A molecular switch for neuroprotective astrocyte reactivity

The intrinsic mechanisms that regulate neurotoxic versus neuroprotective astrocyte phenotypes and their effects on central nervous system degeneration and repair remain poorly understood. Here we show that injured white matter astrocytes differentiate into two distinct C3-positive and C3-negative reactive populations, previously simplified as neurotoxic (A1) and neuroprotective (A2)1,2, which can be further subdivided into unique subpopulations defined by proliferation and differential gene expression signatures. We find the balance of neurotoxic versus neuroprotective astrocytes is regulated by discrete pools of compartmented cyclic adenosine monophosphate derived from soluble adenylyl cyclase and show that proliferating neuroprotective astrocytes inhibit microglial activation and downstream neurotoxic astrocyte differentiation to promote retinal ganglion cell survival. Finally, we report a new, therapeutically tractable viral vector to specifically target optic nerve head astrocytes and show that raising nuclear or depleting cytoplasmic cyclic AMP in reactive astrocytes inhibits deleterious microglial or macrophage cell activation and promotes retinal ganglion cell survival after optic nerve injury. Thus, soluble adenylyl cyclase and compartmented, nuclear- and cytoplasmic-localized cyclic adenosine monophosphate in reactive astrocytes act as a molecular switch for neuroprotective astrocyte reactivity that can be targeted to inhibit microglial activation and neurotoxic astrocyte differentiation to therapeutic effect. These data expand on and define new reactive astrocyte subtypes and represent a step towards the development of gliotherapeutics for the treatment of glaucoma and other optic neuropathies.

Abstract 1509: Longitudinal profiling of high-risk pediatric malignancies using a multiomics approach

For many pediatric cancer patients, commonly used gene-panel sequencing tests yield few actionable results, partly due to the complex genomic alterations present. We hypothesized that an unbiased approach, combining whole-genome (WGS) and RNA sequencing (RNAseq), could overcome this and lead to a more comprehensive understanding of these diseases. While prior studies have evaluated WGS and RNAseq in pediatric cancers, few focused primarily on metastatic or relapsed disease. We also placed special focus on longitudinal profiling of patients, including with additional deep sequencing, to capture tumor evolution at the primary and metastatic sites, and to quantify the utility of resampling.

We assembled a cohort of 191 high-risk pediatric oncology patients, including solid tumors, CNS tumors, and leukemias/lymphomas. We have representation of patients with relapsed/refractory disease (68), metastatic disease at diagnosis (10), rare diagnoses (19), prior cancer history, and estimated overall survival <50%. We characterized 280 samples with WGS (tumor ~60X; germline ~30X) and/or RNAseq (tumor, polyA selected, ≥20 million reads), including multiple samples taken from 85 patients at different time points (diagnosis, resection, relapse, etc.). Variants (SNVs), structural rearrangements (SVs), mutational signatures, and copy-number alterations (CNAs) were identified using WGS. RNAseq was used to profile gene expression outliers, gene fusions, and expression of variants identified by WGS. The integrated results were used to prioritize potentially actionable variants for each patient. For 20 patients (44 samples), we performed targeted deep sequencing of the DNA (~500X) to profile tumor evolution that cannot be captured by WGS.

Multiple sampling from the same patient identified drastic spatial and temporal differences in the genomes and transcriptomes of these tumors. Using the Jaccard index as a measure of concordance between samples shows dynamic changes between samples collected at different time points across multiple modalities (range 0-1, 1 is identical); SNVs ranged from 0.01-0.79, SVs 0.01-0.73, major CNAs 0.07-0.99, minor CNAs 0.38-0.99, up expression outliers 0.12-0.56, down expression outliers 0.04-0.54, and fusions 0-1. Potentially biologically significant differences in therapy-induced mutations by platinum agents were also observed, highlighting the impact of therapy on tumor evolution. Clonal architectures were extracted from deep resequencing and show extensive spatial, temporal, and metastatic heterogeneity in these rare and highly aggressive malignancies that is not captured by WGS alone. Identifying clinically relevant evolution remains a challenge in most patients, but our results suggest that resampling of pediatric tumors at relapse or metastasis will be important for the effectiveness of targeted therapies in the future.

Citation Format: Henry J. Martell, Avanthi T. Shah, Alex G. Lee, Bogdan Tanasa, Stanley G. Leung, Aviv Spillinger, Heng-Yi Liu, Inge Behroozfard, Phuong Dinh, María V. Pons Ventura, Florette K. Hazard, Arun Rangaswami, Sheri L. Spunt, Norman J. Lacayo, Tabitha Cooney, Jennifer G. Michlitsch, Anurag K. Agrawal, Marcus R. Breese, Alejandro Sweet-Cordero. Longitudinal profiling of high-risk pediatric malignancies using a multiomics approach [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 1509.

Directly induced human retinal ganglion cells mimic fetal RGCs and are neuroprotective after transplantation in vivo

Retinal ganglion cell (RGC) replacement therapy could restore vision in glaucoma and other optic neuropathies. We developed a rapid protocol for directly induced RGC (iRGC) differentiation from human stem cells, leveraging overexpression of NGN2. Neuronal morphology and neurite growth were observed within 1 week of induction; characteristic RGC-specific gene expression confirmed identity. Calcium imaging demonstrated γ-aminobutyric acid (GABA)-induced excitation characteristic of immature RGCs. Single-cell RNA sequencing showed more similarities between iRGCs and early-stage fetal human RGCs than retinal organoid-derived RGCs. Intravitreally transplanted iRGCs survived and migrated into host retinas independent of prior optic nerve trauma, but iRGCs protected host RGCs from neurodegeneration. These data demonstrate rapid iRGC generation in vitro into an immature cell with high similarity to human fetal RGCs and capacity for retinal integration after transplantation and neuroprotective function after optic nerve injury. The simplicity of this system may benefit translational studies on human RGCs.

Abstract 54: Integrative analysis of whole-genome and RNA sequencing in high-risk pediatric malignancies

The use of sequencing-based assays for clinical management of pediatric cancer patients has become increasingly common. However, for many pediatric patients, gene panel based sequencing tests yield few actionable results. Given the complex genomic alterations present in many pediatric cancers, especially high-risk solid tumors, we hypothesized that an unbiased approach might reveal more actionable findings and lead to a more comprehensive understanding of these diseases. To accomplish this, we integrated whole-genome sequencing (WGS) with RNAseq in the analysis of a pediatric oncology cohort, with a focus on longitudinal cases to capture potential tumor evolution in metastatic or treated cases.

Our cohort consists of 269 high-risk pediatric oncology patients, including patients with relapsed/refractory disease, metastatic disease at diagnosis, prior cancer history, a rare diagnosis, or an estimated overall survival <50%. Solid tumors, CNS tumors, and leukemia/lymphomas are all represented. In total, 391 samples were characterized using WGS (tumor ~60X; germline ~30X) and/or RNAseq (tumor, polyA selected, ≥20 million reads). For 85 of these patients, multiple samples were collected at different time points (diagnosis, resection, relapse, etc.) to identify changes in the cancer over time. If panel testing was performed as part of their clinical care, a comparison to the integrated WGS/RNA analysis was made. WGS was used to identify variants (SNVs), structural rearrangements (SVs), mutational signatures, and copy-number alterations (CNAs). RNAseq was used to identify gene expression outliers, gene fusions, and confirm the expression of variants identified using WGS. The combination of WGS and RNAseq was then used to identify and prioritize potentially actionable variants for each patient.

Our results show that the integration of WGS and RNAseq can provide more and higher-quality actionable information than either modality alone, whilst also capturing the majority of actionable variants detected by panel sequencing. RNAseq identified not only druggable fusions and expression outliers, but also many rare and novel fusions. WGS provided fusion validation but highlighted the limitations of WGS alone in identifying fusions resulting from complex SVs. Conversely, WGS was adept at capturing genome-wide patterns of CNAs and loss of heterozygosity that are missed by gene-centric panels. Further RNAseq integration enabled prioritization of expressed SNVs as well as CNAs and SVs that significantly alter gene expression. We also used WGS to extract mutational signatures and tracked their evolution across longitudinal samples. We found potentially biologically significant differences in therapy-induced mutations caused by platinum and alkylating agents. Our unbiased approach has enabled further discovery that advances our understanding of these rare and highly aggressive malignancies.

Citation Format: Henry J. Martell, Avanthi Tayi Shah, Alex G. Lee, Bogdan Tanasa, Stanley G. Leung, Aviv Spillinger, Heng-Yi Liu, Inge Behroozfard, Phuong Dinh, Maria V. Pons Ventura, Florette K. Hazard, Arun Rangaswami, Sheri L. Spunt, Norman J. Lacayo, Tabitha Cooney, Jennifer G. Michlitsch, Anurag K. Agrawal, Marcus R. Breese, E. Alejandro Sweet-Cordero. Integrative analysis of whole-genome and RNA sequencing in high-risk pediatric malignancies [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 54.

Identification of cis-regulatory modules for adeno-associated virus-based cell-type-specific targeting in the retina and brain

Adeno-associated viruses (AAVs) targeting specific cell types are powerful tools for studying distinct cell types in the central nervous system (CNS). Cis-regulatory modules (CRMs), e.g., enhancers, are highly cell-type-specific and can be integrated into AAVs to render cell type specificity. Chromatin accessibility has been commonly used to nominate CRMs, which have then been incorporated into AAVs and tested for cell type specificity in the CNS. However, chromatin accessibility data alone cannot accurately annotate active CRMs, as many chromatin-accessible CRMs are not active and fail to drive gene expression in vivo. Using available large-scale datasets on chromatin accessibility, such as those published by the ENCODE project, here we explored strategies to increase efficiency in identifying active CRMs for AAV-based cell-type-specific labeling and manipulation. We found that prescreening of chromatin-accessible putative CRMs based on the density of cell-type-specific transcription factor binding sites (TFBSs) can significantly increase efficiency in identifying active CRMs. In addition, generation of synthetic CRMs by stitching chromatin-accessible regions flanking cell-type-specific genes can render cell type specificity in many cases. Using these straightforward strategies, we generated AAVs that can target the extensively studied interneuron and glial cell types in the retina and brain. Both strategies utilize available genomic datasets and can be employed to generate AAVs targeting specific cell types in CNS without conducting comprehensive screening and sequencing experiments, making a step forward in cell-type-specific research.

MEF2 transcription factors differentially contribute to retinal ganglion cell loss after optic nerve injury

Loss of retinal ganglion cells (RGCs) in optic neuropathies results in permanent partial or complete blindness. Myocyte enhancer factor 2 (MEF2) transcription factors have been shown to play a pivotal role in neuronal systems, and in particular MEF2A knockout was shown to enhance RGC survival after optic nerve crush injury. Here we expanded these prior data to study bi-allelic, tri-allelic and heterozygous allele deletion. We observed that deletion of all MEF2A, MEF2C, and MEF2D alleles had no effect on RGC survival during development. Our extended experiments suggest that the majority of the neuroprotective effect was conferred by complete deletion of MEF2A but that MEF2D knockout, although not sufficient to increase RGC survival on its own, increased the positive effect of MEF2A knockout. Conversely, MEF2A over-expression in wildtype mice worsened RGC survival after optic nerve crush. Interestingly, MEF2 transcription factors are regulated by post-translational modification, including by calcineurin-catalyzed dephosphorylation of MEF2A Ser-408 known to increase MEF2A-dependent transactivation in neurons. However, neither phospho-mimetic nor phospho-ablative mutation of MEF2A Ser-408 affected the ability of MEF2A to promote RGC death in vivo after optic nerve injury. Together these findings demonstrate that MEF2 gene expression opposes RGC survival following axon injury in a complex hierarchy, and further support the hypothesis that loss of or interference with MEF2A expression might be beneficial for RGC neuroprotection in diseases such as glaucoma and other optic neuropathies.

Abstract B20: Integrative analysis of whole-genome and RNA sequencing in high-risk pediatric malignancies

Targeted gene panel sequencing has become increasingly common in the management of pediatric cancer patients. For some patients, these cancer gene panel tests have identified clinically actionable findings, but for many pediatric patients, no actionable alterations are identified. This is in part due to the low mutational burden of pediatric malignancies; thus, an unbiased approach may shed light on potentially actionable findings. To accomplish this, we examined the feasibility and utility of whole-genome sequencing (WGS) and RNA sequencing (RNAseq) in the management of high-risk pediatric oncology patients. We describe our experience with a cohort of over 100 high-risk pediatric oncology patients, with a combination of solid tumors, brain tumors, and hematologic malignancies. The majority of patients were deemed high-risk due to relapsed/refractory disease. A second group of patients was defined as high-risk at time of initial diagnosis due to the presence of metastatic disease, an estimated overall survival of less than 50%, a rare tumor, an undifferentiated tumor, or prior history of another malignancy. When possible, multiple samples from an individual patient were collected (i.e., specimens at biopsy, resection, relapse, and/or from metastatic sites) to allow for evaluation of inter- and intratumoral heterogeneity. Close to 200 tumor samples were available for analysis using WGS and/or RNAseq analysis. Somatic DNA samples were sequenced to an average depth of 60X and germline samples to 30X. WGS samples were analyzed for SNVs, structural rearrangements (SVs), copy-number alterations (CNAs), and mutational signatures. RNAseq was performed to a depth of at least 20 million paired-end reads for each sample. These samples were analyzed to identify known and novel gene-fusions, measure allele specific expression of SNVs, and perform gene-expression outlier analysis. Expression of variants (SNV/SV) identified using WGS were confirmed using RNAseq. For gene expression outliers detected using RNAseq, the WGS data were used to predict possible mechanisms for the aberrant expression (such as CNA, gene fusions, or promoter hijacking). This analysis suggests that WGS and RNAseq analysis is feasible in a clinical setting and can reliably identify variants reported on gene panel tests. Furthermore, the use of WGS/RNAseq results in additional clinically informative findings while also enabling novel research to further advance our understanding of these rare and highly aggressive pediatric malignancies.

Citation Format: Avanthi T. Shah, Marcus R. Breese, Alex G. Lee, Henry J. Martell, Bogdan Tanasa, Stanley G. Leung, Aviv Spillingeer, Heng-Yi Liu, Inge Behroozfard, Phuong Dinh, Florette K. Hazard, Soo-Jin Cho, Arun Rangaswami, Norman J. Lacayo, Sheri L. Spunt, Tabitha Cooney, Jennifer G. Michlitsch, Anurag K. Agarwaal, Alejandro Sweet-Cordero. Integrative analysis of whole-genome and RNA sequencing in high-risk pediatric malignancies [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B20.

Dismissal of RNA Polymerase II Underlies a Large Ligand-Induced Enhancer Decommissioning Program

Nuclear receptors induce both transcriptional activation and repression programs responsible for development, homeostasis, and disease. Here, we report a previously overlooked enhancer decommissioning strategy underlying a large estrogen receptor alpha (ERα)-dependent transcriptional repression program. The unexpected signature for this E₂-induced program resides in indirect recruitment of ERα to a large cohort of pioneer factor basally active FOXA1-bound enhancers that lack cognate ERα DNA-binding elements. Surprisingly, these basally active estrogen-repressed (BAER) enhancers are decommissioned by ERα-dependent recruitment of the histone demethylase KDM2A, functioning independently of its demethylase activity. Rather, KDM2A tethers the E3 ubiquitin-protein ligase NEDD4 to ubiquitylate/dismiss Pol II to abrogate eRNA transcription, with consequent target gene downregulation. Thus, our data reveal that Pol II ubiquitylation/dismissal may serve as a potentially broad strategy utilized by indirectly bound nuclear receptors to abrogate large programs of pioneer factor-mediated, eRNA-producing enhancers.

Mitochondrial Retrograde Signaling in Mammals Is Mediated by the Transcriptional Cofactor GPS2 via Direct Mitochondria-to-Nucleus Translocation

As most of the mitochondrial proteome is encoded in the nucleus, mitochondrial functions critically depend on nuclear gene expression and bidirectional mito-nuclear communication. However, mitochondria-to-nucleus communication pathways in mammals are incompletely understood. Here, we identify G-Protein Pathway Suppressor 2 (GPS2) as a mediator of mitochondrial retrograde signaling and a transcriptional activator of nuclear-encoded mitochondrial genes. GPS2-regulated translocation from mitochondria to nucleus is essential for the transcriptional activation of a nuclear stress response to mitochondrial depolarization and for supporting basal mitochondrial biogenesis in differentiating adipocytes and brown adipose tissue (BAT) from mice. In the nucleus, GPS2 recruitment to target gene promoters regulates histone H3K9 demethylation and RNA POL2 activation through inhibition of Ubc13-mediated ubiquitination. These findings, together, reveal an additional layer of regulation of mitochondrial gene transcription, uncover a direct mitochondria-nuclear communication pathway, and indicate that GPS2 retrograde signaling is a key component of the mitochondrial stress response in mammals.

Abstract PR05: Genomic analysis of osteosarcoma reveals opportunities for targeted therapy

Osteosarcoma (OS) patients who relapse after initial therapy or present with metastatic disease have an extremely poor prognosis. Chemotherapy regimens for these patients have limited efficacy and significant toxicities. Thus, new therapeutic approaches are urgently needed. OS is characterized by numerous copy-number alterations (CNAs) and structural variations (SVs) in cancer-relevant genes. In contrast, recurrent point mutations are not seen. Thus, OS is a C-class (copy number-driven) rather than an M-class (mutation-driven) cancer. However, little is known with regards to whether copy-number alterations can be used to select therapies for aggressive cancers such as OS. The genomic heterogeneity of OS suggests that there may be different oncogenic drivers in subsets of patients. Thus, a systematic effort to identify targetable, patient-specific key driver genes (likely CNAs) is required.

We established a clinically annotated patient-derived tumor xenograft (PDTX) bank of 16 OS samples obtained at diagnosis, after surgical resection, and from metastasis, thus representing the full spectrum of disease. Comparison between PDTXs with a corresponding matched primary tumor demonstrated high correlation in copy number (by WGS for 12 samples) and gene expression (by RNAseq for 13 samples), suggesting that PDTXs are faithful preclinical models for OS. To identify recurrent CNAs, we analyzed this WGS dataset together with a public dataset of OS WGS samples. With this combined dataset of 69 samples from 52 patients, we searched for recurrent CNAs across an actionable cancer gene list and identified genes amplified at least 4-fold in at least 2 samples. The two most frequently amplified genes in OS are CCNE1 and MYC. Other frequent alterations were those in the PI3K pathway (PTEN loss and/or AKT amplification), AURKB amplification, CDK4 amplification, and VEGFA amplification. Importantly, all of these CNAs were reflected in at least one PDTX model. We hypothesized that in OS some of these CNAs are key cancer drivers that can be targeted for cancer treatment. To test this hypothesis, we rank-ordered the CNAs in 9 PDTXs by the amplitude of the copy number gain. We used this simple heuristic to identify candidate drivers for individual samples. We then identified 6 drugs that could be used to target specific amplified genes and tested these drugs in corresponding CNA-matched PDTX. In all cases, we saw significant growth inhibition in matched PDTXs whereas the effect was minimal in PDTXs treated with unmatched therapies. These results support the hypothesis that specific genes within CNA serve as oncogenic drivers in OS and thus outline a feasible approach to personalized, genome-informed therapy for this disease. This work could serve as the necessary preclinical proof of principle for development of a targeted therapy basket trial for OS.

In parallel to these studies and in order to further define the evolutionary trajectory of OS, we have carried out a comprehensive analysis of both spatial and temporal changes that occur in OS samples from the same patient. This has allowed us to begin defining the role of whole-genome duplication events and chromothripsis as well as loss of heterozygosity in the evolution of OS. We are directing our current efforts towards merging this evolutionary analysis with knowledge of possible targetable events to further identify key vulnerabilities that could be exploited for therapeutic benefit.

Citation Format: Leanne Sayles, Marcus Breese, Amanda Koehne, Krystal Straessler, Stanley Leung, Aviv Spillinger, Doug Hawkins, Steven Dubois, Alex Lee, Bogdan Tanasa, Kim Miok, Avanthi Shah, Sheri Spunt, Neyssa Marina, Kim Hazard, Alejandro Sweet-Cordero. Genomic analysis of osteosarcoma reveals opportunities for targeted therapy [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr PR05.

Abstract B49: Quantitating circulating tumor DNA in translocation-positive sarcoma patients using CAPP-Seq

A promising tool for noninvasive disease monitoring is analysis of circulating tumor DNA (ctDNA). Healthy individuals carry 1-10 ng/ml of cell-free DNA (cfDNA) in the blood; in oncology patients, ctDNA, which is released from tumor cells, comprises a fraction of the cfDNA and carries tumor-specific alterations, such as mutations, translocations, and copy number alterations. Most ctDNA assays lack robust translocation detection capabilities, since they are designed for adult cancers, which are commonly characterized by mutations and copy number alterations. Even assays that are designed specifically for translocation detection have inherent limitations. They are often PCR-based with laborious methods. First, the patient’s primary tumor sample is sequenced to determine the unique sequence across the translocation breakpoint. This is followed by design of patient-specific primers that can only be used for that individual patient. We sought to design an off-the-shelf, broadly applicable ctDNA assay for translocation detection across pediatric Ewing sarcoma (ES), osteosarcoma (OS), rhabdomyosarcoma (RMS), and synovial sarcoma (SS).

Recent work by our collaborators at Stanford University led to the development of CAncer Personalized Profiling by deep Sequencing (CAPP-Seq), a method capable of ultraspecific and ultrasensitive detection of ctDNA. Utilizing COSMIC and TCGA data, recent sequencing publications defining the landscape of pediatric sarcomas, and our own in-house sequencing data, we designed a pediatric sarcoma CAPP-Seq selector. This selector is comprised of biotinylated oligonucleotides that tile across the introns where translocation breakpoints occur in these pediatric sarcomas. The selector is applied to a sequencing library prepared from patient cfDNA to enrich for the genomic regions of interest via hybrid capture. The resulting enriched library undergoes next-generation sequencing to allow for detection and quantification of circulating tumor DNA.

We have isolated cfDNA from pediatric sarcoma patients and found that their cfDNA levels are higher than levels found in adult oncology patients and healthy individuals, likely due to a large fraction of contributing ctDNA. We have applied our selector to pretreatment plasma samples from 5 EWS patients, 2 OS patients, 4 RMS patients, and 1 SS patient. We detected translocations in 10/12 of these samples. Tumor was available for 7/12 of these patients, and we were able to confirm our plasma results by whole-genome sequencing of the tumor, as a validation of our findings. Additionally, we have applied our selector to serial plasma samples collected over the course of treatment and found that ctDNA levels correlate with clinical status. We have detected translocations at allelic frequencies <0.01%, demonstrating that our method is ultrasensitive and could be used to detect minimal residual disease. Our work demonstrates that CAPP-Seq can serve as an ultrasensitive, broadly applicable tool for circulating tumor translocation detection and offers promise as a method for noninvasive diagnosis and disease monitoring.

Citation Format: Avanthi Tayi Shah, Tej D. Azad, Jake J. Chabon, Marcus Breese, Bogdan Tanasa, Aviv Spillinger, Stanley G. Leung, Maximilian Diehn, Ash A. Alizadeh, E. Alejandro Sweet-Cordero. Quantitating circulating tumor DNA in translocation-positive sarcoma patients using CAPP-Seq [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr B49.

Abstract B25: Integrative analysis of whole-genome and RNA sequencing in high-risk pediatric malignancies

Clinical use of gene-panel based tumor sequencing has expanded exponentially over the past few years. While in some cases this molecular testing identifies clinically actionable findings, these highly targeted approaches may miss unanticipated, clinically meaningful or novel alterations. In cancers with poorly understood etiologies, including many pediatric solid or high-risk tumors, an unbiased approach may prove more useful. We sought to explore the feasibility and utility of whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) in comparison to commercially available targeted gene-panel testing in pediatric oncology.

Herein we describe our experience with an initial cohort of 58 high-risk pediatric oncology patients (37 solid tumors, 11 brain tumors, and 10 leukemia/lymphomas). The majority of patients (n=40) had relapsed/refractory disease. An additional eighteen patients were defined as high-risk at time of initial diagnosis due to metastatic disease, a rare tumor, prior history of another cancer type, an undifferentiated tumor, or less than 50% survival. A total of 102 samples were obtained from these 58 patients, with 70 samples originating at the primary sites of disease and 32 samples from metastatic sites. Thirty-one samples were chemotherapy/radiation therapy naïve. A combination of WGS and RNA-seq were used to characterize available samples and compared to results from panel testing for that patient (performed as part of their clinical evaluation). Where possible, fresh frozen tissue (FFT) samples were obtained during clinically indicated surgical procedures. When FFT was unavailable, formalin-fixed, paraffin-embedded (FFPE) samples were used. When possible, multiple samples from an individual patient were collected (i.e., specimens obtained at biopsy, resection, relapse, and/or from metastatic sites). Germline DNA was isolated from peripheral blood, with the exception of leukemia patients where saliva was used. Somatic DNA samples were sequenced to an average depth of at least 60X and germline samples to at least 30X. Somatic RNA-seq was performed to a depth of at least 20 million paired-end reads for each sample. In-house as well as published tools and algorithms were used to analyze DNA samples for single-nucleotide variants (SNVs), structural rearrangements, and copy-number alterations. RNA samples were analyzed to identify known and novel gene fusions, to measure allele specific expression of SNVs, and to perform gene-expression outlier analysis.

Consistent with previous observations, the mutational burden across pediatric cancers was low. While common mutations were identified, there was a long tail of mutations that occurred at a low frequency. As anticipated, samples obtained post-chemotherapy had a higher mutational burden than treatment-naïve samples. TP53 was the most commonly mutated gene, but we also identified SNVs in other genes commonly mutated in cancer, such as ASXL1, NOTCH2, and RB1. Other novel recurring variants were discovered, further analysis of which is ongoing. Canonical gene fusions were detected in 8/8 patients as well as potentially novel fusions, confirmation of which is also ongoing. In nearly all patients, variants identified by gene panels were also identified through WGS/RNA-seq analysis; however, in 2 instances, variants reported by gene panel testing were reclassified as germline using our tumor/normal WGS analysis. These results indicate that integrated WGS and RNA-seq analysis is feasible in the clinical setting and can reliably identify variants reported on commercially available gene panel testing. However, this approach also resulted in additional clinically relevant findings and allows for novel discovery that will further advance our understanding of these rare and highly aggressive pediatric malignancies.

Citation Format: Marcus R. Breese, Avanthi T. Shah, Bogdan Tanasa, Alex G. Lee, Stanley G. Leung, Aviv Spillinger, Heng-Yi Liu, Florette K. Hazard, Alejandro Sweet-Cordero. Integrative analysis of whole-genome and RNA sequencing in high-risk pediatric malignancies [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr B25.

Genome-Informed Targeted Therapy for Osteosarcoma

Osteosarcoma is a highly aggressive cancer for which treatment has remained essentially unchanged for more than 30 years. Osteosarcoma is characterized by widespread and recurrent somatic copy-number alterations (SCNA) and structural rearrangements. In contrast, few recurrent point mutations in protein-coding genes have been identified, suggesting that genes within SCNAs are key oncogenic drivers in this disease. SCNAs and structural rearrangements are highly heterogeneous across osteosarcoma cases, suggesting the need for a genome-informed approach to targeted therapy. To identify patient-specific candidate drivers, we used a simple heuristic based on degree and rank order of copy-number amplification (identified by whole-genome sequencing) and changes in gene expression as identified by RNA sequencing. Using patient-derived tumor xenografts, we demonstrate that targeting of patient-specific SCNAs leads to significant decrease in tumor burden, providing a road map for genome-informed treatment of osteosarcoma. SIGNIFICANCE: Osteosarcoma is treated with a chemotherapy regimen established 30 years ago. Although osteosarcoma is genomically complex, we hypothesized that tumor-specific dependencies could be identified within SCNAs. Using patient-derived tumor xenografts, we found a high degree of response for "genome-matched" therapies, demonstrating the utility of a targeted genome-informed approach.This article is highlighted in the In This Issue feature, p. 1.

Abstract 2075: Whole genome sequence analysis informs precision medicine of pediatric cancers

Several recent studies (including BASIC3, iCAT, INFORM, PEDS-MIONCOSEQ) have used whole exome sequencing (WES) and RNA-seq in order to identify targetable chromosomal alterations in a large variety of pediatric cancers. Few studies have attempted to evaluate whether a more comprehensive approach including WGS and RNA-seq could be used to identify novel events relevant to the pathogenesis of advanced pediatric cancer.

We analyzed a total of 59 patients (37 solid tumors, 11 brain tumors, and 10 leukemia/lymphomas) to determine the feasibility of using whole-genome sequencing (WGS) technology in conjunction with RNA-seq in order to identify actionable/druggable alterations in the pediatric cancer genomes. WGS analysis has been performed on 75 samples, that were collected from 45 patients, either at diagnosis or at relapse.

For WGS analysis of germline-tumor pairs, after performing the sequence alignment with BWA-MEM to gender-specific hg38 genomes, we have used and verified a set of computational methods: 1) MuTect2 for SNV calling, 2) cn.mops for CNV calling, 3) DELLY and LUMPY for SV calling.

Here we present our findings on the sets of SNV, CNV, SV, and gene fusions that we have identified by WGSA and RNA-seq, respectively, with a particular emphasis on the druggable alterations, and on the tumor response in the murine PDX models of the pediatric cancers. Consistent with previous observations, the mutational burden across pediatric cancers was low. While common mutations were identified, there was a long-tail of mutations that occurred at a low frequency. As anticipated, samples obtained post-chemotherapy had a higher mutational burden than treatment naive samples. TP53 was the most commonly mutated gene, but we also identified SNVs in other genes commonly mutated in cancer, such as ASXL1, NOTCH2, and RB1.

Other novel recurring variants were discovered, further analysis of which is ongoing. Our results indicate that integrated WGS and RNA-seq analysis is feasible in the clinical setting and can reliably identify variants reported on commercially available gene panel testing. However, this approach also resulted in additional clinically relevant findings and allows for novel discovery that will further advance our understanding of these rare and highly aggressive pediatric malignancies.

Citation Format: Bogdan Tanasa, Alex Lee, Marcus Breese, Avanthi Shah, Stan Leung, Heng-Yi Liu, Aviv Spillinger, Kimberly Hazard, Arun Rangaswami, Sheri Spunt, Norm Lacayo, Tabitha Cooney, Eric Alejandro Sweet-Cordero. Whole genome sequence analysis informs precision medicine of pediatric cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2075.

Abstract 2629: Genome-informed therapy for osteosarcoma

Osteosarcoma (OS) is characterized by numerous copy-number alterations (CNAs) and structural variations (SVs) in cancer-relevant genes. In contrast, recurrent point mutations are not seen. Thus, OS is a “C-class” (copy number driven) rather than an “M-class” (mutation driven) cancer. However, little is known with regards to whether copy-number alterations can be used to select therapies for aggressive cancers such as OS. The genomic heterogeneity of OS suggests that there may be different oncogenic drivers in subsets of patients. Thus, a systematic effort to identify targetable, patient-specific key driver genes (likely CNAs) is required. We established a clinically annotated patient derived tumor xenograft (PDTX) bank of 16 OS samples obtained at diagnosis, after surgical resection and from metastasis, thus representing the full spectrum of disease. Comparison between PDTXs with a corresponding matched primary tumor demonstrated high correlation in copy number (by WGS for 12 samples) and gene expression (by RNAseq for 13 samples), suggesting that PDTXs are faithful preclinical models for OS. To identify recurrent CNAs, we analyzed this WGS dataset together with a public dataset of OS WGS samples. With this combined dataset of 69 samples from 52 patients, we searched for recurrent CNAs across an actionable cancer gene list and identified genes amplified at least 4-fold in at least 2 samples. The two most frequently amplified genes in OS are CCNE1 and MYC. Other frequent alterations were those in the PI3K pathway (PTEN loss and/or AKT amplification), AURKB amplification, CDK4 amplification and VEGFA amplification. Importantly, all of these CNAs were reflected in at least one PDTX model. We hypothesized that in OS some of these CNAs are key cancer drivers that can be targeted for cancer treatment. To test this hypothesis, we rank-ordered the CNAs in 9 PDTXs by the amplitude of the copy number gain. We used this simple heuristic to identify candidate drivers for individual samples. We then identified 6 drugs that could be used to target specific amplified genes and tested these drugs in corresponding CNA-matched PDTX. In all cases, we saw significant growth inhibition in “matched” PDTXs whereas the effect was minimal in PDTXs treated with “unmatched” therapies. These results support the hypothesis that specific genes within CNA serve as oncogenic drivers in OS and thus outline a feasible approach to personalized, genome-informed therapy for this disease. This work could serve as the necessary pre-clinical proof of principle for development of a targeted therapy “basket” trial for OS.

Citation Format: Leanne Sayles, Marcus Breeese, Amanda Koehne, Bogdan Tanasa, Stanley Leung, Alex Lee, Avanthi Shah, krystal Straessler, Kim Hazard, Mi-Ok Kim, Alejandro Sweet-Cordero. Genome-informed therapy for osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2629.

From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data

Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonical and non-canonical miRNA-binding sites from peaks identified by Ago2 Cross-Linked ImmunoPrecipitation associated to high-throughput sequencing (CLIP-seq). Since the quality of peaks is of pivotal importance for the final output of the proposed method, we provide a comprehensive benchmarking of four peak detection programs, namely CIMS, PIPE-CLIP, Piranha and Pyicoclip, on four publicly available Ago2-HITS-CLIP datasets and one unpublished in-house Ago2-dataset in stem cells. We measured the sensitivity, the specificity and the position accuracy toward miRNA binding sites identification, and the agreement with TargetScan. Secondly, we developed a new pipeline, called miRBShunter, to identify canonical and non-canonical miRNA-binding sites based on de novo motif identification from Ago2 peaks and prediction of miRNA::RNA heteroduplexes. miRBShunter was tested and experimentally validated on the in-house Ago2-dataset and on an Ago2-PAR-CLIP dataset in human stem cells. Overall, we provide guidelines to choose a suitable peak detection program and a new method for miRNA-target identification.

Inhibition of Ubc13-mediated Ubiquitination by GPS2 Regulates Multiple Stages of B Cell Development

Non-proteolytic ubiquitin signaling mediated by Lys⁶³ ubiquitin chains plays a critical role in multiple pathways that are key to the development and activation of immune cells. Our previous work indicates that GPS2 (G-protein Pathway Suppressor 2) is a multifunctional protein regulating TNFα signaling and lipid metabolism in the adipose tissue through modulation of Lys⁶³ ubiquitination events. However, the full extent of GPS2-mediated regulation of ubiquitination and the underlying molecular mechanisms are unknown. Here, we report that GPS2 is required for restricting the activation of TLR and BCR signaling pathways and the AKT/FOXO1 pathway in immune cells based on direct inhibition of Ubc13 enzymatic activity. Relevance of this regulatory strategy is confirmed in vivo by B cell-targeted deletion of GPS2, resulting in developmental defects at multiple stages of B cell differentiation. Together, these findings reveal that GPS2 genomic and non-genomic functions are critical for the development and cellular homeostasis of B cells.

Gene Expression Analysis Reveals Distinct Pathways of Resistance to Bevacizumab in Xenograft Models of Human ER-Positive Breast Cancer

Bevacizumab, the recombinant antibody targeting vascular endothelial growth factor (VEGF), improves progression-free but not overall survival in metastatic breast cancer. To seek further insights in resistance mechanisms to bevacizumab at the molecular level, we developed VEGF and non-VEGF-driven ER-positive MCF7-derived xenograft models allowing comparison of tumor response at different timepoints. VEGF gene (MV165) overexpressing xenografts were initially sensitive to bevacizumab, but eventually acquired resistance. In contrast, parental MCF7 cells derived tumors were de novo insensitive to bevacizumab. Microarray analysis with qRT-PCR validation revealed that Follistatin (FST) and NOTCH were the top signaling pathways associated with resistance in VEGF-driven tumors (P<0.05). Based on the presence of VEGF, treatment with bevacizumab resulted in altered patterns of metagenes and PAM50 gene expression. In VEGF-driven model after short and long-term bevacizumab treatments, a change in the intrinsic subtype (luminal to myoepithelial/basal-like) was observed in association with increased expression of genes implicated with cancer stem cell phenotype (P<0.05). Our results show that the presence or absence of VEGF expression affects the response to bevacizumab therapy and gene pathways. In particular, long-term bevacizumab treatment shifts the cancer cells to a more aggressive myoepithelial/basal subtype in VEGF-expressing model, but not in non-VEGF model. These findings could shed light on variable results to anti-VEGF therapy in patients and emphasize the importance of patient stratification based on the VEGF expression. Our data strongly suggest consideration of patient subgroups for treatment and designing novel combinatory therapies in the clinical setting.

GPS2/KDM4A pioneering activity regulates promoter-specific recruitment of PPARγ

Timely and selective recruitment of transcription factors to their appropriate DNA-binding sites represents a critical step in regulating gene activation; however, the regulatory strategies underlying each factor's effective recruitment to specific promoter and/or enhancer regions are not fully understood. Here, we identify an unexpected regulatory mechanism by which promoter-specific binding, and therefore function, of peroxisome proliferator-activator receptor γ (PPARγ) in adipocytes requires G protein suppressor 2 (GPS2) to prime the local chromatin environment via inhibition of the ubiquitin ligase RNF8 and stabilization of the H3K9 histone demethylase KDM4A/JMJD2. Integration of genome-wide profiling data indicates that the pioneering activity of GPS2/KDM4A is required for PPARγ-mediated regulation of a specific transcriptional program, including the lipolytic enzymes adipose triglyceride lipase (ATGL) and hormone-sensitive lipase (HSL). Hence, our findings reveal that GPS2 exerts a biologically important function in adipose tissue lipid mobilization by directly regulating ubiquitin signaling and indirectly modulating chromatin remodeling to prime selected genes for activation.

lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs

While recent studies indicated roles of long non-coding RNAs (lncRNAs) in physiologic aspects of cell-type determination and tissue homeostasis¹ yet their potential involvement in regulated gene transcription programs remain rather poorly understood. Androgen receptor (AR) regulates a large repertoire of genes central to the identity and behavior of prostate cancer cells², and functions in a ligand-independent fashion in many prostate cancers when they become hormone refractory after initial androgen deprivation therapy³. Here, we report that two lncRNAs highly overexpressed in aggressive prostate cancer, PRNCR1 and PCGEM1, bind successively to the AR and strongly enhance both ligand-dependent and ligand-independent AR-mediated gene activation programs and proliferation in prostate cancer cells. Binding of PRNCR1 to the C-terminally acetylated AR on enhancers and its association with DOT1L appear to be required for recruitment of the second lncRNA, PCGEM1, to the DOT1L-mediated methylated AR N-terminus. Unexpectedly, recognition of specific protein marks by PCGEM1-recruited Pygopus2 PHD domain proves to enhance selective looping of AR-bound enhancers to target gene promoters in these cells. In “resistant” prostate cancer cells, these overexpressed lncRNAs can interact with, and are required for, the robust activation of both truncated and full length AR, causing ligand-independent activation of the AR transcriptional program and cell proliferation. Conditionally-expressed short hairpin RNA (shRNA) targeting of these lncRNAs in castration-resistant prostate cancer (CRPC) cell lines strongly suppressed tumor xenograft growth in vivo. Together, these results suggest that these overexpressed lncRNAs can potentially serve as a required component of castration-resistance in prostatic tumors.

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

The functional importance of gene enhancers in regulated gene expression is well established. In addition to widespread transcription of long non-coding RNAs (lncRNAs) in mammalian cells, bidirectional ncRNAs are transcribed on enhancers, and are thus referred to as enhancer RNAs (eRNAs). However, it has remained unclear whether these eRNAs are functional or merely a reflection of enhancer activation. Here we report that in human breast cancer cells 17β-oestradiol (E2)-bound oestrogen receptor α (ER-α) causes a global increase in eRNA transcription on enhancers adjacent to E2-upregulated coding genes. These induced eRNAs, as functional transcripts, seem to exert important roles for the observed ligand-dependent induction of target coding genes, increasing the strength of specific enhancer-promoter looping initiated by ER-α binding. Cohesin, present on many ER-α-regulated enhancers even before ligand treatment, apparently contributes to E2-dependent gene activation, at least in part by stabilizing E2/ER-α/eRNA-induced enhancer-promoter looping. Our data indicate that eRNAs are likely to have important functions in many regulated programs of gene transcription.

DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation

Although liganded nuclear receptors have been established to regulate RNA polymerase II (Pol II)-dependent transcription units, their role in regulating Pol III-transcribed DNA repeats remains largely unknown. Here we report that ~2-3% of the ~100,000-200,000 total human DR2 Alu repeats located in proximity to activated Pol II transcription units are activated by the retinoic acid receptor (RAR) in human embryonic stem cells to generate Pol III-dependent RNAs. These transcripts are processed, initially in a DICER-dependent fashion, into small RNAs (~28-65 nt) referred to as repeat-induced RNAs that cause the degradation of a subset of crucial stem-cell mRNAs, including Nanog mRNA, which modulate exit from the proliferative stem-cell state. This regulation requires AGO3-dependent accumulation of processed DR2 Alu transcripts and the subsequent recruitment of AGO3-associated decapping complexes to the target mRNA. In this way, the RAR-dependent and Pol III-dependent DR2 Alu transcriptional events in stem cells functionally complement the Pol II-dependent neuronal transcriptional program.

P5-06-01: Gene Expression Analysis of Resistance to Bevacizumab in a VEGF-Reinforced Xenograft Model of ER-Positive Breast Cancer

Background: Bevacizumab, a monoclonal antibody targeting vascular endothelial growth factor (VEGF), had promising therapeutic efficacy in breast cancer. However, intrinsic or acquired resistance is common in the clinic. To improve our understanding of the underlying mechanisms of resistance to bevacizumab (BEV), we report the gene expression analysis of resistance to bevacizumab in a VEGF-overexpressing xenograft model of ER-positive breast cancer.

Methods: We developed a nude mouse xenograft model of resistance to anti-VEGF therapy with BEV in which MCF-7 control (ML20) or MCF-7 VEGF (MV165) transfectants were implanted in mammary fat pads, allowed to grow, then treated with BEV, with collection of tumor at early or late time points (while responding (R) to or progressing (NR) on anti-VEGF therapy). To elucidate differentially expressed gene profiling associated with tumor resistance to BEV, we performed whole-genome gene expression analysis (Human WG-6v2 Expression Beadchips, Illumina) and miRNA profiling (TaqMan ***ArrayHuman MicroRNAA+B Cards Set v3.0, Applied Biosystems). Validation of the chosen genes was performed using quantitative real-time RT-PCR (qRT-PCR).

Results: Gene expression analysis revealed differentially regulated genes in the MV165-NR group compared with the MV165-R group. Among the significant genes, Follistatin (FST) and HEY2 were the top genes upregulated in NR compared to R by ANOVA. Expression of HEY2 is induced by the Notch signaling pathway. Using qRT-PCR, we validated the expression of FST and Notch in our system. FST was significantly decreased (Fold change= −3.2; P=0.03) in the R group compared with vehicle in MV165 xenografts. In contrast to R group, FST was upregulated significantly (Fold change= 9.3; P=0.05) in the NR group. Notch4 displayed increased levels of expression in NR group, but it did not reach significance (P=0.23). In addition, correlation of mRNA and miRNA profiles showed that miRNAs targeting FST and Notch4 were differentially regulated in NR group compared to R group in MV165 xenograft tumors. Among the miRNAs, TGF-β-induced oncomiR miR-181a is up-regulated in NR and targets both FST and Notch4. Other miRNAs that target both Notch4 and FST include miR-1, miR-133a, miR-133b, and mir-449b. Conclusion: Our data serve as a potential mechanistic explanation for acquired resistance to bevacizumab. These data may shed light on the transitory effect of BEV observed in the E2100 firstline metastatic breast cancer trial, where VEGF-targeted therapy prolongs progression-free survival in metastatic breast cancer without improving overall survival.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-06-01.

Regulation of Th2 differentiation and Il4 locus accessibility

Helper T cells coordinate immune responses through the production of cytokines. Th2 cells express the closely linked Il4, Il13, and Il5 cytokine genes, whereas these same genes are silenced in the Th1 lineage. The Th1/Th2 lineage choice has become a textbook example for the regulation of cell differentiation, and recent discoveries have further refined and expanded our understanding of how Th2 differentiation is initiated and reinforced by signals from antigen-presenting cells and cytokine-driven feedback loops. Epigenetic changes that stabilize the active or silent state of the Il4 locus in differentiating helper T cells have been a major focus of recent research. Overall, the field is progressing toward an integrated model of the signaling and transcription factor networks, cis-regulatory elements, epigenetic modifications, and RNA interference mechanisms that converge to determine the lineage fate and gene expression patterns of differentiating helper T cells.

A genome-wide Drosophila RNAi screen identifies DYRK-family kinases as regulators of NFAT

Precise regulation of the NFAT (nuclear factor of activated T cells) family of transcription factors (NFAT1-4) is essential for vertebrate development and function. In resting cells, NFAT proteins are heavily phosphorylated and reside in the cytoplasm; in cells exposed to stimuli that raise intracellular free Ca2+ levels, they are dephosphorylated by the calmodulin-dependent phosphatase calcineurin and translocate to the nucleus. NFAT dephosphorylation by calcineurin is countered by distinct NFAT kinases, among them casein kinase 1 (CK1) and glycogen synthase kinase 3 (GSK3). Here we have used a genome-wide RNA interference (RNAi) screen in Drosophila to identify additional regulators of the signalling pathway leading from Ca2+-calcineurin to NFAT. This screen was successful because the pathways regulating NFAT subcellular localization (Ca2+ influx, Ca2+-calmodulin-calcineurin signalling and NFAT kinases) are conserved across species, even though Ca2+-regulated NFAT proteins are not themselves represented in invertebrates. Using the screen, we have identified DYRKs (dual-specificity tyrosine-phosphorylation regulated kinases) as novel regulators of NFAT. DYRK1A and DYRK2 counter calcineurin-mediated dephosphorylation of NFAT1 by directly phosphorylating the conserved serine-proline repeat 3 (SP-3) motif of the NFAT regulatory domain, thus priming further phosphorylation of the SP-2 and serine-rich region 1 (SRR-1) motifs by GSK3 and CK1, respectively. Thus, genetic screening in Drosophila can be successfully applied to cross evolutionary boundaries and identify new regulators of a transcription factor that is expressed only in vertebrates.

A mutation in Orai1 causes immune deficiency by abrogating CRAC channel function

Antigen stimulation of immune cells triggers Ca2+ entry through Ca2+ release-activated Ca2+ (CRAC) channels, promoting the immune response to pathogens by activating the transcription factor NFAT. We have previously shown that cells from patients with one form of hereditary severe combined immune deficiency (SCID) syndrome are defective in store-operated Ca2+ entry and CRAC channel function. Here we identify the genetic defect in these patients, using a combination of two unbiased genome-wide approaches: a modified linkage analysis with single-nucleotide polymorphism arrays, and a Drosophila RNA interference screen designed to identify regulators of store-operated Ca2+ entry and NFAT nuclear import. Both approaches converged on a novel protein that we call Orai1, which contains four putative transmembrane segments. The SCID patients are homozygous for a single missense mutation in ORAI1, and expression of wild-type Orai1 in SCID T cells restores store-operated Ca2+ influx and the CRAC current (I(CRAC)). We propose that Orai1 is an essential component or regulator of the CRAC channel complex.