Use of High-Throughput Sequencing (HTS) of TCRß to Determine the Kinetics of Graft-Versus-Lymphoma (GVL) Effect and T-Cell Repertoire Profiles after Allogeneic Transplant

Abstract Introduction:While allogeneic transplant using non-myeloablative preparative regimen provides a viable alternative with low TRM, the kinetics of GVL effect and the T-cell reconstitution may differ from the myeloablative transplant. In general, the donor cell engraftment is slower using a non-myeloablative regimen and a delayed GVL effect is expected. In this study, we applied the TCRß HTS to determine (1) the kinetics of the GVL effect by quantifying the tumor cell burden prior to and after transplant and (2) the pace of the T-cell reconstitution after transplant. Method: This report included a cohort of 24 patients with advanced stage mycosis fungoides or Sézary Syndrome who underwent allogeneic transplant using a non-myeloablative regimen with total skin electron beam therapy (TSEBT, 24-36 Gy), total lymphoid irradiation (TLI, 8 Gy) and anti-thymocyte globulin (ATG). All patients received G-CSF-mobilized peripheral blood hematopoietic cells with a median donor CD34+ cell dose of 6.9 x 106/kg (range 2.0-12.4) and a median donor CD3+ cell dose of 278.1 x 106/kg (range 134.4-631.0). The unique malignant T-cell clonotype of each individual patient was identified from diagnostic blood/skin samples as the single dominant sequence by TCRß HTS. Blood samples were collected prior to and at different time points after transplant. DNA extracted from PBMC corresponding to approximately 200,000 genomes was used for HTS (Sci. Transl. Med.5:214ra171, 2013) (ImmunoSEQ, Adaptive Biotech). The tumor cell burden (including minimal residual disease, MRD) was expressed as percentage of the malignant clonotype found in the entire T-cell repertoire. Results: Prior to transplant, 21 patients (88%) had detectable disease by TCRß HTS in the blood (<1%: 10 patients, 1-5%: 3 patients, >5%: 8 patients), and 3 patients had no detectable disease in the blood. The percentage of malignant clone decreased in 19 of these 21 patients at day+30 post-transplant, and 2 patients showed stable minimal disease (0.03 and 0.30%, respectively). The reduction of tumor burden was most pronounced in patients with >5% involvement prior to transplant. In these 8 patients, the pre- and day+30 post-transplant disease burden decreased from 77.9 to 0.9%, 23.6 to 9.0%, 21.1 to 8.8%, 11.8 to 1.9%, 11.3 to 0.9%, 10.0 to 0.1%, 6.0 to 1.5% and 5.5 to 0.2%, respectively. This immediate post-transplant GVL effect was not associated with full donor T-cell engraftment (donor CD3+ >95%). The donor T-cell chimerism at day+30 was 94%, 79%, 1%, 90%, 93%, 93%, 23% and 91% for these 8 patients, respectively. Subsequently, 11 of the 24 patients achieved sustained molecular remission in the blood with a median time to achieve molecular remission of 60 days (range 30-540). Patients with full donor T-cell chimerism (n=16) had a higher chance of achieving molecular remission in the blood than those with mixed donor T-cell chimerism (69% vs 0%, p = 0.002). Of these 11 patients who achieved molecular remission in the blood, 8 also achieved molecular remission in the skin at the same time. Of the remaining 3 patients, 2 achieved molecular remission in the skin more than 4 months after achieving remission in the blood, while one patient has yet to achieve molecular remission in the skin. We then analyzed the “T-cell repertoire” at different time points post-transplant by assessing the number of unique T-cell clonotypes in each blood sample from 14 patients who had at least 1-year follow-up. While the size of the T-cell repertoire varied significantly between patients, we observed an overall upward trend within individual patients after transplant (Table). The size of T-cell repertoire did not correlate with the donor CD34+ or CD3+ cell dose in the allograft. Conclusion:By using an extremely sensitive and specific TCRß HTS, we have shown an immediate post-transplant GVL effect in which a full donor engraftment was not required, followed by a subsequent sustained GVL effect that may depend on full donor T-cell engraftment. Our results suggest a different kinetics of GVL effect in different compartments (blood vs skin). We also demonstrate continued expansion of T-cell repertoire profile after allogeneic transplant. Abstract 2473.Table. The number of unique T-cell clonotypes at different time points post-transplantDay+30Day+60Day+90Day+180Day+270Day+360Median7,55010,4177,9428,40013,62820,057Range629 - 60,6441,916 - 63,6911,297 - 82,0591,572 - 66,5916,510 - 42,5651,914 - 57,358 Disclosures No relevant conflicts of interest to declare.

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Lineage–Specific Chimerism and Incidence of Graft-Failure Following T-Cell Replete Haploidentical Transplantation Using Post-Transplant Cyclophosphamide in Eighty-Nine Consecutive Patients From a Single-Center.

Blood ◽

10.1182/blood.v120.21.3030.3030 ◽

2012 ◽

Vol 120 (21) ◽

pp. 3030-3030

Author(s):

Amaani Hussain ◽

Connie A. Sizemore ◽

Xu Zhang ◽

Melissa Sanacore ◽

Stacey Brown ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Graft Failure ◽

Myeloid Cells ◽

Time Points ◽

Post Transplant ◽

Haploidentical Transplantation ◽

Cell Engraftment ◽

Preparative Regimen ◽

Spontaneous Improvement

Abstract Abstract 3030 T-cell replete HLA-haploidentical transplantation using post-transplant cyclophosphamide for prevention of GVHD and graft rejection (Haplo-PTCy) has recently emerged as a valid form of alternative-donor transplantation for patients who lack traditional matched-siblings (MSD) or matched-unrelated donors (MUD). We have demonstrated that patients undergoing Haplo-PTCy can have equivalent rates overall and disease-free survival and equivalent or lower cumulative incidences of GVHD and non-relapse mortality to patients transplanted contemporaneously from MSD and MUD at the same center (Bashey et al ASH 2011 abstract #833). In this study we assessed lineage-specific chimerism, together with incidence and outcome of graft-failure in 89 consecutive first Haplo-PTCy performed for hematologic malignancy in our center between Oct 2005 and Jun 2012. Patient characteristics: M 48, F 41; median age 48 (20–74); Diagnosis AML 28, ALL 16, CLL 11, NHL 9, HL 8, CML 8, MDS 7, MPS 2; median number of matched HLA loci were 5/10 (range 5/10 to 8/10); Median CD34+ and CD3+ cell dose infused were 4.01 × 106/kg (0.84–6.27) and 5.35 × 107/kg (1.4–53.82) respectively. Fifty-eight patients received a marrow graft and 31 received G-CSF mobilized PBSC. The preparative regimen was RIC/NST in 59 (fludarabine 30 mg/m2/d d -6 to -2, TBI 200cGy d-1, cyclophosphamide 14.5 mg/kg/d d-6 & -5, and 50 mg/kg/d d+3 & +4) and myeloablative in 30 (regimen A- fludarabine 30 mg/m2/d d -6 to -2, busulfan 110–130 mg/m2/d d-7 to -4, cyclophosphamide 14.5 mg/kg/d d-3 & -2, and 50 mg/kg/g d+3 & +4 [20 patients] and regimen B- fludarabine 30 mg/m2/d d -7 to -5, TBI 1200 cGy given in 8 fractions between days-4 to -1 and cyclophosphamide 50 mg/kg/d d +3 & +4 [10 patients]). The presence of pre-transplant anti-donor HLA antibodies were assessed using a solid phase assay (Panel Reactive Antibody, PRA, Clinimmune, CO) and by anti-donor cross-matching by flow cytometry (Clinimmune). All donors were selected to provide a negative cross-match using recipient serum and donor T-cells prior to transplant. Engraftment was determined using standard CIBMTR criteria. Lineage-specific chimerism was determined using PCR for short tandem repeats on peripheral blood mononuclear cells separated by CD3 and CD33 expression using immunomagnetic beads on d 30,60,90 and 180 following transplant. Median time to ANC > 500/mm3 was 16d (12–27d) and platelets > 20,000/mm3 was 26d (0–26d). Median T-cell (CD3) and myeloid (CD33) donor chimerisms were 100%, at all time-points assessed from d30–180 (Fig 1). All 30 patients who received a myeloablative Haplo-PTCy had full engraftment of T-cells and myeloid cells starting d +30. However six of 59 patients undergoing RIC/NST Haplo-PTCy had primary failure of T-cell engraftment -median CD3 chimerism (range) for these patients on d 30 and 60 were 0% (0–6%) and 0% (0–14%). Median CD33+ cell chimerism for the same patients on d 30 and 60 respectively were 86% (0–100%) and 45% (0–100%). Four of these patients underwent a second Haplo-PTCy, a median of 105d (range 8–123d) following the first transplant using a different haploidentical donor and the same preparative regimen. In each case the second Haplo-PTCy was successful (CD3+ donor chimerism 100% by d 30–60 in all cases). One patient who was too unwell for second Haplo-PTCy had spontaneous improvement in CD3 chimerism (6–14% d 30–90 improving to 100% d 180) and one patient died of progressive malignancy before a second Haplo-PTCy could be performed. These data demonstrate that full donor chimerism of T-cells and myeloid cells is usual following Haplo-PTCy from the earliest time-points assessed. Engraftment failure was not seen in any patient using the myeloablative regimens described above. Approximately 10% of patients conditioned with the RIC/NST regimen failed to undergo initial T-cell engraftment. However, re-transplantation was successful in all cases when attempted. Late spontaneous improvement of CD3 chimerism is also possible in patients with low level mixed chimerism early post-transplant. Fig 1. Fig 1. Disclosures: No relevant conflicts of interest to declare.

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High-Throughput Sequencing Of T Cell Receptors Detects Signatures Of T Cell Repertoire That Predict MRD Status In Patients With Mantle Cell Lymphoma Undergoing Immunotransplantation

Blood ◽

10.1182/blood.v122.21.4251.4251 ◽

2013 ◽

Vol 122 (21) ◽

pp. 4251-4251

Author(s):

Malek Faham ◽

Joshua Brody ◽

Holbrook E Kohrt ◽

Debra K Czerwinski ◽

Ronald Levy

Keyword(s):

T Cell ◽

Peripheral Blood ◽

Mononuclear Cells ◽

Cell Vaccine ◽

Cell Transplant ◽

T Cell Repertoire ◽

Cell Repertoire ◽

Blood Samples ◽

Post Transplant ◽

Before And After

Background A clinical trial is ongoing at Stanford for MCL patients in first remission that interdigitates an autologous CpG-stimulated tumor cell vaccine with autologous peripheral blood stem cell transplant (PSCT) (NCT00490529). In this trial, blood samples collected before and after vaccination and serially post-transplant are assayed for minimal residual disease (MRD) and for T cell repertoire using the LymphoSIGHT™ sequencing method (Faham et al., Blood 2012). We identified a set of T cell clones that appear to be responding to the vaccine, and therefore we investigated whether the number of these clonotypes was correlated with MRD status. Methods Using universal primer sets, we amplified rearranged IgH variable (V), diversity, and joining (J) gene segments from genomic DNA. Amplified products were sequenced to obtain >1 million reads. The B cell tumor-specific sequence was identified for each patient based on its high frequency in the original tumor biopsy. The presence of the tumor cells was then monitored in serial blood samples with a sensitivity of 1 cell per million leukocytes. The same blood samples were used for amplification, sequencing and analysis of the entire TCRβ repertoire. To facilitate identification of tumor vaccine-induced TCRβ clonotypes, we sequenced the TCRβ repertoire immediately before and after the administration of both the priming vaccination and a booster vaccination. We developed a metric called the vaccine response score (V score). This metric is calculated for each clonotype and reflects the increase in frequency after the initial vaccination AND after the boost. The formula for calculating V score is: V = F1 x F2 x square root [1/ (|F1 – F2| + 1)], where F1 and F2 represent the fold-change of the priming and boost vaccinations, respectively. Clonotypes with a V score >10 were deemed to be vaccination-induced by virtue of these frequency changes. Results In a series of 12 vaccinated patients, the number of clonotypes with V score ≥ 10 ranged between 0 and 262, with a median of 57. We utilized an antigen-specific analysis to validate that clones with high V scores (≥ 10) were in fact tumor-specific. For this analysis, we incubated peripheral blood mononuclear cells (PBMCs) with the tumor and then sequenced the TCRβ repertoire from cells obtained after culture. Clones that were enriched after culture compared to pre-stimulation PBMCs were deemed to be antigen-specific. These clones that are antigen-specific are highly likely to have a high V score compared to a random frequency-matched set of clones (P two tailed = 1.8 x 10-10), providing further evidence that clones with a high V score are tumor-specific. We then analyzed the relationship between V score and clinical outcome. Patients could be stratified into two groups with “high” (> 25) or “low” (<25) numbers of vaccine-responsive clonotypes. Patients in the high V score group, who had larger numbers of putative tumor-specific T cells, were more likely to have sustained molecular remission during the first-year post-transplant compared with patients in the low V score group (P = 0.018) (Figure 1). Conclusions T cell repertoire analysis identified clonotypes responding to the vaccination, and the presence of these vaccine-specific clonotypes correlates with MRD positivity at the important landmark of one year post-PSCT. Further analysis of additional patients enrolled on the MCL trial is ongoing. This data underscores the prognostic relevance of the sequencing-based V score metric and provides a novel approach for assessment of cancer immunotherapy responses. Disclosures: Faham: Sequenta: Employment, Equity Ownership, Membership on an entity’s Board of Directors or advisory committees.

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T cell repertoire remodelling following post-transplant T cell therapy coincides with clinical response

immuneACCESS ◽

10.21417/cs2019jci ◽

2019 ◽

Author(s):

C Smith ◽

D Corvino ◽

L Beagley ◽

S Rehan ◽

MA Neller ◽

...

Keyword(s):

T Cell ◽

Cell Therapy ◽

Clinical Response ◽

T Cell Repertoire ◽

Cell Repertoire ◽

T Cell Therapy ◽

Post Transplant

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Spectratype Analysis of In Vitro Donor Anti-Host T Cell Repertoire Responses Predict Those of In Vivo Post-BMT.

Blood ◽

10.1182/blood.v110.11.2163.2163 ◽

2007 ◽

Vol 110 (11) ◽

pp. 2163-2163

Author(s):

Thea M. Friedman ◽

Kira Goldgirsh ◽

Jenny Zilberberg ◽

Stephanie A. Berger ◽

Joanne Filicko-O’Hara ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

T Cell Responses ◽

T Cell Repertoire ◽

Cell Repertoire ◽

Post Transplant ◽

Cell Responses ◽

Repertoire Analysis ◽

Alloreactive T Cell

Abstract Immunotherapeutic strategies have gained recognition as viable alternatives to more conventional modalities for the treatment of cancer. In this regard, adoptive T cell therapy through allogeneic blood and marrow transplantation (BMT) has provided the strongest evidence that anti-tumor effects could be achieved against hematological malignancies. However, the major complications of BMT still include graft failure, opportunistic infections, disease relapse and graft-versus-host disease (GVHD). The presence of mature donor T cells in the transplant inoculum reduces the incidence of the first three complications, while unfortunately increasing the risk of GVHD, which can be directed against either HLA or minor histocompatibilty antigen (miHA) disparities. Thus, a major objective in the field has been to develop tactics that could facilitate the separation of graft-versus-tumor (GVT) effects from the deleterious effects of GVHD. One such approach would be to selectively deplete donor alloreactive T cells in the donor inoculum while allowing residual T cells to provide some protection against infection and to support a tumor-specific GVT response. For a more targeted approach, delayed donor lymphocyte infusion (DLI) of positively-selected donor GVT-reactive T cells could be used weeks to months post-transplant, if these elements were identifiable. In this regard, TCR Vβ repertoire analysis by CDR3-size spectratyping can be a powerful tool for the characterization of alloreactive T cell responses. Theoretically, molecular analysis of T cell responses in vitro, given the high sensitivity of the PCR-based spectratyping technique, should identify the most potentially critical Vβ families involved in the later development of GVHD and GVT effects in patients. To this end, we tested the hypothesis that T cell repertoire analysis of HLA-matched sibling (SIB) or matched unrelated donors (URD) from in vitro, host-stimulated, mixed lymphocyte cultures (MLC) would be predictive of the TCR-Vβ spectratype analysis of the T cell repertoire in the patient following BMT. In this study, we examined 17 patient pairs and report that for the resolvable Vβ families, we observed overall 71.2 ± 11.9% (mean ± SD.; range 40%–85%) of the in vitro anti-host T cell responses were predictive of those in the patient post-transplant. Of the 28.8% non-predictive Vβ families, 6.9 ± 6.3% (range 0%–27%) exhibited skewing in the MLC but no skewing in the patient post-transplant repertoire, 9.3 ± 6.3% (range 0%–18.8%) exhibited skewing in different peaks within the same Vβ family, and 12.5 ± 10.8% (range 0%–40%) showed skewing in the patient post-transplant and none in the MLC. Taken together, these results suggest that the in vitro MLC T cell responses show good consistency with post-transplant patient responses. Thus, in vitro spectratyping may be useful for predicting the alloreactive T cell responses involved in GVHD and could be used to guide custom-designed select Vβ family T cell-depleted transplants to improve patient outcomes. The additional advantage of this approach is that minimization of GVHD risk can be obtained without any direct knowledge of the specific miHA involved in the individual donor-patient pair.

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T cell repertoire remodeling following post-transplant T cell therapy coincides with clinical response

Journal of Clinical Investigation ◽

10.1172/jci128323 ◽

2019 ◽

Vol 129 (11) ◽

pp. 5020-5032 ◽

Cited By ~ 5

Author(s):

Corey Smith ◽

Dillon Corvino ◽

Leone Beagley ◽

Sweera Rehan ◽

Michelle A. Neller ◽

...

Keyword(s):

T Cell ◽

Cell Therapy ◽

Clinical Response ◽

T Cell Repertoire ◽

Cell Repertoire ◽

T Cell Therapy ◽

Post Transplant

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T Cell Repertoire Evolution After Allogeneic Bone Marrow Transplantation: An Organizational Perspective

10.1101/326744 ◽

2018 ◽

Author(s):

Jeremy A. Meier ◽

Mohamed Fawaz ◽

Hamdi Abdeen ◽

Jason Reed ◽

Christopher G. Kanakry ◽

...

Keyword(s):

Bone Marrow ◽

Bone Marrow Transplantation ◽

T Cell ◽

Clinical Outcomes ◽

Marrow Transplantation ◽

T Cell Subsets ◽

Allogeneic Bone ◽

T Cell Repertoire ◽

Cell Repertoire ◽

Post Transplant

AbstractHigh throughput sequencing (HTS) of human T cell receptors has revealed a high level of complexity in the T cell repertoire. In an attempt to correlate T cell reconstitution with clinical outcomes several measures of T cell repertoire complexity have emerged. However, the associations identified are of a broadly statistical nature, not allowing precise modeling of outcomes based on T cell repertoire development in clinical contexts such as following bone marrow transplantation (BMT). Previous work demonstrated that there is an inherent, mathematically definable order observed in the T cell population that is conserved in a diverse group of donors, and which is perturbed in recipients following BMT. Herein, we use a public database of human leukocyte antigen matched related-donor and recipient T cell receptor (TCR) β sequences to further develop this methodology. TCR β sequencing from unsorted T cells and sorted T cell subsets isolated from peripheral blood samples from BMT donors and recipients show remarkable conservation and symmetry of VJ segment usage in the clonal frequencies, linked to the organization of the gene segments along the TCR locus. This TCR β VJ segment translational symmetry is preserved post-transplant, and even in cases of acute GVHD (aGVHD), suggesting that GVHD occurrence represents a polyclonal donor T cell response to recipient antiges. We also observe that the complexity of the repertoire is significantly diminished after BMT and is not restored even years out post-transplant. The results here provide a new method of quantifying and characterizing post-transplant T cell repertoire reconstitution by further analyzing the mathematical rules governing TCR usage in the context of BMT. This approach may allow for a new means to correlate clinical outcomes with the evolving T cell repertoire post-transplant.

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Characterization of Tcra and Tcrb Repertoires in Acute Myeloid Leukemia Patients before and after Combined Haploidentical and Umbilical Cord Blood Transplant

Blood ◽

10.1182/blood.v124.21.2503.2503 ◽

2014 ◽

Vol 124 (21) ◽

pp. 2503-2503

Author(s):

Houda Alachkar ◽

Poh-Yin Yew ◽

Rui Yamaguch ◽

Kazuma Kiyotani ◽

Hongtao Liu ◽

...

Keyword(s):

T Cell ◽

Cord Blood ◽

Myeloid Leukemia ◽

T Cell Repertoire ◽

Cell Repertoire ◽

Hematopoietic Stem ◽

Time Points ◽

Novel Approach ◽

Cord Blood Transplant

Abstract Rationale: Allogeneic hematopoietic stem cell transplantation (HSCT) remains the most effective therapy for patients with acute myeloid leukemia (AML). The graft-versus-leukemia effect (GVL), mediated by the engrafted T lymphocytes targeting leukemic cells, is thought to play an important role in affecting the overall outcome of patients with AML. Umbilical cord blood (UCB) has emerged as an alternative and effective source of hematopoietic stem cells in high risk patients. We previously reported the hematopoietic reconstitution and clinical outcomes in 45 patients undergoing haplo-cord transplant, a novel approach which combines haploidentical and cord blood grafts to avoid delayed hematopoietic recovery after cord blood transplant (Liu H,et al. Blood. 2011;118(24):6438-45). However, very little is known about immune reconstitution of cord blood cells and whether the emerging immune repertoire correlates with clinical outcome. The great majority of T cell receptors in T lymphocytes are heterodimers of alpha (TCRA) and beta (TCRB) subunits. Somatic recombination combining the VJ (alpha) and VDJ (beta) segments results in an astronomical functional diversity and complexity of TCR receptors, and makes the characterization of their functions a tremendously complex process. To obtain insights into the T-cell repertoire, we have utilized next-generation sequencing (NGS) technology to comprehensively characterize T-cell kinetics and diversity following haplo-cord transplantation. Methods: We evaluated the emerging T-cell repertoire in 10 patients (pts) with high-risk AML enrolled on a clinical trial of haplo-cord transplantation at the University of Chicago. The median age of the pts was 57 years old (range: 26-67) and 3 pts had active disease at the time of transplant. The median UCB dose was 1.6x107 TNC/kg with HLA cord matching of 4/6 in 3 pts and 5/6 or 6/6 in 7 pts. The median overall and disease free survival were 2.4 and 2.2 years, respectively. cDNA was generated from mRNA isolated from peripheral blood mononuclear cells prior to and at sequential time points 30, 100, 180 and 365 days post haplo-cord transplant were sequenced the samples with Ion Personal Genome Machine (PGM) Sequencer and a 400-bp reading kit. We analyzed the sequences by applying a recently developed algorithm in order to determine the VJ and VDJ combinations and CDR3 sequences. Chimerism was determined by microsatellite sequences of DNA of donor and recipient cells. Diversity was calculated for each of TCRA and TCRB using the inverse Simpson’s index. Results: Several clones found in pre-treatment samples obtained from recipients before transplant persisted at low frequency on days 100 and 365 post-transplant suggesting that these clones have evaded the immuno-suppressive conditioning regimens. In order to correlate the diversity of TCRs with the percentage of cord cells in patients’ blood at different time points, we dichotomized patients into cord present (>5%) and cord absent (≤5%) groups, based on the cord blood percentage in blood on day 30 post haplo-cord transplant and correlated it with diversity on day 100. We found that TCRs of pts with >5% cord cells on day 30 post haplo-cord transplant were significantly more diverse (TCRA; P=0.008) and (TCRB; P=0.01) (Fig.1) on day 100 compared to TCRs in patients with <5% cord cells. Four pts achieved a chimersim of >90% cord cells on day 100 post-transplant. Therefore, we examined the correlation between diversity calculated on day 100 and percentage of persisting haplo-identical cells on the same day. We found,, the diversity of TCRB of pts with persistence of >10% haplo-identical cells were 15.05 compared with 72.95 for those with <10% haplo-identical cells on day 100, (P=0.002); similarly, diversity of TCRA was 17 vs 101.6 (P=0.001) in pts with >10% and <10% haplo cells, respectively. Furthermore, we found several recurring clones that were enriched in recipient blood on days 100 and 365. In conclusion, we report a novel approach to specifically characterize the TCR repertoire in AML patients receiving haplo-cord transplant. Our approach provides a valuable comprehensive analysis that defines the kinetics of TCRA and TCRB and the changes in CDR3 diversity. This approach, when applied to a larger patient cohort may provide useful information on whether specific TCR clones can be correlated with infectious complications and clinical outcome. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

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