Role of adenosine deaminase in prostate cancer progression

Prostate cancer (PCa) is the second most common cancer and constitutes about 14.7% of total cancer cases. PCa is highly prevalent and more aggressive in African-American (AA) men than in European-American (EA) men. PCa tends to be highly heterogeneous, and its complex biology is not fully understood. We use metabolomics to better understand the mechanisms behind PCa progression and disparities in its clinical outcome. Adenosine deaminase (ADA) is a key enzyme in the purine metabolic pathway; it was found to be upregulated in PCa and is associated with higher-grade PCa and poor disease-free survival. The inosine-to-adenosine ratio, which is a surrogate for ADA activity was high in PCa patient urine and higher in AA PCa compared to EA PCa. To understand the significance of high ADA in PCa, we established ADA overexpression models and performed various in vitro and in vivo studies. Our studies have revealed that an acute increase in ADA expression during later stages of tumor development enhances in vivo growth in multiple pre-clinical models. Further analysis revealed that mTOR signaling activation could be associated with this tumor growth. Chronic ADA overexpression shows alterations in the cells' adhesion machinery and a decrease in cells' ability to adhere to the extracellular matrix in vitro. Losing cell-matrix interaction is critical for metastatic dissemination which suggests that ADA could potentially be involved in promoting metastasis. This is supported by the association of higher ADA expression with higher-grade tumors and poor patient survival. Overall, our findings suggest that increased ADA expression may promote PCa progression, specifically tumor growth and metastatic dissemination.

Analysis of the Tumor Immune Microenvironment (TIME) in Clear Cell Renal Cell Carcinoma (ccRCC) Reveals an M0 Macrophage-Enriched Subtype: An Exploration of Prognostic and Biological Characteristics of This Immune Phenotype

There is a need to optimize the treatment of clear cell renal cell carcinoma (ccRCC) patients at high recurrence risk after nephrectomy. We sought to elucidate the tumor immune microenvironment (TIME) of localized ccRCC and understand the prognostic and predictive characteristics of certain features. The discovery cohort was clinically localized patients in the TCGA-Kidney Renal Clear Cell Carcinoma (KIRC) project (n = 382). We identified an M0 macrophage-enriched cluster (n = 25) in the TCGA-KIRC cohort. This cluster's median progression-free survival (PFS) and overall survival (OS) were 40.4 and 45.3 months, respectively, but this was not reached in the others (p = 0.0003 and <0.0001, respectively). Gene set enrichment (GSEA) analysis revealed an enrichment of epithelial to mesenchymal transition and cell cycle progression genes within this cluster, and these patients also had a lower predicted response to immune checkpoint blockade (ICB) (4% vs. 20-34%). An M0-enriched cluster (n = 9) with shorter PFS (p = 0.0006) was also identified in the Clinical Proteomics Tumor Analysis Consortium (CPTAC) cohort (n = 94). Through this characterization of the TIME in ccRCC, a cluster of patients defined by enrichment in M0 macrophages was identified that demonstrated poor prognosis and lower predicted ICB response. Pending further validation, this signature can identify localized ccRCC patients at high risk of recurrence after nephrectomy and who may require therapeutic approaches beyond ICB monotherapy.

Development of a Whole-urine, Multiplexed, Next-generation RNA-sequencing Assay for Early Detection of Aggressive Prostate Cancer

BACKGROUND

Despite biomarker development advances, early detection of aggressive prostate cancer (PCa) remains challenging. We previously developed a clinical-grade urine test (Michigan Prostate Score [MiPS]) for individualized aggressive PCa risk prediction. MiPS combines serum prostate-specific antigen (PSA), the TMPRSS2:ERG (T2:ERG) gene fusion, and PCA3 lncRNA in whole urine after digital rectal examination (DRE).

OBJECTIVE

To improve on MiPS with a novel next-generation sequencing (NGS) multibiomarker urine assay for early detection of aggressive PCa.

DESIGN, SETTING, AND PARTICIPANTS

Preclinical development and validation of a post-DRE urine RNA NGS assay (Urine Prostate Seq [UPSeq]) assessing 84 PCa transcriptomic biomarkers, including T2:ERG, PCA3, additional PCa fusions/isoforms, mRNAs, lncRNAs, and expressed mutations. Our UPSeq model was trained on 73 patients and validated on a held-out set of 36 patients representing the spectrum of disease (benign to grade group [GG] 5 PCa).

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

The area under the receiver operating characteristic curve (AUC) of UPSeq was compared with PSA, MiPS, and other existing models/biomarkers for predicting GG ≥3 PCa.

RESULTS AND LIMITATIONS

UPSeq demonstrated high analytical accuracy and concordance with MiPS, and was able to detect expressed germline HOXB13 and somatic SPOP mutations. In an extreme design cohort (n = 109; benign/GG 1 vs GG ≥3 PCa, stratified to exclude GG 2 cancer in order to capture signal difference between extreme ends of disease), UPSeq showed differential expression for T2:ERG.T1E4 (1.2 vs 78.8 median normalized reads, p < 0.00001) and PCA3 (1024 vs 2521, p = 0.02), additional T2:ERG splice isoforms, and other candidate biomarkers. Using machine learning, we developed a 15-transcript model on the training set (n = 73) that outperformed serum PSA and sequencing-derived MiPS in predicting GG ≥3 PCa in the held-out validation set (n = 36; AUC 0.82 vs 0.69 and 0.69, respectively).

CONCLUSIONS

These results support the potential utility of our novel urine-based RNA NGS assay to supplement PSA for improved early detection of aggressive PCa.

PATIENT SUMMARY

We have developed a new urine-based test for the detection of aggressive prostate cancer, which promises improvement upon current biomarker tests.

Prognostic value and therapeutic implications of an integrative molecular subtype and immune content classifier in localized muscle-invasive bladder cancer

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Background: Localized muscle-invasive bladder cancer (MIBC) exhibits heterogeneous molecular features and outcomes, with a 5-year mortality rate of approximately 30%. Immune checkpoint blockade (ICB) has the potential to improve oncological outcomes but molecular tools are needed to identify those most likely to benefit. Here, we integrate transcriptomically derived tumor immune microenvironment (TIME) data with molecular subtypes to create a novel integrative classifier with prognostic and therapeutic implications. Methods: RNAseq data from patients with localized muscle-invasive bladder cancer (MIBC) from the Cancer Genome Atlas BLCA (TCGA-BLCA) project was utilized (n = 187). CIBERSORT was used for immune cell deconvolution, and unsupervised hierarchical clustering divided the cohort based on similar immune profiles. Consensus molecular clustering information for the cohort was obtained from Kamoun et al. Overall survival (OS) of each cluster were analyzed. The tumor immune dysfunction and exclusion (TIDE) tool, which uses a genomic signature validated on immunotherapy treated melanoma patients to model tumor immune evasion, was then used to predict response to ICB. Results: In the TCGA-BLCA cohort, there were two distinct clusters enriched with macrophages, CL1-M0Hi (n = 18) and CL5-M2Hi (n = 35). Compared to the rest of the cohort, these two macrophage enriched clusters combined exhibited a decreased OS (33.1 mo vs. NR, p = 0.01). TIDE tool predicted ICB response was lowest in CL1 (6/18, 33%; p = 0.09), CL5 (12/35, 34%; p = 0.02), and the Ba/Sq molecular cluster (16/57, 28%; p = 1.3x10-5). Patients designated as CL1 or CL5 by immune clustering and Ba/Sq by molecular consensus were combined into a subgroup (n = 20). Compared to the rest of the cohort, this Ba/Sq_MacrophageHi subgroup had a higher body mass index (31.0 vs. 25.8 BMI, p = 0.0004), more whites (95% vs. 64%, p = 0.03), and had a higher stage (80% Stage III/IV vs. 20% Stage I/II, p = 0.05). The Ba/Sq_MacrophageHi cluster demonstrated higher PD-L1 expression (mean Z score 0.15 vs. -0.09; p = 0.008), there was a higher degree of T cell exclusion (mean Z score 0.16 vs. -0.06; p = 0.003) and cancer-associated fibroblasts (mean Z score 0.03 vs. -0.02; p = 3.4x10-5). Overall, the predicted response to ICB by TIDE in the Ba/Sq_MacrophageHi was lower (OR 0.15, 0.03-0.55 p = 0.002) and OS was significantly shorter (median 16.7 mos vs. 54.9 mo, p = 0.04). Conclusions: We demonstrated the prognostic significance of the Basal/Squamous subtype with macrophage enrichment in patients with localized MIBC. Pending further prospective validation, this sub-population may be less amenable to ICB treatment.

Validation of a 22-gene epithelial-mesenchymal transition (EMT) prognostic signature in clear cell renal cell carcinoma

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Background: Current predictors of metastatic progression after radical nephrectomy for localized clear cell renal cell carcinoma (ccRCC) include clinicopathologic features such as tumor stage and grade. The addition of molecular tumor characteristics in a prognostic score may improve risk stratification and patient selection for enhanced follow up strategies or adjuvant therapies. Methods: We retrospectively identified consecutive patients with ccRCC who underwent radical nephrectomy (RNx) for localized disease. Those who developed metastasis were identified. Whole-transcriptome mRNA sequencing of primary tumors was performed followed by gene set enrichment analysis (GSEA) for the most significant cancer hallmark pathways enriched in patients who did or did not develop metastasis. For each patient, the 22-gene epithelial mesenchymal transition (EMT) score was calculated (high vs. low), using cut-offs from a prior study using TCGA data. The prognostic impact of the EMT score was evaluated by performing multivariable cox-proportional hazard testing and Kaplan-Meier (KM) survival analysis. Results: We analyzed 82 patients with median age 62 years and median tumor size 6 ±2.9 cm. The median time to metastasis after radical nephrectomy for patients who developed metastasis (n = 12) was 18.2 months and 31.1 months for patients who did not develop metastasis (n = 70). We observed a significant enrichment of EMT, myogenesis, inflammatory response and hypoxia hallmark pathways in patients with metastasis vs. those without metastasis. Multivariable analysis controlling for relevant clinicopathologic features such as age, sex, tumor size, tumor stage etc. revealed high EMT score to be significantly associated with development of metastasis [hazard ratio (HR) 7.2; 95% CI 1.15-44.8; ]. Conclusions: Here we validate a prognostic 22-gene epithelial mesenchymal transition (EMT) score in patients treated with radical nephrectomy for localized ccRCC. Pending further studies, the EMT score may improve risk stratification and select patients for adjuvant therapy.

Molecular characterization to delineate the clonal evolution of primary prostate cancer with synchronous lymph node metastasis

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Background: Primary prostate cancers (PCa) harbor multiple spatially distinct tumors with significant inter-lesion molecular heterogeneity. This diversity can result in many subclones that compete for biological and clinical dominance. The defining features of primary PCa that give rise to lymph node (LN) metastases is unknown. We performed multiregional targeted DNA/RNA next generation sequencing (NGS) of primary PCa with synchronous LN metastases to identify primary PCa foci capable of metastasis. Methods: Patients who underwent radical prostatectomy and LN dissection with pathologic node positive disease were identified. Punch biopsies were performed from pre-identified regions of cancer on formalin fixed paraffin embedded (FFPE) prostate and LN specimens and DNA/RNA samples were co-isolated. Targeted NGS was performed to characterize the genomic profile of each tumor region and to evaluate gene fusion status of each sample. We compared somatic DNA mutations, copy number alterations (CNA), and gene fusion status between primary and LN disease. Phylogenetic analysis was performed using the Phylip’s dollo and parsimony, neighbor-joining method to determine the likely clonal source of LN metastasis. Results: We analyzed 88 primary tumor (1°) and 23 LN-metastases samples from 14 patients. After quality control, 11 patients (69 and 18 primary and LN tumor samples, respectively) had sufficient quality data for analyses. Seven had evidence of extraprostatic extension (EPE), with phylogenetic analysis supporting this as the source of LN-metastasis in 4 cases. One patient had concordant TP53 and TPR non-synonymous mutations and broad CNAs between all 1°and two LN-metastasis foci, with two of the 1° regions showing high-level CNAs with both LN-metastasis foci. In two patients with pT2N1 disease, sub-clonal seeding and clonal evolution was observed with metastases arising from a GG5 area. Seven had cribriform pattern in both LN and 1° foci. One patient showed CDK12 mutation within the 1° and LN foci. FOXA1 was mutated in two patients within 1° and LN foci. Conclusions: Using targeted DNA/RNA NGS to assess primary PCa and synchronous LN metastases, we demonstrate that LN metastases is related to a combination of histopathologic and genomic factors. This highlights the need to develop robust prognostic biomarkers for identification of novel therapeutic targets for LN metastasis.

The role of spatial transcriptomic profiling to determine androgen receptor signaling and immune infiltration in prostate cancer

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Background: Prostate cancer (PCa) in the transition zone (TZ) accounts for approximately 30% of disease and tends to present with higher PSAs with a lower risk of seminal vesicle invasion, extra-capsular extension, and risk of biochemical recurrence compared with peripheral zone (PZ) tumors. The underlying biological mechanism for these differences is poorly understood. Here, we performed spatial transcriptomic profiling to elucidate the molecular differences between TZ and PZ PCa. Methods: We identified three patients who underwent radical prostatectomy for PCa (one each with PZ only, TZ only, and both PZ and TZ tumors) and used the NanoString’s Digital Spatial Profiling (DSP) platform to quantify whole transcriptomic gene expression data (17,128 genes) in multiple regions of interest (ROI) per patient (42 cancer and 8 normal samples). Four morphology markers to facilitate ROI selection in both cancer and normal areas (SYTO13 for nucleus, PanCK for epithelium, SMA for stroma and CD45 for immune cells) were selected. Raw counts for 17,128 genes were imported to R v.4.1.0 for downstream data analyses. Counts were Q3 normalized and scaled (Z-score) to enable plotting of all genes on the same axes. Differential gene expression analysis using a linear model fit by empirical Bayes moderation, gene set enrichment analysis (GSEA) by cancer hallmarks, XCell gene sets for pathway enrichment and immune cell deconvolution using CIBERSORT was performed. Results: There were grade group (GG) 4 (n=10) and 5 (n=10) tumors in PZ and GG 3 (n=10), 4 (n=11) and 5 (n=1) cancers in TZ regions. We observed distinct gene expression profiles between PZ (n = 20) and TZ (n=22) tumors. Interestingly, androgen receptor (AR) signaling was significantly higher in TZ PCa ROIs compared to PZ ROIs in both GSEA (false discovery rate < 5%) and the androgen subcomponent of the genomic prostate score (p<0.001), regardless of grade, epithelial, stromal or immune component of the region. To standardize the comparison, CIBERSORT’s absolute immune signature scores were only computed for GG4 tumors and found to be significantly higher in PZ GG4 tumors compared to TZ GG4 tumors. Notably, CD4+ memory T cells were significantly higher in PZ GG4 regions compared to TZ GG4 tumor regions (p<0.05). Conclusions: Here, we demonstrate distinct gene expression profiles of PZ and TZ PCa. Specifically, we observed higher AR signaling in TZ cancers and higher levels of immune infiltration on PZ cancers. This is in concordance with prior knowledge that TZ tumors may be associated with higher serum PSA and PZ tumors may be associated with inflammation. Further studies are needed to discern the biological and clinical significance of the different molecular features of PZ and TZ PCa.

The prevalence and density of asymptomatic Plasmodium falciparum infections among children and adults in three communities of western Kenya

BACKGROUND

Further reductions in malaria incidence as more countries approach malaria elimination require the identification and treatment of asymptomatic individuals who carry mosquito-infective Plasmodium gametocytes that are responsible for furthering malaria transmission. Assessing the relationship between total parasitaemia and gametocytaemia in field surveys can provide insight as to whether detection of low-density, asymptomatic Plasmodium falciparum infections with sensitive molecular methods can adequately detect the majority of infected individuals who are potentially capable of onward transmission.

METHODS

In a cross-sectional survey of 1354 healthy children and adults in three communities in western Kenya across a gradient of malaria transmission (Ajigo, Webuye, and Kapsisywa-Kipsamoite), asymptomatic P. falciparum infections were screened by rapid diagnostic tests, blood smear, and quantitative PCR of dried blood spots targeting the varATS gene in genomic DNA. A multiplex quantitative reverse-transcriptase PCR assay targeting female and male gametocyte genes (pfs25, pfs230p), a gene with a transcriptional pattern restricted to asexual blood stages (piesp2), and human GAPDH was also developed to determine total parasite and gametocyte densities among parasitaemic individuals.

RESULTS

The prevalence of varATS-detectable asymptomatic infections was greatest in Ajigo (42%), followed by Webuye (10%). Only two infections were detected in Kapsisywa. No infections were detected in Kipsamoite. Across all communities, children aged 11-15 years account for the greatest proportion total and sub-microscopic asymptomatic infections. In younger age groups, the majority of infections were detectable by microscopy, while 68% of asymptomatically infected adults (> 21 years old) had sub-microscopic parasitaemia. Piesp2-derived parasite densities correlated poorly with microscopy-determined parasite densities in patent infections relative to varATS-based detection. In general, both male and female gametocytaemia increased with increasing varATS-derived total parasitaemia. A substantial proportion (41.7%) of individuals with potential for onward transmission had qPCR-estimated parasite densities below the limit of microscopic detection, but above the detectable limit of varATS qPCR.

CONCLUSIONS

This assessment of parasitaemia and gametocytaemia in three communities with different transmission intensities revealed evidence of a substantial sub-patent infectious reservoir among asymptomatic carriers of P. falciparum. Experimental studies are needed to definitively determine whether the low-density infections in communities such as Ajigo and Webuye contribute significantly to malaria transmission.

Characterization of the tumor immune microenvironment in clear cell renal cell carcinoma (ccRCC): Prognostic value and therapeutic implications of an M0-macrophage enriched subtype

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Background: Metastatic clear cell renal cell carcinoma (ccRCC) has a 5-year survival of 12%, but the number of approved immune checkpoint blockade (ICB) agents is growing, necessitating the need to better identify responders. The composition and role of the tumor immune microenvironment (TIME) has yet to be comprehensively characterized in ccRCC. Here, we leveraged a genomic data driven approach to characterize TIME subtypes in ccRCC. Methods: Whole transcriptome data from patients with local and metastatic disease in the Cancer Genome Atlas KIRC (TCGA-KIRC) project was utilized (n = 537). CIBERSORT was used for immune cell deconvolution, and unsupervised hierarchical clustering divided the cohort based on similar immune profiles. Progression free (PFS) and overall (OS) survival of each cluster was analyzed, and Gene Set Enrichment analysis was performed among clusters. The tumor immune dysfunction and exclusion (TIDE) tool, which uses a genomic signature validated on immunotherapy treated melanoma patients to model tumor immune evasion, was then used to predict response to ICB in the TCGA-KIRC clusters. Results: There was a distinct M0hi cluster identified which demonstrated a higher proportion of patients with stage III/IV disease, decreased PFS and OS (Table). Additionally, the M0hi cluster was characterized by lower PD-L1 expression (ANOVA, p = 0.0045) and an enrichment of epithelial to mesenchymal transition (EMT) hallmark genes [Enrichment Score = 0.64, p = 0.001]. The M0hi cluster also showed a higher degree of T-Cell Exclusion (ANOVA, p = 2.2x10-16), predominance of Cancer Associated Fibroblasts (CAFs; ANOVA, p = 2.2x10-16) and Myeloid Derived Suppressor Cells (MDSCs; ANOVA, p = 4.1x10-10). The M0hi cluster had the lowest predicted response to immunotherapy using the TIDE tool (Table). Conclusions: Comprehensive characterization of the TCGA-KIRC cohort led to identification of a distinct cluster of ccRCC defined molecularly by decreased PD-L1 and increased EMT gene expression and cellularly by enrichment of M0 macrophages, CAFs, MDSCs, and an exclusion of T Cells. Patients within this cluster exhibited aggressive disease and poor predicted response to ICB. These findings warrant further validation to identify appropriate therapeutic approaches for this ccRCC subgroup.[Table: see text]

Tumor size and genomic risk in localized prostate cancer

PURPOSE

Unlike many other cancers, measurement of primary prostate tumor size has no defined role in the management of localized prostate cancer. Here, we assess whether prostate tumor size is associated with aggressive tumor biology using biomarkers of genomic risk.

MATERIALS AND METHODS

We abstracted or imputed tumor size from the primary pathology reports of prostate cancers incorporated in The Cancer Genome Atlas. We used transcriptomic data to estimate the Cell Cycle Progression Score (CCPS, Prolaris), the Genomic Classifier Score (GCS, Decipher) and the Genomic Prostate Score (GPS, OncotypeDx), SChLaP1 expression, and copy number alteration percentage (%CNA) as well as hallmark gene set enrichment analysis.

RESULTS

Tumor size and gene expression data was available for 267 men. On multivariable regression adjusted for Gleason Grade Group and tumor purity, tumor size was independently associated with the calculated (c)GCS, cGPS, SChLaP1 expression, and %CNA (P< 0.05), but not cCCPS. Gene set enrichment analysis demonstrated that tumors <5 cc, when adjusting for Gleason grade group, were enriched for androgen response genes, while tumors >5 cc were enriched for MYC targets and genes associated with epithelial mesenchymal transition.

CONCLUSIONS

Prostate tumor size is independently associated with established markers of genomic risk. This study nominates the size of a primary prostate cancer as candidate for inclusion in future novel risk scores seeking to quantify cancer aggressiveness.

Serial Molecular Profiling of Low-grade Prostate Cancer to Assess Tumor Upgrading: A Longitudinal Cohort Study

BACKGROUND

The potential for low-grade (grade group 1 [GG1]) prostate cancer (PCa) to progress to high-grade disease remains unclear.

OBJECTIVE

To interrogate the molecular and biological features of low-grade PCa serially over time.

DESIGN, SETTING, AND PARTICIPANTS

Nested longitudinal cohort study in an academic active surveillance (AS) program. Men were on AS for GG1 PCa from 2012 to 2017.

INTERVENTION

Electronic tracking and resampling of PCa using magnetic resonance imaging/ultrasound fusion biopsy.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

ERG immunohistochemistry (IHC) and targeted DNA/RNA next-generation sequencing were performed on initial and repeat biopsies. Tumor clonality was assessed. Molecular data were compared between men who upgraded and those who did not upgrade to GG ≥ 2 cancer.

RESULTS AND LIMITATIONS

Sixty-six men with median age 64 yr (interquartile range [IQR], 59-69) and prostate-specific antigen 4.9 ng/mL (IQR, 3.3-6.4) underwent repeat sampling of a tracked tumor focus (median interval, 11 mo; IQR, 6-13). IHC-based ERG fusion status was concordant at initial and repeat biopsies in 63 men (95% vs expected 50%, p <  0.001), and RNAseq-based fusion and isoform expression were concordant in nine of 13 (69%) ERG⁺ patients, supporting focal resampling. Among 15 men who upgraded with complete data at both time points, integrated DNA/RNAseq analysis provided evidence of shared clonality in at least five cases. Such cases could reflect initial undersampling, but also support the possibility of clonal temporal progression of low-grade cancer. Our assessment was limited by sample size and use of targeted sequencing.

CONCLUSIONS

Repeat molecular assessment of low-grade tumors suggests that clonal progression could be one mechanism of upgrading. These data underscore the importance of serial tumor assessment in men pursuing AS of low-grade PCa.

PATIENT SUMMARY

We performed targeted rebiopsy and molecular testing of low-grade tumors on active surveillance. Our findings highlight the importance of periodic biopsy as a component of monitoring for cancer upgrading during surveillance.

Dissection of primary prostate cancer to determine the clonal origin of synchronous lymph node metastasis

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Background: Primary prostate cancer often consists of multiple, genomically-distinct clones. The clonal source of lymph node metastasis in multifocal disease is unknown. We sought to analyze and determine the histopathologic and molecular characteristics of the tumor sub-clones capable of metastasis in primary prostate cancers with synchronous lymph node metastasis. Methods: We identified patients with primary prostate cancer found to have lymph node (LN) metastasis at the time of radical prostatectomy, including those with multifocal disease. Punch biopsies were obtained from multiple regions of primary tumors and LN metastases. Targeted next generation sequencing to assess somatic DNA mutations, copy number alterations (CNA), and TMPRSS2:ERG fusion status. Bioinformatic analyses were performed using in-house developed pipelines. Phylogenetic evolutionary analyses were performed to delineate the primary cancer clone responsible for LN metastasis. Results: We identified 2 patients with LN cancer regions. In one patient, while all four Grade Group (GG) 5 primary tumor (PT) regions showed concordant TP53 and TPR non-synonymous mutations and broad copy number alterations (CNAs) with two LN foci, only two regions shared high level CNAs with both lymph node foci. In this case, a GG1 tumor focus showed no TP53 somatic mutation or CNA overlap with the high-grade tumor or lymph node samples. Critically, phylogenetic analysis revealed that the GG5 PT with extra-prostatic extension (EPE) showed higher concordance with the LN metastases than regions confined to the prostate. In another patient with four PT, phylogenetic analysis revealed that the PT with EPE closely resembled the LN metastasis; both were TMPRSS2:ERG fusion positive share PTEN copy number loss. Two PT (GG1 and 2) appeared to be independent clones and were TMPRSS2:ERG fusion negative. One of the six circulating tumor cells (isolated pre-prostatectomy) from this patient demonstrated a significant PTEN copy loss consistent with the findings in the region of EPE and the LN metastasis. Conclusions: Our findings confirm molecular heterogeneity of primary prostate cancers and homogeneity of LN metastases supporting the use of shared molecular alterations to infer clonal lineage. Our results highlight the critical role of adverse pathologic features, such as grade and EPE, in prostate cancer with synchronous lymph node metastasis.

Whole-Blood Transcriptional Signatures Composed of Erythropoietic and NRF2-Regulated Genes Differ Between Cerebral Malaria and Severe Malarial Anemia

Background

Among the severe malaria syndromes, severe malarial anemia (SMA) is the most common, whereas cerebral malaria (CM) is the most lethal. However, the mechanisms that lead to CM and SMA are unclear.

Methods

We compared transcriptomic profiles of whole blood obtained from Ugandan children with acute CM (n = 17) or SMA (n = 17) and community children without Plasmodium falciparum infection (n = 12) and determined the relationships among gene expression, hematological indices, and relevant plasma biomarkers.

Results

Both CM and SMA demonstrated predominantly upregulated enrichment of dendritic cell activation, inflammatory/Toll-like receptor/chemokines, and monocyte modules, but downregulated enrichment of lymphocyte modules. Nuclear factor, erythroid 2 like 2 (Nrf2)-regulated genes were overexpressed in children with SMA relative to CM, with the highest expression in children with both SMA and sickle cell disease (HbSS), corresponding with elevated plasma heme oxygenase-1 in this group. Erythroid and reticulocyte-specific signatures were markedly decreased in CM relative to SMA despite higher hemoglobin levels and appropriate increases in erythropoietin. Viral sensing/interferon-regulatory factor 2 module expression and plasma interferon-inducible protein-10/CXCL10 negatively correlated with reticulocyte-specific signatures.

Conclusions

Compared with SMA, CM is associated with downregulation of Nrf2-related and erythropoiesis signatures by whole-blood transcriptomics. Future studies are needed to confirm these findings and assess pathways that may be amenable to interventions to ameliorate CM and SMA.

Biologic Significance of Magnetic Resonance Imaging Invisibility in Localized Prostate Cancer

PURPOSE

Multiparametric magnetic resonance imaging (mpMRI) is used widely for prostate cancer (PCa) evaluation. Approximately 35% of aggressive tumors, however, are not visible on mpMRI. We sought to identify the molecular alterations associated with mpMRI-invisible tumors and determine whether mpMRI visibility is associated with PCa prognosis.

METHODS

Discovery and validation cohorts included patients who underwent mpMRI before radical prostatectomy and were found to harbor both mpMRI-visible (Prostate Imaging and Reporting Data System 3 to 5) and -invisible (Prostate Imaging and Reporting Data System 1 or 2) foci on surgical pathology. Next-generation sequencing was performed to determine differential gene expression between mpMRI-visible and -invisible foci. A genetic signature for tumor mpMRI visibility was derived in the discovery cohort and assessed in an independent validation cohort. Its association with long-term oncologic outcomes was evaluated in a separate testing cohort.

RESULTS

The discovery cohort included 10 patients with 26 distinct PCa foci on surgical pathology, of which 12 (46%) were visible and 14 (54%) were invisible on preoperative mpMRI. Next-generation sequencing detected prioritized genetic mutations in 14 (54%) tumor foci (n = 8 mpMRI visible, n = 6 mpMRI invisible). A nine-gene signature (composed largely of cell organization/structure genes) associated with mpMRI visibility was derived (area under the curve = 0.89), and the signature predicted MRI visibility with 75% sensitivity and 100% specificity (area under the curve = 0.88) in the validation cohort. In the testing cohort (n = 375, median follow-up 8 years) there was no significant difference in biochemical recurrence, distant metastasis, or cancer-specific mortality in patients with predicted mpMRI-visible versus -invisible tumors (all P > .05).

CONCLUSION

Compared with mpMRI-invisible disease, mpMRI-visible tumors are associated with underexpression of cellular organization genes. mpMRI visibility does not seem to be predictive of long-term cancer outcomes, highlighting the need for biopsy strategies that detect mpMRI-invisible tumors.

Radiogenomic characterization of multifocal prostate cancer

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Background: Up to 20% of patients with negative multiparametric magnetic resonance imaging (MRI) harbor Gleason score ≥7 prostate cancer (PCa). We sought to elucidate the molecular basis of and determine the prognostic significance of PCa visibility on MRI. Methods: We identified a retrospective cohort of patients who underwent MRI prior to prostatectomy with both MRI visible (PIRADS 3 – 5) and invisible PCa. MRI for each patient was re-reviewed and co-registered with whole-mount histopathology. DNA and RNA were co-isolated from all tumor foci pre-identified on FFPE specimens. High depth, targeted DNA and RNA next generation sequencing was performed to characterize the molecular profile of each tumor focus using the Oncomine Comprehensive Panel (DNA) and a custom targeted RNAseq panel assessing PCa relevant alterations. A multigene RNAseq model was developed and validated in two independent cohorts to predict MRI visible PCa and to determine the prognostic significance of MRI visibility. Results: A total of 26 primary tumor foci from 10 patients were analyzed. Of the 14 (54%) invisible lesions on MRI, 5 (36%) were Gleason 3+4 = 7 and the remainder were Gleason 6. We detected high-confidence prioritized PCa relevant mutations in 54% (14/26) of tumor foci, 43% (6/14) of which were in MRI invisible lesions. Notable point mutations were in APC, AR, ARID1B, ATM, ATRX, BRCA2, FAT1, MAP3K1, NF1, SPEN, SPOP, and TP53. A 9-gene RNA signature, the majority of which were under-expressed cellular organization and structure genes, was developed to predict MRI visibility with an AUC of 0.89. Validation of this signature in an independent data set (n = 16) yielded an AUC of 0.88 with a specificity of 100% for predicting MRI visible tumors. Using this signature in a cohort of 375 patients with clinical follow up, we found that predicted MRI visibility status was not an independent predictor of biochemical recurrence, metastasis-free survival, or PCa specific mortality (all p > 0.05). Conclusions: We observed under-expression of cellular organization and structural genes in MRI visible tumors compared to MRI invisible cancer foci. Using our validated signature to predict MRI visibility status, we found that MRI visibility is not a significant predictor of oncological outcomes.

Molecular characterization of longitudinally tracked prostate cancer foci in men on active surveillance for low-risk disease

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Background: The biological trajectory of Gleason score 6 (GS6) prostate cancer (PCa) in men on active surveillance (AS) is unknown. We herein evaluate the potential for high grade PCa to arise clonally from GS 6 disease and determine the capacity of tissue-based biomarkers to predict grade progression. Methods: Men on AS with GS6 PCa who underwent magnetic resonance imaging/ultrasound (MRI/US) fusion biopsy on two occasions from 2012 through 2017 were enrolled. Tumor foci were tracked and re-sampled using the MRI/US fusion biopsy platform. ERG immunohistochemistry (IHC) and DNA/RNA next generation sequencing (NGS) were performed on formalin-fixed paraffin-embedded (FFPE) initial and repeat biopsy specimens to assess tumor clonality and evaluate candidate molecular markers of PCa grade progression. Results: Sixty-seven men of median age 64 years (IQR 59-69) and PSA 4.9 ng/ml (IQR 3.3-6.4) underwent repeat sampling of a single tracked tumor focus using MRI/US fusion biopsy. The median interval to repeat biopsy was 11 months (IQR 6-13). On repeat biopsy, 31 (46%) men progressed to high-grade (GS≥7) disease (n = 24, GS 3+4 = 7; n = 7, GS ≥4+3 = 7). Among the 67 subjects, ERG IHC status was concordant between initial and repeat biopsy in 64 (96%). Of 134 total specimens obtained (67 initial + 67 repeat biopsies), ERG status determined by NGS was concordant with ERG status by IHC in 132 (99%). Comparing the initial biopsy specimens in men who did versus did not undergo grade progression on follow up biopsy, derived cell cycle progression (CCP) scores (median 57.3 vs. 44.0, p = 0.11) and genomic prostate scores (GPS; median 73.8 vs. 64.4, p = 0.15) were not significantly different. Similarly, expression of FOLH1, PCAT4, SCHLAP1, and SPINK1 on initial biopsy did not significantly differ among men who did and did not undergo grade progression. Conclusions: Use of MRI/US fusion biopsy facilitated resampling of the same clonal focus of cancer over time, with high concordance of ERG status determined by both IHC and NGS. Derived genomic classifiers and candidate individual gene expression markers measured on initial biopsy tissue were not significantly different between patients who progressed and those who did not.

963. Whole Blood Transcriptome Analysis Reveals Differences in Erythropoiesis and Neurologically Relevant Pathways Between Cerebral Malaria and Severe Malarial Anemia

Background

Plasmodium falciparum malaria can rapidly progress to severe disease that can lead to death if left untreated. Severe malaria cases commonly present as severe malarial anemia (SMA), defined in children as hemoglobin (Hb) &lt;5 g/dL with parasitemia, or as cerebral malaria (CM), which manifests as parasitemia with acute neurological deficits and has an inpatient mortality rate of ~20%. The molecular and cellular processes that lead to CM and SMA are unclear.

Methods

In a cross-sectional study, we compared genome-wide transcription profiles of whole blood obtained from Ugandan children with acute CM (n = 17) or SMA (n = 17) and community children without P. falciparum infection (n = 12) who were enrolled in a parent cohort study of severe malaria. We determined the relationships between gene expression, hematological indices, and plasma biomarkers, including inflammatory cytokines.

Results

Both CM and SMA demonstrated enrichment of dendritic cell activation, inflammatory/TLR/chemokines, monocyte, and neutrophil modules but depletion of lymphocyte modules. Neurodegenerative disease and neuroinflammation pathways were enriched in CM. Increased Nrf2 pathway gene expression corresponded with increased plasma heme oxygenase-1 and the heme catabolite bilirubin in a manner specific to children with both SMA and sickle cell disease. Reticulocyte-specific gene expression was markedly decreased in CM relative to SMA despite higher Hb levels and appropriate increases in plasma erythropoietin. Viral sensing/interferon regulatory factor (IRF) 2 module (M111) expression and plasma IP-10 levels both negatively correlated with reticulocyte-specific signatures, but only M111 expression independently predicted decreased reticulocyte-specific gene expression after controlling for leukocyte count, Hb level, parasitemia, and clinical syndrome by multiple regression.

Conclusion

Differences in the blood transcriptome of CM and SMA relate to neurologically relevant pathways and erythropoiesis. Erythropoietic suppression during severe malaria is more pronounced during CM versus SMA and is positively associated with IRF2 blood signatures. Future studies are needed to validate these findings.

Disclosures

All authors: No reported disclosures.