The extended concurrent genes signature for disease-free survival in breast cancer.

BACKGROUND/PURPOSE: Previously we had identified concurrent genes, which highlighted the interplay between copy number variation (CNV) and differential gene expression (GE) for Han Chinese breast cancers. The merit of the approach is to discovery biomarkers not identifiable by conventional GE only data, for which phenotype-correlation or gene variability is the criteria of gene selection. MATERIALS AND METHODS: Thirty-one comparative genomic hybridization (CGH) and 83 GE microarrays were performed, with 29 breast cancers assayed from both platforms. Potential targets were revealed by Genomic Identification of Significant Targets in Cancer (GISTIC) from CGH arrays. Concurrent genes and genes with significant GISTIC scores were used to derive the extended concurrent genes signature, which was consensus from leading edge analysis across all studies and a supervised partial least square (PLS) regression predictive model of disease-free survival was constructed. RESULTS: There were 1584 concurrent genes from 29 samples with both CGH and GE microarrays. Enriched concurrent genes sets for disease-free survival were identified independently from 83 GE arrays and another one with Han Chinese origin as well as three studies of Western origin. For five studies with disease-free survival follow up, prognostic discrepancy was observed between predicted high-risk and low-risk group patients. CONCLUSION: We concluded that through parallel analyses of CGH and GE microarrays, the proposed extended concurrent gene expression signature can identify biomarkers with prognostic values.

HDAC1 and HDAC2 Double Knockout Triggers Cell Apoptosis in Advanced Thyroid Cancer.

Anaplastic thyroid carcinoma (ATC) and squamous thyroid carcinoma (STC) are both rare and advanced thyroid malignancies with a very poor prognosis and an average median survival time of 5 months and less than 20% of affected patients are alive 1 year after diagnosis. The clinical management of both ATC and STC is very similar because they are not particularly responsive to radiotherapy and chemotherapy. This inspired us to explore a novel and effective clinically approved therapy for ATC treatment. Histone deacetylase inhibitor (HDACi) drugs are recently FDA-approved drug for malignancies, especially for blood cell cancers. Therefore, we investigated whether an HDACi drug acts as an effective anticancer drug for advanced thyroid cancers. Cell viability analysis of panobinostat treatment demonstrated a significant IC50 of 0.075 µM on SW579 STC cells. In addition, panobinostat exposure activated histone acetylation and triggered cell death mainly through cell cycle arrest and apoptosis-related protein activation. Using CRISPR/Cas9 to knock out HDAC1 and HDAC2 genes in SW579 cells, we observed that the histone acetylation level and cell cycle arrest were enhanced without any impact on cell growth. Furthermore, HDAC1 and HDAC2 double knockout (KO) cells showed dramatic cell apoptosis activation compared to HDAC1 and HDAC2 individual KO cells. This suggests expressional and biofunctional compensation between HDAC1 and HDAC2 on SW579 cells. This study provides strong evidence that panobinostat can potentially be used in the clinic of advanced thyroid cancer patients.

The Dual Role of an ESCRT-0 Component HGS in HBV Transcription and Naked Capsid Secretion.

The Endosomal Sorting Complex Required for Transport (ESCRT) is an important cellular machinery for the sorting and trafficking of ubiquitinated cargos. It is also known that ESCRT is required for the egress of a number of viruses. To investigate the relationship between ESCRT and hepatitis B virus (HBV), we conducted an siRNA screening of ESCRT components for their potential effect on HBV replication and virion release. We identified a number of ESCRT factors required for HBV replication, and focused our study here on HGS (HRS, hepatocyte growth factor-regulated tyrosine kinase substrate) in the ESCRT-0 complex. Aberrant levels of HGS suppressed HBV transcription, replication and virion secretion. Hydrodynamic delivery of HGS in a mouse model significantly suppressed viral replication in the liver and virion secretion in the serum. Surprisingly, overexpression of HGS stimulated the release of HBV naked capsids, irrespective of their viral RNA, DNA, or empty contents. Mutant core protein (HBc 1-147) containing no arginine-rich domain (ARD) failed to secrete empty virions with or without HGS. In contrast, empty naked capsids of HBc 1-147 could still be promoted for secretion by HGS. HGS exerted a strong positive effect on the secretion of naked capsids, at the expense of a reduced level of virions. The association between HGS and HBc appears to be ubiquitin-independent. Furthermore, HBc is preferentially co-localized with HGS near the cell periphery, instead of near the punctate endosomes in the cytoplasm. In summary, our work demonstrated the importance of an optimum level of HGS in HBV propagation. In addition to an effect on HBV transcription, HGS can diminish the pool size of intracellular nucleocapsids with ongoing genome maturation, probably in part by promoting the secretion of naked capsids. The secretion routes of HBV virions and naked capsids can be clearly distinguished based on the pleiotropic effect of HGS involved in the ESCRT-0 complex.

To compare the performance of prokaryotic taxonomy classifiers using curated 16S full-length rRNA sequences.

BACKGROUND: Taxonomic assignment is a vital step in the analytic pipeline of bacterial 16S ribosomal RNA (rRNA) sequencing. Over the past decade, most research in this field used next-generation sequencing technology to target V3∼V4 regions to analyze bacterial composition. However, focusing on only one or two hypervariable regions limited the taxonomic resolution to the species level. In recent years, third-generation sequencing technology has allowed researchers to easily access full-length prokaryotic 16S sequences and presented an opportunity to attain greater taxonomic depth. However, the accuracy of current taxonomic classifiers in analyzing 16S full-length sequence analysis remains unclear. OBJECTIVE: The purpose of this study is to compare the accuracy of several widely-used 16S sequence classifiers and to indicate the most suitable 16S training dataset for each classifier. METHODS: Both curated 16S full-length sequences and cross-validation datasets were used to validate the performance of seven classifiers, including QIIME2, mothur, SINTAX, SPINGO, Ribosomal Database Project (RDP), IDTAXA, and Kraken2. Different sequence training datasets, such as SILVA, Greengenes, and RDP, were used to train the classification models. RESULTS: The accuracy of each classifier to the species levels were illustrated. According to the experimental results, using RDP sequences as the training data, SINTAX and SPINGO provided the highest accuracy, and were recommended for the task of classifying prokaryotic 16S full-length rRNA sequences. CONCLUSION: The performance of the classifiers was affected by sequence training datasets. Therefore, different classifiers should use the most suitable 16S training data to improve the accuracy and taxonomy resolution in the taxonomic assignment.

CRISPR-mediated knockout of VEGFR2/KDR inhibits cell growth in a squamous thyroid cancer cell line.

Squamous and anaplastic thyroid cancers are the most aggressive and life-threatening cancer types in humans, with the involvement of lymph nodes in 59% of cases and distant metastases in 26% of cases of all thyroid cancers. The median survival of squamous thyroid cancer patients is < 8 months and therefore is of high clinical concern. Here, we show that both VEGFC and VEGFR2/KDR are overexpressed in thyroid cancers, indicating that VEGF/VEGFR signaling plays a carcinogenic role in thyroid cancer development. Using CRISPR/Cas9, we established a KDR knockout (KO) SW579 squamous thyroid cancer cell line that exhibited dramatically decreased colony formation and invasion abilities (30% and 60% reduction, respectively) when compared to scrambled control cells. To validate the potential of KDR as a therapeutic target for thyroid cancers, we used the KDR RTK inhibitor sunitinib. Protein analysis and live/dead assay were performed to demonstrate that sunitinib significantly inhibited cell growth signal transduction and induced cell apoptosis of SW579 cells. These results suggest that selective targeting of KDR may have potential for development into novel anti-cancer therapies to suppress VEGF/VEGFR-mediated cancer development in patients with clinical advanced thyroid cancer.

Platelet-Derived Growth Factor Receptor-α Subunit Targeting Suppresses Metastasis in Advanced Thyroid Cancer In Vitro and In Vivo.

Thyroid cancer is the most common endocrine malignancy. Patients with well-differentiated thyroid cancers, such as papillary and follicular cancers, have a favorable prognosis. However, poorly differentiated thyroid cancers, such as medullary, squamous and anaplastic advanced thyroid cancers, are very aggressive and insensitive to radioiodine treatment. Thus, novel therapies that attenuate metastasis are urgently needed. We found that both PDGFC and PDGFRA are predominantly expressed in thyroid cancers and that the survival rate is significantly lower in patients with high PDGFRA expression. This finding indicates the important role of PDGF/PDGFR signaling in thyroid cancer development. Next, we established a SW579 squamous thyroid cancer cell line with 95.6% PDGFRA gene insertion and deletions (indels) through CRISPR/Cas9. Protein and invasion analysis showed a dramatic loss in EMT marker expression and metastatic ability. Furthermore, xenograft tumors derived from PDGFRA geneedited SW579 cells exhibited a minor decrease in tumor growth. However, distant lung metastasis was completely abolished upon PDGFRA gene editing, implying that PDGFRA could be an effective target to inhibit distant metastasis in advanced thyroid cancers. To translate this finding to the clinic, we used the most relevant multikinase inhibitor, imatinib, to inhibit PDGFRA signaling. The results showed that imatinib significantly suppressed cell growth, induced cell cycle arrest and cell death in SW579 cells. Our developed noninvasive apoptosis detection sensor (NIADS) indicated that imatinib induced cell apoptosis through caspase-3 activation. In conclusion, we believe that developing a specific and selective targeted therapy for PDGFRA would effectively suppress PDGFRA-mediated cancer aggressiveness in advanced thyroid cancers.

Micro-autologous fat transplantation for rejuvenation of the dorsal surface of the aging hand.

BACKGROUND: Rejuvenation of the dorsal surface of the hand for various conditions, such as cutaneous dyschromia, fine wrinkling, skin laxity, visible extensor tendons, and varicosities appear vital to prevent wrist and digit flexion resulting from hiding of the aged appearance of the hand. Numerous fillers have been applied to re-contour the aging dorsal surface of the hand and the results were variable. The micro-autologous fat transplantation (MAFT) technique, proposed by Lin et al. in 2006, has demonstrated its feasibility in facial rejuvenation. In this study, we applied the MAFT technique for the rejuvenation of the dorsal portion of the hand. METHODS: MAFT was performed in 68 female patients. Fat was harvested by performing liposuction, processed, and refined by centrifugation. Purified fat was micro-transplanted to the dorsal surface of the hand in parcels of small volume. RESULTS: The mean age of the patients was 56 years (range, 38-70 years). MAFT was completed in 72 min, on average. The average amount of delivered fat was 13.9 and 13.8 mL for the right and left hands, respectively. The mean follow-up period was 32 months (range, 10-64 months). The 5-point Likert scale revealed that 58.8% of patients were very satisfied and 39.7% were satisfied about their outcome. CONCLUSIONS: MAFT has changed the concept of fat grafting, from an operation with unpredictable clinical results to an easy and reliable procedure. MAFT demonstrated high patient satisfaction with long-term results and is an effective approach to rejuvenate the dorsal surface of the hand.

Surgical site infection and timing of prophylactic antibiotics for appendectomy.

BACKGROUND: Pre-operative prophylactic antibiotics may decrease the frequency of surgical site infection after appendectomy. However, the optimal timing for administration of pre-operative prophylactic antibiotics is unknown. The purpose of this study was to evaluate the effect of timing of prophylactic antibiotics on the frequency of surgical site infection after appendectomy. METHODS: Medical records were reviewed retrospectively for 577 consecutive patients who had appendectomy for acute appendicitis from 2006 to 2009. Quality assurance guidelines for timing of prophylactic antibiotics before the skin incision were changed from 0 to 30 min before the skin incision (before June 2008) to 30 to 60 min before the skin incision (after June 2008). RESULTS: Surgical site infection occurred in 28 patients (4.9%). There was no difference in frequency of surgical site infection with different timing of pre-operative prophylactic antibiotic (pre-operative time 0 to 30 min: 9 infections [3.6%]; 31 to 60 min: 13 infections [5.4%]; 61 to 120 min: 5 infections [7.0%]; >120 min: 1 infection [6.6%]). Multivariable analysis showed that surgical site infection was associated significantly with medical comorbidity but not perforated appendicitis. CONCLUSIONS: The frequency of surgical site infection was independent of timing of preoperative prophylactic antibiotics but was associated with the presence of medical comorbidity.