Report

Landscape of immunogenic tumor antigens in successful immunotherapy of virally induced epithelial cancer

See allHide authors and affiliations

Science  14 Apr 2017:
Vol. 356, Issue 6334, pp. 200-205
DOI: 10.1126/science.aak9510

Targeting nonviral antigens in viral-driven cancer

Adoptive cell transfer harnesses a patient's own T cells to destroy cancer. The strategy can successfully treat epithelial tumors driven by human papillomavirus (HPV), but it remains unclear why only some patients respond. Stevanović et al. examined the antitumor T cell response associated with HPV+ cervical cancers that underwent complete regression. Unexpectedly, reactive T cells were not directed against virally associated antigens, but rather against cancer germline antigens or neoantigens not previously recognized by the immune system. These findings counter the widely held belief that T cell responses against viral antigens are responsible for therapeutic effects in HPV-driven cancers.

Science, this issue p. 200

Abstract

Immunotherapy has clinical activity in certain virally associated cancers. However, the tumor antigens targeted in successful treatments remain poorly defined. We used a personalized immunogenomic approach to elucidate the global landscape of antitumor T cell responses in complete regression of human papillomavirus–associated metastatic cervical cancer after tumor-infiltrating adoptive T cell therapy. Remarkably, immunodominant T cell reactivities were directed against mutated neoantigens or a cancer germline antigen, rather than canonical viral antigens. T cells targeting viral tumor antigens did not display preferential in vivo expansion. Both viral and nonviral tumor antigen–specific T cells resided predominantly in the programmed cell death 1 (PD-1)–expressing T cell compartment, which suggests that PD-1 blockade may unleash diverse antitumor T cell reactivities. These findings suggest a new paradigm of targeting nonviral antigens in immunotherapy of virally associated cancers.

Immunotherapy can induce the regression of certain virally associated epithelial malignancies such as human papillomavirus (HPV)–induced cervical (1), head and neck (2), and anal (3) cancers. The viral oncoproteins expressed by HPV+ tumors are potential candidate tumor regression antigens, as they are immunologically foreign and are constitutively expressed by cancer cells (4). However, evidence supporting their role in immunotherapy-mediated tumor regression is limited. Efforts to induce cancer regression by targeting HPV oncoproteins with antigen-specific immunotherapy, such as therapeutic vaccines, have not been effective (5, 6). Adding chemotherapy to therapeutic vaccines reduces myeloid-derived suppressor cells and augments immunogenicity, but whether this improves the efficacy of vaccine treatments remains unknown (7). It is also intriguing that response rates to programmed cell death 1 (PD-1) immune checkpoint blockade appear to be similar in patients with virus-positive and -negative head and neck carcinomas (2). T cells targeting the protein products of somatic mutations (mutated neoantigens) (811) and epigenetically dysregulated genes (cancer germline antigens) (12, 13) have been implicated in immunotherapy-induced regression of certain nonviral cancers. Thus, one explanation unifying these observations may be that nonviral tumor antigens are targeted in regression of HPV+ cancers. To explore this hypothesis, we performed a global landscape analysis of the viral and nonviral antigens targeted by T cells in patients successfully treated with immunotherapy for a virally associated epithelial cancer.

We studied two patients with HPV+ metastatic cervical carcinoma who experienced complete cancer regression that is ongoing now at 54 months (patient 3775 with HPV16+ squamous cell carcinoma) and at 46 months (patient 3853 with HPV18+ adenocarcinoma) after adoptive transfer of tumor-infiltrating lymphocytes (TILs) (1). The infused T cells, hereafter referred to as TIL-3775 and TIL-3853, were expanded from TIL cultures selected for HPV-E6 and/or HPV-E7 oncoprotein reactivity (1). However, these cultures also contained T cells with uncharacterized antigen specificities. To fully define the antigens targeted by the therapeutic T cells, we combined next-generation sequencing with functional immunological assays and examined T cell reactivity against HPV-encoded antigens, mutated neoantigens, and cancer germline antigens (fig. S1) (14).

We first investigated whether the infused TILs displayed T cell reactivity against HPV-encoded proteins (14). Consistent with prior results, T cells specific for the HPV-E6 and/or HPV-E7 antigens were detected in both patients (Fig. 1, A and B) (1). Reactivity against other HPV proteins was not found (Fig. 1, A and B, and table S1). In TIL-3775, the response against HPV-E6 was CD8+ T cell–mediated, whereas CD4+ and CD8+ T cells recognized HPV-E7 (Fig. 1C). The T cell response against HPV-E7 in TIL-3853 was CD4+ T cell–mediated (Fig. 1D).

Fig. 1 Therapeutic TILs targeted viral and nonviral tumor antigens in two patients with metastatic HPV+ cervical cancer.

(A and B) IFN-γ enzyme-linked immunospot (ELISPOT) assay of TIL-3775 (A) and TIL-3853 (B) compared with pretreatment peripheral blood (PB) T cells from these patients after coculture with autologous dendritic cells (DCs) electroporated with RNA encoding HPV type–specific antigens or glycoprotein 100 (GP100, negative control). (C) Flow cytometric analysis (FCA) of CD137 expression on TIL-3775 and PB T cells cocultured with DCs electroporated with RNA encoding HPV16-E6, HPV16-E7, or GP100. (D) FCA of CD137 expression on TIL-3853 and PB T cells cocultured with DCs electroporated with RNA encoding HPV18-E7 or GP100. (E) IFN-γ ELISPOT assay of TIL-3775 and PB T cells cocultured with DCs electroporated with TMG-1 to TMG-19 RNA or GP100 RNA. (F) FCA of CD137 expression on TIL-3775 and PB T cells upon coculture with DCs electroporated with TMG-1, TMG-5, TMG-18, or GP100 RNA. (G) IFN-γ ELISPOT assay of TIL-3775 cocultured with autologous antigen-presenting cells pulsed with individual mutated 25–amino acid residue (25-mer) peptides encoded in the indicated TMGs (table S2). Mutated 25-mers 3 and 10, encoded in TMG-1 and TMG-5, respectively, could not be synthesized. (H) Reactivity of TIL-3775 to the mutated (MUT) 25-mer peptides encoded by TMG-1 (SETDB1E>D), TMG-5 (METTL17E>K), and TMG-18 (ALDH1A1N>I), or their wild-type (WT) counterparts, pulsed on DCs. Error bars denote SE; N = 3 independent experiments. *P < 0.05, **P < 0.01, two-tailed Student t test; SETDB1E>D P = 0.0033, METTL17E>K P = 0.0388, and ALDH1A1N>I P = 0.0471. (I) IFN-γ ELISPOT assay of TIL-3853 compared with pretreatment PB T cells after coculture with autologous DCs electroporated with RNA encoding the indicated cancer germline antigens (table S1) or GP100 (negative control). (J) FCA of CD137 expression on TIL-3853 and PB T cells upon coculture with DCs electroporated with RNA encoding KK-LC-1 or GP100. In all panels except (H), phorbol 12-myristate 13-acetate and ionomycin (P/I) stimulation was used as a positive control. T cell reactivity was measured at 20 to 24 hours in all coculture assays. “>” denotes off-scale values. All FCAs were pre-gated on live CD3+ T cells. CD4+ T cells are displayed as CD8 T cells in all FCA plots shown. All experiments except (H) were performed as single determinations. All data except (E) and (G) are representative of at least two independent experiments.

We next used the tandem minigene (TMG) approach (15) to investigate whether the infused TILs displayed reactivity against mutated neoantigens (14). TIL-3775 was screened for reactivity against 19 TMG constructs that together encoded 222 identified somatic mutations (14). We detected specific CD8+ T cell–mediated reactivity to TMG-1, TMG-5, and TMG-18 (Fig. 1, E and F). Subsequent screening of individual mutant peptides encoded by the recognized TMGs (table S2) revealed reactivity to neoepitopes derived from SETDB1 (SET domain bifurcated 1), METTL17 (methyltransferase-like 17), and ALDH1A1 (aldehyde dehydrogenase 1 family member A1) (Fig. 1G and fig. S2A). T cells preferentially recognized the mutant peptides (Fig. 1H and fig. S2, B and C). TIL-3853 was also screened for T cell reactivity against 72 identified somatic mutations (14); however, no responses were detected.

Next, the infused TILs were examined for reactivity against cancer germline antigens (14). TIL-3775 did not demonstrate reactivity against any of the seven antigens tested (table S1). TIL-3853 demonstrated CD8+ T cell reactivity against a single cancer germline antigen, KK-LC-1 (Kita-Kyushu lung cancer antigen 1) (Fig. 1, I and J, and table S1). Thus, in addition to T cells targeting the HPV oncoproteins, T cells with reactivity against mutated neoantigens or a cancer germline antigen contributed to the pool of infused T cells in each of the effective treatments.

To characterize the polyclonality of T cell responses targeting the tumor antigens, we identified antigen-specific T cell receptor (TCR) sequences from the infused TILs (fig. S3) using single-cell reverse transcription polymerase chain reaction (14, 16) and/or pairSEQ [a statistical model for pairing TCR α-chain (TCRA) and TCR β-chain (TCRB) sequences; Adaptive Biotechnologies] (14, 17). Paired TCRA and TCRB sequences obtained using these methods (fig. S3 and table S3) were then used to reconstruct TCRs (14, 16). Subsequently, these reconstructed TCRs were cloned into retroviral vectors and were used to genetically engineer autologous peripheral blood T cells (14, 16). For patient 3775, one CD8+ T cell–derived TCR demonstrated specific HPV-E6 recognition; an additional two CD8+ and two CD4+ T cell–derived TCRs displayed HPV-E7 reactivity (Fig. 2A). Five, one, and two CD8+ T cell–derived TCRs demonstrated recognition of mutated SETDB1E>D, METTL17E>K, and ALDH1A1N>I, respectively (Fig. 2A). For patient 3853, one CD4+ T cell–derived TCR conferred specific HPV-E7 reactivity, and one CD8+ T cell–derived TCR recognized KK-LC-1 (Fig. 2B). Thus, T cells targeting viral and nonviral tumor antigens infused into the patients were monoclonal or oligoclonal.

Fig. 2 Immunodominant antitumor T cell responses in therapeutic TILs were directed against mutated neoantigens and the cancer germline antigen KK-LC-1 rather than against HPV antigens.

(A and B) IFN-γ ELISPOT assay of autologous pretreatment PB T cells retrovirally transduced with TCRs identified from infused TILs of patients. (A) Reactivity of PB T cells from patient 3775 transduced with the 13 identified TCRs stimulated with autologous DCs pulsed with peptide pools of HPV16-E6, HPV16-E7, and GP100 (negative control), and wild-type (WT) and mutated (MUT) SETDB1E>D, METTL17E>K, and ALDH1A1N>I 25-mer peptides. The HPV16-E6–specific TCR, two HPV16-E7–specific TCRs (top row, II and III), and all mutated neoantigen–specific TCRs were isolated from antigen-reactive CD8+ T cell populations. Two HPV16-E7–specific TCRs (top row, I and IV) were isolated from an antigen-reactive CD4+ T cell population (14). (B) Reactivity of PB T cells from patient 3853 transduced with the two identified TCRs stimulated with autologous DCs pulsed with peptide pools of HPV18-E7, KK-LC-1, and GP100 (negative control). The HPV18-E7–specific TCR was isolated from an antigen-reactive CD4+ T cell population, and the KK-LC-1–specific TCR was isolated from an antigen-reactive CD8+ T cell population (14). T cell reactivity was measured at 20 to 24 hours in coculture assays. The TCR transduction efficiencies were >40%. P/I stimulation was used as a positive control in all coculture assays (not shown). “>” denotes off-scale values. Experiments were performed as single determinations. Data are representative of two independent experiments. (C and D) Frequency (%) and rank of the individual tumor antigen–specific TCR clonotypes identified in infused TILs, as determined by TCRB deep sequencing. (C) In TIL-3775, all mutation-specific TCR clonotypes (rank 1, 2, 3, 4, 8, 10, 61, and 65), the HPV16-E6–specific TCR clonotype (rank 6), and two HPV16-E7–specific TCR clonotypes (rank 11 and 24) were CD8+. Two HPV16-E7–specific TCR clonotypes (rank 9 and 33) were CD4+. (D) In TIL-3853, the KK-LC-1–specific TCR clonotype (rank 1) was CD8+ and the HPV18-E7–specific TCR clonotype (rank 2) was CD4+. Pie charts display the sum of the frequencies of individual TCR clonotypes with indicated tumor antigen specificity in the infused TILs, as determined by TCRB deep sequencing. (E and F) Functional avidity assessment by IFN-γ enzyme-linked immunosorbent assay (ELISA) of autologous PB T cells transduced with the indicated tumor antigen–specific TCRs cocultured with autologous antigen-presenting cells pulsed with titrated concentrations of cognate T cell epitopes (fig. S4 and table S4). HLA class I–restricted CD8+ T cell–derived TCRs [rank 1, 2, 3, 4, 6, 8, 10, 11, 24, 61, and 65 in TIL-3775 (C); rank 1 in TIL-3853 (D)] were transduced into PB CD8+ T cells, and CD4+ T cell–derived TCRs [rank 9 and 33 in TIL-3775 (C); rank 2 in TIL-3853 (D)] were transduced into PB CD4+ T cells. (E) Functional avidity of 13 TCRs from patient 3775. Reactivity of TCR-transduced T cells (TCR Td) and untransduced T cells (UT) (control T cells) is shown for HPV-specific TCRs; reactivity of TCR-transduced T cells against mutated (MUT) and wild-type (WT) cognate epitopes is shown for mutated neoantigen–specific TCRs. (F) Functional avidity of two TCRs from patient 3853. Reactivity of TCR-transduced T cells and untransduced T cells is shown for HPV-specific TCRs and KK-LC-1–specific TCRs. In (E) and (F), TCR-transduced T cells were enriched to yield >90% pure CD8+ or CD4+ TCR-transduced T cells prior to use in coculture assays. Error bars within symbols in (E) and (F) denote SD of duplicate wells. Data are representative of two independent experiments.

We next used TCRB deep sequencing to determine the relative frequencies of the identified tumor antigen–specific TCR clonotypes in the infused TILs. In TIL-3775, the five HPV-specific and eight mutated neoantigen–specific TCR clonotypes were found at variable frequencies (ranges, 0.7 to 4.7% and 0.1 to 6.9%) and ranks (ranges, 6 to 33 and 1 to 65) (Fig. 2C). The cumulative frequency of mutated neoantigen–specific TCR clonotypes accounted for 35% of TIL-3775, whereas the HPV-specific TCR clonotypes represented 14% (Fig. 2C). In TIL-3853, the KK-LC-1–specific TCR clonotype was the most frequent at 67%, and the HPV-E7–specific TCR clonotype was the second most common at 14% (Fig. 2D). Thus, both patients received TILs that contained a low frequency of HPV-targeted T cells relative to the frequency of nonviral tumor antigen–targeted T cells.

To directly compare the functional avidity of TCRs targeting the viral and nonviral tumor antigens identified in the infused TILs, we cocultured TCR-transduced T cells with antigen-presenting cells pulsed with titrated concentrations of cognate T cell epitopes (fig. S4 and table S4). For patient 3775, the HPV-specific and mutated neoantigen–specific TCRs exhibited functional avidities spanning 10–1 to 10–4 μg/ml and 10–3 to 10–5 μg/ml of cognate peptide, respectively (Fig. 2E). For patient 3853, the HPV-specific and KK-LC-1–specific TCRs displayed recognition of as low as 10–2 μg/ml and 10–3 μg/ml of cognate peptide, respectively (Fig. 2F). Thus, both viral and nonviral tumor antigen–targeting TCRs displayed a range of functional avidities.

We next evaluated the function and persistence of adoptively transferred tumor antigen–specific T cells in the circulation. Posttreatment peripheral blood T cells from both patients displayed specific reactivity against all identified tumor antigens, whereas minimal to no reactivity was detected before treatment (Fig. 3, A and B). In patient 3775, tumor antigen–specific TCR clonotypes represented 27 to 29% of T cells during tumor regression and 2% during remission, whereas they accounted for 0.06% of pretreatment T cells (Fig. 3C). The proportion of HPV-specific T cells relative to mutated neoantigen–specific T cells was similar during tumor regression and remission (Fig. 3C). In patient 3853, tumor antigen–specific TCR clonotypes accounted for 12% of T cells during tumor regression and 3% during remission, whereas they represented 0.003% of pretreatment T cells (Fig. 3D). The frequency of the KK-LC-1–specific TCR clonotype exceeded that of the HPV-specific TCR clonotype by a factor of at least 10 across all time points measured (Fig. 3D). Taken together, infused tumor antigen–reactive T cells in both patients remained functional and persisted at elevated levels in the circulation during tumor regression and remission.

Fig. 3 Repopulation of peripheral blood by infused T cells targeting viral and nonviral tumor antigens throughout cancer regression and remission.

(A and B) Reactivity of PB T cells from before and after treatment was assessed by IFN-γ ELISPOT assay against peptides from tumor antigens identified in patient’s infused TILs. (A) Reactivity of PB T cells from patient 3775, from before treatment and at 1 month after treatment during tumor regression, to peptide pools of HPV16-E6, HPV16-E7, GP100 (negative control), and mutated (MUT) and wild-type (WT) SETDB1E>D, METTL17E>K, and ALDH1A1N>I 9-mer or 25-mer peptides pulsed on autologous DCs. (B) Reactivity of PB T cells from patient 3853, from before treatment and at 0.3 months (tumor regression) and 5.6 months (remission) after treatment, to peptide pools of HPV18-E7, KK-LC-1, and GP100 (negative control) pulsed on autologous DCs. T cell reactivity was measured at 20 to 24 hours in coculture assays. P/I stimulation was used as a positive control. “>” denotes off-scale values. Error bars denote SD of duplicate wells. Data in (A) are representative of two independent experiments; data in (B) are from one experiment because of insufficient availability of patient samples. (C and D) Frequency (f, %) and rank of individual tumor antigen–specific TCR clonotypes, as identified within TIL-3775 (C) and TIL-3853 (D) among PB mononuclear cells (PBMCs) before and after treatment (at the indicated months), were determined by TCRB deep sequencing. (C) For patient 3775, posttreatment samples at 1 and 4.2 months during tumor regression and at 13.4 months during remission were analyzed. Cumulative frequency of mutated neoantigen–specific and HPV-specific TCR clonotypes is indicated; n.d. indicates TCR clonotypes not detected. (D) For patient 3853, posttreatment samples at 1 month during tumor regression and at 5.6 and 10.6 months during remission were analyzed. In all panels, Pre indicates before treatment, Post indicates after treatment, and M indicates month(s).

Cell surface expression of PD-1 on circulating CD8+ T cells functions as a biomarker to identify tumor antigen–specific T cells in metastatic melanoma patients (18), but whether it identifies these T cells in patients with epithelial cancers is unknown. In both patients we studied, a minor population representing ≤10% of CD4+ and CD8+ T cells coexpressed PD-1 in pretreatment peripheral blood (Fig. 4A). Using flow cytometric sorting followed by TCRB deep sequencing, we subsequently identified TCR clonotypes within the circulating PD-1+ and PD-1 T cell populations. Of 13 tumor antigen–specific TCR clonotypes, 12 (including those associated with HPV and mutated neoantigen reactivities) were uniquely detected in the PD-1+ T cell population, but not the PD-1 T cell population, of patient 3775 (Fig. 4B). For patient 3853, both the HPV-specific and KK-LC-1–specific TCR clonotypes were enriched in the PD-1+ T cell population relative to the PD-1 T cell population (Fig. 4C). These findings show that PD-1 expression can identify both viral and nonviral tumor antigen–specific T cells in peripheral blood of cervical cancer patients.

Fig. 4 PD-1 expression identifies both viral and nonviral tumor antigen–specific T cells in the circulation of patients with metastatic cervical carcinoma before treatment.

(A) FCA of PD-1 expression on CD4+ and CD8+ T cells from PB before treatment for patient 3775 (left) and patient 3853 (right). Data are representative of two independent experiments. (B and C) Frequency (%) of tumor antigen–specific TCR clonotypes, as identified for patient 3775 in TIL-3775 (B) and for patient 3853 in TIL-3853 (C) (see Fig. 2, C and D, respectively), within sorted PD-1 and PD-1+ PB CD4+ and CD8+ T cell subsets was determined by TCRB deep sequencing. Graphs display CD4+ and CD8+ TCR clonotypes. The specificity of each TCR clonotype and its rank in the infused TILs is indicated next to the symbol. ND in (B) indicates TCR clonotypes not detected (<0.001%) from the sorted PD-1 population (symbols on the x axis).

This study reveals the targeting of both viral and nonviral tumor antigens by adoptively transferred TILs in complete regression of metastatic HPV+ cervical cancer in two patients. The immunodominant T cell reactivity in infused TILs was directed against mutated neoantigens in one patient (35% of TILs) and the cancer germline antigen KK-LC-1 in another patient (67% of TILs). HPV antigen–targeted T cells represented a subdominant population of administered tumor-specific T cells in both cases (14% of TILs). Given the variety of infused tumor antigen–specific T cells, as well as T cells with undefined specificity, the T cell component(s) responsible for tumor eradication cannot be precisely determined. The relatively high frequency of infused and persisting viral and nonviral tumor antigen–specific T cells suggests that they might have contributed to the cancer regressions. It would have been valuable to test the tumor antigen–specific T cells for autologous tumor recognition. Unfortunately, tumor cell lines from these patients could not be generated. Given this limitation, the immunogenomic approach used in this study was a necessary surrogate to assess T cells for reactivity against patient-specific tumor antigens. Finally, the finding that both viral and nonviral tumor antigen–targeting T cells resided preferentially in the circulating PD-1+ T cell compartment suggests that anti–PD-1 blockade therapy may act through targeting of a variety of tumor antigen–specific T cells in HPV+ cancers. These results have important implications for the development and immune monitoring of immunotherapies for cervical cancer and possibly other virally induced cancers.

The immunogenicity of somatic mutations and of the cancer germline antigen KK-LC-1 in cervical cancer revealed in this study might be exploited for therapeutic benefit. Inactivation of the tumor suppressor proteins p53 and pRb (by the high-risk HPV-E6 and HPV-E7 oncoproteins, respectively) impedes DNA damage repair in HPV-transformed cells (19, 20). Consequently, these cells can accumulate genomic alternations at an accelerated pace, including a variable number of somatic mutations (21, 22) that might be expressed as neoantigens. The immunogenic mutations identified in patient 3775 were unique (23). As such, targeting this class of tumor antigens requires patient-specific personalized therapy (24). By contrast, TILs from patient 3853 targeted KK-LC-1, a shared cancer germline antigen expressed in 40% (12/30) of metastatic cervical cancers we tested. T cell reactivity against KK-LC-1 was detected in TILs from 2/8 additional KK-LC-1+ cervical cancers, which suggests that it is naturally immunogenic (fig. S5). Furthermore, KK-LC-1 is expressed in gastric cancers (81%) (25), triple-negative breast cancers (53%) (26), and non–small cell lung cancers (40%) (27). KK-LC-1 is not expressed in normal non-germline tissues (26), which suggests that it may be safely targeted by T cells. The identified KK-LC-1–specific human leukocyte antigen (HLA)–A*01:01–restricted TCR (fig. S4, B and H) conferred recognition of peptide-pulsed and antigen-positive target cells, as evidenced by interferon-γ (IFN-γ) production (fig. S6, A to C). In addition, KK-LC-1–specific TCR-transduced T cells as well as TIL-3853 produced tumor necrosis factor–α, mobilized CD107a (fig. S6D), and exerted cytolytic activity (fig. S6E) against cancer cell lines in an antigen- and HLA-dependent manner. Thus, these data demonstrate the potential for a novel treatment paradigm of targeting nonviral tumor antigens in virally associated cancers.

HPV+ cancers harbor the E6 and E7 oncoproteins, historically the primary targets for antigen-specific immunotherapies in these malignancies (4). Despite their foreign nature, only 43% (23/54) of cervical cancer TILs were shown to possess oncoprotein reactivity (28, 29). We found that the frequency of oncoprotein-reactive T cells infiltrating the metastatic tumors in our patients was similar to or less than that of mutated neoantigen–specific or cancer germline antigen–specific T cells (table S5), which suggests that viral proteins are not necessarily more immunogenic. Whether T cells solely targeting HPV oncoproteins can cause regression of HPV+ cancers is under investigation in clinical trials (NCT02280811, NCT02858310) using an avid TCR (30) gene therapy approach.

Our findings reveal a previously unrecognized participation of T cells targeting nonviral tumor antigens in the immunotherapy of HPV+ cervical cancer. Analysis of patients who have not responded to immunotherapy may provide additional insight into the importance of T cells targeting this class of tumor antigens. Our study provides impetus for research into the contribution of both viral and nonviral tumor antigen reactivities to the antitumor activity of adoptive T cell therapies and immune checkpoint inhibitors for virally associated malignancies.

Supplementary Materials

www.sciencemag.org/content/356/6334/200/suppl/DC1

Materials and Methods

Figs. S1 to S6

Tables S1 to S5

References (3141)

References and Notes

  1. See supplementary materials.
  2. Acknowledgments: We thank the Division of Cancer Treatment and Diagnosis Tumor Repository at NCI for providing cancer cell lines; A. Mixon, S. Farid, and W. Telford for flow cytometry support; Y.-C. Lu, M. El-Gamil, Y.-F. Li, S. A. Feldman, S. Ilyas, A. Gros, and J. R. Wunderlich for reagents; E. Tran, K. Hanada, L. Jia, and L. Zhang for technical support; S. Steinberg and D. Venzon for assistance with statistical analysis; and all members of the NCI Surgery Branch for helpful discussions. The data reported in this manuscript are tabulated in the main manuscript and the supplementary materials. The raw sequence data are available through the National Center for Biotechnology Information Bioproject database, ID PRJNA342632. S.S. and C.S.H. have filed a patent application (U.S. application no. 62/327,529) that relates to the KK-LC-152-60-specific TCR. This research was supported by the Center for Cancer Research intramural research program of the NCI and the Milstein Family Foundation. B.H. has employment and equity ownership with Adaptive Biotechnologies. H.S.R. has consultancy, equity ownership, patents, and royalties with Adaptive Biotechnologies. Other authors have no potential conflicts of interest.
View Abstract

Stay Connected to Science

Navigate This Article