VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Summary

This protocol describes an approach to interrogate the recombined immunoglobulin heavy chain VDJ regions of lymphomas by deep-sequencing and retrieve VDJ rearrangement and somatic hypermutation status to delineate clonal architecture of individual tumor. Comparing clonal architecture between paired diagnosis and relapse samples reveals lymphoma relapse clonal evolution modes.

Abstract

Understanding tumor clonality is critical to understanding the mechanisms involved in tumorigenesis and disease progression. In addition, understanding the clonal composition changes that occur within a tumor in response to certain micro-environment or treatments may lead to the design of more sophisticated and effective approaches to eradicate tumor cells. However, tracking tumor clonal sub-populations has been challenging due to the lack of distinguishable markers. To address this problem, a VDJ-seq protocol was created to trace the clonal evolution patterns of diffuse large B cell lymphoma (DLBCL) relapse by exploiting VDJ recombination and somatic hypermutation (SHM), two unique features of B cell lymphomas.

In this protocol, Next-Generation sequencing (NGS) libraries with indexing potential were constructed from amplified rearranged immunoglobulin heavy chain (IgH) VDJ region from pairs of primary diagnosis and relapse DLBCL samples. On average more than half million VDJ sequences per sample were obtained after sequencing, which contain both VDJ rearrangement and SHM information. In addition, customized bioinformatics pipelines were developed to fully utilize sequence information for the characterization of IgH-VDJ repertoire within these samples. Furthermore, the pipeline allows the reconstruction and comparison of the clonal architecture of individual tumors, which enables the examination of the clonal heterogeneity within the diagnosis tumors and deduction of clonal evolution patterns between diagnosis and relapse tumor pairs. When applying this analysis to several diagnosis-relapse pairs, we uncovered key evidence that multiple distinctive tumor evolutionary patterns could lead to DLBCL relapse. Additionally, this approach can be expanded into other clinical aspects, such as identification of minimal residual disease, monitoring relapse progress and treatment response, and investigation of immune repertoires in non-lymphoma contexts.

Introduction

Cancer is a clonal disease. Since thirty years ago when Peter C. Nowell proposed the cancer clonal evolution model¹, many studies have tried to dissect clonal populations within tumor samples and reconstruct clonal expansion and evolution patterns that underlie the tumorigenesis process². Recently, whole-genome sequencing has enabled investigators to take a deep look at the clonal heterogeneity and evolution^3,4. However, due to the lack of tractable markers in many cell types, it is difficult to infer the precise clonal architecture and evolutionary path. Fortunately there is a natural clonality marker in mature B cells from which many....

Protocol

1. VDJ Amplification

1.1) DNA Extraction from Tumor Samples

1. Extract DNA from thin sections (10-20 µm) of frozen O.C.T. embedded normal or malignant tissues.
   1. Digest 10-30 thin sections of embedded tissue cut by a cryostat microtome in 4 ml Nucleic Lysis Buffer (0.0075 M Tris HCl, pH 8.2; 0.3 M NaCl; 0.002 M Na₂EDTA) with Proteinase K (0.5 mg/ml, final concentration) and 0.625% SDS in a 15 ml centrifuge tube in a 37 °C water bath overnight.
   2. Add 1 ml of saturated NaCl (5 M) to the digestion mixture and shake vigorously for 15 sec.
   3. Centrifuge at 1,100 x g for 15 min at room temper....

Results

The overall procedure of VDJ sequencing (VDJ-seq), including DNA extraction, recombined VDJ region amplification and purification, sequencing library construction, reads processing, and phylogenetic analysis, is represented in Figure 1. Routinely 5-200 μg DNA can be retrieved from frozen solid tissue sections or 0.5-20 μg DNA from formalin-fixed paraffin-embedded tissue sections. Depending on the quality, rearrangement pattern, and SHM degree of individual samples, a variety of VDJ PCR products from diff.......

Discussion

Because of the nearly unlimited number of iterations of sequence information coded by VDJ rearrangement and SHM at the IGH locus of human B cells, examination of the entire IGH repertoire by high-throughput deep-sequencing proved to be an efficient and comprehensive way to delineate clonal and sub-clonal B-cell populations. Furthermore, this strategy can be used to study the clonal evolution path of B cell tumor development, remission, and relapse by comparing the clonal and sub-clonal architectures of patient samples co.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Ethanol	VWR	89125-170	200 proof, for molecular biology
TE buffer	Life Technologies	12090-015	10 mM Tris·Cl, pH 8.0; 10 mM EDTA
Xylenes	VWR	EM-XX0055-6	500 ml
Proteinase K	Life Technonogies	25530-015	100 mg
Deoxynucleotide triphosphate (dNTP) Solution Mix	Promega	U1515	10 mM each nucleotide
10x PCR Buffer	Roche	11699105001	Without MgCl2
AmpliTaq Gold DNA Polymerase with Gold Buffer and MgCl2	Life Technonogies	4311806	50 µl at 5 U/µl
Specimen Control Size Ladder	Invivoscribe Technologies	2-096-0020	33 reactions
IGH Somatic Hypermutation Assay v2.0 - Gel Detection	Invivoscribe Technologies	5-101-0030	33 reactions, Mix 2 for IGVHFR1 detection
IGH Gene Clonality Assay - Gel Detection	Invivoscribe Technologies	1-101-0020	33 reactions, Tube B for IGVHFR2 detection
GoTaq Flexi DNA Polymerase	Promega	M8291	20 µl at 5 U/µl
10X Tris-Borate-EDTA (TBE) buffer	Corning (cellgro)	46-011-CM	6x1 L
50x TAE BUFFER	VWR	101414-298	1 L
Ethidium bromide solution	Sigma-Aldrich	E1510	10 mg/ml
25 bp DNA Ladder	Life Technologies	10597011	1 µg/µl
100 bp DNA Ladder	Life Technologies	15628-019	1 µg/µl
UltraPure Agarose	Life Technologies	16500-500	500 g
40% Acrylamide/Bis Solution	Bio-Rad Laboratories	1610144	500 ml
QIAquick Gel Extraction Kit	Qiagen	28704	50 columns
Agencourt AMPure XP	Beckman Coulter	A63881
Qubit dsDNA High Sensitivity Assay Kit	Life Technologies	Q32854
High Sensitivity DNA Kit	Agilent Technologies	5067-4626
2100 Bioanalyzer	Agilent Technologies
PhiX Control v3	Illumina	FC-110-3001
MiSeq	Illumina
Qubit 2.0 Fluorometer	Life Technologies	Q32872
Resuspension buffer (Illumina TruSeq DNA Sample Preparation Kit v2)	Illumina	FC-121-2001
End repair mix (Illumina TruSeq DNA Sample Preparation Kit v2)	Illumina	FC-121-2001
A-tailing mix (Illumina TruSeq DNA Sample Preparation Kit v2)	Illumina	FC-121-2001
Ligation mix (Illumina TruSeq DNA Sample Preparation Kit v2)	Illumina	FC-121-2001
DNA adaptor index (Illumina TruSeq DNA Sample Preparation Kit v2)	Illumina	FC-121-2001
Stop ligation buffer (Illumina TruSeq DNA Sample Preparation Kit v2)	Illumina	FC-121-2001
PCR primer cocktail (Illumina TruSeq DNA Sample Preparation Kit v2)	Illumina	FC-121-2001
PCR master mix (Illumina TruSeq DNA Sample Preparation Kit v2)	Illumina	FC-121-2001
Magnetic stand	Life Technologies	4457858
Gel imaging system	Bio-Rad Laboratories	170-8370