Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis

Some overwintering plants acquire competence to flower, after experiencing prolonged cold in winter, through a process termed vernalization. In the crucifer plant Arabidopsis thaliana, prolonged cold induces chromatin-mediated silencing of the potent floral repressor FLOWERING LOCUS C (FLC) by Polycomb proteins. This vernalized state is epigenetically maintained or 'memorized' in warm rendering plants competent to flower in spring, but is reset in the next generation. Here, we show that in early embryogenesis, two homologous B3 domain transcription factors LEAFY COTYLEDON 2 (LEC2) and FUSCA3 (FUS3) compete against two repressive B3-containing epigenome readers and Polycomb partners known as VAL1 and VAL2 for the cis-regulatory cold memory element (CME) of FLC to disrupt Polycomb silencing. Consistently, crystal structures of B3-CME complexes show that B3_FUS3, B3_LEC2 and B3_VAL1 employ a nearly identical binding interface for CME. We further found that LEC2 and FUS3 recruit the scaffold protein FRIGIDA in association with active chromatin modifiers to establish an active chromatin state at FLC, which results in resetting of the silenced FLC to active and erasing the epigenetic parental memory of winter cold in early embryos. Following embryo development, LEC2 and FUS3 are developmentally silenced throughout post-embryonic stages, enabling VALs to bind to the CME again at seedling stages at which plants experience winter cold. Our findings illustrate how overwintering crucifer annuals or biennials in temperate climates employ a subfamily of B3 domain proteins to switch on, off and on again the expression of a key flowering gene in the embryo-to-plant-to-embryo cycle, and thus to synchronize growth and development with seasonal temperature changes in their life cycles.

Acanthopanax senticosus polysaccharide suppressing proliferation and metastasis of the human non-small cell lung cancer NCI-H520 cells is associated with Wnt/β-catenin signaling

Lung cancer (LC) is the highest lethality in all tumors. Non-small cell lung cancer (NSCLC) accounts for about 80% of all LC. Acanthopanax senticosus polysaccharide (ASPS) is extracted from the root of Acanthopanax senticosus (AS). Herein, we examined the effect and molecular mechanism of ASPS on NSCLC. The proliferation, invasion and migration of NCI-H520 cells were detected by cell counting kit-8 (CCK-8), transwell assay and wound healing assay, respectively. The epithelial-mesenchymal transition (EMT) and Wnt/β-catenin pathway-related factors were evaluated using quantitative real-time PCR (QRT-PCR) and western blot assay. Our results observed that ASPS significantly decreased the proliferation of cells at 24 and 48 h. Moreover, ASPS markedly repressed the invasion and migration capacities of cells in a concentration-dependent manner. Besides, ASPS obviously down-regulated the levels of matrix metalloproteinase-2 (MMP-2), MMP-9, fibronectin 1 (FN1), vimentin, wnt3a, phosphorylated-glycogen synthase kinase 3β (p-GSK3β) and cyclin D1, whereas, up-regulating E-cadherin level. The level of GSK3β was not changed in the different groups. ASPS conspicuously inhibited the abilities of proliferation and metastasis in human non-small cell lung cancer cell line NCI-H520 possibly by suppressing Wnt/β-catenin pathway mediated-EMT.

The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor

In plants, flowering time is controlled by environmental signals such as day-length and temperature, which regulate the floral pathway integrators, including FLOWERING LOCUS T (FT), by genetic and epigenetic mechanisms. Here, we identify an H3K27me3 demethylase, JUMONJI 13 (JMJ13), which regulates flowering time in Arabidopsis. Structural characterization of the JMJ13 catalytic domain in complex with its substrate peptide reveals that H3K27me3 is specifically recognized through hydrogen bonding and hydrophobic interactions. Under short-day conditions, the jmj13 mutant flowers early and has increased FT expression at high temperatures, but not at low temperatures. In contrast, jmj13 flowers early in long-day conditions regardless of temperature. Long-day condition and higher temperature induce the expression of JMJ13 and increase accumulation of JMJ13. Together, our data suggest that the H3K27me3 demethylase JMJ13 acts as a temperature- and photoperiod-dependent flowering repressor.

Exosomal Wnt-induced dedifferentiation of colorectal cancer cells contributes to chemotherapy resistance

Cancer stem cells (CSCs) are inherently resistant to chemotherapy, and CSCs in chemotherapy-failed recurrent tumors are enriched; however, the cellular origin of chemotherapy-induced CSC enrichment remains unclear. Communication with stromal fibroblasts may induce cancer cell dedifferentiation into CSCs through secreted factors. We recently demonstrated that fibroblast-derived exosomes promote chemoresistance in colorectal cancer (CRC). Here, we report that fibroblasts confer CRC chemoresistance via exosome-induced reprogramming (dedifferentiation) of bulk CRC cells to phenotypic and functional CSCs. At the molecular level, we provided evidence that the major reprogramming regulators in fibroblast-exosomes are Wnts. Exosomal Wnts were found to increase Wnt activity and drug resistance in differentiated CRC cells, and inhibiting Wnt release diminished this effect in vitro and in vivo. Together, our results indicate that exosomal Wnts derived from fibroblasts could induce the dedifferentiation of cancer cells to promote chemoresistance in CRC, and suggest that interfering with exosomal Wnt signaling may help to improve chemosensitivity and the therapeutic window.

[Meta-analysis on safety and efficacy of dual antiplatelet therapy combining with proton pump inhibitors for patients after percutaneous coronary intervention]

Objective: To analyze the impact of dual antiplatelet (DAPT) therapy combining with or without proton pump inhibitors (PPI) on the main outcomes after percutaneous coronary intervention (PCI). Methods: The PubMed, EMBASE and Cochrane Library were searched for relevant literature and the references obtained from these sources were retrieved manually from inception till September 2017. Inclusion and exclusion criteria were established follow the Cochrane review standard. A total of 977 literatures were included, 193 duplicates were excluded, 74 reviews, case reports, letters and systematic reviews were excluded, 667 literatures were excluded after reading the title and abstract, 34 literatures were excluded due to non-randomized control studies and unrelated outcome indicators, and 9 literatures were finally included with a total of 16 589 patients. RevMan 5.3 software was used to compare the incidence of major adverse cardiovascular events (MACE), cardiogenic death, recurrent myocardial infarction, target vessel revascularization, all-cause death, stent thrombosis, stroke, gastrointestinal bleeding and gastrointestinal events in patients with DAPT combining with or without PPI after PCI. Results: MACE was observed in 8 out of the 9 included literatures, and the results showed that MACE occurred in 561 out of 6 282 patients receiving DAPT combining with PPI therapy and in 951 out of 9 632 patients using DAPT alone (OR=1.15, 95%CI 0.88-1.51, P>0.05). Cardiogenic death was observed in 7 out of the 9 included literatures, and the results showed that cardiogenic death occurred in 172 out of 6 453 patients receiving DAPT combining with PPI treatment and in 321 out of the 9 839 patients using DAPT alone (OR=0.97, 95%CI 0.80-1.18, P>0.05). Recurrent myocardial infarction was observed in 7 out of the 9 included literatures, the results showed 416 out of 6 282 cases in DAPT combining with PPI therapy group experienced recurrent myocardial infarction and 691 out of 9 632 cases in DAPT group experienced recurrent myocardial infarction (OR=1.01, 95%CI 0.89-1.16, P>0.05). Four out of 9 literatures observed revascularization. The results showed that revascularization was performed in 64 out of 2 173 patients receiving DAPT combining with PPI therapy and in 105 out of the 2 770 patients using DAPT alone (OR=1.33, 95%CI 0.55-3.24, P>0.05). All-cause death was observed in 7 out of the 9 included literatures, and the results showed that all-cause death occurred in 172 out of the 6 453 patients in DAPT combining with PPI therapy group and in 321 out of the 9 839 patients using DAPT alone (OR=0.97, 95%CI 0.80-1.18, P>0.05). Three out of the 9 included articles observed stent thrombosis, and the results showed that stent thrombosis occurred in 99 out of 2 997 patients receiving DAPT combining with PPI therapy and in 245 out of the 6 198 patients treated with DAPT (OR=1.07, 95%CI 0.83-1.37, P>0.05). Stroke was observed in 2 out of the 9 included literatures. The results showed that stroke occurred in 5 out of 2 019 patients receiving DAPT combining with PPI therapy, and in 4 out of the 2 033 patients treated with DAPT (OR=1.00, 95%CI 0.29-3.49, P>0.05). Gastrointestinal bleeding was observed in 6 out of the 9 included literatures. The results showed that gastrointestinal bleeding occurred in 26 out of 3 517 patients receiving DAPT combined with PPI therapy, and in 93 out of the 3 506 patients treated with DAPT, gastrointestinal bleeding was significantly lower in the DAPT combining with PPI group than DAPT alone group (OR=0.27, 95%CI 0.17-0.41, P<0.01). Gastrointestinal events were reported in 6 out of the 9 included articles. Similarly, gastrointestinal events were observed in 51 out of 3 517 patients receiving DAPT combined with PPI therapy, and in 190 out of the 3 506 patients treated with DAPT alone, the incidence of gastrointestinal events in the DAPT combined with PPI group was significantly lower than DAPT alone group (OR=0.24, 95%CI 0.14-0.42, P<0.01). Conclusions: The incidence of MACE, cardiogenic death, recurrent myocardial infarction, target vessel revascularization, all-cause death, stent thrombosis and stroke are not affected by DAPT combined with PPI therapy after PCI, while the incidence of gastrointestinal bleeding and gastrointestinal events could be reduced by adding PPI to DAPT in patients undergoing PCI.

Evaluation of short exposure times of antimicrobial wound solutions against microbial biofilms: from in vitro to in vivo

Objectives

Test the performance of topical antimicrobial wound solutions against microbial biofilms using in vitro, ex vivo and in vivo model systems at clinically relevant exposure times.

Methods

Topical antimicrobial wound solutions were tested under three different conditions: (in vitro) 4% w/v Melaleuca oil, polyhexamethylene biguanide, chlorhexidine, povidone iodine and hypochlorous acid were tested at short duration exposure times for 15 min against 3 day mature biofilms of Staphylococcus aureus and Pseudomonas aeruginosa; (ex vivo) hypochlorous acid was tested in a porcine skin explant model with 12 cycles of 10 min exposure, over 24 h, against 3 day mature P. aeruginosa biofilms; and (in vivo) 4% w/v Melaleuca oil was applied for 15 min exposure, daily, for 7 days, in 10 patients with chronic non-healing diabetic foot ulcers complicated by biofilm.

Results

In vitro assessment demonstrated variable efficacy in reducing biofilms ranging from 0.5 log₁₀ reductions to full eradication. Repeated instillation of hypochlorous acid in a porcine model achieved <1 log₁₀ reduction (0.77 log₁₀, P = 0.1). Application of 4% w/v Melaleuca oil in vivo resulted in no change to the total microbial load of diabetic foot ulcers complicated by biofilm (median log₁₀ microbial load pre-treatment = 4.9 log₁₀ versus 4.8 log₁₀, P = 0.43).

Conclusions

Short durations of exposure to topical antimicrobial wound solutions commonly utilized by clinicians are ineffective against microbial biofilms, particularly when used in vivo. Wound solutions should not be used as a sole therapy and clinicians should consider multifaceted strategies that include sharp debridement as the gold standard.

Enhanced broadband spin Hall effects by core-shell nanoparticles

Spin-orbit interaction of light is ubiquitous in any optical system. However, the relevant spin Hall effects are usually weak for the light scattering from nanoparticles, making it challengeable to detect directly in experiment. In this paper, we demonstrate enhanced broadband spin Hall effects by using core-shell nanoparticles. The electric and magnetic dipoles can be tuned by the core-shell nanostructure with great freedom, and are excited simultaneously in a broadband spectrum, resulting in robust enhanced spin Hall shifts. Moreover, the coupling of the electric dipole and electric quadrupole gives rise to enhanced spin Hall shifts at both forward and backward directions. Numerical results from far-field and near-field verify the strong spin-orbit interaction of light. Our work offers a new way to exploit spin Hall effects in superresolution imaging and spin-dependent displacement sensing.

Abstract P4-04-11: A small amount of primary breast cancer shows high tumor mutation burden that may benefit from immune checkpoint inhibitor therapy

Background: Targeted therapy using immune checkpoint inhibitors (ICIs) is a major breakthrough in cancer treatment in the last decade. ICIs like PD1 or PD-L1 antibodies have been shown to be quite effective in cancer like melanoma. However, in most other tumor types including breast cancer, the situation is not as optimistic. Only a small percentage of those patients respond to ICIs therapy. This highlights the importance of identifying biomarkers to predict which patients may benefit from such treatment. Tumor Mutation Burden (TMB) has been shown to be a sensitive marker for ICI treatment. This study is to investigate whether TBM could be used as a biomarker for breast cancer treatment.

Methods: We reviewed next generation sequencing studies of breast cancer. Two such studies with raw data provided were included in our analysis. One study entitled METABRIC performed targeted sequencing of 173 cancer-related genes in around 2500 primary breast cancer tissues. The other study was from TCGA breast cancer project, which performed Whole Exome Sequencing (WES) of around 1000 primary breast cancer samples. Mutation data were downloaded from public data deposit. The number of mutations per sample was calculated. TBM was calculated by divide the coverage in million base pair from that of the total mutation counts.

Results: In METABRIC study, 17272 mutations were identified in 2369 samples, with a median of 7 mutations per sample (95% CI: 6 ˜ 7). The median TMB of METABRIC dataset was 5.8 SNVs/Mb (95% CI: 5 ˜ 5.8). Totally 30 out 2369 (1.3%) samples had a TMB equal or large than 20 SNVs/Mb. In another cohort from TCGA breast cancer study using WES technology, 90172 mutations were identified in 977 samples, with a median of 44 mutations per sample (95% CI: 39 ˜ 50). The median TMB was 1 SNVs/Mb (95% CI: 0.9 ˜ 1.1). Totally 13 out 977 (1.3%) samples had a TMB equal or large than 20 SNVs/Mb.

Conclusions: Breast cancer shows middle to low mutation burden compared to other cancer types. Around 1.3% of breast cancer has quite high TMB of at least 20 SNVs/Mb, which may be qualified for immune checkpoint inhibitors therapy. Our study indicates that TMB may be incorporated as a standard test for late stage breast cancer patients in the clinical practice.

Keywords: Breast cancer, Tumor Mutation Burden, Whole exome sequencing, Targeted sequencing, Immune checkpoint

Citation Format: Wang J, Chen W, Jiang Z, Lin X, Qin T, Yang X, Liu T, Hu H, Li Z, Xie D, Yao H, Song E. A small amount of primary breast cancer shows high tumor mutation burden that may benefit from immune checkpoint inhibitor therapy [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 P4-04-11.

Abstract P2-08-12: Development and validation of prognostic gene signatures for basal-like breast cancer and high grade serous ovarian cancer

Background: Basal-like breast cancer (BLBC) have poor prognosis. Molecular similarities have been reported between BLBC and high grade serous ovarian cancer (HGSOC). To date, there have been no prognostic biomarkers specifically developed for BLBC or HGSOC that can provide risk stratification and inform treatment selections. In this study, we utilized RNA-seq data available from The Cancer Genome Atlas (TCGA) project to develop molecular signatures for risk stratification in BLBC, and further validated these signatures in HGSOC RNA-seq data from TCGA.

Methods: Raw count of RNA-seq data were downloaded from TCGA for 190 BLBC and 374 HGSOC patients. The datasets were annotated with 56963 Ensembl gene IDs. Excluding 31375 gene IDs with no greater than 10 counts in at least 90% of the samples, totally 25228 unique Ensembl gene IDs were used. Progression-free interval (PFI) is the primary study endpoint. Analyses of differentially expressed genes were performed using 3 bioconductor packages: DESEq2, edgeR and voom/limma. Signatures based on commonly identified genes among the 3 analytic methods were established using weighted linear combination of gene expression levels. Their performance was evaluated in the BLBC and HGSOC datasets using Kaplan-Meier survival analysis with log-rank tests and Cox proportional hazard regressions.

Results: Among 190 TNBC patients, 18 had recurrences within 2 years and 40 showed no recurrences for at least 5 years. These patients were used as recurrent vs. non-recurrent cases for differential expression analysis. 307 and 343 genes were differentially expressed based on adjusted p value threshold 0.05 and 0.01 in DESeq2 and edgeR analysis, respectively. voom/limma identified no genes differentially expressed based on adjusted p values, but 228 genes had unadjusted p values &lt; 0.01 and were used in the following analysis. Taken together, 63, 58 and 21 genes were commonly identified by DESeq2/edgeR, DESeq2/limma and edgeR/limma analysis, respectively. All 3 signatures were able to significantly stratify the TNBC full dataset (n=190) using either 20-, 50- or 80-percentile as the cut-points. When evaluated in HGSOC patients using 80-percentile cut-point, both 63- and 58-gene signatures were able to significantly stratify patients into different risk groups (HR 2.16, 95% CI: 1.4-3.34, p &lt; 0.001; HR 2.06, 95% CI: 1.36-3.11, p &lt; 0.001). Multivariate Cox regression adjusting for age, grade and stage showed 63- and 58-gene signatures remained to be statistically significant in stratifying HGSOC patients (p = 0.0005 and 0.001, respectively).

Conclusion: Gene signatures were specifically identified to prognosticate BLBC patients based on RNA-seq data from TCGA project. Which were able to classify HGSOC patients into differential risk groups. With further validations, these signatures may provide additional prognostic tools for clinicians to better manage triple-negative breast cancer that mostly overlap with BLBC, and HGSOC patients who are difficult-to-treat currently.

Disclaimer The views expressed in this article are those of the authors and do not reflect the official policy of the department of Army/Navy/Air Force, Department of Defense, or U.S. government.

Citation Format: Hu H, Zhang Y, Liu J, Raj-Kumar P-K, Yang H, Lee M, Kovatich AJ, Shriver CD. Development and validation of prognostic gene signatures for basal-like breast cancer and high grade serous ovarian cancer [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 P2-08-12.

Abstract P4-08-32: Derivation and validation of a novel prediction model in breast phyllodes tumors after surgery

Aim

This study aimed to develop a nomogram based on clinicopathological features to evaluate the recurrence probability of breast phyllodes tumors following surgery. The criteria for atypia, mitoses, overgrowth, and surgical margin (AMOS) were also validated.

Method

Data from 334 patients with breast phyllodes tumors, who underwent surgical treatment at Sun Yat-sen Memorial Hospital from January 2005 to December 2014, were used to develop a prediction model. Additionally, data of 36 patients from Peking University Shenzhen Hospital and data of 140 patients from Sun Yat-sen University Cancer Center during the same period were used to validate the model. The medical records and tumor slides were retrospectively reviewed. The log-rank and Cox regression tests were used to develop a clinical prediction model of breast phyllodes tumors as well as validating the AMOS criteriaAll statistical analyses were performed using R and STATA.

Results

Of all 334 patients included in the study, 224 had benign, 91 had borderline, and 19 had malignant tumors. The local and distant recurrence rate was 17.7%. The 1-,3-, and 5-year cumulative recurrence-free survival was 98.5%, 97.9%, and 96.8%, respectively. Surgical margin, mitoses, and tumor border were identified as independent risk factors for breast phyllodes tumors. A nomogram was developed based on these three variables. The C-index of internal and external validation was 0.71and 0.67, respectively. The area under the curve of AMOS criteria was 0.59.

Conclusions

The present study model presented a more concise and objective variables to evaluate the recurrence-free survival of patients after surgery compared with that using the AMOS criteria, which is more appropriate for clinical practice and also allows for a more accurate prediction.

Citation Format: Song E, Chao X, Nie Y, Jin X, Tan C, Cui J, Hu H, Yao H. Derivation and validation of a novel prediction model in breast phyllodes tumors after surgery [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 P4-08-32.

Abstract P4-01-26: Circulating cell-free DNA in serum as a marker for the early detection of tumor recurrence in breast cancer patients

Background: Quantitative estimation of circulating cell-free DNA (cfDNA) isolated from serum by noninvasive procedures can serve as a potential biomarker for the early detection of many cancers. However, a simple, straightforward technique is unavailable to estimate the cfDNA in clinical labs. Moreover, the prognostic value of cfDNA in patients with breast cancer (BrCa) is currently under debate. The aim of this study was to develop a simple yet effective quantitative method for measuring the cfDNA in serum and to eventually investigate the relationship between cfDNA and the occurrence of recurrence in BrCa patients.

Methods: A total of 240 patient cases (n=240) were selected and are comprised of different subtypes of breast cancer patients and control individuals. We selected 21 serum samples from patients which showed recurrence after 4-7 years of disease-free survival. For the compare studies, each of the recurrent and non-recurrent serum samples was incubated with the SYBR Green I (2 μM). A standard graph was also made with known DNA concentration to calculate the amount of cfDNA in these recurrent and non-recurrent serum samples. Additionally, a comparative study was also performed with the serum of patients with non-recurrent BrCa versus healthy patients.

Results: We develop a simple fluorescent based measuring technique which can easily estimate the cfDNA in one step. SYBR Green binds to DNA, and as a result, the fluorescence of SYBR Green increases substantially. Global Wilcoxon analyses were performed to compare the cfDNA amount between non-recurrent and recurrent patients. There is a significant difference in fluorescent intensities between recurrent patients' samples versus non-recurrent patients which are directly proportional to the cfDNA levels. The amount of cfDNA is higher in recurrent patient (ratio is 1.3 up; p= 0.03; AUC=0.76) compared to similar non-recurrent patients. While we compared the fluorescence data between normal/healthy patients versus non-recurrent is turned out as non-significant (healthy to non-recurrent ratio = 1.03; p= 0.20, AUC=0.61).

Conclusion: In this current study, we developed a straightforward one-step technique to measure the amount of cfDNA in serum, which can easily translate into a clinical diagnostic tool. To the best of our knowledge, this is the first report which demonstrates serum cfDNA as an early detection marker for recurrent breast cancer patients. The relatively high level of cfDNA in the serum of recurrent breast cancer patients compared to non-recurrent breast cancer patients indicates an uncovered circulating genetic information which triggers the cancer recurrence pathway to relapse cancer in the near future.

Citation Format: Bera A, Eidelman O, Russ E, Landa A, Karaian J, Eklund M, Hu H, Pollard HB, Shriver CD, Srivastava M. Circulating cell-free DNA in serum as a marker for the early detection of tumor recurrence 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 P4-01-26.

[Clinical evaluation of gallbladder and common bile duct stones treated though cholecystostomy tube]

Objective: To investigate the efficacy, feasibility and safety of treatment of gallbladder and common bile duct stones treated through cholecystostomy tube. Methods: The clinical data of 17 patients with gallbladder and common bile duct stones treated through cholecystostomy tube from January 2012 to December 2016 was analyzed retrospectively. Results: Seventeen patients were successfully treated with percutaneous transhepatic gallbladder (PTGD), and 88.2% (15/17) patients had clinical symptom relief. There was no complication happened after PTGD and fistula expansion. All the stones were removed and there was 11.7% (2/17) of gallbladder bleeding, 5.9% (1/17) of pancreatitis, and 5.9% (1/17) of hyperamylasemia after stones extraction. The patients had gone through an average treatment period of 87.8±16.0 days, hospitalization of 5.5±0.6 times and 43.3±4.5 days, cost of 60.0±8.0 thousand, 6.9±0.9 operations, 1.4±0.6 stone extraction operations with the average time of 58.4±21.2 min. The duodenal papillary balloon dilatation rate was 82.4% (14/17). Conclusion: The treatment through cholecystostomy tube is an effective, safe and feasible technique for gallbladder and common bile duct stones. However, there are many shortcomings such as long treatment cycle, large number of hospitalization and operations, difficult operation and high cost.

Transient Ischemic Attack and Carotid Web

BACKGROUND AND PURPOSE

Carotid web was recognized as a cause of ischemic stroke. We sought to determine the clinical and imaging profiles of patients with a carotid web as well as its association with TIA.

MATERIALS AND METHODS

A retrospective review of carotid CT angiography studies and brain MR imaging in patients with TIA during the past 3 years (n = 135) was performed to determine the presence of carotid webs by 2 experienced neuroradiologists according to previously published criteria. Demographics and clinical and imaging characteristics are shown by descriptive statistics for patients with an identified carotid web. The agreement in the detection of carotid webs between 2 neuroradiologists was examined using κ statistics.

RESULTS

There were 12 (8.9%) carotid webs at the symptomatic bifurcation and 1 carotid web (0.7%) at the asymptomatic bifurcation, and no hyperintensity was seen on DWI of these 12 patients. Eight of these 12 (75%) patients with a carotid web were women. None of the 12 patients with a carotid web had major risk factors or other causes of TIA. Fair-to-good interobserver agreement (κ = 0.87) was seen for diagnosing a carotid web with CT angiography. The rate (10/12, 83.3%) of short-term recurrent episodes of TIA in patients with TIA with a carotid web was significantly higher than that of patients without a carotid web (15/123, 12.2%) (P < .001).

CONCLUSIONS

The incidence of carotid web in patients with TIA was 8.9%. There is an association between carotid web and patients with TIA without other identified risks. Carotid web may be an underestimated risk factor for TIA.

Platelet Shp2 negatively regulates thrombus stability under high shear stress

Essentials Shp2 negatively regulates thrombus stability under pathological shear rate. Shp2 suppresses TXA2 receptor-mediated platelet dense granule secretion. Through αIIbβ3 outside-in signaling, Shp2 targets calmodulin-dependent activation of Akt. Shp2 may serve to prevent the formation of unwanted occlusive thrombi. SUMMARY: Background Perpetuation is the final phase of thrombus formation; however, its mechanisms and regulation are poorly understood. Objective To investigate the mechanism of Shp2 in platelet function and thrombosis. Methods and results We demonstrate that the platelet-expressed Src homology region 2 domain-containing protein tyrosine phosphatase Shp2 is a negative regulator of thrombus stability under high shear stress. In a ferric chloride-induced mesenteric arteriole thrombosis model, megakaryocyte/platelet-specific Shp2-deficient mice showed less thrombi shedding than wild-type mice, although their occlusion times were comparable. In accordance with this in vivo phenotype, a microfluidic whole-blood perfusion assay revealed that the thrombi formed on collagen surfaces by Shp2-deficient platelets were more stable under high shear rates than those produced by wild-type platelets. Whereas Shp2 deficiency did not alter platelet responsiveness towards thrombin, ADP and collagen stimulation, Shp2-deficient platelets showed increased dense granule secretion when stimulated by the thromboxane A2 analog U46619. Shp2 appears to act downstream of integrin αIIb β3 outside-in signaling, inhibiting the phosphorylation of Akt (Ser473 and Thr308) and dense granule secretion. Calmodulin was also shown to bind both Shp2 and Akt, linking Shp2 to Akt activation. Conclusions Platelet Shp2 negatively regulates thrombus perpetuation under high shear stress. This signaling pathway may constitute an important mechanism for the prevention of unwanted occlusive thrombus formation, without dramatically interfering with hemostasis.

Aryl hydrocarbon receptor polymorphisms are associated with dry skin phenotypes in Chinese patients with atopic dermatitis

BACKGROUND

Epidermal barrier dysfunction is the initial event in the development of atopic dermatitis (AD). Recent studies have identified a crucial role for the aryl hydrocarbon receptor (AHR) in controlling the gene expression of filaggrin and other skin barrier proteins, suggesting an underlying association between AHR and AD pathogenesis.

AIM

To investigate the role of AHR gene polymorphisms in the susceptibility to AD and in AD-associated phenotypes.

METHODS

We enrolled 487 patients with AD, 210 patients with psoriasis and 226 healthy controls (HCs) from the Han Chinese population, and genotyped two AHR single-nucleotide polymorphisms (rs10249788 and rs2066853) by PCR and subsequent DNA sequencing.

RESULTS

The AHR rs10249788 and rs2066853 polymorphisms were found in both sets of patients (AD and psoriasis) and in HCs, but no significant differences were detected in genotype or allele frequencies between the three groups. However, patients with AD with the rs10249788 (CT/TT) or rs2066853 (AG + AA) genotype were more likely to have severe dry skin scores. In the stratification analysis, the AHR rs2066853 (AG + AA) and rs10249788 (CT + TT) genotypes could predict a higher risk of severe dry skin phenotypes in the male, early-onset and allergic rhinitis subgroups. Furthermore, the combined rs10249788 (CT + TT) and rs2066853 (AG + AA) genotypes led to a higher risk for severe dry skin in patients with AD.

CONCLUSION

AHR polymorphisms are not associated with the risk of AD; however, they may predict a dry skin phenotype in patients with AD.

Cancer Theranostic Applications of Albumin-Coated Tobacco Mosaic Virus Nanoparticles

Nanotechnology holds great promise in cancer drug delivery, and of particular interest are theranostic approaches in which drug delivery and imaging are integrated. In this work, we studied and developed the plant virus tobacco mosaic virus (TMV) as a platform nanotechnology for drug delivery and imaging. Specifically, a serum albumin (SA)-coated TMV formulation was produced. The SA coating fulfils two functions: SA provides a stealth coating for enhanced biocompatibility; it also acts as a targeting ligand enabling efficient tumor accumulation of SA-TMV versus TMV in mouse models of breast and prostate cancer. We demonstrate drug delivery of the chemotherapy doxorubicin (DOX); TMV-delivered DOX outperformed free DOX, resulting in significant delayed tumor growth and increased survival. Furthermore, we demonstrated the ability of SA-coated TMV loaded with chelated Gd(DOTA) for magnetic resonance imaging detection of tumors. In the future, we envision the application of such probes as theranostic, where first imaging is performed to assess whether the nanoparticles are effective at targeting a particular patient tumor. If targeting is confirmed, the therapeutic would be added and treatment can begin. The combination of imaging and therapy would allow to monitor disease progression and therefore inform about the effectiveness of the drug delivery approach.

Complex design of surgical instruments as barrier for cleaning effectiveness, favouring biofilm formation

BACKGROUND

Inadequately reprocessed reusable surgical instruments (RSIs) may harbour infectious agents which may then be transferred to a suitable site for replication.

AIM

To determine the cumulative effect of 20 cycles of contamination, cleaning (manual or manual followed by automated) and steam sterilization on high-complex-design RSIs used for orthopaedic surgery.

METHODS

New flexible medullary reamers and depth gauges were contaminated by soaking in tryptone soya broth, containing 5% sheep blood and 10⁹ cfu/mL of Staphylococcus aureus (ATCC 25923), for 5 min. To mimic a worse-case scenario, RSIs were dried 7 h and subjected to either (a) rinsing in distilled water, (b) manual cleaning or (c) manual plus automated cleaning (reference standard), and steam sterilization. The contamination, cleaning, and sterilization cycle was repeated 20 times. Adenosine triphosphate (ATP) was measured after cleaning procedures; microbial load and residual protein were measured following the 10^th and 20^th reprocessing, in triplicate. Scanning electron microscopy (SEM) was used to confirm soil and biofilm presence on the RSIs after the 20^th reprocessing.

FINDINGS

Manual and manual plus automated cleaning significantly reduced the amount of ATP and protein residues for all RSIs. Viable bacteria were not detected following sterilization. However, SEM detected soil after automated cleaning, and soil, including biofilms, after manual cleaning.

CONCLUSION

Soil and/or biofilms were evident on complex-design RSIs following 20 cycles of contamination and reprocessing, even using the reference standard method of cleaning. Although the depth gauges could be disassembled, biological residues and biofilm accumulated in its lumen. The current design of these RSIs prevents removal of all biological soil and this may have an adverse effect on patient outcome.

PGK1 as an immune target in Kawasaki disease

Kawasaki disease (KD) is an immune-mediated vasculitis with symptoms that mimic febrile illness; the immune origin has been suggested but never proved. First, cell chip technology was used to screen immune targets cells. With the indirect immunofluorescence assay we found that the HeLa cell chip could be recognized by KD patient serum samples. The target cell proteome was extracted as antigens, and antigen recognition reaction was performed using the patients' serum as antibodies and the detected target protein was detected and identified as phosphoglycerate kinase 1 (PGK1). Then PGK1 was produced and tested with enzyme-linked immunosorbent assay (ELISA), Western blotting, immunoprecipitation and competitive inhibition immunofluorescence assay. Immunoglobulin (Ig)G against PGK1 was detected in 46% (23 of 50) sera of KD patients, 13% (five of 38) sera in febrile non-KD patients (FC) and 2·6% (one of 38) sera in healthy donors. As an immune target, PGK1 not only helps understanding of the pathogenesis, it also has potential value in facilitating the laboratory diagnosis of KD.

[Cytotoxic effects of γδT cells on bladder cancer cells and expression of MICA/B in bladder cancer]

OBJECTIVE

To explore the role of γδT cells against bladder cancer and to detect the expression of stress proteins MICA/B recognized by γδT cells in bladder cancer.

METHODS

γδT cells from peripheral blood drawn from 6 bladder cancer patients with pamidronate stimulating were expanded. Flow cytometry was used to detect the purity and expansion folds of γδT cells, and the expression of CD107a on γδT cells after PMA/ionomycin stimulated. The cytotoxicity assay was carried out to test the cytotoxicity of γδT cells against human bladder cancer cell lines. The expression of MICA/B on bladder cancer cell lines and in bladder cancer tissues were detected through flow cytometry and immunohistochemistry respectively.

RESULTS

γδT cells from peripheral blood drawn from 6 bladder cancer patients were successfully expanded. The purity was 75%-94% and the expansion folds were 109-371 times. After being stimulated by PMA/ionomycin, the proportion of CD107a+ γδT cells increased significantly, reaching 40%-82%. γδT cells from the 6 bladder cancer patients showed obvious cytotoxic effects on 3 human bladder cancer cell lines which was enhanced as the effector: the target ratio increased. MICA/B were detected both in 3 bladder cancer cell lines and in 26 bladder cancer tissues. The staining score of MICA/B in invasive bladder cancer was slightly higher than that in non-invasive bladder cancer, and in advanced bladder cancer was higher than that in low grade bladder cancer, but the statistical analysis showed that the staining score of MICA/B was no significant correlation between the tissue and the tumor stages and grades.

CONCLUSION

γδT cells from the peripheral blood of the bladder cancer patients could be successfully expanded in vitro, and showed significant anti-bladder cancer effect. MICA/B were detected both in bladder cancer cell lines and in bladder cancer tissues. The statistical analysis showed that there was no significant correlation between the staining scores of MICA/B in the tissue and the tumor stages and grades.

[Clinical application of partial cystectomy with augmentation cystoplasty for invasive bladder cancer in elderly patients]

OBJECTIVE

To evaluate the clinical effect and safety of biological patch applied in elderly patients with invasive bladder cancer who underwent massive partial cystectomy with augmentation cystoplasty.

METHODS

The clinical data of 2 patients with invasive bladder cancer from October 2016 to March 2017, who underwent the massive partial cystectomy with augmentation cystoplasty were retrospectively reviewed. Case one was an 87-year-old man, with tumor located on the bladder anterior wall, ranging from 5.5 cm×2.5 cm, and the grade of American Society of Anesthesiologists (ASA) being III. Case two was a 77-year-old female, whose lesion was located on the right anterior wall, ranging from 5.2 cm×4.0 cm, and the grade of ASA being II. Both of the patients received a massive partial cystectomy with augmentation cystoplasty. The operative time, estimated blood loss, perioperative and postoperative data and follow-up data, including cystoscopy and urodynamics were recorded and compared. When the P value was less than 0.05, it was statistically significant.

RESULTS

All the operations were successfully performed. The average operative time was (155.0+35.4) min, mean estimated intraoperative blood loss was 20 to 100 mL, and the mean postoperatively hospital stay was eight days. During the 10 to 14 months' follow-up periods, no local recurrence or distant metastasis occurred. Urodynamic data: the maximum urinary flow rate was 16.5 mL/s, and the maximum bladder capacity was 303 mL. The two patients urinated 3-4 times in the day time, 0 to 3 times in the night, 200-300 mL each time, on average. The American Urological Association symptom score was 3 to 5. Partial cystectomy, applied to aged patients with multiple complications and high risk of surgical anesthesia, was able to reduce surgery related complications. For patients with tumor of small size, the normal bladder wall would be enough to recover functional capacity for urine storing after partial cystectomy. For patients with large lesions range and small normal bladder tissues, augmentation cystoplasty would help recover bladder capacity on the condition of negative margin.

CONCLUSION

Massive partial cystectomy with augmentation cystoplasty is safe and effective. It could decrease perioperative morbidity and keep the quality-of-life benefits of bladder preservation, which is worthy of further application for some selected invasive bladder cancer in elderly patients.

A serine protease homologue Bombyx mori scarface induces a short and fat body shape in silkworm

Body shape is one of the most prominent and basic characteristics of any organism. In insects, abundant variations in body shape can be observed both within and amongst species. However, the molecular mechanism underlying body shape fine-tuning is very complex and has been largely unknown until now. In the silkworm Bombyx mori, the tubby (tub) mutant has an abnormal short fat body shape and the abdomen of tub larvae expands to form a fusiform body shape. Morphological investigation revealed that the body length was shorter and the body width was wider than that of the Dazao strain. Thus, this mutant is a good model for studying the molecular mechanisms of body shape fine-tuning. Using positional cloning, we identified a gene encoding the serine protease homologue, B. mori scarface (Bmscarface), which is associated with the tub phenotype. Sequence analysis revealed a specific 312-bp deletion from an exon of Bmscarface in the tub strain. In addition, recombination was not observed between the tub and Bmscarface loci. Moreover, RNA interference of Bmscarface resulted in the tub-like phenotype. These results indicate that Bmscarface is responsible for the tub mutant phenotype. This is the first study to report that mutation of a serine protease homologue can induce an abnormal body shape in insects.

Understanding the microbiome of diabetic foot osteomyelitis: insights from molecular and microscopic approaches

OBJECTIVES

Rigorous visual evidence on whether or not biofilms are involved in diabetic foot osteomyelitis (DFO) is lacking. We employed a suite of molecular and microscopic approaches to investigate the microbiome, and phenotypic state of microorganisms involved in DFO.

METHODS

In 20 consecutive subjects with suspected DFO, we collected intraoperative bone specimens. To explore the microbial diversity present in infected bone we performed next generation DNA sequencing. We used scanning electron microscopy (SEM) and peptide nucleic acid fluorescent in situ hybridization (PNA-FISH) with confocal microscopy to visualize and confirm the presence of biofilms.

RESULTS

In 19 of 20 (95%) studied patients presenting with DFO, it was associated with an infected diabetic foot ulcer. By DNA sequencing of infected bone, Corynebacterium sp. was the most commonly identified microorganism, followed by Finegoldia sp., Staphylococcus sp., Streptococcus sp., Porphyromonas sp., and Anaerococcus sp. Six of 20 bone samples (30%) contained only one or two pathogens, while the remaining 14 (70%) had polymicrobial communities. Using a combination of SEM and PNA-FISH, we identified microbial aggregates in biofilms in 16 (80%) bone specimens and found that they were typically coccoid or rod-shaped aggregates.

CONCLUSIONS

The presence of biofilms in DFO may explain why non-surgical treatment of DFO, relying on systemic antibiotic therapy, may not resolve some chronic infections caused by biofilm-producing strains.

miR-145 is critical for modulation of vascular smooth muscle cell proliferation in human carotid artery stenosis

miR-145 is highly expressed in vascular cells, where it regulates phenotypic switching and vascular homeostasis, but its role in carotid artery stenosis (CAS) is controversial. In the present study, the expression of miR-145 was assessed by real time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) in human samples (both plasma and/or endarterectomy samples) from patients with symptomatic CAS and in controls without CAS. The mouse carotid artery ligation (CAL) model was used to determine the role of miR-145 on vascular smooth muscle cells in vivo (VSMCs) by using a mimic of or an inhibitor of miR-145. We found that miR-145 expression was significantly reduced in the plasma and plaque from patients with CAS (p less than 0.01). The expression of miR-145 in the mouse CAL model, as assessed by qRT-PCR, was significantly reduced compared to the carotid arteries of the control group (p less than 0.01). In vitro, enhancement or inhibition of miR-145 in VSMCs demonstrated that miR-145 significantly inhibited proliferation of VSMCs (p less than 0.05); in vivo, enhancement of miR-145 significantly inhibited neointimal formation in the CAL model (p less than 0.01). These results demonstrate that the expression of miR-145 is reduced in human CAS, miR-145 plays a critical role in CAS by modulation of VSMC proliferation, suggesting that MiR-145 may present a potential therapeutic option for treating CAS.

Effect of cadexomer iodine on the microbial load and diversity of chronic non-healing diabetic foot ulcers complicated by biofilm in vivo

Objectives: The performance of cadexomer iodine was determined against microbial populations from chronic non-healing diabetic foot ulcers (DFUs) complicated by biofilm in vivo, using molecular, microscopy and zymography methods.

Methods: Chronic non-healing DFUs due to suspected biofilm involvement were eligible for enrolment. DNA sequencing and real-time quantitative PCR was used to determine the microbial load and diversity of tissue punch biopsies obtained pre- and post-treatment. Scanning electron microscopy and/or fluorescence in situ hybridization confirmed the presence or absence of biofilm. Zymography was used to determine levels of wound proteases.

Results: Seventeen participants were recruited over a 6 month period. Scanning electron microscopy and or fluorescence in situ hybridization confirmed the presence of biofilm in all samples. Eleven participants exhibited log₁₀ reductions in microbial load after treatment (range 1–2 log₁₀) in comparison with six patients who experienced <1 log₁₀ reduction (P = 0.04). Samples were tested for levels of wound proteases pre- and post-treatment. Reductions in the microbial load correlated to reductions in wound proteases pre- and post-treatment (P = 0.03).

Conclusions: To the best of our knowledge, this study represents the first in vivo evidence, employing a range of molecular and microscopy techniques, of the ability of cadexomer iodine to reduce the microbial load of chronic non-healing DFUs complicated by biofilm. Further analyses correlating log reductions to optimal duration of therapy and improvements in clinical parameters of wound healing in a larger cohort are required.

Inverse association between plasma homocysteine concentrations and type 2 diabetes mellitus among a middle-aged and elderly Chinese population

BACKGROUND AND AIMS

Plasma homocysteine concentrations have been reported to be associated with type 2 diabetes mellitus (T2DM) with controversial findings. The aim of the present study was to investigate the association between plasma homocysteine concentrations and T2DM.

METHODS AND RESULTS

A cross-sectional study including 19,085 eligible participants derived from the Dongfeng-Tongji cohort was conducted. Plasma homocysteine concentrations were measured by Abbott Architect i2000 Automatic analyzer and T2DM was defined according to American Diabetes Association criteria. Logistic regression model was used to explore the association between plasma homocysteine concentrations and T2DM. The prevalence of T2DM was 19.0% in the whole population (mean age 62.9 years), 21.8% in males, and 17.1% in females. In the multivariable logistic regression analyses, compared with those in the lowest quintile, the OR (95% CI) of T2DM was 1.05 (0.92-1.21), 0.99 (0.86-1.14), 0.90 (0.78-1.05), and 0.77 (0.66-0.90) for quintile 2 to quintile 5 of homocysteine concentrations after adjustment for potential confounders (P for trend < 0.0001). Homocysteine concentrations were associated with decreased T2DM prevalence risk (OR = 0.88 per SD increase of homocysteine concentration; 95% CI: 0.84-0.93). A significant interaction between homocysteine concentrations and drinking status on T2DM prevalence risk was observed (P for interaction = 0.03). The inverse association of plasma homocysteine concentrations with T2DM prevalence risk was observed in non-drinkers but not in current drinkers.

CONCLUSION

Plasma homocysteine concentrations were inversely correlated with T2DM among a middle-aged and elderly Chinese population.

Associations between daily cooking duration and the prevalence of diabetes and prediabetes in a middle-aged and elderly Chinese population: A cross-sectional study

Experimental and epidemiological studies indicated that ambient air pollution was positively associated with diabetes. Few studies investigated the associations between household air pollution, for example, daily cooking duration and diabetes or prediabetes. We conducted a cross-sectional study to investigate the associations of daily cooking duration with the prevalence of diabetes and prediabetes among a middle-aged and elderly population. A total of 26 089 individuals (11 250 males and 14 839 females) derived from the Dongfeng-Tongji cohort study were included. Daily cooking duration was assessed by questionnaire. Diabetes and prediabetes were identified according to the criterion of American Diabetes Association. No significant association was observed between daily cooking duration and the prevalence risk of diabetes (odds ratio[OR] = 0.97, 95% confidence interval[CI]: [0.81-1.16], P for trend = .74); however, longer daily cooking duration was associated with higher prevalence risk of prediabetes (OR = 1.26, 95% CI: 1.07-1.47; P for trend = .003) and hyperglycemia (OR = 1.21, 95% CI: 1.05-1.41; P for trend = .005). Our study suggested that daily cooking duration was not associated with diabetes but with higher prevalence risk of prediabetes/hyperglycemia in a middle-aged and elderly Chinese population.

Abstract P4-09-14: Analysis of breast cancer recurrence using gene set enrichment analysis

Background: Even after successful treatment of primary breast tumors, there is a continued risk of recurrence. The risk varies between subtypes and there are ongoing efforts that aim to improve prediction of such risks for individual patients. Detection of subclinical metastases might be achieved by biomarkers in blood. In this study, we profiled protein expression in blood plasma from patients with known clinical outcome (recurrence vs no recurrence) to identify prognostic markers of breast cancer recurrence.

Methods: The subjects and specimens were made available through the Clinical Breast Care Project using IRB-approved protocols. We analyzed blood plasma samples taken at the time of diagnosis from consented patients who subsequently relapsed (33 cases) as well as those with no disease recurrence (31 controls). Based on hormone receptor and lymph node status the samples were grouped as: ER-/HER2- (17 cases/15 controls), ER+/LN+ (10/10) and ER+/LN- (6/6). We used aptamer-based SOMAscan assay platform to study the expression of 1252 proteins. We analyzed the protein expression data by using their coding genes in order to apply the Gene Set Enrichment Analysis method (GSEA v.2, Broad Institute). Pathway databases of KEGG, REACTOME, BIOCARTA and C4 collection were used. Significant gene sets were called at 5% FDR, and overlaps and low coverage gene sets (Tags &lt;70%) were removed. Statistical analysis and clustering were done using R.

Results: Unsupervised clustering showed some difference in signal in the ER+/LN- group. Even though there was a lack of significantly differentiated proteins between the cases and controls of this group, many significant gene sets were identified. After applying the cutoff filters and removing the overlaps, there were 5 gene sets enriched with the pathway collection, involved in B-cell receptor signaling, mRNA metabolism, tight junction and SCF-KIT signaling. Similarly, 9 gene sets from the MORF compendium were differentially expressed with the C4 collection and included neighborhood genes of NME2, ACTG1, EIF3S2, AP2M1, DAP3, UBE2I, NPM1, AATF and NPM1. In contrast, neither differentially expressed proteins nor gene sets were identified from the ER+/LN+ and ER-/HER2- groups. Since the sample size of the ER+/LN- group was small, we conducted a similar analysis by randomly choosing 6 case and control samples in the other two groups respectively. There were still no differentially expressed proteins or gene sets identified above the specified cutoff parameters.

Conclusion: Using plasma protein expression data we identified underlying gene sets differentially expressed between ER+/LN- patients who had cancer recurrence and no recurrence. Many genes in these sets were already known biomarkers (e.g. PTEN, AKT1, STAT3, SET etc.). These results can be used for understanding patterns of recurrence in different cancer subtypes. Further research is needed to estimate the clinical significance of these gene products.

The views expressed in this article are those of the author and do not reflect the official policy of the Department of Army/Navy/Air Force, the Department of Defense, or U.S. Government.

Citation Format: Praveen Kumar A, Kovatich AJ, Biancotto A, Cheung F, Davidson-Moncada JK, Kvecher L, Liu J, Ru Y, Kovatich AW, Deyarmin B, Fantacone-Campbell JL, Hooke JA, Raj Kumar PK, Rui H, Hu H, Shriver CD. Analysis of breast cancer recurrence using gene set enrichment analysis [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 P4-09-14.

Abstract P2-06-04: Use of principal component analyses to select ER-balanced subset for gene centering in PAM50 subtyping

Background: PAM (Prediction Analysis of Microarray) 50 is an established gene expression-based algorithm to classify breast tumors into basal-like, HER2-enriched, luminal A (LA), and luminal B (LB) subtypes. Clinical subtyping is mainly based on immunohistochemistry (IHC) assays of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (Her2) and Ki67 classifying tumors into triple-negative (ER-/PR-/Her2-), Her2+ (ER-/PR-/Her2+), LA (ER+/Her2-/Ki67-), LB1 (ER+/Her2-/Ki67+) and LB2 (ER+/Her2+). These two subtyping methods do not completely match even on comparable subtypes. Nevertheless, the ER-balanced subset for gene-centering in PAM50 subtyping was selected based on clinical status. Here we explored the possibility of using principal component analyses and iterative PAM50 call to refine the selection of an ER balance subset to improve consistency between these methods focusing on LB calls which is more aggressive than LA tumors.

Methods: Normalized gene expression data was obtained from TCGA research network for 712 primary tumors which had IHC status available for ER, PR and Her2. Since Ki67 status was not available LA and LB was discriminated for ER+ cases with Her2- and Her2+ respectively. In house RNA-Seq dataset had 118 primary tumors and were drawn from the Clinical Breast Care Project where breast cancer patients were consented using an IRB-approved protocol. Tumors were selected and processed by laser microdissection. RNA was extracted from tissues using the Illustra triplePrep kit (GE Healthcare). Paired-end mRNA sequencing was performed using the Illumina HiSeq platform. Sequenced reads were processed using PERL based pipeline utilizing PRINSEQ, GSNAP and HTSeq. Principal component analysis (PCA) was done using R. Wilcoxon rank sum test was used for statistical significance (p&lt;0.05).

Results: In both datasets, the PCA map grouping of cases does not perfectly reflect the clinical subtypes. This motivated us to select ER balance subset based on the PC1 separation and IHC subtype. The resulting PAM50 subtypes on PCA map distinguished Basal and LA as two well separated components. Using all of Basal and equal number of LA cases for ER balance subset for PAM50 resulted in increased LB call and a better consistency with IHC LB calls. Among 712 cases in TCGA LB numbers increased from 142 in initial PAM50 call to 203 in ER balanced refined PAM50 call. We noticed that there was significantly higher (p-value = 4.414e-11) MKI67 expression for the 39 cases switch from LA to LB between PAM50 calls. Similar trend was observed in our in-house dataset where majority of the IHC-LB1 cases was called as LB in PAM50. The new method increased LB call from 22 to 27 which in-turn increased consistency between molecular and clinical subtypes from 73 to 79 out of the total of 118 cases.

Conclusion: We show that an iterative PAM50 call coupled with PCA for selection of ER balance set potentially enhanced the consistency of the LB calls with clinical subtyping and that the tumors switched from LA to LB have high MKI67 expression.

The views expressed in this article are those of the author and do not reflect the official policy of the Department of Army/Navy/Air Force, the Department of Defense, or U.S. Government.

Citation Format: Raj-Kumar P-K, Liu J, Kovatich AJ, Kvecher L, Shriver CD, Hu H. Use of principal component analyses to select ER-balanced subset for gene centering in PAM50 subtyping [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 P2-06-04.

Abstract P4-03-04: Targeting the mevalonate pathway in HER2-positive breast cancer to overcome resistance to anti-HER2 therapy

Background: Despite the advent of HER2-targeted therapies for HER2+ breast cancer (BC), including the monoclonal antibody trastuzumab (T) either alone or in combinations, resistance still poses a major clinical challenge. Using our broad panel of HER2+ cell lines made resistant (R) to T alone (TR), and to lapatinib plus T (LTR), we observed that in resistant models where HER2 remains inhibited, especially the LTR derivative, the mevalonate (MVA) pathway is activated and provides an alternative proliferative signal, including the activation of mTOR, to drive resistance. While these resistant cell models were hypersensitive to the widely-used cholesterol-lowering statins, the role of other MVA pathway inhibitors such as zoledronic acid (ZA), which is in clinical use to treat bone metastasis, in overcoming resistance to HER2-targeted therapy has not been explored. Based on recent reports and our preliminary data using reverse phase protein array (RPPA) analysis, the YAP/TAZ transcription factor (TF) emerged as a potential mediator of MVA pathway signaling to mTOR. Here, we investigated the therapeutic efficacy of additional MVA pathway inhibitors and the role of YAP/TAZ in mediating resistance to HER2-targeted therapy.

Methods: HER2+ SKBR3 and AU565 BC cells and their LTR derivatives were used. Changes in cell growth upon genetic and pharmacologic inhibition of the MVA pathway were quantified by methylene blue staining. Luciferase reporter assays and western blots (WB) measured changes in total and phosphorylated (S127 and S381/inactive) YAP protein levels to examine activity of the YAP/TAZ TF complex. To validate the function of YAP/TAZ in resistance, we performed YAP/TAZ knockdown (siRNA), overexpression of dominant-active YAP constructs (S381A, S381/127A), and qRT-PCR assessment of YAP/TAZ target gene expression.

Results: ZA, like simvastatin (Sim), selectively inhibited the growth of resistant cells in a dose-dependent manner. This inhibition was rescued by geranyl geranyl pyrophosphate (GGPP), a downstream metabolite, but not by MVA, an upstream metabolite, indicating the on-target effect of ZA. Further, ZA and Sim combination showed a synergistic growth-inhibitory effect in R but not in parental (P) cells. YAP/TAZ luciferase reporter assays and phosphorylated YAP and total TAZ levels by WB, confirmed the increased activity of YAP/TAZ in R models, which was selectively inhibited by Sim or ZA and was rescued by the corresponding downstream metabolites. YAP/TAZ knockdown selectively inhibited resistant cell growth and mTOR signaling in R vs. P cells, and dominant-active YAP/TAZ rescued the mTOR inhibition by Sim. YAP/TAZ inhibition by siRNA or by Sim significantly decreased the expression of YAP/TAZ target gene survivin in R vs. P cells, and the Sim inhibition was rescued by MVA.

Conclusions: The MVA pathway plays a critical role in mediating resistance to anti-HER2 therapy, which was overcome by Sim and ZA either alone or in combination. Given the synergistic effect of Sim and ZA, their combination may offer a therapeutic strategy to overcome HER2-targeted therapy resistance. Our results also reveal the role of YAP/TAZ in MVA pathway-mediated HER2-targeted therapy resistance, which could suggest new biomarkers and therapeutic targets.

Citation Format: Sethunath V, Hu H, De Angelis C, Veeraraghavan J, Qin L, Rimawi MF, Osborne KC, Schiff R. Targeting the mevalonate pathway in HER2-positive breast cancer to overcome resistance to anti-HER2 therapy [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 P4-03-04.

Abstract P3-16-01: Using the new pan-cancer clinical data resource (TCGA-CDR) to identify breast cancer genomic correlates associating with different survival outcome endpoints

Introduction The Cancer Genome Atlas (TCGA) generated abundant high quality molecular data, however its relatively short-term patient follow-up limited its immediate clinical utility. We led a PanCanAtlas effort to systematically collate, integrate, and quality check the large body of acquired clinicopathologic data, generated 4 primary clinical outcome endpoints for each case, and created a new Pan-Cancer Clinical Data Resource (TCGA-CDR) for public use. We report here on the utility and validity of this TCGA-CDR in relating breast cancer (BC) genomic information to survival endpoints.

Methods Clinicopathologic data from all data files were integrated and processed. Overall survival (OS), disease-specific survival (DSS, an approximation), progression-free interval (PFI), and disease-free interval (DFI)were derived.Tests of the adequacy of the follow-up intervals for each endpoint were performed, and quality evaluation of these endpoints was established by their comparison with different clinical features. As a case study we compared each survival endpoint for significant association (FDR &lt;0.2) with chromosomal aneuploidy.

Results The 4 endpoints were derived for 1097 TCGA BC cases having a median follow-up time of 27.7 months. Median times to events/censorship for OS, DSS, PFI, and DFI were 41.8/25.0, 32.6/26.0, 26.0/25.0, and 25.4/25.0 months respectively. PFI and DFI passed tests for adequate follow-up times; OS and DSS partially passed the same tests signaling some caution with their use in genomic associations.

Using the endpoints, outcomes of patients with ER+ and ER- tumors were compared, along with those of patients with low (I&II) and high (III&IV) stage breast tumors. Univariate analyses suggested patients with ER+ tumors had significantly better survival than patients with ER- tumors when using PFI (p=0.005), DFI (p=0.001), and DSS (p=0.009), with OS not reaching significance (p=0.09). Patients with low stage tumors showed significantly better outcomes than patients with high stage tumors for each endpoint (p&lt;0.001). The 4 endpoints were also evaluated for their significant associations with chromosomal arm aneuploidy. Adjusted for patient age and AJCC stage, tumors with a loss of 8q and 8p (p=0.019, FDR=0.37) had worse PFI; and those with loss of 8q, 20q, and 8p had worse DFI. Tumors with gain of 11q or loss of 14, 7q, 12q, 18q, 20q, 3p, 7p, 8p, 18p, and 20p had worse OS. In contrast, tumors with loss of 16q had better DSS, while those with loss of 3q, 12q, 17q, 18q, 19q, 20q, 3p, 8p, 12p, 18p, 19p, and 20p had worse DSS. The finding that 8p loss associated with worse survival for all 4 endpoints, while 18p loss associated with worse OS and DSS, agrees with literature reports.

Conclusion These findings confirm that PFI and DFI, as extracted from the TCGA-CDR, are valid and appropriate BC survival endpoints, while OS and DSS may be recommended with some caution when employing TCGA data to evaluate new relationships between breast cancer genomic abnormalities and clinical outcomes.

The views expressed in this article are those of the author and do not reflect the official policy of the Department of Army/Navy/Air Force, the Department of Defense, or U.S. Government.

Citation Format: Liu J, Lichtenberg T, Hoadley KA, Cherniack A, Poisson L, Kovatich AJ, Benz C, Thorsson V, TCGA PanCanAtlas Research Network, Shriver CD, Hu H. Using the new pan-cancer clinical data resource (TCGA-CDR) to identify breast cancer genomic correlates associating with different survival outcome endpoints [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 P3-16-01.

Functional Relationship and Gene Ontology Classification of Breast Cancer Biomarkers

Breast cancer is a complex disease that still imposes a significant healthcare burden on women worldwide. The etiology of breast cancer is not known but significant advances have been made in the area of early detection and treatment. The advent of advanced molecular biology techniques, mapping of the human genome and availability of high throughput genomic and proteomic strategies opens up new opportunities and will potentially lead to the discovery of novel biomarkers for early detection and prognostication of breast cancer. Currently, many biomarkers, particularly the hormonal and epidermal growth factor receptors, are being utilized for breast cancer prognosis. Unfortunately, none of the biomarkers in use have sufficient diagnostic, prognostic and/or predictive power across all categories and stages of breast cancer. It is recognized that more useful information can be generated if tumors are interrogated with multiple markers. But choosing the right combination of biomarkers is challenging, because 1) multiple pathways are involved, 2) up to 62 genes and their protein products are potentially involved in breast cancer-related mechanisms and 3) the more markers evaluated, the more the time and cost involved. This review summarizes the current literature on selected biomarkers for breast cancer, discusses the functional relationships, and groups the selected genes based on a Gene Ontology™ classification.

Dietary Intake is Positively Associated with Cognitive Function of a Chinese Older Adults Sample

OBJECTIVE

The relationship between cognitive function and dietary intake in older adults was under-studied in China. This study examined this relationship in a Chinese sample while controlling for the effects of sleep quality and socio demographic confounders.

METHODS

The sample consisted of 340 Chinese older adults (age > 60) who were randomly selected from Wuhan city in central China. Cognitive function was assessed by the Mini-mental State Examination [MMSE], sleep quality by the Pittsburgh Sleep Quality Index [PSQI], and dietary intake by frequencies of intake of meat products, fruits, fish/seafood/aquatic products, nuts and mushroom/algae over the past year. First, confirmatory factor analysis (CFA) was conducted to evaluate the measurement properties of cognitive function, dietary intake, and sleep quality. Second, structural equation modeling (SEM) was conducted to examine the relations of cognitive function, dietary intake, and sleep quality.

RESULTS

Dietary intake was found to be positively related to cognitive function. Older age, lower education status, monthly income, and living alone or without a spouse were significantly associated with poorer cognitive function. SES status had an indirect effect on cognitive function via dietary intake.

CONCLUSION

Dietary intake may be critical to maintain normal cognitive function of older adults in China.

Structure of the Arabidopsis JMJ14-H3K4me3 Complex Provides Insight into the Substrate Specificity of KDM5 Subfamily Histone Demethylases

In chromatin, histone methylation affects the epigenetic regulation of multiple processes in animals and plants and is modulated by the activities of histone methyltransferases and histone demethylases. The jumonji domain-containing histone demethylases have diverse functions and can be classified into several subfamilies. In humans, the jumonji domain-containing Lysine (K)-Specific Demethylase 5/Jumonji and ARID Domain Protein (KDM5/JARID) subfamily demethylases are specific for histone 3 lysine 4 trimethylation (H3K4me3) and are important drug targets for cancer treatment. In Arabidopsis thaliana, the KDM5/JARID subfamily H3K4me3 demethylase JUMONJI14 (JMJ14) plays important roles in flowering, gene silencing, and DNA methylation. Here, we report the crystal structures of the JMJ14 catalytic domain in both substrate-free and bound forms. The structures reveal that the jumonji and C5HC2 domains contribute to the specific recognition of the H3R2 and H3Q5 to facilitate H3K4me3 substrate specificity. The critical acidic residues are conserved in plants and animals with the corresponding mutations impairing the enzyme activity of both JMJ14 and human KDM5B, indicating a common substrate recognition mechanism for KDM5 subfamily demethylases shared by plants and animals and further informing efforts to design targeted inhibitors of human KDM5.

BMI, Waist Circumference and All-Cause Mortality in a Middle-Aged and Elderly Chinese Population

OBJECTIVE

To investigate the association of obesity and all-cause mortality in a sample of middle-aged and elderly population.

DESIGN AND SETTING

Information of participants was collected in the Dongfeng-Tongji study, a perspective cohort study of Chinese occupational population. The main outcome was risk of death after 8.5 years of follow-up.

PARTICIPANTS AND MEASUREMENTS

We examined the association of BMI, waist circumference (WC, and waist-height ratio (WHtR) with all-cause mortality in the Dongfeng-Tongji cohort study (n=26,143). Cox proportional hazard models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CI) for all-cause mortality. Area under the receiver operating characteristic curves and net reclassification improvement (NRI) were used to calculate the power of prediction models.

RESULTS

During a mean of 8.5 years of follow-up, 2,246 deaths were identified. There is a U-shaped association of BMI with all-cause mortality in the middle-aged and elderly Chinese population. Compared with individuals with normal BMI, underweight was positively (HR=2.16, 95% CI: 1.73, 2.69) while overweight (HR=0.75, 95% CI: 0.67, 0.84) and obesity (HR=0.67, 95% CI: 0.56, 0.79) were negatively associated with all-cause mortality after adjustment for potential confounders including WC. In contrast, WC (Q5 vs. Q1, HR=1.55, 95% CI: 1.29, 1.86) and WHtR (Q5 vs.Q1, HR=1.69, 95% CI: 1.40, 2.04) were positively associated with mortality after further adjustment for BMI (P trend < 0.001). Addition of both BMI and WC into the all-cause mortality predictive model significantly increased AUC (P =0.0002) and NRI (NRI = 2.57%, P = 0.0007).

CONCLUSIONS

BMI and WC/WHtR were independently associated with all-cause mortality after mutual adjustment. Combination of BMI and WC/WHtR improved the predictive ability of all-cause mortality risk in the middle-aged and elderly population.

A small-molecule inhibitor of the Wnt pathway (SM04690) as a potential disease modifying agent for the treatment of osteoarthritis of the knee

OBJECTIVES

Osteoarthritis (OA) is a degenerative disease characterized by loss of cartilage and increased subchondral bone within synovial joints. Wnt signaling affects the pathogenesis of OA as this pathway modulates both the differentiation of osteoblasts and chondrocytes, and production of catabolic proteases. A novel small-molecule Wnt pathway inhibitor, SM04690, was evaluated in a series of in vitro and in vivo animal studies to determine its effects on chondrogenesis, cartilage protection and synovial-lined joint pathology.

DESIGN

A high-throughput screen was performed using a cell-based reporter assay for Wnt pathway activity to develop a small molecule designated SM04690. Its properties were evaluated in bone-marrow-derived human mesenchymal stem cells (hMSCs) to assess chondrocyte differentiation and effects on cartilage catabolism by immunocytochemistry and gene expression, and glycosaminoglycan breakdown. In vivo effects of SM04690 on Wnt signaling, cartilage regeneration and protection were measured using biochemical and histopathological techniques in a rodent acute cruciate ligament tear and partial medial meniscectomy (ACLT + pMMx) OA model.

RESULTS

SM04690 induced hMSC differentiation into mature, functional chondrocytes and decreased cartilage catabolic marker levels compared to vehicle. A single SM04690 intra-articular (IA) injection was efficacious in a rodent OA model, with increased cartilage thickness, evidence for cartilage regeneration, and protection from cartilage catabolism observed, resulting in significantly improved Osteoarthritis Research Society International (OARSI) histology scores and biomarkers, compared to vehicle.

CONCLUSIONS

SM04690 induced chondrogenesis and appeared to inhibit joint destruction in a rat OA model, and is a candidate for a potential disease modifying therapy for OA.

Long non-coding RNA CHCHD4P4 promotes epithelial-mesenchymal transition and inhibits cell proliferation in calcium oxalate-induced kidney damage

Kidney stone disease is a major cause of chronic renal insufficiency. The role of long non-coding RNAs (lncRNAs) in calcium oxalate-induced kidney damage is unclear. Therefore, we aimed to explore the roles of lncRNAs in glyoxylate-exposed and healthy mouse kidneys using microarray technology and bioinformatics analyses. A total 376 mouse lncRNAs were differentially expressed between the two groups. Using BLAST, 15 lncRNA homologs, including AU015836 and CHCHD4P4, were identified in mice and humans. The AU015836 expression in mice exposed to glyoxylate and the CHCHD4P4 expression in human proximal tubular epithelial (HK-2) cells exposed to calcium oxalate monohydrate were analyzed, and both lncRNAs were found to be upregulated in response to calcium oxalate. To further evaluate the effects of CHCHD4P4 on the cell behavior, we constructed stable CHCHD4P4-overexpressing and CHCHD4P4-knockdown HK-2 cells. The results showed that CHCHD4P4 inhibited cell proliferation and promoted the epithelial-mesenchymal transition in kidney damage and fibrosis caused by calcium oxalate crystallization and deposition. The silencing of CHCHD4P4 reduced the kidney damage and fibrosis and may thus be a potential molecular target for the treatment of kidney stones.