A New Framework for Performing Cardiac Strain Analysis from Cine MRI Imaging in Mice

Cardiac magnetic resonance (MR) imaging is one of the most rigorous form of imaging to assess cardiac function in vivo. Strain analysis allows comprehensive assessment of diastolic myocardial function, which is not indicated by measuring systolic functional parameters using with a normal cine imaging module. Due to the small heart size in mice, it is not possible to perform proper tagged imaging to assess strain. Here, we developed a novel deep learning approach for automated quantification of strain from cardiac cine MR images. Our framework starts by an accurate localization of the LV blood pool center-point using a fully convolutional neural network (FCN) architecture. Then, a region of interest (ROI) that contains the LV is extracted from all heart sections. The extracted ROIs are used for the segmentation of the LV cavity and myocardium via a novel FCN architecture. For strain analysis, we developed a Laplace-based approach to track the LV wall points by solving the Laplace equation between the LV contours of each two successive image frames over the cardiac cycle. Following tracking, the strain estimation is performed using the Lagrangian-based approach. This new automated system for strain analysis was validated by comparing the outcome of these analysis with the tagged MR images from the same mice. There were no significant differences between the strain data obtained from our algorithm using cine compared to tagged MR imaging. Furthermore, we demonstrated that our new algorithm can determine the strain differences between normal and diseased hearts.

Contralateral breast cancers: Independent cancers or metastases?

A cancer in the contralateral breast in a woman with a previous or synchronous breast cancer is typically considered to be an independent primary tumor. Emerging evidence suggests that in a small subset of these cases the second tumor represents a metastasis. We sought to investigate the issue using massively parallel sequencing targeting 254 genes recurrently mutated in breast cancer. We examined the tumor archives at Memorial Sloan Kettering Cancer Center for the period 1995-2006 to identify cases of contralateral breast cancer where surgery for both tumors was performed at the Center. We report results from 49 patients successfully analyzed by a targeted massively parallel sequencing assay. Somatic mutations and copy number alterations were defined by state-of-the-art algorithms. Clonal relatedness was evaluated by statistical tests specifically designed for this purpose. We found evidence that the tumors in contralateral breasts were clonally related in three cases (6%) on the basis of matching mutations at codons where somatic mutations are rare. Clinical data and the presence of similar patterns of gene copy number alterations were consistent with metastasis for all three cases. In three additional cases, there was a solitary matching mutation at a common PIK3CA locus. The results suggest that a subset of contralateral breast cancers represent metastases rather than independent primary tumors. Massively parallel sequencing analysis can provide important evidence to clarify the diagnosis. However, given the inter-tumor mutational heterogeneity in breast cancer, sufficiently large gene panels need to be employed to define clonality convincingly in all cases.

Abstract S2-02: The landscape of somatic genetic alterations in BRCA1 and BRCA2 breast cancers

Introduction: Women carrying BRCA1 or BRCA2 germline mutations have a 45-80% lifetime risk of developing breast cancer (BC). BRCA1 and BRCA2 are perceived as bona fide tumor suppressor genes, whereby bi-allelic inactivation in tumor cells is required for tumorigenesis. Recent studies have indicated that loss of heterozygosity (LOH) of the wild-type allele of BRCA1 may be heterogeneous and constitute a late event. Therefore, additional somatic events prior to full BRCA1/2 inactivation may be required for tumorigenesis. Given that the somatic events that result in the development of BRCA1/2-BCs and their chronology are not understood, here we sought to define the genomic landscape of BRCA1/2-BCs and whether LOH of BRCA1/2 wild-type allele and/or mutations affecting additional tumor suppressor genes would be clonal or subclonal in these cancers.

Methods: We retrieved 29 BRCA1-BCs and 10 BRCA2-BCs from the Pathology Departments of the authors' institutions. DNA extracted from microdissected tumor and normal breast samples was subjected to targeted capture massively parallel sequencing using either the MSK-IMPACT assay or an assay targeting all exons of 254 genes recurrently mutated in BC or related to DNA repair. Somatic single nucleotide variants, small insertions and deletions and copy number alterations affecting genes present in both sequencing assays (111 genes) were defined using state-of-the-art bioinformatics algorithms. ABSOLUTE and FACETS were employed to define clonal (i.e. present virtually in 100% of the cancer cells of a given case) and subclonal mutations and the presence of LOH of the BRCA1 and BRCA2 wild-type alleles.

Results: Our analysis revealed bi-allelic inactivation of BRCA1 in 28 of 29 BRCA1-BCs (93% harbored LOH of the BRCA1 wild-type allele and 3% harbored a second somatic BRCA1 pathogenic mutation). The only BRCA1-BC lacking bi-allelic inactivation of BRCA1 was an estrogen receptor-positive lobular carcinoma, lacking genomic features consistent with homologous recombination DNA repair defects, diagnosed at 62 years of age. Bi-allelic inactivation of BRCA2 was found in all cases (100% of harbored LOH of the BRCA2 wild-type allele). A clonal somatic 'second hit' resulting in bi-allelic inactivation of BRCA1 or BRCA2 was detected in 76% and 100% of BRCA1-BCs and BRCA2-BCs, respectively. In BRCA1-BCs, TP53 mutations were detected in 76% of cases, and these mutations were found to be clonal in 58% of cases. The repertoire of somatic mutations affecting BRCA1-BCs included clonal somatic mutations or homozygous deletions of known tumor suppressor genes, such as PTEN, RB1, CDKN2A and NF1. In contrast, only 10% of the BRCA2-BCs harbored TP53 somatic mutations. Though clonal somatic mutations in several cancer genes were detected, 40% of BRCA2-BCs had no mutations affecting the cancer genes analyzed.

Conclusions: Bi-allelic inactivation of BRCA1 and BRCA2 are frequent events in BRCA1-BCs and BRCA2-BCs, respectively. In a subset of BRCA1-BCs, however, the second 'hit' appeared to be subclonal, whereas mutations affecting TP53 and other tumor suppressor genes were clonal, supporting the notion that at least in a subset of these tumors, loss of the wild-type allele of BRCA1 may be preceded by inactivation of another tumor suppressor gene.

Citation Format: Geyer FC, Burke KA, Macedo GS, Piscuoglio S, Ng CK, Martelotto LG, Papanastatiou AD, De Filippo MR, Schultheis AM, Brogi E, Robson M, Wen YH, Weigelt B, Schnitt SJ, Tung N, Reis-Filho JS. The landscape of somatic genetic alterations in BRCA1 and BRCA2 breast cancers [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr S2-02.

Abstract P2-03-01: Mutational landscape of breast cancers from PALB2 germline mutation carriers

Background: The PALB2 gene encodes the partner and localizer of the BRCA2 protein, which participates in homologous recombination during DNA repair via an interaction with BRCA1 and BRCA2. Germline mutations in PALB2 are associated with an increased risk of breast cancer, with a cumulative risk of 35% by age 70 in female PALB2 mutant carriers. The aims of this project were to characterize the genomic landscape of PALB2 breast cancers and define the differences in the repertoire of somatic genetic alterations and mutational signatures between PALB2, BRCA1 and BRCA2 breast cancers.

Methods: Representative samples from fourteen breast cancers from patients with known PALB2 germline mutations (seven frame-shift (2 H1170fs, 3 K346fs, 1 T841fs and 1 L531fs), five truncating (3 W1038* and 2 Q775*) and two missense (W1140G and L35P)) were microdissected to ensure a tumor cell content of >70%. DNA samples from microdissected tumors and their matched normal counterparts were subjected to whole exome sequencing on an Illumina HiSeq2000 to a median depth of 118x (range 33-193x). Somatic single nucleotide variations were detected using MuTect, and small insertions and deletions were identified using Strelka and Varscan2. Using ABSOLUTE and FACETS, we investigated the presence of loss of heterozygosity (LOH) of the PALB2 wild-type allele in these tumors. In addition, the mutational signatures and large scale state transitions (LSTs) were defined. The repertoire of somatic mutations identified in PALB2 breast cancers was compared to that of breast cancers from BRCA1 (n=11) and BRCA2 (n=10) germline mutation carriers from The Cancer Genome Atlas study.

Results: PALB2 breast cancers were found to harbor a median of 80 somatic mutations (range 22-286) and one somatic mutation (range 0-13) affecting known cancer genes. Somatic loss of the PALB2 wild-type allele was found in five cases, and in three additional cases, a second PALB2 somatic mutation likely constituted the second 'hit' (two with truncating mutations, Q479* and Q61*, and one with a Q921fs frameshift mutation). Six PALB2 breast cancers displayed the BRCA mutations signature; of these, five had PALB2 bi-allelic inactivation (three LOH of the wild-type allele and two a second PALB2 somatic mutation). 71% of the samples were found to have LSTs, including all cases with a BRCA mutational signature. A significant association between PALB2 bi-allelic inactivation and concurrent BRCA signature and high LST was observed (p=0.015). Breast cancers from PALB2 mutation carriers had fewer somatic TP53 mutations than BRCA1 breast cancers (3/14, 21% vs 9/11, 82%, p=0.004), but no difference in the repertoire of somatic mutations compared to that of BRCA2 breast cancers.

Conclusions: PALB2 breast cancers were found to harbor pathogenic mutations in driver genes, including TP53, PIK3CA, NF1 and NCOR1, however lacked highly recurrent somatic mutations. Unlike BRCA1/2 breast cancers, the majority of breast cancers from PALB2 germline mutation carriers lacked LOH of the PALB2 wild-type allele. Importantly, however, an association between PALB2 bi-allelic inactivation and the BRCA mutational signature and LSTs was observed, providing additional evidence for a homologous recombination-deficient phenotype at least in a subset of PALB2 cancers.

Citation Format: Burke KA, Berman S, Geyer FC, Piscuoglio S, Ng CK, Wen YH, Mannermaa A, Peterlongo P, Tondini C, Janatova M, Soo Hwang T, Ng P-S, Looi LM, Chenevix-Trench G, Southey MC, Weigelt B, Foulkes W, Tischkowitz M, Reis-Filho JS, PALB2 Interest Group. Mutational landscape of breast cancers from PALB2 germline mutation carriers [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-03-01.

Abstract P1-05-03: The genomic landscape of breast metaplastic carcinoma

Introduction: Metaplastic breast carcinoma (MBC) is a rare histologic type of triple-negative breast cancer (TNBC), characterized by the presence of cells displaying squamous and/or mesenchymal differentiation. The transcriptomic profiles of MBCs have been reported to vary according to the type of metaplastic elements. The somatic genetic alterations that underpin this breast cancer subtype remain to be fully characterized. Here we sought to define the genomic landscape of MBCs, whether different subtypes of MBC would be driven by distinct constellations of genetic alterations, and to investigate functionally the impact of mutations affecting WNT pathway genes using non-malignant breast epithelial cells.

Methods: Thirty-five MBCs were retrieved from the pathology department of the authors' institutions and classified into the MBC histologic subtypes. All but one of the MBCs were of triple-negative phenotype. DNA was extracted from microdissected tumor-normal pairs and subjected to whole-exome sequencing. Somatic genetic alterations were identified using state-of-the-art bioinformatics algorithms. The genomic profiles of MBCs were compared to those of 69 common type TNBCs from The Cancer Genome Atlas. Overall mutation rates were compared using the Mann Whitney U test, and the frequency of mutations in each gene was compared using Fisher's exact test. RNA was extracted from a subset of MBCs and subjected to WNT signaling pathway activation analysis with the RT2 Profiler PCR Array. Triple-negative non-malignant breast epithelial cells (MCF10A and MCF12A) and cancer cell lines were utilized for 2D and 3D functional studies.

Results: Whole-exome analysis revealed that MBCs displayed a median of 103 (15-344) somatic mutations, which did not differ from the median number of somatic mutations in common type TNBCs (76, range 14-233). The most frequent recurrently mutated cancer genes included TP53 (69%) and PIK3CA (29%). MBCs more frequently harbored mutations in PI3K pathway genes than common type TNBCs (57% vs 22%, P<0.05), including mutations affecting PIK3CA (29% vs 7%), PIK3R1 (11% vs 0) and PTEN (11% vs 1%). MBCs also more frequently harbored mutations affecting WNT signaling pathway genes (46% vs 26%, P<0.05), including AXIN1 (6% vs 1%), WNT5A (6% vs 0) and APC (3% vs 0). MBC subtype analysis revealed that PIK3CA mutations were only detected in non-chondroid MBCs (53% vs 0), CHERP mutations were only found in chondroid MBCs (25% vs 0), whereas USP5 mutations only found in squamous MBCs (33% vs 0). MBCs with somatic mutations in WNT pathway genes had significantly higher WNT pathway activation than MBCs lacking mutations in these genes (P=0.0244). Consistent with the mesenchymal phenotype frequently exhibited by MBCs, in vitro experiments provided functional evidence that aberrant WNT pathway activation induces an epithelial-to-mesenchymal transition (EMT) phenotype, with downregulation of epithelial markers and upregulation of EMT transcriptional inducers.

Conclusions: MBCs are significantly enriched for mutations affecting PI3K and WNT pathways, highlighting the importance of the dysregulation of the WNT pathway in MBC carcinogenesis. Moreover, our findings suggest that specific mutations are significantly associated with distinct histologic subtypes of MBCs.

Citation Format: Geyer FC, Ng CK, Piscuoglio S, Wen YH, Wen H-C, Pareja F, Eberle CA, Burke KA, Lim RS, Natrajan R, Mariani O, Brogi E, Norton L, Vincent-Salomon A, Weigelt B, Reis-Filho JS. The genomic landscape of breast metaplastic carcinoma [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-03.

Abstract 134: Mutational landscape of breast cancers from PALB2 germline mutation carriers

Introduction: The PALB2 gene encodes the partner and localizer of BRCA2 protein, which interacts with BRCA1/2 and is involved in homologous recombination DNA repair. Germline mutations in PALB2 are associated with an increased risk of breast cancer, with a cumulative risk of 35% by age 70 in female PALB2 mutation carriers. Whether the PALB2 wild-type allele is lost in the development of PALB2 breast cancers has yet to be defined. Further, the repertoire of somatic genetic alterations in these tumors is currently unknown. In this study we sought to characterize the genomic landscape of PALB2 breast cancers and to define the differences in the repertoire of somatic genetic alterations and mutational signatures between PALB2 and BRCA1 and BRCA2 breast cancers.

Material and Methods: Representative samples from nine breast cancers from patients with known PALB2 germline mutations were microdissected. DNA samples from microdissected tumors and matched normal counterparts were subjected to whole exome sequencing on an Illumina HiSeq2000. Somatic mutations were defined using MuTect and insertions and deletions using Strelka and Varscan2. Driver mutations were defined by state-of-the-art bioinformatics methods. Mutational signatures were defined using non-negative matrix factorization. Copy number alterations (CNAs) and regions with loss of heterozygosity were determined using FACETS. The mutational frequency of breast cancers from PALB2 germline mutation carriers was compared to that of breast cancers from BRCA1 (n = 11) and BRCA2 (n = 10) germline mutation carriers from The Cancer Genome Atlas study.

Results: Three patients harbored germline frame-shift PALB2 mutations (2 S1169fs, 1 T841fs), five displayed truncating mutations (3 W1038* and 2 Q775*) and 1 harbored a missense mutation (W1140G, of uncertain significance). Somatic loss of the PALB2 wild-type allele was found in 3 cases, in 2 of which the loss was caused by CNAs and in 1 case it was caused by a somatic PALB2 Q479* mutation. A median of 65 somatic mutations (range 45-223) and a median of 1 driver mutation (range 0-3) were identified per tumor. Cancer genes mutated in PALB2 breast cancers included TP53 (n = 2), PIK3CA (n = 2), NF1 (n = 1) and NCOR1 (n = 1). Six cases displayed mutational signatures consistent with the aging process; the BRCA signature was not found in any of the cases analyzed. Breast cancers from PALB2 mutation carriers had fewer somatic TP53 mutations than BRCA1 breast cancers (2/9, 22% vs 9/11, 82%, p = 0.02). No difference in the repertoire of somatic mutations between PALB2 and BRCA2 breast cancers was observed.

Conclusion: Unlike breast cancers from BRCA1 and BRCA2 mutation carriers, the majority of breast cancers from PALB2 mutation carriers lacked somatic loss of the wild-type allele and none displayed a BRCA mutational signature. No highly recurrently mutated gene was identified, but pathogenic mutations in driver genes (TP53, PIK3CA, NF1 and NCOR1) were found.

Citation Format: Salvatore Piscuoglio, Charlotte KY Ng, Y Hannah Wen, Arto Mannermaa, Paolo Peterlongo, Carlo Tondini, Marketa Janatova, Teo Soo Hwang, Pei-Sze Ng, Lai-Meng Looi, William Foulkes, Georgia Chenevix-Trench, Britta Weigelt, Melissa C. Southey, Marc Tischkowitz, Jorge S. Reis-Filho, PALB2 Interest Group. Mutational landscape of breast cancers from PALB2 germline mutation carriers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 134.

Abstract 91: The mutational landscape of mucinous carcinomas of the breast

Background: Mucinous breast carcinoma (MBC) is a special histologic type of breast cancer, comprising approximately 2% of all invasive breast carcinomas. Morphologically, MBCs are characterized by clusters of tumor cells floating in large amounts of extracellular mucin. MBCs are preferentially of low histologic grade and estrogen receptor (ER)-positive and HER2-negative. MBCs have been shown to lack the hallmark 1q gains and 16q losses found in low-grade ER-positive invasive ductal carcinomas of no special type (IDC-NSTs). Here we sought to characterize the mutational landscape and copy number alterations (CNA) of MBCs by whole exome sequencing analysis.

Material and Methods: Frozen sections from 25 pure MBCs (n = 13 mucinous A (paucicellular), n = 12 mucinous B (hypercellular)) were subjected to microdissection to ensure a tumor cell content >85%. In addition, five cases of mixed mucinous carcinomas composed of mucinous and IDC-NST components were included in this study. In these cases, the MBC and IDC-NST components were microdissected separately. DNA samples extracted from microdissected tumors and matched normal counterparts were subjected to whole exome sequencing on an Illumina HiSeq2000. Somatic single nucleotide variants (SNVs) were identified using MuTect and somatic insertions and deletions (indels) were identified using Strelka and Varscan2. Somatic CNAs were defined using FACETS. Mutational frequencies in MBCs were compared to those of luminal IDC-NSTs from The Cancer Genome Atlas.

Results: A median of 26 (range 5-71) non-synonymous SNVs and indels were identified per MBC. GATA3, mutated in 28% of cases, was the only significantly mutated gene as defined by MutSigCV (q<0.1). Compared to IDC-NSTs of luminal molecular subtype, MBCs were found to harbor significantly fewer mutations in TP53 (3% vs 19%, p<0.001) and PIK3CA (6% vs 41%, p<0.001). Mucinous subtypes A and B did not differ in terms of mutations and/ or CNAs, whereas MBCs of mixed phenotype harbored a greater extent of genomic instability. While MBC and IDC-NST components of mixed MBCs shared the majority of the somatic genetic alterations, indicating their clonal relatedness, mutations and CNAs restricted to either the MBC or the IDC-NST components were also identified. Furthermore, CNA analysis confirmed our previous observations that MBCs, contrary to low-grade ER-positive IDC-NSTs, lack concurrent copy number gains of 1q and 16p and losses of 16q.

Conclusions: Our data suggest that the repertoires of somatic mutations and gene CNAs of MBCs are distinct from those of luminal IDC-NSTs, and that MBCs are an entity distinct from low-grade ER-positive IDC-NSTs not only at the morphologic but also at the genetic level.

Citation Format: Salvatore Piscuoglio, Charlotte KY Ng, Felipe C. Geyer, Carey A. Eberle, Elena Guerini-Rocco, Caterina Marchio, Anne Vincent-Salomon, Jorge S. Reis-Filho, Britta Weigelt. The mutational landscape of mucinous carcinomas of the breast. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 91.

Abstract 4817: Microsatellite instability status in endometrioid endometrial carcinomas is associated with distinct types and patterns of PI3K pathway mutations

Background: Endometrioid endometrial carcinomas (EECs) frequently harbor mutations in the PI3K pathway. In contrast with other cancer types (e.g. breast cancer) where PIK3CA mutations are generally mutually exclusive with PTEN mutations, in EECs mutations affecting these genes often co-occur. Here we sought to determine whether the type and pattern of mutations targeting different components of the PI3K pathway are distinct between microsatellite stable (MSS) and high-level microsatellite instable (MSI-H) EECs, and to define the mutational signatures in MSI-H and MSS EECs.

Methods: Whole exome massively parallel sequencing-based mutation data from EECs of The Cancer Genome Atlas (TCGA) project were used to define the number, type and pattern of mutations affecting PI3K pathway-related genes (i.e., AKT1, INPP4B, MTOR, PIK3CA, PIK3R1 and PTEN). Based on seven MSI markers assessed by TCGA, EECs were classified as MSI-H (n = 70) and MSS (n = 109). POLE ultramutated cases were excluded. Mutational signatures were defined using EMu, a method based upon the expectation-maximization algorithm.

Results: Although the mutation rates of MSS and MSI-H EECs were significantly different, the prevalence of mutations affecting PI3K pathway genes was similar between these two groups (all p>0.05), with the exception of PTEN mutations, which were more prevalent in MSI-H (87%) than in MSS EECs (72%; p = 0.017). The PIK3CA hotspot mutations E542K, E545K, and H1047R were found to be significantly more prevalent in PIK3CA-mutant MSS EECs (36%) than in PIK3CA-mutant MSI-H EECs (13.5%; p = 0.019). In both MSI-H and MSS EECs a mutational signature related to age was identified, characterized by C>T transitions at NpCpG trinucleotides; in MSS tumors a C>T and C>G at TpCpN trinucleotides mutational signature, attributed to the APOBEC family of cytidine deaminases, was identified, whereas in MSI-H tumors, a DNA-MMR deficiency-like signature was found.

Conclusion: Although the prevalence of mutations targeting different components of the PI3K pathway is similar between MSS and MSI-H EECs, PIK3CA hotspot mutations, which result in constitutive kinase activation, are significantly more prevalent in MSS than in MSI-H EECs. We have observed that the mutational processes operating in MSI-H and MSS EECs are distinct, and that the landscape of mutations affecting PI3K pathway-related genes might be shaped by multiple mutational processes in these cancers. Our findings warrant further investigation of the role of different types of PIK3CA mutations in and their predictive impact on distinct subtypes of EECs.

Citation Format: Caterina Marchio, Maria R. De Filippo, Charlotte KY Ng, Robert A. Soslow, Jorge S. Reis-Filho, Britta Weigelt. Microsatellite instability status in endometrioid endometrial carcinomas is associated with distinct types and patterns of PI3K pathway mutations. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4817. doi:10.1158/1538-7445.AM2015-4817

Abstract 2971: Whole exome sequencing reveals heterogeneity within lobular carcinoma in situ (LCIS) and clonal selection in the progression to malignant lesions

INTRODUCTION: Lobular carcinoma in situ (LCIS) is considered both a risk factor and non-obligate precursor of low-grade estrogen receptor-positive breast cancer. We sought to define the mutational repertoire, subclone complexity and heterogeneity of LCIS, and whether invasive lobular carcinomas (ILCs) would stem from specific subclones within a LCIS.

METHODS: Patients with a history of LCIS undergoing therapeutic or prophylactic mastectomy were prospectively enrolled in an IRB approved protocol. Frozen tissue blocks were collected, screened for lesions of interest (LCIS, ductal carcinoma in situ (DCIS), ILC, invasive ductal carcinoma (IDC)) and subject to microdissection and DNA extraction. Matched germline DNA was available for all cases. Whole exome sequencing was performed on a HiSeq2000 (Illumina) and data were aligned to the reference human genome hg19 and processed using GATK. SNVs were called using MuTect, and indels were called using a combination of Varscan and Strelka. Purity and ploidy estimates were calculated by ABSOLUTE. Clonal frequencies were estimated using Pyclone.

RESULTS: 30 LCIS, 10 ILCs, 6 IDCs and 7 DCIS from 15 patients qualified for data analysis, resulting in 18 LCIS-ILC pairs, 22 LCIS-LCIS pairs, 12 LCIS-DCIS pairs, and 14 LCIS-IDC pairs for comparison. 9/18 (50%) LCIS-ILC pairs and 8/22 (36%) LCIS-LCIS pairs were clonally related, supported by several shared mutations (median 18, range 7-81 for LCIS-ILC; median 14, range 5-22 for LCIS-LCIS). All related LCIS-ILC pairs and 6/8 related LCIS-LCIS pairs shared a pathogenic CDH1 mutation; 75% of related LCIS-ILC pairs also shared a PIK3CA hotspot mutation. 7/12 (58%) LCIS-DCIS pairs were found to be clonally related but the number of shared mutations was generally lower than that found in LCIS-ILC pairs (median 9, range 2-11). No evidence of a clonal relationship was found in any of the LCIS-IDC pairs tested. Clonal composition analysis revealed that samples of LCIS display intra-lesion genetic heterogeneity in the form of the presence of a minor clone in 70% of cases. In one case, the LCIS minor subclone (∼15%) constituted the major clone in the ILC and in another case the LCIS minor subclone constituted the major clone in the associated DCIS. The majority of the clonally related lesions were located in the same quadrant of the breast, however evidence of clonality was found in 5 LCIS-LCIS and 3 LCIS-DCIS pairs located in separate quadrants of the breast.

CONCLUSIONS: Intra-lesion genetic heterogeneity is a common phenomenon in LCIS. The dominant clone of a LCIS may not always be the clone directly involved in the progression to malignancy. The spatial relationships of clonally related lesions in this study suggest that anatomy does not always infer clonality, as lesions located in separate quadrants of the breast may be clonally related.

Citation Format: Michail Schizas, Rita A. Sakr, Britta Weigelt, Charlotte KY Ng, Jose Victor S. Carniello, Dilip Giri, Salvatore Piscuoglio, Luciano G. Martelotto, Russell Towers, Victor P. Andrade, Raymond Lim, David B. Solit, Jorge S. Reis-Filho, Tari A. King. Whole exome sequencing reveals heterogeneity within lobular carcinoma in situ (LCIS) and clonal selection in the progression to malignant lesions. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2971. doi:10.1158/1538-7445.AM2015-2971

Abstract 2989: Intra-tumor heterogeneity and clonal changes in the progression of DCIS to invasiveness: Combined tumor bulk and single cell analysis

INTRODUCTION: Ductal carcinoma in situ (DCIS) is a clonal intraductal proliferation of epithelial cells which acts as a non-obligate precursor of invasive breast cancer (IBC), yet the genetic events leading to the acquisition of invasive behavior remain unclear. We hypothesize that DCIS is composed of mosaics of genetically diverse tumor cell clones, and that the process of invasion is an evolutionary bottleneck. To test this hypothesis we performed a detailed characterization of the repertoire of genetic alterations and intra-tumor genetic heterogeneity in synchronously diagnosed DCIS and IBC using NextGen sequencing of bulk tumor and single cells.

METHODS: DNA extracted from fresh frozen, microdissected DCIS, IBC and adjacent normal tissue was subjected to whole exome sequencing on an Illumina HiSeq2000. Reads were aligned to the reference human genome hg19. Single nucleotide variants (SNVs) were called by MuTect, and gene copy number alterations were determined using VarScan2. Single nuclei were isolated from 100μm serial sections microdissected to separate DCIS and IBC. Individual nuclei were FACS-sorted into a 96-well plate, lysed and whole genome amplified. Amplified DNA samples were barcoded, pooled and sequenced on a HiSeq2000. Single cell sequencing data were mapped to the reference genome and uniquely mapped reads were allocated into bins, normalized, segmented and CN values generated.

RESULTS: In 6 cases of synchronous DCIS and IBC, a median of 41 and 47 non-synonymous mutations were found in each component, respectively. The somatic mutations identified in both DCIS and adjacent IBC components affected known driver breast cancer genes, including AKT1, PIK3CA, GATA3, MAP2K4 and TP53. Interestingly, we also found mutations restricted to either DCIS or IBC: ATRX (IBC-3); ALK and PKD2 (IBC-5); ESR1 (DCIS-5). The gene copy number profiles of matched DCIS and IBC were similar in all 6 pairs, however we also identified gene copy number alterations restricted either to DCIS or IBC: 1q gain (IBC-5); 3p and 3q losses (DCIS-6); 12p homozygous deletion (DCIS-4). Single cell sequencing of two cases (3 and 4) revealed that the majority of cells from both DCIS and IBC were derived from a common precursor lineage with shared copy number losses and gains. Both sets of DCIS-IBC pairs in these cases displayed elements of a subclonal structure with dominant clones alongside genetically diverse derivatives as well as genetic heterogeneity reflected in variable copy number alterations and non-modal clones.

CONCLUSION: Synchronous DCIS and IBC share founder genetic events, but also harbor somatic genetic alterations restricted to either the DCIS or IBC components, demonstrating that although DCIS is a precursor of IBC, intra-tumor genetic heterogeneity is present at the DCIS stage. Changes in clonal composition likely take place in the progression from DCIS to IBC.

Citation Format: Rita A. Sakr, Luciano G. Martelotto, Timour Baslan, Charlotte KY Ng, Jude Kendall, Linda Rodgers, Hilary Cox, Mike Riggs, Sean D'Itali, Asya Stepansky, Narciso Olvera, Tari A. King, Britta Weigelt, Jorge S. Reis-Filho, James Hicks. Intra-tumor heterogeneity and clonal changes in the progression of DCIS to invasiveness: Combined tumor bulk and single cell analysis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2989. doi:10.1158/1538-7445.AM2015-2989

Giant Chondrosarcoma of Proximal Humerus in an Adult Female Patient: A Case Report

Chondrosarcoma is the third most common primary tumour of the bone, after myeloma and osteosarcoma. Most of the chondrosarcoma grow slowly and rarely metastasize, and they have an excellent prognosis after adequate surgery. However most of them are chemo or radio-resistant. We report a case of primary chondrosarcoma of proximal humerus in a 36-year-old female who presented with a six years history of left shoulder swelling and restricted range of motion. Trucut biopsy showed a well-differentiated chondrosarcoma. The patient underwent forequarter amputation of left upper limb and was started on chemotherapy following operation.

High-resolution genomic profiling of thyroid lesions uncovers preferential copy number gains affecting mitochondrial biogenesis loci in the oncocytic variants

Oncocytic change is the result of aberrant mitochondrial hyperplasia, which may occur in both neoplastic and non-neoplastic cells and is not infrequent in the thyroid. Despite being a well-characterized histologic phenotype, the molecular causes underlying such a distinctive cellular change are poorly understood. To identify potential genetic causes for the oncocytic phenotype in thyroid, we analyzed copy number alterations in a set of oncocytic (n=21) and non-oncocytic (n=20) thyroid lesions by high-resolution microarray-based comparative genomic hybridization (aCGH). Each group comprised lesions of diverse histologic types, including hyperplastic nodules, adenomas and carcinomas. Unsupervised hierarchical clustering of categorical aCGH data resulted in two distinct branches, one of which was significantly enriched for samples with the oncocytic phenotype, regardless of histologic type. Analysis of aCGH events showed that the oncocytic group harbored a significantly higher number of genes involved in copy number gains, when compared to that of conventional thyroid lesions. Functional annotation demonstrated an enrichment for copy number gains that affect genes encoding activators of mitochondrial biogenesis in oncocytic cases but not in their non-oncocytic counterparts. Taken together, our data suggest that genomic alterations may represent additional/alternative mechanisms underlying the development of the oncocytic phenotype in the thyroid.

Abstract P2-03-08: Mutational landscape of metaplastic breast carcinomas

Introduction: Metaplastic breast carcinoma (MBC) is an aggressive histologic type of breast cancer, which preferentially displays a triple-negative phenotype. These tumors are characterized by the presence of malignant cells exhibiting differentiation towards squamous epithelium or mesenchymal elements, including spindle, chondroid, osseous and rhabdoid differentiation. Unlike other rare histologic types of breast cancer such as adenoid cystic and secretory carcinomas, which are underpinned by the MYB-NFIB and ETV6-NTRK3 fusion genes respectively, pathognomonic genetic alterations have not been identified in MBC. It has been suggested, however, that the frequency of PIK3CA somatic mutations would be significantly higher in MBCs than in other forms of triple-negative disease. Here we sought to characterize the mutational landscape of MBCs by means of high-depth whole exome sequencing analysis.

Material and Methods: Twenty-one triple-negative MBCs were retrieved from the authors’ institutions. Representative sections from frozen blocks were microdissected to ensure tumor cell content greater than 50%. DNA samples extracted from microdissected tumor and matched peripheral blood leukocytes were subjected to high-depth (250x) whole exome sequencing on an Illumina GAIIx or HiSeq2000. Somatic point mutations were called using MuTect and somatic insertions and deletions (indels) were called using Strelka, Varscan2 and Haplotype Caller. Potentially pathogenic mutations were predicted using computational algorithms including PolyPhen-2, Mutation Taster, Mutation Assessor, CHASM and FATHMM. Significantly mutated genes were identified using MutSigCV. Pathway and network enrichment analysis of mutations was performed with Ingenuity Pathway Analysis and HOTNET. The genomic landscape of MBCs was compared with that of triple-negative breast cancers (TNBCs) analyzed as part of The Cancer Genome Atlas project.

Results: A mean of 135 somatic non-synonymous point mutations and indels were identified per MBC. The most frequently mutated gene was TP53, found in 12/21 cases (57%), and the only significantly mutated gene as defined by MutSigCV (q<0.01). The repertoire of somatic mutations found in MBCs was qualitatively similar to that of TNBCs of no special type, and recurrently mutated genes were altered at similar frequencies in MBCs and TNBCs of no special type. When somatic mutations were annotated in pathways and networks, MBCs were found to have potentially pathogenic mutations affecting genes directly related to the PI3K pathway, including pathogenic non-synonymous mutations affecting PIK3CA, PIK3R1, PIK3R2, PIK3C2B, PIK3C2G and PTEN, significantly more frequently than TNBCs of no special type (10 out of 21 MBCs vs. 11 out of 62 TNBCs; Fisher's exact test p-value=0.0099).

Conclusion: The majority (57%) of MBCs harbored non-synonymous mutations affecting TP53. While the frequencies of mutations affecting recurrently mutated genes in MBCs are similar to those found in other forms of TNBCs, MBCs significantly more frequently harbor mutations affecting PI3K pathway-related genes than TNBCs of no special type.

Citation Format: Charlotte KY Ng, Britta Weigelt, Salvatore Piscuoglio, Y Hannah Wen, Maria R De Filippo, Luciano G Martelotto, Rachael Natrajan, Raymond Lim, Edi Brogi, Larry Norton, Anne Vincent-Salomon, Jorge S Reis-Filho. Mutational landscape of metaplastic breast carcinomas [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-03-08.

Abstract P2-03-09: Benchmarking mutation function prediction algorithms using validated cancer driver and passenger mutations

Background: Massively parallel sequencing studies have identified large numbers of mutations of unknown biologic significance. There is a pressing need for computational methods to predict and distinguish neutral from potentially pathogenic mutations accurately, to help identify those mutations worth exploring experimentally and clinically. Although various bioinformatic algorithms are available, they are based on different methodologies and assumptions, and their predictions for the same mutations are not always concordant. In this study, we sought to benchmark the performance of 17 prediction algorithms using functionally validated and pathognomonic mutations.

Methods: We curated the literature for functionally validated and pathognomonic mutations as our positive dataset (i.e. pathogenic mutations). For the negative dataset (i.e. neutral mutations), we retrieved variants from the dbSNP database, including only those with minor allele frequency >25%. We compiled a total of 7975 mutations (875 pathogenic and 7100 neutral). The performance of each prediction algorithm, namely accuracy, specificity, sensitivity, positive predictive value (PPV) and negative predictive value (NPV), were defined using the positive and negative datasets described above. Confidence intervals were calculated by sub-sampling 2/3 of the functionally pathogenic mutations and equal number of neutral mutations 500 times. To reduce the bias introduced by mutations included in the COSMIC database, we excluded those found in COSMIC v67, resulting in 6048 mutations (212 pathogenic and 5835 neutral), and re-evaluated the performance of each prediction algorithm.

Results: Our analysis revealed that the overall accuracy varied considerably, with a median of 87% (range 78%-97%). In terms of accuracy, FATHMM (cancer) statistically outperformed all other prediction algorithms (97%, 95% confidence interval (CI) 96%-98%), followed by MutationTaster 2 (94%, 95% CI 93%-95%). Sensitivity and specificity also varied (median 85%, range 77%-96% and median 89%, range 71%-100%, respectively). The most sensitive prediction algorithm, FATHMM (cancer) (96%, 95% CI 95%-97%) statistically outperformed all others. The most specific prediction algorithm was CHASM (breast) (100%, 95% CI 94%-100%). While CHASM (breast) had the highest PPV (100%, 95% CI 99%-100%), FATHMM (cancer) had statistically better NPV than all other prediction algorithms (96%, 95% CI 95%-97%). When COSMIC mutations were removed, FATHMM (cancer) remained the most accurate (93%, 95% CI 91%-95%) though the difference was not statistically significant. In this context, CanDrA (breast) was the most sensitive prediction algorithm (95%, 95% CI 93%-97%) and had the highest NPV (93%, 95% CI 90%-96%), while CHASM (breast) was the most specific prediction algorithm (100%, 95% CI 99%-100%) and had the best PPV (99%, 95% CI 97%-100%).

Conclusions: Our results demonstrate that functional prediction algorithms varied in performance. Using this dataset of mutations, FATHMM (cancer) outperformed all other prediction algorithms in terms of accuracy, sensitivity and NPV, and remained the most accurate even when mutations catalogued in the COSMIC database were excluded.

Citation Format: Maria R De Filippo, Charlotte KY Ng, Jorge S Reis-Filho, Britta Weigelt. Benchmarking mutation function prediction algorithms using validated cancer driver and passenger mutations [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-03-09.

Abstract PD3-4: Reliability of whole exome sequencing for assessing intratumor heterogeneity from breast tumor biopsies

BACKGROUND: False positive findings introduced by analytical noise in sequencing and bioinformatics pipelines constitute a challenge for accurate massively parallel sequencing (MPS). Reports of intratumor genomic heterogeneity based on MPS rarely estimate the impact of false positive mutation calls. The purpose of this study was to measure apparent genomic heterogeneity in different regions of the same tumor and to assess the technical noise in variant calling in replicate sequencing of the same DNA.

METHODS: Three anatomically distinct biopsies were obtained from 3 different regions of 11 breast cancers (33 samples) including 6 low/intermediate grade, estrogen receptor (ER)-positive and 5 high-grade, triple-negative (TNBC) cancers. DNA from 8 different biopsies was split and independently processed on different days to obtain technical replicates. The NimbleGen SeqCap EZ Exome Library preparation method was used for exome capture and paired-end sequencing of 75 base pair fragments was performed on Illumina HiSeq 2000. Read alignment and variant calling were performed with BWA and GATK haplotype caller. Concordance in variant calls and in minor allele frequencies (MAF) was assessed in the 3 biopsies of the same tumor and 8 technical replicates. We adjusted for uneven sequence coverage and analyzed known germline variants from dbSNP, known cancer related variants from COSMIC separately from novel variants (i.e. not previously reported in dbSNP or COSMIC). We estimated intratumor genomic heterogeneity of genes after removing alterations identified in areas where mapping is difficult and variant calls that had low analytical reliability in the technical replicates.

RESULTS: The mean coverage was over 150X and > 90% of target regions had ≥ 20X coverage. We validated the specificity (98.2%) and sensitivity (86.7%) of the variant calling pipeline on the GIAB reference data. The concordance for germ line SNPs and variants in COSMIC in technical replicates was 94.9% and 92.7%, respectively. Novel variants had very low concordance, 55.9%, in technical replicates. The concordance between MAF estimates from the technical replicates was high (0.974, 0.957 and 0.969 for single nucleotide variations, insertions and deletions, respectively). The concordance for germline SNPs and COSMIC variants in pairwise comparisons of biopsies from the same tumor was 93.2% and 91.1%. For known variants, lower concordance was observed in TNBC (88.3%-98.5%) compared to ER-positive tumors (93.6%-98.8%, P<0.05) indicating greater intratumor heterogeneity. We identified variants in a small number of genes (DNAH9, PPM1E, and MAP3K1) that were called inconsistently in most technical replicates, even after excluding low mappability regions. We assessed intratumor heterogeneity in the triplicate biopsies, after excluding the technically unreliable variants. On average, two different biopsies from the same tumor shared 14272 +/-1379 common variants and differed in 816 +/- 416 variants.

CONCLUSION: We observed heterogeneity to be slightly greater in high-grade, ER-negative compared to low-grade, ER-positive breast cancers. Differences in variants observed in multiple biopsies of the same tumor are only slightly greater than those expected by technical noise alone.

Citation Format: Weiwei Shi, Anees Chagpar, Tingting Jiang, Donald R Lannin, Brigid Killelea, Nina Horowitz, Raymond Lim, James Platt, Charlotte KY Ng, Vikram B Wali, Britta Weigelt, Jorge S Reis-Filho, Christos Hatzis, Lajos Pusztai. Reliability of whole exome sequencing for assessing intratumor heterogeneity from breast tumor biopsies [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr PD3-4.

Abstract P4-02-01: High-depth sequencing of circulating tumor DNA to interrogate the genetics of residual micro-metastatic disease prior to relapse in early breast cancer

Background: The identification of early stage breast cancers that are at high risk of relapse after apparently curative treatment of the primary tumor would allow tailored adjuvant therapy approaches to prevent relapse. We sought to define whether high-depth targeted sequencing of circulating cell-free plasma DNA could be used to interrogate the genetics of residual micro-metastatic disease (RMD) persisting after neoadjuvant treatment in patients with early stage breast cancer.

Methods: In a cohort of 31 patients with early breast cancer receiving neoadjuvant chemotherapy, with no evidence of metastasis at presentation, we collected tumor tissue at baseline with the metastatic relapse if it occurred, and serial plasma samples at baseline, post-surgery, and every 6 months in follow-up. Serial plasma samples were subject to digital PCR mutation tracking to examine for circulating tumor DNA (ctDNA). Four patients had ctDNA detectable prior to clinical relapse. Primary tumor-derived DNA (from 4 cases), serial plasma DNA samples (from 4 cases), and metastases derived DNA (from 2 cases) were subjected to massively parallel sequencing (Illumina HiSeq2000) targeting all exons of 273 genes frequently mutated in breast cancers and/ or a custom AmpliSeq cancer panel (IonTorrent).

Results: Targeted sequencing revealed the presence of 1 to 20 somatic mutations in the early breast cancers at baseline, including 3 PIK3CA H1047L/R and 2 TP53 pathogenic mutations, all of which were detected in the subsequent plasma DNA samples taken prior to relapse. However, in one case an ESR1 E380Q mutation found in the baseline primary breast cancer was undetectable by targeted sequencing in all 3 subsequent plasma samples and in the metastasis; this mutation could not be identified in the metastasis by digital PCR. In two cases plasma DNA sequencing revealed no additional mutations to those identified in the primary tumor, whereas in the other two cases, plasma DNA targeted capture sequencing revealed divergence in the genetics of RMD. In these cases, 1 and 5 somatic mutations were found in the plasma DNA but were not detected in the respective baseline tumors. In particular, an activating FGFR1 K656E mutation, which was not detected by targeted capture sequencing in the primary breast cancer at 355x sequencing depth, was found at a mutant allele fraction (MAF) of 2.6% in the plasma 12 months post-surgery, and was subsequently detected in the distant metastasis at a MAF of 43.4% by targeted sequencing and digital PCR.

Conclusions: Our results provide evidence of clonal shifts in response to neoadjuvant systemic therapy of early breast cancers. In addition, we demonstrate that high-depth targeted capture massively parallel sequencing analysis of plasma ctDNA may help predict the genotype of recurrence prior to the onset of clinically overt metastasis.

Citation Format: Charlotte KY Ng, Britta Weigelt, Isaac Garcia-Murillas, Gaia Schiavon, Sarah Hrebien, Rosalind J Cutts, Peter Osin, Ashutosh Nerurkar, Iwanka Kozarewa, Javier Armisen Garrido, Mitch Dowsett, Ian E Smith, Jorge S Reis-Filho, Nicholas C Turner. High-depth sequencing of circulating tumor DNA to interrogate the genetics of residual micro-metastatic disease prior to relapse in early breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-02-01.

Metaplastic breast carcinomas display genomic and transcriptomic heterogeneity [corrected]

Metaplastic breast carcinoma is a rare and aggressive histologic type of breast cancer, preferentially displaying a triple-negative phenotype. We sought to define the transcriptomic heterogeneity of metaplastic breast cancers on the basis of current gene expression microarray-based classifiers, and to determine whether these tumors display gene copy number profiles consistent with those of BRCA1-associated breast cancers. Twenty-eight consecutive triple-negative metaplastic breast carcinomas were reviewed, and the metaplastic component present in each frozen specimen was defined (ie, spindle cell, squamous, chondroid metaplasia). RNA and DNA extracted from frozen sections with tumor cell content >60% were subjected to gene expression (Illumina HumanHT-12 v4) and copy number profiling (Affymetrix SNP 6.0), respectively. Using the best practice PAM50/claudin-low microarray-based classifier, all metaplastic breast carcinomas with spindle cell metaplasia were of claudin-low subtype, whereas those with squamous or chondroid metaplasia were preferentially of basal-like subtype. Triple-negative breast cancer subtyping using a dedicated website (http://cbc.mc.vanderbilt.edu/tnbc/) revealed that all metaplastic breast carcinomas with chondroid metaplasia were of mesenchymal-like subtype, spindle cell carcinomas preferentially of unstable or mesenchymal stem-like subtype, and those with squamous metaplasia were of multiple subtypes. None of the cases was classified as immunomodulatory or luminal androgen receptor subtype. Integrative clustering, combining gene expression and gene copy number data, revealed that metaplastic breast carcinomas with spindle cell and chondroid metaplasia were preferentially classified as of integrative clusters 4 and 9, respectively, whereas those with squamous metaplasia were classified into six different clusters. Eight of the 26 metaplastic breast cancers subjected to SNP6 analysis were classified as BRCA1-like. The diversity of histologic features of metaplastic breast carcinomas is reflected at the transcriptomic level, and an association between molecular subtypes and histology was observed. BRCA1-like genomic profiles were found only in a subset (31%) of metaplastic breast cancers, and were not associated with a specific molecular or histologic subtype.

Evaluation of candidate spermatogonial markers ID4 and GPR125 in testes of adult human cadaveric organ donors

The optimal markers for human spermatogonial stem cells (SSCs) are not known. Among the genes recently linked to SSCs in mice and other animals are the basic helix-loop-helix transcription factor ID4 and the orphan G-protein-coupled receptor GPR125. While ID4 and GPR125 are considered putative markers for SSCs, they have not been evaluated for coexpression in human tissue. Furthermore, neither the size nor the character of the human spermatogonial populations that express ID4 and GPR125, respectively, are known. A major barrier to addressing these questions is the availability of healthy adult testis tissue from donors with no known reproductive health problems. To overcome this obstacle, we have employed healthy testicular tissue from a novel set of organ donors (n = 16; aged 17-68 years) who were undergoing post-mortem clinical organ procurement. Using immunolabelling, we found that ID4 and GPR125 are expressed on partially overlapping spermatogonial populations and are more broadly expressed in the normal adult human testis. In addition, we found that expression of ID4 remained stable during ageing. These findings suggest that ID4 and GPR125 could be efficacious for identifying previously unrecognized human spermatogonial subpopulations in conjunction with other putative human stem cell markers, both in younger and older donors.

Characterization of the genomic features and expressed fusion genes in micropapillary carcinomas of the breast

Micropapillary carcinoma (MPC) is a rare histological special type of breast cancer, characterized by an aggressive clinical behaviour and a pattern of copy number aberrations (CNAs) distinct from that of grade- and oestrogen receptor (ER)-matched invasive carcinomas of no special type (IC-NSTs). The aims of this study were to determine whether MPCs are underpinned by a recurrent fusion gene(s) or mutations in 273 genes recurrently mutated in breast cancer. Sixteen MPCs were subjected to microarray-based comparative genomic hybridization (aCGH) analysis and Sequenom OncoCarta mutation analysis. Eight and five MPCs were subjected to targeted capture and RNA sequencing, respectively. aCGH analysis confirmed our previous observations about the repertoire of CNAs of MPCs. Sequencing analysis revealed a spectrum of mutations similar to those of luminal B IC-NSTs, and recurrent mutations affecting mitogen-activated protein kinase family genes and NBPF10. RNA-sequencing analysis identified 17 high-confidence fusion genes, eight of which were validated and two of which were in-frame. No recurrent fusions were identified in an independent series of MPCs and IC-NSTs. Forced expression of in-frame fusion genes (SLC2A1-FAF1 and BCAS4-AURKA) resulted in increased viability of breast cancer cells. In addition, genomic disruption of CDK12 caused by out-of-frame rearrangements was found in one MPC and in 13% of HER2-positive breast cancers, identified through a re-analysis of publicly available massively parallel sequencing data. In vitro analyses revealed that CDK12 gene disruption results in sensitivity to PARP inhibition, and forced expression of wild-type CDK12 in a CDK12-null cell line model resulted in relative resistance to PARP inhibition. Our findings demonstrate that MPCs are neither defined by highly recurrent mutations in the 273 genes tested, nor underpinned by a recurrent fusion gene. Although seemingly private genetic events, some of the fusion transcripts found in MPCs may play a role in maintenance of a malignant phenotype and potentially offer therapeutic opportunities.

Abstract S6-06: High-depth massively parallel sequencing reveals heterogeneity between primary tumor and metastatic deposits in de novo metastatic breast cancer patients prior to exposure to systemic therapy

Background: Breast cancers are often composed of mosaics of tumor cells that in addition to the founder genetic events harbor private genetic aberrations. Previous studies comparing the repertoire of mutations in primary breast cancers and their metachronous metastatic deposits that developed after systemic therapy revealed differences in their clonal composition and mutational repertoire. It is unclear, however, whether the differences documented could be attributed to the metastatic process itself or because of selective pressure from systemic therapies. Hence we sought to investigate whether the metastatic process would constitute a biological ‘bottleneck’ resulting in the selection of clones fittest to metastasize. We subjected primary breast cancers and their synchronous metastatic deposits from patients who presented with de novo metastatic disease and who had not received any systemic therapy to gene copy number analysis and high-depth massively parallel sequencing.

Materials and Methods: Frozen primary tumor and distant metastases biopsies were obtained from 7 patients with de novo metastatic disease (i.e. stage IV breast cancer at presentation) enrolled in the ESOPE study (Institut Curie, Paris). DNA samples extracted from microdissected tumors and from peripheral blood were subjected to high-depth (250x) whole exome sequencing and SNP6 copy number profiling. The impact of spatial heterogeneity was further assessed by targeted sequencing of paraffin-embedded samples from additional, independent pre-treatment biopsies of the primary tumor and matched metastasis from the same patients. Driver mutations were defined by bioinformatic methods; for single nucleotide variants (SNVs), CHASM and FATHMM were employed and for insertions/ deletions (indels), only frameshift or truncating mutations in genes normally expressed in breast tissue were included.

Results: In de novo metastatic breast cancers, without any pretreatment, significant genomic differences were observed between primary and metastatic deposits in all cases. A median number of 105 (32-224) and 54 (10-57) SNVs and indels were found, respectively, of which 36 (9-139) and 11 (1-19) were shared between the primary tumors and the de novo metastases, respectively. Although a substantial proportion of driver SNVs and indels were found in common between primary tumors and their respective metastatic deposits (median: 29% (17%-38%)), 50% (25%-78%) of driver SNVs and 79% (60%-90%) of the potentially pathogenic indels were restricted either to the primary or the metastatic deposit, including driver mutations affecting epithelial-to-mesenchymal transition (EMT)-related genes in 3 patients, namely TGFB1, SMAD4 and TCF7L2.

Conclusions: This is, to the best of our knowledge, the first study reporting on the differences in the mutational repertoire between primary tumors and metastatic deposits in de novo metastatic breast cancer patients who have not received systemic therapy. Our findings suggest that the breast cancer metastatic process likely constitutes a biological bottleneck with selection of subclones harboring specific driver genetic aberrations, often affecting EMT-related genes.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr S6-06.

Abstract S4-02: Integrated genomic analyses of members of protein kinase C family identifies subtype specific alterations as novel therapeutic targets

Introduction

Members of the protein kinase C family are serine/threonine kinases that are involved in proliferation, apoptosis, cell survival and migration, and have been implicated in tumorigenesis. Recently PRKCE has been found to be up-regulated in triple-negative (TN) breast cancers and has been proposed as a target for therapeutic intervention. The aims of this study were to determine i) whether different members of the PKC family are dysregulated and/ or mutated in specific subtypes of breast cancer, ii) to investigate the impact of silencing or overexpression of members of the PKC family in cell line models representative of the different breast cancer subtypes.

Material and methods:

We obtained expression and mutational data from the cancer genome atlas (TCGA) project from 567 and 640 samples subjected to microarray-based gene expression profiling and whole exome sequencing, respectively. Pair-wise SAM analysis of TCGA gene expression data was performed to identify differential expression between subgroups (ER+, HER2+ and TN). Potential driver mutations were identified through the algorithm CHASM. Subtype specific dependencies were identified from the re-analysis of publicly available siRNA kinome-wide screens in a panel of 20 breast cancer cell lines. In vitro assessment of gene overexpression was assessed in MCF10A cells by wound healing scratch assays and 3D growth in Matrigel.

Results

PRKCA, B, I and Q were expressed at significantly higher levels in TN breast cancers. Higher expression of PRKCE was significantly associated with ER-negativity, whereas high PRKCD expression was associated with ER-positivity. Analysis of siRNA kinome-wide screen data resulted in a significant reduction in survival associated with PRKCI and PRKCE in ER-negative cells, PRKCQ in triple-negative cells, and PRKCD in ER-positive cells. Furthermore meta-analysis of published exome and whole genome sequencing data identified potentially activating recurrent kinase domain mutations in PRKCB (0.93%), Q (1.25%) and Z (0.93%), with mutations in PRKCZ being associated with higher gene expression. Forced expression of wild-type PRKCQ and PRKCZ in MCF10A cells resulted in the formation of irregular acini in 3D cell culture and expression of wild-type PRKCZ resulted in increased migration.

Conclusions

Differential expression of members of the protein kinase C family, are associated with different molecular subtypes of breast cancer. Furthermore, we have shown that breast cancer cells are dependent upon expression of these family members in vitro, which are associated with different cellular phenotypes.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr S4-02.

Management and prevention of spontaneous pneumothorax using pleurodesis in Hong Kong

BACKGROUND

The practice of pleurodesis for the management and prevention of spontaneous pneumothorax (SP) is uncertain.

DESIGN

A retrospective multicentre analysis of patients admitted to 12 hospitals in Hong Kong with SP in 2004 and who subsequently underwent pleurodesis for the same episode.

RESULTS

Pleurodesis was performed in 394 episodes. Initial medical chemical pleurodesis was performed for 258 (65.5%) patients ('initial medical group'), while 136 (34.5%) underwent initial surgical pleurodesis ('initial surgical group'). Secondary spontaneous pneumothorax (SSP; 237 episodes, 60.2%) was the most common indication for pleurodesis; it was also performed after a first episode of primary spontaneous pneumothorax (PSP) in 22 episodes (5.6%). Tetracycline derivatives (172 episodes, 66.7%) were the most popular sclerosing agents in the initial medical group. Those in the initial medical group were older and were more likely to be males, have SSP, chronic obstructive pulmonary disease and a history of past pleurodesis (P < 0.05) compared to the initial surgical group. Compared to the tetracycline group, more patients who initially received talc slurry had the procedure performed by surgeons, had larger (≥2 cm) pneumothorax or required suction during initial drainage (P < 0.05).

CONCLUSIONS

Despite the availability of international guidelines, there is considerable variation in pleurodesis for SP.

Minocycline and talc slurry pleurodesis for patients with secondary spontaneous pneumothorax

SETTING

Few studies have evaluated the sclerosing efficacy of minocycline, and none have specifically compared its sclerosing efficacy and safety profiles with talc slurry in secondary spontaneous pneumothorax (SSP).

DESIGN

A retrospective analysis was conducted in patients with SSP who underwent chemical pleurodesis from January to December 2004 with minocycline or talc slurry in 12 public hospitals of Hong Kong.

RESULT

There were 121 episodes of minocycline pleurodesis and 64 episodes of talc slurry pleurodesis. Immediate procedural failure were similar in the minocycline and talc slurry groups (21.5% vs. 28.1%, P = 0.31). Presence of interstitial lung disease, ≥ 2 previous episodes of pneumothorax, requiring mechanical ventilation during pleurodesis and persistent air leak before pleurodesis were independently associated with procedural failure. Pain was experienced in respectively 44.6% and 37.5% of the minocycline and the talc slurry groups. Pain was more common in patients receiving high doses of talc (≥ 5 g; P = 0.03). Respiratory distress was found in respectively 1.7% and 1.6% of the minocycline and talc slurry groups.

CONCLUSION

Minocycline and talc slurry had comparable sclerosing efficacy in SSP, with immediate success rates of >70%. Pain was the most common adverse effect and respiratory distress was uncommon. Both appeared to be effective and safe for chemical pleurodesis in SSP.

High prevalence of human papillomavirus DNA detected in cervical swabs from women in southern Selangor, Malaysia

Persistent high-risk human papillomavirus (HPV) infection is known to play an important role in the genesis of cervical cancer. Since new screening and prevention strategies, namely improved HPV testing and HPV vaccination have been aggressively promoted recently, it is crucial to investigate the HPV distribution in Malaysia in order to maximize their cost-effectiveness. This study was therefore conducted to assess the HPV type distribution in the most populous region, the state of Selangor. A total of 200 cervical swab samples were collected in two health-screening campaigns, and also from women attending obstetrics and gynecology clinics in several hospitals in Selangor. DNA extraction was performed and HPV DNA was detected via nested PCR using MY09/MY11 as outer primers and GP5+/GP6+ as inner primers which target the L1 gene of the viral genome. The purified PCR products were subjected to automated DNA sequencing to determine the HPV genotype. Out of 180 β-globin positive samples, 84 (46.7%) were positive for HPV DNA. The most common HPV type found was high-risk oncogenic type 16 (40%), followed by HPV type 18 (3.3%), HPV 33 (1.7%), HPV 31 (0.6%), and low-risk HPV 87 (0.6%). Our study confirmed that nested PCR method is highly sensitive in detecting HPV DNA even in low risk patients. Since a relatively high prevalence rate of HPV infection was found in this population, prompt healthcare policy changes to bring about implementation of early HPV vaccination program is desirable to prevent a high incidence of cervical cancer.

Management of patients admitted with pneumothorax: a multi-centre study of the practice and outcomes in Hong Kong

OBJECTIVE

To examine the management practice of pneumothorax in hospitalised patients in Hong Kong, especially the choice of drainage options and their success rates, as well as the factors associated with procedural failures.

DESIGN

Retrospective study.

SETTING

Multi-centre study involving 12 public hospitals in Hong Kong.

PATIENTS

All adult patients admitted as an emergency in the year 2004 with a discharge diagnosis of 'pneumothorax' were included. Data on the management and outcomes of the various types of pneumothoraces were collected from their case records.

RESULTS

Altogether these patients had 1091 episodes (476 primary spontaneous pneumothoraces, 483 secondary spontaneous pneumothoraces, 87 iatrogenic pneumothoraces, and 45 traumatic pneumothoraces). Conservative treatment was offered in 182 (17%) episodes, which were more common among patients with small primary spontaneous pneumothoraces (71%). Simple aspiration was performed to treat 122 (11%) of such episodes, and had a success rate of 15%. Aspiration failure was associated with having a pneumothorax of size 2 cm or larger (odds ratio=3.7; 95% confidence interval, 1.2-11.5; P=0.03) and a smoking history (4.1; 1.2-14.3; P=0.03). Intercostal tube drainage was employed in 890 (82%) episodes, with a success rate of 77%. Failure of intercostal tube drainage was associated with application of suction (odds ratio=4.1; 95% confidence interval, 2.8-5.9; P<0.001) and presence of any tube complications (1.55; 1.0-2.3; P=0.03). Small-bore catheters (<14 French) were used in 12 (1%) of the episodes only. Tube complications were encountered in 214 (24%) episodes.

CONCLUSION

Notwithstanding recommendations from international guidelines, simple aspiration and intercostal tube drainage with small-bore catheters were not commonly employed in the management of hospitalised patients with the various types of pneumothoraces in Hong Kong.

Design and development of a novel balancer with variable difficulty for training and evaluation

This paper presents a novel, portable and cost-effective balance trainer with the necessary important features to improve the reach of rehabilitation to the masses. There are three factors that contribute to a person's ability to maintain standing balance: Proprioceptive feedback (from the joints), vision, and the vestibular system. These systems can be affected by injury, infection, or brain damage caused by stroke. One example of such injuries is ankle injury. A large focus of the physiotherapy and sports medicine community is using postural-control tasks to prevent, assess and rehabilitate patients. Unfortunately, there are presently two extreme ends of balance training devices. On one end, there is high-end equipment which only large hospitals are capable of buying. On the other end are the simple balance boards which offer limited features. To develop the new balance trainer - the Pro.Balance - therapists at the Singapore General Hospital drafted a new 'wish list' of requirements. The prototype was built at the Nanyang Technological University, Singapore, and was commercialized by Lab Rehab Pte Ltd as the Pro.Balance. The device has a small footprint, incorporating only the most important and frequently used functions. These functions include being able to provide different levels of difficulty, setting different difficulties in different directions, the storing of a patient's performance, real-time visual feedback to aid the patient and different types of modes for different purposes. Springs are used to vary the amount of supporting moments, thus varying the difficulty levels. This paper describes the design and features of the Pro.Balance.

Clinical and economic impact of an antibiotics stewardship programme in a regional hospital in Hong Kong

BACKGROUND

Inappropriate use of antibiotics is one of the important factors attributing to emergence of drug-resistant pathogens. Infection with multidrug-resistant pathogens adversely affects quality of medical care.

CONTEXT

Queen Elizabeth Hospital, an 1800-bed acute service hospital in Hong Kong. Antibiotics are commonly prescribed for treating acute infections.

KEY MEASURES FOR IMPROVEMENT

Reduce inappropriate prescription of broad-spectrum antibiotics and overall antibiotic prescription through implementation of a multidisciplinary antibiotics stewardship programme (ASP).

STRATEGIES FOR CHANGE

A multidisciplinary programme involving policy and guideline formulation, education and feedback, monthly antibiotic consumption and cost monitoring, antimicrobial susceptibility pattern reporting and concurrent feedbacks for commonly prescribed broad-spectrum antibiotics was implemented in 2004. Predefined logistics to prescribe "restricted" antibiotics were formulated and implemented with collaborative efforts from clinical and non-clinical departments. The programme was supported by management at department and hospital levels.

EFFECTS OF CHANGE

Broad-spectrum antibiotics were prescribed inappropriately in 28.9% (n = 192) clinical scenarios. The ASP reduced the restricted and total antibiotic consumption as well as the antibiotics-related costs. Predefined clinical outcomes were not adversely affected. Economic analysis suggested that the extra human cost in running ASP could be offset by savings from antibiotic expenditure.

LESSONS LEARNED

It is cost-effective to implement a multidisciplinary ASP in acute service hospitals as the programme reduces antibiotic consumption and results in overall cost savings. The quality of medical care is not jeopardized as the important clinical outcomes are not adversely affected. The generalisability and sustainability of ASPs in other clinical contexts warrant further studies to ensure the continuous success of this programme.

Two cases of intraperitoneal bladder rupture following vaginal delivery

We report two rare cases of isolated spontaneous intraperitoneal bladder rupture following normal vaginal delivery without concomitant uterine rupture. Two primigravidas, aged 32 years and 34 years, presented following vaginal delivery with abdominal distension and acute renal failure. The initial diagnosis in both cases was severe urosepsis. Definitive diagnosis was achieved after 48 hours. Comparison was made with two of the cases found in the literature and all four cases were reviewed. Laparotomy and bladder repair were performed in all patients with no adverse outcome reported. Two of them were diagnosed only during laparotomy. Key diagnostic clinical features were acute renal failure, new-onset ascites and bowel ileus with sepsis. This rare but life-threatening condition is often diagnosed late. Prompt laparotomy and bladder repair are necessary to prevent an adverse outcome.

Pleuroscopy: our initial experience in Hong Kong

OBJECTIVE

To report our preliminary experience using pleuroscopy for patients with pleural diseases.

DESIGN

Prospective cohort study.

SETTING

Tertiary referral hospital with service input from respiratory physicians and cardiothoracic surgeons in Hong Kong.

PATIENTS

Between April and November 2007, patients with undiagnosed exudative pleural effusions and proven malignant pleural effusions were recruited for diagnostic evaluations and therapeutic interventions, respectively.

INTERVENTION

Pleuroscopy with a semi-rigid thoracoscope performed under local anaesthesia and conscious sedation.

RESULTS

A total of 20 patients (16 males and 4 females; mean age, 63 years) underwent the procedure and were followed up for a mean of 19 weeks. For the 14 patients having diagnostic pleuroscopy, the yield was 79% (11 patients). The 3-month success rate for the six patients undergoing pleurodesis was 83% (five patients). Complications were mild and included self-limiting fever (20%, four patients) and localised subcutaneous emphysema (20%, four patients). No major complications or mortality were noted.

CONCLUSION

Pleuroscopy using a semi-rigid instrument is a safe and efficacious procedure for the management of pleural diseases in suitable patients.

Clinical presentations and outcomes of Penicillium marneffei infections: a series from 1994 to 2004

OBJECTIVES

To describe the clinical presentation, management, and outcomes of patients with Penicillium marneffei infections in a regional hospital in Hong Kong.

DESIGN

Retrospective study.

SETTING

A regional and tertiary human immunodeficiency virus-referral hospital in Hong Kong.

PATIENTS

Those who had penicilliosis during the inclusive period January 1994 to February 2004.

RESULTS

Forty-seven immunocompromised patients (44 being human immunodeficiency virus-positive) with penicilliosis were retrospectively studied. Fever, malaise, and anaemia were the commonest presentations. Most diagnoses were obtained from blood cultures (83%) and lymph node biopsies (34%). Five (11%) died, death being attributable to penicilliosis; four (9%) of them had received no specific antifungal treatment due to late presentation and late diagnosis. The CD4 count of human immunodeficiency virus-infected patients upon diagnosis of penicilliosis was low (median, 20.0 cells/mm3). Most (70%) patients received amphotericin B as an induction treatment, followed by oral itraconazole, although a smaller proportion (21%) received oral itraconazole only. All surviving human immunodeficiency virus-infected patients took highly active antiretroviral treatment and oral itraconazole as secondary prophylaxis after treatment of penicilliosis. The prognosis appeared satisfactory with early diagnosis and administration of appropriate antifungal therapy. Relapse ensued in two (4%) of the patients only.

CONCLUSION

Penicillium marneffei infection in immunocompromised patients is a serious disease with significant mortality if not diagnosed early and treated with appropriate antifungal drugs. Simple investigations like blood culture enable the diagnosis in the majority of cases. Immunocompromised patients who have been successfully treated should receive oral itraconazole as a maintenance therapy to prevent relapse.

Bronchial artery embolisation can be equally safe and effective in the management of chronic recurrent haemoptysis

OBJECTIVE

To examine the efficacy and safety of bronchial artery embolisation in patients with acute major haemoptysis and those with chronic recurrent haemoptysis.

DESIGN

Retrospective review of clinical records.

SETTING

Regional hospital, Hong Kong.

PATIENTS

Clinical records of 70 consecutive patients who had undergone bronchial artery embolisation in Queen Elizabeth Hospital from 1998 to 2003 were reviewed. Altogether 74 bronchial artery embolisation procedures were attempted, 46 (62%) for acute major haemoptysis, and 28 (38%) for chronic recurrent bleeding. Follow-up data were available for 32 patients.

MAIN OUTCOME MEASURES

After bronchial artery embolisation, the Kaplan-Meier method and log-rank tests were used to compare the probability of recurrence in the two patient categories.

RESULTS

Overall immediate control was attained following 99% of the procedures, with a complication rate of 13%; all complications were mild and self-limiting. For the 32 patients (19 having acute major haemoptysis and 13 having chronic recurrent bleeding) with follow-up data available, the overall recurrence rate was 36% (26% in the acute and 47% in chronic group). No statistically significant difference in recurrence probability between the two groups was observed (P=0.24). Presence of active pulmonary tuberculosis was associated with increased risk of recurrence (P=0.005).

CONCLUSION

Bronchial artery embolisation was noted to be effective and safe in both acute major and chronic recurrent haemoptysis.

Postoperative atrial fibrillation independently predicts prolongation of hospital stay after cardiac surgery

AIM

Postoperative atrial fibrillation (AF) occurs in up to 50% of cardiac surgery patients and represents the most common postoperative arrhythmic complication. A reduction of the length of hospital stay is a desirable goal in preventive strategies of postoperative AF. The aim of the present investigation was to determine whether prolonged postoperative hospital stay associated with AF after cardiac surgery surgery is attributable to the arrhythmia itself or to baseline characteristics of patients who develop AF.

METHODS

Patients undergoing elective cardiac surgery in the absence of heart failure and significant left ventricular dysfunction (n = 253; average age 65+/-11 years) were recruited to the present prospective study. Midline sternotomy procedures with standard surgical techniques for normothermic cardiopulmonary bypass in coronary artery bypass grafting and valvular surgery were used.

RESULTS

A total of 99 patients (39.1%) of the study population developed AF during the postoperative period. AF patients were older and more likely to have surgery for valvular heart disease and less likely to have antiarrhythmic drugs including beta-adrenergic blockers than patients without AF, but both patients with and without AF had similar body mass index and duration of surgery. Postoperative hospital stays were longer in patients with AF compared to those without AF (14.9+/-5.7 vs 10.6+/-3.6, respectively; P = 0.001). Multivariate analysis, adjusted for age and postoperative complications, demonstrated that postoperative hospital stay was 14.2+/-5.3 days in patients with AF and 10.8+/-3.8 days in patients without AF (P < 0.01). Treatment with oral antiarrhythmic drugs that reduce AF is associated with a reduction of postoperative hospital stay.

CONCLUSIONS

Despite baseline characteristics differed between patients with and without postoperative AF, most of the prolongation of hospital stay can be attributed to the rhythm disturbance itself.

Benign metastasising leiomyoma: a rare but possible cause of bilateral pulmonary nodules in Chinese patients

We report three cases of benign metastasising leiomyoma, which is a rare cause of multiple lung nodules, in three Hong Kong Chinese females. One patient presented with pleuritic chest pain, another was asymptomatic, while the last presented with haemoptysis. All three patients had previously undergone surgical resection of uterine leiomyomas. Multiple lung nodules mimicking lung metastases were demonstrated on chest radiographs, and all three diagnoses were obtained from lung biopsies. Hormonal therapy was given to two patients with variable responses. To the best of our knowledge, this is the first report of benign metastasising leiomyoma in Hong Kong Chinese population. It highlights the importance of considering this rare and benign disease in premenopausal females presenting with multiple lung nodules.

The spectrum of pathological changes in severe acute respiratory syndrome (SARS)

Aims:  To analyse the lung pathology of severe acute respiratory syndrome (SARS) and correlate the findings with the time sequence of the disease.

Methods and results:  Ten patients with a clinical diagnosis of SARS, and virological confirmation of SARS coronavirus infection were identified. Histology in most cases showed diffuse alveolar damage, from early to late phases, and the changes corresponded to the time sequence. Other variable features include multinucleated giant cells, pneumocytes with cytomegaly and variable amounts of inflammatory cells and foamy macrophages. One case showed superimposed bronchopneumonia. No viral inclusions were found. Coronavirus particles were identified in pneumocytes by electron microscopy.

Conclusions:  The predominant pathological process of SARS is diffuse alveolar damage and, in patients who die from the disease, there is evidence of organization and fibrosis. There are apparently no histological features specific for this disease, and the aetiological diagnosis depends on virological and ultrastructural studies.

Six month radiological and physiological outcomes in severe acute respiratory syndrome (SARS) survivors

BACKGROUND

The long term physiological and radiological outcomes of SARS survivors and their possible determinants are uncertain.

METHODS

SARS survivors in a follow up clinic in a regional hospital underwent high resolution computed tomography (HRCT) of the thorax and lung function tests 6 months after admission to hospital. The associations between the clinical and demographic data of the patients and the physiological and radiological outcomes were examined.

RESULTS

Fifty seven patients took part in the study. Lung function abnormalities were detected in 43 patients (75.4%), with restrictive defects (n = 16) being most common (28.1%). Radiological abnormalities of any degree were detected in 43 patients (75.4%). Only the use of pulse corticosteroids was associated with the presence of CT abnormalities (p = 0.043, OR 6.65, 95% CI 1.06 to 41.73).

CONCLUSIONS

Physiological and radiological abnormalities are still present in a considerable proportion of SARS survivors at 6 months.

Antiarrhythmic Therapy on Prevention of Postoperative Atrial Fibrillation in Patients After Heart Surgery

The incidence of supraventricular arrhythmias is high following open-heart surgery, occurring in 25% to about 50% of patients. The most common of these arrhythmias is atrial fibrillation (AF). Postoperative AF has been associated with increased incidence of other complications and increased hospital length of stay. Atrial arrhythmias are most frequent in the first two to three days after cardiothoracic surgery, but they can occur at any point in the recovery period. Age and concomitant valular heart disease are consistently the independent factors most strongly associated with postoperative atrial fibrillation. Prevention of AF seems to be a reasonable clinical goal, and, consequently, many randomized trials have evaluated the effectiveness of pharmacological and nonpharmacological interventions for prevention of AF. The main indication for AF prophylaxis remains the shorteningof length of hospital stay and possibly reduction in stroke. The optimal treatment strategies for reducing postoperative AF are not well established. Commonly used therapeutic approaches include the use of rate-controlling drugs such as beta-blockers, calcium antagonists, and digoxin. Some pharmacological strategies including beta-blockers, sotalol, and amiodarone have shown to reduce risk of postoperative AF and may reduce length of hospital stay. There is no convincing evidence that reducing postoperative AF reduces stroke. This review summarizes current evidence from randomized controlled trials to estimate the effect of pharmacological and non pharmacologic interventions on the occurrence of AF after open-heart surgery and its effects on postoperative outcome.

Short term outcome and risk factors for adverse clinical outcomes in adults with severe acute respiratory syndrome (SARS)

BACKGROUND

Severe acute respiratory syndrome (SARS) was diagnosed in Hong Kong in over 1700 patients between March and early June 2003.

METHODS

115 patients diagnosed with SARS were admitted to Queen Elizabeth Hospital, a large regional hospital in Hong Kong, from March 2003, of whom 100 were either discharged or were dead at 31 May. The patients were prospectively studied after admission to assess their short term outcomes and the risk factors associated with adverse outcomes, defined as death or the need for mechanical ventilation

RESULTS

At the time of writing 18 patients had died, with a crude mortality rate of 15.7% and a 21 day mortality of 10% (standard error 3%). Thirty nine patients (34%) were admitted to the intensive care unit, 30 of whom (26%) required mechanical ventilation. Multivariate analysis showed that age above 60 (hazards ratio (HR) 3.5, 95% CI 1.2 to 10.2; p=0.02), presence of diabetes mellitus or heart disease (HR 9.1, 95% CI 2.8 to 29.1; p<0.001), and the presence of other comorbid conditions (HR 5.2, 95% CI 1.4 to 19.7; p=0.01) were independently associated with mortality. However, only the presence of diabetes mellitus and/or cardiac disease (HR 7.3, 95% CI 3.1 to 17.4; p<0.001) was associated with adverse outcomes as a whole.

CONCLUSION

SARS is a new disease entity that carries significant morbidity and mortality. Specific clinical and laboratory parameters predicting unfavourable outcomes have been identified.

Outcome of percutaneous nephrostomy for the management of pyonephrosis

OBJECTIVE

The aim of this study was to evaluate the efficacy of percutaneous nephrostomy (PCN) drainage for the interim management of pyonephrosis.

METHODS

Ninety-two consecutive patients [29 men, 63 women; mean age, 57 years; range, 23 to 88] who underwent PCN for the treatment of pyonephrosis from 1996 to 1999 were evaluated retrospectively. The clinical presentation, bacteriology and patient outcomes were analyzed.

RESULTS

The majority [77%] of patients had underlying obstructing urinary calculi. Other causes of obstruction included strictures [9%], papillary necrosis [7%], pelvi-ureteric junction obstruction [4%] and malignant stricture [3%]. The microorganisms cultured were Escherichia coli [30%], Klebsiella [19%], Proteus [8%], Pseudomonas [5%], Enterococcus [5%], and Candida spp [5%]. The microorganisms were sensitive to gentamicin [79%], ceftriaxone [71%], cephalexin [54%], nitrofurantoin [40%], cotrimoxazole [35%], nalidixic acid [32%] and ampicillin [29%]. Only 30% of bladder urine cultures were positive for microorganisms; the addition of PCN cultures improved this yield to 58%. The antibiotic regimen was revised according to the PCN culture whenever there was a discrepancy. After PCN, 69% of patients underwent minimally invasive procedures as definitive treatment of the obstructing lesion. Only 14% of patients required open surgery. There was low procedure-related morbidity [14%] and low overall mortality [2%].

CONCLUSIONS

PCN cultures yield important bacteriological information. The procedure is associated with minimal morbidity, facilitates definitive treatment and provides therapeutic benefit.

Single centre review of radiologically-guided percutaneous nephrostomies: a report of 273 procedures

INTRODUCTION

To evaluate the technical success and complications associated with radiologically-guided percutaneous nephrostomies (PCNs) in a single centre.

MATERIALS AND METHODS

A total of 273 PCNs performed in 190 patients in our hospital over a 3-year period from January 1997 to December 1999 were retrospectively reviewed. The study population consisted of 97 males and 93 females, ranging in age from 13 to 91 years. The main indications were urinary obstruction (77.7%), pyonephrosis (18.3%) and urinary diversion (4%). Demographic variables, technical and risk factors related to the procedure, complications, effect on urine cultures and body temperature; and subsequent patient management were examined.

RESULTS

The technical success rate was 99%. The 30-day mortality was 7.2%, none of which were procedure related. Haemorrhage requiring transfusion occurred in 4.3% while septicaemia affected 3.2% of patients. Drainage catheter complications included catheter dislodgement and blockage which were 11.9% and 4.1%, respectively. Thirty-one per cent of PCNs subsequently underwent ureteric stenting as the definitive treatment modality.

CONCLUSION

Radiologically-guided PCN is a safe procedure with a high technical success rate.

Early investigation of silver-coated Silzone heart valves prosthesis in 126 patients

BACKGROUND AND AIM OF THE STUDY

Permanent silver (Silzone) coating of the sewing cuff of St. Jude Medical prosthetic heart valves may reduce the rate of prosthetic valve endocarditis (PVE). However, the incidence of paravalvular leaks and stroke in patients after implantation of Silzone-coated heart valve prostheses is largely unknown.

METHODS

Complications were analyzed among 126 consecutive patients (78 males, 48 females; mean age 64.7 years; range: 40-80 years) who received Silzone-coated prostheses at our institution between February 1998 and December 1999. Among patients, 94 had aortic valve replacement, 29 mitral valve replacement, and three had aortic and mitral valve replacement. Concomitant cardiac procedures (mainly coronary bypass) were performed in 47 patients (37.3%).

RESULTS

Hospital mortality was 1.6% (2/126) and freedom from valve-related mortality 99.2+/-0.9%. Total follow up was 137.4 patient-years, and 98.4% complete. Strokes or transitory ischemic attacks (TIAs) occurred in four cases (two strokes, two TIAs; stroke rate 1.5%/year; 95% CI 0.4-2.6%/year; stroke+TIA rate 3%/year; 95% CI 0.4-5.25%/year). There was no case of prosthetic valve dysfunction or PVE. Freedom from reoperation due to procedure-associated complications was 97.6% (one aortic dissection, two major bleeds). Paravalvular leak was detected in 19 cases, and graded trivial or mild in 17 cases (11 grade 0-I, six grade I), and moderate in two cases (grade I-II in one, grade II in one). No patient needed reoperation due to paravalvular leak. Left ventricular (LV) function was normal in 80 cases, but was impaired mildly in 20 cases, moderately in 16, and severely in eight. Bicycle exercise testing in 92 patients (73%) showed median exercise performance (81.4+/-23.9% of normal) after correction for age and weight. Cerebral magnetic resonance imaging was performed in 64 patients (50.8%); median MRI score was 2.0+/-1.8 according to a 12-scaled score system.

CONCLUSION

The overall incidence of echocardiographic paravalvular leak graded more than trivial or mild was low (1.6%) in patients followed for a mean of 1.1+/-0.5 years (range: 1-27 months) after valve replacement with Silzone-coated heart valve prostheses. No patient required reoperation due to paravalvular leak; moreover, the stroke rate (1.5%/year) was low in these patients. The present data indicated no significant disadvantages or higher rate of complications related to silver coating compared with other, non-silver-coated prostheses. Future investigation is needed to determine long-term outcome.

Impairment of endothelial function--a possible mechanism for atherosclerosis of a high-fat meal intake

INTRODUCTION

Endothelial dysfunction is known to occur in patients with coronary artery disease. Flow-mediated dilation of the brachial artery using Doppler ultrasound is a non-invasive technique for the assessment of endothelial function. The objective of the study was to use the above method to evaluate the pathophysiology of high-fat (HF) intake on endothelial function in a local population. A popular local dish "nasi-lemak", a source of high saturated fat content from coconut milk, was chosen to represent a local high-fat meal (LHF). In addition, the effects of a Western high-fat (WHF) ("McDonald's") meal and a low-fat (LF) meal control on endothelial function were studied.

MATERIALS AND METHODS

The study population consisted of 10 healthy male non-smoker (mean age 22 +/- 2 years) with normal body mass index, normal fasting sugar and lipid profiles. Nitric oxide dependent flow-mediated dilation and nitric oxide independent (GTN) dilation was assessed by Doppler flow in the brachial artery before and 4 hours after each meal on separate occasions by 2 experienced sonographers blinded to the type of meals.

RESULTS

The baseline brachial artery size, baseline vessel flow and increase in flow after cuff deflation were similar for each of the six arterial studies. In response to reactive hyperaemia after cuff deflation, the endothelium-dependent dilation was significantly different between the meals. There was a marked decrease in endothelium-dependent dilation after the WHF meal compared to the LF meal (8.6 +/- 2.2% vs. -0.8 +/- 1.1%, P < 0.006). There was also a marked decrease in endothelium-dependent dilation after the LHF meal compared to the LF meal (7.7 +/- 2.1% vs. -0.8 +/- 1.1%, P < 0.001). When comparing between the two HF meals, the change in endothelium-dependent dilation was not significant (7.7 vs. 8.6%, P = 0.678). GTN-induced dilation was not significantly different before and after the LF, WHF or LHF (0.1 +/- 0.5% vs. 0.2 +/- 0.9% vs. 1.3 +/- 0.5%, P = 0.094).

CONCLUSION

The results suggest that in a local population, impairment of endothelial function is a possible mechanism in the pathophysiology of atherosclerosis from HF intake, beyond just affecting lipid levels. This effect is observed after both a LHF and a WHF meal intake. This technique to study endothelial function may be a useful non-invasive screening tool in the study of other HF diet choices and provides further information for the education of the influence of dietary choices on atherosclerosis.

Drought-induced guard cell signal transduction involves sphingosine-1-phosphate

Stomata form pores on leaf surfaces that regulate the uptake of CO2 for photosynthesis and the loss of water vapour during transpiration. An increase in the cytosolic concentration of free calcium ions ([Ca2+]cyt) is a common intermediate in many of the pathways leading to either opening or closure of the stomatal pore. This observation has prompted investigations into how specificity is controlled in calcium-based signalling systems in plants. One possible explanation is that each stimulus generates a unique increase in [Ca2+]cyt, or 'calcium signature', that dictates the outcome of the final response. It has been suggested that the key to generating a calcium signature, and hence to understanding how specificity is controlled, is the ability to access differentially the cellular machinery controlling calcium influx and release from internal stores. Here we report that sphingosine-1-phosphate is a new calcium-mobilizing molecule in plants. We show that after drought treatment sphingosine-1-phosphate levels increase, and we present evidence that this molecule is involved in the signal-transduction pathway linking the perception of abscisic acid to reductions in guard cell turgor.

Inductive activity of recombinant human growth and differentiation factor-5

Growth and differentiation factor-5 (GDF-5) is a divergent member of the transforming growth factor-beta/bone morphogenetic protein (BMP) superfamily that is required for proper skeletal patterning and development in the vertebrate limb. Based on the homology of GDF-5 with other bone-inducing BMP family members, the inductive activity of a recombinant form of human GDF-5 (rhGDF-5) was evaluated in a series of in vitro assays and in vivo bone-formation models. The in vitro response to rhGDF-5 resulted in the formation of chondrogenic nodules in fetal rat calvarial cells cultured in the context of collagen or collagen/hyaluronate extracellular matrices. Matrices loaded with rhGDF-5 induced ectopic cartilaginous and osseous tissue when implanted in subcutaneous or intramuscular sites. In non-human primate long-bone-defect and spinal-fusion models, rhGDF-5 combined with a mineralized collagen matrix induced bone formation in a manner equivalent to autogenous bone. These results highlight the unique potential of rhGDF-5 in a wide variety of orthopaedic applications.

Purification and in vitro folding of recombinant human thrombopoietin receptor expressed in Escherichia coli

Thrombopoietin receptor (TPOR) is a member of the cytokine receptor superfamily expressed primarily on hematopoietic cells. TPOR plays an important role in regulating platelet production. Due to its low expression level in human tissue, studies on the biochemical and biophysical properties of TPOR have been limited. In the present study, an extracellular domain of recombinant human TPOR (rh TPOR-EN) was expressed in Escherichia coli as inclusion bodies. Purification was achieved by metal chelated chromatography under denaturing condition and was refolded by gel filtration chromatography. Far UV circular dichroism spectroscopy and surface plasmon resonance experiments were performed to demonstrate that the protein was in a refolded state and could bind with its ligand. Thus, a production and purification scheme was developed by which sufficient quantities of rh TPOR-EN can be made available for biochemical and biophysical characterizations.

Valvuloplasty with glutaraldehyde-treated autologous pericardium in patients with complex mitral valve pathology

BACKGROUND

Severe mitral regurgitation associated with complex mitral valve disease often precludes successful surgical repair. The feasibility and the results of valvuloplasty with glutaraldehyde-treated autologous pericardium remain largely unknown.

METHODS

The cases of 63 patients who underwent operation within an 11-year period were studied. A pretreated autologous pericardial patch was used for leaflet extension plasty, for paracommissural plasty, as a substitute for part of the leaflet, and for reimplantation of ruptured papillary muscles to eliminate severe mitral regurgitation. Patients with a severely calcified annulus after en bloc decalcification had straddling endoventricular pericardial patch annuloplasty for reconstruction of the affected atrioventricular groove. Chordal replacement with a strip of pericardium was chosen if no suitable chordae were available. Pericardium-reinforced suture annuloplasty was used in patients with acute endocarditis resistant to medical therapy. Associated valvuloplasty procedures with Carpentier techniques were also employed.

RESULTS

There were no operative deaths in this series. At a mean follow-up of 61.1 months (range, 4 to 132 months), mitral regurgitation was absent or trivial in 92.1% of patients by echocardiography. Freedom from reoperation was 95.2% at 1 year and 5 years. Thromboembolic events have not been detected. Thirty percent of patients returned to sinus rhythm. Two patients required valve replacement.

CONCLUSIONS

Our beneficial results indicate that glutaraldehyde-treated autologous pericardium is suitable for valvuloplasty. It provides durable and predictable repair of valves that might otherwise need to be replaced because of the complex mitral valve disease. The technique is reliable, allows further efficacious repair possibilities, and improves postoperative outcomes. Whether it can prevent late deterioration and calcification requires more investigation.

Tracer kinetic modeling in nuclear cardiology

The introduction of tracer kinetic modeling techniques in conjunction with nuclear imaging has allowed the assessment of physiologic processes in the myocardium in a noninvasive and quantitative manner. Alongside the development of novel radiopharmaceuticals for both positron emission tomography and single photon emission computed tomography is the clarification of their pharmacology, pharmacokinetics, and modeling strategies for assessment of physiologic rates from imaging data. Image analysis and tracer kinetic modeling techniques used in nuclear cardiology must address unique considerations related to the heart. The most commonly used tracers and modeling techniques are presently discussed, with particular attention given to methods that allow absolute quantitation of physiologic processes. The applications of these techniques are obvious in research protocols and may find more use in future clinical studies.