November 16, 2022

Single‐cell transpo-transcriptome profiling of hematological malignancies – Transposable elements as potential disease biomarkers in hematological malignancies and their implications in disease pathogenesis and physiologic hematopoietic development

1st Call, TPdF

Short Summary

Technical advances in high-throughput RNA sequencing will allow new approaches towards hematological malignancy monitoring. Transposable elements (TE) integrants account for about 50% of human genome DNA content. Their differential expression allows the detection of tissue-specific signatures. However, several considerations are required to design sensitive and specific detection methods based on TEs expression profile. A first step is the calibration of the sequencing technique across selected healthy human circulating blood cells. In addition, TEs display the ability to act as regulators of gene expression, by conferring binding sites for transcription factors (TF). Transcriptional oncogenic drivers using TEs cis-regulatory networks across different cancer types is highly suspected. The exploration of regulatory networks conferred by TEs in hematopoietic development and disease progression is of valuable interest in the era of epigenetic treatments.

Goals

We are going to perform serial high-throughput RNA sequencing on sorted white blood cell subtypes from buffy coats issued from healthy donors. This will allow us to define the required sequencing depth to obtain informative expression signatures across individuals. In a second phase, we are going to confront the data issued from bulk and single-cell RNA sequencing to ascertain the cell-type origin of the detected signal. In parallel, we are building a collaboration with university hospitals to explore the ability of high-throughput RNA sequencing to serve as a disease monitoring tool in stem cell transplant recipients at risk of graft-versus host disease (GVHD).

Our aim is also to characterize epigenetic regulatory networks used by TFs displaying TEs binding patterns throughout the human genome and more specifically oncogenic TFs. We are exploring oncogenic TF-TEs associations by challenging putative regulatory systems, through gene editing and transduction experiments on lymphoblastoid, leukemia and lymphoma cell-lines.

Significance

In the era of personalized oncology, the exploration of new methods of disease monitoring and biological predictors of disease and treatment outcome are essential. High-throughput RNA sequencing exploring TEs expression profile offers a new approach to detect disease-specific signatures. A proof of principle regarding their analytical sensitivity and specificity to efficiently discriminate individuals in an optimized fashion is still lacking. In addition, targeting the noncoding genome is one of the new milestones of cancer research. The identification of regulatory mechanisms of gene expression will increase our understanding of cancer epigenetics but also point out new therapeutic targets.

Background

Minimal residual disease detection (MRD) methods and cancer patient’s stratification according to epigenetic profiling, going beyond current histopathological classifications, are major goals of modern personalized oncology. DNA next-generation sequencing (NGS) and RT-qPCR methods are implemented in the clinic and proved to have a positive impact on early detection of hematological malignancies. In addition, the identification of disease regulatory networks and oncogenic drivers will enrich the repertoire of therapeutic targets and cancer knowledge. Malignancies are regulated by complex transcriptional networks, driven by oncogenic TFs interacting at multiple cis-acting genomic sequences. A fraction of TE integrants serve as regulatory elements of nearby genes, thus shaping the transcriptomic profile of cancer cells but also their normal physiological counterparts in a tissue-specific manner.