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.

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.

Abstract P4-09-19: Comprehensive multiplatform molecular profiling identifies potentially targetable biomarkers in malignant phyllodes tumors of the breast

Introduction: Malignant phyllodes tumors are rare breast malignancies (0.1% of all breast tumors) with limited effective treatment options for recurrent and metastatic disease. Recent trials indicated a potential for anti-angiogenic therapy in soft tissue sarcomas, which led us to investigate these pathways.

Materials and Methods: Thirty-five malignant phyllodes tumors (including two cases with matched primary and metastatic tumors) were profiled using gene sequencing (Next-generation and Sanger), gene copy number analysis (in-situ hybridization), whole genome RNA expression, and protein expression (immunohistochemical assay).

Results: RNA microarray assay showed consistent over-expression of genes involved in angiogenesis including VEGFA, Angiopoietin2, VCAM1, PDGFRA, PTTG1, and CYP3A5 in all cases analyzed (n=5). No mutations in KDR (VEGFR2) were detected (0/26). EGFR protein overexpression was observed in 25/26 (96%) of cases with amplification of the EGFR gene in 8 cases (33%). EGFR gene mutations were identified in 2 cases (8%) including one case with presumed pathogenic V774M mutation and one case with EGFRvIII mutation. The most common mutations included those of TP53 (50%) and PIK3CA (15%) while other mutations (BRCA1, BRCA2, RET, CDH1, MLH1, ATM) were rare affecting single phyllodes cases. Two cases with matched primary and metastatic cancers harbored the same mutations in both sites (PIK3CA/KRAS and RB1 gene mutations, respectively).

Conclusions: Comprehensive multiplatform profiling approach to phyllodes tumors identifies various molecular alterations of which some are potentially actionable. Our data suggests that anti-angiogenic therapy may also be effective in patients with malignant phyllodes tumor. Evaluation of EGFR pathway discovered consistent protein over-expression but rare activating mutations, which necessitates refinement in patient selection targeting these pathways.

Citation Format: Gatalica Z, Vranic S, Ghazalpour A, Xiu J, Ocal I, McGill J, Bender R, Discianno E, Sanati S, Reddy S, Pockaj B. Comprehensive multiplatform molecular profiling identifies potentially targetable biomarkers in malignant phyllodes tumors of the breast. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-09-19.

Comprehensive tumor profiling identifies numerous biomarkers of drug response in cancers of unknown primary site: analysis of 1806 cases

Background

Cancer of unknown primary (CUP) accounts for approximately 3% of all malignancies. Despite extensive laboratory and imaging efforts, the primary site usually cannot be unequivocally confirmed, and the treatment for the most part remains empirical. Recently, identification of common cancer pathway alterations in diverse cancer lineages has offered an opportunity to provide targeted therapies for patients with CUP, irrespective of the primary site.

Patients and Methods

1806 cancers of unknown primary were identified among more than 63,000 cases profiled at Caris Life Sciences. Multiplatform profiling of the tumor samples included immunohistochemistry, gene sequencing and in situ hybridization methods in an effort to identify changes in biomarkers that are predictive of drug responses.

Results

Biomarkers associated with a potential drug benefit were identified in 96% of cases. Biomarkers identified included those associated with potential benefit in nearly all classes of approved cancer drugs (cytotoxic, hormonal, targeted biological drugs). Additionally, biomarkers associated with a potential lack of benefit were identified in numerous cases, which could further refine the management of patients with CUP.

Conclusion

Comprehensive biomarker profiling of CUP may provide additional choices in treatment of patients with these difficult to treat malignancies.

Abstract LB-171: Concordance between protein expression and mRNA expression in the large cohort of cancer patients

Introduction: Immunohistochemical (IHC) analysis of protein expression in clinical specimens has been invaluable in diagnosing, monitoring and guiding treatment in cancer patients. This approach, however, has its limitations including the difficulty to obtain robust and reliable antibodies, the semi quantitative nature of the assay, subjectivity of intensity call, and the lack of specificity to detect clinically relevant isoform expression in tumor specimen. In light of these limitations, RNA expression may be a useful replacement or a complementary approach to IHC in clinical settings. In this study, we compared the concordance between IHC and mRNA expression levels as measured by microarray using a large cohort of cancer patients spanning multiple lineages.

Methods: 10246 patient samples that included 40 tumor types were utilized in this study. Transcript and protein expression levels were measured for ESR1, AR, KIT, ERBB2 (Her2), RRM1, and ERCC1. Transcript levels were measured by Illumina's HumanHT-12 microarray (v4), and IHC was performed using the following antibodies: SP1 (ESR1), AR27 (AR), 4B5 (Her2), 8F1 (ERCC1), anti-CD117 polyclonal (KIT), and 10526-1-AP (RRM1).

Results: We observed a significant correlation between ERBB2, ESR1, and KIT with IHC data. Of the 3 probes on the microarray measuring ERBB2, only one probe mapping to the 3’ end of the two ERBB2 isoforms showed significant association with IHC data. For KIT, IHC and mRNA expression correlated well across, thymic carcinomas, poorly differentiated neuroendocrine tumors, melanoma, GIST, and head and neck cancer. For ESR1, significant correlations were observed for uterine sarcoma, endometrial carcinoma, and breast adenocarcinoma. Cervical cancers and ovarian surface epithelial carcinomas showed diminished association, and there was a lack of association in NSCLC and neuroendocrine carcinoid tumors. For AR, we observed strong correlation only in prostate tumors. ERCC1 and RRM1 mRNA expressions did not correlate well with protein expression in any of the tumor lineages examined.

Conclusion: These observations suggest that measuring mRNA via microarray has the potential to serve as a surrogate for IHC in clinical setting. The mixed associations observed for some of the genes exhibited lineage specificity suggesting that the relation between microarray results and IHC may be driven by the tissue-specific expression of isoforms, differential expression of genes in the stromal cells, and the technical limitations of each platform including the specificity of either the probes used to measure mRNA or antibodies used to measure protein expression. As such, combining the two platforms in the clinical setting may provide a more complete assessment of gene expression in tumor samples.

Citation Format: Anatole Ghazalpour, Wangjuh Sting Chen, Wenhsiang Wen, Zoran Gatalica, Ryan Bender. Concordance between protein expression and mRNA expression in the large cohort of cancer patients. [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 LB-171. doi:10.1158/1538-7445.AM2014-LB-171

Molecular profiling of infiltrating urothelial carcinoma of bladder and nonbladder origin

BACKGROUND

Infiltrating UC represents the second most common genitourinary malignancy. Advanced UC has a poor prognosis and new treatments are needed. Molecular profiling of UC might identify biomarkers associated with targeted therapies or chemotherapeutics, providing physicians with new treatment options.

MATERIALS AND METHODS

Five hundred thirty-seven cases of locally advanced or metastatic UC of the bladder, 74 nonbladder, and 55 nonurothelial bladder cancers were profiled using mutation analysis, in situ hybridization, and immunohistochemistry assays for biomarkers predictive of therapy response.

RESULTS

Molecular profiling of UC showed high overexpression of topoisomerase 2α, common phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha and/or phosophatase and tensin homolog (PTEN) alterations in nonbladder (27%) and bladder UC (21%), and rare gene mutations across subtypes. Compared with nonbladder, bladder UC consistently exhibited more frequent abnormal protein expression, including HER2 (10% vs. 3%; P = .04), tyrosine protein c-Kit receptor kinases (11% vs. 5%), c-Met proto-oncogene, receptor tyrosine kinases (25% vs. 8%), androgen receptor (16% vs. 6%), O(6)-methylguanine-methyltransferase (63% vs. 43%), ribonucleotide reductase M1 (32% vs. 11%), Serum protein acidic and rich in cysteine (SPARC) (69% vs. 33%), and topoisomerase 1 (63% vs. 39%). Bladder UC also exhibited increased amplification of HER2 (12% vs. 2%; P = .06).

CONCLUSION

Comprehensive molecular profiling of UC identified a large number of biomarkers aberrations that might direct treatment in conventional chemotherapies and targeted therapies, not currently recommended in this population. As a group, bladder UC exhibited higher levels of actionable biomarkers, suggesting that UC from different primary sites and non-UC are driven by different molecular pathways. These differences could have clinical implications resulting in different treatment regimens depending on the site of origin of UC.

Molecular profiling of infiltrating urothelial carcinoma of the bladder

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Background: Infiltrating urothelial carcinoma (UC) is the most common variant of urinary bladder cancer. The prognosis for muscle infiltrating or metastatic UC of the bladder is poor with no major advances made in the last 20 years. We investigated a large cohort of such patients for specific genetic/biomarker alterations and compared them to other, less common urothelial malignancies. Methods: We reviewed 602 cases; 518 cases (86%) were locally advanced or metastatic UCs of the bladder and the remaining 84 cases (14%) were non-bladder UCs. Multiple methodologies for optimal assessment of biomarker expression (Caris Molecular Intelligence, Caris Life Sciences, Phoenix, AZ) were employed: Mutation analysis (Next-generation sequencing, Sanger, pyrosequencing, qPCR, RFLP), in-situ hybridization (fluorescent and chromogenic), immunohistochemistry, and RNA fragment analysis. Results: Bladder UC showed slightly higher rates of HER2/neu gene amplification (12% in bladder vs. 6% non-bladder, p=0.32) and EGFR gene amplification (22% vs. 12%, p=0.25). HER2/neu and EGFR protein expressions were more common in the bladder than in non-bladder sites (10% vs. 1%, p=0.03, and 77% vs. 60%, p=0.5, respectively). Pathogenic mutations in HER2/neu and EGFR were rare. Although c-Kit and c-Met receptor kinases were more frequently overexpressed in bladder than in non-bladder cancers (10% vs. 6% and 25% vs. 8%, respectively), activating mutations were also rare. PIK3CA and/or PTEN mutations were more frequently observed in non-bladder (27%) than in bladder UCs (21%). Non-bladder UC harbored high FGFR3 gene mutation (33%), which was not observed in any of the UC of the bladder (p=0.02). TP53 gene mutations were frequently identified in both bladder and in non-bladder cancers (49% vs. 27%, respectively, p=0.15), while KRAS was frequently mutated in the bladder adenocarcinomas (56%, p<0.001). Other therapeutically targetable biomarkers over-expressed in bladder UC compared to non-bladder UC included androgen receptor (16% vs. 8%, p=0.07) and MGMT (63% vs. 47%). Conclusions: Comprehensive molecular profiling of urothelial carcinoma identifies a number of potentially actionable targets, which can be managed by the novel treatment modalities.

Molecular profiling of advanced refractory prostate cancer

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Background: Prostate cancer is the second leading cause of cancer-related death among men in the U.S. Forty percent of men diagnosed will develop metastatic disease, which has few treatment options. We aim to describe the molecular profile of prostate cancer tumors and potential for novel therapeutic options. Methods: We reviewed profiling data of over 330 patients from a large referral laboratory (Caris Life Sciences, Phoenix, AZ) for biomarkers of drug response. Multiple methodologies were employed: sequencing (NGS, Sanger, pyrosequencing), in-situ hybridization (fluorescent and chromogenic), and immunohistochemistry. Results: High expression was observed for AR, MRP1, TOPO1, TLE3 and EGFR, with positivity rates of 89%, 87%, 63%, 48%, and 47%, respectively. Low expression was observed for TS, PGP, TUBB3, RRM1, PTEN and MGMT, with negativity rates of 94%, 87%, 75%, 69%, 54%, and 45%, respectively. Gene copy number increases for EGFR and cMYC were observed in 13% of patients. Sequencing data showed a 48% mutation rate for TP53, 18% for PTEN, 9% for CTNNB1, 8% for PIK3CA, 5% for RB1, ATM, and cMET, and approximately 2% for K/HRAS, ERBB4, ALK, BRAF, and cKIT. Targeted therapy options include imatinib for patients with high cKIT or PDGFRA (9 to 10%) and cetuximab for patients with EGFR positivity (13 to 47%). Promising agents may be considered, including cabozantinib, based on 4% of cohort with cMET aberrations or PAM pathway inhibitors (BEZ234, everolimus) based on approximately 30% of cohort with PIK3CA pathway activation. Lastly, HDAC inhibitors have recently been linked to cMYC driven cancers (13% amplified). 5-FU, gemcitabine, and temozolomide chemotherapies may be options, as approximately 70% of cohort with low TS, RRM1, or MGMT. Biomarker guidance for common prostate cancer drugs such as cabazitaxel is also provided, based on approximately 70% of cohort with low TUBB3 or PGP, or high TLE3. Also, continued dependence on androgen signaling is exhibited by 89% of cohort with high AR, indicating potential utility of anti-androgen agents like enzalutamide. Conclusions: Tumor profiling identified small subsets of patients that may benefit from targeted agents approved for other solid tumors (imatinib, cetuximab), promising therapies in clinical trials (cabozantinib) or agents not routinely used for prostate cancer (gemcitabine).

Neurophysiological correlates of motor and working memory performance following subthalamic nucleus stimulation

Subthalamic nucleus (STN) deep brain stimulation (DBS) has become an accepted treatment for the motor manifestations of Parkinson disease (PD). The beneficial motor effects of STN DBS are likely due to modulation of BG output to frontal cortical regions associated with motor control, but the underlying neurophysiology of STN DBS effects, especially at the level of the cortex, is not well understood. In this study, we examined the effects of STN DBS on motor disability and visual working memory, a cognitive process supported by pFC. We tested 10 PD participants off medications, ON and OFF stimulation, along with 20 normal controls on a visual working memory task while simultaneously recording cortical EEG. In the OFF state, PD patients had poor motor function, were slower and less accurate in performing the working memory task, and had greater amplitudes and shorter latencies of the N200 ERP response. DBS improved clinical motor function, reduced N200 amplitudes, and increased N200 latencies but had little effect on working memory performance. We conclude that STN DBS normalizes neurophysiological activity in fronto striatal circuits and this may independently affect motor and cognitive function.

Frequency distribution of SPARC in triple-negative breast cancer patients

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Background: SPARC (secreted protein acid rich in cysteine) belongs to a group of extracellular matrix proteins and promotes adhesion of cells from the matrix. It plays an important role in tumor development in breast cancer and has a significant bearing on patient prognosis and long term survival. It is also known to predict response to nab-paclitaxel in certain tumor types including breast cancer. In 2005, FDA approved a solvent free formulation of paclitaxel for the treatment of metastatic breast cancer that utilizes albumin bound (nab) technology (nab-paclitaxel). Clinical studies have shown that nab-paclitaxel is significantly more effective than paclitaxel. Our study evaluated the frequency distribution of SPARC among triple negative breast cancer patients in which identification of a novel therapeutic target is warranted.

Methods: In a total of 951 breast cancer patients, we analyzed tumor SPARC expression by immunohistochemistry (IHC) using a monoclonal (R&D Systems) and a polyclonal antibody (Exalpha Biologicals). Immunoreactivity was assessed by scoring the percentage of cells stained in each field and by the intensity of staining. A cutoff point of 2+ and >30% stained tumor cells were considered as positive.

Results: From our analysis of 951 breast cancer patients profiled, a total of 165 patients (17%) were triple negative for ER, PR and HER2. Within this pathologic subtype, 29% patients stained positive with SPARC monoclonal antibody and 21% stained positive with SPARC polyclonal antibody. The correlation of SPARC tumor staining with hormone receptor status will be presented in detail.

Conclusions: We conclude that SPARC over-expression is a functionally important feature of a subset of triple negative breast cancer patients. The triple negative subset of tumors generally has a more aggressive clinical course and does not benefit from conventional targeted therapies. Our study suggests that nab-paclitaxel may serve as a therapeutic agent for the subset of triple negative patients that over-express SPARC. To the best of our knowledge, this is the first study involving a large patient pool in which SPARC has been investigated in a single clinical laboratory using standardized IHC with two different SPARC antibodies.

Supermassive black holes do not correlate with galaxy disks or pseudobulges

The masses of supermassive black holes are known to correlate with the properties of the bulge components of their host galaxies. In contrast, they seem not to correlate with galaxy disks. Disk-grown 'pseudobulges' are intermediate in properties between bulges and disks; it has been unclear whether they do or do not correlate with black holes in the same way that bulges do. At stake in this issue are conclusions about which parts of galaxies coevolve with black holes, possibly by being regulated by energy feedback from black holes. Here we report pseudobulge classifications for galaxies with dynamically detected black holes and combine them with recent measurements of velocity dispersions in the biggest bulgeless galaxies. These data confirm that black holes do not correlate with disks and show that they correlate little or not at all with pseudobulges. We suggest that there are two different modes of black-hole feeding. Black holes in bulges grow rapidly to high masses when mergers drive gas infall that feeds quasar-like events. In contrast, small black holes in bulgeless galaxies and in galaxies with pseudobulges grow as low-level Seyfert galaxies. Growth of the former is driven by global processes, so the biggest black holes coevolve with bulges, but growth of the latter is driven locally and stochastically, and they do not coevolve with disks and pseudobulges.

Estimating adjusted risk difference (RD) and number needed to treat (NNT) measures in the Cox regression model

In medical research, risk difference (RD) and number needed to treat (NNT) measures for survival times have been mainly proposed without consideration of covariates. In this paper, we develop adjusted RD and NNT measures for use in observational studies with survival time outcomes within the framework of the Cox proportional hazards regression model taking the distribution of confounders into account. We consider the typical situation of a cohort study in which the effect of an exposure on a survival time outcome is investigated and important covariates have to be taken into account. The exposure effect described by means of the RD and NNT measures in dependence on whether the effect of allocating an exposure to unexposed persons (number needed to be exposed) or that of removing an exposure from exposed persons (exposure impact number) is considered. Estimation of these adjusted RD and NNT measures is performed by using the average RD approach recently developed for logistic regression. To determine standard errors and confidence intervals for these estimators we use two approaches, the delta method with respect to the regression coefficients of the Cox model and bootstrapping and compare each other. The performance of these estimators is assessed by performing Monte Carlo simulations demonstrating clear advantages of the bootstrap method. The proposed method for point and interval estimation of adjusted RD and NNT measures in the Cox model is illustrated by means of data of the Düsseldorf Obesity Mortality Study (DOMS).