Dysregulation of intracellular signaling networks underpins cancer. Yet, resolving signaling networks within distinct or rare cell types in cancer in vivo has been unattainable. Here we develop INSIGHT by integrating cell sorting with mass spectrometry to enable quantitative phosphoproteomics and proteomics of discrete cell types from fixed tissues. Using INSIGHT, we map the signaling network within disseminating glioblastoma cells from patient-derived xenografts implanted in mice. Disseminating tumor cells undergo a proteome-wide shift from proliferative to mesenchymal, neural progenitor-like cell states. In parallel, signaling network and global kinase activity are rewired, transitioning from cell cycle-associated circuitries to those governing synaptic function, neuronal migration, and ion channel activity. Changes begin at the tumor margin and persist in distant brain parenchyma. Hornerin and phosphorylation of Ca²⁺-permeable GluA2 at Y876 were identified as mediators of glioblastoma progression. INSIGHT enables systems-level dissection of cell-type-specific signaling circuitries in vivo across wide range of biological systems.

Malignant glioma is incurable. Using a mouse genetic mosaic system to generate sporadic Trp53,Nf1-null OPCs, we previously identified oligodendrocyte precursor cell (OPC) as a cell-of-origin of glioma. Here, we report that pre-malignant Trp53,Nf1-null OPCs outcompete wildtype counterparts during their expansion. Blocking competition by mutating/strengthening wildtype OPCs impeded both pre-malignant progression and malignant expansion of glioma. "In-tissue" phosphoproteomic profiling revealed an enrichment of phosphopeptides related to RNA splicing and protein translation at the peak of cell competition, suggesting that competitiveness may stem from unique protein species. Among candidates was mTORC1, whose pharmacological inhibition or genetic disruption resulted in a loss of competitiveness in our mouse model. Finally, analysis of patient biopsies and interrogating the role of individual gliomagenic mutations in OPC competition supported its relevance in human gliomas. Together, these findings identified the driving role of competitive interactions among OPCs in gliomagenesis, and suggest unconventional therapeutic strategies to target this process.

Glioblastoma (GBM) is an aggressive primary brain cancer with few effective therapies. Stereotactic needle biopsies are routinely used for diagnosis; however, the feasibility and utility of investigative biopsies to monitor treatment response remains ill-defined. Here, we demonstrate the depth of data generation possible from routine stereotactic needle core biopsies and perform highly resolved multi-omics analyses, including single-cell RNA sequencing, spatial transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics on standard biopsy tissue obtained intra-operatively. We also examine biopsies taken from different locations and provide a framework for measuring spatial and genomic heterogeneity. Finally, we investigate the utility of stereotactic biopsies as a method for generating patient-derived xenograft (PDX) models. Multimodal dataset integration highlights spatially mapped immune cell-associated metabolic pathways and validates inferred cell-cell ligand-receptor interactions. In conclusion, investigative biopsies provide data-rich insight into disease processes and may be useful in evaluating treatment responses.

Although effective for immunologically hot tumors, immune checkpoint inhibitors minimally affect tumors that are not T cell inflamed, including breast cancer. An alternate strategy to combat immune cold breast tumors may be to reeducate innate immunity. This study identifies strategies to skew neutrophils to acquire tumoricidal properties. Systemic Toll-like receptor (TLR)–induced inflammation, concomitant with mitochondrial complex I inhibition in breast tumors, increases neutrophil cytotoxicity against breast cancer cells and independently of CD8+ T cell immunity. These therapy-entrained neutrophils enhance secretory granule production, increasing expression of the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase machinery and inducing a respiratory burst. Moreover, systemic administration of TLR agonists elevates nuclear factor κB signaling in neutrophils to increase production of secretory granule and NADPH oxidase machinery components, whereas complex I inhibitors are required to potentiate oxidative damage. In summary, we describe a class of neutrophils, educated by the combined action of inflammatory mediators and metabolic inhibitors, having tumoricidal functions.

Recurrent glioblastoma (rGBM) is incurable, and routine clinical monitoring is often insufficient to uncover mechanisms of treatment failure in clinical trials. To improve clinical monitoring and mechanistic insights from rGBM trials, we are conducting a Break Through Cancer collaborative clinical trial in which tumor biopsies are collected and subjected to multi-omic profiling at up to 6 timepoints in each patient over a 4 month period of treatment with intratumorally delivered oncolytic herpesvirus (HSV) (CAN-3110, aka rQNestin34.5v.2). Here we report findings from the first two patients in this study. Longitudinal sampling was feasible and well-tolerated, with 96 serial rGBM biopsy cores being obtained over a 4 month period from the two patients. Routine pathology confirmed infiltrating glioma with some necrosis and gliosis at the time of trial enrollment, and serial radiologic monitoring showed increased contrast enhancement consistent with continued tumor growth throughout the therapy period for both patients. In contrast, longitudinal multi-omic profiling revealed decreasing tumor cell density, changes in tumor cell states, increased immune infiltration/activation, and increased HLA protein expression following therapy. In addition to time-dependent changes, we also observed spatially driven changes. Biopsy sites further from HSV injection sites had higher tumor cell densities and HLA class II protein expression, while biopsies closer to HSV injection sites had higher immune activation and MHCI signatures. Functional profiling of TCR specificity also revealed increasing frequency of anti-HSV CD4/8 T cell clones following therapy, consistent with a treatment-induced intratumoral immune response. These results show that longitudinal tissue sampling during rGBM clinical trials is well tolerated and, even with a small number of patients, can reveal critical mechanistic insights into a therapy’s impact that would be missed via routine clinical monitoring. (clinicaltrials.gov NCT03152318)

Glioblastoma (GBM) is an aggressive primary brain cancer with few effective therapies. Standard endpoints such as overall survival, progression free survival or radiology are coarse markers of treatment response, and there is a strong need to improve the current understanding of how the tumor, host immune system and tumor microenvironment respond to therapies. Currently, few opportunities exist to obtain additional tissue samples to understand tumor responses apart from initial surgery. This lack of visibility into tumor and immune co-evolution under treatment is a fundamental limitation in our ability to develop and advance new GBM therapies. Stereotactic needle biopsies are routinely used for diagnosis; however, the feasibility and utility of investigative biopsies to monitor treatment response remains ill-defined. The goal of the present study was the investigate the feasibility of performing highly resolved multi-omics analyses on routine stereotactic biopsy samples obtained during surgery. Single-cell RNA sequencing, spatial transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics was performed on standard biopsy tissue obtained intra-operatively. We also examine biopsies taken from different locations and provide a framework for measuring spatial and genomic heterogeneity. Finally, we investigate the utility of stereotactic biopsies as a method for generating patient-derived xenograft (PDX)models Optimized workflows resulted in sufficient yield to perform single cell RNA sequencing of biopsy samples and matched spatial proteomic profiling. MHC Class I immunopeptidomics and phosphoproteomics was generated and cross referenced to single cell gene expression data. Spatial proteomics data was integrated with single cell RNA sequencing and spatial metabolomics data. Multi-modal dataset integration highlights spatially mapped immune cell-associated metabolic pathways and validates inferred cell-cell ligand-receptor interactions. Intra- and inter-regional biopsy variance was also quantified. Finally, patient derived xenografts were generated using needle core biopsies. In conclusion, investigative biopsies provide data-rich insight into disease processes and will likely play an increasingly important role in evaluating treatment responses going forward.

Recurrent glioblastoma (rGBM) remains incurable. One barrier to the development of effective rGBM therapies is the difficulty in collecting posttreatment tumor tissue. Serial multiomic assays from longitudinal rGBM biopsies may uncover tumor responses to a treatment. Here, we obtained 97 serial rGBM biopsy cores over 4 months from the first two patients participating in a clinical trial of repeated intratumoral dosing of the immunotherapeutic agent CAN-3110. Multiomic analysis of the biopsy cores revealed therapeutic effects, including longitudinal and spatial reshaping of the rGBM's microenvironment, expansion of new T cell tissue-resident effector memory clonotypes against CAN-3110 epitopes and other undetermined antigens, and expression of human leukocyte antigen (HLA)-presented immunopeptides, including cancer testis antigens. Moreover, serial integrated multimodal analyses provided evidence of therapeutic responses to CAN-3110 despite traditional magnetic resonance imaging indicating progression. Clinically, the two treated patients achieved a pathologic response or stable clinical disease, respectively. These results show the value of longitudinal tissue sampling to understand rGBM's evolution during administration of an investigational therapy.

Abstract Macrophages are a type of immune cell that play a crucial role in the tumor microenvironment. In tumors, macrophages can be polarized towards a pro-inflammatory phenotype, referred to as M1, or towards an anti-inflammatory and tumor-promoting phenotype, referred to as M2. M2 macrophages promote tumor growth by secreting cytokines that increase tumor proliferation, angiogenesis, and dampen the immune response from other immune cells such as T cells and dendritic cells. The balance between M1 and M2 macrophages in the tumor microenvironment is critical in determining the outcome of cancer progression and response to therapy. By understanding the pathways that lead to macrophage polarization, we can develop therapeutics that inhibit this process and support an anti-tumor macrophage response. Co-culture is a powerful model to study interactions between different cell types. We created co-cultures with macrophages and glioblastoma multiforme (GBM) cells to understand how these cell-cell interactions can lead to altered cell phenotype. Several studies have looked at the interaction of two populations using a transwell system where one cell population is placed in a well with a permeable membrane and the other population is placed below, allowing for the exchange of soluble factors. However, this does not account for an important mode of cell-cell interaction, which is physical contact. Therefore, we tested how macrophages derived from primary monocytes polarized in the context of conditioned media (supernatant), cell lysate, and direct co-culture. We used U87-MG as a model GBM cell line. We assayed the M2 phenotype by using flow cytometry with CD163 as a marker. Our findings show that direct co-culture is crucial for promoting macrophage M2 polarization. Using our in vitro model for tumor-induced macrophage polarization, we conducted phosphoproteomic analysis to characterize signals associated with this phenotypic change. To study how co-culture induced differential signaling in tumor populations and macrophages, we devised a method to fix cells to preserve cell signaling, followed by separation using flow cytometry and LC-MS/MS analysis of individual cell populations. We created co-cultures of U87-MG tumor cells and macrophage-differentiated THP-1 cells, a monocyte cell line. We then tested whether our method could reliably separate the different populations, whether we could detect altered signals due to co-culture, and showcase how separating cell populations yields information that could not be gathered from bulk analysis of co-cultures. Our data shows that the analysis was highly reproducible and that the signaling from cells separated from co-culture was highly similar to signaling in cells that were grown individually. However, some phosphorylation residues were uniquely upregulated in the co-culture condition, pointing to signaling that may occur in response to tumor interaction. Citation Format: Alicia D. D'Souza, Rachit Mukkamala, Ryuhjin Ahn, Forest M. White. Characterizing signaling in macrophage-GBM cell coculture [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5365.

Dysregulation of intracellular signaling networks underpins cancer. However, a systems-level elucidation of how signaling networks within distinct cell subpopulations drive cancer progression in vivo has been unattainable due to technical limitations. We developed INSIGHT (INvestigating SIGnaling network of specific cell subpopulation in Heterogeneous Tissue), a new platform technology combining fluorescence-activated cell sorting with ultra-sensitive mass spectrometry to enable phosphoproteomic characterization of rare and discrete cell subpopulations from fixed tissues. We demonstrated the broad utility of INSIGHT by analyzing the oligodendroglial cell-specific signaling network in the mouse brain. We then applied INSIGHT to investigate the rare, disseminated tumor cell subpopulation in glioblastoma patient-derived xenograft models. INSIGHT uncovered a global rewiring of signaling networks with tumor cell dissemination, marked by a transition from proliferation-associated signaling in the primary tumor cells to signaling associated with postsynapse, neuronal migration, and ion homeostasis in disseminated tumor cells. We reveal interconnections between signaling circuitries within the networks, with numerous proteins, including GluA2, exhibiting altered phosphorylation without protein expression changes, emphasizing the role of post-translational modifications in glioblastoma dissemination. We validated key phosphorylation changes and inferred differentially active kinases with tumor spread to offer new systems-level insights into glioblastoma dissemination mechanisms in vivo. INSIGHT is generally applicable to a wide range of biological systems without genetic engineering and provides quantitative phosphorylation and protein expression data for selected cell subpopulations from heterogeneous tissues. ### Competing Interest Statement The authors have declared no competing interest.

Vaccines and immunotherapies that target peptide-major histocompatibility complexes (peptide-MHCs) have the potential to address multiple unmet medical needs in cancer and infectious disease. Designing vaccines and immunotherapies to target peptide-MHCs requires accurate identification of target peptides in infected or cancerous cells or tissue, and may require absolute or relative quantification to identify abundant targets and measure changes in presentation under different treatment conditions. Internal standard parallel reaction monitoring (also known as 'SureQuant') can be used to validate and/or quantify MHC peptides previously identified by using untargeted methods such as data-dependent acquisition. SureQuant MHC has three main use cases: (i) conclusive confirmation of the identities of putative MHC peptides via comparison with an internal synthetic stable isotope labeled (SIL) peptide standard; (ii) accurate relative quantification by using pre-formed heavy isotope-labeled peptide-MHC complexes (hipMHCs) containing SIL peptides as internal controls for technical variation; and (iii) absolute quantification of each target peptide by using different amounts of hipMHCs loaded with synthetic peptides containing one, two or three SIL amino acids to provide an internal standard curve. Absolute quantification can help determine whether the abundance of a peptide-MHC is sufficient for certain therapeutic modalities. SureQuant MHC therefore provides unique advantages for immunologists seeking to confidently validate antigenic targets and understand the dynamics of the MHC repertoire. After synthetic standards are ordered (3-4 weeks), this protocol can be carried out in 3-4 days and is suitable for individuals with mass spectrometry experience who are comfortable with customizing instrument methods.

Central to successful cancer immunotherapy is effective T cell antitumor immunity. Multiple targeted immunotherapies engineered to invigorate T cell-driven antitumor immunity rely on identifying the repertoire of T cell antigens expressed on the tumor cell surface. Mass spectrometry-based survey of such antigens (“immunopeptidomics”) combined with other omics platforms and computational algorithms has been instrumental in identifying and quantifying tumor-derived T cell antigens. In this review, we discuss the types of tumor antigens that have emerged for targeted cancer immunotherapy and the immunopeptidomics methods that are central in MHC peptide identification and quantification. We provide an overview of the strength and limitations of mass spectrometry-driven approaches and how they have been integrated with other technologies to discover targetable T cell antigens for cancer immunotherapy. We highlight some of the emerging cancer immunotherapies that successfully capitalized on immunopeptidomics, their challenges, and mass spectrometry-based strategies that can support their development.

Abstract The GL261-luc2 and CT2A-luc syngeneic tumor lines are frequently used as immunocompetent orthotopic mouse models of human glioblastoma (huGBM), but demonstrate distinct differences in response to immune checkpoint blockade. Whereas GL261-luc2 is readily responsive to several immunotherapies, CT2A-luc is broadly resistant to diverse immunotherapeutic modalities. To decipher the cell-intrinsic mechanisms that drive immunotherapy resistance in CT2A-luc and to define the aspects of human cancer biology that these lines can best model, we systematically compared their genomic and phenotypic profiles. The transcriptional profiles of GL261-luc2 and CT2A-luc tumors resembled those of huGBM, despite neither line sharing the canonical genetic or histologic features of huGBM. Both models exhibited striking hypermutation and contained clonal hotspot mutations in RAS genes (Kras p.G12C in GL261-luc2 and Nras p.Q61L in CT2A-luc), which have only been identified in <1% of huGBM tumors. CT2A-luc distinctly displayed mesenchymal differentiation, upregulated angiogenesis, and multiple defects in antigen presentation machinery and interferon response pathways – confirmed at the genomic, transcriptomic, and proteomic levels. CT2A-luc uniquely contained multiple mutations in antigen presentation machinery genes that were computationally predicted to have deleterious biologic effects, including a clonal p.A275P missense mutation in Psmb8 (a subunit of the immunoproteasome, which degrades proteins into peptides for loading onto MHC class I) and a clonal p.Y488C missense mutation in Tap1 (which transports peptides into the endoplasmic reticulum for loading onto MHC class I). CT2A-luc also distinctly exhibited a single-copy loss of a chromosomal segment involving 4qC4 (FDR-adjusted p=0.04), which encompassed multiple type I IFN genes, as well as a single-copy loss of 10qD2-10qD3 (FDR-adjusted p=0.04), which contained Stat2, Stat6, and Ifng. Consistent with our observation of down-regulated IFN response pathways in CT2A-luc, phosphoproteomic analysis revealed decreased phosphorylation of several members of the JAK/STAT pathway in ex vivo CT2A-luc tumors, including Ptpn11 (i.e., Shp2), Il13ra1, and Stat3 - together suggesting reduced JAK/STAT signaling. Additionally, CT2A-luc demonstrated substantial baseline secretion of the CCL-2, CCL-5, and CCL-22 chemokines, all of which are known to play important roles as myeloid chemoattractants, in marked contrast to GL261-luc2. The defect in MHC class I expression could be overcome in CT2A-luc by interferon-γ treatment, which may underlie the modest efficacy of some immunotherapy combinations for CT2A-luc. Thus, CT2A-luc may be an informative preclinical model of immunotherapy resistance due to its mesenchymal differentiation and antigen presentation machinery deficits. Citation Format: Bryan Iorgulescu, Neil Ruthen, Ryuhjin Ahn, Eleni Panagioti, Prafulla Gokhale, Martha Neagu, Maria Speranza, Benjamin Eschle, Kara Soroko, Raziye Piranlioglu, Meenal Datta, Shanmugarajan Krishnan, Kathleen Yates, Gregory Baker, Rakesh Jain, Mario Suva, Donna Neuberg, Forest White, E. Chiocca, Gordon Freeman, Arlene Sharpe, Catherine Wu, David Reardon. Antigen presentation deficiency and mesenchymal differentiation underlie resistance to immunotherapy in the murine syngeneic CT2A tumor model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2990.

Abstract Pediatric-type diffuse high grade gliomas are aggressive brain cancers in children which to date lack effective treatment options and remain largely understudied. Even though genomic markers including histone H3 K27M and G34R mutations have been identified, their functional implications on signaling networks remain to be described. Phosphoproteomics might be able to uncover activated signaling pathways which could open up new paths for treatment. Here we analyzed formalin-fixed paraffin-embedded (FFPE) sections from K27M mutated, G34R mutated and histone H3 wild type patient tumors (n = 14) using phosphoproteomics. Our workflow not only enables the comprehensive characterization of phosphoserines and threonines but also of phosphotyrosines which, despite being rare modifications (0.1-1% of all phosphorylations), are known to play an important role in cancer. We found that signaling networks were distinct between the different tumor subtypes. For phosphotyrosines, tumor subtype accounted for the largest source of variation in the data (44% of variance) as determined by principle component analysis. The separation by subtype could also be seen from serine and threonine phosphoproteomics and proteomics, but was not as striking as for the phosphotyrosine data. Differential abundance analysis, partial least squares discriminant analysis and self-organizing maps revealed deregulated signaling networks between subtypes. The most downregulated pathway in K27M compared to wild type tumors was enriched for proteins involved in the epigenetic regulation of gene expression (FDR<5%), which is in accordance with the remodeling of the epigenome taking place in K27M mutated tumors. In addition, we could identify signaling networks (e.g. EGFR signaling) which were activated in a few individual patients independent of their subtype and might be targetable. Our study provides insights into the signaling landscape of pediatric-type diffuse high grade gliomas. Recognizing deregulated signaling networks across subtypes and in individual patients could offer new avenues for personalized therapy.

Glioblastoma (GBM) is a primary brain cancer with an abysmal prognosis and few effective therapies. The ability to investigate the tumor microenvironment before and during treatment would greatly enhance both understanding of disease response and progression, as well as the delivery and impact of therapeutics. Stereotactic biopsies are a routine surgical procedure performed primarily for diagnostic histopathologic purposes. The role of investigative biopsies - tissue sampling for the purpose of understanding tumor microenvironmental responses to treatment using integrated multi-modal molecular analyses ('Multi-omics") has yet to be defined. Secondly, it is unknown whether comparatively small tissue samples from brain biopsies can yield sufficient information with such methods. Here we adapt stereotactic needle core biopsy tissue in two separate patients. In the first patient with recurrent GBM we performed highly resolved multi-omics analysis methods including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics from biopsy tissue that was obtained from a single procedure. In a second patient we analyzed multi-regional core biopsies to decipher spatial and genomic variance. We also investigated the utility of stereotactic biopsies as a method for generating patient derived xenograft models in a separate patient cohort. Dataset integration across modalities showed good correspondence between spatial modalities, highlighted immune cell associated metabolic pathways and revealed poor correlation between RNA expression and the tumor MHC Class I immunopeptidome. In conclusion, stereotactic needle biopsy cores are of sufficient quality to generate multi-omics data, provide data rich insight into a patient's disease process and tumor immune microenvironment and can be of value in evaluating treatment responses. One sentence summary:Integrative multi-omics analysis of stereotactic needle core biopsies in glioblastoma.

Immunotherapy clinical trials have not shown efficacy in glioblastoma (GBM), arguably the deadliest of all cancers. A microenvironment, characterized by a paucity of T cells recognizing tumor peptides displayed on major histocompatibility complexes of tumor cells is one of the main reasons for GBM’s evasion. Virotherapy provides the opportunity to reshape the GBM TME towards pro-inflammatory phenotype. Data from a recent clinical trial with herpes simplex-1 based oncolytic virus (oHSV) have shown that the administration of these agents leads to a rapid influx of CD8 T cells, and activation of myeloid cells, suggesting that oHSV may offer an in-situ vaccination approach to increase availability of actionable antigens. C57BL/6-derived GBM models do not mimic the outcome observed with patient derived tumors in terms of virus replication. To decipher the impact of oHSV on tumor antigen specific responses, better immunocompetent models are needed. To assess whether oHSV treatment modulates the immunopeptidome profile (IP) of tumor, we used two transplantable GEMM-derived GBM models, 1620 and 1694. Both have wild type human EGFR, loss of Pten and Cdkn2a in BALB/c background. These models were more receptive to infection than CT2A. In vivo, virus persisted in tumors for up to 6 days, but not for 4 days in CT2A. IP analyses revealed that oHSV promotes epitope presentation on tumor cells and in TME. Moreover, low dose of virus efficiently induced antigen availability in both models though it differentially modulated the MHC ligandome. Using two new GBM models, we showed that an oncolytic virus used in clinical trial with recurrent GBM (NCT03152318) modulates IP of tumors, and low dose of virus is sufficient to induce the presentation of tumor epitopes. This project is supported by Bridge Fund given to Drs. Chiocca and White and P01 CA236749 to Dr. Chiocca.

BackgroundThe GL261 and CT2A syngeneic tumor lines are frequently used as immunocompetent orthotopic mouse models of human glioblastoma (huGBM) but demonstrate distinct differences in their responses to immunotherapy.MethodsTo decipher the cell-intrinsic mechanisms that drive immunotherapy resistance in CT2A-luc and to define the aspects of human cancer biology that these lines can best model, we systematically compared their characteristics using whole exome and transcriptome sequencing, and protein analysis through immunohistochemistry, Western blot, flow cytometry, immunopeptidomics, and phosphopeptidomics.ResultsThe transcriptional profiles of GL261-luc2 and CT2A-luc tumors resembled those of some huGBMs, despite neither line sharing the essential genetic or histologic features of huGBM. Both models exhibited striking hypermutation, with clonal hotspot mutations in RAS genes (Kras p.G12C in GL261-luc2 and Nras p.Q61L in CT2A-luc). CT2A-luc distinctly displayed mesenchymal differentiation, upregulated angiogenesis, and multiple defects in antigen presentation machinery (e.g. Tap1 p.Y488C and Psmb8 p.A275P mutations) and interferon response pathways (e.g. copy number losses of loci including IFN genes and reduced phosphorylation of JAK/STAT pathway members). The defect in MHC class I expression could be overcome in CT2A-luc by interferon-γ treatment, which may underlie the modest efficacy of some immunotherapy combinations. Additionally, CT2A-luc demonstrated substantial baseline secretion of the CCL-2, CCL-5, and CCL-22 chemokines, which play important roles as myeloid chemoattractants.ConclusionAlthough the clinical contexts that can be modeled by GL261 and CT2A for huGBM are limited, CT2A may be an informative model of immunotherapy resistance due to its deficits in antigen presentation machinery and interferon response pathways.

List of candidate genes identified from the shRNA screens in both MDA-MB-231 and BT-549 cells