bims-tumhet 2021-08-15 papers

Issue of 2021–08–15
three papers selected by
Sergio Marchini, Humanitas Research

Methods Mol Biol. 2021 ;2351 353-368

Low-Input Whole-Genome Bisulfite Sequencing.

DNA methylation can regulate gene expression by modulating chromatin accessibility and transcription factor binding on promoter and enhancer regions. Whole-genome bisulfite sequencing (WGBS) represents the most informative and comprehensive analysis to profile the DNA methylation status of all the cytosines at single-base resolution. However, most of the available protocols recommend an amount of input DNA (50 ng-5μg) that makes the WGBS unsuitable for limited samples and cell populations. In this chapter, we provide complete protocol to perform WGBS libraries from very low-input DNA. This protocol is recommended for the analysis of the whole-genome DNA methylation pattern in rare cell populations, like a defined stem cell population isolated from animal models or human samples.

Keywords: DNA methylation; Enhancer methylation; Low-input DNA; Promoter methylation; WGBS

DOI: https://doi.org/10.1007/978-1-0716-1597-3_20

Semin Oncol. 2021 Jul 14. pii: S0093-7754(21)00038-5. [Epub ahead of print]

Liquid Biopsy, the hype vs. hope in molecular and clinical oncology.

Abhishek Mohanty, Sambit K Mohanty, Sipra Rout, Chinmaya Pani.

The molecular landscape of tumors has been traditionally established using a biopsy or resection specimens. These modalities result in sampling bias that offer only a single snapshot of tumor heterogeneity. Over the last decade intensive research towards alleviating such a bias and obtaining an integral yet accurate portrait of the tumors, evolved to the use of established molecular and genetic analysis using blood and several other body fluids, such as urine, saliva, and pleural effusions as liquid biopsies. Genomic profiling of the circulating markers including circulating cell-free tumor DNA (ctDNA), circulating tumor cells (CTCs) or even RNA, proteins, and lipids constituting exosomes, have facilitated the diligent monitoring of response to treatment, allowed one to follow the emergence of drug resistance, and enumerate minimal residual disease. The prevalence of tumor educated platelets (TEPs) and our understanding of how tumor cells influence platelets are beginning to unearth TEPs as a potentially dynamic component of liquid biopsies. Here, we review the biology, methodology, approaches, and clinical applications of biomarkers used to assess liquid biopsies. The current review addresses recent technological advances and different forms of liquid biopsy along with upcoming challenges and how they can be integrated to get the best possible tumor-derived genetic information that can be leveraged to more precise therapies for patient as liquid biopsies become increasingly routine in clinical practice.

Keywords: Circulating tumor DNA (ctDNA); Circulating tumor RNA (ctRNA); Circulating tumor cells (CTCs); Liquid Biopsy; Tumor Educated Platelets, TEPs; tissue biopsy; tumor metastasis

DOI: https://doi.org/10.1053/j.seminoncol.2021.06.002

Oncogene. 2021 Aug 13.

Spontaneous and inherited TP53 genetic alterations.

Arnold J Levine.

The p53 protein is a transcription factor that prevents tumors from developing. In spontaneous and inherited cancers there are many different missense mutations in the DNA binding domain of the TP53 gene that contributes to tumor formation. These mutations produce a wide distribution in the transcriptional capabilities of the mutant p53 proteins with over four logs differences in the efficiencies of forming cancers in many diverse tissue types. These inherited and spontaneous TP53 mutations produce proteins that interact with both genetic and epigenetic cellular modifiers of p53 function and their inherited polymorphisms to produce a large number of diverse phenotypes in individual patients. This manuscript reviews these variables and discusses how the combinations of TP53 genetic alterations interact with genetic polymorphisms, epigenetic alterations, and environmental factors to begin predicting and modifying patient outcomes and provide a better understanding for new therapeutic opportunities.

DOI: https://doi.org/10.1038/s41388-021-01991-3