Huhehasi Wu

Whole-Genome Tiling Array Analysis of Mycobacterium leprae RNA Reveals High Expression of Pseudogenes and Noncoding Regions

Whole-genome sequence analysis of Mycobacterium leprae has revealed a limited number of protein-coding genes, with half of the genome composed of pseudogenes and noncoding regions. We previously showed that some M. leprae pseudogenes are transcribed at high levels and that their expression levels change following infection. In order to clarify the RNA expression profile of the M. leprae genome, a tiling array in which overlapping 60-mer probes cover the entire 3.3-Mbp genome was designed. The array was hybridized with M. leprae RNA from the SHR/NCrj-rnu nude rat, and the results were compared to results from an open reading frame array and confirmed by reverse transcription-PCR. RNA expression was detected from genes, pseudogenes, and noncoding regions. The signal intensities obtained from noncoding regions were higher than those from pseudogenes. Expressed noncoding regions include the M. leprae unique repetitive sequence RLEP and other sequences without any homology to known functional noncoding RNAs. Although the biological functions of RNA transcribed from M. leprae pseudogenes and noncoding regions are not known, RNA expression analysis will provide insights into the bacteriological significance of the species. In addition, our study suggests that M. leprae will be a useful model organism for the study of the molecular mechanism underlying the creation of pseudogenes and the role of microRNAs derived from noncoding regions.

Expression of adipose differentiation-related protein (ADRP) and perilipin in macrophages infected with Mycobacterium leprae.

Mycobacterium leprae survives and replicates within a lipid droplet stored in the enlarged phagosome of histiocytes, a typical feature of lepromatous leprosy that is thought to be an important nutrient source for the bacillus. However, the underlying mechanisms by which lipids accumulate within phagosomes remain unclear. Recently, it was revealed that the lipid droplet-associated proteins, including ADRP and perilipin, play essential roles in lipid accumulation in adipocytes or macrophages. Therefore, we attempted to examine the role of these proteins in leprosy pathogenesis. ADRP and perilipin localized to the phagosomal membrane, which contains M. leprae in skin biopsy specimens of lepromatous leprosy. ADRP expression was transiently increased after phagocytosis in THP-1 cells. However, high levels of ADRP expression persisted only when live M. leprae, but not dead bacilli or latex beads, was added. Furthermore, although peptidoglycan, a Toll-like receptor 2 ligand, suppressed the expression levels of ADRP and perilipin, M. leprae infection inhibited this suppression. These results suggest that live M. leprae has the ability to actively induce and support ADRP/perilipin expression to facilitate the accumulation of lipids within the phagosome and to further maintain a suitable environment for the intracellular survival within the macrophage.

Fragments of Genomic DNA Released by Injured Cells Activate Innate Immunity and Suppress Endocrine Function in the Thyroid

Activation of innate and acquired immune responses, which can be induced by infection, inflammation, or tissue injury, may impact the development of autoimmunity. Although stimulation of cells by double-stranded DNA (dsDNA) has been shown to activate immune responses, the role of self-genomic DNA fragments released in the context of sterile cellular injury is not well understood. Using cultured thyroid cells, we show that cell injury prompts the release of genomic DNA into the cytosol, which is associated with the production of type I interferons, inflammatory cytokines, and chemokines. Molecules necessary for antigen processing and presentation to lymphocytes are also induced in thyroid cells by injury. dsDNA strongly suppressed the expression of sodium/iodide symporter and radioiodine uptake. To identify molecules responsible for sensing cytosolic dsDNA, we directly identified the cellular proteins that bound a dsDNA Sepharose column by mass spectrometry. Our analysis identified histone H2B, which was previously demonstrated to be an essential factor that mediates the activation of innate immunity induced by dsDNA. Knockdown of histone H2B using specific small interfering RNA abolished cell injury-induced innate immune activation and increased sodium/iodide symporter expression. These results indicate that genomic DNA fragments released by cell injury are recognized by extrachromosomal histone H2B, which results in the activation of genes involved in both innate and acquired immune responses in thyroid cells and suppression of thyroid function. These results suggest that sterile thyroid injury, in the absence of infection, may be sufficient to trigger autoimmune reaction and to induce thyroid dysfunction.

Tryptophan aspartate‐containing coat protein (CORO1A) suppresses Toll‐like receptor signalling in Mycobacterium leprae infection

Mycobacterium leprae is an intracellular pathogen that survives within the phagosome of host macrophages. Several host factors are involved in producing tolerance, while others are responsible for killing the mycobacterium. Tryptophan aspartate‐containing coat protein (TACO; also known as CORO1A or coronin‐1) inhibits the phagosome maturation that allows intracellular parasitization. In addition, the Toll‐like receptor (TLR) activates the innate immune response. Both CORO1A and TLR‐2 co‐localize on the phagosomal membrane in the dermal lesions of patients with lepromatous leprosy. Therefore, we hypothesized that CORO1A and TLR‐2 might interact functionally. This hypothesis was tested by investigating the effect of CORO1A in TLR‐2‐mediated signalling and, inversely, the effect of TLR‐2‐mediated signalling on CORO1A expression. We found that CORO1A suppresses TLR‐mediated signal activation in human macrophages, and that TLR2‐mediated activation of the innate immune response resulted in suppression of CORO1A expression. However, M. leprae infection inhibited the TLR‐2‐mediated CORO1A suppression and nuclear factor‐κB activation. These results suggest that the balance between TLR‐2‐mediated signalling and CORO1A expression will be key in determining the fate of M. leprae following infection.

Excess iodide decreases transcription of NIS and VEGF genes in rat FRTL-5 thyroid cells.

Although it is well known that an excess of iodide suppresses thyroid function and blood flow in vivo, the underlying molecular mechanisms are not fully known. The functional effect of iodide occurs at multiple steps, which include inhibition of sodium/iodide symporter (NIS) expression, transient block of organification, and inhibition of hormonal release. The vascular effect likely involves suppression of the vascular endothelial growth factor (VEGF) gene. In this report, we show that excess iodide coordinately suppresses the expression of the NIS and VEGF genes in FRTL-5 thyroid cells. We also demonstrate that the mechanism of iodide suppression of NIS gene expression is transcriptional, which is synergized by the addition of thyroglobulin. Based on the findings of reporter gene assays and electrophoretic gel mobility shift analysis, we also report two novel DNA binding proteins that responded specifically to iodide and modulated NIS promoter activity. The results suggest that excess iodide affects thyroid vascular function in addition to iodide uptake. This study provides additional insights into the mechanism of action of excess iodide on thyroid function.

Analysis of Mycobacterium leprae gene expression using DNA microarray.

Mycobacterium leprae, the causative agent of leprosy, does not grow under in vitro condition, making molecular analysis of this bacterium difficult. For this reason, bacteriological information regarding M. leprae gene function is limited compared with other mycobacterium species. In this study, we performed DNA microarray analysis to clarify the RNA expression profile of the Thai53 strain of M. leprae grown in footpads of hypertensive nude rats (SHR/NCrj-rnu). Of 1605 M. leprae genes, 315 showed signal intensity twofold higher than the median. These genes include Acyl-CoA metabolic enzymes and drug metabolic enzymes, which might be related to the virulence of M. leprae. In addition, consecutive RNA expression profile and in silico analyses enabled identification of possible operons within the M. leprae genome. The present results will shed light on M. leprae gene function and further our understanding of the pathogenesis of leprosy.

Detection of RNA expression from pseudogenes and non-coding genomic regions of Mycobacterium leprae.

We have previously reported that some pseudogenes are expressed in Mycobacterium leprae (M. leprae), the causative agent of leprosy, and that their expression levels alter upon infection of macrophages. We attempted to further examine the expression of pseudogene and non-coding genomic region in M. leprae, in this study. 19 Pseudogenes, 17 non-coding genomic regions, and 21 coding genes expression in M. leprae maintained in the footpads of the hypertensive nude rat (SHR/NCrj-rnu) were examined by reverse transcriptase polymerase chain reaction (RT-PCR). The expression of some of these pseudogenes, non-coding genomic regions and coding genes were also examined in M. leprae from skin smear specimens obtained from patients with lepromatous leprosy by RT-PCR. Transcripts from pseudogenes, non-coding genomic regions and coding genes examined in this study were clearly observed in M. leprae. The expression patterns of some of these transcripts vary greatly among different leprosy patients. These results indicate that some of pseudogenes and non-coding genomic regions are transcribed in M. leprae and analysis of RNA expression patterns including pseudogene and non-coding genomic region in M. leprae may be useful in understanding the pathological states of infected patients.

Expression of a thyroglobulin (Tg) variant in mouse kidney glomerulus

Thyroglobulin (Tg) is an essential substrate for thyroid hormone biosynthesis whose production is primarily limited to the thyroid follicular cell. We have previously identified an approximately 1.2 kb fragment of Tg mRNA in cultured mouse mesangial cells, and in the present study provide evidence showing that this transcript is transcribed and translated into a unique protein (kTg) in the kidney, but not the thyroid gland. Cloning of kTg from a mouse kidney cDNA library showed that transcription starts in the middle of intron 41 of the Tg gene and continues in-frame with the remaining coding sequence of thyroid-derived Tg beginning with exon 42. Translation of this mRNA is predicted to yield a protein of 367 amino acids (40 kDa) containing a unique 13 amino acid sequence serving as a signal peptide followed by a 354 amino acid segment identical to the carboxy-terminal end of thyroid Tg. Western blot analysis with an antibody directed against the C-terminus of thyroid Tg detected a 40 kDa protein expressed in the kidney. Immunohistochemistry with this antibody showed that immunoreactive Tg was localized in podocytes and the mesangial area of the renal glomerulus. A part of a homologous transcript was also detected in human kidney, and the kTg protein was recognized by sera from Hashimotos thyroiditis but not from controls. Together these results suggest that a unique low molecular weight variant of Tg is expressed in the kidney, where it could serve both physiological and pathological roles, including that of an autoantigen.