Correlation of HER2 Protein Level With mRNA Level Quantified by RNAscope in Breast Cancer

Trastuzumab deruxtecan (T-DXd) has been approved by the US Food and Drug Administration (FDA) to treat patients with metastatic HER2-positive and HER2-low breast cancer, and clinical trials are examining its efficacy against early-stage breast cancer. Current HER2 immunohistochemical (IHC) assays are suboptimal in evaluating HER2-low breast cancers and identifying which patients would benefit from T-DXd. HER2 expression in 526 breast cancer tissue microarray (TMA) cores was measured using the FDA-approved PATHWAY and HercepTest IHC assays, and the corresponding RNA levels were evaluated by RNAscope. HER2 protein levels by regression analysis using a quantitative immunofluorescence score against cell line arrays with known HER2 protein levels determined by mass spectrometry were available in 48 of the cores. RNAscope was also performed in 32 metastatic biopsies from 23 patients who were subsequently treated with T-DXd, and the results were correlated with response rate. HER2 RNA levels by RNAscope strongly correlated with HER2 protein levels (P < .0001) and with HER2 IHC H-scores from the PATHWAY and HercepTest assays (P < .0001). However, neither protein levels nor RNA levels significantly differed between cases scored 0, ultralow, and 1+ by PATHWAY and HercepTest. The RNA levels were significantly higher (P = .030) in responders (6.4 ± 8.2 dots/cell, n = 12) than those in nonresponders (2.6 ± 2.2, n = 20) to T-DXd. RNAscope is a simple assay that can be objectively quantified and is a promising alternative to current IHC assays in evaluating HER2 expression in breast cancers, especially HER2-low cases, and may identify patients who would benefit from T-DXd.

The use of transcutaneous electrical nerve stimulation along with functional tasks for immediate pain relief in individuals with knee osteoarthritis

BACKGROUND

Knee pain is the major complaint in individuals with knee osteoarthritis (OA), and the effects of transcutaneous electrical nerve stimulation (TENS) on knee pain are controversial. The present study applied TENS along with functional tests to investigate its effect on pain level in individuals with mild to moderate knee OA.

METHODS

Twenty volunteers with knee OA classification of graded 2-3 performed four functional tests (stair climb test - SCT, timed up and go test - TUG, 6-minute walk test - 6MWT, knee extensor strength test - KES, and 2-step test from the locomotive syndrome risk test - LSR_2ST) while wearing either an active or inactive TENS. Knee pain level before and after each test was self-accessed by the visual analog scale (VAS). The effect of TENS (active vs. inactive) on pain level was submitted to statistical analyses.

RESULTS

Knee pain during SCT, TUG, and LSR_2ST tests was significantly lower when subjects used the active TENS, compared to using the inactive unit. The effect of the active TENS on pain level was also more significant in subjects with no anxiety or depression.

CONCLUSIONS

The results provided evidence of immediate pain relief in individuals with mild to moderate knee OA when TENS is applied along with functional activities, that usually induced pain in people with knee OA.

Galectin-3 and PTEN expression in pancreatic ductal adenocarcinoma, pancreatic neuroendocrine neoplasms and gastrointestinal tumors on fine-needle aspiration cytology

OBJECTIVE

Galectin-3 has been implicated in the carcinogenesis of pancreatic ductal adenocarcinoma (PDAC). Its applicability in pancreatic fine-needle aspiration (FNA) in separating malignant from benign lesions has never been addressed. In addition, a correlation between Galectin-3 and tumor suppressor phosphatase and tensin homolog (PTEN) and their potential diagnostic value has never been tested.

STUDY DESIGN

This study analyzed Galectin-3 immunohistochemical expression in FNA cell blocks of PDAC, pancreatic neuroendocrine neoplasms (PNEN), gastrointestinal stromal tumors (GIST) and non-tumor pancreatic tissue. In parallel, Galectin-3 and PTEN levels were evaluated in a tumor tissue microarray (TMA).

RESULTS

Forty-four of 46 PDAC FNA and 32 of 33 PDAC TMA demonstrated tumor-specific Galectin-3 positivity. In contrast, Galectin-3 was not detected in PNEN and GIST. Total loss of PTEN was displayed by 26 of 33 PDAC, while non-neoplastic tissues all retained PTEN expression.

CONCLUSION

Galectin-3 could be a valuable marker to help diagnose PDAC and rule out PNEN and GIST. In addition, PTEN positivity strongly argues against a diagnosis of PDAC. These data also advocate their potential diagnostic roles in the work up of challenging cytologic cases requiring ancillary test confirmation.

SOX10 expression in malignant melanoma, carcinoma, and normal tissues

Sry-related HMg-Box gene 10 (SOX10) is a nuclear transcription factor that plays an important role in melanocytic cell differentiation. It has been shown to be a sensitive marker of melanoma including spindle and desmoplastic subtypes. We assessed its frequency of expression in melanoma, carcinoma, benign nevi, and non-neoplastic tissues with routine immunohistochemistry for SOX10. The 109 primary melanoma included 49 epithelioid, 19 spindle cell, 22 desmoplastic, and 19 mixed spindle cell/desmoplastic melanoma. All primary, except 8 desmoplastic melanoma, and 11 metastatic melanoma were strongly and diffusely nuclear SOX10-positive. Six desmoplastic melanoma had ≤10% cells positive, and 2 were <50% positive, all of 3+ intensity. Eighteen of 149 (12%) breast carcinoma were SOX10-positive. All 24 ovarian, 23 endometrial, 26 lung, and 25 colon carcinoma were SOX10-negative. All 43 benign nevi, 18 dysplastic nevi, 68 non-neoplastic and benign skins, and all 56 non-neoplastic breast tissue were SOX10-positive. The sensitivity and specificity for SOX10 in the diagnosis of melanoma are 1.0 and 0.93, respectively; the positive and negative predictive values are 0.87 and 1.0, respectively. SOX10 is a sensitive, specific marker for melanoma. As benign nevi also express SOX10, it cannot be used to differentiate between benign and malignant pigmented skin lesions. Only a small number of breast carcinoma (12%), and breast lobules, express SOX10; no carcinoma of the ovary, endometrium, lung, or colon expressed SOX10.

Automated and manual human papilloma virus in situ hybridization and p16 immunohistochemistry: comparison in metastatic oropharyngeal carcinoma

OBJECTIVES

We compared the efficacy of automated and manual human papilloma virus (HPV) in situ hybridization (ISH) and p16 immunohistochemical staining (IHC) in fine needle aspiration (FNA) of metastatic oropharyngeal carcinoma.

STUDY DESIGN

A total of 41 FNA cell blocks (CB) were evaluated. HPV ISH was interpreted as positive if a minimum of one tumor cell showed punctate dot-like nuclear positivity. p16 was interpreted as positive if ≥70% of tumor cells showed brown nuclear and cytoplasmic staining.

RESULTS

Thirty of 41 CB (73%) were positive by automated HPV ISH, 25 of 41 CB (60%) with manual HPV ISH. Eighteen of 41 CB (43%) were positive for p16 IHC. Twelve of 41 CB (29%) with automated HPV ISH and 2 of 41 CB (4%) with the manual method were positive at 10× magnification. Three of 41 CB (7%) with automated HPV ISH and 14 of 41 CB (34%) with the manual method were positive at 20× magnification. Fifteen of 41 CB (36%) with automated HPV ISH and 9 of 41 CB (21%) with the manual method were positive at 40-60× magnification.

CONCLUSION

Automated HPV ISH plays a more significant role in determining the HPV status in CB. However, the failure to use high magnification in the evaluation can give false-negative results.

Phosphohistone H3 and Ki-67 labeling indices in cytologic specimens from well-differentiated neuroendocrine tumors of the gastrointestinal tract and pancreas: a comparative analysis using automated image cytometry

BACKGROUND

Ki-67 proliferation index was recently incorporated in the grading of neuroendocrine neoplasms (NENs) of the gastrointestinal tract (GIT) and pancreas. These are now divided into well-differentiated neuroendocrine tumors (WDNETs, grades 1 and 2) and poorly differentiated neuroendocrine carcinomas (grade 3). While Ki-67 is an established proliferation marker in NENs, phosphohistone H3 (PHH3), a newer marker of mitotic activity, is not.

METHODS

We determined Ki-67 and PHH3 indices on cytologic samples from WDNETs of the GIT and pancreas using an automated cellular imaging system (ACIS®).

RESULTS

There was a strong correlation between Ki-67 and PHH3 indices generated by ACIS on cytologic samples. However, in some cases the two stains caused conflicting grades within the same tumor.

CONCLUSION

Both antibodies stain cells in different phases of the cell cycle which may cause discordant grades, thus affecting patient management and prognostication. Ki-67 staining is stronger than PHH3, making 'hot spots' easier to identify on ACIS. Ki-67 is more ideal than PHH3 for staining NENs, especially in tumors with borderline grades. Because PHH3 generates lower mitotic indices it should not be used as a proliferation marker in NENs until its expression has been further characterized.

Laboratory based experiments to assess the use of green and food based compost to improve water quality in a Sustainable Drainage (SUDS) device such as a swale

Many tonnes of compost are generated per year due to door step composting of both garden and kitchen waste. Whilst there are commercial outlets for the finer grade of compost (<10mm) in plant nurseries, there is little demand for the coarser material (>25 mm). This paper reports part of a WRAP-sponsored (Waste Resources Action Programme) study which investigated the potential for green (GC) and mixed green and food (MC) composts to be incorporated into Sustainable Drainage (SUDS) devices such as swales, and replace the topsoil (TS) onto which turf is laid or grass seed distributed. However, it is not known whether compost can replace TS in terms of pollutant remediation, both the trapping of polluted particulates and in dealing with hydrocarbons such as oil, but also from a biofilm development and activity perspective. Using laboratory based experiments utilising leaching columns and an investigation of microbiological development in the composts studied, it was found that many of the differences in performance between MC and GC were insignificant, whilst both composts performed better in terms of pollutant retention than TS. Mixed compost in particular could be used in devices where there may be oil spillages, such as the lorry park of a Motorway Service Area due to its efficiency in degrading oil. Samples of GC and MC were found to contain many of the bacteria and fungi necessary for an active and efficient biofilm which would be an argument in their favour for replacement of TS and incorporation in swales.

Combined double CK5/P63 stain: useful adjunct test for diagnosing pulmonary squamous cell carcinoma

Increasing demand for accurate differentiation of pulmonary squamous cell carcinoma (SQCC) from other subtypes can be challenging for pathologists. This is more so in fine-needle aspirations (FNA) since the sample is small and SQCC may show degenerative changes and necrosis that distort the cellular features. Immunohistochemistry (IHC) is a valuable adjunct, and CK5/6 and P63 immunoreactivity is found to be basically restricted to SQCC. In our study, we evaluated the efficiency of CK5/P63 double staining in the diagnosis of pulmonary SQCC in cell blocks (CB) of lung FNA. We used a cohort including 24 CB of lung SQCC and 34 CB of lung adenocarcinomas (ADC). IHC was performed for CK5/P63 double stain. Seventeen of 24 (70%) lung SQCC were positive for the double stain CK5/P63. Two (8%) were positive for CK5 alone and two (8%) were positive for P63 alone. Thus, a total 19 of 24(79%) SQCC of the lung were positive for CK5 and P63 each. In ADC, no immunoreactivity was detected for CK5 alone or combined CK5/P63. Three of 34(8%) ADC were positive for P63. This first study of double staining of CK5/P63 in FNA CB shows a sensitivity of 70% and specificity of 100% for SQCC of the lung. When each marker staining alone is included, the sensitivity for CK5 and P63 increases to 79% each. This double stain can help in the diagnosis of pulmonary SQCC with an accuracy of 88% and a positive predictive value of 100%.

TTF-1 and Napsin A double stain: a useful marker for diagnosing lung adenocarcinoma on fine-needle aspiration cell blocks

BACKGROUND

Immunohistochemistry (IHC) for thyroid transcription factor-1 (TTF-1) is used to confirm the diagnosis of lung adenocarcinoma. Napsin A also has shown positivity in lung adenocarcinoma. A combined double stain for TTF-1 and napsin A has been proposed to achieve higher sensitivity and specificity. In this study, the authors evaluated the utility of this double stain in the diagnosis of lung adenocarcinoma in cell blocks of fine-needle aspirates (FNA).

METHODS

The authors used a cohort comprising 35 FNA cell blocks of lung adenocarcinoma and 24 FNA cell blocks of lung squamous cell carcinoma (SqCCA). IHC was performed; expressions of TTF-1 as brown nuclear stain and of napsin A as red cytoplasmic stain were identified.

RESULTS

Twenty-six of 35 (74%) lung adenocarcinomas were positive for double staining with TTF-1/napsin A. Of 35 lung adenocarcinomas, only 2 (5%) were positive for TTF-1 alone and 3 (8%) were positive for napsin A alone. For the double stain TTF-1/napsin A, 3 of 24 (12%) lung SqCCAs were positive for both. Six of 24 (25%) cases were positive for TTF-1 alone, and none were positive for napsin A alone. For lung adenocarcinoma, TTF-1/napsin A has a sensitivity of 74%, specificity of 87%, accuracy of 79%, and a positive predictive value of 89%.

CONCLUSIONS

The double IHC stain, TTF-1/napsin A, for the identification of pulmonary adenocarcinoma in FNA cell block materials was diagnostically useful. The use of napsin A alone demonstrated a greater degree of accuracy and appeared diagnostically useful as a single IHC stain.

Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences

The Afrotropical mosquito Anopheles gambiae sensu stricto, a major vector of malaria, is currently undergoing speciation into the M and S molecular forms. These forms have diverged in larval ecology and reproductive behavior through unknown genetic mechanisms, despite considerable levels of hybridization. Previous genome-wide scans using gene-based microarrays uncovered divergence between M and S that was largely confined to gene-poor pericentromeric regions, prompting a speciation-with-ongoing-gene-flow model that implicated only about 3% of the genome near centromeres in the speciation process. Here, based on the complete M and S genome sequences, we report widespread and heterogeneous genomic divergence inconsistent with appreciable levels of interform gene flow, suggesting a more advanced speciation process and greater challenges to identify genes critical to initiating that process.

Image cytometric validation of breast carcinoma markers (ER, HER2 and MIB-1) using tissue microarrays: rabbit monoclonal vs. FDA-approved antibodies

OBJECTIVE

To use the ACIS III (Dako, Carpinteria, California, U.S.A.) with tissue microarrays (TMAs) to compare rabbit monoclonal antibodies (RMab) for ER, HER2, and MIB-1 with FDA-approved monoclonal (FMab) and polyclonal (FPab) antibodies.

STUDY DESIGN

TMAs of 43 breast cancers were used. Immunohistochemistry was performed using RMab (LabVision, Fremont, California, U.S.A.): ER (SP1; 1/100), HER2 (SP3; 1/100), and MIB-1 (SP6; 1/200). FMPab (Dako) used: ER (1D5; 1/50), HercepTest kit and MIB-1 (MIB-1; 1/160). The stained TMAs were quantitated visually and by image cytometry (ACIS III).

RESULTS

The overall agreement between RMab and FMab for ER using visual (98.45%) and image analysis (97.56%) was excellent, with a kappa level of 0.89 and 0.94, respectively. For HER2, the overall agreement between RMab and FPab was fair for visual (67.44%) and substantial (87.50%) for image analysis, with a kappa level of 0.32 and 0.72, respectively. For MIB-1, there was fair (64.29%) to poor (43.33%) agreement between MIB-1 RMab and FMab using visual and image analysis, with a kappa level of 0.47 and 0.16, respectively.

CONCLUSION

RMabs for ER (SP1) and HER2 (SP3) are almost comparable to their counterpart, FDA antibodies; however, MIB-1 RMab (SP6) shows poor concordance with FMab in TMA. Image analysis shows a better concordance than visual quantitation assessment specifically for ER and HER2.

Ensembl Genomes: extending Ensembl across the taxonomic space

Ensembl Genomes (http://www.ensemblgenomes.org) is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community, which we consider as essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimised data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

Current distribution under electrodes in relation to stimulation current and skin blood flow: are modern electrodes really providing the current distribution during stimulation we believe they are?

Carbonized rubber electrodes were tested extensively when they were first developed 30 years ago, but modern carbonized rubber electrodes have not received the type of scrutiny that the first electrodes received. Modern electrodes differ from the original electrodes in that they come with a self-adhesive electrode gel called hydrogel as part of their composition. The present study was undertaken to examine the current distribution and impedance characteristics of five brands of carbonized rubber electrodes and to examine the current distribution between electrodes during electrical stimulation in six subjects. Several different electrode sizes were tested between 3 and 10 cm. The current flow between the electrodes was determined by measuring the voltage across the skin on human subjects in 15 discrete locations between the electrodes. Blood flow was also measured between the electrodes with a laser Doppler flow meter to assess the physiological effect of current distribution on the skin at several skin temperatures. The results of these studies showed that at low currents, such as is used in TENS, very little current is actually applied through the skin due to the high impedance of the electrodes. At current levels normally used for electrical stimulation for functional movement, while current flow is better in most electrodes, it is very uneven, resulting in high current density in the centre of the electrodes and a fall off of at least 50% in current intensity at the edges of the electrode. There was very little difference in current density between small and large electrodes due to the high current density in the centre. Skin blood flow altered the movement of current between the electrodes and also may contribute to electrode performance. The implication of these studies is that electrode design needs to be altered for better current distribution, especially at low stimulation currents.

A phase III multi-institutional randomized study of immunization with the gp100: 209–217(210M) peptide followed by high-dose IL-2 compared with high-dose IL-2 alone in patients with metastatic melanoma

CRA9011

Background: In a phase II study, 13 (42%) of 31 patients with metastatic melanoma receiving high-dose (HD) IL-2 plus gp100:209–217(210M) peptide experienced objective responses (S.A. Rosenberg, et al, Nature Medicine 4: 321–327, 1998). Other studies showed a lower response rate (RR) but no randomized studies have been done. Methods: A prospective randomized phase III trial was conducted at 21 centers with 185 patients. Eligibility: stage IV or locally advanced stage III cutaneous melanoma, HLA A0201, no brain metastases, eligible for HD IL-2, and no previous HD IL-2 or gp100:209–217(210M). Arm 1 received HD IL-2 alone (720,000 IU/kg/dose) and Arm 2 gp100:209–217(210M) peptide + Montanide ISA followed by HD IL-2. The primary objective was clinical response. Secondary objectives were toxicity, disease free/progression free survival, immunologic response and quality of life. Central HLA typing, pathology review, and blinded response assessment were done at the NIH. Central data monitoring was done by The EMMES Corp. and a Data Safety Monitoring Board. Results: Numbers of patients enrolled, treated, and evaluable for response in Arm 1 were 94, 93, and 93 respectively; in Arm 2 91, 86, and 86. Toxicities were consistent with HD IL-2 ± vaccine. Investigator assessed RR showed significant improvement in overall RR for Arm 2=22.1% vs 9.7% (P=0.0223, Chi-Square) and progression free survival (PFS) in favor of Arm 2=2.9 months (1.7–4.5) vs 1.6 (1.5–1.8) (P=0.0101). Median overall survival favors Arm 2=17.6 months (11.8–26.6) vs 12.8 (8.7–16.3) (P=0.0964). Blinded response review is ongoing. Conclusions: RR and PFS were superior with peptide vaccine and HD IL-2 compared to HD IL-2 alone. This represents the first evidence of clinical benefit of vaccination in patients with melanoma.

[Table: see text]

A phase III multi-institutional randomized study of immunization with the gp100: 209–217(210M) peptide followed by high-dose IL-2 compared with high-dose IL-2 alone in patients with metastatic melanoma

CRA9011

The full, final text of this abstract will be available in Part II of the 2009 ASCO Annual Meeting Proceedings, distributed onsite at the Meeting on May 30, 2009, and as a supplement to the June 20, 2009, issue of the Journal of Clinical Oncology.

[Table: see text]

Randomized phase II study of the safety and efficacy of a human anti-αv integrin monoclonal antibody (CNTO 95) alone and in combination with dacarbazine in patients with stage IV metastatic melanoma: 12-month results

9029

Objectives: Evaluate the safety and efficacy of CNTO 95, a human anti-αv integrin monoclonal antibody, when administered alone or in combination with dacarbazine (DTIC). Methods: Patients with Stage IV metastatic melanoma were randomized 1:1:1:1 to receive 5 or 10mg/kg CNTO 95 alone, or DTIC (1000mg/m2) + either 10mg/kg CNTO 95 or placebo administered intravenously once every 3 weeks for 8 cycles in the absence of disease progression or unacceptable toxicity. DTIC arms were blinded; single-agent arms were open-label. The primary endpoint was progression free survival (PFS); secondary endpoints included partial response (PR), complete response (CR), stable disease (SD) and overall survival (OS). Major safety endpoints included the incidence of adverse events (AEs) and serious AEs (SAEs). Results: Patients were randomized to receive 5mg/kg CNTO 95 (n=32), 10mg/kg CNTO 95 (n=33), CNTO 95+DTIC (n=32), or placebo+DTIC (n=32). Baseline demographics were similar across groups. The median PFS for CNTO 95+DTIC was 75 days, placebo+DTIC was 54 days and both CNTO 95 alone arms were 42 days. Six patients achieved PR (2–10mg/kg CNTO 95, 1-CNTO 95+DTIC, 3-placebo+DTIC); one patient achieved CR (CNTO 95+DTIC). A higher proportion (43.3%) of patients achieved SD ≥ 12 wks in the CNTO 95+DTIC group compared with the other 3 groups (<20.0%). The median survival was 11.0 months for the patients in the CNTO 95+DTIC arm, 9.8 months and 14.9 months for the 5mg/kg and 10mg/kg arms, and 8.0 months for those in the DTIC control arm. The most common AEs were headache, nausea, fatigue, pyrexia, vomiting and transient uveitic reactions. Three patients (1–5mg/kg, 2-CNTO 95+DTIC) discontinued treatment due to AEs. A higher proportion of patients experienced SAEs in the placebo+DTIC group (29.0%) than in the 5mg/kg (12.9%), 10mg/kg (16.2%) or CNTO 95+DTIC (18.8%) groups. Conclusions: CNTO 95 alone or combined with DTIC was generally well tolerated. In patients with Stage IV metastatic melanoma, a trend toward improvement in PFS, OS and disease control was demonstrated with CNTO 95+DTIC.

Centocor, Centocor Research and Development, Inc.

Centocor Research and Development, Inc.

Johnson & Johnson

Centocor Research and Development, Inc.

No significant financial relationships to disclose.

Effects of a 2-, 3- and 4-electrode stimulator design on current dispersion on the surface and into the limb during electrical stimulation in controls and patients with wounds

Electrical stimulation is a widely used modality in the field of physical therapy and exercise physiology. The most common method for the application of electrical stimulation is a two-electrode system where one electrode is the source and the other is a reference. However, recent studies report that a more effective delivery system can be achieved if more than two electrodes are used. In the present investigation, the circuitry to deliver electrical stimulation through a 2-, 3- or 4-electrode delivery system was designed. The system was evaluated by its ability to deliver current on the surface of the skin as well as deep into the quadriceps muscle in six control subjects and in and around wounds in six other subjects. The results of the experiments showed that much better depth of penetration was achieved in a 4-electrode system (one electrode was on the opposite side of the limb and three electrodes were on top of the limb) than in either a 2- or a 3-electrode delivery system. In non-wounded skin, given the same current from the stimulator, the current in the quadriceps muscle was found to be double with a 4-electrode versus a 2-electrode system. In wounds, this same finding was seen. Here, blood flow, an indicator of the effectiveness of electrical stimulation in wounds, was three times higher if a multi-channel stimulator was used versus a 2-channel stimulator. Thus a multi-channel electrical stimulation system is more effective than a 2-electrode system.

Triple-negative breast carcinoma in women from Vietnam and the United States: characterization of differential marker expression by tissue microarray

Triple-negative breast carcinoma accounts for approximately 15% of all breast cancers. It is characterized by an aggressive clinical history, high rate of local relapse, and association with the basal epithelial-like subtype. Variations in breast cancer subtype and clinical outcome often exist across racial and ethnic lines. Therefore, the aim of this study was to compare the immunohistochemical and clinicopathologic characteristics of triple-negative breast carcinoma in women living in Vietnam with those from the United States. Invasive triple-negative breast carcinoma of patients from the 2 populations was characterized by tissue microarray for the expression of basal cytokeratins (CK5/6, CK7, CK14), luminal cytokeratins (CK8, CK18, CK19), and markers associated with the basal phenotype (cKit, epithelial growth factor receptor, P-cadherin, p53, and p63). Significant differences in expression between the 2 populations were not observed for the basal cytokeratins. However, epithelial growth factor receptor and P-cadherin, markers associated with the basal phenotype, were underexpressed in Vietnamese patients. Of the luminal cytokeratins, CK8 was overexpressed and CK18 was underexpressed in the Vietnamese women. Significant differences were also observed regarding the clinicopathologic characteristics. Triple-negative breast carcinoma in Vietnamese women was smaller and less likely to be grade III. In addition, it was more frequently of ductal histologic type and less often medullary or metaplastic. These differences in histology and marker expression suggest that triple-negative breast carcinoma has unique biological characteristics in women from Vietnam and the United States, and may follow a unique clinical course in each of the 2 populations.

Ensembl 2009

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).

Claudin-7 and claudin-8: immunohistochemical markers for the differential diagnosis of chromophobe renal cell carcinoma and renal oncocytoma

Claudin-7 and claudin-8 code for tight junction proteins expressed in distal nephron epithelium. In a recent oligonucleotide microarray study, we identified claudin-7 and claudin-8 as candidate markers to distinguish chromophobe renal cell carcinoma from other renal tumors, including oncocytoma. Distinction of these lesions can be difficult by light microscopy but is clinically important because chromophobe renal cell carcinoma has malignant biological potential, whereas renal oncocytoma is benign. Claudin-7 and claudin-8 expression was studied by immunohistochemistry in 11 chromophobe renal cell carcinomas and 17 oncocytomas using formalin-fixed paraffin-embedded tissue sections of tumor with adjacent nonneoplastic kidney. Steam antigen retrieval was performed before immunohistochemistry. Specificity was verified by negative control reactions without primary antibody and appropriate membranous staining patterns in positive control tissues (colon carcinoma and adjacent nonneoplastic kidney). Claudin-7 protein was expressed in a membranous pattern in 10 of 11 chromophobe renal cell carcinomas and 4 of 17 oncocytomas (P < .01). Claudin-8 was expressed in multiple patterns: In oncocytoma, 11 of 17 cases showed cytoplasmic, 4 of 17 membranous, and 2 of 17 negative reactions. In chromophobe renal cell carcinoma, 0 of 11 cases showed cytoplasmic, 3 of 11 membranous, and 8 of 11 negative reactions (P < .01). The immunohistochemical pattern of membranous claudin-7 and negative claudin-8 was seen in 7 of 11 chromophobe renal cell carcinomas and 1 of 17 oncocytomas (63% sensitivity, 84% specificity, 88% positive predictive value for chromophobe renal cell carcinoma). Negative claudin-7 and cytoplasmic claudin-8 were observed in 10 of 17 oncocytomas and 0 of 11 chromophobe renal cell carcinomas (59% sensitivity, 100% specificity and positive predictive value for oncocytoma). The distal nephron proteins claudin-7 and claudin-8 have potential use as immunohistochemical biomarkers in the differential diagnosis of chromophobe renal cell carcinoma and oncocytoma. Expression of claudin-7 and claudin-8 may reflect the relationship of chromophobe renal cell carcinoma and oncocytoma to intercalated cells of the cortical collecting duct. It may be necessary to identify additional biomarkers to include with claudin-7 and claudin-8 in a larger immunohistochemical panel to improve diagnostic sensitivity and specificity.

Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase

High-throughput genome sequencing techniques have now reached vector biology with an emphasis on those species that are vectors of human pathogens. The first mosquito to be sequenced was Anopheles gambiae, the vector for Plasmodium parasites that cause malaria. Further mosquitoes have followed: Aedes aegypti (yellow fever and dengue fever vector) and Culex pipiens (lymphatic filariasis and West Nile fever). Species that are currently in sequencing include the body louse Pediculus humanus (Typhus vector), the triatomine Rhodnius prolixus (Chagas disease vector) and the tick Ixodes scapularis (Lyme disease vector). The motivations for sequencing vector genomes are to further understand vector biology, with an eye on developing new control strategies (for example novel chemical attractants or repellents) or understanding the limitations of current strategies (for example the mechanism of insecticide resistance); to analyse the mechanisms driving their evolution; and to perform an exhaustive analysis of the gene repertory. The proliferation of genomic data creates the need for efficient and accessible storage. We present VectorBase, a genomic resource centre that is both involved in the annotation of vector genomes and act as a portal for access to the genomic information (http://www.vectorbase.org).

Ensembl 2008

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein–DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

Claudin-7 immunohistochemistry in renal tumors: a candidate marker for chromophobe renal cell carcinoma identified by gene expression profiling

CONTEXT

The differential diagnosis of eosinophilic renal tumors can be difficult by light microscopy. In particular, chromophobe renal cell carcinoma (RCC) is difficult to distinguish from oncocytoma. This differential diagnosis is important because chromophobe RCC is malignant, whereas oncocytoma is benign. Furthermore, chromophobe RCC has distinct malignant potential and prognosis compared with eosinophilic variants of other RCC subtypes. Immunohistochemistry is useful for distinguishing chromophobe RCC from other subtypes of renal carcinoma, but no expression marker reliably separates chromophobe RCC from oncocytoma.

OBJECTIVE

In a previous gene expression microarray analysis of renal tumor subtypes, we found the distal nephron markers claudin-7 and claudin-8 to be overexpressed in chromophobe RCC versus oncocytoma and other tumor subtypes. We have confirmed similar findings in independent microarray data and validated differential claudin-7 protein expression by immunohistochemistry.

DESIGN

Immunohistochemical analysis of claudin-7 in 36 chromophobe RCCs, 43 oncocytomas, 42 clear cell RCCs, and 29 papillary RCCs.

RESULTS

Membranous claudin-7 expression was detected in 67% chromophobe RCCs, compared with 0% clear cell RCCs, 28% papillary RCCs, and 26% oncocytomas (P < .001).

CONCLUSIONS

Based on microarray and immunohistochemical data, we propose claudin-7 to be a candidate expression marker for distinguishing chromophobe RCC from other renal tumor subtypes, including the morphologically similar oncocytoma. The clinical utility of claudin-7 should be validated in independent studies of renal tumors, possibly in combination with additional targets in a multiplex immunohistochemical panel.

A phase II study of YM155, a novel survivin suppressant, administered by 168 hour continuous infusion in patients with unresectable stage III or stage IV melanoma

8538

Background: In cell line studies, YM155 showed markedly potent antiproliferative activity against melanoma with 50% growth inhibition (GI50) values ranging from 0.35 nM to 910 nM. In melanoma tumor-bearing mouse xenograft models, YM155 showed significant antitumor activity including regression of tumors, at doses ranging from 1 to 10 mg/kg/day. Methods: Chemotherapy naive patients with unresectable Stage III or IV melanoma were eligible. The primary endpoint was tumor response defined by RECIST criteria. Secondary endpoints included progression-free survival and toxicity. A Simon's two stage minimax design was utilized with the first stage requiring 1 response (N=27) and a total of 2 responses required at the conclusion of stage II (N=29). Patients were considered evaluable if they completed 2 cycles. YM155 was given as a 168-hour (7-day) continuous infusion every three weeks (1 cycle) at a dose of 4.8 mg/m2/day. Results: Enrollment is complete at 34 pts in order to reach 29 evaluable with treatment ongoing. Results are available for the first 26 pts. Median age was 59 y/o, (range 29 - 88) with ECOG PS of 0–1. There is one objective response of intrabdominal lymph nodes based on Investigator assessment at Cycle 2 confirmed at Cycle 4; another patient had a minor response (24% reduction) at Cycle 6 (currently at Cycle 8). Two subjects have shown stable disease after 6 cycles and remain on study. The median number of cycles is 3 (range 1 - 9). Two of 26 pts reported a grade 3 AE considered possibly related to YM155 (chest pain - nos and catheter related thrombosis). Nineteen of 26 pts have discontinued the study (18 PD, 1 withdrew consent). Conclusions: YM155 induced responses in 2 pts and was generally well tolerated. Given this encouraging response as a single agent, studies of YM155 combined with other agents are under consideration.

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Subgroup analysis of efficacy and safety analysis of a randomized, double-blinded controlled phase II study of STA-4783 in combination with paclitaxel in patients with metastatic melanoma

8528

Background: STA-4783 (S), an inducer of heat shock protein 70 (hsp70) is a bis-thiobenzoylhydrazide compound. S leads to up-regulation of hsp70 in tumor cell lines. Xenograft models of solid tumors showed synergistic anti-tumor activity in combination with paclitaxel (P). The combination P + S, in phase I and II studies, showed dose-related hsp70 induction (evidence of biological activity) and tolerability. Methods: Eligibility was based on a diagnosis of metastatic cutaneous melanoma, ECOG <=2, and prior treatment with 1 or no chemotherapy regimens. A total of 81 patients (pts) were randomized 2:1 (P 80 mg/m2 + S 213 mg/m2:P 80 mg/m2) 3 weeks out of 4 at 21 US clinical sites. The primary endpoint was progression free survival (PFS); secondary endpoints were response rate (RR), and adverse events (AEs). Results: Based on intent-to-treat analysis, the median PFS was 3.68 months (m) for P + S vs. 1.84 m in the P only arm (p=.035). RR was 15.1% in the P + S arm and 3.6% in the P arm. Subgroup analysis showed chemo- naive pts (n=23) with P + S showed a median PFS of 8.28 m vs. 2.40 in the P arm (n=9). For pts with 1 prior chemotherapy, (n=29), PFS on P + S was 3.12 m vs. 1.77 m on P (n=19). Of 19 pts who crossed over at progression, data are available for 14. PFS ranged from 0.72 to 5.5 m. Three of the 14 evaluable pts treated with P alone had rapid progression (0.95, 1.6, and 1.7 m) then significant inversion of the time to progression with the addition of S to P (2.3, 5.5, and 4.2 m) suggesting study drug effect. Scans were done at identical intervals (8 weeks). The proportion of pts with AEs of grade 3 or higher was 54% (n=52) in the P + S group and 57% in the P group (n=28); pts on P received a median of 2 cycles, while pts in the P + S group received a median of 4. Adverse events leading to discontinuation were low in both groups: 10% for the P + S, and 14% for P. Conclusions: The addition of S to P showed an increase in PFS vs. P alone particularly in chemo-naïve pts. A few pts failing single agent P appeared to benefit from P + S. Despite the additional treatment duration in the P + S group the drugs were well- tolerated, and showed mainly P related adverse events. A phase III study is planned to confirm a role for P + S in metastatic melanoma.

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Ensembl 2007

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of chordate genome sequences. Over the past year the number of genomes available from Ensembl has increased from 15 to 33, with the addition of sites for the mammalian genomes of elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat and european hedgehog; the fish genomes of stickleback and medaka and the second example of the genomes of the sea squirt (Ciona savignyi) and the mosquito (Aedes aegypti). Some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology/paralog annotations based on gene trees.

Cell surface glycoconjugate abnormalities and corneal epithelial wound healing in the pax6+/- mouse model of aniridia-related keratopathy

PURPOSE

Congenital aniridia due to heterozygosity for Pax6 is associated with ocular surface disease, including keratopathy. This study investigated how defects in glycoconjugate component of the cell surface of Pax6+/- could cause the abnormal cellular migration phenotypes associated with the disease.

METHODS

Immunohistochemistry, lectin-based histochemistry, conventional staining techniques, and proteomic assays were performed on eyes and cultured corneal epithelial cells from wild-type and Pax6+/- littermates. Wild-type cells were manipulated in culture to replicate the glycoconjugate abnormalities found in Pax6 heterozygotes and determine the consequences for wound healing.

RESULTS

Multiple glycoconjugate defects were found in Pax6-mutant cells. Lectin cytochemistry of corneal epithelial cells suggested a partial failure of glycoprotein trafficking. Blocking cell surface carbohydrate moieties in wild-type corneal cells caused wound-healing delays similar to those seen in untreated Pax6+/- cells.

CONCLUSIONS

Alterations to the cell surface glycoconjugate signature of Pax6+/- corneal epithelia restrict the ability of cells to initiate migration in response to wounding. This underlies the observed wound-healing delay in cultured Pax6+/- epithelia.

The roles of calcium signaling and ERK1/2 phosphorylation in a Pax6+/- mouse model of epithelial wound-healing delay

Background

Congenital aniridia caused by heterozygousity at the PAX6 locus is associated with ocular surface disease including keratopathy. It is not clear whether the keratopathy is a direct result of reduced PAX6 gene dosage in the cornea itself, or due to recurrent corneal trauma secondary to defects such as dry eye caused by loss of PAX6 in other tissues. We investigated the hypothesis that reducing Pax6 gene dosage leads to corneal wound-healing defects. and assayed the immediate molecular responses to wounding in wild-type and mutant corneal epithelial cells.

Results

Pax6^+/- mouse corneal epithelia exhibited a 2-hour delay in their response to wounding, but subsequently the cells migrated normally to repair the wound. Both Pax6^+/+ and Pax6^+/- epithelia activated immediate wound-induced waves of intracellular calcium signaling. However, the intensity and speed of propagation of the calcium wave, mediated by release from intracellular stores, was reduced in Pax6^+/- cells. Initiation and propagation of the calcium wave could be largely decoupled, and both phases of the calcium wave responses were required for wound healing. Wounded cells phosphorylated the extracellular signal-related kinases 1/2 (phospho-ERK1/2). ERK1/2 activation was shown to be required for rapid initiation of wound healing, but had only a minor effect on the rate of cell migration in a healing epithelial sheet. Addition of exogenous epidermal growth factor (EGF) to wounded Pax6^+/- cells restored the calcium wave, increased ERK1/2 activation and restored the immediate healing response to wild-type levels.

Conclusion

The study links Pax6 deficiency to a previously overlooked wound-healing delay. It demonstrates that defective calcium signaling in Pax6^+/- cells underlies this delay, and shows that it can be pharmacologically corrected. ERK1/2 phosphorylation is required for the rapid initiation of wound healing. A model is presented whereby minor abrasions, which are quickly healed in normal corneas, transiently persist in aniridic patients, compromising the corneal stroma.

Neuroendocrine cancer of the kidney: Clinical implications of expression microarray analysis

20093

Background: Conventional clinical trial strategies cannot be used to develop new therapies for rare malignancies. Neuroendocrine neoplasms of the kidney are extremely rare. Here we compare the gene expression profiles of a neuroendocrine tumor from a 32 year old male with a horseshoe kidney, a large renal primary and metastatic thyroid lesions to the profiles of other cancers. Response to systemic therapy is also reported. The ultimate objective of this project is to identify new therapeutic targets for patient-specific cancer therapy. Methods: After informed consent, tissue from the patient was analyzed by cytology and immunohistochemistry. Total RNA was isolated from formalin-fixed paraffin-embedded archival reference tissues with Arcturus Paradise Reagents. Gene expression was analyzed with Affymetrix X3P arrays of the entire expressed genome. A supervised significance analysis of microarrays (SAM) procedure, using 400 data permutations, was performed to identify gene products that were differentially expressed. Clinical outcomes were documented in the patient’s medical record on the basis of standard medical imaging. Results: Cytology, immunohistochemistry and microarray studies revealed similar patterns for the primary and metastatic lesions. Gene expression profiles of the patient’s kidney and thyroid lesions, as well as other kidney and neuroendocrine tumors, identified 11 genes overexpressed significantly in the neuroendocrine tumors. Each was associated with neuroendocrine biology. The patient had a mixed response to chemotherapy with gemcitabine and cisplatin and progressive disease after 3 monthly treatments with sandostatin. He awaits assessment of response to metaiodobenzylguanidine (MIBG). Conclusions: Gene expression profiling was effective in characterizing an unusual case of renal cancer with metastasis to thyroid, though no new therapeutic target has yet been identified. Comparing response or resistance to therapy with microarray analysis may prove to be an effective strategy for developing patient-specific cancer therapy. This work was supported, in part, by a VA Merit Review Award.

No significant financial relationships to disclose.

Proliferation (MIB-1 Expression) in Oligodendrogliomas

Expression of to nuclear antigen Ki-67 (MIB-1) has been linked to proliferative activity and prognosis in a variety of tumors. The authors assessed three techniques for quantitating MIB-1 (expression in oligodendrogliomas, correlating results with mitotic activity and prognosis. Formalin-fixed, paraffin-embedded sections of 38 oligodendrogliomas were immunostained using monoclonal MIB-l. Proliferation index (PI) was quantitated by visual estimation, CAS-200, and AC1S image analysis. MIB-1 expression and mitotic count were correlated with overall survival and recurrence (disease-free survival), defined clinically and radiographically as new tumor growth. Mean follow-up was 54 months (range 1-276). Mean PI quantitated by the three methods was statistically similar (Visual 10.5%, CAS-200, 12.2%, CAIS 11.2%). PI results by all three techniques correlated significantly with each other; visual and CAS-200 PI correlated with mitotic index. Overall and disease-free survivals were similar for patients with PIs above and below the mean by both image cytometric assays; visually estimated PIs below the mean, versus above the mean, correlated with improved disease-free survival. The authors show a significant correlation between MIB-1 PI using the visual method and recurrence in patients with oligodendrogliomas. The objectivity and speed of the image analysis systems make them an attractive alternative to visual estimation, and larger series should be analyzed for prognostic value.

Rapid Intraoperative Immunohistochemical Evaluation of Sentinel Lymph Nodes for Metastatic Breast Carcinoma

OBJECTIVE

Sentinel lymph node (SLN) biopsy is an integral part of the surgical management of patients with breast cancer. Rapid immunohistochemistry (RIHC) has the potential to increase detection of metastatic carcinoma at the time of frozen section consultation. The authors assessed the accuracy and turnaround time of a newly developed RIHC method for pancytokeratin (RIHC-CK).

METHODS

Sixty-six SLNs from 32 patients with breast carcinoma were examined for metastasis using the Zymed Sentinel Lymph Node Rapid IHC Kit. Intraoperative frozen sections (6 mum) of the SLNs were incubated with Zymed anti-pan-cytokeratin/HRP conjugate, diaminobenzidine (DAB), and stained with hematoxylin. Slides were ready within 8 minutes and were interpreted as positive or negative for metastatic carcinoma. Results were compared with previous intraoperative touch preparations, frozen sections, hematoxylin and eosin (Perm H&E), and AEl/3-immunostained permanent sections (Perm CK).

RESULTS

Fourteen lymph nodes (19%) in 13 patients tested positive for metastatic carcinoma in Perm H&E, the gold standard. RIHC-CK had the highest sensitivity (92%) of the intraoperative tests, compared with touch preparations (64%) and frozen sections (80%). RIHC-CK showed 94% accuracy, compared with 96% (frozen section) and 93% (touch preparation). The RIHC technique took 8 minutes and was easy to perform and interpret.

CONCLUSIONS

Zymed RIHC is a sensitive method for detecting breast cancer metastases in SLNs. The speed, accuracy, and ease of interpretation of the test allow for recognition of micrometastases (<2 mm) that might otherwise be undetectable by current methods of intraoperative evaluation. The prognostic significance and effect on surgical management of micrometastases in SLNs have yet to be determined.

Embryonic poly(A)-binding protein stimulates translation in germ cells

The function of poly(A)-binding protein 1 (PABP1) in poly(A)-mediated translation has been extensively characterized. Recently, Xenopus laevis oocytes and early embryos were shown to contain a novel poly(A)-binding protein, ePABP, which has not been described in other organisms. ePABP was identified as a protein that binds AU-rich sequences and prevents shortening of poly(A) tails. Here, we show that ePABP is also expressed in X. laevis testis, suggesting a more general role for ePABP in gametogenesis. We find that ePABP is conserved throughout vertebrates and that mouse and X. laevis cells have similar tissue-specific ePABP expression patterns. Furthermore, we directly assess the role of ePABP in translation. We show that ePABP is associated with polysomes and can activate the translation of reporter mRNAs in vivo. Despite its relative divergence from PABP1, we find that ePABP has similar functional domains and can bind to several PABP1 partners, suggesting that they may use similar mechanisms to activate translation. In addition, we find that PABP1 and ePABP can interact, suggesting that these proteins may be bound simultaneously to the same mRNA. Finally, we show that the activity of both PABP1 and ePABP increases during oocyte maturation, when many mRNAs undergo polyadenylation.

Angiogenic and lymphangiogenic microvessel density in breast carcinoma: correlation with clinicopathologic parameters and VEGF-family gene expression

Angiogenesis and lymphangiogenesis are essential for breast cancer progression and are regulated by vascular endothelial growth factors (VEGF). To determine clinical and molecular correlates of these processes, we measured blood and lymphatic vascular microvessel density in 29 invasive carcinomas (22 ductal, six lobular, one papillary), using the vascular marker CD31 and the novel lymphatic marker D2-40. Microvessel density was assessed microscopically and by image cytometry, and was compared with tumor histology, grade, stage, lymph node metastasis, hormone receptors, HER2/neu status, and expression of VEGF, VEGF-C and VEGF-D by immunohistochemistry or quantitative RT-PCR. Strong correlation was observed between visual and image cytometric microvessel density using D2-40 but not CD31 (P=0.016 and 0.1521, respectively). Image cytometric CD31 microvessel density correlated with tumor size, grade, stage and lymph node metastasis (P=0.0001, 0.0107, 0.0035 and 0.0395, respectively). D2-40 microvessel density correlated with tumor stage (P=0.0123 by image cytometry) and lymph node metastasis (P=0.0558 by microscopy). Immunohistochemical VEGF signal in peritumoral blood vessels correlated with image cytometric CD31 and D2-40 microvessel density (P=0.022 and 0.0012, respectively), consistent with the role of VEGF in blood and lymphatic vascular growth. Intratumoral VEGF-C and VEGF-D expression by quantitative RT-PCR correlated with D2-40 (P=0.0291 by image cytometry) but not with CD31 microvessel density, which could suggest a selective role of VEGF-C and VEGF-D in lymphangiogenesis. CD31 and D2-40 microvessel density correlated significantly with several prognostic factors, including lymph node metastasis. Thus, measurements of angiogenesis and lymphangiogenesis may have utility for breast cancer pathology, particularly for estimation of metastatic risk.