Patent Description:
The present disclosure relates to methods of calculating a change in an individual's immune repertoire.

Through the process of homeostasis, the immune system maintains a certain number and repertoire of T and B lymphocytes, collectively referred to as an individual's "immune repertoire. " An individual's immune repertoire constantly changes, however, as a result of continuous cell turnover and the exposure to antigens. Such immune repertoire changes may include, for example, the generation of new (naive) T and B lymphocytes, expansion of active T and B lymphocytes, and the formation of new memory T and B lymphocytes.

Immune therapies and cellular therapies are becoming increasingly popular tools for the treatment of cancer and autoimmune disease. Immune therapies may include antibody treatments to modulate immune pathways or to boost a patient's immune response to a disease. Cellular therapies may include exposing a patient's blood or white blood cells to a disease antigen ex vivo and subsequently reintroducing the treated blood or white blood cells to the patient. While conventional methods utilize synthetic small molecules to target particular disease pathways, immune therapies and cellular therapies may act by educating a patient's immune system to fight disease.

When in a disease state, or during treatment of such disease state, a patient's immune system mobilizes to fight the disease. As a result, the turnover rate of the immune repertoire may change. A measurement of such change may give an indication of the effectiveness of the treatment. Currently, however, no tools or methods are available which would allow scientists or physicians to measure the immune repertoire turnover rate; current methods, such as white blood cell counts and flow cytometry, are not ideal. Measuring a patient's white blood cell count provides only the total number of lymphocytes or the number of cells that belong to lymphocyte category, and flow cytometry allows classification of T and B lymphocytes based on surface markers. Neither of these methods, however, provide an accurate measurement of the immune repertoire turnover rate. As such, current methods are not ideal for the evaluation of therapeutic results of therapies, such as immune therapies, the generation of markers for pre-screening patients, and the identification of those patients best fit for a particular therapy. What is needed, therefore, is a tool to classify T and B lymphocytes at the single cell level based on the differentiallyexpressed T or B lymphocyte receptors and a method of utilizing this information to determine a change in an individual's immune repertoire. <CIT> relates to the measurement and comparison of immune diversity by high-throughput sequencing. <CIT> relates to the quantitative assessment of human T-cell repertoire recovery after allogeneic hematopoietic stem cell transplantation. <CIT> relates to sequence-based measures of the immune response. <CIT> relates to methods of treating diseases, the methods comprising deliberate tumor insult and sequencing of the T cell repertoire before and after the insult in order to detect and sequence the TCR alpha and beta loci of highly expanded T cell clonotypes. <CIT> relates to tracking of donor-reactive TCR as a biomarker in transplantation. Wang et al. , discloses that high throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. <CIT> relates to characterization of the adaptive immune response to vaccination or infection using immune repertoire sequencing. <CIT> relates to a method for evaluating an immunorepertoire.

The present invention relates to a method of calculating the change in the immune repertoire of a patient, comprising the steps of:.

wherein the first and second samples comprise white blood cells; wherein the Delta Index is calculated from two samples collected at different time periods, and wherein the Delta Index provides a measurement of the difference in the level of immune cell diversity in the two samples at the different time periods. In certain embodiments, the immune repertoire change rate is determined at a time point before, during or after a health event. The presently disclosed methods allow for the analysis of a vast amount of sequencing data while eliminating sampling and sequencing inconsistencies that have previously made the calculation of immune repertoire changes impossible.

The disclosure can be better understood with reference to the following figures.

The inventor has developed a method for calculating the change in the immune repertoire of an individual; the individual may be one who is suffering from a disease or undergoing therapy for the treatment of a disease. The method uses the difference between the level of immune cell diversity seen in an individual, for example before, during or after a health event; this difference may be used to determine the effect of a disease, or the effect of a treatment regime, on the individual. Such a health event may include a natural occurrence (i.e., the onset of a disease) or an artificial occurrence (i.e., the commencement of disease treatment). The difference in the level of immune cell diversity is referred to as the Delta Index. The Delta Index is defined as in claim <NUM>; it represents a quantitative change (up or down regulation of CDR3s) and qualitative change (gain or loss of clones) of an individual's most dynamic immune cells over time. The third complementaritydetermining region (CDR3) is a region whose nucleotide sequence is unique to each T or B cell clone. The most dynamic immune cells within an individual's immune system are referred to as the immune repertoire Impact Range. The Impact Range is defined as in claim <NUM>. The Impact Range may include other numbers of clones, for example the <NUM>,<NUM> or <NUM>,<NUM> clones displaying the biggest change. As used herein, "immune cells" refers to T lymphocytes and/or B lymphocytes.

Also disclosed is a method for assessing the rate of change in an individual's most dynamic immune cells over time comprising the following steps: (a) collecting at least two sample populations of white blood cells from a subject; (b) separately amplifying polynucleotides from each population of white blood cells in a reaction mix comprising target-specific nested primers to produce a set of first amplicons, at least a portion of the target-specific nested primers comprising additional nucleotides which, during amplification, serve as a template for incorporating into the first amplicons a binding site for at least one common primer; (c) separately transferring a portion of each of the first reaction mixes containing the first amplicons to second reaction mixes comprising at least one common primer; (d) for each population, amplifying, using the at least one common primer, the first amplicons to produce a set of second amplicons; (e) sequencing each of the second amplicons to identify the frequency of specific CDR3 regions present in the sample; (f) normalizing the CDR3 frequency data; (g) comparing the normalized CDR3 frequency data of the first sample and the second sample to determine the absolute difference between the frequency of each CDR3 sequence; (h) determining the CDR3 sequences common to the first sample and the second sample with the largest frequency changes; and (i) determining the sequences from step (h) with the highest degree of change. As used herein, "subject" means either a human or an animal.

It has previously been difficult to assess the immune system in a broad manner, as the number and variety of cells in a human or animal immune system is so large that sequencing more than a small subset of cells has been impractical. The inventor developed a semi-quantitative PCR method (arm-PCR, described in more detail in <CIT>), which provides increased sensitivity and specificity over previously-available methods, while producing semi-quantitative results. It is this ability to increase specificity and sensitivity, and thereby increase the number of targets detectable within a single sample, that makes the method ideal for detecting relative numbers of clonotypes of the immune repertoire. The inventor has more recently discovered that using this sequencing method allows him to compare the change, or turnover rate, of the immune repertoire of individual subjects, which has led to the development of the present method. The method has been used to evaluate subjects who are undergoing treatment for a particular disease, for example cancer. The inventor has demonstrated that a change in the immune repertoire diversity can be readily detected using the methods of the invention. These methods may therefore be useful as indicators of treatment effectiveness, much as cell counts and biochemical tests are currently used in clinical practice.

Clonotypes of an immune repertoire are determined by the rearrangement of Variable (V), Diverse (D) and Joining (J) gene segments through somatic recombination in the early stages of immunoglobulin (Ig) and T cell receptor (TCR) production of the immune system. The V(D)J rearrangement can be amplified and detected from T cell receptor alpha, beta, gamma, and delta chains, as well as from immunoglobulin heavy chain (IgH) and light chains (IgK, IgL). Cells may be obtained from a patient by obtaining peripheral blood, lymphoid tissue, cancer tissue, or tissue or fluids from other organs and/or organ systems, for example. Techniques for obtaining these samples, such as blood samples, are known to those of skill in the art. "Quantifying clonotypes," as used herein, means counting, or obtaining a reliable approximation of, the numbers of cells belonging to a particular clonotype. Cell counts may be extrapolated from the number of sequences detected by PCR amplification and sequencing.

The CDR3 region, comprising about <NUM>-<NUM> nucleotides, encompasses the junction of the recombined variable (V), diversity (D) and joining (J) segments of the gene. It encodes the binding specificity of the receptor and is useful as a sequence tag to identify unique V(D)J rearrangements.

Arm-PCR may be used for the amplification of CDR3 regions from T cells, B cells, and/or subsets of T or B cells. The term "population" of cells, as used herein, therefore encompasses what are generally referred to as either "populations" or "sub-populations" of cells. Large numbers of amplified products may then be efficiently sequenced using next-generation sequencing platforms.

The arm-PCR method provides highly sensitive, semi-quantitative amplification of multiple polynucleotides in one reaction. The arm-PCR method may also be performed by automated methods in a closed cassette system (iCubate®, Huntsville, Ala. ), which is beneficial in the present method because the repertoires of various T and B cells, for example, are so large. In the arm-PCR method, target numbers are increased in a reaction driven by DNA polymerase, which is the result of target-specific primers being introduced into the reaction. An additional result of this amplification reaction is the introduction of binding sites for common primers which will be used in a subsequent amplification by transferring a portion of the first reaction mix containing the first set of amplicons to a second reaction mix comprising common primers. "At least one common primer," as used herein, refers to at least one primer that will bind to such a binding site, and includes pairs of primers, such as forward and reverse primers. This transfer may be performed either by recovering a portion of the reaction mix from the first amplification reaction and introducing that sample into a second reaction tube or chamber, or by removing a portion of the liquid from the completed first amplification, leaving behind a portion, and adding fresh reagents into the tube in which the first amplification was performed. In either case, additional buffers, polymerase, etc., may then be added in conjunction with the common primers to produce amplified products for detection. The amplification of target molecules using common primers gives a semi-quantitative result wherein the quantitative numbers of targets amplified in the first amplification are amplified using common, rather than target-specific primers - making it possible to produce significantly higher numbers of targets for detection and to determine the relative numbers of cells comprising various rearrangements within a patient's blood sample. Also, combining the second reaction mix with a portion of the first reaction mix allows for higher concentrations of target-specific primers to be added to the first reaction mix, resulting in greater sensitivity in the first amplification reaction. It is the combination of specificity and sensitivity, along with the ability to achieve quantitative results by use of a method such as the arm-PCR method that allows a sufficiently sensitive and quantitative assessment of the type and number of clonotypes in a population of cells to produce a Delta Index that is of diagnostic use.

Clonal expansion due to recognition of antigen results in a larger population of cells that recognize that particular antigen, and evaluating cells by their relative numbers provides a method for determining whether an antigen exposure has influenced expansion of antibody-producing B cells or receptor-bearing T cells. This is helpful for evaluating whether there may be a particular population of cells prevalent in individuals who have been diagnosed with a particular disease. For example, the method may be especially helpful in evaluating whether or not a treatment or vaccine has achieved the desired immune response in individuals to whom the treatment or vaccine has been given.

Primers for amplifying and sequencing variable regions of immune system cells are available commercially, and have been described in publication such as the inventor's published patent applications <CIT> and <CIT>.

There are several commercially available high-throughput sequencing technologies, such as Hoffman-LaRoche, Inc. 's <NUM> sequencing system. In the <NUM>° sequencing method, for example, the A and B adaptor are linked onto PCR products either during PCR or ligated on after the PCR reaction. The adaptors are used for amplification and sequencing steps. When done in conjunction with the arm-PCR technique, A and B adaptors may be used as common primers (which are sometimes referred to as "communal primers" or "superprimers") in the amplification reactions. After A and B adaptors have been physically attached to a sample library (such as PCR amplicons), a single-stranded DNA library is prepared using techniques known to those of skill in the art. The single-stranded DNA library is immobilized onto specifically-designed DNA capture beads. Each bead carries a unique singled-stranded DNA library fragment. The bead-bound library is emulsified with amplification reagents in a water-in-oil mixture, producing microreactors, each containing just one bead with one unique sample-library fragment. Each unique sample library fragment is amplified within its own microreactor, excluding competing or contaminating sequences. Amplification of the entire fragment collection is done in parallel. For each fragment, this results in copy numbers of several million per bead. Subsequently, the emulsion PCR is broken while the amplified fragments remain bound to their specific beads. The clonally amplified fragments are enriched and loaded onto a PicoTiterPlate® device for sequencing. The diameter of the PicoTiterPlate® wells allows for only one bead per well. After addition of sequencing enzymes, the fluidics subsystem of the sequencing instrument flows individual nucleotides in a fixed order across the hundreds of thousands of wells each containing a single bead. Addition of one (or more) nucleotide(s) complementary to the template strand results in a chemilluminescent signal recorded by a CCD camera within the instrument. The combination of signal intensity and positional information generated across the PicoTiterPlate® device allows the software to determine the sequence of more than <NUM>,<NUM>,<NUM> individual reads, each is up to about <NUM> base pairs, with the GS FLX system.

In one embodiment of the invention, sequencing information from the CDR3 region of T cells, B cells, and/or subsets of T or B cells is obtained from a single patient. As illustrated in <FIG>, these cells may be collected at varying time points. For example, multiple samples may be collected from the same patient at the same time point (PAT1S1, PAT1S2). In this embodiment, samples are collected before the commencement of a treatment regime. As will be described in more detail below, analysis of sequence information from samples taken at the same time point allows for the establishment of an initial or baseline immune repertoire turnover rate of the patient's most dynamic immune cells. The methods of the invention are practiced on samples collected from the same patient at different time points (PAT1S1, PAT2S1) (<FIG>). In one embodiment, samples may be collected before, during and after a treatment regime, the timing of which may be dictated by the patient's practitioner. Analysis of this sequence information allows one to determine a change in the immune repertoire turnover rate of the patient's most dynamic immune cells resulting from the treatment regime.

Differences in how the sample is collected, the number of cells collected, the number of sequencing reads obtained (i.e., the number of sequences obtained from a sample) and the number of CDR3 sequences sampled makes comparison of two samples impossible without first normalizing the samples to a common read count. A reference must therefore be established as a basis of comparison for later measurements. Therefore, having obtained the sequences using a quantitative and/or semi-quantitative method, the data is then normalized to account for such differences.

<FIG> and <FIG> illustrate the process of calculating the baseline change in the immune repertoire. Column A of <FIG> represents raw sequence data for a number of CDR3 regions of a population of immune cells from a first patient sample. As is evident from column A, each detected gene sequence has an accompanying frequency of <NUM> million (reads). In one embodiment of the invention, each sample is normalized to <NUM> million reads to account for these discrepancies. In this embodiment, a normalized read count is obtained by multiplying the read count (i.e., the number of times each unique CDR3 sequence is detected in the sample) for each CDR3 sequence by a normalization factor (<NUM> million/total number of reads for the sample) (column B), which is then divided by <NUM> million (column C). Although the present example normalizes the read count to <NUM> million, the count may be normalized to other cell concentrations in other embodiments.

To establish a baseline repertoire turnover rate for an individual, the normalized sequence data from two samples collected at a single time period (PAT1S1 and PAT1S2) are then compared. Referring now to <FIG>, the absolute difference between the frequencies of each CDR3 read count in each sample is determined (column D). Because the present method is used to determine the change in an individual's immune repertoire, all quantitative changes (i.e., the increase or decrease in the frequency of a unique CDR3 sequence) are included in these calculations. In an additional embodiment, the absolute difference between the frequencies of each CDR3 sequence will also include qualitative changes. For example, the fact that a specific CDR3 sequence may be present in the first sample but absent from the second sample (or vice versa) will be in the calculations for determining the absolute difference in clonotype diversity between the two samples.

Referring again to <FIG>, the next step in determining the baseline immune repertoire turnover rate for a patient includes the calculation of the Impact Range of the two samples (column E). As used herein, the Impact Range is calculated by determining the percentage of the patient's immune repertoire contributed by the most dynamic clones, as further defined in claim <NUM>. It is necessary to determine the Impact Range so that sampling differences between the two populations may be eliminated. As described previously, such sampling inconsistencies may include, for example, differences in the number of cells included in the patient sample, differences in the amplification efficiency during arm-PCR, introduction of sequencing bias and differences in sequencing depth. The presence of these sample variables makes it impossible to compare the frequency variability between the two populations. Normalizing the sequencing data to <NUM> million reads, as described above, helps to eliminate some of these inconsistencies. However, further steps, such as calculating the Impact Range, must be taken to enable the analysis of the vast amount of sequencing data and to allow for the direct comparison of the two samples. The variables discussed above will mask any frequency changes and make such a comparison impossible. The Impact Range is determined by calculating the percent of the patient's immune repertoire contributed by the <NUM> CDR3 clones with the biggest frequency difference between samples, as defined in claim <NUM>. As illustrated in <FIG>, other numbers of clones may be included in the calculation of the Impact Range in other embodiments, for example the <NUM>,<NUM> or <NUM>,<NUM> clones with the biggest frequency difference between the samples.

In the next step illustrated in <FIG>, column F, the Delta Index is calculated for the two samples. As used herein, the Delta Index is as defined in claim <NUM>; it represents the total percentage of the sequenced CDR3 clones within the Impact Range that exhibit a frequency difference between the first and second samples. In the example illustrated in <FIG>, column H, the Impact Range of samples <NUM> and <NUM> (averaged) is <NUM>%, indicating that the <NUM> most dynamic CDR3 clones make up <NUM>% of the sequenced immune repertoire of the patient. In the final step, the Delta Index is calculated for the two samples. In this embodiment, the Delta Index is the percentage of the CDR3 clones included in the Impact Range that has changed between sample <NUM> and sample <NUM>. As illustrated in <FIG>, column H, the Delta Index of <NUM>% is a calculation of the baseline immune repertoire turnover for the patient, calculated from two samples collected at the same time point, for example, before the start of a health event.

After establishing the baseline immune repertoire turnover rate, the Delta Index can then be calculated for two samples collected at different time periods. In one embodiment, a first sample may be collected before the start of treatment and a second sample collected during, or after the treatment is completed. As illustrated in <FIG>, the raw CDR3 sequence data from two samples collected at different time points (PAT1S1 and PAT2S1) is: (<NUM>) normalized; (<NUM>) the absolute difference between the frequencies calculated; (<NUM>) the Impact Range of the two samples is calculated; and (<NUM>) the Delta Index determined for the two samples. These steps are performed in the same manner as described previously in regard to <FIG> (i.e., the same manner as in calculating the baseline Delta Index). As further illustrated in <FIG>, the signal to noise ratio of the Delta Index calculation may then be determined by comparing the baseline Delta Index to the experimental Delta Index, as illustrated by the following calculation:<MAT>.

In the embodiment illustrated in <FIG>, the selection of an Impact Range of <NUM> produces the lowest signal to noise ratio and provides results with less noise.

The present invention allows for the calculation of the repertoire rate of the most dynamic immune cells. The steps of the method involve the manipulation of vast amounts of sequence data, for example when normalizing sample sizes, obtaining frequency values for each CDR3, obtaining absolute frequency changes, and calculating Impact Ranges. These calculations are necessary to take into account that some clones may be upregulated during a health event, others may be downregulated, some clones may disappear at a second time point, and some new clones may appear at a different time point. The present invention overcomes these problems by determining overall repertoire changes and quantifying the changes associated with each CDR3. The present methods allow for the analysis of a vast amount of sequencing data while eliminating sampling and sequencing inconsistencies that have previously made the comparison of immune repertoire changes impossible.

Two whole blood samples were collected from each of two healthy individuals at three month intervals. Two next generation sequencing (NGS) protocols were performed on the samples from each individual. RNA was extracted from, on average, <NUM> million cells, and arm-PCR was used to generate the NGS library. Sequencing was performed using the Illumina HiSeq® instrument.

<FIG> illustrates the calculated Delta Index for several sample groups:.

Two whole blood samples were collected from each of <NUM> healthy individuals at three month intervals. Two NGS protocols were performed on the samples from each individual. RNA was extracted from, on average, <NUM> million cells, and arm-PCR was used to generate the NGS library. Sequencing was performed using the Illumina HiSeq® instrument. On average, <NUM> million T cell receptor molecules were sequenced for each sample (<NUM> million total reads per individual). Approximately <NUM>,<NUM> to <NUM>,<NUM> unique CDR3 sequences were obtained from each sample.

Table <NUM> illustrates the results of analyzing close to <NUM> million sequence reads (one read = one molecule), including the calculated Delta Index, with a range of <NUM>% to <NUM>%, with an average of <NUM>%.

Samples were obtained from <NUM> breast cancer patients undergoing neoadjuvant treatment, i.e., chemotherapy before surgery to reduce the tumor burden before surgery.

Peripheral blood samples were collected pre- and post-treatment. Two NGS protocols were performed on the samples from each individual. RNA was extracted from, on average, <NUM> million cells, and arm-PCR was used to generate the NGS library. Sequencing was performed using the Illumina HiSeq® instrument. As illustrated in Table <NUM>, the calculated Delta Index range was from <NUM>% to <NUM>%, with an average <NUM>%.

These calculated Delta Index ranges indicate a significantly higher repertoire turnover rate as compared to that observed for healthy individuals (Table <NUM>). Calculating the immune repertoire turnover rate, using the methodologies described herein, offers several advantages compared with current methods. The methodologies disclosed herein may, for example, help to evaluate treatment outcomes or to indicate the onset of a disease state.

Claim 1:
A method of calculating the change in the immune repertoire of a patient, comprising the steps of:
(a) quantifying CDR3 clonotypes of immune cells in a population or subpopulation of immune cells in a first sample and a second sample collected from the same patient;
(b) calculating frequency data for the first sample and the second sample by identifying the frequency of each CDR3 clonotype;
(c) normalizing the frequency data for the first sample and the second sample;
(d) determining the absolute difference in the frequency of each CDR3 clonotype present in the first sample and the second sample;
(e) determining at least <NUM> CDR3 clonotypes common to the first sample and the second sample with the largest frequency change;
(f) determining an Impact Range parameter that is obtained by calculating the percentage of the patient's immune repertoire contributed by the at least <NUM> CDR3 clonotypes; and
(g) determining a Delta Index parameter by calculating the total percentage of the CDR3 clonotypes within the Impact Range that exhibit a frequency difference between the first and second samples;
wherein the first and second samples comprise white blood cells;
wherein the Delta Index is calculated from two samples collected at different time periods, and
wherein the Delta Index provides a measurement of the difference in the level of immune cell diversity in the two samples at the different time periods.