Background: Cell lines are commonly used in various kinds of biomedical research in the world. However, it remains uncertain whether genomic alterations existing in primary tumor tissues are represented in cell lines and whether cell lines carry cell line-specific genomic alterations. This study was performed to answer these questions. Methods: Array-based comparative genomic hybridization (CGH) was employed with 4030 bacterial artificial chromosomes (BACs) that cover the genome at 1.0 megabase resolution to analyze DNA copy number aberrations (DCNAs) in 35 primary breast tumors and 24 breast cancer cell lines. DCNAs were compared between these two groups. A tissue microdissection technique was applied to primary tumor tissues to reduce the contamination of samples by normal tissue components. Results: The average number of BAC clones with DCNAs was 1832 (45.3% of spotted clones) and 971 (24.9%) for cell lines and primary tumor tissues, respectively. Gains of 1q and 8q and losses of 8p, 11q, 16q and 17p were detected in >50% of primary cancer tissues. These aberrations were also frequently detected in cell lines. In addition to these alterations, the cell lines showed recurrent genomic alterations including gains of 5p14-15, 20q11 and 20q13 and losses of 4p13-p16, 18q12, 18q21, Xq21.1 and Xq26-q28 that were barely detected in tumor tissue specimens. These are considered to be cell line-specific DCNAs. The frequency of the HER2 amplification was high in both cell lines and tumor tissues, but it was statistically different between cell lines and primary tumors (P = 0.012); 41.3 ± 29.9% for the cell lines and 15.9 ± 18.6% for the tissue specimens. Conclusions: Established cell lines carry cell lines-specific DCNAs together with recurrent aberrations detected in primary tumor tissues. It must therefore be emphasized that cell lines do not always represent the genotypes of parental tumor tissues.

Temporal coherence is one of the most fundamental characteristics of light, connecting to spectral information through the Fourier transform relationship between time and frequency. Interferometers with a variable path-length difference (PLD) between the two branches have widely been employed to characterize temporal coherence properties for broad spectral regimes. Hard X-ray interferometers reported previously, however, have strict limitations in their operational photon energies, due to the specific optical layouts utilized to satisfy the stringent requirement for extreme stability of the PLD at sub-ångström scales. The work presented here characterizes the temporal coherence of hard X-ray free-electron laser (XFEL) pulses by capturing single-shot interferograms. Since the stability requirement is drastically relieved with this approach, it was possible to build a versatile hard X-ray interferometer composed of six separate optical elements to cover a wide photon energy range from 6.5 to 11.5 keV while providing a large variable delay time of up to 47 ps at 10 keV. A high visibility of up to 0.55 was observed at a photon energy of 10 keV. The visibility measurement as a function of time delay reveals a mean coherence time of 5.9 ± 0.7 fs, which agrees with that expected from the single-shot spectral information. This is the first result of characterizing the temporal coherence of XFEL pulses in the hard X-ray regime and is an important milestone towards ultra-high energy resolutions at micro-electronvolt levels in time-domain X-ray spectroscopy, which will open up new opportunities for revealing dynamic properties in diverse systems on timescales from femtoseconds to nanoseconds, associated with fluctuations from ångström to nanometre spatial scales.

X-ray optics were implemented for advanced ultrafast X-ray experiments with different techniques at the hard X-ray beamline BL3 of SPring-8 Ångstrom Compact free-electron LAser. A double channel-cut crystal monochromator (DCCM) and compound refractive lenses (CRLs) were installed to tailor the beam conditions. These X-ray optics can work simultaneously with an arrival-timing monitor that compensates for timing jitter and drift. Inner-walls of channel-cut crystals (CCs) in the DCCM were processed by plasma chemical vaporization machining to remove crystallographic damage. Four-bounced reflection profiles of the CCs were investigated and excellent diffraction qualities were achieved. The use of CRLs enabled two-dimensional X-ray focusing with a spot size of ∼1.5 µm × 1.5 µm full width at half-maximum, while keeping reasonable throughputs for a wide photon energy range of 5−15 keV.

The performance of a hard X-ray split-and-delay optical (SDO) system with a wavefront division scheme was investigated at the hard X-ray free-electron laser facility SACLA. For the wavefront division, beam splitters made of edge-polished perfect Si(220) crystals were employed. We characterized the beam properties of the SDO system, and investigated its capabilities for beam manipulation and diagnostics. First, it was confirmed that shot-to-shot non-invasive diagnostics of pulse energies for both branches in the SDO system was feasible. Second, nearly ideal and identical focal profiles for both branches were obtained with a spot size of ∼1.5 µm in full width at half-maximum. Third, a spatial overlap of the two focused beams with a sub-µm accuracy was achieved by fine tuning of the SDO system. Finally, a reliable tunability of the delay time between two pulses was confirmed. The time interval was measured with an X-ray streak camera by changing the path length of the variable-delay branch. Errors from the fitted line were evaluated to be as small as ±0.4 ps over a time range of 60 ps.

As a means to achieving highly sensitive bioluminescence imaging of deep tissues utilizing the firefly luciferin-luciferase (L-L) reaction, we previously reported a luciferin analogue, AkaLumine, which exhibits high cell-permeability and emits near-infrared (NIR) light with high tissue-penetration by the L-L reaction. However, while AkaLumine enables us to observe targets in deep tissues, its poor solubility in aqueous media limits its utility for in vivo imaging. Herein, to address this issue, we have synthesized three AkaLumine derivatives with N-heterocyclic aromatic rings as new red luciferin analogues that have substantially higher solubility than that of AkaLumine in phosphate buffered saline solution. One of the derivatives (herein termed seMpai) exhibits an emission maximum at 675 nm upon L-L reaction with Photinus pyralis luciferase and presents an activity in mouse-tissue imaging similar to that of AkaLumine. It is hoped that seMpai will extend the application of high-sensitivity NIR bioluminescence imaging in a wide range of biomedical research fields.

Purpose.: The prognosis of patients with esophageal carcinoma is poor. To identify genomic alterations associated with poor patient prognosis, we analyzed whole DNA copy number profiles of esophageal squamous carcinomas (ESCs) using array-based comparative genomic hybridization (aCGH). Materials and Methods.: Twenty-one operated and two biopsied cases of esophageal squamous cancer were examined for study. Each sample was laser microdissected to obtain pure cancer cell populations. The extracted DNA was analyzed using aCGH. Results.: One of the most representative alterations was a previously reported amplification at 11q13.3. In addition, some novel alterations, such as deletion of 16p13.3, were identified. Of the 19 patients who were reassessed more than 5 years after the operation, nine were still living and 10 had died from disease recurrence. When aCGH profiles from the surviving group and the deceased group were compared, significant differences were recognized in 68 of 4,030 bacterial artificial chromosome (BAC) clones. Almost half of these clones were present at nine limiting regions in 4q, 13q, 20q, and Xq. For 22 of these 68 BAC clones, there also was a significant difference in the Kaplan-Meier survival curve, using the log-rank test, when comparing patients who had an alteration in a particular clone with those who did not. Conclusions.: aCGH study of esophageal squamous cancer clearly identified BAC clones that are related to the prognosis of patients. These clones give us the opportunity to determine specific genes that are associated with cancer progression.