Background State‐of‐art non‐invasive diagnosis processes for bladder cancer (BLCA) harbour shortcomings such as low sensitivity and specificity, unable to distinguish between high‐ (HG) and low‐grade (LG) tumours, as well as inability to differentiate muscle‐invasive bladder cancer (MIBC) and non‐muscle‐invasive bladder cancer (NMIBC). This study investigates a comprehensive characterization of the entire DNA methylation (DNAm) landscape of BLCA to determine the relevant biomarkers for the non‐invasive diagnosis of BLCA. Methods A total of 304 samples from 224 donors were enrolled in this multi‐centre, prospective cohort study. BLCA‐specific DNAm signature discovery was carried out with genome‐wide bisulfite sequencing in 32 tumour tissues and 12 normal urine samples. A targeted sequencing assay for BLCA‐specific DNAm signatures was developed to categorize tumour tissue against normal urine, or MIBC against NMIBC. Independent validation was performed with targeted sequencing of 259 urine samples in a double‐blinded manner to determine the clinical diagnosis and prognosis value of DNAm‐based classification models. Functions of genomic region harbouring BLCA‐specific DNAm signature were validated with biological assays. Concordances of pathology to urine tumour DNA (circulating tumour DNA [ctDNA]) methylation, genomic mutations or other state‐of‐the‐art diagnosis methods were measured. Results Genome‐wide DNAm profile could accurately classify LG tumour from HG tumour (LG NMIBC vs. HG NMIBC: p = .038; LG NMIBC vs. HG MIBC, p = .00032; HG NMIBC vs. HG MIBC: p = .82; Student's t ‐test). Overall, the DNAm profile distinguishes MIBC from NMIBC and normal urine. Targeted‐sequencing‐based DNAm signature classifiers accurately classify LG NMIBC tissues from HG MIBC and could detect tumours in urine at a limit of detection of less than .5%. In tumour tissues, DNAm accurately classifies pathology, thus outperforming genomic mutation or RNA expression profiles. In the independent validation cohort, pre‐surgery urine ctDNA methylation outperforms fluorescence in situ hybridization (FISH) assay to detect HG BLCA ( n = 54) with 100% sensitivity (95% CI: 82.5%–100%) and LG BLCA ( n = 26) with 62% sensitivity (95% CI: 51.3%–72.7%), both at 100% specificity (non‐BLCA: n = 72; 95% CI: 84.1%–100%). Pre‐surgery urine ctDNA methylation signature correlates with pathology and predicts recurrence and metastasis. Post‐surgery urine ctDNA methylation ( n = 61) accurately predicts recurrence‐free survival within 180 days, with 100% accuracy. Conclusion With the discovery of BLCA‐specific DNAm signatures, targeted sequencing of ctDNA methylation outperforms FISH and DNA mutation to detect tumours, predict ...
Single cell chromatin accessibility sequencing (scATAC) reconstructs developmental trajectory by phenotypic similarity. However, inferring the exact developmental trajectory is challenging. Here we show a simple, accurate and phenotypic-neutral measure of cell developmental hierarchy – the fraction of accessible clock-like differential methylation loci (ClockDML). As cell undergone mitosis, heterogeneity of chromatin accessibility on ClockDML reduced, providing a measure of mitotic age. We developed a method, EpiTrace, that counts the fraction of opened ClockDML from scATAC data to determine cell age and perform lineage tracing. EpiTrace derived cell age shows concordance to known developmental hierarchies, correlates well with DNA methylation-based clocks, and is complementary with mutation-based lineage tracing, RNA velocity, and stemness predictions. Applying EpiTrace to human scATAC data revealed a multitude of novel biological insights with clinically relevant implications, ranging from hematopoiesis, organ development, tumor biology and immunity to cortical gyrification. Our work discovered a universal epigenomic hallmark during cellular development, which facilitates the study of cellular hierarchies and organismal aging.
SummaryPreeclampsia, a life-threatening pregnancy complication characterized by hypertension and multiorgan damage, affects 2-5% of pregnancies and causes 76,000 deaths per year. Most preeclampsia associated syndromes immediately dispel after removal of placenta, indicating a casual role of placenta in the pathogenesis. Failed transformation of spiral artery due to insufficient invasion and excessive apoptosis of trophoblast suggested developmental defects in preeclampsia placenta. However, the underlying molecular mechanisms that affected placenta development in preeclampsia remained elusive. Here we show that, in preeclampsia placenta, the epigenetic landscape formed during extraembryonic tissue differentiation was disrupted: dramatic chromatin accessibility shift affected known and novel genes implicated in preeclampsia. DNA methylation defects in preeclampsia affected lineage-defining PcG-controlled loci in trophectoderm. LTR12 retrotransposons associated with VCT/SCT-specific genes were hypermethylated. Meanwhile, hundreds of PcG-regulated EVT-specific gene promoters, which otherwise undergone post-ZGA extraembryonic-tissue-specific de novo methylation, were hypomethylated and hyper-activated. Together, these epigenetic defects resulted in placenta developmental delay in preeclampsia. The defective methylation pattern could be detected in serum cfDNA, and could be used to accurately predict preeclampsia at early pregnancy weeks in independent validation cohorts. Our data suggests that the preeclampsia placenta represents a stalled state of epigenetic reprogramming en route of development from trophectoderm to normal placenta.
Bladder cancer (BLCA) is a most common urological tumours with high rate of recurrence, which needs long‐term of follow‐up. To date, diagnosis and surveillance of BLCA still rely on cystoscopy, an invasive and expensive method that increases the difficulty for routine follow‐up. Therefore, exploring new biomarkers or tests is an effective way to improve the current clinical management of BLCA. Recent years, liquid biopsy has received increasing attention, especially for its great potential for clinical application in the non‐invasive detection of tumours. In addition, liquid biopsy involves a wide range of biomarkers, including DNA, RNA, proteins, extracellular vesicles and metabolites in blood, urine or other body fluids. For BLCA, urine is a most ideal body fluid to achieve non‐invasive diagnosis and surveillance. Here, we address recent developments of urine‐based biomarkers or tests for clinical diagnostic challenges in BLCA, such as early detection, minimal residual, recurrence monitoring and therapeutic response. Meanwhile, the many challenges of urine biomarkers that need to be overcome are also discussed.
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