Patterns of Local Recurrence and Risk of Skin Recurrence in Soft Tissue Sarcomas After Surgical Resection

PURPOSE

Although there is a theoretical risk of skin seeding during surgical resection of soft tissue sarcomas (STSs), current consensus guidelines recommend against routine use of bolus during radiation therapy (RT). However, the risk of skin recurrence has not been systematically assessed. We aimed to assess the patterns of local recurrence (LR) in patients with STS treated with surgery with or without RT.

METHODS AND MATERIALS

We performed a retrospective analysis of adults with STSs evaluated at our institution between 2007 and 2021. For patients who developed LR, the depth was evaluated. Progression-free survival and overall survival were analyzed from time of first LR using the Kaplan-Meier method. Cumulative incidence of distant metastasis was calculated with competing risk analysis from date of LR.

RESULTS

Of the 206 patients evaluated, 20 had LR (9.7%). Among patients with LR, 5 patients (25.0%) were treated with surgery alone and 15 patients (75.0%) with surgery and RT. In patients treated with RT, 46.7% had preoperative RT, 53.3% had postoperative RT, and bolus was used in 46.7%. Surgical margins were close (<1 mm) in 4 patients (20.0%) and positive in 10 patients (50.0%). LR occurred in the deep subfascial tissue in 9 patients (45%), subcutaneous tissue in 10 patients (50.0%), and skin in 1 patient (5.0%). The patient with a skin recurrence was treated with surgery alone, and the tumor involved the skin at presentation. In patients treated with RT, LR occurred within the RT field in 13 patients (86.7%). At 1 year after LR, progression-free survival was 70.3%, overall survival was 81.7%, and cumulative incidence of distant metastasis was 5.9%.

CONCLUSIONS

Skin recurrences were rare after surgical resection of STSs and only occurred in a tumor that involved the skin at initial presentation. These findings support current recommendations against routine use of bolus in STSs not involving the skin at presentation.

Antitumor Immune Responses in B2M-Deficient Cancers

β2-microglobulin (B2M) is a critical component of the MHC class I molecule and is required to present tumor antigens to T cells. Its loss results in acquired resistance to immune checkpoint blockade (ICB) therapies. However, there have been well-documented cases of B2M-inactivated tumors responding to ICB, justifying investigation of how an antitumor immune response can be generated to tumors without surface MHC class I. We knocked out B2M in three murine models with varying baseline MHC class I expression and sensitivity to anti-programmed death receptor (PD-1) therapy and analyzed the immune responses. MC38 and YUMMER2.1 without B2M responded to anti-PD-1 alone or with an IL2 agonist, and this was mediated by CD4+ T cells and natural killer (NK) cells. The more aggressive B16 without B2M expression only partially responded to the IL2 agonist, and this was dependent on NK cells. When analyzing nearly 300 pretreatment biopsies from patients with melanoma receiving PD-1 blockade-based therapies, we found infrequent B2M mutations or homozygous loss but more frequent LOH or copy-number gains. B2M LOH was enriched in biopsies from patients without response to therapy, and these biopsies were more frequently infiltrated by activated NK cells. We conclude that in the absence of B2M, activation of CD4+ T cells and NK cells can mediate responses to murine models of PD-1 blockade therapy. In addition, in human melanoma, the intratumoral presence of activated NK cells upon partial B2M loss likely selects against tumor escape through low surface MHC class I expression.

Surgical Outcomes in Patients Treated with 5-Day Preoperative Radiotherapy for Soft Tissue Sarcoma

PURPOSE/OBJECTIVE(S)

Treatment for high-risk soft tissue sarcoma (STS) of the extremity/trunk includes radiation therapy (RT) and surgical resection. Initial results of a phase 2 single arm trial of 5-day preoperative RT demonstrated acceptable safety and local control. Here we report an update of detailed surgical outcomes among patients treated with 5-day preoperative RT alone on the original phase 2 study, as well as an ongoing expansion cohort.

MATERIALS/METHODS

We conducted an updated analysis of surgical complications from a previously reported phase 2 trial of 50 patients with high-risk extremity/trunk STS treated with 5-day preoperative RT (30 Gy over 5 consecutive daily fractions) and surgery. The current analysis includes additional patients from an ongoing IRB-approved expansion cohort of the phase 2 study, which was designed to compare wound complication rates between patients receiving neoadjuvant chemotherapy and those receiving RT alone. However, given that the primary endpoint of this study has not matured, here we present only the data for patients treated with 5-day preoperative RT alone (n = 44; data cutoff date: February 17, 2022). We generated a secure prospective patient database and extracted data including demographic variables, cancer characteristics and surgical outcomes. Minimum post-operative follow-up was 90 days. Statistical analysis was performed using R (v4.2).

RESULTS

From a total of 94 patients, mean age was 57 (17-90), 40 (42.5%) were female, 10 (10.6%) were diabetic and 8 patients (8.5%) were active smokers or had a >10 pack-year smoking history. Median follow up was 24 months (IQR 10.6-41.8). The most common histologic diagnosis was undifferentiated pleomorphic sarcoma (n = 38, 40.4%). The most common location was the lower extremity (n = 57, 60.6%). Overall, 26 (27.7%) patients experienced surgical wound complications. In the lower extremity, wound complications occurred in 18 patients (31.6%). In all other sites, wound complications occurred in 8 patients (21.6%) (p = 0.41). Twenty-seven (28.7%) cases required local tissue advancement for primary closure and 12 of these patients (44.4%) experienced a wound complication (p = 0.04). Wound dehiscence occurred in 18 patients at a median duration of 43.5 days (IQR 40.3-85.3) from surgery, comprising 69.2% of all wound complications. Secondary surgical intervention was required in 28 patients (29.8%), of which 7 were oncologic re-excisions and 15 were irrigation and debridement. On multivariate analysis, the use of advancement flaps (OR = 5.39; p = 0.004) and diabetes (OR = 4.08; p = 0.07) were associated with wound complications.

CONCLUSION

Five-day preoperative RT for STS results in rates of wound complications comparable to standard fractionation. We identified local advancement flaps as the primary factor associated with wound complications. STS of the lower extremity that require complex closure warrant close attention for dehiscence.

Patterns of local recurrence and risk of skin recurrence in soft tissue sarcomas after surgical resection

PURPOSE/OBJECTIVE(S)

Soft tissue sarcomas (STSs) are rare, heterogeneous tumors primarily managed surgically with radiotherapy (RT) added to improve local control. Although there is a theoretical risk of skin seeding at the time of surgery, current ASTRO Clinical Practice Guidelines recommend against routine use of bolus during pre-operative or post-operative radiotherapy for STS due to increased risk of skin toxicity without clear benefit. However, in the modern era with contemporary treatment planning techniques, the risk of skin recurrence has not been assessed. We performed a detailed analysis of the patterns of local recurrence (LR) in patients with STS treated with surgical resection with or without RT.

MATERIALS/METHODS

We performed a retrospective analysis of 206 adult patients with extremity or trunk STSs evaluated in the Department of Radiation Oncology at our institution over 14 years (2007-2021) and identified all patients with LR. The depth of the recurrence and location relative to the radiation field in patients treated with radiotherapy was evaluated. Progression free survival (PFS) and overall survival (OS) were analyzed using the Kaplan-Meier method, and cumulative incidence of distant metastasis (CIDM) was calculated with competing risk analysis from the date of LR.

RESULTS

Of the 206 patients evaluated, 20 experienced a LR after surgical resection with or without RT. Among patients with a LR, 5 patients (25.0%) were treated with surgery alone and 15 patients (75.0%) received surgery and RT. In patients treated with RT, 46.7% had pre-operative RT, 53.3% had post operative RT, and bolus was used in 5 patients (33.3%). Surgical margins were close (<1mm) in 4 patients (20.0%) and positive in 10 patients (50.0%). Tumor grade was intermediate/high in 15 patients (75%) and the median tumor size was 9 cm (range 5-12). LR occurred in the muscle in 8 patients (40%), subcutaneous tissue in 11 patients (55.0%), and skin in 1 patient (5.0%). The patient with a skin recurrence was treated with surgery alone and the tumor involved the skin at presentation. In the patients treated with RT, LR occurred within radiation field in 10 patients (66.7%). Median follow up time after local recurrence was 12.9 months. At 3 years after LR, PFS was 43.9%, OS was 81.7%, and CIDM was 16.7%.

CONCLUSION

Skin recurrences were exceedingly rare after surgical resection of STSs, and only occurred in a tumor that involved the skin at initial presentation. Due to the increased dose to the normal skin and subcutaneous tissues when bolus is used, which increases risk of toxicity, these findings support current recommendations against routine use of bolus in STSs not involving the skin at presentation.

IGF2BP3 as a Prognostic Biomarker in Well-Differentiated/Dedifferentiated Liposarcoma

BACKGROUND

Although IGF2BP3 has been implicated in tumorigenesis and poor outcomes in multiple cancers, its role in soft-tissue sarcoma (STS) remains unknown. Preliminary data have suggested an association with IGF2BP3 expression among patients with well-differentiated/dedifferentiated liposarcoma (WD/DD LPS), a disease where molecular risk stratification is lacking.

METHODS

We examined the survival associations of IGF2BP3 via univariate and multivariate Cox regression in three unique datasets: (1) the Cancer Genome Atlas (TCGA), (2) an in-house gene microarray, and (3) an in-house tissue microarray (TMA). A fourth dataset, representing an independent in-house TMA, was used for validation.

RESULTS

Within the TCGA dataset, IGF2BP3 expression was a poor prognostic factor uniquely in DD LPS (OS 1.6 vs. 5.0 years, p = 0.009). Within the microarray dataset, IGF2BP3 expression in WD/DD LPS was associated with worse survival (OS 7.7 vs. 21.5 years, p = 0.02). IGF2BP3 protein expression also portended worse survival in WD/DD LPS (OS 3.7 vs. 13.8 years, p < 0.001), which was confirmed in our validation cohort (OS 2.7 vs. 14.9 years, p < 0.001). In the multivariate model, IGF2BP3 was an independent risk factor for OS, (HR 2.55, p = 0.034).

CONCLUSION

IGF2BP3 is highly expressed in a subset of WD/DD LPS. Across independent datasets, IGF2BP3 is also a biomarker of disease progression and worse survival.

Adaptation of the Tumor Antigen Presentation Machinery to Ionizing Radiation

Ionizing radiation (IR) can reprogram proteasome structure and function in cells and tissues. In this article, we show that IR can promote immunoproteasome synthesis with important implications for Ag processing and presentation and tumor immunity. Irradiation of a murine fibrosarcoma (FSA) induced dose-dependent de novo biosynthesis of the immunoproteasome subunits LMP7, LMP2, and Mecl-1, in concert with other changes in the Ag-presentation machinery (APM) essential for CD8+ T cell-mediated immunity, including enhanced expression of MHC class I (MHC-I), β2-microglobulin, transporters associated with Ag processing molecules, and their key transcriptional activator NOD-like receptor family CARD domain containing 5. In contrast, in another less immunogenic, murine fibrosarcoma (NFSA), LMP7 transcripts and expression of components of the immunoproteasome and the APM were muted after IR, which affected MHC-I expression and CD8+ T lymphocyte infiltration into NFSA tumors in vivo. Introduction of LMP7 into NFSA largely corrected these deficiencies, enhancing MHC-I expression and in vivo tumor immunogenicity. The immune adaptation in response to IR mirrored many aspects of the response to IFN-γ in coordinating the transcriptional MHC-I program, albeit with notable differences. Further investigations showed divergent upstream pathways in that, unlike IFN-γ, IR failed to activate STAT-1 in either FSA or NFSA cells while heavily relying on NF-κB activation. The IR-induced shift toward immunoproteasome production within a tumor indicates that proteasomal reprogramming is part of an integrated and dynamic tumor-host response that is specific to the stressor and the tumor and therefore is of clinical relevance for radiation oncology.

The landscape of drug sensitivity and resistance in sarcoma

Sarcomas are a family of rare malignancies composed of over 100 distinct histological subtypes. The rarity of sarcoma poses significant challenges in conducting clinical trials to identify effective therapies, to the point that many rarer subtypes of sarcoma do not have standard-of-care treatment. Even for established regimens, there can be substantial heterogeneity in responses. Overall, novel, personalized approaches for identifying effective treatments are needed to improve patient out-comes. Patient-derived tumor organoids (PDTOs) are clinically relevant models representative of the physiological behavior of tumors across an array of malignancies. Here, we use PDTOs as a tool to better understand the biology of individual tumors and characterize the landscape of drug resistance and sensitivity in sarcoma. We collected n=194 specimens from n=126 sarcoma patients, spanning 24 distinct subtypes. We characterized PDTOs established from over 120 biopsy, resection, and metastasectomy samples. We leveraged our organoid high-throughput drug screening pipeline to test the efficacy of chemotherapeutics, targeted agents, and combination therapies, with results available within a week from tissue collection. Sarcoma PDTOs showed patient-specific growth characteristics and subtype-specific histopathology. Organoid sensitivity correlated with diagnostic subtype, patient age at diagnosis, lesion type, prior treatment history, and disease trajectory for a subset of the compounds screened. We found 90 biological pathways that were implicated in response to treatment of bone and soft tissue sarcoma organoids. By comparing functional responses of organoids and genetic features of the tumors, we show how PDTO drug screening can provide an orthogonal set of information to facilitate optimal drug selection, avoid ineffective therapies, and mirror patient outcomes in sarcoma. In aggregate, we were able to identify at least one effective FDA-approved or NCCN-recommended regimen for 59% of the specimens tested, providing an estimate of the proportion of immediately actionable information identified through our pipeline.

Highlights

Standardized organoid culture preserve unique sarcoma histopathological featuresDrug screening on patient-derived sarcoma organoids provides sensitivity information that correlates with clinical features and yields actionable information for treatment guidanceHigh-throughput screenings provide orthogonal information to genetic sequencingSarcoma organoid response to treatment correlates with patient response to therapyLarge scale, functional precision medicine programs for rare cancers are feasible within a single institution.

Abstract IA012: Intratumoral activation of double-stranded RNA sensors induces systemic immune response to irradiated sarcoma

Background: Undifferentiated pleomorphic sarcoma (UPS) is a common aggressive sarcoma subtype for which existing therapies are ineffective. Immune checkpoint blockade (ICB) is effective in a minority of patients. Most UPS tumors have a predominantly myeloid infiltrate, a highly plastic cellular population with the potential to serve as a substrate for immunotherapy. Radiotherapy (RT), a standard therapy for UPS, can also drive myeloid cells into the tumor. Based on abundant expression of pattern recognition receptors (PRRs) by myeloid cells, we hypothesized that intratumoral injection of a PRR agonist would leverage pre-existing and RT-associated myeloid cells by redirecting them to prime adaptive anti-tumor immunity. Methods: We used BO-112, a nanoplexed double-stranded ribonucleic acid that activates PRRs, most of which are not typically activated by RT. We used an ICB-resistant mouse model, in which tumor cells derived from a KrasG12D/−P53−/− model of UPS are used to establish large tumors in flanks of C57BL/6J mice. Tumor-bearing mice were treated with RT (8 Gy x 3 fractions daily) ± BO-112 (30 ug/dose). Tumor volume and survival between groups were compared by ANOVA and log-rank test, respectively. To test the role of lymphocytes, the study was repeated in RAG−/−gc−/− mice. Kinetic analysis of myeloid and T cells was performed in the tumors and lymph nodes (LN) on days 15, 21, 26 using high-dimensional flow cytometry. To evaluate the fate of monocytes, LysM-eGFP monocytes were intratumorally transferred following treatment, with subsequent analysis of tumors and LNs on days 16, 18, 21. Results: We detected significantly improved tumor control starting from day 16 with mean tumor volume of 240 mm3 in the combination group compared to 490 mm3 in BO112, 790 mm3 in RT, and 875mm3 in mock groups (p&lt;0.0001) which translated into a maximal survival advantage in the combination group (p&lt;0.005), which was associated with both local and systemic increase in IFNg+ CD8 T cells. In RAG−/−gc−/− mice, the benefit of combination therapy was completely negated. Despite the lymphocyte-dependent effect, myeloid cells were preferentially targeted by BO-112. In the combination therapy group (compared to mock), we observed an early reduction in Ly6ChiMHCII+ cells (p&lt;0.05) within the tumor followed by a progressive increase of the same population in the draining LN over time (p=0.01). In parallel, we observed trafficking of adoptively transferred intratumoral eGFP+ monocytes from the tumor to dLNs in response to BO-112 and RT. Conclusions: Local-only therapy of BO-112 and RT yields a lymphocyte-dependent anti-tumor immune response in an immunotherapy-resistant model of UPS. Longitudinal analysis of locoregional immune responses and adoptive transfer experiments indicate that combination BO-112 and RT induces tumor-to-dLN myeloid trafficking that may bridge an adaptive response and confer therapeutic effect. An ongoing phase 1 dose escalation study testing the combination of RT, BO-112 and nivolumab is currently accruing.

Citation Format: Anusha Kalbasi. Intratumoral activation of double-stranded RNA sensors induces systemic immune response to irradiated sarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA012.

Engineered IL13 variants direct specificity of IL13Rα2-targeted CAR T cell therapy

IL13Rα2 is an attractive target due to its overexpression in a variety of cancers and rare expression in healthy tissue, motivating expansion of interleukin 13 (IL13)-based chimeric antigen receptor (CAR) T cell therapy from glioblastoma into systemic malignancies. IL13Rα1, the other binding partner of IL13, is ubiquitously expressed in healthy tissue, raising concerns about the therapeutic window of systemic administration. IL13 mutants with diminished binding affinity to IL13Rα1 were previously generated by structure-guided protein engineering. In this study, two such variants, termed C4 and D7, are characterized for their ability to mediate IL13Rα2-specific response as binding domains for CAR T cells. Despite IL13Rα1 and IL13Rα2 sharing similar binding interfaces on IL13, mutations to IL13 that decrease binding affinity for IL13Rα1 did not drastically change binding affinity for IL13Rα2. Micromolar affinity to IL13Rα1 was sufficient to pacify IL13-mutein CAR T cells in the presence of IL13Rα1-overexpressing cells in vitro. Interestingly, effector activity of D7 CAR T cells, but not C4 CAR T cells, was demonstrated when cocultured with IL13Rα1/IL4Rα-coexpressing cancer cells. While low-affinity interactions with IL13Rα1 did not result in observable toxicities in mice, in vivo biodistribution studies demonstrated that C4 and D7 CAR T cells were better able to traffic away from IL13Rα1+ lung tissue than were wild-type (WT) CAR T cells. These results demonstrate the utility of structure-guided engineering of ligand-based binding domains with appropriate selectivity while validating IL13-mutein CARs with improved selectivity for application to systemic IL13Rα2-expressing malignancies.

Abstract 3605: Human chimeric orthogonal IL9 receptor signaling promotes stemness and polyfunctionality for adoptive T cell therapy of cancer

Background: Orthogonal cytokine-receptor pairs allow selective in vivo manipulation of T cells after adoptive cell therapy (ACT) of cancer. Using mouse models, we previously described a chimeric orthogonal receptor (o9R) comprised of an orthogonal IL-2Rβ extracellular domain (ECD) and an IL-9R intracellular domain (ICD). Adoptive transfer of tumor-specific T cells engineered with o9R showed superior anti-tumor activity in mice treated with orthogonal IL-2 (oIL2). To evaluate the translational potential of o9R signaling, we generated and evaluated a human chimeric orthogonal IL-2Rβ ECD/IL-9R ICD (ho9R).

Methods: We hypothesized that ho9R in tumor-specific T cells would result in distinct signaling, phenotypic and functional properties compared to the human orthogonal IL-2Rβ (ho2R), mirroring our observations in the mouse system. Activated T cells were retrovirally transduced with two vectors: one encoding either ho9R or ho2R and another encoding a T cell receptor (TCR) specific for NY-ESO-1 in the context of HLA*0201. Transduced and sorted T cells were exposed to mouse serum albumin-bound human orthogonal IL2 (MSA-hoIL2) or wildtype IL-2 (MSA-hIL2) for 20 mins to evaluate STAT-1, -3 and -5 phosphorylation. We assessed proliferation and memory differentiation of transduced T cells cultured in MSA-hoIL2 or MSA-hIL2 for one week or after repetitive tumor challenge using an HLA*0201+ NY-ESO-1+ melanoma tumor cell line (M407-nRFP) in the presence of MSA-hoIL2 or MSA-hIL2. After four tumor challenges, T cells were restimulated to quantify intracellular cytokine production. Comparisons between ho2R and ho9R T cells were made using unpaired t-tests or 2-way ANOVA.

Results: Consistent with the mouse system, human T cells signaling through ho9R activated pSTAT-1, -3 and -5, whereas ho2R signaling primarily activated pSTAT5. Similar to the mouse system, ho9R signaling resulted in weaker proliferation than ho2R or wildtype IL-2 signaling (p&lt;0.001). Despite weaker proliferation, ho9R signaling expanded a population of TSCM cells (CD45RA+CD27+CCR7+CD95+; p&lt;0.0001). The difference in T cell phenotype between ho9R/NYESO1-TCR and ho2R/NYESO1-TCR T cells persisted even after four challenges with M407-nRFP in the presence of MSA-hoIL2: ho9R/NYESO1-TCR T cells retained more CD45RA+CD27+ and TSCM cells (p&lt;0.01), and expressed higher levels of CD62L (p&lt;0.05) and CXCR3 (p&lt;0.001). Upon re-exposure to antigen after four tumor challenges, ho9R/NYESO1-TCR T cells expressed more IFNγ, TNFα, and IL-2 (p&lt;0.0001) and exhibited greater polyfunctionality than ho2R/NYESO1-TCR T cells.

Conclusion: In tumor-specific T cells ho9R signaling activates STAT-1, -3, and -5, promotes stemness, and maintains effector polyfunctionality despite repetitive antigen stimulation, providing human evidence for its potential in adoptive T cell therapy of cancer.

Citation Format: Mito Tariveranmoshabad, Leon L. Su, Amy L. Sun, Lora K. Picton, Antoni Ribas, K. Christopher Garcia, Anusha Kalbasi. Human chimeric orthogonal IL9 receptor signaling promotes stemness and polyfunctionality for adoptive T cell therapy of cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3605.

Abstract 3490: IGF2BP3 (IMP3) expression is associated with worse survival in well-differentiated/dedifferentiated (WD/DD) liposarcoma

Background: Liposarcoma (LPS) is an understudied form of soft tissue sarcoma (STS). The well-differentiated (WD) and de-differentiated (DD) subtypes of LPS are associated with indolent and aggressive disease courses, respectively, but this histologic stratification fails to fully capture disease heterogeneity. Molecular approaches may help refine prognostication and inform treatment intensification. Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3 or IMP3), is an RNA-binding protein that regulates gene expression by controlling mRNA stability and has been implicated in tumorigenesis and poor prognosis in many cancers. We hypothesized IGF2BP3 would refine the prognostication of LPS beyond its WD/DD histologic status.

Methods: We examined the association between IGF2BP3 gene or protein expression and clinical data in four datasets: (1) patients with STS subtypes (n=206) in the cancer genome atlas (TCGA) database, (2) an in-house gene microarray of lipomatous tumors (n=71), LPS cell lines (n=3) and patient-derived xenografts (PDX, n=3), (3) an in-house tissue microarray (TMA) of lipomatous tumors (n=115), LPS cell lines (n=3) and PDXs (n=3) and (4) an in-house TMA of WD/DD LPS (n=71). IGF2BP3 protein expression in TMAs was quantified by immunohistochemistry (IHC). IGF2BP3 gene and protein expression values from identical samples were compared by Pearson correlation (n=43). The Kaplan-Meier method and log-rank test were used to compare survival outcomes.

Results: In the TCGA cohort, which does not include WD LPS, IGF2BP3 expression was a poor prognostic factor solely in DD LPS (n=50, median overall survival (mOS): 1.6 vs 5.0 years, p=0.009). Among gene microarray samples, IGF2BP3 expression was highest in DD LPS (n=18) compared to WD LPS (n=29) and lipoma (n=7) by paired t-tests (p=0.03 and 0.002, respectively) and IGF2BP3 expression was associated with worse survival in WD/DD LPS (mOS 7.7 vs 21.5 years, p=0.02). In both TMAs, IGF2BP3 expression (&gt;25% cell positivity/core) portended worse survival in WD/DD LPS (mOS (3): 3.7 vs 13.8 years, p&lt;0.001 and mOS (4): 2.7 vs 14.9 years, p&lt;0.001). IGF2BP3 was not expressed in myxoid LPS (n=21) or lipoma (n=8) samples. Gene and protein expression of IGF2BP3 were positively correlated in WD/DD LPS (r2 = 0.69). IGF2BP3 expression was more strongly associated with survival than LPS differentiation status (mOS: 7.0 (DD) vs 15.2 years (WD), p=0.02). Furthermore, all LPS cell lines and PDXs demonstrated high gene and protein expression of IGF2BP3.

Conclusion: IGF2BP3 is highly expressed in a subset of LPS. Across independent datasets, IGF2BP3 is also a biomarker of disease progression and worse survival, and may stratify patients more effectively than histologic differentiation. Mechanistic studies of IGF2BP3 in LPS tumorigenesis and progression using aforementioned LPS cell lines and PDX models are ongoing.

Citation Format: Kyle D. Klingbeil, Jack Pengfei Tang, Sarah M. Dry, Fritz C. Eilber, Dinesh S. Rao, Brian E. Kadera, Anusha Kalbasi. IGF2BP3 (IMP3) expression is associated with worse survival in well-differentiated/dedifferentiated (WD/DD) liposarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3490.

Abstract 3446: Radiation and intratumoral activation of double-stranded RNA sensors redirects myeloid cells and primes adaptive immunity

Background: Undifferentiated pleomorphic sarcoma (UPS) is a common aggressive sarcoma subtype for which existing therapies are ineffective. Immune checkpoint blockade (ICB) is effective in a minority of patients whose tumors harbor a pre-existing lymphocytic response. However, most UPS tumors have a myeloid infiltrate, a highly plastic cellular population with the potential to serve as a substrate for immunotherapy. Radiotherapy (RT), a standard therapy for UPS, can also drive myeloid cells into the tumor. Based on abundant expression of pattern recognition receptors (PRRs) by myeloid cells, we hypothesized that intratumoral injection of a PRR agonist would leverage pre-existing and RT-associated myeloid cells by redirecting them to prime adaptive anti-tumor immunity.

Methods: We used BO-112, a nanoplexed double-stranded ribonucleic acid that activates PRRs, most of which are not typically activated by RT. We used an ICB-resistant mouse model, in which tumor cells derived from a KrasG12D/-P53-/- model of UPS are used to establish large tumors in flanks of C57BL/6J mice. Tumor-bearing mice were treated with RT (8 Gy x 3 fractions daily) starting on day 8 ± BO-112 (30 ug/dose) on days 8 and 10. Tumor growth and survival between groups were compared by ANOVA and log-rank test, respectively. To test the role of lymphocytes, the study was repeated in RAG-/-gc-/- mice. Kinetic analysis of myeloid and T cells was performed in the tumors and lymph nodes (LN) on days 15, 21, 26 using high-dimensional flow cytometry. To evaluate the fate of monocytes, LysM-eGFP monocytes were intratumorally transferred following treatment, with subsequent analysis of tumors and LNs on days 16, 18, 21.

Results: Tumor control was significantly improved in the combination group starting from day 16 with mean tumor volume of 240 mm3 in the combination group compared to 490 mm3 in BO112, 790 mm3 in RT, and 875mm3 in mock groups (p&lt;0.0001) which translated into a maximal survival advantage in the combination group (p&lt;0.005). However, in RAG-/-gc-/- mice, this benefit of combination therapy was completely negated. This therapeutic combination appeared to drive an early reduction in Ly6ChiMHCII+ cells (p&lt;0.05) within the tumor followed by a progressive increase of the same population in the draining LN over time (p=0.01). In parallel, we observed trafficking of adoptively transferred intratumoral eGFP+ monocytes from the tumor to dLNs in response to BO-112 and RT.

Conclusions: Local-only therapy of BO-112 and RT yields a lymphocyte-dependent anti-tumor immune response in an immunotherapy-resistant model of UPS. Longitudinal analysis of locoregional immune responses and adoptive transfer experiments indicate that combination BO-112 and RT induces tumor-to-dLN myeloid trafficking that may bridge an adaptive response and confer therapeutic effect.

Citation Format: Jie Deng, Scott C. Chin, Mito Tariveranmoshabad, Danielle S. Graham, Hailey R. Lee, Marisol Quintero, Dorthe Schaue, Anusha Kalbasi. Radiation and intratumoral activation of double-stranded RNA sensors redirects myeloid cells and primes adaptive immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3446.

Abstract 3818: Infrequent chromosomal loss and recurrent gains lead to imbalanced expression of HLA genes in melanoma

Introduction: Loss-of-heterozygosity (LOH) events in chromosome 6p, comprising the human leukocyte antigen (HLA) genes, have been reported in about 10% of cutaneous melanoma (compared to 20-40% of squamous cell carcinomas), while copy number gains in this region have been observed in over 50% of melanoma. Recent studies focused in HLA allelic loss have been restricted to DNA-based approaches, and have not been validated orthogonally at the RNA or protein levels. Here, using clinical melanoma biopsies and patient-derived melanoma cell lines, we show that genetic alterations in HLA genes results in imbalanced allele expression, subsequently skewing antigen presentation by melanoma cells.

Methods: Whole exome and RNA sequencing (WES, RNAseq) analyses were performed on 760 melanoma biopsies and 60 patient-derived melanoma cell lines. Patient-matched normal WES was used to perform HLA haplotyping across Class I and II HLA genes. Tumor WES was analyzed for copy number alterations in chromosome 6, identifying which alleles were lost or gained. Differential expression of HLA alleles was quantified in tumor RNAseq, correlating the allelic imbalance at the DNA and RNA levels. Melanoma cell lines heterozygous for HLA-A*02, A*03, and A*24 were analyzed by flow cytometry for surface-level HLA protein expression using allele-specific antibodies to quantify allelic densities and compare the imbalance of HLA-A alleles at the DNA, RNA, and protein levels.

Results: Across 760 melanoma biopsies, copy number alterations in chromosome 6p were identified in 76% of tumors; 12% had LOH, and 54% had copy number gains that resulted in imbalanced copies of alleles. In paired tumor WES and RNAseq (N=682), genetic imbalance was correlated with imbalanced expression of HLA alleles in the classical Class I HLA genes (Spearman rho=0.64-0.7; p=2.2e-16); this association was strengthened in tumors with high tumor cellularity, and was not associated with the total expression of the HLA genes.These patterns were explored in a 60 patient-derived melanoma cell lines with matched tumor WES and RNAseq, confirming that alleles gained at the genetic level were also expressed at higher levels than alleles that were not gained or lost. In 10 cell lines heterozygous for either HLA-A*02, A*03, or A*24, allelic imbalance at the DNA and RNA level resulted in correlative imbalanced surface presentation of alleles at the protein level.

Conclusions: Evaluation of paired tumor WES and RNAseq revealed orthogonal validation of HLA allelic imbalance, and analysis in cell lines suggested that these patterns were likely tumor intrinsic. Experimental validation of these findings at the protein level suggests that antigen presentation density can be modulated by chromosomal gains, and not just allelic loss, in HLA genes. This knowledge is important for the design of cancer vaccines or T cell therapies targeting neoantigens presented by HLA class I complexes.

Citation Format: Katie M. Campbell, Justin Saco, Egmidio Medina, Meelad Amouzgar, Shannon M. Pfeiffer, Cynthia R. Gonzalez, Gabriela Steiner, Ameya Champhekar, Cristina Puig Saus, Jesse Zaretsky, Gabriel Abril Rodriguez, Agustin Vega-Crespo, Ignacio Baselga Carretero, Mito Tariveranmoshabad, Anusha Kalbasi, Christine Spencer, Zachary L. Skidmore, Malachi Griffith, Obi L. Griffith, Daniel K. Wells, Antoni Ribas. Infrequent chromosomal loss and recurrent gains lead to imbalanced expression of HLA genes in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3818.

Retrospective analysis of adjuvant treatment for localized, operable uterine leiomyosarcoma

OBJECTIVE

Currently, there is no standard adjuvant treatment protocol for localized uterine leiomyosarcoma (uLMS) as clinical trials to address this question have been retrospective, underpowered, or undermined by slow accrual rates. The aim of this study is to determine the benefit of adjuvant chemotherapy for uLMS.

METHODS

We reviewed the medical records of localized uLMS patients who had underwent adjuvant therapy after upfront surgery between 2000 and 2020. The cases were blinded for review. We evaluated the influence of various clinical characteristics and different types of adjuvant therapies on specific outcomes.

RESULTS

Sixty-eight patients (median age: 50 years) were included for analysis. Forty of 68 (58.8%) patients received adjuvant chemotherapy +/- radiation therapy and 25 patients (38.6%) did not receive any adjuvant therapy. At a median follow-up time of 43.3 months, 45 patients (66.1%) had relapsed disease. The median disease-free survival (mDFS) for all patients was 23.1 months. Patients who received any adjuvant treatment (chemotherapy and/or radiation) trended toward a longer mDFS compared with those who did not receive any adjuvant therapy (29.7 vs. 14.1 months, p = 0.26). Patients who received adjuvant chemotherapy alone had a longer, but nonstatistically significant mDFS compared with those who did not receive any adjuvant treatment (22.2 vs. 14.1 months, p = 0.18). Additionally, univariate analysis found that tumor size large than 10 cm, and a mitotic rate >10/10hpf were independent prognostic factors for worse DFS.

CONCLUSIONS

Though DFS was more favorable among those who received adjuvant therapy, it was not statistically significant, and thus based on this data adjuvant therapy for resected uLMS is still in question.

Spatial profiling reveals association between WNT pathway activation and T-cell exclusion in acquired resistance of synovial sarcoma to NY-ESO-1 transgenic T-cell therapy

BACKGROUND

Genetically engineered T-cell immunotherapies for adoptive cell transfer (ACT) have emerged as a promising form of cancer treatment, but many of these patients develop recurrent disease. Furthermore, delineating mechanisms of resistance may be challenging since the analysis of bulk tumor profiling can be complicated by spatial heterogeneity.

METHODS

Tumor samples were collected from a patient with synovial sarcoma who developed acquired resistance to ACT targeting NY-ESO-1. Biopsies (primary, progressive metastasis, and recurrence) were subjected to bulk tumor DNA and RNA sequencing, as well as high-dimensional spatial profiling of RNA and protein targets. Untreated and progressive lesions were compared with identified patterns associated with acquired resistance to ACT.

RESULTS

Gene expression patterns due to immune activity and infiltration were diluted in bulk tumor sequencing. The metastasis was enriched for tumor regions with increased CTNNB1 (encoding beta-catenin), which were negatively associated with the expression of T-cell surface proteins and antigen presentation machinery. Spatial profiling was most highly concordant with bulk sequencing in the lesions with decreased spatial heterogeneity.

CONCLUSIONS

Complementary use of bulk and spatial profiling enables more accurate interrogation of tumor specimens, particularly to address complex questions regarding immunotherapeutic mechanisms. Our study uses this approach to demonstrate a mechanism of T-cell exclusion and resistance to cellular immunotherapy in synovial sarcoma.

Germline biomarkers predict toxicity to anti-PD1/PDL1 checkpoint therapy

BACKGROUND

There is great interest in finding ways to identify patients who will develop toxicity to cancer therapies. This has become especially pressing in the era of immune therapy, where toxicity can be long-lasting and life-altering, and primarily comes in the form of immune-related adverse effects (irAEs). Treatment with the first drugs in this class, anti-programmed death 1 (anti-PD1)/programmed death-ligand 1 (PDL1) checkpoint therapies, results in grade 2 or higher irAEs in up to 25%-30% of patients, which occur most commonly within the first 6 months of treatment and can include arthralgias, rash, pruritus, pneumonitis, diarrhea and/or colitis, hepatitis, and endocrinopathies. We tested the hypothesis that germline microRNA pathway functional variants, known to predict altered systemic stress responses to cancer therapies, would predict irAEs in patients across cancer types.

METHODS

MicroRNA pathway variants were evaluated for an association with grade 2 or higher toxicity using four classifiers on 62 patients with melanoma, and then the panel's performance was validated on 99 patients with other cancer types. Trained classifiers included classification trees, LASSO-regularized logistic regression, boosted trees, and random forests. Final performance measures were reported on the training set using leave-one-out cross validation and validated on held-out samples. The predicted probability of toxicity was evaluated for its association, if any, with response categories to anti-PD1/PDL1 therapy in the melanoma cohort.

RESULTS

A biomarker panel was identified that predicts toxicity with 80% accuracy (F1=0.76, area under the curve (AUC)=0.82) in the melanoma training cohort and 77.6% accuracy (F1=0.621, AUC=0.778) in the pan-cancer validation cohort. In the melanoma cohort, the predictive probability of toxicity was not associated with response categories to anti-PD1/PDL1 therapy (p=0.70). In the same cohort, the most significant biomarker of toxicity in RAC1, predicting a greater than ninefold increased risk of toxicity (p<0.001), was also not associated with response to anti-PD1/PDL1 therapy (p=0.151).

CONCLUSIONS

A germline microRNA-based biomarker signature predicts grade 2 and higher irAEs to anti-PD1/PDL1 therapy, regardless of tumor type, in a pan-cancer manner. These findings represent an important step toward personalizing checkpoint therapy, the use of which is growing rapidly.

Abstract CT221: A phase I study of intratumoral BO-112 and nivolumab for resectable soft tissue sarcoma

Background: BO-112 is a double stranded synthetic RNA formulated with polyethyleneimine. By mimicking a viral infection, it mobilizes the immune system, including activation of dendritic cells, CD8 T-cell infiltration, induction of interferons, and enhancement of immunogenic cell death. Intratumoral (IT) BO-112 has been tested both alone and in combination with anti-PD-1 therapies in a phase I trial (NCT02828098), which showed an overall response rate (ORR) of 11% and disease control rate (DCR) of 46% in patients with multiple tumor types and a tolerable safety profile. While anti-PD1 therapies have shown promise in select subtypes of soft tissue sarcoma (STS), their overall efficacy in STS has been limited. We hypothesize that BO-112, in combination with radiotherapy (RT), may reverse resistance to anti-PD1 therapy in a subset of patients with STS.

Methods: This is an exploratory phase I study of IT BO-112 in combination with nivolumab in patients with STS planning to undergo neoadjuvant RT (NCT04420975) and surgery. BO-112 at a dose of 1 mg will be administered intratumorally on days 1, 8 and 15; nivolumab 240 mg will be administered intravenously on days 8 and 22. Patients will receive 5 fractions of neoadjuvant RT between day 8 and 12, followed by surgical resection between days 26 and 50. Twenty patients with newly diagnosed high grade histologically confirmed STS of the extremity, trunk or retroperitoneum amenable for IT injection will be included. Allowed histological subtypes are undifferentiated pleomorphic sarcoma, myxofibrosarcoma, leiomyosarcoma, dedifferentiated liposarcoma and synovial sarcoma.The primary objective is to explore the safety of BO-112 in combination with nivolumab in patients undergoing preoperative RT. The study includes stopping rules based on the frequency of dose limiting toxicities. As an exploratory single arm pilot study results will be reported using purely descriptive statistics. Tumor and blood specimens collected at baseline, at each IT BO-112 injection, and surgery will allow evaluation of the dynamic changes in tumor immune infiltration, T cell receptor repertoire, and tumor necrosis. These dynamic changes, along with putative biomarkers, such as baseline tumor mutational load, copy number alterations, tumor immune composition, tumor and immune gene expression signatures, and PD-L1 expression, will be related to individual subject tumor responses. The 2-year rate of local recurrence and distant metastasis will also be assessed. This study began accrual in December 2020 and is open.

Citation Format: Anusha Kalbasi, Fritz C. Eilber, Arun Singh, Bartosz Chmielowski, Nicholas Bernthal, Brooke Crawford, Joseph G. Crompton, Varand Ghazikhanian, Leanne Seeger, Kambiz Motamedi, Michael L. Douek, Carol Felix, Vincent Basehart, Helena Escuin-Ordinas, Marisol Quintero, Sonia Macia. A phase I study of intratumoral BO-112 and nivolumab for resectable soft tissue sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr CT221.

Abstract NG11: Orthogonal IL-9 receptor signaling reprograms T cells to obviate conditioning chemotherapy before adoptive cell therapy

Background: Adoptive cell therapy using genetically engineered T cells - such as chimeric antigen receptor (CAR) or T cell receptor (TCR) modified T cells - is an effective therapy for patients with cancer. However, successful adoptive cell therapies (ACT) require conditioning chemotherapy in order to deplete a patient's endogenous T cells. Patients may also be treated with interleukin-2 (IL2) to promote expansion of adoptively transferred cells, causing significant toxicity and resulting in counterproductive expansion of regulatory T cells. A synthetic orthogonal IL2 (oIL2) can be used to selectively expand adoptively transferred T cells engineered with a synthetic orthogonal interleukin-2 receptor (oIL2R) in vivo, without activating the wildtype IL2 receptor of endogenous T cells. In a lymphodepleted host treated with oIL2, the oIL2R-engineered tumor-specific T cells were equally as effective as tumor-specific T cells treated with wildtype IL2. We hypothesized that selective expansion of adoptively transferred cells using orthogonal interleukin/interleukin-receptor pairs may circumvent the need for lymphodepletion prior to ACT. Methods: To evaluate the impact of orthogonal interleukin signaling on efficacy of adoptively transferred tumor-specific T cells, we used gp100-specific pmel-1 T cells and the gp100+ B16-F10 mouse melanoma model. Activated pmel-1 T cells were engineered with retroviral vectors encoding one of two orthogonal interleukin receptors designed by our collaborator (Dr. Christopher Garcia): orthogonal interleukin-2 receptor (oIL2R) or orthogonal interleukin-9 receptor (oIL9R). The oIL2R consists of a mutant IL2Rb chain that selectively binds orthogonal IL2 (oIL2), but does not bind wildtype IL2. In turn, oIL2 does not bind the wildtype IL2Rb. The oIL9R consists of the extracellular and transmembrane domains of the oIL2R, but the intracellular domain of IL9Ra. Thus, both orthogonal interleukin receptors are activated upon stimulation with oIL2. T cells engineered with oIL9R signal through STAT1, STAT3 and STAT5, compared to oIL2R T cells which predominantly signal through STAT5. We hypothesized that orthogonal interleukin signaling through the IL-9 receptor pathway may promote superior anti-tumor efficacy because this signaling pathway results in activation of STAT1, STAT3, and STAT5 signaling, in contrast to primarily STAT5 signaling activation observed with IL-2 signaling. Sorted oIL2 or oIL9R pmel-1 T cells were used for downstream experiments. For in vivo experiments, tumor-bearing mice were lymphodepleted (or not) with total body irradiation one day prior to adoptive cell transfer (ACT) of 4.0-6.0 × 106 gp100-activated pmel-1 T cells. Mice were also treated with mIL2 or oIL2 for 5 consecutive days starting on the day of adoptive transfer. Tumor volume and survival were assessed. Peripheral blood was examined for adoptively transferred pmel-1 T cells (Thy1.1+CD8+) at various timepoints. Tumors and spleens from mice were harvested for analysis by multiplex immunohistochemistry (IHC) and mass cytometry. In vitro, oIL2 and/or oIL9R pmel-1 T cells were cultured with either wildtype murine IL-2 (mIL2) or orthogonal IL-2 (oIL2). Proliferation was quantified and T cell phenotype was evaluated by flow cytometry. Activated C3H splenocytes transduced with oIL2R and oIL9R were used as a secondary model. After coculture with mIL2 or oIL2, oIL2R and oIL9R pmel-1 T cells were cocultured with nuclear RFP+ B16-F10 tumor cells at various effector:target ratios to assess cell killing and cytokine production. Results: In the absence of lymphodepletion, pmel-1 T cells administered with mIL2 do not expand in vivo and do not have anti-tumor efficacy against B16-F10 tumor-bearing mice. Consistent with our hypothesis, oIL2R pmel-1 T cells expand and persist in vivo even in the absence of lymphodepletion when mice are treated with oIL2 but not mIL2 (53.7 versus 10.8 Thy1.1+CD8+ cells per 10mL blood; P=0.01). However, this improved expansion and persistence did not result in improved anti-tumor efficacy or survival for mice treated with oIL2R pmel-1 T cells and oIL2 in the absence of lymphodepletion across multiple experiments. We next evaluated the expansion and persistence of oIL9R pmel-1 T cells in vivo in the absence of lymphodepletion. Similar to oIL2R pmel-1 T cells, oIL9R pmel-1 T cells expand and persist in vivo even in the absence of lymphodepletion when mice are treated with oIL2 but not mIL2 (108.8 versus 5.7 Thy1.1+CD8+ cells per 10mL blood; P=0.004). But unlike the oIL2R pmel-1 T cells, adoptive transfer of oIL9R pmel-1 T cells in mice treated with oIL2 (versus mIL2) did result in delayed tumor growth and prolonged survival in the absence of lymphodepletion (mean tumor volume 155mm3 versus 1736mm3, P=0.02; Log-rank test, P=0.002). Thus, while both oIL2R and oIL9R pmel-1 T cells can expand in vivo after ACT in the absence of lymphodepletion, only oIL9R pmel-1 T cells result in anti-tumor efficacy and prolonged survival. We hypothesized that other functional differences between oIL9R and oIL2R T cells are responsible for the discrepancy in anti-tumor activity. We found that oIL9R pmel-1 T cells have improved tumor infiltration. Tumors from mice treated with oIL2R and oIL9R pmel-1 T cells were examined by mass cytometry. Of 18 phenotypic opt-SNE clusters, the only cluster with differential abundance was the cluster assigned to adoptively transferred pmel-1 T cells, which was present at greater abundance in tumors from mice treated with oIL9R pmel-1 T cells (log2(fold change) = 2.45, P=1.86 × 10−5). This data was corroborated by multiplex IHC, which demonstrated a higher quantity of CD8+ and CD8+PD1+ T cells in tumors from mice treated with oIL9R pmel-1 T cells, compared to oIL2R pmel-1 T cells. In vitro, oIL9R pmel-1 T cells, but not oIL2R pmel-1 T cells, upregulate lymphocyte homing marker CD62L upon exposure to oIL2 (P&lt;0.0001). In addition, oIL9R pmel-1 T cells lose expression of CD44, indicating a shift toward a naïve/T-stem cell memory phenotype, which is associated with improved anti-tumor efficacy. These phenotypic changes were corroborated in activated C3H T cells engineered with oIL9R T cells and exposed to oIL2. oIL9R pmel-1 T cells exposed to oIL2 for 48 hours prior to coculture with B16-F10 tumor cells had superior in vitro tumor killing than oIL2R pmel-1 T cells exposed to oIL2 (16.6% versus 58.2% tumor confluence at 70 hours, P=0.001). Likewise, oIL9R pmel-1 T cells exposed to oIL2 for 48 hours prior to coculture produced higher amounts of IFNg (15,318 versus 11,530 pg/mL, P=0.03). Conclusions: ACT with oIL9R reprogrammed pmel-1 T cells induce antitumor activity in the absence of conditioning chemotherapy. The oIL9R genetically programmed T cells have superior effector function upon encountering antigen and have improved in vivo activity through diverse effects on T cell phenotype, trafficking and function in non-lymphodepleted hosts. This opens a path toward obviating conditioning chemotherapy prior to ACT in patients with cancer.

Citation Format: Anusha Kalbasi, Mito Tariveranmoshabad, Helena Escuin-Ordenas, Sarah Kremer, Leon L. Su, Lora Picton, AnushaGiulia Parisi, Christopher Garcia, Antoni Ribas. Orthogonal IL-9 receptor signaling reprograms T cells to obviate conditioning chemotherapy before adoptive cell therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr NG11.

Recurrence and disease-specific survival after 10-year disease-free interval in patients with primary retroperitoneal liposarcoma: Implications for long-term surveillance

11546

Background: Surveillance imaging of patients with retroperitoneal liposarcoma (RP-LPS) following surgical resection is based on a projected risk of locoregional and distant recurrence. The duration of surveillance is not well defined as the long-term natural history of RP-LPS after treatment is poorly understood. We evaluate a cohort of RP-LPS patients—without evidence of disease 10 years following initial resection—to assess the long-term risk of recurrence and disease-specific survival (DSS). Methods: The prospectively maintained UCLA Sarcoma Database was used to identify RP-LPS patients who demonstrated 10-year progression-free survival (10yr-PFS) after initial diagnosis and treatment. Patients in the 10yr-PFS cohort were subsequently evaluated for recurrence and DSS. Time intervals start at date of initial surgical resection. Cox proportional hazards models were used to determine factors associated with recurrence and DSS. Results: From 1972-2010, 76 patients with RP-LPS had at least 10 years of follow-up. Of these, 37 (49%) demonstrated 10yr-PFS. Median follow-up was 15 years (range 10-35 years). Among the 10yr-PFS patients, 43% (16/37) developed a recurrence >10 years after the initial surgery, and 19% (7/37) died of disease. Neither long-term recurrence nor DSS were significantly associated with age, sex, tumor size, LPS subtype, surgical margin, or peri-operative treatment with radiation or chemotherapy (Table). Conclusions: Patients with primary RP-LPS treated with surgical resection +/- multimodality therapy have a long-term risk of recurrence and disease-specific death that is unacknowledged by current surveillance imaging guidelines. Among the patients with a 10yr-PFS, 43% developed a recurrence and 19% died of disease. These findings suggest a need for lifelong surveillance imaging in patients with RP-LPS.[Table: see text]

Prediction of soft tissue sarcoma response to radiotherapy using longitudinal diffusion MRI and a deep neural network with generative adversarial network-based data augmentation

PURPOSE

The goal of this study was to predict soft tissue sarcoma response to radiotherapy (RT) using longitudinal diffusion-weighted MRI (DWI). A novel deep-learning prediction framework along with generative adversarial network (GAN)-based data augmentation was investigated for the response prediction.

METHODS

Thirty soft tissue sarcoma patients who were treated with five-fraction hypofractionated radiation therapy (RT, 6Gy×5) underwent diffusion-weighted MRI three times throughout the RT course using an MR-guided radiotherapy system. Pathologic treatment effect (TE) scores, ranging from 0-100%, were obtained from the post-RT surgical specimen as a surrogate of patient treatment response. Patients were divided into three classes based on the TE score (TE ≤ 20%, 20% < TE < 90%, TE ≥ 90%). Apparent diffusion coefficient (ADC) maps of the tumor from the three time points were combined as 3-channel images. An auxiliary classifier generative adversarial network (ACGAN) was trained on 20 patients to augment the data size. A total of 15,000 synthetic images were generated for each class. A prediction model based on a previously described VGG-19 network was trained using the synthesized data, validated on five unseen validation patients, and tested on the remaining five test patients. The entire process was repeated seven times, each time shuffling the training, validation, and testing datasets such that each patient was tested at least once during the independent test stage. Prediction performance for slice-based prediction and patient-based prediction was evaluated.

RESULTS

The average training and validation accuracies were 86.5% ± 1.6% and 84.8% ± 1.8%, respectively, indicating that the generated samples were good representations of the original patient data. Among the seven rounds of testing, slice by slice prediction accuracy ranged from 81.6% to 86.8%. The overall accuracy of the independent test sets was 83.3%. For patient-based prediction, 80% was achieved in one round and 100% was achieved in the remaining six rounds. The mean accuracy was 97.1%.

CONCLUSION

This study demonstrated the potential to use deep learning to predict the pathologic treatment effect from longitudinal DWI. Accuracies of 83.3% and 97.1% were achieved on independent test sets for slice-based and patient-based prediction respectively.

Metastasis and Immune Evasion from Extracellular cGAMP Hydrolysis

Cytosolic DNA is characteristic of chromosomally unstable metastatic cancer cells, resulting in constitutive activation of the cGAS-STING innate immune pathway. How tumors co-opt inflammatory signaling while evading immune surveillance remains unknown. Here, we show that the ectonucleotidase ENPP1 promotes metastasis by selectively degrading extracellular cGAMP, an immune-stimulatory metabolite whose breakdown products include the immune suppressor adenosine. ENPP1 loss suppresses metastasis, restores tumor immune infiltration, and potentiates response to immune checkpoint blockade in a manner dependent on tumor cGAS and host STING. Conversely, overexpression of wild-type ENPP1, but not an enzymatically weakened mutant, promotes migration and metastasis, in part through the generation of extracellular adenosine, and renders otherwise sensitive tumors completely resistant to immunotherapy. In human cancers, ENPP1 expression correlates with reduced immune cell infiltration, increased metastasis, and resistance to anti-PD-1/PD-L1 treatment. Thus, cGAMP hydrolysis by ENPP1 enables chromosomally unstable tumors to transmute cGAS activation into an immune-suppressive pathway. SIGNIFICANCE: Chromosomal instability promotes metastasis by generating chronic tumor inflammation. ENPP1 facilitates metastasis and enables tumor cells to tolerate inflammation by hydrolyzing the immunotransmitter cGAMP, preventing its transfer from cancer cells to immune cells.This article is highlighted in the In This Issue feature, p. 995.

Radiotherapy Remains Underused in the Treatment of Soft-Tissue Sarcomas: Disparities in Practice Patterns in the United States

BACKGROUND

Practice patterns of radiation therapy (RT) use for soft-tissue sarcoma (STS) remain quite variable, despite clinical practice guidelines recommending the addition of RT to surgery for patients with high-grade STS, particularly for larger tumors. Using the National Cancer Database (NCDB), we assessed patterns of overall RT use, neoadjuvant versus adjuvant treatment, and specific RT modalities in this population.

PATIENTS AND METHODS

Patients aged ≥18 years with stage II/III STS in 2004 through 2015 were identified from the NCDB. Patterns of care were assessed using multivariable logistic regression analysis.

RESULTS

Of 27,426 total patients, 11,654 (42%) were treated with surgery alone versus 15,772 (58%) with RT in addition to surgery, with no overall increase in RT use over the study period. Notable clinical predictors of receipt of RT included tumor size (>5 cm), grade III, and tumors arising in the extremities. Conversely, female sex, older age (≥70 years), Black race, noncommercial insurance coverage, farther distance to treatment, and poor performance status were negative predictors of RT use. Of those receiving RT, 27% were treated with neoadjuvant RT and 73% with adjuvant RT. The proportion of those receiving neoadjuvant RT increased over time. Relevant factors associated with neoadjuvant RT included treatment at academic centers, larger tumor size, and extremity tumors. Of those who received RT with a modality specified as either intensity-modulated RT (IMRT) or 3D conformal RT (3DCRT), 61% were treated with IMRT and 39% with 3DCRT. The proportion of patients treated with IMRT increased over time. Relevant factors associated with IMRT use included treatment at academic centers, commercial insurance coverage, and larger and nonextremity tumors.

CONCLUSIONS

Although use of neoadjuvant RT and IMRT has increased over time, a significant number of patients with STS are not receiving adjuvant or neoadjuvant RT. Our findings also note potential sociodemographic disparities and highlight the concern that not all patients with STS are being equally considered for RT.

Comparison and evaluation of distortion correction techniques on an MR-guided radiotherapy system

PURPOSE

To evaluate two distortion correction techniques for diffusion-weighted single-shot echo-planar imaging (DW-ssEPI) on a 0.35 T magnetic resonance-guided radiotherapy (MRgRT) system.

METHODS

The effects of sequence optimization through enabling parallel imaging (PI) and selecting appropriate bandwidth on spatial distortion were first evaluated on the 0.35 T MRgRT system using a spatial integrity phantom. Field map (FM) and reversed gradient (RG) corrections were then performed on the optimized protocol to further reduce distortion. An open-source toolbox was used to quantify the spatial displacement before and after distortion correction. To evaluate ADC accuracy and repeatability of the optimized protocol, as well as impacts of distortion correction on ADC values, the optimized protocol was scanned twice on a diffusion phantom. The calculated ADC values were compared with reference ADCs using paired t-test. Intraclass correlation coefficient (ICC) between the two repetitions, as well as between before and after FM/RG correction was calculated to evaluate ADC repeatability and effects of distortion correction. Six patients were recruited to assess the in-vivo performance. The optimal distortion correction technique was identified by visual assessment. To quantify distortion reduction, tumor and critical structures were contoured on the turbo spin echo (TSE) image (reference image), the DW-ssEPI image, and the distortion corrected images independently by two radiation oncologists. Mean distance to agreement (MDA) and DICE coefficient between contours on the reference images and the diffusion images were calculated. Tumor apparent diffusion coefficient (ADC) values from the original DW-ssEPI images and the distortion corrected images were compared using Bland-Altman analysis.

RESULTS

Sequence optimization played a vital role in improving the spatial integrity, and spatial distortion was proportional to the total readout time. Before the correction, distortion of the optimized protocol (PI and high bandwidth) was 1.50 ± 0.89 mm in a 100 mm radius and 2.21 ± 1.39 mm in a 175 mm radius for the central plane. FM corrections reduced the distortions to 0.42 ± 0.27 mm and 0.67 ± 0.49 mm respectively, and RG reduced distortion to 0.40 ± 0.22 mm and 0.64 ± 0.47 mm, respectively. The optimized protocol provided accurate and repeatable ADC quantification on the diffusion phantom. The calculated ADC values were consistent before and after FM/RG correction. For the patient study, the FM correction was unable to reduce chemical shift artifacts whereas the RG method successfully mitigated the chemical shift. MDA reduced from 2.52 ± 1.29 mm to 1.11 ± 0.72 mm after the RG correction. The DICE coefficient increased from 0.80 ± 0.13 to 0.91 ± 0.06. A Bland-Altman plot showed that there was a good agreement between ADC measurements before and after application of the RG correction.

CONCLUSION

Two distortion correction techniques were evaluated on a commercial low-field MRgRT system. Overall, the RG correction was able to drastically improve spatial distortion and preserve ADC accuracy.

Clinical Development and Evaluation of Megavoltage Topogram for Fast Patient Alignment on Helical Tomotherapy

Purpose

To develop and evaluate a fast patient localization tool using megavoltage (MV)-topogram on helical tomotherapy.

Methods and Materials

Eighty-one MV-topogram pairs for 18 pelvis patients undergoing radiation were acquired weekly under an institutional review board–approved clinical trial. The MV-topogram imaging protocol requires 2 orthogonal acquisitions at static gantry angles of 0 degrees and 90 degrees for a programed scan length. A MATLAB based in-house software was developed to reconstruct the MV-topograms offline. Reference images (digitally reconstructed topograms, digitally reconstructed topograms) were generated using the planning computed tomography and tomotherapy geometry. The MV-topogram based alignment was determined by registering the MV-topograms to the digitally reconstructed topogram using bony landmark on commercial MIM software. The daily shifts in 3 translational directions determined from MV-topograms were compared with the megavoltage computed tomography (MVCT) based patient shifts. Linear-regression and two one-sided tests equivalence tests were performed to investigate the relation and equivalence between the 2 techniques. Seventy-eight MV-topogram pairs for 19 head and neck patients were included to validate the finding.

Results

The magnitudes of alignment differences of (MVCT − MV-topogram) (and standard deviations) were −0.3 ± 2.1, −0.8 ± 2.4, and 1.6 ± 1.7 mm for pelvis and 0.6 ± 1.2, 0.8 ± 4.2, 1.6 ± 2.6 mm for head and neck; the linear-regression coefficients between 2 imaging techniques were 1.18, 1.10, 0.94, and 0.86, 0.63, 0.38 in the lateral, longitudinal, vertical directions for pelvis and head and neck, respectively. The acquisition time for a pair of MV-topograms was up to 12.7 times less than MVCT scans (coarse scan mode) while covering longer longitudinal length.

Conclusions

MV-topograms showed equivalent clinical performance to the standard MVCT with significantly less acquisition time for pelvis and H&N patients. The MV-topogram can be used as an alternative or complimentary tool for bony landmark-based patient alignment on tomotherapy.

Uncoupling interferon signaling and antigen presentation to overcome immunotherapy resistance due to JAK1 loss in melanoma

Defects in tumor-intrinsic interferon (IFN) signaling result in failure of immune checkpoint blockade (ICB) against cancer, but these tumors may still maintain sensitivity to T cell-based adoptive cell therapy (ACT). We generated models of IFN signaling defects in B16 murine melanoma observed in patients with acquired resistance to ICB. Tumors lacking Jak1 or Jak2 did not respond to ICB, whereas ACT was effective against Jak2 KO tumors, but not Jak1 KO tumors, where both type I and II tumor IFN signaling were defective. This was a direct result of low baseline class I major histocompatibility complex (MHC I) expression in B16 and the dependency of MHC I expression on either type I or type II IFN signaling. We used genetic and pharmacologic approaches to uncouple this dependency and restore MHC I expression. Through independent mechanisms, overexpression of NLRC5 (nucleotide-binding oligomerization domain-like receptor family caspase recruitment domain containing 5) and intratumoral delivery of BO-112, a potent nanoplexed version of polyinosinic:polycytidylic acid (poly I:C), each restored the efficacy of ACT against B16-Jak1 KO tumors. BO-112 activated double-stranded RNA (dsRNA) sensing (via protein kinase R and Toll-like receptor 3) and induced MHC I expression via nuclear factor κB, independent of both IFN signaling and NLRC5. In summary, we demonstrated that in the absence of tumor IFN signaling, MHC I expression is essential and sufficient for the efficacy of ACT. For tumors lacking MHC I expression due to deficient IFN signaling, activation of dsRNA sensors by BO-112 affords an alternative approach to restore the efficacy of ACT.

Conserved Interferon-γ Signaling Drives Clinical Response to Immune Checkpoint Blockade Therapy in Melanoma

We analyze the transcriptome of baseline and on-therapy tumor biopsies from 101 patients with advanced melanoma treated with nivolumab (anti-PD-1) alone or combined with ipilimumab (anti-CTLA-4). We find that T cell infiltration and interferon-γ (IFN-γ) signaling signatures correspond most highly with clinical response to therapy, with a reciprocal decrease in cell-cycle and WNT signaling pathways in responding biopsies. We model the interaction in 58 human cell lines, where IFN-γ in vitro exposure leads to a conserved transcriptome response unless cells have IFN-γ receptor alterations. This conserved IFN-γ transcriptome response in melanoma cells serves to amplify the antitumor immune response. Therefore, the magnitude of the antitumor T cell response and the corresponding downstream IFN-γ signaling are the main drivers of clinical response or resistance to immune checkpoint blockade therapy.

Treatment effect prediction for sarcoma patients treated with preoperative radiotherapy using radiomics features from longitudinal diffusion-weighted MRIs

The objective of this study was to explore radiomics features from longitudinal diffusion-weighted MRIs (DWIs) for pathologic treatment effect prediction in patients with localized soft tissue sarcoma (STS) undergoing hypofractionated preoperative radiotherapy (RT). Thirty patients with localized STS treated with preoperative hypofractionated RT were recruited to this longitudinal imaging study. DWIs were acquired at three time points using a 0.35 T MRI-guided radiotherapy system. Treatment effect score (TES) was obtained from the post-surgery pathology as a surrogate of treatment outcome. Patients were divided into two groups based on TES. Response prediction was first performed using a support vector machine (SVM) with only mean apparent diffusion coefficient (ADC) or delta ADC to serve as the benchmark. Radiomics features were then extracted from tumor ADC maps at each of the three time points. Logistic regression and SVM were constructed to predict the TES group using features selected by univariate analysis and sequential forward selection. Classification performance using SVM with features from different time points and with or without delta radiomics were evaluated. Prediction performance using only mean ADC or delta ADC was poor (area under the curve (AUC) < 0.7). For the radiomics study using features from all time points and corresponding delta radiomics, SVM significantly outperformed logistic regression (AUC of 0.91 ± 0.05 v.s. 0.85 ± 0.06). Prediction AUC values using single or multiple time points without delta radiomics were all below 0.74. Including delta radiomics of mid- or post-treatment relative to the baseline drastically boosted the prediction. In this work, an SVM model was built to predict the TES using radiomics features from longitudinal DWI. Based on this study, we found that use of mean ADC, delta ADC, or radiomics features alone was not sufficient for response prediction, and including delta radiomics features of mid- or post-treatment relative to the baseline can optimize the prediction of TES, a pathologic and clinical endpoint.

Abstract 3166: The degree of conserved interferon gamma signaling guides response to immune checkpoint blockade therapy

The long-lasting responses to immune blockade therapy in a subset of patients with melanoma remain largely unexplained. We assessed baseline and on-therapy biopsies from 118 patients with advanced melanoma treated with the anti-PD-1 antibody nivolumab alone (N = 82) or in combination with the anti-CTLA-4 antibody ipilimumab (N = 36) (CheckMate 038 study). There were 46 progressive disease (PD) cases, 26 stable disease (SD) cases, and 46 complete or partial response (CRPR) cases. Tumors were analyzed by RNA sequencing. RNAseq bulk immune cell deconvolution revealed that the largest immune cell change on-treatment was an increase in CD8+ T cell infiltration for patients regardless of treatment or clinical response (P &lt; 0.04, 0.02, 2e-4 for PD, SD, CRPR). In CRPR, there was a corresponding increase in CD4+ T cells (P &lt; 2e-4), Tregs (P &lt; 9e-4), NK cells (P &lt; 3e-5) and macrophages (P &lt; 3e-5). Principal component analysis showed that T cell infiltration was the best organizer of the RNAseq biopsies; 3694 genes were correlated or negatively correlated with T cell infiltration.

Analysis of 58 human melanoma cell lines exposed in vitro to interferon-gamma (IFNγ) for 6 hours showed a conserved response to this cytokine in all cell lines able to signal through the IFNγ receptor (N = 46), including an increase in antigen presentation machinery, an increase in expression of IFNγ signaling molecules representing a signal amplification, and production of chemokines that attract other immune cells, while there was a decrease in cell cycle and WNT signaling pathways. These same gene sets are present in the list of genes correlated and negatively correlated with T cell infiltration in the patient data, as well as the list of genes significantly up- or down-regulated in CRPR cases. Only cell lines with JAK1 or JAK2 mutations (N = 12) did not exhibit this conserved response; in fact, these mutants had no genes with at least a 2-fold change.

Analysis of the patient biopsies using the IFNγ regulated gene sets revealed that in CRPR cases there was a large increase in HLA expression (P &lt; 0.04, 4e-3, 8e-4 for HLA-A, HLA-B, HLA-C), along with a corresponding large decrease in WNT signaling (P &lt; 3e-4), a driver of immune exclusion. We did not find genomic alterations (in the subset of cases that we exome sequenced) or gene expression differences pre-treatment to explain the greater response in the CRPR cases, including no JAK1/2 mutations. The lack of naturally occurring mutations disabling IFNγ signaling in our baseline biopsies is likely selected for by the role IFNγ plays in up-regulating PD-L1 expression necessary for establishing the anti-PD1 immune blockade. Using RNAseq immune cell deconvolution, the 36 CRPR cases (16 monotherapy, 20 combination) had significantly larger CD8+ T cell infiltration pre-treatment (P &lt; 8e-4 compared to PD cases). Therefore, our data showed that the strength of the antitumor T cell response and corresponding downstream IFNγ signaling is the main driver of response or resistance to immune checkpoint blockade therapy.

Citation Format: Catherine Grasso, Jennifer Tsoi, Mykola Onyshchenko, Gabriel Abril-Rodriguez, Ameya Champhekar, Egmidio Medina, Davis Torrejon, Daniel Shin, Michael Quist, Petra Ross-Mcdonald, Megan Wind-Rotolo, Daniel Speiser, Anusha Kalbasi, Anthony Ribas. The degree of conserved interferon gamma signaling guides response to immune checkpoint blockade therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3166.

Low Rates of Chemotherapy Use for Primary, High-Grade Soft Tissue Sarcoma: A National Cancer Database Analysis

BACKGROUND

There is conflicting evidence regarding the role of chemotherapy for high-grade soft tissue sarcoma (STS) in adults. We sought to characterize patterns of chemotherapy use, including multiagent and neoadjuvant chemotherapy, in the United States.

PATIENTS AND METHODS

Using the National Cancer Database, we identified 19,969 adult patients who underwent surgical resection for primary high-grade STS from 2004 to 2016. Using logistic regression, we examined factors associated with overall, multiagent, and neoadjuvant chemotherapy use.

RESULTS

Chemotherapy was administered to 22% (n=4,377) of the study population. Among patients treated using chemotherapy, 85% received multiagent treatment and 47% received neoadjuvant treatment. On multivariate analysis, factors associated with chemotherapy use included tumor size, depth, histology, and primary site; receipt of radiation treatment; younger age; higher patient income; and academic treatment facility. Factors associated with multiagent chemotherapy use included tumor histology, tumor primary site, and younger age. Factors associated with neoadjuvant chemotherapy use included tumor size, depth, margin status, and primary site; receipt of radiation treatment; higher patient income; academic treatment facility type; and distance to treatment facility. Treatment at a high-volume facility was the only factor associated with overall, multiagent, and neoadjuvant chemotherapy use. No significant temporal trend was seen in overall, multiagent, or neoadjuvant chemotherapy use.

CONCLUSIONS

Overall chemotherapy use was low (22%). The variability in chemotherapy use was driven by clinical, patient, demographic, and facility factors. Among patients treated with chemotherapy, the use of multiagent chemotherapy was high (85%), and nearly half received neoadjuvant therapy. There was a discrepancy in the use of chemotherapy-including neoadjuvant and multiagent chemotherapy-between high- and low-volume treatment centers.

Prioritization of SARS-CoV-2 epitopes using a pan-HLA and global population inference approach

SARS-CoV-2 T cell response assessment and vaccine development may benefit from an approach that considers the global landscape of the human leukocyte antigen (HLA) proteins. We predicted the binding affinity between 9-mer and 15-mer peptides from the SARS-CoV-2 peptidome for 9,360 class I and 8,445 class II HLA alleles, respectively. We identified 368,145 unique combinations of peptide-HLA complexes (pMHCs) with a predicted binding affinity less than 500nM, and observed significant overlap between class I and II predicted pMHCs. Using simulated populations derived from worldwide HLA frequency data, we identified sets of epitopes predicted in at least 90% of the population in 57 countries. We also developed a method to prioritize pMHCs for specific populations. Collectively, this public dataset and accessible user interface (Shiny app: https://rstudio-connect.parkerici.org/content/13/) can be used to explore the SARS-CoV-2 epitope landscape in the context of diverse HLA types across global populations.

Overcoming Genetically Based Resistance Mechanisms to PD-1 Blockade

Mechanism-based strategies to overcome resistance to PD-1 blockade therapy are urgently needed. We developed genetic acquired resistant models of JAK1, JAK2, and B2M loss-of-function mutations by gene knockout in human and murine cell lines. Human melanoma cell lines with JAK1/2 knockout became insensitive to IFN-induced antitumor effects, while B2M knockout was no longer recognized by antigen-specific T cells and hence was resistant to cytotoxicity. All of these mutations led to resistance to anti-PD-1 therapy in vivo. JAK1/2-knockout resistance could be overcome with the activation of innate and adaptive immunity by intratumoral Toll-like receptor 9 agonist administration together with anti-PD-1, mediated by natural killer (NK) and CD8 T cells. B2M-knockout resistance could be overcome by NK-cell and CD4 T-cell activation using the CD122 preferential IL2 agonist bempegaldesleukin. Therefore, mechanistically designed combination therapies can overcome genetic resistance to PD-1 blockade therapy. SIGNIFICANCE: The activation of IFN signaling through pattern recognition receptors and the stimulation of NK cells overcome genetic mechanisms of resistance to PD-1 blockade therapy mediated through deficient IFN receptor and antigen presentation pathways. These approaches are being tested in the clinic to improve the antitumor activity of PD-1 blockade therapy.This article is highlighted in the In This Issue feature, p. 1079.

How Technology Is Improving the Multidisciplinary Care of Sarcoma

Sarcomas are rare tumors but comprise a wide histologic spectrum. Advances in technology have emerged to address the biologic complexity and challenging diagnosis and treatment of this disease. The diagnostic approach to sarcomas has historically been based on morphologic features, but technologic advances in immunohistochemistry and cytogenetic/molecular testing have transformed the interdisciplinary work-up of mesenchymal neoplasms in recent years. On the therapeutic side, technologic advances in the delivery of radiation have made it a linchpin in the treatment of localized and oligometastatic sarcoma. In this review, we discuss recent advances in the pathologic diagnosis of sarcomas and discuss select sarcoma types that illustrate how newly discovered diagnostic, prognostic, and predictive biomarkers have refined existing classification schemes and substantially shaped our diagnostic approach. Such examples include conventional and epithelioid malignant peripheral nerve sheath tumors (MPNSTs), emerging entities in the group of round cell sarcomas, and other mesenchymal neoplasms with distinct cytogenetic aberrations. Recent advances in radiation oncology, including intensity-modulated, stereotactic, MRI-guided, and proton radiotherapy (RT), will be reviewed in the context of neoadjuvant or adjuvant localized soft-tissue sarcoma and oligometastatic or oligoprogressive disease. Innovations in translational research are expected to be introduced into clinical practice over the next few years and will likely continue to affect the rapidly evolving field of sarcoma diagnostics and therapy.

Tumor Size Matters-Understanding Concomitant Tumor Immunity in the Context of Hypofractionated Radiotherapy with Immunotherapy

The purpose of this study was to determine the dynamic contributions of different immune cell subsets to primary and abscopal tumor regression after hypofractionated radiation therapy (hRT) and the impact of anti-PD-1 therapy. A bilateral syngeneic FSA1 fibrosarcoma model was used in immunocompetent C3H mice, with delayed inoculation to mimic primary and microscopic disease. The effect of tumor burden on intratumoral and splenic immune cell content was delineated as a prelude to hRT on macroscopic T1 tumors with 3 fractions of 8 Gy while microscopic T2 tumors were left untreated. This was performed with and without systemic anti-PD-1. Immune profiles within T1 and T2 tumors and in spleen changed drastically with tumor burden in untreated mice with infiltrating CD4+ content declining, while the proportion of CD4+ Tregs rose. Myeloid cell representation escalated in larger tumors, resulting in major decreases in the lymphoid:myeloid ratios. In general, activation of Tregs and myeloid-derived suppressor cells allow immunogenic tumors to grow, although their relative contributions change with time. The evidence suggests that primary T1 tumors self-regulate their immune content depending on their size and this can influence the lymphoid compartment of T2 tumors, especially with respect to Tregs. Tumor burden is a major confounding factor in immune analysis that has to be taken into consideration in experimental models and in the clinic. hRT caused complete local regression of primary tumors, which was accompanied by heavy infiltration of CD8+ T cells activated to express IFN-γ and PD-1; while certain myeloid populations diminished. In spite of this active infiltrate, primary hRT failed to generate the systemic conditions required to cause abscopal regression of unirradiated microscopic tumors unless PD-1 blockade, which on its own was ineffective, was added to the RT regimen. The combination further increased local and systemically activated CD8+ T cells, but few other changes. This study emphasizes the subtle interplay between the immune system and tumors as they grow and how difficult it is for local RT, which can generate a local immune response that may help with primary tumor regression, to overcome the systemic barriers that are generated so as to effect immune regression of even small abscopal lesions.

A Phase II Trial of 5-Day Neoadjuvant Radiotherapy for Patients with High-Risk Primary Soft Tissue Sarcoma

PURPOSE

In a single-institution phase II study, we evaluated the safety of a 5-day dose-equivalent neoadjuvant radiotherapy (RT) regimen for high-risk primary soft tissue sarcoma.

PATIENTS AND METHODS

Patients received neoadjuvant RT alone (30 Gy in five fractions) to the primary tumor with standard margins. The primary endpoint was grade ≥2 late-radiation toxicity. Major wound complications, local recurrences, and distant metastases were also examined. In exploratory analysis, we evaluated germline biomarkers for wound toxicity and the effects of the study on treatment utilization.

RESULTS

Over 2 years, 52 patients were enrolled with median follow-up of 29 months. Seven of 44 evaluable patients (16%) developed grade ≥2 late toxicity. Major wound complications occurred in 16 of 50 patients (32%); a signature defined by 19 germline SNPs in miRNA-binding sites of immune and DNA damage response genes, in addition to lower extremity tumor location, demonstrated strong predictive performance for major wound complications. Compared with the preceding 2-year period, the number of patients treated with neoadjuvant RT alone at our institution increased 3-fold, with a concomitant increase in the catchment area.

CONCLUSIONS

A shorter 5-day neoadjuvant RT regimen results in favorable rates of wound complications and grade ≥2 toxicity after 2-year follow-up. Five-day RT significantly increased utilization of neoadjuvant RT at our high-volume sarcoma center. With further validation, a putative germline biomarker for wound complications may guide safer RT utilization.

Pathologic discordance in sarcomas: Prospective comparison of external and sarcoma center pathologic diagnosis

11020

Background: With more than 80 different histologic subtypes, sarcomas are a unique pathologic challenge. As therapeutic decisions have become histology-specific, obtaining an accurate pathologic diagnosis is critical in guiding treatment decisions. The aim of this study is to determine the discordance between the diagnosis rendered by an external non-specialized pathologist and pathologic re-review by a specialized sarcoma pathologist at a high-volume sarcoma center. Methods: Patients who presented at the UCLA Multidisciplinary Sarcoma Conference (MSC) in 2017 that had a pathologic diagnosis from an outside facility were included in this study. All specimens underwent pathologic re-review at UCLA by an experienced sarcoma pathologist. The pathology was classified as concordant (identical diagnoses), minor discordance (difference with minor impact on prognosis/therapy) and major discordance (difference with significant impact on prognosis/therapy). Results: 1350 patients were presented at the UCLA MSC in 2017. Of the 635 new patients, 196 presented with an outside pathologic diagnosis and underwent pathologic re-review at UCLA. 44% (n = 87) were concordant, 22% (n = 43) had minor discordance, and 34% (n = 66) had major discordance. Major discordance included substantial discrepancies in histologic subtype (n = 24, 36%), benign/malignant mismatch (n = 23, 35%), diagnostic from non-diagnostic (n = 12, 18%) and major grading discrepancy (n = 7, 11%). Major discordance was most often seen in biopsies [needle (n = 27, 32%), incisional (n = 30, 44%)] as compared to resection (n = 9, 21%). Conclusions: 56% of external non-specialized sarcoma pathologic diagnoses were discordant from specialized sarcoma pathologist review, 34% of which were major discordances. Pathologic re-review of a presumed sarcoma by a specialized sarcoma pathologist is critical for both patient care and investigational studies. [Table: see text]

Overcoming genetically based resistance mechanisms to PD-1 blockade

2584

Background: Mechanism-based strategies to overcome resistance to anti-PD1 therapy are urgently needed. Using CRISPR/Cas9 genome editing tools, we developed acquired resistant models through JAK1/2 and B2M loss of function (LoF) mutations in human melanoma cell lines and in the murine MC38 colon carcinoma, known for high mutational load and good response to anti-PD-1. We hypothesized that the downstream activation of the IFN-receptor pathway or the activation of natural killer (NK) cells would overcome this resistance. Methods: We studied signaling changes in four human cell lines (parental and LoFs) exposed to IFN-gamma using RNAseq. In addition, we analyzed the in-vivo antitumor activity in MC38 variants with anti-PD1 and characterized the tumor microenvironment using mass cytometry (CyTOF). Finally, we tested strategies to overcome resistance mechanisms with SD-101 (TLR-9 agonist) and bempegaldesleukin (NKTR-214, CD-122 biased agonist) with the extent of CD8 and NK1.1 depletion. Results: RNAseq differential gene expression analysis showed that the IFN-gamma induced increased expression of antigen presenting machinery, IFN-gamma signaling and chemokines (CXCL9/10) was lost in JAK1/2-LoF human melanoma cell lines. The significant antitumor activity of anti-PD-1 against MC38 parental cell line was lost in JAK1/2 and B2M LoF sublines, and CyTOF analysis revealed that anti-PD-1 therapy was unable to increase tumor CD8+ T-effectors in these LoF tumors. The intratumoral administration of SD-101 (50 μg/injection q4dx3wks) was able to overcome local resistance even in non-injected sites in JAK1/2 and IFNAR-type-I LoF tumors, and systemic administration of bempegaldesleukin (0.8 mg/kg, q9dx2, i.v.) was able to overcome resistance in B2M LoF with significantly increased survival (Table). Depletion studies showed complete abrogation of anti-tumor response with anti-NK1.1 in JAK1 LoF and B2M LoF, and partial abrogation with anti-NK1.1 or anti-CD8 in JAK2 LoF tumors. Conclusions: Even in the extreme setting of genetic resistance to PD-1 blockade by JAK1/2 LoF, resistance can be overcome by SD-101, a TLR9 agonist, while resistance of B2M LoF can be overcome by bempegaldesleukin (NKTR-214), a CD-122 biased agonist. Our findings support the testing of these rational mechanistic strategies in patients with a-PD1 resistance. [Table: see text]

Retrospective analysis of adjuvant treatment for localized, operable uterine leiomyosarcoma

11072

Background: Surgery is the standard of care for uterine leiomyosarcoma, but recurrence rates are high and outcomes are poor. Standard adjuvant treatment of localized uterine leiomyosarcoma(uLMS) has not yet been established as clinical trials to address this question have been small or hindered by slow accrual. Methods: We reviewed the medical records of patients with uLMS who underwent upfront surgery between 2000-2018. We evaluated the clinical characteristics and adjuvant therapy on outcomes. Patient characteristics and treatment outcomes were described using descriptive statistics. Kaplan-Meier survival analysis was used for DFS. Cox proportional hazard regression was used to compare difference between groups. Results: 59 patients with a median age of 52 years were analyzed and the median time from surgery to adjuvant treatment was 47 days. 48/59 (81.4%) underwent TAH-BSO. 64.4% were FIGO stage I, 16.9% were stage II and 6.7% were stage III. The median tumor size was 11 cm (range: 3-21cm) and the median mitotic rate was 13 mitoses/ 10 high-power fields (HPF), (range: 1-63). 34/59 (57.6%) of patients received adjuvant chemotherapy +/- radiation therapy and 25 patients (42.3%) did not receive adjuvant treatment. With a median follow-up time of 42.8 months, 42 patients (71.2%) had disease relapse and 15 (35.7%) had pulmonary metastases. The median disease-free survival (mDFS) for all patients was 23.1 months. Any adjuvant treatment (chemotherapy or radiation) had a trend toward longer mDFS than no adjuvant treatment (36.6 vs 13.6 months, p = 0.14). Patients who had adjuvant chemotherapy had a non-significant longer mDFS compared to who did not receive any adjuvant treatment (33.8 vs 13.6 months, p = 0.18). Patients with stage I disease had trend towards higher mDFS in the chemotherapy group, it was not statistically significant (29.7 vs 16.6 months, p = 0.59). Multivariate analysis found that the independent prognostic factors for worse DFS included tumor size larger than 10 cm, and mitotic rate over 10/ 10HPF. More morcellated specimens were found in non-adjuvant treatment arm (36%) compare to 8% in adjuvant arm. In the non-treatment arm, 14 patients had recurrences within 6 months. Conclusions: In a retrospective uLMS population, the mDFS was 23.1 months. Tumor size > 10cm and mitotic rate > 10/10 HPF were independent prognostic factors for lower DFS. The non-treatment group had a significantly higher number of patient with morcellization and relapsed within 6 months, confounding analyses of the impact of adjuvant chemotherapy.

Interleukin 32 expression in human melanoma

Background

Various proinflammatory cytokines can be detected within the melanoma tumor microenvironment. Interleukin 32 (IL32) is produced by T cells, NK cells and monocytes/macrophages, but also by a subset of melanoma cells. We sought to better understand the biology of IL32 in human melanoma.

Methods

We analyzed RNA sequencing data from 53 in-house established human melanoma cell lines and 479 melanoma tumors from The Cancer Genome Atlas dataset. We evaluated global gene expression patterns associated with IL32 expression. We also evaluated the impact of proinflammatory molecules TNFα and IFNγ on IL32 expression and dedifferentiation in melanoma cell lines in vitro. In order to study the transcriptional regulation of IL32 in these cell lines, we cloned up to 10.5 kb of the 5′ upstream region of the human IL32 gene into a luciferase reporter vector.

Results

A significant proportion of established human melanoma cell lines express IL32, with its expression being highly correlated with a dedifferentiation genetic signature (high AXL/low MITF). Non IL32-expressing differentiated melanoma cell lines exposed to TNFα or IFNγ can be induced to express the three predominant isoforms (α, β, γ) of IL32. Cis-acting elements within this 5′ upstream region of the human IL32 gene appear to govern both induced and constitutive gene expression. In the tumor microenvironment, IL32 expression is highly correlated with genes related to T cell infiltration, and also positively correlates with high AXL/low MITF dedifferentiated gene signature.

Conclusions

Expression of IL32 in human melanoma can be induced by TNFα or IFNγ and correlates with a treatment-resistant dedifferentiated genetic signature. Constitutive and induced expression are regulated, in part, by cis-acting sequences within the 5′ upstream region.

Electronic supplementary material

The online version of this article (10.1186/s12967-019-1862-y) contains supplementary material, which is available to authorized users.

A Pilot Trial of the Combination of Transgenic NY-ESO-1-reactive Adoptive Cellular Therapy with Dendritic Cell Vaccination with or without Ipilimumab

PURPOSE

Transgenic adoptive cell therapy (ACT) targeting the tumor antigen NY-ESO-1 can be effective for the treatment of sarcoma and melanoma. Preclinical models have shown that this therapy can be improved with the addition of dendritic cell (DC) vaccination and immune checkpoint blockade. We studied the safety, feasibility, and antitumor efficacy of transgenic ACT with DC vaccination, with and without CTLA-4 blockade with ipilimumab.

PATIENTS AND METHODS

Freshly prepared autologous NY-ESO-1-specific T-cell receptor (TCR) transgenic lymphocytes were adoptively transferred together with NY-ESO-1 peptide-pulsed DC vaccination in HLA-A2.1-positive subjects alone (ESO, NCT02070406) or with ipilimumab (INY, NCT01697527) in patients with advanced sarcoma or melanoma.

RESULTS

Six patients were enrolled in the ESO cohort, and four were enrolled in the INY cohort. Four out of six patients treated per ESO (66%), and two out of four patients treated per INY (50%) displayed evidence of tumor regression. Peripheral blood reconstitution with NY-ESO-1-specific T cells peaked within 2 weeks of ACT, indicating rapid in vivo expansion. Tracking of transgenic T cells to the tumor sites was demonstrated in on-treatment biopsies via TCR sequencing. Multiparametric mass cytometry of transgenic cells demonstrated shifting of transgenic cells from memory phenotypes to more terminally differentiated effector phenotypes over time.

CONCLUSIONS

ACT of fresh NY-ESO-1 transgenic T cells prepared via a short ex vivo protocol and given with DC vaccination, with or without ipilimumab, is feasible and results in transient antitumor activity, with no apparent clinical benefit of the addition of ipilimumab. Improvements are needed to maintain tumor responses.

A germline microRNA-based biomarker signature of immune-associated toxicity to anti-PD1/PDL1 therapy

96

Background: Treatment with anti-PD1/anti-PDL1 agents is associated with toxicity termed immune related adverse events (iRAEs). While the prevalence of Grade 2 and higher iRAEs is approximately 25-30%, biomarkers have not been previously identified. We tested the hypothesis that functional, germ-line mutations would predict iRAEs. Methods: Four classifiers were trained on a set of 61 melanoma patients evaluated for toxicity and response. Subjects were classified as experiencing high toxicity (≥ Grade 2) vs low toxicity (< Grade 2). Performance of the classifiers was tested on a validation set of 89 cancer patients with a variety of cancer types, with the most common being GU and NSCLC. Classifiers were built for each treatment of marker data including classification trees, LASSO-regularized logistic regression, boosted trees (BT), and random forests. The final performance measures, accuracy, specificity, sensitivity, negative predictive value, positive predictive value, area under the curve (AUC), and F1 score, were reported on the categorical treatment of the training data using leave-one-out cross validation on the validation data. We also evaluated the association between our most significant toxicity biomarker and response to anti-PD1/PDL1 therapy. Results: Within the melanoma training sample, we found a biomarker signature where toxicity is predicted with 79.0% accuracy (F1 = .714, AUC = .827) using BT. The same biomarker panel also accurately predicted toxicity in the validation cohort with 85.6% accuracy (F1 = .760, AUC = .883). Of the most predictive biomarkers, three were in microRNA binding sites in RAC1, CD274, and KRAS, two in immune related genes IL2RA and FCGR2A, and one in the DNA repair gene ATM. Our most significant biomarker in RAC1 did not predict response to anti-PD1/PDL1 treatment (p=0.91). Conclusions: We have identified a germ-line biomarker signature which predicts Grade 2 or higher iRAEs for patients treated with anti-PD1/anti-PDL1 therapy, regardless of cancer type, and does not predict an increased likelihood of response to these therapies. These findings are an important step in defining how to better safely personalize immune therapy, whose use is growing rapidly.

SD-101 in Combination with Pembrolizumab in Advanced Melanoma: Results of a Phase Ib, Multicenter Study

PD-1 inhibitors are approved for treating advanced melanoma, but resistance has been observed. This phase Ib trial evaluated intratumoral SD-101, a synthetic CpG oligonucleotide that stimulates Toll-like receptor 9 (TLR9), in combination with pembrolizumab in patients with unresectable or metastatic malignant melanoma. The most common adverse events related to SD-101 were injection-site reactions and transient, mild-to-moderate "flu-like" symptoms. Among the 9 patients naïve to anti-PD-1 therapy, the overall response rate (ORR) was 78%. The estimated 12-month progression-free survival rate was 88%, and the overall survival rate was 89%. Among 13 patients having prior anti-PD-1 therapy, the ORR was 15%. RNA profiling of tumor biopsies demonstrated increased CD8⁺ T cells, natural killer cells, cytotoxic cells, dendritic cells, and B cells. The combination of intratumoral SD-101 and pembrolizumab was well tolerated and induced broad immune activation in the tumor microenvironment with durable tumor responses in both peripheral and visceral lesions.Significance: These early data demonstrate that the combination of pembrolizumab with intratumoral SD-101 is well tolerated and can induce immune activation at the tumor site. Combining an intratumoral TLR9 innate immune stimulant with PD-1 blockade can potentially increase clinical efficacy with minimal additional toxicity relative to PD-1 blockade alone. Cancer Discov; 8(10); 1250-7. ©2018 AACR. This article is highlighted in the In This Issue feature, p. 1195.

Antigen Presentation Keeps Trending in Immunotherapy Resistance

Through a gain-of-function kinome screen, MEX3B was identified as a mediator of resistance to T-cell immunotherapy not previously identified using CRISPR-based screens. MEX3B is a posttranscriptional regulator of HLA-A, validating the critical role of tumor-intrinsic antigen presentation in T-cell immunotherapy and indicating a new putative molecular target. Clin Cancer Res; 24(14); 3239-41. ©2018 AACRSee related article by Huang et al., p. 3366.