Re-expression of Selected Epigenetically Silenced Candidate Tumor Suppressor Genes in Cervical Cancer by TET2-directed Demethylation

DNA hypermethylation is extensively explored as therapeutic target for gene expression modulation in cancer. Here, we re-activated hypermethylated candidate tumor suppressor genes (TSGs) (C13ORF18, CCNA1, TFPI2, and Maspin) by TET2-induced demethylation in cervical cancer cell lines. To redirect TET2 to hypermethylated TSGs, we engineered zinc finger proteins (ZFPs), which were first fused to the transcriptional activator VP64 to validate effective gene re-expression and confirm TSG function. ChIP-Seq not only revealed enriched binding of ZFPs to their intended sequence, but also considerable off-target binding, especially at promoter regions. Nevertheless, results obtained by targeted re-expression using ZFP-VP64 constructs were in line with cDNA overexpression; both revealed strong growth inhibition for C13ORF18 and TFPI2, but not for CCNA1 and Maspin. To explore effectivity of locus-targeted demethylation, ZFP-TET2 fusions were constructed which efficiently demethylated genes with subsequent gene re-activation. Moreover, targeting TET2 to TFPI2 and C13ORF18, but not CCNA1, significantly decreased cell growth, viability, and colony formation in cervical cancer cells compared to a catalytically inactive mutant of TET2. These data underline that effective re-activation of hypermethylated genes can be achieved through targeted DNA demethylation by TET2, which can assist in realizing sustained re-expression of genes of interest.

Prolonged re-expression of the hypermethylated gene EPB41L3 using artificial transcription factors and epigenetic drugs

Epigenetic silencing of tumor suppressor genes (TSGs) is considered a significant event in the progression of cancer. For example, EPB41L3, a potential biomarker in cervical cancer, is often silenced by cancer-specific promoter methylation. Artificial transcription factors (ATFs) are unique tools to re-express such silenced TSGs to functional levels; however, the induced effects are considered transient. Here, we aimed to improve the efficiency and sustainability of gene re-expression using engineered zinc fingers fused to VP64 (ZF-ATFs) or DNA methylation modifiers (ZF-Tet2 or ZF-TDG) and/or by co-treatment with epigenetic drugs [5-aza-2'-deoxycytidine or Trichostatin A (TSA)]. The EPB41L3-ZF effectively bound its methylated endogenous locus, as also confirmed by ChIP-seq. ZF-ATFs reactivated the epigenetically silenced target gene EPB41L3 (∼ 10-fold) in breast, ovarian, and cervical cancer cell lines. Prolonged high levels of EPB41L3 (∼ 150-fold) induction could be achieved by short-term co-treatment with epigenetic drugs. Interestingly, for otherwise ineffective ZF-Tet2 or ZF-TDG treatments, TSA facilitated re-expression of EPB41L3 up to twofold. ATF-mediated re-expression demonstrated a tumor suppressive role for EPB41L3 in cervical cancer cell lines. In conclusion, epigenetic reprogramming provides a novel way to improve sustainability of re-expression of epigenetically silenced promoters.

Current Smoking is Associated with Decreased Expression of miR-335-5p in Parenchymal Lung Fibroblasts

Cigarette smoking causes lung inflammation and tissue damage. Lung fibroblasts play a major role in tissue repair. Previous studies have reported smoking-associated changes in fibroblast responses and methylation patterns. Our aim was to identify the effect of current smoking on miRNA expression in primary lung fibroblasts. Small RNA sequencing was performed on lung fibroblasts from nine current and six ex-smokers with normal lung function. MiR-335-5p and miR-335-3p were significantly downregulated in lung fibroblasts from current compared to ex-smokers (false discovery rate (FDR) <0.05). Differential miR-335-5p expression was validated with RT-qPCR (p-value = 0.01). The results were validated in lung tissue from current and ex-smokers and in bronchial biopsies from non-diseased smokers and never-smokers (p-value <0.05). The methylation pattern of the miR-335 host gene, determined by methylation-specific qPCR, did not differ between current and ex-smokers. To obtain insights into the genes regulated by miR-335-5p in fibroblasts, we overlapped all proven miR-335-5p targets with our previously published miRNA targetome data in lung fibroblasts. This revealed Rb1, CARF, and SGK3 as likely targets of miR-335-5p in lung fibroblasts. Our study indicates that miR-335-5p downregulation due to current smoking may affect its function in lung fibroblasts by targeting Rb1, CARF and SGK3.

Marked TGF-β-regulated miRNA expression changes in both COPD and control lung fibroblasts

COPD is associated with disturbed tissue repair, possibly due to TGF-β-regulated miRNA changes in fibroblasts. Our aim was to identify TGF-β-regulated miRNAs and their differential regulation and expression in COPD compared to control fibroblasts. Small RNA sequencing was performed on TGF-β-stimulated and unstimulated lung fibroblasts from 15 COPD patients and 15 controls. Linear regression was used to identify TGF-β-regulated and COPD-associated miRNAs. Interaction analysis was performed to compare miRNAs that responded differently to TGF-β in COPD and control. Re-analysis of previously generated Ago2-IP data and Enrichr were used to identify presence and function of potential target genes in the miRNA-targetome of lung fibroblasts. In total, 46 TGF-β-regulated miRNAs were identified in COPD and 86 in control fibroblasts (FDR < 0.05). MiR-27a-5p was the most significantly upregulated miRNA. MiR-148b-3p, miR-589-5p and miR-376b-3p responded differently to TGF-β in COPD compared to control (FDR < 0.25). MiR-660-5p was significantly upregulated in COPD compared to control (FDR < 0.05). Several predicted targets of miR-27a-5p, miR-148b-3p and miR-660-5p were present in the miRNA-targetome, and were mainly involved in the regulation of gene transcription. In conclusion, altered TGF-β-induced miRNA regulation and differential expression of miR-660-5p in COPD fibroblasts, may represent one of the mechanisms underlying aberrant tissue repair and remodelling in COPD.

Genomic profiling of post-transplant lymphoproliferative disorders using cell-free DNA

Diagnosing post-transplant lymphoproliferative disorder (PTLD) is challenging and often requires invasive procedures. Analyses of cell-free DNA (cfDNA) isolated from plasma is minimally invasive and highly effective for genomic profiling of tumors. We studied the feasibility of using cfDNA to profile PTLD and explore its potential to serve as a screening tool. We included seventeen patients with monomorphic PTLD after solid organ transplantation in this multi-center observational cohort study. We used low-coverage whole genome sequencing (lcWGS) to detect copy number variations (CNVs) and targeted next-generation sequencing (NGS) to identify Epstein-Barr virus (EBV) DNA load and somatic single nucleotide variants (SNVs) in cfDNA from plasma. Seven out of seventeen (41%) patients had EBV-positive tumors, and 13/17 (76%) had stage IV disease. Nine out of seventeen (56%) patients showed CNVs in cfDNA, with more CNVs in EBV-negative cases. Recurrent gains were detected for 3q, 11q, and 18q. Recurrent losses were observed at 6q. The fraction of EBV reads in cfDNA from EBV-positive patients was 3-log higher compared to controls and EBV-negative patients. 289 SNVs were identified, with a median of 19 per sample. SNV burden correlated significantly with lactate dehydrogenase levels. Similar SNV burdens were observed in EBV-negative and EBV-positive PTLD. The most commonly mutated genes were TP53 and KMT2D (41%), followed by SPEN, TET2 (35%), and ARID1A, IGLL5, and PIM1 (29%), indicating DNA damage response, epigenetic regulation, and B-cell signaling/NFkB pathways as drivers of PTLD. Overall, CNVs were more prevalent in EBV-negative lymphoma, while no difference was observed in the number of SNVs. Our data indicated the potential of analyzing cfDNA as a tool for PTLD screening and response monitoring.

Mutational heterogeneity between different regional tumour grades of clear cell renal cell carcinoma

Only a limited number of studies have explored the possible associations between tumour grade and mutated genes in clear cell renal cell carcinoma (ccRCC), and we set out to investigate this further using a multiple sampling and next generation sequencing (NGS) approach in a series of ccRCCs. Multiple regions were sampled from formalin-fixated paraffin-embedded ccRCC tumour blocks from seven patients. In 27 samples from six patients, we performed targeted NGS using a custom 42-gene panel based on the most frequently mutated genes in ccRCC reported in public databases. In four samples from the seventh patient, we performed whole exome sequencing (WES) and array comparative genomic hybridisation for detection of copy number variants (CNVs). Mutated genes and the tumour grades of the samples in which they had been identified were compared both within and between all individual tumours. CNVs were compared across all samples from patient 7. We identified clear genetic heterogeneity within and across tumours, but VHL mutations were seen in all patients. Looking across all samples, we identified eleven genes that were only mutated in samples with one particular tumour grade. However, these genes were never mutated in all samples with that tumour grade. Increasing chromosomal instability corresponded with increasing tumour grade, but we observed minimal association between tumour grade and total mutational load in the WES data. Our study confirms the genetic heterogeneity and tumour grade heterogeneity of ccRCC. Although a relatively small number of samples was analysed, genes were identified that could potentially be specific, though insensitive, markers of higher ccRCC tumour grades.

Does left atrial epicardial conduction time reflect atrial fibrosis and the risk of atrial fibrillation recurrence after thoracoscopic ablation? Post hoc analysis of the AFACT trial

OBJECTIVES

To determine the association between left atrial epicardial conduction time (LAECT), fibrosis and atrial fibrillation (AF) recurrence after thoracoscopic surgical ablation of persistent AF.

SETTING

Single tertiary care centre in the Netherlands.

PARTICIPANTS

Patients with persistent AF from the randomised Atrial Fibrillation Ablation and Autonomic Modulation via Thoracoscopic Surgery (AFACT)-trial were included. Patients eligible for thoracoscopic AF ablation were included, full inclusion and exclusion criteria were previously published. All patients underwent thoracoscopic ablation, encompassing pulmonary vein isolation with an additional roof and trigone lesion. In patients with conduction block across the roof and trigone lesion, LAECT was measured. LAECT was defined as the time to local activation at one side of the roofline on pacing from the opposite side. Collagen fibre density was quantified from left atrial appendage histology.

OUTCOME MEASURES

Primary outcome: AF recurrence during 2 years of follow-up.

RESULTS

121 patients were included, of whom 35(29%) were women, age was 60.4±7.8 and 51% (62) had at least one AF recurrence during 2 years of follow-up. LAECT was longer in patients with versus without AF recurrence (182±43 ms vs 147±29 ms, p<0.001). LAECT was longer in older patients, in patients with a higher body mass index (BMI) and in patients using class IC antiarrhythmic drugs. LAECT was shorter in patients with higher collagen fibre density. A previously failed catheter ablation, LAECT and BMI were independently associated with AF recurrence.

CONCLUSION

LAECT is correlated with collagen fibre density and BMI and is independently associated with AF recurrence in patients with persistent AF. In these patients, LAECT appears to reflect substrate characteristics beyond clinical AF type and left atrial volume.

TRIAL REGISTRATION NUMBER

NCT01091389.

Abstract 2989: An all-in-one transcriptome-based assay to identify therapy-related biomarkers in lung cancer

Background. In the past decade, treatment of advanced stage lung cancer patients guided by somatic aberrations has become routine practice. Different molecular tests are being applied to detect all targetable mutations and fusions. However, in most cases tissue biopsies are small, hampering multiple independent diagnostic tests. To optimize diagnostic testing we developed an all-in-one transcriptome-based assay.

Methods. We have developed a targeted next generation sequencing protocol that uses total RNA as input and is based on the Single Primed enrichment Technology (SPET). We included 11 cell lines, four frozen biopsies, 12 pleural effusion samples and 32 FFPE samples with in total 41 known mutations (including EGFR n=15; KRAS n=11; BRAF n=2; PIK3CA n=3 ), 21 fusion genes (including ALK n=15; ROS n=3) and 3 cases of MET exon14 skipping.

Results. We confirmed presence of 32 out of 41 mutations, 19 out of 23 fusions and all three cases of exon skipping by our assay. Besides confirming the fusions, we were also able to identify the fusion gene partner for all detected fusion transcripts. For the samples for which we failed to detect the mutations or fusions, the read depth of the target region was less than four, indicating low expression, low tumor content or insufficient unique reads. Independent RNA-based ddPCR on six unconfirmed mutations were all positive, albeit with low numbers of mutant droplets in some cases. One of three undetected fusions was positive in a NanoString fusion gene detection assay. For one of two negative cases, the fusion was most likely false positive by FISH, as this patient was FISH-break positive for both ALK and RET, which is never reported before.

Conclusions. This study proved feasibility of this targeted all-in-one transcriptome-based assay for simultaneous detection of mutations and fusions even in relatively small FFPE tissue biopsies. Moreover, we were able to detect the fusion partner genes in all positive cases. We expect that for routine diagnostic testing using an enrichment for tumor cell-rich areas of recently prepared FFPE blocks, the success rate of the all-in-one transcriptome approach will reach similar sensitivity as currently used diagnostic tests.

Citation Format: Klaas Kok, Jiacong Wei, Anna A. Rybczynska, Pei Meng, Martijn M. Terpstra, Anthonie J. van der Wekken, Jeroen T. Hiltermann, Ed Schuuring, Harry J. Groen, Anke van den Berg. An all-in-one transcriptome-based assay to identify therapy-related biomarkers in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2989.

Abstract 4757: Whole exome sequencing reveals a distinct mutation pattern in metastatic small cell lung cancer compared to non-small cell lung cancer

Purpose: Lung cancer is divided into two main groups, small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), the latter subdivided in squamous, large cell and adenocarcinoma. Many studies have shown intra-tumor heterogeneity in lung cancer with multiple minor clones characterized by their own specific mutational landscape. These minor clones can become predominant under selective pressure caused by therapy. Aim of our study is to investigate the relation between primary lung cancer and multiple distant metastases using whole exome sequencing.

Materials and methods: Normal tissue, primary lung tumor, and multiple metastases were obtained from 2 SCLC and 3 NSCLC patients resulting in a total of 29 samples (Table 1). DNA was isolated from total, macro-dissected, or laser micro-dissected tissue to obtain a purity of at least 80% tumor cells. Library preparation was based on the SureSelect All Exon V5 bait (Agilent) and paired-end sequencing was done using Illumina® HiSeq2000. Genome analysis toolkit (GATK) was used to analyze data and the 1000-Genome database was used to remove single nucleotide polymorphisms.

Patients' characteristics and overview of sequenced metastases samplesSubtypeSexAge at diagnosisCOPDSmokingPack yearTime interval between diagnosis and death (days)No. of somatic mutationsMetastasesLarge cell carcinomaMale65YesYes302308446Lymph node (1x)Adrenal gland (1x)Squamous cell carcinomaMale68YesYes&gt;100111306Liver (1x)Spleen (1x)Heart (1x)AdenocarcinomaFemale51NoNo02579Liver (1x)Lymph nodes (2x)Ovary (1x)Vertebra (1x)Jejunum (1x)Small cell carcinoma-1Female79YesYes&gt;508347Liver (1x)Adrenal gland (1x)Small cell carcinoma-2Female58YesYes406260Liver (1x)Lymph nodes (4x)

Results: In four patients more than 70% of the observed variants were true somatic mutations. In the adenocarcinoma patient, only 32% of the variants were called as true somatic mutations. After excluding personal variants, 79 to 446 true somatic mutations were observed in any of the tumor samples of the five lung cancer patients (Table 1). Comparison of the mutations observed in the primary and metastatic samples revealed that around 50% of the mutations were shared between all tumor samples of the three NSCLC patients, whereas more than 95% of mutations were shared in all samples of the two SCLC patients.

Conclusion: We found a high percentage of metastasis specific mutations in NSCLC patients. In contrast, SCLC patients show a limited number of metastasis specific mutations, consistent with the aggressiveness of these tumor and the very poor prognosis.

Citation Format: Ali Saber, Klaas Kok, Martijn M. Terpstra, Wim Timens, Sijmen Aukema, T. Jeroen Hiltermann, Harry J. M. Groen, Anke van den Berg. Whole exome sequencing reveals a distinct mutation pattern in metastatic small cell lung cancer compared to non-small cell lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4757. doi:10.1158/1538-7445.AM2015-4757

P1837HFpEF reverses in more than a quarter of patients after thoracoscopic AF ablation

Purpose

To evaluate the proportion of patients in whom parameters that define the diagnosis of HFpEF and HFmrEF persist versus normalize upon elimination of AF.

Background

Atrial fibrillation (AF) and heart failure with preserved or mid-range ejection fraction (HFpEF or HFmrEF) concur in many patients. Distinction between these two diagnoses remains challenging as one can cause or exacerbate the other. Adequate patient selection for invasive AF treatment is crucial to improve rhythm outcome.

Methods

Patients underwent thoracoscopic ablation, consisting of pulmonary vein isolation (PVI) alone or PVI with additional lines in the case of persistent AF. Patients were prospectively followed-up. HFmrEF or HFpEF was defined as left ventricular ejection fraction (LVEF) ≥40% or ≥50% respectively and N-terminal prohormone of brain natriuretic peptide (NT-proBNP) levels >125 pg/ml. Patients who remained free from AF, or any atrial tachycardia of more than 30 seconds, at 6 months postoperatively, were included in this study. Patients with AF recurrences during this period were excluded. The primary outcome was the change of NT-proBNP at 6 month follow-up.

Results

From 2008 to 2017, 92 patients undergoing thoracoscopic AF ablation fulfilled the aforementioned criteria and were included. Of these patients, mean age was 61±8 years and 66 (72%) were male. Median NT-proBNP was 366 pg/ml (128–2916) and mean LVEF was 53±7%. Thirty (35%) patients had a LVEF of 40–49%. Six months after elimination of AF, NT-proBNP was <125 pg/ml (Figure 1A: median 87 (50–122) vs 459 (137 – 2916) pg/ml at baseline; p<0.001) in 26 patients (28%), whereas in the remaining patients NT-proBNP was unchanged (Figure 1B: median 298 (126–1568) vs. 318 (128–2387) pg/ml at baseline; p=0.011).

Figure 1. NT-proBNP alterations after thoracoscopic AF ablation from baseline to 6 month follow-up. A. Patients with normalization of NT-proBNP. B. Patients with unchanged high levels of NT-proBNP.

Conclusion

In 28% of patients the diagnostic criteria of HFpEF/HFmrEF are caused by AF and normalize upon elimination of AF with thoracoscopic ablation.

P1017Thoracoscopic AF ablation is a successful treatment for patients with a giant left atrium

Background

Severely enlarged left atrial (LA) volume is associated with a considerable ineffective outcome of ablation for atrial fibrillation (AF). Therefore, in patients with AF and a giant atrial volume catheter ablation is not recommended. However, thoracoscopic AF ablation is being performed in patients with AF and giant LA, but with unknown efficacy.

Purpose

To determine efficacy of thoracoscopic AF ablation in patients with AF and a giant LA.

Methods

Patients underwent thoracoscopic AF ablation (paroxysmal AF) plus additional left atrial ablations (persistent AF) and were prospectively followed. Giant LA was defined as left atrial volume index (LAVI)≥50 ml/m2, outcome was also assessed for LAVI≥55 ml/m2. Follow-up was performed with ECGs and 24-hour Holters every three months. After a 3-month blanking period, all AADs were discontinued. Primary outcome was recurrence of any atrial tachycardia ≥30 sec during one year of follow-up.

Results

Between 2008–2017, 357 patients underwent thoracoscopic AF ablation. At baseline, giant LA was diagnosed in 72 (20.2%) patients (mean LAVI: 59.5±9.6 ml/m2), while 285 (79.8%) had a smaller left atrium (mean LAVI: 36.3±7.8 ml/m2), p<0.001. Giant LA patients were older (mean: 61.7±6.9 vs 59.3±9.0 years, p=0.03) and more often diagnosed with persistent AF (n=60, 83.3%) compared to control (n=164, 57.5%), p<0.001. Sex (female: n=19, 26.4% vs n=79, 27.7%, p=0.82) and history of AF (median: 4.0 [IQR: 2.0–6.0] vs 4.0 [IQR: 2.0–8.0] years, p=0.10) were equally distributed. Freedom of any atrial tachycardia did not differ significantly between both groups (n=43, 59.7% vs n=195, 68.4%, log rank p=0.91), figure. This was similar for the cut-off of LAVI≥55 ml/m2: n=24/43 (55.8%) vs n=214/314 (68.2%), p=0.15). AF recurred in 16 (22.2%) patients with giant LA compared to 55 (19.3%) patients, while atrial tachycardia recurred in 21 (29.2%) vs 56 (19.6%) patients, respectively, p=0.06.

Kaplan-Meier analysis of AF recurrence i

Conclusion

Thoracoscopic AF ablation is an effective therapy in patients with a giant LA. Thoracoscopic AF ablation may therefore be a feasible treatment for patients with a giant LA.