Satoshi Ito

Aberrant PD-L1 expression through 3′-UTR disruption in multiple cancers

Successful treatment of many patients with advanced cancer using antibodies against programmed cell death 1 (PD-1; also known as PDCD1) and its ligand (PD-L1; also known as CD274) has highlighted the critical importance of PD-1/PD-L1-mediated immune escape in cancer development. However, the genetic basis for the immune escape has not been fully elucidated, with the exception of elevated PD-L1 expression by gene amplification and utilization of an ectopic promoter by translocation, as reported in Hodgkin and other B-cell lymphomas, as well as stomach adenocarcinoma. Here we show a unique genetic mechanism of immune escape caused by structural variations (SVs) commonly disrupting the 3 region of the PD-L1 gene. Widely affecting multiple common human cancer types, including adult T-cell leukaemia/lymphoma (27%), diffuse large B-cell lymphoma (8%), and stomach adenocarcinoma (2%), these SVs invariably lead to a marked elevation of aberrant PD-L1 transcripts that are stabilized by truncation of the 3-untranslated region (UTR). Disruption of the Pd-l1 3-UTR in mice enables immune evasion of EG7-OVA tumour cells with elevated Pd-l1 expression in vivo, which is effectively inhibited by Pd-1/Pd-l1 blockade, supporting the role of relevant SVs in clonal selection through immune evasion. Our findings not only unmask a novel regulatory mechanism of PD-L1 expression, but also suggest that PD-L1 3-UTR disruption could serve as a genetic marker to identify cancers that actively evade anti-tumour immunity through PD-L1 overexpression.

Use of telemedicine in periodic screening of diabetic retinopathy.

Telemedicine was used for taking ocular fundus images of diabetic patients, which were subsequently sent by electronic mail to experienced ophthalmologists at a university hospital. The ophthalmologists provided reports on the patients to the internists. The objective of the study was to evaluate the effectiveness of this telemedicine system. A total of 279 diabetic patients were admitted to the Third Department of Internal Medicine of Yokohama City University Hospital, School of Medicine, for blood sugar control or for education on lifestyle between April, 1999, and October, 2000. The subjects did not have eye disease nor diabetic retinopathy when evaluated by an ophthalmologist (at either Yokohama City University Hospital or other facility) within 3 months before enrollment in the study. After dilation of the pupil, fundus images were taken of each eye from four angles using a nonmydriatic fundus camera. The images were transmitted by electronic mail to the Division of Ophthalmology of Tokyo University Branch Hospital along with other patient information. The ophthalmologists there evaluated the images on the screen according to Fukudas classification of diabetic retinopathy. They sent ophthalmologic reports to the internists at the Third Department of Internal Medicine of Yokohama City University Hospital, School of Medicine, and recommended whether the patient should be seen by his/her regular ophthalmologist earlier than the next scheduled visit. Fundus images were obtained at the time of admission, at 1, 3, and 6 months after discharge, and at every 6 months thereafter. Out of the images of 1170 eyes obtained at various time points from the 279 patients, 1076 (92.0%) were successfully evaluated by the ophthalmologists at the University of Tokyo, while 60 (5.1%) could not be evaluated and there was a communication problem for the images of 34 eyes. The ophthalmologists determined that 5 eyes of 3 patients required further evaluation by the patients regular ophthalmologist based on the images transferred by telemedicine. No patient dropped out during the study period.

A single acetylation of 18 S rRNA is essential for biogenesis of the small ribosomal subunit in Saccharomyces cerevisiae.

Background: Post-transcriptional modifications of rRNAs play important roles in biogenesis and function of ribosome. Results: Identification of an essential RNA acetyltransferase Rra1p responsible for forming N4-acetylcytidine at position 1773 in 18 S rRNA. Conclusion: Rra1p and ac4C1773 are required for pre-18 S rRNA processing. Significance: Rra1p modulates 40 S subunit biogenesis through a single acetylation of 18 S rRNA by sensing nuclear acetyl-CoA concentration. Biogenesis of eukaryotic ribosome is a complex event involving a number of non-ribosomal factors. During assembly of the ribosome, rRNAs are post-transcriptionally modified by 2′-O-methylation, pseudouridylation, and several base-specific modifications, which are collectively involved in fine-tuning translational fidelity and/or modulating ribosome assembly. By mass-spectrometric analysis, we demonstrated that N4-acetylcytidine (ac4C) is present at position 1773 in the 18 S rRNA of Saccharomyces cerevisiae. In addition, we found an essential gene, KRE33 (human homolog, NAT10), that we renamed RRA1 (ribosomal RNA cytidine acetyltransferase 1) encoding an RNA acetyltransferase responsible for ac4C1773 formation. Using recombinant Rra1p, we could successfully reconstitute ac4C1773 in a model rRNA fragment in the presence of both acetyl-CoA and ATP as substrates. Upon depletion of Rra1p, the 23 S precursor of 18 S rRNA was accumulated significantly, which resulted in complete loss of 18 S rRNA and small ribosomal subunit (40 S), suggesting that ac4C1773 formation catalyzed by Rra1p plays a critical role in processing of the 23 S precursor to yield 18 S rRNA. When nuclear acetyl-CoA was depleted by inactivation of acetyl-CoA synthetase 2 (ACS2), we observed temporal accumulation of the 23 S precursor, indicating that Rra1p modulates biogenesis of 40 S subunit by sensing nuclear acetyl-CoA concentration.

Human NAT10 is an ATP-dependent RNA acetyltransferase responsible for N4-acetylcytidine formation in 18 S ribosomal RNA (rRNA).

Background: Post-transcriptional modifications of rRNAs play important roles in biogenesis and function of ribosome. Results: NAT10 is an ATP-dependent RNA acetyltransferase responsible for N4-acetylcytidine formation of 18 S rRNA. Conclusion: NAT10 and ac4C1842 are required for pre-18 S rRNA processing. Significance: 40 S subunit formation is regulated by a single acetylation of 18 S rRNA, implying a regulatory mechanism for ribosome biogenesis by sensing the cellular energy budget. Human N-acetyltransferase 10 (NAT10) is known to be a lysine acetyltransferase that targets microtubules and histones and plays an important role in cell division. NAT10 is highly expressed in malignant tumors, and is also a promising target for therapies against laminopathies and premature aging. Here we report that NAT10 is an ATP-dependent RNA acetyltransferase responsible for formation of N4-acetylcytidine (ac4C) at position 1842 in the terminal helix of mammalian 18 S rRNA. RNAi-mediated knockdown of NAT10 resulted in growth retardation of human cells, and this was accompanied by high-level accumulation of the 30 S precursor of 18 S rRNA, suggesting that ac4C1842 formation catalyzed by NAT10 is involved in rRNA processing and ribosome biogenesis.

Clinical factors associated with the symptoms of constipation in patients with diabetes mellitus: a multicenter study

Changes in treatment protocols for patients with diabetes mellitus (DM) may influence the functions of the digestive tract. This study examined possible clinical factors associated with the symptoms of constipation in patients with DM.

D3M: detection of differential distributions of methylation levels

MOTIVATIONnDNA methylation is an important epigenetic modification related to a variety of diseases including cancers. We focus on the methylation data from Illuminas Infinium HumanMethylation450 BeadChip. One of the key issues of methylation analysis is to detect the differential methylation sites between case and control groups. Previous approaches describe data with simple summary statistics or kernel function, and then use statistical tests to determine the difference. However, a summary statistics-based approach cannot capture complicated underlying structure, and a kernel function-based approach lacks interpretability of results.nnnRESULTSnWe propose a novel method D(3)M, for detection of differential distribution of methylation, based on distribution-valued data. Our method can detect the differences in high-order moments, such as shapes of underlying distributions in methylation profiles, based on the Wasserstein metric. We test the significance of the difference between case and control groups and provide an interpretable summary of the results. The simulation results show that the proposed method achieves promising accuracy and shows favorable results compared with previous methods. Glioblastoma multiforme and lower grade glioma data from The Cancer Genome Atlas show that our method supports recent biological advances and suggests new insights.nnnAVAILABILITY AND IMPLEMENTATIONnR implemented code is freely available from https://github.com/ymatts/D3M/ CONTACT: ymatsui@med.nagoya-u.ac.jp or shimamura@med.nagoya-u.ac.jpnnnSUPPLEMENTARY INFORMATIONnSupplementary data are available at Bioinformatics online.

Cancer evolution simulation identifies possible principles underlying intratumor heterogeneity

Cancer arises from accumulation of somatic mutations and accompanying evolutionary selection for growth advantage. During the evolutionary process, an ancestor clone branches into multiple clones, yielding intratumor heterogeneity. However, principles underlying intratumor heterogeneity have been poorly understood. Here, to explore the principles, we built a cellular automaton model, termed the BEP model, which can reproduce the branching cancer evolution in silico. We then extensively searched for conditions leading to high intratumor heterogeneity by performing simulations with various parameter settings on a supercomputer. Our result suggests that multiple driver genes of moderate strength can shape subclonal structures by positive natural selection. Moreover, we found that high mutation rate and a stem cell hierarchy can contribute to extremely high intratumor heterogeneity, which is characterized by fractal patterns, through neutral evolution. Collectively, This study identified the possible principles underlying intratumor heterogeneity, which provide novel insights into the origin of cancer robustness and evolvability.

Detection and Recognition of Moving Objects by Using Motion Invariants

Motion invariant features, which are called either absolute or relative invariant linear features, are useful for detection and recognition of moving objects from image streams. We conducted simple experiments using these invariant features. The first experiment tested our method for moving object recognition with a fixed camera using absolute invariant linear features. In the second experiment, another method was used to detect moving objects with a moving camera using both relative and absolute invariant linear features. The results of these experiments confirmed the effectiveness of the proposed methods

Shape Optimization Using an Adjoint Variable Method in ITBL Grid Environment

To decrease the fluid drag force on the surface of a specified object subjected to an unsteady flow, under a constant volume condition, the adjoint variable method is formulated by using FEM. Based on the Lagrange multiplier method (a conditional variational principle), this method consists of the state equation, the adjoint equation and the sensitivity equation. To solve the equations effectively using the steepest descent method, a parallel algorithm that finds the Armijos line-search step size is constructed. The shape optimization code for solving a large scale 3D problem using a parallel algorithm was implemented on ITBL using the HPC-MW library. Results show that, by using shape optimization, the fluid drag force on the object can be reduced by about 17.5%. (authors)

Node-based parallel computing of three-dimensional incompressible flows using the free mesh method

The present report discusses node-based parallel computing of three-dimensional incompressible flows using a node-based finite element method named the free mesh method (FMM). The FMM has two advantages over the finite element method. One advantage of the FMM is that this method is quite suitable for massively parallel computing because all computational procedures, from the mesh generation to the solution of a system of equations, can be performed in parallel in terms of nodes. Another advantage of the FMM is that finite element mesh is not required as input data so that the analyst need only prepare data concerning the nodes in the analysis domain. The present method is implemented on distributed memory systems, such as a parallel supercomputer Hitachi SR8000. The performance of the proposed method is demonstrated by computing a lid-driven cavity problem. A numerical example is used to show that the FMM can achieve high parallel performance by a simple distribution operation of computational loads among multiprocessors.