Circulating Tumor DNA Analysis in Advanced Urothelial Carcinoma: Insights from Biological Analysis and Extended Clinical Follow-up

PURPOSE

To investigate whether circulating tumor DNA (ctDNA) assessment in patients with muscle-invasive bladder cancer predicts treatment response and provides early detection of metastatic disease.

EXPERIMENTAL DESIGN

We present full follow-up results (median follow-up: 68 months) from a previously described cohort of 68 neoadjuvant chemotherapy (NAC)-treated patients who underwent longitudinal ctDNA testing (712 plasma samples). In addition, we performed ctDNA evaluation of 153 plasma samples collected before and after radical cystectomy (RC) in a separate cohort of 102 NAC-naïve patients (median follow-up: 72 months). Total RNA sequencing of tumors was performed to investigate biological characteristics of ctDNA shedding tumors.

RESULTS

Assessment of ctDNA after RC identified metastatic relapse with a sensitivity of 94% and specificity of 98% using the expanded follow-up data for the NAC-treated patients. ctDNA dynamics during NAC was independently associated with patient outcomes when adjusted for pathologic downstaging (HR = 4.7; P = 0.029). For the NAC-naïve patients, ctDNA was a prognostic predictor before (HR = 3.4; P = 0.0005) and after RC (HR = 17.8; P = 0.0002). No statistically significant difference in recurrence-free survival for patients without detectable ctDNA at diagnosis was observed between the cohorts. Baseline ctDNA positivity was associated with the Basal/Squamous (Ba/Sq) subtype and enrichment of epithelial-to-mesenchymal transition and cell cycle-associated gene sets.

CONCLUSIONS

ctDNA is prognostic in NAC-treated and NAC-naïve patients with more than 5 years follow-up and outperforms pathologic downstaging in predicting treatment efficacy. Patients without detectable ctDNA at diagnosis may benefit significantly less from NAC, but additional studies are needed.

Abstract 5600: Utility of circulating tumor DNA and transcriptomic profiling in predicting outcome in muscle invasive bladder cancer patients

Background: Standard treatment of localized muscle invasive bladder cancer (MIBC) is neoadjuvant chemotherapy (NAC) followed by radical cystectomy (RC); however, only 40-50% respond to NAC and approx. 50% experience relapse. Evaluation of treatment efficacy and early detection of relapse are therefore major clinical challenges.

Methods: We present a clinical update of a previously described cohort of 68 patients who received NAC prior to RC (NAC cohort; Christensen et al. JCO 2019; median follow-up (FU) of 58 months) together with evaluation of a retrospectively collected cohort of 120 patients who did not receive NAC (no-NAC cohort; median FU of 71 months). Circulating tumor DNA (ctDNA) was analyzed before NAC (NAC cohort, n=63), prior to RC (NAC cohort, n=67; no-NAC cohort, n=115) and after RC (NAC cohort, n=66; no-NAC cohort, n=37) using Signatera™. RNA-seq was performed on 176 tumors.

Results: Updated clinical FU for the NAC cohort showed that ctDNA-positive patients had significantly worse recurrence-free survival (RFS) compared to ctDNA-negative patients (before NAC: HR=16, 95%CI=3.6-70.5, p=0.0002; during surveillance after RC: HR=27.6, 95%CI=7.9-96.9, p<0.0001). After NAC prior to RC, 84% (52/62) of patients were ctDNA-negative, and of these 81% (42/52) achieved pathological complete response (pCR), while none of the ctDNA-positive patients achieved pCR (PPV 100%; NPV 81%). For the no-NAC cohort, presence of ctDNA was also prognostic at both time points (before RC: HR=2.5, 95%CI=1.4-4.4, p=0.001; single time point after RC: HR=10.1, 95%CI=3.2-31.6, p<0.0001). In both cohorts, transcriptomic pathway analysis showed an enrichment of oncogenic pathways, namely EMT and hypoxia (q<0.0001), in tumors from ctDNA-positive patients (n=62/142). This may reflect a more aggressive cancer phenotype of ctDNA shedding tumors. Among those who were ctDNA-positive after NAC (n=7) we found enrichment of EMT (q<0.0001) and TGF-β signaling (q=0.005), whereas there was enrichment of anti-tumor immune pathways, including IFNα and IFNγ response (q=0.03 and q=0.04), in patients with ctDNA clearance after NAC (n=11). Similarly, we found upregulation of IFNα and IFNγ response pathways (q<0.0001) in ctDNA-negative patients without relapse in the no-NAC cohort (n=34/57). Finally, we classified all tumors according to the MIBC consensus classes and found more Ba/Sq tumors among the ctDNA-positive patients (p<0.0001). We are currently investigating the potential clinical benefit of receiving NAC in ctDNA-positive and -negative patients by comparing the NAC and no-NAC treated patients.

Conclusion: Presence of ctDNA was associated with worse prognosis for both NAC and no-NAC treated patients. Transcriptomic analysis of primary tumors showed that anti-tumor immune responses may be associated with a particularly good outcome whereas EMT may be promoting more aggressive disease.

Citation Format: Sia Viborg Lindskrog, George Laliotis, Karin Birkenkamp-Demtröder, Iver Nordentoft, Philippe Lamy, Elshaddai Z. White, Natalia Pajak, Tine G. Andreasen, Punashi Dutta, Meenakshi Malhotra, Shruti Sharma, Mark Calhoun, Adam ElNaggar, Minetta C. Liu, Mads Agerbæk, Jørgen B. Jensen, Lars Dyrskjøt. Utility of circulating tumor DNA and transcriptomic profiling in predicting outcome in muscle invasive bladder cancer patients. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5600.

Abstract A030: Deciphering the micro-RNA landscape of AKT isoforms and its clinical impact in patients with lung adenocarcinoma

Over the last 25 years, AKT kinase has been thoroughly investigated and characterized as a crucial regulator of cellular homeostasis, affecting a plethora of essential molecular functions. The three identified isoforms of this kinase, namely AKT1, AKT2 and AKT3, often display opposing and antagonizing cellular functions. One of these important cellular functions is the expression and activation of micro-RNAs (miRNAs), an important RNA process that epigenetically regulates the human transcriptome. In the context of human cancer and based on several reports, AKT kinase has been associated with aberrant expression of oncogenic miRNAs, that in turn hijack oncogenic pathways, leading to tumor progression, metastasis and resistance to therapy, especially in lung adenocarcinoma (LUAD). Nevertheless, a comprehensive analysis of the impact of each AKT isoform on the regulation and enrichment of a specific miRNA signature in lung adenocarcinoma has yet to be performed. Here, we were willing to elucidate the miRNA epigenetic landscape and downstream targets, driven by each AKT isoform, and its clinical importance in patients with lung adenocarcinoma. To this extent, we utilized RNA-Seq and Small RNA-Seq data from The Cancer Genome Atlas (TCGA-LUAD) to identify the miRNA signatures related with the expression of each AKT isoform in LUAD. Gene Set Enrichment Analysis from RNA-Seq and miRNA levels analysis from Small RNA-Seq, identified a unique miRNA signature for each AKT isoform, demonstrating their largely opposing effect in miRNA profiling. In parallel analysis, in silico target analysis of the top 50 regulated miRNAs, demonstrated another set of unique targets for each isoform-dependent miRNA signature, which is involved in metabolism, DNA damage, RNA processing, cell survival, immune response and metastasis. More importantly, clinical and survival analysis revealed that the top 50 Differentially regulated miRNAs, ranked by q-value, for each isoform correlated with poor progression free survival in patients with LUAD. Collectively, our atlas of AKT isoform-driven miRNA landscapes implicates AKT as a global effector of miRNA landscape in lung adenocarcinoma. Due to the lack of reliable isoform-specific AKT inhibitors, the identification of the oncogenic miRNA networks regulated by each isoform, acts as an important transnational resource for the design and testing of inhibitors that bypass AKT inhibition toxicity, sparing its impactful physiological functions.

Citation Format: George Laliotis, Pauline Lin. Deciphering the micro-RNA landscape of AKT isoforms and its clinical impact in patients with lung adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A030.

Abstract A031: Deciphering the transcriptomic landscape of AKT isoforms and its prognostic impact in patients with lung adenocarcinoma

AKT kinase is a regulator of several crucial biological functions including metabolism, cell cycle progression and proliferation. Its three isoforms, namely AKT1, AKT2 and AKT3, although they display significant similarities in their sequences, their functions largely differ and often antagonize each other. In the context of human cancer, several studies have previously demonstrated that each three of the AKT isoforms often act as oncogenes or tumor suppressors in the same type of cancer, and especially in lung adenocarcinoma (LUAD). These differences could be attributed to the plethora of different targets and pathways that they directly regulate through phosphorylation or indirectly through different intermediate effectors. One of these targets and pathways can be the regulation of transcription. Based on recent reports, several transcription factors can be directly phosphorylated by AKT kinase in human cancer, globally changing their chromatin occupancy and transcriptional landscape, thus altering transcription regulation. Nevertheless, a comprehensive analysis of the impact of each AKT isoform on transcription regulation and transcription factor enrichment in lung adenocarcinoma was yet to be performed. Here, we were willing to elucidate the genome-wide transcriptional landscape, driven by each AKT isoform, and its prognostic effect in patients with lung adenocarcinoma. To this extent, we utilized Next-Generation Sequencing data from The Cancer Genome Atlas (TCGA) to identify the transcriptomic changes related with the expression of each isoform in LUAD patients. Gene Set Enrichment Analysis revealed enrichment of unique pathways between the three isoforms. In parallel analysis, Transcription Factor enrichment and ATAC-Seq analysis from the same LUAD patients revealed a unique set of transcription factors that are differentially enriched between each AKT isoform group. More importantly, clinical and survival analysis revealed that the top 50 Differentially Expressed Genes (DEG), ranked by q-value, for each isoform correlated with poor overall survival, prognosis free survival, acting as potential prognostic factor in patients with LUAD. In addition, by analyzing publicly available LUAD datasets, through Gene Expression Omnibus (GEO), we demonstrate that the same gene signature is also enriched in relapsing patients. Collectively, our atlas of AKT isoform-mediated transcriptomic landscapes establishes a role of the AKT isoforms in the regulation of transcription by governing transcription factor occupancy in target genes. Given the lack of isoform specific AKT inhibitors, the deep knowledge of the transcriptional landscape driven by each isoform in human lung adenocarcinoma, can open new avenues on the design of precision-medicine markers and therapeutics that can preserve the normal AKT functions, while targeting the oncogenic pathways that these isoforms regulate.

Citation Format: George Laliotis, Pauline Lin. Deciphering the transcriptomic landscape of AKT isoforms and its prognostic impact in patients with lung adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A031.

Abstract B032: Pancancer genomic analysis reveals histone H3K36 and H3K27 modifiers and readers as prognostic factors in patients with cancer

Histone modifications are a crucial component of the epigenetic regulation of human transcriptome and cellular homeostasis. Among these modifications, lysine (K) methylation in various sites of histones is orchestrated by a complex network of histone writers - methyltransferases, and histone erasers - demethylases. Furthermore, the establishment of histone lysine methylation is recognized by a variety of adaptor proteins, also known as histone readers, and mediate their signaling importance through formation of other protein complexes, affecting a plethora of cellular functions such as transcription, RNA splicing, DNA-damage response and proliferation. Among other modifications, the Histone H3 Lysine 27 (K27) and Lysine 36 (K36) methylations have been implicated in a plethora of human diseases, with their misregulation to be prominent for human cancer and developmental defects. Cancer cells usually hijack these pathways through mutations and/or aberrant expression of these modifiers, promoting cancer growth and metastatic potential. Nevertheless, regardless of the major therapeutic potential of these pathways, a comprehensive pan-cancer analysis for the prevalence and impact of genomic alterations of Histone H3K27 and H3K36 methylation modifiers in human cancer has not been undergone yet. Here, we sought to identify the genomic alterations of these effectors through a pan-cancer analysis of Whole Exome Sequence data (WES) from The Cancer Genome Atlas (TCGA). To this extent, we analyzed 11,194 patients samples with 33 different types of human cancer, available through cbioportal.org, for genomic alterations in 32 histone H3K27 and H3K36 modifiers and readers. The most common genomic alterations were observed in KDM6B, BRPF1, KDM6A, SETD2 and NSD1 (5%, 5%, 4% and 4% respectively). Interestingly, the patient group with genomic alterations was significantly most likely to present with concurrent oncogenic alterations in TP53, PIK3CA, TERT, ARID1A and KMT2A, among other alterations. Furthermore, our analysis demonstrated that several of these alterations co-occur (p<0.0001). More importantly, clinical and survival analysis revealed poor overall survival in the pan-cancer group of patients with genomic alterations of these modifiers (HR = 1.14, p=0.031), demonstrating the oncogenic and prognostic importance of these mutations in human cancer. Collectively, our pan-cancer analysis implicates the histone H3K27 and H3K36 modifiers and erasers as a major oncogenic pathway and their alterations as an important driver for human cancer, and sets the stage for further pre-clinical and translational research on the potential therapeutic potential of this pathway.

Citation Format: George Laliotis, Pauline Lin. Pancancer genomic analysis reveals histone H3K36 and H3K27 modifiers and readers as prognostic factors in patients with cancer. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr B032.