Exclusion of the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy in HPCX1-linked families

Several linkage studies provided evidence for the presence of the hereditary prostate cancer locus, HPCX1, at Xq27-q28. The strongest linkage peak of prostate cancer overlies a variable region of ~750 kb at Xq27 enriched by segmental duplications (SDs), suggesting that the predisposition to prostate cancer may be a genomic disorder caused by recombinational interaction between SDs. The large size of SDs and their sequence similarity make it difficult to examine this region for possible rearrangements using standard methods. To overcome this problem, direct isolation of a set of genomic segments by in vivo recombination in yeast (a TAR cloning technique) was used to perform a mutational analysis of the 750 kb region in X-linked families. We did not detect disease-specific rearrangements within this region. In addition, transcriptome and computational analyses were performed to search for nonannotated genes within the Xq27 region, which may be associated with genetic predisposition to prostate cancer. Two candidate genes were identified, one of which is a novel gene termed SPANXL that represents a highly diverged member of the SPANX gene family, and the previously described CDR1 gene that is expressed at a high level in both normal and malignant prostate cells, and mapped 210 kb of upstream the SPANX gene cluster. No disease-specific alterations were identified in these genes. Our results exclude the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy. Adjacent regions appear to be the most likely candidates to identify the elusive HPCX1 locus.

Abstract 994: Colorectal cancer, adenoma and normal whole genome methylation sequencing in Africa Americans

Background: Colorectal adenoma (CRA) to cancer (CRC) progression involves epigenetic changes including DNA methylation. Here we performed whole genome Bisulfite Next-Generation Sequencing (WGBNGS) on a normal, a tubular adenoma and a tumor patients’ tissue DNA to elucidate epigenetic drivers in normal to cancer progression. Patients and Methods: Genomic DNA was isolated from fresh frozen tissues from a patient with normal colon, from a tubular adenoma lesion (20X depth was performed on these DNA samples., Alignment, mapping and CpG methylation analyses were done. Pyrosequencing and immunohistochemistry (IHC) were used to confirm selected methylation target genes. Results: We identified 94 unique CpG sites hypermethylated in 4 novel genes in adenoma compared to normal and 180 unique CpG sites in 7 genes in cancer. Ingenuity pathway analysis (IPA) showed that the methylated genes including a novel gene ATXN7L1 were involved in WNT pathway, ubiquitination process and cross-talk with B-catenin, in the adenoma. Three of the hypermethylated genes in cancer were, Loc100506436: a novel gene with 17 unique CpG sites (EGFR pathway, cRNA CpG site hypermethylated is part of MEK1/2), GPNMB with 7 unique CpG sites (membrane protein likely in complexes with integrins) and TNFAIP2 with 8 unique CpG sites (its role was noted in Head and neck cancer). IHC confirmed the lack of GPNMB expression in cancer tissues. Conclusion: This work provides insight into differential CpG island methylation profiles in CRA, CRC vs. normal colon tissue and provides a window into the more complex factors, including alteration of known and novel genes as multiple CpG methylation drivers in colorectal carcinogenesis. Investigations into the possible roles of the novel genes targets in the context of early and prognostic methylation biomarker are underway.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 994. doi:1538-7445.AM2012-994

Multidrug resistance-linked gene signature predicts overall survival of patients with primary ovarian serous carcinoma

PURPOSE

This study assesses the ability of multidrug resistance (MDR)-associated gene expression patterns to predict survival in patients with newly diagnosed carcinoma of the ovary. The scope of this research differs substantially from that of previous reports, as a very large set of genes was evaluated whose expression has been shown to affect response to chemotherapy.

EXPERIMENTAL DESIGN

We applied a customized TaqMan low density array, a highly sensitive and specific assay, to study the expression profiles of 380 MDR-linked genes in 80 tumor specimens collected at initial surgery to debulk primary serous carcinoma. The RNA expression profiles of these drug resistance genes were correlated with clinical outcomes.

RESULTS

Leave-one-out cross-validation was used to estimate the ability of MDR gene expression to predict survival. Although gene expression alone does not predict overall survival (OS; P = 0.06), four covariates (age, stage, CA125 level, and surgical debulking) do (P = 0.03). When gene expression was added to the covariates, we found an 11-gene signature that provides a major improvement in OS prediction (log-rank statistic P < 0.003). The predictive power of this 11-gene signature was confirmed by dividing high- and low-risk patient groups, as defined by their clinical covariates, into four specific risk groups on the basis of expression levels.

CONCLUSION

This study reveals an 11-gene signature that allows a more precise prognosis for patients with serous cancer of the ovary treated with carboplatin- and paclitaxel-based therapy. These 11 new targets offer opportunities for new therapies to improve clinical outcome in ovarian cancer.

Sarcomatoid carcinoma of the hand: a clinical case with an aggressive and uncommon presentation

Cutaneous sarcomatoid carcinoma is a high-grade malignancy. We describe a clinical case of an aggressive sarcomatoid carcinoma in an 87-year-old woman, who presented to the outpatients department with a haemorrhagic nodule on the dorsum of her right hand. By the time of excision 3 weeks later, the nodule had enlarged to 100 × 90 × 65 mm in size. On histological examination, a poorly differentiated carcinoma was seen, with both carcinomatous and sarcomatous elements, in keeping with a sarcomatoid carcinoma. The tumour was positive for cytokeratin, epithelial, smooth-muscle actin, and vimentin stains. Two months later, the patient presented with a recurrent growth on the excised scar along with numerous large right axillary lymph nodes. A right axillary dissection along with excision of the growth confirmed tumour recurrence with metastasis to lymph nodes. Soon after, the patient developed cerebral metastasis, which proved fatal. This case thus highlights the aggressive potential of sarcomatoid carcinoma.

Regulation of global gene expression in human Loa loa infection is a function of chronicity

Background

Human filarial infection is characterized by downregulated parasite-antigen specific T cell responses but distinct differences exist between patients with longstanding infection (endemics) and those who acquired infection through temporary residency or visits to filarial-endemic regions (expatriates).

Methods and Findings

To characterize mechanisms underlying differences in T cells, analysis of global gene expression using human spotted microarrays was conducted on CD4⁺ and CD8⁺ T cells from microfilaremic Loa loa-infected endemic and expatriate patients. Assessment of unstimulated cells showed overexpression of genes linked to inflammation and caspase-associated cell death, particularly in endemics, and enrichment of the Th1/Th2 canonical pathway in endemic CD4⁺ cells. However, pathways within CD8⁺ unstimulated cells were most significantly enriched in both patient groups. Antigen (Ag)-driven gene expression was assessed to microfilarial Ag (MfAg) and to the nonparasite Ag streptolysin O (SLO). For MfAg-driven cells, the number of genes differing significantly from unstimulated cells was greater in endemics compared to expatriates (p<0.0001). Functional analysis showed a differential increase in genes associated with NFkB (both groups) and caspase activation (endemics). While the expatriate response to MfAg was primarily a CD4⁺ pro-inflammatory one, the endemic response included CD4⁺ and CD8⁺ cells and was linked to insulin signaling, histone complexes, and ubiquitination. Unlike the enrichment of canonical pathways in CD8⁺ unstimulated cells, both groups showed pathway enrichment in CD4⁺ cells to MfAg. Contrasting with the divergent responses to MfAg seen between endemics and expatriates, the CD4⁺ response to SLO was similar; however, CD8⁺ cells differed strongly in the nature and numbers (156 [endemics] vs 36 [expatriates]) of genes with differential expression.

Conclusions

These data suggest several important pathways are responsible for the different outcomes seen among filarial-infected patients with varying levels of chronicity and imply an important role for CD8⁺ cells in some of the global changes seen with lifelong exposure.

Infection with the filarial parasite Loa loa causes a parasite-specific downregulation of T cell responses. However, differences exist (clinical and immunologic) between patients born and living in filarial endemic regions (endemics) and those who become infected during travel or short-term residency (expatriates). T cell responses are more depressed in endemics while expatriates have more clinical “allergic-type” symptoms. In this study, we showed that these differences reflect transcriptional differences within the T cell compartment. Using microarrays, we examined global gene expression in both CD4⁺ and CD8⁺ T cells of microfilaremic endemic and expatriate patients and found differences not only ex vivo, but also to parasite and, for CD8⁺ cells, to nonparasite antigens. Functional analysis showed that endemic patients expressed genes linked to inflammatory disease and caspase associated cell death at homeostasis while expatriates tended to have a more activation-induced gene profile at homeostasis and a CD4⁺ inflammatory response to parasite antigen. Patient groups were similar in their CD4⁺ response to nonparasite antigen but strongly differed in their CD8⁺ responses, demonstrating the potential global ramifications of chronic, longstanding infection. Our study describes potential transcriptional mechanisms for the variability seen in patients with different levels of exposure to and chronicity of filarial infection.

A new whole genome amplification method for studying clonal evolution patterns in malignant colorectal polyps

To identify the genetic drivers of colorectal tumorigenesis, we applied array comparative genomic hybridization (aCGH) to 13 formalin-fixed paraffin-embedded (FFPE) samples of early, localized human colon adenocarcinomas arising in high-grade adenomas (so-called "malignant polyps"). These lesions are small and hence the amount of DNA is limited. Additionally, the quality of DNA is compromised due to the fragmentation as a consequence of formalin fixation. To overcome these problems, we optimized a newly developed isothermal whole genome amplification system (NuGEN Ovation® WGA FFPE System). Starting with 100 ng of FFPE DNA, the amplification system produced 4.01 ± 0.29 μg (mean ± standard deviation) of DNA. The excellent quality of amplified DNA was further indicated by a high signal-to-noise ratio and a low derivative log(2) ratio spread. Both, the amount of amplified DNA and aCGH performance were independent of the age of the FFPE blocks and the associated degradation of the extracted DNA. We observed losses of chromosome arms 5q and 18q in the adenoma components of the malignant polyp samples, while the embedded early carcinomas revealed losses of 8p, 17p, and 18, and gains of 7, 13, and 20. Aberrations detected in the adenoma components were invariably maintained in the embedded carcinomas. This approach demonstrates that using isothermally whole genome amplified FFPE DNA is technically suitable for aCGH. In addition to demonstrating the clonal origin of the adenoma and carcinoma part within a malignant polyp, the gain of chromosome arm 20q was an indicator for progression from adenoma to carcinoma.

Genome and transcriptome profiles of CD133-positive colorectal cancer cells

Colorectal carcinomas (CRC) might be organized hierarchically and contain a subpopulation of tumorigenic, putative cancer stem cells that are CD133 positive. We studied the biological and genetic characteristics of such cells in CRC cell lines and primary tumors. Three CRC cell lines were sorted in CD133 positive and negative fractions. The respective genetic aberration profiles were studied using array comparative genomic hybridization (aCGH) and expression profiling. Tumorigenicity for each cellular population was tested by injection into nude mice. Additionally, we compared CD133+ and CD133- cells of 12 primary colorectal tumors using laser capture microdissection and aCGH. Three of five CRC cell lines displayed both CD133+ and CD133- cells, but tumorigenicity of these subfractions did not differ significantly and aCGH revealed essentially identical genomic imbalances. However, 96 genes were differentially expressed between the two populations. Array comparative genomic hybridization analysis after laser capture microdissection of CD133+ and CD133- areas in primary colorectal tumors revealed genetic differences in 7 of 12 cases. The use of cell lines for studying genomic alterations that define cancer stem cell characteristics, therefore, seems questionable. In contrast, CD133+ cells in primary cancer samples showed a unique genomic aberration profile. In conclusion, our data suggest that CD133 positivity defines a genetically distinct cellular compartment in primary CRC, which potentially includes tumor initiating cells.

Clinical relevance of multidrug resistance gene expression in ovarian serous carcinoma effusions

The presence of tumor cells in effusions within serosal cavities is a clinical manifestation of advanced-stage cancer and is generally associated with poor survival. Identifying molecular targets may help to design efficient treatments to eradicate these aggressive cancer cells and improve patient survival. Using a state-of-the-art TaqMan-based qRT-PCR assay, we investigated the multidrug resistance (MDR) transcriptome of 32 unpaired ovarian serous carcinoma effusion samples obtained at diagnosis or at disease recurrence following chemotherapy. MDR genes were selected a priori based on an extensive curation of the literature published during the last three decades. We found three gene signatures with a statistically significant correlation with overall survival (OS), response to treatment [complete response (CR) vs other], and progression free survival (PFS). The median log-rank p-values for the signatures were 0.023, 0.034, and 0.008, respectively. No correlation was found with residual tumor status after cytoreductive surgery, treatment (with or without chemotherapy) and stage defined according to the International Federation of Gynecology and Obstetrics. Further analyses demonstrated that gene expression alone can effectively predict the survival outcome of women with ovarian serous carcinoma (OS, log-rank p = 0.0000; and PFS, log-rank p = 0.002). Interestingly, the signature for overall survival is the same in patients at first presentation and those who had chemotherapy and relapsed. This pilot study highlights two new gene signatures that may help in optimizing the treatment for ovarian carcinoma patients with effusions.

Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview

BACKGROUND

DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes.

RESULTS

Each significant difference in gene-gene association represents a Differentially Associated Pair (DAP). Our tools include several choices of filtering methods, gene-gene association metrics, statistical testing methods and multiple comparison adjustments. Network results are easily displayed in Cytoscape. Analyses of glioma experiments and microarray simulations demonstrate the utility of these tools.

CONCLUSIONS

DAPfinder is a new friendly-user tool for reconstruction and comparison of biological networks.

Prevalence of hepatitis B virus infection in non-Hodgkin lymphoma: a systematic review and meta-analysis

BACKGROUND AND AIM

A recent meta-analysis has demonstrated an association between hepatitis C virus and non-Hodgkin lymphoma (NHL). There is also evidence on the association between hepatitis B virus (HBV) and NHL. The aim of this study was to evaluate this evidence using a meta-analytic approach.

METHODS

We searched the MEDLINE database from 1962 to 2008 for case-control studies that have reported the association of HBV with NHL. We calculated the odds ratio (OR) and 95% confidence intervals (CI) to assess the prevalence of HBV infection and pooled the results using three different statistical models.

RESULTS

Our search yielded 12 studies with 11 studies (3262 NHL patients, 1,523,205 controls) evaluating HBV infection in NHL and one study (3888 HBV-infected individuals, 205,203 controls) that had investigated for NHL in HBV infection. The OR of detecting HBV infection in NHL when compared with the control population was 2.56 (95% CI, 2.24-2.92) by the fixed effects model; 2.61 (95% CI, 2.29-2.98) by the exact method and 2.67 (95% CI, 2.04-3.49) by the random effects model suggesting a high prevalence of HBV carrier state in lymphoma. There was evidence of statistical heterogeneity which disappeared after exclusion of retrospective studies on sensitivity analysis.

CONCLUSIONS

The results of this study suggest a possible causal relation between HBV infection and NHL which needs to be confirmed by experimental and epidemiological studies. In countries where prevalence of HBV infection is 1% or more, it may be prudent to screen patients with NHL for occult HBV infection.

Prevalence of hepatitis B virus infection in non-Hodgkin lymphoma: a systematic review and meta-analysis

BACKGROUND AND AIM

A recent meta-analysis has demonstrated an association between hepatitis C virus and non-Hodgkin lymphoma (NHL). There is also evidence on the association between hepatitis B virus (HBV) and NHL. The aim of this study was to evaluate this evidence using a meta-analytic approach.

METHODS

We searched the MEDLINE database from 1962 to 2008 for case-control studies that have reported the association of HBV with NHL. We calculated the odds ratio (OR) and 95% confidence intervals (CI) to assess the prevalence of HBV infection and pooled the results using three different statistical models.

RESULTS

Our search yielded 12 studies with 11 studies (3262 NHL patients, 1,523,205 controls) evaluating HBV infection in NHL and one study (3888 HBV-infected individuals, 205,203 controls) that had investigated for NHL in HBV infection. The OR of detecting HBV infection in NHL when compared with the control population was 2.56 (95% CI, 2.24-2.92) by the fixed effects model; 2.61 (95% CI, 2.29-2.98) by the exact method and 2.67 (95% CI, 2.04-3.49) by the random effects model suggesting a high prevalence of HBV carrier state in lymphoma. There was evidence of statistical heterogeneity which disappeared after exclusion of retrospective studies on sensitivity analysis.

CONCLUSIONS

The results of this study suggest a possible causal relation between HBV infection and NHL which needs to be confirmed by experimental and epidemiological studies. In countries where prevalence of HBV infection is 1% or more, it may be prudent to screen patients with NHL for occult HBV infection.

Prevalence of hepatitis B virus infection in non-Hodgkin lymphoma: a systematic review and meta-analysis

BACKGROUND AND AIM

A recent meta-analysis has demonstrated an association between hepatitis C virus and non-Hodgkin lymphoma (NHL). There is also evidence on the association between hepatitis B virus (HBV) and NHL. The aim of this study was to evaluate this evidence using a meta-analytic approach.

METHODS

We searched the MEDLINE database from 1962 to 2008 for case-control studies that have reported the association of HBV with NHL. We calculated the odds ratio (OR) and 95% confidence intervals (CI) to assess the prevalence of HBV infection and pooled the results using three different statistical models.

RESULTS

Our search yielded 12 studies with 11 studies (3262 NHL patients, 1,523,205 controls) evaluating HBV infection in NHL and one study (3888 HBV-infected individuals, 205,203 controls) that had investigated for NHL in HBV infection. The OR of detecting HBV infection in NHL when compared with the control population was 2.56 (95% CI, 2.24-2.92) by the fixed effects model; 2.61 (95% CI, 2.29-2.98) by the exact method and 2.67 (95% CI, 2.04-3.49) by the random effects model suggesting a high prevalence of HBV carrier state in lymphoma. There was evidence of statistical heterogeneity which disappeared after exclusion of retrospective studies on sensitivity analysis.

CONCLUSIONS

The results of this study suggest a possible causal relation between HBV infection and NHL which needs to be confirmed by experimental and epidemiological studies. In countries where prevalence of HBV infection is 1% or more, it may be prudent to screen patients with NHL for occult HBV infection.

Microarray-based analysis of differential gene expression between infective and noninfective larvae of Strongyloides stercoralis

BACKGROUND

Differences between noninfective first-stage (L1) and infective third-stage (L3i) larvae of parasitic nematode Strongyloides stercoralis at the molecular level are relatively uncharacterized. DNA microarrays were developed and utilized for this purpose.

METHODS AND FINDINGS

Oligonucleotide hybridization probes for the array were designed to bind 3,571 putative mRNA transcripts predicted by analysis of 11,335 expressed sequence tags (ESTs) obtained as part of the Nematode EST project. RNA obtained from S. stercoralis L3i and L1 was co-hybridized to each array after labeling the individual samples with different fluorescent tags. Bioinformatic predictions of gene function were developed using a novel cDNA Annotation System software. We identified 935 differentially expressed genes (469 L3i-biased; 466 L1-biased) having two-fold expression differences or greater and microarray signals with a p value<0.01. Based on a functional analysis, L1 larvae have a larger number of genes putatively involved in transcription (p = 0.004), and L3i larvae have biased expression of putative heat shock proteins (such as hsp-90). Genes with products known to be immunoreactive in S. stercoralis-infected humans (such as SsIR and NIE) had L3i biased expression. Abundantly expressed L3i contigs of interest included S. stercoralis orthologs of cytochrome oxidase ucr 2.1 and hsp-90, which may be potential chemotherapeutic targets. The S. stercoralis ortholog of fatty acid and retinol binding protein-1, successfully used in a vaccine against Ancylostoma ceylanicum, was identified among the 25 most highly expressed L3i genes. The sperm-containing glycoprotein domain, utilized in a vaccine against the nematode Cooperia punctata, was exclusively found in L3i biased genes and may be a valuable S. stercoralis target of interest.

CONCLUSIONS

A new DNA microarray tool for the examination of S. stercoralis biology has been developed and provides new and valuable insights regarding differences between infective and noninfective S. stercoralis larvae. Potential therapeutic and vaccine targets were identified for further study.

High recombination rates and hotspots in a Plasmodium falciparum genetic cross

Background

The human malaria parasite Plasmodium falciparum survives pressures from the host immune system and antimalarial drugs by modifying its genome. Genetic recombination and nucleotide substitution are the two major mechanisms that the parasite employs to generate genome diversity. A better understanding of these mechanisms may provide important information for studying parasite evolution, immune evasion and drug resistance.

Results

Here, we used a high-density tiling array to estimate the genetic recombination rate among 32 progeny of a P. falciparum genetic cross (7G8 × GB4). We detected 638 recombination events and constructed a high-resolution genetic map. Comparing genetic and physical maps, we obtained an overall recombination rate of 9.6 kb per centimorgan and identified 54 candidate recombination hotspots. Similar to centromeres in other organisms, the sequences of P. falciparum centromeres are found in chromosome regions largely devoid of recombination activity. Motifs enriched in hotspots were also identified, including a 12-bp G/C-rich motif with 3-bp periodicity that may interact with a protein containing 11 predicted zinc finger arrays.

Conclusions

These results show that the P. falciparum genome has a high recombination rate, although it also follows the overall rule of meiosis in eukaryotes with an average of approximately one crossover per chromosome per meiosis. GC-rich repetitive motifs identified in the hotspot sequences may play a role in the high recombination rate observed. The lack of recombination activity in centromeric regions is consistent with the observations of reduced recombination near the centromeres of other organisms.

CD4 cell count recovery in HIV/TB co-infected patients versus TB uninfected HIV patients

BACKGROUND

There is lack of data comparing the improvement in CD4 count following antitubercular (ATT) and antiretroviral therapy (ART) in patients presenting with Human Immunodeficiency Virus/Tuberculosis (HIV/TB) dual infection compared with CD4 matched cohort of TB uninfected HIV patients initiated on ART. We sought to test the hypothesis; TB additionally contributes to reduction in CD4 count in HIV/TB co-infected patients and this would result in greater improvement in count following treatment compared with CD4 matched TB uninfected individuals.

MATERIALS AND METHODS

In a retrospective cohort study design we studied the change in CD4 cell counts in two groups of patients - those with CD4 cell count >100 cells / mm 3 (Group 1) and <100/mm 3 (Group 2) at presentation. In each group the change in CD4 cell count in dually infected patients following six-month ATT and ART was compared to cohorts of CD4 matched TB uninfected patients initiated on ART.

RESULTS

In Group 1 (52 patients) dually infected subjects' CD4 count improved from 150 cells/ mm 3 to 345 cells/mm 3 (P=0.001). In the control TB uninfected patients, the change was from 159 cells/mm 3 to 317 cells/mm 3 (P=0.001). Additional improvement in dually infected patients compared to the control group was not statistically significant (P=0.24). In Group 2 (65 patients) dually infected subjects count improved from 49 cells/mm3 to 249 cells/mm 3 (P=0.001) where as in control TB uninfected patients improvement was from 50 cells/ mm 3 to 205 cells/mm 3 (P=0.001), there being statistically significant additional improvement in dually infected subjects (P=0.01).

CONCLUSION

Greater increment in CD4 counts with ATT and ART in dually infected patients suggests that TB additionally influences the reduction of CD4 counts in HIV patients.

Abstract P2-06-11: Ramifications of HER2/ER/PR Guidelines from ASCO/CAP for Translational Cancer Research Using a Cohort from a Tertiary Care Centre in Ontario

Background: A transdisciplinary team from basic science, pathology, clinical and biostatistics was assembled to establish a framework with which to take novel laboratory biomarkers and targets to clinical validation. Human epidermal growth factor receptor (HER2), estrogen (ER) and progesterone (PR) receptor are of important prognostic and predictive value and drivers of systemic therapy for breast cancer (BC). As a first step, the current ASCO/CAP guidelines were used to re-assign centrally reviewed tumour specimens and compare to the clinically assigned scores for ER/PR and HER2.

Methods: With REB approval, a cohort of 62 cases of non-metastatic invasive BC with banked tumour specimens was assembled between 2005 and 2007. Clinico-pathological information for each case was retrospectively obtained from the medical file and entered into an anonymized database. Full section slides were originally stained by routine immunohistochemistry (IHC). Categorical clinical scores for ER/PR (negative-neg/weak/positive-pos) were compared to the continuous scores assigned in a blinded fashion using ASCO/CAP criteria (% pos/H-score). Categorical clinical scores obtained with duplicate IHC antibody staining of full sections for HER2 (neg/equivocal-eq/pos) were compared to those obtained from IHC assessments of triplicate 6mm cores in a tissue microarray (TMA) that were assigned to be neg/eq/pos using ASCO/CAP criteria. A senior breast pathologist adjudicated discordant specimens. Exact Fisher tests were used to compare the two sets of categorical assessments.

Results: Mean age was 43.5 years, (range 29-49). The majority of the cohort (59.7%) had N0 disease and received adjuvant chemotherapy (74.2%); 72.6% of the cohort was alive at the time of this analysis. Score means and ranges of ER/PR are displayed below. Two of 16 clinically ER neg cases (12.5%) were rescored as pos and 0/43 clinically ER pos cases were rescored as neg, P&lt;0.0001. Two of 13 clinically PR neg cases (15.4%) were rescored as pos and 4/46 clinically PR pos cases (8.7%) were rescored as neg, (P&lt;0.0001). HER2 status was reassessed for 51 cases, 41 of which (80%) had concordant scores (P&lt;0.0001). Thirty-nine (76%) cases were classified as HER2 neg on TMA, 7 of which (18%) were eq on routine IHC and neg by fluorescence in situ hybridization. In routine IHC, 15.7% of tumours were eq. Four TMA cases were eq (7.8%%); with routine IHC, one of these was neg, one eq, and two were pos. Eight patients were HER2 pos in both assessments.

ER/PR scores

Conclusions: Systemic therapy recommendations could be impacted in a small but substantive number of cases by the methodology used for biomarker assessment and scoring, particularly near threshold values. This study illustrates that the scoring criteria used may be an important contributor to variability in correlative biomarker studies. Consideration should be given to routine systematic reassessment with continuous scoring for biomarker data proposed for use in correlative science studies.

Direct measurement of the electron density of extended femtosecond laser pulse-induced filaments

We present direct time- and space-resolved measurements of the electron density of femtosecond laser pulse-induced plasma filaments. The dominant nonlinearity responsible for extended atmospheric filaments is shown to be field-induced rotation of air molecules.

Relevance of opt-out screening for HIV in emergency and pre-surgery patients in a tertiary care center in Northern India: a pilot study

OBJECTIVE

A preliminary opt-out screening study for HIV was conducted in a tertiary care hospital in India according to Center for Disease Control (CDC) guidelines. A total of 876 cases were screened for HIV during August 2007 to December 2007 using tests approved by the National AIDS Control Organization (NACO).

RESULTS

Data indicates that the prevalence of HIV in emergency and pre-surgical setting was 21 per thousand at the tertiary care center. Positivity rate in the pediatric population was 20.9 per thousand while in adults it was 21.4 per thousand. Most patients were totally unsuspected. Nearly 40000 patients seek admission annually to the emergency department alone. Thus nearly 700 to 800 patients may be missed every year if one does not resort to such a practice.

CONCLUSION

Since India has the second largest number of HIV cases in the world, opt-out screening program and testing in an emergency setting, as recommended by CDC, is extremely relevant. Logistics of implementation of this policy need to be worked out at a national level.

Genome-wide analysis of novel splice variants induced by topoisomerase I poisoning shows preferential occurrence in genes encoding splicing factors

RNA splicing is required to remove introns from pre-mRNA, and alternative splicing generates protein diversity. Topoisomerase I (Top1) has been shown to be coupled with splicing by regulating serine/arginine-rich splicing proteins. Prior studies on isolated genes also showed that Top1 poisoning by camptothecin (CPT), which traps Top1 cleavage complexes (Top1cc), can alter RNA splicing. Here, we tested the effect of Top1 inhibition on splicing at the genome-wide level in human colon carcinoma HCT116 and breast carcinoma MCF7 cells. The RNA of HCT116 cells treated with CPT for various times was analyzed with ExonHit Human Splice Array. Unlike other exon array platforms, the ExonHit arrays include junction probes that allow the detection of splice variants with high sensitivity and specificity. We report that CPT treatment preferentially affects the splicing of splicing-related factors, such as RBM8A, and generates transcripts coding for inactive proteins lacking key functional domains. The splicing alterations induced by CPT are not observed with cisplatin or vinblastine and are not simply due to reduced Top1 activity, as Top1 downregulation by short interfering RNA did not alter splicing like CPT treatment. Inhibition of RNA polymerase II (Pol II) hyperphosphorylation by 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (DRB) blocked the splicing alteration induced by CPT, which suggests that the rapid Pol II hyperphosphorylation induced by CPT interferes with normal splicing. The preferential effect of CPT on genes encoding splicing factors may explain the abnormal splicing of a large number of genes in response to Top1cc.

Liposomal amphotericin B (Fungisome) for the treatment of cryptococcal meningitis in HIV/AIDS patients in India: a multicentric, randomized controlled trial

BACKGROUND

There is need to investigate the use of liposomal amphotericin B in cryptococcal meningitis in India.

AIMS

To compare the efficacy, safety, duration of treatment and cost of two doses of liposomal amphotericin B (Amp B) (Fungisome) in cryptococcal meningitis in HIV/AIDS patients.

SETTINGS AND DESIGN

Prospective, randomized, multicenter study in tertiary care hospitals across India.

MATERIALS AND METHODS

Adult patients with culture-proven cryptococcal meningitis with HIV/AIDS were randomized to receive either 1 (Group A) or 3 mg/kg/day of Fungisome (Group B). Clinical efficacy and tolerability, laboratory evaluations and mycological response were assessed daily, twice weekly and weekly respectively. The patients were assessed at four and eight-week follow-up.

STATISTICS

We calculated average and standard deviation for the various parameters.

RESULTS

The time to show clinical response was 13.66 days (1 mg) and 9.55 days (3 mg). In Group B (n=6 complete response), 50% patients responded within one week by microbial conversion, 83% in two weeks and 100% in three weeks. Patients with 1 mg dose (n=4 complete response), none showed microbial conversion within one week, 75% responded in two weeks, whereas one patient took four weeks. The average duration of treatment was 36.5+/-14.4 and 26.5+/-5.89 (S.D.) days in 1 and 3 mg/kg/day respectively. Drug was tolerated with little renal, hepatic or hematological toxicity. The cost was found to be 3.81 lacs and 1.74 lacs with 3mg/kg/day and 1mg/kg/day respectively.

CONCLUSION

Higher dose showed better efficacy and quicker microbial conversion of Cerebrospinal fluid (CSF) (cerebrospinal fluid) than 1 mg/kg/day. It shortened the duration of treatment in days by 27% while drug cost almost doubled (

CLINICAL TRIAL REGISTRATION NUMBER

ISRCTN 52812742).

Abstract LB-51: Correlation of expression of MDR-associated genes with outcome in primary ovarian serous carcinoma

We have been developing tools to reproducibly correlate the expression of multidrug-resistance (MDR)-associated genes with response to chemotherapy in primary cancers. This study reports the results of a novel MDR gene expression analysis of primary serous carcinoma of the ovary utilizing a TaqMan Low Density Array (TLDA) chip which includes 380 previously characterized multidrug resistance (MDR)-associated genes that were initially identified in cultured cancer cells. Primary tumor samples from 133 patients from 4 sites were studied. All patients were subsequently treated with standard chemotherapy and had known clinical outcome. A 13 gene signature was identified whose expression added statistical power to the risk status of the patients based on standard clinical parameters (age, CA125, and success of surgical debulking) (log-rank statistic p=0.02). When subsets of patients with defined clinical risk were studied, we found that a subset of clinically high risk patients that had low expression of the 13 gene signature had a better outcome than would be predicted by purely clinical criteria. Similarly, clinically low risk patients with high expression of the 13 gene signature had a poorer prognosis. Since the mechanism of action of the 13 MDR genes involved in the signature are well-understood, it might be possible to devise therapeutic strategies to some of these targets with the goal of improving clinical outcome.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-51.

Steroid responsive prolonged thrombocytopenia in dengue

Prolonged thrombocytopenia in a usual case of dengue virus infection is uncommon. Dengue-related thrombocytopenia is self-limiting and responds within 3-5 days. An underlying immunological disorder may be responsible for delayed return of platelet count to a normal level. We present a case of prolonged thrombocytopenia in a case of dengue hemorrhagic fever. The response to steroids suggests a possible immunological dysfunction.

Ion selectivity from local configurations of ligands in solutions and ion channels

Probabilities of numbers of ligands proximal to an ion lead to simple, general formulae for the free energy of ion selectivity between different media. That free energy does not depend on the definition of an inner shell for ligand-counting, but other quantities of mechanistic interest do. If analysis is restricted to a specific coordination number, then two distinct probabilities are required to obtain the free energy in addition. The normalizations of those distributions produce partition function formulae for the free energy. Quasi-chemical theory introduces concepts of chemical equilibrium, then seeks the probability that is simplest to estimate, that of the most probable coordination number. Quasi-chemical theory establishes the utility of distributions of ligand-number, and sharpens our understanding of quasi-chemical calculations based on electronic structure methods. This development identifies contributions with clear physical interpretations, and shows that evaluation of those contributions can establish a mechanistic understanding of the selectivity in ion channels.

An integrative computational model for intestinal tissue renewal

OBJECTIVES

The luminal surface of the gut is lined with a monolayer of epithelial cells that acts as a nutrient absorptive engine and protective barrier. To maintain its integrity and functionality, the epithelium is renewed every few days. Theoretical models are powerful tools that can be used to test hypotheses concerning the regulation of this renewal process, to investigate how its dysfunction can lead to loss of homeostasis and neoplasia, and to identify potential therapeutic interventions. Here we propose a new multiscale model for crypt dynamics that links phenomena occurring at the subcellular, cellular and tissue levels of organisation.

METHODS

At the subcellular level, deterministic models characterise molecular networks, such as cell-cycle control and Wnt signalling. The output of these models determines the behaviour of each epithelial cell in response to intra-, inter- and extracellular cues. The modular nature of the model enables us to easily modify individual assumptions and analyse their effects on the system as a whole.

RESULTS

We perform virtual microdissection and labelling-index experiments, evaluate the impact of various model extensions, obtain new insight into clonal expansion in the crypt, and compare our predictions with recent mitochondrial DNA mutation data.

CONCLUSIONS

We demonstrate that relaxing the assumption that stem-cell positions are fixed enables clonal expansion and niche succession to occur. We also predict that the presence of extracellular factors near the base of the crypt alone suffices to explain the observed spatial variation in nuclear beta-catenin levels along the crypt axis.

Chromosomal copy number changes of locally advanced rectal cancers treated with preoperative chemoradiotherapy

Standard treatment of rectal cancer patients comprises preoperative chemoradiotherapy followed by radical surgery. However, clinicians are faced with the problem that response rates vary from one individual to another. Predictive biomarkers would therefore be helpful. To identify genomic imbalances that might assist in stratifying tumors into responsive or nonresponsive categories, we used metaphase comparative genomic hybridization to prospectively analyze pretherapeutic biopsies from 42 patients with locally advanced rectal cancers. These patients were subsequently treated with 5-fluorouracil-based preoperative chemoradiotherapy. Based on downsizing of the T-category, 21 rectal cancers were later classified as responsive, while the other 21 were nonresponsive. Comparing these two groups, we could show that gains of chromosomal regions 7q32 approximately q36 and 7q11 approximately q31, as well as amplifications of 20q11 approximately q13, were significantly associated with responsiveness to preoperative chemoradiotherapy (P<0.05). However, the probability of detecting these copy number changes by chance is high (P=0.21). Our primary results suggest that pretherapeutic evaluation of chromosomal copy number changes may be of value for response prediction of rectal cancers to preoperative chemoradiotherapy. This will require validation in a larger cohort of patients.

Evaluation of current methods used to analyze the expression profiles of ATP-binding cassette transporters yields an improved drug-discovery database

The development of multidrug resistance (MDR) to chemotherapy remains a major challenge in the treatment of cancer. Resistance exists against every effective anticancer drug and can develop by multiple mechanisms. These mechanisms can act individually or synergistically, leading to MDR, in which the cell becomes resistant to a variety of structurally and mechanistically unrelated drugs in addition to the drug initially administered. Although extensive work has been done to characterize MDR mechanisms in vitro, the translation of this knowledge to the clinic has not been successful. Therefore, identifying genes and mechanisms critical to the development of MDR in vivo and establishing a reliable method for analyzing highly homologous genes from small amounts of tissue is fundamental to achieving any significant enhancement in our understanding of MDR mechanisms and could lead to treatments designed to circumvent it. In this study, we use a previously established database that allows the identification of lead compounds in the early stages of drug discovery that are not ATP-binding cassette (ABC) transporter substrates. We believe this can serve as a model for appraising the accuracy and sensitivity of current methods used to analyze the expression profiles of ABC transporters. We found two platforms to be superior methods for the analysis of expression profiles of highly homologous gene superfamilies. This study also led to an improved database by revealing previously unidentified substrates for ABCB1, ABCC1, and ABCG2, transporters that contribute to MDR.

Preoperative chemoradiotherapy in locally advanced rectal cancer: correlation of a gene expression-based response signature with recurrence

Preoperative chemoradiotherapy is recommended for locally advanced rectal cancer (UICC stage II/III). We recently demonstrated that responsive and nonresponsive tumors showed differential expression levels of 54 genes. In this follow-up study, we investigated the relationship between this gene set and disease-free (DFS) and overall survival (OS). Pretherapeutic biopsies from 30 participants in the CAO/ARO/AIO-94 trial of the German Rectal Cancer Study Group were analyzed using gene expression microarrays. Statistical analysis was performed to identify differentially expressed genes between recurrent and nonrecurrent tumors and to correlate these changes with disease recurrence and outcome. After a median follow-up of 59 months, seven of eight patients with recurrent disease was a nonresponder, and one responsive tumor recurred. Response to chemoradiotherapy was significantly correlated with an improved DFS (log rank P=0.028), whereas OS did not differ significantly (P=0.11). Applying a class comparison analysis, we identified 20 genes that were differentially expressed between recurrent and nonrecurrent tumors (P<0.001). Analyzing the first two principal components of the 54 genes previously identified to predict response, we observed that this response signature correlated with an increased risk of cancer recurrence. These data suggest that the genetic basis of local response also affects the genetic basis of tumor recurrence. Genes that are indicative of nonresponse to preoperative chemoradiotherapy might also be linked to an increased risk of tumor recurrence.

CellMiner: a relational database and query tool for the NCI-60 cancer cell lines

Background

Advances in the high-throughput omic technologies have made it possible to profile cells in a large number of ways at the DNA, RNA, protein, chromosomal, functional, and pharmacological levels. A persistent problem is that some classes of molecular data are labeled with gene identifiers, others with transcript or protein identifiers, and still others with chromosomal locations. What has lagged behind is the ability to integrate the resulting data to uncover complex relationships and patterns. Those issues are reflected in full form by molecular profile data on the panel of 60 diverse human cancer cell lines (the NCI-60) used since 1990 by the U.S. National Cancer Institute to screen compounds for anticancer activity. To our knowledge, CellMiner is the first online database resource for integration of the diverse molecular types of NCI-60 and related meta data.

Description

CellMiner enables scientists to perform advanced querying of molecular information on NCI-60 (and additional types) through a single web interface. CellMiner is a freely available tool that organizes and stores raw and normalized data that represent multiple types of molecular characterizations at the DNA, RNA, protein, and pharmacological levels. Annotations for each project, along with associated metadata on the samples and datasets, are stored in a MySQL database and linked to the molecular profile data. Data can be queried and downloaded along with comprehensive information on experimental and analytic methods for each data set. A Data Intersection tool allows selection of a list of genes (proteins) in common between two or more data sets and outputs the data for those genes (proteins) in the respective sets. In addition to its role as an integrative resource for the NCI-60, the CellMiner package also serves as a shell for incorporation of molecular profile data on other cell or tissue sample types.

Conclusion

CellMiner is a relational database tool for storing, querying, integrating, and downloading molecular profile data on the NCI-60 and other cancer cell types. More broadly, it provides a template to use in providing such functionality for other molecular profile data generated by academic institutions, public projects, or the private sector. CellMiner is available online at .

DNA fingerprinting of the NCI-60 cell line panel

The National Cancer Institute's NCI-60 cell line panel, the most extensively characterized set of cells in existence and a public resource, is frequently used as a screening tool for drug discovery. Because many laboratories around the world rely on data from the NCI-60 cells, confirmation of their genetic identities represents an essential step in validating results from them. Given the consequences of cell line contamination or misidentification, quality control measures should routinely include DNA fingerprinting. We have, therefore, used standard DNA microsatellite short tandem repeats to profile the NCI-60, and the resulting DNA fingerprints are provided here as a reference. Consistent with previous reports, the fingerprints suggest that several NCI-60 lines have common origins: the melanoma lines MDA-MB-435, MDA-N, and M14; the central nervous system lines U251 and SNB-19; the ovarian lines OVCAR-8 and OVCAR-8/ADR (also called NCI/ADR); and the prostate lines DU-145, DU-145 (ATCC), and RC0.1. Those lines also show that the ability to connect two fingerprints to the same origin is not affected by stable transfection or by the development of multidrug resistance. As expected, DNA fingerprints were not able to distinguish different tissues-of-origin. The fingerprints serve principally as a barcodes.

Perception and knowledge of clinical trials and factors affecting participation of regional and rural cancer patients of North Queensland

e17558

Background: The best treatment option for most cancers is participation in clinical trials. Participation in trials is generally low and among rural patients it is likely to be even lower. The aim of this study was to assess knowledge about and attitudes towards clinical trials among rural and regional cancer patients of North Queensland. Methods: A questionnaire-based survey was conducted in outpatient clinics at the Townsville Cancer Centre on all types of cancer patients. Results: The mean age of the 178 participants was 56 years and 45.4% lived in rural or remote areas. Median distance to the trial centre (Townsville) for rural participants was 180 km (range 80 - 1300 km). Being asked whether they would take part in a RCT, 13.2% of participants said no, 56.3% said yes, and 30.5% were unsure. There were no significant relationships between willingness to participate and rurality (p = 0.896) or education level (p = 0.943). For the majority of patients, the number of clinic visits and blood tests required did not matter. Cost of travel (41.1% rural/remote; 23.5% regional; p < 0.001) and the need for family or friends to accompany (38.9% rural/remote; 24.1% regional; p = 0.021) were more important for rural/remote than regional patients as factors affecting participation. Only 16.4% of participants were aware of early studies. After education, percentage of patients willing to participate in phase I and II studies were 57% and 84%, respectively. Rural patients were less willing to participate in phase I studies than regional patients (33.9% vs 52.6%, p = 0.029). Conclusions: Rural patients are as interested in participating in clinical trials as urban patients except for phase 1 trials and should not be excluded because of rurality. Knowledge of trials is poor and there is a need for education early. Cost of travel seems more important for rural patients and as such budgets should include cost of travel to encourage participation of rural patients.

No significant financial relationships to disclose.