Identification of a rare copy number polymorphic gain at 3q12.2 with candidate genes for familial endometriosis

Endometriosis is a complex disease that affects 10-15% of women of reproductive age. Familial studies show that relatives of affected patients have a higher risk of developing the disease, implicating a genetic role for this disorder. Little is known about the impact of germline genomic copy number variant (CNV) polymorphisms on the heredity of the disease. In this study, we describe a rare CNV identified in two sisters with familial endometriosis, which contain genes that may increase the susceptibility and progression of this disease. We investigated the presence of CNVs from the endometrium and blood of the sisters with endometriosis and normal endometrium of five women as controls without the disease using array-CGH through the Agilent 2x400K platform. We excluded common CNVs that were present in the database of genomic variation. We identified, in both sisters, a rare CNV gain affecting 113kb at band 3q12.2 involving two candidate genes: ADGRG7 and TFG. The CNV gain was validated by qPCR. ADGRG7 is located at 3q12.2 and encodes a G protein-coupled receptor influencing the NF-kappaβ pathway. TFG participates in chromosomal translocations associated with hematologic tumor and soft tissue sarcomas, and is also involved in the NF-kappa B pathway. The CNV gain in this family provides a new candidate genetic marker for future familial endometriosis studies. Additional longitudinal studies of affected families must confirm any associations between this rare CNV gain and genes involved in the NF-kappaβ pathway in predisposition to endometriosis.

FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer

Fatty acid synthase (FASN) catalyzes the synthesis of long-chain saturated fatty acids and is overexpressed during prostatic tumorigenesis, where it is the therapeutic target in several ongoing trials. However, the mechanism of FASN upregulation in prostate cancer remains unclear. Here, we examine FASN gene CpG methylation pattern by InfiniumEPIC profiling and whole-genome bisulfite sequencing across multiple racially diverse primary and metastatic prostate cancer cohorts, comparing with FASN protein expression as measured by digitally quantified IHC assay and reverse phase protein array analysis or FASN gene expression. We demonstrate that the FASN gene body is hypomethylated and overexpressed in primary prostate tumors compared with benign tissue, and FASN gene methylation is significantly inversely correlated with FASN protein or gene expression in both primary and metastatic prostate cancer. Primary prostate tumors with ERG gene rearrangement have increased FASN expression and we find evidence of FASN hypomethylation in this context. FASN expression is also significantly increased in prostate tumors from carriers of the germline HOXB13 G84E mutation compared with matched controls, consistent with a report that HOXB13 may contribute to epigenetic regulation of FASN in vitro. However, in contrast to previous studies, we find no significant association of FASN expression or methylation with self-identified race in models that include ERG status across two independent primary tumor cohorts. Taken together, these data support a potential epigenetic mechanism for FASN regulation in the prostate which may be relevant for selecting patients responsive to FASN inhibitors.

SIGNIFICANCE

Here, we leverage multiple independent primary and metastatic prostate cancer cohorts to demonstrate that FASN gene body methylation is highly inversely correlated with FASN gene and protein expression. This finding may shed light on epigenetic mechanisms of FASN regulation in prostate cancer and provides a potentially useful biomarker for selecting patients in future trials of FASN inhibitors.

Pan-cancer genomic analysis shows hemizygous PTEN loss tumors are associated with immune evasion and poor outcome

In tumors, somatic mutations of the PTEN suppressor gene are associated with advanced disease, chemotherapy resistance, and poor survival. PTEN loss of function may occur by inactivating mutation, by deletion, either affecting one copy (hemizygous loss) leading to reduced gene expression or loss of both copies (homozygous) with expression absent. Various murine models have shown that minor reductions in PTEN protein levels strongly influence tumorigenesis. Most PTEN biomarker assays dichotomize PTEN (i.e. presence vs. absence) ignoring the role of one copy loss. We performed a PTEN copy number analysis of 9793 TCGA cases from 30 different tumor types. There were 419 (4.28%) homozygous and 2484 (25.37%) hemizygous PTEN losses. Hemizygous deletions led to reduced PTEN gene expression, accompanied by increased levels of instability and aneuploidy across tumor genomes. Outcome analysis of the pan-cancer cohort showed that losing one copy of PTEN reduced survival to comparable levels as complete loss, and was associated with transcriptomic changes controlling immune response and the tumor microenvironment. Immune cell abundances were significantly altered for PTEN loss, with changes in head and neck, cervix, stomach, prostate, brain, and colon more evident in hemizygous loss tumors. These data suggest that reduced expression of PTEN in tumors with hemizygous loss leads to tumor progression and influences anticancer immune response pathways.

Association of self-identified race and genetic ancestry with the immunogenomic landscape of primary prostate cancer

The genomic and immune landscapes of prostate cancer differ by self-identified race. However, few studies have examined the genome-wide copy number landscape and immune content of matched cohorts with genetic ancestry data and clinical outcomes. Here, we assessed prostate cancer somatic copy number alterations (sCNA) and tumor immune content of a grade-matched, surgically treated cohort of 145 self-identified Black (BL) and 145 self-identified White (WH) patients with genetic ancestry estimation. A generalized linear model adjusted with age, preoperative prostate-specific antigen (PSA), and Gleason Grade Group and filtered for germline copy number variations (gCNV) identified 143 loci where copy number varied significantly by percent African ancestry, clustering on chromosomes 6p, 10q, 11p, 12p, and 17p. Multivariable Cox regression models adjusted for age, preoperative PSA levels, and Gleason Grade Group revealed that chromosome 8q gains (including MYC) were significantly associated with biochemical recurrence and metastasis, independent of genetic ancestry. Finally, Treg density in BL and WH patients was significantly correlated with percent genome altered, and these findings were validated in the TCGA cohort. Taken together, our findings identify specific sCNA linked to genetic ancestry and outcome in primary prostate cancer and demonstrate that Treg infiltration varies by global sCNA burden in primary disease.

An mTORC1-mediated negative feedback loop constrains amino acid-induced FLCN-Rag activation in renal cells with TSC2 loss

The mechanistic target of rapamycin complex 1 (mTORC1) integrates inputs from growth factors and nutrients, but how mTORC1 autoregulates its activity remains unclear. The MiT/TFE transcription factors are phosphorylated and inactivated by mTORC1 following lysosomal recruitment by RagC/D GTPases in response to amino acid stimulation. We find that starvation-induced lysosomal localization of the RagC/D GAP complex, FLCN:FNIP2, is markedly impaired in a mTORC1-sensitive manner in renal cells with TSC2 loss, resulting in unexpected TFEB hypophosphorylation and activation upon feeding. TFEB phosphorylation in TSC2-null renal cells is partially restored by destabilization of the lysosomal folliculin complex (LFC) induced by FLCN mutants and is fully rescued by forced lysosomal localization of the FLCN:FNIP2 dimer. Our data indicate that a negative feedback loop constrains amino acid-induced, FLCN:FNIP2-mediated RagC activity in renal cells with constitutive mTORC1 signaling, and the resulting MiT/TFE hyperactivation may drive oncogenesis with loss of the TSC2 tumor suppressor.

Association between pathogenic germline mutations in BRCA2 and ATM and tumor-infiltrating lymphocytes in primary prostate cancer

Pathogenic mutations in homologous recombination (HR) DNA repair genes may be associated with increased tumor mutational burden and numbers of tumor-infiltrating lymphocytes (TIL). Though HR-deficient prostate tumors have been anecdotally associated with improved responses to immunotherapy, it is unclear whether HR mutations or HR deficiency (HRD) scores predict for increased T-cell densities in this cancer. We evaluated 17 primary prostate tumors from patients with pathogenic germline BRCA2 mutations (gBRCA2) and 21 primary prostate tumors from patients with pathogenic germline ATM (gATM) mutations, which were compared to 19 control tumors lacking HR gene mutations, as well as the TCGA prostate cancer cohort. HRD score was estimated by targeted sequencing (gBRCA2 and gATM) or by SNP microarray (TCGA). Tumor-associated T-cell densities were assessed using validated automated digital image analysis of CD8 and FOXP3 immunostaining (gBRCA2 or gATM) or by methylCIBERSORT (TCGA). CD8 + and FOXP3 + T-cell densities were significantly correlated with each other in gBRCA2 and gATM cases. There was no significant difference between CD8 + or FOXP3 + TIL densities in gBRCA2 or gATM cases compared to controls. In the TCGA cohort, HRD score was associated with predicted CD8 + and FOXP3 + TILs. Associations were also seen for HRD score and TIL density among the germline-mutated cases. In contrast to mismatch repair-deficient primary prostate tumors, cancers from germline BRCA2 or ATM mutation carriers do not appear to be associated with elevated TIL density. However, measures of genomic scarring, such as HRD score, may be associated with increased tumor-infiltrating T-cells.

GPNMB expression identifies TSC1 /2/ mTOR ‐associated and MiT family translocation‐driven renal neoplasms

GPNMB (glycoprotein nonmetastatic B) and other TFE3/TFEB transcriptional targets have been proposed as markers for microphthalmia (MiT) translocation renal cell carcinomas (tRCCs). We recently demonstrated that constitutive mTORC1 activation via TSC1/2 loss leads to increased activity of TFE3/TFEB, suggesting that the pathogenesis and molecular markers for tRCCs and TSC1/2‐associated tumors may be overlapping. We examined GPNMB expression in human kidney and angiomyolipoma (AML) cell lines with TSC2 and/or TFE3/TFEB loss produced using CRISPR–Cas9 genome editing as well as in a mouse model of Tsc2 inactivation‐driven renal tumorigenesis. Using an automated immunohistochemistry (IHC) assay for GPNMB, digital image analysis was employed to quantitatively score expression in clear cell RCC (ccRCC, n = 87), papillary RCC (papRCC, n = 53), chromophobe RCC (chRCC, n = 34), oncocytoma (n = 4), TFE3‐ or TFEB‐driven tRCC (n = 56), eosinophilic solid and cystic RCC (ESC, n = 6), eosinophilic vacuolated tumor (EVT, n = 4), and low‐grade oncocytic tumor (LOT, n = 3), as well as AML (n = 29) and perivascular epithelioid cell tumors (PEComas, n = 8). In cell lines, GPNMB was upregulated following TSC2 loss in a MiT/TFE‐ and mTORC1‐dependent fashion. Renal tumors in Tsc2^+/− A/J mice showed upregulation of GPNMB compared with normal kidney. Mean GPNMB expression was significantly higher in tRCC than in ccRCC (p < 0.0001), papRCC (p < 0.0001), and chRCC (p < 0.0001). GPNMB expression in TSC1/2/MTOR alteration‐associated renal tumors (including ESC, LOT, AML, and PEComa) was comparable to that in tRCC. The immunophenotype of tRCC and TSC1/2/MTOR alteration‐associated renal tumors is highly overlapping, likely due to the increased activity of TFE3/TFEB in both, revealing an important caveat regarding the use of TFE3/TFEB‐transcriptional targets as diagnostic markers. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Reciprocal YAP1 loss and INSM1 expression in neuroendocrine prostate cancer

Neuroendocrine prostate cancer (NEPC) is a rare but aggressive histologic variant of prostate cancer that responds poorly to androgen deprivation therapy. Hybrid NEPC-adenocarcinoma (AdCa) tumors are common, often eluding accurate pathologic diagnosis and requiring ancillary markers for classification. We recently performed an outlier-based meta-analysis across a number of independent gene expression microarray datasets to identify novel markers that differentiate NEPC from AdCa, including up-regulation of insulinoma-associated protein 1 (INSM1) and loss of Yes-associated protein 1 (YAP1). Here, using diverse cancer gene expression datasets, we show that Hippo pathway-related genes, including YAP1, are among the top down-regulated gene sets with expression of the neuroendocrine transcription factors, including INSM1. In prostate cancer cell lines, transgenic mouse models, and human prostate tumor cohorts, we confirm that YAP1 RNA and YAP1 protein expression are silenced in NEPC and demonstrate that the inverse correlation of INSM1 and YAP1 expression helps to distinguish AdCa from NEPC. Mechanistically, we find that YAP1 loss in NEPC may help to maintain INSM1 expression in prostate cancer cell lines and we further demonstrate that YAP1 silencing likely occurs epigenetically, via CpG hypermethylation near its transcriptional start site. Taken together, these data nominate two additional markers to distinguish NEPC from AdCa and add to data from other tumor types suggesting that Hippo signaling is tightly reciprocally regulated with neuroendocrine transcription factor expression. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

The Role of Somatic Mutations on the Immune Response of the Tumor Microenvironment in Prostate Cancer

Immunotherapy has improved patient survival in many types of cancer, but for prostate cancer, initial results with immunotherapy have been disappointing. Prostate cancer is considered an immunologically excluded or cold tumor, unable to generate an effective T-cell response against cancer cells. However, a small but significant percentage of patients do respond to immunotherapy, suggesting that some specific molecular subtypes of this tumor may have a better response to checkpoint inhibitors. Recent findings suggest that, in addition to their function as cancer genes, somatic mutations of PTEN, TP53, RB1, CDK12, and DNA repair, or specific activation of regulatory pathways, such as ETS or MYC, may also facilitate immune evasion of the host response against cancer. This review presents an update of recent discoveries about the role that the common somatic mutations can play in changing the tumor microenvironment and immune response against prostate cancer. We describe how detailed molecular genetic analyses of the tumor microenvironment of prostate cancer using mouse models and human tumors are providing new insights into the cell types and pathways mediating immune responses. These analyses are helping researchers to design drug combinations that are more likely to target the molecular and immunological pathways that underlie treatment failure.

Transcriptional landscape of PTEN loss in primary prostate cancer

BACKGROUND

PTEN is the most frequently lost tumor suppressor in primary prostate cancer (PCa) and its loss is associated with aggressive disease. However, the transcriptional changes associated with PTEN loss in PCa have not been described in detail. In this study, we highlight the transcriptional changes associated with PTEN loss in PCa.

METHODS

Using a meta-analysis approach, we leveraged two large PCa cohorts with experimentally validated PTEN and ERG status by Immunohistochemistry (IHC), to derive a transcriptomic signature of PTEN loss, while also accounting for potential confounders due to ERG rearrangements. This signature was expanded to lncRNAs using the TCGA quantifications from the FC-R2 expression atlas.

RESULTS

The signatures indicate a strong activation of both innate and adaptive immune systems upon PTEN loss, as well as an expected activation of cell-cycle genes. Moreover, we made use of our recently developed FC-R2 expression atlas to expand this signature to include many non-coding RNAs recently annotated by the FANTOM consortium. Highlighting potential novel lncRNAs associated with PTEN loss and PCa progression.

CONCLUSION

We created a PCa specific signature of the transcriptional landscape of PTEN loss that comprises both the coding and an extensive non-coding counterpart, highlighting potential new players in PCa progression. We also show that contrary to what is observed in other cancers, PTEN loss in PCa leads to increased activation of the immune system. These findings can help the development of new biomarkers and help guide therapy choices.

Abstract 2431: mTORC1 paradoxically drives MiT/TFE activity and lysosomal biogenesis in tuberous sclerosis complex

Background: Tuberous Sclerosis Complex (TSC) is characterized by TSC1/2 loss, dysregulated mTORC1 signaling & renal tumors (angiomyolipomas (AML) & renal cell carcinoma (RCC)). The MiT/TFE transcription factors (MITF/TFE3/TFEB) drive autophagy/lysosomal biogenesis & are negatively regulated by mTORC1. However, this model raises a paradox in cancer, where elevated lysosomal activity must persist with mTORC1 activity. We recently showed that epidermal Tsc1 loss paradoxically increases MiT/TFE-activity (https://www.jci.org/articles/view/128287). Intriguingly, TFE3/TFEB gene rearrangements/amplifications and TSC1/2 loss are mutually exclusive drivers in PEComas & RCC. This raises the possibility that TSC1/2 loss & TFE3/TFEB gene rearrangements have overlapping cellular consequences. Here, we address the hypothesis that MiT/TFE-driven lysosomal biogenesis drives tumorigenesis in TSC.

Design: We used HEK293T cells +/- CRISPR deletion (KO) of TSC1, 2 or both, to examine: a) Lysosomal gene enrichment by RNA-seq/GSEA, b) Expression of MiT/TFE & lysosomal markers (immunoblotting, qRT-PCR & IF), c) MiT/TFE localization (IF & nuclear fraction immunoblots), d) MiT/TFE activity (4X-CLEAR luciferase assays, qRT-PCR, cathepsin processing, autophagic flux, LC3 puncta). We analysed spontaneous renal tumors in Tsc2 +/- mice for MIT/TFE protein/gene expression (IHC, IF & qRT-PCR analyses of laser capture micro-dissected (LCM) renal tumors). We examined MIT/TFE proteins/lysosomal markers in FFPE samples of renal PEComas & eosinophilic solid & cystic (ESC) RCC & normal kidney.

Results: RNA-seq/GSEA showed enrichment of lysosomal gene sets in TSC1/2 KO cells compared to controls. TSC2 KO cells had increased expression of lysosomal transcripts & proteins in cellular lysates & lysosomal fractions. TSC1, 2 & 1/2 KO cells showed increased nuclear TFEB/TFE3 (IF/nuclear-fraction immunoblots), compared to controls. MiT/TFE activity in 4X-CLEAR luciferase reporter assays was increased in TSC2 KO cells compared to controls. Treatment of TSC2 KO cells with chloroquine increased lipidated LC3-II, indicating increased autophagic flux. TSC2 KO cells also showed increased LC3-labelled puncta by IF. We analyzed renal tumors in Tsc2 +/- mice, where elevated mTORC1 signaling was confirmed by p-S6 IHC. Expression of lysosomal proteins (LAMP1, Lamtor 1, Rag C, Cathepsin B) & nuclear localization of TFE3 & TFEB was increased in these lesions by IF/IHC, compared to normal kidney. We performed LCM on renal tumors from Tsc2 +/- mice & found levels of MiT/TFE transcriptional targets to be significantly enriched in tumors compared to normal kidney. We analyzed TFE3 expression in 10 cases of ESC- RCC with sporadic bi-allelic TSC1/2 mutations & 2 cases of TSC-associated RCC; 8/10 cases showed elevated nuclear TFE3.

Conclusions: Elevated MiT/TFE levels & activity may represent oncogenic drivers in human & murine renal tumors in TSC.

Citation Format: Kaushal V. Asrani, Daniela Salles, Juhyung Woo, Adrianna Mendes, Sanjana Murali, Thiago Vidotto, Pedram Argani, Edward Gabrielson, Tamara Lotan. mTORC1 paradoxically drives MiT/TFE activity and lysosomal biogenesis in tuberous sclerosis complex [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 2431.

Sexual Dimorphism in Outcomes of Non-muscle-invasive Bladder Cancer: A Role of CD163+ Macrophages, B cells, and PD-L1 Immune Checkpoint

BACKGROUND

Non-muscle-invasive bladder cancer (NMIBC) is over three times as common in men as it is in women; however, female patients do not respond as well to immunotherapeutic treatments and experience worse clinical outcomes than their male counterparts. Based on the established sexual dimorphism in mucosal immune responses, we hypothesized that the tumor immune microenvironment of bladder cancer differs between the sexes, and this may contribute to discrepancies in clinical outcomes.

OBJECTIVE

To determine biological sex-associated differences in the expression of immune regulatory genes and spatial organization of immune cells in tumors from NMIBC patients.

DESIGN SETTING AND PARTICIPANTS

Immune regulatory gene expression levels in tumors from male (n = 357) and female (n = 103) patients were measured using whole transcriptome profiles of tumors from the UROMOL cohort. Multiplexe immunofluorescence was performed to evaluate the density and spatial distribution of immune cells and immune checkpoints in tumors from an independent cohort of patients with NMIBC (n = 259 males and n = 73 females).

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Transcriptome sequencing data were analyzed using DESeq2 in R v4.0.1, followed by application of the Kruskal-Wallis test to determine gene expression differences between tumors from males and females. Immunofluorescence data analyses were conducted using R version 3.5.3. Survival analysis was performed using survminer packages.

RESULTS AND LIMITATIONS

High-grade tumors from female patients exhibited significantly increased expression of B-cell recruitment (CXCL13) and function (CD40)-associated genes and the immune checkpoint genes CTLA4, PDCD1, LAG3, and ICOS. Tumors from female patients showed significantly higher infiltration of PD-L1+ cells and CD163+ M2-like macrophages than tumors from male patients. Increased abundance of CD163+ macrophages and CD79a+ B cells were associated with decreased recurrence-free survival.

CONCLUSIONS

These novel findings highlight the necessity of considering sexual dimorphism in the design of future immunotherapy trials in NMIBC.

PATIENT SUMMARY

In this study, we measured the abundance of various immune cell types between tumors from male and female patients with non-muscle-invasive bladder cancer. We demonstrate that tumors from female patients have a significantly higher abundance of immunosuppressive macrophages that express CD163. Higher abundance of tumor-associated CD163-expressing macrophages and B cells is associated with shorter recurrence-free survival in both male and female patients.

Assessment of MYC/PTEN Status by Gene-Protein Assay in Grade Group 2 Prostate Biopsies

This study leveraged a gene-protein assay to assess MYC and PTEN status at prostate cancer biopsy and examined the association with adverse outcomes after surgery. MYC gain and PTEN loss were simultaneously assessed by chromogenic in situ hybridization and immunohistochemistry, respectively, using 277 Grade Group 2 needle biopsies that were followed by prostatectomy. The maximal size of cribriform Gleason pattern 4 carcinoma (CRIB), the presence of intraductal carcinoma (IDC), and percentage of Gleason pattern 4 carcinoma at biopsy were also annotated. MYC gain or PTEN loss was present in 19% and 18% of biopsies, respectively, whereas both alterations were present in 9% of biopsies. Tumors with one or both alterations were significantly more likely to have non-organ-confined disease (NOCD) at radical prostatectomy. In logistic regression models, including clinical stage, tumor volume on biopsy, and presence of CRIB/IDC, cases with MYC gain and PTEN loss remained at higher risk for NOCD (odds ratio, 6.23; 95% CI, 1.74-24.55; P = 0.005). The area under the curve for a baseline model using CAPRA variables (age, prostate-specific antigen, percentage of core involvement, clinical stage) was increased from 0.68 to 0.69 with inclusion of CRIB/IDC status and to 0.75 with MYC/PTEN status. Dual MYC/PTEN status can be assessed in a single slide and is independently associated with increased risk of NOCD for Grade Group 2 biopsies.

Risk Stratification of Prostate Cancer Through Quantitative Assessment of PTEN Loss (qPTEN)

BACKGROUND

Phosphatase and tensin homolog (PTEN) loss has long been associated with adverse findings in early prostate cancer. Studies to date have yet to employ quantitative methods (qPTEN) for measuring of prognostically relevant amounts of PTEN loss in postsurgical settings and demonstrate its clinical application.

METHODS

PTEN protein levels were measured by immunohistochemistry in radical prostatectomy samples from training (n = 410) and validation (n = 272) cohorts. PTEN loss was quantified per cancer cell and per tissue microarray core. Thresholds for identifying clinically relevant PTEN loss were determined using log-rank statistics in the training cohort. Univariate (Kaplan-Meier) and multivariate (Cox proportional hazards) analyses on various subpopulations were performed to assess biochemical recurrence-free survival (BRFS) and were independently validated. All statistical tests were two-sided.

RESULTS

PTEN loss in more than 65% cancer cells was most clinically relevant and had statistically significant association with reduced BRFS in training (hazard ratio [HR] = 2.48, 95% confidence interval [CI] = 1.59 to 3.87; P < .001) and validation cohorts (HR = 4.22, 95% CI = 2.01 to 8.83; P < .001). The qPTEN scoring method identified patients who recurred within 5.4 years after surgery (P < .001). In men with favorable risk of biochemical recurrence (Cancer of the Prostate Risk Assessment - Postsurgical scores <5 and no adverse pathological features), qPTEN identified a subset of patients with shorter BRFS (HR = 5.52, 95% CI = 2.36 to 12.90; P < .001) who may be considered for intensified monitoring and/or adjuvant therapy.

CONCLUSIONS

Compared with previous qualitative approaches, qPTEN improves risk stratification of postradical prostatectomy patients and may be considered as a complementary tool to guide disease management after surgery.

STAT1 associated immune checkpoint expression and immune cell localization represent adaptive immune resistance in high-grade serous ovarian cancer

High-grade serous carcinoma (HGSC) is a deadly malignancy leading to ~70% of the 140,000 ovarian cancer deaths each year. Resistance to platinum chemotherapy followed by recurrence and an incurable disease occurs in most HGSC patients. Contemporary immune checkpoint blockade therapies have shown minimal efficacy in this cancer. Our previous investigations established that tumour interferon (IFN) activation status and CD8+ T cell density are predictors of chemotherapy response in HGSC. Furthermore, we also showed that the IFN induced chemokine CXCL10 is a key determinant of increased survival via immune cell recruitment in the tumour immune microenvironment (TIME). Given that signal transducer and activator of transcription 1 (STAT1) is central to the feed forward loops of cellular IFN responses, we investigated STAT1 associated transcriptomic alterations and spatial profiles of immune cells in 204 pre-treatment HGSC tumours.

RNA-sequencing based whole transcriptomic profiling revealed that higher STAT1 expression significantly correlated with higher immunomodulatory gene expression, including immune checkpoints and activators, in both chemotherapy sensitive and resistant tumours. Findings were independently validated in a cohort of 379 HGSC tumour RNA-Seq profiles from The Cancer Genome Atlas Network ovarian cancer dataset. Multiplex immunofluorescence based spatial profiling of CD8+ T cells, FoxP3+ T regulatory T cells, CD68+M1, and CD163+ M2 macrophages and expression of PD-L1, PD-1, IDO1 immune checkpoints was performed. Findings from our study provide evidence for IFN mediated adaptive immune resistance in the HGSC TIME and will potentially inform the design of rational chemo-immunotherapy approaches.

M2 macrophages, B cells, and PD-L1 immune checkpoint protein exhibit sexual dimorphism in the outcomes of non-muscle invasive bladder cancer

Non-muscle-invasive bladder cancer (NMIBC) is more than three times as common in men as it is in women. However, female patients with NMIBC do not respond as well to immunotherapeutic treatments and experience worse clinical outcomes than their male counterparts. The underlying causes of these discrepancies have yet to be fully elucidated.

We hypothesized that sexual dimorphism in the tumor immune microenvironment (TIME) may contribute to the inferior clinical outcomes observed in female patients with NMIBC. To test this hypothesis, we investigated immune-associated gene expression in tumors from male (n=357) and female (n=103) patients. High-grade tumors from female patients exhibited significantly increased expression of B cell-associated genes CD40 and CXCL13, and the immune checkpoint genes CTLA4, PDCD1, LAG3, and ICOS.

Based on these differences, we utilized multiplexed immunofluorescence to evaluate the density and spatial distribution of 12 immune cell markers (CD79a, CD3, CD8, FoxP3, Ki67, CD103, CD163, GATA3, CK5, IDO1, PD-1, and PD-L1) in tumors from an independent cohort of 332 patients with NMIBC (n=259 males and n=73 females). Tumors from female patients showed significantly higher infiltration of PD-L1+ cells and CD163+ M2-like macrophages compared to tumors from male patients. Notably, increased abundance of CD163+ macrophages and CD79a+ B cells were independently associated with decreased recurrence-free survival.

This study has the potential to inform the rational utilization of immunomodulatory treatments for NMIBC based on the TIME of both male and female patients. Furthermore, these novel findings highlight the necessity of considering sexual dimorphism in the design of future immunotherapy trials.

Plasma cells are enriched in localized prostate cancer in Black men and are associated with improved outcomes

Black men die more often of prostate cancer yet, interestingly, may derive greater survival benefits from immune-based treatment with sipuleucel-T. Since no signatures of immune-responsiveness exist for prostate cancer, we explored race-based immune-profiles to identify vulnerabilities. Here we show in multiple independent cohorts comprised of over 1,300 patient samples annotated with either self-identified race or genetic ancestry, prostate tumors from Black men or men of African ancestry have increases in plasma cell infiltrate and augmented markers of NK cell activity and IgG expression. These findings are associated with improved recurrence-free survival following surgery and nominate plasma cells as drivers of prostate cancer immune-responsiveness.

Abstract A04: DNA damage repair gene mutations and associated tumor immune landscape as biomarkers of response to immunotherapy in muscle-invasive urothelial cancer

Molecular subtyping of urothelial cancer (UC) has significantly advanced the understanding of bladder tumor heterogeneity and development of prognostic and predictive biomarkers. Evolving evidence across cancers strongly suggests that tumor immunoediting has a profound impact on the behavior of cancer cells and their adaptation to the coevolving microenvironment and response to treatment. In alignment with this concept, recent immune checkpoint blockade (ICB) therapies in UC have demonstrated the predictive potential of mutations in the DNA damage repair (DDR). A comprehensive understanding of DDR mutation-associated expression of immune regulatory genes could thus aid in expansion of current immunotherapies and predictive biomarkers for the design of patient-tailored combination treatments. We thus investigated the pretreatment tumor transcriptomic profiles of the five recently described molecular subtypes of muscle-invasive urothelial cancer (MIUC; n=408) from the Genomic Data Commons, to determine subtype-specific immune cell abundance, expression of 67 immune regulatory genes, and association with DDR gene mutation profiles. Analysis using CIBERSORT immune cell abundance determination tool showed significant differences in immune cell profiles and abundance between MIUC subtypes. Expression patterns of a selected panel of 67 genes including both immune-stimulatory and -inhibitory genes showed significant associations with subtypes and DDR mutation status. Findings from our study provide compelling evidence for coexpression of multiple immune checkpoint genes including PD-1, PD-L1, IDO1, TIGIT, TIM-3, TGFB1, LAG3, and others, that potentially contribute to compensatory immune evasion in bladder tumors. Our findings also emphasize the urgent need for biomarker discovery approaches that combine molecular subtype, DDR gene mutation status, tumor immune landscape classification, and immune checkpoint gene expression to increase the number of patients responding to immunotherapies.

Citation Format: Thiago Vidotto, Sarah Nersesian, Charles Graham, David Robert Siemens, Madhuri Koti. DNA damage repair gene mutations and associated tumor immune landscape as biomarkers of response to immunotherapy in muscle-invasive urothelial cancer [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2019 May 18-21; Denver, CO. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(15_Suppl):Abstract nr A04.

Emerging role of PTEN loss in evasion of the immune response to tumours

Mutations in PTEN activate the phosphoinositide 3-kinase (PI3K) signalling network, leading to many of the characteristic phenotypic changes of cancer. However, the primary effects of this gene on oncogenesis through control of the PI3K-AKT-mammalian target of rapamycin (mTOR) pathway might not be the only avenue by which PTEN affects tumour progression. PTEN has been shown to regulate the antiviral interferon network and thus alter how cancer cells communicate with and are targeted by immune cells. An active, T cell-infiltrated microenvironment is critical for immunotherapy success, which is also influenced by mutations in DNA damage repair pathways and the overall mutational burden of the tumour. As PTEN has a role in the maintenance of genomic integrity, it is likely that a loss of PTEN affects the immune response at two different levels and might therefore be instrumental in mediating failed responses to immunotherapy. In this review, we summarise findings that demonstrate how the loss of PTEN function elicits specific changes in the immune response in several types of cancer. We also discuss ongoing clinical trials that illustrate the potential utility of PTEN as a predictive biomarker for immune checkpoint blockade therapies.

Interferon associated adaptive immune resistance represented by immune checkpoint expression and immune cell localization in high-grade serous ovarian cancer

High-grade serous carcinoma (HGSC) is a deadly malignancy leading to ~70% of the 140,000 ovarian cancer deaths globally each year. Resistance to platinum chemotherapy followed by recurrence and an incurable disease occurs in most HGSC patients. Contemporary immune checkpoint blockade therapies have shown minimal efficacy in this cancer. Our previous investigations established that tumour interferon (IFN) activation status and CD8+ T cell density are predictors of chemotherapy response in HGSC. Furthermore, we also showed that IFN induced chemokine CXCL10 is a key determinant of increased survival via immune cell recruitment in the tumour immune microenvironment (TIME). Given that signal transducer and activator of transcription 1 (STAT1) is central to the feed forward loops of cellular IFN responses, we investigated STAT1 associated transcriptomic alterations and spatial profiles of immune cells in 204 pre-treatment HGSC tumours.

RNA-sequencing based whole transcriptomic profiling revealed that higher STAT1 expression significantly correlated with higher immunomodulatory gene expression, including immune checkpoints and activators, in both chemotherapy sensitive and resistant tumours. Findings were independently validated in a cohort of 379 HGSC tumour RNA-Seq profiles from The Cancer Genome Atlas Network ovarian cancer dataset. Multiplex immunofluorescence based spatial profiling of CD8+ T cells, FoxP3+ T regulatory T cells, CD68+M1, and CD163+ M2 macrophages and expression of PD-L1, PD-1, IDO1 immune checkpoints was performed. Findings from our study provide evidence for IFN mediated adaptive immune resistance in the HGSC TIME and will potentially inform the design of rational chemo-immunotherapy approaches.

Abstract A31: High aneuploidy levels are linked to a reduced immune-cell abundance in metastatic castrate-resistant prostate cancer

Single-agent immunotherapeutic approaches are promising for treating castrate-resistant prostate cancer (CRPC) patients; however, to date no significant improvement in survival has been reported. Mixed response to therapy occurs because metastatic lesions are highly heterogeneous. These lesions exhibit distinct genomic changes that are linked to a tumor microenvironment that is often poorly populated by immune cells. In other tumor types, a high percent genome altered (e.g., aneuploidy) associates with an overall reduction in immune response in the primary tumor microenvironment. However, the association between genomic changes and immune cell composition is poorly understood in metastatic prostate cancers. Thus, we quantified the abundance of 22 immune cell types in 330 tumors from two independent public domain CRPC cohorts and 491 primary prostate tumors from TCGA using the Absolute Mode from CIBERSORT. The estimation in CRPC was performed using whole-transcriptome data from West Coast Dream Team (Abida et al., 2019; n=212) and East Coast Dream Team (Robinson et al., 2015; n=117) samples. We did not identify any significant correlations between mutational load and immune cell abundance in the three investigated cohorts. In primary tumors, aneuploidy was weakly negatively correlated with CD8+ and CD4+ T-cell abundance (R=-0.14 and R=-0.09, P&lt;0.05). Overall, metastatic lesions demonstrated a low absolute abundance of the majority of immune cell subtypes, with higher levels of CD8+ T-cells, memory CD4+ T-cells, macrophages, and plasma cells. We found that bone lesions had the lowest abundance of CD8+ T-cells (Kruskal-Wallis, p=0.05) and the highest abundance of macrophages (P&lt;0.0001) compared to lymph node and liver samples. Overall, aneuploidy was negatively correlated with immune cell abundance in both metastatic cohorts (Spearman correlation, P&lt;0.05). Interestingly, lymph node metastases showed the strongest negative correlation between aneuploidy and T-cell abundance in both West and East cohorts (R=-0.36 and R=-0.32, respectively, p&lt;0.01). Our preliminary results show that the extent of chromosomal aberrations in CRPC is significantly associated with underlying immune cell infiltrates. These results have potential implications for future immunotherapy trials in prostate cancer.

Citation Format: Thiago Vidotto, Daniela C. Salles, Tamara L. Lotan. High aneuploidy levels are linked to a reduced immune-cell abundance in metastatic castrate-resistant prostate cancer [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A31.

CDKN1B Deletions are Associated with Metastasis in African American Men with Clinically Localized, Surgically Treated Prostate Cancer

PURPOSE

The potential biological determinants of aggressive prostate cancer in African American (AA) men are unknown. Here we characterize prostate cancer genomic alterations in the largest cohort to date of AA men with clinical follow-up for metastasis, with the aim to elucidate the key molecular drivers associated with poor prognosis in this population.

EXPERIMENTAL DESIGN

Targeted sequencing was retrospectively performed on 205 prostate tumors from AA men treated with radical prostatectomy (RP) to examine somatic genomic alterations and percent of the genome with copy-number alterations (PGA). Cox proportional hazards analyses assessed the association of genomic alterations with risk of metastasis.

RESULTS

At RP, 71% (145/205) of patients had grade group ≥3 disease, and 49% (99/202) were non-organ confined. The median PGA was 3.7% (IQR = 0.9%-9.4%) and differed by pathologic grade (P < 0.001) and stage (P = 0.02). Median follow-up was 5 years. AA men with the highest quartile of PGA had increased risks of metastasis (multivariable: HR = 13.45; 95% CI, 2.55-70.86; P = 0.002). The most common somatic mutations were SPOP (11.2%), FOXA1 (8.3%), and TP53 (3.9%). The most common loci altered at the copy number level were CDKN1B (6.3%), CHD1 (4.4%), and PTEN (3.4%). TP53 mutations and deep deletions in CDKN1B were associated with increased risks of metastasis on multivariable analyses (TP53: HR = 9.5; 95% CI, 2.2-40.6; P = 0.002; CDKN1B: HR = 6.7; 95% CI, 1.3-35.2; P = 0.026).

CONCLUSIONS

Overall, PGA, somatic TP53 mutations, and a novel finding of deep deletions in CDKN1B were associated with poor prognosis in AA men. These findings require confirmation in additional AA cohorts.

Serotonin synthesis protects the mouse colonic crypt from DNA damage and colorectal tumorigenesis

Serotonin (5-HT) signaling pathways are thought to be involved in colorectal tumorigenesis (CRT), but the role of 5-HT synthesis in the early steps of this process is presently unknown. In this study, we used carcinogen treatment in the tryptophan hydroxylase 1 knockout (Tph1KO) and transgenic (Tph1^fl/fl Villin^Cre ) mouse models defective in 5-HT synthesis to investigate the early mutagenic events associated with CRT. Our observations of the colonic crypt post-treatment followed a timeline designed to understand how disruption of 5-HT synthesis affects the initial steps leading to CRT. We found Tph1KO mice had decreased development of both allograft tumors and colitis-related CRT. Interestingly, carcinogenic exposure alone induced multiple colon tumors and increased cyclooxygenase-2 (Ptgs2) expression in Tph1KO mice. Deletion of interleukin 6 (Il6) in Tph1KO mice confirmed that inflammation was a part of the process. 5-HT deficiency increased colonic DNA damage but inhibited genetic repair of specific carcinogen-related damage, leading to CRT-related inflammatory reactions and dysplasia. To validate a secondary effect of 5-HT deficiency on another DNA repair pathway, we exposed Tph1KO mice to ionizing radiation and found an increase in DNA damage associated with reduced levels of ataxia telangiectasia and Rad3 related (Atr) gene expression in colonocytes. Restoring 5-HT levels with 5-hydroxytryptophan treatment decreased levels of DNA damage and increased Atr expression. Analysis of Tph1^fl/fl Villin^Cre mice with intestine-specific loss of 5-HT synthesis confirmed that DNA repair was tissue specific. In this study, we report a novel protective role for 5-HT synthesis that promotes DNA repair activity during the early stages of colorectal carcinogenesis. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

DNA damage repair gene mutations and their association with tumor immune regulatory gene expression in muscle invasive bladder cancer subtypes

BACKGROUND

Molecular subtyping of urothelial cancer (UC) has significantly advanced the understanding of bladder tumor heterogeneity and development of prognostic and predictive biomarkers. Evolving evidence across cancers strongly suggests that tumor immunoediting has a profound impact on the behaviour of cancer cells and their adaptation to the co-evolving microenvironment and response to treatment. In alignment with these concepts, recent immune checkpoint blockade (ICB) therapies in UC have demonstrated the predictive potential of mutations in the DNA damage repair (DDR) genes. A comprehensive understanding of DDR gene inactivation associated expression of immune regulatory genes could thus aid in expansion of current immunotherapies and predictive biomarkers for the design of patient-tailored combination treatments.

METHODS

We investigated pre-treatment tumor transcriptomic profiles of the five recently described molecular subtypes of muscle invasive urothelial cancer (MIUC; n = 408) from The Cancer Genome Atlas, to determine subtype specific immune cell abundance, expression of 67 immune regulatory genes, and association with DDR gene inactivation (via mutation, copy number alteration) profiles.

RESULTS

Analysis using CIBERSORT immune cell abundance determination tool showed significant differences in immune cell profiles and abundance between MIUC subtypes. Expression patterns of a selected panel of 67 genes including both immune stimulatory and inhibitory genes, showed significant associations with subtypes, and DDR gene mutation status.

CONCLUSION

Findings from our study provide compelling evidence for co-expression of multiple immune checkpoint genes including, PD-1, PD-L1, IDO1, TIGIT, TIM-3, TGFB1, LAG3, and others, that potentially contribute to compensatory immune evasion in bladder tumors. Our findings also emphasize the urgent need for biomarker discovery approaches that combine molecular subtype, DDR gene mutation status, tumor immune landscape classification, and immune checkpoint gene expression to increase the number of patients responding to immunotherapies.

PTEN-deficient prostate cancer is associated with an immunosuppressive tumor microenvironment mediated by increased expression of IDO1 and infiltrating FoxP3+ T regulatory cells

BACKGROUND

Accumulating evidence shows that tumor cell-specific genomic changes can influence the cross talk between cancer cells and the surrounding tumor microenvironment (TME). Loss of the PTEN tumor suppressor gene is observed in 20% to 30% of prostate cancers (PCa) when first detected and the rate increases with PCa progression and advanced disease. Recent findings implicate a role for PTEN in cellular type I interferon response and immunosuppression in PCa. However, the way that PTEN inactivation alters antitumor immune response in PCa is poorly understood.

MATERIALS AND METHODS

To investigate the changes associated with PTEN loss and an immunosuppressive TME in PCa, we used CIBERSORT to estimate the relative abundance of 22 immune-cell types from 741 primary and 96 metastatic tumors. Our in silico findings were then validated by immunohistochemical analysis of immune cells and IDO1 and PDL1 checkpoint proteins in a cohort of 94 radical prostatectomy specimens.

RESULTS

FoxP3+ T regulatory cells (Tregs) were significantly increased in PTEN-deficient PCa in all three public domain cohorts. Loss of PTEN in bone metastases was associated with lower CD8+ T-cell abundance, but in liver metastasis, FoxP3+ Tregs were present at higher levels. PTEN-deficient lymph node metastasis had a distinct profile, with high levels of CD8+ T cells. Moreover, we found that metastatic PCa presents higher abundance of FoxP3+ Treg when compared to primary lesions. Since PTEN-deficient tumors are likely to be immunosuppressed as a consequence of increased FoxP3+ Tregs, we then evaluated the localization and expression of IDO1, PDL1 immune checkpoints, and the corresponding density of FoxP3+ Treg and CD8+ T cells using our validation cohort (n = 94). We found that IDO1 protein expression and FoxP3+ Treg density were higher in neoplastic glands compared with benign adjacent tissue. Moreover, higher densities of FoxP3+ Treg cells in both stromal (P = 0.04) and tumor (P = 0.006) compartments were observed in PTEN-deficient tumors compared to tumors that retained PTEN activity. Similarly, IDO1 protein expression was significantly increased in the tumor glands of PTEN-deficient PCa (P < 0.0001). Spearman correlation analysis showed that IDO1 expression was significantly associated with FoxP3+ Treg and CD8+ T-cell density (P < 0.01).

CONCLUSIONS

Our findings imply that PTEN deficiency is linked to an immunosuppressive state in PCa with distinct changes in the frequency of immune cell types in tumors from different metastatic sites. Our data suggest that determining PTEN status may also help guide the selection of patients for future immunotherapy trials in localized and metastatic PCa.

Abstract 5736: In silico analysis shows that PTEN loss and AR overexpression are associated with increased CD8+ T-cell and Treg density and earlier disease recurrence in prostate cancer

PTEN loss occurs in 20-30% prostate cancers (PCa), is associated with worse outcome, and regulates the type I interferon response through the interferon regulatory factor 3 (IRF3). Both PTEN loss and the overexpression of the androgen receptor (AR) promote castrate-resistant PCa leading to a more aggressive disease. To characterize the associations between PTEN loss and AR expression in immune cell infiltration in the tumor microenvironment (TME), we conducted an in silico analysis in two PCa cohorts. RNAseq and gene expression array data were imputed in CIBERSORT to evaluate the relative frequency of 22 immune infiltrating cells in the TME. PTEN was lost in 19.7% (97/491) and 19.8% (26/131) in the TCGA and MSKCC cohorts, respectively. AR was overexpressed in 56% (279/491) and 54% (71/131) of the TCGA and MSKCC cohorts, respectively. Remarkably, AR overexpression was associated with decreased CD8+ T-cells infiltration in both the TCGA (p&lt;0.0001) and MSKCC (p=0.001) cohorts. In addition we found that PTEN loss was associated with increased Treg infiltration in both the TCGA (p=0.002) and MSKCC (p&lt;0.0001) cohorts. PTEN loss was also associated with low plasma cell infiltration in both the TCGA and MSKCC cohorts (p=0.001 and p=0.002, respectively). More detailed analysis of the MSKCC cohort showed that PTEN loss correlated with increased CD8+ T-cell density in the TME (p&lt;0.0001). When we compared the immune cell infiltration profile from the primary and metastatic tumors in the MSKCC cohort, we found an increased infiltration of memory B-cell, Treg, and active dendritic cells (p&lt;0.0001, p=0.005, and p=0.002, respectively) in the metastatic tumors. We then investigated the association between PTEN and AR expression with the most common immunotherapeutic targets. We found that PTEN loss was associated with increased PD-1 expression in MSKCC cohort (p&lt;0.0001) and with reduced PD-L1 expression in the TCGA cohort (p=0.006). Increased AR expression correlated with reduced PD-1 expression in both TCGA and MSKCC cohorts (p&lt;0.0001) and with reduced CTLA-4 expression in TCGA cohort (p=0.009). There was a positive association between PD-1 and CTLA-4 expression with CD8+ T-cell and Treg infiltration in both cohorts. Log-rank analysis showed that PTEN loss and high Treg infiltration predicted earlier disease recurrence in both the TCGA and MSKCC cohorts (p=0.021 and p=0.027, respectively). In addition, combined PTEN loss and increased CD8+ T-cell infiltration promotes earlier disease recurrence in both the TCGA and MSKCC cohorts (p=0.05 and p=0.029, respectively). These findings imply that the immune cell profile in the TME can be influenced by changes in the expression of PTEN and AR, suggesting that novel immunotherapies may promote better responses in castrate-resistant PCa.

Citation Format: Thiago Vidotto, Madhuri Koti, Jeremy A. Squire. In silico analysis shows that PTEN loss and AR overexpression are associated with increased CD8+ T-cell and Treg density and earlier disease recurrence in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5736.

PTEN loss affects the immune and inflammatory response in prostate cancer

Loss of the PTEN tumor suppressor gene occurs in 20-30% of prostate cancer (PCa) cases and is associated with worse disease outcome. Recent evidence highlights the role of inflammation in the tumor microenvironment (TME) and its association with PCa disease progression. The aim of this study is to determine if PTEN genomic loss is associated with the inflammatory response mediated by IFN regulated pathways in the TME. We performed an in silico analysis of genomic and corresponding transcriptomic profiles PCa tumors (n=493) from the Genomic Data Commons (GDC) cohort to identify significant alterations in immune response pathways when PTEN was lost. We identified 449 genes of interest using the Gene ontology (GO) Biological Function in Nexus Expression 3.0 with the keywords “Immune” and “Inflammatory”. We detected that 104 tumors (21%) had either homozygous or hemizygous loss of PTEN. We also found significant associations between PTEN loss, 17p loss and 21q loss (TMPRSS2-ERG fusion gene). PTEN loss was directly associated with worse PCa outcome. Of the 449 selected immune genes, 124 (28%) were differentially expressed when the PTEN loss group was compared to the PTEN intact group. Different cytokines and chemokines presented differential expression by comparing PTEN loss vs. PTEN intact PCa samples. IL13RA1, CXCL9, CXCL10, CXCL11 and CXCL14 showed upregulation in PTEN loss group (P<0.0001), while CXCL12 was found to be downregulated in PTEN loss group. DAVID enrichment analysis showed upregulation of 16 pathways, including RIG-I-like signaling pathway (P<0.0001), chemokine signaling pathway (P<0.0001), and toll-like receptor signaling pathway (P<0.0001). In addition, we identified ten downregulated pathways, including cytokine-cytokine receptor interaction pathway (P<0.003) and intestinal immune network for IgA production pathway (P<0.006). The 25 most differentially expressed genes were associated directly with type I and II IFN response. Collectively, our findings based on in silico studies suggest that PCa with PTEN loss exhibits dysregulated Type I and II IFN response that permits progression to an aggressive disease phenotype. Future investigations will be required to define the mechanisms underlying these correlations, and their role in PCa disease progression so that inflammation biomarker can be therapeutically exploited using immunotherapies.

Distinct subtypes of genomic PTEN deletion size influence the landscape of aneuploidy and outcome in prostate cancer

Background

Inactivation of the PTEN tumor suppressor gene by deletion occurs in 20-30% of prostate cancer tumors and loss strongly correlates with a worse outcome. PTEN loss of function not only leads to activation of the PI3K/AKT pathway, but is also thought to affect genome stability and increase levels of tumor aneuploidy. We performed an in silico integrative genomic and transcriptomic analysis of 491 TCGA prostate cancer tumors. These data were used to map the genomic sizes of PTEN gene deletions and to characterize levels of instability and patterns of aneuploidy acquisition.

Results

PTEN homozygous deletions had a significant increase in aneuploidy compared to PTEN tumors without an apparent deletion, and hemizygous deletions showed an intermediate aneuploidy profile. A supervised clustering of somatic copy number alterations (SCNA) demonstrated that the size of PTEN deletions was not random, but comprised five distinct subtypes: (1) "Small Interstitial" (70 bp-789Kb); (2) "Large Interstitial" (1-7 MB); (3) "Large Proximal" (3-65 MB); (4) "Large Terminal" (8-64 MB), and (5) "Extensive" (71-132 MB). Many of the deleted fragments in each subtype were flanked by low copy repetitive (LCR) sequences. SCNAs such as gain at 3q21.1-3q29 and deletions at 8p, RB1, TP53 and TMPRSS2-ERG were variably present in all subtypes. Other SCNAs appeared to be recurrent in some deletion subtypes, but absent from others. To determine how the aneuploidy influenced global levels of gene expression, we performed a comparative transcriptome analysis. One deletion subtype (Large Interstitial) was characterized by gene expression changes associated with angiogenesis and cell adhesion, structure, and metabolism. Logistic regression demonstrated that this deletion subtype was associated with a high Gleason score (HR = 2.386; 95% C.I. 1.245-4.572), extraprostatic extension (HR = 2.423, 95% C.I. 1.157-5.075), and metastasis (HR = 7.135; 95% C.I. 1.540-33.044). Univariate and multivariate Cox Regression showed that presence of this deletion subtype was also strongly predictive of disease recurrence.

Conclusions

Our findings indicate that genomic deletions of PTEN fall into five different size distributions, with breakpoints that often occur close LCR regions, and that each subtype is associated with a characteristic aneuploidy signature. The Large Interstitial deletion had a distinct gene expression signature that was related to cancer progression and was also predictive of a worse prognosis.

Abstract B58: The effect of differential miRNA expression in glioblastoma multiforme molecular subtypes

Glioblastoma multiforme (GBM) is characterized by a distinct profile of specific miRNAs that regulate pathways of therapeutic importance, such as cell proliferation, apoptosis, cell cycle regulation, migration, invasion, and angiogenesis. Recently, the molecular classification of gliomas was updated, and three methylation clusters with distinct prognostic values for GBM were characterized. The aim of this research is to evaluate the expression, the functional roles, and the target genes of the miRNAs that have potential value for diagnosis, prognosis, and treatment in patients within the newest molecular subgroup classification of GBM. First, we performed an in silico analysis 606 GBM samples from the Genome Data Commons (GDC) cohort. Based on the methylation subgroups of gliomas recently published (Cecarelli et al., 2016), we performed a comparison of the miRNA expression between LGm4, LGm5, and LGm6 subgroups through Nexus Expression 3.0 (Biodiscovery). The comparison between LGm4 x LGm6 indicated that eight miRNAs were upregulated, while 17 were downregulated. The LGm5 x LGm4 comparison showed two downregulated miRNAs, and the LGm5 x LGm6 comparison showed one upregulated miRNA. By comparing the differentially expressed miRNAs found in our analysis with two other in silico studies, we found an overlap of 54% of the differentially expressed miRNAs. We will now evaluate the expression levels of the upregulated miRNAs obtained through the in silico analysis of samples of the Hospital of Clinics - Faculty of Medicine of Ribeirão Preto (HCFMRP/USP) through a customized nCounter NanoString panel of 24 miRNA. We will also evaluate the plasma exosomal miRNAs from the same patients using the same 24 miRNA nCounter NanoString panel. By identifying the most significant miRNAs regulating cell proliferation and invasive behavior in this tumor, we will be able to use expression levels of the most informative miRNA to both guide the molecular diagnosis of GBM and facilitate future targeted therapeutics for this aggressive disease.

Citation Format: Livia Ferreira Silva Verzola, Thiago Vidotto, Jeremy Andrew Squire. The effect of differential miRNA expression in glioblastoma multiforme molecular subtypes [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr B58.

Abstract B30: PTEN loss associates with type I and II IFN response in prostate cancer

PTEN gene deletion and protein loss occurs in 20-30% of prostate cancer (PCa) cases and leads to poor disease outcome. Loss of the PTEN tumor suppressor gene activates the PI3 kinase pathway and also appears to alter cellular interferon (IFN) responses. Recent evidence highlights the role of inflammation in the tumor microenvironment (TME) and its association with PCa disease progression. It is thus important to establish whether IFN response inflammatory biomarkers in PCa tumors are predictive of disease outcome in the context of PTEN status. The aim of this study is to determine if PTEN genomic and protein loss is associated with IFN response in the TME. We performed an in silico analysis of genomic and corresponding transcriptomic profiles PCa tumors (n=493) from the Genomic Data Commons (GDC) cohort to identify significant alterations in immune response pathways when PTEN was lost. Nexus Copy Number, v8.0 (BioDiscovery, Santa-Clara, CA, USA) was used for normalization, segmentation, and identification of corresponding copy number events of all genomic files in the GDC cohort. The GDC RNAseq dataset comprises the expression of 20,532 genes that were filtered using standard thresholds from Nexus Expression 3.0 (BioDiscovery, Santa-Clara, CA, USA). The filtering resulted in 6081 genes. Genes of interest were identified using the Gene Ontology (GO) Biological Function in Nexus Expression 3.0 with the keywords “Immune” and “Inflammatory” (http://geneontology.org/). Of the 449 selected immune genes, 124 (28%) were differentially expressed when the PTEN-loss group was compared to the PTEN-intact group. DAVID enrichment analysis showed upregulation of 16 pathways, in which three were directly associated with immune and inflammatory responses, including retinoic acid-inducible gene I (RIG-I-like) receptor signaling pathway (P&lt;0.0001), chemokine signaling pathway (P&lt;0.0001), and Toll-like receptor signaling pathway (P&lt;0.0001). In addition, we identified ten downregulated pathways, including cytokine-cytokine receptor interaction pathway (P&lt;0.003) and intestinal immune network for IgA production pathway (P&lt;0.006). We then selected the 25 most differentially expressed genes from the three upregulated and two downregulated pathways described above to compare the cohort of 218 prostate cancer tumors from MSKCC (in which 11% had PTEN loss) to the GDC cohort. The direction of differential gene expression was identical for 19/25 (76%) genes, in both cohorts having similarly altered PTEN-dependent changes in expression of immune and inflammatory response genes. The 25 most differentially expressed genes were associated directly with type I and II IFN response, indicating that PTEN loss affects the TME probably through the IRF3-IFN axis. Collectively, our findings based on in silico studies suggest that PCa with PTEN loss exhibits dysregulated Type I and II IFN response that permits progression to an aggressive disease phenotype. Future investigations will be required to define the mechanisms underlying these correlations, and their role in PCa disease progression so that inflammation biomarker can be therapeutically exploited using immunotherapies.

Citation Format: Thiago Vidotto, Jeremy Andrew Squire, Madhuri Koti. PTEN loss associates with type I and II IFN response in prostate cancer [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr B30.

Abstract 716: STAT1 expression in the tumor-stroma microenvironment is influenced by loss of PTEN in prostate cancer

The prostate cancer (PCa) microenvironment is an admixture of stromal cells, such as lymphocytes, fibroblasts, myofibroblasts and blood vessel endothelium. The reactive stromal microenvironment of PCa facilitates tumor growth through cytokine and chemokine-mediated cell signaling. STAT1, a transcription factor, induces cell cycle arrest, apoptosis and modulates immune and inflammatory response through IFN-á/ã cytokine activation. IFN-á/ã may be secreted in response to PI3K/AKT activation, since this pathway is associated with JAK/STAT signaling. In addition, the PI3K/AKT pathway can become activated when the PTEN prognostic biomarker is deleted in PCa. The rationale for this project is that the immediate stromal microenvironment of PCa may become pro-tumorigenic as a result of induction of inflammatory cytokines caused by PTEN deletions and activation of PI3K/AKT. We performed FISH analysis of the PTEN gene on 172 cores on a PCa tissue microarray (TMA) derived from 43 patients with intermediate risk disease. Analysis of cytoplasmic and nuclear STAT1 in both the tumor and stromal compartments was performed on each TMA core using immunohistochemistry (IHC) to determine whether the tumor PTEN deletion status was associated with STAT1 expression. In each core, tumor and stromal cell histologies were evaluated independently to estimate the percentage area that was stained positive by IHC. The staining was graded as percentage of positive cells with 0 (negative), 1 (less than 10%), 2 (11% to 50%), and 3 (more than 51%). We found that STAT1 expression in stroma was increased when the PTEN gene in the adjacent tumor was homozygously deleted (p = 0,04). We also showed that mean STAT1 expression in benign tissue cores was reduced when compared to the average score from tumor tissue with one (p = 0.01) or two copies (p = 0.03) of the PTEN gene. STAT1 expression and PTEN gene copy numberPTEN copy numberMean STAT1 in StromaMean STAT1 in Tumor&gt;2 copies0.410.822 copies0.510.651 copy0.600.700 copies0.850.85

These results suggest that the STAT1 pathway may be influenced by PTEN loss in this tumor, suggesting that the JAK/STAT inflammatory pathway may have future clinical applications in PCa.

Citation Format: Thiago Vidotto, Clarissa G. Picanço-Albuquerque, Fabiano P. Saggioro, Rodolfo Borges dos Reis, David Robert Siemens, Madhuri Koti, Jeremy A. Squire. STAT1 expression in the tumor-stroma microenvironment is influenced by loss of PTEN in prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 716.

Characterization of 12 microsatellite loci for Hypochaeris chillensis (Asteraceae) and cross-amplification in related species

PREMISE OF THE STUDY

Hypochaeris is considered a biological model to understand evolutionary processes in the vascular flora of South America, particularly from the temperate portion of the continent. We report the development and characterization of microsatellite markers for H. chillensis to assess the genetic variability and patterns of population structure of the species. •

METHODS AND RESULTS

Twelve microsatellite primers were isolated using a CT- and GT-enriched genomic library. PCR amplification detected one to five alleles, with 2.91 alleles per locus on average. Tested for cross-amplification, all primer pairs were successfully amplified in 10 South American species and in the putative ancestor of the group, H. angustifolia. •

CONCLUSIONS

The microsatellites can be used to assess genetic diversity and population structure of H. chillensis. Application in other species will focus on the elucidation of adaptive radiation of the genus in South America.