Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma

Immune checkpoint blockade (CPB) improves melanoma outcomes, but many patients still do not respond. Tumor mutational burden (TMB) and tumor-infiltrating T cells are associated with response, and integrative models improve survival prediction. However, integrating immune/tumor-intrinsic features using data from a single assay (DNA/RNA) remains underexplored. Here, we analyze whole-exome and bulk RNA sequencing of tumors from new and published cohorts of 189 and 178 patients with melanoma receiving CPB, respectively. Using DNA, we calculate T cell and B cell burdens (TCB/BCB) from rearranged TCR/Ig sequences and find that patients with TMBhigh and TCBhigh or BCBhigh have improved outcomes compared to other patients. By combining pairs of immune- and tumor-expressed genes, we identify three gene pairs associated with response and survival, which validate in independent cohorts. The top model includes lymphocyte-expressed MAP4K1 and tumor-expressed TBX3. Overall, RNA or DNA-based models combining immune and tumor measures improve predictions of melanoma CPB outcomes.

Abstract 6670: Combined signals from tumor and immune cells predict outcomes of checkpoint inhibition in melanoma

Cancer immunotherapy with checkpoint blockade has improved survival and outcomes in melanoma, but still a majority of patients do not respond. Both high tumor mutation burden (TMB) and high T cell infiltration have been associated with response, but integrative models based on DNA or RNA assays have not been comprehensively explored and validated. Focusing on melanomas from patients receiving checkpoint blockade, we generated new and aggregated existing datasets of whole exome sequencing (WES) (n = 189 total) and bulk RNA sequencing (n = 154 total) to derive genomic and transcriptomic factors that predict survival and response to immunotherapy in melanoma.

We quantified T and B cell infiltrates using rearranged T cell receptor (TCR) and immunoglobulin (Ig) sequences, respectively, from DNA or RNA sequencing. High levels of rearranged TCR reads or rearranged Ig reads in RNA-seq were associated with survival (P = 0.0046, P = 0.015) and response (P = 0.0034, P = 0.047). We created RNA-based metrics of T and B cell burden (TCBRNA or BCBRNA) by normalizing the number of rearranged TCR reads by the total number of mapped reads. When we analyzed WES data in patients for whom DNA and RNA were extracted from the same region, we found that the TCBDNA correlated with TCBRNA (rho = 0.73) and BCBDNA with BCBRNA (rho = 0.41), demonstrating that the level of lymphocyte infiltration can be estimated using rearranged TCR or Ig reads from tumor WES alone.

We found that TCBDNA and BCBDNA both associated with survival (P = 0.0023 and 0.0089). In a combined model, patients with high TMB and high TCB DNA survived longer (P = 2.4e-4, HR = 2.68) and had a higher response rate (Fisher P = 0.028). This combined model was superior to models with TMB or TCBDNA alone. Similarly, patients with high TMB and high BCBDNA had longer survival and higher response rates (log-rank P = 0.0029, HR = 2.64, Fisher P = 0.015). We reanalyzed stage III/IV melanomas from TCGA and found that the TMB high, TCBDNA high subgroup had increased survival (P = 0.007).

Next, clustering of tumor transcriptomes identified 5 tumor subtypes based on melanocyte differentiation, immune infiltration and keratin levels. These melanoma subtypes were associated with survival outcomes after immunotherapy (P = 0.019). We found that TBX3, a tumor-expressed transcription factor enriched in poorly differentiated melanomas, was over-expressed among non-responders within the immune-infiltrated subtype and among all patients (P = 3.9e-4, P = 8.7e-5). Patients whose tumors had high immune infiltrate and low expression of TBX3 had longer survival (P = 1.6e-5, HR = 3.39), however this subgroup did not have longer survival in an independent cohort (n = 73, P = 0.10, HR = 2.63). In conclusion, we demonstrate both RNA-based (immune infiltrate and tumor subtype) and DNA-based metrics (TMB/TCB or TMB/BCB) can be used as pre-treatment predictors of survival after checkpoint blockade in melanoma.

Citation Format: Samuel S. Freeman, Moshe Sade-Feldman, Jaegil Kim, Chip Stewart, Arvind Ravi, Monica Arniella, Keren Yizhak, Ignaty Leshchiner, Liudmila Elagina, Oliver Spiro, Dimitri Livitz, Daniel Rosebrock, François Aguet, Jian Carrot-Zhang, Anna Gonye, Gavin Ha, Ziao Lin, Jonathan H. Chen, Dennie T. Frederick, Michal Barzily-Rokni, Marc R. Hammond, Hans Vitzthum, Shauna M. Blackmon, Yunxin J. Jiao, Donald P. Lawrence, Lyn M. Duncan, Anat Stemmer-Rachamimov, Jennifer A. Wargo, Keith T. Flaherty, Genevieve M. Boland, Ryan J. Sullivan, Matthew Meyerson, Gad Getz, Nir Hacohen. Combined signals from tumor and immune cells predict outcomes of checkpoint inhibition in melanoma [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 6670.

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

Treatment of cancer has been revolutionized by immune checkpoint blockade therapies. Despite the high rate of response in advanced melanoma, the majority of patients succumb to disease. To identify factors associated with success or failure of checkpoint therapy, we profiled transcriptomes of 16,291 individual immune cells from 48 tumor samples of melanoma patients treated with checkpoint inhibitors. Two distinct states of CD8+ T cells were defined by clustering and associated with patient tumor regression or progression. A single transcription factor, TCF7, was visualized within CD8+ T cells in fixed tumor samples and predicted positive clinical outcome in an independent cohort of checkpoint-treated patients. We delineated the epigenetic landscape and clonality of these T cell states and demonstrated enhanced antitumor immunity by targeting novel combinations of factors in exhausted cells. Our study of immune cell transcriptomes from tumors demonstrates a strategy for identifying predictors, mechanisms, and targets for enhancing checkpoint immunotherapy.

Resistance to checkpoint blockade therapy through inactivation of antigen presentation

Treatment with immune checkpoint blockade (CPB) therapies often leads to prolonged responses in patients with metastatic melanoma, but the common mechanisms of primary and acquired resistance to these agents remain incompletely characterized and have yet to be validated in large cohorts. By analyzing longitudinal tumor biopsies from 17 metastatic melanoma patients treated with CPB therapies, we observed point mutations, deletions or loss of heterozygosity (LOH) in beta-2-microglobulin (B2M), an essential component of MHC class I antigen presentation, in 29.4% of patients with progressing disease. In two independent cohorts of melanoma patients treated with anti-CTLA4 and anti-PD1, respectively, we find that B2M LOH is enriched threefold in non-responders (~30%) compared to responders (~10%) and associated with poorer overall survival. Loss of both copies of B2M is found only in non-responders. B2M loss is likely a common mechanism of resistance to therapies targeting CTLA4 or PD1.

Abstract LB-C05: Early exosome mRNA changes are associated with improved progression free survival of metastatic melanoma patents on ipilimumab: Identification of a novel exosome mRNA signature of ipilimumab response

Background: The recent approval of several new targeted therapies for metastatic melanoma (including ipilimumab, an anti-CTLA-4 therapy) has introduced a new challenge for physicians to determine which drug(s) provide the most benefit to an individual patient. More effective strategies using blood or tissue biomarkers to identify patients who are responding (or not responding) to a particular therapy are needed.

Exosomes are abundantly released from tumors into biofluids such as plasma and carry nucleic acids and proteins from the cell of origin. This enables a non-invasive way to monitor a patient's tumor status in real-time. However, despite the many advantages of a liquid biopsy over traditional and invasive biopsy of primary tumors, there are challenges. Specifically, a biofluid-based cancer test for a tumor-specific exosome signature must be identified against a background of exosomes originating from non-malignant cells.

Here we set out to identify early changes in exosome mRNA that predict six month progression free survival (PFS) of metastatic melanoma patients treated with ipilimumab. To facilitate the identification of gene changes related to ipilimumab treatment, we examined exosome mRNA from patient plasma with and without exclusion of non-tumor exosomes. We predicted that depletion of normal reticulocyte exosomes using an anti-glycophorin A platform would enrich tumor-derived exosomes in plasma and reveal rapid exosome mRNA changes between baseline and week 2 or week 4 of treatment.

Methods: Plasma was obtained from 17 patients with metastatic melanoma before receiving ipilimumab (baseline) and longitudinally throughout treatment. Response to therapy was determined by RECIST. Patients who achieved at least six months PFS from start of ipilimumab (n = 7) were compared to patients with progressed disease (PD) on ipilimumab (n = 10).

Matched patient plasma samples at baseline and week 2 or week 4 were analyzed. The plasma exosome mRNA signature using the glycophorin A exclusion method was compared with total plasma exosome mRNA from the same patient samples. Analysis of exosomal mRNA utilized the OpenArray® Human Inflammation Panel. Fold change in gene expression between baseline and week 2 or 4 was calculated.

Results: Targeting glycophorin A to remove normal reticulocyte exosomes from plasma enriched the RNA profile compared to total exosome profiling. Of the 587 genes examined, the exclusion platform revealed 28 genes that were significantly increased between baseline and 2-4 weeks in the majority of patients who went on to achieve 6 month PFS, and decreased in patients with PD. This signature included immune-related genes such as CCR5, INFAR1, LTB, MALT1 and TNFSF8. In contrast, the exosome mRNA signature without the exclusion platform revealed only four genes that changed between baseline and week 2 or 4: A2M, CD163, TLR1 and TNFSF10.

Conclusions: We have developed a platform to exclude normal exosomes from plasma which increases the power to discriminate early exosome mRNA changes associated with improved progression free survival in metastatic melanoma patients in response to ipilimumab. Future work will focus on refining and validating the mRNA signature.

Citation Format: Christine M. Coticchia, Ryan J. Sullivan, Keith T. Flaherty, James D. Hurley, Lan Hu, Shauna M. Blackmon, Graham Brock, Vincent T. O'Neill, Johan Skog. Early exosome mRNA changes are associated with improved progression free survival of metastatic melanoma patents on ipilimumab: Identification of a novel exosome mRNA signature of ipilimumab response. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr LB-C05.

Palliative care and hospice use among melanoma patients treated with immunotherapy

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Background: PD-1/PD-L1 inhibitors (PD-1/PD-L1i) have revolutionized the treatment of patients with metastatic melanoma. However, little is known about the supportive care needs and use of palliative care (PC) services in these patients. We sought to assess rates and correlates of PC consultation and hospice use among melanoma patients treated with PD-1/PD-L1i. Methods: We retrospectively collected data on all patients with melanoma treated with PD-1/PD-L1i at the Massachusetts General Hospital (MGH) from May 2009 to March 2015. We determined rates of PC consultation and hospice use in this sample. We used logistic regression with purposeful selection of covariates to identify correlates of PC consultation. Results: Of 122 patients treated at MGH (mean age = 61.2 years), most were married (n = 91, 75%) and college educated (n = 66, 54%). Overall, 83 patients (68%) experienced autoimmune toxicities, 22 (18%) had liver metastases, 87 (71%) had cancer progression and 44 (36%) died during our study period. We found that 36 patients (30%) received PC consultation during their treatment course; 9 (25%) of these occurred over 6 months prior to the patients’ death, and 11 (31%) in their last month of life. Among the patients who died, 36 (82%) received hospice services, and 11 (31%) enrolled in hospice during their last week of life. In our regression model, younger age, having cancer progression and presence of liver metastases correlated with increased likelihood of receiving PC consultation. Conclusions: Melanoma patients treated with immunotherapy often receive PC and hospice services late in their treatment course. These data underscore the difficulty understanding when to involve hospice and PC for these patients, and highlight the need for further PC research in this patient population. Additionally, younger age, presence of cancer progression and liver metastases were associated with receiving PC consultation, thus suggesting the need for integrated PC services among certain subpopulations of these patients. [Table: see text]

Dispase facilitates posterior vitreous detachment during vitrectomy in young pigs

PURPOSE

To evaluate the role of intravitreal dispase in conjunction with pars plana vitrectomy to facilitate the creation of a posterior vitreous detachment (PVD) in young pig eyes.

METHODS

Twenty-four eyes of 24 animals were randomized to receive an intravitreal injection of dispase (50 microg/0.05 mL) or phosphate buffered saline (PBS) immediately after core vitrectomy and before attempted creation of a posterior cortical vitreous detachment. Following a 15-minute waiting period, surgical creation of a posterior vitreous separation was attempted by aspiration of the posterior vitreous immediately adjacent to the optic disk. Eyes were evaluated postoperatively by clinical examination (1, 4, and 8 weeks) and electroretinography (4 and 8 weeks), after which they were enucleated for light, scanning, and transmission electron microscopy.

RESULTS

Based on intraoperative findings and postoperative scanning electron microscopy, eyes receiving intravitreal dispase exhibited a higher incidence of PVD compared to eyes receiving PBS (P = 0.029). Electroretinographic responses recorded at postoperative weeks 4 and 8 were similar in both dispase and PBS eyes compared to the unoperated fellow eyes. Clinical examinations, including indirect ophthalmoscopy, were indistinguishable between the PBS eyes and 11 of 12 eyes in the dispase group. Light and transmission electron microscopy demonstrated no differences in the retina between the dispase eyes and the PBS operated controls.

CONCLUSION

Dispase is a useful adjunct in facilitating surgical creation of a PVDin young pig eyes.

Early loss of synaptic protein PSD-95 from rod terminals of rhodopsin P347L transgenic porcine retina

Retinitis pigmentosa (RP), a type of retinal degeneration involving first rod and then slow cone photoreceptor degeneration, can be caused by any of a number of mutations in different genes. In the cases of mutations affecting rod-specific genes such as rhodopsin, it is unclear how the mutations may cause degeneration of cones. We have used the porcine retina, which is rod-dominated and has an abundance of cones, to study the mutation-induced changes in both rod and cone photoreceptors. Like patients with the same mutation, rhodopsin P347L transgenic swine manifest rod-cone degeneration. In addition, the rod bipolar cells fail to form synaptic connections with rods; instead, they form ectopic synapses with cones. The mechanisms that prevent the formation of the rod-rod bipolar cell synaptic connection are not known. We used specific antibodies and immunocytochemistry to show that the synaptic protein, PSD-95, is present in both normal and transgenic porcine retinas. During neonatal development, however, PSD-95 is lost from rod terminals in the transgenic swine. This loss is virtually complete (90%) by postnatal day 5, at a time when greater than 80% of rod cell bodies still remain. Furthermore, the remaining rods retain their outer segments and their gross morphology appears relatively normal. In contrast, PSD-95 expression continues in cone terminals, even in 10-month-old transgenic swine, where the rods have all disappeared and the cones show signs of severe degeneration. These results suggest that loss of PSD-95 may not be a general consequence of the deteriorating cell. Rather, the very early and selective loss of PSD-95 from the rod terminals may be causally related to the absence of rod-rod bipolar cell synapses in the rhodopsin P347L transgenic retina.