Optimization of duplex digital PCR for the measurement of SARS-CoV-2 RNA

Quantitative PCR (qPCR) is the gold standard for detecting nucleic acid sequences specific to the target pathogen. For COVID-19 diagnosis, several molecular assays have been developed. In this study, we present an optimization strategy for the measurement of SARS-CoV-2 RNA via multiplex qPCR and digital PCR (dPCR). Compared to qPCR, both droplet and chip-based dPCR, which are known to be more sensitive and accurate, showed a better resilience to suboptimal assay compositions and cycling conditions following the proposed optimizations. In particular, the formation of heterodimers among assays greatly interfered with qPCR results, but only minimally with dPCR results. In dPCR, existing heterodimers lowered the PCR efficiency, producing a dampened fluorescent signal in positive partitions. This can be corrected by adjusting the PCR cycling conditions, after which dPCR shows the capability of measuring the expected copy number. In addition, we present a process to improve the existing RdRp assay by correcting the primer sequences and matching the melting temperature, ultimately producing highly sensitive and robust assays. The results of this study can reduce the cost and time of SARS-CoV-2 diagnosis while increasing accuracy. Furthermore, our results suggest that dPCR is a reliable method for the accurate measurement of nucleic acid targets.

Digital PCR for the characterization of reference materials

Well-characterized reference materials support harmonization and accuracy when conducting nucleic acid-based tests (such as qPCR); digital PCR (dPCR) can measure the absolute concentration of a specific nucleic acid sequence in a background of non-target sequences, making it ideal for the characterization of nucleic acid-based reference materials. National Metrology Institutes are increasingly using dPCR to characterize and certify their reference materials, as it offers several advantages over indirect methods, such as UV-spectroscopy. While dPCR is gaining widespread adoption, it requires optimization and has certain limitations and considerations that users should be aware of when characterizing reference materials. This review highlights the technical considerations of dPCR, as well as its role when developing and characterizing nucleic acid-based reference materials.

Development of SARS-CoV-2 packaged RNA reference material for nucleic acid testing

Nucleic acid tests to detect the SARS-CoV-2 virus have been performed worldwide since the beginning of the COVID-19 pandemic. For the quality assessment of testing laboratories and the performance evaluation of molecular diagnosis products, reference materials (RMs) are required. In this work, we report the production of a lentiviral SARS-CoV-2 RM containing approximately 12 kilobases of its genome including common diagnostics targets such as RdRp, N, E, and S genes. The RM was measured with multiple assays using two different digital PCR platforms. To measure the homogeneity and stability of the lentiviral SARS-CoV-2 RM, reverse transcription droplet digital PCR (RT-ddPCR) was used with in-house duplex assays. The copy number concentration of each target gene in the extracted RNA solution was then converted to that of the RM solution. Their copy number values are measured to be from 1.5 × 105 to 2.0 × 105 copies/mL. The RM has a between-bottle homogeneity of 4.80-8.23% and is stable at 4 °C for 1 week and at -70 °C for 6 months. The lentiviral SARS-CoV-2 RM closely mimics real samples that undergo identical pre-analytical processes for SARS-CoV-2 molecular testing. By offering accurate reference values for the absolute copy number of viral target genes, the developed RM can be used to improve the reliability of SARS-CoV-2 molecular testing.

The Dangers of Using Cq to Quantify Nucleic Acid in Biological Samples: A Lesson From COVID-19

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA quantities, measured by reverse transcription quantitative PCR (RT-qPCR), have been proposed to stratify clinical risk or determine analytical performance targets. We investigated reproducibility and how setting diagnostic cutoffs altered the clinical sensitivity of coronavirus disease 2019 (COVID-19) testing.

METHODS

Quantitative SARS-CoV-2 RNA distributions [quantification cycle (Cq) and copies/mL] from more than 6000 patients from 3 clinical laboratories in United Kingdom, Belgium, and the Republic of Korea were analyzed. Impact of Cq cutoffs on clinical sensitivity was assessed. The June/July 2020 INSTAND external quality assessment scheme SARS-CoV-2 materials were used to estimate laboratory reported copies/mL and to estimate the variation in copies/mL for a given Cq.

RESULTS

When the WHO-suggested Cq cutoff of 25 was applied, the clinical sensitivity dropped to about 16%. Clinical sensitivity also dropped to about 27% when a simulated limit of detection of 106 copies/mL was applied. The interlaboratory variation for a given Cq value was >1000 fold in copies/mL (99% CI).

CONCLUSION

While RT-qPCR has been instrumental in the response to COVID-19, we recommend Cq (cycle threshold or crossing point) values not be used to set clinical cutoffs or diagnostic performance targets due to poor interlaboratory reproducibility; calibrated copy-based units (used elsewhere in virology) offer more reproducible alternatives. We also report a phenomenon where diagnostic performance may change relative to the effective reproduction number. Our findings indicate that the disparities between patient populations across time are an important consideration when evaluating or deploying diagnostic tests. This is especially relevant to the emergency situation of an evolving pandemic.

Metrological framework to support accurate, reliable, and reproducible nucleic acid measurements

Nucleic acid analysis is used in many areas of life sciences such as medicine, food safety, and environmental monitoring. Accurate, reliable measurements of nucleic acids are crucial for maximum impact, yet users are often unaware of the global metrological infrastructure that exists to support these measurements. In this work, we describe international efforts to improve nucleic acid analysis, with a focus on the Nucleic Acid Analysis Working Group (NAWG) of the Consultative Committee for Amount of Substance: Metrology in Chemistry and Biology (CCQM). The NAWG is an international group dedicated to improving the global comparability of nucleic acid measurements; its primary focus is to support the development and maintenance of measurement capabilities and the dissemination of measurement services from its members: the National Metrology Institutes (NMIs) and Designated Institutes (DIs). These NMIs and DIs provide DNA and RNA measurement services developed in response to the needs of their stakeholders. The NAWG members have conducted cutting edge work over the last 20 years, demonstrating the ability to support the reliability, comparability, and traceability of nucleic acid measurement results in a variety of sectors.

Comparison of two digital PCR methods for EGFR DNA and SARS-CoV-2 RNA quantification

BACKGROUND

The COVID-19 pandemic caused by the severe acute SARS-CoV-2 virus has undeniably highlighted the importance of reliable nucleic acid quantification. Digital PCR (dPCR) is capable of the absolute quantification of nucleic acids.

METHOD

By using the droplet dPCR (QX200) and the digital real-time PCR (LOAA), the copy numbers were compared via multiple assays for three distinct targerts; EGFR DNA, SARS-CoV-2 and HIV-1 RNA.

RESULTS

The droplet dPCR and digital real-time PCR showed similar copy numbers for both DNA and RNA quantification. When the limit of detection (LOD) and limit of quantitation (LOQ) of each method were estimated for DNA and RNA targets, the digital real-time PCR showed a higher sensitivity and precision especially with low copy number targets.

CONCLUSION

The breath of nucleic acid testing in diagnostic applications continues to expand. In this study we applied common diagnostic targets to a novel digital real-time PCR methodology. It performed comparably to the established dPCR method with distinctive advantages and disadvantages for implementing in laboratories. These rapidly developing dPCR systems can be applied to benefit the accurate and sensitive nucleic acid testing for various clinical areas.

Colorectal cancer cells differentially impact migration and microRNA expression in endothelial cells

Angiogenesis is an essential step in cancer progression and metastasis. Changes in the microRNA (miRNA or miR) expression profiles of endothelial cells (ECs) elicited by cancer cells promote angiogenesis. Vascular endothelial growth factor (VEGF), a key pro-angiogenic factor, influences miRNA expression in ECs; however, the exact role that VEGF serves in miRNA regulation during angiogenesis is poorly defined. The present study aimed to demonstrate the differential angiogenic effects on human umbilical vein endothelial cells (HUVECs) of five different colorectal cancer (CRC) cell lines by in vitro HUVEC migration and angiogenesis assays in response to CRC-conditioned medium (CM). Among the tested CMs, LoVo was the most effective cell line in eliciting HUVEC angiogenic phenotypes, at least partially due to its high VEGF level. It was also observed that pro-angiogenesis-regulatory miRNAs (angio-miRNA) miR-296, miR-132, miR-105 and miR-200 were upregulated in the VEGF-rich LoVo CM compared with the VEGF-scarce SW620 CM. In addition, treatment with VEGF receptor 2 inhibitor downregulated the pro-angio-miRNAs, with the exception of miR-132, suggesting that VEGF, as well as additional signaling, is required for angio-miRNA expression. Quantitative analyses on pro-angio-miRNA target expression suggested that independent pathways may be involved in the regulation of their expression. Overall, the data from the present study indicated that multiple paracrine factors, including VEGF secreted by CRCs, effectively modulated angio-miRNA expression, thus impacting their target expression and the angiogenic phenotypes of HUVECs.

A novel population of extracellular vesicles smaller than exosomes promotes cell proliferation

Background

Extracellular vesicles (EVs) play important roles in intercellular communication by delivering RNA, lipid, and proteins to neighboring or distant cells. Identification and classification of EVs secreted from diverse cell types are essential for understanding their signaling properties.

Methods

In this study, EVs from the culture media were isolated by ultracentrifugation and analyzed by electron microscopy (EM) and nanoparticle tracking analyses. Conditioned media (CM) from HEK293 cells culture grown either in serum-free (SF) or 10% fetal bovine serum (FBS) containing media were centrifuged at 100,000×g to separate the SN_Δ supernatant and the P100 pellet in which exosomes are enriched. Then, the SN_Δ fraction was centrifuged at 200,000×g to yield the P200 pellet fraction containing novel EVs smaller than exosomes. The exosomal markers in the EV subgroups were examined by western blotting and immune-EM, and the functional analyses of EVs were conducted on HEK293 and THP-1 cell culture.

Results

We identified a new group of EVs in the P200 fraction that was smaller than exosomes in size. Typical exosome markers such as Hsp70, TSG101, and CD63 were found in both P100 exosomes and the P200 vesicles, but CD81 was highly enriched in exosomes but not in the P200 vesicles. Furthermore, chemicals that inhibit the major exosome production pathway did not decrease the level of P200 vesicles. Therefore, these small EVs indeed belong to a distinguished group of EVs. Exosomes and the P200 vesicles were found in CM of human cell lines as well as FBS. Addition of the exosomes and the P200 vesicles to human cell cultures enhanced exosome production and cell proliferation, respectively.

Conclusions

Our study identifies a novel population of EVs present in the P200 fraction. This EV population is distinguished from exosomes in size, protein contents, and biogenesis pathway. Furthermore, exosomes promote their own production whereas the P200 vesicles support cell proliferation. In sum, we report a new group of EVs that are distinct physically, biologically and functionally from exosomes.

Electronic supplementary material

The online version of this article (10.1186/s12964-019-0401-z) contains supplementary material, which is available to authorized users.

ADAMTS Sol narae cleaves extracellular Wingless to generate a novel active form that regulates cell proliferation in Drosophila

Wnt/ Wingless (Wg) is essential for embryonic development and adult homeostasis in all metazoans, but the mechanisms by which secreted Wnt/Wg is processed remain largely unknown. A Drosophila Sol narae (Sona) is a member of ADisintegrin And Metalloprotease with ThromboSpondin motif (ADAMTS) family, and positively regulates Wg signaling by promoting Wg secretion. Here we report that Sona and Wg are secreted by both conventional Golgi and exosomal transports, and Sona cleaves extracellular Wg at the two specific sites, leading to the generation of N-terminal domain (NTD) and C-terminal domain (CTD) fragments. The cleaved forms of extracellular Wg were detected in the extracellular region of fly wing discs, and its level was substantially reduced in sona mutants. Transient overexpression of Wg-CTD increased wing size while prolonged overexpression caused lethality and developmental defects. In contrast, Wg-NTD did not induce any phenotype. Moreover, the wing defects and lethality induced by sona RNAi were considerably rescued by Wg-CTD, indicating that a main function of extracellular Sona is the generation of Wg-CTD. Wg-CTD stabilized cytoplasmic Armadillo (Arm) and had genetic interactions with components of canonical Wg signaling. Wg-CTD also induced Wg downstream targets such as Distal-less (Dll) and Vestigial (Vg). Most importantly, Cyclin D (Cyc D) was induced by Wg-CTD but not by full-length Wg. Because Sona also induces Cyc D in a cell non-autonomous manner, Wg-CTD generated by Sona in the extracellular region activates a subset of Wg signaling whose major function is the regulation of cell proliferation.

Abstract P2-08-53: Tumor elasticity and clinicopathologic factors affecting neoadjuvant chemotherapy response in breast cancer patients

Background: Neoadjuvant chemotherapy for breast cancer has been increased. Many studies have reported on clinicopathologic factors to predict neoadjuvant chemotherapy response. Elastography, which is usually used to differentiate benign and malignant tumors, can be performed to evaluate tissue elasticity during conventional ultrasonography. The purpose of this study was to determine the clinicopathologic factors, including tumor elasticity, that affect neoadjuvant chemotherapy response in stage II or III breast cancer patients.

Methods: From April 2014 to March 2017, 95 patients received neoadjuvant chemotherapy for clinical stage IIa-IIIc primary breast cancer. To evaluate tumor elasticity, strain elastography was performed in 74 patients before neoadjuvant chemotherapy. Patients were divided into two groups by the Tsukuba elasticity scoring system (soft group ≤3 vs. hard group ≥4). Histologic type, nuclear grade, tumor infiltrating lymphocytes (TILs), tumor cellularity, characteristics of stroma, and hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) status were evaluated using core needle biopsy specimens obtained before neoadjuvant chemotherapy. Pathologic complete response (pCR) was defined as the absence of invasive carcinoma in breast (ypT0 and ypTis) and axillary lymph node (ypN0). Residual cancer burden (RCB) was also calculated in 79 cases and the cases were categorized into 2 groups; favorable RCB group (RCB-0 and I) and unfavorable RCB group (RCB-II and III).

Results: The mean age of patients was 46.43±8.62 years (range, 27-71 years) and the mean initial tumor size was 3.63±1.95cm (range, 2.1-12.8cm). Twenty-four patients (32.4%) were categorized into the soft group and 50 patients (67.6%) into the hard group. The mean tumor cellularity on core needle biopsy specimens and characteristics of stroma were not significantly different between the two groups (p=0.35 and p=0.79, respectively). Twenty-two patients achieved pCR (23.2%). The patients with pCR were more likely to have estrogen receptor (ER) or progesterone receptor (PR) negative breast cancer (p=0.04 and p=0.03). The rate of nuclear grade 3 was higher in patients with pCR than those without (p=0.03). Tumor elasticity was not correlated with pCR (p=0.28). Thirty patients (38.0%) achieved favorable RCB and forty-nine patients (62.0%) had unfavorable RCB. Not only the rates of ER negativity (p=0.05), PR negativity (p=0.03), nuclear grade 3 (p=0.01), and high TILs level (≥ 10%) (p=0.04) but also the mean TILs level (p=0.05) were significantly higher in the favorable RCB group compared withthe unfavorable RCB group. No significant difference in tumor elasticity was observed between the two groups (p=0.30). In univariate analyses, nuclear grade 3 (p=0.03), and high TILs level (≥10%) (p=0.04) were significantly correlated with favorable RCB. HR negativity was an independent predictor of favorable RCB in multivariate analysis (odds ratio, 2.93; 95% confidence interval, 1.04-8.28; p=0.04).

Conclusion: Tumor elasticity was not associated with pCR or RCB. HR negativity was an independent predictor for favorable RCB.Nuclear grade and TILs were also potential predictive factors for neoadjuvant chemotherapy response.

Citation Format: Park JY, Choi JE, Bae YK, Lee SJ. Tumor elasticity and clinicopathologic factors affecting neoadjuvant chemotherapy response in breast cancer patients [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-08-53.

An ADAMTS Sol narae is required for cell survival in Drosophila

Cell survival is essential for all living organisms to cope against multiple environmental insults. Intercellular signaling between dying and surviving cells plays an important role to ensure compensatory proliferation, preventing tissue loss after environmental stresses. Here, we show that Sol narae (Sona), a Disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) in Drosophila is required for cell survival. sona exhibited a positive genetic interaction with Death-associated inhibitor of apoptosis 1 (Diap1), and a negative genetic interaction with reaper (rpr). Transcription patterns of sona, Diap1, and rpr genes in the pouch region of wing discs were coordinately changed after irradiation. Interestingly, there was a negative correlation in the expression levels of Sona and DIAP1, and both cell types, one with high Sona level and the other with high Diap1 level, were resistant to irradiation-induced cell death. The sona-expressing cells rarely entered into cell cycle themselves but promoted the nearby cells to proliferate in irradiation conditions. We found that these sona-expressing cells are able to upregulate Cyclin D (Cyc D) and increase tissue size. Furthermore, transient Sona overexpression increased survival rate and promoted development of flies in irradiation conditions. We propose that the two types of radiation-resistant cells, one with high Sona level and the other with high Diap1 level, communicate with dying cells and between each other for cell survival and proliferation in response to irradiation.

Assessment of Digital PCR as a Primary Reference Measurement Procedure to Support Advances in Precision Medicine

BACKGROUND

Genetic testing of tumor tissue and circulating cell-free DNA for somatic variants guides patient treatment of many cancers. Such measurements will be fundamental in the future support of precision medicine. However, there are currently no primary reference measurement procedures available for nucleic acid quantification that would support translation of tests for circulating tumor DNA into routine use.

METHODS

We assessed the accuracy of digital PCR (dPCR) for copy number quantification of a frequently occurring single-nucleotide variant in colorectal cancer (KRAS c.35G>A, p.Gly12Asp, from hereon termed G12D) by evaluating potential sources of uncertainty that influence dPCR measurement.

RESULTS

Concentration values for samples of KRAS G12D and wild-type plasmid templates varied by <1.2-fold when measured using 5 different assays with varying detection chemistry (hydrolysis, scorpion probes, and intercalating dyes) and <1.3-fold with 4 commercial dPCR platforms. Measurement trueness of a selected dPCR assay and platform was validated by comparison with an orthogonal method (inductively coupled plasma mass spectrometry). The candidate dPCR reference measurement procedure showed linear quantification over a wide range of copies per reaction and high repeatability and interlaboratory reproducibility (CV, 2%-8% and 5%-10%, respectively).

CONCLUSIONS

This work validates dPCR as an SI-traceable reference measurement procedure based on enumeration and demonstrates how it can be applied for assignment of copy number concentration and fractional abundance values to DNA reference materials in an aqueous solution. High-accuracy measurements using dPCR will support the implementation and traceable standardization of molecular diagnostic procedures needed for advancements in precision medicine.

Abstract P5-22-03: Arm node preserving surgery in primary breast cancer patients : 5 year experience

Background:

Lymphedema is one of the major complications of axillary lymph node dissection (ALND) in patients with breast cancer. Axillary reverse mapping (ARM) is the technique to find lymphatic drainage from the arm during ALND. The purpose of this study is to evaluate the efficacy of arm node preserving surgery using ARM for reducing the incidence of lymphedema after axillary lymph node dissection in breast cancer patients and its oncologic safety.

Methods:

From January 2009 to October 2014, 167 patients with primary breast cancer were included. In all patients, 1 mCi of 99mTc-phytate was injected at the ipsilateral subareolar plexus and for axillary reverse mapping, 2.5mL of methylene blue was injected into the subcutaneous area of the medial intermuscular groove of the ipsilateral upper arm. The injection site was massaged for at least 5 minutes with the arm lifted above the heart level. At least 15 minutes later, ALND was performed and blue-stained arm nodes were identified. Arm nodes that were enlarged, hard or looked suspicious for metastasis were removed and all other arm nodes were preserved. Arm circumference at 10cm proximal to the medial epicondyle were measured pre- and post-operatively for 2 years. Circumference difference between both upper arms (CD) was evaluated and lymphedema was defined as CD of ≥ 2cm. Follow-up studies were performed every 6 months for 5 years and then annually using mammography, ultrasonography, and/or positron emission tomography.

Results:

Among 167 patients, 125 patients (74.9%) had their arm node preserved (ANP) and 42 (25.1%) patients had their arm node removed (ANR). Statistically significant difference in the mean number of harvested nodes was observed between ANP group (17.85±6.74) and ANR group (20.17±6.08) (p=0.05). The mean number of total identified blue stained arm nodes were 1.35±0.84. The mean follow-up period for measurement of arm circumference was 16.62±8.36 months. The last measured CD between both upper arms was 0.19±0.67cm in ANP group and 0.67±0.92cm in ANP group (p=0.003). 20 patients complained subjective symptoms of lymphedema, 7 patients in ANP group and 13 patients in ANR group (5.6% vs 31%, p&lt;0.001). Among them, one patient in ANP group and 6 patients in ANR group were diagnosed with lymphedema ( 0.8% vs 14.3%, p=0.001). The other 13 patients' CDs between both upper arms were below objective criteria of lymphedema. Follow-up studies were performed for 59.4±22.40 months. There were 16 cases of distant metastasis, 12 cases in ANP group, 4 cases in ANR group (9.6% vs 9.5%, p=1). Two patients in ANP group had distant metastasis and ipsilateral axillary recurrence simultaneously, but their TNM stages were already IIIc and IIb at the diagnosis. There's no solitary axillary recurrence.

Conclusion:

Arm node preserving surgery using axillary reverse mapping in breast cancer patients can reduce the incidence of lymphedema after axillary lymph node dissection and it simultaneously has oncologic safety.

Citation Format: Park JY, Choi JE, Bae YK, Lee SJ. Arm node preserving surgery in primary breast cancer patients : 5 year experience [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-22-03.

Differential Expression Patterns of Irf3 and Irf7 in Pediatric Lymphoid Disorders

Interferon regulatory factors (IRFs) are multifunctional transcriptional factors. To define the role of IRFs in lymphoid disorders, we determined the expression patterns of IRF3 and IRF7 by immunohistochemistry in 5 normal lymph nodes, 12 reactive hyperplastic lymph nodes, and 27 pediatric lymphomas. IRF3 was prominently expressed in the nuclei of the histiocytes, and was expressed very weakly in the cytoplasm of most of the lymphocytes of the normal lymph nodes. However, IRF7 was expressed strongly in the nuclei of over 50% of the lymphocytes throughout the normal lymph nodes, but the histiocytes and fibroblasts were spared. In the reactive hyperplastic lymph nodes, the number of IRF3- and IRF7-positive cells in the nuclei was elevated. In the lymphomas, the number of IRF3-positive cells in the nucleus appeared to have decreased, and the cells were scattered throughout the lymphoma tissue in no specific pattern. However, in most cases the number of IRF7-positive cells was elevated.

These results suggested that IRF3 was activated principally in the histiocytes and T cells under inflammatory conditions, but IRF3 activation was attenuated in cases of lymphoma. However, the number of IRF7-positive cells was found to be elevated in the reactive hyperplastic lymph nodes and pediatric lymphoma.

The migrations of Drosophila muscle founders and primordial germ cells are interdependent

Caudal visceral mesoderm (CVM) cells migrate from posterior to anterior of the Drosophila embryo as two bilateral streams of cells to support the specification of longitudinal muscles along the midgut. To accomplish this long-distance migration, CVM cells receive input from their environment, but little is known about how this collective cell migration is regulated. In a screen we found that wunen mutants exhibit CVM cell migration defects. Wunens are lipid phosphate phosphatases known to regulate the directional migration of primordial germ cells (PGCs). PGC and CVM cell types interact while PGCs are en route to the somatic gonadal mesoderm, and previous studies have shown that CVM impacts PGC migration. In turn, we found here that CVM cells exhibit an affinity for PGCs, localizing to the position of PGCs whether mislocalized or trapped in the endoderm. In the absence of PGCs, CVM cells exhibit subtle changes, including more cohesive movement of the migrating collective, and an increased number of longitudinal muscles is found at anterior sections of the larval midgut. These data demonstrate that PGC and CVM cell migrations are interdependent and suggest that distinct migrating cell types can coordinately influence each other to promote effective cell migration during development.

Comparative analysis of gene expression profiles for several migrating cell types identifies cell migration regulators

Cell migration is an instrumental process that ensures cells are properly positioned to support the specification of distinct tissue types during development. To provide insight, we used fluorescence activated cell sorting (FACS) to isolate two migrating cell types from the Drosophila embryo: caudal visceral mesoderm (CVM) cells, precursors of longitudinal muscles of the gut, and hemocytes (HCs), the Drosophila equivalent of blood cells. ~350 genes were identified from each of the sorted samples using RNA-seq, and in situ hybridization was used to confirm expression within each cell type or, alternatively, within other interacting, co-sorted cell types. To start, the two gene expression profiling datasets were compared to identify cell migration regulators that are potentially generally-acting. 73 genes were present in both CVM cell and HC gene expression profiles, including the transcription factor zinc finger homeodomain-1 (zfh1). Comparisons with gene expression profiles of Drosophila border cells that migrate during oogenesis had a more limited overlap, with only the genes neyo (neo) and singed (sn) found to be expressed in border cells as well as CVM cells and HCs, respectively. Neo encodes a protein with Zona pellucida domain linked to cell polarity, while sn encodes an actin binding protein. Tissue specific RNAi expression coupled with live in vivo imaging was used to confirm cell-autonomous roles for zfh1 and neo in supporting CVM cell migration, whereas previous studies had demonstrated a role for Sn in supporting HC migration. In addition, comparisons were made to migrating cells from vertebrates. Seven genes were found expressed by chick neural crest cells, CVM cells, and HCs including extracellular matrix (ECM) proteins and proteases. In summary, we show that genes shared in common between CVM cells, HCs, and other migrating cell types can help identify regulators of cell migration. Our analyses show that neo in addition to zfh1 and sn studied previously impact cell migration. This study also suggests that modification of the extracellular milieu may be a fundamental requirement for cells that undergo cell streaming migratory behaviors.

Abstract P1-11-13: Re-excision rate in breast conservation surgery after neoadjuvant chemotherapy

Background : The goal of neoadjuvant chemotherapy is to reduce tumor size and convert mastectomy to breast-conservation surgery (BCS). In response to neoadjuvant chemotherapy, the regression rate and pattern of breast cancer is variable. And the re-excision rate to secure negative resection margin is reported limitedly in this case. The purpose of this study was to compare the re-excision rate and BCS success rate of patients who received and who did not received neoadjuvant chemotherapy.

Method : In this retrospective cohort study, between January 2009 and December 2012, total 256 women were included who had clinical T2 breast cancer and were planed to receive BCS as initial operation or neoadjuvant chemotherapy. Fifty-nine patients of them received neoadjuvant chemotherapy. Clinical data were collected including age, preoperative or initial clinical tumor size, mammographic microcalcifications, ultrasound multifocality and axillary nodal status, retrospectively. In the resected specimen from BCS, we reviewed the pathologic tumor size, multifocality, histologic type, hormone receptor and Her-2-neu status, ki67, DCIS and EIC component. The re-excision rate and BCS success rate were investigated. Univariate analysis and regression model were used for identify clinicopathologic factors associated with re-excision. To reduce the effect of selection bias, propensity score matching-based anaylsis was also performed.

Results : Of the 256 patients, 178 patients (90.4%, 178/197) received BCS finally in neoadjuvant group and 56 patients (94.9%, 56/59) in non-neoadjuvant group (p=0.406). There was no statistical difference in the re-excision rate between two groups (35.6% (21/59) in neoadjuvant group vs 34.0% (67/197) in non-neoadjuvant group, p=0.946). In propensity-matched cohorts (N=118), the re-excision rate was same in two groups (35.6% (21/59) in neoadjuvant group vs 35.6% (21/59) in non-neoadjuvant group, p=1.000). BCS success rate was higher in neoadjuvant group(94.9% 56/59) than non-neoadjuvant group (86.4%(51/59)), but there was no statistical difference (p=0.205). In this cohorts, clinicopathologic factors associated with re-excision were pathologic multifocality (OR=4.56, p=0.0142), high ki67 (≥50%) (OR=0.7, p=0.0243) and DCIS component (OR=2.67, p=0.0261) in logistic regression model.

Conclusion: This study showed neoadjuvant chemotherapy could increase the BCS success rate but could not decrease the re-excision rate. The re-excision rate is more associated with pathologic finding rather than effect of neoadjuvant chemotherapy.

Citation Format: Song JH, Park JY, Choi JE, Bae YK, Lee SJ. Re-excision rate in breast conservation surgery after neoadjuvant chemotherapy [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-11-13.

Abstract P3-13-06: The efficacy and long term results of intraoperative frozen section analysis to access resection margin in ductal carcinoma in situ

Introduction

Breast conserving surgery (BCS) is a standard procedure for early breast cancer and resection margin state is the most important risk factor of local recurrence. Re-operation is generally conducted in 20∼40% after initial BCS to achieve negative margins, especially in breast cancer with carcinoma in situ components. In this study, we analyzed the long-term follow up results and efficacy of BCS using intraoperative frozen section analysis to access resection margin in ductal carcinoma in situ (DCIS) patients.

Methods

Between 2004 and 2006, 1016 patients were diagnosed with primary breast cancer and received breast cancer surgery. Among them, BCS was attempted as an initial operation for 523 patients. Superior, inferior, medial and lateral margin of resected specimen were evaluated according to the intraoperative frozen section analysis. If tumor cells existed less than 2mm from resected specimen margin, intraoperative further resection was done and if the further resection was impossible, initial BCS was converted to mastectomy. All medical records and pathologic reports were reviewed retrospectively.

Results

Of the 523 patients who had to undergo BCS, 13.3% (70/523) were converted to mastectomy during initial BCS. The number of the patients who had either only DCIS or invasive carcinoma c carcinoma in situ component was 372 (71.1%, 372/523) and 17.2% (64/372) were converted to mastectomy. One hundred fifty one (28.9%, 151/523) patients had only invasive carcinoma and 3.97% (6/151) were converted to mastectomy. In this study, we analyzed 94 patients who had to undergo BCS with DCIS. The rate of intraoperative conversion to mastectomy was 13.8% (13/94) and 81 patients had successful BCS with 0∼3 times of intraoperative frozen section analysis. There were no differences between patients who had BCS and final mastectomy in clinicopathologic characteristics such as physical examination of tumor, age of patients, DCIS subtypes, nuclear polymorphism, presence of necrosis, ER, PR, HER2 and Ki67. After permanent biopsy was reported, in 5 patients, resected specimen had tumor cells within less than 2mm from resected margin, not inked margin. They had no reoperations and no recurrences. Mean follow up period was 76.6 months. One locoregional and 3 local recurrences in BCS patients and 1 local recurrence in mastectomy patients were found. There was no difference in disease free survival between two groups (95.1% vs 92.3%, p=0.659). In these DCIS patients, reoperation rate was 0%.

Conclusion

Intraoperative frozen section analysis during BCS to access resection margin helps to avoid reoperations and increase intraoperative success rate of BCS in DCIS. It also shows oncological safe long term results. Further studies are needed to resolve the problem with cost-effectiveness of intraoperative frozen section analysis.

Citation Format: Choi JE, Yeu KJ, Park JY, Kang SH, Lee SJ, Bae YK. The efficacy and long term results of intraoperative frozen section analysis to access resection margin in ductal carcinoma in situ. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-13-06.

Abstract P5-07-07: Prognostic value of mutant TP53 in basal breast cancer

Backgrounds; p53 is a tumor suppressor gene that plays an important role in cell cycle control and apoptosis. In the breast cancer, mutant tumor protein (TP53) is expressed in approximately 30% and patients with mutant TP53 often tend to have poor response to chemotherapy and poor prognosis than those with normal TP53. But, according to a recent study, TP53 inactivation could cause to significant DNA damage and to eventual cell death by mitotic catastrophe. We investigated the expression frequency and prognostic value of mutant TP53 using tissue microarrays of 898 invasive breast cancers.

Patients and methods; From January 1995 to December 2005 at Yeungnam university hospital, patients who diagnosed with the primary invasive breast cancer and received operation were included in this study. Patients with bilateral breast cancer or distant metastasis at the time of diagnosis were excluded. According to the immunohistochemical results of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor 2 (HER2), Ki67, epidermal growth factor (EGFR) and cytokeratin (CK) 5/6, we classified patients into 6 subgroups, luminal A, luminal B1, B2, HER2-enriched, normal breast-like (triple negative nonbasal) and basal-like breast cancers. Immunohistochemical staining for TP53 was performed and we defined more than 10% stain of tumor cell as mutant TP53-positive. Distribution and prognostic significance of mutant TP53 in each subgroup was investigated.

Results; In 898 invasive breast cancers, mutant TP53 was identified in 33.5% (301/898). Each expression frequency of mutant TP53 was 10.9% (42/385) in luminal A, 32.1% (45/140) in luminal B1, 50.0% (34/68) in luminal B2, 63.7% (72/113) in HER2-enriched, 54.7% (35/64) in normal breast-like and 57.0% (73/128) in basal-like subtype, respectively. In whole breast cancer patients, patients with mutant TP53 tended to have poor overall survival (OS) and disease free survival (DFS). However, there was no statistical significance (p = 0.187 and p = 0.651). But, in 128 patients with basal-like breast cancer, mutant TP53 showed good prognosis in both OS and DFS (p = 0.003 and p = 0.021). In basal-like breast cancer, the expression of mutant TP53 had no association with other clinicopathologic factors such as tumor size, lymph node metastasis, histological grade, lymphovascular invasion etc. and 98.4% (126/128) patients received adjuvant chemotherapy. In multivariate anaylsis, expression of mutant TP53 was an independent prognostic factor for OS and DFS in basal-like breast cancers (p = 0.008 and p = 0.012).

Conclusions: This study showed that basal-like breast cancer with mutant TP53 has a good outcome in both OS and DFS. Further studies are needed to identify the action mechanism of mutant TP53.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-07-07.

Clinical significance of insulin-growth factor 1 and insulin-growth factor 1 receptor expression in gastrointestinal stromal tumors

BACKGROUND/AIMS

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors in the gastrointestinal tract and are mostly driven by KIT and PDGFRA-activation mutations. However, other signaling pathways are involved in pathogenesis and proliferation of GISTs. This study investigates the prognostic significance of insulin-like growth factor 1 (IGF1) and IGF1 receptor (IGF1R) and the role of succinate dehydrogenase subunit B (SDHB) in GISTs.

METHODOLOGY

Immunohistochemistry (IHC) for IGF1, IGF1R and SDHB was performed in total of 165 GISTs.

RESULTS

The overexpression of IGF1 was evident in tumors with high mitotic count, large tumor size and was correlated with high risk of malignant behavior. IGF1R overexpression was correlated with IGF overexpression, high mitotic count and high risk of malignant behavior. Loss of expression for SDHB was found in only 2 gastric GISTs.

CONCLUSIONS

The overexpression of IGF1 and IGF1R can be useful marker to predict relapse and aggressive behavior in GISTs and has prognostic implications.

Abstract P5-04-07: Epithelial-mesenchymal transition phenotype in breast cancers is associated with clinicopathologic factors indicating aggressive biologic behavior and poor clinical outcome

Epithelial-mesenchymal transition (EMT) is defined by the loss of epithelial characteristics and the acquisition of a mesenchymal phenotype. EMT in epithelial tumors is a reversible process and expected to be involved in invasion, metastasis and chemoresistance of cancer cells. EMT-inducing factors down-regulate E-cadherin and up-regulate extracellular matrix proteins such as fibronectin. Cancer tissue may display a wide spectrum of expression phenotypes of EMT-related proteins. However, little is known about the clinical significance of the different EMT phenotypes in breast cancers. We investigated expression pattern of EMT-related proteins, E-cadherin and fibronectin in 1,498 invasive breast carcinomas by using immunohistochemistry on tissue microarrays. EMT phenotypes were divided into complete type (E-cadherin-negative and fibronectin-positive); incomplete type, including hybrid (E-cadherin-positive and fibronectin-positive) and null (E-cadherin-negative and fibronectin-negative) types; and a wild type (E-cadherin-positive and fibronectin-negative). We correlated EMT phenotype with clinicopathologic characteristics and patients survival. Loss of E-cadherin was observed in 140 (9.3%) cases and fibronectin was expressed in cancer cells of 320 (21.4%) cases. Twenty three (1.5%) cases were categorized as complete type, 414 (27.6%) as incomplete type (hybrid type, 297; null type, 117), and 1,061 (70.8%) as wild type. Complete EMT phenotype was significantly associated with advanced pT stage, lymph node metastasis, high histological grade, and triple negativity (p &lt; 0.001). Overall survival and disease-free survival rates were significantly worse in the complete type, better in the incomplete type and best in the wild type (p = 0.002 and p &lt; 0.001, respectively). In multivariate Cox proportional hazard model analysis, the complete EMT phenotype was not an independent prognostic factor for both overall and disease-free survival. In conclusion, breast cancer patients with EMT phenotype showed less favorable outcomes than those with wild type as it was strongly associated with clinicopathologic factors indicating aggressive biologic behavior.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-04-07.

The role of FGF signaling in guiding coordinate movement of cell groups: guidance cue and cell adhesion regulator?

Cell migration influences cell-cell interactions to drive cell differentiation and organogenesis. To support proper development, cell migration must be regulated both temporally and spatially. Mesoderm cell migration in the Drosophila embryo serves as an excellent model system to study how cell migration is controlled and influences organogenesis. First, mesoderm spreading transforms the embryo into a multilayered form during gastrulation and, subsequently, cells originating from the caudal visceral mesoderm (CVM) migrate along the entire length of the gut. Here we review our studies, which have focused on the role of fibroblast growth factor (FGF) signaling, and compare and contrast these two different cell migration processes: mesoderm spreading and CVM migration. In both cases, FGF acts as a chemoattractant to guide cells’ directional movement but is likely not the only signal that serves this role. Furthermore, FGF likely modulates cell adhesion properties since FGF mutant phenotypes share similarities with those of cell adhesion molecules. Our working hypothesis is that levels of FGF signaling differentially influence cells’ response to result in either directional movement or changes in adhesive properties.

P3-04-04: Patterns of Distant Metastasis According to the Molecular Subtypes of Breast Cancer; Results of 529 Breast Cancer Patients

Backgrounds; Distant metastasis from breast cancer arises from various sites. But few studies concerning factors that can predict metastasis patterns in breast cancer has been reported. In this study, we analyzed the effect of breast cancer molecular subtypes on distant metastasis patterns and tried to determine factors that predict metastasis sites.

Patients and methods; From January 1995 to January 2004 at Yeungnam university hospital, patients diagnosed with the primary invasive breast cancer and received treatments were included in this study. Patients with bilateral breast cancer or distant metastasis at diagnosis were excluded. After analyzing estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor 2 (HER2), epidermal growth factor (EGFR) and cytokeratin (CK) 5/6 status, we classified patients into 5 categories, luminal A, luminal B, HER2−enriched, basal-like, and normal (triple negative nonbasal) breast cancers. Distant metastatic patterns of each category were analyzed.

Results; 529 patients were eligible for tissue microassay analysis and median follow-up period was 7.7 years. In this period, total 82 patients (15.5%) had locoregional relapse or distant metastasis and distant metastasis were identified in 54 patients (10.2%). Each distant metastatic rate was 10.5% (33/313) in luminal A, 8.7% (4/46) in luminal B, 10.2% (6/59) in HER2−enriched, 7.9% (7/89) in basal-like, and 18.2% (4/22) in normal subtype. Most frequent site of distant metastasis in all patients was bone and such result was consistent with Luminal A subtype. Liver metastasis was most frequent in Luminal B subtype, lung metastasis in HER2 enriched and normal subtype and brain metastasis in basal-like subtype.

P3-07-16: The Efficacy of Arm Node Preserving Surgery Using Axillary Reverse Mapping for Preventing Lymphedema in Patients with Breast Cancer

Background

Lymphedema affects over 20% of breast cancer patients undergoing axillary dissection. Axillary reverse mapping (ARM) technique to identify and preserve arm node during sentinel lymph node biopsy (SLNB) or axillary lymph node dissection (ALND) was developed to prevent lymphedema. The purpose of this study was to investigate the location and the metastatic rate of the arm node, and finally to evaluate the short term incidence of lymphedema after arm node preserving surgery.

Patients and Methods

From January 2009 to October 2010, 97 breast cancer patients who underwent ARM were enrolled. 2.5ml blue dye was injected in ipsilateral upper inner arm. After at least 20 minutes after injection, SLNB or ALND was performed in the usual manner and blue stained arm nodes and/or lymphatics were identified. We checked arm circumference at baseline and average of 8.8 months after operation in ALND cases and 13.7 months in SLNB cases. Patients were divided into two groups, arm node preserved group (70 patients in ALND, 10 patients in SLNB) and unpreserved group (13 patients in ALND, 4 patients in SLNB). The difference of arm circumference between preoperative and postoperative was checked in these groups.

Results: The mean number of identified blue stained arm nodes was 1.4±0.6. The arm nodes were found in the inferolateral side of axillary and thoracodorsal vessels in 57 patients (58.76%), the inferomedial side in 37 patients (38.14%), the superolateral side in 2 patients (2.06%), and the superomedial side in 1 patient (1.04%). In the majority of patients (92%), arm nodes were located between the lower level of the axillary vein and just below the second intercostal brachial nerve.

In arm node unpreserved group, 2 patients had metastasis in their arm node. The one had a common pathway between the arm node and the sentinel lymph node. Another did not have a common pathway, but had extranodal extension with N3 metastasis. Among ALND patients, in arm node preserved group, the difference of arm circumference between preoperative and postoperative in ipsilateral and contralateral arm was 0.27cm and 0.07cm, respectively, whereas 0.47cm and −0.03cm in unpreserved group, and one lymphedema was found after 6 months. No difference was found between arm node preserved and unpreserved group amoung SLNB patients (0.21cm and 0.39cm in in preserved group, 0.2cm and 0.02cm in unpreserved group).

Abstract P4-08-05: Delineation of HER2 Gene Status in Korean Breast Cancers by Standardized Immunohistochemistry (IHC) and Silver In Situ Hybridization (SISH): Comparison of Local IHC Result with Central IHC and SISH Results

Background: Amplification of the human epidermal growth factor receptor 2 (HER2) gene and concomitant protein overexpression are present in 20-25% of breast cancers. HER2 overexpression and/or gene amplification is associated with a worse clinical outcome and an important predictive marker for sensitivity to anthracycline-based chemotherapy and HER2- targeted therapy. In Korea, the HER2 status has usually been assessed by immunohistochemistry (IHC) in the laboratories. To verify the preanalytic, analytic, and postanalytic factors of IHC in multi-institutions, we assessed the interlaboratory variability of HER2 IHC by comparing the local IHC with the central IHC and SISH results, as a first step toward building a nationwide quality assurance program.

Methods: The Breast Pathology Study Group of Korean Society of Pathologists collected 1,198 breast carcinoma samples from 7 university-based hospitals and constructed 56 tissue microarray (TMA) blocks with triplicate of 1 mm cores. Local IHC results for HER2 were obtained from 1,130 patients. We performed IHC (PATHWAY anti-HER2/neu (4B5) rabbit monoclonal antibody, Ventana Medical Systems) and SISH (INFORM HER2 DNA Probe Kit, Ventana Medical Systems) for HER2 on the TMA sections using the automated Benchmark platform (Ventana Medical Systems). We interpreted the results according to the American Society of Clinical Oncology/College of American Pathologists guidelines. Results from local IHC were compared with central IHC and SISH. The concordant rates between central IHC and SISH results were also calculated.

Results: The total percentage of cases in each category of local IHC score was: 0/1+, 70.4%; 2+, 8.8% (range among hospitals, 0-36%); and 3+, 20.8% (10.8-28.8%). The percentage of central IHC results (1,110 patients) in each category was: 0/1+, 79.7%; 2+, 3.6% (1.1-8.3%); and 3+, 16.7% (13.1-18.8%). SISH results were obtained from 1,033 patients: negative, 79.5%; equivocal, 0.2% (0-1.6%); and positive, 20.3% (19.2-22.6%). SISH amplifications in each local IHC category were observed as follows: 0/1+, 4.3% (0.6-10%); 2+, 18.8% (5.6-66.7%); and 3+, 71.2% (50-97.3%). When considering the central SISH as gold standard, 3% of cases (30/995) were false negative and 6.3% (63/995) were false positive in local IHC. In central lab, the concordance rates between IHC 3+ and SISH-positive, and IHC 0/1+ and SISH-negative were 95.5% and 98%, respectively.

Conclusions: The results of central IHC and SISH markedly decreased the interlaboratory variability of HER2 status. The measurement of HER2 gene amplification by SISH was less affected by the preanalytic factors than the measurement of overexpression of HER2 protein by IHC. Because the rate of false positivity is higher than that of false negativity in the local IHC, the quality assurance program needs to be focused on decreasing not only the false negativity, but also the false positivity of HER2 IHC in local laboratories

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-08-05.

Current trends in the epidemiological and pathological characteristics of gastrointestinal stromal tumors in Korea, 2003-2004

Despite remarkable progress in understanding and treating gastrointestinal stromal tumors (GISTs) during the past two decades, the pathological characteristics of GISTs have not been made clear yet. Furthermore, concrete diagnostic criteria of malignant GISTs are still uncertain. We collected pathology reports of 1,227 GISTs from 38 hospitals in Korea between 2003 and 2004 and evaluated the efficacy of the NIH and AFIP classification schemes as well as the prognostic factors among pathologic findings. The incidence of GISTs in Korea is about 1.6 to 2.2 patients per 100,000. Extra-gastrointestinal GISTs (10.1%) are more common in Korea than in Western countries. In univariate analysis, gender, age, tumor location, size, mitosis, tumor necrosis, vascular and mucosal invasions, histologic type, CD34 and s-100 protein expression, and classifications by the NIH and AFIP criteria were found to be significantly correlated with patient's survival. However, the primary tumor location, stage and classification of the AFIP criteria were prognostically significant in predicting patient's survival in multivariate analysis. The GIST classification based on original tumor location, size, and mitosis is more efficient than the NIH criteria in predicting patient's survival, but the mechanism still needs to be clarified through future studies.

The CIL-1 PI 5-phosphatase localizes TRP Polycystins to cilia and activates sperm in C. elegans

BACKGROUND

C. elegans male sexual behaviors include chemotaxis and response to hermaphrodites, backing, turning, vulva location, spicule insertion, and sperm transfer, culminating in cross-fertilization of hermaphrodite oocytes with male sperm. The LOV-1 and PKD-2 transient receptor potential polycystin (TRPP) complex localizes to ciliated endings of C. elegans male-specific sensory neurons and mediates several aspects of male mating behavior. TRPP complex ciliary localization and sensory function are evolutionarily conserved. A genetic screen for C. elegans mutants with PKD-2 ciliary localization (Cil) defects led to the isolation of a mutation in the cil-1 gene.

RESULTS

Here, we report that a phosphoinositide (PI) 5-phosphatase, CIL-1, regulates TRPP complex ciliary receptor localization and sperm activation. cil-1 does not regulate the localization of other ciliary proteins, including intraflagellar transport (IFT) components, sensory receptors, or other TRP channels in different cell types. Rather, cil-1 specifically controls TRPP complex trafficking in male-specific sensory neurons and does so in a cell-autonomous fashion. In these cells, cil-1 is required for normal PI(3)P distribution, indicating that a balance between PI(3,5)P2 and PI(3)P is important for TRPP localization. cil-1 mutants are infertile because of sperm activation and motility defects. In sperm, the CIL-1 5-phosphatase and a wortmannin-sensitive PI 3-kinase act antagonistically to regulate the conversion of sessile spermatids into motile spermatozoa, implicating PI(3,4,5)P3 signaling in nematode sperm activation.

CONCLUSION

Our studies identify the CIL-1 5-phosphatase as a key regulator of PI metabolism in cell types that are important in several aspects of male reproductive biology.

Analysis of microsatellite instability, protein expression and methylation status of hMLH1 and hMSH2 genes in gastric carcinomas

BACKGROUND/AIMS

Microsatellite instability (MSI) is a manifestation of a defective DNA mismatch repair system. It is caused by germline mutations of mismatch repair genes or CpG islands hypermethylation. The majority of cancers of hereditary nonpolyposis colorectal cancer (HNPCC) syndrome have MSI+ phenotype. The colorectal cancers show distinctive clinicopathological characteristics and prognoses according to the MSI status. However, there is a wide variety of results between MSI and clinicopathological parameters in gastric carcinomas.

METHODOLOGY

Five hundred and twenty-one surgically resected gastric carcinomas were studied and the correlation with clinicopathological parameters, MSI status by using five microsatellite markers, expression of hMLH1 and hMSH2 protein by immunohistochemical stain, and methylation of hMLH1 and hMSH2 by methylation-specific polymerase chain reaction was analyzed.

RESULTS

There were 50 (9.6%) high-frequency MSI (MSI-H) cases. The MSI-H gastric carcinomas were associated with older age, expanding type by Ming's classification, lymphatic invasion, tumor multiplicity, losses of hMLH1 and hMSH2 protein expressions. The methylation frequency of hMLH1 was 75.5% in MSI-H gastric carcinomas.

CONCLUSIONS

Our results suggest that epigenetic inactivation of hMLH1 might play a role in the carcinogenesis of MSI-H gastric carcinomas. The immunohistochemical stain for hMLH1 protein expression could be used in routine diagnostic methods for predicting MSI status.

Identification of genes involved in the ciliary trafficking of C. elegans PKD-2

Ciliary membrane proteins are important extracellular sensors, and defects in their localization may have profound developmental and physiological consequences. To determine how sensory receptors localize to cilia, we performed a forward genetic screen and identified 11 mutants with defects in the ciliary localization (cil) of C. elegans PKD-2, a transient receptor potential polycystin (TRPP) channel. Class A cil mutants exhibit defects in PKD-2::GFP somatodendritic localization while Class B cil mutants abnormally accumulate PKD-2::GFP in cilia. Further characterization reveals that some genes mutated in cil mutants act in a tissue-specific manner while others are likely to play more general roles in such processes as intraflagellar transport (IFT). To this end, we identified a Class B mutation that disrupts the function of the cytoplasmic dynein light intermediate chain gene xbx-1. Identification of the remaining mutations will reveal novel molecular pathways required for ciliary receptor localization and provide further insight into mechanisms of ciliary signaling.

Sensory roles of neuronal cilia: cilia development, morphogenesis, and function in C. elegans

In the free-living nematode Caenorhabditis elegans, cilia are found on the dendritic endings of sensory neurons. C. elegans cilia are classified as 'primary' or 'sensory' according to the '9+0' axonemal ultrastructure (nine doublet outer microtubules with no central microtubule pair) and lack of motility, characteristics of '9+2' cilia. The C. elegans ciliated nervous system allows the animal to perceive environmental stimuli and make appropriate developmental, physiological, and behavioral decisions. In vertebrates, the biological significance of primary cilia had been largely neglected. Recent findings have placed primary/sensory cilia in the center of cellular signaling and developmental processes. Studies using genetic model organisms such as C. elegans identified the link between ciliary dysfunction and human ciliopathies. Future studies in the worm will address important basic questions regarding ciliary development, morphogenesis, specialization, and signaling functions.

General and cell-type specific mechanisms target TRPP2/PKD-2 to cilia

Ciliary localization of the transient receptor potential polycystin 2 channel (TRPP2/PKD-2) is evolutionarily conserved, but how TRPP2 is targeted to cilia is not known. In this study, we characterize the motility and localization of PKD-2, a TRPP2 homolog, in C. elegans sensory neurons. We demonstrate that GFP-tagged PKD-2 moves bidirectionally in the dendritic compartment. Furthermore, we show a requirement for different molecules in regulating the ciliary localization of PKD-2. PKD-2 is directed to moving dendritic particles by the UNC-101/adaptor protein 1 (AP-1) complex. When expressed in non-native neurons, PKD-2 remains in cell bodies and is not observed in dendrites or cilia, indicating that cell-type specific factors are required for directing PKD-2 to the dendrite. PKD-2 stabilization in cilia and cell bodies requires LOV-1, a functional partner and a TRPP1 homolog. In lov-1 mutants, PKD-2 is greatly reduced in cilia and forms abnormal aggregates in neuronal cell bodies. Intraflagellar transport (IFT) is not essential for PKD-2 dendritic motility or access to the cilium, but may regulate PKD-2 ciliary abundance. We propose that both general and cell-type-specific factors govern TRPP2/PKD-2 subcellular distribution by forming at least two steps involving somatodendritic and ciliary sorting decisions.

Intraflagellar transport is required for the vectorial movement of TRPV channels in the ciliary membrane

The membranes of all eukaryotic motile (9 + 2) and immotile primary (9 + 0) cilia harbor channels and receptors involved in sensory transduction (reviewed by). These membrane proteins are transported from the cytoplasm onto the ciliary membrane by vesicles targeted for exocytosis at a point adjacent to the ciliary basal body. Here, we use time-lapse fluorescence microscopy to demonstrate that select GFP-tagged sensory receptors undergo rapid vectorial transport along the entire length of the cilia of Caenorhabditis elegans sensory neurons. Transient receptor potential vanilloid (TRPV) channels OSM-9 and OCR-2 move in ciliary membranes at rates comparable to the intraflagellar transport (IFT) machinery located between the membrane and the underlying axonemal microtubules. OSM-9 motility is disrupted in certain IFT mutant backgrounds. Surprisingly, motility of transient receptor potential polycystin (TRPP) channel PKD-2 (polycystic kidney disease-2), a mechano-receptor, was not detected. Our study demonstrates that IFT, previously shown to be necessary for transport of axonemal components, is also involved in the motility of TRPV membrane protein movement along cilia of C. elegans sensory cells.

Casein kinase II and calcineurin modulate TRPP function and ciliary localization

Cilia serve as sensory devices in a diversity of organisms and their defects contribute to many human diseases. In primary cilia of kidney cells, the transient receptor potential polycystin (TRPP) channels polycystin-1 (PC-1) and polycystin-2 (PC-2) act as a mechanosensitive channel, with defects resulting in autosomal dominant polycystic kidney disease. In sensory cilia of Caenorhabditis elegans male-specific neurons, the TRPPs LOV-1 and PKD-2 are required for mating behavior. The mechanisms regulating TRPP ciliary localization and function are largely unknown. We identified the regulatory subunit of the serine-threonine casein kinase II (CK2) as a binding partner of LOV-1 and human PC-1. CK2 and the calcineurin phosphatase TAX-6 modulate male mating behavior and PKD-2 ciliary localization. The phospho-defective mutant PKD-2(S534A) localizes to cilia, whereas a phospho-mimetic PKD-2(S534D) mutant is largely absent from cilia. Calcineurin is required for PKD-2 ciliary localization, but is not essential for ciliary gene expression, ciliogenesis, or localization of cilium structural components. This unanticipated function of calcineurin may be important for regulating ciliary protein localization. A dynamic phosphorylation-dephosphorylation cycle may represent a mechanism for modulating TRPP activity, cellular sensation, and ciliary protein localization.

Primary clear cell sarcoma of bone

Clear cell sarcoma is a rare soft tissue sarcoma of young adults with melanocytic differentiation. It occurs predominantly in the soft tissue of extremities, typically involving tendons and aponeuroses. Primary clear cell sarcoma of bone is extremely rare. We report a case of primary clear cell sarcoma of the right first metatarsal in a 48-year-old woman and provide a literature review of the entity.

Allergenicity test of genetically modified soybean in Sprague Dawley rats

Allergenicity of genetically-modified (GM) soybean was evaluated in male Sprague Dawley rats. To confirm the GM soybean used in this study, the polymerase chain reaction (PCR) was performed using the chromosomal DNA of soybeans. The PCR result provided the clear discrimination of genetically-modified (GM) soybeans. To evaluate the allergenicity of GM soybean and non-GM control one, the soybean homogenate was sensitized subcutaneously 3 times a week for 3 weeks. The doses of soybean were 0, 2 and 20 mg/kg in the protein basis. A week after the last sensitization, antisera were recovered from individual animals. When the sera were injected intradermally on the clipped back of unsensitized rats with various dilutions, followed by a challenge with 20 mg/kg of soybean homogenate containing 1% Evans blue, no sign of passive cutaneous anaphylaxis reaction was detected. In addition, when the sera were treated in the cultures of peritoneal mast cells, the increase of histamine release by anti-(GM soybean) sera was not observed when compared to that by anti-(non-GM soybean) sera. The present results indicate that the GM soybean might not act as a strong allergen in male Sprague Dawley rats.

Analysis of upstream elements in the HuC promoter leads to the establishment of transgenic zebrafish with fluorescent neurons

HuC encodes an RNA binding protein homologous to Drosophila elav that serves as an excellent early marker for differentiating neurons. We have characterized the promoter of the zebrafish HuC gene by examining the ability of 5'-upstream fragments to drive expression of green fluorescent protein (GFP) in live embryos. We determined that 2.8 kb of the 5'-flanking sequence is sufficient to restrict GFP gene expression to neurons. The core promoter spans 251 base pairs and contains a CCAAT box and one SP1 sequence but no TATA box is present near the transcription start site. A putative MyT1 binding site and at least 17 E-box sequences are necessary to maintain the neuronal specificity of HuC expression. Interestingly, sequential removal of the putative MyT1 binding site and 14 distal E boxes does not appear to abolish neuronal expression; rather, it leads to a progressive expansion of GFP expression into muscle cells. Further removal of the three proximal E boxes eliminates neuronal and muscle specificity of GFP expression and leads to ubiquitous expression of GFP in the whole body. Identification of key components of the HuC promoter has led to the establishment of a stable zebrafish transgenic line (HuC-GFP) in which GFP is expressed specifically in neurons. We crossed mind bomb (mib) fish with this line to visualize their neurogenic phenotype in live mib(-/-) mutant embryos. This cross illustrates how HuC-GFP fish could be used in the future to identify and analyze zebrafish mutants with an aberrant pattern of early neurons.

Cooperative roles of Bozozok/Dharma and Nodal-related proteins in the formation of the dorsal organizer in zebrafish

In vertebrates, specification of the dorso-ventral axis requires Wnt signaling, which leads to formation of the Nieuwkoop center and the Spemann organizer (dorsal organizer), through the nuclear accumulation of beta-catenin. Zebrafish bozozok/dharma (boz) and squint (sqt), which encode a homeodomain protein and a Nodal-related protein, respectively, are required for the formation of the dorsal organizer. The zygotic expression of boz and sqt in the dorsal blastoderm and dorsal yolk syncytial layer (YSL) was dependent on the maternally derived Wnt signal, and their expression at the late blastula and early gastrula stages was dependent on the zygotic expression of their own genes. The dorsal organizer genes, goosecoid (gsc) and chordin (din), were ectopically expressed in wild-type embryos injected with boz or sqt RNA. The expression of gsc strictly depended on both boz and sqt while the expression of din strongly depended on boz but only partially depended on sqt and cyclops (cyc, another nodal-related gene). Overexpression of boz in embryos defective in Nodal signaling elicited the ectopic expression of din but not gsc and resulted in dorsalization, implying that boz could induce part of the organizer, independent of the Nodal proteins. Furthermore, boz; sqt and boz;cyc double mutants displayed a severely ventralized phenotype with anterior truncation, compared with the single mutants, and boz;sqt;cyc triple mutant embryos exhibited an even more severe phenotype, lacking the anterior neuroectoderm and notochord, suggesting that Boz/Dharma and the Nodal-related proteins cooperatively regulate the formation of the dorsal organizer.

Overexpression of neurogenin induces ectopic expression of HuC in zebrafish

Several basic helix-loop-helix (bHLH) transcription factors are known to be involved in vertebrate neurogenesis. To investigate their roles in zebrafish neurogenesis, we isolated cDNAs for homologues of neurogenin and Math(-1)/atonal. The transcription of neurogenin was first detectable in zebrafish nervous system at late gastrulation stage. The expression of zebrafish neurogenin precedes and overlaps that of HuC, one of the earliest neuronal precursor markers. Injection of neurogenin mRNA into early stage zebrafish embryos induced ectopic expression of HuC. These results suggest that neurogenin may participate in the generation of HuC-expressing cells, implying its role in neuronal determination in zebrafish.

Protective effect of methylcellulose and other polymers on insect cells subjected to laminar shear stress

The relative sensitivity of two insect cell lines to laminar shear stress was determined, and the protective effect of polymers added to the growth media of two insect cell lines, Trichoplusia ni (TN-368) and Spodoptera frugiperda (SF-9), was evaluated. TN-368 and SF-9 cells were found to be equally sensitive to laminar shear stress. Methylcellulose [0.5% (w/v) Dow E4M Methocel] and dextran [4.5% (w/v)] increased the resistance of suspended cells to lysis due to laminar shear stress by factors of up to 76 and 28, respectively, compared to cells in media without additives. It was observed that the protective effect of Pluronic F-68 was concentration-dependent: 0.2% and 0.3% (w/v) F-68 increased the resistance of SF-9 cells to shear stress by factors of 15 and 42, respectively. However, increasing the concentration to 0.5% did not significantly increase the cells' resistance compared to 0.3% (w/v). F-68 at 0.2% only increased the resistance of TN-368 cells by a factor of 6. It is believed that the protection is a result of the polymer adsorbing to the cell membrane. None of the polymer additives tested had a significant effect on SF-9 or TN-368 growth rate.