Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes

BACKGROUND

In rheumatoid arthritis (RA), the activation of T and B cell clones specific for self-antigens leads to the chronic inflammation of the synovium. Here, we perform an in-depth quantitative analysis of the seven chains that comprise the adaptive immune receptor repertoire (AIRR) in RA.

RESULTS

In comparison to controls, we show that RA patients have multiple and strong differences in the B cell receptor repertoire including reduced diversity as well as altered isotype, chain, and segment frequencies. We demonstrate that therapeutic tumor necrosis factor inhibition partially restores this alteration but find a profound difference in the underlying biochemical reactivities between responders and non-responders. Combining the AIRR with HLA typing, we identify the specific T cell receptor repertoire associated with disease risk variants. Integrating these features, we further develop a molecular classifier that shows the utility of the AIRR as a diagnostic tool.

CONCLUSIONS

Simultaneous sequencing of the seven chains of the human AIRR reveals novel features associated with the disease and clinically relevant phenotypes, including response to therapy. These findings show the unique potential of AIRR to address precision medicine in immune-related diseases.

Immune repertoire analysis of normal Chinese donors at different ages

OBJECTIVES

This study investigated the characteristics of the immune repertoire in normal Chinese individuals of different ages.

MATERIALS AND METHODS

In this study, all seven receptor chains from both B and T cells in peripheral blood of 16 normal Chinese individuals from two age groups were analyzed using high-throughput sequencing and dimer-avoided multiplex PCR amplification. Normal in this study is defined as no chronic, infectious or autoimmune disease within 6 months prior to blood draw.

RESULTS

We found that compared with the younger group, the clonal expression of T-cell receptor repertoire increased in the older group, while diversity decreased. In addition, we found that the T-cell receptor repertoire was more significantly affected by age than the B-cell receptor repertoire, including significant differences in the use of the unique TCR-alpha and TCR-beta V-J gene combinations, in the two groups of normal participants. We further analyzed the degree of complementarity determining region 3 sequence sharing between the two groups, and found shared TCR-alpha, TCR-gamma, immunoglobulin-kappa and immunoglobulin-lambda chain complementarity determining region 3 sequences in all subjects.

CONCLUSION

Taken together, our study gives us a better understanding of the immune repertoire of different normal Chinese people, and these results can be applied to the treatment of age-related diseases. Immune repertoire analysis also allows us to observe participant's wellness, aiding in early-stage diagnosis.

Analysis of human BCR-IgH from genomic DNA with UMI incorporation

Immune repertoire analysis can be performed from practically any biological sample as long as viable nucleic acid can be extracted. While using RNA as a template has its benefits, gDNA is often preferred as gDNA is often easier to obtain, especially from difficult samples. In addition, since each cell may only have one copy of the successfully rearranged V(D)J, it may better reflect the quantity of cells. In other words, identification of a successfully rearranged V(D)J will not be skewed by expression levels as the relationship should be one cell to one V(D)J rearrangement.

We developed a new set of BCR-IgH specific primers to target the gDNA V(D)J region while also incorporating unique molecular indices (UMI) through our proprietary dimer avoided multiplex PCR technology. The inclusion of UMI with gDNA amplification allows each cell to be counted since the relationship of one V(D)J per cell will be maintained and will have a unique barcode added during the processing. The inclusion of UMI also assists with the elimination of PCR and sequencing error, which will lead to more confident analysis of low frequency clones and hypermutations. The primers were first tested on a BCR-IgH synthetic library. The sequencing result demonstrated >85% correlation with the known synthetic library gene expression. These results showed that the new gDNA BCR-IgH panel was sufficient at amplifying all known J gene targets.

Presently, we have also applied this method to gDNA extracted from B cell enriched PBMC samples including the spike-in of a known BCR clone at various concentrations. To our knowledge, this is the first assay of its kind to incorporate UMI into BCR-IgH gDNA to capture both the BCR repertoire and true cell frequency.

Shared B cell but not T cell intratumoral immune repertoire among patients with low grade appendiceal mucinous neoplasms

Introduction: Low grade mucinous appendiceal neoplasms (LAMNs) are indolent tumors that present with widespread peritoneal metastases. Despite standard of care cytoreductive surgery and heated intraperitoneal chemotherapy (CRS-HIPEC), patients with LAMNs often recur within 1–3 years and respond poorly to chemotherapy.

Methods & Results: Histopathologic review identified clusters of lymphocytes associated with epithelial hypercellularity among larger pools of mucin. Utilizing dimer avoidance multiplex-PCR and next generation sequencing, we explored the adaptive immune response in patients with recurrent LAMNs (n=10). Bulk sequencing of tumor tissue following initial CRS-HIPEC revealed a predominant expression of B cell over T cell receptors (mean expression: 0.5% Vα, 1.4% Vβ, 0.01% Vδ, 12.6% IgH, 47.6% Igκ, 37.8% Igλ). Very interestingly, we observed a heightened IgE fraction (8.4%±1.1) in patients with LAMNs, greater than both healthy donor blood (0.57%±0.36, p<0.0001, n=239) and pretreated high-grade tumors (n=66, 3.3%±2.4, p<0.0001). Although the TCR repertoire was extremely private in patients, the BCR repertoire included several shared public and private clones: 11 IgH private CDR3s shared between 2 patients, 64 Igκ public CDR3s shared among >7 patients, 261 private Igκ CDR3s shared among 3 patients, 20 public Igλ CDR3s shared among >7 patients, and 137 private Igλ CDR3s shared between 2 patients, an intriguing and unexpected finding.

Conclusions:

This, we believe, is the first report of adaptive immunity in low grade mucinous neoplasms that identifies a skewed but diverse infiltration of T and B cells, that warrants study in additional patients.

A human monoclonal antibody blocks malaria transmission and defines a highly conserved neutralizing epitope on gametes

Malaria elimination requires tools that interrupt parasite transmission. Here, we characterize B cell receptor responses among Malian adults vaccinated against the first domain of the cysteine-rich 230 kDa gamete surface protein Pfs230, a key protein in sexual stage development of P. falciparum parasites. Among nine Pfs230 human monoclonal antibodies (mAbs) that we generated, one potently blocks transmission to mosquitoes in a complement-dependent manner and reacts to the gamete surface; the other eight show only low or no blocking activity. The structure of the transmission-blocking mAb in complex with vaccine antigen reveals a large discontinuous conformational epitope, specific to domain 1 of Pfs230 and comprising six structural elements in the protein. The epitope is conserved, suggesting the transmission-blocking mAb is broadly functional. This study provides a rational basis to improve malaria vaccines and develop therapeutic antibodies for malaria elimination.

CTLA-4 expression by B-1a B cells is essential for immune tolerance

CTLA-4 is an important regulator of T-cell function. Here, we report that expression of this immune-regulator in mouse B-1a cells has a critical function in maintaining self-tolerance by regulating these early-developing B cells that express a repertoire enriched for auto-reactivity. Selective deletion of CTLA-4 from B cells results in mice that spontaneously develop autoantibodies, T follicular helper (Tfh) cells and germinal centers (GCs) in the spleen, and autoimmune pathology later in life. This impaired immune homeostasis results from B-1a cell dysfunction upon loss of CTLA-4. Therefore, CTLA-4-deficient B-1a cells up-regulate epigenetic and transcriptional activation programs and show increased self-replenishment. These activated cells further internalize surface IgM, differentiate into antigen-presenting cells and, when reconstituted in normal IgH-allotype congenic recipient mice, induce GCs and Tfh cells expressing a highly selected repertoire. These findings show that CTLA-4 regulation of B-1a cells is a crucial immune-regulatory mechanism.

HMGB1 Promotes Myeloid Egress and Limits Lymphatic Clearance of Malignant Pleural Effusions

Pleural effusions, when benign, are attributed to cardiac events and suffusion of fluid within the pleural space. When malignant, lymphatic obstruction by tumor and failure to absorb constitutively produced fluid is the predominant formulation. The prevailing view has been challenged recently, namely that the lymphatics are only passive vessels, carrying antigenic fluid to secondary lymphoid sites. Rather, lymphatic vessels can be a selective barrier, efficiently coordinating egress of immune cells and factors within tissues, limiting tumor spread and immune pathology. An alternative explanation, offered here, is that damage associated molecular pattern molecules, released in excess, maintain a local milieu associated with recruitment and retention of immune cells associated with failed lymphatic clearance and functional lymphatic obstruction. We found that levels of high mobility group box 1 (HMGB1) were equally elevated in both benign and malignant pleural effusions (MPEs) and that limited diversity of T cell receptor expressing gamma and delta chain were inversely associated with these levels in MPEs. Acellular fluid from MPEs enhanced γδ T cell proliferation in vitro, while inhibiting cytokine production from γδ T cells and monocytes as well as restricting monocyte chemotaxis. Novel therapeutic strategies, targeting HMGB1 and its neutralization in such effusions as well as direct delivery of immune cells into the pleural space to reconstitute normal physiology should be considered.

Analysis of BCR-IgH from genomic DNA with UMI incorporation

NGS of T and B cell immune receptors has become routine in immunological studies. While using RNA as a template has its benefits, gDNA is often preferred by those collecting the sample as DNA is often easier to obtain, especially from difficult samples or samples that have been in long-term storage. In addition, since each cell may only have one copy of the successfully rearranged V(D)J, it may reflect the quantity of the repertoire better. In other words, identification of a successfully rearranged V(D)J will not be skewed by expression levels as the relationship should be one cell to one V(D)J rearrangement. Here, we describe the development of a new set of BCR-IgH specific primers to target the gDNA V(D)J region while also incorporating unique molecular indices (UMI) through our proprietary dimer avoided multiplex PCR technology. The inclusion of UMI with gDNA amplification allows each cell to be counted uniquely since the relationship of one V(D)J per cell will be maintained. Thus, both the identity and the frequency of the B-cell can be captured directly, while allowing for the elimination of PCR and sequencing error. The newly developed panel was tested on a BCR-IgH Synthetic Library. The results demonstrate a high degree of correlation with the known BCR-IgH Synthetic Library (R20.956) including coverage of all known V and J gene targets. Currently, gDNA extracted from B-cell enriched PBMC samples are being tested. This method has important implications for monitoring aberrant clonotypes in blood cancers since the frequency of a clonotype can be directly quantified, even under conditions when one clonotype is expanded.

A comparison of single cell capture methods and amplification strategies to pair alpha and beta

Immune repertoire amplification of T cell receptors coupled to NGS provides detailed, sequence-level insight into the immune system which can be beneficial for the development of personalized therapies. However, information related to the cognate pairing of alpha and beta chains is lost once RNA extraction is performed on the bulk sample. We have previously presented low through-put (iPair) and high throughput methods for single cell pairing of the alpha and beta receptor chain. Here, we compare different methods to amplify and pair alpha and beta from single cells, as well as track CDR3 rankings from the same sample when sorted for iPair, high throughput pairing, and bulk repertoire. Template switch oligo (TSO) with 5′ cell barcoding, 3′ cell barcoding, and iRepertoire’s multiplex primers were used independently to amplify cDNA from the same cells. The cells are sorted CD14-CD4+ with 1% Jurkat cell line spiked in. Eight thousand cells from the same population were loaded onto 2 different platforms to capture single cells: a droplet-based capture and a microwell array capture. The results demonstrate that the dominant CDR3 pairs in single cell data (regardless of capture method) match the dominant CDR3 clones in bulk repertoire. All single cell methods compared accurately called the 1% Jurkat spike-in and the top paired CDR3.

Complete multi-chain adaptome amplification from whole blood and PBMC via novel dam-PCR technology

Profiling the immune repertoire through NGS allows detailed, sequence-specific insight into the adaptive immune response. One of the key challenges during immune receptor amplification is the formation of dimers, which can compete with the immune amplicons of interest during library preparation. Therefore, we developed a novel PCR technique, dimer-avoided multiplex PCR (dam-PCR), that effectively avoids primer dimer formation and allows for the all-in-one qualitative amplification of all BCR and TCR receptors in a single, quantitative reaction. Here, we present this technology’s capabilities of bias-free immune repertoire amplification, even for low frequency CDR3s. First, we demonstrate the ability of this method to accurately detect a Jurkat cell line that was spiked into pre-screened sorted donor CD4+ cells at 1%, 0.1%, 0.01%, 0.001%, and 0.0001%. RNA from each spike-in percentage was extracted and amplified in duplicate using our standard amplification protocol to assess repeatability of CDR3 discovery between replicates, as well as establish the limits of detection and quantitation. Then, we demonstrate the method’s ability to amplify a synthetic repertoire, created by spiking RNA from two individuals of known repertoire into each other at 75%, 50%, and 25%. The mixed RNA, as well as pure RNA from each individual, was then amplified to assess correlation between the predicted repertoire and amplified repertoire at each spike-in percentage. For both the Jurkat cell level spike-in test, as well as the RNA level spike-in test, the amplified repertoire was successfully predicted at an R2 value of > 0.99. This single reaction method will allow for a cost effective, all-inclusive, and quantitative analysis of immune repertoires.

T cell receptor repertoire detection from dry blood spots

Immune repertoire amplification of T cell receptors (TCRs) coupled with high throughput sequencing provides detailed insight into the immune system. A common starting sample type is total RNA extracted from whole blood by venipuncture. However, the costs, participant burden, regulatory constraints, and logistics associated with venipuncture and RNA handling are major barriers to clinical application or community-based research on various diseases. This study aims to identify TCR repertoires from dry blood spots (DBS), a method that could help collect real-world data for biomarker applications. Finger-prick blood was collected onto a Whatman filter card, and RNA was extracted from DBS. Fully automated multiplex PCR was performed to generate a TCRβ chain library for next generation sequencing (NGS) analysis of unique CDR3s (uCDR3). According to statistical analysis and laboratory confirmation, forty 2-mm punch disks from the filter cards were enough to detect the shared top clones and have a strong correlation in uCDR3 discovery with whole blood. uCDR3 discovery was not affected by storage temperatures (room temperature or −20°C) or storage durations (1, 14, and 28 days) when compared to whole blood. About 74 – 90% of top 50 uCDR3 clones of whole blood could also be detected from DBS. The DBS-based TCR repertoire profiling method is minimally invasive, provides convenient sampling, and incorporates fully automated library preparation. The system is sensitive to low RNA input, and the results are highly correlated with whole blood uCDR3 discovery allowing study scale-up to better understand the relationship and mutual influences between the immune repertoire and various disease states.

Complete all-in-one immune repertoire profiling of newborn babies via novel dimer-avoided multiplex PCR (dam-PCR)

There is an increased demand for immune repertoire profiling in both basic research as well as in various clinical settings, such as during vaccine development, lymphocyte tracking in minimal residual disease (MRD), hematopoietic stem cell transplant recovery monitoring, immunotherapy development, and immunological monitoring for prognosis purposes during treatment. Although next generation sequencing of the immune repertoire allows detailed, sequence-specific insight into the adaptive immune response, it usually focuses on only one or two receptor chains. One of the key challenges during immune receptor amplification is the formation of dimers, which can compete with the immune amplicons of interest during library preparation. We therefore developed a novel PCR technique, dimer-avoided multiplex PCR, that allows amplification of both BCRs and TCRs in a single, quantitative multiplex reaction. Our method generates next generation sequencing libraries for all TCR and BCR loci including TCR-beta, TCR-alpha, TCR-delta, TCR-gamma, BCR-IgH, and BCR-IgK and IgL. Here, we report the application of this method to investigate the immune repertoire of cord blood from newborn babies. Our study revealed the vast diversity and abundance of babies’ immune repertoire, the composition of TCR and BCR loci, and the sharing status of unique CDR3s among newborns. This single reaction, cost effective, all-inclusive, and quantitative immune-profiling analysis method shows promise for future applications in both basic research and clinical settings.

Physical cognate pairing of mouseTCR alpha-beta VDJ-rearrangements with phenotype directly from FACS sorted cells

Phenotypic characterization of single cells paired with immune receptor information can provide valuable insight into T cell function, which may be beneficial for the development of personalized therapies. In order to comprehensively analyze T cell function and specificity, it is necessary to integrate antigen receptor sequencing with phenotypic markers at the single cell level. We therefore developed a sensitive technology called iPair+™ that enables the simultaneous amplification and sequencing of paired mouse TCR alpha and beta chains with functional gene markers in a single, sorted immune cell via a combination of flow cytometry, multiplex PCR, and next generation sequencing. We utilized iPair+™ to study CD4 and CD8 T cells isolated from treated and non-treated mice from a breast cancer model. CDR3 diversity, clonality, and frequency were analyzed together with 80+ phenotypic genes. When cells isolated from both treated and non-treated mice were compared, we found gene expression levels changed significantly with treatment. Our data demonstrates that genes that were upregulated prior to treatment were associated with cancer growth, while genes upregulated after treatment were associated with T cell activation and function in cancer repression or growth inhibition. Our study indicates that iPair+ technology could reveal important insights into T cell function, clonal development, and immunotherapy response during treatment.

A novel method for high throughput TCR single cell VDJ-pairing with phenotypic analysis

Single cell transcriptional analysis reveals a wealth of information that is obscured when analyzing the RNA of a sample en masse. Furthermore, it is important to know the identity of the TCR chain VDJ-rearrangement associated with the phenotypic state. This information can provide direct calculations of clonal frequency in various cell subsets, tracking of specific lymphocytes with treatment, and reveal paired information for both chains of the receptor for downstream Car-T development. Here, we discuss a novel method that identifies paired VDJ-rearrangements for both TCR alpha and beta chains from single cells barcoded via the BD Rhapsody Express single cell system. The phenotype of the cell is obtained using the BD Rhapsody RNA-seq kit, while the receptor information is amplified from the same cDNA using an iRepertoire-derived method incorporating a multiplex mix of primers associated with both the TCR alpha and beta loci. This targeted-seq strategy requires less read depth when compared to template-switch approaches. In one experiment, 3,000 TCR-beta unique CDR3 (uCDR3) were identified from ~7,000 barcoded cells using 1.5 million NGS reads with a 0.83 Pearson correlation upon repeat. Approximately 1,000 TCR alpha-beta paired uCDR3 were also called from the data. Additionally, the BD phenotyping results independently verify the immune repertoire data since the TCR beta chain constant gene overlays with the TCR-beta uCDR3 clonotypes for CD4+ and CD8+ subsets but is largely absent in the CD14+ monocyte population for both analyses. Thus, the developed technology provides the ability to simultaneously pair both alpha and beta chains for thousands of T-cells while obtaining information related to the functional status of each cell.

Belimumab promotes negative selection of activated autoreactive B cells in systemic lupus erythematosus patients

Belimumab has therapeutic benefit in active systemic lupus erythematosus (SLE), especially in patients with high-titer anti-dsDNA antibodies. We asked whether the profound B cell loss in belimumab-treated SLE patients is accompanied by shifts in the immunoglobulin repertoire. We enrolled 15 patients who had been continuously treated with belimumab for more than 7 years, 17 matched controls, and 5 patients who were studied before and after drug initiation. VH genes of sort-purified mature B cells and plasmablasts were subjected to next-generation sequencing. We found that B cell-activating factor (BAFF) regulates the transitional B cell checkpoint, with conservation of transitional 1 (T1) cells and approximately 90% loss of T3 and naive B cells after chronic belimumab treatment. Class-switched memory B cells, B1 B cells, and plasmablasts were also substantially depleted. Next-generation sequencing revealed no redistribution of VH, DH, or JH family usage and no effect of belimumab on representation of the autoreactive VH4-34 gene or CDR3 composition in unmutated IgM sequences, suggesting a minimal effect on selection of the naive B cell repertoire. Interestingly, a significantly greater loss of VH4-34 was observed among mutated IgM and plasmablast sequences in chronic belimumab-treated subjects than in controls, suggesting that belimumab promotes negative selection of activated autoreactive B cells.

iPair and iPair+: cognate pairing of human TCR alpha and beta V-regions and phenotypic analysis of single cells using NGS

Immune repertoire amplification of T and B cell receptors coupled to NGS provides detailed, sequence-level insight into the immune system. However, information related to the cognate pairing of alpha and beta chains is lost once RNA extraction is performed on the entire sample (or bulk sample). Here, we describe a very sensitive method that allows for the amplification of both human TCR alpha and beta chains including additional phenotypic markers from single cells in the same reaction well. We have reduced the RT-PCR chemistry as low as 1.5 μL, thus providing a cost-effective method to analyze single cells from standard FACs instruments. Plate processing procedures are also simplified since RT-PCR of all targets can be performed in the same plate. Under optimal conditions, the amplification success rate is greater than 90%, with successfully identified pairs as high as 75% of those amplified. During the first round of PCR, RT-PCR is performed with nested, multiplex primers covering both the alpha and beta locus (iPair) and 30 phenotypic markers (iPair+). Communal forward and reverse binding sites are included on the 5′ end of the inside primers. Included on the reverse primer is an in-line 6 nt barcode, which serves as a plate identifier so that multiple 96-well plates may be multiplexed in the same sequencing flow cell. After RT-PCR1, the first round PCR1 products are rescued using beads. A second PCR is performed with dual-indexed primers that complete the sequencing adaptors introduced during PCR1 and provide plate positional information for the sequenced products. An analysis tool has also been developed to help visualize pairing across a plate and to identify those pairs that would be likely candidates for further investigation.

Immune Repertoire Diversity Correlated with Mortality in Avian Influenza A (H7N9) Virus Infected Patients

Specific changes in immune repertoires at genetic level responding to the lethal H7N9 virus are still poorly understood. We performed deep sequencing on the T and B cells from patients recently infected with H7N9 to explore the correlation between clinical outcomes and immune repertoire alterations. T and B cell repertoires display highly dynamic yet distinct clonotype alterations. During infection, T cell beta chain repertoire continues to contract while the diversity of immunoglobulin heavy chain repertoire recovers. Patient recovery is correlated to the diversity of T cell and B cell repertoires in different ways – higher B cell diversity and lower T cell diversity are found in survivors. The sequences clonally related to known antibodies with binding affinity to H7 hemagglutinin could be identified from survivors. These findings suggest that utilizing deep sequencing may improve prognostication during influenza infection and could help in development of antibody discovery methodologies for the treatment of virus infection.

iRock 2.0 and the iR-Processor: an automated immune repertoire library preparation platform for NGS (TECH2P.919)

Immune repertoire amplification of T and B cell receptors coupled to Next Generation Sequencing (NGS) provides detailed sequence-level insight into the immune system. Previously, we described the automation of a patented, nested multiplex PCR method (arm-PCR) to amplify an immune repertoire, inclusively and semi-quantitatively, on the iR-Processor, an instrument developed by iCubate, Inc. The iR-Processor is an open development platform for diagnostic panels consisting of a closed-cassette and the iR-Processor. The cassette is pre-loaded with the reagents necessary for library preparation, and the iR-Processor instructs the cassette to perform the necessary liquid handling steps and PCR for library generation. Template RNA is added to the cassette with the RT enzyme. iRock 2.0 represents an improved method in which all of the first round cDNA is rescued prior to library generation with a pair of universal primers. Once PCR is complete, residual primer-dimers are removed by magnetic selection of the primary product in the cassette. The amplified library is eluted from the magnetic beads by the user and is directly ready for sequencing using the Illumina MiSeq. The sequencing results from repeat amplification experiments of the TCRβ chain from the same individual and between individuals are compared. The results demonstrate high repeatability among shared CDR3 sequences and an improvement in the percentage of shared CDR3 discovery upon repetition.

Automation of immune repertoire amplification on the iC-Processor (TECH1P.851)

Immune repertoire amplification of T and B cell receptors coupled to Next Generation Sequencing (NGS) provides detailed sequence-level insight into the immune system. Previously, we developed a patented, nested multiplex PCR method (arm-PCR) to amplify an immune repertoire, inclusively and semi-quantitatively. Here, we describe the automation of this process in cassette format on the iC-system (iCubate, Inc.) and compare the sequencing results from repeat amplification experiments of the TCRβ and human Ig heavy chains from the same individual. The iC-system is an open, nested multiplex PCR diagnostic development platform, which allows for the development of automated diagnostic panels in a closed cassette format. In addition to the automation, the closed format helps to reduce contamination of the laboratory environment with multiplex primers. Template RNA is added to the cassette at the appropriate concentration with RT enzyme. After two sets of PCR, residual primer-dimers are removed by magnetic selection of the primary product in the cassette. The cassette is then removed from the iC-Processor, and the amplified library is eluted from the magnetic beads. The amplified immune library is directly ready for pooling, QC, and sequencing using the Illumina MiSeq NGS platform. Repeat amplification experiments from the same individual using this automated approach demonstrated high repeatability among shared CDR3 sequences for both the TCRβ and Ig heavy chains.

Breast cancer diagnosis by high throughput sequencing of T cell receptors from peripheral blood samples (TUM2P.905)

T cells play vital roles in the identification and elimination of transformed cells. It might be possible to diagnose cancer by reading imprints on the immune system made by cancer cells. High-throughput immune repertoire sequencing allows the depiction of T cell repertoire details at a nucleotide resolution and enables us to search for cancer-specific biomarkers. RNA was isolated from whole blood in breast cancer and matched controls and the CDR3 region of the TCR beta chain amplified and sequenced by Illumina next-generation sequencing platform. Initial studies showed around 200 breast cancer-specific CDR3 sequences. Two thirds of those CDR3 sequences show a pattern of convergent evolution, i.e., the same CDR3 peptide sequence is coded by different sequences. To leverage those disease-specific CDR3’s for diagnostics, we developed a novel metric called immune repertoire sharing index (SI) to measure the similarity between a repertoire and the disease library. With SI, we were able to predict breast cancer cases with both the sensitivity and the specificity around 90%. The diagnostics process requires only 10ml peripheral blood. We hypothesized that the immune repertoire sequencing and sharing index method could be generalized to other diseases. An ‘ultimate diagnostics’ may be emerged where taking one sample, with one procedure; hundreds of diseases can be diagnosed by evaluating immune repertoires.

Biomarker: long term study of breast cancer specific CDR3s in peripheral blood (TUM2P.894)

We have identified a group of T cell receptors, represented by their unique CDR3 sequences, that are closely associated with breast cancer. Multiplex PCR was used to amplify the T cell receptor beta (TCRβ) inclusively and semi-quantitatively; the amplicons were sequenced with the Illumina HiSeq platform. Here, we report a longitudinal study where one patient’s peripheral blood samples were evaluated for repertoire changes before and after the treatment. At regular intervals over four years, we collected five peripheral blood samples from the patient. The blood samples were sorted into Tc, Tr, Th, and NKT cell subsets, and the TCRβ genes were amplified and sequenced. We have also sequenced the TCRβ from the patient’s surgically removed breast cancer tissue. We have identified two kinds of biomarkers for breast cancer: public and private biomarkers. The public biomarkers are those CDR3s that are shared with other patients who were also diagnosed with breast cancer; the private biomarkers are expressed exclusively within a particular patient and are also found in the disease tissue. The study has shown that a group of CDR3s can be used as breast cancer-specific biomarkers because they are tightly associated with breast cancer patients, and their expression level can be quantitatively measured from peripheral blood. The discovery of this new class of cancer specific biomarkers will facilitate the development of new drugs and also improve the utility of existing therapies.

DNA polymerase preference determines PCR priming efficiency

Background

Polymerase chain reaction (PCR) is one of the most important developments in modern biotechnology. However, PCR is known to introduce biases, especially during multiplex reactions. Recent studies have implicated the DNA polymerase as the primary source of bias, particularly initiation of polymerization on the template strand. In our study, amplification from a synthetic library containing a 12 nucleotide random portion was used to provide an in-depth characterization of DNA polymerase priming bias. The synthetic library was amplified with three commercially available DNA polymerases using an anchored primer with a random 3’ hexamer end. After normalization, the next generation sequencing (NGS) results of the amplified libraries were directly compared to the unamplified synthetic library.

Results

Here, high throughput sequencing was used to systematically demonstrate and characterize DNA polymerase priming bias. We demonstrate that certain sequence motifs are preferred over others as primers where the six nucleotide sequences at the 3’ end of the primer, as well as the sequences four base pairs downstream of the priming site, may influence priming efficiencies. DNA polymerases in the same family from two different commercial vendors prefer similar motifs, while another commercially available enzyme from a different DNA polymerase family prefers different motifs. Furthermore, the preferred priming motifs are GC-rich. The DNA polymerase preference for certain sequence motifs was verified by amplification from single-primer templates. We incorporated the observed DNA polymerase preference into a primer-design program that guides the placement of the primer to an optimal location on the template.

Conclusions

DNA polymerase priming bias was characterized using a synthetic library amplification system and NGS. The characterization of DNA polymerase priming bias was then utilized to guide the primer-design process and demonstrate varying amplification efficiencies among three commercially available DNA polymerases. The results suggest that the interaction of the DNA polymerase with the primer:template junction during the initiation of DNA polymerization is very important in terms of overall amplification bias and has broader implications for both the primer design process and multiplex PCR.

R10K update: NGS of immune repertoire for biomarker discoveries (P3241)

The natural duty of the adaptive immune system is to detect any internal and external threats and mount specific and measured reactions accordingly. Therefore, the immune repertoire is rich in specific diagnostic markers. We have developed a novel multiplex PCR method, which can amplify the CDR3 regions from a sample inclusively and semi-quantitatively. The PCR products can be sequenced directly with different next generation sequencing platforms. A software package was developed to filter out amplification and sequencing errors, identify CDR3 sequences and perform routine repertoire analysis. The R10K project (www.R10K.org) is organized and supported by the HudsonAlpha Institute for Biotechnology, a nonprofit research institute specialized in genomic research. The project is an international collaborative effort to sequence 10,000 samples and study 100 diseases. Our pilot studies have demonstrated that disease specific repertoire changes can be detected. Quantitatively, the changes in repertoire diversity can be used as a biomarker for disease staging and measuring treatment response. Qualitatively, detection of disease specific CDR3s can be used for early diagnosis of diseases, including cancer, autoimmune diseases, inflammatory diseases, and infectious diseases. The R10K project is open to collaborators; the IP rights are shared among collaborators, participating institutions and companies. The data will be publicly available as each study is completed.

Evaluation of three next generation sequencing platforms for immune repertoire sequencing (58.10)

The advent of next generation sequencing (NGS) techniques, combined with a semi-quantitative multiplex PCR method, enables us to comprehensively profile the lymphocyte receptor diversity (immune repertoire) of the entire collection of B or T cells from a particular sample. Different NGS platforms vary in read length, throughput, sequencing error rate and error pattern, hands-on time, turnaround time and price. Three popular NGS techniques (Illumina HiSeq, 454 FLX and Ion Torrent) were employed to sequence amplicons from T cell receptor clones generated with arm-PCR in order to evaluate the usage of those techniques on immune repertoire sequencing. The error pattern and rate of the three techniques in the context of T cell receptor sequences were profiled. Based on the differences of the three techniques, we discuss the usage of each NGS platform in the context of immune repertoire sequencing.

R10K: an international collaborative project for biomarker discovery (58.7)

The R10K Project is an international collaborative effort to sequence the immune repertoire (T and B cells) from 10,000 samples that cover 100 diseases. We have developed a novel multiplex PCR method, which can amplify targets from a complex genetic material, inclusively and semi-quantitatively. This easy-to-use technology has been successfully applied to amplify immune repertoire libraries from peripheral blood samples or other tissue samples. The natural duty of the adaptive immune system is to detect any internal and external threats and mount specific and measured reactions accordingly. Our pilot studies have demonstrated that immune repertoire sequencing can be used to measure this specific response and identify disease-related T cell CDR3s. Therefore, analyzing the immune repertoire of several disease states with high throughput sequencing may lead to the discovery of disease-specific biomarkers for diagnosis, prognosis, and treatment evaluations. The R10K project is organized and supported by the HudsonAlpha Institute for Biotechnology, a non-profit research institute specialized in genomic research. A Scientific Advisory Board has been established to help identify projects from online submitted proposals. The R10K data will be made public 6 months after it has been generated.

Identification and temporal monitoring of breast cancer-associated T cell receptors with high throughput sequencing (46.23)

Tumor-specific antigens may trigger an immune response that leads to T lymphocytes infiltrating the tumor tissue. We have developed a method to study the immune repertoire of a sample by utilizing a patented multiplex PCR amplification strategy, arm-PCR (Patent No. 7,999,092), coupled with high throughput sequencing (Wang et al., PNAS 2010). Using this method, we studied a patient’s surgically removed breast cancer tissue, the nearby normal tissue, and sorted peripheral blood. The patient’s sorted peripheral blood was also examined three months, six months, and one year post-surgery. Dominant T cell clones with specific CDR3 sequences were identified from the breast cancer tissue. Some of these same clones were found expressed at high levels in the nearby normal tissue and peripheral CD8+ cells. After treatment, dynamic changes in these cancer-associated clones were apparent, demonstrating the capability of the current technology to identify specific T cells associated with a patient’s cancer tissue. These specific T cells can serve as personalized biomarkers for prognosis, treatment evaluations, and early detection of recurrence. They can also be used to develop personalized treatment strategies. Currently, this study has been extended to examine 10 additional breast cancer patients.

High throughput sequencing identified specific T cells from breast cancer tissue and peripheral blood (48.37)

Tumor specific antigens may trigger an immune response that leads to T lymphocytes infiltrating the tumor tissue. We have developed methods using high throughput sequencing technology to study the immune repertoire within a sample (Wang et al., PNAS 2010). Using this method, we studied a patient’s surgically removed breast cancer tissue, the nearby normal tissue, and sorted peripheral blood. Dominant T cell clones with specific CDR3 sequences were identified from the breast cancer tissue. The same clones were found expressed at high levels in the nearby normal tissue and peripheral CD8+ cells. The clones were also expressed at low levels in other subsets of T cells in peripheral blood. Peripheral blood was collected after lumpectomy and radiation therapy from the same patient and subsets of T cells were sequenced. The study demonstrated the capability to identify specific T cells associated with a patient’s cancer tissue. These specific T cells can serve as personalized biomarkers for prognosis, treatment evaluations and early detection of recurrent tumors. Identification of these cancer specific T cells also make it possible to design personalized treatment strategies.

Development of an alternative method for the identification and production of antigen-specific monoclonal antibodies (65.16)

A critical step in the production of monoclonal antibodies (Abs) is the initial identification of the antigen-specific Abs, which is usually performed by multiple rounds of panning in both hybridoma and phage display. We have developed an alternative method that allows for the rapid and direct identification of antigen-specific Abs from peripheral blood via high-throughput immune repertoire sequencing and LC MS/MS peptide matching. Our B-cell repertoire technology combines novel amplicon rescued multiplex PCR (arm-PCR, patent pending) with high-throughput gene sequencing to access the sequence of a broad spectrum of heavy and light chain V-regions. As a proof of concept, we have sequenced the immune repertoire of 2 healthy individuals at various time points after administration of the 2009-2010 seasonal influenza vaccine. Antigen-specific Abs were purified directly from immune peripheral blood serum and identified using LC MS/MS peptide sequencing, exploiting the B-cell repertoire gene sequencing results as a database for identification. During our study, several unique peptides were successfully matched for each individual’s response to both Flu A strains in the vaccine. Future work includes the development of a method to rapidly clone and express these identified Abs in a human in vitro glycoexpression system. The recombinant Abs will then be tested for their ability to bind flu hemagglutinin, demonstrating the utility of our technology towards the production of mAbs.

Profiling the pattern of human immunoglobulin SHM and CSR in B memory cells via high-throughput sequencing (62.11)

One of the defining features of the adaptive immune system is that it adapts its response during an infection to improve its recognition of the pathogen. The adaptive feature is best embodied in the genetic alteration mechanism of somatic hypermutation (SHM) and class-switch recombination (CSR) as they are only activated to increase recognition to a previously encountered pathogen. Due to the limited number of sequence data, the hypermutation pattern such as mutation rate, and the distribution of mutation spots remains poorly understood. Using the combination of arm-PCR and high-throughput sequencing, we have determined about one million cDNA sequences of human immunoglobulin genes in B memory cells isolated from the peripheral blood from two subjects at various time points after administration of the 2009-2010 flu vaccine. We identified the location of the hypermutations, the distribution of mutation rate, mutation patterns of different classes of immunoglobulin, and the impact on primer design for immunoglobulin genes.