The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758

We present a genome assembly of Caretta caretta (the Loggerhead sea turtle; Chordata, Testudines, Cheloniidae), generated from genomic data from two unrelated females. The genome sequence is 2.13 gigabases in size. The assembly has a busco completion score of 96.1% and N50 of 130.95 Mb. The majority of the assembly is scaffolded into 28 chromosomal representations with a remaining 2% of the assembly being excluded from these.

THU0253 FATIGUE AND PAIN REMAIN PROMINENT AND IMPACTFUL IN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS (SLE): A CROSS-SECTIONAL SURVEY OF SLE PATIENTS IN THE UNITED STATES

Background:

Systemic lupus erythematosus (SLE) is a chronic autoimmune inflammatory condition impacting multiple organ systems.1,2SLE affects approximately 1.5 million Americans, disproportionately females of reproductive age, and is more prevalent in non-Caucasian populations.3Fatigue and pain are some of the most prominent symptoms of SLE, contributing to the heavy disease burden and disruption to daily life.4This study aimed to further understand the burden of SLE. Lilly worked with the Lupus Foundation of America (LFA) and Evidera to develop the SLE-UPDATE (Understanding Preferences, Disease Activity and Treatment Expectations) survey.

Objectives:

To understand the patient-perceived symptom burden of SLE, in particular pain and fatigue, within the current landscape of therapeutic options. This study also focused on current treatment patterns in SLE patients.

Methods:

This was a cross-sectional, non-interventional, online survey study conducted in partnership with the LFA. English-speaking United States patients aged ≥18 years with a self-reported diagnosis of SLE completed the survey following online screening and informed consent. Descriptive data are presented by means (standard deviation [SD]) for continuous measures, and frequency (n, %) for dichotomous measures. Demographic, clinical, and patient-reported outcomes were collected including the FACIT-Fatigue (range 0-52, higher scores indicate less fatigue), Pain Numerical Rating Scale (NRS) (0 [none] to 10 [worst imaginable]), Worst Joint Pain NRS (0 [none] to 10 [worst imaginable]), and the LupusPRO, a validated, lupus-specific quality of life (QoL) instrument (range 0-100, higher scores indicate better QoL).

Results:

A total of 500 patients with SLE completed the survey. Patients were predominantly female (75%), white/Caucasian (76%), with a mean age of 42.6 years and mean disease duration of 11.1 years.

Most patients with SLE rated their overall condition as either good (38%) or fair (31%), with 8% rating poor and 7% excellent. Current non-biologic prescription medication use included: antimalarials 42%, corticosteroids 33%, immunosuppressants 33%, nonsteroidal anti-inflammatory drugs (NSAID) 32%, other analgesics 15% and 10% were using tofacitinib. Biologic therapies were being used by only 19%, including intravenous (IV) Benlysta (37%),subcutaneous(SC) Benlysta (25%), rituximab (17%), and 22% were using other biologics. Fatigue was the most commonly reported symptom (69%), with 40% of patients ranking fatigue as their most bothersome SLE symptom. Forty eight percent of patients with current fatigue rated the severity as moderate and 33% as severe. The mean (SD) FACIT-Fatigue score was 22.9 (12.0). The next most commonly reported symptoms were joint stiffness (57%), sleep problems (55%), joint pain/swelling (53%), and muscle pain (52%). Sixty percent of patients reported experiencing pain all or most of the time over the past seven days. A total of 30% of patients with current joint pain/swelling rated it as severe, and 24% of patients with current joint stiffness rated it as severe. The mean scores for Worst pain NRS and Worst Joint Pain NRS were both 5.8 out of 10.

The LupusPRO domains indicated by respondents as the most impacted by SLE were Emotional Health, Pain/Vitality, and Lupus Medications.

Conclusion:

Fatigue, followed by pain and joint stiffness, were the most common patient-reported symptoms contributing to the overall SLE disease burden. Further research could highlight the efforts required to address the inadequacies in treatment and management of pain and fatigue in this patient population.

Disclosure of Interests:

Julie Birt Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Monica Hadi: None declared, Nashmel Sargalo: None declared, Ella Brookes: None declared, Paul Swinburn: None declared, Leslie Hanrahan: None declared, Karin Tse: None declared, Natalia Bello Vega Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Kirstin Griffing Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Maria Silk Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Laure Delbecque Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Diane L Kamen Consultant of: Consulted on SLE survey development for Lilly and consulted on SLE trial protocol development for EMD Serono in 2019

AB1338-HPR GLOBAL PATIENT PERSPECTIVE ON TOP CHALLENGES IN LUPUS CARE AND RESEARCH PARTICIPATION

Background:

The Addressing Lupus Pillars for Health Advancement (ALPHA) Project is a global consensus initiative to identify, prioritize and address top barriers in lupus drug development, clinical care and access to care. The Lupus Foundation of America convenes ALPHA with Tufts Center for the Study of Drug Development and a Global Advisory Committee of lupus experts representing clinician-scientists, industry and patients.

Objectives:

Collect global patient input to determine alignment with the lupus clinician-scientist community on prior published consensus of top lupus barriers.

Methods:

A 23-question online Qualtrics survey was developed to identify challenges across lupus diagnosis, clinical care and research participation. The survey, available in English, Spanish, Korean and simplified Chinese, was fielded in November 2019 to people with lupus and caregivers of children <18 with lupus. SPSS 26 and SAS 9.4 were used for descriptive statistics and sub-analysis.

Results:

Analysis included only consented responses with ≥ 68% survey completion (n=3,447) received across 83 countries. 95% were female with a mean age of 45. Respondents reported being White (57%), Black or of African descent (14%), Hispanic or Latino (18%) and Asian (10%). 65% resided in the US while 35% resided in countries outside of the US. 97% were people with lupus while 3% were caregivers to children <18 with lupus.

Highest ranked challenges were similar globally and across children and adults: medication side effects, lack of treatment options and high out-of-pocket costs. Managing side effects ranked significantly higher (p<.05) outside of the US (48%) compared to US (40%). 50% of caregivers reported managing side effects as the top challenge for children compared to 43% of adults (p<.05). Research participation was low (24%) and lower among children (16%). The top reason for not participating in a clinical trial was not being asked by their doctor.

Conclusion:

This global survey revealed that medication side effects and lack of effective treatments are top challenges for people with lupus, including children. Most respondents were never asked by their doctors to participate in a clinical trial, which may explain difficulties in trial recruitment. These barriers are consistent with prior published barriers identified by the clinician-scientist community.

Acknowledgments:

ALPHA sponsors: EMD Serono, GSK, Aurinia, Mallinckrodt

Disclosure of Interests:

Karin Tse: None declared, Yaritza Peña: None declared, Kathleen Arntsen: None declared, Sang-Cheol Bae: None declared, Lauren Bloch Consultant of: Faegre Drinker Consulting is a division of Faegre Drinker Biddle & Reath, a law and consulting firm that represents patient advocacy organizations and sponsors developing drugs, Ian N. Bruce Grant/research support from: Genzyme Sanofi, GSK, and UCB, Consultant of: Eli Lilly, AstraZeneca, UCB, Iltoo, and Merck Serono, Speakers bureau: UCB, Karen Costenbader Grant/research support from: Merck, Consultant of: Astra-Zeneca, Bradley Dickerson Employee of: Aurinia, Thomas Dörner Grant/research support from: Janssen, Novartis, Roche, UCB, Consultant of: Abbvie, Celgene, Eli Lilly, Roche, Janssen, EMD, Speakers bureau: Eli Lilly, Roche, Samsung, Janssen, Kenneth Getz: None declared, Amy Kao Employee of: EMD Serono, Susan Manzi: None declared, Eric F. Morand Grant/research support from: AstraZeneca, Consultant of: AstraZeneca, Speakers bureau: AstraZeneca, Sandra Raymond: None declared, Brad H Rovin Grant/research support from: GSK, Consultant of: GSK, Laura Schanberg Grant/research support from: Sobi, BMS, Consultant of: Aurinia, UCB, Sanofi, Victoria Werth Grant/research support from: Biogen, Celgene, Gilead, Janssen, Viela, Consultant of: Biogen, Gilead, Janssen, Abbvie, GSK, Resolve, AstraZeneca, Amgen, Eli Lilly, EMD Serono, BMS, Viela, Kyowa Kirin, Joan Von Feldt Shareholder of: GSK, Employee of: GSK, David Zook Consultant of: Faegre Drinker Consulting is a division of Faegre Drinker Biddle & Reath, a law and consulting firm that represents patient advocacy organizations and sponsors developing drugs, Leslie Hanrahan: None declared

The Genome of the Steller Sea Lion (Eumetopias jubatus)

The Steller sea lion is the largest member of the Otariidae family and is found in the coastal waters of the northern Pacific Rim. Here, we present the Steller sea lion genome, determined through DNA sequencing approaches that utilized microfluidic partitioning library construction, as well as nanopore technologies. These methods constructed a highly contiguous assembly with a scaffold N50 length of over 14 megabases, a contig N50 length of over 242 kilobases and a total length of 2.404 gigabases. As a measure of completeness, 95.1% of 4104 highly conserved mammalian genes were found to be complete within the assembly. Further annotation identified 19,668 protein coding genes. The assembled genome sequence and underlying sequence data can be found at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA475770.

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer

High-grade serous ovarian cancer (HGSC) exhibits extensive malignant clonal diversity with widespread but non-random patterns of disease dissemination. We investigated whether local immune microenvironment factors shape tumor progression properties at the interface of tumor-infiltrating lymphocytes (TILs) and cancer cells. Through multi-region study of 212 samples from 38 patients with whole-genome sequencing, immunohistochemistry, histologic image analysis, gene expression profiling, and T and B cell receptor sequencing, we identified three immunologic subtypes across samples and extensive within-patient diversity. Epithelial CD8+ TILs negatively associated with malignant diversity, reflecting immunological pruning of tumor clones inferred by neoantigen depletion, HLA I loss of heterozygosity, and spatial tracking between T cell and tumor clones. In addition, combinatorial prognostic effects of mutational processes and immune properties were observed, illuminating how specific genomic aberration types associate with immune response and impact survival. We conclude that within-patient spatial immune microenvironment variation shapes intraperitoneal malignant spread, provoking new evolutionary perspectives on HGSC clonal dispersion.

The Genome of the Beluga Whale (Delphinapterus leucas)

The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus Delphinapterus. The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue. Assembled sequence and all of the underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the Bioproject accession number PRJNA360851A.

The whole-genome landscape of medulloblastoma subtypes

Current therapies for medulloblastoma, a highly malignant childhood brain tumour, impose debilitating effects on the developing child, and highlight the need for molecularly targeted treatments with reduced toxicity. Previous studies have been unable to identify the full spectrum of driver genes and molecular processes that operate in medulloblastoma subgroups. Here we analyse the somatic landscape across 491 sequenced medulloblastoma samples and the molecular heterogeneity among 1,256 epigenetically analysed cases, and identify subgroup-specific driver alterations that include previously undiscovered actionable targets. Driver mutations were confidently assigned to most patients belonging to Group 3 and Group 4 medulloblastoma subgroups, greatly enhancing previous knowledge. New molecular subtypes were differentially enriched for specific driver events, including hotspot in-frame insertions that target KBTBD4 and ‘enhancer hijacking’ events that activate PRDM6. Thus, the application of integrative genomics to an extensive cohort of clinical samples derived from a single childhood cancer entity revealed a series of cancer genes and biologically relevant subtype diversity that represent attractive therapeutic targets for the treatment of patients with medulloblastoma.

Genomic analysis of 491 medulloblastoma samples, including methylation profiling of 1,256 cases, effectively assigns candidate drivers to most tumours across all molecular subgroups.

Medulloblastomas are highly malignant brain tumours that develop during childhood. Paul Northcott and colleagues analysed the whole-genome sequences of 491 medulloblastomas in order to characterize the genomic landscape across tumours and identify new drivers and mutational signatures. Their integrative genomic analyses, including methylation profiling of 1,256 medulloblastomas, identifies subgroup-specific driver mutations and suggests additional tumour subtypes. The authors assign driver mutations to a high proportion of the less well characterized Group 3 and Group 4, which together contribute to more than 60% of all medulloblastomas.

Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways

Malignant rhabdoid tumors (MRTs) are rare lethal tumors of childhood that most commonly occur in the kidney and brain. MRTs are driven by SMARCB1 loss, but the molecular consequences of SMARCB1 loss in extra-cranial tumors have not been comprehensively described and genomic resources for analyses of extra-cranial MRT are limited. To provide such data, we used whole-genome sequencing, whole-genome bisulfite sequencing, whole transcriptome (RNA-seq) and microRNA sequencing (miRNA-seq), and histone modification profiling to characterize extra-cranial MRTs. Our analyses revealed gene expression and methylation subgroups and focused on dysregulated pathways, including those involved in neural crest development.

MEN1 mutations in Hürthle cell (oncocytic) thyroid carcinoma

CONTEXT AND OBJECTIVE

Oncocytic thyroid carcinoma, also known as Hürthle cell thyroid carcinoma, accounts for only a small percentage of all thyroid cancers. However, this malignancy often presents at an advanced stage and poses unique challenges to patients and clinicians. Surgical resection of the tumor accompanied in some cases by radioactive iodine treatment, radiation, and chemotherapy are the established modes of therapy. Knowledge of the perturbed oncogenic pathways can provide better understanding of the mechanism of disease and thus opportunities for more effective clinical management.

DESIGN AND PATIENTS

Initially, two oncocytic thyroid carcinomas and their matched normal tissues were profiled using whole genome sequencing. Subsequently, 72 oncocytic thyroid carcinomas, one cell line, and five Hürthle cell adenomas were examined by targeted sequencing for the presence of mutations in the multiple endocrine neoplasia I (MEN1) gene.

RESULTS

Here we report the identification of MEN1 loss-of-function mutations in 4% of patients diagnosed with oncocytic thyroid carcinoma. Whole genome sequence data also revealed large regions of copy number variation encompassing nearly the entire genomes of these tumors.

CONCLUSION

Menin, a ubiquitously expressed nuclear protein, is a well-characterized tumor suppressor whose loss is the cause of MEN1 syndrome. Menin is involved in several major cellular pathways such as regulation of transcription, control of cell cycle, apoptosis, and DNA damage repair pathways. Mutations of this gene in a subset of Hürthle cell tumors point to a potential role for this protein and its associated pathways in thyroid tumorigenesis.

Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling

High-grade serous ovarian cancer (HGSC) is characterized by poor outcome, often attributed to the emergence of treatment-resistant subclones. We sought to measure the degree of genomic diversity within primary, untreated HGSCs to examine the natural state of tumour evolution prior to therapy. We performed exome sequencing, copy number analysis, targeted amplicon deep sequencing and gene expression profiling on 31 spatially and temporally separated HGSC tumour specimens (six patients), including ovarian masses, distant metastases and fallopian tube lesions. We found widespread intratumoural variation in mutation, copy number and gene expression profiles, with key driver alterations in genes present in only a subset of samples (eg PIK3CA, CTNNB1, NF1). On average, only 51.5% of mutations were present in every sample of a given case (range 10.2-91.4%), with TP53 as the only somatic mutation consistently present in all samples. Complex segmental aneuploidies, such as whole-genome doubling, were present in a subset of samples from the same individual, with divergent copy number changes segregating independently of point mutation acquisition. Reconstruction of evolutionary histories showed one patient with mixed HGSC and endometrioid histology, with common aetiologic origin in the fallopian tube and subsequent selection of different driver mutations in the histologically distinct samples. In this patient, we observed mixed cell populations in the early fallopian tube lesion, indicating that diversity arises at early stages of tumourigenesis. Our results revealed that HGSCs exhibit highly individual evolutionary trajectories and diverse genomic tapestries prior to therapy, exposing an essential biological characteristic to inform future design of personalized therapeutic solutions and investigation of drug-resistance mechanisms.

Complete genomic landscape of a recurring sporadic parathyroid carcinoma

Parathyroid carcinoma is a rare endocrine malignancy with an estimated incidence of less than 1 per million population. Excessive secretion of parathyroid hormone, extremely high serum calcium level, and the deleterious effects of hypercalcaemia are the clinical manifestations of the disease. Up to 60% of patients develop multiple disease recurrences and although long-term survival is possible with palliative surgery, permanent remission is rarely achieved. Molecular drivers of sporadic parathyroid carcinoma have remained largely unknown. Previous studies, mostly based on familial cases of the disease, suggested potential roles for the tumour suppressor MEN1 and proto-oncogene RET in benign parathyroid tumourigenesis, while the tumour suppressor HRPT2 and proto-oncogene CCND1 may also act as drivers in parathyroid cancer. Here, we report the complete genomic analysis of a sporadic and recurring parathyroid carcinoma. Mutational landscapes of the primary and recurrent tumour specimens were analysed using high-throughput sequencing technologies. Such molecular profiling allowed for identification of somatic mutations never previously identified in this malignancy. These included single nucleotide point mutations in well-characterized cancer genes such as mTOR, MLL2, CDKN2C, and PIK3CA. Comparison of acquired mutations in patient-matched primary and recurrent tumours revealed loss of PIK3CA activating mutation during the evolution of the tumour from the primary to the recurrence. Structural variations leading to gene fusions and regions of copy loss and gain were identified at a single-base resolution. Loss of the short arm of chromosome 1, along with somatic missense and truncating mutations in CDKN2C and THRAP3, respectively, provides new evidence for the potential role of these genes as tumour suppressors in parathyroid cancer. The key somatic mutations identified in this study can serve as novel diagnostic markers as well as therapeutic targets.

Clonal evolution of high-grade serous ovarian carcinoma from primary to recurrent disease

High-grade serous carcinoma (HGSC) is the most common and fatal form of ovarian cancer. While most tumours are highly sensitive to cytoreductive surgery and platinum- and taxane-based chemotherapy, the majority of patients experience recurrence of treatment-resistant tumours. The clonal origin and mutational adaptations associated with recurrent disease are poorly understood. We performed whole exome sequencing on tumour cells harvested from ascites at three time points (primary, first recurrence, and second recurrence) for three HGSC patients receiving standard treatment. Somatic point mutations and small insertions and deletions were identified by comparison to constitutional DNA. The clonal structure and evolution of tumours were inferred from patterns of mutant allele frequencies. TP53 mutations were predominant in all patients at all time points, consistent with the known founder role of this gene. Tumours from all three patients also harboured mutations associated with cell cycle checkpoint function and Golgi vesicle trafficking. There was convergence of germline and somatic variants within the DNA repair, ECM, cell cycle control, and Golgi vesicle pathways. The vast majority of somatic variants found in recurrent tumours were present in primary tumours. Our findings highlight both known and novel pathways that are commonly mutated in HGSC. Moreover, they provide the first evidence at single nucleotide resolution that recurrent HGSC arises from multiple clones present in the primary tumour with negligible accumulation of new mutations during standard treatment.

Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia

Genomic profiling has identified a subtype of high-risk B-progenitor acute lymphoblastic leukemia (B-ALL) with alteration of IKZF1, a gene expression profile similar to BCR-ABL1-positive ALL and poor outcome (Ph-like ALL). The genetic alterations that activate kinase signaling in Ph-like ALL are poorly understood. We performed transcriptome and whole genome sequencing on 15 cases of Ph-like ALL and identified rearrangements involving ABL1, JAK2, PDGFRB, CRLF2, and EPOR, activating mutations of IL7R and FLT3, and deletion of SH2B3, which encodes the JAK2-negative regulator LNK. Importantly, several of these alterations induce transformation that is attenuated with tyrosine kinase inhibitors, suggesting the treatment outcome of these patients may be improved with targeted therapy.

Use of mutation profiles to refine the classification of endometrial carcinomas

The classification of endometrial carcinomas is based on pathological assessment of tumour cell type; the different cell types (endometrioid, serous, carcinosarcoma, mixed, undifferentiated, and clear cell) are associated with distinct molecular alterations. This current classification system for high-grade subtypes, in particular the distinction between high-grade endometrioid (EEC-3) and serous carcinomas (ESC), is limited in its reproducibility and prognostic abilities. Therefore, a search for specific molecular classifiers to improve endometrial carcinoma subclassification is warranted. We performed target enrichment sequencing on 393 endometrial carcinomas from two large cohorts, sequencing exons from the following nine genes: ARID1A, PPP2R1A, PTEN, PIK3CA, KRAS, CTNNB1, TP53, BRAF, and PPP2R5C. Based on this gene panel, each endometrial carcinoma subtype shows a distinct mutation profile. EEC-3s have significantly different frequencies of PTEN and TP53 mutations when compared to low-grade endometrioid carcinomas. ESCs and EEC-3s are distinct subtypes with significantly different frequencies of mutations in PTEN, ARID1A, PPP2R1A, TP53, and CTNNB1. From the mutation profiles, we were able to identify subtype outliers, ie cases diagnosed morphologically as one subtype but with a mutation profile suggestive of a different subtype. Careful review of these diagnostically challenging cases suggested that the original morphological classification was incorrect in most instances. The molecular profile of carcinosarcomas suggests two distinct mutation profiles for these tumours: endometrioid-type (PTEN, PIK3CA, ARID1A, KRAS mutations) and serous-type (TP53 and PPP2R1A mutations). While this nine-gene panel does not allow for a purely molecularly based classification of endometrial carcinoma, it may prove useful as an adjunct to morphological classification and serve as an aid in the classification of problematic cases. If used in practice, it may lead to improved diagnostic reproducibility and may also serve to stratify patients for targeted therapeutics.

Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data

Motivation: The study of cancer genomes now routinely involves using next-generation sequencing technology (NGS) to profile tumours for single nucleotide variant (SNV) somatic mutations. However, surprisingly few published bioinformatics methods exist for the specific purpose of identifying somatic mutations from NGS data and existing tools are often inaccurate, yielding intolerably high false prediction rates. As such, the computational problem of accurately inferring somatic mutations from paired tumour/normal NGS data remains an unsolved challenge.

Results: We present the comparison of four standard supervised machine learning algorithms for the purpose of somatic SNV prediction in tumour/normal NGS experiments. To evaluate these approaches (random forest, Bayesian additive regression tree, support vector machine and logistic regression), we constructed 106 features representing 3369 candidate somatic SNVs from 48 breast cancer genomes, originally predicted with naive methods and subsequently revalidated to establish ground truth labels. We trained the classifiers on this data (consisting of 1015 true somatic mutations and 2354 non-somatic mutation positions) and conducted a rigorous evaluation of these methods using a cross-validation framework and hold-out test NGS data from both exome capture and whole genome shotgun platforms. All learning algorithms employing predictive discriminative approaches with feature selection improved the predictive accuracy over standard approaches by statistically significant margins. In addition, using unsupervised clustering of the ground truth ‘false positive’ predictions, we noted several distinct classes and present evidence suggesting non-overlapping sources of technical artefacts illuminating important directions for future study.

Availability: Software called MutationSeq and datasets are available from http://compbio.bccrc.ca.

Contact:saparicio@bccrc.ca

Supplementary information:Supplementary data are available at Bioinformatics online.

Clinicopathologic findings in Jamaican men with prostate cancer

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Background: Jamaican men appear to have higher age adjusted incidence rates (302/100K) than African Americans (250/100K) and Caucasians (182/100K). The purpose of this study is to examine the clinicopathologic findings in Jamaican born men presenting to Memorial Sloan-Kettering Cancer Center over a five-year period.

Methods: We reviewed the records of 150 Jamaican-born men seen at MSKCC for prostate cancer between 2003 and 2008. Age at diagnosis, highest pretreatment PSA levels, Gleason scores, and clinical stage were tabulated. Pathologic T and N stage was included for patients undergoing prostatectomy.

Results: 23 patients were excluded because the diagnosis of prostate cancer was not confirmed. The mean age at diagnosis was 59 years (37-77). The median PSA was 8 ng/mL (1-7,400 ng/mL). The distribution of Gleason scores was Gleason 6: 51 patients (40%), Gleason 7: 57 patients (45%), and Gleason 8-10: 19 patients (15%). 92% (75/81) of the men had organ confined disease by (cT1-2) by DRE. Of 46 men who had prostatectomy, 31 (67%) had organ confined disease (p T2) and 84% (37/44) were node negative.

Conclusions: Without a comparison cohort, no firm conclusions can be drawn. But, Jamaican born men presenting to MSKCC for treatment of prostate cancer do not seem to have unusually adverse pretreatment characteristics or more advanced pathological findings at prostatectomy. Our results may be affected by referral bias in favor of patients with lower risk disease. Further research is needed to determine if Jamaican men with prostate cancer present with more advanced stage or higher grade disease than men in the general population.

No significant financial relationships to disclose.

ARID1A mutations in endometriosis-associated ovarian carcinomas

BACKGROUND

Ovarian clear-cell and endometrioid carcinomas may arise from endometriosis, but the molecular events involved in this transformation have not been described.

METHODS

We sequenced the whole transcriptomes of 18 ovarian clear-cell carcinomas and 1 ovarian clear-cell carcinoma cell line and found somatic mutations in ARID1A (the AT-rich interactive domain 1A [SWI-like] gene) in 6 of the samples. ARID1A encodes BAF250a, a key component of the SWI–SNF chromatin remodeling complex. We sequenced ARID1A in an additional 210 ovarian carcinomas and a second ovarian clear-cell carcinoma cell line and measured BAF250a expression by means of immunohistochemical analysis in an additional 455 ovarian carcinomas.

RESULTS

ARID1A mutations were seen in 55 of 119 ovarian clear-cell carcinomas (46%), 10 of 33 endometrioid carcinomas (30%), and none of the 76 high-grade serous ovarian carcinomas. Seventeen carcinomas had two somatic mutations each. Loss of the BAF250a protein correlated strongly with the ovarian clear-cell carcinoma and endometrioid carcinoma subtypes and the presence of ARID1A mutations. In two patients, ARID1A mutations and loss of BAF250a expression were evident in the tumor and contiguous atypical endometriosis but not in distant endometriotic lesions.

CONCLUSIONS

These data implicate ARID1A as a tumor-suppressor gene frequently disrupted in ovarian clear-cell and endometrioid carcinomas. Since ARID1A mutation and loss of BAF250a can be seen in the preneoplastic lesions, we speculate that this is an early event in the transformation of endometriosis into cancer. (Funded by the British Columbia Cancer Foundation and the Vancouver General Hospital–University of British Columbia Hospital Foundation.).

The completion of the Mammalian Gene Collection (MGC)

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide.

Anatomy of the subtalar joint and imaging of talo-calcaneal coalition

Talo-calcaneal coalitions may be intra-articular or extra-articular in position and may be classified as fibrous, cartilaginous or osseous in morphology. Fibrous coalitions, particularly extra-articular talo-calcaneal coalitions, may have cross-sectional imaging findings that resemble normal anatomic variants, particularly the medial talo-calcaneal ligament and to a lesser extent the presence of an accessory articular facet between the posterior margin of the sustentaculum and postero-medial process of the talus. Typically, in the adult fibrous coalition, there will be some osseous deformity at the entheses, allowing differentiation from a medial talo-calcaneal ligament. The anatomy of the subtalar joint and its ligamentous supports, normal anatomic variations and their corresponding imaging appearance are reviewed in the first part of this article. In the second part, the various forms of talo-calcaneal coalition and their imaging appearance are reviewed.

Immuno-prophylaxis of babies borne to hepatitis B carrier mothers

OBJECTIVES

To examine the efficacy of current hepatitis B immuno-prophylaxis and estimate the prevalence of S-mutant infections among local newborn babies.

DESIGN

Prospective study.

SETTING

Regional hospital, Hong Kong.

PATIENTS

A total of 137 newborn babies delivered between the period of November 2000 and 30 June 2001 inclusive, whose mothers were chronic hepatitis B surface antigen carriers.

RESULTS

Of the 121 infants who were followed up for 12 months, three were found to be chronic hepatitis B virus carriers, giving a vertical transmission rate of 2.5%. One (0.8%) was suspected to be infected by the S-mutant. All the three hepatitis B virus carrier babies were born to mothers with hepatitis B e antigen, but none to the eight mothers suspected to have S-mutants. Of 119 (98.3%) infants who developed hepatitis B surface antibody upon follow-up at 12 months, 35 were found to have hepatitis B e antigen at birth. All were born to hepatitis B e antigen-positive mothers. Only three of the 35 babies were found to be hepatitis B virus carriers. Most babies lost the hepatitis B e antigen by 6 months of age; only the infected babies had the antigen persisting at 1 year of age. The non-infected infants' hepatitis B e antigen is likely transplacental.

CONCLUSIONS

Our hepatitis B virus prophylaxis programme was effective at preventing perinatal infection and the non-infected infants' hepatitis B e antigen was likely transplacental.

Glycerol kinase deficiency presenting with hypodipsia, osmotic diuresis and severe hypernatraemia

A Chinese boy with glycerol kinase deficiency is reported. His presentation with severe hypernatraemia secondary to hypodipsia and glycerol-induced osmotic diuresis is unusual and not previously described in the literature.

Esophageal atresia and achalasialike esophageal dysmotility

A 14-year-old boy presented with regurgitation, malnutrition, and chronic lung insufficiency with a history of successful repair of esophageal atresia and tracheoesophageal fistula in the newborn period. Barium swallow and manometry results showed achalasia. Hellar operation with antireflux procedure resulted in complete symptomatic relief. Histology and immunohistochemistry including PGP9.5, MAP5, cKit, and nNOS of myotomy specimen showed intact innervation. Although esophageal dysmotility after esophageal atresia repair usually is caused by gastroesophageal reflux and incoordination of peristalsis, the possibility of achalasia should also be considered, because a casual relationship between esophageal atresia and achalasia may exist.

Severe cow's milk protein allergy in a Chinese neonate

Cow's milk protein allergy is a growing problem in developed countries. We report the case of a Chinese infant, born at term, who presented on day 28 with severe growth failure, chronic diarrhoea, and metabolic acidosis. Investigations supported a diagnosis of cow's milk protein allergy. This was confirmed by withdrawing and reintroducing the relevant infant formula under controlled clinical conditions. Both acidosis and diarrhoea were seen to resolve, and 'catch-up' growth was evident after introduction of an elemental infant formula. Early recognition of this problem leads to a rapid 'cure', as seen in this case. However, later presentation with other atopic conditions has been reported.

A survey of elderly diabetic patients attending a community clinic in Hong Kong

A cross-sectional survey was conducted on Chinese diabetic patients attending a community clinic in Hong Kong. A questionnaire, physical examination and blood tests were administered. Of 155 adults with diabetes mellitus recruited, the mean age was 63 years (SD 10.3), 77.4% were female and 41.9% illiterate. Half the patients achieved adequate knowledge scores. Knowledge was found to be associated with education level (OR 4.3, 95% CI 1.8, 10.0), longer disease duration (OR 3.2, 95% CI 1.4, 7.4) and complications (OR 0.3, 95% CI 0.1, 0.8). No correlation was found between knowledge and attitude or practice. Attitude was found to be associated with practice (OR 1.2, 95% CI 1.0, 1.3) and male gender (OR 2.9, 95% CI 1.1, 7.5); practice was associated with hypertension (0.5, 95% CI 0.2, 0.9). Older less educated Chinese diabetic patients can be educated about diabetes management, but knowledge does not always translate into practice.

Once daily mometasone furoate aqueous nasal spray is as effective as twice daily beclomethasone dipropionate for treating perennial allergic rhinitis patients

BACKGROUND

Perennial allergic rhinitis is chronic and persistent, may lead to a constellation of secondary complaints including sinusitis, mouth-breathing, and some symptoms resembling a permanent cold, and often requires constant medical intervention. Well-tolerated nasal corticosteroids, alone or in combination with antihistamines, have been found to be very effective in treating this condition.

OBJECTIVE

To compare the effectiveness and tolerability of mometasone furoate aqueous suspension, a new once daily nasal spray, to placebo vehicle and to beclomethasone dipropionate, administered twice daily, in patients with perennial allergic rhinitis.

METHODS

This was a randomized, double-blind, placebo-controlled, double-dummy, parallel group study, in 427 patients age 12 years and older at 24 centers in Canada and Europe. Patients allergic to at least one perennial allergen, confirmed by medical history, skin testing, and adequate symptomatology were eligible to receive one of the following regimens for 3 months: mometasone furoate, 200 micrograms only daily; beclomethasone dipropionate, 200 micrograms twice daily (400 micrograms total dose); or placebo vehicle control. The primary efficacy variable was the change from baseline in total AM plus PM diary nasal symptom score over the first 15 days of treatment.

RESULTS

Three hundred eighty-seven patients were valid for efficacy. For the primary efficacy variable, mometasone furoate was significantly (P < or = .01) more effective than placebo and was indistinguishable from beclomethasone dipropionate. Similar trends were seen among individual symptoms, physician symptom evaluations, and therapeutic response. There was no evidence of tachyphylaxis. All treatments were well tolerated.

CONCLUSIONS

Mometasone furoate nasal spray adequately controls symptoms of perennial allergic rhinitis, offers the advantage of once daily treatment, and is well tolerated.

Characterization of natural toxins with inhibitory activity against serine/threonine protein phosphatases

Recent studies suggest that the ability to inhibit the activity of certain serine/threonine protein phosphatases underlies the toxicity of several natural compounds including: okadaic acid, microcystin-LR, nodularin, calyculin A and tautomycin. To characterize further the actions of these toxins, this study compares the inhibitory effects of okadaic acid, chemical derivatives of okadaic acid, microcystin-LR, microcystin-LA, nodularin, calyculin A and tautomycin on the activity of serine/threonine protein phosphatases types 1 (PP1), 2A (PP2A) and a recently identified protein phosphatase purified from bovine brain (PP3). This study shows that, like PP1 and PP2A, the activity of PP3 is potently inhibited by okadaic acid, both microcystins, nodularin, calyculin A and tautomycin. Further characterization of the toxins employing the purified catalytic subunits of PP1, PP2A and PP3 under identical experimental conditions indicates that: (a) okadaic acid, microcystin-LR, and microcystin-LA inhibit PP2A and PP3 more potently than PP1 (order of potency PP2A > PP3 > PP1); (b) nodularin inhibits PP1 and PP3 at a similar concentration that is slightly higher than that which affects PP2A, and (c) both calyculin A and tautomycin show little selectivity among the phosphatases tested. This study also shows that the chemical modification of the (C1) carboxyl group of okadaic acid can have a profound influence on the inhibitory activity of this toxin. Esterification of okadaic acid, producing methyl okadaate, or reduction, producing okadaol, greatly decreases the inhibitory effects against all three enzymes tested. Further reduction, producing 1-nor-okadaone, or acetylation, producing okadaic acid tetraacetate, results in compounds with no inhibitory activity. In contrast, the substitution of alanine (-LA) for arginine (-LR) in microcystin has no apparent effect on the inhibitory activity against PP1, PP2A or PP3.

Okadaic acid inhibits PDGF-induced proliferation and decreases PDGF receptor number in C3H/10T1/2 mouse fibroblasts

Okadaic acid is both a potent inhibitor of protein serine/threonine phosphatases and a tumor promoter in the mouse skin model. We have previously shown that at non-toxic nanomolar concentrations okadaic acid reversibly inhibits induction (promotion) by PDGF of transformed cells by the 'complete' and 'two-stage' protocols in the C3H/10T1/2 mouse fibroblast transformation assay. In the present study we have demonstrated that treatment of confluent and proliferatively quiescent C3H/10T1/2 mouse fibroblasts with low doses of okadaic acid inhibits the platelet-derived growth factor (PDGF)-induced mitogenic response. This inhibition is accompanied by a loss of PDGF binding sites, a decreased PDGF-induced phosphatidylinositol turnover and a decrease in the PDGF-induced intracellular calcium signal. The decrease in the PDGF-generated intracellular signalling processes represents a mechanism by which okadaic acid inhibits PDGF-induced proliferation and the promotion of in vitro neoplastic transformation by PDGF.

Differences in mediator release between allergic rhinitis and asthma

To determine why patients with allergic rhinitis alone differ in their airway response to inhaled allergen compared to patients with allergic asthma, bronchial lavage was performed in 10 subjects with allergic asthma and in five subjects with allergic rhinitis, before and after inhalation challenge with antigen to produce an immediate asthmatic reaction. Before antigen challenge, the subjects with asthma had higher absolute neutrophil counts in the lavage fluid. After antigen challenge, the subjects with asthma released significant amounts of bronchoconstrictive mediators, such as histamine and thromboxane B2 into the lavage fluid, whereas subjects with rhinitis alone did not. There was also a significant increase in prostaglandin E2 in the subjects with asthma after antigen challenge. Nonimmunologic bronchoconstriction with methacholine inhalation challenge in six other subjects with asthma did not demonstrate an increase in any of the lavage fluid mediator levels that were measured. A positive correlation was found between methacholine provocative concentration causing a 20% drop in FEV1 and the concentration of prostaglandin E2 in the lavage fluid before challenge. The significance of this observation has yet to be determined. The results suggest that subjects with allergic asthma differ from subjects with rhinitis alone in their capacity to release more mediators into the airways on antigen challenge. It is not known whether this increase in mediators is due to increase in the number of mast cells in the airways or due to increase in mediator releasability from the mast cells of subjects with asthma.

Dilemmas in counselling: the EEC syndrome

A family with the EEC syndrome is reported. Two sibs have the classical form of the condition with ectrodactyly, ectodermal dysplasia, and clefting. Their mother, however, has only minimal evidence, with preaxial polydactyly of the right hand and duplication of the terminal phalanx of the second toe of the left foot with 3/4 syndactyly. The dilemmas faced by the genetic counsellor are discussed in this variable autosomal dominant condition.

Congenital absence of insulin-secreting cells

A male infant was diagnosed as having diabetes mellitus 1 d after birth and died on the third day. Histological examination of the pancreas showed small and inconspicuous islets of Langerhans that were completely devoid of insulin-secreting cells. There was no evidence of insulitis.

The allergic patient and advances in immunology

Our understanding of the basic pathogenetic mechanism of human allergic diseases was made possible by the discovery of IgE and the identification of this immunoglobulin as the key molecule in the mediation of human allergic reactions. The modern immunological principles in connection with the immediate hypersensitivity reaction can be applied to the management of allergic patients in terms of rational approaches in the areas of diagnosis and treatment.