Update of a prognostic survival model in head and neck squamous cell carcinoma patients treated with immune checkpoint inhibitors using an expansion cohort

Background

Immune checkpoint inhibitors (ICI) treatment in recurrent/metastatic (R/M) head and neck squamous cell carcinoma (HNSCC) offers new therapeutic venues. We have previously developed a predictive survival model in this patient population based on clinical parameters, and the purpose of this study was to expand the study cohort and internally validate the model.

Methods

A single institutional retrospective analysis of R/M HNSCC patients treated with ICI. Clinical parameters collected included p-16 status, hemoglobin (Hb), albumin (Alb), lactate dehydrogenase (LDH), neutrophil, lymphocyte and platelet counts. Cox proportional hazard regression was used to assess the impact of patient characteristics and clinical variables on survival. A nomogram was created using the rms package to generate individualized survival prediction.

Results

201 patients were included, 47 females (23%), 154 males (77%). Median age was 61 years (IQR: 55-68). P-16 negative (66%). Median OS was 12 months (95% CI: 9.4, 14.9). Updated OS model included age, sex, absolute neutrophil count, absolute lymphocyte count, albumin, hemoglobin, LDH, and p-16 status. We stratified patients into three risk groups based on this model at the 0.33 and 0.66 quantiles. Median OS in the optimal risk group reached 23.7 months (CI: 18.5, NR), 13.8 months (CI: 11.1, 20.3) in the average risk group, and 2.3 months (CI: 1.7, 4.4) in the high-risk group. Following internal validation, the discriminatory power of the model reached a c-index of 0.72 and calibration slope of 0.79.

Conclusions

Our updated nomogram could assist in the precise selection of patients for which ICI could be beneficial and cost-effective.

AKT3-mediated IWS1 phosphorylation promotes the proliferation of EGFR-mutant lung adenocarcinomas through cell cycle-regulated U2AF2 RNA splicing

AKT-phosphorylated IWS1 regulates alternative RNA splicing via a pathway that is active in lung cancer. RNA-seq studies in lung adenocarcinoma cells lacking phosphorylated IWS1, identified a exon 2-deficient U2AF2 splice variant. Here, we show that exon 2 inclusion in the U2AF2 mRNA is a cell cycle-dependent process that is regulated by LEDGF/SRSF1 splicing complexes, whose assembly is controlled by the IWS1 phosphorylation-dependent deposition of histone H3K36me3 marks in the body of target genes. The exon 2-deficient U2AF2 mRNA encodes a Serine-Arginine-Rich (RS) domain-deficient U2AF65, which is defective in CDCA5 pre-mRNA processing. This results in downregulation of the CDCA5-encoded protein Sororin, a phosphorylation target and regulator of ERK, G2/M arrest and impaired cell proliferation and tumor growth. Analysis of human lung adenocarcinomas, confirmed activation of the pathway in EGFR-mutant tumors and showed that pathway activity correlates with tumor stage, histologic grade, metastasis, relapse after treatment, and poor prognosis.

RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis

Background

RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules. However, this technology produces a vast amount of data requiring sophisticated computational approaches for their analysis than other traditional technologies such as Real-Time PCR or microarrays, strongly discouraging non-expert users. For this reason, dozens of pipelines have been deployed for the analysis of RNA-Seq data. Although interesting, these present several limitations and their usage require a technical background, which may be uncommon in small research laboratories. Therefore, the application of these technologies in such contexts is still limited and causes a clear bottleneck in knowledge advancement.

Results

Motivated by these considerations, we have developed RNAdetector, a new free cross-platform and user-friendly RNA-Seq data analysis software that can be used locally or in cloud environments through an easy-to-use Graphical User Interface allowing the analysis of coding and non-coding RNAs from RNA-Seq datasets of any sequenced biological species.

Conclusions

RNAdetector is a new software that fills an essential gap between the needs of biomedical and research labs to process RNA-Seq data and their common lack of technical background in performing such analysis, which usually relies on outsourcing such steps to third party bioinformatics facilities or using expensive commercial software.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04211-7.

Use of cetuximab added to weekly chemotherapy to improve progression-free survival in patients with recurrent metastatic head and neck squamous cell carcinoma after progression on immune checkpoint inhibitors

6038

Background: Immune checkpoint inhibitors (ICI) are currently approved in the treatment of patients (pts) with recurrent-metastatic (R/M) head and neck squamous cell carcinoma (HNSCC). The majority of pts will progress on ICI. Little is known regarding the best treatment approach for this patient population. We previously showed that the combination of weekly carboplatin, paclitaxel and cetuximab was associated with reduced risk of grade 3/4 toxicities, which makes it an ideal regimen in this setting. Here; we report the outcomes of pts with R/M HNSCC who were treated with chemotherapy alone vs weekly chemotherapy plus cetuximab after progression on ICI. Methods: Between January 15th 2016 and April 9th 2020, 154 pts who progressed on ICI were analyzed. Among these pts, 64 had received subsequent systemic therapy and met the inclusion criteria. Progression Free Survival (PFS) was defined as the time elapsed between initiation of subsequent chemotherapy and tumor progression or death. Overall Survival (OS) was defined as the time elapsed between initiation of subsequent chemotherapy to death. Descriptive statistics and Cox regression were used to explore study variables. Results: 64 pts received subsequent chemotherapy after progression on ICI. 28 pts (44%) received a combination of weekly chemotherapy plus cetuximab. This regimen included carboplatin AUC 1.5, paclitaxel 45 mg/m2, and cetuximab loading dose of 400mg/m2 followed by weekly dose of 250 mg/m2. 36 pts (56%) received chemotherapy alone without cetuximab. These regimens included capecitabine, afatinib, and gemcitabine, among others. Sex: 51 males (80%), 13 females (20%), age (median): 61 (IQR: 53-66), tumor site: oropharynx 32 (50%), oral cavity 11 (17%), larynx 8 (12%), other sites 13 (21%). P16 status: negative 36 (56%), positive 28 (44%). Prior ICI drug: pembrolizumab 34 (53%), nivolumab 26 (41%), ipilimumab + nivolumab 4 (6%). Median follow up: 9 months (IQR: 5-13). Overall response rate: weekly chemotherapy plus cetuximab 32%, chemotherapy alone 22% (p = 0.4). Pts who received chemotherapy alone had a median PFS of 3.2 months (CI: 2-5) vs 5.6 months (CI: 4.3-10.1) in the weekly chemotherapy plus cetuximab group. After adjusting for p16 status and prior ICI drug, PFS was improved in the group that received weekly chemotherapy plus cetuximab vs. chemotherapy alone (HR: 0.52; CI: 0.28-0.98; p = 0.042). Median OS was 10 months (CI: 8.5-NR) in the weekly chemotherapy plus cetuximab group vs 8.7 months (CI: 5.7-13.8) in the chemotherapy alone group (HR: 0.84; CI: 0.4-1.8; p = 0.8). Conclusions: Pts with R/M HNSCC who progressed on ICI experience longer PFS with the addition of cetuximab to weekly chemotherapy. Further investigation in a larger cohort of pts is needed to fully assess the impact on survival for this treatment combination.

Expansion cohort validation of a clinical predictive model for head and neck cancer survival in patients treated with immune checkpoint inhibitors

6030

Background: Immune checkpoint inhibitors (ICI) therapy is approved for patients (pts) with recurrent-metastatic (R/M) head and neck squamous cell carcinoma (HNSCC). The majority of pts will die within two years of diagnosis. We have shown that pretreatment clinical characteristics may predict overall survival (OS). Here, we expand our analysis to a total of 201 pts. Methods: Between January 15,2016 and April 9, 2020, 201 pts with R/M HNSCC were treated with ICI as first, second line and beyond. Data on p16 status, hemoglobin (Hb), albumin, lactate dehydrogenase (LDH), neutrophil, platelet and lymphocyte count was recorded initially. OS was defined from the start of ICI to death. Progression Free Survival (PFS) was defined from the start of ICI to disease progression (PD) or death. A nomogram was created using the rms package to generate individualized survival prediction. Results: 201 pts were analyzed, sex: 154 male (77%), 47 female (23%), median age 61 (IQR: 55-68). ICI drug: pembrolizumab 100 (50%), nivolumab 91 (45%), ipilimumab+nivolumab 10 (5%). Line of therapy: First: 98 (49%), second and beyond: 103 (51%). Tumor site: oropharynx 84 (42%), oral cavity 45 (22%), others 72 (36%). p16 status: negative 132 (66%), positive 69 (34%). Laboratory values: Median neutrophil count: 4.58 (IQR: 3.43-6.47), Median lymphocyte count: 0.69 (IQR: 0.47-1.08), Median Platelet count: 229 (IQR: 187-300), hemoglobin (Hb) normal/low 101/100 (50%/50%), albumin: normal/low 156/45 (78%/22%), LDH: normal/high 124/77 (62%/38%). Overall response rate: 36 (18%). Median OS: 12 months (CI: 9.4-14.8), median PFS: 4 months (CI: 3.5-5.7). The variables associated with OS were neutrophil count (high) [HR 1.28 (1.08 – 1.51), p=0.004], lymphocyte count (high) [HR 0.75 (0.60 – 0.95), p=0.015], albumin (low) [HR 2.06 (1.37 – 3.10), p<0.001], hemoglobin (low) [HR 1.64 (1.14 – 2.35), p=0.007], LDH (high) [HR 1.78 (1.23 – 2.56), p=0.002] and p16 status (positive) [HR 0.58 (0.39-0.87), p=0.009]. Using the prognostic index of the chosen model, we stratified patients into three risk groups at the 33rd and 66th percentile. Median OS in the good risk group was 24 months (CI: 18.5-NR), average risk group 13.8 months (CI: 11-20), poor risk group 2.3 months (CI: 1.7-4.4). The discrimination of the model after internal validation was c-index of 0.72. Conclusions: A small percentage of R/M HNSCC pts treated with ICI have good long-term survival outcomes. In a larger cohort, we internally validated the utilization of a simple, inexpensive and widely accessible nomogram based on clinical and laboratory variables which can predict OS in this patient population.

Abstract PO010: The inhibition of IWS1 phosphorylation promotes genomic instability, the cGAS/STING pathway activation and PD-L1 levels, through the U2AF2 alternative RNA splicing and Sororin expression

We have previously shown that the loss of IWS1 phosphorylation promotes the alternative RNA splicing of U2 Associated-Factor 2 (U2AF2), resulting in transcripts lacking exon 2 in lung adenocarcinoma cells. This exon encodes part of the U2AF65 Serine-Rich (SR) Domain, which is required for its binding with pre-mRNA Processing factor 19 (Prp19). We have also shown that inhibition of the pathway results in the downregulation of cell cycle division associated 5 (CDCA5), and its protein product Sororin, a phosphorylation target and regulator of ERK and member of the cohesin complex, leading to G2/M phase arrest, sister-chromatid cohesion defects, impaired cell proliferation and tumor growth in mouse xenografts models. Here, we show that the loss of IWS1 results in genomic instability and accumulation of cytosolic dsDNA, an effect rescued by the expression of Sororin. The dsDNA is censored by cyclic GMP-AMP synthetase (cGAS), activating the STING/TBK1 pathway. The latter leads to increased expression of Interferon Regulatory Factor-3 (IRF-3) targets along with PD-L1. More importantly, IWS1 phosphorylation, U2AF2 RNA splicing pattern and Sororin expression negatively correlate with the cGAS/STING pathway and PD-L1 expression in lung adenocarcinoma patients. These results highlight the role of IWS1 phosphorylation-dependent RNA splicing in governing genomic stability, and proposes this axis as a novel drug target for a synergy with PD-L1/PD-1 blockade in lung adenocarcinoma patients.

Citation Format: Georgios I. Laliotis, Evangelia Chavdoula, Abdul Kaba, Alessandro La Ferlita, Vollter Anastas, Arturo Orlacchio, Lalit Sehgal, David P. Carbone, Vincenzo Coppola, Philip N. Tsichlis. The inhibition of IWS1 phosphorylation promotes genomic instability, the cGAS/STING pathway activation and PD-L1 levels, through the U2AF2 alternative RNA splicing and Sororin expression [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr PO010.

Abstract PO088: Sensitivity of cancer cells to oncolytic viruses is defined by IWS1 phosphorylation dependent epigenetic regulation of U2AF2 splicing and nucleocytoplasmic export of type I IFN transcripts

We have previously shown that loss of IWS1 phosphorylation promotes the alternative RNA splicing of U2 Associated-Factor 2 (U2AF2), resulting in transcripts lacking exon 2. This exon encodes part of the Serine-Rich (SR) domain of U2AF65, which is responsible for its binding with pre-mRNA Processing Factor 19 (Prp19). Here, we show that whereas both U2AF65 isoforms bind cytoplasmic accumulation response elements (CAR-E) of intronless mRNAs, the loading of Prp19 occurs only in exon 2-containing U2AF65, in cells expressing phosphorylated IWS1, promoting their nucleocytoplasmic export. Furthermore, this Prp19 loading is RNA Pol II dependent. Given that IFNA1 and IFNB1 are among the target genes, the expression of IFNα and IFNβ was decreased in cells deficient in IWS1 phosphorylation, and their sensitivity to the oncolytic VSV and Reovirus virus infection was increased accordingly. More importantly, treatment of the lung adenocarcinoma cells with the pan-AKT inhibitor, MK2206 phenocopied the loss of IWS1 phosphorylation and showed increased sensitivity to oncolytic viral infection. These data identify a novel mechanism by which the AKT/p-IWS1 axis, via the epigenetic regulation of alternative RNA splicing, contribute to the sensitivity to oncolytic viruses.

Citation Format: Georgios I. Laliotis, Adam D. Kenney, Evangelia Chavdoula, Arturo Orlacchio, Vollter Anastas, Alessandro La Ferlita, Abdul Kaba, Lalit Sehgal, Vincenzo Coppola, Jacob S. Yount, Philip N. Tsichlis. Sensitivity of cancer cells to oncolytic viruses is defined by IWS1 phosphorylation dependent epigenetic regulation of U2AF2 splicing and nucleocytoplasmic export of type I IFN transcripts [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr PO088.

Abstract PO-011: IWS1 phosphorylation promotes tumor growth and predicts poor prognosis in EGFR mutant lung adenocarcinoma patients, through the epigenetic regulation of U2AF2 RNA splicing

Our previous studies have shown that IWS1 (Interacts with Spt6) is a phosphorylation target of AKT and regulates the alternative RNA splicing of FGFR2, linking IWS1 with human Non-Small Cell Lung Cancer. To further address the role of IWS1 in alternative RNA splicing in lung cancer, we performed an RNA-seq study using lung adenocarcinoma cells in which IWS1 was knocked down or replaced by its phosphorylation site mutant. The results identified a novel, exon 2 deficient splice variant of the splicing factor U2 Associated-Factor 2 (U2AF2), whose abundance increases, upon the loss of phosphorylated IWS1. This exon encodes part of the U2AF65 Serine-Rich (SR) Domain, which is required for its binding with pre-mRNA Processing factor 19 (Prp19). Here, we show that U2AF2 exon 2 inclusion depends on phosphorylated IWS1, by promoting histone H3K36 trimethylation and the assembly of LEDGF/SRSF1 splicing complexes, in a cell-cycle specific manner. Inhibition of the pathway results in the downregulation of cell cycle division associated 5 (CDCA5), and its protein product, Sororin, a phosphorylation target of ERK and member of the cohesin complex, essential of G2/M phase progression. We also reveal the existence of a novel Sororin/ERK feedback loop controlled by the epigenetic regulation of U2AF2 RNA splicing, downstream of IWS1 phosphorylation. Given that the U2AF2 RNA splicing is regulated through the cell cycle and controls Sororin, our data unravel a novel RNA splicing pattern which is regulated through the cell cycle and feedbacks towards its regulation. Impairment of this signaling pathway leads to leading to G2/M phase arrest, impaired cell proliferation and tumor growth in mouse xenografts models, an effect more pronounced in EGFR mutant cells. Analysis of lung adenocarcinoma samples revealed strong correlations between IWS1 phosphorylation, U2AF2 RNA splicing, and Sororin/p-ERK levels, especially in EGFR, as opposed to K-RAS mutant patients. More importantly, IWS1 phosphorylation and U2AF2 RNA splicing pattern are positively correlated with tumor stage, grade and metastasis, and associated with poor survival in the same patients. This work highlights the instrumental role of the AKT/p-IWS1 axis to alternative RNA splicing in governing cell cycle progression and tumorigenesis and proposes this axis as a novel drug target in EGFR mutant lung adenocarcinoma, by concomitantly affecting the epigenetic regulation of RNA processing and oncogenic signals.

Citation Format: Georgios I. Laliotis, Evangelia Chavdoula, Maria D. Paraskevopoulou, Abdul Kaba, Alessandro La Ferlita, Vollter Anastas, Arturo Orlacchio, Vasiliki Taraslia, Ioannis Vlachos, Marina Capece, Artemis Hatzigeorgiou, Dario Palmieri, Salvatore Alaimo, Christos Tsatsanis, Lalit Sehgal, David P. Carbone, Vincenzo Coppola, Philip N. Tsichlis. IWS1 phosphorylation promotes tumor growth and predicts poor prognosis in EGFR mutant lung adenocarcinoma patients, through the epigenetic regulation of U2AF2 RNA splicing [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PO-011.

Abstract 3649: Alternative RNA splicing of U2AF2, induced by AKT3-phosphorylated IWS1, promotes tumor growth, by activating a CDCA5-pERK positive feedback loop

A phosphoproteomics study of isogenic cell lines expressing the 3 different Akt isoforms identified 606 proteins that are phosphorylated by at least one isoform. About 30 of these proteins were involved in various steps of RNA processing. One of them, IWS1, is a transcription elongation factor, which was originally identified in the yeast Saccharomyces cerevisiae, as a protein that interacts with the histone H3/H4 chaperone Spt6 or as a suppressor of TATA binding protein (TBP) mutations that impair post-recruitment transcriptional activation. The human IWS1 is an 819aa protein, which contains a C-terminal domain that is similar to domain I of the transcription elongation factor TFIIS, and to related domains in Elongin A and the Mediator Complex subunit 26 (Med26). IWS1 was shown to be phosphorylated, primarily by Akt3, at two neighboring sites (Ser720/Thr721). To address the role of phosphorylated IWS1 in RNA processing, we performed an RNA-seq study, using human lung adenocarcinoma cell lines in which IWS1 was knocked down or replaced by its phosphorylation site mutant. This identified the splicing factor U2AF2 as a target of IWS1 phosphorylation. Specifically, phosphorylated IWS1 regulated the alternative splicing of U2AF2 and its loss resulted in U2AF2 transcripts lacking exon 2. This exon encodes part of the U2AF2 Serine-Rich (SR) Domain, required for the binding of U2AF2 with Prp19. Exploring the mechanism of this alternative splicing event revealed that the loss of phosphorylated IWS1 interferes with the recruitment of the histone H3K36 trimethyltransferase SETD2 to an Spt6/IWS1/Aly complex, which assembles on the Ser-2-phosphorylated CTD of RNA-Pol II. The absence of SETD2 recruitment to this complex impairs histone H3K36 trimethylation and the assembly of LEDGF/SRSF1 splicing complexes inthe U2AF2 gene, resulting in the exclusion of exon 2 from the mature U2AF2 mRNA transcript. The loss of the U2AF2/Prp19 interaction results in the downregulation of CDCA5, a component of the cohesin complex, giving rise to genomic instability. Phosphorylation of CDCA5 by p-ERK at Ser79 and Ser209 has a major impact in the regulation of cell proliferation and cancer stem cell renewal, although does not affect its role in the cohesin complex. The effect of phosphorylated CDCA5 on cell proliferation appears to depend on the transcriptional regulation of a set of genes involved in the control of the G2/M phase of the cell cycle, including Cyclin B1 and CDK1. Overall, these data describe a novel pathway, which starts with the phosphorylation of IWS1 by AKT3 and results in the epigenetic modulation of RNA splicing and cell cycle regulation. The importance of this pathway to human cancer was confirmed by meta-analysis of pre-existing patient data, tumor xenograft models and prospective studies on human lung adenocarcinomas.

Citation Format: Georgios I. Laliotis, Evangelia Chavdoula, Maria D. Paraskevopoulou, Vollter Anastas, Ioannis Vlachos, Vasiliki Tarasslia, Artemis Hatzigeorgiou, Dario Palmieri, Abdul Kaba, Marina Capece, Arturo Orlacchio, Lalit Sehgal, Vincenzo Coppola, Philip N. Tsichlis. Alternative RNA splicing of U2AF2, induced by AKT3-phosphorylated IWS1, promotes tumor growth, by activating a CDCA5-pERK positive feedback loop [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 3649.

Abstract LB-183: Sensitivity of cancer cells to oncolytic viruses is defined by IWS1 phosphorylation dependent epigenetic regulation of U2AF2 splicing and nucleocytoplasmic export of type I IFN transcripts

We have previously shown that phosphorylation of IWS1 by AKT (primarily AKT3) at Ser720/Thr721 promotes the binding of SETD2 to an Spt6/IWS1/Aly-Ref transcription elongation complex. This complex is bound via Spt6 to the Ser2-phosphorylated CTD of RNA Pol II. We have also shown that this results in the AKT-dependent trimethylation of Histone H3 at K36, a histone modification that contributes to the regulation of alternative splicing, and that this splicing pathway plays an important role in lung cancer. Here, we show that one of the genes targeted for alternative splicing via this mechanism is U2AF2, which encodes the splicing factor U2AF65. The predominant alternatively spliced U2AF2 transcript in cells which have lost IWS1, and in cells in which IWS1 is not phosphorylated, lacks exon 2, which encodes the SR domain of U2AF65. U2AF65 lacking the SR domain does not bind Prp19, a member of a seven-protein complex, which also contributes to RNA processing. U2AF65 and Prp19, along with the TREX complex, bind Cytoplasmic Accumulation Response Elements (CAR-E) in naturally intronless mRNAs and promotes their nucleocytoplasmic export. Examples of mRNAs whose transport is regulated by this mechanism include IFNα1, IFNβ1, HSPBP3 and c-Jun. Based on these data, we predicted that the production of type I IFNs would be dependent on IWS1 phosphorylation by AKT and that inhibition of this pathway would lead to increased sensitivity of cells to virus infection. Indeed, type I IFN production was decreased in such cells and infection with Vesicular Stomatitis Virus (VSV) was accordingly increased. In addition, whereas U2AF65 binds CAR-E elements in the RNA of type I interferons independent of IWS1 phosphorylation, the binding of Prp19 to the same RNA elements occured only in cells expressing AKT-phosphorylated IWS1. These data identify a mechanism by which AKT inhibits viral infection and suggest that inhibition of the AKT/IWS1 axis will increase the sensitivity of cancer cells to infection by oncolytic viruses.

Citation Format: Georgios I. Laliotis, Adam D. Kenney, Arturo Orlacchio, Vincenzo Coppola, Jacob S. Yount, Philip N. Tsichlis. Sensitivity of cancer cells to oncolytic viruses is defined by IWS1 phosphorylation dependent epigenetic regulation of U2AF2 splicing and nucleocytoplasmic export of type I IFN transcripts [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 LB-183.