The Current Achievements of Multi-Gene Panel Tests in Clinical Settings for Patients with Non-Small-Cell Lung Cancer.

Some multi-gene panel tests have been implemented in clinical settings to guide targeted therapy in non-small-cell lung cancer (NSCLC) in Japan. The current performance of multi-gene panel tests under the condition that the Oncomine Dx Target Test (ODxTT) and Amoy Dx Pan Lung Cancer PCR panel (AmoyDx-multi) are available remains relatively unknown. We retrospectively reviewed consecutive patients with NSCLC, whose FFPE samples were considered for genetic testing.

Complex phenotypic heterogeneity of combined hepatocellular-cholangiocarcinoma with a homogenous promoter mutation.

To clarify the mechanism underlying the development and poor prognosis of combined hepatocellular-cholangiocarcinoma (cHCC-CCA), we characterized liver cancer driver mutations and poor prognostic markers in both the HCC and intrahepatic CCA (iCCA) components of a cHCC-CCA tumor. The telomerase reverse transcriptase () promoter mutation C228T was quantified by digital polymerase chain reaction using DNA from multiple microdissected cancer components of a single cHCC-CCA nodule. The protein expression of cancer-related markers, including TERT, was examined by serial thin-section immunohistochemistry and double-staining immunofluorescence.

Close-to-lesion transbronchial biopsy: a novel technique to improve suitability of specimens for genetic testing in patients with peripheral pulmonary lesions.

Bronchoscopy with radial-probe endobronchial ultrasound, a guide sheath, and electromagnetic navigation can improve the diagnostic yield of peripheral lung nodules. However, the suitability of specimens for genetic analysis remains unsatisfactory. We hypothesized that a transbronchial biopsy performed after closely approaching the bronchoscope tip to the lesion might provide more suitable specimens for genetic analysis.

Clinical importance of the range of detectable variants between the Oncomine Dx target test and a conventional single-gene test for EGFR mutation.

Although we have experienced some cases with discordant results between the Oncomine Dx target test (ODxTT) and conventional single gene tests for detecting EGFR alterations, the clinical efficacy of EGFR-TKIs in these discordant cases remains little known. We retrospectively reviewed consecutive patients with non-small-cell lung cancer whose FFPE samples were simultaneously submitted for the ODxTT, and a PNA-LNA PCR clamp test. We evaluated the clinical efficacy of EGFR-TKIs in patients with discordant results between the two tests, focusing on the common EGFR mutations.

Physical Activity Estimated by the Wearable Device in Lung Disease Patients: Exploratory Analyses of Prospective Observational Study.

Physical activity is a potential parameter to assess the severity or prognosis of lung disease. However, the differences in physical activity between healthy individuals and patients with lung disease remain unclear. The analyses in this report are a combined analysis of four cohorts, including a healthy control cohort, in a prospective study designed to evaluate wearable device-estimated physical activity in three cohorts: the lung cancer cohort, the interstitial pneumonia cohort, and the COPD cohort (UMIN000047834).

Comparison of the analytical performance of the Oncomine dx target test focusing on bronchoscopic biopsy forceps size in non-small cell lung cancer.

Background: Next-generation sequencing (NGS) has been implemented in clinical oncology to analyze multiple genes and to guide targeted therapy. Although the pathological diagnosis and biomarker tests for patients with advanced lung cancer have mostly been obtained with small biopsy samples, especially with bronchoscopic approaches, the performance for NGS with respect to the different sizes of biopsy forceps remains little known.

Methods: We retrospectively reviewed consecutive patients with non-small cell lung cancer, whose FFPE samples were obtained by endobronchial biopsy/transbronchial biopsy and were submitted for the Oncomine Dx Target Test (ODxTT).

Guanine damage by singlet oxygen from SYBR Green I in liquid crystalline DNA.

It is known that double-stranded DNA (dsDNA) turns into a liquid crystalline phase by the addition of a high concentration of polymer with salt. SYBR Green I (SG) is a well-known sensitive fluorescent stain for dsDNA, and is intercalated in liquid crystalline DNA. Formation of the liquid crystalline dsDNA-SG complex has been confirmed by CD spectral measurements, fluorescence spectral measurements and confocal fluorescence microscopy.

The effect of spermidine on guanine decomposition via photoinduced electron transfer in DNA.

Spermidine, a trivalent organic cation, induced DNA structural changes and suppressed guanine photooxidative decomposition via electron transfer through pyrene-modified DNA. On the other hand, adding higher concentrations of spermidine resulted in DNA condensation. The efficiency of guanine decomposition in condensed pyrene-modified DNA was promoted remarkably.

Detection of apoptosis and matrical degeneration within the intervertebral discs of rats due to passive cigarette smoking.

Although low-back pain is considered to be associated with cigarette smoking, the influence of cigarette smoking on the intervertebral discs (IVD) has not been confirmed. We established a rat model of passive cigarette smoking-induced IVD degeneration, and investigated the cytohistological changes in the IVD and the accompanying changes in gene expression. IVD from rats exposed to 8 weeks of passive cigarette smoking were stained with Elastica van Gieson, and exhibited marked destruction of the supportive structure of the reticular matrix in the nucleus pulposus (NP).

Drastic promotion of guanine oxidation via electron transfer in Ψ-type DNA.

We investigated the effects of a crowded environment on guanine oxidation in pyrene-modified oligonucleotides by photoinduced electron transfer. We observed drastic promotion of guanine oxidation in Ψ (psi; polymer- and salt-induced)-type DNA.

Caution for simple sequence repeat number variation in the mitochondrial DNA D-loop to determine cancer-specific variants.

The mitochondrial DNA (mtDNA) displacement loop (D-loop) is often altered in various cancer types, including with regard to simple sequence repeat number variation (SSRNV), which includes the C-tract and CA-tract. However, because of mitochondrial heteroplasmy and slippage errors by the Taq DNA polymerase used in polymerase chain reaction (PCR) analysis, it is difficult to precisely evaluate mtDNA D-loop SSRNV experimentally. In this study, to precisely determine cancer-specific variants in mtDNA SSRNV, various microscopic portions of cancerous tissues and normal control tissues were obtained from a patient with breast cancer, followed by laser-capture microdissection of formalin-fixed paraffin-embedded specimens.

Contradictory intrahepatic immune responses activated in high-load hepatitis C virus livers compared with low-load livers.

We found a HLA class II histocompatibility antigen gene, DQ alpha 1 chain (HLA-DQA1), that was expressed more than 9-fold higher in high-load hepatitis C virus (HCV) livers than low-load HCV livers using transcriptomics of chronic HCV-infected livers. To further investigate this finding, we examined which cells were positive for HLA-DQA1 and what liver immune responses were different between HCV-high and -low livers. HLA-DQA1-positive cells were significantly increased in the HCV-high group, and most positive cells were identified as non-parenchymal sinusoid cells and lymphocytic infiltrates in the portal area.

Particular gene upregulation and p53 heterogeneous expression in -mutated maxillary carcinoma.

It has been demonstrated that tumor protein p53 () mutation in maxillary squamous cell carcinoma, is more treatment-resistant compared with the carcinoma without mutation. However, the association between mutation and treatment resistance remains unclear. As a first step in understanding the biological differences between tumors with and without mutation, a comprehensive gene expression analysis of maxillary squamous cell carcinoma with or without mutation was performed.

Assessment of the quality of DNA from various formalin-fixed paraffin-embedded (FFPE) tissues and the use of this DNA for next-generation sequencing (NGS) with no artifactual mutation.

Formalin-fixed, paraffin-embedded (FFPE) tissues used for pathological diagnosis are valuable for studying cancer genomics. In particular, laser-capture microdissection of target cells determined by histopathology combined with FFPE tissue section immunohistochemistry (IHC) enables precise analysis by next-generation sequencing (NGS) of the genetic events occurring in cancer. The result is a new strategy for a pathological tool for cancer diagnosis: 'microgenomics'.

Transglutaminase 2 is upregulated in primary hepatocellular carcinoma with early recurrence as determined by proteomic profiles.

The mechanism of early recurrence of hepato-cellular carcinoma (HCC) is not well understood. To examine whether early intrahepatic metastasis of HCC can be determined by the reliable molecular characteristics of the primary HCC, we focused on early-stage tumors of primary and solitary HCC cases. Proteomic differences were investigated between two groups, 11 early (recurrence within 12 months) and 10 late (no recurrence within 48 months) HCC cases, using two-dimensional fluorescence difference gel electrophoresis.

Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions.

The Qubit fluorometer is a DNA quantification device based on the fluorescence intensity of fluorescent dye binding to double-stranded DNA (dsDNA). Qubit is generally considered useful for checking DNA quality before next-generation sequencing because it measures intact dsDNA. To examine the most accurate and suitable methods for quantifying DNA for quality assessment, we compared three quantification methods: NanoDrop, which measures UV absorbance; Qubit; and quantitative PCR (qPCR), which measures the abundance of a target gene.

Passive cigarette smoking changes the circadian rhythm of clock genes in rat intervertebral discs.

We aimed to elucidate the molecular changes in intervertebral discs (IVDs) caused by passive smoking. Rats were subjected to 8 weeks of passive smoking; thereafter, their lumbar vertebrae were harvested. The annulus fibrosus and cartilage endplate (AF/CEP) were harvested together, and the nucleus pulposus (NP) was isolated separately.

Transmembrane serine protease TMPRSS2 activates hepatitis C virus infection.

Unlabelled: The human liver reacts to hepatitis C virus (HCV) with a balanced response consisting of host anti- and proviral activities. To explore these subtle host responses, we used oligonucleotide microarrays to investigate the differential gene expression between two groups of liver samples with high and low HCV loads (>100-fold difference). We identified and validated 26 genes that were up-regulated in livers with high HCV loads, including transmembrane protease serine 2 (TMPRSS2).

CLEC4M-positive and CD81-negative Huh7 cells are not susceptible to JFH-1 HCVcc infection but mediate transinfection.

C-type lectin domain family 4, member M (CLEC4M), a trans-membrane protein specifically expressed in liver sinusoidal endothelial cells, is considered a candidate receptor for hepatotropism of hepatitis C virus (HCV). CLEC4M was previously reported to capture artificial HCVpp (pseudoparticle) and transmit it to hepatocytes (transinfection) via CLEC4M-positive cells. It is still not known whether CLEC4M acts as a receptor for HCVcc (cell-culture-produced HCV) transinfection or whether CLEC4M is an entry receptor for HCVcc.