ABSTRACT
Follicular lymphoma is an incurable malignancy, with transformation to an aggressive subtype representing a critical event during disease progression. Here we performed whole-genome or whole-exome sequencing on 10 follicular lymphoma-transformed follicular lymphoma pairs followed by deep sequencing of 28 genes in an extension cohort, and we report the key events and evolutionary processes governing tumor initiation and transformation. Tumor evolution occurred through either a 'rich' or 'sparse' ancestral common progenitor clone (CPC). We identified recurrent mutations in linker histone, JAK-STAT signaling, NF-κB signaling and B cell developmental genes. Longitudinal analyses identified early driver mutations in chromatin regulator genes (CREBBP, EZH2 and KMT2D (MLL2)), whereas mutations in EBF1 and regulators of NF-κB signaling (MYD88 and TNFAIP3) were gained at transformation. Collectively, this study provides new insights into the genetic basis of follicular lymphoma and the clonal dynamics of transformation and suggests that personalizing therapies to target key genetic alterations in the CPC represents an attractive therapeutic strategy.
Subject(s)
Cell Transformation, Neoplastic/genetics , Disease Progression , Genomics/methods , Lymphoma, Follicular/genetics , Lymphoma, Follicular/physiopathology , Base Sequence , CREB-Binding Protein/genetics , Cluster Analysis , Cohort Studies , DNA-Binding Proteins/genetics , Enhancer of Zeste Homolog 2 Protein , Exome/genetics , High-Throughput Nucleotide Sequencing , Histones/genetics , Humans , Intracellular Signaling Peptides and Proteins/genetics , Molecular Sequence Annotation , Molecular Sequence Data , Mutagenesis , Mutation/genetics , Myeloid Differentiation Factor 88/genetics , Neoplasm Proteins/genetics , Nuclear Proteins/genetics , Phylogeny , Polycomb Repressive Complex 2/genetics , Polymorphism, Single Nucleotide/genetics , Sequence Analysis, DNA , Trans-Activators/genetics , Tumor Necrosis Factor alpha-Induced Protein 3ABSTRACT
BACKGROUND: Deep sequencing of single cell-derived cDNAs offers novel insights into oncogenesis and embryogenesis. However, traditional library preparation for RNA-seq analysis requires multiple steps with consequent sample loss and stochastic variation at each step significantly affecting output. Thus, a simpler and better protocol is desirable. The recently developed hyperactive Tn5-mediated library preparation, which brings high quality libraries, is likely one of the solutions. RESULTS AND CONCLUSIONS: Here, we tested the applicability of hyperactive Tn5-mediated library preparation to deep sequencing of single cell cDNA, optimized the protocol, and compared it with the conventional method based on sonication. This new technique does not require any expensive or special equipment, which secures wider availability. A library was constructed from only 100 ng of cDNA, which enables the saving of precious specimens. Only a few steps of robust enzymatic reaction resulted in saved time, enabling more specimens to be prepared at once, and with a more reproducible size distribution among the different specimens. The obtained RNA-seq results were comparable to the conventional method. Thus, this Tn5-mediated preparation is applicable for anyone who aims to carry out deep sequencing for single cell cDNAs.
