CRISPR-mediated TGFBR2 knockout renders human ovarian cancer tumor-infiltrating lymphocytes resistant to TGF-β signaling

Background

The correlation between elevated T-cell infiltration and improved survival of ovarian cancer (OvCa) patients suggests that endogenous tumor-infiltrating lymphocytes (TIL) possess some degree of antitumor activity that can be harnessed for OvCa immunotherapy. We previously optimized a protocol for ex vivo OvCa TIL expansion for adoptive cell therapy, which is now being tested in a clinical trial at our institution (NCT03610490). Building on this success, we embarked on genetic modification of OvCa TIL to overcome key immunosuppressive factors present in the tumor microenvironment. Here, we present the preclinical optimization of CRISPR/Cas9-mediated knockout of the TGF-β receptor 2 (TGFBR2) in patient-derived OvCa TIL.

Methods

OvCa TILs were generated from four patients’ tumor samples obtained at surgical resection and subjected to CRISPR/Cas9-mediated knockout of TGFBR2 before undergoing a rapid expansion protocol. TGFBR2-directed gRNAs were comprehensively evaluated for their TGFBR2 knockout efficiency and off-target activity. Furthermore, the impact of TGFBR2 knockout on TIL expansion, function, and downstream signaling was assayed.

Results

TGFBR2 knockout efficiencies ranging from 59±6% to 100%±0% were achieved using 5 gRNAs tested in four independent OvCa TIL samples. TGFBR2 knockout TIL were resistant to immunosuppressive TGF-β signaling as evidenced by a lack of SMAD phosphorylation, a lack of global transcriptional changes in response to TGF-β stimulation, equally strong secretion of proinflammatory cytokines in the presence and absence of TGF-β, and improved cytotoxicity in the presence of TGF-β. CRISPR-modification itself did not alter the ex vivo expansion efficiency, immunophenotype, nor the TCR clonal diversity of OvCa TIL. Importantly for clinical translation, comprehensive analysis of CRISPR off-target effects revealed no evidence of off-target activity for our top two TGFBR2-targeting gRNAs.

Conclusions

CRISPR/Cas9-mediated gene knockout is feasible and efficient in patient-derived OvCa TIL using clinically-scalable methods. We achieved efficient and specific TGFBR2 knockout, yielding an expanded OvCa TIL product that was resistant to the immunosuppressive effects of TGF-β. This study lays the groundwork for clinical translation of CRISPR-modified TIL, providing opportunities for engineering more potent TIL therapies not only for OvCa treatment, but for the treatment of other solid cancers as well.

172 Overcoming immunosuppressive TGF-β signaling in human ovarian cancer-derived tumor infiltrating lymphocytes via non-viral CRISPR engineering

Background

Our ongoing clinical trial for the treatment of melanoma with TGF-β-resistant tumor-infiltrating lymphocytes (TIL) [TGF-β dominant negative receptor 2 (TGFβDNR2) transduced-TIL] has yielded long-term responses in checkpoint refractory patients (NCT01955460). Building on this success, we sought to extend the impact of TGF-β–resistant TIL therapy to additional cancers while optimizing a non-viral alternative to transduction with a TGFβDNR2. Ovarian cancer (OvCa), which is characterized by an abundance of TGF-β, a dysfunctional immune infiltrate, and a paucity of novel treatment options, is an ideal candidate for TGF-β–resistant TIL therapy. Here, we present an optimized and clinically-scalable method for CRISPR/Cas9-mediated deletion of the TGF-β receptor (TGFBR2) in OvCa TIL.

Methods

OvCa TIL were generated from tumor fragments1 and subjected to CRISPR-mediated knockout of TGFBR2 before going through a rapid expansion protocol. Resistance of TGFBR2-knockout TIL to TGF-β signaling was evaluated via quantification of downstream SMAD-2/-3 phosphorylation, global transcriptional changes upon TGF-β exposure, and cytokine release following TCR stimulation in the presence of TGF-β. The impact of CRISPR modification on TIL expansion and TCR clonal diversity was evaluated. Finally, the risk of off-target CRISPR activity throughout the genome was evaluated using Target Enriched GUIDE-seq (TEG-seq)2 followed by next generation sequencing (NGS) validation of putative off-target sites.

Results

Using five TGFBR2-directed guide RNAs (gRNAs), we achieved gene disruption efficiencies ranging from 48%–90%, which correlated inversely with the degree of SMAD phosphorylation after TGF-β exposure (r=-0.9440, p=0.0158, n=4 donors) (figure 1A-C). TGF-β exposure induced a strong transcriptional response in wild-type TIL but had little to no effect on TGFBR2-knockout TIL (figure 2). TGFBR2-knockout TIL functioned well in the presence of exogenous TGF-β as evidenced by equally strong secretion of pro-inflammatory cytokines in the presence and absence of TGF-β (figure 3). CRISPR-modification did not hamper the ex vivo expansion efficiency nor the TCR clonal diversity of expanded OvCa TIL (figure 4). Using TEG-seq, we identified ≤5 low-probability off-target sites for gRNA-#3 and gRNA-#4, each of which were attributed to background sequencing artifacts upon further validation by NGS of specific amplicons (figure 5).

Abstract 172 Figure 1

(A) Genomic-level TGFBR2 knockout efficiency using 5 different gRNAs as evidenced by NGS of specific amplicons (n=1 TIL donor). (B) SMAD-2 and SMAD-3 phosphorylation in TGFBR2 knockout TIL vs. control TIL after 30 min exposure to TGF-β1. The left panel shows representative histograms of phospho-SMAD staining, and the right panel shows quantification of cells positive for phospho-SMAD-2/-3 after TGF-β exposure (n=4 TIL donors). The statistical significance of each experimental condition compared to the non-transfected control is shown. (C) Inverse correlation of TGFBR2 knockout efficiency and TGF-β-mediated SMAD phosphorylation.

Abstract 172 Figure 2

Top 100 differentially expressed genes in non-transfected (WT) TIL exposed to TGF-β. TGFBR2 knockout (KO) TIL display minimal gene expression changes upon TGF-β exposure (n=3 technical replicates).

Abstract 172 Figure 3

TIL were collected after 14 days of expansion and re-stimulated with 300 ng/mL plate-bound anti-CD3 in the presence of 3000 IU/mL IL2 and 10 ng/mL human TGF-β1 or vehicle. Cell culture supernatant was collected after 72 hrs of stimulation and assayed for the presence of 10 proinflammatory cytokines (IFN-γ, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p70, IL-13, and TNF-α). For TIL with intact TGFBR2 (non-transfected and Cas9 mock transfected TIL), the production of many pro-inflammatory cytokines decreased significantly in the presence of TGF-β. Conversely, TGFBR2 knockout TIL (generated using gRNA #3 or gRNA #4) retain cytokine secretion in the presence of TGF-β. IL-12p70 was below the limit of detection in this assay and is therefore not presented.

Abstract 172 Figure 4

(A) Control and CRISPR-modified OvCa TIL expand with equal efficiency during a 14-day rapid expansion protocol. Fold expansions ranging from 1000× - 3000× were observed across 4 independent patient samples. (B) The TCR clonal diversity of TIL after 14-day expansion was assessed by TCRB sequencing. Productive Simpson Clonality was equivalent in CRISPR-modified TIL compared to control TIL samples.

Abstract 172 Figure 5

TEG-seq revealed 3 putative off-target sites for gRNA #3 and 5 putative off-target sites for gRNA #4. The aligned sequences show similarities and differences between the gRNA sequence and the reference genome site. Dots represent exact matches in the reference genome compared to the gRNA sequence. Dashes represent missing bases, lower-case letters represent extra bases, and upper-case letters represent a base mismatch. Validation by NGS of specific amplicons confirmed the presence of TEG-seq Tag integration and large indels at the on-target cleavage sites for gRNA #3 and #4, indicating successful Cas9 editing and Tag integration in our experiment. NGS validation revealed that all putative low probability off-target sites were background artifacts as evidenced by the lack of Tag identification and lack of large indels.

Conclusions

CRISPR/Cas9-mediated knockout of TGFBR2 is feasible and efficient in patient-derived OvCa TIL using clinically-scalable methods that yield little to no evidence of off-target activity. This study lays the groundwork for clinical translation of CRISPR-modified, TGF-β-resistant TIL for OvCa treatment, which will not only provide a novel immunotherapy for OvCa patients but also a platform for engineering more potent TIL therapies in general.

References

Sakellariou-Thompson D, Forget MA, Hinchcliff E, Celestino J, Hwu P, Jazaeri AA, et al. Potential clinical application of tumor-infiltrating lymphocyte therapy for ovarian epithelial cancer prior or post-resistance to chemotherapy. Cancer Immunology, Immunotherapy: CII 2019;68(11):1747–57.

Tang PZ, Ding B, Peng L, Mozhayskiy V, Potter J, Chesnut JD. TEG-seq: an ion torrent-adapted NGS workflow for in cellulo mapping of CRISPR specificity. Bio Techniques 2018;65(5):259–67.

Ethics Approval

All procedures performed were in accordance with the 1975 Helsinki declaration. Ethical approval and tissue from surgical resections used to expand TIL were both obtained under protocols (PA16-0912 and LAB02-188) approved by the Institutional Review Board of The University of Texas MD Anderson Cancer Center. Written informed consent was obtained from all individual participants included in the study for their specimens and data to be used in research and for publication.

Aurora kinase inhibition sensitizes melanoma cells to T-cell-mediated cytotoxicity

Although immunotherapy has achieved impressive durable clinical responses, many cancers respond only temporarily or not at all to immunotherapy. To find novel, targetable mechanisms of resistance to immunotherapy, patient-derived melanoma cell lines were transduced with 576 open reading frames, or exposed to arrayed libraries of 850 bioactive compounds, prior to co-culture with autologous tumor-infiltrating lymphocytes (TILs). The synergy between the targets and TILs to induce apoptosis, and the mechanisms of inhibiting resistance to TILs were interrogated. Gene expression analyses were performed on tumor samples from patients undergoing immunotherapy for metastatic melanoma. Finally, the effect of inhibiting the top targets on the efficacy of immunotherapy was investigated in multiple preclinical models. Aurora kinase was identified as a mediator of melanoma cell resistance to T-cell-mediated cytotoxicity in both complementary screens. Aurora kinase inhibitors were validated to synergize with T-cell-mediated cytotoxicity in vitro. The Aurora kinase inhibition-mediated sensitivity to T-cell cytotoxicity was shown to be partially driven by p21-mediated induction of cellular senescence. The expression levels of Aurora kinase and related proteins were inversely correlated with immune infiltration, response to immunotherapy and survival in melanoma patients. Aurora kinase inhibition showed variable responses in combination with immunotherapy in vivo, suggesting its activity is modified by other factors in the tumor microenvironment. These data suggest that Aurora kinase inhibition enhances T-cell cytotoxicity in vitro and can potentiate antitumor immunity in vivo in some but not all settings. Further studies are required to determine the mechanism of primary resistance to this therapeutic intervention.