scholarly journals Intron retention as a novel source of cancer neoantigens

2018 ◽  
Author(s):  
Alicia C. Smart ◽  
Claire A. Margolis ◽  
Harold Pimentel ◽  
Meng Xiao He ◽  
Diana Miao ◽  
...  
Keyword(s):  
Cancer Vaccine ◽  
Immune Checkpoint ◽  
Vaccine Development ◽  
Intron Retention ◽  
Immune Checkpoint Blockade ◽  
Checkpoint Blockade ◽  
Sequencing Data ◽  
Transcriptional Dysregulation ◽  
Retained Intron ◽  
Personalized Cancer

Personalized cancer vaccine strategies directed at tumor neoantigens derived from somatic mutations in the DNA are currently under prospective evaluation1, 2. Alterations in tumor RNA, rather than DNA, may also represent a previously-unexplored source of neoantigens. Here, we show that intron retention, a widespread feature of cancer transcriptomes3, 4, represents a novel source of tumor neoantigens. We developed an in silico approach to identify retained intron neoantigens from RNA sequencing data and applied this methodology to tumor samples from patients with melanoma treated with immune checkpoint blockade5, 6, discovering that the retained intron neoantigen burden in these samples augments the DNA-derived, somatic neoantigen burden. We validated the existence of retained intron derived neoantigens by implementing this technique on cancer cell lines with mass spectrometry-derived immunopeptidome data7, 8, revealing that retained intron neoantigens were complexed with MHC I experimentally. Unexpectedly, we observed a trend toward lack of clinical benefit from immune checkpoint blockade in high retained intron load-tumors, which harbored transcriptional signatures consistent with cell cycle dysregulation and DNA damage repair. Our results demonstrate the contribution of transcriptional dysregulation to the overall burden of tumor neoantigens, provide a foundation for augmenting personalized cancer vaccine development with a new class of tumor neoantigens, and demonstrate how global transcriptional dysregulation may impact selective response to immune checkpoint blockade.Statement of significanceWe developed and experimentally validated a computational pipeline to identify a novel class of tumor neoantigens derived from RNA-based intron retention, which is prevalent throughout cancer transcriptomes. The discovery of transcriptionally-derived tumor neoantigens expands the tumor immunopeptidome and contributes potential substrates for personalized cancer vaccine development.

The prognostic and predictive implications of the 12-chemokine score in muscle invasive bladder cancer.

2021 ◽  
Vol 39 (6_suppl) ◽  
pp. 466-466
Author(s):  
Logan Zemp ◽  
Anders E. Berglund ◽  
Jasreman Dhillon ◽  
Ryan Putney ◽  
Youngchul Kim ◽  
...  
Keyword(s):  
Overall Survival ◽  
Bladder Cancer ◽  
Immune Checkpoint ◽  
Immune Cell ◽  
Progression Free Survival ◽  
Immune Checkpoint Blockade ◽  
Checkpoint Blockade ◽  
Sequencing Data ◽  
Lymphoid Aggregate ◽  
Type Iii

466 Background: Adaptive anti-tumor immunity can be orchestrated by lymph node-like immune cell aggregates within the tumor microenvironment (TME) called tertiary lymphoid structures (TLSs). TLSs are postulated to be the gateway of lymphocyte infiltration into the TME, and are privileged sites for coordinated tumor antigen presentation and lymphocyte priming, differentiation, and proliferation, leading to a robust tumor-specific immune response. A 12-chemokine metagene grouping (12-CK score) has previously been described that correlates with the presence of TLSs in other solid tumor types. In this study, we explored the prognostic implication of the 12-CK score in bladder cancer and its correlation with the presence of TLSs. Methods: Cystectomy specimens from 132 patients with bladder cancer were arrayed on Affymetrix microarrays. 12-CK scores were normalized with > 1 denoting high scores (12-CKHi). Immunohistochemistry (IHC) antibody staining was performed for DC-LAMP, CD20, CD4, and CD8. A GU pathologist scored TLSs into Types I-III, with type III representing fully developed TLSs. The Fisher’s exact test was used to test the associations between the 12-CK scores and the type of lymphoid aggregate. Overall survival was estimated using the Kaplan Meier method. Findings were validated using 12-CK scores extracted from TCGA transcriptome sequencing data and the IMvigor210CoreBiologies package. Results: Twenty-five (n = 25) patients had 12CK scores > 1 and were classified as 12CK-High. Pathologic review of 43 bladder tumor specimens confirmed higher levels of Type III TLS patients (33% vs. 9%, p = 0.03), B cells (p = 0.002), CD8 T cells (p = 0.01), and activated DC (p = 0.01) in 12-CKHi compared to 12-CKLo. 12-CKHi was found to have a progression-free survival (PFS, HR 0.29, p = 0.003, Fig1a), disease specific survival (DSS, HR 0.29, p = 0.004, Fig1b), and overall survival (OS, HR 0.55, p = 0.03, fig1c) advantage compared to 12-CKLo in the Moffitt patient cohort. These results were validated using the publically available RNA expression data from TCGA. TCGA patients with 12-CKHi (18%,n = 72) had improved PFS ( HR 0.55, p = 0.007, fig1d), DSS (HR = 0.40, p = 0.002, fig1e), and 0S (HR = 0.59, p = 0.01, fig1f). From the IMVIGOR-210 patient who were 12-CKHi were more likely to have a complete response (p < 0.05, fig1g) and have a 11.2mo OS benefit (fig1h) after treatment using atezolizumab. Conclusions: Three important findings emerged from the current study: 12CK-High scores corresponded with formation of TLS in the TME; favorable prognosis in surgically treated MIBC patients; and CR in atezolizumab-treated patients. The findings herein suggest the 12CK gene signature to be a clinically actable biomarker for predicting response to immune checkpoint blockade. We believe the 12CK signature may serve as an important tool to refine patient selection for immune checkpoint blockade treatment.

scholarly journals Enhanced Antitumor Response to Immune Checkpoint Blockade Exerted by Cisplatin-Induced Mutagenesis in a Murine Melanoma Model

2021 ◽  
Vol 11 ◽  
Author(s):  
Falih M. Gorgun ◽  
Steven G. Widen ◽  
Douglas S. Tyler ◽  
Ella W. Englander
Keyword(s):  
Immune Cells ◽  
Immune Checkpoint ◽  
Tumor Regression ◽  
Ex Vivo ◽  
Immune Surveillance ◽  
Immune Checkpoint Blockade ◽  
Checkpoint Blockade ◽  
Sequencing Data ◽  
Melanoma Model

Sequencing data from different types of cancers including melanomas demonstrate that tumors with high mutational loads are more likely to respond to immune checkpoint blockade (ICB) therapies. We have previously shown that low-dose intratumoral injection of the chemotherapeutic DNA damaging drug cisplatin activates intrinsic mutagenic DNA damage tolerance pathway, and when combined with ICB regimen leads to tumor regression in the mouse YUMM1.7 melanoma model. We now report that tumors generated with an in vitro cisplatin-mutagenized YUMM1.7 clone (YUMM1.7-CM) regress in response to ICB, while an identical ICB regimen alone fails to suppress growth of tumors generated with the parental YUMM1.7 cells. Regressing YUMM1.7-CM tumors show greater infiltration of CD8 T lymphocytes, higher granzyme B expression, and higher tumoral cell death. Similarly, ex-vivo, immune cells isolated from YUMM1.7-CM tumors-draining lymph nodes (TDLNs) co-incubated with cultured YUMM1.7-CM cells, eliminate the tumor cells more efficiently than immune cells isolated from TDLNs of YUMM1.7 tumor-bearing mice. Collectively, our findings show that in vitro induced cisplatin mutations potentiate the antitumor immune response and ICB efficacy, akin to tumor regression achieved in the parental YUMM1.7 model by ICB administered in conjunction with intratumoral cisplatin injection. Hence, our data uphold the role of tumoral mutation burden in improving immune surveillance and response to ICB, suggesting a path for expanding the range of patients benefiting from ICB therapy.

Analysis of Advanced Melanomas Changed from Immune Checkpoint Blockade Therapy to Palliative Care

2018 ◽  
Vol 80 (1) ◽  
pp. 51-55
Author(s):  
Ai KAJITA ◽  
Osamu YAMASAKI ◽  
Tatsuya KAJI ◽  
Hiroshi UMEMURA ◽  
Keiji IWATSUKI
Keyword(s):  
Palliative Care ◽  
Immune Checkpoint ◽  
Immune Checkpoint Blockade ◽  
Checkpoint Blockade

Potential immunotherapy for Alzheimer disease and age-related dementia

2019 ◽  
Vol 21 (1) ◽  
pp. 21-25 ◽  
Keyword(s):  
Immune System ◽  
Alzheimer Disease ◽  
Cross Talk ◽  
Immune Checkpoint ◽  
Short Review ◽  
Immune Checkpoint Blockade ◽  
Checkpoint Blockade ◽  
New Approach ◽  
Age Related ◽  
The Brain

Emerging results support the concept that Alzheimer disease (AD) and age-related dementia are affected by the ability of the immune system to contain the brain's pathology. Accordingly, well-controlled boosting, rather than suppression of systemic immunity, has been suggested as a new approach to modify disease pathology without directly targeting any of the brain's disease hallmarks. Here, we provide a short review of the mechanisms orchestrating the cross-talk between the brain and the immune system. We then discuss how immune checkpoint blockade directed against the PD-1/PD-L1 pathways could be developed as an immunotherapeutic approach to combat this disease using a regimen that will address the needs to combat AD.

Potential immunotherapy for Alzheimer disease and age-related dementia

2019 ◽  
Vol 21 (1) ◽  
pp. 21-25 ◽  
Keyword(s):  
Immune System ◽  
Alzheimer Disease ◽  
Cross Talk ◽  
Immune Checkpoint ◽  
Short Review ◽  
Immune Checkpoint Blockade ◽  
Checkpoint Blockade ◽  
New Approach ◽  
Age Related ◽  
The Brain

Emerging results support the concept that Alzheimer disease (AD) and age-related dementia are affected by the ability of the immune system to contain the brain’s pathology. Accordingly, well-controlled boosting, rather than suppression of systemic immunity, has been suggested as a new approach to modify disease pathology without directly targeting any of the brain’s disease hallmarks. Here, we provide a short review of the mechanisms orchestrating the cross-talk between the brain and the immune system. We then discuss how immune checkpoint blockade directed against the PD-1/PD-L1 pathways could be developed as an immunotherapeutic approach to combat this disease using a regimen that will address the needs to combat AD.

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