Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Colon cancer-derived oncogenic EGFR G724S mutant identified by whole genome sequence analysis is dependent on asymmetric dimerization and sensitive to cetuximab

Background

Inhibition of the activated epidermal growth factor receptor (EGFR) with either enzymatic kinase inhibitors or anti-EGFR antibodies such as cetuximab, is an effective modality of treatment for multiple human cancers. Enzymatic EGFR inhibitors are effective for lung adenocarcinomas with somatic kinase domain EGFR mutations while, paradoxically, anti-EGFR antibodies are more effective in colon and head and neck cancers where EGFR mutations occur less frequently. In colorectal cancer, anti-EGFR antibodies are routinely used as second-line therapy of KRAS wild-type tumors. However, detailed mechanisms and genomic predictors for pharmacological response to these antibodies in colon cancer remain unclear.

Findings

We describe a case of colorectal adenocarcinoma, which was found to harbor a kinase domain mutation, G724S, in EGFR through whole genome sequencing. We show that G724S mutant EGFR is oncogenic and that it differs from classic lung cancer derived EGFR mutants in that it is cetuximab responsive in vitro, yet relatively insensitive to small molecule kinase inhibitors. Through biochemical and cellular pharmacologic studies, we have determined that cells harboring the colon cancer-derived G719S and G724S mutants are responsive to cetuximab therapy in vitro and found that the requirement for asymmetric dimerization of these mutant EGFR to promote cellular transformation may explain their greater inhibition by cetuximab than small-molecule kinase inhibitors.

Conclusion

The colon-cancer derived G719S and G724S mutants are oncogenic and sensitive in vitro to cetuximab. These data suggest that patients with these mutations may benefit from the use of anti-EGFR antibodies as part of the first-line therapy.

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

Translating whole-exome sequencing (WES) for prospective clinical use may have an impact on the care of patients with cancer; however, multiple innovations are necessary for clinical implementation. These include rapid and robust WES of DNA derived from formalin-fixed, paraffin-embedded tumor tissue, analytical output similar to data from frozen samples and clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival formalin-fixed, paraffin-embedded tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a 'long tail' of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15 out of 16 patients. In one patient, previously undetected findings guided clinical trial enrollment, leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine.

Somatic mutation of CDKN1B in small intestine neuroendocrine tumors

The diagnosed incidence of small intestine neuroendocrine tumors (SI-NETs) is increasing, and the underlying genomic mechanisms have not yet been defined. Using exome- and genome-sequence analysis of SI-NETs, we identified recurrent somatic mutations and deletions in CDKN1B, the cyclin-dependent kinase inhibitor gene, which encodes p27. We observed frameshift mutations of CDKN1B in 14 of 180 SI-NETs, and we detected hemizygous deletions encompassing CDKN1B in 7 out of 50 SI-NETs, nominating p27 as a tumor suppressor and implicating cell cycle dysregulation in the etiology of SI-NETs.

Meso-Rex shunt using deep femoral vein conduit: first report

The Meso-Rex shunt (MRS) procedure was first described in 1992 by de VILLE et al. for the treatment of extrahepatic portal vein obstruction (EHPVO) in paediatric liver transplant patients. This technique provides more physiological relief of portal hypertension compared to the porto-systemic shunts, which can lead to long-term complications such as hyperammonaemia and hepato-pulmonary syndrome. Different conduits as autologous and cryopreserved veins or prosthetic grafts have been previously reported. We present herein the first case of a MRS using the autologous deep femoral vein in a 17-year-old female patient affected by EHPVO from unknown reasons.

Mutational heterogeneity in cancer and the search for new cancer-associated genes

Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour-normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.

Punctuated evolution of prostate cancer genomes

The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of genome-wide alterations has not been profiled extensively in this disease. We sequenced the genomes of 57 prostate tumors and matched normal tissues to characterize somatic alterations and to study how they accumulate during oncogenesis and progression. By modeling the genesis of genomic rearrangements, we identified abundant DNA translocations and deletions that arise in a highly interdependent manner. This phenomenon, which we term "chromoplexy," frequently accounts for the dysregulation of prostate cancer genes and appears to disrupt multiple cancer genes coordinately. Our modeling suggests that chromoplexy may induce considerable genomic derangement over relatively few events in prostate cancer and other neoplasms, supporting a model of punctuated cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we charted a path of oncogenic events along which chromoplexy may drive prostate carcinogenesis.

Safety and sample adequacy of renal transplant surveillance biopsies

PURPOSE

To report on the safety and adequacy of surveillance biopsy for detecting subclinical lesions in clinically stable renal grafts.

MATERIALS AND METHODS

We established an in-patient surveillance biopsy program with the elective performance of a renal transplant biopsy during the first year after renal transplantation. All biopsies in our centre were performed or supervised by the same operator. Patients were admitted to the hospital the day of biopsy and were discharged after 24h of observation. All patients were biopsied in supine position, using a 16-gauge needle with a spring-loaded gun (Bard) under real-time ultrasound guidance. Complication rates were retrospectively scored using the patients' charts and blood counts before and after biopsy. Major complications were defined as those requiring an intervention for resolution, a transfusion of blood products or an invasive procedure (angiography or surgery), and those that led to acute renal obstruction or failure, septicaemia, graft loss or death. In all other cases complications were considered minor. An adequate biopsy was defined as the presence of 7 or more glomeruli and at least one artery in the biopsy specimen.

RESULTS

We performed 282 surveillance biopsies in 248 patients between January 2006 and December 2011. None of the complications were major. We observed 6% minor complications (n = 17). 5.6% (n = 16) of the complications were related to bleeding, with macroscopic haematuria as the most common condition (n = 10; 3.5%), followed by pain (n = 6; 2.1%) eighter due to a perinephric hematoma (n = 5) or a subcutaneous hematoma (n = 1). The biopsies contained a median number of 9 glomeruli (range 0-39) with 70% of biopsies containing at least 7 glomeruli and one artery.

CONCLUSION

The procedure for taking surveillance biopsies was proven to be safe. There were no major complications and only rare minor complications. The majority of the samples were adequate for histological examination.

Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity

The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With a 5-year survival rate of ~15%, the identification of new therapeutic targets for EAC is greatly important. We analyze the mutation spectra from whole-exome sequencing of 149 EAC tumor-normal pairs, 15 of which have also been subjected to whole-genome sequencing. We identify a mutational signature defined by a high prevalence of A>C transversions at AA dinucleotides. Statistical analysis of exome data identified 26 significantly mutated genes. Of these genes, five (TP53, CDKN2A, SMAD4, ARID1A and PIK3CA) have previously been implicated in EAC. The new significantly mutated genes include chromatin-modifying factors and candidate contributors SPG20, TLR4, ELMO1 and DOCK2. Functional analyses of EAC-derived mutations in ELMO1 identifies increased cellular invasion. Therefore, we suggest the potential activation of the RAC1 pathway as a contributor to EAC tumorigenesis.

Abstract 5135: Analysis of formalin-fixed paraffin-embedded (FFPE) samples

The availability of large numbers of formalin-fixed, paraffin-embedded (FFPE) tumor DNA samples, together with accurate and specific clinical annotations, can be a great resource for in-depth analysis of correlations of somatic and germline DNA alterations with clinical outcome. However, the effects of this tissue preservation technique on next-generation DNA sequencing technologies and downstream analyses are still being investigated. Furthermore, usually the archives of such FFPE samples do not include matched normal tissue, which complicates the process of identifying somatic alterations. We are in the process of analyzing lung adenocarcinoma, colorectal and prostate patient datasets, which contain both an FFPE and a fresh-frozen tumor together with a matched blood normal sample. The availability of both a frozen and an FFPE tumor sample enables us to compare the detected somatic point mutations and indels, taking into account the fact that these pairs are produced from different aliquots of DNA. This analysis includes calculating the power to detect variants in the FFPE sample given that they have been observed in the fresh frozen tumor, as well as the validation rate of clonal SNVs between the two samples. We are also developing a method for classification of SNVs as germline or somatic without a paired normal sample by taking advantage of the fact that most tumor samples contain a substantial fraction of normal cells. Because stromal contamination has a different effect on the allelic fraction of somatic vs. germline SNVs, we can apply algorithms to estimate tumor purity and absolute somatic copy numbers in order to distinguish the two types of events. We present preliminary results from these analyses.

Citation Format: Petar Stojanov, Scott L. Carter, Ivan Imaz Rosshandler, Andrey Sivachenko, Alberto Salido Guadarrama, Karla Vazquez, Sandra Romero Cordoba, Kristian Cibulskis, Carrie Sougnez, Douglas Voet, Gordon Saksena, Lee Lichtenstein, Lihua Zou, Scott Frazer, Chip Stewart, Rameen Beroukhim, Matthew Meyerson, Michael S. Lawrence, Gad Getz. Analysis of formalin-fixed paraffin-embedded (FFPE) samples. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5135. doi:10.1158/1538-7445.AM2013-5135

Abstract 1112: Whole exome and whole genome sequence analysis of lung adenocarcinoma

Lung adenocarcinoma is the leading cause of cancer-related death worldwide. Recent molecular characterization of this disease through large-scale sequencing efforts has identified distinct subsets driven by mutant oncogenes or kinase fusion proteins, many of which can be inhibited with targeted therapies. Despite these advances, almost half of all lung cancers still lack an identifiable driver. Here, we describe the genomic profiling of 230 normal-paired lung adenocarcinoma samples included as part of The Cancer Genome Atlas (TCGA) effort. All samples were subjected to whole exome analysis, copy number profiling and a subset were also subjected to whole genome sequencing. Mutation calling was performed with the MuTect algorithm. To identify significantly mutated genes, we used the MutSig CV algorithm, a statistically rigorous analysis that takes into account nucleotide context, gene-expression, replication time, and somatic background mutation rate. Mutation rate in lung adenocarcinoma was quite high with an average of 242 mutations/tumor observed (median: 161, range: 11-1328). In total, we identified mutations in over 13,500 genes of which 10 genes reached statistical significance (q<0.1). One significant gene was excluded from further analyses as it was not expressed in RNA-seq data. In addition to mutant genes with established roles in lung adenocarcinoma (e.g. TP53, KRAS, STK11, EGFR, RB1, KEAP1, and BRAF), we also identified other statistically significant mutant genes whose role in lung tumorigenesis is presently unclear. These included mutations in the RNA-binding protein RBM10, and the integrin protein ITGAL. Although statistically insignificant by a small degree, we also identified mutations in the splicing factor U2AF1, and the SWI/SNF complex proteins SMARCA4 and ARID1A. We are currently analyzing whole genome sequences to confirm these events, and identify known and novel fusion events that may be contributing to tumorigenesis. In conclusion, we have analyzed the exomes of 230 lung adenocarcinoma samples and identified known and unknown mutations in this disease. Ultimately, these data will be integrated with ongoing expression, methylation, pathway, miRNA, and proteomic analyses. At its conclusion, this effort will represent the most comprehensive profiling of lung adenocarcinoma samples to date, and will provide a detailed integrative picture of the molecular mechanisms contributing to this disease.

Citation Format: Juliann Chmielecki, Mara Rosenberg, Marcin Imielinski, Bryan Hernandez, Michael Lawrence, Andrey Sivachenko, Kristian Cibulskis, Douglas Voet, Carrie Sougnez, Stacey Gabriel, Gad Getz, Matthew Meyerson, The Cancer Genome Atlas Research Network. Whole exome and whole genome sequence analysis of lung adenocarcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1112. doi:10.1158/1538-7445.AM2013-1112

Abstract 4601: Punctuated evolution of prostate cancer genomes

The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of alterations across the entire genome has not been profiled extensively in this disease. We sequenced the genomes of 55 primary prostate tumors and matched normal tissues to catalogue somatic alterations and to study how they accumulate during oncogenesis and progression. By implementing an algorithm to identify genomic alterations that arise together, we found abundant sets of DNA rearrangements and deletions that may occur simultaneously in a single cell. This phenomenon, which we term “chromoplexy," frequently accounts for the dysregulation of prostate cancer genes including PTEN, NKX3-1, TP53 and CDKN1B. The somatic fusion of TMPRSS2 and ERG, which occurs in approximately half of prostate cancers, predominantly arises with additional genomic rearrangements in the context of chromoplexy. We further demonstrate that TMPRSS2-ERG fusion-positive tumors display a unique profile of chromoplexy, with complex chains of rearrangements that may fuse DNA from four or more distinct chromosomes.

In prostate cancer and other neoplasms, chromoplexy induces considerable genomic derangement in a series of relatively few events. In several instances, multiple cancer genes from non-contiguous regions of the genome appear to be disrupted simultaneously by this process, suggesting a model of punctuated progression during cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we constructed a path of oncogenic events along which chromoplexy drives prostate carcinogenesis.

Citation Format: Sylvan C. Baca, Davide Prandi, Michael S. Lawrence, Juan Miguel Mosquera, Alessandro Romanel, Yotam Drier, Kyung Park, Naoki Kitabayashi, Theresa Y. MacDonald, Eliezer Van Allen, Gregory V. Kryukov, Jean-Philippe Theurillat, T. David Soong, Elizabeth Nickerson, Daniel Auclair, Ashutosh Tewari, Himisha Beltran, Robert C. Onofrio, Gunther Boysen, Candace Guiducci, Christopher E. Barbieri, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Douglas Voet, Gordon Saksena, Michelle R. Cipicchio, Kristin Ardlie, Philip W. Kantoff, Michael F. Berger, Stacey B. Gabriel, Todd R. Golub, Matthew Meyerson, Eric S. Lander, Olivier Elemento, Gad Getz, Francesca Demichelis, Mark A. Rubin, Levi A. Garraway. Punctuated evolution of prostate cancer genomes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4601. doi:10.1158/1538-7445.AM2013-4601

Abstract 4017: Dissecting the clonal hierarchy of cancer-driving genomic lesions

Characterizing the genomic evolution of cancer is critical to understanding disease progression and identifying potential therapeutic targets. By examining the clonal hierarchy of genomic lesions in common tumors, it would be possible to reconstruct the path of oncogenic events that drive carcinogenesis. Reliable assessment of such paths from high-throughput genome sequencing data is complicated by the admixture of normal DNA in tumor samples and by reduced data signal for highly subclonal events. We introduce an approach that exploits individuals’ genetic background by using the abundant germline SNP genotype data provided by whole genome sequence coverage to assess the clonality of genomic alterations, including copy number changes, rearrangements, and point mutations.

We developed a novel algorithm, CLONET (CLONality Estimate in Tumors), which analyzes patient-specific heterozygous SNP loci (informative SNPs) and mono-allelic somatic deletions to assess levels of stromal DNA admixture and infer the clonal status of each aberration. For every mono allelic deletion, CLONET assesses the allelic fractions of informative SNPs to determine the apparent proportion of normal cells DNA. Next, through a conservative use of simulation-based error estimates, deletions with the lowest proportions of normal DNA reads are considered clonal. For point mutations, the tumor allelic fraction is corrected for stromal DNA admixture level and subclonality is inferred when it differs significantly from the expected value for clonal lesions. Similarly, the proportions of reads that span each side of a putative breakpoint involved in a rearrangement are matched against the expected values. CLONET also addresses tumor aneuploidy by searching for chromosomes with coverage and allelic fractions of informative SNPs not consistent with a diploid genome.

CLONET was tested on 55 whole genome sequences from prostate cancers, a highly heterogeneous tumor type, to catalogue the accumulation of somatic alterations during oncogenesis and progression. In 98% of the cases CLONET made confident assessment of admixture and clonality. We observed consistent clonal lesions involving NKX3-1, the 3Mb region between TMPRSS2 and ERG and FOXP1, as well as early point mutations in SPOP and FOXA1. Overall, we observed a higher rate of subclonal protein-coding point mutation versus deletions (p-value < 10−7). We validated this approach by IHC and FISH for predicted clonal and sub-clonal events. A predicted subclonal homozygous deletion of CHD1 was confirmed by FISH that demonstrated the presence of both nuclei with homozygous and with hemizygous deletion of CHD1. Finally, to assess the general validity of CLONET, we analyzed data from 53 additional tumor genomes, including 25 melanomas and 28 lung adenocarcinomas.

In summary, our results imply the existence of consensus paths of tumor carcinogenesis that favor dysregulation of cancer genes in a defined sequence.

Citation Format: Davide Prandi, Sylvan C. Baca, Michael S. Lawrence, Juan Miguel Mosquera, Alessandro Romanel, Yotam Drier, Kyung Park, Naoki Kitabayashi, Theresa Y. MacDonald, Eliezer Van Allen, Gregory V. Kryukov, Jean-Philippe Theurillat, T. David Soong, Elizabeth Nickerson, Daniel Auclair, Ashutosh Tewari, Himisha Beltran, Robert C. Onofrio, Gunther Boysen, Candace Guiducci, Christopher E. Barbieri, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Gordon Saksena, Douglas Voet, Alex H. Ramos, Wendy Winckler, Michelle Cipicchio, Kristin Ardlie, Philip W. Kantoff, Michael F. Berger, Stacey B. Gabriel, Todd R. Golub, Matthew Meyerson, Eric S. Lander, Olivier Elemento, Gad Getz, Francesca Demichelis, Mark A. Rubin, Levi A. Garraway. Dissecting the clonal hierarchy of cancer-driving genomic lesions. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4017. doi:10.1158/1538-7445.AM2013-4017

A landscape of driver mutations in melanoma

Despite recent insights into melanoma genetics, systematic surveys for driver mutations are challenged by an abundance of passenger mutations caused by carcinogenic UV light exposure. We developed a permutation-based framework to address this challenge, employing mutation data from intronic sequences to control for passenger mutational load on a per gene basis. Analysis of large-scale melanoma exome data by this approach discovered six novel melanoma genes (PPP6C, RAC1, SNX31, TACC1, STK19, and ARID2), three of which-RAC1, PPP6C, and STK19-harbored recurrent and potentially targetable mutations. Integration with chromosomal copy number data contextualized the landscape of driver mutations, providing oncogenic insights in BRAF- and NRAS-driven melanoma as well as those without known NRAS/BRAF mutations. The landscape also clarified a mutational basis for RB and p53 pathway deregulation in this malignancy. Finally, the spectrum of driver mutations provided unequivocal genomic evidence for a direct mutagenic role of UV light in melanoma pathogenesis.

Melanoma genome sequencing reveals frequent PREX2 mutations

Melanoma is notable for its metastatic propensity, lethality in the advanced setting, and association with ultraviolet (UV) exposure early in life¹. To obtain a comprehensive genomic view of melanoma, we sequenced the genomes of 25 metastatic melanomas and matched germline DNA. A wide range of point mutation rates was observed: lowest in melanomas whose primaries arose on non-UV exposed hairless skin of the extremities (3 and 14 per Mb genome), intermediate in those originating from hair-bearing skin of the trunk (range = 5 to 55 per Mb), and highest in a patient with a documented history of chronic sun exposure (111 per Mb). Analysis of whole-genome sequence data identified PREX2 - a PTEN-interacting protein and negative regulator of PTEN in breast cancer² - as a significantly mutated gene with a mutation frequency of approximately 14% in an independent extension cohort of 107 human melanomas. PREX2 mutations are biologically relevant, as ectopic expression of mutant PREX2 accelerated tumor formation of immortalized human melanocytes in vivo. Thus, whole-genome sequencing of human melanoma tumors revealed genomic evidence of UV pathogenesis and discovered a new recurrently mutated gene in melanoma.

Abstract 5056: A glimpse into the somatic mutation landscape of melanoma through exome sequencing of 121 tumor-normal pairs

Melanoma is an aggressive skin cancer of melanocytic origin characterized by high metastatic potential and mutation rate. Affording a survey of the wide breadth of genomic lesions found in melanoma, we present here an analysis of the somatic mutations discovered in the sequenced exomes of 121 melanoma tumor-normal pairs. We identify frequent genomic alterations both in genes previously implicated in melanoma (BRAF, NRAS, TP53, CDKN2A, PTEN) as well as in several genes whose role in melanoma tumorigenesis has not yet been established and thus are of particular interest. To do so we implement a novel method to increase the identification of genes that are significantly recurrently mutated in melanoma in the setting of its exceptionally high mutation rate. A preponderance of C>T transitions (∼85%) in the observed mutational profile reflects a history of DNA damage due to UV radiation, though the majority of somatic mutations in known melanoma genes are not C>T events. Our study broadens understanding of the genomic lesions involved in melanoma tumorigenesis, and we expect our analysis approach to inform future genomic studies of cancer lineages with similarly high mutation rates.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5056. doi:1538-7445.AM2012-5056

Contrast-enhanced ultrasonography in hepatosplenic sarcoidosis

We report a case of a 38-year-old woman with atypical pain in the left lower hemi-abdomen. On abdominal B-mode ultrasonography the liver was normal; the spleen showed multiple subcentimetric hypoechoic nodules. A multidetector CT-examination revealed multiple small low-attenuation nodules in the liver and the spleen, suggestive for metastatic disease. Contrast-enhanced ultrasound (CEUS) revealed two hypoechoic nodules in the liver that were visible in the portal phase and disappeared in the late phase. The focal splenic lesions were visible as irregular hypo-enhancing nodules. An MRI examination, including T1, T2 and contrast-enhanced images, could not confirm the exact nature of the lesions. A core biopsy of a splenic nodule yielded non-caseating epithelioid cell granulomas. Different complementary examinations were normal and hepatosplenic sarcoidosis was diagnosed. The pain in the left lower hemi-abdomen was ascribed to irritable bowel syndrome.

The mutational landscape of head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a common, morbid, and frequently lethal malignancy. To uncover its mutational spectrum, we analyzed whole-exome sequencing data from 74 tumor-normal pairs. The majority exhibited a mutational profile consistent with tobacco exposure; human papillomavirus was detectable by sequencing DNA from infected tumors. In addition to identifying previously known HNSCC genes (TP53, CDKN2A, PTEN, PIK3CA, and HRAS), our analysis revealed many genes not previously implicated in this malignancy. At least 30% of cases harbored mutations in genes that regulate squamous differentiation (for example, NOTCH1, IRF6, and TP63), implicating its dysregulation as a major driver of HNSCC carcinogenesis. More generally, the results indicate the ability of large-scale sequencing to reveal fundamental tumorigenic mechanisms.

The genomic complexity of primary human prostate cancer

Prostate cancer is the second most common cause of male cancer deaths in the United States. However, the full range of prostate cancer genomic alterations is incompletely characterized. Here we present the complete sequence of seven primary human prostate cancers and their paired normal counterparts. Several tumours contained complex chains of balanced (that is, 'copy-neutral') rearrangements that occurred within or adjacent to known cancer genes. Rearrangement breakpoints were enriched near open chromatin, androgen receptor and ERG DNA binding sites in the setting of the ETS gene fusion TMPRSS2-ERG, but inversely correlated with these regions in tumours lacking ETS fusions. This observation suggests a link between chromatin or transcriptional regulation and the genesis of genomic aberrations. Three tumours contained rearrangements that disrupted CADM2, and four harboured events disrupting either PTEN (unbalanced events), a prostate tumour suppressor, or MAGI2 (balanced events), a PTEN interacting protein not previously implicated in prostate tumorigenesis. Thus, genomic rearrangements may arise from transcriptional or chromatin aberrancies and engage prostate tumorigenic mechanisms.

Abstract 1139: Complete characterization of prostate cancer genomes by massively parallel sequencing

Prostate cancer is the most common type of cancer diagnosed among men in the United States, accounting for 200,000 new cases and 27,000 deaths per year. Prior genetic studies have shown that chromosomal rearrangements comprise a major mechanism of oncogene activation in prostate cancer. For example, androgen-regulated gene fusions involving ETS family transcription factors are present in the majority of prostate cancers, yet the full repertoire of genomic alterations driving prostate carcinogenesis and progression remains unknown. Toward this end, recent technological advances have made it possible to characterize the full complement of somatic mutations in a single tumor through whole genome sequencing.

We are using massively parallel sequencing technology to characterize the complete genomes of several primary prostate adenocarcinomas at >30x coverage. All samples are high-grade primary tumors (Gleason grade 7 to 9) and include cases with and without known ETS family translocations. For each tumor, we are also obtaining >30x sequence coverage of matched normal DNA from blood of these same patients in order to determine the somatic component of the overall variation we observe. Our results indicate that translocations and other chromosomal rearrangements occur frequently in prostate cancer, at a rate of >100 per genome. Further, we have discovered many nonsynonymous sequence mutations (point mutations and indels) in each tumor, some of which may represent novel candidate drivers of tumor progression. The overall rate of somatic point mutations is approximately 1 per Megabase. Integrated analysis of all genomes reveals both recurrent and private alterations. Together, these results illuminate potential avenues for target discovery and demonstrate the unparalleled value in performing complete genome sequencing in this malignancy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1139.

Pulsating tumour in the clavicular region of a chronic haemodialysis patient with ipsilateral vascular access catheter

We describe the case of a 70-year-old woman who presented with a pulsating mass in the left supraclavicular region during a haemodialysis session. The frequency of the pulsations, parallel to that of the dialysis-related blood flow cycle, without blood loss at the exit site, indicated that this observation could potentially be attributed to a rupture of the silastic material in the subcutaneous track of the catheter. Our hypothesis was confirmed after removal of the catheter.

Free DIEAP and SGAP flap breast reconstruction after abdominal/gluteal liposuction

Perforator flaps are widely used in our unit for breast reconstruction. They provide ample tissue with minimal donor site morbidity together with long lasting aesthetic results. Increasing number of patients may have liposuction procedure which may jeopardise areas such as the abdomen and the buttock which are the donor sites for perforator-free flaps in breast reconstruction. Therefore, liposuction has been considered as a relative contraindication of raising perforator flaps. Six patients who had previous liposuction of the donor sites underwent autologous breast reconstruction with perforator-free flaps. Colour Duplex imaging was obtained in all cases preoperatively in order to evaluate the blood supply to the flap and to map the perforators. There were five deep inferior epigastric artery flaps (DIEP) and one superior gluteal artery perforator (SGAP) flap used. Total flap survival was obtained in all cases. Postoperative course was uneventful. Our results showed that raising perforator flaps after liposuction of the donor sites is possible. Preoperative radiological evaluation of the perforators is mandatory for such difficult cases.

Visceral and testicular calcifications as part of the phenotype in pseudoxanthoma elasticum: ultrasound findings in Belgian patients and healthy carriers

Occasionally calcifications in abdominal organs, breasts and testicles have been reported in pseudoxanthoma elasticum (PXE) patients. In the present study, an ultrasound evaluation was performed of the abdomen and--in male patients--of the testicles in 17 PXE patients and 17 heterozygous carriers. Blood samples were taken to evaluate calcium load, liver and kidney function. Calcifications in liver, kidneys and spleen were detected in 59% of the patients and in 23.5% of healthy carriers. Parameters of kidney and liver function were normal in both groups, suggesting that the calcifications have no direct effect on organ function. Testicular ultrasound revealed parenchymous calcifications in all males investigated. Widespread, small hyperechogenic foci resembling testicular microlithiasis were seen. In some carriers, focal calcifications were identified. The current data suggest that visceral and testicular calcifications are part of the phenotype of PXE patients. Their presence in some of the healthy carriers are suggestive of subclinical manifestations in these relatives. The natural history and long-term effects of the parenchymal calcifications remain to be elucidated. As testicular microlithiasis may be associated with a higher risk for malignancy, regular clinical and ultrasound follow-up seems indicated in these patients.

[Treatment of iatrogenic femoral pseudoaneurysms by ultrasound-guided percutaneous thrombin injection: effectiveness and complications]

AIM

We retrospectively assessed the effectiveness of ultrasound-guided percutaneous thrombin injection in the treatment of iatrogenic femoral pseudoaneurysms and registered the occurrence of complications in the systemic circulation.

METHODS

We performed ultrasound-guided thrombin injection in 26 iatrogenic femoral pseudoaneurysms: 24 were classified as single en 2 as complex. We registered the volume and the pseudoaneurysm neck measurements, as well as the complication rate.

RESULTS

Ultrasound-guided percutaneous thrombin injection led to a successful obliteration of pseudoaneurysm in 25 out of 26 cases (96.2%). The thrombin amount varied between 250 and 1000 IU. A thrombosis of the common femoral artery after the thrombin injection occurred only in one patient.

CONCLUSION

Ultrasound-guided percutaneous thrombin injection is effective and safe in the treatment of iatrogenic femoral pseudoaneurysms provided the exclusion criteria are respected. Complications are rare.

Ultrasound and CT changes of liver parenchyma in acute schistosomiasis

Acute schistosomiasis in travellers to endemic regions often remains unrecognized. Early diagnosis is important to avoid progression to chronic disease. Diagnosis is based on clinical, epidemiological and laboratory data. The role of imaging techniques as diagnostic tools remains to be established in acute clinical schistosomiasis. We describe hypodense nodules in the liver on ultrasound and CT scanning in a patient with acute schistosomiasis (Katayama syndrome). To our knowledge this is the first description of nodular hepatic lesions in acute schistosomiasis.

Rational design, analysis, and potential utility of GM-CSF antagonists

Granulocyte-macrophage colony-stimulating factor (GM-CSF) is an important cytokine involved in many immune and inflammatory processes and is believed to act in the early stages of immune responses. GM-CSF stimulates antigen-presenting cells, enhancing antigen presentation and inducing macrophage tumoricidal activity. GM-CSF binds to specific cellular receptors that are potential targets for pharmacological design. Rational design of small-molecule mimics is an important approach to pharmacophore design. One of the strategies in the development of small-molecular mimics of larger polypeptyde ligands is analysis of alternative ligands that bind the same site as does the native ligand. Molecular studies of GM-CSF-receptor interactions have led to the development of interaction site analogs and the development of an "anti-anti-GM-CSF" recombinant antibody (rAb) analog of a site on GM-CSF important for biological activity and receptor binding. This rAb and a peptide derived from the rAb first complementarity determining region (CDR) sequence bind to a monoclonal anti-GM-CSF antibody that mimics the GM-CSFR alpha chain, compete with GM-CSF for binding to GM-CSF receptor alpha chain (GM-CSFR alpha), and are specific biological antagonists. Molecular modeling of the rAb suggests structural similarity with a site previously implicated in GM-CSF binding to the GM-CSFR alpha. Two cyclic peptides, 1785 and 1786, also were developed on the basis of structural analysis of the GM-CSF region mimicked by anti-anti-GM-CSF recombinant antibody (rAb) 23.2. These peptides were designed to mimic structurally the positions of specific residues on the B and C helicies of human GM-CSF implicated in receptor binding and bioactivity. Both 1785 and 1786 were recognized specifically by polyclonal anti-GM-CSF antibody. 1786 also competitively inhibited binding of GM-CSF to the GM-CSF receptor and demonstrated antagonist bioactivity, as shown by its reversal of GM-CSF's ability to inhibit apoptosis of the GM-CSF-dependent cell line MO7E. These studies support the role of residues on the GM-CSF B and C helicies in receptor binding and bioactivity and suggest strategies for mimicking binding sites on four-helix bundle proteins with cyclic peptides.

Effect of nifedipine on superior mesenteric artery impedance in humans

OBJECTIVE

In a randomized, double-blind placebo-controlled study the acute effect of sublingual nifedipine (10 mg) on the superior mesenteric artery pulsatility index (p.i.) was studied over 60 min in 12 healthy subjects (Age 43 y).

METHODS

p.i. was considered as a parameter of vascular resistance and was calculated as the peak-to-peak amplitude of the waveform divided by the mean amplitude. p.i. measurements were performed with the subject resting and fasting and were made 5, 10, 15, 30, 45 and 60 min for 1 hour after nifedipine (10 mg) or placebo. Arterial blood pressure and heart rate were measured at the same times.

RESULTS

Placebo administration failed to change arterial blood pressure, heart rate or p.i. 5 min after 10 mg sublingual nifedipine, p.i. had significantly decreased from 5.0 to 3.8, with a nonsignificant decrease in arterial blood pressure and an increase in heart rate. By 15 min after nifedipine administration p.i. had further decreased to 3.1, and there was a concomitant significant decrease in mean arterial blood pressure and increase in heart rate. Sixty minutes after drug intake p.i. and arterial blood pressure were still below baseline not significant but the heart rate remained significantly increased.

CONCLUSION

Our data indicate that in healthy subjects sublingual administration of nifedipine had a vasodilator effect (decrease in p.i.) on the superior mesenteric vascular bed.

Use of tissue type plasminogen activator in neonates: case reports and review of the literature

Recombinant tissue type plasminogen activator (rt-PA) has been used successfully in neonates for resolution of thrombotic processes, both arterial and venous. We report on 2 neonates with vena cava inferior thrombosis and with biochemical evidence of liver dysfunction in whom rt-PA treatment had to be interrupted because of significant bleeding tendency, without complete resolution of the thrombus. Therapy failure may be due to the age of the thrombus and the systemic way of administration, bypassing the site of the thrombus by collateral circulation. Impaired liver function may result in decreased degradation of rt-PA with prolonged effect and higher risk for bleeding complications. We suggest that lower doses should be administered in these patients.

Rational design of granulocyte-macrophage colony-stimulating factor antagonist peptides

Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a member of the four-helix bundle family of cytokines/growth factors which exhibit several activities. It is a hematopoietic growth factor, a cytokine involved in inflammatory and immune processes, an adjunct for cancer therapy, and an anti-tumor immunomodulator. Studies of interactions between GM-CSF and its receptor and identification of small peptides presenting binding capacity to the receptor are important goals for the development of GM-CSF analogs. Here we describe the study of two cyclic peptides, 1785 and 1786, developed based on structural analysis of the GM-CSF region mimicked by anti-anti-GM-CSF recombinant antibody 23.2. These peptides were designed to structurally mimic the positions of specific residues on the B and C helices of human GM-CSF implicated in receptor binding and bioactivity. Both 1785 and 1786 were specifically recognized by polyclonal anti-GM-CSF antibody (stronger for 1786 than 1785). 1786 also competitively inhibited binding of GM-CSF to the GM-CSF receptor on HL-60 cells and demonstrated antagonist bioactivity, as shown by its reversal of GM-CSF's ability to inhibit apoptosis of the GM-CSF-dependent cell line MO7E. These studies support the role of residues on the GM-CSF B and C helices in receptor binding and bioactivity and suggest strategies for mimicking binding sites on four-helix bundle proteins with cyclic peptides.

Influence of central command and ergoreceptors on the splanchnic circulation during isometric exercise

The splanchnic circulation can make a major contribution to blood flow changes. However, the role of the splanchnic circulation in the reflex adjustments to the blood pressure increased during isometric exercise is not well documented. The central command and the muscle chemoreflex are the two major mechanisms involved in the blood pressure response to isometric exercise. This study aimed to examine the behaviour of the superior mesenteric artery during isometric handgrip (IHG) at 30% maximal voluntary contraction (MVC). The pulsatility index (PI) of the blood velocity waveform of the superior mesenteric artery was taken as the study parameter. A total of ten healthy subjects [mean age, 21.1 (SEM 0.3) years] performed an IHG at 30% MVC for 90 s. At 5 s prior to the end of the exercise, muscle circulation was arrested for 90 s to study the effect of the muscle chemoreflex (post exercise arterial occlusion, PEAO). The IHG at 30% MVC caused a decrease in superior mesenteric artery PI, from 4.84 (SEM 1.57) at control level to 3.90 (SEM 1.07) (P = 0.015). The PI further decreased to 3.17 (SEM 0.70) (P = 0.01) during PEAO. Our results indicated that ergoreceptors may be involved in the superior mesenteric artery vasodilatation during isometric exercise.

Recombinant antibodies in bioactive peptide design

Granulocyte-macrophage colony-stimulating factor (GM-CSF) is important in many immune and inflammatory processes. GM-CSF binds to specific cellular receptors which belong to a recently described supergene family. These receptors are potential targets for pharmacologic design, and such design depends on a molecular understanding of ligand-receptor interactions. One approach to dissecting out critical intermolecular interactions is to develop analogs of specific interaction sites of potential importance. Monoclonal antibodies have been employed for these purposes in prior studies. Here we present application of recombinant antibody technology to the development of analogs of a site on GM-CSF bound by a neutralizing anti-GM-CSF monoclonal antibody. Polyclonal antisera with high titer neutralizing activity against human GM-CSF were developed in BALB/c mice. Purified immunoglobulins were prepared and used to immunize syngeneic mice. Anti-anti-GM-CSF was developed which demonstrated biological antagonist activity against GM-CSF-dependent cellular proliferation. RNA was extracted from spleen cells of mice with biologically active anti-anti-GM-CSF, cDNA synthesized, and polymerase chain reaction performed with primers specific for murine kappa light chain V regions. Polymerase chain reaction products were cloned into the pDABL vector and an expression library developed. This was screened with anti-GM-CSF neutralizing mAb 126.213, and several binding clones isolated. One clone (23.2) which inhibited 126.213 binding to GM-CSF was sequenced revealing a murine kappa light chain of subgroup III. Comparison of the 23.2 sequence with the human GM-CSF sequence revealed only weak sequence similarity of specific complementarity determining regions (CDRs) with human GM-CSF. Structural analysis revealed potential mimicry of specific amino acids in the CDR I, CDR II and FR3 regions of 23.2 with residues on the B and C helices of GM-CSF. A synthetic peptide analog of the CDR I was bound by 126.213, specifically antagonized GM-CSF binding to cells and blocked GM-CSF bioactivity. These studies indicate the feasibility of using recombinant antibody libraries as sources of interaction site analogs.

Influence and interference of isosorbide dinitrate and food intake on superior mesenteric artery impedance in humans

The influence of isosorbide dinitrate (ISDN) and food ingestion on superior mesenteric artery impedance was investigated in 24 healthy volunteers (age 40 +/- 2.7 years). Superior mesenteric artery circulation was assessed by duplex ultrasound. Pulsatility index (PI) was considered as a parameter of vascular resistance and was calculated as the peak-to-peak amplitude of the waveform divided by the mean amplitude. The subjects were randomly allocated to four groups (ISDN, meal, ISDN + meal, meal + ISDN). PI measurements were performed in resting and fasting conditions and serially for 1 h after sublingual 5 mg ISDN, ingestion of a 300-kcal, 300-ml mixed liquid meal; sublingual 5 mg ISDN followed 10 min later by the test meal; and ingestion of the test meal followed 5 min later by sublingual 5 mg ISDN. Five minutes after 5 mg sublingual ISDN, PI had increased from 6.8 to 12.4, while after intake of a meal PI had decreased from 7.6 to 4.9. Separate effects of 5 mg ISDN and meal intake lasted for at least 1 h. The reflex vasoconstrictive effect of 5 mg ISDN on the superior mesenteric artery circulation was counterbalanced by ingestion of a meal in healthy volunteers.

Granulocyte-macrophage colony-stimulating factor mimicry and receptor interactions

Development of small molecular mimics of larger polypeptide ligands is an important approach to pharmacophore design. One strategy for the development of such mimics is analysis of alternative ligands that bind to the same site as the native ligand. These allow examination of the structural and chemical constraints for binding within the setting of diverse backbone geometries. The use of antireceptor antibodies as alternative ligands has allowed the development of biologically active peptides in several ligand-receptor systems. This technology has been applied to the study of interactions between human granulocyte-macrophage colony-stimulating factor (GM-CSF) and its receptor (GM-CSFR). GM-CSF is one of a family of signal-transducing cytokines and growth factors characterized by a four-helix bundle core structure. The GM-CSFR is comprised of an alpha-chain (GM-CSFR alpha) specific for GM-CSF, and a beta-chain (beta c) shared with the interleukin-3 and interleukin-5 receptors. At least two sites on GM-CSF have been implicated in the GM-CSF-GM-CSFR alpha/beta c ternary complex. In studies summarized here, synthetic peptide analogs of GM-CSF sequences were designed and used to map neutralizing epitopes. One neutralizing epitope corresponded to the A helix of GM-CSF, and a synthetic analog displayed biological activity as a GM-CSF antagonist in vitro, suggesting interaction with the GM-CSFR alpha/beta c complex. A second peptide comprising the B and C helices was recognized by monoclonal neutralizing antibodies and similarly displayed antagonist activity. Recombinant antibody (rAb) technology was also employed. An expression library of rAbs from mice immunized with neutralizing anti-GM-CSF antibodies was developed and screened with a neutralizing anti-GM-CSF monoclonal antibody. One clone which displayed receptor binding activity exhibited structural similarity with epitopes on GM-CSF previously implicated as interaction sites with the neutralizing monoclonal antibody. A synthetic peptide analog of the rAb inhibited GM-CSF bioactivity. Critical contact residues were predicted on the basis of structural similarity of the rAb peptide and GM-CSF. These studies indicate the feasibility of using rAbs in bioactive peptide design, providing lead compounds and information regarding contact residues for drug design.

Influence of isosorbide dinitrate on superior mesenteric artery impedance in humans

In a randomized, double-blind, placebo-controlled crossover study the acute effect of isosorbide dinitrate (ISDN) on the superior mesenteric artery velocity waveform was studied in 10 healthy subjects (mean age 48.2 years) over a 10-minute period. The superior mesenteric artery pulsatility index (PI), which quantifies the blood velocity waveform, increased from the second minute following sublingual administration of 5 mg ISDN (basal PI 4.88 +/- 0.32) and reached its upper level (8.22 +/- 1.38) from the fourth minute on. In comparison with placebo, the significant rise of PI (second minute) occurred before the significant decrease of systolic blood pressure (ninth minute) and before the significant increase in the heart rate (fourth minute). Diastolic and mean arterial blood pressures remained unchanged. These observations suggest an immediate vasoconstrictive effect of ISDN on the resistance vessels of the vascular bed of the superior mesenteric artery.

Neurosyphilis presenting with optic neuropathy. Report of a case and review

A patient with neurosyphilis, presenting with severe ocular impairment due to optic neuropathy, is described. In such a case, a low index of clinical suspicion and improper use of syphilitic serologic tests may delay diagnosis. However, specific tests of serum and cerebrospinal fluid are mandatory for the diagnosis. Treatment evaluation necessitates the follow-up of serology and cerebrospinal fluid cell count. Recent changes of therapy recommendations in subjects with neurosyphilis and in those syphilitic patients co-infected with HIV are mentioned.

Arcuate ligament syndrome mimicking celiac occlusion

In a patient with weight loss and a systolic epigastric murmur, aortography demonstrated positional celiac axis occlusion. Color Doppler imaging of the celiac axis showed occlusion in the supine position, but patency was documented during deep inspiration and with the patient in the upright position. This report documents a rare example of extreme celiac axis compression with position-dependent celiac patency.

Noninvasive diagnosis of superior sagittal sinus thrombosis in a neonate

A newborn boy presented within the first day of life with moaning, anemia, and thrombocytopenia. The clinical syndrome resulted from thrombosis of the posterior part of the superior sagittal sinus due to impression at birth of the tip of the occipital squama. Both computed tomography and ultrasound scans were valuable noninvasive tools for documentation of the thrombus itself and the cerebral sequelae. Color Doppler ultrasound scan confirmed the absence and reappearance of flow in the superior sagittal sinus.

Leptomeningeal cyst: early diagnosis by color Doppler imaging

A newborn with a leptomeningeal cyst over the anterior fontanelle due to birth trauma is described. Color Doppler flow sonograms were helpful to diagnose the leptomeningocele in its early stages and to differentiate it from a cephalhematoma or subgaleal haemorrhage by demonstrating cerebro-fugal flow in an arterial connection between the extracranial fluid collection and the dural space.

Floating thrombi: diagnosis and follow-up by duplex ultrasound

The clinical features and evolution of floating thrombi (FT) diagnosed by duplex ultrasound were examined. In 76 consecutively diagnosed above-knee deep venous thromboses the prevalence of FT was 18%. Of 44 FT diagnosed in 39 patients, 18 (39%) were located in the common femoral, 12 (26%) in the popliteal and seven (15%) in the external iliac veins. Serial duplex examinations revealed that 31% of FT in the iliofemoral segment disappeared 33% remained unchanged and 36% adhered to the vein wall within 2 weeks following diagnosis. After 3 months, 87% of the floating segments had disappeared, irrespective of the localization or therapeutic regimen. Thirteen patients experienced pulmonary embolism before (12/13) or following (4/13) diagnosis of floating thrombosis; three of four superficial femoral vein FT embolized. Fifteen per cent of the patients with FT died during the study period and 28% of the thrombi were associated with a malignant neoplasm; the incidence of malignancy was 60% in superficial and 39% in common femoral vein FT.

Pseudoxanthoma elasticum: similar autosomal recessive subtype in Belgian and Afrikaner families

A multidisciplinary survey of the clinical and genetic characteristics of 26 Belgian and 32 Afrikaner families with biopsy-proven pseudoxanthoma elasticum (PXE) was undertaken. The major PXE phenotype emerging from this study is very similar in both patient groups and is characterized by severe ophthalmologic manifestations with variable, mild cutaneous and vascular symptoms. In the families with more than one affected relative, segregation analysis is compatible with autosomal recessive inheritance in both groups. It is suggested that the PXE phenotype of these Belgian and Afrikaner patients is distinct from the other recognized PXE subtypes. The phenotypic resemblance in both patient groups raises the question whether a similar genetic mechanism is involved.

Crystallization and preliminary X-ray studies of recombinant human granulocyte-macrophage colony stimulating factor

Human granulocyte-macrophage colony stimulating factor (hGM-CSF) is an important regulator of growth and differentiation for mononuclear and polymorphonuclear phagocytes. Here we report the crystallization and preliminary X-ray studies of Escherichia coli-expressed hGM-CSF. The crystals are orthorhombic, with the space group P212121, and have unit cell dimensions a = 46.62 A, b = 58.73 A and c = 126.42 A. Recombinant hGM-CSF crystals diffract X-rays to 2.4 A resolution and are thus suitable for X-ray structural studies.