COVID-19 sequelae among competitive athletes: a systematic review

Background

During the COVID-19 pandemic, several professional athletes from different sports were infected by SARS-CoV-2. The aim of this systematic review was to evaluate the currently available scientific evidence regarding the cardiological, pulmonary, psychological, and combined sequelae, in professional athletes.

Methods

The present systematic review was performed following the PRISMA statements, thereby searching on 3 databases: PubMed, ISI Web of Science, Scopus. Primary studies published between January 2020 and March 2022, investigating symptomatic and instrumental sequelae in competitive athletes after COVID-19 infection, were included.

Results

A total of 1,957 articles were screened, finally 18 were included (6 cohort studies, 2 case-control studies and 10 cross-sectional studies). Studies’ sample size ranged from a minimum of 12 to 1908 athletes playing different sports. In addition, the studies examined the following type of sequelae: 12 cardiological, 2 psychological, 1 pulmonary and 3 combined. Regarding the cardiological field, the prevalence of anomalies in instrumental examinations ranged 0-27.89% for first level tests (echocardiography, electrocardiogram, troponin), and 0-6.21% for second level tests (cardiac magnetic resonance). The prevalence of myocarditis and pericarditis in the athletes ranged from 0 to 3.33%, whereby the prevalence of myocarditis was in the range 0-2.32% and that of pericarditis in the range 0-2.22%.

Conclusions

The results show that post SARS-CoV-2 infection cardiac sequelae have a quite low prevalence among competitive athletes included in our review, but it would be important to set up a gradual and continuous testing approach to preserve sports performance. Public health framework, such as vaccination campaign, is important both at European and international level in order to address potential consequences of infectious diseases among competitive athletes.

Key messages

• It is important to monitor all COVID-19 sequelae in European competitive athletes playing different sports.

• Considering anti-COVID-19 vaccination in competitive athletes as an important preventive measure, to limit the circulation of the virus and the physical consequences that may occur.

Characterization of disease-propagating stem cells responsible for myeloproliferative neoplasm-blast phase

Chronic myeloproliferative neoplasms (MPN) frequently evolve to a blast phase (BP) that is almost uniformly resistant to induction chemotherapy or hypomethylating agents. We explored the functional properties, genomic architecture, and cell of origin of MPN-BP initiating cells (IC) using a serial NSG mouse xenograft transplantation model. Transplantation of peripheral blood mononuclear cells (MNC) from 7 of 18 patients resulted in a high degree of leukemic cell chimerism and recreated clinical characteristics of human MPN-BP. The function of MPN-BP ICs was not dependent on the presence of JAK2V617F, a driver mutation associated with the initial underlying MPN. By contrast, multiple MPN-BP IC subclones coexisted within MPN-BP MNCs characterized by different myeloid malignancy gene mutations and cytogenetic abnormalities. MPN-BP ICs in 4 patients exhibited extensive proliferative and self-renewal capacity, as demonstrated by their ability to recapitulate human MPN-BP in serial recipients. These MPN-BP IC subclones underwent extensive continuous clonal competition within individual xenografts and across multiple generations, and their subclonal dynamics were consistent with functional evolution of MPN-BP IC. Finally, we show that MPN-BP ICs originate from not only phenotypically identified hematopoietic stem cells, but also lymphoid-myeloid progenitor cells, which were each characterized by differences in MPN-BP initiating activity and self-renewal capacity.

Abstract P3-09-15: Value-added clinical tumor/normal whole exome and whole transcriptome sequencing versus a DNA and RNA tumor only gene panel for managing breast cancer

As sequencing technologies advance, there is increasing interest in the value of more comprehensive molecular profiling techniques. Our laboratory has clinically validated two next generation sequencing (NGS) assays for detecting somatic variants in solid tumors. The Sema4 Signal Solid Tumor Panel, utilizes the Thermo Fisher 161 gene Oncomine Comprehensive v3 assay and the Sema4 Signal Whole Exome/Transcriptome Sequencing (WES/WTS) assay consists of whole transcriptome RNAseq for the tumor and whole exome sequencing for the tumor and normal DNA on the Illumina NovaSeq. We compiled a cohort of 224 breast tumors from 211 patients encompassing 10 histological subtypes (BRCA (102), IDC (74), ILC (21), BRCANOS (11), BRCNOS (4), IBC (1), ACBC (1), IMMC (1), MBC (2), MDLC (2), Other (5)). A total of 209 specimens were analyzed by our Solid Tumor panel, and 15 were analyzed by WES/WTS. ER/PR/HER2 status was available for 212 tumors with 36 triple-negative, 123 ER(+)/PR(+)/HER2(-), and 23 ER(+)/PR(+)/HER2(+). Treatment history was available for 151 patients. Of the 118 patients who self-reported racial identity, 8 identified as Asian, 33 identified as Black or African American, 77 identified as white. Sequencing with either the 161 gene panel or WES/WTS detected clinically significant variants in 95% (213/224) of the tumors sequenced. Targetable PIK3CA variants were reported in 36% (80/224) of tumors, as well as CCND1 amplification (16%, 26/224) and ESR1 resistance variants (10%, 24/224). Tier 1 drugs were reported in 35% (79/224) of tumors, as well as tier 2 drugs (4%, 10/224). At least 2 patients had tumor specimens obtained at time points spanning 18 or more months and acquired ESR1 p.Y537S and p.Y537C resistance mutations in the later specimens. A patient with triple-negative specimens, obtained in 2018 and 2020, had no change in clinically significant variants but had loss of variants of unknown significance in the later sample. Panel sequencing and WES/WTS are comparable in terms of known variant detection, but panel-based testing has considerable limitations for assessing disease progression and genomic complexity. For the 15 WES/WTS specimens, we were able to determine additional molecular features, including complex copy number state, which has relevance to prognostic information, tumor mutation burden, homologous recombination deficiency, and differential gene expression. Moreover, WES of the tumor and normal specimens resolved multiple germline variants that had been reported as somatic variants in a tumor-only report from a patient with triple-negative breast cancer. Our findings support the adoption of tumor/normal WES/WTS as a standard diagnostic tool for breast cancer patients.

Citation Format: Kimberly S. Cole, Zhiqiang Li, Amy Tiersten, Wanying Zhang, Hussam Al-Kateb, Feras M. Hantash, Michael R. Rossi, Scott Newman, Xiang Zhou, Eric E. Schadt, Rong Chen, William K. Oh, Marc Y. Fink. Value-added clinical tumor/normal whole exome and whole transcriptome sequencing versus a DNA and RNA tumor only gene panel for managing breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-09-15.

The genomic profiling and MAMLD1 expression in human and canines with Cushing's disease

BACKGROUND

Cushing's disease (CD) is defined as hypercortisolemia caused by adrenocorticotropic hormone (ACTH)-secreting pituitary adenomas (corticotroph PA) that afflicts humans and dogs. In order to map common aberrant genomic features of CD between humans and dogs, we performed genomic sequencing and immunostaining on corticotroph PA.

METHODS

For inclusion, humans and dog were diagnosed with CD. Whole exome sequencing (WES) was conducted on 6 human corticotroph PA. Transcriptome RNA-Seq was performed on 6 human and 7 dog corticotroph PA. Immunohistochemistry (IHC) was complete on 31 human corticotroph PA. Corticotroph PA were compared with normal tissue and between species analysis were also performed.

RESULTS

Eight genes (MAMLD1, MNX1, RASEF, TBX19, BIRC5, TK1, GLDC, FAM131B) were significantly (P < 0.05) overexpressed across human and canine corticotroph PA. IHC revealed MAMLD1 to be positively (3+) expressed in the nucleus of ACTH-secreting tumor cells of human corticotroph PA (22/31, 70.9%), but absent in healthy human pituitary glands.

CONCLUSIONS

In this small exploratory cohort, we provide the first preliminary insights into profiling the genomic characterizations of human and dog corticotroph PA with respect to MAMLD1 overexpression, a finding of potential direct impact to CD microadenoma diagnosis. Our study also offers a rationale for potential use of the canine model in development of precision therapeutics.

Critical role of ASCT2-mediated amino acid metabolism in promoting leukaemia development and progression

Amino acid (AA) metabolism is involved in diverse cellular functions, including cell survival and growth, however it remains unclear how it regulates normal hematopoiesis versus leukemogenesis. Here, we report that knockout of Slc1a5 (ASCT2), a transporter of neutral AAs, especially glutamine, results in mild to moderate defects in bone marrow and mature blood cell development under steady state conditions. In contrast, constitutive or induced deletion of Slc1a5 decreases leukemia initiation and maintenance driven by the oncogene MLL-AF9 or Pten deficiency. Survival of leukemic mice is prolonged following Slc1a5 deletion, and pharmacological inhibition of ASCT2 also decreases leukemia development and progression in xenograft models of human acute myeloid leukemia. Mechanistically, loss of ASCT2 generates a global effect on cellular metabolism, disrupts leucine influx and mTOR signaling, and induces apoptosis in leukemic cells. Given the substantial difference in reliance on ASCT2-mediated AA metabolism between normal and malignant blood cells, this in vivo study suggests ASCT2 as a promising therapeutic target for the treatment of leukemia.

Multi-faceted computational assessment of risk and progression in oligodendroglioma implicates NOTCH and PI3K pathways

Oligodendrogliomas are diffusely infiltrative gliomas defined by IDH-mutation and co-deletion of 1p/19q. They have highly variable clinical courses, with survivals ranging from 6 months to over 20 years, but little is known regarding the pathways involved with their progression or optimal markers for stratifying risk. We utilized machine-learning approaches with genomic data from The Cancer Genome Atlas to objectively identify molecular factors associated with clinical outcomes of oligodendroglioma and extended these findings to study signaling pathways implicated in oncogenesis and clinical endpoints associated with glioma progression. Our multi-faceted computational approach uncovered key genetic alterations associated with disease progression and shorter survival in oligodendroglioma and specifically identified Notch pathway inactivation and PI3K pathway activation as the most strongly associated with MRI and pathology findings of advanced disease and poor clinical outcome. Our findings that Notch pathway inactivation and PI3K pathway activation are associated with advanced disease and survival risk will pave the way for clinically relevant markers of disease progression and therapeutic targets to improve clinical outcomes. Furthermore, our approach demonstrates the strength of machine learning and computational methods for identifying genetic events critical to disease progression in the era of big data and precision medicine.

Common cancer-driver mutations and their association with abnormally methylated genes in lung adenocarcinoma from never-smokers

OBJECTIVES

Lung adenocarcinoma in never-smokers accounts for 15-20% of all lung cancer. Although targetable mutations are more prevalent in these tumors, the biological and clinical importance of coexisting and/or mutually exclusive abnormalities is just emerging. This study evaluates the relationships between common genetic and epigenetic aberrations in these tumors.

MATERIALS AND METHODS

Next-generation sequencing was employed to screen 20 commonly mutated cancer-driver genes in 112 lung adenocarcinomas from never-smokers. The relationship of these mutations with cancer-related methylation of 59 genes, and geographical/ethnic differences in the prevalence for mutations compared to multiple East Asian never-smoker lung adenocarcinoma cohorts was studied.

RESULTS

The most common driver mutation detected in 40% (45/112) of the tumors was EGFR, followed by TP53 (18%), SETD2 (11%), and SMARCA4 (11%). Over 72% (81/112) of the cases have mutation of at least one driver gene. While 30% (34/112) of the tumors have co-mutations of two or more genes, 42% (47/112) have only one driver gene mutation. Differences in the prevalence for some of these mutations were seen between adenocarcinomas in East Asian versus US (mainly Caucasian) never-smokers including a significantly lower rate of EGFR mutation among the US patients. Interestingly, aberrant methylation of multiple cancer-related genes was significantly associated with EGFR wildtype tumors. Among 15 differentially methylated genes by EGFR mutation, 14 were more commonly methylated in EGFR wildtype compared to mutant tumors. These findings were independently validated using publicly available data.

CONCLUSION

Most lung adenocarcinomas from never-smokers harbor targetable mutation/co-mutations. In the absence of EGFR mutation that drives 40% of these tumors, EGFR wildtype tumors appear to develop by acquiring aberrant promoter methylation that silences tumor-suppressor genes.

The Impact of Smoking and TP53 Mutations in Lung Adenocarcinoma Patients with Targetable Mutations-The Lung Cancer Mutation Consortium (LCMC2)

Purpose: Multiplex genomic profiling is standard of care for patients with advanced lung adenocarcinomas. The Lung Cancer Mutation Consortium (LCMC) is a multi-institutional effort to identify and treat oncogenic driver events in patients with lung adenocarcinomas.Experimental Design: Sixteen U.S. institutions enrolled 1,367 patients with lung cancer in LCMC2; 904 were deemed eligible and had at least one of 14 cancer-related genes profiled using validated methods including genotyping, massively parallel sequencing, and IHC.Results: The use of targeted therapies in patients with EGFR, ERBB2, or BRAF p.V600E mutations, ALK, ROS1, or RET rearrangements, or MET amplification was associated with a survival increment of 1.5 years compared with those with such mutations not receiving targeted therapy, and 1.0 year compared with those lacking a targetable driver. Importantly, 60 patients with a history of smoking derived similar survival benefit from targeted therapy for alterations in EGFR/ALK/ROS1, when compared with 75 never smokers with the same alterations. In addition, coexisting TP53 mutations were associated with shorter survival among patients with EGFR, ALK, or ROS1 alterations.Conclusion: Patients with adenocarcinoma of the lung and an oncogenic driver mutation treated with effective targeted therapy have a longer survival, regardless of prior smoking history. Molecular testing should be performed on all individuals with lung adenocarcinomas irrespective of clinical characteristics. Routine use of massively parallel sequencing enables detection of both targetable driver alterations and tumor suppressor gene and other alterations that have potential significance for therapy selection and as predictive markers for the efficacy of treatment. Clin Cancer Res; 24(5); 1038-47. ©2017 AACR.

aCGHViewer: A Generic Visualization Tool for aCGH Data

Array-Comparative Genomic Hybridization (aCGH) is a powerful high throughput technology for detecting chromosomal copy number aberrations (CNAs) in cancer, aiming at identifying related critical genes from the affected genomic regions. However, advancing from a dataset with thousands of tabular lines to a few candidate genes can be an onerous and time-consuming process. To expedite the aCGH data analysis process, we have developed a user-friendly aCGH data viewer (aCGHViewer) as a conduit between the aCGH data tables and a genome browser. The data from a given aCGH analysis are displayed in a genomic view comprised of individual chromosome panels which can be rapidly scanned for interesting features. A chromosome panel containing a feature of interest can be selected to launch a detail window for that single chromosome. Selecting a data point of interest in the detail window launches a query to the UCSC or NCBI genome browser to allow the user to explore the gene content in the chromosomal region. Additionally, aCGHViewer can display aCGH and expression array data concurrently to visually correlate the two. aCGHViewer is a stand alone Java visualization application that should be used in conjunction with separate statistical programs. It operates on all major computer platforms and is freely available at http://falcon.roswellpark.org/aCGHview/ .

Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms

The Overlay Tool© has been developed to combine high throughput data derived from various microarray platforms. This tool analyzes high-resolution correlations between gene expression changes and either copy number abnormalities (CNAs) or loss of heterozygosity events detected using array comparative genomic hybridization (aCGH). Using an overlay analysis which is designed to be performed using data from multiple microarray platforms on a single biological sample, the Overlay Tool© identifies potentially important genes whose expression profiles are changed as a result of losses, gains and amplifications in the cancer genome. In addition, the Overlay Tool© will incorporate loss of heterozygosity (LOH) probability data into this overlay procedure. To facilitate this analysis, we developed an application which computationally combines two or more high throughput datasets (e.g. aCGH/expression) into a single categorized dataset for visualization and interrogation using a gene-centric approach. As such, data from virtually any microarray platform can be incorporated without the need to remap entire datasets individually. The resultant categorized (overlay) data set can be conveniently viewed using our in-house visualization tool, aCGHViewer© (Shankar et al. 2006), which serves as a conduit to public databases such as UCSC and NCBI, to rapidly investigate genes of interest.

Next-generation sequencing and clinical outcomes of patients with lung adenocarcinoma treated with stereotactic body radiotherapy

BACKGROUND

Genetic aberrations are well characterized in lung adenocarcinomas (LACs) and clinical outcomes have been influenced by targeted therapies in the advanced setting. Stereotactic body radiotherapy (SBRT) is the standard-of-care therapy for patients with nonoperable, early-stage LAC, but to the authors' knowledge, no information is available regarding the impact of genomic changes in these patients. The current study sought to determine the frequency and clinical impact of genetic aberrations in this population.

METHODS

Under an Institutional Review Board-approved protocol, the records of 242 consecutive patients with early-stage lung cancers were reviewed; inclusion criteria included LAC histology with an adequate tumor sample for the successful use of next-generation sequencing and fluorescence in situ hybridization testing. Univariate analysis was performed to identify factors associated with clinical outcomes.

RESULTS

LAC samples from 98 of the 242 patients were reviewed (40.5%), of whom 45 patients (46.0%) had genetic testing. The following mutations were noted: KRAS in 20.0% of samples, BRAF in 2.2% of samples, SMAD family member 4 (SMAD4) in 4.4% of samples, epidermal growth factor receptor (EGFR) in 15.6% of samples, STK1 in 2.2% of samples, tumor protein 53 (TP53) in 15.6% of samples, and phosphatase and tensin homolog (PTEN) in 2.2% of samples. The following gene rearrangements were observed: anaplastic lymphoma kinase (ALK) in 8.9% of samples, RET in 2.2% of samples, and MET amplification in 17.8% of samples. The median total delivered SBRT dose was 50 grays (range, 48-60 grays) over a median of 5 fractions (range, 3-8 fractions). The KRAS mutation was associated with worse local control (odds ratio [OR], 3.64; P<.05). MET amplification was associated with worse regional (OR, 4.64; P<.05) and distant (OR, 3.73; P<.05) disease control.

CONCLUSIONS

To the authors' knowledge, the current series is the first to quantify genetic mutations and their association with clinical outcomes in patients with early-stage LAC treated with SBRT. KRAS mutations were associated with worse local control and MET amplification was associated with worse regional and distant disease control, findings that need to be validated in a prospective setting. Cancer 2017;123:3681-3690. © 2017 American Cancer Society.

CD36-positive B-lymphoblasts Predict Poor Outcome in Children With B-lymphoblastic Leukemia

Objective We observed that pediatric patients with B lymphoblastic leukemia which expressed CD36 at diagnosis seemed to have worse outcome than patients whose blasts did not. Here, we describe the patient, disease characteristics, pathological, molecular, and genetic features and outcomes of patients with CD36+ B-LL compared to patients with CD36- B-LL. Methods We retrospectively reviewed all flow cytometry reports from September 2008 to December 2015 to identify patients diagnosed at our institution with CD36 expression on B lymphoblasts. CD36- control patients were chosen from our leukemia database and matched 2:1 to CD36+ patients for National Cancer Institute (NCI) risk group at diagnosis. We reviewed diagnostic marrow slides for cytoplasmic granules and abstracted clinical data from patient charts. To identify underlying genetic abnormalities, clinical FISH testing and RNA sequencing was performed on 5 of our CD36+ patients, and RNA-seq data from the NIH Therapeutically Applicable Research to Generate Effective Treatments (TARGET) ALL Expansion Phase 2 data set were examined. Results Twenty-five of 366 (6.83%) patients diagnosed at our institution in the study period had CD36+ blasts. With a median follow-up of 5.32 years, 5-year event-free survival (EFS) and overall survival (OS) were significantly worse for CD36+ patients compared to CD36- patients who were NCI Standard Risk at diagnosis (EFS: 60% ± 15.49 vs 95% ± 4.87, P = .016; OS: 90% ± 9.5 vs 100%, P = .019). NCI Standard Risk patients whose blasts were both CD36+ and had granules had the worst survival compared to CD36- patients without granules (EFS 25% ± 21.65 vs 95% ± 4.87, P = .0004). From our CD36+ patients and the TARGET database, we found 2 ABL2 mutations, 1 PDGFRB mutation, and 2 NRAS mutations. Conclusions For NCI Standard Risk patients, CD36 expression on B-lymphoblasts identifies patients with B-LL who have especially poor outcome. This may be due to underlying genetic abnormalities that may be amenable to targeted therapy.

Molecular signatures of class II HLA and p-16 status as an immune-based classification of OPSCC relying on known predictors of sensitivity to PD-1 blockade

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Background: PD-1 inhibitors are known to have significant clinical activity in head and neck squamous cell cancer (SCCHN); there is, however, no selection criterion for SCCHN patients who may benefit from PD-1 inhibition. Utilizing RNA-seq analysis we explored a set of human genes encoding leukocyte antigens (HLAs) as part of a 37-gene panel predictive of response in melanoma patients to PD-1 inhibitors (Chen et al, Cancer Discov. 2016 Aug;6(8):827-37).We investigated whether this panel could define an immune-based classification of oropharyngeal squamous cell carcinoma (OPSCC). Methods: We have applied a minimal mutation and copy number content (151 genes) using an Agilent Clearseq DNA and an extensive Illumina Truseq RNA panel providing key information on gene fusions, differential gene expression, coding mutation and metagenomics on 47 SCCHN FFPE samples including 27 OPSCC. We performed an unsupervised hierarchical clustering of the samples. Two clusters with high and low expression were noted. Fisher’s exact test was performed to determine if the samples in each clusters were associated with p16 as a surrogate marker for HPV status. The same procedure was repeated on Level 3 transcriptome data from the TCGA via GDC data portal. Results: A set of fourteen immune related HLA antigen genes were identified within the 37-gene panel predictive to response to PD-1 inhibitors in p16+ versus - OPSCC (p = 0.015).We applied the same set of immune related HLA genes on the 103 patient samples from TCGA with known p16 status. When applied on all samples, there was no correlation between the HLA gene expression and p16 status (p = 0.1366); however, when restricted to OPSCC patients there was a high correlation with p16 status (p = 0.0047). Conclusions: We have identified a set of immune related HLA type II genes that are over-expressed in p16 positive OPSCC. This opens the door for further evaluation of these genes to better understand the immune related factors affecting the biology of HPV-associated OPSCC and its response to PD-1 inhibitors. (This research was supported by a grant NCI R21 CA182661-01A1to NFS and GZC).

Landscape of genetic alterations in oropharyngeal squamous cell carcinoma (OPSCC) based on RNA-seq and WES analysis of FFPE samples and correlation with data from TCGA

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Background: Whole human exome sequencing (WES) has identified well characterized somatic mutations (such as TP53, CDKN2A, PIK3CA and HRAS) in patients with squamous cell carcinoma of the head and neck (SCCHN). We sought to optimize a combined RNA-seq and WES approach for identifying actionable mutations and gene expression signatures in p16 + versus - OPSCC. Methods: Relying on formalin fixed and paraffin embedded (FFPE) samples we applied a minimal mutation and copy number content (151 genes) on DNA and an extensive RNA panel on a total of 27 OPSCC (22 p16 +, and 5 p16 -). SAMSeq was used to identify the differentially expressed genes. Unsupervised hierarchical clustering of the TCGA OPSCC samples with available p16 status (n = 31) was performed for external validation of the results. Statistical significance was further tested by Fisher’s exact test. Results: We identified a gene signature differentially expressed in p16+ and p16- OPSCC. External validation showed a significant association between gene expression and p16 status (P = 0.00033). We did not however find an association with mutation burden and smoking history. A number of pathways associated with this gene signature such as NCAM1 may have relevant biologic implications in OPSCC. Conclusions: Our results underscore the reliability of integrating data from FFPE samples in distinguishing gene signatures characteristic of p16 + versus p16- OPSCC; these signatures need to be further explored for their biologic relevance in OPSCC (This research was supported by a grant NCI R21 CA182661-01A1to NFS and GZC).

Molecular impact of selective NFKB1 and NFKB2 signaling on DLBCL phenotype

Diffuse large B-cell lymphoma (DLBCL) has been categorized into two molecular subtypes that have prognostic significance, namely germinal center B-cell like (GCB) and activated B-cell like (ABC). Although ABC-DLBCL has been associated with NF-κB activation, the relationships between activation of specific NF-κB signals and DLBCL phenotype remain unclear. Application of novel gene expression classifiers identified two new DLBCL categories characterized by selective p100 (NF-κB2) and p105 (NF-κB1) signaling. Interestingly, our molecular studies showed that p105 signaling is predominantly associated with GCB subtype and histone mutations. Conversely, most tumors with p100 signaling displayed ABC phenotype and harbored ABC-associated mutations in genes such as MYD88 and PIM1. In vitro, MYD88 L265P mutation promoted p100 signaling through TAK1/IKKα and GSK3/Fbxw7a pathways, suggesting a novel role for this protein as an upstream regulator of p100. p100 signaling was engaged during activation of normal B cells, suggesting p100's role in ABC phenotype development. Additionally, silencing p100 in ABC-DLBCL cells resulted in a GCB-like phenotype, with suppression of Blimp, IRF4 and XBP1 and upregulation of BCL6, whereas introduction of p52 or p100 into GC cells resulted in differentiation toward an ABC-like phenotype. Together, these findings identify specific roles for p100 and p105 signaling in defining DLBCL molecular subtypes and posit MYD88/p100 signaling as a regulator for B-cell activation.

Targeting adhesion signaling in KRAS, LKB1 mutant lung adenocarcinoma

Loss of LKB1 activity is prevalent in KRAS mutant lung adenocarcinoma and promotes aggressive and treatment-resistant tumors. Previous studies have shown that LKB1 is a negative regulator of the focal adhesion kinase (FAK), but in vivo studies testing the efficacy of FAK inhibition in LKB1 mutant cancers are lacking. Here, we took a pharmacologic approach to show that FAK inhibition is an effective early-treatment strategy for this high-risk molecular subtype. We established a lenti-Cre-induced Kras and Lkb1 mutant genetically engineered mouse model (KL_Lenti) that develops 100% lung adenocarcinoma and showed that high spatiotemporal FAK activation occurs in collective invasive cells that are surrounded by high levels of collagen. Modeling invasion in 3D, loss of Lkb1, but not p53, was sufficient to drive collective invasion and collagen alignment that was highly sensitive to FAK inhibition. Treatment of early, stage-matched KL_Lenti tumors with FAK inhibitor monotherapy resulted in a striking effect on tumor progression, invasion, and tumor-associated collagen. Chronic treatment extended survival and impeded local lymph node spread. Lastly, we identified focally upregulated FAK and collagen-associated collective invasion in KRAS and LKB1 comutated human lung adenocarcinoma patients. Our results suggest that patients with LKB1 mutant tumors should be stratified for early treatment with FAK inhibitors.

Genomic Analysis in the Practice of Surgical Neuropathology: The Emory Experience

The evaluation of central nervous system tumors increasingly relies on molecular genetic methods to aid in classification, offer prognostic information, and predict response to therapy. Available assays make it possible to assess genetic losses, amplifications, translocations, mutations, or the expression levels of specific gene transcripts or proteins. Current molecular diagnostics frequently use a panel-based approach and whole genome analysis, and generally rely either on DNA sequencing or on hybridization-based methodologies, such as those used in cytogenomic microarrays. In some cases, immunohistochemistry can be used as a surrogate for genetic analysis when the mutation of interest consistently results in overexpression or underexpression of a known protein product. In surgical neuropathology practice, the diagnostic workup of diffuse gliomas, medulloblastomas, low-grade circumscribed gliomas, as well as other diseases, now routinely incorporates the results of genomic studies. Here we summarize our institution's current approach to diagnostic surgical neuropathology, using these contemporary molecular diagnostic applications.

Use of liquid biopsy for detection of renal cell carcinoma

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Background: Circulating tumor DNA (ctDNA) displays characteristics of an ideal serum biomarker. We sought to develop whole-exome sequencing of ctDNA to interrogate commonly mutated genes in renal cell carcinoma (RCC) for early tumor detection through a single blood sample. Methods: Patients with solid renal tumors and healthy controls provided 40 mL blood from which purified plasma cell-free DNA was prepared. A multiplex bar-coded polymerase chain reaction amplification using the Fluidigm Access Array was performed to prepare sequencing libraries for the Illumina HiSeq platform. Galaxy workflow was then utilized to identify mutations within the plasma cell-free DNA samples and results were compared to buffy coat sequencing containing control DNA for each individual’s sample. The following genes were queried: VHL, PBRM1, SETD2, BAP1, KDM5C, KIT, NFE2L2, MET, TP53, CDKN2A, FGFR3, PIK3CA, BRAF, and MUC4. Criteria for calling mutations included adequate frequency by overall count and percentage of reads, identification in all overlapping sequences and presence of buffy coat-derived control DNA for comparison with <0.5% containing the mutation. Results: Of the preoperative RCC patients, 20/30 (67%) had detectable somatic mutations compared to 2/48 (4.2%) controls. These included nonsynonymous, frameshift, stop-gain, and splice site mutations. Mutations were detected in RCC patients with both early and advanced stage disease, including a patient with a 1.1 x 0.7 x 0.5 cm tumor. Mutations were seen in all genes assayed. Conclusions: The majority of RCC patients of various stages and histology had ctDNA detected in a single preoperative blood sample. Comparatively, only two of the control patients sampled were ctDNA positive. Controls will be followed to identify the possible sources of ctDNA. Developing such non-invasive methods for RCC detection has the potential to enhance both diagnosis and surveillance of renal malignancy, even in the setting of small renal masses.

Abstract 3607: An evaluation of NGS to identify gene fusions using RNA from FFPE solid tumor samples

Gene fusions have long been considered strong drivers of cellular transformation, making the accurate and precise assessment of these variants a necessity for any tumor profiling assay. Recent studies have indicated the utility of next-generation sequencing (NGS) for tumor profiling due to increasing data output and decreasing costs of the technology. Unfortunately, because a critical facet of NGS is the evaluation of short DNA fragments, sufficiently covering all possible breakpoint regions (many of which are intronic) has proven difficult and costly. Recent studies have indicated that NGS may prove better at detecting gene fusions using RNA instead of DNA, given the higher probability of breakpoint-spanning reads. This allows for de-novo discovery of fusion partners without knowing the precise breakpoint and guarantees expression of the fusion transcript. To that end, Illumina is developing a novel method for simultaneous library preparation from low input amounts of degraded DNA and RNA from a single FFPE tumor sample. With a turnaround time from nucleic acid to data of less than 4 days, this enrichment-based assay surveys 170 genes for single nucleotide variants and small indels, 57 genes for gene amplifications, 55 genes for fusions and four genes for splice variants. To determine the limit of detection for gene fusions, a panel of different synthetic RNA transcripts were prepared in vitro, pooled at equal molar amounts, and spiked into 20ng of cell line RNA (MCF-7). Fusions were detected over several orders of magnitude down to 1×10-8 picomoles, equivalent to 3 to 15 fusion transcripts per cell. In addition, a similar range of fusion detection was observed when RNA from two different cell lines were mixed, as when RNA from a cell line with high expression of an FGFR2-COL14A1 fusion was mixed in proportional amounts with RNA from a different cell line where FGFR2 is minimally expressed. Importantly, our method allowed for fusion detection from as little as 100 picograms of cell line RNA. We then tested our new method on previously characterized FFPE solid tumor samples harboring known gene rearrangements identified by FISH and other methods. Not only was the NGS method able to detect the majority of previously characterized variants, including EML4-ALK and SDC4-ROS1, it also identified the gene fusions and their uncharacterized fusions partners by combining the non-targeted sequence information gained from using an enrichment-based assay with novel fusion calling algorithms. From this information, we were able to glean new insights into the structure of the rearrangements and how the gene fusions may be involved in tumorigenesis. These results indicate that NGS can identify fusions from the low amounts of degraded RNA from solid tumor samples, identify fusion partners not uncovered by current technologies, and further emphasizes the advantage of NGS in solid tumor profiling.

Citation Format: Julianna Tdr Parks, Luo Byron, Brian Crain, Snedecor June, Zhao Chen, Tingting Du, Gabriel L. Sica, Taofee K. Owonikoko, Stewart G. Neill, Scott Newman, Debra F. Saxe, Jennifer S. LoCoco, Han-Yu Chuang, Charles Lin, Kathryn M. Stephens, Michael R. Rossi, Matthew C. Friedenberg. An evaluation of NGS to identify gene fusions using RNA from FFPE solid tumor samples. [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 3607.

Abstract LB-348: Developing a personalized anti-metastatic therapy to treat KRAS, LKB1-mutant lung adenocarcinoma

LKB1 is the 2rd most commonly mutated tumor suppressor gene in human lung adenocarcinoma, is commonly co-mutated with KRAS, and leads to more aggressive, treatment-resistant tumors in mouse models. The identification of druggable signaling molecules that result from specific alterations in LKB1 could result in a personalized clinical strategy to target this high-risk patient population. We have previously published that LKB1 acts to limit focal adhesion kinase (FAK) activity in human lung cancer cells to restrict cell adhesion and migration. Based on our prior published data we hypothesize that FAK pathway inhibition will suppress invasion and metastasis in LKB1-mutant tumors in vivo. To investigate our hypothesis, we have designed the first rolling-enrollment pre-clinical mouse trial to target invasion and metastasis using a small-molecule FAK inhibitor. To enroll mice with early-stage lung adenocarcinoma, we developed a novel lentiviral-Cre induced KrasG12D; Lkb1fl/fl genetically engineered mouse model (GEMM) (KLLLenti) that develops 100% adenocarcinomas, expresses a luciferase reporter gene, and has elevated levels of active FAK in late stage invasive tumors. Importantly, short-term treatment of KLLLenti mice with a pharmacologic FAK inhibitor potently suppresses the invasive progression of primary tumors. Moreover, long-term treatment results in improved progression-free survival, and delays metastatic spread to the lymph nodes. We further pursue mechanistic studies to investigate how LKB1-mutant tumor tissue gains a metastatic advantage in vivo, and using a combination of 3D tumor spheroid assays, and multiphoton microscopy, present results that LKB1-mutant tumors use a unique form of hybrid invasion that relies both on cell:cell and cell-matrix adhesion, and in doing so, are equipped to more efficiently invade into the collagen-dense microenvironment of the lung. We will also present data that similar molecular and cell biologic phenotypes can be found in a subset of KRAS, LKB1-mutant human clinical samples. Our studies suggest that when used early, FAK inhibitors may be a viable clinical strategy to prevent or delay metastasis in the KRAS, LKB1-mutant patient population, and begin to define alternate escape pathways by which this highly invasive cell population may escape first-line therapy.

Citation Format: Melissa Gilbert-Ross, Jessica Konen, Junghui Koo, John Shupe, Gabriel L. Sica, Zhengjia Chen, Brian S. Robinson, Madhusmita Behera, Michael R. Rossi, Geoffrey H. Smith, Charles E. Hill, Suresh M. Ramalingam, Haian Fu, Fadlo R. Khuri, Wei Zhou, Adam Marcus. Developing a personalized anti-metastatic therapy to treat KRAS, LKB1-mutant lung adenocarcinoma. [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 LB-348.

Patient-derived xenografts faithfully replicated clinical outcome in a phase II co-clinical trial of arsenic trioxide in relapsed small cell lung cancer

Background

SCLC has limited treatment options and inadequate preclinical models. Promising activity of arsenic trioxide (ASO) recorded in conventional preclinical models of SCLC supported the clinical evaluation of ASO in patients. We assessed the efficacy of ASO in relapsed SCLC patients and in corresponding patient-derived xenografts (PDX).

Methods

Single arm, Simon 2-stage, phase II trial to enroll patients with relapsed SCLC who have failed at least one line of therapy. ASO was administered as an intravenous infusion over 1–2 h daily for 4 days in week 1 and for 2 days in weeks 2–6 of an 8-week cycle. Treatment continued until disease progression. Pretreatment tumor biopsy was employed for PDX generation through direct implantation into subcutaneous pockets of SCID mice without in vitro manipulation and serially propagated for five generations. Ex vivo efficacy of cisplatin (3 mg/kg i.p. weekly) and ASO (3.75 mg/kg i.p. every other day) was tested in PDX representative of platinum sensitive and platinum refractory SCLC.

Results

The best response in 17 evaluable patients was stable disease in 2 (12 %), progressive disease in 15 (88 %) patients and median time-to-progression of seven (range 1–7) weeks. PDX was successfully grown in 5 of 9 (56 %) transplanted biopsy samples. Serially-propagated PDXs preserved characteristic small cell histology and genomic stability confirmed by immunohistochemistry, short tandem repeat (STR) profiling and targeted sequencing. ASO showed in vitro cytotoxicity but lacked in vivo efficacy against SCLC PDX tumor growth.

Conclusions

Cisplatin inhibited growth of PDX derived from platinum-sensitive SCLC but was ineffective against PDX from platinum-refractory SCLC. Strong concordance between clinical and ex vivo effects of ASO and cisplatin in SCLC supports the use of PDX models to prescreen promising anticancer agents prior to clinical testing in SCLC patients.

Trial Registration The study was registered at http://www.clinicaltrials.gov (NCT01470248)

Electronic supplementary material

The online version of this article (doi:10.1186/s12967-016-0861-5) contains supplementary material, which is available to authorized users.

Gene integrated set profile analysis: a context-based approach for inferring biological endpoints

The identification of genes with specific patterns of change (e.g. down-regulated and methylated) as phenotype drivers or samples with similar profiles for a given gene set as drivers of clinical outcome, requires the integration of several genomic data types for which an 'integrate by intersection' (IBI) approach is often applied. In this approach, results from separate analyses of each data type are intersected, which has the limitation of a smaller intersection with more data types. We introduce a new method, GISPA (Gene Integrated Set Profile Analysis) for integrated genomic analysis and its variation, SISPA (Sample Integrated Set Profile Analysis) for defining respective genes and samples with the context of similar, a priori specified molecular profiles. With GISPA, the user defines a molecular profile that is compared among several classes and obtains ranked gene sets that satisfy the profile as drivers of each class. With SISPA, the user defines a gene set that satisfies a profile and obtains sample groups of profile activity. Our results from applying GISPA to human multiple myeloma (MM) cell lines contained genes of known profiles and importance, along with several novel targets, and their further SISPA application to MM coMMpass trial data showed clinical relevance.

Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies

We tested and clinically validated a targeted next-generation sequencing (NGS) mutation panel using 80 formalin-fixed, paraffin-embedded (FFPE) tumor samples. Forty non-small cell lung carcinoma (NSCLC), 30 melanoma, and 30 gastrointestinal (12 colonic, 10 gastric, and 8 pancreatic adenocarcinoma) FFPE samples were selected from laboratory archives. After appropriate specimen and nucleic acid quality control, 80 NGS libraries were prepared using the Illumina TruSight tumor (TST) kit and sequenced on the Illumina MiSeq. Sequence alignment, variant calling, and sequencing quality control were performed using vendor software and laboratory-developed analysis workflows. TST generated ≥500× coverage for 98.4% of the 13,952 targeted bases. Reproducible and accurate variant calling was achieved at ≥5% variant allele frequency with 8 to 12 multiplexed samples per MiSeq flow cell. TST detected 112 variants overall, and confirmed all known single-nucleotide variants (n = 27), deletions (n = 5), insertions (n = 3), and multinucleotide variants (n = 3). TST detected at least one variant in 85.0% (68/80), and two or more variants in 36.2% (29/80), of samples. TP53 was the most frequently mutated gene in NSCLC (13 variants; 13/32 samples), gastrointestinal malignancies (15 variants; 13/25 samples), and overall (30 variants; 28/80 samples). BRAF mutations were most common in melanoma (nine variants; 9/23 samples). Clinically relevant NGS data can be obtained from routine clinical FFPE solid tumor specimens using TST, benchtop instruments, and vendor-supplied bioinformatics pipelines.

Listeria Monocytogenes: an uncommon pathogen of cervical necrotizing fasciitis

The aim of this paper is to present a unique case of neck-necrotizing fasciitis caused by Listeria Monocytogenes in a young woman, successfully treated by surgery and IV antibiotic therapy. Necrotizing fasciitis is a rare, rapidly progressing and potentially life-threatening infection that infrequently occurs in the head and neck region. Pathogens involved in necrotizing fasciitis are heterogeneous and include aerobic and anaerobic bacteria. To the best of our knowledge, this is the only case of neck necrotizing fasciitis caused by Listeria Monocytogenes studied in literature so far.

Anaplastic lymphoma kinase (ALK) gene alteration in signet ring cell carcinoma of the gastrointestinal tract

OBJECTIVES

ALK-EML4 translocation is an established driver aberration in non-small cell lung cancer (NSCLC), with reported predilection for cases with signet ring histology. We assessed the presence of anaplastic lymphoma kinase (ALK) gene rearrangements in signet ring cancers arising in the stomach and colon.

METHODS

Histologically confirmed cases of signet ring adenocarcinoma of the stomach or the colon were identified. The presence of the classic ALK and EML4 fusion gene was initially determined by fluorescence in-situ hybridization (FISH) technique. Immunohistochemistry (IHC) was performed using two previously validated antibodies, ALK1 clone (1:100; DAKO) and 5A4 (Novocastra, Leica Biosystems) along with positive controls of ALK-translocated lung cancer.

RESULTS

We employed 42 cases of signet ring carcinoma diagnosed between 2001 and 2011; 25 gastric and 17 colon cancer. Median age 63.3 years; male/female 17/25; race, black 47.5%, white 47.5%, others, 5%; stage I, 21.4%; stage II, 31%; stage III, 26.2%; stage IV, 21.4%. One of 42 cases (2.3%) was positive for ALK translocation by FISH using the standard criteria of at least 15% positive cells for the break-apart signal (50-70 cells enumerated per case). Using a less restrictive cut-off of 10% positive cells, 7 cases (16%) were considered possibly positive. None of the 'possibly positive' cases was found to harbor ALK translocation by another molecular testing approach (IHC). IHC with two previously validated monoclonal antibodies showed 0 of 42 (0%) cases positive.

CONCLUSIONS

ALK gene rearrangement is very rare in gastrointestinal cancers and enrichment strategy focusing on signet ring cell histology did not significantly improve the detection rate.

A Translational, Pharmacodynamic, and Pharmacokinetic Phase IB Clinical Study of Everolimus in Resectable Non-Small Cell Lung Cancer

PURPOSE

The altered PI3K/mTOR pathway is implicated in lung cancer, but mTOR inhibitors have failed to demonstrate efficacy in advanced lung cancer. We studied the pharmacodynamic effects of everolimus in resectable non-small cell lung cancer (NSCLC) to inform further development of these agents in lung cancer.

EXPERIMENTAL DESIGN

We enrolled 33 patients and obtained baseline tumor biopsy and 2[18F]fluoro-2-deoxy-D-glucose-positron emission tomography/computed tomography (FDG-PET/CT) imaging followed by everolimus treatment (5 or 10 mg daily, up to 28 days), or without intervening treatment for controls. Target modulation by everolimus was quantified in vivo and ex vivo by comparing metabolic activity on paired PET scans and expression of active phosphorylated forms of mTOR, Akt, S6, eIF4e, p70S6K, 4EBP1, and total Bim protein between pretreatment and posttreatment tissue samples.

RESULTS

There were 23 patients on the treatment arm and 10 controls; median age 64 years; 22 tumors (67%) were adenocarcinomas. There was a dose-dependent reduction in metabolic activity (SUVmax: 29.0%, -21%, -24%; P = 0.014), tumor size (10.1%, 5.8%, -11.6%; P = 0.047), and modulation of S6 (-36.1, -13.7, -77.0; P = 0.071) and pS6 (-41.25, -61.57, -47.21; P = 0.063) in patients treated in the control, 5-mg, and 10-mg cohorts, respectively. Targeted DNA sequencing in all patients along with exome and whole transcriptome RNA-seq in an index patient with hypersensitive tumor was employed to further elucidate the mechanism of everolimus activity.

CONCLUSIONS

This "window-of-opportunity" study demonstrated measurable, dose-dependent, biologic, metabolic, and antitumor activity of everolimus in early-stage NSCLC.

Comprehensive genomic profiling of cancer of the appendix to reveal new routes to targeted therapies

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Background: Cancers of the appendix are rare forms of malignancy that include two major mucin producing tumors, mucinous adenocarcinoma (MA) and goblet cell carcinoid (GCC). There is no clear standard of care for management of these malignancies. We queried whether comprehensive genomic profiling (CGP) of MA and GCC would reveal differences in the pattern of genomic alterations (GA) of these two subtypes of appendiceal cancer and serve as a guide for targeted therapies for this disease. Methods: DNA was extracted from 40 microns of FFPE sections from 20 clinically advanced appendiceal carcinomas (9 GCC and 11 MA). Comprehensive genomic profiling was performed on hybridization-captured, adaptor ligation based libraries to a high mean coverage depth of >600X for 3,230 exons of 182 cancer-related genes, plus 37 introns from 14 genes frequently rearranged in cancer. The results were evaluated for all classes of GA including base substitutions, short insertions and deletions, copy number alterations and fusions/rearrangements. Clinically relevant GAs were defined as GAs linked to drugs on the market or under evaluation in mechanism driven clinical trials. Results: Base substitutions in KRAS were seen in 73% of MA and 11% of GCCs. TP53 mutations were seen in 64% of MA and 22% of GCCs. MYC (36%), SMAD4 (27%), and APC (27%) mutations were found in MA but were absent in GCC. Other GA of low frequency, but clinically relevant in both subsets included ERBB2, GNAS, ARID1A, PIK3CA, NRAS, CTNNB1, BRCA1, BRAF, KDR, PTEN, MCL1, IDH1, FBXW7, and RICTOR. Conclusions: KRAS and TP53 mutations are common in appendiceal MA, but rare in appendiceal GCCs. This confirms the differences in biology and has implications regarding the use of targeted therapies such as anti-EGFR antibody treatments. The high frequency of clinically relevant genomic alterations uncovered in this study that can potentially serve as targets for therapies, either approved or in clinical trials, raises hope that CGP can lead to improvement in outcomes for patients with this aggressive form of malignancy.

Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines

We describe open, reproducible pipelines that create an integrated genomic profile of a cancer and use the profile to find mutations associated with disease and potentially useful drugs. These pipelines analyze high-throughput cancer exome and transcriptome sequence data together with public databases to find relevant mutations and drugs. The three pipelines that we have developed are: (1) an exome analysis pipeline, which uses whole or targeted tumor exome sequence data to produce a list of putative variants (no matched normal data are needed); (2) a transcriptome analysis pipeline that processes whole tumor transcriptome sequence (RNA-seq) data to compute gene expression and find potential gene fusions; and (3) an integrated variant analysis pipeline that uses the tumor variants from the exome pipeline and tumor gene expression from the transcriptome pipeline to identify deleterious and druggable mutations in all genes and in highly expressed genes. These pipelines are integrated into the popular Web platform Galaxy at http://usegalaxy.org/cancer to make them accessible and reproducible, thereby providing an approach for doing standardized, distributed analyses in clinical studies. We have used our pipeline to identify similarities and differences between pancreatic adenocarcinoma cancer cell lines and primary tumors.

Abstract 1227: Preserved histological and molecular phenotypes following serial in vivo propagation of patient-derived xenografts of small cell lung cancer

Background: Limited availability of tissue samples is a major impediment to small cell lung cancer (SCLC) research but patient-derived xenograft (PDX) offers a potential alternative. The high genomic instability of SCLC necessitates the need to establish whether the molecular characteristics of PDXs are preserved across serial propagation in mice.

Method: PDX were raised using biopsy samples from patients with relapsed SCLC under an IRB-approved protocol. Image guided or bronchoscopic biopsies were directly implanted subcutaneously into SCID mice within 60 minutes of collection and without in vitro culture. Tumor growth was monitored and animals were sacrificed while overall tumor size remained &lt;2g. Harvested tumors were immediately re-implanted into a new set of 5 mice for up to 5 generations while freezing remnant tumor samples in liquid nitrogen for future use. Tumor histology was assessed by standard H&E and immunohistochemistry for neuroendocrine markers (NSE, chromogranin and Synaptophysin). Harvested DNA from tumor samples from all generations of PDX using QiAmp DNA Mini Kit was employed for targeted sequencing at greater than 2,000x coverage on the Illumina MiSeq instrument. A 17-gene panel including frequently encountered genetic aberrations in lung cancer (EGFR, KRAS, TP53, STK11, PTEN, NRAS, ERBB2, MET, NF1 and PIK3CA) was used to characterize molecular phenotype of PDX samples. Molecular homogeneity was assessed by comparing the genetic profile of each PDX across all generations. All identified mutations were compared to the COSMIC database.Results: We have successfully raised PDX from 5 of 9 patient biopsies with a lag time from initial implantation to adequate tumor growth ranging between 1.5 and 11 months. Propagation of PDX across generations has been performed for 5 generations (1PDX), 3 generations (2PDXs), 2 generations (2PDXs) and 1 generation (1PDX). There was good preservation of tumor histology assessed by H&E and IHC across generations. Mutations in TP53 gene (c.422G&gt;A[p.Cys141Tyr]; c.913A&gt;T[p.Lys305Ter], c.488A&gt;G[p.Tyr163Cys], c.892G&gt; [p.Glu298Ter]) detected in tumor samples from the first generation mice were preserved across all subsequent generations tested. Additionally, there were no new aberrations detected in this panel of 17 genes when comparing early to later generations of PDX. Conclusions: Despite the high degree of genomic instability expected in SCLC, serially propagated PDX of SCLC maintained histologic and molecular characteristics across many generations. Our finding that original tumor characteristics remain well preserved in PDX supports future use of this resource as reliable platform for translational research in SCLC.Supported through the Georgia Cancer Coalition Distinguished Scholar Award and NIH/NCI 5K23CA164015 grant to TK Owonikoko

Citation Format: Taofeek Kunle Owonikoko, Guojing Zhang, Gabriel L. Sica, Hyun S. Kim, Onyinye C. Ogee-Nwankwo, Suresh S. Ramalingam, Michael R. Rossi, Fadlo R. Khuri. Preserved histological and molecular phenotypes following serial in vivo propagation of patient-derived xenografts of small cell lung cancer. [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 1227. doi:10.1158/1538-7445.AM2014-1227

Abstract 922: Evaluating markers of cisplatin sensitivity and survival in small cell lung cancer

Background: Molecular characterization of small cell lung cancer (SCLC) can lead to improved outcome through the identification of tumor subtypes with differential clinical outcome and response to treatment. We characterized SCLC cell lines and patient samples by a combination of a genome-wide and a custom expression panel to assess expression changes associated with cisplatin sensitivity, in the case of cell lines, and overall survival, in terms of SCLC patients.Method: SCLC cell lines (H69, H128, H146, H526, H187, H209, D53, DMS153, and DMS114) and 79 archival samples of pulmonary neuroendocrine tumor samples were employed. Sensitivity to cisplatin, and PARP inhibitor, veliparib was determined by MTS assay. In order to identify expression profiles characteristic of sensitive and insensitive cell lines, gene expression for untreated and treated cells was obtained from Illumina microarray gene expression and NanoString platforms. Comparisons of expression were performed between treated cell lines and controls using a combination of ANOVA and empirical variance distributions to assess sensitivity. Prognostic impact of differentially expressed genes in cell lines was assessed in patients using gene expression obtained by NanoString and protein expression by immunohistochemistry (IHC). Kaplan Meier Method, Logrank test, and Cox proportional hazard model were employed for testing differences in survival. Additionally, a quantile survival analyses was performed to identify patient subgroups associated with early and/or late changes in expression.Results: Unsupervised analysis of the Illumina probesets identified a 23 gene panel with differential expression between cell lines with differing platinum sensitivity: Sensitive - GLS, UBEC2, HACL1, MSI2 and LOC100129585; insensitive - CENPE, CRYGS, FAM83D, FLJ44342, GNA12, LOC88523, LRDD, N4BP2L2, SLC35A3, SPC25; shared - AURKA, CENPA, DLGAP5, HMMR, KIF20B, LOC100129585, LOC100131735, RBMX, SFRS3. Unsupervised analysis of expression data from Illumina and nCounter NanoString showed considerable concordance in cluster patterns. The Cox regression models of gene expression on overall survival identified LOC100131735 as a predictive marker and, SLC35A3, SPC25, DLGAP5 and UBE2C genes as prognostic biomarkers. Concomitantly high expression of SLC35A3 and GLS genes characterized SCLC with prolonged survival (Logrank p=0.025) while a trend toward reduced risk of death (HR: 0.798; 95%CI, 0.375-1.700, p=0.559) was observed with high GLS protein expression.Conclusions: Our use of both cell line and patient SCLC data has provided evidence of markers characteristics of cisplatin insensitivity that also show a relation with poor overall survival in patients. Additional studies to fully understand the mechanisms underlying such markers are currently underway. Supported through the Georgia Cancer Coalition Distinguished Scholar Award and NIH 5K23CA164015 grant to TK Owonikoko

Citation Format: Taofeek Kunle Owonikoko, Guojing Zhang, Gabriel L. Sica, Zhengjia Chen, Jeffrey M. Switchenko, Sungjin Kim, Anthony A. Gal, Suresh S. Ramalingam, Xingming Deng, Michael R. Rossi, Jeanne Kowalski, Fadlo R. Khuri. Evaluating markers of cisplatin sensitivity and survival in small cell lung cancer. [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 922. doi:10.1158/1538-7445.AM2014-922

Mutation and Transcriptional Profiling of Formalin-Fixed Paraffin Embedded Specimens as Companion Methods to Immunohistochemistry for Determining Therapeutic Targets in Oropharyngeal Squamous Cell Carcinoma (OPSCC): A Pilot of Proof of Principle

The role of molecular methods in the diagnosis of head and neck cancer is rapidly evolving and holds great potential for improving outcomes for all patients who suffer from this diverse group of malignancies . However, there is considerable debate as to the best clinical approaches, particularly for Next Generation Sequencing (NGS). The choices of NGS methods such as whole exome, whole genome, whole transcriptomes (RNA-Seq) or multiple gene resequencing panels, each have strengths and weakness based on data quality, the size of the data, the turnaround time for data analysis, and clinical actionability. There have also been a variety of gene expression signatures established from microarray studies that correlate with relapse and response to treatment, but none of these methods have been implemented as standard of care for oropharyngeal squamous cell carcinoma (OPSCC). Because many genomic methodologies are still far from the capabilities of most clinical laboratories, we chose to explore the use of a combination of off the shelf targeted mutation analysis and gene expression analysis methods to complement standard anatomical pathology methods. Specifically, we have used the Ion Torrent AmpliSeq cancer panel in combination with the NanoString nCounter Human Cancer Reference Kit on 8 formalin-fixed paraffin embedded (FFPE) OPSCC tumor specimens, (4) HPV-positive and (4) HPV-negative. Differential expression analysis between HPV-positive and negative groups showed that expression of several genes was highly likely to correlate with HPV status. For example, WNT1, PDGFA and OGG1 were all over-expressed in the positive group. Our results show the utility of these methods with routine FFPE clinical specimens to identify potential therapeutic targets which could be readily applied in a clinical trial setting for clinical laboratories lacking the instrumentation or bioinformatics infrastructure to support comprehensive genomics workflows. To the best of our knowledge, these preliminary experiments are among the earliest to combine both mutational and gene expression profiles using Ion Torrent and NanoString technologies. This reports serves as a proof of principle methodology in OPSCC.

Poly (ADP) ribose polymerase enzyme inhibitor, veliparib, potentiates chemotherapy and radiation in vitro and in vivo in small cell lung cancer

Poly (ADP) ribose polymerase (PARP) plays a key role in DNA repair and is highly expressed in small cell lung cancer (SCLC). We investigated the therapeutic impact of PARP inhibition in SCLC. In vitro cytotoxicity of veliparib, cisplatin, carboplatin, and etoposide singly and combined was determined by MTS in 9 SCLC cell lines (H69, H128, H146, H526, H187, H209, DMS53, DMS153, and DMS114). Subcutaneous xenografts in athymic nu/nu mice of H146 and H128 cells with relatively high and low platinum sensitivity, respectively, were employed for in vivo testing. Mechanisms of differential sensitivity of SCLC cell lines to PARP inhibition were investigated by comparing protein and gene expression profiles of the platinum sensitive and the less sensitive cell lines. Veliparib showed limited single-agent cytotoxicity but selectively potentiated (≥50% reduction in IC₅₀) cisplatin, carboplatin, and etoposide in vitro in five of nine SCLC cell lines. Veliparib with cisplatin or etoposide or with both cisplatin and etoposide showed greater delay in tumor growth than chemotherapy alone in H146 but not H128 xenografts. The potentiating effect of veliparib was associated with in vitro cell line sensitivity to cisplatin (CC = 0.672; P = 0.048) and DNA-PKcs protein modulation. Gene expression profiling identified differential expression of a 5-gene panel (GLS, UBEC2, HACL1, MSI2, and LOC100129585) in cell lines with relatively greater sensitivity to platinum and veliparib combination. Veliparib potentiates standard cytotoxic agents against SCLC in a cell-specific manner. This potentiation correlates with platinum sensitivity, DNA-PKcs expression and a 5-gene expression profile.

Multiplatform assessment of anaplastic lymphoma kinase (ALK) gene rearrangement in signet ring cell carcinoma of the gastrointestinal tract

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Background: ALK-EML4 translocation is an established driver aberration in NSCLC, with reported predilection for cases with signet ring histology. We assessed the presence of ALK gene rearrangements in signet ring cancers arising in the stomach and colon. Methods: Histologically confirmed cases of signet ring adenocarcinoma of the stomach or the colon were identified from the pathology archive of Emory University Hospital. Presence of the classic ALK and EML4 fusion gene was initially determined by fluorescence in-situ hybridization (FISH) method. Cases showing break-apart signal in more than 15% of enumerated cells were considered positive; at least 10% of enumerated cells was considered “possibly positive”. Immunohistochemistry of the fused gene product was assessed using previously validated antibodies ALK1 clone (1:100; DAKO) and 5A4 (Novocastra, Leica Biosystems) and positive controls of ALK-translocated lung cancer. Positive or possibly positive cases by FISH were further analyzed by RT-PCR using specific primers for the most common translocation pairs (EML4 Ex13/ALK Ex20 and EML4 Ex6/ALK Ex20) along with positive (H228, HEK293) and negative (H460, H1975) control cell lines. Results: We retrieved 44 cases of signet ring carcinoma diagnosed between 2001 and 2011; 26 gastric and 18 colon cancer. Median age - 63 yrs; M/F 17/27; Black - 47.5%; White - 47.5%; Others - 5%; Stage I - 21.4%; II - 31%; III - 26.2; IV - 21.4%. One of 44 cases (2.3%) was positive for ALK translocation by FISH using the standard criteria of at least 15% positive cells for the break-apart signal (50-70 cells counted per case). 7 cases (16%) were considered possibly positive [1 of 18 (6%) colon cancer and 6 of 26 (26%) gastric cancer cases]. IHC showed 0 of 44 (0%) cases positive. Molecular analysis using RT-PCR did not confirm the suspected ALK gene rearrangements in any of the 7 cases considered possibly positive by FISH. Conclusions: The overall frequency of ALK gene rearrangement detected by FISH in signet ring cancer of the GI tract was low, but appears comparable to the reported frequency in lung cancer. Signet ring histology failed to enrich for cases with ALK gene translocation in this histologic subtype.

Evaluation of phosphatidylinositol-3-kinase catalytic subunit (PIK3CA) and epidermal growth factor receptor (EGFR) gene mutations in pancreaticobiliary adenocarcinoma

BACKGROUND

Phosphatidylinositol-3-kinase (PI3K) activation involves the epidermal growth factor receptor (EGFR) and plays an important role in cell survival signaling in pancreaticobiliary cancer. EGFR gene mutations have been correlated with clinical response to EGFR inhibitors in patients with advanced non-small cell lung cancer. This study examined the prevalence of PIK3CA and EGFR mutations in pancreaticobiliary cancer where erlotinib, an EGFR inhibitor, is approved for therapy.

METHODS

Thirty patients who underwent pancreatectomy for pancreaticobiliary carcinoma were identified. Genomic DNA was extracted from formalin fixed paraffin embedded tumor and adjacent normal tissue, and exons 9 and 20 (for the PIK3CA gene) and exons 18-21 (for the EGFR gene) were amplified by PCR and sequenced. Literature review on EGFR and/or PIK3CA mutations in pancreaticobiliary adenocarcinomas was conducted.

RESULTS

No mutations in either PIK3CA or EGFR genes were identified. The study identified one synonymous single nucleotide polymorphism (SNP) (rs1050171) in the coding region of EGFR. A previously unreported change, suspected to be a SNP, was observed in intron 18 of EGFR (IVS18+15, C>T). Review of the literature showed EGFR mutation rate of 2% and 10.5% in pancreatic and biliary tract carcinomas, respectively. PIK3CA mutations were found in 3.6% and 11.7% of pancreatic and biliary tract carcinomas, respectively.

CONCLUSIONS

A low prevalence of EGFR or PIK3CA mutations exists in pancreatic cancer (<5%), indicating that mutation screening may not be as useful in determining prognosis or response to targeted inhibition.

Heterogeneity of primary glioblastoma cells in the expression of caspase-8 and the response to TRAIL-induced apoptosis

Recent studies suggest that cancer stem cells (CSCs) are responsible for cancer resistance to therapies. We therefore investigated how glioblastoma-derived CSCs respond to the treatment of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). Neurospheres were generated from glioblastomas, characterized for CSC properties including self-renewal, cell differentiation and xenograft formation capacity, and analyzed for TRAIL-induced apoptosis, CASP8 genomic status, and caspase-8 protein expression. The neurosphere NSC326 was sensitive to TRAIL-induced apoptosis as evidenced by cell death and caspase-8, -3, and -7 enzymatic activities. In contrast, however, the neurosphere NSC189 was TRAIL-resistant. G-banding analysis identified five chromosomally distinguishable cell populations in the neurospheres. Fluorescence in situ hybridization revealed the variation of chromosome 2 copy number in these populations and the loss of CASP8 locus in 2q33-34 region in a small set of cell populations in the neurosphere. Immunohistochemistry of NSC189 cell blocks revealed the lack of caspase-8 protein in a subset of neurosphere cells. Western blotting and immunohistochemistry of human glioblastoma tumors demonstrated the expression of caspase-8 protein in the vast majority of the tumors as compared to normal human brain tissues that lack the caspase-8 expression. This study shows heterogeneity of glioblastomas and derived CSCs in the genomic status of CASP8, expression of caspase-8, and thus responsiveness to TRAIL-induced apoptosis. Clinic trials may consider genomic analysis of the cancer tissue to identify the genomic loss of CASP8 and use it as a genomic marker to predict the resistance of glioblastomas to TRAIL apoptosis pathway-targeted therapies.