KRAS mutation effects on the 2-[18F]FDG PET uptake of colorectal adenocarcinoma metastases in the liver

Background

Deriving individual tumor genomic characteristics from patient imaging analysis is desirable. We explore the predictive value of 2-[18F]FDG uptake with regard to the KRAS mutational status of colorectal adenocarcinoma liver metastases (CLM).

Methods

2-[18F]FDG PET/CT images, surgical pathology and molecular diagnostic reports of 37 patients who underwent PET/CT-guided biopsy of CLM were reviewed under an IRB-approved retrospective research protocol. Sixty CLM in 39 interventional PET scans of the 37 patients were segmented using two different auto-segmentation tools implemented in different commercially available software packages. PET standard uptake values (SUV) were corrected for: (1) partial volume effect (PVE) using cold wall-corrected contrast recovery coefficients derived from phantom spheres with variable diameter and (2) variability of arterial tracer supply and variability of uptake time after injection until start of PET scan derived from the tumor-to-blood standard uptake ratio (SUR) approach. The correlations between the KRAS mutational status and the mean, peak and maximum SUV were investigated using Student’s t test, Wilcoxon rank sum test with continuity correction, logistic regression and receiver operation characteristic (ROC) analysis. These correlation analyses were also performed for the ratios of the mean, peak and maximum tumor uptake to the mean blood activity concentration at the time of scan: SUR_MEAN, SUR_PEAK and SUR_MAX, respectively.

Results

Fifteen patients harbored KRAS missense mutations (KRAS+), while another 3 harbored KRAS gene amplification. For 31 lesions, the mutational status was derived from the PET/CT-guided biopsy. The Student’s t test p values for separating KRAS mutant cases decreased after applying PVE correction to all uptake metrics of each lesion and when applying correction for uptake time variability to the SUR metrics. The observed correlations were strongest when both corrections were applied to SUR_MAX and when the patients harboring gene amplification were grouped with the wild type: p ≤ 0.001; ROC area under the curve = 0.77 and 0.75 for the two different segmentations, respectively, with a mean specificity of 0.69 and sensitivity of 0.85.

Conclusion

The correlations observed after applying the described corrections show potential for assigning probabilities for the KRAS missense mutation status in CLM using 2-[18F]FDG PET images.

Naturally occurring R225W mutation of the gene encoding AMP-activated protein kinase (AMPK)gamma(3) results in increased oxidative capacity and glucose uptake in human primary myotubes

AIMS/HYPOTHESIS

AMP-activated protein kinase (AMPK) has a broad role in the regulation of glucose and lipid metabolism making it a promising target in the treatment of type 2 diabetes mellitus. We therefore sought to characterise for the first time the effects of chronic AMPK activation on skeletal muscle carbohydrate metabolism in carriers of the rare gain-of-function mutation of the gene encoding AMPKgamma(3) subunit, PRKAG3 R225W.

METHODS

Aspects of fuel metabolism were studied in vitro in myocytes isolated from vastus lateralis of PRKAG3 R225W carriers and matched control participants. In vivo, muscular strength and fatigue were evaluated by isokinetic dynamometer and surface electromyography, respectively. Glucose uptake in exercising quadriceps was determined using [(18)F]fluorodeoxyglucose and positron emission tomography.

RESULTS

Myotubes from PRKAG3 R225W carriers had threefold higher mitochondrial content (p < 0.01) and oxidative capacity, higher leak-dependent respiration (1.6-fold, p < 0.05), higher basal glucose uptake (twofold, p < 0.01) and higher glycogen synthesis rates (twofold, p < 0.05) than control myotubes. They also had higher levels of intracellular glycogen (p < 0.01) and a trend for lower intramuscular triacylglycerol stores. R225W carriers showed remarkable resistance to muscular fatigue and a trend for increased glucose uptake in exercising muscle in vivo.

CONCLUSIONS/INTERPRETATION

Through the enhancement of skeletal muscle glucose uptake and increased mitochondrial content, the R225W mutation may significantly enhance exercise performance. These findings are also consistent with the hypothesis that the gamma(3) subunit of AMPK is a promising tissue-specific target for the treatment of type 2 diabetes mellitus, a condition in which glucose uptake and mitochondrial function are impaired.

Stable expression in yeast of the mature form of human telomerase RNA depends on its association with the box H/ACA small nucleolar RNP proteins Cbf5p, Nhp2p and Nop10p

Telomerase is a ribonucleoprotein (RNP) particle required for the replication of telomeres. The RNA component, termed hTR, of human telomerase contains a domain structurally and functionally related to box H/ACA small nucleolar RNAs (snoRNAs). Furthermore, hTR is known to be associated with two core components of H/ACA snoRNPs, hGar1p and Dyskerin (the human counterpart of yeast Cbf5p). To assess the functional importance of the association of hTR with H/ACA snoRNP core proteins, we have attempted to express hTR in a genetically tractable system, Saccharomyces cerevisiae. Both mature non-polyadenylated and polyadenylated forms of hTR accumulate in yeast. The former is associated with all yeast H/ACA snoRNP core proteins, unlike TLC1 RNA, the endogenous RNA component of yeast telomerase. We show that the presence of the H/ACA snoRNP proteins Cbf5p, Nhp2p and Nop10p, but not Gar1p, is required for the accumulation of mature non-polyadenylated hTR in yeast, while accumulation of TLC1 RNA is not affected by the absence of any of these proteins. Our results demonstrate that yeast telomerase is unrelated to H/ACA snoRNPs. In addition, they show that the accumulation in yeast of the mature RNA component of human telomerase depends on its association with three of the four core H/ACA snoRNP proteins. It is likely that this is the case in human cells as well.

Genetic and physical interactions involving the yeast nuclear cap-binding complex

Yeast strains lacking the yeast nuclear cap-binding complex (yCBC) are viable, although impaired in growth. We have taken advantage of this observation to carry out a genetic screen for components that show synthetic lethality (SL) with a cbp20-Delta cbp80-Delta double mutation. One set of SL interactions was due to mutations that were complemented by components of U1 small nuclear RNP (snRNP) and the yeast splicing commitment complex. These interactions confirm the role of yCBC in commitment complex formation. Physical interaction of yCBC with the commitment complex components Mud10p and Mud2p, which may directly mediate yCBC function, was demonstrated. Unexpectedly, we identified multiple SL mutations that were complemented by Cbf5p and Nop58p. These are components of the two major classes of yeast small nucleolar RNPs, which function in the maturation of rRNA precursors. Mutants lacking yCBC were found to be defective in rRNA processing. Analysis of the yCBC deletion phenotype suggests that this is likely to be due to a defect in the splicing of a subset of ribosomal protein mRNA precursors.

Cloning and characterization of the KlDIM1 gene from Kluyveromyces lactis encoding the m2(6)A dimethylase of the 18S rRNA

The KlDIM1 gene encoding the m2(6)A rRNA dimethylase was cloned from a Kluyveromyces lactis genomic library using a PCR amplicon from the Saccharomyces cerevisiae ScDIM1 gene as probe. The KlDIM1 gene encodes a 320-amino acid protein which shows 81% identity to ScDim1p from S. cerevisiae and 25% identity to ksgAp from Escherichia coli. Complementation of the kasugamycin-resistant ksgA-mutant of E. coli lacking dimethylase activity demonstrates that KlDim1p is the functional homologue of the bacterial enzyme. Multiple alignment of dimethylases from prokaryotes and yeasts shows that the two yeast enzymes display distinctive structural motives including a putative nuclear localization signal.

Update of the viroid and viroid-like sequence database: addition of a hepatitis delta virus RNA section

Recently, we developed and made available an online database that includes all the reported (to our knowledge) viroid and viroid-like RNA sequences [Bussire,F., Lafontaine,D. and Perreault,J.-P. (1996)Nucleic Acids Res.24, 1793-1798]. We report here an update of this catalogue which includes the addition of a new section devoted to human hepatitis delta virus (vHDV) sequences. This new section comprises all available vHDV sequences, irrespective of their completeness, which have been either published or were available from nucleic acid libraries. Additional structural characteristics of the vHDV genome, such as the positions of the self-catalytic domains, the antigen open reading frames, etc., are also included. The catalogue is available on the World Wide Web (see text) in a user-friendly form. It should provide an excellent reference point for further molecular studies of these small circular pathogenic RNAs.

One-step PCR mediated strategy for the construction of conditionally expressed and epitope tagged yeast proteins

With the availability of the complete yeast genomic sequence, techniques which allow the rapid functional analysis of genes of interest are of increasing importance. Here we report a technique which allows the initial characterisation of genes of interest, through the construction of conditionally expressed mutations for functional analyses and the generation of epitope-tagged fusion proteins for immuno-localisation and immuno-purification, entirely by PCR.

Compilation and analysis of viroid and viroid-like RNA sequences

We have created a catalogue comprising all viroid and viroid-like RNA sequences which to our knowledge have been either published or were available from on-line sequence libraries as of October 1, 1995. In the development of this catalogue nomenclature ambiguities were removed, the likely ancestral sequence of most species was determined and the most stable secondary structures of these sequences were predicted using the MulFold package. Only viroids of PSTVd-type possessed a rod-like secondary structure, while most other viroids adopted branched secondary structures. Several viroids have predicted secondary structures that include either a Y or cruciform structure reminiscent of the tRNA-like end of virus genomes at an extremity. However, it remains unknown whether or not these predicted structures are adopted in solution, and if they serve a particular function in vivo. Additional information such as the position of the self-catalytic domains are included in the catalogue. An analysis of the data compilated in the catalogue is included. The catalogue will be available on the world wide web (http://www.callistro.si.usherb.ca/jpperra), on computer disk and in printed form. It should provide an excellent reference point for further studies.

Trans-acting factors in yeast pre-rRNA and pre-snoRNA processing

The major intermediates in the pathway of pre-rRNA processing in yeast and other eukaryotes were originally identified by biochemical analyses. However, as a result of the analysis of the effects of mutations in trans-acting factors, the yeast pre-rRNA processing pathway is now characterized in far more detail than that of other eukaryotes. These analyses have led to the identification of processing sites and intermediates that were either too close in size or too short lived to detected by biochemical analyses alone. In addition, it was generally unclear whether pre-rRNA processing steps were endonucleolytic or exonucleolytic; analyses of trans-acting factors is now revealing a complex mixture of endonucleolytic and exonucleolytic processing steps. Many of the small nucleolar RNAs (snoRNAs) are excised from larger precursors. Analyses of trans-acting factors are also revealing details of pre-snoRNA processing in yeast. Interestingly, factors involved in pre-snoRNA processing turn out to be components that also function in pre-rRNA processing, suggesting a potential mechanism for the coregulation of rRNA and snoRNA synthesis. In general, very little is known about the regulation of pre-rRNA processing steps. The best candidate for a system regulating specific pre-rRNA processing reactions has recently been revealed by the analysis of a yeast pre-RNA methylase. Here we will review recent data on the trans-acting factors involved in yeast ribosome synthesis and discuss how these analyses have contributed to our current view of this complex process.

The 18S rRNA dimethylase Dim1p is required for pre-ribosomal RNA processing in yeast

The m6(2)A1779m6(2)A1780 dimethylation at the 3' end of the small subunit rRNA has been conserved in evolution from bacteria to eukaryotes. The yeast 18S rRNA dimethylase gene DIM1 was cloned previously by complementation in Escherichia coli and shown to be essential for viability in yeast. A conditional GAL10::dim1 strain was constructed to allow the depletion of Dim1p from the cell. During depletion, dimethylation of the pre-rRNA is progressively inhibited and pre-rRNA processing at cleavage sites A1 and A2 is concomitantly lost. In consequence, the mature 18S rRNA and its 20S precursor drastically underaccumulate. This has the effect of preventing the synthesis of nonmethylated rRNA. To test whether the processing defect is a consequence of the absence of the dimethylated nucleotides or of the Dim1p dimethylase itself, a cis-acting mutation was created in which both dimethylated adenosines are replaced by guanosine residues. Methylation cannot occur on this mutant pre-rRNA, but no clear pre-rRNA processing defect is seen. Moreover, methylation of the wild-type pre-rRNA predominantly occurs after cleavage at sites A1 and A2. This shows that formation of the m6(2)A1779m6(2)A1780 dimethylation is not required for pre-rRNA processing. We propose that the binding of Dim1p to the pre-ribosomal particle is monitored to ensure that only dimethylated pre-rRNA molecules are processed to 18S rRNA.

Intra- and intermolecular nonenzymatic ligations occur within transcripts derived from the peach latent mosaic viroid

We report here the nonenzymatic self-ligation of transcripts corresponding to the peach latent mosaic viroid (PLMVd). This is the first description of this process with viroid sequences, although it has been reported to occur with human hepatitis delta virus RNA. Self-ligation occurs when the 5'-hydroxyl and the 2',3'-cyclic phosphate termini produced by the hammerhead self-cleavage of the viroid RNA are juxtaposed by the viroid rod-like structure, and a phosphodiester bond is formed between the two following hydrolysis of the cyclic phosphate. Unit-length transcripts undergo intramolecular folding, and their subsequent self-ligation produces circular molecules. The self-ligation observed in vitro may contribute to PLMVd circularization during rolling circle replication; however, this does not exclude the possibility that a host RNA ligase catalyzes the ligation steps in vivo. Like self-cleavage, self-ligation is probably an ancestral reaction, and the enzyme-catalyzed ligation most likely evolved from this primitive mechanism. Furthermore, the intermolecular self-ligation of annealed transcripts derived from PLMVd is demonstrated, suggesting a possible mechanism for sequence reassortment in viroids.

The DIM1 gene responsible for the conserved m6(2)Am6(2)A dimethylation in the 3'-terminal loop of 18 S rRNA is essential in yeast

Biogenesis of cytoplasmic ribosomes universally involves methylation of ribosomal RNA. Little genetic evidence is available about the functional role(s) of this conserved posttranscriptional modification. The only known methylase gene involved in rRNA maturation is ksgA in Escherichia coli, which directs dimethylation of two adjacent adenosines (m6(2)A1518m6(2)A1519) in the loop of a conserved hairpin near the 3'-end of 16 S rRNA. This tandem methylation is the only rRNA modification common to pro and eukaryotes. Disruption of ksgA confers resistance to the aminoglycoside antibiotic kasugamycin without significantly impairing viability. Here we report the cloning of the DIM1 gene encoding the homolog 18 S rRNA dimethylase in Saccharomyces cerevisiae. The yeast enzyme is evolutionary related to the ksgA protein. It carries a distinctive lysine-rich-N-terminal extension with a potential protein kinase C phosphorylation site. Like ksgA, DIM1 belongs to the erm family of prokaryotic 23 S rRNA dimethylases responsible for erythromycin resistance. Surprisingly, disruption of DIM1 turns out to be lethal in yeast.

Direction of transcription in bacteriophage T5 first-step transfer DNA

The transcription of the T5 first-step transfer genes A2 and A3 has been shown to proceed from right to left (i.e., from A3 to A2) on the T5 DNA molecule.