Purpose:

TNF-related apoptosis inducing ligand (TRAIL) expression by immune cells contributes to antitumor immunity. A naturally occurring splice variant of TRAIL, called TRAILshort, antagonizes TRAIL-dependent cell killing. It is unknown whether tumor cells express TRAILshort and if it impacts antitumor immunity.

Experimental Design:

We used an unbiased informatics approach to identify TRAILshort expression in primary human cancers, and validated those results with IHC and ISH. TRAILshort-specific mAbs were used to determine the effect of TRAILshort on tumor cell sensitivity to TRAIL, and to immune effector cell dependent killing of autologous primary tumors.

Results:

As many as 40% of primary human tumors express TRAILshort by both RNA sequencing and IHC analysis. By ISH, TRAILshort expression is present in tumor cells and not bystander cells. TRAILshort inhibition enhances cancer cell lines sensitivity to TRAIL-dependent killing both in vitro and in immunodeficient xenograft mouse models. Immune effector cells isolated from patients with B-cell malignancies killed more autologous tumor cells in the presence compared with the absence of TRAILshort antibody (P < 0.05).

Conclusions:

These results identify TRAILshort in primary human malignancies, and suggest that TRAILshort blockade can augment the effector function of autologous immune effector cells.

See related commentary by de Miguel and Pardo, p. 5546

Translational Relevance

This work shows that primary human tumors express TRAILshort, which antagonizes tumor cell killing by immune effector cells, yet this restriction can be overcome by inhibiting TRAILshort with TRAILshort-specific antibodies.

The human immune system is capable of identifying and eliminating tumor cells, and it is increasingly recognized that effective cancer therapy requires the presence of an effective immune response. New therapies which target T-cell inhibitory pathways have revolutionized cancer therapy, and yet only a minority of patients with cancer derives benefit from immunotherapy. Consequently, there remains a need to identify new targets for intervention, which further enhance the ability of immune effector cells to kill tumor targets.

TNF-related apoptosis inducing ligand (TRAIL) is a proapoptotic death-inducing ligand, which can cause the death of tumor cells, or virally infected cells in vitro while sparing untransformed or uninfected cells (1). TRAIL is expressed by activated T cells and NK cells (2), arguing for a role of TRAIL in the innate and adaptive immune response. Knockout studies support that contention, because TRAIL−/− mice have normal lymphoid and myeloid cell development (3), yet develop spontaneous lymphoid and stromal tumors after >500 days (4). Similarly in response to the genotoxic carcinogen methylcholanthrene, TRAIL−/− mice have enhanced rates of fibrosarcoma development in comparison to WT parental mice (5). Notwithstanding that the regulation of TRAIL in mice is less complex than in humans (mice have one TRAIL receptor, whereas humans have 4), the loss of TRAIL receptor in mice has similar effects. Deletion of the TRAIL receptor in mice enhances tumorigenesis in a lymphoma-prone Eμ-myc mouse, and increases diethylnitrosamine-induced (DEN-induced) hepatocarcinogenesis (6). Similarly, tumor growth and progression (metastasis) are accelerated in the TRAIL−/− (4) and TRAILR−/− mice (6). Finally, neutralizing antibodies against TRAIL, which prevent it from interacting with the TRAIL receptor, cause increased oncogenesis in mice treated with methylcholanthrene; and in mice implanted with tumors, antibody neutralization of TRAIL increase rates of tumor growth and metastasis (7, 8). Thus, neutralization of the TRAIL/TRAIL receptor axis favors tumor development.

TRAIL is a transmembrane protein, which forms homo-trimers and this trimerization is critical for TRAIL's pro-apoptotic effect (9). TRAIL can bind to four membrane bound receptors, TRAIL receptor R1, R2, R3, and R4, and to one soluble receptor, osteoprotegerin. Apoptotic signaling is mediated by the two membrane-bound TRAIL receptors, TRAIL-R1 and TRAIL-R2, which signal through intracellular death domains (DD), to recruit intracellular FAS-associated DD protein leading to activation of initiator caspases 8 and 10, through proximity-induced autocatalysis. Caspase 8/10 activation leads to cleavage and activation of downstream effector caspases, including caspase 3, which induces cleavage of a wide array of cellular proteins and caspase-activated nucleases, ultimately resulting in the phenotypic changes of apoptosis (10).

In our previous studies on the effects of HIV infection on regulation of the TRAIL:TRAIL receptor axis, we discovered that cells from HIV-infected patients make a novel splice variant of TRAIL, which is present in plasma and tissue culture supernatants, which antagonizes the pro-apoptotic effects of TRAIL (11). This protein, named TRAILshort, is a 101-amino acid polypeptide that shares the first 90 amino acids with full-length TRAIL, but has a distinct 11-amino acid C terminus. Because TRAILshort is produced as a consequence of a splicing event that excises exons 3 and 4 from the normal 5 exon protein, TRAILshort is missing cysteine 230, and exists as a monomer, and lacks apoptosis-inducing activity (11). Moreover, TRAILshort binds preferentially to TRAIL-R1 and -R2, and inhibits the pro-apoptotic activity of full-length TRAIL, thereby acting as a dominant negative ligand (12). Interestingly, TRAILshort is found in extracellular vesicles, which are elaborated from TRAILshort expressing cells, and these vesicles can confer TRAIL resistance upon otherwise TRAIL-sensitive bystander, neighboring cells (12). Finally, we have observed that interfering with TRAILshort function using inhibitory antibodies alters T-cell dynamics following acute HIV infection in vitro (13, 14).

We now know that TRAILshort is induced by type I IFN signaling and Toll-like receptor (TLR) activation, suggesting that other diseases may be associated with elevated TRAILshort expression. In this report, we sought to identify other disease states in which TRAILshort is expressed.

Cell culture

Uninfected primary peripheral blood mononuclear cells (PMBC) were isolated from donor apheresis cones using density gradient centrifugation. The following cell lines were also used: Jurkat (ATCC), HBL-1 (Ansell Lab, Mayo Clinic), OCI-LY3 (DSMZ), JeKo-1 (ATCC), RPMI8226 (ATCC), BCWM.1 (Ansell Lab, Mayo Clinic), Ovcar8 (NCI-DTP), Hovtax2 (John Copland Lab, Mayo Clinic), Cov362 (ECACC), Caov3 (ATCC), Ovcar5 (NCI-DTP) PEO1 (ECACC) TYK-nu (JCRB), L3.6 (Daniel Billadeau Lab, Mayo Clinic), BxPC-3 (ATCC;), HepG2 (ATCC), HLE (JCRB), EM-Meso (Tobias Peikert Lab, Mayo Clinic); MDA-MB231 (ATCC), and Sk-Mel-28 (ATCC). TRAIL knockout Jurkat T cells were described previously (13).

Animal studies

Mouse protocols were reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) at the Mayo Clinic and animal procedures followed IACUC guidelines.

Gene Expression Omnibus analysis

All publicly available RNA-sequencing data from NCBI's Sequencing Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra) were downloaded and processed with an internal gene expression quantification pipeline. In brief, FASTQ files were run through the pre-processing package fastp (https://github.com/OpenGene/fastp) to obtain high-quality reads. Gene and isoform expression levels were estimated using salmon (https://salmon.readthedocs.io/en/latest/salmon.html). Each sample from the SRA was further annotated with the nferX Natural Language Processing (NLP) software (proprietary and unpublished) for disease phenotypes based on available sample descriptions in the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). Significance was determined with the Fisher exact test, where the first group was presence in the top 5% expressing samples for a transcript [based on transcripts per million (TPM)] and the second was presence in the bottom 25% expressing samples. The final output was an enrichment score [reported as -log(p-val)] for each disease phenotype (Supplementary Table S1).

The Cancer Genome Atlas analysis

Isoform-level gene expression data from The Cancer Genome Atlas (TCGA, http://gdac.broadinstitute.org) was used to estimate transcript abundance. The nonnormalized isoform counts and transcript abundance estimates were generated by the TCGA Research Network: https://cancergenome.nih.gov/. Isoform expression values from Broad DAC were named in the general format: (SUBTYPE.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms__ data.data.txt). The “scaled estimate” value found in these files was transformed to TPM by multiplication with 1e6. We then extracted the expression values for TRAILshort (‘uc003fie.2’) and visualized this across multiple tissues. R code and data for this plot has been deposited in github (https://github.com/egarciarivera/rcode/tree/master/trail_short_tcga). Cutoffs were set as follows, with 3 TPM representing baseline level of expression for any gene (15), 10 TPM being the approximately 90th percentile (high), and 20 TPM being the approximately 95th percentile (very high) of TRAILshort expression.

IHC staining

Five millimeters od sections of formalin-fixed paraffin-embedded (FFPE) tissues were retrieved for 20 minutes using Epitope retrieval 2 (EDTA; Leica), and incubated in protein block (Dako) for 5 minutes. The TRAILshort primary antibody (clone 2.2 at 1 μg/μL) or appropriate isotype control antibody were diluted to 1:800 in background reducing diluent (Dako) and incubated for 15 minutes. Slides were counterstained with hematoxylin, washed, and dehydrated in ethanol prior to permanent coverslipping in xylene-based medium.

RNA ISH

Deparaffinized FFPE slides were pretreated with RNAScope Hydrogen Peroxidase (Advanced Cell Diagnostics, ACD), then 1× RNAScope Target Retrieval Reagents (ACD) followed by RNAScope Protease III (ACD) at 40°C. Slides were hybridized with a positive control probe BA-Hs-PPIB-3zz (ACD), a negative control probe BA-DapB-3zz (ACD), and a target probe BA-Hs-TNFSF10-tv2-E2E3 (ACD) for 2 hours at 40°C inside a HybEZ oven. Thereafter, amplification was performed per manufacturer's instructions. Signal detection was performed using a mix of BaseScope Red A and Red B (ACD) at a ratio of 60:1 at room temperature for 10 minutes. Slides were then rinsed in tap water, counterstained, and mounted.

IncuCyte cell killing assay

Adherent cells were seeded in a flat-bottom 96-well plate at a density of 104 cells/well. For suspension cells, 96-well plates were precoated with 50 μL of poly-l-ornithine for 1 hour at RT then washed twice. Assays were performed as described previously (12), using the IncuCyte platform (Essen BioScience) and IncuCyte caspase 3/7 apoptosis detection reagent that was added immediately after cells were plated, but before the indicated treatments. Cells were monitored every 2 hours for up to 60 hours by anti-active caspase 3 staining in triplicate. The pan-caspase inhibitor Q-VD was used where indicated (Sigma Aldrich).

Flow cytometry and PCR

Cells were collected and washed twice, blocked in 5% FBS for 30 minutes on ice, and stained using a CF555-labeled TRAILshort (Clone 2.2) antibody, a phycoerythrin (PE)-labeled CD253 TRAIL antibody (Abcam), and an FITC-labeled death receptor 5 (DR5) antibody (Thermo Fisher Scientific) for 1 hour on ice. TUNEL staining was performed according to manufacturer's protocol (Roche). TMRE staining was performed as described previously (11). Flow cytometry was performed using a Becton Dickinson LSR Fortessa X20 and FACS Diva Software. The primers and conditions for real-time PCR assessment of TRAILshort have been described previously (11).

Antibody humanization

Variable heavy (VH) and light (VL) regions of the TRAILshort murine antibody were sequenced and compared using BLASTp (NCBI) to identify homology with known human VH and VL antibody sequences. The four most homologous candidates to the murine sequences were identified taking into account framework homology, maintenance of key framework residues, and canonical loop structure (based on a combined IMGT/Kabat CDR labelling approach). The four humanized VH domains and four humanized VL domains were synthesized and cloned into the pD2610-v13 mammalian expression vector (Atum) in a combinatorial manner on an IgG1 Fc backbone. Resultant recombinant chimeric antibodies were purified and assessed by surface plasmon resonance (Supplementary Fig. S1) using a Biacore 2000 instrument for kinetic interaction analyses (Biaffin). This identified clone HC2LC3, with an equilibrium dissociation constant (KD) of 3.8 × 10–12 M (Supplementary Fig. S3) that also effectively synergized with sk-TRAIL to kill Jurkat T cells in vitro (Supplementary Fig. S4). The HC2LC3 clone was selected for further testing.

TRAILshort antibody in vivo safety assessment

An in vivo safety assessment of anti-TRAILshort antibody was performed by injecting 10 C57-BL/6 mice (five male, five female) with 10 mg/kg anti-TRAILshort antibody (clone 2.2) and observing mice twice daily for 7 days.

NSG mouse xenograft model

A single cell clone of Jurkat cells stably expressing firefly luciferase (Jurkat-Luc; obtained from Dr. Douglas K. Graham, Emory University, GA; ref. 16) was used for mouse experiments, and five million cells injected via tail vein injection into NSG mice as described previously (16). HBL-1 cells harvested during log-phase growth were injected subcutaneously into the right dorsal region NSG mice as described previously (17). In vivo tumor burden for Jurkat-Luc cells was determined twice weekly by measuring the whole-body luciferase activity with an IVIS200 imaging system or, in the case of HBL-1 cells, by blinded measurement using calipers. After nearly 20 days (range 20–30 days) when tumors had become established, mice were randomly assigned to treatment groups and were monitored daily.

Quantification and statistical analysis

For the time-dependent cell killing experiments, the AUC was compared using the two-sample t test. For mouse xenograft experiments, the log-rank test was used to assess differences in overall survival between treatment groups. Changes in tumor volume (or luminescence) over time were compared between treatment groups using linear regression, with an endpoint reflecting the last day when all mice were alive. Statistical analyses were performed using R (version 3.5.1; ref. 18). Statistical significance was defined as P < 0.05, and all tests were two-sided.

Data and software availability

Study approval

All the human-derived samples were obtained in compliance with IRB-approved protocols (Mayo IRB nos. 118-01 and 1827-00).

TRAILshort transcripts are associated with human disease

To determine the potential clinical significance of TRAILshort expression we used unbiased isoform level gene expression data from 253,200 samples across 6,600 studies in GEO, and identified TRAILshort transcripts in 117,500 samples, and significant enrichment (>10) of TRAILshort expression in patients with active infectious diseases consistent with our earlier publications (Supplementary Table S1; refs. 11–14), and identified a novel association of TRAILshort enrichment with human malignancy, as 15 of 25 disease states in which enrichment was observed occurred in patients with malignant diagnoses.

TRAILshort transcripts are highly prevalent in human cancers

TCGA database (19) identified that nearly 40% of primary human malignancies express TRAILshort transcripts. Specifically, TRAILshort expression of >3 TPM (which represents the baseline level of expression for any gene; ref. 15) was observed in 40% of cases, whereas 10% of malignancies express TRAILshort at high levels (>10 TPM), and nearly 5% of malignancies had very high levels of TRAILshort (>20 TPM; Fig. 1A). TRAILshort transcripts were significantly coassociated with 66 different transcripts (P < 0.05, Fig. 1B) and 63 of 66 (95%) of those genes are type I IFN regulated, suggesting a common pathway of induction. Interestingly HPV-positive tumors expressed more TRAILshort transcripts that HPV-negative tumors (mean ± SE of HPV-positive 17.6 ± 1.9 TPM, vs. HPV-negative 11.9 ± 0.6 TPM, P = 0.006, Fig. 1C) consistent with HPV activation of TLR7 (20, 21), and the known ability of TLR7 activation to induce TRAILshort expression (12).

Figure 1.

TRAILshort is prevalent within human cancer tissues. A, Tissues within the TCGA dataset were queried for the presence of TRAILshort transcripts, and data are expressed as TPM according to tissue type. B, Pearson's correlation coefficients (PCC) identified 66 gene transcripts coassociated with expression of TRAILshort transcripts, and the functional clustering is shown. C, TRAILshort transcripts were compared between HPV-positive (N = 97) and HPV-negative (N = 422) tumors in the TCGA dataset; depicted are mean ± SE; P = 0.0061 by two-tailed Mann–Whitney test. D–F, The indicated tissues were stained by IHC for TRAILshort protein expression (brown staining), or by ISH for TRAILshort mRNA expression (red dots indicated with black arrowheads). D, Angioimmunoblastic T-cell lymphoma (AITL) and peripheral T-cell lymphoma not otherwise specified (PTCL NOS) stain positive for TRAILshort mRNA (red dots with black arrowheads; top, RNA ISH, scale bar = 60 μm) as well as by IHC (bottom, scale bar = 300 μm). E, Oropharyngeal squamous cell carcinoma (SCC) tissue was stained by ISH using a negative control probe, DapB top panels, and no signal is detected, yet TRAILshort mRNA is detected by ISH in the malignant tissue indicated by the red dots (highlighted by black arrowheads), but not in the nonmalignant adjacent tissue. Scale bar = 60 μm for all panels. F, TRAILshort protein detected by IHC (top) or TRAILshort mRNA detected by ISH (bottom) in malignant (left panels) or nonmalignant (right) cervical squamous epithelium.

Figure 1.

TRAILshort is prevalent within human cancer tissues. A, Tissues within the TCGA dataset were queried for the presence of TRAILshort transcripts, and data are expressed as TPM according to tissue type. B, Pearson's correlation coefficients (PCC) identified 66 gene transcripts coassociated with expression of TRAILshort transcripts, and the functional clustering is shown. C, TRAILshort transcripts were compared between HPV-positive (N = 97) and HPV-negative (N = 422) tumors in the TCGA dataset; depicted are mean ± SE; P = 0.0061 by two-tailed Mann–Whitney test. D–F, The indicated tissues were stained by IHC for TRAILshort protein expression (brown staining), or by ISH for TRAILshort mRNA expression (red dots indicated with black arrowheads). D, Angioimmunoblastic T-cell lymphoma (AITL) and peripheral T-cell lymphoma not otherwise specified (PTCL NOS) stain positive for TRAILshort mRNA (red dots with black arrowheads; top, RNA ISH, scale bar = 60 μm) as well as by IHC (bottom, scale bar = 300 μm). E, Oropharyngeal squamous cell carcinoma (SCC) tissue was stained by ISH using a negative control probe, DapB top panels, and no signal is detected, yet TRAILshort mRNA is detected by ISH in the malignant tissue indicated by the red dots (highlighted by black arrowheads), but not in the nonmalignant adjacent tissue. Scale bar = 60 μm for all panels. F, TRAILshort protein detected by IHC (top) or TRAILshort mRNA detected by ISH (bottom) in malignant (left panels) or nonmalignant (right) cervical squamous epithelium.

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TRAILshort protein and message are detected in human cancer biopsies

We assessed primary human cancer tissues for TRAILshort protein by IHC, using a mouse monoclonal anti-TRAILshort antibody which we have validated previously (11), and by TRAILshort message specific ISH. The anti-TRAILshort antibody was developed and validated to recognize the unique C-terminal 11 amino acids encoded by TRAILshort (13). The TRAILshort ISH probes target the novel splice junction not present in full-length TRAIL message. Staining was optimized using the TRAILshort negative HeLa cell line (transfected with control vector), or Hela cells transfected with TRAILshort (Supplementary Figs. S1A and S1B). Once optimized, TRAILshort message and protein were evaluated in multiple primary cancer specimens (Supplementary Figs. S1C–S1E). TRAILshort message was confined to tumor cells, whereas TRAILshort protein was more diffuse, consistent with TRAILshort being contained with extracellular vesicles, and present within the microenvironment (11, 12).

Multiple tumor types identified by informatics analyses to be TRAILshort positive, stained positive for TRAILshort mRNA by ISH, whereas some tissues (e.g., urothelial carcinoma) were negative for TRAILshort mRNA (Supplementary Fig. S1E). We also assessed lymphomas for example angioimmunoblastic T-cell lymphoma (AITL) and peripheral T-cell lymphoma not otherwise specified (PTCL NOS), had detectable TRAILshort expression by both ISH and IHC (Fig. 1D, top and bottom, respectively). In total, ISH was carried out for 82 human cancer tissue sections. Thirty-one (37.8%) of these tissues were positive for TRAILshort by ISH, and positive staining was detected most commonly in squamous cell carcinomas (from cervical, tonsillar, and/or oropharyngeal sources), lymphomas, and pancreatic adenocarcinomas (Supplementary Table S2). Within single tissue sections that contained both malignant tissue (e.g., oropharyngeal squamous cell carcinoma) and nonmalignant tissue (non-neoplastic squamous epithelium), TRAILshort ISH detected TRAILshort in neoplastic cells but not the non-neoplastic squamous epithelium (Fig. 1E). Similarly, TRAILshort protein and mRNA were detected in malignant squamous epithelium from the cervix (Fig. 1F, left), but not in nonmalignant squamous epithelium from the same tissue section (Fig. 1F, right).

TRAILshort expression protects human cancer cell lines from the death inducing effects of TRAIL agonists

TRAILshort protects HIV-infected T cells from death induced by TRAIL (13). Using the same antibody we used to neutralize TRAILshort, we now tested the effect of that antibody on TRAIL-induced killing of TRAILshort-expressing cancer cell lines. In initial experiments, a TRAIL agonist [super killer (sk)-TRAIL] induced minimal death of the TRAILshort-expressing cell line HBL-1, and that killing was significantly augmented by the addition of a TRAILshort neutralizing antibody (Fig. 2A); by contrast, the TRAILshort antibody had no impact on TRAIL-induced killing of the TRAILshort-negative RPMI8226 cell line. Across the cell lines tested, 6 of 23 cell lines (26%) tested showed a significant increase in cell killing imparted by the TRAILshort antibody (Fig. 2CG), whereas other tumors (Fig. 2D) and noncancerous PBMCs (Fig. 2I) were unaffected by anti-TRAILshort antibody, suggesting that TRAILshort antibody might selectively impact TRAIL sensitivity of a subset of malignant cells. Transcriptional profiles of five responsive cell lines and nine nonresponsive cell lines, were compared (Fig. 2H), revealing 27 differentially expressed transcripts, with significant enrichment (P < 0.0001) of type I IFN-induced genes.

Figure 2.

Neutralization of TRAILshort enhances TRAIL-induced cell killing. Human cancer cell lines were assessed for TRAILshort and TRAIL receptor 2 expression, and in parallel tested for cell killing in response to skTRAIL, with or without TRAILshort antibody. TRAILshort and TRAIL receptor 2 expression is shown for (A) HBL1 cells or (B) RPMI 8226 cells (red histogram = isotype control staining; blue = TRAILshort or TRAILR2), and these cells were tested for cell killing in response to recombinant TRAIL (skTRAIL) alone, anti TRAILshort antibody alone, or the combination. Cell killing curves performed as in A and B, shown for (C) JeKo-1, (D) HLE, (E) SK-MEL-28, (F) Ovcar-5, (G) PEO1, and (I) primary PBMCs. H, The transcriptional profile of anti-TRAILshort-responsive cell lines was compared with that of anti-TRAILshort-non-responsive cell lines to generate a heat map, which identified differentially expressed genes. IFN response genes are indicated by an asterisk.

Figure 2.

Neutralization of TRAILshort enhances TRAIL-induced cell killing. Human cancer cell lines were assessed for TRAILshort and TRAIL receptor 2 expression, and in parallel tested for cell killing in response to skTRAIL, with or without TRAILshort antibody. TRAILshort and TRAIL receptor 2 expression is shown for (A) HBL1 cells or (B) RPMI 8226 cells (red histogram = isotype control staining; blue = TRAILshort or TRAILR2), and these cells were tested for cell killing in response to recombinant TRAIL (skTRAIL) alone, anti TRAILshort antibody alone, or the combination. Cell killing curves performed as in A and B, shown for (C) JeKo-1, (D) HLE, (E) SK-MEL-28, (F) Ovcar-5, (G) PEO1, and (I) primary PBMCs. H, The transcriptional profile of anti-TRAILshort-responsive cell lines was compared with that of anti-TRAILshort-non-responsive cell lines to generate a heat map, which identified differentially expressed genes. IFN response genes are indicated by an asterisk.

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Mechanism of action of TRAILshort neutralization

To further understand the mechanism by which TRAILshort antagonism alters cell fate, we focused on Jurkat T cells, which we have previously observed to further upregulate TRAILshort in response to HIV infection (12, 13). Because TRAIL receptor signaling can lead to apoptosis in susceptible cells or cell proliferation in resistant cells (22), we investigated the effects of TRAILshort antagonism on apoptosis and cell proliferation. First, we demonstrated that Jurkat T cells are partially susceptible to TRAIL-induced apoptosis, which is inhibited by the pan-caspase inhibitor QVD (Fig. 3A). As TRAILshort is a splice variant of TRAIL, genetic deletion of TRAIL necessarily deletes TRAILshort. Taking advantage of this, we next compared cell death induced by TRAIL in wild-type (WT) or CRISPR Cas/9-deleted TRAIL (and thus TRAILshort) Jurkat T cells. When WT or TRAIL knockout (KO) Jurkat T cells were treated with skTRAIL, TRAIL-induced apoptosis (measured by loss of mitochondrial outer membrane potential (Fig. 3B) or DNA end-nick labeling (Fig. 3C) was markedly increased in the TRAIL-deficient Jurkats compared with the WT Jurkats, consistent with TRAILshort antagonizing the proapoptotic effects of TRAIL. We then confirmed surface TRAILshort expression in uninfected WT Jurkat T cells (Fig. 3D).

Figure 3.

Neutralization of TRAILshort does not alter cell proliferation nor activation, but enhances apoptotic cell death. A, Jurkat T cells were treated with control, sk-TRAIL, or sk-TRAIL plus the pan-caspase inhibitor QVD for 24 hours and assessed for apoptosis by Annexin V/PI staining and active caspase 3/LIVE/DEAD staining by flow cytometry. Etoposide was used as a positive control. B, WT Jurkat T cells or Jurkat T cells genetically deficient in TRAIL by CRISPR (TRAIL KO) were treated with skTRAIL or vehicle control for 12 hours and mitochondrial depolarization assessed by tetramethylrhodamine, ethyl ester, perchlorate (TMRE) staining and flow cytometry. Carbonyl cyanide m-chlorophenylhydrazone (CCCP) was used as a positive control. Percentage of TMRE low cells is enumerated. C, WT and TRAIL KO Jurkat T cells were treated with skTRAIL or control for 12 hours and DNA fragmentation assessed by TUNEL staining and flow cytometry. DNAse treatment was used as positive control. The percentage of TUNEL positive cells is enumerated. D, Jurkat T cells were assessed for surface expression of TRAILshort by flow cytometry. E and F, Ten thousand Jurkat T cells were treated with either an isotype control antibody (5 μg/mL), recombinant pre-aggregated sk-TRAIL (1 ng/mL, unless unresponsive in which case 10 ng/mL was used), mouse anti-TRAILshort antibody (5 μg/mL, unless otherwise noted), or a combination of isotype control and either sk-TRAIL or mouse anti-TRAILshort antibody at low, medium, or high concentration (1.25, 2.5, or 5 μg/mL), plus sk-TRAIL as indicated. The number of caspase 3/7 positive cells was monitored every 2 hours. All experiments were performed in triplicate. Data are represented as mean ± SE. Significance shown in A and B compares sk-TRAIL + anti-TRAILshort versus sk-TRAIL alone. G, Jurkat cells were treated with sk-TRAIL plus anti-TRAILshort antibody in the presence of or absence of the pan-caspase inhibitor Q-VD to test the caspase-dependence of apoptosis. H, WT Jurkat cells were treated with nothing, isotype control, anti-TRAILshort antibody or anti-CD3/CD28 microbeads and assessed for surface expression of CD69 (at 3 days) and CFSE dilution (at 5 days).

Figure 3.

Neutralization of TRAILshort does not alter cell proliferation nor activation, but enhances apoptotic cell death. A, Jurkat T cells were treated with control, sk-TRAIL, or sk-TRAIL plus the pan-caspase inhibitor QVD for 24 hours and assessed for apoptosis by Annexin V/PI staining and active caspase 3/LIVE/DEAD staining by flow cytometry. Etoposide was used as a positive control. B, WT Jurkat T cells or Jurkat T cells genetically deficient in TRAIL by CRISPR (TRAIL KO) were treated with skTRAIL or vehicle control for 12 hours and mitochondrial depolarization assessed by tetramethylrhodamine, ethyl ester, perchlorate (TMRE) staining and flow cytometry. Carbonyl cyanide m-chlorophenylhydrazone (CCCP) was used as a positive control. Percentage of TMRE low cells is enumerated. C, WT and TRAIL KO Jurkat T cells were treated with skTRAIL or control for 12 hours and DNA fragmentation assessed by TUNEL staining and flow cytometry. DNAse treatment was used as positive control. The percentage of TUNEL positive cells is enumerated. D, Jurkat T cells were assessed for surface expression of TRAILshort by flow cytometry. E and F, Ten thousand Jurkat T cells were treated with either an isotype control antibody (5 μg/mL), recombinant pre-aggregated sk-TRAIL (1 ng/mL, unless unresponsive in which case 10 ng/mL was used), mouse anti-TRAILshort antibody (5 μg/mL, unless otherwise noted), or a combination of isotype control and either sk-TRAIL or mouse anti-TRAILshort antibody at low, medium, or high concentration (1.25, 2.5, or 5 μg/mL), plus sk-TRAIL as indicated. The number of caspase 3/7 positive cells was monitored every 2 hours. All experiments were performed in triplicate. Data are represented as mean ± SE. Significance shown in A and B compares sk-TRAIL + anti-TRAILshort versus sk-TRAIL alone. G, Jurkat cells were treated with sk-TRAIL plus anti-TRAILshort antibody in the presence of or absence of the pan-caspase inhibitor Q-VD to test the caspase-dependence of apoptosis. H, WT Jurkat cells were treated with nothing, isotype control, anti-TRAILshort antibody or anti-CD3/CD28 microbeads and assessed for surface expression of CD69 (at 3 days) and CFSE dilution (at 5 days).

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TRAIL-induced apoptosis of Jurkat T cells was augmented in the presence of TRAILshort antibody (Fig. 3E), an effect that was dose dependent (Fig. 3F) and inhibited by the pan caspase inhibitor QVD (Fig. 3G). These data argue that the antibody effect impacts cell death signaling. Altogether, these data indicate that TRAILshort protects Jurkat T cells from TRAIL-induced killing, and that cell death occurring in the setting of anti-TRAILshort antibody plus recombinant TRAIL is apoptotic in nature.

Finally, we assessed the impact of anti-TRAILshort antibody alone on proliferation, and found that treatment of Jurkat T cells with anti-TRAILshort antibody does not lead to activation nor proliferation (Fig. 3H) compared with isotype control antibody.

Anti-TRAILshort antibody exerts antitumor effect in human leukemia/lymphoma xenografts

We next assessed putative antitumor effects of TRAILshort antibodies in vivo. An in vivo safety assessment of anti-TRAILshort antibody in C57-BL/6 mice demonstrated no morbidity, mortality, abnormalities in hematology or chemistry, or pathology at necropsy (Supplementary Document S1). For these proof-of-concept studies, we did not measure or optimize pharmacokinetics.

Next, nonobese diabetic, severe combined-immunodeficient, common γ-chain deficient (NSG) mice were implanted with luciferease expressing Jurkat T leukemia cells, and the tumor was allowed to become established for nearly 20 days (16). Starting on day 20 after tumor injection, mice received 10 mg/kg of either anti-TRAILshort antibody or isotype control; the treatment was repeated weekly. Treatment with anti-TRAILshort antibody alone resulted in both decreased tumor burden through day 31 (the last day all mice remained alive, Fig. 4A, P = 0.04) and prolonged survival over the full period of observation (Fig. 4B, P < 0.0001) compared with isotype control antibody.

Figure 4.

Anti-TRAILshort antibody alone or in combination with a TRAIL agonist has antitumor effects in Jurkat T cell and HBL-1 xenograft models. A and B, Non-obese diabetic, severe combined-immunodeficient, common γ-chain deficient (NSG) mice were implanted with Jurkat human T leukemia cells expressing luciferase by intravenous injection, and tumors were allowed to become established. Mice were treated weekly with mouse anti-TRAILshort antibody (clone 2.2) alone or isotype control antibody. Mice were imaged twice weekly and followed for (A) total body luminescence over time and (B) survival. C and D, Mice injected with luciferase expressing Jurkat T cells were administered a single injection of mouse anti-TRAILshort antibody (clone 2.2) followed 24 hours later by a single injection of anti-TRAIL-R2 antibody, and followed for (C) mouse whole body luminescence over time (P = 0.0008) and (D) mouse survival (P = 0.07). E–H, NSG mice were implanted with HBL-1 cells by intravenous injection, and tumors were allowed to become established. These mice were treated weekly with anti-TRAIL short antibody or isotype control alone (E and F), or followed the next day by anti-TRAILR2 antibody (G and H), and tumors measured and followed for (E and G) tumor size and (F and H) survival. Results shown are mean ± SD.

Figure 4.

Anti-TRAILshort antibody alone or in combination with a TRAIL agonist has antitumor effects in Jurkat T cell and HBL-1 xenograft models. A and B, Non-obese diabetic, severe combined-immunodeficient, common γ-chain deficient (NSG) mice were implanted with Jurkat human T leukemia cells expressing luciferase by intravenous injection, and tumors were allowed to become established. Mice were treated weekly with mouse anti-TRAILshort antibody (clone 2.2) alone or isotype control antibody. Mice were imaged twice weekly and followed for (A) total body luminescence over time and (B) survival. C and D, Mice injected with luciferase expressing Jurkat T cells were administered a single injection of mouse anti-TRAILshort antibody (clone 2.2) followed 24 hours later by a single injection of anti-TRAIL-R2 antibody, and followed for (C) mouse whole body luminescence over time (P = 0.0008) and (D) mouse survival (P = 0.07). E–H, NSG mice were implanted with HBL-1 cells by intravenous injection, and tumors were allowed to become established. These mice were treated weekly with anti-TRAIL short antibody or isotype control alone (E and F), or followed the next day by anti-TRAILR2 antibody (G and H), and tumors measured and followed for (E and G) tumor size and (F and H) survival. Results shown are mean ± SD.

Close modal

Next, we combined TRAILshort antibody with a TRAIL agonist, in this case anti-TRAIL R2 antibody (23). NSG mice engrafted with luciferase expressing Jurkat cells (as in Fig. 4A) were treated with a single dose of either anti-TRAILshort antibody (clone 2.2) or isotype control, followed 24 hours later with anti-TRAIL-R2 (24). Mice receiving the anti-TRAILshort antibody followed by the TRAIL agonist had significantly decreased tumor burden compared with isotype antibody plus TRAIL agonist-treated mice (Supplementary Fig. S2, representative images at day 45, Fig. 4C, P = 0.0008). Furthermore, although three of nine mice treated with isotype control antibody succumbed to the tumor, all anti-TRAILshort antibody treated mice survived until the end of observation on day 56 (the predefined end of the experiment, Fig. 4D, P = 0.07).

In a second, orthogonal, validated in vivo xenograft model (17), NSG mice were injected subcutaneously with HBL-1 cells, and subsequently treated with anti-TRAILshort antibody or isotype control alone (Fig. 4E and F) or in combination with a TRAIL receptor agonist antibody (anti-TRAIL-R2, Fig. 4G and H). Mice treated with anti-TRAILshort antibody alone had significant reductions in tumor volumes compared with isotype control treatments through day 37 (the last day all mice remained alive, Fig. 4E) with apparent but nonsignificant effect on survival (Fig. 4F). When antiTRAIL-R2 antibody was added to anti-TRAILshort antibodies in this experimental system, mice receiving anti-TRAILshort antibody plus anti-TRAIL-R2 also had significantly reduced tumor volumes (P < 0.0001, Fig. 4G) but also had improvement in survival compared with mice treated with isotype control plus anti-TRAIL-R2 (P = 0.058, Fig. 4H).

These xenograft data indicate that anti-TRAIL short antibody has modest antitumor effects both alone and in combination with a TRAIL agonist, suggesting in vivo relevance of inhibiting TRAILshort with therapeutic antibodies. Optimizing of pharmacokinetics and/or combining this therapy with tumor specific T cells might further enhance this modest therapeutic effect, and further improve survival rates in vivo.

Effect of TRAILshort antibody on fresh tumor cells isolated from patients undergoing splenectomy for malignant diagnoses

We next obtained cells freshly harvested from patients undergoing splenectomy for suspected malignancy. These splenocyte preparations are known to contain mixtures of tumor cells (most of them of B-cell lineage) and immune effector cells including T cells. For these experiments we used a fully humanized anti-TRAILshort antibody clone HC2LC3, with a KD of 3.8 × 10−12 M (Supplementary Figs. S3 and S4).

To begin, freshly harvested splenocytes (containing malignant B cells as well as immune effector cells) were treated immediately with anti-TRAILshort antibody (HC2LC3), or isotype control antibody, alone or in combination with the TRAIL agonist skTRAIL, and cell death analyzed. A total of 26 samples were tested (Supplementary Table S3), and 21 of those ultimately had a malignant diagnosis, whereas five cases were nonmalignant immune thrombocytopenia purpura (ITP) or reactive follicular hyperplasia.

Of the 21 cases with a malignant diagnosis, nine (43%)—mostly B-cell lymphomas—were killed in response to anti-TRAILshort antibody in combination with sk-TRAIL (representative examples in Fig. 5A). Reassuringly, none of the cells harvested from patients with nonmalignant diagnoses died in response to TRAILshort antibody alone or in combination with skTRAIL (Supplementary Table S3) similar to what we previously observed with healthy PBMC (Fig. 2I). Thirteen of the malignant tumors were also tested by ISH for TRAILshort expression and six were positive (Supplementary Table S3, representative example in Fig. 5C and D), and of those tumors shown to be TRAILshort positive by ISH, five of six (83%) died in response to TRAILshort antibody in combination with skTRAIL.

Figure 5.

Humanized anti-TRAILshort antibodies have antitumor activity in primary human tumor samples ex vivo. Ten thousand splenocytes harvested from human patients with suspected malignancies were treated within 4 hours of harvest with isotype control antibody (5 μg/mL), recombinant pre-aggregated sk-TRAIL (1 ng/mL), humanized anti-TRAILshort antibody (5 μg/mL), the combination of isotype control antibody and sk-TRAIL, or humanized anti-TRAILshort antibody at low medium or high dose (1.25, 2.5, or 5 μg/mL) plus sk-TRAIL as indicated. A, Representative patient samples in which splenocyte death was augmented by the addition of anti-TRAILshort antibody to the TRAIL agonist skTRAIL. B, Representative patient samples in which splenocyte death was induced with anti-TRAILshort antibody treatment alone. C, Splenic tissue from the patient with Mantle cell lymphoma from B, was stained for TRAILshort expression by ISH (red dots and arrows), and (D) IHC (brown staining). E, CD8 T cells from the splenocyte suspension were analyzed by flow cytometry using CD3/CD8 and TRAIL antibodies; TRAIL expression in CD3+CD8+ cells is shown. F, Surface TRAIL expression was examined in peripheral CD3+CD8+ T cells from healthy donors by flow cytometry, in unstimulated conditions or (G) stimulated with tetanus toxoid (recall antigen) ex vivo for 24 hours, histogram shows pooled results from three donors.

Figure 5.

Humanized anti-TRAILshort antibodies have antitumor activity in primary human tumor samples ex vivo. Ten thousand splenocytes harvested from human patients with suspected malignancies were treated within 4 hours of harvest with isotype control antibody (5 μg/mL), recombinant pre-aggregated sk-TRAIL (1 ng/mL), humanized anti-TRAILshort antibody (5 μg/mL), the combination of isotype control antibody and sk-TRAIL, or humanized anti-TRAILshort antibody at low medium or high dose (1.25, 2.5, or 5 μg/mL) plus sk-TRAIL as indicated. A, Representative patient samples in which splenocyte death was augmented by the addition of anti-TRAILshort antibody to the TRAIL agonist skTRAIL. B, Representative patient samples in which splenocyte death was induced with anti-TRAILshort antibody treatment alone. C, Splenic tissue from the patient with Mantle cell lymphoma from B, was stained for TRAILshort expression by ISH (red dots and arrows), and (D) IHC (brown staining). E, CD8 T cells from the splenocyte suspension were analyzed by flow cytometry using CD3/CD8 and TRAIL antibodies; TRAIL expression in CD3+CD8+ cells is shown. F, Surface TRAIL expression was examined in peripheral CD3+CD8+ T cells from healthy donors by flow cytometry, in unstimulated conditions or (G) stimulated with tetanus toxoid (recall antigen) ex vivo for 24 hours, histogram shows pooled results from three donors.

Close modal

In a subset of patient samples above, splenocytes were killed by TRAILshort antibody alone (Fig. 5B), suggesting the presence of an endogenous source of TRAIL. Tumor infiltrating T cells have been reported to express high levels of TRAIL (25–27), and T-cell activation by phorbol esters or mitogen further enhances TRAIL expression (28). We therefore assessed purified CD8 positive cells from a mantle cell lymphoma case and observed TRAIL expression by CD8 positive cells (Fig. 5E). Moreover, freshly isolated CD3+CD8+ T cells from healthy donors, expressed low levels of surface TRAIL (Fig. 5F), and consistent with the original descriptions of TRAIL expression by T cells, we observed that T-cell stimulation by recall antigen (in this case tetanus toxoid) further enhances T-cell expression of TRAIL (P < 0.05, Fig. 5G).

Given that some tumor cells express TRAILshort, that TRAILshort blocks TRAIL-mediated cell death, and that both antigen stimulated CD8 T cells and tumor-infiltrating CD8+ cells express TRAIL, we tested the hypothesis that the ability of tumor infiltrating immune effector cells to kill autologous tumors might be antagonized by TRAILshort, and enhanced by neutralization of TRAILshort (Fig. 6). Cells from splenocyte suspensions were separated into CD8+ cells and the remaining cells pooled, stained with a lipophilic red die, and considered as tumor target cells. Autologous activated CD8+ cells, and red target cells were mixed at varying effector: target cell ratios (according to the number of available cells, range 1:1 to 5:1) and cell death assessed in the red tumor target cells (Fig. 6A). The number of tumor cells (red) that became caspase 3/7 positive (green) was minimal when tumor cells were incubated alone. The addition of CD8+ cells alone to the tumor target cells did not significantly alter tumor cell killing. However, activated CD8+ cells plus TRAILshort antibody, but not control antibody, resulted in significantly increased CD8+ cell killing of target tumor cells (P < 0.05, Fig. 6BD), in three (23%) of 13 patient samples tested. Altogether, these data indicate that anti-TRAILshort antibody can augment the ability of autologous effector cells to kill tumor targets.

Figure 6.

Humanized anti-TRAILshort antibodies augment antitumor activity of immune effector cells ex vivo. A, CD8+ cells were positively selected from bulk patient splenocytes, and cocultured with autologous target cells (bulk splenocytes after CD8 cell removal stained with cell tracker red) at the indicated effector to target ratios, in the presence or absence of anti-TRAILshort antibody, and cell death was measured over time in the red target cell population. B–D, Representative data of the number of Caspase 3/7 positive target cells in coculture from three patient samples with response to anti-TRAILshort antibody.

Figure 6.

Humanized anti-TRAILshort antibodies augment antitumor activity of immune effector cells ex vivo. A, CD8+ cells were positively selected from bulk patient splenocytes, and cocultured with autologous target cells (bulk splenocytes after CD8 cell removal stained with cell tracker red) at the indicated effector to target ratios, in the presence or absence of anti-TRAILshort antibody, and cell death was measured over time in the red target cell population. B–D, Representative data of the number of Caspase 3/7 positive target cells in coculture from three patient samples with response to anti-TRAILshort antibody.

Close modal

TRAIL is upregulated on activated T cells including tumor-infiltrating T cells (2), and their interaction with TRAIL receptor 1 and/or 2 expressing tumor cells should logically result in the killing of the tumor cells. Paradoxically that does not occur, leading multiple groups to speculate and test the hypothesis that supplying more, or more powerful, TRAIL agonists might result in effective tumor killing—to limited success. Here we show that TRAILshort is highly expressed in a subset of primary human cancers, and we provide proof of concept that inhibiting the production of TRAILshort genetically or inhibiting the function of TRAILshort using first-generation antibodies, enhances autologous immune effector cell killing of tumors.

Because the concept of immune surveillance against malignant and/or infected cells was first proposed, it has become an overarching principle of pathophysiology. As new immune effector mechanisms are described, new pathways of immune escape are invariably unmasked. In such cases, Darwinian pressures favor the survival of cancerous cell clones which escape immune surveillance pathways. It therefore follows that immune cell killing of cancer cells through TRAIL would be antagonized in cancer clones in which TRAILshort is expressed. Moreover, it suggests that this mechanism of immune escape would eventually be shared across a diverse collection of cancerous cell types and virally infected cells.

Alterations in the TRAIL:TRAIL receptor axis are known to impact outcomes of both infectious diseases, as well as cancer. For example, TRAIL receptor deficiency in mice increases influenza virus replication and morbidity (29), increases rates of lymphomagenesis, and enhances spread of certain malignancies (3–6, 30). TRAIL axis inactivation in humans may have similar implications, as null mutations in TRAIL receptor genes have been linked to primary human cancers (31, 32). Consistent with that model, TRAILshort antagonism of TRAIL-mediated immune surveillance results has the following pathophysiologic correlates: elevated TRAILshort is associated with higher viral loads (11) and low levels of TRAILshort is associated with Elite control of HIV infection (14), and as we demonstrate herein using preclinical models that TRAILshort impairs immune control of cancer.

Alternative splicing enhances the diversity of proteins expressed by a single gene often resulting in protein variants with disparate or opposing functions (33, 34). Splice variants of genes that impact apoptosis, cell cycle and repair, cell–cell, and cell–matrix interactions, have been associated with neoplasia and metastasis (35, 36). For example, CD44 is normally involved in cell adhesion, migration, and cell–matrix interactions; however, CD44 splice variant 6 independently imparts metastatic potential to an otherwise nonmetastatic pancreatic adenocarcinoma cell line (37, 38), and this effect can be inhibited by mAbs targeting CD44 (39). The observation of that TRAILshort impairs T-cell control of tumors furthers the importance of alternate splicing in immune surveillance (40).

There is also ample precedent for soluble isoforms of membrane bound proteins altering biology. B cell Maturation antigen (BCMA) is a cell surface protein expressed universally on myeloma cells, and is required for optimum survival of plasma cells (41). BCMA serves as a receptor for the cytokines BAFF and APRIL, which promote B cell growth, maturation and survival. Soluble BCMA exists in plasma of patients with multiple myeloma, where it binds circulating BAFF, thus preventing BAFF mediated normal B cell development and plasma cell survival (42). Similarly soluble PD-1 (sPD-1) occurs due to alternative splicing (43), and sPD1 isoforms enhance T cell proliferation in vitro. In contrast, whereas membrane associated PDL1 binding to the PD1 receptor reduces T cell proliferation and inhibits apoptosis of regulatory T cells, soluble PDL1 (sPDL1) results from matrix metalloprotease mediated cleavage (44), and exposure of T cells to sPDL-1 causes their death by apoptosis (45). Furthermore, high levels of sPDL-1 in sera are associated with impaired survival of patients with myeloma, lymphoma (46) and melanoma (47).

While no tumors that are TRAILshort negative are impacted by TRAILshort antibody, it is noteworthy that not all cell types that express TRAILshort become sensitized to TRAIL mediated killing following the addition of TRAILshort antibodies. This situation has parallels to the emerging observation that PDL1 positive tumors are not always sensitive to treatment with PDL1 inhibitors (48, 49). From a biologic perspective, it is likely that other factors which impact TRAIL signaling should modify the biologic response to TRAILshort inhibition, for example as the relative expression of death inducing versus decoy TRAIL receptors, levels of anti-apoptotic Bcl2 family members, and expression of different cFLIP isoforms, or IAP family members. Future work will explore these hypotheses at the molecular level.

Polymorphisms in TRAIL have been associated with an increased risk of lymphoma, suggesting a role for TRAIL in B-cell lymphomagenesis (50). Consequently, the TRAIL pathway has been targeted in B-cell malignancies for example using TRAIL agonists in patients with non-Hodgkin lymphoma and multiple myeloma, as well as other malignancies, with uniformly disappointing results. Our results may shed light on a reason for these failures—failure to eliminate TRAIL receptor bearing tumors is not due to TRAIL deficiency (as often T cells from these patients have sufficient TRAIL expression) but rather there is an excess of TRAILshort, which antagonizes the effect of endogenous TRAIL.

Our results establish proof of concept that both in vitro and in vivo, TRAILshort expressed by human cancers antagonizes the TRAIL:TRAIL receptor axis, that TRAILshort is a functional dominant negative TRAIL receptor ligand that inhibits the pro-apoptotic effects of full-length TRAIL, and finally that immune escape afforded by TRAILshort can be partially reversed by TRAILshort-specific antibody.

E. Garcia-Rivera reports other from nference (equity) outside the submitted work. J.R. Anderson holds equity in Splissen Therapeutics, a company that has licensed related technology. M. Aravamudan reports other from Splissen (nference has a small equity interest in Splissen) during the conduct of the study; other from nference (equity) outside the submitted work; and is the founder and CEO of nference, an Analytics/Software company. R.J. Buick reports other from Fusion Antiobidies Ltd (Fusion Antiobodies Ltd received payment for the antibody humanization work from Mayo Clinic) during the conduct of the study; and is an employee of Fusion Antibodies Ltd, who were paid to perform the antibody humanization work. A.J. Novak reports other from Celgene/BMS (research collaboration) outside the submitted work. S.S. Kenderian reports grants from Novartis, Gilead, Kite, Juno, Celgene, MorPhosys, Sunesis, Lentigen, Humanigen, and Tolero, and other from Humanigen (advisory board), Kite (advisory board), and Juno (advisory board) outside the submitted work; and is listed as a co-inventor on and receives royalties from a patent in the field of CAR Immunotherapy, licensed to Novartis, Humanigen, and Mettaforge. A.D. Badley reports other from Zentalis (equity), other from Nference (equity), and personal fees from AbbVie (consulting fees) outside the submitted work; is listed as a co-inventor on a patent regarding TRAILshort therapeutics uses licensed to Splissen Therapeutics; and is on the scientific advisory board of Nference and Zentalis, has equity shares for that work, and is the founder and president of Splissen Therapeutics. No potential conflicts of interest were disclosed by the other authors.

F. Aboulnasr: Formal analysis, investigation, visualization, methodology, writing-review and editing. A. Krogman: Investigation and methodology. R.P. Graham: Formal analysis, methodology, writing-review and editing. N.W. Cummins: Formal analysis, writing-review and editing. A. Misra: Investigation, writing-review and editing. E. Garcia-Rivera: Software, formal analysis, validation and investigation. J.R. Anderson: Data curation, formal analysis, visualization, writing-review and editing. S. Natesampillai: Investigation and methodology. N. Kogan: Software, formal analysis and validation. M. Aravamudan: Software and formal analysis. Z. Nie: Investigation. T.D.Y. Chung: Data curation. R. Buick: Methodology. A.L. Feldman: Resources, writing-review and editing. R.L. King: Formal analysis, writing-review and editing. A.J. Novak: Resources. S.M. Ansell: Resources. S. Kenderian: Investigation and methodology. A.D. Badley: Conceptualization, resources, data curation, formal analysis, supervision, funding acquisition, validation, investigation, visualization, methodology, writing-original draft, writing-review and editing.

This work was supported by grants AI110173 and AI120698 from NIAID, by P50CA97274 and P50CA102701 from the NCI. Some results presented here are in whole or part based upon data generated by the TCGA Research Network: http://cancergenome.nih.gov/. We would like to thank Eric C. Polley (Department of Biomedical Statistics and Informatics) for his assistance with data analysis and critical manuscript review.

The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

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