Heterogeneity of colorectal cancers and extraction of discriminator gene signatures for personalized prediction of prognosis.

Dissected specimens of colorectal cancer (CRC) have been intensively studied using molecular sketches (gene signatures) to obtain a set of discriminator gene signatures for accurate prognosis prediction in individual patients. The discriminators obtained so far are not universally applicable, as the gene sets reflect the method and site of the study. In this study, we show that dissected stage II and III CRC samples are significantly heterogeneous in molecular sketches, and are not appropriate sources for discriminator extraction unless handled individually. To search for an accurate discriminator gene set for prediction of metastases, we need to start with less heterogeneous stage II CRC. We examined 198 (92 stage II and 106 stage III) CRC dissected samples for the predictability of discriminator gene signatures by analyzing stage II CRC alone, stage III alone, or in combination. The best predictive power of discriminator genes was obtained only when these genes were extracted and validated with stage II CRC samples. An accurate discriminator gene set for the prediction of CRC metastases can be obtained by focusing on stage II CRC samples.

Regulation of PLAP-1 expression in periodontal ligament cells.

Periodontal-ligament-associated protein-1 (PLAP-1) is preferentially expressed in the periodontal ligament (PDL) and encodes a novel small leucine-rich repeat proteoglycan protein. PLAP-1 expression was induced during the course of cytodifferentiation of PDL cells into mineralized-tissue-forming cells in vitro, suggesting the possible involvement of PLAP-1 in the mineralization process of PDL cells. In this study, we hypothesized that PLAP-1 expression is regulated by mineralization-related cytokines in PDL cells. PLAP-1 expression was clearly down-regulated when the cytodifferentiation of PDL cells was reversibly inhibited by fibroblast growth factor-2 (FGF-2). In contrast, bone morphogenetic protein-2 (BMP-2) enhanced PLAP-1 expression. Up-regulation of PLAP-1 expression by BMP-2 was confirmed at the protein level when PDL cells were immunostained with anti-PLAP-1 polyclonal antibody. These results revealed the cytokine-mediated regulatory mechanisms of PLAP-1 expression and suggested that PLAP-1 expression may be associated with the process of cytodifferentiation of PDL cells.

PCR-array gene expression profiling of hepatocellular carcinoma.

Many trials using DNA microarrays have been reported for various human malignancies, but an efficient molecular diagnostic system has yet to be established. Here, we adopted a high throughput quantitative PCR-array system based on adaptor-tagged competitive PCR (ATAC-PCR), as a novel technique for gene expression profiling of hepatocellular carcinoma (HCC). This PCR-array contained 3,072 genes derived from three different cDNA libraries, including 298 additional known genes suspected to be involved in hepatocarcinogenesis. Using this PCR-array with 20 pairs of liver tissues (20 HCC, 20 surrounding nontumor liver), we identified a total of 117 genes differing in expression levels in the two liver tissues. Hierarchical clustering analysis and principal component analysis with these genes revealed distinct gene expression patterns in the HBV-positive group and the HCV-positive groups. Among 117 genes, only 7 (GPAA1, TMEM9, FACL4, ADFP, MAWBP, PACE4, FOS) were common to both groups. In conclusion, this PCR-array analysis with an appropriate set of genes is considered useful for gene expression profiling of HCC, and we identified some genes which may play a common key role in hepatocarcinogenesis.

Comparative evaluation of diagnostic guidelines for sudden infant death syndrome (SIDS) in Japan.

It is a well-recognized fact among professionals that the diagnosis of sudden infant death syndrome (SIDS) involves difficult elements; a SIDS diagnosis is not uniform throughout Japan; and such a diagnosis is not made based on any internationally recognized definition. Faced with this situation, guidelines have been prepared and proposals have been made to standardize and improve the accuracy of SIDS diagnoses, viz. the following three can be cited: "guideline for diagnosis of SIDS" prepared by a Study Group of the Ministry of Health and Welfare; "case studies of SIDS" and a "guideline for its diagnosis" prepared by the Case Study Committee of Japan SIDS Research Society; and a "proposal on the principles of medico-legal pathology concerning SIDS", included in the research report supported by a Grant-in-Aid for Scientific Research from the Ministry of Education. In the current study, a comparison was made focusing on the discrepancies among these three documents. The major discrepancies among these three are: (1) handling of the patient's age (by months or years) in the diagnosis of SIDS; (2) dealing with those cases for which no autopsy has been conducted; (3) attitudes concerning whether sleeping in a prone posture is a cause for asphyxia and (4) opinions concerning the aspiration of vomited milk. It is anticipated that these discrepancies will invite confusion and affect judgments and recognition of SIDS-related cases that will be brought to court. It is essential that those involved with these three documents have an opportunity at the earliest time to discuss the matter and come to a uniform understanding.

Research for improving the autopsy rate for infant death--medical economic assessment of the forensic autopsy system in Japan.

The rate at which autopsies are performed in Japan for cases of infant death is not adequate for diagnosing sudden infant death syndrome (SIDS). In Japan, it will be necessary to increase the autopsy rate at the time of infant deaths in order to improve the certainty of diagnosing SIDS and improving the accuracy of determining the cause of death with respect to infant death. The objective of this research is to provide basic documentation required for administrative implementation of this objective. In Japan, the Medical Examiner System and its related Approved Autopsy System are not deployed nationwide. The estimated budget in the case of deploying the Medical Examiner System nationwide for the purpose of improving the infant death autopsy rate is in excess of 5 trillion yen, and that in the case of deploying the Approved Autopsy System nationwide is estimated at roughly 130 million US dollars. However, since the rate of autopsies performed for SIDS has not changed following the implementation of approved autopsies, the efficacy of the Approved Autopsy System has come to be viewed questionably. In addition, it is also necessary to enact legislation that mandates the conducting of autopsies for all cases of infant death as is done in Scandinavia. The required cost in the case of performing autopsies for all cases of abnormal infant death is estimated at 200,000-700,000 US dollars and is considered to be within a range that could be implemented through local government regulations. In addition, the cost per body of an autopsy performed at the State Crime Laboratory in the State of Arkansas in the US in 1999 was about 6000 US dollars. In contrast, the same cost at the Tokyo Medical Examiner Office is much less at only about 4000 US dollars.

Study to increase the frequency of autopsies performed for cases of infant deaths--proposed revision of the law on postmortem examination and corpse preservation and other related regulations.

By definition, sudden infant death syndrome (SIDS) requires diagnosis through exclusion by conducting an autopsy. To obtain a reliable diagnosis of this disease, an autopsy is essential. However, the frequency with which autopsies are conducted in Japan is not sufficient to meet the need associated with the diagnosis of SIDS. To improve this frequency, various public policies, such as nationwide implementation of the administrative autopsy system (medical examiner system), the application of the practice of autopsy approved by families, and legally required autopsies, are being considered; but none has been put into practice. On the other hand, attention has been called to the fact that the Law on postmortem examination and corpse preservation, which was instituted at the end of the Second World War, requires updating. In the current report, it is proposed that the following be added to Article 8, item 3 of this Law: "the Metropolitan or Prefectural Governor must insist that an autopsy be conducted on all cases of a sudden and unexpected death of an infant to investigate the cause of this death." At present, the annual incidence of SIDS in Japan is reported to be 500. To put the above-recommended legal requirement into practice, the estimated annual addition to the budget, if conducted as approved or an administrative autopsy, will be in the order of 150,000-500,000 dollar, which is within the prescribed limits for an appropriation.

A study on how to increase the sudden infant death syndrome (SIDS) autopsy rate.

To clarify the real cause of death of sudden infant death syndrome (SIDS), it is the most urgent and important subject to increase the autopsy rate of SIDS. So, we make following three proposals. (1) SIDS must be reported to the police. (2) Autopsy of SIDS must be performed in the area where a medical examiner's system is established. (3) Medical examiner's system or similar system must be established in all big cities. (4) It is desirable to perform autopsy in the area having no medical examiner's system by judicial autopsy or pathological autopsy by pathologists having diploma in postmortem medical examination.

Detection of cardiomyocyte apoptosis in forensic autopsy cases.

The purpose of the present study was to determine reliable parameters for the detection of apoptotic cells for use as a diagnostic marker during the early stage of acute myocardial infarction (AMI) in forensic autopsy cases. Myocardial tissues taken from forensic autopsy cases were examined by immunohistochemical and molecular-biological methods using the terminal deoxynucleotidyl transferase-mediated dUTP biotin nick end-labelling (TUNEL) and the DNA laddering methods. In cases of AMI with a time period between 2 h from onset to death and 20 h post-mortem time, the nuclei of cardiomyocytes were stained positive with the TUNEL method and DNA fragmentation of myocardial cells was detected by agarose gel electrophoresis. Similar findings were obtained in cases of carbon monoxide (CO) intoxication. However, no apoptotic cells were found in other cases such as methamphetamine (MAP) intoxication, tetrodotoxin intoxication, alcohol intoxication, asphyxia, head injury, heart injury or myocarditis. These findings suggested that it would be possible to apply TUNEL-positive cells as a diagnostic marker during the early stages of AMI.

Expression of a novel member of the ATP1G1/PLM/MAT8 family, phospholemman-like protein (PLP) gene, in the developmental process of mouse cerebellum.

We have identified a new member of the ATP1G1/PLM/MAT8 family, named phospholemman-like protein (PLP), from a mouse cerebellum cDNA library. The family consists of small transmembrane proteins that modulate the activities of some ion channels. The deduced amino acid sequence of PLP consists of 93 residues that contain the ATP1G1/PLM/MAT8 motif and a single transmembrane domain, and is most similar to the sequence of mouse phospholemman. In situ hybridization analysis showed that the PLP gene is highly expressed in cerebellar granule cells. PLP expression is elevated in the postnatal developing cerebellum. Thus, it may be implicated in the proliferation, differentiation, and axon elongation of granule cells as they mature and migrate to the internal granule layer.

Expression profile of active genes in human periodontal ligament and isolation of PLAP-1, a novel SLRP family gene.

Periodontal ligament (PDL) is one of the most important tissues in maintaining the homeostasis of tooth and tooth-supporting tissue, periodontium. In this study, we investigated the expression profile of active genes in the human PDL obtained by collecting sequences with a 3'-directed cDNA library, which faithfully represents the composition of the mRNA population. We succeeded in obtaining a total of 1752 cDNA sequences by sequencing randomly selected clones and identified a total of 1318 different species as gene signatures (GS) by their sequence identity, 344 of which were known genes in the GenBank, and 974 of which were new genes. The resulting expression profile showed that collagen type I and type III were the most abundant genes and that osteogenesis-related proteins, such as SPARC/osteonectin and osteoblast specific factor 2, were highly expressed. By comparing the expression profile of PDL with 44 profiles similarly obtained with unrelated human cell/tissue, nine novel genes, which are probably expressed specifically in PDL, were discovered. Among them, we cloned a full-length cDNA of GS5096, which is frequently expressed in freshly-isolated periodontal tissue. We found that it encodes a novel protein, which is a new member of the class I small leucine-rich repeat proteoglycan family, and designated it PLAP-1 (periodontal ligament associated protein-1). PLAP-1 mRNA expression was confirmed in in vitro-maintained PDL cells and was enhanced during the course of the cytodifferentiation of the PDL cells into mineralized tissue-forming cells such as osteoblasts and cementoblasts. These findings suggest the involvement of PLAP-1 in the mineralized matrix formation in PDL tissues.

DNA testing of Klinefelter's syndrome in a criminal case using XY chromosomal STR multiplex-PCR.

We report genetic typing of Klinefelter's syndrome applied to casework in forensic DNA testing. In this case, by using extracted DNA from body samples (muscle and bones), we could identify two distinct X alleles in two out of three X-STR loci (HPRTB and ARA), in addition to Y alleles (DYS390, DYS393). The extra X was found to have originated from father, and the victim turned out to have 47XXY Klinefelter's syndrome. The victim was a 30-year-old male, born from relatively elderly parents as a second child. His father was a severe alcoholic and had been malnourished for more than 20 years at the moment of his birth. He exhibited slight mental retardation as a child, and belonged to a criminal group as an adult. The method presented here was useful to accurately diagnose sex chromosomal abnormality instead of conventional chromosomal analysis and Xg blood group typing. A subtype of this syndrome, 48 XXXY or mosaic, for example, could be identified if the intensity of the overlapped X bands were calculated.

Construction of preferential cDNA microarray specialized for human colorectal carcinoma: molecular sketch of colorectal cancer.

cDNA microarray analyses can be used to identify candidate genes that play important roles in human carcinogenesis. To gain insight into the molecular sketch of colorectal cancer, we have constructed cDNA microarrays specialized for colorectal cancer, which we named "Colonochip" by selecting genes that are expressed in colorectal cancer, normal colonic mucosa, and liver metastatic cancer tissues. This microarray contained 4608 nonredundant cDNA clones from over 30,000 cDNA clones derived from the three types of human cDNA libraries, as well as clones from 170 additional conventional major genes suspected to be involved in colorectal carcinogenesis, according to literatures. Using this "Colonochip," we were able to identify 59 genes showing twofold or more differential expression between primary cancer and normal colonic mucosa, potent candidates for diagnosis, and therapy of colorectal cancer for further studies.

Identifying sex chromosome abnormalities in forensic DNA testing using amelogenin and sex chromosome short tandem repeats.

Forensic DNA laboratories worldwide have begun using multiplexed STR systems to decrease analysis time and increase sample throughput. The loci used in these systems are basically "nonsense" regions of human DNA. However, due to the chromosome on which some of these loci are located, various genetic abnormalities can sometimes be detected. This paper will show one such abnormality--Klinefelter's Syndrome--and the process used to show the possibility of this defect in two undiagnosed males using peak height ratios at the Amelogenin locus, and X-Y STRs.

Pesticide poisoning initially suspected as a natural death.

A pesticide poisoning victim suspected initially as having died a natural death was autopsied. The victim was a 47-year-old male. Macroscopically, signs of acute death and, in particular, general erosion in the mucosa of the airways and esophagus were observed. In the gastric contents, which had a pungent smell and a greenish-brown color, 5.00 g/L of propanil, 1.27 g/L of carbaryl, 0.38 g/L of ethylbenzene, and 0.32 g/L of xylene were detected. In the blood (serum), 21.6 mg/L of propanil, 8.1 mg/L of carbaryl, 1.7 mg/L of ethylbenzene, and 4.0 mg/L of xylene were identified. Postmortem methemoglobinemia (45%) was recognized. The cause of death was considered to have been pesticide poisoning; propanil was probably most responsible for his death. The police considered the case to be "death with illness as the suspected cause." By performing an autopsy, however, we were able to clarify that the cause of death was pesticide poisoning.

[Cardiac lesions in methamphetamine abusers].

Various cardiac lesions such as hypertrophy, disarray and fibrosis similar to HCM, were often found in the heart of methamphetamine (MA) abusers. Myolysis, eosinophilic changes, contraction band necrosis and small round cell infiltration were also observed. Male ddy mouse were administered MA 1 mg/kg subcutaneously every day for 4 weeks. Their hearts revealed many cardiac changes such as hypertrophy, myolysis, contraction band necrosis, disarrangement of myofibers, saw-like cytoplasm, side-to-side connection of cardiac cells and vascuolative degeneration microscopically, and crysterosis of mitochondria, enlargement of sarcoplasmic reticulum and hypercontraction electronmicroscopically. These changes are thought to be similar to that of MA abusers, so it is certified that MA has toxic effect on the heart. Moreover, these changes could not be found when beta-blocker or calcium antagonist was premedicated. To elucidate the mechanisms of MA cardiac toxicity, we have designed some experiments. When MA (15 mg or 20 mg/kg) was administered on rats, cardiac lipid peroxidates, as a marker of free radical, increased rapidly. When rats were feeded for 7 weeks with Vitamin E deficient diet, 10 mg/kg MA administration was enough to increase lipid peroxidates. Simultaneous ECG observation revealed various arrhythmia such as VPB, A-V block and intraventricular conduction delay. In the investigation of contractile protein, although we could not find differences in the isozyme pattern of myosin heavy chain between MA groups (1 mg/kg for 8 and 12 weeks) and control group, Mg2+ ATPase activity of myocardial actomyosin at 0.1 microM Ca2+ increased significantly in 12 weeks MA group. We also found MA induced cardiac toxicity in cultured myocytes. Primary cultured adult rat myocytes were exposed to MA (1 x 10(-5) M and 1 x 10(-3) M) for 1 to 24 h in the presence and absence of 1 x 10(-5) M propranolol. After 24-h MA treatment, cellular granulation, swelling and hypercontraction and release of CPK were observed both with and without propranolol treatment. These findings suggest that MA may exert direct toxic effects on the heart.

Application of in situ PCR to diagnose pneumonia in medico-legal autopsy cases.

In situ polymerase chain reaction (in situ PCR) can detect specific sequences of DNA, such as those of micro-organisms in human tissue samples. In forensic medicine, there are many cases implicated with infection, and pneumonia is an especially common finding in autopsy cases. In the present study, we tried to detect the presence of bacterial infections in lung tissue samples. The experiment was performed with ten paraffin-embedded lung tissue samples, including three non-pneumonia cases using specific primers for Streptococcus pneumoniae, Staphylococcus aureus, Streptococcus equisimilis, and a DIG Oligonucleotide 3'-End Labeling Kit (Boehringer Mannheim). The findings showed that at least one or all three species of bacterial flora in the alveoli could be detected in all seven pneumonia cases, and that some leukocyte cytoplasms, after antigen-antibody and color emission chemical reactions, were also observed to have changed color due to phagocytosis. Detection of bacterial DNA in the leukocyte cytoplasm is a sign of vital reaction and differentiates between antemortem and postmortem infection. The present findings revealed that in situ PCR had the advantage that it helped identifying specific bacteria in the lung tissues with pneumonia.

A novel mutation of the KAL1 gene in monozygotic twins with Kallmann syndrome.

OBJECTIVE: Kallmann syndrome is defined by the association of hypogonadotropic hypogonadism and anosmia. The KAL1 gene is responsible for the X-linked form of Kallmann syndrome. In this study we describe monozygotic twins with Kallmann syndrome due to the same mutation in the KAL1 gene. DESIGN: We studied male monozygotic twins with Kallmann syndrome. METHODS: We analyzed the KAL1 gene using the PCR-direct sequencing method. The twins' mother was examined for the identified mutation. RESULTS: We identified a 14 bp deletion from codon 419 in exon 9 (Pro419del14) in both KAL1 genes of the twins. This was a novel mutation in the KAL1 gene and was responsible for Kallmann syndrome. As Pro419del14 was not detected in the mother of the twins, Pro419del14 was a germline mutation originating from them. These monozygotic twins showed different LH and FSH responses to LH-RH stimulation and different phenotypes such as complications, physiques and psychiatric characters. CONCLUSIONS: We report an identical KAL1 gene mutation in the monozygotic twins with Kallmann syndrome. As these monozygotic twins showed different phenotypes in some respects, we suggest that factors other than mutations in the KAL1gene affect the symptomatic features of Kallmann syndrome.

Gene expression profiling of mouse postnatal cerebellar development.

Expression patterns of 1,869 genes were determined using adapter-tagged competitive PCR (ATAC-PCR) at 6 time points during mouse postnatal cerebellar development. The expression patterns were classified into 12 clusters that were further assembled into 3 groups by hierarchical cluster analysis. Among the 1,869 genes, 1,053 known genes were assigned to 90 functional categories. Statistically significant correlation between the clusters or groups of gene expression and the functional categories was ascertained. Genes involved in oncogenesis or protein synthesis were highly expressed during the earlier stages of development. Those responsible for brain functions such as neurotransmitter receptor and synapse components were more active during the later stages of development. Many other genes also showed expression patterns in accordance with literature information. The gene expression patterns and the inferred functions were in good agreement with anatomical as well as physiological observations made during the developmental process.

BodyMap: a collection of 3' ESTs for analysis of human gene expression information.

BodyMap is a collection of site-directed 3' expressed sequence tags (ESTs) (gene signatures, GSs) that contains the transcript compositions of various human tissues and was the first systematic effort to acquire gene expression data. For the construction of BodyMap, cDNA libraries were made, preserving abundance information and histologic resolutions of tissue mRNAs. By sequencing 164,000 randomly selected clones, 88,587 GSs that represent chromosomally coded transcripts have been collected from 51 human organs and tissues. They were clustered into 18,722 independent 3' termini from transcripts, and more than 3000 of these were not found among ESTs assembled in UniGene (Build 75). Assessment of the prevalence of polyadenylation signals and comparison with GenBank cDNAs indicated that there was no significant contamination by internally primed cDNAs or genomic fragments but that there was a relatively high incidence (12%) of alternative polyadenylation sites. We evaluated the sensitivity and resolution of expression information in BodyMap by in silico Northern hybridization and selection of tissue-specific gene probes. BodyMap is a unique resource for estimation of the absolute abundance of transcripts and selection of gene probes for efficient hybridization-based gene expression profiling.

Analysis of citrulline in rat brain tissue after perfusion with haloperidol by liquid chromatography-mass spectrometry.

We have investigated the potential of high-performance liquid chromatography (HPLC) coupled to mass spectrometry (MS) to determine enrichments of citrulline as a marker for in vivo nitric oxide (NO) production in brain tissue. The analysis of citrulline as the butyl ester derivative was evaluated using two types of ionization: electron spray ionization (ESI) and atmospheric pressure chemical ionization (APCI). APCI-MS appeared to be more suitable for determination of citrulline than ESI-MS, because the ion intensity of the protonated molecule ion [M+H]+, m/z 232, of citrulline in the former was about twelve times higher than in the latter. The chromatography was carried out on a reversed C8 column with the mobile phase consisting of 15% acetonitrile: 85% H2O: 0.2% acetic acid (v/v). The calibration curve had good linearity within the concentration range investigated (5 ng to 500 ng/ml). The limit of determination was estimated to be ca. 1 ng/ml of standard solution. The method was applied to the analysis of citrulline in the brain dialysate obtained from rat after perfusion of the striatum with haloperidol (HP, 0.1 mM). It is concluded that APCI-MS in combination with HPLC can be successfully applied to determination of citrulline in brain tissue, thus providing a useful tool for assessment of in vivo NO production.