Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data

Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models

Recent studies exploring the impact of methylation in tumor evolution suggest that although the methylation status of many of the CpG sites are preserved across distinct lineages, others are altered as the cancer progresses. Because changes in methylation status of a CpG site may be retained in mitosis, they could be used to infer the progression history of a tumor via single-cell lineage tree reconstruction. In this work, we introduce the first principled distance-based computational method, Sgootr, for inferring a tumor's single-cell methylation lineage tree and for jointly identifying lineage-informative CpG sites that harbor changes in methylation status that are retained along the lineage. We apply Sgootr on single-cell bisulfite-treated whole-genome sequencing data of multiregionally sampled tumor cells from nine metastatic colorectal cancer patients, as well as multiregionally sampled single-cell reduced-representation bisulfite sequencing data from a glioblastoma patient. We show that the tumor lineages constructed reveal a simple model underlying tumor progression and metastatic seeding. A comparison of Sgootr against alternative approaches shows that Sgootr can construct lineage trees with fewer migration events and with more in concordance with the sequential-progression model of tumor evolution, with a running time a fraction of that used in prior studies. Lineage-informative CpG sites identified by Sgootr are in inter-CpG island (CGI) regions, as opposed to intra-CGIs, which have been the main regions of interest in genomic methylation-related analyses.

Recent Advances in High-sensitivity In Situ Hybridization and Costs and Benefits to Consider When Employing These Methods

In situ hybridization (ISH), which visualizes nucleic acids in tissues and cells, is a powerful tool in histology and pathology. Over 50 years since its invention, multiple attempts have been made to increase the sensitivity and simplicity of these methods. Therefore, several highly sensitive in situ hybridization methods have been developed that offer researchers a wide range of options. When selecting these in situ hybridization variants, their signal-amplification principles and characteristics must be understood. In addition, from a practical point of view, a method with good monetary and time-cost performance must be chosen. This review introduces recent high-sensitivity in situ hybridization variants and presents their principles, characteristics, and costs.

Circular GOLPH3 RNA exerts oncogenic effects in vitro by regulating the miRNA-1299/LIF axis in oral squamous cell carcinoma

Circular RNAs, which are a novel subclass of noncoding RNAs, are reported to be involved in various biological processes. Aberrant expression of circular RNAs may promote cancer progression. The function of circular GOLPH3 RNA (circGOLPH3) in oral squamous cell carcinoma (OSCC) is unclear. In this study, the circGOLPH3 levels in OSCC cell lines were determined using quantitative real-time polymerase chain reaction (qRT-PCR). Gain-of-function and loss-of-function experiments were performed to evaluate the roles of circGOLPH3 in OSCC. Cell counting kit 8, migration, and invasion assays were performed to determine the functions of circGOLPH3. The mechanism of circGOLPH3 in OSCC was investigated using qRT-PCR, western blotting, luciferase activity, and RNA pull-down analyses. Furthermore, the function of circGOLPH3 in vivo was evaluated. circGOLPH3 derived from GOLPH3 was mainly localized to the cytoplasm and exhibited high stability. The expression of circGOLPH3 was upregulated in OSCC cells. circGOLPH3 promoted the growth of OSCC in vitro and in vivo. Additionally, circGOLPH3 upregulated OSCC cell migration and invasion. Mechanistically, circGOLPH3 functioned as a microRNA sponge and downregulated miR-1299 expression. miR-1299 downregulated the expression of LIF by targeting its 3’-untranslated region. Inhibition of the circGOLPH3/miR-1299/LIF axis suppressed the growth, migration, and invasion of OSCC cells. These findings indicate that the circGOLPH3/miR-1299/LIF axis promotes OSCC cell growth, migration, and invasion and that this axis is a potential therapeutic target for OSCC.

OUP accepted manuscript

MOTIVATION

Cancer develops through a process of clonal evolution in which an initially healthy cell gives rise to progeny gradually differentiating through the accumulation of genetic and epigenetic mutations. These mutations can take various forms, including single-nucleotide variants (SNVs), copy number alterations (CNAs) or structural variations (SVs), with each variant type providing complementary insights into tumor evolution as well as offering distinct challenges to phylogenetic inference.

RESULTS

In this work, we develop a tumor phylogeny method, TUSV-ext, which incorporates SNVs, CNAs and SVs into a single inference framework. We demonstrate on simulated data that the method produces accurate tree inferences in the presence of all three variant types. We further demonstrate the method through application to real prostate tumor data, showing how our approach to coordinated phylogeny inference and clonal construction with all three variant types can reveal a more complicated clonal structure than is suggested by prior work, consistent with extensive polyclonal seeding or migration.

AVAILABILITY AND IMPLEMENTATION

https://github.com/CMUSchwartzLab/TUSV-ext.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.