Characterization of tumor evolution by functional clonality and phylogenetics in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a molecularly heterogeneous solid malignancy, and its fitness may be shaped by how its tumor cells evolve. However, ability to monitor tumor cell evolution is hampered by the presence of numerous passenger mutations that do not provide any biological consequences. Here we develop a strategy to determine the tumor clonality of three independent HCC cohorts of 524 patients with diverse etiologies and race/ethnicity by utilizing somatic mutations in cancer driver genes. We identify two main types of tumor evolution, i.e., linear, and non-linear models where non-linear type could be further divided into classes, which we call shallow branching and deep branching. We find that linear evolving HCC is less aggressive than other types. GTF2IRD2B mutations are enriched in HCC with linear evolution, while TP53 mutations are the most frequent genetic alterations in HCC with non-linear models. Furthermore, we observe significant B cell enrichment in linear trees compared to non-linear trees suggesting the need for further research to uncover potential variations in immune cell types within genomically determined phylogeny types. These results hint at the possibility that tumor cells and their microenvironment may collectively influence the tumor evolution process.

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvements in germline SV detection. However, current long-read SV detection methods do not generalize well to the analysis of somatic SVs in tumor genomes with complex rearrangements, heterogeneity, and aneuploidy. Here, we present Severus: a method for the accurate detection of different types of somatic SVs using a phased breakpoint graph approach. To benchmark various short- and long-read SV detection methods, we sequenced five tumor/normal cell line pairs with Illumina, Nanopore, and PacBio sequencing platforms; on this benchmark Severus showed the highest F1 scores (harmonic mean of the precision and recall) as compared to long-read and short-read methods. We then applied Severus to three clinical cases of pediatric cancer, demonstrating concordance with known genetic findings as well as revealing clinically relevant cryptic rearrangements missed by standard genomic panels.

UGDH promotes tumor-initiating cells and a fibroinflammatory tumor microenvironment in ovarian cancer

BACKGROUND

Epithelial ovarian cancer (EOC) is a global health burden, with the poorest five-year survival rate of the gynecological malignancies due to diagnosis at advanced stage and high recurrence rate. Recurrence in EOC is driven by the survival of chemoresistant, stem-like tumor-initiating cells (TICs) that are supported by a complex extracellular matrix and immunosuppressive microenvironment. To target TICs to prevent recurrence, we identified genes critical for TIC viability from a whole genome siRNA screen. A top hit was the cancer-associated, proteoglycan subunit synthesis enzyme UDP-glucose dehydrogenase (UGDH).

METHODS

Immunohistochemistry was used to characterize UGDH expression in histological and molecular subtypes of EOC. EOC cell lines were subtyped according to the molecular subtypes and the functional effects of modulating UGDH expression in vitro and in vivo in C1/Mesenchymal and C4/Differentiated subtype cell lines was examined.

RESULTS

High UGDH expression was observed in high-grade serous ovarian cancers and a distinctive survival prognostic for UGDH expression was revealed when serous cancers were stratified by molecular subtype. High UGDH was associated with a poor prognosis in the C1/Mesenchymal subtype and low UGDH was associated with poor prognosis in the C4/Differentiated subtype. Knockdown of UGDH in the C1/mesenchymal molecular subtype reduced spheroid formation and viability and reduced the CD133 + /ALDH high TIC population. Conversely, overexpression of UGDH in the C4/Differentiated subtype reduced the TIC population. In co-culture models, UGDH expression in spheroids affected the gene expression of mesothelial cells causing changes to matrix remodeling proteins, and fibroblast collagen production. Inflammatory cytokine expression of spheroids was altered by UGDH expression. The effect of UGDH knockdown or overexpression in the C1/ Mesenchymal and C4/Differentiated subtypes respectively was tested on mouse intrabursal xenografts and showed dynamic changes to the tumor stroma. Knockdown of UGDH improved survival and reduced tumor burden in C1/Mesenchymal compared to controls.

CONCLUSIONS

These data show that modulation of UGDH expression in ovarian cancer reveals distinct roles for UGDH in the C1/Mesenchymal and C4/Differentiated molecular subtypes of EOC, influencing the tumor microenvironmental composition. UGDH is a strong potential therapeutic target in TICs, for the treatment of EOC, particularly in patients with the mesenchymal molecular subtype.

Tumor biology and immune infiltration define primary liver cancer subsets linked to overall survival after immunotherapy

Primary liver cancer is a rising cause of cancer deaths in the US. Although immunotherapy with immune checkpoint inhibitors induces a potent response in a subset of patients, response rates vary among individuals. Predicting which patients will respond to immune checkpoint inhibitors is of great interest in the field. In a retrospective arm of the National Cancer Institute Cancers of the Liver: Accelerating Research of Immunotherapy by a Transdisciplinary Network (NCI-CLARITY) study, we use archived formalin-fixed, paraffin-embedded samples to profile the transcriptome and genomic alterations among 86 hepatocellular carcinoma and cholangiocarcinoma patients prior to and following immune checkpoint inhibitor treatment. Using supervised and unsupervised approaches, we identify stable molecular subtypes linked to overall survival and distinguished by two axes of aggressive tumor biology and microenvironmental features. Moreover, molecular responses to immune checkpoint inhibitor treatment differ between subtypes. Thus, patients with heterogeneous liver cancer may be stratified by molecular status indicative of treatment response to immune checkpoint inhibitors.

NF-κB Signaling Modulates miR-452-5p and miR-335-5p Expression to Functionally Decrease Epithelial Ovarian Cancer Progression in Tumor-Initiating Cells

Epithelial ovarian cancer (EOC) remains the fifth leading cause of cancer-related death in women worldwide, partly due to the survival of chemoresistant, stem-like tumor-initiating cells (TICs) that promote disease relapse. We previously described a role for the NF-κB pathway in promoting TIC chemoresistance and survival through NF-κB transcription factors (TFs) RelA and RelB, which regulate genes important for the inflammatory response and those associated with cancer, including microRNAs (miRNAs). We hypothesized that NF-κB signaling differentially regulates miRNA expression through RelA and RelB to support TIC persistence. Inducible shRNA was stably expressed in OV90 cells to knockdown RELA or RELB; miR-seq analyses identified differentially expressed miRNAs hsa-miR-452-5p and hsa-miR-335-5p in cells grown in TIC versus adherent conditions. We validated the miR-seq findings via qPCR in TIC or adherent conditions with RELA or RELB knocked-down. We confirmed decreased expression of hsa-miR-452-5p when either RELA or RELB were depleted and increased expression of hsa-miR-335-5p when RELA was depleted. Either inhibiting miR-452-5p or mimicking miR-335-5p functionally decreased the stem-like potential of the TICs. These results highlight a novel role of NF-κB TFs in modulating miRNA expression in EOC cells, thus opening a better understanding toward preventing recurrence of EOC.

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies

BACKGROUND

The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples.

RESULTS

We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy.

CONCLUSIONS

A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.

Implementation of ensemble machine learning algorithms on exome datasets for predicting early diagnosis of cancers

Classification of different cancer types is an essential step in designing a decision support model for early cancer predictions. Using various machine learning (ML) techniques with ensemble learning is one such method used for classifications. In the present study, various ML algorithms were explored on twenty exome datasets, belonging to 5 cancer types. Initially, a data clean-up was carried out on 4181 variants of cancer with 88 features, and a derivative dataset was obtained using natural language processing and probabilistic distribution. An exploratory dataset analysis using principal component analysis was then performed in 1 and 2D axes to reduce the high-dimensionality of the data. To significantly reduce the imbalance in the derivative dataset, oversampling was carried out using SMOTE. Further, classification algorithms such as K-nearest neighbour and support vector machine were used initially on the oversampled dataset. A 4-layer artificial neural network model with 1D batch normalization was also designed to improve the model accuracy. Ensemble ML techniques such as bagging along with using KNN, SVM and MLPs as base classifiers to improve the weighted average performance metrics of the model. However, due to small sample size, model improvement was challenging. Therefore, a novel method to augment the sample size using generative adversarial network (GAN) and triplet based variational auto encoder (TVAE) was employed that reconstructed the features and labels generating the data. The results showed that from initial scrutiny, KNN showed a weighted average of 0.74 and SVM 0.76. Oversampling ensured that the accuracy of the derivative dataset improved significantly and the ensemble classifier augmented the accuracy to 82.91%, when the data was divided into 70:15:15 ratio (training, test and holdout datasets). The overall evaluation metric value when GAN and TVAE increased the sample size was found to be 0.92 with an overall comparison model of 0.66. Therefore, the present study designed an effective model for classifying cancers which when implemented to real world samples, will play a major role in early cancer diagnosis.

Abstract 1339: Interleukin 4 Producing CD4 T cells initiate a crucial event for lung cancer development

Lung cancer remains one of the leading causes of mortality of cancer patients. Kinase-dead Ikkα knock-in (KA/KA) mice develop CD4 T cell-derived autoimmune disease. Previously, we reported spontaneous lung squamous cell carcinoma (SCC) associated with increase macrophage and CD4 T cell numbers in KA/KA mice. Depleting macrophages dampens lung SCC development in KA/KA mice, but a lot of CD4 T cells remain in the lungs. The activity of CD4 T cells in lung SCC development is unknown. In this study, we attempted to investigate the role of CD4 T cells in lung SCC development. We performed adoptive CD4 T cell transfer experiment and found that KA/KA CD4 T cell transfer, not WT CD4 T cells, recruited marked macrophages to the lungs and induced lung SCC in KA/KA;Rag1-/- mice. The CD4 T cells isolated from the lungs of KA/KA mice and KA/KA;Rag1-/- mice with KA/KA CD4 T cell transfer expressed elevated PD-1, IL-4, IL-5, Il-13, and Il-21 levels compared to WT mice. We found that Il4 ablation, not Il5 deletion, reduced macrophage recruitment and blocked SCC development in KA/KA;Il4-/- mice as well as unlike KA/KA CD4 T cells, KA/KA;Il4-/- CD4 T cells did not induce spontaneous lung SCC in KA/KA;Rag1-/- mice with KA/KA;Il4-/- CD4 T cell injections. Taken together, the finding highlights a pathogenic role of IL-4-producing CD4 T cells in lung carcinogenesis.

Citation Format: Gajendra Jogdand, Sayantan Banerjee, Gongping Shi, Jami Willet Brown, Amit Singh, Yongmei Zhao, Jyoti Shetty, Bao Tran, Yinling Hu. Interleukin 4 Producing CD4 T cells initiate a crucial event for lung cancer development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1339.

Proteasome inhibition alters mitotic progression through the upregulation of centromeric α-Satellite RNAs

Cell cycle progression requires control of the abundance of several proteins and RNAs over space and time to properly transit from one phase to the next and to ensure faithful genomic inheritance in daughter cells. The proteasome, the main protein degradation system of the cell, facilitates the establishment of a proteome specific to each phase of the cell cycle. Its activity also strongly influences transcription. Here, we detected the upregulation of repetitive RNAs upon proteasome inhibition in human cancer cells using RNA‐seq. The effect of proteasome inhibition on centromeres was remarkable, especially on α‐Satellite RNAs. We showed that α‐Satellite RNAs fluctuate along the cell cycle and interact with members of the cohesin ring, suggesting that these transcripts may take part in the regulation of mitotic progression. Next, we forced exogenous overexpression and used gapmer oligonucleotide targeting to demonstrate that α‐Sat RNAs have regulatory roles in mitosis. Finally, we explored the transcriptional regulation of α‐Satellite DNA. Through in silico analyses, we detected the presence of CCAAT transcription factor‐binding motifs within α‐Satellite centromeric arrays. Using high‐resolution three‐dimensional immuno‐FISH and ChIP‐qPCR, we showed an association between the α‐Satellite upregulation and the recruitment of the transcription factor NFY‐A to the centromere upon MG132‐induced proteasome inhibition. Together, our results show that the proteasome controls α‐Satellite RNAs associated with the regulation of mitosis.

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.

Abstract 224: Evaluation of next generation sequencing of DNA and RNA from archival formalin-fixed, paraffin-embedded pancreatic cancer tissue: A pilot study of the SEER-linked virtual tissue repository

As formalin-fixed, paraffin-embedded (FFPE) tissue is being utilized for next-generation sequencing (NGS) in research and clinical settings, we conducted a study through the Surveillance, Epidemiology and End Results (SEER)-Linked Virtual Tissue Repository (VTR) Pilot Program to determine the quality of sequencing data obtained using FFPE-derived DNA and RNA. Forty-eight pancreatic ductal adenocarcinoma (PDAC) patients, comprising 24 case-control pairs based on survival time (≥5 years [cases] vs <24 months [controls]), were selected. Participating SEER registries obtained selected diagnostic tissue blocks collected clinically and stored for 4-18 years. DNA and RNA were extracted from the FFPE specimens for 36 patients (18 pairs). Whole genome (WGS) and whole exome sequencing (WES) were performed on tumor and normal DNA from 16 patients, and a methylation array was conducted on tumor DNA from 6 of these patients. RNA-Seq was conducted on tumor RNA from 36 patients. The median coverage depths for tumor were above 300x for WES and 60x for WGS. However, the majority of sequencing reads (>60%) were duplicates. Concordant mutations (SNVs, MNVs and indels) were >50% by WGS and WES from the majority of samples (n=11, 69%), and the most common discordant mutations were C>T. On average, mutant allele frequencies (MAFs) were 20% in coding regions and 15% across the whole genome, consistent with tumor content as measured by methylation analysis for five tumor samples (18%, 22%, 28%, 42%, and 50%). WES and/or WGS revealed that specimens for five of 27 PDAC subjects tested had a high fraction of variants overlapping with germline variants in dbSNP (≥20%), indicating that tumor cellularity was low among these samples. TP53, KRAS, CDKN2A, SMAD4, and RNF43 were the most frequently mutated genes from these specimens, consistent with genes reported in studies using fresh frozen tissue. Point mutations comprised most of the gene variants, and indels were found in CDKN2A, SMAD4, and RNF43. Most of the mutation status (e.g. missense, nonsense or indels) were concordantly called by WES and WGS (e.g., 81% for TP53, 100% CDKN2A, 94% SMAD4, and 94% RNF43). Most discordant calls were mutations identified by WES but not WGS (e.g., 8 [50%] for KRAS and 3 [19%] TP53). All samples yielded RNA-Seq reads with <30% exonic mapping, 39% (14) of which had <10% exonic mapping. Our study provided important evidence for NGS applications on DNA and RNA from archival PDAC FFPE tissue specimens stored for up to 18 years. These findings demonstrate that, with sufficient tumor content and coverage depth, FFPE-derived DNA is adequate for identifying somatic driver gene mutations in PDAC patients and that the it is feasible to utilize the population-based, SEER-Linked VTR as an infrastructure for obtaining diagnostic tissue for molecular studies.

Citation Format: Yao Yuan, Alison Van Dyke, Valentina Petkov, Alyssa Tuan, Aatur Singhi, Lynn Matrisian, Lola Rahib, John Pearson, Katia Nones, Nicola Waddell, Yongmei Zhao, Tsai-wei Shen, Bao Tran, Jyoti Shetty, Elizabeth Gillanders, Danielle Carrick, Rosemary Cress, Lloyd Mueller, Brenda Hernandez, Charles Lynch, Thomas Tucker, Xiao-Cheng Wu, Lynne Penberthy. Evaluation of next generation sequencing of DNA and RNA from archival formalin-fixed, paraffin-embedded pancreatic cancer tissue: A pilot study of the SEER-linked virtual tissue repository [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 224.

Drugs Targeting Tumor-Initiating Cells Prolong Survival in a Post-Surgery, Post-Chemotherapy Ovarian Cancer Relapse Model

Disease recurrence is the major cause of morbidity and mortality of ovarian cancer (OC). In terms of maintenance therapies after platinum-based chemotherapy, PARP inhibitors significantly improve the overall survival of patients with BRCA mutations but is of little benefit to patients without homologous recombination deficiency (HRD). The stem-like tumor-initiating cell (TIC) population within OC tumors are thought to contribute to disease recurrence and chemoresistance. Therefore, there is a need to identify drugs that target TICs to prevent relapse in OC without HRD. RNA sequencing analysis of OC cells grown in TIC conditions revealed a strong enrichment of genes involved in drug metabolism, oxidative phosphorylation and reactive oxygen species (ROS) pathways. Concurrently, a high-throughput drug screen identified drugs that showed efficacy against OC cells grown as TICs compared to adherent cells. Four drugs were chosen that affected drug metabolism and ROS response: disulfiram, bardoxolone methyl, elesclomol and salinomycin. The drugs were tested in vitro for effects on viability, sphere formation and markers of stemness CD133 and ALDH in TICs compared to adherent cells. The compounds promoted ROS accumulation and oxidative stress and disulfiram, elesclomol and salinomycin increased cell death following carboplatin treatment compared to carboplatin alone. Disulfiram and salinomycin were effective in a post-surgery, post-chemotherapy OC relapse model in vivo, demonstrating that enhancing oxidative stress in TICs can prevent OC recurrence.

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Gene expression analysis by RNA sequencing (RNA-seq) enables unique insights into clinical samples that can potentially lead to mechanistic understanding of the basis of various diseases as well as resistance and/or susceptibility mechanisms. However, FFPE tissues, which represent the most common method for preserving tissue morphology in clinical specimens, are not the best sources for gene expression profiling analysis. The RNA obtained from such samples is often degraded, fragmented, and chemically modified, which leads to suboptimal sequencing libraries. In turn, these generate poor quality sequence data that may not be reliable for gene expression analysis and mutation discovery. In order to make the most of FFPE samples and obtain the best possible data from low quality samples, it is important to take certain precautions while planning experimental design, preparing sequencing libraries, and during data analysis. This includes the use of appropriate metrics for precise sample quality control (QC), identifying the best methods for various steps during the sequencing library generation, and careful library QC. In addition, applying correct software tools and parameters for sequence data analysis is critical in order to identify artifacts in RNA-seq data, filter out contamination and low quality reads, assess uniformity of gene coverage, and measure the reproducibility of gene expression profiles among biological replicates. These steps can ensure high accuracy and reproducibility for profiling of very heterogeneous RNA samples. Here we describe the various steps for sample QC, library preparation and QC, sequencing, and data analysis that can help to increase the amount of useful data obtained from low quality RNA, such as that obtained from FFPE-RNA tissues.

Durvalumab with or without tremelimumab in patients with recurrent or metastatic head and neck squamous cell carcinoma: EAGLE, a randomized, open-label phase III study

BACKGROUND

Targeting the programmed cell death protein 1 (PD-1)/programmed cell death ligand 1 (PD-L1) axis has demonstrated clinical benefit in recurrent/metastatic head and neck squamous cell carcinoma (R/M HNSCC). Combining immunotherapies targeting PD-L1 and cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) has shown evidence of additive activity in several tumor types. This phase III study evaluated the efficacy of durvalumab (an anti-PD-L1 monoclonal antibody) or durvalumab plus tremelimumab (an anti-CTLA-4 monoclonal antibody) versus standard of care (SoC) in R/M HNSCC patients.

PATIENTS AND METHODS

Patients were randomly assigned to receive 1 : 1 : 1 durvalumab (10 mg/kg every 2 weeks [q2w]), durvalumab plus tremelimumab (durvalumab 20 mg/kg q4w plus tremelimumab 1 mg/kg q4w × 4, then durvalumab 10 mg/kg q2w), or SoC (cetuximab, a taxane, methotrexate, or a fluoropyrimidine). The primary end points were overall survival (OS) for durvalumab versus SoC, and OS for durvalumab plus tremelimumab versus SoC. Secondary end points included progression-free survival (PFS), objective response rate, and duration of response.

RESULTS

Patients were randomly assigned to receive durvalumab (n = 240), durvalumab plus tremelimumab (n = 247), or SoC (n = 249). No statistically significant improvements in OS were observed for durvalumab versus SoC [hazard ratio (HR): 0.88; 95% confidence interval (CI): 0.72-1.08; P = 0.20] or durvalumab plus tremelimumab versus SoC (HR: 1.04; 95% CI: 0.85-1.26; P = 0.76). The 12-month survival rates (95% CI) were 37.0% (30.9-43.1), 30.4% (24.7-36.3), and 30.5% (24.7-36.4) for durvalumab, durvalumab plus tremelimumab, and SoC, respectively. Treatment-related adverse events (trAEs) were consistent with previous reports. The most common trAEs (any grade) were hypothyroidism for durvalumab and durvalumab plus tremelimumab (11.4% and 12.2%, respectively), and anemia (17.5%) for SoC. Grade ≥3 trAE rates were 10.1%, 16.3%, and 24.2% for durvalumab, durvalumab plus tremelimumab, and SoC, respectively.

CONCLUSION

There were no statistically significant differences in OS for durvalumab or durvalumab plus tremelimumab versus SoC. However, higher survival rates at 12 to 24 months and response rates demonstrate clinical activity for durvalumab.

TRIAL REGISTRATION

ClinicalTrials.gov: NCT02369874.

A Thpok-Directed Transcriptional Circuitry Promotes Bcl6 and Maf Expression to Orchestrate T Follicular Helper Differentiation

The generation of high-affinity neutralizing antibodies, the objective of most vaccine strategies, occurs in B cells within germinal centers (GCs) and requires rate-limiting "help" from follicular helper CD4⁺ T (Tfh) cells. Although Tfh differentiation is an attribute of MHC II-restricted CD4⁺ T cells, the transcription factors driving Tfh differentiation, notably Bcl6, are not restricted to CD4⁺ T cells. Here, we identified a requirement for the CD4⁺-specific transcription factor Thpok during Tfh cell differentiation, GC formation, and antibody maturation. Thpok promoted Bcl6 expression and bound to a Thpok-responsive region in the first intron of Bcl6. Thpok also promoted the expression of Bcl6-independent genes, including the transcription factor Maf, which cooperated with Bcl6 to mediate the effect of Thpok on Tfh cell differentiation. Our findings identify a transcriptional program that links the CD4⁺ lineage with Tfh differentiation, a limiting factor for efficient B cell responses, and suggest avenues to optimize vaccine generation.

Clinical deterioration despite syringomyelia resolution after successful foramen magnum decompression for Chiari malformation - Case series

INTRODUCTION

Neurosurgical treatment is recommended for symptomatic syringomyelia and the post-operative radiological resolution of the syringomyelia is associated with an improvement or at least stability of the patient's pre-operative symptoms.

METHODS

We reviewed syringomyelia treatment in our centre over the last five years for clinical outcome, surgical complications, post operative MRI and long term symptom resolution.

RESULTS

50 cases of symptomatic syringomyelia underwent foramen magnum decompression and expansile watertight duroplasty. While the outcomes for majority are similar to what published in literature, three of them developed typical syringomyelia symptoms after initial good recovery and radiological resolution of syrinx.

CONCLUSION

Syringomyelia symptoms may appear or worsen following successful surgical treatment and radiological resolution of syrinx and it is important to counsel young people and their family regarding this.

Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies

Background: Trichoplusia ni derived cell lines are commonly used to enable recombinant protein expression via baculovirus infection to generate materials approved for clinical use and in clinical trials. In order to develop systems biology and genome engineering tools to improve protein expression in this host, we performed de novo genome assembly of the Trichoplusia ni-derived cell line Tni-FNL. Methods: By integration of PacBio single-molecule sequencing, Bionano optical mapping, and 10X Genomics linked-reads data, we have produced a draft genome assembly of Tni-FNL. Results: Our assembly contains 280 scaffolds, with a N50 scaffold size of 2.3 Mb and a total length of 359 Mb. Annotation of the Tni-FNL genome resulted in 14,101 predicted genes and 93.2% of the predicted proteome contained recognizable protein domains. Ortholog searches within the superorder Holometabola provided further evidence of high accuracy and completeness of the Tni-FNL genome assembly. Conclusions: This first draft Tni-FNL genome assembly was enabled by complementary long-read technologies and represents a high-quality, well-annotated genome that provides novel insight into the complexity of this insect cell line and can serve as a reference for future large-scale genome engineering work in this and other similar recombinant protein production hosts.

Single-cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma

Intratumor molecular heterogeneity of hepatocellular carcinoma is partly attributed to the presence of hepatic cancer stem cells (CSCs). Different CSC populations defined by various cell surface markers may contain different oncogenic drivers, posing a challenge in defining molecularly targeted therapeutics. We combined transcriptomic and functional analyses of hepatocellular carcinoma cells at the single-cell level to assess the degree of CSC heterogeneity. We provide evidence that hepatic CSCs at the single-cell level are phenotypically, functionally, and transcriptomically heterogeneous. We found that different CSC subpopulations contain distinct molecular signatures. Interestingly, distinct genes within different CSC subpopulations are independently associated with hepatocellular carcinoma prognosis, suggesting that a diverse hepatic CSC transcriptome affects intratumor heterogeneity and tumor progression.

CONCLUSION

Our work provides unique perspectives into the biodiversity of CSC subpopulations, whose molecular heterogeneity further highlights their role in tumor heterogeneity, prognosis, and hepatic CSC therapy. (Hepatology 2018;68:127-140).

Efficiency of fenofibrate in facilitating the reduction of central macular thickness in diabetic macular edema

PURPOSE

The purpose of this study is to study the benefit of addition of oral fenofibrate to the current regimen of diabetic macular edema (DME) management and quantify its effect on macular thickness and visual function in DME.

METHODS

Fifty-three eyes of 50 patients were randomized into treatment (Group A) (oral fenofibrate 160 mg/day) and control groups (Group B). Both groups underwent treatment of DME as per the standard treatment protocol of our hospital including intravitreal injections (anti-vascular endothelial growth factor/steroid) and grid laser. Patients were followed up every 2 months to note the visual acuity and central macular thickness (CMT) for 6 months.

RESULTS

Our groups were matched with respect to age (P = 0.802), mean diabetic age (P = 0.878), serum HbA1C levels (P = 0.523), and serum triglyceride levels (P = 0.793). The mean reduction in CMT was 136 μ in Group A and 83 μ in Group B at the end of 6 months. This difference was statistically significant (P = 0.031). Visual acuity improvement was 0.15 in Group A and 0.11 in Group B at the end of 6 months (P = 0.186). On subgroup analysis in Group A, we found that there was no difference in reduction of CMT between hypertensives and normotensives (P = 0.916), in patients with normal triglyceride levels and increased triglyceride levels (P = 0.975).

CONCLUSION

Addition of fenofibrate to the standard protocol of DME management seems to facilitate reduction of CMT and probably have an added benefit on the visual functions.

Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma

BACKGROUND

Diffuse large B-cell lymphomas (DLBCLs) are phenotypically and genetically heterogeneous. Gene-expression profiling has identified subgroups of DLBCL (activated B-cell-like [ABC], germinal-center B-cell-like [GCB], and unclassified) according to cell of origin that are associated with a differential response to chemotherapy and targeted agents. We sought to extend these findings by identifying genetic subtypes of DLBCL based on shared genomic abnormalities and to uncover therapeutic vulnerabilities based on tumor genetics.

METHODS

We studied 574 DLBCL biopsy samples using exome and transcriptome sequencing, array-based DNA copy-number analysis, and targeted amplicon resequencing of 372 genes to identify genes with recurrent aberrations. We developed and implemented an algorithm to discover genetic subtypes based on the co-occurrence of genetic alterations.

RESULTS

We identified four prominent genetic subtypes in DLBCL, termed MCD (based on the co-occurrence of MYD88L265P and CD79B mutations), BN2 (based on BCL6 fusions and NOTCH2 mutations), N1 (based on NOTCH1 mutations), and EZB (based on EZH2 mutations and BCL2 translocations). Genetic aberrations in multiple genes distinguished each genetic subtype from other DLBCLs. These subtypes differed phenotypically, as judged by differences in gene-expression signatures and responses to immunochemotherapy, with favorable survival in the BN2 and EZB subtypes and inferior outcomes in the MCD and N1 subtypes. Analysis of genetic pathways suggested that MCD and BN2 DLBCLs rely on "chronic active" B-cell receptor signaling that is amenable to therapeutic inhibition.

CONCLUSIONS

We uncovered genetic subtypes of DLBCL with distinct genotypic, epigenetic, and clinical characteristics, providing a potential nosology for precision-medicine strategies in DLBCL. (Funded by the Intramural Research Program of the National Institutes of Health and others.).

ONC201 kills breast cancer cells in vitro by targeting mitochondria

We report a novel mechanism of action of ONC201 as a mitochondria-targeting drug in cancer cells. ONC201 was originally identified as a small molecule that induces transcription of TNF-related apoptosis-inducing ligand (TRAIL) and subsequently kills cancer cells by activating TRAIL death receptors. In this study, we examined ONC201 toxicity on multiple human breast and endometrial cancer cell lines. ONC201 attenuated cell viability in all cancer cell lines tested. Unexpectedly, ONC201 toxicity was not dependent on either TRAIL receptors nor caspases. Time-lapse live cell imaging revealed that ONC201 induces cell membrane ballooning followed by rupture, distinct from the morphology of cells undergoing apoptosis. Further investigation found that ONC201 induces phosphorylation of AMP-dependent kinase and ATP loss. Cytotoxicity and ATP depletion were significantly enhanced in the absence of glucose, suggesting that ONC201 targets mitochondrial respiration. Further analysis indicated that ONC201 indirectly inhibits mitochondrial respiration. Confocal and electron microscopic analysis demonstrated that ONC201 triggers mitochondrial structural damage and functional impairment. Moreover, ONC201 decreased mitochondrial DNA (mtDNA). RNAseq analysis revealed that ONC201 suppresses expression of multiple mtDNA-encoded genes and nuclear-encoded mitochondrial genes involved in oxidative phosphorylation and other mitochondrial functions. Importantly, fumarate hydratase deficient cancer cells and multiple cancer cell lines with reduced amounts of mtDNA were resistant to ONC201. These results indicate that cells not dependent on mitochondrial respiration are ONC201-resistant. Our data demonstrate that ONC201 kills cancer cells by disrupting mitochondrial function and further suggests that cancer cells that are dependent on glycolysis will be resistant to ONC201.

Control of Regulatory T Cell Differentiation by the Transcription Factors Thpok and LRF

The CD4⁺ lineage-specific transcription factor Thpok is required for intrathymic CD4⁺ T cell differentiation and, together with its homolog LRF, supports CD4⁺ T cell helper effector responses. However, it is not known whether these factors are needed for the regulatory T cell (Treg) arm of MHC class II responses. In this study, by inactivating in mice the genes encoding both factors in differentiated Tregs, we show that Thpok and LRF are redundantly required to maintain the size and functions of the postthymic Treg pool. They support IL-2-mediated gene expression and the functions of the Treg-specific factor Foxp3. Accordingly, Treg-specific disruption of Thpok and Lrf causes a lethal inflammatory syndrome similar to that resulting from Treg deficiency. Unlike in conventional T cells, Thpok and LRF functions in Tregs are not mediated by their repression of the transcription factor Runx3. Additionally, we found that Thpok is needed for the differentiation of thymic Treg precursors, an observation in line with the fact that Foxp3⁺ Tregs are CD4⁺ cells. Thus, a common Thpok-LRF node supports both helper and regulatory arms of MHC class II responses.

Abstract 4423: Deep sequencing of lung cancer samples using different library preparation methods produces discordant short non-coding RNA profiles

Background: RNA-seq is the new standard for profiling coding and non-coding RNAs in a cell. This study compared two methods for miRNA library preparation from NEB and Qiagen. Our goal was to evaluate overall performance in terms of coverage, known miRNA detection, novel miRNA detection, isomiR detection, and tRNA fragment (tRF) detection.

Methods: We performed short RNA-seq on 4 lung cancer tumor-normal pairs. We used two library preparation kits: NEB Next Small RNA kit and Qiagen Qiaseq. All 16 preparations were sequenced on an Illumina NextSeq 550 using NextSeq High V2 chemistry and 75 bp single-end reads were obtained. After adapter removal and quality trimming reads were mapped to the hg19 human genome assembly using the Bowtie2 and SHRiMP packages.

Results: On average read yield was 46 million reads. A significantly higher portion of the sequenced reads survived adapter removal and quality trimming in the NEB preparations (96.5%) compared to the Qiagen (72.9%). The portion that could be uniquely mapped to hg19 was lower for the NEB kit (41.1%) than for the Qiagen (50.8%).NEB performed better (39.6%) compared with Qiagen (36.9%). Qiagen preparations had lengths between 20 and 25 bp whereas more than half of the mapped reads in the NEB preparation were 26 bp or longer.

At the miRNA arm level the Qiagen kit detected significantly more known miRNAs (792) with 10 or more reads, compared with NEB (576). The same 530 miRNA arms were identified by both kits. There was no discernible pattern in the ID’s or the sequence composition of the miRNAs that were identified by each kit. The detection of novel miRNAs was also higher with Qiagen (102), compared with NEB (82). The same 79 novel miRNAs were identified by both.

The Qiagen kit detected nearly twice as many isomiRs (5,316) with 10 or more reads compared to NEB (2,958). The same 2,631 isomiRs were identified by both kits. However, isomiR detection across samples was more consistent with the NEB kit.

When we computed pairwise Pearson correlations of normal samples, using the most highly expressed miRNAs in each sample, the NEB kit exhibited higher consistency (0.98) compared with the Qiagen kit (0.95). Pearson correlations of tumor samples showed even higher consistency for NEB (0.96) than Qiagen (0.89). Unsurprisingly, Pearson correlations of like samples across the NEB and Qiagen kits was very low: 0.42 for normal and 0.56 for tumor samples. RIN value did not seem to affect the overall performance of either kit.

Lastly, we compared tRFs. Here, the differences were very pronounced. For multiple choices of the support threshold the NEB and Qiagen profiles agreed on approximately 33% of the reported tRFs.

Conclusions: Library preparation kits give rise to both consistent and divergent results. End users interested in the detection of miRNAs, isomiRs or tRFs may derive greater utility by selecting one kit over another.

Citation Format: Brid M. Ryan, Phillipe Loher, Khadijah Mitchell, Adriana Zingone, Yongmei Zhao, Jyoti Shetty, Bao Tran, Isidore Rigoutsos. Deep sequencing of lung cancer samples using different library preparation methods produces discordant short non-coding RNA profiles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4423. doi:10.1158/1538-7445.AM2017-4423

Management of Complex Ovarian Cysts in Newborns - Our Experience

Aims: To analyse the clinical presentation, clinicopathological correlation and management of complex ovarian cysts in newborn and infants.

Materials and Methods: Over a period of 6 years (2009-2015), 25 newborns who were diagnosed to have ovarian cyst on antenatal ultrasound, were followed up. We collected data in the form of clinical features, radiological findings, pathology and mode of treatment.

Results: Of the 25 fetuses who were diagnosed to have ovarian cysts, fourteen (56%) underwent spontaneous regression by 6-8 months. Eight were operated in newborn period while 3 were operated in early infancy. Seven had ovarian cyst on right side, 4 had on left side. Eight babies underwent laparoscopy while 3 underwent laparotomy. Histopathology showed varied features of hemorrhagic cyst with necrosis and calcification, serous cystadenoma with hemorrhage, benign serous cyst with hemorrhage and simple serous cyst. Post-operative recovery was uneventful in all.

Conclusion: All the ovarian cysts detected antenatally in female fetuses need close follow-up after birth. Since spontaneous regression is known, only complex or larger cysts need surgical intervention, preferably by laparoscopy. Majority of the complex cysts show atrophic ovarian tissue hence end up in oophorectomy but simple cysts can be removed preserving normal ovarian tissue whenever possible.

Histone H3 Lysine 27 demethylases Jmjd3 and Utx are required for T-cell differentiation

Although histone H3 lysine 27 trimethylation (H3K27Me3) is associated with gene silencing, whether H3K27Me3 demethylation affects transcription and cell differentiation in vivo has remained elusive. To investigate this, we conditionally inactivated the two H3K27Me3 demethylases, Jmjd3 and Utx, in non-dividing intrathymic CD4(+) T-cell precursors. Here we show that both enzymes redundantly promote H3K27Me3 removal at, and expression of, a specific subset of genes involved in terminal thymocyte differentiation, especially S1pr1, encoding a sphingosine-phosphate receptor required for thymocyte egress. Thymocyte expression of S1pr1 was not rescued in Jmjd3- and Utx-deficient male mice, which carry the catalytically inactive Utx homolog Uty, supporting the conclusion that it requires H3K27Me3 demethylase activity. These findings demonstrate that Jmjd3 and Utx are required for T-cell development, and point to a requirement for their H3K27Me3 demethylase activity in cell differentiation.

Abstract OT3-2-11: A phase II study of letrozole and lapatinib followed by an addition of everolimus in postmenopausal women with advanced endocrine resistant breast cancer (BC)

Background: Several preclinical studies demonstrated that crosstalk between growth factor receptor pathways, particularly HER2, and ER signaling confers resistance to endocrine therapy (ET). There are emerging data showing the involvement of immune system and miRNA with endocrine resistance. EGF30008 trial showed a benefit of lapatinib in combination with letrozole, mainly in HER2-positive (HER+) metastatic BC (MBC) while a subset analysis of this trial showed that HER2-negative (HER2-) patients (pts) with acquired endocrine resistance may also benefit from this combination. Our preclinical study suggests that everolimus is synergistic with letrozole and lapatinib.

Trial Design: This is a single arm phase II study for postmenopausal women with hormone receptor-positive MBC progressing after aromatase inhibitor, tamoxifen, or fulvestrant. The total target accrual is 76 pts (38 HER2+ pts and 38 HER- pts). In the first phase of the study, pts will be treated with letrozole and lapatinib (1,500 mg daily). Upon disease progression, pts will enter the second phase where everolimus (5 mg daily) will be added to letrozole and the dose of lapatinib will be reduced to 1,250 mg daily. For correlative studies, peripheral blood samples will be serially collected to evaluate for serum HER2 extracellular domain (ECD), circulating miRNAs, PC cell-derived growth factor (GP88), immune regulatory cells including myeloid-derived suppressor cells, NK cells, and Treg cells. These parameters will be correlated with tumor response. In pts with accessible tumors, optional serial biopsies will be performed at baseline and upon progression in each phase of the study. The tumor tissue will be tested for total HER1, HER2, and HER2 expressions as well as HER2:HER2 homodimers, HER2:HER3 heterodimers, HER1:HER2 heterodimers, p95, and HER3/PI3K (p85 subunit) using VeraTag assay.

Statistical Method: The primary objective is to evaluate the clinical benefit rate (CBR: CR, PR, SD > 24 weeks) of the combination of letrozole and lapatinib as well as the combination of everolimus, letrozole, and lapatinib. This is a three-stage design which is an extension of the Simon's two-stage design. The sample size is based on the assumption that a CBR below 10% (null hypothesis) would indicate ineffective therapy and the statistical power is set at a higher CBR of 30% which we consider is plausible. Therefore, if 0 of the first 10 pts in each cohort have clinical benefit, the study will be closed; otherwise additional 8 pts will be enrolled. If ≤ 1 of the total 18 pts has clinical benefit, the study will be closed; otherwise an additional 9 pts will be enrolled. If ≤ 5 pts have clinical benefit the therapy is considered not promising; and if ≥ 6 pts of the total of 27 have clinical benefit, the therapy is considered worth pursuing. This design has ∼90% probability to accept the therapy for further trials if the true CBR is indeed at least 30% and 10% probability to accept it if the true clinical benefit is indeed below 10%.

To date, there are a total of 6 pts enrolled. Accrual is currently ongoing. Please contact ntait@umm.edu for further information.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr OT3-2-11.

Interleukin-27 treated human macrophages induce the expression of novel microRNAs which may mediate anti-viral properties

Interleukin-27 (IL-27) is a pleiotropic cytokine which plays important and diverse roles in the immune system. We have previously demonstrated that IL-27 induces potent anti-viral effects against HIV-1, HIV-2, SIV, HSV-2, KSHV and influenza viruses in macrophages. This induction occurred in an interferon (IFN) independent manner and involved down regulation of SPTBN1. MicroRNAs (miRNAs) are critical regulators of mRNA translation and turnover. There have been reports that some miRNAs inhibit viral replication. In this study, we hypothesized that IL-27 could induce the expression of novel miRNAs in macrophages which may have functional relevance in terms of anti-viral activity and primary monocytes were differentiated into macrophages using either M-CSF (M-Mac) or a combination of M-CSF and IL-27 (I-Mac) for seven days. Following this, total RNA was extracted from these cells and deep sequencing was performed, in parallel with gene expression microarrays. Using the novel miRNA discovery software, miRDeep, seven novel miRNAs were discovered in these macrophages. Four of which were preferentially expressed in I-Mac (miR-SX1, -SX2, -SX3 and -SX6) whilst three were detected in both M-Mac and I-Mac (miR-SX4, -SX5 and -SX7). The expression of six of the seven novel miRNAs was highly correlated with qRT-PCR using specific primer/probes designed for the novel miRNAs. Gene expression microarray further demonstrated that a number of genes were potentially targeted by these differentially expressed novel miRNAs. Finally, several of these novel miRNAs (miR-SX1, -SX4, -SX5, -SX6 and -SX7) were shown to target the open reading frames of a number of viruses (including HSV-1, HSV-2 and HHV-8) which may partially explain the anti-viral properties observed.

P4-12-13: A Multi-Center Randomized Controlled Double Blind Trial Assessing the Effect of Acupuncture in Reducing Musculoskeletal Symptoms in Breast Cancer Patients Taking Aromatase Inhibitors: First Interim Analysis

Background: Aromatase inhibitors (AIs) are recommended as first-line adjuvant hormonal therapy in postmenopausal women with hormone-receptor-positive breast cancer, as monotherapy or sequential therapy after tamoxifen. AI-associated musculoskeletal symptoms (AIMSS) occur in approximately 50% of women receiving AIs and in some may result in discontinuation of treatment. Symptom management is essential to ensure that breast cancer patients receive the full recommended duration of AI therapy. We conducted a randomized, placebo-controlled trial to evaluate the effect of acupuncture on AIMSS and report the first interim analysis.

Method: Postmenopausal women with early stage breast cancer, experiencing AIMSS, who had not had acupuncture in the year prior to the study, were eligible. Patients were randomized to 8 weekly acupuncture or sham acupuncture. Health assessment questionnaire disability index (HAQ-DI ranging 0–3.0) and pain visual analog scale (VAS ranging 0–100) were used to assess clinical musculoskeletal disorder severity at weeks 0, 4, 8, and 12 or 24. Change in HAQ-DI (ΔHAQ-DI) and VAS scores (ΔVAS) from baseline were compared between patients receiving acupuncture versus sham acupuncture using exact Wilcoxon rank sum test. Serum samples were collected for measurements of estrogens and beta endorphin concentrations and cytokine profile before and after the intervention to evaluate the etiology of AIMSS and the mechanism of acupuncture in treating AIMSS.

Results: Between May 2008 and June 2011, 48 patients were enrolled, 2 patients were not evaluable due to noncompliance to treatment and lost to follow up, 10 were still receiving treatment and therefore not evaluable. Thirty-six were evaluable, and were equally distributed between the real and sham acupuncture groups. Baseline characteristics were balanced between the two groups with regard to age, race, and body mass index (BMI) with the exception that baseline mean HAQ-DI was higher in the acupuncture group (0.9 vs 0.55, p=0.04). White/Black/Asian: 26/7/3, Median (range): age: 61 (45-82); BMI (kg/m2): 31.1 (22.9−59.6). At week 8, both groups showed a wide range of ΔHAQ-DI (ΔHAQ-DI =HAQ-DIweek8-HAQ-DIbaseline): from −1.38 to 0.5 in the acupuncture group versus from −1 to 0.12 in sham acupuncture group. There was no statistically significant difference in mean ΔHAQ-DI between the real and sham acupuncture groups (−0.33 vs −0.33, p=0.87). Eleven patients in each group (61%) reported decreased HAQ-DI scores, which correlated with improved function. There was no difference in mean ΔVAS between the real and sham acupuncture groups (−9.27 vs −13.82, p=0.67). No significant side effects were reported. Changes in other time points and in serum biomarkers will be presented at the meeting.

Conclusions: The majority of breast cancer patients experiencing AIMSS who participated in our study reported a reduced HAQ-DI score both from acupuncture and sham acupuncture. We did not observe significant differences between responses to real versus sham acupuncture after 8 weekly treatments. The study remains open to accrual to reach 50 evaluable patients.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P4-12-13.

Sublingual misoprostol: a better choice for cervical priming before manual vacuum aspiration

BACKGROUND

Misoprostol is effective for cervical priming before manual vacuum aspiration (MVA). Aim of study was to determine whether sublingual misoprostol with a shorter interval of 2 hours before MVA would be as effective as its standard vaginal administration.

STUDY DESIGN

This randomized control trial included 82 women randomly assigned to receive 400 mcg of misoprostol, either sublingually or vaginally. MVA was performed 2 hours and 3 hours after in sublingual and vaginal group, respectively.

RESULTS

Cervical dilatation of 8 mm was achieved within 2 hours in sublingual group. Mean time taken for procedure (14.4 ± 5.3: sublingual group and 16.2 ± 5.7: vaginal group), and blood loss was comparable (12.2 ± 9.7 ml in sublingual group and 13.7 ± 8.5 ml in vaginal group).

CONCLUSION

2 hour of cervical priming with 400 mcg of sublingual misoprostol before MVA was as good as 3 hours with vaginal administration of the same dose.

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

BACKGROUND

Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species.

RESULTS

The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions, although, surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between P. ultimum and more host-specific oomycete species. Although we observed a high degree of orthology with Phytophthora genomes, there were novel features of the P. ultimum proteome, including an expansion of genes involved in proteolysis and genes unique to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report of these in a genome outside the metazoans.

CONCLUSIONS

Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage-specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae.

Production of ethanol from winter barley by the EDGE (enhanced dry grind enzymatic) process

BACKGROUND

US legislation requires the use of advanced biofuels to be made from non-food feedstocks. However, commercialization of lignocellulosic ethanol technology is more complex than expected and is therefore running behind schedule. This is creating a demand for non-food, but more easily converted, starch-based feedstocks other than corn that can fill the gap until the second generation technologies are commercially viable. Winter barley is such a feedstock but its mash has very high viscosity due to its high content of beta-glucans. This fact, along with a lower starch content than corn, makes ethanol production at the commercial scale a real challenge.

RESULTS

A new fermentation process for ethanol production from Thoroughbred, a winter barley variety with a high starch content, was developed. The new process was designated the EDGE (enhanced dry grind enzymatic) process. In this process, in addition to the normal starch-converting enzymes, two accessory enzymes were used to solve the beta-glucan problem. First, beta-glucanases were used to hydrolyze the beta-glucans to oligomeric fractions, thus significantly reducing the viscosity to allow good mixing for the distribution of the yeast and nutrients. Next, beta-glucosidase was used to complete the beta-glucan hydrolysis and to generate glucose, which was subsequently fermented in order to produce additional ethanol. While beta-glucanases have been previously used to improve barley ethanol production by lowering viscosity, this is the first full report on the benefits of adding beta-glucosidases to increase the ethanol yield.

CONCLUSIONS

In the EDGE process, 30% of total dry solids could be used to produce 15% v/v ethanol. Under optimum conditions an ethanol yield of 402 L/MT (dry basis) or 2.17 gallons/53 lb bushel of barley with 15% moisture was achieved. The distillers dried grains with solubles (DDGS) co-product had extremely low beta-glucan (below 0.2%) making it suitable for use in both ruminant and mono-gastric animal feeds.

SpermCheck Fertility, an immunodiagnostic home test that detects normozoospermia and severe oligozoospermia

BACKGROUND

A simple and inexpensive home sperm test could be of considerable value to couples attempting to conceive and to men curious about their fertility potential. A two-strip lateral flow immunochromatographic diagnostic device that allows men to evaluate their sperm count at low cost in the privacy of their own homes is described.

METHODS

The ability of SpermCheck Fertility to predict sperm counts obtained using a hemacytometer procedure based on standard World Health Organization methodology was assessed. Test results obtained by lay users were also compared with those obtained by trained laboratory professionals, and the ease of use of the device was evaluated in consumer studies.

RESULTS

A total of 225 semen samples were analyzed in the method comparison, and the performance of SpermCheck Fertility was excellent with over 96% of all samples correctly classified as normozoospermic (> or =2 x 10(7) sperm/ml), oligozoospermic (5 x 10(6)-2 x 10(7) sperm/ml) or severely oligozoospermic (<5 x 10(6) sperm/ml). Consumer studies with 164 lay users demonstrated that SpermCheck Fertility was easy to use. Lay users and laboratory professionals agreed 95% of the time when reading the same test independently. Overall, the correct response rate on a 20-question survey about the test was over 97%.

CONCLUSIONS

SpermCheck Fertility is a simple and reliable immunodiagnostic test that can quickly inform men as to whether their sperm count is normal, low or very low. This home test can assist couples in deciding whether to seek comprehensive clinical evaluation of the fertility status of the male partner.

The pattern of childhood blindness in Karnataka, South India

PURPOSE

To determine the causes of severe visual impairment and blindness in children in schools for the blind in southern Karnataka state of India.

METHOD

Children aged less than 16 years with a visual acuity of < 6/60 in the better eye, attending the residential schools for the blind were examined in 2005-2006, in the Karnataka state in the south of India. History taking, visual acuity estimation, external ocular examination, retinoscopy, and fundoscopy were done on all students. Refraction and low vision work-up done where indicated. The anatomical and etiological causes of severe visual impairment (< 6/60-3/60) and blindness (< 3/60 in the better eye) were classified using the World Health Organization's prevention of blindness programs' record system.

RESULTS

A total of 1,179 students were examined, 891 of whom fulfilled the eligibility criteria. The major anatomical sites of visual loss were congenital anomalies (microphthalmos, anophthalmos) (321, 35.7%), corneal conditions (mainly scarring due to vitamin A deficiency, measles, trauma) (133, 14.9%), cataract or aphakia in 102 (11.4%), and retinal disorders (mainly dystrophies) in 177 children (19.9%). Nearly one-fourth of children were blind from conditions which could have been prevented or treated (27.8%), 87 of whom were referred for surgery. Low vision devices improved near acuity in 27 children (3%), and 43 (4.8%) benefited from refraction.

CONCLUSIONS

Congenital anomalies, cataract, and retinal conditions account for most of the blindness in children.

Using comparative genomics to reorder the human genome sequence into a virtual sheep genome

BACKGROUND

Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes?

RESULTS

A sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped with high sensitivity and low specificity onto the frameworks of the human, dog, and cow genomes. To maximize genome coverage, the coordinates of all BAC end sequence hits to the cow and dog genomes were also converted to the equivalent human genome coordinates. The 84,624 sheep BACs (about 5.4-fold genome coverage) with paired ends in the correct orientation (tail-to-tail) and spacing, combined with information from sheep BAC comparative genome contigs (CGCs) built separately on the dog and cow genomes, were used to construct 1,172 sheep BAC-CGCs, covering 91.2% of the human genome. Clustered non-tail-to-tail and outsize BACs located close to the ends of many BAC-CGCs linked BAC-CGCs covering about 70% of the genome to at least one other BAC-CGC on the same chromosome. Using the BAC-CGCs, the intrachromosomal and interchromosomal BAC-CGC linkage information, human/cow and vertebrate synteny, and the sheep marker map, a virtual sheep genome was constructed. To identify BACs potentially located in gaps between BAC-CGCs, an additional set of 55,668 sheep BACs were positioned on the sheep genome with lower confidence. A coordinate conversion process allowed us to transfer human genes and other genome features to the virtual sheep genome to display on a sheep genome browser.

CONCLUSION

We demonstrate that limited sequencing of BACs combined with positioning on a well assembled genome and integrating locations from other less well assembled genomes can yield extensive, detailed subgene-level maps of mammalian genomes, for which genomic resources are currently limited.

Equatorial segment protein (ESP) is a human alloantigen involved in sperm-egg binding and fusion

The equatorial segment of the sperm head is known to play a role in fertilization; however, the specific sperm molecules contributing to the integrity of the equatorial segment and in binding and fusion at the oolemma remain incomplete. Moreover, identification of molecular mediators of fertilization that are also immunogenic in humans is predicted to advance both the diagnosis and treatment of immune infertility. We previously reported the cloning of Equatorial Segment Protein (ESP), a protein localized to the equatorial segment of ejaculated human sperm. ESP is a biomarker for a subcompartment of the acrosomal matrix that can be traced through all stages of acrosome biogenesis (Wolkowicz et al, 2003). In the present study, ESP immunoreacted on Western blots with 4 (27%) of 15 antisperm antibody (ASA)-positive serum samples from infertile male patients and 2 (40%) of 5 ASA-positive female sera. Immunofluorescent studies revealed ESP in the equatorial segment of 89% of acrosome-reacted sperm. ESP persisted as a defined equatorial segment band on 100% of sperm tightly bound to the oolemma of hamster eggs. Antisera to recombinant human ESP inhibited both oolemmal binding and fusion of human sperm in the hamster egg penetration assay. The results indicate that ESP is a human alloantigen involved in sperm-egg binding and fusion. Defined recombinant sperm immunogens, such as ESP, may offer opportunities for differential diagnosis of immune infertility.

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of approximately 65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome. The sequences reported in this paper have been deposited in the GenBank database (accession nos. CZ 250707-CZ 257443 and DX 390731-DX 389174).

The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease

Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.

Human, mouse, and rat genome large-scale rearrangements: stability versus speciation

Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300 syntenic blocks identified are segments of over 40 Mb without any detected interspecies rearrangements, as well as regions with frequently broken synteny and extensive rearrangements. As closely related species, mouse and rat share the majority of the breakpoints and often have the same types of rearrangements when compared with the human genome. However, the breakpoints not shared between them indicate that mouse rearrangements are more often interchromosomal, whereas intrachromosomal rearrangements are more prominent in rat. Centromeres may have played a significant role in reorganizing a number of chromosomes in all three species. The comparison of the three species indicates that genome rearrangements follow a path that accommodates a delicate balance between maintaining a basic structure underlying all mammalian species and permitting variations that are necessary for speciation.

Genetic analysis of an Indian family with members affected with juvenile-onset primary open-angle glaucoma

PURPOSE

Glaucoma is the second leading cause of blindness. In India, approximately 1.5 million people are blind due to glaucoma. Mutations in the MYOC gene located at the GLC1A locus on chromosome 1q21-q31 have been found in patients with juvenile-onset primary open-angle glaucoma (J-POAG). The purpose of the present study was to identify the genetic cause of glaucoma in a four-generation Indian family affected with J-POAG.

METHODS

Peripheral blood samples were obtained from individuals for genomic DNA isolation. To determine if this family was linked to the GLC1A locus, haplotyping analysis was carried out using microsatellite markers from the GLC1A candidate region. Exon-specific primers from exon 3 of the MYOC gene were used to amplify DNA samples from individuals. Mutation analysis was carried out using PCR-SSCP and DNA sequence analyses.

RESULTS

Pedigree analysis suggested that glaucoma in this family segregated as an autosomal dominant trait. Of six patients, five had J-POAG and one had adult-onset POAG (A-POAG). Haplotype analysis suggested linkage of this family to the GLC1A locus. Mutation and sequence analyses showed a novel missense mutation, c.821C > G (p.P274R), in the C-terminal olfactomedin domain coded by exon 3 of the MYOC gene. One patient was found to be homozygous for this mutation with a severe phenotype.

CONCLUSIONS

This study reports a novel missense mutation in a four-generation Indian family with all but one member affected with J-POAG. The total number of mutations described so far in the MYOC gene, including the one reported here, is 59 with a clustering of 52 mutations in exon 3.

Confirmation of linkage and refinement of the RP28 locus for autosomal recessive retinitis pigmentosa on chromosome 2p14-p15 in an Indian family

PURPOSE

To report the linkage analysis of retinitis pigmentosa (RP) in an Indian family.

METHODS

Individuals were examined for symptoms of retinitis pigmentosa and their blood samples were withdrawn for genetic analysis. The disorder was tested for linkage to known 14 adRP and 22 arRP loci using microsatellite markers.

RESULTS

Seventeen individuals including seven affecteds participated in the study. All affected individuals had typical RP. The age of onset of the disease ranged from 8-18 years. The disorder in this family segregated either as an autosomal recessive trait with pseudodominance or an autosomal dominant trait. Linkage to an autosomal recessive locus RP28 on chromosome 2p14-p15 was positive with a maximum two-point lod score of 3.96 at theta=0 for D2S380. All affected individuals were homozygous for alleles at D2S2320, D2S2397, D2S380, and D2S136. Recombination events placed the minimum critical region (MCR) for the RP28 gene in a 1.06 cM region between D2S2225 and D2S296.

CONCLUSIONS

The present data confirmed linkage of arRP to the RP28 locus in a second Indian family. The RP28 locus was previously mapped to a 16 cM region between D2S1337 and D2S286 in a single Indian family. Haplotype analysis in this family has further narrowed the MCR for the RP28 locus to a 1.06 cM region between D2S2225 and D2S296. Of 15 genes reported in the MCR, 14 genes (KIAA0903, OTX1, MDH1, UGP2, VPS54, PELI1, HSPC159, FLJ20080, TRIP-Br2, SLC1A4, KIAA0582, RAB1A, ACTR2, and SPRED2) are either expressed in the eye or retina. Further study needs to be done to test which of these genes is mutated in patients with RP linked to the RP28 locus.