Identifying DNA methylation biomarkers for non-endoscopic detection of Barrett's esophagus

We report a biomarker-based non-endoscopic method for detecting Barrett's esophagus (BE) based on detecting methylated DNAs retrieved via a swallowable balloon-based esophageal sampling device. BE is the precursor of, and a major recognized risk factor for, developing esophageal adenocarcinoma. Endoscopy, the current standard for BE detection, is not cost-effective for population screening. We performed genome-wide screening to ascertain regions targeted for recurrent aberrant cytosine methylation in BE, identifying high-frequency methylation within the CCNA1 locus. We tested CCNA1 DNA methylation as a BE biomarker in cytology brushings of the distal esophagus from 173 individuals with or without BE. CCNA1 DNA methylation demonstrated an area under the curve of 0.95 for discriminating BE-related metaplasia and neoplasia cases versus normal individuals, performing identically to methylation of VIM DNA, an established BE biomarker. When combined, the resulting two biomarker panel was 95% sensitive and 91% specific. These results were replicated in an independent validation cohort of 149 individuals who were assayed using the same cutoff values for test positivity established in the training population. To progress toward non-endoscopic esophageal screening, we engineered a well-tolerated, swallowable, encapsulated balloon device able to selectively sample the distal esophagus within 5 min. In balloon samples from 86 individuals, tests of CCNA1 plus VIM DNA methylation detected BE metaplasia with 90.3% sensitivity and 91.7% specificity. Combining the balloon sampling device with molecular assays of CCNA1 plus VIM DNA methylation enables an efficient, well-tolerated, sensitive, and specific method of screening at-risk populations for BE.

Abstract 213: Sarcolemma Genes Related to the Transverse Tubule Structure Are Mostly Not Expressed in Differentiating Human iPSC-derived Cardiomyocytes

Background: Transverse tubules (TT) are tunnel-like extensions of sarcolemma studded with ion channels coupling excitation, through the cytoplasm, to contraction in the sarcomere of matured cardiomyocytes (CMs). Expression timing of sub-cellular TT-related genes (TT-rgs) in individual human iPSC-derived CMs (hiPSC-CMs) has not yet been reported.

Objective: Map out the gene program of TT-rgs by sub-cellular locations during hiPSC-CM differentiation using single-cell transcriptomics (scRNA Seq.).

Methods: hiPSC-CMs were differentiated from 2 commercially available lines using sequential GSK3 and Wnt signaling inhibition. The %CMs were assayed by flow cytometry for sarcomeric myosin heavy chain protein, a CM biomarker. Baseline cells (iPSCs, n=24) and day 14 (n=45), 30 (n=64), and 60 (n=5) post differentiation cells were sampled for scRNA Seq. using the Fluidigm C1 platform. We categorized 73 TT-rgs by cellular location of the coded protein (i.e. sarcomere, cytoplasm or sarcolemma). The expression pattern for each location was categorized as induced, repressed, or neither based on the median transcript per million for each individual cell normalized to iPSCs.

Results: CMs increased from <1% in iPSCs to 21%, 37% and 59% at D14, D30 and D60 post differentiation (adj. p <0.03 by ANOVA), respectively. 33 genes (45%) had no detectable RNA while 21 (29%) were induced to D60. See table.

Conclusion: Single-cell transcriptomes in differentiating hiPSC-CMs revealed a discordance between sarcolemma (mostly not expressed) and sarcomeric genes being induced. Defining timing and within cell variability of TT sub-cellular genes will be critical to understand human CM maturation.

Abstract 212: Adrenergic Signaling Genes Are Not All Expressed During Myogenesis in Individual Human iPSC-derived Cardiomyocytes

Background: Adrenergic receptors (AR) in an individual cardiomyocyte (CM) are not uniformly expressed at the single-cell level (Myagmar et al., 2017). The timing and cellular distribution of AR signaling (ARS) genes in individual human iPSC-derived CMs (hiPSC-CMs) have not yet been reported.

Objective: To map out the transcription program of ARS genes during hiPSC-CM myogenesis using single-cell transcriptomics (scRNA Seq.).

Methods: 132 ARS in CM genes curated by the Kyoto Encyclopedia of Genes and Genomes were studied. The CMs were derived from 2 commercially available hiPSC lines using sequential GSK3 and Wnt signaling inhibition. The CMs were assayed by flow cytometry with sarcomeric myosin heavy chain (MYHC6/7) protein, a biomarker of myogenesis. Baseline cells (iPSCs, n=24) and day 14 (n=45), 30 (n=64), and 60 (n=5) post differentiation cells were sampled for scRNA Seq. using the Fluidigm C1 platform. Data from 10 somatic cell preparations and iPSCs defined the signal specificity and biological noise in the system. The expression patterns were categorized as induced, repressed, or neither based on the median transcript per million for individual cells normalized to iPSCs. A p -value of <0.05 by ANOVA was used for significance.

Results: The CMs had spontaneous contractions by D14 and increased from <1% in iPSCs to 21%, 37% and 59% at D14, D30 and D60 post differentiation (adj. p <0.03) respectively. None of the iPSCs had MYH6/7 transcripts, while >90% of differentiating cells did. MYH6/7 median expression increased 15-fold from D14 to D30 (p<0.0001) and 60-fold to D60 (p<0.06). Of 132 ARS genes, 60 (44%) had no detectable expression out to D60. Of the 72 genes with expression, 18 (25%) were induced in parallel to MYH6/7, while 22 (31%) were repressed. The remaining 32 genes (44%) had no distinctive pattern. From 18 induced genes (14% of all), 8 were sarcomeric genes that preceded expression to most ARS genes without induction (86% of all).

Conclusion: Single-cell transcriptomes in derived hiPSC-CMs revealed a lack of uniformity between upstream ARS genes and early sarcomeric genes. Defining the timing and cell-to-cell variability of the ARS gene program will be critical to understanding its mechanistic relationship to the sarcomeric gene program in humans.