A signature of enhanced proliferation associated with response and survival to anti-PD-L1 therapy in early-stage non-small cell lung cancer

In early-stage non-small cell lung cancer, the combination of neoadjuvant anti-PD-L1 and subablative stereotactic body radiation therapy (SBRT) is associated with higher rates of major pathologic response compared to anti-PD-L1 alone. Here, we identify a 140-gene set, enriched in genes characteristic of highly proliferating cells, associated with response to the dual therapy. Analysis of on-treatment transcriptome data indicate roles for T and B cells in response. The 140-gene set is associated with disease-free survival when applied to the combined trial arms. This 140-gene set identifies a subclass of tumors in all 7 of The Cancer Genome Atlas tumor types examined. Worse survival is associated with the 140-gene signature in 5 of these tumor types. Collectively, our data support that this 140-gene set, discovered in association with response to combined anti-PD-L1 and SBRT, identifies a clinically aggressive subclass of solid tumors that may be more likely to respond to immunotherapies.

The evolution of metastatic upper tract urothelial carcinoma through genomic-transcriptomic and single-cell protein markers analysis

The molecular characteristics of metastatic upper tract urothelial carcinoma (UTUC) are not well understood, and there is a lack of knowledge regarding the genomic and transcriptomic differences between primary and metastatic UTUC. To address these gaps, we integrate whole-exome sequencing, RNA sequencing, and Imaging Mass Cytometry using lanthanide metal-conjugated antibodies of 44 tumor samples from 28 patients with high-grade primary and metastatic UTUC. We perform a spatially-resolved single-cell analysis of cancer, immune, and stromal cells to understand the evolution of primary to metastatic UTUC. We discover that actionable genomic alterations are frequently discordant between primary and metastatic UTUC tumors in the same patient. In contrast, molecular subtype membership and immune depletion signature are stable across primary and matched metastatic UTUC. Molecular and immune subtypes are consistent between bulk RNA-sequencing and mass cytometry of protein markers from 340,798 single cells. Molecular subtypes at the single-cell level are highly conserved between primary and metastatic UTUC tumors within the same patient.

Cysteine induces mitochondrial reductive stress in glioblastoma through hydrogen peroxide production

Glucose and amino acid metabolism are critical for glioblastoma (GBM) growth, but little is known about the specific metabolic alterations in GBM that are targetable with FDA-approved compounds. To investigate tumor metabolism signatures unique to GBM, we interrogated The Cancer Genome Atlas for alterations in glucose and amino acid signatures in GBM relative to other human cancers and found that GBM exhibits the highest levels of cysteine and methionine pathway gene expression of 32 human cancers. Treatment of patient-derived GBM cells with the FDA-approved single cysteine compound N-acetylcysteine (NAC) reduced GBM cell growth and mitochondrial oxygen consumption, which was worsened by glucose starvation. Normal brain cells and other cancer cells showed no response to NAC. Mechanistic experiments revealed that cysteine compounds induce rapid mitochondrial H2O2 production and reductive stress in GBM cells, an effect blocked by oxidized glutathione, thioredoxin, and redox enzyme overexpression. From analysis of the clinical proteomic tumor analysis consortium (CPTAC) database, we found that GBM cells exhibit lower expression of mitochondrial redox enzymes than four other cancers whose proteomic data are available in CPTAC. Knockdown of mitochondrial thioredoxin-2 in lung cancer cells induced NAC susceptibility, indicating the importance of mitochondrial redox enzyme expression in mitigating reductive stress. Intraperitoneal treatment of mice bearing orthotopic GBM xenografts with a two-cysteine peptide induced H2O2 in brain tumors in vivo. These findings indicate that GBM is uniquely susceptible to NAC-driven reductive stress and could synergize with glucose-lowering treatments for GBM.

The nuclear factor ID3 endows macrophages with a potent anti-tumour activity

Macrophage activation is controlled by a balance between activating and inhibitory receptors1-7, which protect normal tissues from excessive damage during infection8,9 but promote tumour growth and metastasis in cancer7,10. Here we report that the Kupffer cell lineage-determining factor ID3 controls this balance and selectively endows Kupffer cells with the ability to phagocytose live tumour cells and orchestrate the recruitment, proliferation and activation of natural killer and CD8 T lymphoid effector cells in the liver to restrict the growth of a variety of tumours. ID3 shifts the macrophage inhibitory/activating receptor balance to promote the phagocytic and lymphoid response, at least in part by buffering the binding of the transcription factors ELK1 and E2A at the SIRPA locus. Furthermore, loss- and gain-of-function experiments demonstrate that ID3 is sufficient to confer this potent anti-tumour activity to mouse bone-marrow-derived macrophages and human induced pluripotent stem-cell-derived macrophages. Expression of ID3 is therefore necessary and sufficient to endow macrophages with the ability to form an efficient anti-tumour niche, which could be harnessed for cell therapy in cancer.

Neoadjuvant durvalumab plus radiation versus durvalumab alone in stages I-III non-small cell lung cancer: survival outcomes and molecular correlates of a randomized phase II trial

We previously reported the results of a randomized phase II trial (NCT02904954) in patients with early-stage non-small cell lung cancer (NSCLC) who were treated with either two preoperative cycles of the anti-PD-L1 antibody durvalumab alone or combined with immunomodulatory doses of stereotactic radiation (DRT). The trial met its primary endpoint of major pathological response, which was significantly higher following DRT with no new safety signals. Here, we report on the prespecified secondary endpoint of disease-free survival (DFS) regardless of treatment assignment and the prespecified exploratory analysis of DFS in each arm of the trial. DFS at 2 and 3 years across patients in both arms of the trial were 73% (95% CI: 62.1-84.5) and 65% (95% CI: 52.5-76.9) respectively. For the exploratory endpoint of DFS in each arm of the trial, three-year DFS was 63% (95% CI: 46.0-80.4) in the durvalumab monotherapy arm compared to 67% (95% CI: 49.6-83.4) in the dual therapy arm. In addition, we report post hoc exploratory analysis of progression-free survival as well as molecular correlates of response and recurrence through high-plex immunophenotyping of sequentially collected peripheral blood and gene expression profiles from resected tumors in both treatment arms. Together, our results contribute to the evolving landscape of neoadjuvant treatment regimens for NSCLC and identify easily measurable potential biomarkers of response and recurrence.

Immunogenomic Landscape of Neuroendocrine Prostate Cancer

PURPOSE

Patients with neuroendocrine prostate cancer (NEPC) are often managed with immunotherapy regimens extrapolated from small-cell lung cancer (SCLC). We sought to evaluate the tumor immune landscape of NEPC compared with other prostate cancer types and SCLC.

EXPERIMENTAL DESIGN

In this retrospective study, a cohort of 170 patients with 230 RNA-sequencing and 104 matched whole-exome sequencing data were analyzed. Differences in immune and stromal constituents, frequency of genomic alterations, and associations with outcomes were evaluated.

RESULTS

In our cohort, 36% of the prostate tumors were identified as CD8+ T-cell inflamed, whereas the remaining 64% were T-cell depleted. T-cell-inflamed tumors were enriched in anti-inflammatory M2 macrophages and exhausted T cells and associated with shorter overall survival relative to T-cell-depleted tumors (HR, 2.62; P < 0.05). Among all prostate cancer types in the cohort, NEPC was identified to be the most immune depleted, wherein only 9 out of the 36 total NEPC tumors were classified as T-cell inflamed. These inflamed NEPC cases were enriched in IFN gamma signaling and PD-1 signaling compared with other NEPC tumors. Comparison of NEPC with SCLC revealed that NEPC had poor immune content and less mutations compared with SCLC, but expression of checkpoint genes PD-L1 and CTLA-4 was comparable between NEPC and SCLC.

CONCLUSIONS

NEPC is characterized by a relatively immune-depleted tumor immune microenvironment compared with other primary and metastatic prostate adenocarcinoma except in a minority of cases. These findings may inform development of immunotherapy strategies for patients with advanced prostate cancer.

Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells

The rarity of malignant Hodgkin and Reed Sternberg (HRS) cells in classic Hodgkin lymphoma (cHL) limits the ability to study the genomics of cHL. To circumvent this, our group has previously optimized fluorescence-activated cell sorting to purify HRS cells. Using this approach, we now report the whole-genome sequencing landscape of HRS cells and reconstruct the chronology and likely etiology of pathogenic events leading to cHL. We identified alterations in driver genes not previously described in cHL, APOBEC mutational activity, and the presence of complex structural variants including chromothripsis. We found that high ploidy in cHL is often acquired through multiple, independent chromosomal gains events including whole-genome duplication. Evolutionary timing analyses revealed that structural variants enriched for RAG motifs, driver mutations in B2M, BCL7A, GNA13, and PTPN1, and the onset of AID-driven mutagenesis usually preceded large chromosomal gains. This study provides a temporal reconstruction of cHL pathogenesis.

SIGNIFICANCE

Previous studies in cHL were limited to coding sequences and therefore not able to comprehensively decipher the tumor complexity. Here, leveraging cHL whole-genome characterization, we identify driver events and reconstruct the tumor evolution, finding that structural variants, driver mutations, and AID mutagenesis precede chromosomal gains. This article is highlighted in the In This Issue feature, p. 171.

A Genome-Wide RNAi Screen Reveals Common Host-Virus Gene Signatures: Implication for Dengue Antiviral Drug Discovery

Dengue is the most common mosquito-borne viral disease that in recent years has become a major international public health concern. Dengue is a tropical neglected disease with increasing global incidences, affecting millions of people worldwide, and without the availability of specific treatments to combat it. The identification of host-target genes essential for the virus life cycle, for which effective modulators may already exist, would provide an alternative path to a rapid drug development of the much needed antidengue agents. For this purpose, we performed the first genome-wide RNAi screen, combining two high-content readouts for dengue virus infection (DENV E infection intensity) and host cell toxicity (host cell stained nuclei), against an arrayed lentiviral-based short hairpin RNA library covering 16,000 genes with a redundancy of at least 5 hairpins per gene. The screen identified 1924 gene candidates in total; of which, 1730 gene candidates abrogated dengue infection, whereas 194 gene candidates were found to enhance its infectivity in HEK293 cells. A first pass clustering analysis of hits revealed a well-orchestrated gene-network dependency on host cell homeostasis and physiology triggering distinct cellular pathways for infectivity, replication, trafficking, and egress; a second analysis revealed a comprehensive gene signature of 331 genes common to hits identified in 28 published RNAi host-viral interaction screens. Taken together, our findings provide novel antiviral molecular targets with the potential for drug discovery and development.

The Cytidine Deaminase APOBEC3G Contributes to Cancer Mutagenesis and Clonal Evolution in Bladder Cancer

Mutagenic processes leave distinct signatures in cancer genomes. The mutational signatures attributed to APOBEC3 cytidine deaminases are pervasive in human cancers. However, data linking individual APOBEC3 proteins to cancer mutagenesis in vivo are limited. Here, we showed that transgenic expression of human APOBEC3G promotes mutagenesis, genomic instability, and kataegis, leading to shorter survival in a murine bladder cancer model. Acting as mutagenic fuel, APOBEC3G increased the clonal diversity of bladder cancer, driving divergent cancer evolution. Characterization of the single-base substitution signature induced by APOBEC3G in vivo established the induction of a mutational signature distinct from those caused by APOBEC3A and APOBEC3B. Analysis of thousands of human cancers revealed the contribution of APOBEC3G to the mutational profiles of multiple cancer types, including bladder cancer. Overall, this study dissects the mutagenic impact of APOBEC3G on the bladder cancer genome, identifying that it contributes to genomic instability, tumor mutational burden, copy-number loss events, and clonal diversity.

SIGNIFICANCE

APOBEC3G plays a role in cancer mutagenesis and clonal heterogeneity, which can potentially inform future therapeutic efforts that restrict tumor evolution. See related commentary by Caswell and Swanton, p. 487.

Tumor-intrinsic IRE1α signaling controls protective immunity in lung cancer

IRE1α-XBP1 signaling is emerging as a central orchestrator of malignant progression and immunosuppression in various cancer types. Employing a computational XBP1s detection method applied to TCGA datasets, we demonstrate that expression of the XBP1s mRNA isoform predicts poor survival in non-small cell lung cancer (NSCLC) patients. Ablation of IRE1α in malignant cells delays tumor progression and extends survival in mouse models of NSCLC. This protective effect is accompanied by alterations in intratumoral immune cell subsets eliciting durable adaptive anti-cancer immunity. Mechanistically, cancer cell-intrinsic IRE1α activation sustains mPGES-1 expression, enabling production of the immunosuppressive lipid mediator prostaglandin E2. Accordingly, restoring mPGES-1 expression in IRE1αKO cancer cells rescues normal tumor progression. We have developed an IRE1α gene signature that predicts immune cell infiltration and overall survival in human NSCLC. Our study unveils an immunoregulatory role for cancer cell-intrinsic IRE1α activation and suggests that targeting this pathway may help enhance anti-tumor immunity in NSCLC.

Abstract 1309: Patient-derived tumor organoids as a platform to study radiation-exposed neoantigens

Focal radiation therapy (RT) can increase tumor immunogenicity and T cell-mediated tumor rejection when combined with immune checkpoint blockade (ICB). Our prior findings in patients and in preclinical studies suggest that one mechanism whereby RT increases tumor immunogenicity is by enhancing the expression of neoantigens.1,2 In response to RT, cells rapidly transcribe and translate hundreds of genes associated with the DNA damage response (DDR), protein turnover and cellular stress. Genes in these pathways are frequently mutated in cancer. Thus, we hypothesized that the presence of immunogenic mutations in genes upregulated by radiation could help predict the benefits of RT used in combination with ICB. In order to develop such a predictor, we built an in vitro system to study the RT-induced transcriptional response of primary human tumors cultured as patient-derived tumor organoids (PDO). PDOs were established from 2 breast cancer (BC), 4 non-small cell lung cancer (NSCLC) and 3 colorectal cancer (CRC) patients. PDOs were irradiated with doses of 5 to 8 Gy daily for 3 days (n=4) or left untreated (UT, n=4) and cultured for 24h prior to RNA extraction. RNA sequencing was carried out using a NovaSeq6000 sequencer (Illumina) to a depth of 30 million reads. Differential expression analysis between RT and UT samples was performed using DESeq2 and significantly perturbed genes were defined as genes with fold change greater than 1.5 and adjusted p-value cutoff of 0.05. In total we detected an average of 15,000+/-800 protein coding genes per sample and the number of genes modulated by RT was found to vary with cancer type. This ranged from an average of 3.9+/-1.6% genes upregulated by RT in NSCLC to 12.1+/-2.5% in CRC organoids. There were 104 and 490 genes commonly upregulated by RT in NSCLC and CRC, respectively. One of the BC PDOs is a triple-negative BC and the other HR+ and despite this difference, we identified 24 commonly upregulated genes. Gene Set Enrichment Analysis (GSEA), revealed enrichments in DDR and pro-inflammatory signaling pathways among the upregulated genes. Whole exome sequencing and paired normal tissue was used to determine the variants and predicted neoantigens for these PDOs. In one of the EGFR mutated NSCLC PDOs we found that among the genes transcriptionally upregulated by RT, 18 carried somatic mutations predicted to be antigenic. The presentation of these neoantigens is being investigated by mass spectrometry analysis of the immunopeptidome eluted from surface MHC-I molecules. Similar investigations are being carried out in the other models. Overall, results support the feasibility of identifying a common signature of RT upregulated genes in PDOs. This will provide a system to predict RT- exposed neoantigens. [1] Formenti et al. Nat. Med. 2018;24(12):1845-1851, [2] Lhuillier et al. J. Clin. Invest. 2021;131(5):e138740

Citation Format: Samantha J. Van Nest, Jared Capuano, Bhavneet Bhinder, Martin G. Klatt, Tuo Zhang, M. Laura Martin, Silvia C. Formenti, Olivier Elemento, Nils-Petter Rudqvist, Sandra Demaria. Patient-derived tumor organoids as a platform to study radiation-exposed neoantigens [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 1309.

Global evolution of the tumor microenvironment associated with progression from preinvasive invasive to invasive human lung adenocarcinoma

To investigate changes in the tumor microenvironment (TME) during lung cancer progression, we interrogate tumors from two chest computed tomography (CT)-defined groups. Pure non-solid (pNS) CT density nodules contain preinvasive/minimally invasive cancers, and solid density nodules contain invasive cancers. Profiling data reveal a dynamic interaction between the tumor and its TME throughout progression. Alterations in genes regulating the extracellular matrix and genes regulating fibroblasts are central at the preinvasive state. T cell-mediated immune suppression is initiated in preinvasive nodules and sustained with rising intensity through progression to invasive tumors. Reduced T cell infiltration of the cancer cell nests is more frequently associated with preinvasive cancers, possibly until tumor evolution leads to a durable, viable invasive phenotype accompanied by more varied and robust immune suppression. Upregulation of immune checkpoints occurs only in the invasive nodules. Throughout progression, an effector immune response is present but is effectively thwarted by the immune-suppressive elements.

Collision tumors revealed by prospectively assessing subtype-defining molecular alterations in 904 individual prostate cancer foci

BACKGROUND

Prostate cancer is multifocal with distinct molecular subtypes. The utility of genomic subtyping has been challenged due to inter- and intrafocal heterogeneity. We sought to characterize the subtype-defining molecular alterations of primary prostate cancer across all tumor foci within radical prostatectomy (RP) specimens and determine the prevalence of collision tumors.

METHODS

From the Early Detection Research Network cohort, we identified 333 prospectively collected RPs from 2010 to 2014 and assessed ETS-related gene (ERG), serine peptidase inhibitor Kazal type 1 (SPINK1), phosphatase and tensin homolog (PTEN), and speckle type BTB/POZ protein (SPOP) molecular status. We utilized dual ERG/SPINK1 immunohistochemistry and fluorescence in situ hybridization to confirm ERG rearrangements and characterize PTEN deletion, as well as high-resolution melting curve analysis and Sanger sequencing to determine SPOP mutation status.

RESULTS

Based on index focus alone, ERG, SPINK1, PTEN, and SPOP alterations were identified in 47.5%, 10.8%, 14.3%, and 5.1% of RP specimens, respectively. In 233 multifocal RPs with ERG/SPINK1 status in all foci, 139 (59.7%) had discordant molecular alterations between foci. Collision tumors, as defined by discrepant ERG/SPINK1 status within a single focus, were identified in 29 (9.4%) RP specimens.

CONCLUSION

Interfocal molecular heterogeneity was identified in about 60% of multifocal RP specimens, and collision tumors were present in about 10%. We present this phenomenon as a model for the intrafocal heterogeneity observed in previous studies and propose that future genomic studies screen for collision tumors to better characterize molecular heterogeneity.

FUNDING

Early Detection Research Network US National Cancer Institute (NCI) 5U01 CA111275-09, Center for Translational Pathology at Weill Cornell Medicine (WCM) Department of Pathology and Laboratory Medicine, US NCI (WCM SPORE in Prostate Cancer, P50CA211024-01), R37CA215040, Damon Runyon Cancer Research Foundation, US MetLife Foundation Family Clinical Investigator Award, Norwegian Cancer Society (grant 208197), and South-Eastern Norway Regional Health Authority (grant 2019016 and 2020063).

Pan-cancer analysis reveals molecular patterns associated with age

Older age is a strong risk factor for several diseases, including cancer. The etiology and biology of age-associated differences among cancers are poorly understood. To address this knowledge gap, we aim to delineate differences in tumor molecular characteristics between younger and older patients across a variety of tumor types from The Cancer Genome Atlas. We show that these groups exhibit widespread molecular differences in select tumor types. Our work shows that tumors in younger individuals exhibit a dysregulated molecular aging phenotype and are associated with hallmarks of premature senescence. Additionally, we find that these tumors are enriched for driver gene mutations, resulting in homologous recombination defects. Lastly, we observe a trend toward decreased immune infiltration and function in older patients and find that, immunologically, young tumor tissue resembles aged healthy tissue. Taken together, we find that tumors from young individuals possess unique characteristics that may be leveraged for therapy.

Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes

The cohesin complex plays critical roles in genomic stability and gene expression through effects on 3D architecture. Cohesin core subunit genes are mutated across a wide cross-section of cancers, but not in germinal center (GC) derived lymphomas. In spite of this, haploinsufficiency of cohesin ATPase subunit Smc3 was shown to contribute to malignant transformation of GC B-cells in mice. Herein we explored potential mechanisms and clinical relevance of Smc3 deficiency in GC lymphomagenesis. Transcriptional profiling of Smc3 haploinsufficient murine lymphomas revealed downregulation of genes repressed by loss of epigenetic tumor suppressors Tet2 and Kmt2d. Profiling 3D chromosomal interactions in lymphomas revealed impaired enhancer-promoter interactions affecting genes like Tet2, which was aberrantly downregulated in Smc3 deficient lymphomas. Tet2 plays important roles in B-cell exit from the GC reaction, and single cell RNA-seq profiles and phenotypic trajectory analysis in Smc3 mutant mice revealed a specific defect in commitment to the final steps of plasma cell differentiation. Although Smc3 deficiency resulted in structural abnormalities in GC B-cells, there was no increase of somatic mutations or structural variants in Smc3 haploinsufficient lymphomas, suggesting that cohesin deficiency largely induces lymphomas through disruption of enhancer-promoter interactions of terminal differentiation and tumor suppressor genes. Strikingly, the presence of the Smc3 haploinsufficient GC B-cell transcriptional signature in human patients with GC-derived diffuse large B-cell lymphoma (DLBCL) was linked to inferior clinical outcome and low expression of cohesin core subunits. Reciprocally, reduced expression of cohesin subunits was an independent risk factor for worse survival int DLBCL patient cohorts. Collectively, the data suggest that Smc3 functions as a bona fide tumor suppressor for lymphomas through non-genetic mechanisms, and drives disease by disrupting the commitment of GC B-cells to the plasma cell fate.

Abstract PO-036: Immunological characterization of mouse HR+ mammary tumors relapsing after radiation therapy

Background. Hormone receptor (HR)+ breast cancer (BC) causes the majority of BC-related deaths in the US (Siegel, Miller et al. 2020). Standard treatment includes surgery, endocrine therapy +/- chemotherapy or radiation therapy (RT), depending on surgical procedure and risk assessment). However, approximately 50% of patients with HR+ do not experience disease eradication after standard-of-care therapy, ultimately relapse and succumb to the disease. It has been postulated that such cases of relapse reflect situations in which treatment is unable to elicit a strong immune response that would enable long-term disease control. Objective and procedures. To obtain insights into the immunological alterations accompanying disease relapse in HR+ BC exposed to RT, we harnessed an endogenous model of BC driven in immunocompetent mice by the implantation of a slow-release medroxyprogesterone acetate (MPA, M) pellet and oral administration of the carcinogen DMBA (D). This model recapitulates multiple key aspects of human luminal B BC, including a relatively ´cold´ microenvironment in basal conditions and hence limited sensitivity to PD-1 blockage (Buque, Bloy et al. 2020). To identify immunological alterations associated with disease relapse after RT, we undertook an in-depth characterization of the tumor (by DNAseq and RNAseq) and systemic (by flow cytometry on the splenic compartment) microenvironment of C57BL/6 female mice bearing tumors that recovered normal growth after either 21 Gy in a single fraction, or 3 consecutive doses of 10 Gy each (10 Gy X 3, total dose 30 Gy), which we previously demonstrated to mediate differential local control of the disease, with the latter approach being more efficient. Results. We observed a trend for reduction in splenic macrophage activation and abundance of B cells, T cells and NKT cells amongst tumors relapsing after single-dose vs fractionated RT, alongside an increased abundance of immunosuppressive TREG cells, elevated markers of exhaustion in both CD4+ and CD8+ cells and limited responsiveness to ex vivo stimulation in terms of TNFalpha secretion. Moreover, mice with M/D-driven tumors relapsing after single-dose RT exhibited a more pronounced secretion of IL17 by splenic CD8+ cells, which has been previously associated with immunosuppression in the BC microenvironment (Chabab, Barjon et al. 2020). As compared to control tumor-naïve mice, the splenocytes of mice with M/D-driven tumors relapsing after fractionated RT were sub-efficient at responding to ex vivo stimulation with cytokine and effector molecules, potentially linked to disease progression. DNAseq and RNAseq data are being analyzed and results will be available shortly. Impact: Identifying immunological correlates of relapse after RT can direct strategies to overcome resistance in HR+ BC patients, the majority of BC patients. If successful, this can inform therapeutic approaches to enable superior therapeutic responses in patients with HR+ BC, hence significantly reducing BC-related deaths.

Citation Format: Norma Bloy, Aitziber Buque, Giulia Petroni, Takahiro Yamazaki, Ai Sato, Bhavneet Bhinder, Olivier Elemento, Silvia C. Formenti, Lorenzo Galluzzi. Immunological characterization of mouse HR+ mammary tumors relapsing after radiation therapy [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr PO-036.

Artificial Intelligence in Cancer Research and Precision Medicine

Artificial intelligence (AI) is rapidly reshaping cancer research and personalized clinical care. Availability of high-dimensionality datasets coupled with advances in high-performance computing, as well as innovative deep learning architectures, has led to an explosion of AI use in various aspects of oncology research. These applications range from detection and classification of cancer, to molecular characterization of tumors and their microenvironment, to drug discovery and repurposing, to predicting treatment outcomes for patients. As these advances start penetrating the clinic, we foresee a shifting paradigm in cancer care becoming strongly driven by AI. SIGNIFICANCE: AI has the potential to dramatically affect nearly all aspects of oncology-from enhancing diagnosis to personalizing treatment and discovering novel anticancer drugs. Here, we review the recent enormous progress in the application of AI to oncology, highlight limitations and pitfalls, and chart a path for adoption of AI in the cancer clinic.

Smc3 dosage regulates B cell transit through germinal centers and restricts their malignant transformation

During the germinal center (GC) reaction, B cells undergo extensive redistribution of cohesin complex and three-dimensional reorganization of their genomes. Yet, the significance of cohesin and architectural programming in the humoral immune response is unknown. Herein we report that homozygous deletion of Smc3, encoding the cohesin ATPase subunit, abrogated GC formation, while, in marked contrast, Smc3 haploinsufficiency resulted in GC hyperplasia, skewing of GC polarity and impaired plasma cell (PC) differentiation. Genome-wide chromosomal conformation and transcriptional profiling revealed defects in GC B cell terminal differentiation programs controlled by the lymphoma epigenetic tumor suppressors Tet2 and Kmt2d and failure of Smc3-haploinsufficient GC B cells to switch from B cell- to PC-defining transcription factors. Smc3 haploinsufficiency preferentially impaired the connectivity of enhancer elements controlling various lymphoma tumor suppressor genes, and, accordingly, Smc3 haploinsufficiency accelerated lymphomagenesis in mice with constitutive Bcl6 expression. Collectively, our data indicate a dose-dependent function for cohesin in humoral immunity to facilitate the B cell to PC phenotypic switch while restricting malignant transformation.

Common germline-somatic variant interactions in advanced urothelial cancer

The prevalence and biological consequences of deleterious germline variants in urothelial cancer (UC) are not fully characterized. We performed whole-exome sequencing (WES) of germline DNA and 157 primary and metastatic tumors from 80 UC patients. We developed a computational framework for identifying putative deleterious germline variants (pDGVs) from WES data. Here, we show that UC patients harbor a high prevalence of pDGVs that truncate tumor suppressor proteins. Deepening somatic loss of heterozygosity in serial tumor samples is observed, suggesting a critical role for these pDGVs in tumor progression. Significant intra-patient heterogeneity in germline-somatic variant interactions results in divergent biological pathway alterations between primary and metastatic tumors. Our results characterize the spectrum of germline variants in UC and highlight their roles in shaping the natural history of the disease. These findings could have broad clinical implications for cancer patients.

Abstract 2011: HER2 expression and M2-like tumor infiltrating macrophages associated with Cabazitaxel activity in gastric cancer

Gastric cancer (GC), responsible for ~700,000 deaths worldwide annually, is a dismal disease, with median survival for metastatic disease less than 1 year. We examined the efficacy and safety of cabazitaxel, a novel 3rd generation taxane, in the 2nd line treatment setting in advanced GC. Comprehensive correlative studies were performed to identify genetic aberrations or tumor microenvironment signatures associated with cabazitaxel activity.

Patients with previously treated GC were eligible for this multicenter phase II study of single agent cabazitaxel (NCT01757171). The progression-free survival (PFS) rate at 3-mo using RECIST 1.1 was 28% (95%CI 17-42%) in taxane-naïve and 35% (95%CI 16-57%) in taxane treated cohorts. A fresh tissue biopsy of the tumor and matching adjacent non-tumor tissue was obtained from each of the 66 patients (87% of the study population) and was examined using whole exome sequencing (WES) and bulk RNAseq. We performed CIBERSORT deconvolution of the RNA expression data into its constituent immune cell types. Tumor samples were segregated into those with high or low macrophage M2 levels using the cohort specific median M2 abundance as the threshold. 26 tumor samples were examined for validation of the M2 signature by immunohistochemistry (IHC) using CD68 (pan-macrophage), CD163 (M2), and iNOS (M1) markers.

GC WES showed numerous somatic alterations including missense mutations, chromosomal rearrangements, SNVs, small indels and CNAs with prevalent mutations in TP53 (26/47 cases), RHOA, and RTK/RAS signaling. Clinically actionable alterations included BRAF V600E, EGFR amplifications (10/47) and HER2 amplifications (8/47). One patient had a KRAS Q61H mutation predictive of resistance to a broad spectrum of RTK inhibitors. Other alterations included mutations in RTK signaling components, deletions of MTOR and STK11 suppressor gene and mutations in PI3K/mTOR pathway.

We found that HER2 amplification was significantly more prevalent in responders, 50% HER2 positive among patients with PR/SD vs 10% in patients with PD (p=0.003). Patients with HER2 positive tumors had better PFS (p=0.04) and OS (45% 2-year survival vs 15%, p=0.002). Deconvolution analysis revealed an enrichment of an M2 macrophage signature in a cohort of patients having an improved PFS (45% vs 20% at 12 months, p=0.031). IHC analysis also showed M2 enrichment in 65% tissue samples examined (n=26). The M2-like macrophage signature was associated with improved outcome independent of HER2 amplification/ over-expression. In 8 out of 10 matched on-treatment biopsies, the M2-like signature significantly decreased post treatment.

We have identified two novel biomarkers, HER2 overexpression and M2-high tumor macrophage signature, associated with improved outcomes in patients with GC treated with cabazitaxel. Additional correlative analyses and integration are underway.

Citation Format: Sandipto Sarkar, Prashant K. Thakkar, Heinz Lenz, Peter Enzinger, Andrew H. Ko, Allyson J. Ocean, Yao Lu, Chao Zhang, Bhavneet Bhinder, Olga Plotnikova, Nikita Kotlov, Feliz Frenkel, Aleksander Bagaev, Olivier Elemento, Doron Betel, Paraskevi Giannakakou, Meredith E. Pittman, Manish A. Shah. HER2 expression and M2-like tumor infiltrating macrophages associated with Cabazitaxel activity in gastric cancer [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 2011.

Abstract 859: Deep learning predicts expression-based molecular subtypes and immune status of urothelial cancer using digital pathology slides

RNA-sequencing (RNA-seq) has revealed intrinsic subtypes of urothelial carcinoma (UC). We have recently developed a molecular classifier to separate UC tumors to ‘hot' and ‘cold' based on the expression of immune-related genes. Both molecular subtype and immune-status correlate with response to different treatments, however, RNA-seq data is not readily available for all tumors thus limiting our ability to predict treatment response. We hypothesized that a deep learning approach can predict urothelial cancer molecular subtype and classify immune cell levels from pathology tissue slides. To test this hypothesis, we developed a deep learning model to classify urothelial carcinoma subtypes from hematoxylin and eosin (H&E) stained tissue sections using BASE47 luminal-basal classification and our immune-status classifiers based on RNA-seq data from patients in the TCGA dataset as ground truth. Patches of 2048x2048 pixels were generated from 446 whole slide images (WSIs) resulting in a total of 79,053 images. 70% of the patients were used for training, and 15% are being used as a validation set. The remaining 15% of the data will be a blind test set. We used the Resnet-18 architecture, which performed best based on empirical testing (high accuracy while minimizing overfitting). We performed a color normalization step based on the Vahadane algorithm (IEEE Trans Med Imaging. 2016;35(8):1962 71) to analyze the predictive performance and generalizability of the model compared to non-normalized slides. We also used gradient-weighted class activation mapping to highlight the regions of the tissue that may be important for classification. After 20 epochs of training, we achieved a 74% patch prediction accuracy on the validation set with a ROC-AUC of 0.80 for non-normalized immune cell classification. For normalized images, we achieved a 70% patch prediction accuracy on the validation set with a ROC-AUC of 0.75. For the luminal-basal subtype classification task, we achieved a 68% patch wise accuracy on the validation set with a ROC-AUC of 0.76 for normalized data and 68% patch-wise accuracy with a ROC-AUC of 0.74 for non-normalized data. We are currently testing the model on an internal urothelial cancer cohort at Weill Cornell Medicine. Our data demonstrates the utility of deep learning methods in predicting UC molecular subtype and immune status from digital pathology slides. This data has important implications for predicting prognosis and treatment response in UC patients.

Citation Format: Matthew Bryan Brendel, Pegah Khosravi, Emily Tse, Lilly Gu, Kyrillus Shohdy, Rohan Bareja, Bhavneet Bhinder, Olivier Elemento, Bishoy Faltas, Iman Hajirasouliha. Deep learning predicts expression-based molecular subtypes and immune status of urothelial cancer using digital pathology slides [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 859.

Multicenter Phase II Study of Cabazitaxel in Advanced Gastroesophageal Cancer: Association of HER2 Expression and M2-Like Tumor-Associated Macrophages with Patient Outcome

PURPOSE

We examined cabazitaxel, a novel next-generation taxoid, in patients with metastatic gastric cancer in a multicenter phase II study.

PATIENTS AND METHODS

Patients who have progressed on one or more prior therapies for locally advanced, unresectable, or metastatic disease were eligible, and prior taxane therapy was allowed. Taxane-naïve and pretreated cohorts were analyzed independently for efficacy. The primary endpoint for both cohorts was progression-free survival (PFS) using RECIST 1.1, using a Simon's two-stage design (10% significance and 80% power) for both cohorts. Comprehensive molecular annotation included whole exome and bulk RNA sequencing.

RESULTS

Fifty-three patients enrolled in the taxane-naïve cohort (Arm A) and 23 patients in the prior-taxane cohort (Arm B), from January 8, 2013, to April 8, 2015: median age 61.7 years (range, 35.5-91.8 years), 66% male, 66% Caucasian. The most common adverse events included neutropenia (17% Arm A and 39% Arm B), fatigue/muscle weakness (13%), and hematuria (12%). In Arm A, the 3-month PFS rate was 28% [95% confidence interval (CI), 17%-42%] and did not meet the prespecified efficacy target. The 3-month PFS rate in Arm B was 35% (95% CI, 16%-57%) and surpassed its efficacy target. HER2 amplification or overexpression was associated with improved disease control (P = 0.003), PFS (P = 0.04), and overall survival (P = 0.002). An M2 macrophage signature was also associated with improved survival (P = 0.031).

CONCLUSIONS

Cabazitaxel has modest activity in advanced gastric cancer, including in patients previously treated with taxanes. Her2 amplification/overexpression and M2 high macrophage signature are potential biomarkers for taxane efficacy that warrant further evaluation.

Demographic and genetic factors influence the abundance of infiltrating immune cells in human tissues

Despite infiltrating immune cells having an essential function in human disease and patients' responses to treatments, mechanisms influencing variability in infiltration patterns remain unclear. Here, using bulk RNA-seq data from 46 tissues in the Genotype-Tissue Expression project, we apply cell-type deconvolution algorithms to evaluate the immune landscape across the healthy human body. We discover that 49 of 189 infiltration-related phenotypes are associated with either age or sex (FDR < 0.1). Genetic analyses further show that 31 infiltration-related phenotypes have genome-wide significant associations (iQTLs) (P < 5.0 × 10-8), with a significant enrichment of same-tissue expression quantitative trait loci in suggested iQTLs (P < 10-5). Furthermore, we find an association between helper T cell content in thyroid tissue and a COMMD3/DNAJC1 regulatory variant (P = 7.5 × 10-10), which is associated with thyroiditis in other cohorts. Together, our results identify key factors influencing inter-individual variability of immune infiltration, to provide insights on potential therapeutic targets.

Integrative Molecular Analysis of Patients With Advanced and Metastatic Cancer

PURPOSE

We developed a precision medicine program for patients with advanced cancer using integrative whole-exome sequencing and transcriptome analysis.

PATIENTS AND METHODS

Five hundred fifteen patients with locally advanced/metastatic solid tumors were prospectively enrolled, and paired tumor/normal sequencing was performed. Seven hundred fifty-nine tumors from 515 patients were evaluated.

RESULTS

Most frequent tumor types were prostate (19.4%), brain (16.5%), bladder (15.4%), and kidney cancer (9.2%). Most frequently altered genes were TP53 (33%), CDKN2A (11%), APC (10%), KTM2D (8%), PTEN (8%), and BRCA2 (8%). Pathogenic germline alterations were present in 10.7% of patients, most frequently CHEK2 (1.9%), BRCA1 (1.5%), BRCA2 (1.5%), and MSH6 (1.4%). Novel gene fusions were identified, including a RBM47-CDK12 fusion in a metastatic prostate cancer sample. The rate of clinically relevant alterations was 39% by whole-exome sequencing, which was improved by 16% by adding RNA sequencing. In patients with more than one sequenced tumor sample (n = 146), 84.62% of actionable mutations were concordant.

CONCLUSION

Integrative analysis may uncover informative alterations for an advanced pan-cancer patient population. These alterations are consistent in spatially and temporally heterogeneous samples.

Abstract 134: Immunogenomic landscape of neuroendocrine prostate cancer (NEPC)

Background: NEPC is a histological subtype of advanced prostate cancer, predominantly arising clonally from castrate resistant prostate adenocarcinoma (CRPC) as a mechanism of resistance. Given current immunotherapeutic strategies only showing modest clinical benefit in prostate cancer patients and NEPC having clinical features aligned with small cell lung carcinoma (SCLC) we investigated the immune landscape of NEPC in relation to prostate cancer subtypes and SCLC to identify potential targets.

Methods: We evaluated RNA-seq from a 190 patient cohort including benign prostate (n=29; 25 PCa matched), localized prostate adenocarcinoma (PCa; n=68), hormone-naïve metastatic prostate adenocarcinoma (mPCa; n=11), CRPC (n=54), NEPC (n=25; 11 de novo) with follow-up data, and SCLC (n=28) (Rudin et al., Nat Gen 2012). Additionally, 234 prostate cancer patients had tumor mutational burden (TMB) determined by WES. Unsupervised clustering of FPKMs was performed to identify a 232 gene, immune-rich cluster, used to categorize immune status and prioritize validation of targets by IHC.

Results: Prostate cancer is known to have a relatively low TMB. Similarly, the median TMB of NEPC is akin to CRPC (38.0 vs 37.0 p = 0.44) while significantly lower than SCLC (38.0 vs 142.5, p &lt;0.001). Unsupervised assessment identified a predominantly ‘cold’ immune status across subtypes, with ‘hot’ tumors (n=8) associated with metastatic tumors of the LN and bone and ‘intermediate’ NEPC tumors (n=9) associated with de novo cases. Worse overall survival was associated with intermediate vs cold T-cell immune status (66.5 mo vs 101.5 mo; p &lt;0.001). Further analysis of NEPC showed lower expression of cytokines (p&lt;0.01) as well as variation in checkpoint markers. Specifically, NEPC tumors had significantly lower expression of PD1 in relation to CRPC (p = 0.0001) and SCLC (p = &lt;0.0001), higher PDL1 expression than CRPC (p = 0.05) but comparable with SCLC (p = 0.93) and lower PDL2 expression than PCa and SCLC (p = 0.03; &lt;0.001, respectively).

Conclusion: NEPC is characterized by a relatively ‘cold’ tumor immune microenvironment similar to other metastatic prostate cancer subtypes but higher PDL1 expression comparable to SCLC. Association of colder tumors with treatment-induced disease, inverse correlation between survival outcome and immune infiltration, as well as novel expression changes in cytokines and checkpoint markers support further investigation into the immune landscape and potential targets for NEPC.

Citation Format: Alison M. Ferguson, Bhavneet Bhinder, Vincenza Conteduca, Michael Sigouros, Andrea Sboner, David Nanus, Scott Tagawa, David Rickman, Olivier Elemento, Himisha Beltran. Immunogenomic landscape of neuroendocrine prostate cancer (NEPC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 134.

Immunogenomic landscape of neuroendocrine prostate cancer (NEPC)

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Background: Prostate cancer (PCa) shows limited clinical benefit from current immunotherapy strategies. NEPC is a histologic subtype of advanced PCa that most often arises clonally from castrate resistant prostate adenocarcinoma (CRPC) as a mechanism of resistance, but shares pathologic, clinical, and molecular features with small cell lung carcinoma (SCLC). We investigated the immune landscape of NEPC in relation to other PCa subtypes and SCLC to identify potential immunological targets. Methods: We evaluated RNA-seq from 190 patients comprising benign prostate (n = 29; 25 PCa matched), localized PCa (n = 68), hormone-naïve metastatic prostate adenocarcinoma (mPCa; n = 11), CRPC (n = 54), NEPC (n = 25) with follow-up data, and SCLC (n = 28) (Rudin et al., Nat Gen 2012). Additionally, 290 patients had WES data available for tumor mutational burden (TMB). Unsupervised clustering of FPKMs was performed to identify an immune rich cluster of 232 genes, which was used to categorize immune status and prioritize validation of select targets by IHC. Results: Median TMB of NEPC was similar to CRPC (38.0 vs 37.0 p= 0.44) but significantly lower than SCLC (38.0 vs 142.5, p< 0.001). Unsupervised assessment of T-cell related gene expression identified a predominantly cold immune status across subtypes, with hot (n = 8) tumors associated with metastatic tumors of the LN and bone. Worse overall survival was seen with intermediate vs cold T-cell immune status (66.5 mo vs 101.5 mo; p < 0.001). Further analysis of NEPC showed lower expression of cytokines ( p< 0.01) and variation in checkpoint markers. Specifically, NEPC had significantly lower expression of PD1 in relation to CRPC ( p= 0.0001) and SCLC ( p = < 0.0001), higher PDL1 than CRPC ( p= 0.05) but comparable with SCLC ( p= 0.93) and lower PDL2 than PCa and SCLC ( p= 0.03; < 0.001, respectively). Conclusions: NEPC is characterized by a relatively ‘cold’ tumor immune microenvironment similar to other metastatic prostate cancer subtypes but higher PDL1 expression comparable to SCLC. The inverse correlation between survival outcome and immune infiltration, as well as the novel expression changes in cytokines and checkpoint markers support further investigation into the immune landscape and potential targets for NEPC.

Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome

BACKGROUND

To further our understanding of immunopeptidomics, improved tools are needed to identify peptides presented by major histocompatibility complex class I (MHC-I). Many existing tools are limited by their reliance upon chemical affinity data, which is less biologically relevant than sampling by mass spectrometry, and other tools are limited by incomplete exploration of machine learning approaches. Herein, we assemble publicly available data describing human peptides discovered by sampling the MHC-I immunopeptidome with mass spectrometry and use this database to train random forest classifiers (ForestMHC) to predict presentation by MHC-I.

RESULTS

As measured by precision in the top 1% of predictions, our method outperforms NetMHC and NetMHCpan on test sets, and it outperforms both these methods and MixMHCpred on new data from an ovarian carcinoma cell line. We also find that random forest scores correlate monotonically, but not linearly, with known chemical binding affinities, and an information-based analysis of classifier features shows the importance of anchor positions for our classification. The random-forest approach also outperforms a deep neural network and a convolutional neural network trained on identical data. Finally, we use our large database to confirm that gene expression partially determines peptide presentation.

CONCLUSIONS

ForestMHC is a promising method to identify peptides bound by MHC-I. We have demonstrated the utility of random forest-based approaches in predicting peptide presentation by MHC-I, assembled the largest known database of MS binding data, and mined this database to show the effect of gene expression on peptide presentation. ForestMHC has potential applicability to basic immunology, rational vaccine design, and neoantigen binding prediction for cancer immunotherapy. This method is publicly available for applications and further validation.

Immune reprogramming via PD-1 inhibition enhances early-stage lung cancer survival

Success of immune checkpoint inhibitors in advanced non-small-cell lung cancer (NSCLC) has invigorated their use in the neoadjuvant setting for early-stage disease. However, the cellular and molecular mechanisms of the early immune responses to therapy remain poorly understood. Through an integrated analysis of early-stage NSCLC patients and a Kras mutant mouse model, we show a prevalent programmed cell death 1/programmed cell death 1 ligand 1 (PD-1/PD-L1) axis exemplified by increased intratumoral PD-1+ T cells and PD-L1 expression. Notably, tumor progression was associated with spatiotemporal modulation of the immune microenvironment with dominant immunosuppressive phenotypes at later phases of tumor growth. Importantly, PD-1 inhibition controlled tumor growth, improved overall survival, and reprogrammed tumor-associated lymphoid and myeloid cells. Depletion of T lymphocyte subsets demonstrated synergistic effects of those populations on PD-1 inhibition of tumor growth. Transcriptome analyses revealed T cell subset-specific alterations corresponding to degree of response to the treatment. These results provide insights into temporal evolution of the phenotypic effects of PD-1/PD-L1 activation and inhibition and motivate targeting of this axis early in lung cancer progression.

Evaluation of Compound Optical Interference in High-Content Screening

Compound optical interference remains an inherent problem in chemical screening and has been well documented for biochemical assays and less so for automated microscopy-based assays. It has also been the assumption that the latter should not suffer from such interference because of the washing steps involved in the process, thus eliminating the residual nonspecific compound effects. Instead, these compounds may have no relevance to the actual target, and as such, compound optical interference contributes to a number of false-positives, resulting in a high attrition rate during subsequent follow-up studies. In this report, we analyze the outcome of a high-content screen using enhanced green fluorescent protein as a reporter in a gain-of-function cell-based assay in search of modulators of the micro RNA (miRNA) biogenesis pathway. Using a previously validated image-based biosensor, we screened a diverse library collection of ~315,000 compounds covering natural and synthetic derivatives in which 1130 positives were identified to enhance green fluorescence expression. Lateral confirmation and dose-response studies revealed that all of these compounds were the result of optical interference and not specific inhibition of miRNA biogenesis. Here, we highlight the chemical classes that are susceptible to compound optical interference and discuss their implications in automated microscopy-based assays.

Towards a better cancer precision medicine: systems biology meets immunotherapy

Systems biology approaches that embrace the complexity of cancer are starting to gain traction in the development of new anticancer therapeutic strategies. In this review we describe how genomic analyses are helping improve our understanding of response to immunotherapy, a front-runner in cancer treatment. We argue that systems-level approaches are needed to help understand the concerted impact of tumor-specific and immune-specific molecular features on clinical outcomes, predict responders and unravel the complexity of tumor ecosystems. This integrated approach will propel immunotherapy into the exciting world of precision medicine.

Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care

We describe Exome Cancer Test v1.0 (EXaCT-1), the first New York State-Department of Health-approved whole-exome sequencing (WES)-based test for precision cancer care. EXaCT-1 uses HaloPlex (Agilent) target enrichment followed by next-generation sequencing (Illumina) of tumour and matched constitutional control DNA. We present a detailed clinical development and validation pipeline suitable for simultaneous detection of somatic point/indel mutations and copy-number alterations (CNAs). A computational framework for data analysis, reporting and sign-out is also presented. For the validation, we tested EXaCT-1 on 57 tumours covering five distinct clinically relevant mutations. Results demonstrated elevated and uniform coverage compatible with clinical testing as well as complete concordance in variant quality metrics between formalin-fixed paraffin embedded and fresh-frozen tumours. Extensive sensitivity studies identified limits of detection threshold for point/indel mutations and CNAs. Prospective analysis of 337 cancer cases revealed mutations in clinically relevant genes in 82% of tumours, demonstrating that EXaCT-1 is an accurate and sensitive method for identifying actionable mutations, with reasonable costs and time, greatly expanding its utility for advanced cancer care.

Proteasome Addiction Defined in Ewing Sarcoma Is Effectively Targeted by a Novel Class of 19S Proteasome Inhibitors

Ewing sarcoma is a primitive round cell sarcoma with a peak incidence in adolescence that is driven by a chimeric oncogene created from the fusion of the EWSR1 gene with a member of the ETS family of genes. Patients with metastatic and recurrent disease have dismal outcomes and need better therapeutic options. We screened a library of 309,989 chemical compounds for growth inhibition of Ewing sarcoma cells to provide the basis for the development of novel therapies and to discover vulnerable pathways that might broaden our understanding of the pathobiology of this aggressive sarcoma. This screening campaign identified a class of benzyl-4-piperidone compounds that selectively inhibit the growth of Ewing sarcoma cell lines by inducing apoptosis. These agents disrupt 19S proteasome function through inhibition of the deubiquitinating enzymes USP14 and UCHL5. Functional genomic data from a genome-wide shRNA screen in Ewing sarcoma cells also identified the proteasome as a node of vulnerability in Ewing sarcoma cells, providing orthologous confirmation of the chemical screen findings. Furthermore, shRNA-mediated silencing of USP14 or UCHL5 in Ewing sarcoma cells produced significant growth inhibition. Finally, treatment of a xenograft mouse model of Ewing sarcoma with VLX1570, a benzyl-4-piperidone compound derivative currently in clinical trials for relapsed multiple myeloma, significantly inhibited in vivo tumor growth. Overall, our results offer a preclinical proof of concept for the use of 19S proteasome inhibitors as a novel therapeutic strategy for Ewing sarcoma. Cancer Res; 76(15); 4525-34. ©2016 AACR.

Generating a neoantigen map of advanced urothelial carcinoma by whole exome sequencing

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Background: immune-checkpoint blockade is a promising treatment of advanced urothelial carcinoma (UC) that unleashes pre-existing immune responses against recognized tumor antigens. Somatic mutations lead to the formation of neoantigens, which are highly antigenic mutant proteins. Methods: Our objective was to generate a neoantigen map through analysis of whole exome sequencing data of our cohort of patients (pts) with platinum-resistant UC. Whole exome sequencing (WES) data from 73 prospectively collected UC samples from 34 patients were analyzed using our neoantigen prediction pipeline. We defined neoantigens as mutant nonamers with high affinity binding to predicted class I MHC molecules for each patient. HLA haplotypes were inferred from WES of matched germline DNA. Results: A significant correlation between global somatic mutation rates, and neo-epitope burden was observed (R2 = 0.93), a similar correlation was observed between single nucleotide variants (SNV) and neo-epitope burdens (R2 = 0.94). We identified a strong positive correlation between the numbers of pack-years of smoking and neoepitope burden in patients with advanced UC (p = 0.0004). No correlation between global somatic mutational and predicted neoepitope burdens with overall survival was identified. Metastatic samples had a trend of harboring more SNVs (median 49 vs. 22, P = 0.13), and neoepitopes (median 17 vs 12, P = 0.22) compared to primary samples. Interestingly, only 32% of total SNVs and 8 % of neoepitopes (with binding affinities of ≤ 50nM) that were initially identified, reappeared in metastatic samples from the same patients obtained at a later time point. A significant selection against strong binding neo-epitopes was observed in subsequent samples from metastatic tumors (p-value < 0.005). Conclusions: A strong correlation between mutational burden and predicted neoantigenic load was observed in UC. Neoantigenic signatures were shaped by environmental exposures such as smoking. The significant heterogeneity in primary and metastatic neoantigens was possibly due to immunoediting as the tumor evolved. These findings may have important implications for selecting patients for immunotherapeutic approaches.

A 1536-well fluorescence polarization assay to screen for modulators of the MUSASHI family of RNA-binding proteins

RNA-binding proteins (RBPs) can act as stem cell modulators and oncogenic drivers, but have been largely ignored by the pharmaceutical industry as potential therapeutic targets for cancer. The MUSASHI (MSI) family has recently been demonstrated to be an attractive clinical target in the most aggressive cancers. Therefore, the discovery and development of small molecule inhibitors could provide a novel therapeutic strategy. In order to find novel compounds with MSI RNA binding inhibitory activity, we have developed a fluorescence polarization (FP) assay and optimized it for high throughput screening (HTS) in a 1536-well microtiter plate format. Using a chemical library of 6,208 compounds, we performed pilot screens, against both MSI1 and MSI2, leading to the identification of 7 molecules for MSI1, 15 for MSI2 and 5 that inhibited both. A secondary FP dose-response screen validated 3 MSI inhibitors with IC50 below 10 μM. Out of the 25 compounds retested in the secondary screen only 8 demonstrated optical interference due to high fluorescence. Utilizing a SYBR-based RNA electrophoresis mobility shift assay (EMSA), we further verified MSI inhibition of the top 3 compounds. Surprisingly, even though several aminoglycosides were present in the library, they failed to demonstrate MSI inhibitor activity challenging the concept that these compounds are pan-active against RBPs. In summary, we have developed an in vitro strategy to identify MSI specific inhibitors using an FP HTS platform, which will facilitate novel drug discovery for this class of RBPs.

Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion

Many cancer cells consume large quantities of glutamine to maintain TCA cycle anaplerosis and support cell survival. It was therefore surprising when RNAi screening revealed that suppression of citrate synthase (CS), the first TCA cycle enzyme, prevented glutamine-withdrawal-induced apoptosis. CS suppression reduced TCA cycle activity and diverted oxaloacetate, the substrate of CS, into production of the nonessential amino acids aspartate and asparagine. We found that asparagine was necessary and sufficient to suppress glutamine-withdrawal-induced apoptosis without restoring the levels of other nonessential amino acids or TCA cycle intermediates. In complete medium, tumor cells exhibiting high rates of glutamine consumption underwent rapid apoptosis when glutamine-dependent asparagine synthesis was suppressed, and expression of asparagine synthetase was statistically correlated with poor prognosis in human tumors. Coupled with the success of L-asparaginase as a therapy for childhood leukemia, the data suggest that intracellular asparagine is a critical suppressor of apoptosis in many human tumors.

A simple method for analyzing actives in random RNAi screens: introducing the "H Score" for hit nomination & gene prioritization

Due to the numerous challenges in hit identification from random RNAi screening, we have examined current practices with a discovery of a variety of methodologies employed and published in many reports; majority of them, unfortunately, do not address the minimum associated criteria for hit nomination, as this could potentially have been the cause or may well be the explanation as to the lack of confirmation and follow up studies, currently facing the RNAi field. Overall, we find that these criteria or parameters are not well defined, in most cases arbitrary in nature, and hence rendering it extremely difficult to judge the quality of and confidence in nominated hits across published studies. For this purpose, we have developed a simple method to score actives independent of assay readout; and provide, for the first time, a homogenous platform enabling cross-comparison of active gene lists resulting from different RNAi screening technologies. Here, we report on our recently developed method dedicated to RNAi data output analysis referred to as the BDA method applicable to both arrayed and pooled RNAi technologies; wherein the concerns pertaining to inconsistent hit nomination and off-target silencing in conjugation with minimal activity criteria to identify a high value target are addressed. In this report, a combined hit rate per gene, called "H score", is introduced and defined. The H score provides a very useful tool for stringent active gene nomination, gene list comparison across multiple studies, prioritization of hits, and evaluation of the quality of the nominated gene hits.

A novel high throughput 1536-well Notch1 γ -secretase AlphaLISA assay

The Notch pathway plays a crucial role in cell fate decisions through controlling various cellular processes. Overactive Notch signal contributes to cancer development from leukemias to solid tumors. γ-Secretase is an intramembrane protease responsible for the final proteolytic step of Notch that releases the membrane-tethered Notch fragment for signaling. Therefore, γ-secretase is an attractive drug target in treating Notch-mediated cancers. However, the absence of high throughput γ-secretase assay using Notch substrate has limited the identification and development of γ- secretase inhibitors that specifically target the Notch signaling pathway. Here, we report on the development of a 1536- well γ-secretase assay using a biotinylated recombinant Notch1 substrate. We effectively assimilated and miniaturized this newly developed Notch1 substrate with the AlphaLISA detection technology and demonstrated its robustness with a calculated Z' score of 0.66. We further validated this optimized assay by performing a pilot screening against a chemical library consisting of ~5,600 chemicals and identified known γ-secretase inhibitors e.g. DAPT, and Calpeptin; as well as a novel γ-secretase inhibitor referred to as KD-I-085. This assay is the first reported 1536-well AlphaLISA format and represents a novel high throughput Notch1-γ-secretase assay, which provides an unprecedented opportunity to discover Notch-selective γ-secretase inhibitors that can be potentially used for the treatment of cancer and other human disorders.

Discovery of a dicer-independent, cell-type dependent alternate targeting sequence generator: implications in gene silencing & pooled RNAi screens

There is an acceptance that plasmid-based delivery of interfering RNA always generates the intended targeting sequences in cells, making it as specific as its synthetic counterpart. However, recent studies have reported on cellular inefficiencies of the former, especially in light of emerging gene discordance at inter-screen level and across formats. Focusing primarily on the TRC plasmid-based shRNA hairpins, we reasoned that alleged specificities were perhaps compromised due to altered processing; resulting in a multitude of random interfering sequences. For this purpose, we opted to study the processing of hairpin TRCN#40273 targeting CTTN; which showed activity in a miRNA-21 gain-of-function shRNA screen, but inactive when used as an siRNA duplex. Using a previously described walk-through method, we identified 36 theoretical cleavage variants resulting in 78 potential siRNA duplexes targeting 53 genes. We synthesized and tested all of them. Surprisingly, six duplexes targeting ASH1L, DROSHA, GNG7, PRKCH, THEM4, and WDR92 scored as active. QRT-PCR analysis on hairpin transduced reporter cells confirmed knockdown of all six genes, besides CTTN; revealing a surprising 7 gene-signature perturbation by this one single hairpin. We expanded our qRT-PCR studies to 26 additional cell lines and observed unique knockdown profiles associated with each cell line tested; even for those lacking functional DICER1 gene suggesting no obvious dependence on dicer for shRNA hairpin processing; contrary to published models. Taken together, we report on a novel dicer independent, cell-type dependent mechanism for non-specific RNAi gene silencing we coin Alternate Targeting Sequence Generator (ATSG). In summary, ATSG adds another dimension to the already complex interpretation of RNAi screening data, and provides for the first time strong evidence in support of arrayed screening, and questions the scientific merits of performing pooled RNAi screens, where deconvolution of up to genome-scale pools is indispensable for target identification.

Modulators of the microRNA biogenesis pathway via arrayed lentiviral enabled RNAi screening for drug and biomarker discovery

MicroRNAs (miRNAs) are small endogenous and conserved non-coding RNA molecules that regulate gene expression. Although the first miRNA was discovered well over sixteen years ago, little is known about their biogenesis and it is only recently that we have begun to understand their scope and diversity. For this purpose, we performed an RNAi screen aimed at identifying genes involved in their biogenesis pathway with a potential use as biomarkers. Using a previously developed miRNA 21 (miR-21) EGFP-based biosensor cell based assay monitoring green fluorescence enhancements, we performed an arrayed short hairpin RNA (shRNA) screen against a lentiviral particle ready TRC1 library covering 16,039 genes in 384-well plate format, and interrogating the genome one gene at a time building a panoramic view of endogenous miRNA activity. Using the BDA method for RNAi data analysis, we nominate 497 gene candidates the knockdown of which increased the EGFP fluorescence and yielding an initial hit rate of 3.09%; of which only 22, with reported validated clones, are deemed high-confidence gene candidates. An unexpected and surprising result was that only DROSHA was identified as a hit out of the seven core essential miRNA biogenesis genes; suggesting that perhaps intracellular shRNA processing into the correct duplex may be cell dependent and with differential outcome. Biological classification revealed several major control junctions among them genes involved in transport and vesicular trafficking. In summary, we report on 22 high confidence gene candidate regulators of miRNA biogenesis with potential use in drug and biomarker discovery.

Chemical & RNAi screening at MSKCC: a collaborative platform to discover & repurpose drugs to fight disease

Memorial Sloan Kettering Cancer Center (MSKCC) has implemented the creation of a full service state-of-the-art High-throughput Screening Core Facility (HTSCF) equipped with modern robotics and custom-built screening data management resources to rapidly store and query chemical and RNAi screening data outputs. The mission of the facility is to provide oncology clinicians and researchers alike with access to cost-effective HTS solutions for both chemical and RNAi screening, with an ultimate goal of novel target identification and drug discovery. HTSCF was established in 2003 to support the institution's commitment to growth in molecular pharmacology and in the realm of therapeutic agents to fight chronic diseases such as cancer. This endeavor required broad range of expertise in technology development to establish robust and innovative assays, large collections of diverse chemical and RNAi duplexes to probe specific cellular events, sophisticated compound and data handling capabilities, and a profound knowledge in assay development, hit validation, and characterization. Our goal has been to strive for constant innovation, and we strongly believe in shifting the paradigm from traditional drug discovery towards translational research now, making allowance for unmet clinical needs in patients. Our efforts towards repurposing FDA-approved drugs fructified when digoxin, identified through primary HTS, was administered in the clinic for treatment of stage Vb retinoblastoma. In summary, the overall aim of our facility is to identify novel chemical probes, to study cellular processes relevant to investigator's research interest in chemical biology and functional genomics, and to be instrumental in accelerating the process of drug discovery in academia.

Death induced by CD95 or CD95 ligand elimination

CD95 (Fas/APO-1), when bound by its cognate ligand CD95L, induces cells to die by apoptosis. We now show that elimination of CD95 or CD95L results in a form of cell death that is independent of caspase-8, RIPK1/MLKL, and p53, is not inhibited by Bcl-xL expression, and preferentially affects cancer cells. All tumors that formed in mouse models of low-grade serous ovarian cancer or chemically induced liver cancer with tissue-specific deletion of CD95 still expressed CD95, suggesting that cancer cannot form in the absence of CD95. Death induced by CD95R/L elimination (DICE) is characterized by an increase in cell size, production of mitochondrial ROS, and DNA damage. It resembles a necrotic form of mitotic catastrophe. No single drug was found to completely block this form of cell death, and it could also not be blocked by the knockdown of a single gene, making it a promising way to kill cancer cells.

An image-based biosensor assay strategy to screen for modulators of the microRNA 21 biogenesis pathway

microRNAs (miRNAs) are evolutionary conserved, small endogenous non-coding, RNA molecules. Although their mode of action has been extensively studied, little is known about their biogenesis. As their altered expression has been implicated in many diseases, small molecules that would modulate their expression are sought after. They are generated through the concerted action of several complexes which promote their transcription, maturation, export, trafficking, and loading of mature miRNA into silencing complexes. An increasing number of studies have suggested that each of these steps serves as a regulatory junction in the process, and therefore provides an intervention point. For this purpose, we have developed a simple image-based assay strategy to screen for such modulators. Here, we describe its successful implementation which combines the use of a microRNA 21 (miR-21) synthetic mimic together with an EGFP based reporter cell line, where its expression is under the control of miR-21, to monitor EGFP expression in a format suitable for HTS. The strategy was further validated using a small panel of known gene modulators of the miRNA pathway. A screen was performed in duplicate against a library of 6,912 compounds and identified 48 initial positives exhibiting enhanced EGFP fluorescence intensity. 42 compounds were found to be inherently fluorescent in the green channel leaving the remaining 6 as potential inhibitors and with a positive rate of 0.09%. Taken together, this validated strategy offers the opportunity to discover novel and specific inhibitors of the pathway through the screening of diverse chemical libraries.

Systematic analysis of RNAi reports identifies dismal commonality at gene-level and reveals an unprecedented enrichment in pooled shRNA screens

RNA interference (RNAi) has opened promising avenues to better understand gene function. Though many RNAi screens report on the identification of genes, very few, if any, have been further studied and validated. Data discrepancy is emerging as one of RNAi main pitfalls. We reasoned that a systematic analysis of lethality-based screens, since they score for cell death, would examine the extent of hit discordance at inter-screen level. To this end, we developed a methodology for literature mining and overlap analysis of several screens using both siRNA and shRNA flavors, and obtained 64 gene lists censoring an initial list of 7,430 nominated genes. We further performed a comparative analysis first at a global level followed by hit re-assessment under much more stringent conditions. To our surprise, none of the hits overlapped across the board even for PLK1, which emerged as a strong candidate in siRNA screens; but only marginally in the shRNA ones. Furthermore, EIF5B emerges as the most common hit only in the shRNA screens. A highly unusual and unprecedented result was the observation that 5,269 out of 6,664 nominated genes (~80%) in the shRNA screens were exclusive to the pooled format, raising concerns as to the merits of pooled screens which qualify hits based on relative depletions, possibly due to multiple integrations per cell, data deconvolution or inaccuracies in intracellular processing causing off-target effects. Without golden standards in place, we would encourage the community to pay more attention to RNAi screening data analysis practices, bearing in mind that it is combinatorial in nature and one active siRNA duplex or shRNA hairpin per gene does not suffice credible hit nomination. Finally, we also would like to caution interpretation of pooled shRNA screening outcomes.

A high-content assay strategy for the identification and profiling of ABCG2 modulators in live cells

ABCG2 is a member of the ATP-binding cassette (ABC) family of transporters, the overexpression of which has been implicated in resistance to various chemotherapeutic agents. Though a number of cell-based assays to screen for inhibitors have been reported, they do not provide a content-rich platform to discriminate toxic and autofluorescent compounds. To fill this gap, we developed a live high-content cell-based assay to identify inhibitors of ABCG2-mediated transport and, at the same time, assess their cytotoxic effect and potential optical interference. We used a pair of isogenic U87MG human glioblastoma cell lines, with one stably overexpressing the ABCG2 transporter. JC-1 (J-aggregate-forming lipophilic cation 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazol carbocyanine iodide) was selected as the optimal reporter substrate for ABCG2 activity, and the resulting assay was characterized by a Z' value of 0.50 and a signal-to-noise (S/N) ratio of 14 in a pilot screen of ∼ 7,000 diverse chemicals. The screen led to the identification of 64 unique nontoxic positives, yielding an initial hit rate of 1%, with 58 of them being confirmed activity. In addition, treatment with two selected confirmed positives suppressed the side population of U87MG-ABCG2 cells that was able to efflux the Hoechst dye as measured by flow cytometry, confirming that they constitute potent new ABCG2 transporter inhibitors. Our results demonstrate that our live cell and content-rich platform enables the rapid identification and profiling of ABCG2 modulators, and this new strategy opens the door to the discovery of compounds targeting the expression and/or trafficking of ABC transporters as an alternative to functional inhibitors that failed in the clinic.