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Phosphoproteomic analysis expands our understanding of cancer biology. However, the feasibility of phosphoproteomic analysis using endoscopically collected tumor samples, especially with regards to dynamic changes upon drug treatment, remains unknown in stage IV gastric cancer. Here, we conducted a phosphoproteomic analysis using paired endoscopic biopsy specimens of pre- and post-treatment tumors (Ts) and non-tumor adjacent tissues (NATs) obtained from 4 HER2-positive gastric cancer patients who received trastuzumab-based treatment and from pre-treatment Ts and NATs of 4 HER2-negative gastric cancer patients. Our analysis identified 14,622 class 1 phosphosites with 12,749 quantified phosphosites and revealed molecular changes by HER2 positivity and treatment. An inhibitory signature of the ErbB signaling was observed in the post-treatment HER2-positive T group compared with the pre-treatment HER2-positive T group. Phosphoproteomic profiles obtained by a case-by-case review using paired pre- and post-treatment HER2-positive T could be utilized to discover predictive or resistant biomarkers. Furthermore, these data nominated therapeutic kinase targets which were exclusively activated in the patient unresponded to the treatment. The present study suggests that a phosphoproteomic analysis of endoscopic biopsy specimens provides information on dynamic molecular changes which can individually characterize biologic features upon drug treatment and identify therapeutic targets in stage IV gastric cancer.

Understanding the interaction between intense terahertz (THz) electromagnetic fields and spin systems has been gaining importance in modern spintronics research as a unique pathway to realize ultrafast macroscopic magnetization control. In this work, we used intense THz pulses with pulse energies in the order of 10 mJ/pulse generated from the terahertz free electron laser (THz-FEL) to irradiate the ferromagnetic domains of ErFeO3 single crystal. It was found that the domain shape can be locally reconfigured by irradiating the THz − FEL pulses near the domain boundary. Observed domain reconfiguration mechanism can be phenomenologically understood by the combination of depinning effect and the entropic force due to local thermal gradient exerted by terahertz irradiation. Our finding opens up a new possibility of realizing thermal-spin effects at THz frequency ranges by using THz-FEL pulses.

With rapid advances occurring in terahertz (THz) radiation generation techniques, the interaction between matter and intense THz fields has become an important research topic. Among different types of THz radiation sources, the free electron laser (FEL) is a promising experimental tool that is expected to pave the way for new forms of material processing, control of phase transitions, and serve as a test bench for extreme operating conditions in high-speed small-size electrical and magnetic devices through the exploitation of strong THz electrical and magnetic fields without the presence of interband electronic excitation. In the current work, we irradiated Ge2Sb2Te5 phase change memory material with intense THz pulse trains from an FEL and observed THz-induced surface changes due to damage as a precursor to ablation and the formation of fine surface undulations whose spatial period is comparable to or slightly smaller than the wavelength of the excitation THz pulses in the material. The formation of undulations as well as the fact that no significant thermal effect was observed below the volume expansion threshold suggests that THz-induced effects mainly contributed to the observed changes. To the best of our knowledge, this is the first experimental observation of THz-induced undulations (so-called “LIPSS”), which are of potential importance for laser material processing.

Abnormality in cellular phosphorylation is closely related to oncogenesis. Thus, kinase inhibitors, especially tyrosine kinase inhibitors (TKIs), have been developed as anti-cancer drugs. Genomic analyses have been used in research on TKI sensitivity, but some types of TKI resistance have been unclassifiable by genomic data. Therefore, global proteomic analysis, especially phosphotyrosine (pY) proteomic analysis, could contribute to predict TKI sensitivity and overcome TKI-resistant cancer. In this study, we conducted deep phosphoproteomic analysis to select active kinase candidates in colorectal cancer intrinsically resistant to Cetuximab. The deep phosphoproteomic data were obtained by performing immobilized metal-ion affinity chromatography-based phosphoproteomic and highly sensitive pY proteomic analyses. Comparison between sensitive (LIM1215 and DLD1) and resistant cell lines (HCT116 and HT29) revealed active kinase candidates in the latter, most of which were identified by pY proteomic analysis. Remarkably, genomic mutations were not assigned in most of these kinases. Phosphorylation-based signaling network analysis of the active kinase candidates indicated that SRC-PRKCD cascade was constitutively activated in HCT116 cells. Treatment with an SRC inhibitor significantly inhibited proliferation of HCT116 cells. In summary, our results based on deep phosphoproteomic data led us to propose novel therapeutic targets against cetuximab resistance and showed the potential for anti-cancer therapy.

The hatcing enzyme gene (HE) encodes a protease that is indispensable for the hatching process and is conserved during vertebrate evolution. During teleostean evolution, it is known that HE experienced a drastic transfiguration of gene structure, namely, losing all of its introns. However, these facts are contradiction with each other, since intron-less genes typically lose their original promoter because of duplication via mature mRNA, called retrocopy. Here, using a comparative genomic assay, we showed that HEs have changed their genomic location several times, with the evolutionary timings of these translocations being identical to those of intron-loss. We further showed that HEs maintain the promoter sequence upstream of them after translocation. Therefore, teleostean HEs are unique genes which have changed intra- (exon-intron) and extra-genomic structure (genomic loci) several times, although their indispensability for the reproductive process of hatching implies that HE genes are translocated by retrocopy with their promoter sequence.

We demonstrate photoacoustic wave propagation with a plane wavefront in liquid water using a terahertz (THz) laser pulse. The THz light can effectively generate the photoacoustic wave in water because of strong absorption via a stretching vibration mode of the hydrogen bonding network. The excitation of a large-area water surface irradiated by loosely focused THz light produces a plane photoacoustic wave. This is in contrast with conventional methods using absorbers or plasma generation using near-infrared laser light. The photoacoustic wave generation and plane wave propagation are observed using a system with a THz free-electron laser and shadowgraph imaging. The plane photoacoustic wave is generated by incident THz light with a small radiant exposure of

Many attempts have been made to reproduce the three-dimensional (3D) cancer behavior. For that purpose, Matrigel, an extracellular matrix from Engelbreth-Holm-Swarm mouse sarcoma cell, is widely used in 3D cancer models such as scaffold-based spheroids and patient-derived organoids. However, severe ion suppression caused by contaminants from Matrigel hampers large-scale phosphoproteomics. In the present study, we successfully performed global phosphoproteomics from Matrigel-embedded spheroids and organoids. Using acetone precipitations of tryptic peptides, we identified more than 20,000 class 1 phosphosites from HCT116 spheroids. Bioinformatic analysis revealed that phosphoproteomic status are significantly affected by the method used for the recovery from the Matrigel, i.e., Dispase or Cell Recovery Solution. Furthermore, we observed the activation of several phosphosignalings only in spheroids and not in adherent cells which are coincident with previous study using 3D culture. Finally, we demonstrated that our protocol enabled us to identify more than 20,000 and nearly 3,000 class 1 phosphosites from 1.4 mg and 150 μg of patient-derived organoid, respectively. Additionally, we were able to quantify phosphosites with high reproducibility (r = 0.93 to 0.95). Our phosphoproteomics protocol is useful for analyzing the phosphosignalings of 3D cancer behavior and would be applied for precision medicine with patient-derived organoids.

As terahertz (THz) frequencies correspond to those of the intermolecular vibrational modes in a polymer, intense THz wave irradiation affects the macromolecular polymorph, which determines the polymer properties and functions. THz photon energy is quite low compared to the covalent bond energy; therefore, conformational changes can be induced “softly,” without damaging the chemical structures. Here, we irradiate a poly(3-hydroxybutylate) (PHB) / chloroform solution during solvent casting crystallization using a THz wave generated by a free electron laser (FEL). Morphological observation shows the formation of micrometer-sized crystals in response to the THz wave irradiation. Further, a 10−20% increase in crystallinity is observed through analysis of the infrared (IR) absorption spectra. The peak power density of the irradiating THz wave is 40 MW/cm2, which is significantly lower than the typical laser intensities used for material manipulation. We demonstrate for the first time that the THz wave effectively induces the intermolecular rearrangement of polymer macromolecules.