Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Functional annotation of a full-length mouse cDNA collection

The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.

Relocalization of apoptosis-inducing factor in photoreceptor apoptosis induced by retinal detachment in vivo

Apoptosis-inducing factor (AIF) is a novel mediator in apoptosis. AIF is a flavoprotein that is normally confined to the mitochondrial intermembrane space, yet translocates to the nucleus in several in vitro models of apoptosis. To investigate the role of AIF in the apoptotic process in vivo, we induced retinal detachment (RD) by subretinal injection of sodium hyaluronate, either in Brown Norway rats or in C3H mice. Apoptotic DNA fragmentation, as determined by terminal nick-end labeling, was most prominent 3 days after RD. The subcellular localization of AIF was examined by immunohistochemistry and immunoelectron microscopy. In normal photoreceptor cells, AIF was present in the mitochondrion-rich inner segment. However, AIF was found in the nucleus after RD. Photoreceptor apoptosis developed similarly in C3H control mice, and in mice bearing the gld or lpr mutations, indicating that cell death occurs independently from the CD95/CD95 ligand system. Both the mitochondrio-nuclear transition of AIF localization and the nuclear DNA fragmentation were inhibited by subretinal application of brain-derived neurotrophic factor. To our knowledge, this is the first description of AIF relocalization occurring in a clinically relevant, in vivo model of apoptosis.

Targeted gene transfer to corneal endothelium in vivo by electric pulse

A novel method of in vivo targeted gene transfer to intentionally selected areas of the corneal endothelium was developed. Plasmid DNA with the lacZ gene coding for beta-galactosidase was injected into the anterior chamber of adult Wistar rats, and eight pulses of electricity at intensities ranging from 5 to 40 V/cm were delivered for 50 ms to the cornea with a specially designed electric probe in order to determine the effect of gene transfer on the corneal endothelial cells. Gene expression was visualized by enzymatic color reaction using X-gal in enucleated eyes on days 1, 3, 7, 14 and 21 after gene transfer. The treated eyes were then photographed and the X-gal-positive areas were evaluated by an image analyzer. The ratios of the areas (X-gal-positive area/area of entire corneal endothelium x 100%) were then calculated to determine gene transfection efficiency. The expression of beta-galactosidase was clearly detected in the cytoplasm of the corneal endothelial cells as early as day 1 and lasted until day 21. The most intense gene expression was observed on days 1 and 3 (5.21% on day 1 and 6.45% on day 3). The expression of beta-galactosidase on day 3 was most evident following delivery of 20 V electric pulses (0.09% at 5 V, 0.03% at 10 V, 6.45% at 20 V). beta-Galactosidase expression was limited to the corneal endothelial cells in highly selected areas and no beta-galactosidase expression was detected in any other intra- or axtraocular tissues. In addition, no cell damage was apparent in the cornea and no inflammation was detected in any other intraocular tissues. Thus, low-voltage electric pulses successfully transferred the gene of interest to highly selective areas of the corneal endothelium without inducing any pathological changes. This targeted gene transfer method appears to have great potential for use in gene therapy for ocular diseases.

Microglial localization of alpha-interferon receptor in human brain tissues

The localization of the alpha-interferon receptor (alpha-IFNR) was examined in human brain tissues from neurologically normal, Alzheimer's disease (AD) and cerebral infarction cases, using one antibody (IFNaR3) which preferentially recognizes alpha 2-IFN receptor and a second antibody (anti-p40) which recognizes the soluble alpha-IFN alpha/beta receptor. In all cases, microglial cells were stained with the antibodies. In infarct brains, macrophages were intensely labeled for alpha-IFNR. The anti-p40 antibody also showed capillary staining which might be due to residual blood plasma. On Western blots, IFNaR3 recognized only a 210 kDa alpha-IFN/receptor complex, indicating its localization in microglial cells. The anti-p40 antibody recognized this complex as well as four other major materials of lower molecular weight. These results suggest that alpha-IFNR protein is constitutively expressed in microglial cells.

Utility of colorimetric end-tidal carbon dioxide detector for monitoring during prehospital cardiopulmonary resuscitation

The purpose of this study was to evaluate a colorimetric end-tidal CO2 (ETCO2) detector (EASY CAP) as a monitor during prehospital cardiopulmonary resuscitation (CPR) without tracheal intubation. This detector was used for 121 patients during CPR with a laryngeal mask airway or face mask by authorized emergency lifesaving technicians. At 7 to 15 minutes after the initiation of CPR, ETCO was <0.5% in 30 cases (group A), 0.5% to 2.0% in 46 cases (group B) and >2.0% in 45 cases (group C). The rate of return of spontaneous circulation was 17% in group A, 24% in group B, and 48% in group C (groups A v C, P < .01). There was a significant difference in the rate of hospital admission between groups A and C. The ETCO2 value may be useful for monitoring during prehospital CPR with a laryngeal mask airway or face mask.

Retinal functional change caused by adenoviral vector-mediated transfection of LacZ gene

We examined the effect of insertion of an exogenous gene on retinal function to assess the rationale of adenoviral vector-mediated gene transfer for future gene therapy. An adenoviral vector expressing bacterial LacZ (AdCALacZ) was injected into the eyes of adult rats either intravitreally (group A) or subretinally (group B), and the gene expression and retinal function were thus examined at different time points after gene transfer for 3 weeks. X-Gal histostaining showed that neural retinal cells were transfected in group A and that retinal pigment epithelial cells were transfected in group B. The gene transfer was more efficient in group B (54.4% of the fixed retinal area was stained) than in group A (10.4%). The electroretinogram (ERG) revealed retinal dysfunction in the AdCALacZ-transfected rats even at the stage in which the histological damage was not apparent by electron microscopy and immunohistochemical studies for cytokeratin, S-100 protein, and glial fibrillary acidic protein. The ERG change was correlated with the intensity of inflammation, and retinal function recovered to the original level by 3 weeks, along with a diminution of inflammation. Functional changes were more evident in eyes treated with AdCALacZ than in those infected with adenoviral vector with no exogenous gene; however, no histological difference was observed between these groups, indicating that the insertion of exogenous gene itself affects retinal function. The results showed that different kinds of retinal cells could be gene-transferred by an adenoviral vector, depending on the application method. The retinal dysfunction caused by each adenoviral transfection method was caused by inflammation and the insertion of exogenous gene, and this retinal dysfunction was recoverable. In future gene therapy, special attention should be given to the method of exogenous gene insertion in the retina.

Increased expression of angiotensin-converting enzyme in retinas of diabetic rats

PURPOSE

The aim of this study was to examine the localization and the changes in the amount of angiotensin-converting enzyme (ACE) and the relationship between the renin-angiotensin (RA) system and vascular endothelial growth factor (VEGF)/VEGF-receptor system in the retinas of diabetic rats.

METHODS

Immunohistochemical localization of ACE, VEGF, and VEGF-receptor fetal liver kinase-1 (Flk-1) was examined in cryosections of the retinas of streptozotocin-injected diabetic rats. A semi-quantitative comparison of diabetic rats with age-matched controls was also performed by counting the ACE- or Flk-1-positive vessels per microscopic field.

RESULTS

ACE immunoreactivity was localized in the retinal vessel walls, and the percentages of ACE-positive vessels were significantly increased in the retinas of diabetic rats maintained 3 to 5 months. Both VEGF and Flk-1 signals increased simultaneously with the increment of ACE immunoreactivity.

CONCLUSIONS

ACE, expressed in the retinal vessel walls, increases simultaneously with the increment of both VEGF and Flk-1 in the retinas of diabetic rats, suggesting that upregulation of ACE might play some role in the progression of diabetic retinopathy through the VEGF/VEGF receptor system.

Differential expression of major gap junction proteins, connexins 26 and 32, in rat mammary glands during pregnancy and lactation

We examined the expression pattern of two major gap junction proteins, connexin 26 (Cx26) and connexin 32 (Cx32), in rat mammary glands during pregnancy and lactation. Immunohistochemically the two different Cxs were coexpressed in acinar cells and were independently modulated according to the physiological cell activity. Western blot analysis demonstrated that Cx26 gradually increased from early pregnancy, while Cx32 rapidly and dramatically increased at 16 h after parturition, and that both Cxs reached a maximum early in lactation. Increased expression of both Cxs was confirmed by Northern blot analysis showing that their mRNA transcripts were significantly induced on the day of parturition. We also analyzed double-immunofluorescent staining for Cx26 and Cx32 on a confocal laser scanning microscope, in order to examine colocalization of these Cxs in situ. Cx26 immunoreactivity mostly overlapped with Cx32-positive sites in acinar cells of lactating mammary glands, indicating that both Cxs were colocalized together in the same gap junctional plaques in lactation. These results suggest that upregulation of Cx26 and Cx32 in acinar cells at lactating stages, with colocalization in the same gap junctional plaques, may be important for control of secretion by acinar cells in rat mammary glands.

Invasion of brain by neurovirulent influenza A virus after intranasal inoculation

We examined the immunohistochemical localization of neurovirulent influenza A virus (WSN and R404BP) in the brains and lungs of C3H/HeN and A2G mice 3 days after intranasal inoculation, as well as in A2G mice 3 days after intracerebral inoculation. The invasion of brain by R404BP virus was greater than that of WSN in both mouse strains. The areas of infection were less extensive in Mx gene(+) A2G mice than in the Mx gene(-) C3H/HeN mice, which is consistent with previous reports. Major involvement was seen in various catecholaminergic neurons, capillaries, meninges and ependymal areas. Olfactory and trigeminal nerves were not positive for the WSN antigen. These results show that, in the early phase of infection, influenza A virus invades, probably through hematogenous spread, and particularly affects catecholaminergic neurons.

Immunocytochemical studies of major gap junction proteins in rat salivary glands

We examined protein components of the gap junctions between acinar cells of the parotid, sublingual and submandibular glands of the rat, using type-specific antibodies directed against major gap junction proteins, connexin32 (Cx32) and connexin26 (Cx26). Double-immunofluorescence microscopy revealed that fluorescent spots of both connexins in the parotid and sublingual glands were distributed between the apposed regions of acinar cells. They appeared together, or were co-localized. The intensity of the Cx26-associated fluorescent signals was relatively weak in the submandibular glands compared with the other glands and was absent from some acini. When present, these spots were always co-localized with Cx32 immunoreactive positive spots. The results suggest that Cx32 and Cx26 in rat salivary glands are colocalized within the same gap junctional plaques when simultaneously expressed by the same acinar cells.

Computational analysis of full-length mouse cDNAs compared with human genome sequences

Although the sequencing of the human genome is complete, identification of encoded genes and determination of their structures remain a major challenge. In this report, we introduce a method that effectively uses full-length mouse cDNAs to complement efforts in carrying out these difficult tasks. A total of 61,227 RIKEN mouse cDNAs (21,076 full-length and 40,151 EST sequences containing certain redundancies) were aligned with the draft human sequences. We found 35,141 non-redundant genomic regions that showed a significant alignment with the mouse cDNAs. We analyzed the structures and compositional properties of the regions detected by the full-length cDNAs, including cross-species comparisons, and noted a systematic bias of GENSCAN against exons of small size and/or low GC-content. Of the cDNAs locating the 35,141 genomic regions, 3,217 did not match any sequences of the known human genes or ESTs. Among those 3,217 cDNAs, 1,141 did not show any significant similarity to any protein sequence in the GenBank non-redundant protein database and thus are candidates for novel genes.

Comparative study of magnetic resonance and CT scan imaging in cases of severe head injury

The distribution, frequency, and appearance of head injuries were evaluated with MRI and CT in a prospective study of 155 patients with acute (n = 124) and chronic (n = 31) head injuries. MRI was significantly more sensitive than CT in the detection of intraaxial injury at any stage. In severe cases, central structure lesions were detected in approximately 80% of patients. Severity on admission was compatible with MR findings. However it was difficult to decide on neurobehavioural prognosis from initial MRI findings only.

Leech extracellular hemoglobin: two globin strains that are akin to vertebrate hemoglobin alpha and beta chains

Leech (Whitmania edentula, Haemadipsa zeylanica var. japonica and Erpobdella lineata) extracellular hemoglobins are basically composed of three constituent subunits, a dimer (D1 and D2 chains) and two monomers (M1 and M2 chains). We isolated these four chains from respective species by a combination of reversed-phase chromatography on a Resource RPC column and gel-filtration on a Superdex 75 column. The apparent molecular masses of the four globin chains were estimated by SDS-PAGE analysis to be 13 kDa (M1), 16 kDa (M2; 19 kDa in its reduced form) and about 27 kDa for the dimer subunit (13 kDa for D1; 15 kDa for D2), regardless of the source. The amino (N)-terminal segments (21-30 residues) from twelve globin chains of the above three species were determined and aligned. It was found that the twelve sequences could be separated into two distinct globin groups A and B. This finding supports the original idea of "two globin strains in annelid hemoglobin", which was proposed without any evidence for leech hemoglobins. Comparing the sequences in the three classes of Annelida, Hirudinea, Oligochaeta and Polychaeta, we found two invariant amino acids, Cys and Trp, which are interposed by eleven amino acid residues. Furthermore, the globin chains belonging to strain A were readily discernible as they had three more invariants, Ser-13, Asp-16 and Trp-28, while the globin chains of strain B had two more invariants, Lys-12 and Arg-27. Consequently, we propose that each of the three classes of Annelida have two distinct groups of globin chains that are akin to vertebrate hemoglobin alpha and beta chains.

Associated movement as a sequel to thoracotomy: aberrant regeneration to the latissimus dorsi muscle

We describe two patients with unusual associated movements as a sequel to thoracotomy. The two patients developed involuntary twitchings of the latissimus dorsi, which were induced by contractions of the adjacent muscles, the serratus anterior muscle in patient 1 and the external intercostal muscle in patient 2, after lobectomy for lung cancer. Electrophysiological and radiological studies showed that aberrant regeneration from the adjacent nerves to the denervated latissimus dorsi could be responsible for the associated movements.

Immunohistochemistry of a cytoplasmic dynein (MAP 1C)-like molecule in rodent and human brain tissue: an example of molecular mimicry between cytoplasmic dynein and influenza A virus

Immunohistochemistry with an antibody to influenza A/Aichi/2/68 (H3N2) virus was performed using normal mouse, rat and human brain tissues. Dot-like or filamentous structures in the neuronal cytoplasm were clearly stained. Axons were also stained, but weakly. Lewy bodies in Parkinson's disease substantia nigra were also positive. Immunoscreening of the antibody using mouse brain cDNA revealed that this antibody recognized the heavy chain of cytoplasmic dynein. Immunoblot analysis also showed that the reactive molecule was the same size as cytoplasmic dynein (microtubule-associated protein 1 C). This is an example of molecular mimicry between cytoplasmic dynein and influenza A virus, and the antibody appears to be useful for the localization on cytoplasmic dynein in the central nervous system.

[A case of sepsis by Neisseria meningitidis beginning with pneumonia during a trip abroad]

A 62-year-male presented a high fever and a dry cough during a trip to Australia. He was admitted to a hospital as soon as be returned to Japan. The next day after returning to Japan, he was transferred to our hospital with septic shock and loss of consciousness. Neisseria meningitidis was cultured from his blood. N. meningitidis is rare in Japan. However its seems common, in some foreign countries. With these findings, it can be postulated that N. meningitidis might be one of the etiological agents of the imported infectious disease.

Optimization of lymphapheresis for manufacturing autologous CAR-T cells

Collection of CD3+ lymphocytes via lymphapheresis is essential for manufacturing autologous chimeric antigen receptor (CAR) T cells. Optimization of timing and procedures for lymphapheresis for each patient is critical because patients often have progressive diseases and receive medications that could reduce T cell counts. We conducted a retrospective study of clinical data from 28 patients who underwent lymphapheresis for CD19-directed CAR-T therapy with tisagenlecleucel to identify factors that could affect CD3+ lymphocyte yields. The numbers of CD3+ cells in peripheral blood were significantly correlated with CD3+ cell yields (correlation coefficient r = 0.84), which enabled us to estimate the volume of blood to process before apheresis. We also found that small cell ratio (SCR) at the apheresis site precisely reflected the proportion of lymphocytes, especially in patients without circulating blasts (coefficient of determination: r² = 0.9). We were able to predict the CD3+ cell yield and prevent excessive apheresis by measuring pre-apheresis circulating CD3+ cell counts and monitoring SCR. Collectively, these results will help us to establish a strategy for optimization of lymphapheresis procedures for CAR-T cell production on a patient-by-patient basis.