Best practices for multimodal clinical data management and integration: An atopic dermatitis research case

BACKGROUND

In clinical research on multifactorial diseases such as atopic dermatitis, data-driven medical research has become more widely used as means to clarify diverse pathological conditions and to realize precision medicine. However, modern clinical data, characterized as large-scale, multimodal, and multi-center, causes difficulties in data integration and management, which limits productivity in clinical data science.

METHODS

We designed a generic data management flow to collect, cleanse, and integrate data to handle different types of data generated at multiple institutions by 10 types of clinical studies. We developed MeDIA (Medical Data Integration Assistant), a software to browse the data in an integrated manner and extract subsets for analysis.

RESULTS

MeDIA integrates and visualizes data and information on research participants obtained from multiple studies. It then provides a sophisticated interface that supports data management and helps data scientists retrieve the data sets they need. Furthermore, the system promotes the use of unified terms such as identifiers or sampling dates to reduce the cost of pre-processing by data analysts. We also propose best practices in clinical data management flow, which we learned from the development and implementation of MeDIA.

CONCLUSIONS

The MeDIA system solves the problem of multimodal clinical data integration, from complex text data such as medical records to big data such as omics data from a large number of patients. The system and the proposed best practices can be applied not only to allergic diseases but also to other diseases to promote data-driven medical research.

Synthesis of causal and surrogate models by non-equilibrium thermodynamics in biological systems

We developed a model to represent the time evolution phenomena of life through physics constraints. To do this, we took into account that living organisms are open systems that exchange messages through intracellular communication, intercellular communication and sensory systems, and introduced the concept of a message force field. As a result, we showed that the maximum entropy generation principle is valid in time evolution. Then, in order to explain life phenomena based on this principle, we modelled the living system as a nonlinear oscillator coupled by a message and derived the governing equations. The governing equations consist of two laws: one states that the systems are synchronized when the variation of the natural frequencies between them is small or the coupling strength through the message is sufficiently large, and the other states that the synchronization is broken by the proliferation of biological systems. Next, to simulate the phenomena using data obtained from observations of the temporal evolution of life, we developed an inference model that combines physics constraints and a discrete surrogate model using category theory, and simulated the phenomenon of early embryogenesis using this inference model. The results show that symmetry creation and breaking based on message force fields can be widely used to model life phenomena.

Multifaceted analysis of cross-tissue transcriptomes reveals phenotype-endotype associations in atopic dermatitis

Atopic dermatitis (AD) is a skin disease that is heterogeneous both in terms of clinical manifestations and molecular profiles. It is increasingly recognized that AD is a systemic rather than a local disease and should be assessed in the context of whole-body pathophysiology. Here we show, via integrated RNA-sequencing of skin tissue and peripheral blood mononuclear cell (PBMC) samples along with clinical data from 115 AD patients and 14 matched healthy controls, that specific clinical presentations associate with matching differential molecular signatures. We establish a regression model based on transcriptome modules identified in weighted gene co-expression network analysis to extract molecular features associated with detailed clinical phenotypes of AD. The two main, qualitatively differential skin manifestations of AD, erythema and papulation are distinguished by differential immunological signatures. We further apply the regression model to a longitudinal dataset of 30 AD patients for personalized monitoring, highlighting patient heterogeneity in disease trajectories. The longitudinal features of blood tests and PBMC transcriptome modules identify three patient clusters which are aligned with clinical severity and reflect treatment history. Our approach thus serves as a framework for effective clinical investigation to gain a holistic view on the pathophysiology of complex human diseases.

Combined plasma metabolomic and transcriptomic analysis identify histidine as a biomarker and potential contributor in SLE pathogenesis

OBJECTIVES

To investigate metabolite alterations in the plasma of SLE patients to identify novel biomarkers and provide insight into SLE pathogenesis.

METHODS

Patients with SLE (n = 41, discovery cohort and n = 37, replication cohort), healthy controls (n = 30 and n = 29) and patients with RA (n = 19, disease control) were recruited. Metabolic profiles of the plasma samples were analysed using liquid chromatography-time-of-flight mass spectrometry and capillary electrophoresis-time-of-flight mass spectrometry. Transcriptome data was analysed using RNA-sequencing for 18 immune cell subsets. The importance of histidine (His) in plasmablast differentiation was investigated by using mouse splenic B cells.

RESULTS

We demonstrate that a specific amino acid combination including His can effectively distinguish between SLE patients and healthy controls. Random forest and partial least squares-discriminant analysis identified His as an effective classifier for SLE patients. A decrease in His plasma levels correlated with damage accrual independent of prednisolone dosage and type I IFN signature. The oxidative phosphorylation signature in plasmablasts negatively correlated with His levels. We also showed that plasmablast differentiation induced by innate immune signals was dependent on His.

CONCLUSIONS

Plasma His levels are a potential biomarker for SLE patients and are associated with damage accrual. Our data suggest the importance of His as a pathogenic metabolite in SLE pathogenesis.

THU0225 INTEGRATIVE PLASMA METABOLOME AND TRANSCRIPTOME ANALYSIS REVEALED THE IMPORTANCE OF HISTIDINE HOMEOSTASIS IN SLE PATHOGENESIS WITH POTENTIAL FOR IMPROVED SLE PATIENTS STRATIFICATION

Background:

Recently, immunometabolism has gathered attention of many immunologists. It has been widely recognized that metabolic reprogramming in each immune cell brings different effects on different cells and is important for regulating their functions. Along with the progress of statistical genetics, serum metabolites were shown to be under genetic regulations1). Metabolic changes are now considered not only to be mere phenotypes of cells but also to be key factors for controlling immune cell differentiation, proliferation and function through regulating gene expressions eventually. Although genome-wide association studies have brought deep insights into SLE pathogenesis, the precise pathway from genome to metabolome has been largely unknown, and vice versa.

Objectives:

The aim of this study is to investigate metabolomic regulation in SLE in relation to gene expressions by integrating plasma metabolome data and transcriptome data.

Methods:

We collected plasma samples from patients with SLE (n=57) who met the 1997 American College of Rheumatology criteria for SLE. Gender- and age-matched healthy controls (HCs) (n=56) were recruited. Metabolic profiles focusing on 39 amino acids were analyzed with liquid chromatography (LC)-mass spectrometry. Transcriptome data of SLE patients were obtained from our RNA-sequencing data of each immune cell subset (total 19 subsets). Whole-genome sequencing was also performed.

Results:

Our previous experiment showed that about 160 peaks were detected from comprehensive LC-TOFMS and amino acids were useful for distinguishing SLE patients from HCs. Both partial least squares discriminant analysis (PLS-DA) and random forest, a machine learning algorithm, revealed the importance of histidine (His), one of the essential amino acids, to classify SLE patients from HCs, whose plasma level was lower in SLE patients. In addition, inverse correlation between His level and titer of ds-DNA as well as damage index (SDI) was detected. His level was correlated neither with PSL dosage nor with type I interferon (IFN) signature. Receiver operating characteristic (ROC) analysis showed the best predictability for SLE with the combination of specific amino acids including His. Our transcriptome analysis has revealed the significance of oxidative phosphorylation (OXPHOS) in B cells for SLE pathogenesis. Interestingly, OXPHOS signature was inversely correlated with His level in SLE B cells.

Conclusion:

His may be an important factor for SLE pathogenesis especially in B cells independently from IFN signal. SLC15A4, a transporter of His on lysosome, is one of the SLE GWAS SNPs and has been reported to play an important role in IFN production in B cells through regulation of TLR7/9 activation 2). We also identified that SLE patients with risk allele of SLC15A4 had tendency to show higher plasma His level, indicating His homeostasis could become a novel treatment target for SLE. Moreover, the inverse correlation of His level to SDI as well as OXPHOS signature suggests that His might play a key role for promoting organ damages in SLE.

References:

[1]Nat Genet.2017;49:568. 2)Immunity. 2014;41:375. 3)Semin Arthritis Rheum.2019;48:1142

Disclosure of Interests: :

Yukiko Iwasaki: None declared, Yusuke Takeshima: None declared, Masahiro Nakano: None declared, Mineto Ota: None declared, Yasuo Nagafuchi: None declared, Akari Suzuki: None declared, Yuta Kochi: None declared, Tomohisa Okamura: None declared, Takaho Endo: None declared, Ichiro Miki: None declared, Kazuhiro Sakurada: None declared, Kazuhiko Yamamoto Grant/research support from: Astellas, BMS, MitsubishiTanabe, Pfizer, Ayumi, Takeda, Chugai, Eisai, Taisho Toyama, UCB, and ImmunoFuture, Keishi Fujio Grant/research support from: Astellas, BMS, MitsubishiTanabe, Pfizer, Ayumi, Takeda, Chugai, Eisai, Taisho Toyama, Eli Lilly, Sanofi, and UCB

Development and validation of a deep-learning model for scoring of radiographic finger joint destruction in rheumatoid arthritis

Objective

The purpose of this research was to develop a deep-learning model to assess radiographic finger joint destruction in RA.

Methods

The model comprises two steps: a joint-detection step and a joint-evaluation step. Among 216 radiographs of 108 patients with RA, 186 radiographs were assigned to the training/validation dataset and 30 to the test dataset. In the training/validation dataset, images of PIP joints, the IP joint of the thumb or MCP joints were manually clipped and scored for joint space narrowing (JSN) and bone erosion by clinicians, and then these images were augmented. As a result, 11 160 images were used to train and validate a deep convolutional neural network for joint evaluation. Three thousand seven hundred and twenty selected images were used to train machine learning for joint detection. These steps were combined as the assessment model for radiographic finger joint destruction. Performance of the model was examined using the test dataset, which was not included in the training/validation process, by comparing the scores assigned by the model and clinicians.

Results

The model detected PIP joints, the IP joint of the thumb and MCP joints with a sensitivity of 95.3% and assigned scores for JSN and erosion. Accuracy (percentage of exact agreement) reached 49.3–65.4% for JSN and 70.6–74.1% for erosion. The correlation coefficient between scores by the model and clinicians per image was 0.72–0.88 for JSN and 0.54–0.75 for erosion.

Conclusion

Image processing with the trained convolutional neural network model is promising to assess radiographs in RA.

Identification of NR5A1 (SF-1/AD4BP) gene expression modulators by large-scale gain and loss of function studies

Nuclear receptor subfamily 5, group A, member 1 (NR5A1 previously known as SF-1/AD4BP) is a transcription factor involved in the development of adrenal/gonadal tissues and steroidogenic lineage cell differentiation in adult somatic stem cells. To understand the cellular signaling network that regulates NR5A1 gene expression, loss of function screening with an siRNA kinome library, and gain of function screening with an addressable full-length cDNA library representing one quarter of the human genome was carried out. The NR5A1 gene expression was activated in mesenchymal stem cells by siRNA directed against protein kinase C (PKC)-delta, erb-B3, RhoGAP (ARHGAP26), and hexokinase 2, none of which were previously known to be involved in the NR5A1 gene expression. Among these, we identified crosstalk between erb-B3 and PKC-delta signaling cascades. In addition, the gain of function studies indicated that sex-determining region Y (SRY)-box 15 (SOX15), TEA domain family member 4, KIAA1257 (a gene of unknown function), ADAM metallopeptidase with thrombospondin type 1 motif 6, Josephin domain containing 1, centromere protein, TATA box-binding protein-associated factor 5-like RNA polymerase, and inducible T-cell co-stimulator activate NR5A1 gene expression. These results provide new insights into the molecular mechanisms of NR5A1 gene expression.

Heterogeneity of pluripotent marker gene expression in colonies generated in human iPS cell induction culture

Induction of pluripotent stem cells from human fibroblasts has been achieved by the ectopic expression of two different sets of four genes. However, the mechanism of the pluripotent stem cell induction has not been elucidated. Here we identified a marked heterogeneity in colonies generated by the four-gene (Oct3/4, Sox2, c-Myc, and Klf4) transduction method in human neonatal skin-derived cells. The four-gene transduction gave a higher probability of induction for archetypal pluripotent stem cell marker genes (Nanog, TDGF, and Dnmt3b) than for marker genes that are less specific for pluripotent stem cells (CYP26A1 and TERT) in primary induction culture. This tendency may reflect the molecular mechanism underlying the induction of human skin-derived cells into pluripotent stem cells. Among the colonies induced by the four-gene transduction, small cells with a high nucleus-to-cytoplasm ratio could be established by repeated cloning. Subsequently established cell lines were similar to human embryonic stem cells as well as human induced pluripotent stem (iPS) cells derived from adult tissue in morphology, gene expression, long-term self-renewal ability, and teratoma formation. Genome-wide single-nucleotide polymorphism array analysis of the human iPS cell line indicates that the induction process did not induce DNA mutation.

Surgical resection of tumors located in subcortex of language area

OBJECT

Although functional mapping facilitates the planning of surgery in and around eloquent areas, the resection of tumors adjacent to language areas remains challenging. In this report, we took notice that the language areas (Broca's and Wernicke's) present at the perisylvian fissure. We posit that if there is non-essential language area on the inner surface of the Sylvian fissure, safe tumor resection may be possible even if the tumor is located under the language cortex.

METHODS

The study population consisted of 5 patients with intrinsic brain tumors (frontal glioma, n = 3; temporal cavernous angioma, n = 1; primary malignant central nervous system lymphoma, n = 1) located in the perisylvian subcortex, in the language-dominant hemisphere. All patients underwent awake surgery and we performed intra-operative bipolar cortical functional language mapping. When the tumor was located under the language area, the Sylvian fissure was opened and the inner surface of the opercular cortex was exposed with the patient asleep, and additional functional mapping of that cortex was performed. This enabled us to remove the tumor from the non-functioning cortex. In our series, 4 of 5 patients had not language function on the inner surface of the operculum. Only one patient, a 52-year-old man with frontal glioblastoma (Case 3) had language function on the inner surface of the frontal operculum.

CONCLUSION

We suggest that even perisylvian tumors located in the subcortex of the language area may be resectable via the nonfunctioning intrasylvian cortex by a transopercular approach without resultant language dysfunction.

Single-cell-derived mesenchymal stem cells overexpressing Csx/Nkx2.5 and GATA4 undergo the stochastic cardiomyogenic fate and behave like transient amplifying cells

Bone marrow-derived stromal cells can give rise to cardiomyocytes as well as adipocytes, osteocytes, and chondrocytes in vitro. The existence of mesenchymal stem cells has been proposed, but it remains unclear if a single-cell-derived stem cell stochastically commits toward a cardiac lineage. By single-cell marking, we performed a follow-up study of individual cells during the differentiation of 9-15c mesenchymal stromal cells derived from bone marrow cells. Three types of cells, i.e., cardiac myoblasts, cardiac progenitors and multipotent stem cells were differentiated from a single cell, implying that cardiomyocytes are generated stochastically from a single-cell-derived stem cell. We also demonstrated that overexpression of Csx/Nkx2.5 and GATA4, precardiac mesodermal transcription factors, enhanced cardiomyogenic differentiation of 9-15c cells, and the frequency of cardiomyogenic differentiation was increased by co-culturing with fetal cardiomyocytes. Single-cell-derived mesenchymal stem cells overexpressing Csx/Nkx2.5 and GATA4 behaved like cardiac transient amplifying cells, and still retained their plasticity in vivo.

Age-related changes in haematology and serum chemistry of Weiser-Maples guineapigs (Cavia porcellus)

Age-related changes in haematology and serum chemistry values were examined in male and female Weiser-Maples guineapigs (Cavia porcellus). Haematological changes that significantly (P<0.01) correlated with ageing were increased white blood cell and neutrophil counts in both sexes, decreased lymphocyte counts in both sexes, decreased reticulocyte and platelet counts in males, and decreased basophil counts in females. For serum chemistry, increases in total protein, triglycerides, blood urea nitrogen and creatinine were seen in both sexes, along with increases in total cholesterol in males and sodium in females. Decreased alkaline phosphatase in both sexes and decreased chloride in males were significantly (P<0.01) associated with age. These age-related changes are compared with the published literature.

Multimodal strategy for managing meningiomas in the elderly

BACKGROUND

The incidence of brain tumors in elderly patients is increasing. It has become possible to treat meningiomas in the elderly by several modalities. We developed a successful multimodal strategy to treat these patients.

METHODS

We registered 35 patients with meningiomas. Symptomatic meningiomas were treated surgically at the time of diagnosis (n=19). Of the 16 asymptomatic meningiomas, 5 were removed at the time of diagnosis. The other asymptomatic meningiomas (n=11) were treated conservatively and when the tumors increased in size, surgical treatment was considered. "Operated" patients with residual or recurrent tumors underwent radiosurgery with a gamma knife.

FINDINGS

Surgical mortality and morbidity were 4% and 16%, respectively. Of the 25 "operated" patients, 21 (84.0%) had a good Karnofsky scale (> or =80%) at discharge. In all but two of the 11 patients with asymptomatic, conservatively treated meningiomas, the tumors did not increase during the follow-up period. Gamma knife radiosurgery, performed to treat 3 residual and 1 recurrent tumor, resulted in very good tumor control and none of the tumors increased after gamma knife surgery.

CONCLUSIONS

Meningiomas in elderly patients require a multimodal approach. Our strategy, which includes surgery, radiosurgery, and conservative treatment, resulted in good tumor control and made it possible for patients to pursue their activities of daily life.

Physical and functional interaction between BH3-only protein Hrk and mitochondrial pore-forming protein p32

Bcl-2 homology domain (BH) 3-only proteins of the proapoptotic Bcl-2 subfamily play a key role as initiators of mitochondria-dependent apoptosis. To date, at least 10 mammalian BH3-only proteins have been identified, and it is now being realized that they have different roles and mechanisms of regulation in the transduction of apoptotic signals to mitochondria. Hrk/DP5 is one of the mammalian BH3-only proteins implicated in a variety of physiological and pathological apoptosis, yet the molecular mechanism involved in Hrk-mediated apoptosis remains poorly understood. In an attempt to identify cellular proteins participating in Hrk-mediated apoptosis, we have conducted yeast two-hybrid screening for Hrk-interacting proteins and isolated p32, a mitochondrial protein that has been shown to form a channel consisting of its homotrimer. In vitro binding, co-immunoprecipitation, as well as immunocytochemical analyses verified specific interaction and colocalization of Hrk and p32, both of which depended on the presence of the highly conserved C-terminal region of p32. Importantly, Hrk-induced apoptosis was suppressed by the expression of p32 mutants lacking the N-terminal mitochondrial signal sequence (p32(74-282)) and the conserved C-terminal region (p32 (1-221)), which are expected to inhibit binding of Hrk competitively to the endogenous p32 protein and to disrupt the channel function of p32, respectively. Furthermore, small interfering RNA-mediated knockdown of p32 conferred protection against Hrk-induced apoptosis. Altogether, these results suggest that p32 may be a key molecule that links Hrk to mitochondria and is critically involved in the regulation of Hrk-mediated apoptosis.

Regulation of oxidative stress by ATM is required for self-renewal of haematopoietic stem cells

The 'ataxia telangiectasia mutated' (Atm) gene maintains genomic stability by activating a key cell-cycle checkpoint in response to DNA damage, telomeric instability or oxidative stress. Mutational inactivation of the gene causes an autosomal recessive disorder, ataxia-telangiectasia, characterized by immunodeficiency, progressive cerebellar ataxia, oculocutaneous telangiectasia, defective spermatogenesis, premature ageing and a high incidence of lymphoma. Here we show that ATM has an essential function in the reconstitutive capacity of haematopoietic stem cells (HSCs) but is not as important for the proliferation or differentiation of progenitors, in a telomere-independent manner. Atm-/- mice older than 24 weeks showed progressive bone marrow failure resulting from a defect in HSC function that was associated with elevated reactive oxygen species. Treatment with anti-oxidative agents restored the reconstitutive capacity of Atm-/- HSCs, resulting in the prevention of bone marrow failure. Activation of the p16(INK4a)-retinoblastoma (Rb) gene product pathway in response to elevated reactive oxygen species led to the failure of Atm-/- HSCs. These results show that the self-renewal capacity of HSCs depends on ATM-mediated inhibition of oxidative stress.

Differential effects of DNA tumor virus genes on the expression profiles, differentiation, and morphogenetic reprogramming potential of epithelial cells

The availability of cell lines that retain their differentiation programs is important for the study of differentiated cell types and the development of cell therapies. DNA tumor virus genes are often used to establish cell lines from primary culture for the analysis of cell-specific functions. To ascertain whether viral immortalizing or transforming genes differed in their effects on cellular differentiation programs, the E1A 12S (WT12S) gene of adenovirus and the large T antigen (LT) gene of SV40 were used to derive stable cell lines from primary kidney. The resultant cell types exhibited very different morphologies, growth and behavior patterns, differentiation states, and plasticities. Renal cells immortalized by LT exhibited branching tubulogenesis in response to Matrigel. This was in contrast to their behavior under normal culture conditions, wherein they were less differentiated, very nonadhesive, very rapidly growing, and transformed. These cells coexpressed adult epithelial (keratin) and embryonic mesenchymal (vimentin, osteopontin, FSP1, PAX-2, and WT1) genes. WT12S-immortalized cells grown on or in Matrigel formed cysts or tubules, consistent with their expression profiles, which consisted of both epithelial and adult kidney markers (E-cadherin, alpha-catenin, circumferential actin filaments (CAF), alkaline phosphatase, aminopeptidase M, BMP7, or podocalyxin), but not embryonic/mesenchymal markers (PAX-2 or WT1). The WT12S-expressing cells were well differentiated, adhesive, slow growing, and nontransformed. Thus, cells expressing WT12S maintained their original differentiation status and were less sensitive to reprogramming, while cells expressing LT were dedifferentiated, but had the potential for reprogramming by exogenous factors.

Large scale isolation of non-uniform shear stress-responsive genes from cultured human endothelial cells through the preparation of a subtracted cDNA library

To investigate the molecular mechanisms responsible for the regional selectivity of early atherogenesis, we have applied a non-uniform shear stress to cultured human umbilical vein endothelial cells (HUVEC). We used a microcarrier culture system and a combination of subtraction and reverse-subtraction methods to isolate a number of genes upregulated by shear stress. The resultant subtracted library includes several known genes (e.g. MCP-1, TM) whose responsiveness to shear stress has been previously reported, indicating that the library is enriched for genes upregulated by shear stress. Also included are atherosclerosis-related genes (e.g. CTGF, IL-8) whose responsiveness to shear stress had not been demonstrated, other known genes whose relationship to atherosclerosis had not been reported, and novel genes. Some responsive to centrifugal force and shear stress (RECS) genes are also upregulated following stimulation by steady laminar shear stress in a parallel plate chamber. Interestingly, the library includes ET-1 and PAI, which are well known atherogenic factors that are downregulated by laminar shear stress. This implies that turbulent shear stress has effects on HUVEC that are different from those elicited by laminar shear stress. Importantly, analysis of specimens taken from human aorta showed that several RECS genes are transcriptionally upregulated in atherosclerotic lesions, suggesting that the subtracted library includes novel therapeutic targets for the treatment of atherosclerosis.

Cadmium accumulation augments contraction and phosphoinositide hydrolysis of vascular smooth muscles

Effects of cadmium accumulation in blood vessels on vasoconstriction and hydrolysis of phosphoinositides were investigated using aortas isolated from rats. The aortic strips were incubated with cadmium chloride (10 microM) for 24 hr and then washed out (cadmium accumulation). In the cadmium-accumulated aortas, contractile responses to KCl and 5-hydroxytryptamine were augmented compared to the control incubated with a vehicle. The degree of the augmentation by cadmium was higher in 5-hydroxytryptamine contraction than in KCl contraction. The level of 5-hydroxytryptamine-induced contraction relative to KCl-induced contraction (expressed as percent of maximum KCl contraction in each strip) was also significantly increased in the cadmium-accumulated aortas as compared to the control. Cadmium pretreatment augmented 5-hydroxytryptamine-stimulated inositol monophosphate accumulation, while there was no difference in the basal level of inositol monophosphate between the cadmium-accumulated aortas and the control. These results suggest that cadmium accumulation increases vasocontractility, in part because of the facilitation of phosphoinositide hydrolysis.

Involvement of protein kinase C-epsilon in signal transduction of thrombopoietin in enhancement of interleukin-3-dependent proliferation of primitive hematopoietic progenitors

We studied the effect of thrombopoietin (TPO) on interleukin-3 (IL-3)-dependent bone marrow cell colony formation of mice to clarify the role of protein kinase C (PKC) in the signal transduction of TPO for the proliferation of primitive hematopoietic progenitors. TPO alone hardly yielded colonies. However, TPO in combination with IL-3 increased colony numbers synergistically from 2- to 4-fold, compared with those supported by IL-3 alone. Serial observation of colony development showed that TPO may hasten the appearance of colonies by shortening the dormant period (G(0)) of primitive progenitors. Immunocytochemical studies on PKC isoforms in progenitor cells stimulated with TPO have revealed that the expression pattern of PKC-epsilon is changed, but not that of PKC-alpha, -beta, -gamma, -delta, or -zeta. Selective PKC inhibitors, such as calphostin C and GF 109203X, and PKC-epsilon-specific translocation inhibitor peptide abrogated the enhancing effect of TPO on IL-3-dependent colony formation and the changes in the intracellular expression pattern of PKC-epsilon. These data taken together suggest that TPO has a direct effect on primitive progenitors and enhances IL-3-dependent colony formation, at least partly through the activation of PKC-epsilon.

Development of rigor mortis is not affected by muscle volume

There is a hypothesis suggesting that rigor mortis progresses more rapidly in small muscles than in large muscles. We measured rigor mortis as tension determined isometrically in rat musculus erector spinae that had been cut into muscle bundles of various volumes. The muscle volume did not influence either the progress or the resolution of rigor mortis, which contradicts the hypothesis. Differences in pre-rigor load on the muscles influenced the onset and resolution of rigor mortis in a few pairs of samples, but did not influence the time taken for rigor mortis to reach its full extent after death. Moreover, the progress of rigor mortis in this muscle was biphasic; this may reflect the early rigor of red muscle fibres and the late rigor of white muscle fibres.

Onset of rigor mortis is earlier in red muscle than in white muscle

Rigor mortis is thought to be related to falling ATP levels in muscles postmortem. We measured rigor mortis as tension determined isometrically in three rat leg muscles in liquid paraffin kept at 37 degrees C or 25 degrees C--two red muscles, red gastrocnemius (RG) and soleus (SO) and one white muscle, white gastrocnemius (WG). Onset, half and full rigor mortis occurred earlier in RG and SO than in WG both at 37 degrees C and at 25 degrees C even though RG and WG were portions of the same muscle. This suggests that rigor mortis directly reflects the postmortem intramuscular ATP level, which decreases more rapidly in red muscle than in white muscle after death. Rigor mortis was more retarded at 25 degrees C than at 37 degrees C in each type of muscle.

Diagnosis of cyanide intoxication by measurement of cytochrome c oxidase activity

Cytochrome c oxidase (CCO), a mitochondrial enzyme, is inactivated by cyanide or carbon monoxide (CO) intoxication. We measured CCO activity, in the major organs of the rat at various times after death caused by cyanide intoxication. Tissue samples were homogenized, and the CCO activity in the mitochondrial fraction was measured using ferrous cytochrome c as the substrate. The CCO activity inhibition was highest in the brain, although the cyanide concentration was lowest level. As a result of this and the clinical symptoms displayed, we consider the brain to be the primary organ of cyanide intoxication. As cyanide is highly toxic to humans, in small amounts and many patients and victims have already had some medical care, it is difficult to detect cyanide in criminal investigations. The CCO activities in various organs remained significantly low for 2 days after the cyanide intoxication, suggesting that the diagnosis may be possible by measuring not only the cyanide concentration but also the CCO activity.

RIZ, the retinoblastoma protein interacting zinc finger gene, is mutated in genetically unstable cancers of the pancreas, stomach, and colorectum

The retinoblastoma protein interacting zinc finger (RIZ) gene is a candidate tumor suppressor gene on 1p36, a region frequently rearranged in a wide variety of human tumors. As the RIZ gene harbors several microsatellites within its coding region, it is a candidate for an inactivating mutation in microsatellite instability (MSI) mediated carcinogenesis. In this study, we examined mutations of two poly adenine tracts, A(8) and A(9), within the coding region of the RIZ gene, in MSI-high (MSI-H) primary cancers occurring in the pancreas, stomach, and colorectum. Frameshift mutations were found in one (10%) of 10 pancreatic, four (36%) of 11 gastric, and two (25%) of eight colorectal cancers. These results indicate that mutations of the RIZ gene play an important role in the pathogenesis of some MSI-H cancers.

Rho-associated kinase phosphorylates MARCKS in human neuronal cells

Myristoylated alanine-rich C kinase substrate (MARCKS) is a filamentous actin bundling protein and has multiple sites for phosphorylation, by which the biochemical function is negatively regulated. However, the role of such phosphorylation in physiological functions, particularly in neuronal functions, is not well understood. Using a phosphorylation-site specific antibody, we detected the phosphorylation of MARCKS at Ser159 by various protein kinases. Rho-kinase, protein kinase A, and protein kinase C, could introduce (32)P into human recombinant MARCKS in vitro and the phosphorylation site was confirmed to be the Ser159 residue. In human neuronal teratoma (NT-2) cells, lysophosphatidic acid (LPA) induced MARCKS phosphorylation dose- and time-dependently. This phosphorylation was sensitive to Rho-kinase inhibitor HA1077. However, the phosphorylation induced by PDBu was lesser sensitive. In a skinned NTera-2 cell system, Ca(2+)-independent and GTP gamma S/ATP-stimulated phosphorylation at Ser159 was also sensitive to pre-treatment C3 toxin and HA1077. These findings suggest that the Ser159 residue of MARCKS is a target of LPA-stimulated Rho-kinase in neuronal cells.

Thiol-oxidizing agent diamide and acidic pH enhance lipid peroxidation of rat heart mitochondria and cardiolipin-cytochrome c complex

In this study, we investigated lipid peroxidation in rat heart mitochondria hydrolyzed by phospholipase A2 (PLA2) and lipid peroxidation in a mitochondrial-mimetic lipid peroxidation system, where phospholipids such as cardiolipin (CL) and cytochrome c (Cyt c) were first mixed together and then PLA2 and calcium chloride were added to the mixture (CL-Cyt c-PLA2 system). Production of hydroperoxy and hydroxy compounds of linoleic acid (LA) in the mixture was measured by high performance liquid chromatography. The ratio of the total amount of hydroperoxy and hydroxy compounds of LA to that of LA was calculated as an index for lipid peroxidation (1000 x mol/mol). The index for lipid peroxidation in the rat heart mitochondria hydrolyzed by PLA2 at the physiological pH of 7.4 was 22.8 +/- 2.2 (mean +/- SD, n = 4) and that at the acidic pH of 6.7 was 41.8 +/- 2.0. In the presence of the thiol (SH)-oxidizing agent diamide, the index was 47.0 +/- 2.6 (pH 7.4). In the CL-Cyt c-PLA2 system, lipid peroxidation seemed to be due to three mechanisms: (1) oxidation of the LA (nonreleased form) constituent of CL by Cyt c (oxidation of CL by Cyt c); (2) oxidation of free LA, released from CL, involving the oxidation of CL by Cyt c (free LA oxidation by the CL-Cyt c complex); and (3) oxidation of free LA, released from CL, by Cyt c and calcium ions (LA-Cyt c-Ca system). The lipid peroxidation of the CL-Cyt c-PLA2 system was also enhanced by the addition of diamide and by an acidic pH of 6.7. The fact that the SH-oxidizing agent enhanced the lipid peroxidation in the CL-Cyt c-PLA2 system suggested that SH groups in the hemoprotein played an inhibitory role in lipid peroxidation in the system.

Structure, expression and mutational analysis of the hBRAG gene on 10q in the frequently deleted region in human endometrial cancer

We previously reported that chromosome arm 10q is one of the target regions of allelic loss in human endometrial cancer. To identify the gene in this region responsible for endometrial cancer, we further characterized this region and localized the hBRAG gene. The function of hBRAG has not yet been fully studied, and there is the possibility that this gene works as a tumor suppressor. This gene consist of 7 exons and 6 introns encoding 503 amino acids; all the introns start with GT and end with AG in agreement with the GT-AG rule. Expression of this gene was studied by Northern hybridization and suppressed expression was observed in one (SK-UT-1B) of the six endometrial cancer cell lines. Mutation analysis in 38 primary EC tissues and six EC cell lines disclosed no genetic alterations. The genomic structure of hBRAG elucidated in this study should contribute to the future analysis of the hBRAG gene.

[A case of giant skull myofibroma occupying left anterior cranial fossa]

We report a rare case of giant skull myofibroma occupying left anterior cranial fossa. A 53-year-old woman presented with left exophthalmos for 2 years. Neurological examination showed left exophthalmos, disturbance of bilateral visual acuity, and bitemporal hemianopsia. A CT scan revealed an ossifing mass at left anterior cranial fossa. On magnetic resonance images, the tumor showed iso-intensity on T 1-weighted image, heterogeneous high intensity on T 2-weighted image, and was heterogeneously well-enhanced after administration of Gd-DTPA. The tumor was fed mainly by middle meningeal artery. The patient underwent surgery and the tumor was removed totally. Histological diagnosis of the tumor was myofibroma. The patient has been followed every other month by MRI without any adjuvant therapy. There has been no tumor recurrence for 19 months. There is no other myofibroma in her body, therefore the patient was diagnosed as solitary myofibroma of the skull. Our case is the first report of solitary myofibroma of the skull because we could not find any reports on solitary myofibroma of the skull in the past literature.

cis-9,10-Methylenehexadecanoic acid inhibits contractility and actomyosin ATPase activity of guinea pig myocardium

Superfusion with a cyclopropane fatty acid, cis-9, 10-methylenehexadecanoic acid (10-300 microM), reduced the contractility of papillary muscle isolated from guinea pigs in a dose-dependent manner. cis-9,10-Methylenehexadecanoic acid also inhibited the Mg(2+)-ATPase activity of guinea pig papillary myocardium by about 40% at 400 microM. Since cis-9, 10-methylenehexadecanoic acid 4 microM inhibited the K(+)-EDTA-ATPase activity inherent in myosin's catalytic activity by about 25%, the fatty acid was thought to interact with the catalytic center of the myosin molecule.

[Radiation induced glioblastoma: a case report]

We report a surgical case of a 54-year-old woman with a radiation induced glioblastoma. At the age of 34, the patient was diagnosed to have a non-functioning pituitary adenoma. It was partially removed followed by 50 Gy focal irradiation with a 5 x 5 cm lateral opposed field. Twenty years later, she suffered from rapidly increasing symptoms such as aphasia and right hemiparesis. MRI showed a large mass lesion in the left temporal lobe as well as small mass lesions in the brain stem and the right medial temporal lobe. These lesions situated within the irradiated field. Magnetic resonance spectroscopy revealed relatively high lactate signal and decreased N-acetyl aspartate, choline, creatine and phosphocreatine signals. Increased lactate signal meant anaerobic metabolism that suggested the existence of a rapidly growing malignant tumor. Thus, we planned surgical removal of the left temporal lesion with the diagnosis of a radiation induced malignant glioma. The histological examination revealed a glioblastoma with radiation necrosis. MIB-1 staining index was 65%. Postoperatively, her symptoms improved, but she died from pneumonia 1 month after the surgery. An autopsy was obtained. The lesion of the left temporal lobe was found to have continuity to the lesion in the midbrain, the pons and the right temporal lobe as well. High MIB-1 staining index suggested that a radiation induced glioblastoma had high proliferative potential comparing with a de novo and a secondary glioblastoma.

Effect of cytochrome c on the linoleic acid-degrading activity of porcine leukocyte 12-lipoxygenase

Hemoproteins are known to have quasilipoxygenase activity that converts linoleic acid (LA) to its hydroperoxides. However, it is not still clear whether, like lipoxygenases, hemoproteins can produce LA hydroperoxides when the LA is part of a mixture containing many different saturated and unsaturated fatty acids. In this study, we found that such hemoprotein as cytochrome c (Cyt c) did not produce LA hydroperoxides from the phospholipase A(2) (PL-A(2)) hydrolysis products of egg yolk phosphatidylcholine (PC). We also found that traces of hydroperoxides and a high concentration of the target unsaturated fatty acid (LA) needs to be present in a fatty acid mixture before the quasi-lipoxygenase activity of Cyt c becomes apparent. We also attempted to elucidate how Cyt c interact with porcine leukocyte 12-lipoxygenase (12-LOX). Hemoproteins are known to possess pseudo-lipohydroperoxidase activity, and can remove the hydroperoxides of unsaturated fatty acids from a reaction mixture. However, we found that Cyt c catalyzed the reaction by which hydroperoxides degrade LA, and thus enhanced the LA-degrading activity of 12-LOX. This hemoprotein-induced promotion of the ability of 12-LOX to degrade LA was observed even when the reaction mixture contained many different saturated and unsaturated fatty acids.

Postmortem changes in cytochrome c oxidase activity in various organs of the rat and in human heart

Cytochrome c oxidase (COX), a mitochondrial enzyme, is inactivated by cyanide or carbon monoxide (CO) intoxication. To test whether cytochrome c has potential as an indicator of these toxins in cadavers, we measured COX activity in the main organs of the rat, and in the human heart, at various times after death. Each tissue sample or organ was homogenized and the COX activity in the mitochondrial fraction was measured using ferrous cytochrome c as the substrate. COX activity was significantly higher in rat brain, heart and kidney than in lung and liver from 0 to 4 days after death. The loss of COX activity was significantly slower in the brain and heart than in the lung, liver and kidney. Most importantly, COX activity correlated with the time-since-death for each of the rat organs we tested (r2=0.70-0.95), but for the human heart (r2=0.47). It may be possible that COX activity is likely to be a useful indicator of the time-since-death, and is worth pursuing as an indicator of the tissue cyanide and CO content.

[A successfully operated case of choriocarcinoma with recurrent intratumoral hemorrhage]

A 12-year-old boy with primary intracranial choriocarcinoma of the pineal region suffered from repeated intratumoral hemorrhage over a short period. Neuroradiological images demonstrated a pineal-region tumor with intratumoral hemorrhage and obstructive hydrocephalus. HCG-beta subunit concentration of his serum and cerebrospinal fluid was abnormally high. After the 24.2Gy irradiation, the tumor was removed almost totally. After the operation, we treated him with additional radiation and chemotherapy using ifosfamide, cisplatin, and etoposide (namely ICE therapy). No recurrence or metastasis has been noted, and he was in good condition during the 22 months since the operation. At present he receives maintenance ICE therapy every 3 months. Choriocarcinoma involves a high possibility of intratumoral fatal hemorrhage, so a radical operation is recommended as soon as possible.

Nurr1, an orphan nuclear receptor, is a transcriptional activator of endogenous tyrosine hydroxylase in neural progenitor cells derived from the adult brain

Adult rat-derived hippocampal progenitor cells express many of the molecules implicated in midbrain dopaminergic determination, including FGF receptors 1, 2 and 3, the sonic hedgehog receptor components Smo and Ptc, and the region-specific transcription factors Ptx3 and Nurr1. Here we use undifferentiated progenitors to probe the events leading to the dopaminergic phenotype and find that the influences of Nurr1 can be temporally and mechanistically uncoupled from the patterning influences of sonic hedgehog and FGF-8 or the more generic process of neuronal differentiation itself. In gain-of-function experiments, Nurr1 is able to activate transcription of the tyrosine hydroxylase gene by binding a response element within a region of the tyrosine hydroxylase promoter necessary for midbrain-specific expression. This activation is mediated through a retinoid X receptor independent mechanism and occurs in all precursors, regardless of differentiation status. Overexpression of Nurr1 does not affect proliferation or stimulate neuronal differentiation and has no influence on the expression of other dopaminergic markers. This uncoupling of tyrosine hydroxylase expression from other dopaminergic markers suggests that the midbrain dopaminergic identity is dictated by a combination of pan-dopaminergic (e.g., Shh/FGF-8) and region-specific (Nurr1) mechanisms.

A 'keyhole lesion' gunshot wound in an adipocere case

A corpse completely converted into adipocere and showing two adjacent bone defects--a typical gunshot entrance wound and a keyhole lesion--is reported. Postmortem changes, a comminuted fracture of the cranial base, and destruction of the bullets made it impossible to determine the direction of fire through the keyhole lesion. Gunshot wounds may show various atypical forms, including keyhole lesions, and especially in old corpses, the distinction between an entrance wound and an exit wound can be very difficult, even if a careful complete autopsy is performed.

Identification of cis-9,10-methylenehexadecanoic acid in submitochondrial particles of bovine heart

Submitochondrial particles of bovine heart were hydrolyzed by phospholipase A2 and the products were analyzed by liquid chromatography electrospray ionization-mass spectrometry. We found a fatty acid with a molecular mass of 268 Da and a retention time longer than that of linoleic acid. Next, we synthesized organically cis-9,10-methylenehexadecanoic acid, which has a molecular mass similar to that of the extracted fatty acid, and characterized its high performance liquid chromatography and gas chromatography-mass spectrometry profiles. Using these data we were able to identify endogenous cis-9,10-methylenehexadecanoic acid in rat and human heart and liver tissues that had been hydrolyzed by phospholipase A2. This fatty acid was not detected in tissue extracts that had not been hydrolyzed by phospholipase A2. Similar amounts of cis-9, 10-methylenehexadecanoic acid were measured in tissue extracts after total hydrolysis. These results suggest that cis-9, 10-methylenehexadecanoic acid is a fatty acid component, in the sn-2 position, of phospholipids in some mammalian tissue.

Calcium is required for quasi-lipoxygenase activity of hemoproteins

Bovine and guinea pig heart homogenates, porcine leukocyte homogenate, and human hemolysate were found to vigorously oxidize linoleic acid, with lipoxygenase-like activity, to its hydroperoxy, epoxy, hydroxy-epoxy, and keto compounds in the presence of calcium chloride. In the absence of calcium, the reaction was significantly reduced. Attempts to characterize this quasi-lipoxygenase activity revealed that calcium potentiated the quasi-lipoxygenase activities of hemoproteins (hemoglobin, myoglobin, myeloperoxidase, catalase, cytochrome c) and hemin at the physiological pH of 7.5. Lipid peroxidation by hemoproteins was inhibited by albumin and erythrocyte membranes in blood, as well as by a low concentration of calcium in cells. However, it seems possible that in extracellular fluid, which contains a high concentration of calcium and a low concentration of albumin, hemoprotein released from damaged cells could oxidize unsaturated fatty acids derived by phospholipase-A2 from phospholipids of damaged cellular membranes. In a model of quasi-lipoxygenase activation under such conditions, lipids of erythrocyte membranes were oxidized by hemoglobin in the presence of phospholipase-A2 and calcium. The effect of nitrogen oxide, paraquat, and bleomycin on oxidation by hemoproteins and hemin was also discussed.

HA1077, a protein kinase inhibitor, inhibits calponin phosphorylation on Ser175 in porcine coronary artery

Calponin is a thin filament-associated protein which has been implicated in the modulation of the contractile state of smooth muscle via its interaction with actin and inhibition of the actin-activated myosin Mg-ATPase. This inhibitory effect is alleviated by phosphorylation of calponin at Ser175 in vitro by protein kinase C. The issue of calponin phosphorylation in intact smooth muscle in response to agonists that activate protein kinase C is controversial. We have produced a monoclonal antibody that specifically recognizes calponin phosphorylated at Ser175 and used it to analyze calponin phosphorylation in porcine coronary arterial smooth muscle stimulated with prostaglandin F2alpha or phorbol 12,13-dibutylate (PDB). Calponin phosphorylation increased rapidly in response to prostaglandin F2alpha concomitant with the increase in tension. Calponin was then dephosphorylated while force was maintained. Tension development in response to PDB was significantly slower, but again calponin phosphorylation paralleled force development. In this case, calponin dephosphorylation was very slow, consistent with prolonged activation of protein kinase C. The protein kinase inhibitors, HA1077 (1-5-(isoquinoline sulfonyl)-homopiperazine HCl) and HA1100 (1-hydroxy HA1077; 1-(hydroxy-5-isoquinoline sulfonyl-homopiperazine), inhibited tension development and calponin phosphorylation in a concentration-dependent manner with similar ED50 values in response to prostaglandin F2alpha and PDB. These results support physiological roles for calponin in force development in smooth muscle in response to agonists which trigger protein kinase C activation and in the latch state, i.e., force maintenance at low energy cost. Furthermore, the vasodilator effect of HA1077 and HA1100 is more likely due to inhibition of protein kinase C than of myosin light chain kinase.

A 39,X/40,XY true hermaphrodite mouse with normal ovarian function

A cryptorchid mouse with a 39,X/40,XY chromosome constitution was identified among 414 offspring born in the departmental XO mouse breeding colony. This mouse had a small testis on the left, with no sign of spermatogenesis, and a normal ovary on the right with several corpora lutea.

Dynamics of myosin light chain phosphorylation at Ser19 and Thr18/Ser19 in smooth muscle cells in culture

Using the specific antibodies pLC1 and pLC2 for mono- and diphosphorylated 20-kDa myosin light chain (MLC20) at Ser19 and at both Thr18 and Ser19, respectively, we visualized the dynamics of the MLC20 phosphorylation in rabbit aortic smooth muscle cells (cell line SM-3) stimulated with PGF2alpha. In the resting state, the diphosphorylated form was located in the peripheral region of the cell, such as the leading edge or the adhesion plaque, and the monophosphorylated form was located not only in the peripheral region but also on a discontinuous fibrillary structure along the long axis of the cell. After stimulation with 30 microM PGF2alpha, although localization of the monophosphorylated form changed little, the content of the diphosphorylated form increased and the distribution spread along the fibrillary structure to an extent the same as or similar to that of the monophosphorylated form, which colocalized with actin filament bundles. The diphosphorylation of MLC20 was more sensitive to protein kinase inhibitors, HA-1077, HA-1100, staurosporine, wortmannin, and ML-9, than was the monophosphorylation. In light of these observations, we propose that MLC20 diphosphorylation and monophosphorylation are regulated by different mechanisms.

Calcium ions potentiate lipoxygenase activity of cytochrome c at the physiological pH

Cytochrome c oxidized linoleic acid, with lipoxygenase-like activity, to 9-hydroperoxy-10,12-octadecadienoic acid (9-HpODE), 13-hydroperoxy-9,11-octadecadienoic acid (13-HpODE), 13-keto-9,11-octadecadienoic acid (13-KODE), and hydroxy-epoxy-octadecenoic acids (HEPOs) in the presence of calcium chloride at the physiological pH of 7.5. In the absence of calcium, the reaction was remarkably reduced. Statistically significant increase of 13-KODE was observed 1 min after the reaction was started by adding calcium. Calcium chloride at concentrations as low as 30 microM caused statistically significant increase of 13-KODE production in the presence of 1 microM cytochrome c, and cytochrome c at concentrations as low as 10 nM caused statistically significant increase of 13-KODE production in the presence of 2 mM calcium. The addition of bleomycin enhanced the reaction, and the addition of adriamycin attenuated the reaction. The same oxidized linoleic acid products were found in the submitochondrial particles which were hydrolyzed by phospholipase-A2 in the presence of calcium. Lipoxygenase activity potentiated by calcium may be involved in the lipid peroxidation in the submitochondrial particles hydrolyzed by phospholipase-A2.