Germline Exome Sequencing for Men with Testicular Germ Cell Tumor Reveals Coding Defects in Chromosomal Segregation and Protein-targeting Genes

BACKGROUND

Testicular germ cell tumor (TGCT) is the most common cancer among young White men. TGCT is highly heritable, although there are no known high-penetrance predisposition genes. CHEK2 is associated with moderate TGCT risk.

OBJECTIVE

To identify coding genomic variants associated with predisposition to TGCT.

DESIGN, SETTING, AND PARTICIPANTS

The study involved 293 men with familial or bilateral (high risk; HR)-TGCT representing 228 unique families and 3157 cancer-free controls.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

We carried out exome sequencing and gene burden analysis to identify associations with TGCT risk.

RESULTS AND LIMITATIONS

Gene burden association identified several genes, including loss-of-function variants of NIN and QRSL1. We identified no statistically significant association with the sex- and germ-cell development pathways (hypergeometric overlap test: p = 0.65 for truncating variants, p = 0.47 for all variants) or evidence of associations with the regions previously identified via genome-wide association studies (GWAS). When considering all significant coding variants together with genes associated with TGCT on GWAS, there were associations with three major pathways: mitosis/cell cycle (Gene Ontology identity GO:1903047: observed/expected variant ratio [O/E] 6.17, false discovery rate [FDR] 1.53 × 10-11), co-translational protein targeting (GO:0006613: O/E 18.62, FDR 1.35 × 10-10), and sex differentiation (GO:0007548: O/E 5.25, FDR 1.90 × 10-4).

CONCLUSIONS

To the best of our knowledge, this study is the largest to date on men with HR-TGCT. As in previous studies, we identified associations with variants for several genes, suggesting multigenic heritability. We identified associations with co-translational protein targeting, and chromosomal segregation and sex determination, identified via GWAS. Our results suggest potentially druggable targets for TGCT prevention or treatment.

PATIENT SUMMARY

We searched for gene variations that increase the risk of testicular cancer and found numerous new specific variants that contribute to this risk. Our results support the idea that many gene variants inherited together contribute to the risk of testicular cancer.

Immunologic predictors of vaccine responsiveness in patients with lymphoma and CLL

Patients with B-cell lymphomas have altered cellular components of vaccine responses due to malignancy and therapy, and the optimal timing of vaccination relative to therapy remains unknown. SARS-CoV-2 vaccines created an opportunity for new insights in vaccine timing because patients were challenged with a novel antigen across multiple phases of treatment. We studied serologic mRNA vaccine response in retrospective and prospective cohorts with lymphoma and CLL, paired with clinical and research immune parameters. Reduced serologic response was observed more frequently during active therapies, but non-response was also common within observation and post-treatment groups. Total IgA and IgM correlated with successful vaccine response. In individuals treated with CART-19, non-response was associated with reduced B and T follicular helper cells. Predictors of vaccine response varied by disease and therapeutic group, and therefore further studies of immune health during and after cancer therapies are needed to allow individualized vaccine timing.

Biallelic BRCA Loss and Homologous Recombination Deficiency in Nonbreast/Ovarian Tumors in Germline BRCA1/2 Carriers

PURPOSE

Breast and ovarian tumors in germline BRCA1/2 carriers undergo allele-specific loss of heterozygosity, resulting in homologous recombination deficiency (HRD) and sensitivity to poly-ADP-ribose polymerase (PARP) inhibitors. This study investigated whether biallelic loss and HRD also occur in primary nonbreast/ovarian tumors that arise in germline BRCA1/2 carriers.

METHODS

A clinically ascertained cohort of BRCA1/2 carriers with a primary nonbreast/ovarian cancer was identified, including canonical (prostate and pancreatic cancers) and noncanonical (all other) tumor types. Whole-exome sequencing or clinical sequencing results (n = 45) were analyzed. A pan-cancer analysis of nonbreast/ovarian primary tumors from germline BRCA1/2 carriers from The Cancer Genome Atlas (TCGA, n = 73) was used as a validation cohort.

RESULTS

Ages of nonbreast/ovarian cancer diagnosis in germline BRCA1/2 carriers were similar to controls for the majority of cancer types. Nine of 45 (20%) primary nonbreast/ovarian tumors from germline BRCA1/2 carriers had biallelic loss of BRCA1/2 in the clinical cohort, and 23 of 73 (32%) in the TCGA cohort. In the combined cohort, 35% and 27% of primary canonical and noncanonical BRCA tumor types, respectively, had biallelic loss. High HRD scores (HRDex > 42) were detected in 81% of tumors with biallelic BRCA loss compared with 22% (P < .001) of tumors without biallelic BRCA loss. No differences in genomic profile, including mutational signatures, mutation spectrum, tumor mutational burden, or microsatellite instability, were found in primary nonbreast/ovarian tumors with or without biallelic BRCA1/2 loss.

CONCLUSION

A proportion of noncanonical primary tumors have biallelic loss and evidence of HRD. Our data suggest that assessment of biallelic loss and HRD could supplement identification of germline BRCA1/2 mutations in selection of patients for platinum or PARP inhibitor therapy.

Efficient recall of Omicron-reactive B cell memory after a third dose of SARS-CoV-2 mRNA vaccine

We examined antibody and memory B cell responses longitudinally for ∼9-10 months after primary 2-dose SARS-CoV-2 mRNA vaccination and 3 months after a 3rd dose. Antibody decay stabilized between 6 and 9 months, and antibody quality continued to improve for at least 9 months after 2-dose vaccination. Spike- and RBD-specific memory B cells remained durable over time, and 40%-50% of RBD-specific memory B cells simultaneously bound the Alpha, Beta, Delta, and Omicron variants. Omicron-binding memory B cells were efficiently reactivated by a 3rd dose of wild-type vaccine and correlated with the corresponding increase in neutralizing antibody titers. In contrast, pre-3rd dose antibody titers inversely correlated with the fold-change of antibody boosting, suggesting that high levels of circulating antibodies may limit the added protection afforded by repeat short interval boosting. These data provide insight into the quantity and quality of mRNA-vaccine-induced immunity over time through 3 or more antigen exposures.

A human breast atlas integrating single-cell proteomics and transcriptomics

The breast is a dynamic organ whose response to physiological and pathophysiological conditions alters its disease susceptibility, yet the specific effects of these clinical variables on cell state remain poorly annotated. We present a unified, high-resolution breast atlas by integrating single-cell RNA-seq, mass cytometry, and cyclic immunofluorescence, encompassing a myriad of states. We define cell subtypes within the alveolar, hormone-sensing, and basal epithelial lineages, delineating associations of several subtypes with cancer risk factors, including age, parity, and BRCA2 germline mutation. Of particular interest is a subset of alveolar cells termed basal-luminal (BL) cells, which exhibit poor transcriptional lineage fidelity, accumulate with age, and carry a gene signature associated with basal-like breast cancer. We further utilize a medium-depletion approach to identify molecular factors regulating cell-subtype proportion in organoids. Together, these data are a rich resource to elucidate diverse mammary cell states.

Abstract OT2-18-01: Harnessing olaparib, palbociclib, and endocrine therapy (HOPE): Phase I/II trial of olaparib, palbociclib and fulvestrant in patients with BRCA1/2-associated, hormone receptor-positive, HER2-negative metastatic breast cancer

Background: Hormone receptor-positive (HR+) metastatic breast cancer (MBC) that occurs in the context of a germline or somatic BRCA1 or BRCA2 (BRCA1/2) mutation has dual drivers: hormone receptor signaling and homologous recombination deficiency. The PALOMA-3 trial studied the selective estrogen receptor downregulator fulvestrant and the CDK4 and CDK6 inhibitor (CDK4/6i) palbociclib in patients with HR+ MBC. Compared with fulvestrant and placebo, combination fulvestrant and palbociclib demonstrated significant and clinically meaningful improvements in progression-free survival (PFS) and overall survival. The OlympiAD trial examined patients with HER2-negative MBC and a germline BRCA1/2 mutation who were treated with the poly(ADP-ribose) polymerase inhibitor (PARPi) olaparib or non-platinum chemotherapy. Olaparib resulted in improved PFS, double the response rate, and a lower risk of disease progression or death compared to chemotherapy. Despite these remarkable therapeutic advances, resistance to treatment inevitably develops and contributes to mortality in patients with MBC. Targeting dual therapeutic drivers concurrently may delay or circumvent resistance; however, olaparib and palbociclib have overlapping hematologic toxicity and the safety of combined olaparib, palbociclib and fulvestrant has not been determined. Methods: HOPE (NCT03685331) is a phase I/II clinical trial to evaluate the safety and efficacy of olaparib, palbociclib and fulvestrant in patients with HR+ MBC and a pathogenic or likely pathogenic germline or somatic variant in BRCA1/2. Eligible patients are biological males, postmenopausal females, or premenopausal females on ovarian suppression who have an ECOG performance status 0-1, measureable/evaluable breast cancer, any/no prior endocrine therapy, and 0-2 prior lines of chemotherapy for MBC. Prior platinum chemotherapy is allowed for curative intent treatment if completed at least 12 months prior to diagnosis of metastatic disease, or for MBC if there was no progression during therapy. Prior PARPi and prior CDK4/6i are permitted without restriction during phase I, and are permitted during phase II provided there was no progression on these therapies. Treatment (28-day cycles) consists of: olaparib 300mg by mouth twice daily continuously; fulvestrant 500mg intramuscularly on day 1 of each cycle and day 15 of the first cycle; and oral palbociclib once daily on days 1-21. For phase I, palbociclib dose is based on dosing cohort. Dose Levels (DL) are: DL 0 (starting level), 75mg; DL 1, 100mg; DL 2, 125mg. Phase I treatment begins with a 28-day safety run-in of fulvestrant and olaparib alone. For phase II, palbociclib will be dosed at MTD. Subjects will have archival tissue collection or fresh biopsy at baseline as well as research blood samples for cfDNA analysis at baseline, at progression, and at all scan timepoints (every 3 cycles). The phase I primary endpoint is determination of MTD. A 3+3 dose escalation design will be utilized with a 30% rate of dose limiting toxicity (DLT) deemed acceptable, and 6 patients treated at a dose for it to be declared MTD. This schema yields a minimum of 2 and a maximum of 18 patients on the phase I. For the phase II trial, the primary endpoint is PFS estimated using Kaplan-Meier methods and secondary efficacy endpoints are objective response rate and 24-week clinical benefit rate. The phase II trial will evaluate 54 subjects to provide 80% power to detect an increase in PFS from 7 months with olaparib monotherapy to 10 months. Exploratory objectives include examination of baseline tissue for PARPi predictive biomarkers and measures of tumor immunogenicity as well as serial serum evaluation for reversion mutations. Enrollment has begun.

Citation Format: Alexandra Torres, Carey Kokkonen, Mary Oladeji, Kurt D'Andrea, Rosemarie Mick, Vivek Narayan, Michael Mallamaci, Gayle Ewing, Hayley Knollman, Nadine M. Tung, Mark Robson, Katherine L. Nathanson, Susan Domchek, Payal D. Shah. Harnessing olaparib, palbociclib, and endocrine therapy (HOPE): Phase I/II trial of olaparib, palbociclib and fulvestrant in patients with BRCA1/2-associated, hormone receptor-positive, HER2-negative metastatic breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr OT2-18-01.

Rapid induction of antigen-specific CD4+ T cells is associated with coordinated humoral and cellular immunity to SARS-CoV-2 mRNA vaccination

SARS-CoV-2 mRNA vaccines have shown remarkable clinical efficacy, but questions remain about the nature and kinetics of T cell priming. We performed longitudinal antigen-specific T cell analyses on healthy SARS-CoV-2-naive and recovered individuals prior to and following mRNA prime and boost vaccination. Vaccination induced rapid antigen-specific CD4+ T cell responses in naive subjects after the first dose, whereas CD8+ T cell responses developed gradually and were variable in magnitude. Vaccine-induced Th1 and Tfh cell responses following the first dose correlated with post-boost CD8+ T cells and neutralizing antibodies, respectively. Integrated analysis revealed coordinated immune responses with distinct trajectories in SARS-CoV-2-naive and recovered individuals. Last, whereas booster vaccination improved T cell responses in SARS-CoV-2-naive subjects, the second dose had little effect in SARS-CoV-2-recovered individuals. These findings highlight the role of rapidly primed CD4+ T cells in coordinating responses to the second vaccine dose in SARS-CoV-2-naive individuals.

Identification of 22 susceptibility loci associated with testicular germ cell tumors

Testicular germ cell tumors (TGCT) are the most common tumor in young white men and have a high heritability. In this study, the international Testicular Cancer Consortium assemble 10,156 and 179,683 men with and without TGCT, respectively, for a genome-wide association study. This meta-analysis identifies 22 TGCT susceptibility loci, bringing the total to 78, which account for 44% of disease heritability. Men with a polygenic risk score (PRS) in the 95th percentile have a 6.8-fold increased risk of TGCT compared to men with median scores. Among men with independent TGCT risk factors such as cryptorchidism, the PRS may guide screening decisions with the goal of reducing treatment-related complications causing long-term morbidity in survivors. These findings emphasize the interconnected nature of two known pathways that promote TGCT susceptibility: male germ cell development within its somatic niche and regulation of chromosomal division and structure, and implicate an additional biological pathway, mRNA translation.

Abstract 1352: Genetic susceptibility to immune-related adverse events among melanoma patients treated with ipilimumab

Background: Ipilimumab is an immune checkpoint inhibitor used to treat melanoma. Although the development of immune-related adverse events (irAEs) among patients treated with ipilimumab is well documented, little is known about factors that may increase risk of irAEs. We conducted a genome-wide association study (GWAS) to examine the genetic susceptibility to irAEs in response to ipilimumab monotherapy.

Methods: In partnership with Bristol Myers Squibb BMS, extant genotype data and clinical information were obtained on melanoma patients treated with ipilimumab monotherapy from three clinical trials. Only patients who were treatment naïve were included in our analyses. We defined our outcome as the occurrence of a serious irAE, grade 3 or higher. We first analyzed data from 294 subjects, 79 with severe irAE, enrolled on CA184-169 for whom genotyping was completed using the Affymetrix 6 array. After appropriate quality control, SNP associations were determined using logistic regression models that were adjusted for ancestry, ECOG status, ipilimumab dosage (3 mg/kg vs 10 mg/kg), and number of doses (&lt;4 vs 4+). Next, we analyzed data from 175 subjects, 63 with severe irAE, enrolled on CA209-067 or CA209-069 for whom genotyping was completed using the Illumina MegaEX array; and SNP associations were similarly determined after adjustment for ancestry, trial, and number of doses (&lt;4 vs 4+). Summary statistics from the two analyses were combined using a fixed-effect meta-analysis. Because of the small sample size, we used a sub-genome-wide significance level of 1 × 10-5 to indicate potentially important findings.

Results: The most statistically significant marker (rs55981606, p=1.39 × 10-7) and a second independent marker (rs72712605, p=6.33 × 10-6) mapped to a non-coding region on chromosome 9. We identified a marker (rs65949485, p = 9.38 × 10-6) intragenic between the SHQ1 and GXYLT2 genes, both of which are involved in the Notch signaling pathway. Markers proximal to NR2F2 (rs13270533, p=7.8 × 10-6) and within SAMD12 (rs13270533, p = 9.23 × 10-6) were also identified; the latter two genes have been implicated as being oncogenic. Additionally, we identified several markers implicating genes involved in inflammation, specifically macrophage activation, including TLE1 (rs3739581, p = 9.25 × 10-7), SLC16A4 (rs2271885, p=9.23 × 10-6) and CYP2J2 (rs427970, p=2.03 × 10-6).

Conclusions: Results from our meta-analysis suggest that genes related to inflammation processes and those with known contributions to oncogenesis may play a role in the development of severe irAEs resulting from ipilimumab monotherapy. If further validated, these findings may provide the foundation to advance models to discriminate patients with a high likelihood of suffering irAE allowing for heightened surveillance of symptom onset or joint decision making for alternative therapies.

Citation Format: John Pluta, Lu Qian, Kurt D'Andrea, Chunzhe Duan, Benita Weathers, Megan Wind-Rotolo, Peter Kanetsky, Katherine Nathanson. Genetic susceptibility to immune-related adverse events among melanoma patients treated with ipilimumab [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1352.

Distinct antibody and memory B cell responses in SARS-CoV-2 naïve and recovered individuals following mRNA vaccination

Novel mRNA vaccines for SARS-CoV-2 have been authorized for emergency use. Despite their efficacy in clinical trials, data on mRNA vaccine-induced immune responses are mostly limited to serological analyses. Here, we interrogated antibody and antigen-specific memory B cells over time in 33 SARS-CoV-2 naïve and 11 SARS-CoV-2 recovered subjects. SARS-CoV-2 naïve individuals required both vaccine doses for optimal increases in antibodies, particularly for neutralizing titers against the B.1.351 variant. Memory B cells specific for full-length spike protein and the spike receptor binding domain (RBD) were also efficiently primed by mRNA vaccination and detectable in all SARS-CoV-2 naive subjects after the second vaccine dose, though the memory B cell response declined slightly with age. In SARS-CoV-2 recovered individuals, antibody and memory B cell responses were significantly boosted after the first vaccine dose; however, there was no increase in circulating antibodies, neutralizing titers, or antigen-specific memory B cells after the second dose. This robust boosting after the first vaccine dose strongly correlated with levels of pre-existing memory B cells in recovered individuals, identifying a key role for memory B cells in mounting recall responses to SARS-CoV-2 antigens. Together, our data demonstrated robust serological and cellular priming by mRNA vaccines and revealed distinct responses based on prior SARS-CoV-2 exposure, whereby COVID-19 recovered subjects may only require a single vaccine dose to achieve peak antibody and memory B cell responses. These findings also highlight the utility of defining cellular responses in addition to serologies and may inform SARS-CoV-2 vaccine distribution in a resource-limited setting.

Seasonal human coronavirus antibodies are boosted upon SARS-CoV-2 infection but not associated with protection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread within the human population. Although SARS-CoV-2 is a novel coronavirus, most humans had been previously exposed to other antigenically distinct common seasonal human coronaviruses (hCoVs) before the coronavirus disease 2019 (COVID-19) pandemic. Here, we quantified levels of SARS-CoV-2-reactive antibodies and hCoV-reactive antibodies in serum samples collected from 431 humans before the COVID-19 pandemic. We then quantified pre-pandemic antibody levels in serum from a separate cohort of 251 individuals who became PCR-confirmed infected with SARS-CoV-2. Finally, we longitudinally measured hCoV and SARS-CoV-2 antibodies in the serum of hospitalized COVID-19 patients. Our studies indicate that most individuals possessed hCoV-reactive antibodies before the COVID-19 pandemic. We determined that ∼20% of these individuals possessed non-neutralizing antibodies that cross-reacted with SARS-CoV-2 spike and nucleocapsid proteins. These antibodies were not associated with protection against SARS-CoV-2 infections or hospitalizations, but they were boosted upon SARS-CoV-2 infection.

Deep immune profiling of MIS-C demonstrates marked but transient immune activation compared to adult and pediatric COVID-19

Pediatric COVID-19 following SARS-CoV-2 infection is associated with fewer hospitalizations and often milder disease than in adults. A subset of children, however, present with Multisystem Inflammatory Syndrome in Children (MIS-C) that can lead to vascular complications and shock, but rarely death. The immune features of MIS-C compared to pediatric COVID-19 or adult disease remain poorly understood. We analyzed peripheral blood immune responses in hospitalized SARS-CoV-2 infected pediatric patients (pediatric COVID-19) and patients with MIS-C. MIS-C patients had patterns of T cell-biased lymphopenia and T cell activation similar to severely ill adults, and all patients with MIS-C had SARS-CoV-2 spike-specific antibodies at admission. A distinct feature of MIS-C patients was robust activation of vascular patrolling CX3CR1+ CD8+ T cells that correlated with the use of vasoactive medication. Finally, whereas pediatric COVID-19 patients with acute respiratory distress syndrome (ARDS) had sustained immune activation, MIS-C patients displayed clinical improvement over time, concomitant with decreasing immune activation. Thus, non-MIS-C versus MIS-C SARS-CoV-2 associated illnesses are characterized by divergent immune signatures that are temporally distinct from one another and implicate CD8+ T cells in the clinical presentation and trajectory of MIS-C.

Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications

Coronavirus disease 2019 (COVID-19) is currently a global pandemic, but human immune responses to the virus remain poorly understood. We used high-dimensional cytometry to analyze 125 COVID-19 patients and compare them with recovered and healthy individuals. Integrated analysis of ~200 immune and ~50 clinical features revealed activation of T cell and B cell subsets in a proportion of patients. A subgroup of patients had T cell activation characteristic of acute viral infection and plasmablast responses reaching >30% of circulating B cells. However, another subgroup had lymphocyte activation comparable with that in uninfected individuals. Stable versus dynamic immunological signatures were identified and linked to trajectories of disease severity change. Our analyses identified three immunotypes associated with poor clinical trajectories versus improving health. These immunotypes may have implications for the design of therapeutics and vaccines for COVID-19.

Mutation Rates in Cancer Susceptibility Genes in Patients With Breast Cancer With Multiple Primary Cancers

PURPOSE

Women with breast cancer have a 4%-16% lifetime risk of a second primary cancer. Whether mutations in genes other than BRCA1/2 are enriched in patients with breast and another primary cancer over those with a single breast cancer (S-BC) is unknown.

PATIENTS AND METHODS

We identified pathogenic germline mutations in 17 cancer susceptibility genes in patients with BRCA1/2-negative breast cancer in 2 different cohorts: cohort 1, high-risk breast cancer program (multiple primary breast cancer [MP-BC], n = 551; S-BC, n = 449) and cohort 2, familial breast cancer research study (MP-BC, n = 340; S-BC, n = 1,464). Mutation rates in these 2 cohorts were compared with a control data set (Exome Aggregation Consortium [ExAC]).

RESULTS

Overall, pathogenic mutation rates for autosomal, dominantly inherited genes were higher in patients with MP-BC versus S-BC in both cohorts (8.5% v 4.9% [P = .02] and 7.1% v 4.2% [P = .03]). There were differences in individual gene mutation rates between cohorts. In both cohorts, younger age at first breast cancer was associated with higher mutation rates; the age of non-breast cancers was unrelated to mutation rate. TP53 and MSH6 mutations were significantly enriched in patients with MP-BC but not S-BC, whereas ATM and PALB2 mutations were significantly enriched in both groups compared with ExAC.

CONCLUSION

Mutation rates are at least 7% in all patients with BRCA1/2 mutation-negative MP-BC, regardless of age at diagnosis of breast cancer, with mutation rates up to 25% in patients with a first breast cancer diagnosed at age < 30 years. Our results suggest that all patients with breast cancer with a second primary cancer, regardless of age of onset, should undergo multigene panel testing.

Abstract 2500: Copy number variation in recurrent BRCA1/2 germline mutation-associated breast and ovarian cancers

Carriers of pathogenic germline mutations in BRCA1/2 are highly predisposed to breast and ovarian cancers. Although their primary tumors respond to DNA-damaging agents, such as platinum-based chemotherapy and poly (ADP-ribose) polymerase inhibitors (PARPi), these malignancies often return as therapy-resistant recurrences. To identify genetic mechanisms of therapeutic resistance, we performed whole exome sequencing on 41 pairs of matched primary/recurrent breast and ovarian tumors from 27 BRCA1/2 mutation carriers. The cohort consisted of 14 ovarian cancer patients (nine BRCA1, five BRCA2) and 13 breast cancer patients (nine BRCA1, four BRCA2). Five patients received PARPi, 17 patients received platinums, and all patients received some type of chemotherapy prior to recurrence. First, we performed a segmentation analysis to assess copy number variation (CNVs) in each tumor. We calculated homologous recombination deficiency (HRD) scores for each tumor, but found no significant differences between matched primary/recurrent pairs. We noted that primary tumors had a relatively high average HRD score (55/100), which remained high in recurrences (52/100). Next, we totaled arm-level CNVs to generate aneuploidy scores for each tumor. Using a Wilcoxon signed rank test, we found that aneuploidy scores were significantly higher in recurrences than in matched primary tumors (p=0.007). This finding suggests that recurrences have more arm-level CNVs than primary tumors, but that acquired genomic abnormalities are not caused by HRD per se. Instead, arm-level CNVs indicate that replication errors or genome doubling events are more common in recurrences than in primary tumors. Lastly, we annotated all tumors' CNVs with genes to interrogate potential effects on signaling pathways, including CNVs exclusive to each recurrence. Using Gene Set Enrichment Analysis with Hallmark gene sets, we identified pathways significantly (FDR q&lt;0.30) affected by losses (CN≤1) and gains (CN≥4) from primary tumor CNVs, recurrent tumor CNVs, and recurrence-exclusive CNVs. All three CNV sets showed gains encompassing interferon gamma response genes and losses of Hedgehog signaling genes. Primary tumor losses were enriched for reactive oxygen species and cholesterol homeostasis genes. Recurrent tumor and recurrence-exclusive gains were enriched for UV-responsive and MTORC1 signaling gene sets, which may enhance survival in the presence of DNA-damaging or cytotoxic chemotherapies. These findings suggest that CNVs encompass different genes in recurrences compared to matched primary tumors. Further, differences in gene dosage and downstream signaling could represent novel therapeutic targets for recurrent tumors. Ultimately, we found that CNVs grant insights into the genomic and signaling processes that underlie acquired therapeutic resistance in BRCA1/2 mutation-associated cancers.

Citation Format: Jennifer Brady Shah, Bradley Wubbenhorst, John Pluta, Caitlin Feltcher, Lauren Schmucker, Kurt D'Andrea, Heather Symecko, Catherine Ruan, Anupma Nayak, Kara N. Maxwell, Susan Domchek, Katherine L. Nathanson. Copy number variation in recurrent BRCA1/2 germline mutation-associated breast and ovarian cancers [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 2500.

Association of Filaggrin Loss-of-Function Variants With Race in Children With Atopic Dermatitis

Importance

Atopic dermatitis (AD) is a common chronic illness that has been associated with variation in the filaggrin gene (FLG). Four variants are most often evaluated.

Objectives

To comprehensively describe and compare results from targeted sequencing of FLG loss-of-function (LoF) variants in children of African and European ancestry and the association of these variants with onset and persistence of AD.

Design, Setting, and Participants

This prospective US cohort study assessed the genetic subcohort of the Pediatric Eczema Elective Registry (PEER). Children with mild to moderate AD were included in the analysis. Massively parallel sequencing (MPS) was used to focus on FLG LoF variation in white and African American children. Patients were enrolled from June 2005 through July 2017. Data were analyzed from January 25 through May 10, 2019.

Main Outcomes and Measures

Associations of FLG LoF variation with white and African American ancestry and with the risk and persistence of AD.

Results

A total of 741 children were included in the analysis (394 [53.2%] female and 347 [46.8%] male; mean [SD] age at onset, 1.97 [2.72] years); of these, 394 (53.2%) were white, 326 (44.0%) were African American, and 21 (2.8%) were of other ancestries. Using MPS technology, 23 FLG LoF variants were found in children with AD. The prevalence of FLG LoF variants was 177 participants (23.9%) in the full cohort, 124 white participants (31.5%), and 50 African American participants (15.3%). The odds ratio for carrying any FLG LoF variant in a white child compared with an African American child with AD was 2.44 (95% CI, 1.76-3.39). Some FLG LoF variants are only found in children of a specific ancestry (eg, p.S3316* and p.R826* were not seen in white patients). Children with an FLG LoF were more likely to have persistent AD (odds ratio, 0.67; 95% CI, 0.56-0.80).

Conclusions and Relevance

The FLG LoF variants in a US cohort of children with mild to moderate AD differ significantly by race and their association with the persistence of AD. Conventional testing of the 4 frequently evaluated variants is inadequate. Any planned genetic diagnostic test for AD based on FLG LoF variants must be inclusive and not rely on the most frequently studied variants.

Association between fine mapping thymic stromal lymphopoietin and atopic dermatitis onset and persistence

BACKGROUND

Atopic dermatitis (AD) is a common chronic relapsing skin disease. Genetic variants have been associated with skin barrier function and immune regulation. Thymic stromal lymphopoietin (TSLP), an immune regulator, has been previously associated with AD.

OBJECTIVE

To fine map TSLP and evaluate associations with the onset and persistence of AD.

METHODS

TSLP variation was determined using targeted massively parallel sequencing in a longitudinal cohort of children with AD. Evaluations included linkage disequilibrium and the persistence of AD for as many as 10 years of follow-up. The association between the presence of AD and rs1898671 variation was evaluated in a second independent cohort.

RESULTS

The minor variant frequency for rs1898671 was 23.5% (95% CI, 21.4%-25.8%). This variant was not in linkage disequilibrium with other TSLP variants in the longitudinal cohort (n = 741). White children with AD were less likely to have rs1898671 variant (odds ratio [OR], 1.41; 95% CI, 1.20-1.66) than Genome Aggregation Database controls. Children with AD and the rs1898671 variant during follow-up were more likely to have remission than children who were wild type for rs1898671 (OR, 1.56; 95% CI, 1.26-1.91). In the second cohort (n = 585), the rs1898671 variant was less prevalent in those with AD than those without. The protective effect was greater in rs1898671 heterozygotes (OR, 1.91; 95% CI, 1.34-2.75) than homozygotes (OR, 1.28; 95% CI, 0.61-2.70).

CONCLUSION

TSLP and specifically rs1898671 are important in the pathogenesis of AD and could represent a potential clinical target for the development of therapies to treat individuals with AD.

A single dose of neoadjuvant PD-1 blockade predicts clinical outcomes in resectable melanoma

Immunologic responses to anti-PD-1 therapy in melanoma patients occur rapidly with pharmacodynamic T cell responses detectable in blood by 3 weeks. It is unclear, however, whether these early blood-based observations translate to the tumor microenvironment. We conducted a study of neoadjuvant/adjuvant anti-PD-1 therapy in stage III/IV melanoma. We hypothesized that immune reinvigoration in the tumor would be detectable at 3 weeks and this response would correlate with disease-free survival. We identified a rapid and potent anti-tumor response, with 8/27 patients experiencing a complete or major pathological response after a single dose of anti-PD-1, all of whom remain disease-free. These rapid pathologic and clinical responses were associated with accumulation of exhausted CD8 T cells in the tumor at 3 weeks with reinvigoration in the blood observed as early as 1 week. Transcriptional analysis demonstrated a pre-treatment immune signature (Neoadjuvant Response Signature) that was associated with clinical benefit. In contrast, patients with disease recurrence displayed mechanisms of resistance including immune suppression, mutational escape, and/or tumor evolution. Neoadjuvant anti-PD-1 treatment is effective in high-risk resectable stage III/IV melanoma. Pathological response and immunological analyses after a single neoadjuvant dose can be used to predict clinical outcome and to dissect underlying mechanisms in checkpoint blockade.

Uncommon Filaggrin Variants Are Associated with Persistent Atopic Dermatitis in African Americans

Atopic dermatitis (AD) is a common illness that has been associated with filaggrin gene (FLG) loss of function (LoF) variation. In African Americans, a group that commonly has AD and has not been well studied, FLG LoF variation is rarely found. Our objective was to use massively parallel sequencing to evaluate FLG LoF variation in children of African ancestry to evaluate the association between FLG LoF variation and AD and AD persistence. We studied 262 African American children with AD. Nine unique FLG exon 3 LoF variants were identified for an overall minor variant frequency of 6.30% (95% confidence interval [CI] = 4.37-8.73). The most common variants were p.R501X (1.72%, 95% CI = 0.79-3.24), p.S3316X (1.34%, 95% CI = 0.54-2.73), and p.R826X (0.95%, 95% CI = 0.31-2.2). Over an average follow-up period of 96.4 (95% CI = 92.0-100.8) months, African American children with FLG LoF were less likely to be symptom free (odds ratio = 0.36, 95% CI = 0.14-0.89, P = 0.027) compared with a FLG wild-type child. In contrast to previous reports, uncommon FLG LoF variants in African American children exist and are associated with AD and more persistent AD. In contrast to Europeans, no FLG LoF variants predominate in African American children. Properly determining FLG LoF status requires advanced sequencing techniques.

Erratum: Author Correction: The contribution of pathogenic variants in breast cancer susceptibility genes to familial breast cancer risk

[This corrects the article DOI: 10.1038/s41523-017-0024-8.].

Abstract 4265: Risks of familial breast cancer associated with known and proposed breast cancer susceptibility genes

A better understanding of gene-specific risks for development of breast cancer will lead to improved screening, prevention, and therapeutic strategies for individuals identified to carry germline mutations. We performed targeted massively-parallel sequencing to identify mutations and large genomic rearrangements in 26 known or proposed breast cancer susceptibility genes in 2134 BRCA-negative women with familial breast cancer (FBC). A case-control analysis was performed comparing the frequency of internally classified mutations identified in FBC cases to that in non-Finnish European controls from the Exome Aggregation Consortium (ExAC) excluding samples from The Cancer Genome Atlas. Including large genomic rearrangements, mutations were identified in 8.2% of FBC cases compared to 6.2% of ExAC controls, including mutations in high-penetrance genes (0.6% in cases vs. 0.1% in controls), moderate-penetrance genes (3.7% vs 1.7%), and seven cases with two mutations (0.3%). The remainder of FBC cases and ExAC controls had mutations in proposed breast cancer genes (1.6% of cases vs 2.4% of controls), Lynch syndrome genes (0.5% vs. 0.5%) or were heterozygous MUTYH carriers (1.5% vs. 1.5%). Case-control analysis demonstrated significant associations with FBC for ATM, PALB2, and TP53 mutations (OR&gt;3.0, p&lt;10-4), BARD1 mutations (OR=3.2, p=0.012), and CHEK2 truncating mutations (OR=1.6, p=0.041). Our results therefore demonstrate that only approximately 4% of BRCA1/2 negative FBC patients have mutations in genes definitively associated with breast cancer at this time. Large case-control studies are needed to fully evaluate the breast cancer risks associated with moderate penetrance and proposed breast cancer susceptibility genes.

Citation Format: Kara N. Maxwell, Thomas Paul Slavin, Jenna M. Lilyquist, Joseph Vijai, Susan L. Neuhausen, Steven N. Hart, Vignesh Ravichandran, Tinu Thomas, Ann Maria, Kasmintan A. Schrader, Raymond Moore, Chunling Hu, Brad Wubbenhorst, Brandon M. Wenz, Kurt D'Andrea, Susan M. Domchek, Mark E. Robson, Paulo Peterlongo, Paolo Radice, James M. Ford, Judy E. Garber, Csilla Szabo, Kenneth Offit, Katherine L. Nathanson, Fergus J. Couch, Jeffrey N. Weitzel. Risks of familial breast cancer associated with known and proposed breast cancer susceptibility genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4265. doi:10.1158/1538-7445.AM2017-4265

The contribution of pathogenic variants in breast cancer susceptibility genes to familial breast cancer risk

Understanding the gene-specific risks for development of breast cancer will lead to improved clinical care for those carrying germline mutations in cancer predisposition genes. We sought to detail the spectrum of mutations and refine risk estimates for known and proposed breast cancer susceptibility genes. Targeted massively-parallel sequencing was performed to identify mutations and copy number variants in 26 known or proposed breast cancer susceptibility genes in 2134 BRCA1/2-negative women with familial breast cancer (proband with breast cancer and a family history of breast or ovarian cancer) from a largely European–Caucasian multi-institutional cohort. Case–control analysis was performed comparing the frequency of internally classified mutations identified in familial breast cancer women to Exome Aggregation Consortium controls. Mutations were identified in 8.2% of familial breast cancer women, including mutations in high-risk (odds ratio > 5) (1.4%) and moderate-risk genes (2 < odds ratio < 5) (2.9%). The remaining familial breast cancer women had mutations in proposed breast cancer genes (1.7%), Lynch syndrome genes (0.5%), and six cases had two mutations (0.3%). Case–control analysis demonstrated associations with familial breast cancer for ATM, PALB2, and TP53 mutations (odds ratio > 3.0, p < 10⁻⁴), BARD1 mutations (odds ratio = 3.2, p = 0.012), and CHEK2 truncating mutations (odds ratio = 1.6, p = 0.041). Our results demonstrate that approximately 4.7% of BRCA1/2 negative familial breast cancer women have mutations in genes statistically associated with breast cancer. We classified PALB2 and TP53 as high-risk, ATM and BARD1 as moderate risk, and CHEK2 truncating mutations as low risk breast cancer predisposition genes. This study demonstrates that large case–control studies are needed to fully evaluate the breast cancer risks associated with mutations in moderate-risk and proposed susceptibility genes.

Women with the heritable form of breast cancer often harbor mutations in cancer-linked genes other than the usual suspects, BRCA1 and BRCA2. Slavin, Maxwell, Lilyquist, Joseph, and colleagues from major national and international cancer centers studied 2134 women with familial breast cancer who tested negative for BRCA1/2 gene mutations. The researchers sequenced 26 known or proposed breast cancer susceptibility genes and found mutations in approximately 1 in every 12 of the study subjects. They then further broke down the susceptibility genes into those that confer high-, moderate- or low-risk—although not all the proposed breast cancer genes reached statistical significance and, as such, their clinical importance remains unclear. The results support adding some of the high- and moderate-risk genes to multi-panel diagnostic tests that aim to determine the likelihood of a women developing heritable breast cancer.

T-cell invigoration to tumour burden ratio associated with anti-PD-1 response

Despite the success of monotherapies based on blockade of programmed cell death 1 (PD-1) in human melanoma, most patients do not experience durable clinical benefit. Pre-existing T-cell infiltration and/or the presence of PD-L1 in tumours may be used as indicators of clinical response; however, blood-based profiling to understand the mechanisms of PD-1 blockade has not been widely explored. Here we use immune profiling of peripheral blood from patients with stage IV melanoma before and after treatment with the PD-1-targeting antibody pembrolizumab and identify pharmacodynamic changes in circulating exhausted-phenotype CD8 T cells (T_ex cells). Most of the patients demonstrated an immunological response to pembrolizumab. Clinical failure in many patients was not solely due to an inability to induce immune reinvigoration, but rather resulted from an imbalance between T-cell reinvigoration and tumour burden. The magnitude of reinvigoration of circulating T_ex cells determined in relation to pretreatment tumour burden correlated with clinical response. By focused profiling of a mechanistically relevant circulating T-cell subpopulation calibrated to pretreatment disease burden, we identify a clinically accessible potential on-treatment predictor of response to PD-1 blockade.

Abstract PR05: Peripheral blood immune profiling of anti-PD-1 therapy in human melanoma reveals a link between T cell re-invigoration and tumor burden that predicts response

Despite the clinical success of PD-1 based therapies in human melanoma patients, the majority of patients do not have durable clinical benefit from anti-PD-1 monotherapy. A major challenge remains identifying which patients will respond to anti-PD-1 therapy and defining the underlying reasons for successful response versus treatment failure. Pre-existing T cell infiltration and/or PD-L1 expression in tumors may predict clinical responses; however, the use of blood-based profiling to understand the immunologic mechanism of PD-1 blockade has been less explored. Here we used detailed immune profiling of peripheral blood from stage IV melanoma patients before and after pembrolizumab (pembro), and identified pharmacodynamic changes in circulating exhausted-phenotype CD8 T cells (TEX). Robust induction of Ki67 in this subset of circulating CD8 T cells post-therapy (re-invigoration) occurred in 78% of patients indicating strong, on target immunological effects of PD-1 blockade in most patients studied here. Despite this high immunological response rate, the objective clinical response rate in this cohort was less than 40%. Ki67 in CD8 T cells alone did not predict clinical outcomes and, in fact, higher systemic immune activation at baseline was associated with lower overall survival. Rather, the magnitude of re-invigoration of circulating TEX in relation to pre-treatment tumor burden correlated with clinical response. We identified a TEX re-invigoration to tumor burden ratio which could be used to predict clinical response and overall survival as early as 6 weeks post therapy. Consistent observations were found in a second independent cohort and suggest that clinical failure of PD-1 blockade in many patients may not solely be due to an inability to induce immune re-invigoration but rather, an imbalance between T cell re-invigoration and tumor burden. Thus, by focused profiling of a mechanistically relevant circulating T cell subpopulation calibrated to pre-treatment disease burden, we identify a clinically accessible predictor of response to PD-1 blockade. These findings also provide a framework for dissecting distinct types of treatment failures in melanoma and have implications for stratifying patients into additional immunotherapeutic treatment approaches.

Citation Format: Alexander Huang, Michael A. Postow, Robert J. Orlowski, Rosemarie Mick, Bertram Bengsch, Sasi Manne, Wei Xu, Shannon Harmon, Matthew Adamow, Deborah Kuk, Katherine Panangeas, Cristina Carerra, Phillip Wong, Felix Quagliarello, Kristen E. Pauken, Ramin S. Herati, Suzanne McGettigan, Shawn Kothari, Sangeeth M. George, Brandon Wenz, Kurt D'Andrea, Xiaowei Xu, Ravi K. Amaravadi, Giorgos Karakousis, Lynn M. Schuchter, Katherine L. Nathanson, Jedd D. Wolchok, Tara C. Gangadhar, John Wherry. Peripheral blood immune profiling of anti-PD-1 therapy in human melanoma reveals a link between T cell re-invigoration and tumor burden that predicts response [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr PR05.

Copy Number Changes Are Associated with Response to Treatment with Carboplatin, Paclitaxel, and Sorafenib in Melanoma

PURPOSE

Copy number alterations have been shown to be involved in melanoma pathogenesis. The randomized phase III clinical trial E2603: carboplatin, paclitaxel, ± sorafenib (CP vs. CPS) offers a large collection of tumor samples to evaluate association of somatic mutations, genomic alterations, and clinical outcomes, prior to current FDA-approved therapies.

EXPERIMENTAL DESIGN

Copy number and mutational analysis on 119 pretreatment samples was performed.

RESULTS

CPS therapy was associated with improved progression-free survival (PFS) compared with CP in patients with tumors with RAF1 (cRAF) gene copy gains (HR, 0.372; P = 0.025) or CCND1 gene copy gains (HR, 0.45; P = 0.035). CPS therapy was associated with improved overall survival (OS) compared with CP in patients with tumors with KRAS gene copy gains (HR, 0.25; P = 0.035). BRAF gene copy gain and MET amplification were more common in samples with V600K versus V600E mutations (P < 0.001), which was validated in The Cancer Genome Atlas (TCGA) dataset.

CONCLUSIONS

We observed improved treatment response with CPS in patients with melanoma whose tumors have RAF1 (cRAF), KRAS, or CCND1 amplification, all of which can be attributed to sorafenib targeting CRAF. These genomic alterations should be incorporated in future studies for evaluation as biomarkers.

Abstract 2990: Evidence for diverse mechanisms of tumorigenesis in breast and ovarian tumors of BRCA1/2 carriers

Germline mutations in the tumor suppressors BRCA1 and BRCA2 lead to increased risks of breast and ovarian cancers at least in part due to their roles in homologous recombination based double stranded DNA repair. Genetic alterations including loss of the wild-type BRCA1/2 allele, PTEN loss and TP53 mutations are thought to contribute to genomic instability in susceptible tissues and therefore tumor formation. In order to further investigate the mechanisms of tumorigenesis in BRCA1/2 carriers, we performed whole exome sequencing of 39 breast and ovarian tumors and matched blood germline DNA. Sequencing data were analyzed using GATK and MuTECT for variant calls and ngCGH and Sequenza for copy number analysis. Using cellularity corrected tumor versus germline allele frequency calculations, we found no evidence of loss of heterozygosity (LOH) in 17% of BRCA1 tumors (n = 4 of 24) and 40% of BRCA2 tumors (n = 6 of 15). Genomic instability as measured by percentage of genome in the diploid state showed that BRCA1/2 tumors with no evidence of LOH had decreased genomic instability (average% genome diploid 76+27% vs 57+16%, p = 0.01) with no difference in the overall somatic mutation rate (average 50+71 vs 83+156 single nucleotide variants per megabase, p = NS). While there were also no significant differences in the average number of predicted deleterious somatic mutations in BRCA1/2 tumors with no LOH versus tumors with LOH (n = 13+15 vs 13+6, p = NS), tumors without LOH were significantly less likely to have mutations or loss in TP53 or loss of PTEN (50% versus 93%, p = 0.007). Of the ten tumors with no LOH, five were from patients who had received prior cytotoxic chemotherapy. Other tumors with no LOH were from patients with atypical presentations including a mixed histology epithelial ovarian tumor in a BRCA1 carrier, and a triple negative breast cancer in a 70 year old BRCA2 carrier. Of the 29 tumors with evidence of LOH, no patient had received cytotoxic chemotherapy for a prior malignancy or in the neoadjuvant setting. No recurrent driver mutations other than TP53 mutations were identified in the BRCA1/2 tumors with or without LOH. Twenty-six pathogenic likely driver mutations were identified in 25 cancer genes outside of TP53, including NRAS, PIK3CA, and ABL2. Our results indicate that approximately 75% of tumors in BRCA1/2 germline mutation carriers arise via a classic pathway involving LOH of the wildtype allele, loss of function of TP53 and/or PTEN and significant genomic instability. However, approximately 25% of tumors may arise via an alternative pathway, possibly related to prior chemotherapy in some cases. Further studies are needed to determine the molecular and clinical factors associated with this proposed classic versus atypical pathway of tumorigenesis in BRCA1/2 carriers and whether these characteristics are associated with outcomes such as survival and platinum and/or PARP inhibitor sensitivity.

Citation Format: Kara N. Maxwell, Daniel De Sloover, Bradley Wubbenhorst, Brandon Wenz, Nicole Lunceford, Lyndsey Emery, Kurt D'Andrea, Robert D. Daber, Michael D. Feldman, Susan M. Domchek, Katherine L. Nathanson. Evidence for diverse mechanisms of tumorigenesis in breast and ovarian tumors of BRCA1/2 carriers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2990. doi:10.1158/1538-7445.AM2015-2990

Pathway-based analysis of GWAs data identifies association of sex determination genes with susceptibility to testicular germ cell tumors

Genome-wide association (GWA) studies of testicular germ cell tumor (TGCT) have identified 18 susceptibility loci, some containing genes encoding proteins important in male germ cell development. Deletions of one of these genes, DMRT1, lead to male-to-female sex reversal and are associated with development of gonadoblastoma. To further explore genetic association with TGCT, we undertook a pathway-based analysis of SNP marker associations in the Penn GWAs (349 TGCT cases and 919 controls). We analyzed a custom-built sex determination gene set consisting of 32 genes using three different methods of pathway-based analysis. The sex determination gene set ranked highly compared with canonical gene sets, and it was associated with TGCT (FDRG = 2.28 × 10(-5), FDRM = 0.014 and FDRI = 0.008 for Gene Set Analysis-SNP (GSA-SNP), Meta-Analysis Gene Set Enrichment of Variant Associations (MAGENTA) and Improved Gene Set Enrichment Analysis for Genome-wide Association Study (i-GSEA4GWAS) analysis, respectively). The association remained after removal of DMRT1 from the gene set (FDRG = 0.0002, FDRM = 0.055 and FDRI = 0.009). Using data from the NCI GWA scan (582 TGCT cases and 1056 controls) and UK scan (986 TGCT cases and 4946 controls), we replicated these findings (NCI: FDRG = 0.006, FDRM = 0.014, FDRI = 0.033, and UK: FDRG = 1.04 × 10(-6), FDRM = 0.016, FDRI = 0.025). After removal of DMRT1 from the gene set, the sex determination gene set remains associated with TGCT in the NCI (FDRG = 0.039, FDRM = 0.050 and FDRI = 0.055) and UK scans (FDRG = 3.00 × 10(-5), FDRM = 0.056 and FDRI = 0.044). With the exception of DMRT1, genes in the sex determination gene set have not previously been identified as TGCT susceptibility loci in these GWA scans, demonstrating the complementary nature of a pathway-based approach for genome-wide analysis of TGCT.

Abstract 933: Copy number changes are associated with BRAF and NRAS mutations and response to treatment with carboplatin, paclitaxel and sorafenib

Copy number alterations, both gains and losses, have been shown to be involved in melanoma pathogenesis and may provide novel targets for treatment. Previous observations have additionally suggested that specific copy number profiles may be associated with BRAF, NRAS and WT/WT status. The randomized, phase III clinical trial E2603: carboplatin, paclitaxel, +/- sorafenib (CP vs. CPS) offers the largest available collection of tumor samples from patients with well annotated clinical outcome to evaluate these associations. We evaluated copy number variants (CNVs) using array Comparative Genomic Hybridization in melanoma tumor samples from patients treated on this trial. Genomic DNA was hybridized on SurePrint G4 human CGH microarrays 2 x 440 K (Agilent). Copy number gains and losses were ≥ 0.3 or ≤ -0.3 on a log2 scale, respectively (Nexus BioDiscovery, Inc). In 119 melanoma tumor samples, 45% had BRAF mutations, 24% NRAS mutations, and 24% without either (designated WT), CNVs were evaluated in an initial set of 26 genes known to be involved in melanoma pathogenesis. Overall genomic instability, as measured by number of genes with CNVs, was associated with poor ECOG performance status (P=0.007) and marginally significant for more organs with metastatic involvement (P=0.06), and is consistent with other studies suggesting that genomic instability is a predictor of worsened outcome. We further explored the association between copy number and somatic mutation status. Not surprisingly, BRAF gene amplification was observed in 91% of BRAF mutant melanoma tumor samples (P&lt;0.001, as compared to 66% of NRAS/WT samples). The average value of BRAF copy number was higher in tumor samples with BRAF V600K mutations compared to samples with BRAF V600E mutations (1.11 v 0.55, P&lt;0.001). MET, also on chr 7, was found to be amplified in 59% of BRAF mutated melanoma tumor samples. The average value of MET copy number was also higher in BRAF V600K mutant compared to BRAF V600E mutant melanoma (0.53 v 0.27, P=0.04), which may contribute to the differing clinical behaviors of melanomas with the two mutations. Patients with BRAF copy number gain had a trend towards lower overall response rate to either treatment compared to diploid (15.2% v 29.6%, OR=0.37, P=0.08). Patients with NRAS copy number gain receiving CPS had significantly improved overall survival compared to patients receiving CP alone (HR=0.35, P=0.03) in multivariable Cox model. We had previously found a trend suggesting an improved clinical response and PFS in patients with NRAS mutant melanoma treated with CPS as compared to CP. Our present study demonstrates an association between CNVs and treatment response to CP or CPS, as well as an association with somatic mutations. In addition, distinct cooperating genomic events identified in somatic mutation cohorts, such as MET and BRAF V600K gain, may contribute to the pathogenesis of melanoma tumors.

Citation Format: Melissa A. Wilson, Fengmin Zhao, Sanika Khare, Richard Letrero, Kurt D'Andrea, David L. Rimm, John M. Kirkwood, Harriet M. Kluger, Sandra J. Lee, Lynn M. Schuchter, Keith T. Flaherty, Katherine L. Nathanson. Copy number changes are associated with BRAF and NRAS mutations and response to treatment with carboplatin, paclitaxel and sorafenib. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 933. doi:10.1158/1538-7445.AM2014-933

Correlation of somatic mutations and clinical outcome in melanoma patients treated with Carboplatin, Paclitaxel, and sorafenib

PURPOSE

Sorafenib is an inhibitor of VEGF receptor (VEGFR), platelet-derived growth factor receptor (PDGFR), and RAF kinases, amongst others. We assessed the association of somatic mutations with clinicopathologic features and clinical outcomes in patients with metastatic melanoma treated on E2603, comparing treatment with carboplatin, paclitaxel ± sorafenib (CP vs.

CPS) EXPERIMENTAL DESIGN

Pretreatment tumor samples from 179 unique individuals enrolled on E2603 were analyzed. Genotyping was performed using a custom iPlex panel interrogating 74 mutations in 13 genes. Statistical analysis was performed using Fisher exact test, logistic regression, and Cox proportional hazards models. Progression-free survival (PFS) and overall survival were estimated using Kaplan-Meier methods.

RESULTS

BRAF and NRAS mutations were found at frequencies consistent with other metastatic melanoma cohorts. BRAF-mutant melanoma was associated with worse performance status, increased number of disease sites, and younger age at diagnosis. NRAS-mutant melanoma was associated with better performance status, fewer sites of disease, and female gender. BRAF and NRAS mutations were not significantly predictive of response or survival when treated with CPS versus CP. However, patients with NRAS-mutant melanoma trended toward a worse response and PFS on CP than those with BRAF-mutant or WT/WT melanoma, an association that was reversed for this group on the CPS arm.

CONCLUSIONS

This study of somatic mutations in melanoma is the last prospectively collected phase III clinical trial population before the era of BRAF-targeted therapy. A trend toward improved clinical response in patients with NRAS-mutant melanoma treated with CPS was observed, possibly due to the effect of sorafenib on CRAF.

Expression of drug targets in patients treated with sorafenib, carboplatin and paclitaxel

Introduction

Sorafenib, a multitarget kinase inhibitor, targets members of the mitogen-activated protein kinase (MAPK) pathway and VEGFR kinases. Here we assessed the association between expression of sorafenib targets and biomarkers of taxane sensitivity and response to therapy in pre-treatment tumors from patients enrolled in ECOG 2603, a phase III comparing sorafenib, carboplatin and paclitaxel (SCP) to carboplatin, paclitaxel and placebo (CP).

Methods

Using a method of automated quantitative analysis (AQUA) of in situ protein expression, we quantified expression of VEGF-R2, VEGF-R1, VEGF-R3, FGF-R1, PDGF-Rβ, c-Kit, B-Raf, C-Raf, MEK1, ERK1/2, STMN1, MAP2, EB1 and Bcl-2 in pretreatment specimens from 263 patients.

Results

An association was found between high FGF-R1 and VEGF-R1 and increased progression-free survival (PFS) and overall survival (OS) in our combined cohort (SCP and CP arms). Expression of FGF-R1 and VEGF-R1 was higher in patients who responded to therapy ((CR+PR) vs. (SD+PD+ un-evaluable)).

Conclusions

In light of the absence of treatment effect associated with sorafenib, the association found between FGF-R1 and VEGF-R1 expression and OS, PFS and response might reflect a predictive biomarker signature for carboplatin/paclitaxel-based therapy. Seeing that carboplatin and pacitaxel are now widely used for this disease, corroboration in another cohort might enable us to improve the therapeutic ratio of this regimen.

Tumor genetic analyses of patients with metastatic melanoma treated with the BRAF inhibitor dabrafenib (GSK2118436)

PURPOSE

Dabrafenib is a selective inhibitor of V600-mutant BRAF kinase, which recently showed improved progression-free survival (PFS) as compared with dacarbazine, in metastatic melanoma patients. This study examined potential genetic markers associated with response and PFS in the phase I study of dabrafenib.

EXPERIMENTAL DESIGN

Baseline (pretreatment or archival) melanoma samples were evaluated in 41 patients using a custom genotyping melanoma-specific assay, sequencing of PTEN, and copy number analysis using multiplex ligation amplification and array-based comparative genomic hybridization. Nine patients had on-treatment and/or progression samples available.

RESULTS

All baseline patient samples had BRAF(V600E/K) confirmed. Baseline PTEN loss/mutation was not associated with best overall response to dabrafenib, but it showed a trend for shorter median PFS [18.3 (95% confidence interval, CI, 9.1-24.3) vs. 32.1 weeks (95% CI, 24.1-33), P=0.059]. Higher copy number of CCND1 (P=0.009) and lower copy number of CDKN2A (P=0.012) at baseline were significantly associated with decreased PFS. Although no melanomas had high-level amplification of BRAF, the two patients with progressive disease as their best response had BRAF copy gain in their tumors.

CONCLUSIONS

Copy number changes in CDKN2A, CCND1, and mutation/copy number changes in PTEN correlated with the duration of PFS in patients treated with dabrafenib. The results suggest that these markers should be considered in the design and interpretation of future trials with selective BRAF inhibitors in advanced melanoma patients.

Abstract 2280: Targeted massively parallel sequencing identifies a limited number of clinically actionable variants in women with early onset breast cancer

Approximately 5-10% of breast cancers are likely attributable to single gene mutations. Multiple breast cancer susceptibility genes have been identified; however, there is insufficient information on the clinical benefit of testing for variants in many of these genes outside of BRCA1, BRCA2, TP53 and PTEN. To obtain further information on the spectrum of variants in breast cancer susceptibility genes, we performed massively parallel sequencing using targeted capture of 28 known or proposed breast cancer susceptibility genes in over 250 patients with breast cancer diagnosed under age 40, negative clinical BRCA1 and BRCA2 testing and no personal or family history of ovarian cancer. Sixty-five percent of the patients had a family history of breast cancer. Breast cancers were triple negative in 26% of the patients; 70% of the patients presented with Stage II or greater disease. Positive control mutations in BRCA1, BRCA2, PALB2, CHEK2, MSH2 and BRCC3 were identified using the targeted panel. In analysis of the first 98 study patients, 46+/8 total variants were identified on average per patient with a median read depth of 131. Of the 4,483 total variants identified in the 98 patients, ten variants that are known to be or are likely functionally significant were identified in ten patients (10%). One patient had the CHEK2 1100delC mutation, and another the known deleterious TP53 mutation, P151T. Four of the functionally significant variants are novel frameshift or nonsense mutations in ATM, BRIP1, BARD1 and MRE11A. Four variants predicted to affect splicing, located within the first two nucleotides within the intron, were identified in CHEK2 (3) and MUTYH (1) and are therefore likely to be functionally significant. In addition, 29 patients (29%) were found to carry 27 variants predicted to be deleterious missense variants by multiple variant calling software programs and found at less than 1% frequency in the control population, but are of unclear functional significance as they are either novel or functionally untested. These potentially deleterious variants were identified in ATM (4), RAD50 (3), BRCA2 (3), BARD1 (2), BRCA1 (2), MLH1 (2), NBS (2), BRIP1 (1), CHEK2 (1), MCPH1 (1), MRE11A (1), MSH6 (1), PMS1 (1), and PMS2 (1). These data show that massively parallel sequencing has the ability to identify multiple potentially causative variants in known breast cancer susceptibility genes in patients who present with early onset breast cancer. However, only rare patients, 1% in our initial sample, which will be reported in full, have actionable mutations given current clinical management guidelines. Given the difficulty in determining the functional significance of novel variants, outside of truncating mutations, there is a great deal of uncertainty about how these findings can be translated into improvements in patient care.

Citation Format: Kara N. Maxwell, Bradley Wubbenhorst, Richard Letrero, Kurt D'Andrea, Jacqueline Powers, Jill E. Stopfer, Susan M. Domchek, Katherine L. Nathanson. Targeted massively parallel sequencing identifies a limited number of clinically actionable variants in women with early onset breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2280. doi:10.1158/1538-7445.AM2013-2280

Abstract 5557: Mutation analysis of melanoma tumor samples from ECOG 2603 clinical trial

The BRAF kinase, a member of the MAP kinase pathway, has emerged as an attractive molecule to target in melanoma. In an initial attempt to target BRAF in melanoma, a randomized, phase III trial (ECOG 2603) of carboplatin, paclitaxel, and sorafenib versus carboplatin, paclitaxel, and placebo was performed. Patients enrolled on the trial had either unresectable, locally advanced Stage III or Stage IV melanoma. We analyzed patients’ tumor samples for 74 mutations in 13 genes using a custom iPlex (Sequenom). We have preliminarily analyzed 157 tumor samples from patients enrolled in this clinical trial. Analysis of the initial data set demonstrates that 62 samples (42%, 62/148, 95% CI 34%,50%) carried BRAF mutations - 60 samples with V600 and two samples having a BRAF V601 mutation. Thirty eight samples (26%, 38/148, 95% CI 19%,33%) were positive for NRAS mutations, with 33 with Q61, two G12 and three G13 mutations. With the exception of one tumor sample, the BRAF and NRAS mutations were negatively correlated with each other, consistent with prior observations. We also observed a number of rare mutations in our samples including one in AKT1, one in AKT3, four in CDK4, five in beta-catenin, two in GNAQ and three in KIT. The results of this study demonstrated no difference between the two treatment arms in OS and PFS and no association with treatment outcome and BRAF and NRAS mutations. Consequently, the treatment arms were collapsed, and we examined the relationship of BRAF and NRAS mutations with OS and PFS. Interestingly, our data demonstrated that the BRAF and NRAS mutations did not correlate with OS or PFS. This sample population is unique in that it provides a large data set of melanoma tumor samples, all of whom were entered on a clinical trial, unselected for pre-existing mutations. Using the Sequenom assay platform, we have identified a number of mutations in a subset of genes known to be involved in melanoma in patient tumor samples. In the future, these tumor samples will be informative as we continue to examine and identify additional genetic alterations in melanoma, providing information regarding the natural history and distribution of certain mutations. Future studies will use array comparative genomic hybridization to further investigate additional somatic mutations occurring in melanoma tumors and correlate these with clinical outcome, as well as provide insight into the pathogenesis of melanoma. These results may lead to further opportunities for clinical trials.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5557. doi:1538-7445.AM2012-5557

Integrative genomic analyses of sporadic clear cell renal cell carcinoma define disease subtypes and potential new therapeutic targets

Sporadic clear cell renal cell carcinoma (ccRCC), the most common type of adult kidney cancer, is often associated with genomic copy number aberrations on chromosomes 3p and 5q. Aberrations on chromosome 3p are associated with inactivation of the tumor suppressor gene von-Hippel Lindau (VHL), which activates the hypoxia-inducible factors HIF1α and HIF2α. In contrast, ccRCC genes on chromosome 5q remain to be defined. In this study, we conducted an integrated analysis of high-density copy number and gene expression data for 54 sporadic ccRCC tumors that identified the secreted glycoprotein STC2 (stanniocalcin 2) and the proteoglycan VCAN (versican) as potential 5q oncogenes in ccRCCs. In functional assays, STC2 and VCAN each promoted tumorigenesis by inhibiting cell death. Using the same approach, we also investigated the two VHL-deficient subtypes of ccRCC, which express both HIF1α and HIF2α (H1H2) or only HIF2α (H2). This analysis revealed a distinct pattern of genomic aberrations in each group, with the H1H2 group displaying, on average, a more aberrant genome than the H2 group. Together our findings provide a significant advance in understanding ccRCCs by offering a molecular definition of two subtypes with distinct characteristics as well as two potential chromosome 5q oncogenes, the overexpression of which is sufficient to promote tumorigenesis by limiting cell death.

A second independent locus within DMRT1 is associated with testicular germ cell tumor susceptibility

Susceptibility to testicular germ cell tumors (TGCT) has a significant heritable component, and genome-wide association studies (GWASs) have identified association with variants in several genes, including KITLG, SPRY4, BAK1, TERT, DMRT1 and ATF7IP. In our GWAS, we genotyped 349 TGCT cases and 919 controls and replicated top hits in an independent set of 439 cases and 960 controls in an attempt to find novel TGCT susceptibility loci. We identified a second marker (rs7040024) in the doublesex and mab-3-related transcription factor 1 (DMRT1) gene that is independent of the previously described risk allele (rs755383) at this locus. In combined analysis that mutually conditions on both DMRT1 single nucleotide polymorphism markers, TGCT cases had elevated odds of carriage of the rs7040024 major A allele [per-allele odds ratio (OR) = 1.48, 95% confidence interval (CI) 1.23, 1.78; P = 2.52 × 10(-5)] compared with controls, while the association with rs755383 persisted (per allele OR = 1.26, 95% CI 1.08, 1.47, P = 0.0036). In similar analyses, the association of rs7040024 among men with seminomatous tumors did not differ from that among men with non-seminomatous tumors. In combination with KITLG, the strongest TGCT susceptibility locus found to date, men with TGCT had greatly elevated odds (OR = 14.1, 95% CI 5.12, 38.6; P = 2.98 × 10(-7)) of being double homozygotes for the risk (major) alleles at DMRT (rs7040024) and KITLG (rs4474514) when compared with men without TGCT. Our findings continue to corroborate that genes influencing male germ cell development and differentiation have emerged as the major players in inherited TGCT susceptibility.

Abstract 346: Integrative genomic analysis of sporadic clear cell renal cell carcinoma

Sporadic clear cell Renal Cell Carcinoma (ccRCC) is the most common type of adult kidney cancer. Using high-density copy-number profiling and gene expression profiles, we performed an integrated genomic analysis of 54 sporadic tumor samples. We took a two pronged approach, focusing on 1) all samples and 2) comparing ccRCCs that express both HIF1α and HIF2α (H1H2) and those that express only HIF2α (H2), sub-types of ccRCC that we previously described. For all samples at a frequency over 10%, we identified regions of amplification on 1q, 5q, 7q, 8q, 12p, and 20q, and regions of deletion on 1p, 3p, 6q, 8p, 9p, and 14q, as previously described. We used our integrative analysis to identify target genes that had consistent copy-number and gene expression changes (e.g. amplified and upregulated or deleted and downregulated) within regions on chromosomes 5 and 7. Combining our data with an independent dataset (Beroukhim et al., 2009) and including a literature based analysis, we were able to narrow down to three target genes, which we subsequently validated using a renal cancer cell line. We then compared genomic changes in H1H2 and H2 ccRCCs. Prior data suggested that H2 ccRCCs have increased expression of genes involved in double strand break repair, thus potentially greater genomic stability. Using high-density copy-number data, we have confirmed that H2 tumors have significantly fewer genomic aberrations compared to H1H2 tumors (for amplifications p=0.032 and for deletions p=0.003). In addition, using GISTIC, we found that deletion of chromosome 6 is significantly more common in H1H2 tumors (p&lt;0.001), whereas deletion of chromosome 9 is significantly more common in H2 tumors (p&lt;0.001). Of note, deletion of chromosome 9 previously has been associated with poor prognosis. Thus, correlations between the copy-number data and gene expression profiles indicate that the H1H2 and H2 classes of ccRCC tumors may each have a distinct set of drivers of tumorigenesis; target gene validation for these groups is underway. These experiments provide novel insights into the biology of clear cell Renal Cell Carcinoma (ccRCC).

Beroukhim et al. Patterns of Gene Expression and Copy-Number Alternations in von-Hippel Lindau Disease-Associated and Sporadic Clear Cell Carcinoma of the Kidney. Can Res 2009; 69: (11):4674-81.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 346. doi:10.1158/1538-7445.AM2011-346