RAF1 amplification drives a subset of bladder tumors and confers sensitivity to MAPK-directed therapeutics

Bladder cancer is a genetically heterogeneous disease, and novel therapeutic strategies are needed to expand treatment options and improve clinical outcomes. Here, we identified a unique subset of urothelial tumors with focal amplification of the RAF1 (CRAF) kinase gene. RAF1-amplified tumors had activation of the RAF/MEK/ERK signaling pathway and exhibited a luminal gene expression pattern. Genetic studies demonstrated that RAF1-amplified tumors were dependent upon RAF1 activity for survival, and RAF1-activated cell lines and patient-derived models were sensitive to available and emerging RAF inhibitors as well as combined RAF plus MEK inhibition. Furthermore, we found that bladder tumors with HRAS- or NRAS-activating mutations were dependent on RAF1-mediated signaling and were sensitive to RAF1-targeted therapy. Together, these data identified RAF1 activation as a dependency in a subset making up nearly 20% of urothelial tumors and suggested that targeting RAF1-mediated signaling represents a rational therapeutic strategy.

Twists and turns from "tumor in tumor" profiling: surveillance of chronic lymphocytic leukemia (CLL) leads to detection of a lung adenocarcinoma, whose genomic characterization alters the original hematologic diagnosis

Comprehensive characterization of somatic genomic alterations has led to fundamental shifts in our understanding of tumor biology. In clinical practice, these studies can lead to modifications of diagnosis and/or specific treatment implications, fulfilling the promise of personalized medicine. Herein, we describe a 78-yr-old woman under surveillance for long-standing untreated chronic lymphocytic leukemia (CLL). Molecular studies from a peripheral blood specimen revealed a TP53 p.V157F mutation, whereas karyotype and fluorescence in situ hybridization (FISH) identified a 17p deletion, trisomy 12, and no evidence of IGH-CCND1 rearrangement. Positron emission tomography-computed tomography scan identified multistation intra-abdominal lymphadenopathy and a pulmonary nodule, and subsequent pulmonary wedge resection confirmed the presence of a concurrent lung adenocarcinoma. Targeted next-generation sequencing of the lung tumor identified an EGFR in-frame exon 19 deletion, two TP53 mutations (p.P152Q, p.V157F), and, unexpectedly, a IGH-CCND1 rearrangement. Follow-up immunohistochemistry (IHC) studies demonstrated a cyclin D1–positive lymphoid aggregate within the lung adenocarcinoma. The presence of the TP53 p.V157F mutation in the lung resection, detection of an IGH-CCND1 rearrangement, and cyclin D1 positivity by IHC led to revision of the patient's hematologic diagnosis and confirmed the extranodal presence of mantle cell lymphoma within the lung mass, thus representing a “tumor in tumor.” Manual review of the sequencing data suggested the IGH-CCND1 rearrangement occurred via an insertional event, whose size precluded detection by original FISH studies. Thus, routine imaging for this patient's known hematologic malignancy led to detection of an unexpected solid tumor, whose subsequent precision medicine studies in the solid tumor redefined the original hematological diagnosis.

Abstract 2059: AI - optimized genomic homologous recombination deficiency test (HRDScar) to predict platinum and PARP inhibitor responses in high-grade serous ovarian cancer

High-grade serous ovarian cancer (HGSC) is the most common and most lethal subtype of ovarian cancer. More than half of the HGSCs are defective in Homologous Recombination DNA repair (HRD), and sensitive to Poly-ADP Ribose Polymerase (PARP) inhibitors. Recently, a genomic HRD test based on three types of genomic scarring events (Large scale transitions; LST, Telomeric Allelic Imbalance TAI, Loss of Heterozygosity LOH) was shown to predict which patients benefit the most from PARP inhibitors. The HRD test, however, was originally designed and optimized in breast cancer, and therefore the details of genomic scarring events occurring in ovarian cancers are unknown.

To characterize the genomic scarring events and define an optimal cut-off for HRDScar biomarker in ovarian cancer, we are using large publicly available dataset from the TCGA. We selected 103 HRD samples based on somatic and germline mutations, gene deletions or hypermethylation in the BRCA1/2 and RAD51 paralog genes, and 34 HR proficient (HRP) samples without any mutation, deletion or hypermethylation of the HR genes. To identify the detailed features of LOH, LST and TAI scarring events, we employed state-of-the-art machine-learning algorithm and statistics to optimally separate the HRD-samples from HRP in the TCGA SNP array dataset. Our new optimized genomic footprints and cut-offs showed improved accuracy to separate HRD from HRP compared to the previous algorithm (accuracy of 0.89 vs 0.79). The optimized HRDScar showed reliable performance in NGS-derived data and correlated with mutational signature 3 (p=2.2e-16, r2=0.5). Interestingly, the HRDScar levels also positively correlated with an HRD score derived from an ex-vivo RAD51-based functional assay for HRD performed in the prospective HERCULES samples (n=72). Using two independent validation cohorts (PCAWG, HERCULES), our optimized HRDScar more accurately predicted progression-free survival (PFS) and overall survival (OS) when compared to previous algorithms. Importantly, improved prediction of PFS was detected especially in patients without BRCA1/2 alterations (p= 1.9e-04, HR=0.70). We are in the process of analyzing HRDScar from a clinical trial involving PARP inhibitor Niraparib (TOPACIO/Keynote-162 (NCT02657889)) enabling direct association of the HRDScar to clinical outcomes. In conclusion, HRDScar shows promise as a fully optimized algorithm that can be used for improved selection of patients for PARP inhibitor therapies in HGSC.

Citation Format: Fernando Perez-Villatoro, Jaana Oikkonen, Manuela Tumiati, Julia Casado, Sakari Hietanen, Johanna Hynninen, Elizabeth P. Garcia, Panagiotis Konstantinopoulos, Sampsa Hautaniemi, Liisa Kauppi, Anniina Färkkilä. AI - optimized genomic homologous recombination deficiency test (HRDScar) to predict platinum and PARP inhibitor responses in high-grade serous ovarian cancer [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 2059.

Abstract 5671: Alignment of TMB measured on clinical samples: Phase IIB of the Friends of Cancer Research TMB Harmonization Project

Introduction:

Tumor mutational burden (TMB) is the number of somatic mutations per megabase in a tumor's genome and has shown promise as a predictive biomarker of response to immune checkpoint inhibitors across several cancers. TMB is typically measured by whole exome sequencing (WES TMB) or by targeted next-generation sequencing gene panels (panel TMB). As more assays are developed to estimate TMB, harmonization is emerging as an unmet need and is a key goal of the Friends of Cancer Research (Friends) TMB Harmonization Project. Phase I of the Harmonization Project demonstrated correlation between panel TMB and WES TMB using TCGA data and defined theoretical sources of variability across panels. In phase IIA, sustainable TMB reference standard materials generated from human derived cell lines were used to characterize variability in TMB measurements across panels and assessed for utility in TMB alignment. Phase IIB aims to characterize variability in TMB measurements in clinical samples and to establish best practices for estimating and aligning TMB in order to improve consistency across panels.

Methods:

Fifteen laboratories (16 targeted gene panels) at different stages of development participated in phase IIB. Thirty formalin-fixed paraffin-embedded (FFPE) samples with >30% tumor content were acquired; tumor DNA was isolated by a single reference lab. TMB values were calculated for DNA extracted from lung (N=10), bladder (N=10), and gastric tumors (N=10) using WES and a uniform bioinformatics pipeline agreed upon by all Consortium members. DNA samples were also sent to all laboratories, and each used their own sequencing and bioinformatics pipelines to estimate TMB from the genes represented in their respective panels. For each tumor sample, a median across panel TMB estimates was calculated; individual panel TMB estimates were translated to fold-changes relative to the sample median to quantify variability. Association between WES TMB (reference) and panel TMB will be assessed by regression analysis; dependence of association on cancer type was investigated.

Results:

A subset of tumor samples (9 bladder, 7 lung, and 5 gastric) was analyzed using 11 panels at the time of abstract submission. Median panel TMB values ranged 0.60 - 40.26 across samples, with median of median values of 5.35. Fold-change from sample-level medians ranged 0x - 6.67x. Assessment of these clinical samples by WES and all 16 gene panels, as well as regression analysis results, are forthcoming.

Conclusions:

The Friends TMB Harmonization Project has made substantial progress in characterization of TMB measurement variability and association between WES TMB and panel TMB. These are important steps toward alignment of TMB estimates generated by different gene panels which may improve the interpretation of findings within clinical development programs and ultimately enhance the usefulness of this predictive biomarker in clinical decision making.

Citation Format: Diana M. MERINO, Laura M. Yee, Lisa M. McShane, P. Mickey Williams, Tomas Vilimas, Rajesh Patidar, J. Carl Barrett, Shu-Jen Chen, Jen-Hao Cheng, Jeffrey M. Conroy, Dinesh Cyanam, Kenneth R. Eyring, David A. Fabrizio, Vincent Funari, Elizabeth P. Garcia, Sean T. Glenn, Christopher D. Gocke, Vikas Gupta, Lisa M. Haley, Matthew D. Hellmann, Laurel Keefer, Lauryn R. Keeler, Brett Kennedy, Alexander J. Lazar, Laura E. MacConaill, Kristen L. Meier, Arnaud Papin, Naiyer A. Rizvi, Ethan Sokol, Phillip Stafford, John F. Thompson, Warren Tom, Victor J. Weigman, Mingchao Xie, Chen Zhao, Mark D. Stewart, Jeff Allen. Alignment of TMB measured on clinical samples: Phase IIB of the Friends of Cancer Research TMB Harmonization Project [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 5671.

Biallelic PTCH1 Inactivation Is a Dominant Genomic Change in Sporadic Keratocystic Odontogenic Tumors

Keratocystic odontogenic tumors (KCOTs) are locally aggressive odontogenic neoplasms with recurrence rates of up to 60%. Approximately 5% of KCOTs are associated with nevoid basal cell carcinoma (Gorlin) syndrome and 90% of these show genomic inactivation of the PTCH1 gene encoding Patched 1. Sporadic KCOTs reportedly have PTCH1 mutations in 30% of cases, but previous genomic analyses have been limited by low tumor DNA yield. The aim of this study was to identify recurrent genomic aberrations in sporadic KCOTs using a next-generation sequencing panel with complete exonic coverage of sonic hedgehog (SHH) pathway members PTCH1, SMO, SUFU, GLI1, and GLI2. Included were 44 sporadic KCOTs from 23 female and 21 male patients with a median age of 50 years (range, 10 to 82 y) and located in the mandible (N=33) or maxilla (N=11). Sequencing identified PTCH1 inactivating mutations in 41/44 (93%) cases, with biallelic inactivation in 35 (80%) cases; 9q copy neutral loss of heterozygosity targeting the PTCH1 locus was identified in 15 (34%) cases. No genomic aberrations were identified in other sequenced SHH pathway members. In summary, we demonstrate PTCH1 inactivating mutations in 93% of sporadic KCOTs, indicating that SHH pathway alterations are a near-universal event in these benign but locally aggressive neoplasms. The high frequency of complete PTCH1 loss of function may provide a rational target for SHH pathway inhibitors to be explored in future studies.

Genomic profiling of pleomorphic and florid lobular carcinoma in situ reveals highly recurrent ERBB2 and ERRB3 alterations

Pleomorphic LCIS (P-LCIS) and florid LCIS (F-LCIS) are morphologic variants distinguished from classic LCIS by marked nuclear pleomorphism and/or an expansile growth pattern with or without necrosis. Given the rarity of these LCIS variants, little data exist regarding their molecular pathogenesis, natural history, and optimal management. The purpose of this study was to genomically profile LCIS variants to gain further insight into their biology. Nineteen cases of pure LCIS variants (17 P-LCIS, 2 F-LCIS) diagnosed on core needle biopsy at our institution from 2006 to 2017 were included, five of which were upgraded to invasive cancer at excision. Macrodissected lesions were analyzed by a hybrid-capture next generation sequencing assay that surveyed exonic sequences of 447 genes for mutations and copy number variations (CNVs) and 191 regions across 60 genes for structural rearrangements. LCIS variants were all confirmed as E-cadherin negative by immunohistochemistry. Receptor profiles among the 17 P-LCIS cases included HR+/HER2- (nine cases), HR+/HER2+ (three cases), HR-/HER2+ (two cases), and HR-/HER2- (three cases). The two F-LCIS cases were HR+/HER2- and HR+/HER2+. All LCIS variants had genetic alterations consistent with a lobular phenotype including 1q gain (16 cases), 16q loss (18 cases), and CDH1 mutations (18 cases). Highly recurrent ERBB2 alterations were noted including mutations (13 cases) and amplifications (six cases). Other significant alterations included mutations in PIK3CA (six cases), RUNX1 (four cases), ERBB3 (four cases), and CBFB (three cases), as well as amplification of CCND1 (five cases). A TP53 mutation was identified in one case of HR-/HER2+ P-LCIS with signet ring cell features that lacked 1q gain and 16q loss. P-LCIS and F-LCIS contain genetic alterations characteristic of lobular neoplasia; however, these LCIS variants are distinguished from classical LCIS reported in the literature by their highly recurrent ERBB2 alterations.

ViroPanel: Hybrid Capture and Massively Parallel Sequencing for Simultaneous Detection and Profiling of Oncogenic Virus Infection and Tumor Genome

Precision cancer medicine aims to classify tumors by site, histology, and molecular testing to determine an individualized profile of cancer alterations. Viruses are a major contributor to oncogenesis, causing 12% to 20% of all human cancers. Several viruses are causal of specific types of cancer, promoting dysregulation of signaling pathways and resulting in carcinogenesis. In addition, integration of viral DNA into the host (human) genome is a hallmark of some viral species. Tests for the presence of viral infection used in the clinical setting most often use quantitative PCR or immunohistochemical staining. Both approaches have limitations and need to be interpreted/scored appropriately. In some cases, results are not binary (virus present/absent), and it is unclear what to do with a weakly or partially positive result. In addition, viral testing of cancers is performed separately from tests to detect human genomic alterations and can thus be time-consuming and use limited valuable specimen. We present a hybrid-capture and massively parallel sequencing approach to detect viral infection that is integrated with targeted genomic analysis to provide a more complete tumor profile from a single sample.

Abstract 1611: High quality next generation sequencing results for breast cancer using dual-mode biopsy tissue preservation

Introduction: Formalin-fixed paraffin-embedded (FFPE) tissue is commonly used for molecular analysis, including for next generation sequencing (NGS). In an effort to improve the quality of molecular results in small tissue samples, we developed a novel biopsy transport device that splits the biopsy sample longitudinally for dual-mode preservation by freezing (for biomolecular analysis) and formalin (for the evaluation of histologic features without freezing artifact). In this feasibility study we compared NGS results from samples acquired by the new device with those obtained using standard biopsy handling procedures.

Methods: Following informed consent, biopsy samples were obtained ex-vivo by a breast imaging radiologist under ultrasound guidance from invasive cancers in two mastectomy specimens using a standard biopsy needle (Mission 14G, CR Bard). A reference sample (REF) was placed directly into 10% neutral buffered formalin. An experimental sample (EXP) was placed in the new device, ink marked on one end for orientation and sectioned longitudinally. After sectioning, one half-sample was formalin fixed and one half was frozen and then stored at -80 degrees until further processing. The REF samples and one half of the EXP samples were fixed for 24 hours then processed routinely into FFPE blocks. DNA was extracted from the REF sample and the frozen EXP half-sample and evaluated using NGS Oncopanel (targeted exome sequencing, Illumina) at 25ng, 50ng and 100ng input template.

Results: The formalin-fixed EXP halves maintained high quality of tissue histology with minimal artifacts. The number of unique, aligned, high-quality reads was on average 1.85-fold greater in the EXP specimens relative to the paired REF samples for all three template amounts in both tumors that were analyzed (range 1.58-fold to 2.29-fold; p=0.0016). More than twice as many high-quality reads were present in the EXP specimens for Tier 2 and Tier 3 mutations (TP53, PIK3CA and GATA3) at the lowest template amounts (average 2.40-fold at 25ng). Copy number reads showed lower cutoff scores (a measure of signal variability across segments) in EXP samples than in REF samples (p=0.0052).

Conclusions: Dual-mode preservation of core biopsy samples by freezing and formalin can be done with the new device and it provides equivalent quality of histology sections. Preservation of biopsy samples by freezing rather than formalin improved the quality of NGS evaluation in all samples down to 25ng input template, both for single variant analysis and for copy number detection. Longitudinal sectioning of the tissue samples allows for assessment of tumor purity and for macrodissection of the oriented frozen half-sample as needed. These improvements allow for greater confidence in variant and copy number calls with lower input template amounts.

Citation Format: Deborah A. Dillon, Elizabeth P. Garcia, Michele Baltay, Krishan Taneja, Teri Bowman, Eva C. Gombos, Tom Gal, Stuart G. Silverman, Erez Nevo, Shoshan Nevo. High quality next generation sequencing results for breast cancer using dual-mode biopsy tissue preservation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1611.

Somatic mutations in CDH1 and CTNNB1 in primary carcinomas at 13 anatomic sites

Metastases are involved in most cancer deaths. Evidence has suggested that cancer cell detachment from primary tumors might occur largely via the mechanism of epithelial-mesenchymal transition (EMT) activated by epigenetic events, but data addressing other possible triggers of detachment, particularly genetic mutations, have been limited. Using the Profile study of cancer genomics at Dana-Farber Cancer Institute, we examined somatic mutations in the EMT genes CDH1 in 5,106 primary carcinomas and CTNNB1 in 7,578 primary carcinomas across 13 anatomic sites: urinary bladder, breast, colon/rectum, endometrium, esophagus, kidney, lung, ovary, pancreas, prostate, skin (non-melanoma), stomach, and thyroid. For each gene and anatomic site, we calculated the prevalence of primary carcinomas with at least one mutation. Across all anatomic sites, 4% of carcinomas had at least one CDH1 mutation and 4% of carcinomas had at least one CTNNB1 mutation. By anatomic site, the observed prevalence of carcinomas with at least one mutation was less than 5% at 10 sites for CDH1 and 12 sites for CTNNB1. Tumor stage data were available for a subset of breast, colorectal, lung, and prostate tumors. Among patients from this subset who were diagnosed with regional or distant disease, only 4% had a CDH1 mutation and 1% had a CTNNB1 mutation in the primary tumor. The low mutation prevalences, especially among those with diagnoses of regional or distant disease, suggest that somatic mutations in CDH1 and CTNNB1 are unlikely to explain a substantial proportion of cancer cell detachment from primary carcinomas originating at most anatomic sites.

Validation of OncoPanel: A Targeted Next-Generation Sequencing Assay for the Detection of Somatic Variants in Cancer

CONTEXT

- The analysis of somatic mutations across multiple genes in cancer specimens may be used to aid clinical decision making. The analytical validation of targeted next-generation sequencing panels is important to assess accuracy and limitations.

OBJECTIVE

- To report the development and validation of OncoPanel, a custom targeted next-generation sequencing assay for cancer.

DESIGN

- OncoPanel was designed for the detection of single-nucleotide variants, insertions and deletions, copy number alterations, and structural variants across 282 genes with evidence as drivers of cancer biology. We implemented a validation strategy using formalin-fixed, paraffin-embedded, fresh or frozen samples compared with results obtained by clinically validated orthogonal technologies.

RESULTS

- OncoPanel achieved 98% sensitivity and 100% specificity for the detection of single-nucleotide variants, and 84% sensitivity and 100% specificity for the detection of insertions and deletions compared with single-gene assays and mass spectrometry-based genotyping. Copy number detection achieved 86% sensitivity and 98% specificity compared with array comparative genomic hybridization. The sensitivity of structural variant detection was 74% compared with karyotype, fluorescence in situ hybridization, and polymerase chain reaction. Sensitivity was affected by inconsistency in the detection of FLT3 and NPM1 alterations and IGH rearrangements due to design limitations. Limit of detection studies demonstrated 98.4% concordance across triplicate runs for variants with allele fraction greater than 0.1 and at least 50× coverage.

CONCLUSIONS

- The analytical validation of OncoPanel demonstrates the ability of targeted next-generation sequencing to detect multiple types of genetic alterations across a panel of genes implicated in cancer biology.

Institutional implementation of clinical tumor profiling on an unselected cancer population

BACKGROUND. Comprehensive genomic profiling of a patient's cancer can be used to diagnose, monitor, and recommend treatment. Clinical implementation of tumor profiling in an enterprise-wide, unselected cancer patient population has yet to be reported. METHODS. We deployed a hybrid-capture and massively parallel sequencing assay (OncoPanel) for all adult and pediatric patients at our combined cancer centers. Results were categorized by pathologists based on actionability. We report the results for the first 3,727 patients tested. RESULTS. Our cohort consists of cancer patients unrestricted by disease site or stage. Across all consented patients, half had sufficient and available (>20% tumor) material for profiling; once specimens were received in the laboratory for pathology review, 73% were scored as adequate for genomic testing. When sufficient DNA was obtained, OncoPanel yielded a result in 96% of cases. 73% of patients harbored an actionable or informative alteration; only 19% of these represented a current standard of care for therapeutic stratification. The findings recapitulate those of previous studies of common cancers but also identify alterations, including in AXL and EGFR, associated with response to targeted therapies. In rare cancers, potentially actionable alterations suggest the utility of a "cancer-agnostic" approach in genomic profiling. Retrospective analyses uncovered contextual genomic features that may inform therapeutic response and examples where diagnoses revised by genomic profiling markedly changed clinical management. CONCLUSIONS. Broad sequencing-based testing deployed across an unselected cancer cohort is feasible. Genomic results may alter management in diverse scenarios; however, additional barriers must be overcome to enable precision cancer medicine on a large scale. FUNDING. This work was supported by DFCI, BWH, and the National Cancer Institute (5R33CA155554 and 5K23CA157631).

Detection of Mismatch Repair Deficiency and Microsatellite Instability in Colorectal Adenocarcinoma by Targeted Next-Generation Sequencing

Mismatch repair protein deficiency (MMR-D) and high microsatellite instability (MSI-H) are features of Lynch syndrome-associated colorectal carcinomas and have implications in clinical management. We evaluate the ability of a targeted next-generation sequencing panel to detect MMR-D and MSI-H based on mutational phenotype. Using a criterion of >40 total mutations per megabase or >5 single-base insertion or deletion mutations in repeats per megabase, sequencing achieves 92% sensitivity and 100% specificity for MMR-D by immunohistochemistry in a training cohort of 149 colorectal carcinomas and 91% sensitivity and 98% specificity for MMR-D in a validation cohort of 94 additional colorectal carcinomas. False-negative samples are attributable to tumor heterogeneity, and next-generation sequencing results are concordant with analysis of microsatellite loci by PCR. In a subset of 95 carcinomas with microsatellite analysis, sequencing achieves 100% sensitivity and 99% specificity for MSI-H in the combined training and validation set. False-positive results for MMR-D and MSI-H are attributable to ultramutated cancers with POLE mutations, which are confirmed by direct sequencing of the POLE gene and are detected by mutational signature analysis. These findings provide a framework for a targeted tumor sequencing panel to accurately detect MMR-D and MSI-H in colorectal carcinomas.

Morphologic correlates of molecular alterations in extrauterine Müllerian carcinomas

Extrauterine high-grade serous carcinomas can exhibit various histologic patterns including (1) classic architecture that is papillary, micropapillary and infiltrative and (2) solid, endometrioid, and transitional (ie, SET) patterns. Although the SET pattern has been associated with germline BRCA mutations, potential molecular underpinnings have not been fully investigated. DNA was isolated from 174 carcinomas of the fallopian tube, ovary, or peritoneum. Targeted next-generation sequencing was performed and single-nucleotide and copy number variants were correlated with morphologic subtype. Overall, 79% of tumors were classified as high-grade serous carcinoma (n=138), and the most common mutations in high-grade serous carcinomas were TP53 (94%), BRCA1 (25%), BRCA2 (11%), and ATM (7%). Among chemotherapy-naive high-grade serous carcinomas, 40 cases exhibited classic morphology and 40 cases had non-classic morphology (SET or ambiguous features). Mutations in homologous recombination pathways were seen across all tumor histotypes. High-grade serous carcinomas with homologous recombination mutations were six times more likely to be associated with non-classic histology (P=0.002) and were significantly more likely to be platinum sensitive and have improved progression-free survival (PFS) (P=0.007 and P=0.004, respectively). In a multivariate analysis adjusted for age, homologous recombination mutation status and increased copy number variants were independently associated with improved PFS (P=0.008 and P=0.005, respectively). These findings underscore the potential significance of variant morphologic patterns and comprehensive genomic analysis in high-grade serous carcinomas with potential implications for pathogenesis, as well as response to targeted therapies.

KRAS and NKX2-1 Mutations in Invasive Mucinous Adenocarcinoma of the Lung

INTRODUCTION

Mucinous differentiation is observed in a subset of lung adenocarcinomas with unique clinical and pathological features, but the biology of these neoplasms is poorly understood.

METHODS

We apply targeted next-generation sequencing to characterize the mutational profiles of 21 invasive mucinous adenocarcinomas, mixed mucinous/nonmucinous adenocarcinomas, and adenocarcinomas with mucinous features of the lung and validate key findings on 954 additional lung adenocarcinomas from our institution and 514 lung adenocarcinomas from The Cancer Genome Atlas.

RESULTS

Sequencing identifies pathogenic mutations in the oncogenes Kirsten rat sarcoma viral oncogene homolog (KRAS), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), erb-b2 receptor tyrosine kinase 2 (ERBB2), and anaplastic lymphoma receptor tyrosine kinase (ALK) and recurrent mutations in tumor protein p53 (TP53), serine/threonine kinase 11 (STK11), NK2 homeobox 1 (NKX2-1), and SET domain containing 2 (SETD2). In the combined discovery and validation cohorts, we identify nine neoplasms with distinct molecular and pathological features. All are invasive mucinous adenocarcinomas or mixed mucinous/nonmucinous adenocarcinomas with mutations of KRAS and frameshift or nonsense mutations of NKX2-1. Immunohistochemical analysis shows that these neoplasms are associated with altered differentiation states, including loss of expression of the pulmonary marker thyroid transcription factor 1 (also called Nkx2.1) and expression of gastrointestinal markers.

CONCLUSIONS

These findings describe recurrent NKX2-1 mutations in invasive mucinous adenocarcinomas of the lung and support NKX2-1 as a lineage-specific tumor suppressor gene in lung carcinogenesis.

Abstract 2991: Detection of gene rearrangements using OncoPanel: a targeted next-generation sequencing assay

Identification of structural gene rearrangements is vital for cancer patients as these events can provide definitive diagnoses, prognostic value, and influence the course of treatment. While FISH, karyotype analysis and aCGH array have traditionally been used to identify and confirm the presence of structural variants, the advent of next generation sequencing has enabled genetic testing including detection of multiple structural variants (SVs) from genomic DNA. To this end, we have developed and validated Oncopanel, a cancer-specific targeted next generation sequencing (NGS) assay designed to detect SNVs, indels, and copy number alterations across 300 genes, and 35 clinically actionable or informative SVs. Each rearrangement was specifically targeted by baiting genomic locations frequently identified to contain breakpoints reported in the literature and publicly available databases. Using BreaKmer, an internally developed SV detection tool (Nucleic Acids Res. 2014 Nov 26, doi: 10.1093/nar/gku1211), rearrangements, including the exact breakpoint coordinates and the genes involved in or adjacent to the breakpoint(s), were identified. Here we examine the utility of Oncopanel using genomic DNA to identify structural variants.

We report the results of 3,291 cancer patients tested in our personalized cancer medicine program (Profile), a joint venture between Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Boston Children's Hospital. As compared to conventional cytogenetics, FISH analysis, and molecular detection by PCR methods, Oncopanel's overall sensitivity and specificity for SVs was 81.4% and 100%, respectively. Most discordant results were identified in (1) tumors with SVs involving the IGH enhancer regions (60% of discordant results), or (2) in samples with < 20% tumor (25% of discordant results). Several SVs involving the IGH enhancer regions were missed likely due to lack of Oncopanel coverage. Oncopanel was designed to target a finite sequence pool, but due to IGH enhancer region's large size (1.2Mb), only a small portion of this region was specifically interrogated. Inclusion of all possible IGH enhancer sequences would have hampered the effectiveness of SNV, indel and copy number alteration detection for other cancer critical genes. Discrepant Oncopanel and cytogenetic results were also observed in samples with low tumor purity likely due to masking of variant sequences by stromal contamination.

In conclusion, we find that Oncopanel has utility to detect structural variants with a sensitivity of 92%, barring detection of rearrangements involving IGH, and a specificity of 100%. Based on the baiting strategy, detection of many rearrangements can also be interrogated in parallel with SNV, indel and CNV detection resulting in reduced sample input requirements and the inclusion of precise information regarding the breakpoints and the class of rearrangement identified.

Citation Format: Elizabeth P. Garcia, Azra H. Ligon, Ryan P. Abo, Paola S. Dal Cin, Stanislawa Weremowicz, Priyanka Shivdasani, Phani K. Davineni, Dimity L. Zepf, Matthew D. Ducar, Paul Van Hummelen, Yonghui Jia, Frank C. Kuo, Lynette M. Sholl, Laura E. MacConaill, Neal I. Lindeman. Detection of gene rearrangements using OncoPanel: a targeted next-generation sequencing assay. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2991. doi:10.1158/1538-7445.AM2015-2991

BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers

Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially for ‘targeted’ resequencing efforts. This is critically important in the clinical setting where targeted resequencing is frequently being applied to rapidly assess clinically actionable mutations in tumor biopsies in a cost-effective manner. We present BreaKmer, a novel approach that uses a ‘kmer’ strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants. Relative to four publically available algorithms, BreaKmer detected SV with increased sensitivity and limited calls in non-tumor samples, key features for variant analysis of tumor specimens in both the clinical and research settings.

Abstract 5321: BreaKmer: Detection of structural rearrangements in targeted next-generation sequencing data using kmers

Targeted next-generation sequencing (NGS) to capture genes or regions of interest has proven to be a cost-effective alternative to whole genome sequencing (WGS), particularly for cancer research and clinical cancer care. In this context, biologically or clinically relevant selected genes/regions are sequenced to several hundred-fold coverage. However, current algorithms and tools for detecting large structural variants (SVs), such as translocations, fail to achieve either high specificity or sensitivity, due to the fact that most available methods were designed for WGS data, and thus do not take advantage of the reduced size and higher coverage of targeted sequencing to improve SV calling.

We developed a novel method, BreaKmer, to detect indels, rearrangements, and translocations from single sample targeted genomic reads. The algorithm extracts mis-mapped single or paired-end NGS reads. From these reads, hypothesized to contain SV breakpoints, contigs are built with a kmer strategy: reads are broken into k-length substrings or kmers, and those occurring in the reference are filtered. The remaining kmers represent sequences containing any sequence variant from the reference, ranging from single nucleotides to larger variants. Contigs are assembled from reads containing sample specific kmers. SVs are called based on alignment of the contigs to the reference sequence. With paired-end (PE) reads, discordantly mapped paired reads are extracted and coupled with SV calls that are made.

To demonstrate BreaKmer, we analyzed NGS data from 166 samples enriched using 3 different capture panels (ranging from 305-504 genes). Our dataset contained 25 cancer specimens with known translocation events verified by orthogonal clinical methods and a negative control set of 141 ‘normal’ samples with no known SVs. The samples represented DNA extracted from FFPE, fresh frozen, blood and cell lines. Among 25 samples, 15 had additional replicate samples. Mean target coverage over all the samples was on average 150x. Specimens were barcoded at library preparation and pooled, followed by hybrid-capture targeting cancer genes and sequenced 2x100bp PE.

All translocation events from the 25 test samples and their replicates (46) were detected by BreaKmer. An additional 19 translocations were detected among all the samples and their replicates, while no translocation calls were made for the 141 negative control samples.

Our novel kmer strategy to detect SVs displayed high sensitivity and specificity. We reliably detected rearrangements of ALK, BCL2-IGH, BCR-ABL1 from lung adenocarcinoma, B-cell lymphoma, and chronic myeloid leukemia samples, respectively; indicating real clinical utility of this algorithm. In addition, our tool effectively detects other SV types - such as indels in FLT3 and KIT, among other genes. Our algorithm thus serves a pressing need for improved SV detection in targeted NGS data, particularly in precision cancer medicine.

Citation Format: Ryan P. Abo, Elizabeth P. Garcia, Matthew Ducar, Ravali Adusumilli, Marc Breneiser, Vanessa Rojas-Rudilla, Lynette M. Sholl, Neal I. Lindeman, Matthew L. Meyerson, William C. Hahn, Paul Van Hummelen, Laura E. MacConaill. BreaKmer: Detection of structural rearrangements in targeted next-generation sequencing data using kmers. [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 5321. doi:10.1158/1538-7445.AM2014-5321

Scalable transcriptional analysis routine--multiplexed quantitative real-time polymerase chain reaction platform for gene expression analysis and molecular diagnostics

We report the development of a new technology for simultaneous quantitative detection of multiple targets in a single sample. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. STAR demonstrated similar or better sensitivity and precision compared to two commonly used methods, SYBR Green-based and TaqMan probe-based real-time reverse transcriptase-polymerase chain reaction. STAR can be used as a flexible platform for building a variety of applications to monitor gene expression, from single gene assays to assays analyzing the expression level of multiple genes. Using severe acute respiratory syndrome (SARS) corona virus as a model system, STAR technology detected single copies of the viral genome in a two-gene multiplex. Blinded studies using RNA extracted from various tissues of a SARS-infected individual showed that STAR correctly identified all samples containing SARS virus and yielded negative results for non-SARS control samples. Using alternate priming strategies, STAR technology can be adapted to transcriptional profiling studies without requiring a priori sequence information. Thus, STAR technology offers a flexible platform for development of highly multiplexed assays in gene expression analysis and molecular diagnostics.

Calcium channel and NMDA receptor activities differentially regulate nuclear C/EBPbeta levels to control neuronal survival

Insulin-like growth factor-1 (IGF-1) promotes the survival of cerebellar granule neurons by enhancing calcium influx through L-type calcium channels, whereas NMDA receptor-mediated calcium influx can lead to excitotoxic death. Here we demonstrate that L and NMDA receptor channel activities differentially regulate the transcription factor C/EBPbeta to control neuronal survival. Specifically, we show that L channel-dependent calcium influx results in increased CaMKIV activity, which acts to decrease nuclear C/EBPbeta levels. Conversely, NMDA receptor-mediated influx rapidly elevates nuclear C/EBPbeta and induces excitotoxic death via activation of the calcium-dependent phosphatase, calcineurin. Moderate levels of AMPA receptor activity stimulate L channels to improve survival, whereas higher levels stimulate NMDA receptors and reduce neuronal survival, suggesting differential synaptic effects. Finally, N-type calcium channel activity reduces survival, potentially by increasing glutamate release. Together, these results show that the L-type calcium channel-dependent survival and NMDA receptor death pathways converge to regulate nuclear C/EBPbeta levels, which appears to be pivotal in these mechanisms.

Multiple trafficking signals regulate kainate receptor KA2 subunit surface expression

The kainate receptor subunit KA2 does not form functional homomeric channels despite its structural similarity to the functional glutamate receptor 5-7subunits and high agonist binding affinity in in vitro assays. In this study, we first demonstrate that homomeric KA2 receptors fail to reach the plasma membrane and then identify the molecular mechanisms preventing surface expression. Specifically, we show that KA2 subunits form homooligomeric receptors that are confined to the endoplasmic reticulum (ER). We then demonstrate that, in both heterologous expression systems and primary neurons, the intracellular retention of KA2 is not caused by subunit misfolding but, rather, is mediated through discrete protein trafficking signals, including an arginine-rich ER retention/retrieval motif and a di-leucine endocytic sequence in the C terminus of the KA2 subunit. Disruption of these motifs results in ER exit and surface expression of KA2 homomeric receptors that remain nonfunctional. Furthermore, our data suggest that the ER retention/retrieval signal in KA2 is sterically shielded during heteromeric assembly, allowing delivery of functional heteromeric receptors to the plasma membrane. Taken together, our results illustrate novel regulatory mechanisms that control the intracellular trafficking and surface expression of kainate receptors.

Allosteric regulation and spatial distribution of kainate receptors bound to ancillary proteins

A diverse range of accessory proteins regulates the behaviour of most ligand- and voltage-gated ion channels. For glutamate receptor 6 (GluR6) kainate receptors, two unrelated proteins, concanavalin-A (Con-A) and postsynaptic density protein 95 (PSD-95), bind to extra- and intracellular domains, respectively, but are reported to exert similar effects on GluR6 desensitization behaviour. We have tested the hypothesis that distinct allosteric binding sites control GluR6 receptors via a common transduction pathway. Rapid agonist application to excised patches revealed that neither Con-A nor PSD-95 affect the onset of desensitization. The rate of desensitization elicited by 10 mM L-glutamate was similar in control (taufast = 5.5 +/- 0.4 ms), Con-A-treated patches (taufast = 6.1 +/- 0.5 ms) and patches containing PSD-95 and GluR6 receptors (taufast = 4.7 +/- 0.6 ms). Likewise, the time course of recovery from GluR6 desensitization was similar in both control and Con-A conditions, whereas PSD-95 accelerated recovery almost twofold. Peak and steady-state (SS) dose-response relationships to glutamate were unchanged by lectin treatment (e.g. control, EC50(SS) = 31 +/- 28 microM vs Con-A, EC50(SS) = 45 +/- 9 microM, n = 6), suggesting that Con-A does not convert non-conducting channels with high agonist affinity into an open conformation. Instead, we demonstrate that the effects of Con-A on macroscopic responses reflect a shift in the relative contribution of different open states of the channel. In contrast, the effect of PSD-95 on recovery behaviour suggests that the association between kainate receptors and cytoskeletal proteins regulates signalling at glutamatergic synapses. Our results show that Con-A and PSD-95 regulate kainate receptors via distinct allosteric mechanisms targeting selective molecular steps in the transduction pathway.

The PDZ1 domain of SAP90. Characterization of structure and binding

The structural features of the PDZ1 domain of the synapse-associated protein SAP90 have been characterized by NMR. A comparison with the structures of the PDZ2 and PDZ3 domains of SAP90 illustrates significant differences, which may account for the unique binding properties of these homologous domains. Within the postsynaptic density, SAP90 functions as a molecular scaffold with a number of the protein-protein interactions mediated through the PDZ1 domain. Here, using fluorescence anisotropy and NMR chemical shift analysis, we have characterized the association of PDZ1 to the C-terminal peptides of the GluR6 subunit of the kainate receptor, voltage-gated K(+) channel Kv1.4, and microtubule-associate protein CRIPT, all of which are known to associate with SAP90. The latter two, which possess the consensus sequence for binding to PDZ domains (T/S-X-V-oh), have low micromolar binding affinities (1.5-15 microm). The C terminus of GluR6, RLPGKETMA-oh, lacking the consensus sequence, binds to PDZ1 of SAP90 with an affinity of 160 microm. The NMR data illustrate that although all three peptides occupy the binding groove capped by the GLGF loop of PDZ1, specific differences are present, consistent with the variation in binding affinities.

Kainate receptor activation induces mixed lineage kinase-mediated cellular signaling cascades via post-synaptic density protein 95

Kainate receptor glutamate receptor 6 (GluR6) subunit-deficient and c-Jun N-terminal kinase 3 (JNK3)-null mice share similar phenotypes including resistance to kainite-induced epileptic seizures and neuronal toxicity (Yang, D. D., Kuan, C-Y., Whitmarsh, A. J., Rincon, M., Zheng, T. S., Davis, R. J., Rakis, P., and Flavell, R. (1997) Nature 389, 865-869; Mulle, C., Seiler, A., Perez-Otano, I., Dickinson-Anson, H., Castillo, P. E., Bureau, I., Maron, C., Gage, F. H., Mann, J. R., Bettler, B., and Heinemmann, S. F. (1998) Nature 392, 601-605). This suggests that JNK activation may be involved in GluR6-mediated excitotoxicity. We provide evidence that post-synaptic density protein (PSD-95) links GluR6 to JNK activation by anchoring mixed lineage kinase (MLK) 2 or MLK3, upstream activators of JNKs, to the receptor complex. Association of MLK2 and MLK3 with PSD-95 in HN33 cells and rat brain preparations is dependent upon the SH3 domain of PSD-95, and expression of GluR6 in HN33 cells activated JNKs and induced neuronal apoptosis. Deletion of the PSD-95-binding site of GluR6 reduced both JNK activation and neuronal toxicity. Co-expression of dominant negative MLK2, MLK3, or mitogen-activated kinase kinase (MKK) 4 and MKK7 also significantly attenuated JNK activation and neuronal toxicity mediated by GluR6, and co-expression of PSD-95 with a deficient Src homology 3 domain also inhibited GluR6-induced JNK activation and neuronal toxicity. Our results suggest that PSD-95 plays a critical role in GluR6-mediated JNK activation and excitotoxicity by anchoring MLK to the receptor complex.

SAP90 binds and clusters kainate receptors causing incomplete desensitization

The mechanism of kainate receptor targeting and clustering is still unresolved. Here, we demonstrate that members of the SAP90/PSD-95 family colocalize and associate with kainate receptors. SAP90 and SAP102 coimmunoprecipitate with both KA2 and GluR6, but only SAP97 coimmunoprecipitates with GluR6. Similar to NMDA receptors, GluR6 clustering is mediated by the interaction of its C-terminal amino acid sequence, ETMA, with the PDZ1 domain of SAP90. In contrast, the KA2 C-terminal region binds to, and is clustered by, the SH3 and GK domains of SAP90. Finally, we show that SAP90 coexpressed with GluR6 or GluR6/KA2 receptors alters receptor function by reducing desensitization. These studies suggest that the organization and electrophysiological properties of synaptic kainate receptors are modified by association with members of the SAP90/PSD-95 family.

A presynaptic inositol-5-phosphatase

Synaptojanin is a nerve terminal protein of relative molecular mass 145,000 which appears to participate with dynamin in synaptic vesicle recycling. The central region of synaptojanin defines it as a member of the inositol-5-phosphatase family, which includes the product of the gene that is defective in the oculocerebrorenal syndrome of Lowe. Synaptojanin has 5-phosphatase activity and its amino-terminal domain is homologous with the yeast protein Sac1 (Rsd1), which is genetically implicated in phospholipid metabolism and in the function of the actin cytoskeleton. The carboxy terminus, which is of different lengths in adult and developing neurons owing to the alternative use of two termination sites, is proline-rich, consistent with the reported interaction of synaptojanin with the SH3 domains of Grb2 (refs 1, 2). Synaptojanin is the only other major brain protein besides dynamin that binds the SH3 domain of amphiphysin, a presynaptic protein with a putative function in endocytosis. Our results suggest a link between phosphoinositide metabolism and synaptic vesicle recycling.

v- and t-SNAREs in neuronal exocytosis: a need for additional components to define sites of release

Synaptic vesicle recycling is a specialized form of membrane recycling which takes place in all cells between early endosomes and the plasmalemma. Synaptic vesicles exocytosis is highly regulated and occurs only at presynaptic active zones. In contrast, exocytosis of endosome-derived vesicles of the housekeeping recycling pathway takes place constitutively and throughout the cell surface. Since v- and t-SNAREs play a key role in membrane interactions leading to fusion, unique v- and t-SNAREs may be implicated in synaptic vesicle exocytosis. It was found, however, that the same v-SNAREs of the synaptobrevin family are found both on synaptic vesicles and on endosome-derived vesicles which undergo constitutive fusion. Likewise, t-SNAREs which act as plasmalemmal receptors for synaptic vesicles are not restricted to synaptic active zones. Thus, v- and t-SNAREs interactions may define which organelles can fuse with the plasmalemma, but require additional components to define properties of the exocytotic reaction which are specific for distinct classes of secretory organelles.

rbSec1A and B colocalize with syntaxin 1 and SNAP-25 throughout the axon, but are not in a stable complex with syntaxin

rbSec1 is a mammalian neuronal protein homologous to the yeast SEC1 gene product which is required for exocytosis. Mutations in Sec1 homologues in the nervous systems of C. elegans and D. melanogaster lead to defective neurotransmitter secretion. Biochemical studies have shown that recombinant rbSec1 binds syntaxin 1 but not SNAP-25 or synaptobrevin/VAMP, the two proteins which together with syntaxin 1 form the synaptic SNARE complex. In this study we have examined the subcellular localization of rbSec1 and the degree of interaction between rbSec1 and syntaxin 1 in situ. rbSec1, which we show here to be represented by two alternatively spliced isoforms, rbSec1A and B, has a widespread distribution in the axon and is not restricted to the nerve terminal. This distribution parallels the localization of syntaxin 1 and SNAP-25 along the entire axonal plasmalemma. rbSec1 is found in a soluble and a membrane-associated form. Although a pool of rbSec1 is present on the plasmalemma, the majority of membrane-bound rbSec1 is not associated with syntaxin 1. We also show that rbSec1 is not part of the synaptic SNARE complex or of the syntaxin 1/SNAP-25 complex we show to be present in non-synaptic regions of the axon. Thus, in spite of biochemical studies demonstrating the high affinity interaction of rbSec1 and syntaxin 1, our results indicate that rbSec1 and syntaxin 1 are not stably associated. They also suggest that the function of rbSec1, syntaxin 1, and SNAP-25 is not restricted to synaptic vesicle exocytosis at the synapse.

A rat brain Sec1 homologue related to Rop and UNC18 interacts with syntaxin

Sec1 is a hydrophilic protein that plays an essential role in exocytosis from the yeast Saccharomyces cerevisiae. Two high copy suppressors of mutations in the Sec1 gene, SSO1 and SSO2, were recently identified that encode proteins of the syntaxin family. Syntaxin (a T-SNARE), together with SNAP-25 and synaptobrevin/VAMP (a T- and a V-SNARE, respectively), is thought to form the core of the docking-fusion complex in synaptic vesicle exocytosis. Proteins that exhibit similarity to Sec1 were identified in the nervous system of Drosophila melanogaster (Rop) and Caenorhabditis elegans (UNC18). Based on the amino acid sequence alignment of Sec1, Rop, and UNC18, we have used a PCR-based approach to isolate a rat brain cDNA encoding a Sec1 homologue. The cDNA hybridizes to a 3.5-kb brain-specific mRNA by Northern blot analysis and encodes a protein of 593 amino acids (rbSec1). Antibodies raised against a central portion of rbSec1 recognize a 67.5-kDa protein in total homogenates of rat brain but not of nonneuronal tissues. When incubated with a Triton X-100 brain extract, rbSec1-glutathione S-transferase (GST) fusion protein, but not GST protein alone, specifically interacts with syntaxin but not with SNAP-25 or synaptobrevin/VAMP. We conclude that the function of proteins of the Sec1 family in membrane fusion involves an interaction with a T-SNARE.

Influence of major histocompatibility complex class I, class II and TLA genes on tumor rejection

T lymphocytes recognize antigen associated with MHC class I and/or class II gene products. Recognition of malignant cells is therefore dependent on presentation of tumor associated antigen(s) by MHC molecules. We have studied immunity to tumors that have down-regulated class I expression. These studies demonstrate a requirement for class I antigens, but suggest that additional factors may also be required for tumor-specific immunity. The MHC also encodes TLA class I antigens, whose function is unknown. Our studies suggest that these molecules function is unknown. Our studies suggest that T lymphocytes, specifically in tumor cells that do not express H-2K or H-2D moieties. Other studies are aimed at improving tumor-specific Th cell generation by producing class II+ tumor cells. The success of these experiments indicates that this approach may be a potentially useful immunotherapy.

Embryonal carcinoma cells express Qa and Tla class I genes of the major histocompatibility complex

The murine major histocompatibility complex encodes H-2K and H-2D transplantation antigens and other class I-like proteins called Qa and Tla molecules; the functions of the Qa/Tla molecules are not known. That they may participate in embryonic cell-cell interactions and/or play a role in immune responses against tumors has been speculated. We have studied two murine embryonal carcinoma tumors, 402AX and PCC4, that are rejected in vivo immunologically, although they do not express H-2K or H-2D antigens. Transplantation studies with these cells suggest that rejection is mediated by class-I-like major histocompatibility complex antigens. As a first step in evaluating Qa/Tla function(s), we have characterized expression of class I-like genes and proteins in 402AX and PCC4 cells. Northern (RNA) blot hybridizations, polymerase chain reaction studies, and cDNA cloning experiments demonstrate that EC lines transcribe genes allelic to the Tla region gene "37", Qa-2 region gene "Q7", and another, previously uncharacterized, class I-like gene. Immunoprecipitation studies show that the embryonal carcinoma tumor cells contain low levels of beta 2-microglobulin expressed in association with non-H-2K, non-H-2D class I-like proteins.

Allogeneic H-2 antigen expression is insufficient for tumor rejection

Murine A strain (KkDdLd) sarcoma I (SaI) tumor cells have been transfected with a cloned H-2Kb gene. The resulting clones (SKB clones) stably express high levels of a molecule that is serologically and biochemically indistinguishable from the H-2Kb antigen. SKB clones are not susceptible to cytotoxic T lymphocyte-mediated lysis by H-2Kb-specific bulk, cloned, or H-2Kb-restricted lymphocytic choriomeningitis virus-specific effectors. Survival times of A/J and B10.A mice challenged i.p. with the H-2Kb-expressing transfectants and the parental SaI cells are similar, suggesting that the presence of an allogeneic major histocompatibility complex class I antigen on the surface of this tumor line is insufficient for tumor rejection.

Transperitoneal conversion of the ureter after Wertheim's operation with lymphadenectomy

The incidence of ureteral fistula occurring after Wertheim's operation with lymphadenectomy, performed at our Department since 1953, has been high. Therefore, in 1970, a new procedure (a modification of the technique proposed by Novak) was attempted: the peritoneal flaps were used to cover the pelvic wall, which was previously completely cleaned to assure total lymphadenectomy. Thus a new bed is provided for the isolated ureter, which is prevented from falling into the retroperitoneal space. One hundred and thirty-three cases were operated on according to this technique and the incidence of ureteral fistulas fell from 10 to 0.75 per cent. Intravenous urographies taken two, six and ten months after the operation showed good results. All patients in this series who underwent this operation had previously had irradiation.