Noninvasive diagnosis of TRIT1-related mitochondrial disorder by measuring i6 A37 and ms2 i6 A37 modifications in tRNAs from blood and urine samples.

Subsets of mitochondrial transfer RNA (tRNA) contain the N6 -isopentenyladenosine (i6 A) or 2-methylthio-N6 -isopentenyladenosine (ms2 i6 A) modification at position A37, which is adjacent to an anticodon. These modifications are essential for efficient protein translation in mitochondria and contribute to energy metabolism. The first step in i6 A and ms2 i6 A modifications is catalyzed by tRNA isopentenyltransferase, which is encoded by the TRIT1 gene. Herein, we report a girl with a developmental delay, frequent episodes of seizures induced by febrile illness, and myoclonic epilepsy who had compound heterozygous missense mutations in TRIT1. A mass spectrometry analysis of RNA nucleoside obtained from the subject's peripheral blood and urine showed a marked decrease in both i6 A and ms2 i6 A modifications. These results suggest that the mitochondrial disorder was caused by defective tRNA isopentenylation arising from a loss-of-function mutation in TRIT1. Furthermore, the present observations suggest that noninvasive biochemical analysis using peripheral blood and urine samples are sufficient for the diagnosis of TRIT1-related disorders, making muscle biopsy for the direct measurement of oxidative phosphorylation unnecessary. Such biochemical analyses before the start of antiepileptic medications would be beneficial to avoid hepatotoxicity in patients with possible mitochondrial disorders.

Identification of urinary exosomal noncoding RNAs as novel biomarkers in chronic kidney disease.

In chronic kidney disease (CKD), the decline in the glomerular filtration rate is associated with increased morbidity and mortality and thus poses a major challenge for healthcare systems. While the contribution of tissue-derived miRNAs and mRNAs to CKD progression has been extensively studied, little is known about the role of urinary exosomes and their association with CKD. Exosomes are small, membrane-derived endocytic vesicles that contribute to cell-to-cell communication and are present in various body fluids, such as blood or urine. Next-generation sequencing approaches have revealed that exosomes are enriched in noncoding RNAs and thus exhibit great potential for sensitive nucleic acid biomarkers in various human diseases. Therefore, in this study we aimed to identify urinary exosomal ncRNAs as novel biomarkers for diagnosis of CKD. Since up to now most approaches have focused on the class of miRNAs, we extended our analysis to several other noncoding RNA classes, such as tRNAs, tRNA fragments (tRFs), mitochondrial tRNAs, or lincRNAs. For their computational identification from RNA-seq data, we developed a novel computational pipeline, designated as ncRNASeqScan. By these analyses, in CKD patients we identified 30 differentially expressed ncRNAs, derived from urinary exosomes, as suitable biomarkers for early diagnosis. Thereby, miRNA-181a appeared as the most robust and stable potential biomarker, being significantly decreased by about 200-fold in exosomes of CKD patients compared to healthy controls. Using a cell culture system for CKD indicated that urinary exosomes might indeed originate from renal proximal tubular epithelial cells.

The degradation rates of cytoplasmic tRNA, rRNA and mRNA in rats are elevated after infection with Nippostrongylus brasiliensis.

The effects of a parasitic infection with the nematode Nippostrongylus brasiliensis on the degradation rates of cytoplasmic tRNA, rRNA and mRNA in rats have been investigated by measuring the renal excretion rates of the modified RNA catabolites N6-threoninocarbonyladenosine, pseudouridine and 7-methylguanine. Between days 9 and 13 post-infection when the expulsion of N. brasiliensis is usually the most pronounced, the degradation rates of the different RNA classes were significantly higher than in the control rats (P < 0.05) by, on average, +24% (tRNA), +34% (rRNA) and +26% (mRNA). We suspect that the elevated degradation rates of RNA are related to an increased production of reactive oxygen species by the host during the expulsion of N. brasiliensis.

Excretion of RNA catabolites by rats with hepatoma transplants.

Rats with transplants of Morris Hepatoma 5123 excreted in their urine greater than normal amounts of modified nucleosides and bases, catabolites of RNA. Despite rapid growth of the neoplasm, the elevated levels did not appear until 22 days after inoculation with the tumor. With tumor progression, there were increased levels and number of these catabolites. This study also suggests that the source of the elevated RNA catabolites is mainly from the host RNA rather than from tumor tissue and also that mRNA and rRNA as well as tRNA may contribute to the urinary levels.

Transfer RNA breakdown products in the urine of asbestos workers.

Patients with malignant mesothelioma, a neoplasia strongly associated with previous asbestos exposure, excrete in the urine high levels of modified purines, pyrimidines, and their ribosides, breakdown products of transfer RNA. The urinary excretion levels of modified nucleosides were measured in 47 male insulation workers with long term exposure to asbestos and, therefore, at high neoplastic risk. The nucleoside levels of 44 male control subjects were used for comparison. Asbestos-related radiographic changes were found in 70% of the exposed individuals. An increasing severity of radiographic alterations was associated with a greater frequency of elevated nucleoside clusters, especially in m'A, m'I, m'G, and m2(2)G. Duration since onset of exposure was directly related to pseudouridine, m'I, and m2(2)G. Though cigarette smoking contributes to the development of asbestos-related lung cancer, data are presented that support the hypothesis that asbestos exposure is the more important factor related to the elevated values of nucleosides. It was concluded, therefore, that measuring nucleoside levels in populations at high risk of developing certain kinds of cancer may provide a useful diagnostic tool for detecting "preclinical" biochemical changes that may be predictive of future neoplastic manifestations.

Study of nucleic acid metabolism in two astronauts.

During the last years data have evidenced that alteration in nucleic acid metabolism, expecially increased urinary excretion of modified nucleosides reflects physiological changes in living organism. In relation with the Soyuz-36-Salyut-6-Soyuz-35 mission in 1980 urinary nucleoside excretion of two astronauts /B.F., V.K./ were traced. Individual daily urine samples were collected for 4 days before starting and 6 days after landing and were analysed with improved analytical procedures /affinity chromatography, high Performance liquid chromatography/. Levels of 1-methylinosine, 1-methylguanosine and N,2,2-dimethylguanosine in urine were determined. Thus recorded changes differ considerably at two astronauts. One of the /V.K./ excreted nucleosides normally, another /B.F./ showed increase to 200-400 % levels excretion of above nucleosides on the second day after landing. The peak values disappeared on the 3-6 days after. To interpret this phenomenon extreme factors of space-flight /weightlessness, stress, radiations, etc./ have to be taken into consideration. However, we attach importance to training of astronauts. During the last decade data have evidenced that alterations in the metabolism of nucleic acids especial increased urinary excretion of modified nucleosides reflects physiological and in some cases pathological changes in living organism. In relation with the Soyuz-36-Salyut-6-Soyuz 35 mission urinary excretion of certain modified nucleosides of two astronauts /B.F. and V.K./ were measured. The aim of the measurements was: how the metabolism of transfer ribonucleic acids /tRNAs/ referring to cosmic flight, how it is reflected in urinary excretions of modified nucleosides. For these purposes we studied the excretion of methylguanosine, dimethylguanosine and methylinosine. These nucleosides are the normal minor components of tRNA.

Urinary excretion of modified nucleosides in patients with malignant mesothelioma.

Transfer RNA is the most complex biomacromolecule in both structure and function. The complexity of its structure is caused by a large variety of enzymes which add modifying groups to the four bases after the primary synthesis. The most abundant of these enzymes are the transfer RNA methylases, which add methyl groups at various positions in the macromolecule. These methylating enzymes were found to be, without exception, aberrantly hyperactive in every malignant tumor examined. In turn, every malignant tumor contains a few transfer RNAs that are different in structure from the transfer RNAs in the normal tissue. Again, there is no exception. These are the first qualitatively different biochemical components of every malignant cell, not more or less but different transfer RNAs. The late Alexander Gutman observed that cancer patients excrete in their urine elevated levels of certain methylated bases. From the structure of these bases and our knowledge of their method of synthesis, it became apparent that most of them come from the breakdown of transfer RNA. Their elevation in the urine stems from an extraordinarily high rate of turnover of transfer RNAs in tumor tissue. Highly sophisticated, sensitive methods of analysis were developed for the determination of the modified nucleosides in the urine of cancer patients. When related to the creatinine level of the urine, some of the modified nucleosides and products derived from them were elevated in a large variety of tumors. Perhaps more importantly, it was found that these elevated levels return to normal after effective chemotherapy. Thus, these markers may also be useful in monitoring the effectiveness of therapy. We report here initial studies on the detection of cancer in asbestos workers and possible premalignant conditions in workers with asbestosis.

tRNA breakdown products as markers for cancer.

Seven breakdown products of tRNA were quantitated by high pressure liquid chromatography in urine and were related to the creatinine content. In the urine of 26 of 27 patients with 13 different malignancies, there was an elevation of one or more of these "markers." The levels of excretion vary approximately with the stage of the disease.

Composition, associated tissue methyltransferase activity, and catabolic end products of transfer RNA from carcinogen-induced hepatoma and normal monkey livers.

This investigation was designed to explore transfer RNA (TRNA) methyltransferase activity, urinary excretion levels of tRNA degradation products, and tRNA base composition in normal monkeys and in those with hepatocellular carcinomas induced by N-nitrosodiethylamine. After the development of the tumor, 24-hr urine specimens were collected, the monkeys were sacrificed, and the livers were removed for tRNA isolation and methyltransferase activity studies. The tRNA methyltransferase activity and capacity and the urinary excretion levels for selected tRNA degradation products (pseudouridine, N2,N2-dimethylguanosine, 1-methylinosine, 7-methylguanine, and beta-aminoisobutyric acid) were elevated for the hepatoma-bearing monkeys when compared to those with normal liver. The isolated tRNA pools were analyzed by high-resolution liquid chromatography, and similar base compositions were found for the hepatoma-bearing and normal monkeys. With the use of methyl-deficient Escherichia coli tRNA as the methyl receptor and the analytical procedure for tRNA anlysis, the methylating ability of the tRNA methyltransferases in hepatoma and normal liver extracts was determined. The hepatoma methyltransferase homogenates were found to produce increased levels of 7-methylguanine, N2,N2-dimethylguanine, and thymine, while the normal liver extracts gave higher levels of N2-methylguanine. These differences were not apparent in the base composition of the tRNA pools. The increased urinary excretion and higher methyltransferase activity of the hepatoma-bearing monkeys without an apparent increase in the methylated base content of their tRNA suggest increased tRNA tf individual isoaccepting tRNA's would be missed by analyzing the tRNA pools. The variations in the individual tRNA methyltransferase activities of the hepatoma and normal liver homogenates indicate a difference in the methlation of their tRNA's.

Determination of trimethylsilyl methylated nucleic acid bases in urine by gas-liquid chromatography.

A method for the determination of the urinary excretion level of methylated nucleic acid bases by gas-liquid chromatography (GLC) has been developed. A clean-up procedure prior to GLC analysis consisted of hydrolysis, filtration, charcoal adsorption, and anion exchange. Studies to determine optimum derivatization conditions for conversion of the methylated bases to their trimethylsilyl derivatives and to evaluate GLC parameters and columns to obtain the best separation were conducted. Application of the method was shown by determining the excretion levels of methylated bases in urine of normal controls and of patients with various types of malignancy.

High-resolution liquid chromatographic analysis of methylated purine and pyrimidine bases in transfer RNA.

Methylated and major purine and pyrimidine bases were separated and quantified by high-resolution liquid chromatography after hydrolyzing transfer ribonucleic acids (tRNAs). Separation was accomplished by eluting the hydrolyzed samples from an anion-exchange column with a concentration gradient of ammonium acetate at pH 9.2. Isolated sample of tRNA were hydrolyzed to the free bases with a trifluoroacetic acid-formic acid mixture of 200 degrees. Detection limits of 100-200 ng/ml were measured for the methylated bases; analytical data are reported for ten methylated bases plus the four major bases of calf liver and rat liver tRNA.