Rapid nongenomic estrogen signaling controls alcohol drinking behavior

The sex steroid hormone estrogen is a key modulator of numerous physiological processes and adaptive behaviors, but it may also be co-opted to drive maladaptive behaviors. While many behavioral roles for estrogen signaling have been shown to occur through canonical genomic signaling mechanisms via nuclear receptors, estrogen can also act in a neurotransmitter-like fashion at membrane-associated estrogen receptors to rapidly regulate neuronal function. Early alcohol drinking confers greater risk for alcohol use disorder in women than men, and binge alcohol drinking is correlated with high circulating estrogen but a causal role for estrogen in alcohol drinking has not been established. Here, we demonstrate that gonadally intact female mice consume more alcohol and display an anxiolytic phenotype when they have elevated levels of ovarian-derived estrogen across the estrous cycle. We found that rapid, nongenomic estrogen signaling at membrane-associated estrogen receptor alpha in the bed nucleus of the stria terminalis (BNST) is necessary and sufficient for the pro-alcohol drinking effects of ovarian estrogen signaling, regardless of the transcriptional program of a high ovarian estrogen state. We further show that a population of corticotropin-releasing factor (CRF) BNST neurons (BNSTCRF) is a critical mediator of these effects, as high estrogen rapidly enhances synaptic excitation of BNSTCRF neurons and promotes their role in driving binge alcohol drinking. These findings show a causal role for endogenous, ovarian-derived estrogen in hormonal modulation of risky alcohol consumption and provide the first demonstration of a purely rapid, nongenomic signaling mechanism of ovarian estrogen in the brain controlling behavior in gonadally intact females.

High burden of clonal hematopoiesis in first responders exposed to the World Trade Center disaster

The terrorist attacks on the World Trade Center (WTC) created an unprecedented environmental exposure to aerosolized dust, gases and potential carcinogens. Clonal hematopoiesis (CH) is defined as the acquisition of somatic mutations in blood cells and is associated with smoking and exposure to genotoxic stimuli. Here we show that deep targeted sequencing of blood samples identified a significantly higher proportion of WTC-exposed first responders with CH (10%; 48 out of 481) when compared with non-WTC-exposed firefighters (6.7%; 17 out of 255; odds ratio, 3.14; 95% confidence interval, 1.64-6.03; P = 0.0006) after controlling for age, sex and race/ethnicity. The frequency of somatic mutations in WTC-exposed first responders showed an age-related increase and predominantly affected DNMT3A, TET2 and other CH-associated genes. Exposure of lymphoblastoid cells to WTC particulate matter led to dysregulation of DNA replication at common fragile sites in vitro. Moreover, mice treated with WTC particulate matter developed an increased burden of mutations in hematopoietic stem and progenitor cell compartments. In summary, the high burden of CH in WTC-exposed first responders provides a rationale for enhanced screening and preventative efforts in this population.

Abstract 2238: A novel comprehensive breakpoint-targeted assay for clinically actionable RNA fusions and aberrant RNAs in solid tumors

Background: Gene fusions are major drivers of cancer and their accurate detection is key for supporting diagnosis and therapy selection. There are more than 65,000 annotated gene fusion events. Current fusions detection strategies are limited to amplicon panels querying only a small number of genes, or whole exome capture based assays, which can reduce sensitivity. With these technologies, multiple small panels are required to capture all relevant fusions, which is prohibitive for small biopsies like fine needle aspirates. Hence, clinical grade assays able to accurately detect a comprehensive set of the most clinically relevant gene fusions for solid tumors are needed.

Methods: We isolated total nucleic acid (TNA) from 141 FFPE tumor specimens or a control sample (Seraseq) and performed pair-ended, strand-specific hybridization-based RNA sequencing on a Next-Seq 500. We selected 252 fusion genes from NCCN and WHO guidelines, published clinical studies, and the 120 most frequent curated fusions in solid tumors from COSMIC (v91). These fusions are clinically relevant to most frequent cancers, including breast, colorectal, lung, lymphoma, pancreatic, prostate, salivary gland, sarcomas, and thyroid cancers. Chimeric probes were synthetized targeting fusion RNA sequences for 2230 selected breakpoints and exon junction regions of aberrant RNAs, including EGFRvIII, MET exon 14 skipping, ARv7 and ARv9. We also targeted the full coding region of 27 genes whose change in expression may suggest translocations and mutations, or have diagnostic value. Fusions were called by a custom pipeline using 3 fusion callers and a machine-learning algorithm. The PCR-based Archer FusionPlex assays and RT-PCR followed by Sanger were used as orthogonal validation methods.

Results: This single RNA fusion assay can detect at least 1194 unique known fusions pairs involving 1104 genes, as compared to 63 or 47 fusion genes from other commercially available NGS assays. On 141 FFPE samples from various tumor types, we detected 100/106 fusions reported in our CLIA laboratory Archer Sarcoma and Comprehensive Thyroid & Lung (CTL) panels. We also identified 41 additional high confidence fusions missed by Archer but confirmed by Sanger sequencing. Thus, the assay has 95.9% (141/147) sensitivity and 100% specificity, as all fusions were confirmed by either orthogonal assay. We also detected MET exon 14 skipping, EGFRvIII and ARv7 variants. Importantly, in two samples we detected MET exon 14 skipping not predicted from DNA mutation analysis showing the sensitivity of the approach. Notably, several of the 41 additional fusions are novel and were targeted by only one of the breakpoints.

Conclusion: We developed a novel and efficient breakpoint targeted fusion detection RNA-seq assay from extracted TNA from FFPE samples that can comprehensively profile thousands of clinically actionable RNA fusions and aberrant RNAs in solid tumors.

Citation Format: Fernando J. Lopez-Diaz, Steven P. Rivera, Chenyin Ou, Christophe Magnan, Brad Thomas, Tibor Gyuris, Yanglong Mou, Segun Jung, Madhuri Paul, Forrest Blocker, Shari Brown, Jacqueline Lekostaj, Ryan Bender, Sally Agersborg, Lawrence M. Weiss, Vincent Funari. A novel comprehensive breakpoint-targeted assay for clinically actionable RNA fusions and aberrant RNAs in solid tumors [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 2238.

Abstract 2208: A comprehensive genomic profiling approach to detect functional translocations and genomic alterations in a single tube workflow

Background: To comprehensively profile mutations in hematologic malignancies, we developed a targeted multimodal NGS assay that can detect SNVs, InDels, fusions, gene expression, and copy number variations from total nucleic acid (TNA) in a single tube workflow.

Methods: TNA was extracted from peripheral blood and bone marrow specimens from patients with hematologic cancers. TNA was used to prepare libraries then sequenced on a NovaSeq 6000. DNA variants were compared to results from DNA NGS assays and RNA fusions were compared to FISH and RT-PCR.

Results: Our multimodal NGS assay can efficiently use TNA to detect mutations simultaneously within the DNA and RNA in a single tube workflow. From 100 fusion positive samples, we detected fusions in all samples and >25 different fusions were detected. Our NGS assay was 100% concordant with the BCR-ABL1 qRT-PCR assay in samples with an IS value of >0.5, 92.7% concordant with the ArcherDX Heme NGS assay, and 100% sensitive in detecting high-confidence fusions. In 5 previously tested BCR-ABL1 positive samples, we confirmed the RNA expression as well as detected pathogenic DNA variants, including JAK2 p.V617F, U2AF1 p.S34F, ASXL1 p.E635Rfs*15, BRCA p.S1982Rfs*22, and DNMT3A p.S708Vfs*71. In another patient, we found multiple pathogenic mutations (ASXL1 and JAK2), in addition to a BCR-FGFR1 fusion. Two PML(e4)-RARA and PML(e6)-RARA isoforms were detected and confirmed in one sample, illustrating the high resolution that could be used to help monitor the patient. Three fusions involving CXCR4 (CXCR4-FOSL2, CXCR4-DDX5, and ARID5A-CXCR4), a receptor known to promote proliferation, migration and resistance to chemotherapy were also detected in addition to CXCR4 over-expression in three patients. In another patient, we confirmed a KMKT2A-ARHGEF12/del(11)(q23q23) aberration by NGS that was missed by cytogenetics. In one sample, we confirmed expression of 3 out of 4 different MYC fusions (MYC-BCL6, MYC-IgH, IgH-MYC); only NGS could identify the fusion orientation, illustrating the high resolution of NGS over FISH. In several patients with IgH-BCL1 translocations, we expected BCL1 overexpression. Although DNA PCR results were mostly negative, we discovered increased expression in a subset of these samples. This suggests that despite the detection of the fusion by FISH, a subset may lack gene expression which may suggest a different biological or clinical significance.

Conclusion: Our findings demonstrate the value that a comprehensive profile provides to diagnostic tests. NGS has high resolution and by targeting RNA we can detect more fusions than traditional DNA approaches. Comparison of FISH and NGS results show that detecting a functional mutation maybe important for characterizing a disease. However, both may need to be combined for a complete picture to improve detection and characterization of various hematologic diseases.

Citation Format: Cynthie Wong, Brad Thomas, Yanglong Mou, Christophe Magnan, Segun Jung, Tibor Gyuris, Francys Alarcon, Eve Shinbrot, Fei Ye, Ryan Bender, Sally Agersborg, Lawrence Weiss, Vincent Funari. A comprehensive genomic profiling approach to detect functional translocations and genomic alterations in a single tube workflow [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 2208.

Facilitated self-assembly of a prevascularized dermal/epidermal collagen scaffold

Introduction: Resurfacing complex full thickness wounds requires free tissue transfer which creates donor site morbidity. We describe a method to fabricate a skin flap equivalent with a hierarchical microvascular network. Materials & methods: We fabricated a flap of skin-like tissue containing a hierarchical vascular network by sacrificing Pluronic^® F127 macrofibers and interwoven microfibers within collagen encapsulating human pericytes and fibroblasts. Channels were seeded with smooth muscle and endothelial cells. Constructs were topically seeded with keratinocytes. Results: After 28 days in culture, multiphoton microscopy revealed a hierarchical interconnected network of macro- and micro-vessels; larger vessels (>100 μm) were lined with a monolayer endothelial neointima and a subendothelial smooth muscle neomedia. Neoangiogenic sprouts formed in the collagen protodermis and pericytes self-assembled around both fabricated vessels and neoangiogenic sprouts. Conclusion: We fabricated a prevascularized scaffold containing a hierarchical 3D network of interconnected macro- and microchannels within a collagen protodermis subjacent to an overlying protoepidermis with the potential for recipient microvascular anastomosis.

Abstract 182: A comprehensive genomic profiling approach to interrogate hematologic malignancies using a novel multimodal next generation sequencing assay in a single-tube

Background: Many new guidelines require a comprehensive genomic profiling approach for diagnosis, risk stratification and therapy decisions. Limitations in sample quantity and throughput may limit the number of single biomarker tests (FISH, karyotyping, sequencing, qRT-PCR, etc.) that can be performed for the patient. There are currently multiple commercial NGS assay options for total nucleic acid, however they involve independent parallel workflows and twice the amount of sample and effort. Here we developed a novel consolidated DNA/RNA workflow in a single-tube assay utilizing custom QIAseq multimodal chemistry. This simplified workflow enables a discovery approach of all critical DNA/RNA abnormalities in hematologic malignancies, extending our NGS capabilities to large structural changes, RNA fusions and expression.

Methods: 297 Heme-focused genes and 14 chromosomes were targeted in the genome, along with 213 RNA genes targeting 712 exons involved in known fusions in the transcriptome using a custom QIAseq workflow. Captured DNA/RNA targets from 135 patients were sequenced with unique dual indices on an Illumina's NovaSeq 6000. Coverage and variant allele frequency from all gene and chromosomal targets in 25 disease free patients was compared to the same genomic targets in 76 patients that were referred for a suspected hematological malignancy (e.g. MDS, CML, AML, ALL, etc.). We compared results from our custom algorithm to karyotyping and FISH. In addition, we assessed the relationship between structural changes and the average mutation load for each indication. Positives gene fusions were confirmed by qRT-PCR or Sanger sequencing.

Results: Cytogenetic abnormalities in 30/32 patients were confirmed by karyotyping and FISH; two cases with abnormalities were missed by NGS. NGS detected additional abnormalities not detected by cytogenetics, including a case of loss of chr17 including deletion of driver genes, NF1 and SUZ12. No significant relationship between chromosome abnormalities and tumor mutation burden was observed. However, patients referred for myeloid disorders with structural abnormalities had a significantly higher mutational burden (p<9.12x10−7). Mutational load in these patients was significantly associated with chromosome 17 abnormalities, primarily loss (p<0.013). qRT-PCR confirmed 100% of BCR-ABL fusions (p210, p190) in all patients (59/59) with International Scale (IS) percentages ranging from 2.4-100%. Notably, we confirmed two clinically significant fusions, SET-NUP214 and RUNX1-RUNX1T1 in two patients not previously interrogated by qRT-PCR. The SET-NUP214 fusion is normally associated with acute lymphoblastic leukemia (ALL) was identified in a patient with suspected CML. We also confirmed PCALM-MLLT10 gene fusion was detected in a commercial universal human RNA reference material, commonly used in expression profiling studies.

Conclusions: This study confirms the validity and utility of simple but efficient comprehensive genomic profiling for use in hematologic malignancies. Coupled with FISH and cytogenetics tests, NGS can offer a better diagnostic and prognostic testing service for patients with hematologic disease to assist in treatment selection as well as precise patient care.

Citation Format: Segun C. Jung, YongXin Yu, Yanglong Mou, Hyunjun Nam, Cynthie Wong, Samuel Koo, Brad Thomas, Forrest Blocker, Derek Lyle, Ryan Bender, Sally Agersborg, Lawrence M. Weiss, Vincent A. Funari. A comprehensive genomic profiling approach to interrogate hematologic malignancies using a novel multimodal next generation sequencing assay in a single-tube [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 182.

Abstract 3170: Different genomic mutations signatures are associated to specific PD-L1/TMB states on lung cancer with potential value for patients screening for immunotherapy

Objective: PD-L1 expression and Tumor Mutation Burden (TMB) have independently emerged as prospective biomarkers of response to anti PD1-/PDL1 checkpoint inhibitors. However, TMB has not fully proven its value as a biomarker of Immunotherapy response in lung cancer. Moreover, FDA-approved CDx PD-L1 expression alone is not an optimal biomarker for checkpoint inhibitors and combined use of MSI, TMB and PD-L1 protein levels has been proposed. Here we present the correlation between genomic landscape, including TMB and MSI with PDL1 IHC in lung cancer specimens to help identify immunogenomic profiles for stratification of patients for check-point inhibitors therapies evaluation.

Methods: 874 FFPE clinical samples across cancer types were characterized in our CLIA/CAP accredited clinical laboratory using a CLIA-validated NGS-based assay that interrogates SNVs, indels, TMB and Microsatellite Status (27 MS markers) using a 323 gene panel. TMB (mutations/Mb) is categorized as low (≤7), intermediate (7<TMB≤15) and high: (greater than 15). The de-identified aggregated results paired with PD-L1 IHC data from 424 lung cancer samples were analyzed and correlations between PD-L1 tumor proportion scores (TPS) and TMB results were made. In silico analyses were also performed on 5939 lung cancer samples from public databases.

Results: The detected TMB median in lung cancer was 8.6 (range 0-126.4). Median PD-L1 TPS was 7%, with 26% of samples being PD-L1 negative (TPS<1%), 44% Low expressing (≥1-49%) and 31% High (≥50%). All samples were MSS. We found poor correlation between PD-L1 expression and TMB in NSCLC (r2=0.266). We classified samples based on TMB and PD-L1 TPS and found mutational correlations specific to in each of the following groups: PD-L1 High/TMB Low, PD-L1 High/TMB High, PD-L1 Low/TMB High, PD-L1 High/TMB High, and PD-L1 Neg/TMB High. Of note 67% (34/51) of PD-L1 High/TMB Low samples presented mutations either on EGFR (12%), KRAS (23.5%) or in genes from known driver TRK/MAPK pathways, whereas only KRAS was part of the frequently mutated gene signature with 36.5% (13/36) samples mutated on PD-L1 High/TMB High samples. Neither EGFR nor KRAS were found frequently mutated on PD-L1 Low/TMB High group (n=46). Strikingly the top 12 most frequently mutated genes on PD-L1 Neg/TMB High tumors were TP53, LRP1B, SPTA1, SMARCA4, GNAS, ALK, FGFR2, SLIT2, ROS1, AMER1, FAT1, and MED12. We found statistically significant co-occurrences between LRP1B and 7 other genes from this signature in additional 5939 lung cancer patients assessed.

Conclusions: TMB and PD-L1 results do not correlate in lung cancer specimens. Common genomic alteration signatures might define subsets of lung cancer tumors with no PD-L1 expression to complement TMB and PD-L1 on the selection criteria for patients whom may benefit from checkpoint inhibitors.

Citation Format: Fernando J. Lopez-Diaz, Lauryn Keeler, Forrest Blocker, Shiloh Sprankles, Ryan Bender, Sally Agersborg, Lawrence Weiss, Vincent Funari. Different genomic mutations signatures are associated to specific PD-L1/TMB states on lung cancer with potential value for patients screening for immunotherapy [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 3170.

Abstract P4-09-15: A large study of PIK3CA mutations in the community setting identifies varying degree of mutation positivity rates across age groups in advanced HR+, HER2- breast cancer patients using an FDA RT-PCR cleared test

Background: The phosphatidylinositol 3-kinase (PI3K) gene encoding the catalytic component p110, PIK3CA, is one of the most frequently mutated genes in breast cancer. [1]

PIK3CA mutational status and prevalence have been studied in various clinical trial settings but not sufficiently studied in the community setting. In the SOLAR-1 trial, PIK3CA mutations were detected in approximately 40% of hormone receptor (HR) positive, human epidermal growth factor receptor 2 (HER2)-negative breast cancer patients where the mutation rate in exon 20 was similar to that in exon 9 (33.7% vs 29.9%). [2-3] In other HER2-positive breast cancer trials, the PIK3CA mutation rate was 21.4% in the GeparStudies, 22.5% in NeoALTTO, and 20.4% in the CHERLOB study, where mutations in exon 20 were twice as high as in exon 9 (14.5% vs 7.2%). [4-6]

Methods: An unselected female cohort of 1281 patients with advanced stage HR-positive, HER2-negative breast cancer seen in the community setting was included in this study, with an average age of 62.9 years. Age groups by the decade ranged from < 30 years old to > 80 years old respectively: 6, 46, 124, 274, 390, 332, 109 patients. The breast tumor tissues used in this study were formalin-fixed, paraffin-embedded (FFPE). Mutational status was determined by an U.S. Food & Drug Administration (FDA) cleared test kit, and processed in accordance with the labeling instructions. [7-8] This PIK3CA kit was a real-time qualitative PCR test for the detection of 11 mutations in the PIK3CA gene (Exon 7: C420R; Exon 9: E542K, E545A, E545D [1635G>T only], E545G, E545K, Q546E, Q546R; and Exon 20: H1047L, H1047R, H1047Y) using genomic DNA (gDNA) extracted from (FFPE) breast tumor tissue.

Results: PIK3CA mutations were detected at 37.5% (N=481) of patient samples.

Mutation positivity rates differed depending on the patient age groups. For patients under the age of 30 or in their 30s, mutation positivity rates were 16.7% and 17.4% respectively while the positivity rates were substantially higher in older age groups: 37.9% (40s), 31% (50s), 41.3% (60s), 39.2% (70s) and 45% (> 80 years old).

The specific mutations identified varied for the different age groups. Patients under the age of 30 or in their 30s, the p.E545K variant appeared to be the predominant point mutation. In contrast, patients in the 50 years old age group and older had mutations across all detectable mutational hotspots in exon 7, 9 and 20.

Conclusion: PIK3CA is one of the most frequently mutated genes in breast cancer. This study marks the first large cohort assessment of PIK3CA mutation status within the community setting using an FDA-cleared assay. In this study, the mutation positivity rate of 37.5% in the community setting is similar to the ~40% in clinical trial settings.

Refernces:

1. Cancer Genome Atlas Network: Nature 490:61-70, 2012

2. André F, et al. N Engl J Med 2019;380: 1929-40

3. Rugo H, et al. Cancer Res 2019;79(13 Suppl):Abstract CT142

4. Loibl S, et al. Annals of Oncology 27: 1519–1525, 2016

5. Majewski IJ, et al. J Clin Oncol 2015; 33: 1334–1339

6. Guarneri V, et al. Oncologist 2015; 20: 1001–1010

7. P190001 - therascreen® PIK3CA RGQ Kit Instructions for Use (Handbook). Accessed August 29, 2019

8. P190004 - therascreen® PIK3CA RGQ PCR Kit Instructions for Use (Handbook). Accessed August 29, 2019

Citation Format: Alex C Chan, Lawrence M Weiss, Ryan Bender. A large study of PIK3CA mutations in the community setting identifies varying degree of mutation positivity rates across age groups in advanced HR+, HER2- breast cancer patients using an FDA RT-PCR cleared test [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-09-15.

Hyperbaric oxygen therapy for iatrogenic arterial gas embolism after CT-guided lung biopsy : A case report

Iatrogenic arterial gas embolism (AGE) can be life-threatening. The only causal treatment is immediate hyperbaric oxygen therapy (HBOT). This article reports on a case of a 74-year-old male patient who underwent computed tomography (CT)-guided lung biopsy of suspect nodules after squamous cell carcinoma of the tonsils. During puncture, sudden cardiovascular arrest occurred. The CT scan documented severe arterial gas embolism in the aorta, spinal canal, left heart ventricle, and brain. The patient was then transferred to our hospital for HBOT. After the first HBOT, an additional CT scan showed regression of all gas inclusions. In the treatment of gas embolism, HBOT is considered the gold standard and is indispensable. It is primarily used to reduce acute bubble effects and to avoid secondary bubble effects. Unfortunately, the long persisting gas occlusions and perfusion deficits led to severe hypoxic brain damage and a poor prognosis for the patient. In this case report we present the management of (iatrogenic) arterial gas embolism and point out the necessity of immediate HBOT. Furthermore, we discuss the pathophysiology leading to arterial gas embolism on the basis of the gas laws.

Testing the Gaussianity of the Human EEG During Anesthesia

The Gaussian properties of human EEGs, which were measured over various stages of general anesthesia, were tested. The basis of the method was to describe the EEG signals by autoregressive models and to test the normality of the regression residuals with the Shapiro-Wilk statistic. The results show that in general the human EEG during anesthesia can be considered as a realization of a Gaussian stochastic process.

Application of Adjusted Survival Curves to Renal Transplant Data

An important means in the analysis of survival time data is the estimation and graphical representation of survival probabilities. In this paper unifactorial parametric and non-parametric survival curve estimators and two types of adjusted survival curves based on a parametric multifactorial approach are applied to renal transplant data. It is shown that the resulting survival curves can differ substantially. The unifactorial survival curves yield biased results in case of serious disequilibrium in the data. This drawback of the unifactorial methods has been overcome by the use of adjusted survival curves which take possible distortions in the data set into account. The benefits of adjusted survival curves in assessing potentially prognostic factors are elucidated by the application to data from renal transplantation.

Intervention Effects in the Case of Heterogeneity between Three Subgroups

Background: Usually, statistical tests for interactions are applied to investigate potential effect modifiers. If an effect modifier, consisting of three categories, is found to be statistically significant, the application of pairwise interaction tests is indicated. In this case, the problem of non-transitive relations may occur if the significance level is fixed at 0.05 for all tests.

Objective: To develop an algorithm for which non-transitive relations do not occur.

Methods: A hierarchical testing procedure is applied, based on the heterogeneity statistic Q. In a first step the interaction will be tested for the three trial subgroups altogether, applying the significance level α = 0.05 (global test). If a significant interaction is proven in the first step, pairwise tests for interaction will be applied in a second step. Theoretical data scenarios will be considered and p-values will be calculated for the pairwise tests. Based on these results the significance level for pairwise testing will be determined.

Results: Fixing the significance level at 0.05 for all tests, the problem of non-transitive relations is mostly relevant, if the difference in the effects between the three trial subgroups is approximately 3.5 standard errors and the effect of the ‘middle’ trial subgroup is not close to one of the other two effects. This problem vanishes when the significance level is set to α = 0.22. We propose to select α = 0.20 to get a more ’even’ and simple value.

Conclusions: By increasing the significance level for the pairwise tests to 0.20, non-transitive relations are virtually avoidable. The proposed hierarchical testing procedure represents a clear practical guidance to perform subgroup analyses in the framework of systematic reviews.

Multi-platform molecular profiling of a large cohort of glioblastomas reveals potential therapeutic strategies

Glioblastomas (GBM) are the most aggressive and prevalent form of gliomas with abysmal prognosis and limited treatment options. We analyzed clinically relevant molecular aberrations suggestive of response to therapies in 1035 GBM tumors. Our analysis revealed mutations in 39 genes of 48 tested. IHC revealed expression of PD-L1 in 19% and PD-1 in 46%. MGMT-methylation was seen in 43%, EGFRvIII in 19% and 1p19q co-deletion in 2%. TP53 mutation was associated with concurrent mutations, while IDH1 mutation was associated with MGMT-methylation and TP53 mutation and was mutually exclusive of EGFRvIII mutation. Distinct biomarker profiles were seen in GBM compared with WHO grade III astrocytoma, suggesting different biology and potentially different treatment approaches. Analysis of 17 metachronous paired tumors showed frequent biomarker changes, including MGMT-methylation and EGFR aberrations, indicating the need for a re-biopsy for tumor profiling to direct subsequent therapy. MGMT-methylation, PR and TOPO1 appeared as significant prognostic markers in sub-cohorts of GBM defined by age. The current study represents the largest biomarker study on clinical GBM tumors using multiple technologies to detect gene mutation, amplification, protein expression and promoter methylation. These data will inform planning for future personalized biomarker-based clinical trials and identifying effective treatments based on tumor biomarkers.

[Autologous Skin Cell Transplantation and Medical Needling for Repigmentation of Depigmented Burn Scars on UV-protected and UV-exposed Skin]

Background: Burn scars remain a serious physical and psychological problem for the affected people. Both clinical studies and basic scientific research have shown that medical needling can significantly increase the quality of burn scars with comparatively low risk and stress for the patient related to skin elasticity, moisture, erythema and transepidermal water loss. However, medical needling does not influence repigmentation of large hypopigmented scars. Objective: The goal is to evaluate whether both established methods - needling (improvement of scar quality) and non-cultured autologous skin cell suspension (NCASCS) "ReNovaCell" (repigmentation) - can be combined. So far, 20 patients with mean age of 33 years (6-60 years) with deep second and third degree burn scars have been treated. The average treated tissue surface was 94 cm² (15-250 cm²) and was focused on areas like face, neck, chest and arm. Methods: Medical needling is performed using a roller covered with 3 mm long needles. The roller is vertically, horizontally and diagonally rolled over the scar, inducing microtrauma. Then, NCASCS is applied, according to the known protocol. The patients have been followed up for 15 months postoperatively. The scars were subdivided into "UV-exposed" and "UV-protected" to discover whether the improved repigmentation is due to transfer of melanocytes or to reactivation of existing melanocytes after exposure to UV or the sun. Results: The objective measures show improved pigmentation in both UV-exposed and UV-protected groups. Melanin increases 1 year after NCASCS treatment in the UV-protected group are statistically significant. Conclusion: Medical needling in combination with NCASCS shows promise for repigmentation of burn scars, even in sun protected scars.

Abstract 2750: Mutations on the homologous recombination pathway in 13 cancer types

Homologous recombination (HR) is important in DNA double-strand break repair. HR defects promote carcinogenesis and are associated with selective sensitivity to PARP-inhibitors and DNA-damaging agents. We collected 1029 tumor samples in 13 cancer types and used next-generation sequencing (NGS) to survey genes in the HR pathway. NGS on 591 genes was performed using formalin-fixed paraffin-embedded samples on the Illumina NextSeq platform (Caris Life Sciences, AZ). Mutations in as low as 5% of cells can be detected with > 99% confidence. Deletions larger than 27bp may not be detected by this method. Pathogenic or presumed pathogenic variants are counted as mutations. The table summarizes mutation rates of 7 key genes—ATM, BRCA1, BRCA2, CHEK1, CHEK2, PALB2 and PTEN—included in this pilot study. Another 17 HR genes—ATR, ATRX, BARD1, BLM, BRIP1, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCL, MRE11A, NBN, RAD50, RAD51, and RAD51B—were also analyzed. PTEN mutations were seen in 6.3% of tumors, ATM in 5%, BRCA1 in 2%, BRCA2 in 2%, PALB2 in 1%, and CHEK2 in 1%. No CHEK1 mutations were observed. Overall, 15% of tumors carry at least one mutation in any of the 7 key genes. The highest mutation rates were seen in endometrial (43%), glioblastoma (34%), and gastric cancers (23%). The highest rates of ATM (9.7%), BRCA2 (6.5%), and PALB2 (6.5%) were seen in gastric cancer, while the highest CHEK2 (5.6%), BRCA1 (7.3%) and PTEN (44%) mutations were seen in cholangiocarcinoma, ovarian and endometrial tumors, respectively. One 53-year old pt with metastatic poorly-differentiated gastric adenocarcinoma experienced ongoing radiographic partial response and dramatic symptom relief following 4 cycles of FOLFOX without surgery; tumor analysis revealed a nonsense PALB2 (S326*) gene mutation, while the other 23 HR genes were wild type. ERCC1 showed intact expression by IHC. Mutation rates of 7 genes on the HR pathway in 13 cancer typesEndometrialATMBRCA1BRCA2CHEK1CHEK2PALB2PTENAny of the 7 genesEndometrial (N = 35)00002.9%3.0%44.1%42.9%GBM (N = 47)2.1%2.1%000030.4%34.0%Gastric (N = 31)9.7%06.5%006.5%022.6%Bladder (N = 38)2.6%05.4%00010.8%18.4%Kidney (N = 41)2.5%0005.0%010.0%17.1%Ovarian (N = 82)3.7%7.3%1.2%01.2%01.3%14.6%Breast (N = 108)4.6%2.8%1.9%00.9%1.0%3.8%13.9%Cholangiocarcinoma (N = 36)2.8%02.8%05.6%02.9%13.9%CRC(N = 254)6.3%2.0%1.6%00.4%04.0%13.0%Pancreatic (N = 62)4.8%1.6%3.2%001.7%3.3%12.9%NSCLC(N = 234)6.5%00.9%001.4%2.6%11.1%Neuroendocrine(N = 35)2.9%000005.7%8.6%Esophageal (N = 26)3.8%000004.0%7.7%Overall(N = 1029)5.0%1.6%1.6%00.8%0.8%6.3%15.2%

Thus, mutation rates of at least 8 to 43% in the HR pathway are reported from 13 cancer types. This method can potentially identify responders to DNA-damaging agents including platinum.

Citation Format: Joanne Xiu, Ryan Bender, Brian Abbott, Zoran Gatalica, Sandeep Reddy, Mohamed Salem, Shelly Seward. Mutations on the homologous recombination pathway in 13 cancer types. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2750.

Abstract 2735: Clinico-pathological and molecular features associated with TP53 mutation in 3457 molecularly-profiled colorectal cancers (CRCs)

Deregulation of the p53 tumor suppressor gene (TP53) is a key event contributing to transformation and aggressive metastatic features of CRC. Patients with TP53 mutation are often resistant to therapy and carry a poor prognosis. We investigated TP53 mutation in a cohort of 3457 CRCs to identify molecular features specific to TP53-mutated CRC tumors. The 3457 CRC clinical samples were evaluated for tumor profiling (Caris Life Sciences, Phoenix, AZ). Tests included Sanger or next generation sequencing (NGS), protein expression by immunohistochemistry (IHC) and gene amplification by in situ hybridization (ISH). TP53 mutation was observed in 2106 or 61% of CRCs analyzed. 2018 or 96% of these mutant TP53 tumors carried one TP53 mutation, 83 (4%) carried 2 mutations, 4 carried 3 and 1 tumor carried 4 mutations. Among the ∼2200 mutations found in TP53, 37% were found at one of the six hotspots within the DNA binding domain (R175, G245, R248, R249, R273 and R282). Overall, 1554 (71%) were missense mutations, 367 (17%) nonsense, 209 (9.5%) frameshift, 45 (2%) small in-frame in-dels, and 25 (1.1%) mutations that affect splicing. In this cohort, TP53 mutation was more prevalent in male patients (64% vs. 57%, P<0.0001) and was more likely to occur in tumors that originated from the left colon (69%) as compared to the right colon (45%, p<0.0001). TP53 mutation rate was not correlated with patient age, histology or whether the tumor sample was taken from the primary or metastatic sites. When the molecular features of TP53-mutated tumors were compared to those of wild-type TP53, mutated tumors carried significantly higher Her2 IHC expression (2.5% vs. 1.0%, p = 0.0039) and gene amplification (3.7% vs. 1.4%, p = 0.0002), as well as higher MGMT (61% vs. 53%, p<0.0001) and TOPO2A expression (92% vs. 81%, p<0.0001). On the other hand, lower EGFR expression (57.4% vs. 70%, p<0.0001), PTEN expression (47.9% vs. 61%, p<0.0001), microsatellite instability (2.5% vs. 11.5%, p<0.0001), ERCC1 (18% vs. 24%, p<0.0001) and TS expression (31% vs. 38%, p<0.0001) were associated with TP53-mutated tumors. TP53-mutated CRCs carried higher rates of APC mutation (63% vs. 53%, p<0.0001), but lower rates of KRAS (46% vs. 54%, p<0.0001), PIK3CA (11.6% vs. 22%, p<0.0001), PTEN (2% vs. 5.2%, p<0.0001), GNAS (1% vs. 8.3%, p<0.0001) and AKT1 (0.6% vs. 1.7%, p = 0.0016) mutation. In this cohort of 3457 molecularly profiled CRCs, TP53 mutation was more prevalent in males and tumors that originated from the left colon. Distinct molecular features associated with TP53 mutation in CRC included lower frequency of PI3K/Akt/mTor pathway activation and were more likely to be microsatellite stable.. Our findings suggest differential presence of therapeutic targets in CRC tumors based on TP53 mutation status.

Citation Format: Joanne Xiu, Thierry Soussi, Ryan Bender, Sandeep Reddy, Wafik S. El-Deiry. Clinico-pathological and molecular features associated with TP53 mutation in 3457 molecularly-profiled colorectal cancers (CRCs). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2735.

Abstract 3928: Caveolin-1: Beyond a marker for basal-like breast cancers

Introduction: Caveolin-1 (Cav1) is associated with basal-like triple-negative (ER-/PR-/Her2-) breast cancers (TNBC). Its biological contribution to this subtype has not been fully explored and controversy persists regarding the molecular role of Cav1 in carcinogenesis. Experimental Procedures: Thirty-four TNBC (17 Cav1+/17 Cav1-) patients molecularly-profiled with a commercial assay (Caris Life Sciences, AZ) were evaluated retrospectively. Cav1 status was determined by immunohistochemistry (caveolin-1 polyclonal; ≥2+ ≥50%). The majority of specimens (28/34) used for profiling were from primary breast sites and contained ≥50% neoplastic cells. The transcriptomes were profiled using Illumina's HumanHT-12 microarray (v4). Data were normalized using mean normalization procedure. Differential expression analysis was performed using R's Limma package. Pathway analysis was carried out using R's signaling pathway impact analysis (SPIA) package with 69 cancer, immunity, and cell signaling related KEGG pathways. Results: Using a cutoff of two-fold and adjusted p-value of 0.05, we identified 954 genes differentially expressed between Cav1+/- TNBC patients. Included in these were 31 genes which were found to be up-regulated by over five- fold and 3 genes down-regulated by over five fold in Cav1+ TNBC. Genes of notable interest for their role in cell signaling, cell adhesion, tumor invasion and metastasis, included an up-regulation of TGFBR2, SPARC, integrins (ITGA11, ITGB5, ITGBL1), cell adhesion proteins (LAMB3, COL5A3) and molecules which facilitate tumor invasion (LAMB3, MMP1, MMP2, MMP9). In addition, genes found to be down-regulated in Cav1+ patients and notable for their roles in promoting epithelial-mesenchymal-transition (EMT) included Claudin 3(CLD3) and CA125/MUC16 (Mucin 16). We also detected an approximately two-fold down-regulation of CDKN2A in Cav1+ patients. Using SPIA pathway analysis, 12 pathways were found to be differentially activated in Cav1+ vs. Cav1- TNBC. The most differentially activated pathways were the focal adhesion pathway (p = 4.51E-18), PI3k-Akt signaling pathway (p = 2.01E-6) and TGF-β and MAPK signaling pathways (p = 0.005, 0.014, respectively). Conclusions: Differential gene expression patterns and pathway analyses provide evidence for distinct profiles for gene expression between Cav1+/- TNBC. Cav1+ TNBC patients exhibit up-regulation of genes important for cell signaling, extracellular matrix remodeling and tumor invasion, and down-regulation of genes that may facilitate EMT and loss of cell cycle control. The focal adhesion pathway, as well as TGF-β, PI3K and MAPK signaling pathways, were identified as differentially activated among Cav1+/- TNBC. Taken together, these data support the role of Cav1+ in identifying a subtype of TNBC that may have a greater risk for invasion and metastasis. The correlation of this subtype with prognosis and drug response should be investigated in future studies.

Citation Format: Rebecca A. Feldman, Zoran Gatalica, Semir Vranic, Ryan Bender, Sandeep Reddy, Anatole Ghazalpour. Caveolin-1: Beyond a marker for basal-like breast cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3928.

Combination of medical needling and non-cultured autologous skin cell transplantation (renovacell) for repigmentation of hypopigmented burn scars in children and young people

Burn scars remain a serious physical and psychological problem for the affected. Clinical studies as well as basic scientific research have shown that Medical Needling can significantly increase the quality of burn scars with comparatively low risk and stress for the patient with regards to skin elasticity, moisture, erythema and transepidermal water loss. However, Medical Needling has no influence on repigmentation of large hypopigmented scars. The goal is to evaluate whether both established methods - Needling (improvement of scar quality) and ReNovaCell (repigmentation) - can be combined. So far, eight patients with mean age of 20 years (6-28 years) with deep second and third degree burn scars have been treated. The average treated tissue surface was 76cm² (15-250cm²) and was focused on areas like face, neck, chest and arm. Medical Needling is performed using a roller covered with 3mm long needles. The roller is vertically, horizontally and diagonally rolled over the scar, inducing microtrauma. Then, non-cultured autologous skin cell suspension (ReNovaCell) is applied, according to the known protocol. The patients were followed 12 months postoperatively. Pigmentation changes were measured objectively, and with patient and observer ratings. Patient satisfaction/preference was also obtained. We present the final study results. Taken together, pigmentation ratings and objective measures indicate improvement in six of the study participants. Melanin increase seen 12 months after ReNovaCell treatment in the study group as a whole is notable. Medical Needling in combination with ReNovaCell shows promise for repigmentation of burn scars.

Mutations in the Kinase Domain of the HER2/ERBB2 Gene Identified in a Wide Variety of Human Cancers

The HER2 (official name ERBB2) gene encodes a membrane receptor in the epidermal growth factor receptor family amplified and overexpressed in adenocarcinoma. Activating mutations also occur in several cancers. We report mutation analyses of the HER2 kinase domain in 7497 histologically diverse cancers. Forty-five genes, including the kinase domain of HER2 with HER2 IHC and dual in situ hybridization, were analyzed in tumors from 7497 patients with cancer, including 850 breast, 770 colorectal, 910 non-small cell lung, 823 uterine or cervical, 1372 ovarian, and 297 pancreatic cancers, as well as 323 melanomas and 2152 other solid tumors. Sixty-nine HER2 kinase domain mutations were identified in tumors from 68 patients (approximately 1% of all cases, ranging from absent in sarcomas to 4% in urothelial cancers), which included previously published activating mutations and 13 novel mutations. Fourteen cases with coexisting HER2 mutation and amplification and/or overexpression were identified. Fifty-two of 68 patients had additional mutations in other analyzed genes, whereas 16 patients (23%) had HER2 mutations identified as the sole driver mutation. HER2 mutations coexisted with HER2 gene amplification and overexpression and with mutations in other functionally important genes. HER2 mutations were identified as the only driver mutation in a significant proportion of solid cancers. Evaluation of anti-HER2 therapies in nonamplified, HER2-mutated cancers is warranted.

Combination of medical needling and non-cultured autologous skin cell transplantation (ReNovaCell) for repigmentation of hypopigmented burn scars

Burn scars remain a serious physical and psychological problem for the affected people. Clinical studies as well as basic scientific research have shown that medical needling can significantly increase the quality of burn scars with comparatively low risk and stress for the patient with regards to skin elasticity, moisture, erythema and transepidermal water loss. However, medical needling has no influence on repigmentation of large hypopigmented scars. The goal of this study is to evaluate whether two established methods - needling (for improvement of scar quality) and non-cultured autologous skin cell suspension (for repigmentation) - can be successfully combined. Twenty subjects with mean age of 33 years (6-60 years) with scars from deep second and third degree burns have been treated. The average treated surface area was 94cm² (15-250cm²) and was focused on prominent areas such as the face, neck, chest and arm. Percutaneous collagen induction or "medical needling" was performed using a roller covered with 3mm long needles. The roller is vertically, horizontally and diagonally rolled over the scar, inducing microtrauma. Then, non-cultured autologous skin cell suspension (NCASCS) was produced and applied using the ReNovaCell Autologous Cell Harvesting Device (Avita Medical), according to the manufacturer's instructions. The patients were followed 12 months postoperatively. Pigmentation changes were measured objectively, as well as with patient and observer ratings. Patient satisfaction/preference was also obtained. Taken together, the pigmentation ratings and objective measures indicate individual improvement in 17 of the study participants. The melanin increases seen 12 months after NCASCS treatment are statistically significant. Medical needling in combination with NCASCS shows promise for repigmentation of burn cars.