Direct mRNA Sequencing Research Articles

LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data.

While several well-established quality control (QC) tools are available for short reads sequencing data, there is a general paucity of computational tools that provide long read metrics in a fast and comprehensive manner across all major sequencing platforms (such as PacBio, Oxford Nanopore, Illumina Complete Long Read) and data formats (such as ONT POD5, FAST5, basecall summary files and PacBio unaligned BAM). Additionally, none of the current tools provide support for summarizing Oxford Nanopore basecall signal or comprehensive base modification (methylation) information from genomic data. Furthermore, nowadays a single PromethION flowcell on the Oxford Nanopore platform can generate terabytes of signal data, which cannot be handled by existing tools designed for small-scale flowcells. To address these challenges, here we present LongReadSum, a multi-threaded C++ tool which provides fast and comprehensive QC reports on all major aspects of sequencing data (such as read, base, base quality, alignment, and base modification metrics) and produce basecalling signal intensity information from the Oxford Nanopore platform. We demonstrate use cases to analyze cDNA sequencing, direct mRNA sequencing, reduced representation methylation sequencing (RRMS) through adaptive sequencing, as well as whole genome sequencing (WGS) data using diverse long-read platforms.

Abstract PO1-23-11: Differential m6A modification identified by direct RNA sequencing in endocrine- resistant and sensitive breast cancer cells

Abstract A major limitation of current adjuvant treatments for the ~ 70% of breast cancer patients with estrogen receptor α–expressing (ER+) primary breast tumors is the development of acquired and adaptive endocrine therapy (ET) resistance and metastatic spread. Chemical modifications of transcribed RNAs alters their cellular location, stability, and, for mRNAs, translation into proteins. N-6 methyladenosine (m6A) is the most common modification of mRNA. We tested the hypothesis that m6A epitranscriptomic changes alters the transcriptome resulting in changes in targets in pathways contributing to the metastatic cascade in ET-resistant breast cancer cells. We used an unbiased approach of direct mRNA sequencing using the Oxford Nanopore MinION platform on polyA-selected mRNA from MCF-7 luminal A breast cancer cells and ER+, ET-resistant LCC9 breast cancer cells treated with vehicle control or 100 nM 4-hydroxytamoxifen (4-OHT) for 24 h. In addition, MCF-7 cells were treated with the METTL3 (the catalytic methyltransferase that adds the methyl group from S-adenosylmethionine (SAM) to the adenosine on the N6 position) inhibitor STM2457 to identify m6A positions and transcripts directly regulated by METTL3 activity. Computational analysis directly identified m6A locations in transcripts. We examined the differential modification rate (DMR) between MCF-7 cells +/STM2457 treatment, between MCF-7 and LCC9 cells with vehicle control treatment or with 4-OHT treatment and within each cell line with 4-OHT treatment. We identified 183 and 3,097 genes with m6A DMRs between vehicle-treated and 4-OHT-treated MCF-7 and LCC9 cells, respectively. For 4-OHT-treated cells, we identified 2,401 and 2,638 genes with m6A DMRs in MCF-7 and LCC9 cells respectively with 1,760 genes in common. We identified many genes with multiple m6A modifications, e.g., AMIGO2 appeared to have 14 m6A sites at DRACH motifs in MCF-7 cells, but none were m6A modified in LCC9 cells. Enrichment by Pathway Maps, Process Networks, and GO Processes were performed. Overall, our data suggest a role for altered m6A positions in transcripts and pathways involved in ET-resistance in breast cancer. Citation Format: Belinda Petri, Bailey Valdes, Kellianne Piell, Eric Rouchka, Carolyn Klinge. Differential m6A modification identified by direct RNA sequencing in endocrine- resistant and sensitive breast cancer cells [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-23-11.

Unraveling the RNA Tapestry: A Symphony of Innovations in m6A Research Technology

AbstractThis review navigates the evolving landscape of N6‐methyladenosine (m6A) research approaches, emphasizing the importance of advanced technology in understanding RNA epigenetics. Beginning with the fundamentals of m6A and the need for high‐ throughput methods, the investigation progresses from low‐throughput approaches to high‐throughput technologies, encompassing antibody‐dependent and antibody‐free sequencing methods, as well as nanopore‐based direct mRNA sequencing and computation methods for m6A detection. Spatial techniques and imaging tools for m6A are also introduced in addition. The discussion of their special applications emphasizes the biological significance of absolute quantification, single‐nucleotide resolution, single‐molecule detection, and single‐cell profiling. The review concludes with a vision of ideal approaches that combine current technologies for comprehensive m6A sequencing, with the potential to further our understanding of gene regulation, cellular diversity, and their roles in health and disease.

Epigenetic landscape of intestinal cell line HT29 cocultured with Lacticaseibacillus.

Aim: To investigate the changes in epigenetic landscape of HT29 cells upon coculture with the Lacticaseibacillus.Materials & methods: Histone and m6A mRNA modifications were examined by biochemical and NGS-based methods including western blotting, colorimetric assays, ChIP-Seq and direct mRNA sequencing. LC-MS was performed to identify Lacticaseibacillus secretome.Results: In cocultured HT29 cells global enrichment of H3K9ac and H3K4me3 and depletion of H3K9me3 mark was observed; mean genic positional signals showed depletion of H3K9ac and H3K4me3 at the TSS but enrichment in the upstream region; m6A methylation was altered in mRNAs corresponding to specific gene pathways; Lacticaseibacillus HU protein interacts with histone H3.Conclusion: Lacticaseibacillus can epigenetically alter specific genetic pathways in human intestinal cells.

Cumulative autophagy insufficiency in mice leads to progression of β-cell failure

Autophagy is known to play a pivotal role in β-cell function. While the lifelong inhibition of autophagy through Atg7 deletion in β cells has been demonstrated to lead to impaired glucose tolerance together with β-cell dysfunction, the temporal association between autophagy inhibition and β-cell dysfunction remains unclear. To address such questions, inducible β-cell-specific Atg7-knockout (iβAtg7KO) mice were generated, and autophagy inhibition was induced for two different time durations. Whereas 2 weeks of Atg7 ablation was sufficient to induce autophagy deficiency, confirmed by the accumulation of p62, iβAtg7KO mice exhibited normal glucose tolerance. In contrast, prolonged autophagy deficiency for 6 weeks resulted in glucose intolerance together with impaired insulin secretion. Direct mRNA sequencing and pathway analysis revealed that the gene set associated with insulin secretion was downregulated only after the 6-week prolonged autophagy inhibition. Furthermore, we identified a novel gene, Sprr1a, which was expressed at more than 50-fold higher levels during both the 2-week and 6-week autophagy inhibition. These findings suggest that autophagy insufficiency cumulatively leads to β-cell failure after a certain interval, accompanied by stepwise alterations of gene expression patterns.

Exploring the potential of mRNA for taxonomic delineation of marine benthic eukaryotes.

Direct sequencing of mRNA isolated from environmental samples has been commonly used to analyze the functional activity of ambient communities and, occasionally used for taxonomic identification. Here we assess the viability of using mRNA for investigating the species composition of marine benthic eukaryotes. Total RNA was extracted from sediments sampled close to fish farms and mRNA was sequenced after poly-A enrichment on an Illumina MiSeq sequencer. We investigated the origin of both raw reads and assembled contigs by aligning them to the NCBI non-redundant (nr/nt) nucleotide database. Although sequences were predominantly of eukaryotic origin, the analyses were complicated both by experimental and database artefacts. These issues were addressed by applying filtering procedures that removed the majority of ambiguous sequences from downstream analyses. These processes resulted in a set of 436 high-confidence contigs, the vast majority of which mapped to benthic organisms. Our alignments were dominated by annelids, consistent with burrowing groups found in a parallel morphological analysis. This study shows that it is possible to obtain adequate taxonomic information from the RNA of an eukaryotic community from a limited sample at a moderate cost, demonstrates how both laboratory and in silico artefacts can be overcome through appropriate bioinformatic procedures, and finally highlights some of the drawbacks and caveats of using NCBI as a reference database for such a dataset.

Splice variants of mRNA of cytochrome P450 genes: analysis by the nanopore sequencing method in human liver tissue and HepG2 cell line

The analysis of cytochrome P450 transcripts was carried out by the nanopore sequencing in liver tissue samples of three donors and HepG2 line cells. It has been demonstrated that direct mRNA sequencing with a MinION nanopore sequencer (Oxford Nanopore Technologies) allows one to obtained quantitative profiles for transcripts (and their splice variants) of cytochrome P450 superfamily genes encoding isoforms involved in metabolism of the large (~80%) part of drugs. The splice variant profiles substantially differ for donors. The cytochrome P450 gene expression at the transcript level is significantly weaker in cells of the HepG2 line compared with that in the normal liver tissue. This limits the capability of the direct mRNA nanopore sequencing for studying alternative splicing of cytochrome P450 transcripts in HepG2 cells. Both quantitative and qualitative profiles of the cytochrome P450 gene expression at the transcript level are notably differ in human liver tissue and HepG2 cells.

LIQA: long-read isoform quantification and analysis

Long-read RNA sequencing (RNA-seq) technologies can sequence full-length transcripts, facilitating the exploration of isoform-specific gene expression over short-read RNA-seq. We present LIQA to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read direct mRNA sequencing or cDNA sequencing data. LIQA incorporates base pair quality score and isoform-specific read length information in a survival model to assign different weights across reads, and uses an expectation-maximization algorithm for parameter estimation. We apply LIQA to long-read RNA-seq data from the Universal Human Reference, acute myeloid leukemia, and esophageal squamous epithelial cells and demonstrate its high accuracy in profiling alternative splicing events.

LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing

BackgroundLong-read RNA-Seq techniques can generate reads that encompass a large proportion or the entire mRNA/cDNA molecules, so they are expected to address inherited limitations of short-read RNA-Seq techniques that typically generate < 150 bp reads. However, there is a general lack of software tools for gene fusion detection from long-read RNA-seq data, which takes into account the high basecalling error rates and the presence of alignment errors.ResultsIn this study, we developed a fast computational tool, LongGF, to efficiently detect candidate gene fusions from long-read RNA-seq data, including cDNA sequencing data and direct mRNA sequencing data. We evaluated LongGF on tens of simulated long-read RNA-seq datasets, and demonstrated its superior performance in gene fusion detection. We also tested LongGF on a Nanopore direct mRNA sequencing dataset and a PacBio sequencing dataset generated on a mixture of 10 cancer cell lines, and found that LongGF achieved better performance to detect known gene fusions over existing computational tools. Furthermore, we tested LongGF on a Nanopore cDNA sequencing dataset on acute myeloid leukemia, and pinpointed the exact location of a translocation (previously known in cytogenetic resolution) in base resolution, which was further validated by Sanger sequencing.ConclusionsIn summary, LongGF will greatly facilitate the discovery of candidate gene fusion events from long-read RNA-Seq data, especially in cancer samples. LongGF is implemented in C++ and is available at https://github.com/WGLab/LongGF.

The green impact: bacterioplankton response toward a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches.

Phytoplankton blooms exhibit a severe impact on bacterioplankton communities as they change nutrient availabilities and other environmental factors. In the current study, the response of a bacterioplankton community to a Phaeocystis globosa spring bloom was investigated in the southern North Sea. For this purpose, water samples were taken inside and reference samples outside of an algal spring bloom. Structural changes of the bacterioplankton community were assessed by amplicon-based analysis of 16S rRNA genes and transcripts generated from environmental DNA and RNA, respectively. Several marine groups responded to bloom presence. The abundance of the Roseobacter RCA cluster and the SAR92 clade significantly increased in bloom presence in the total and active fraction of the bacterial community. Functional changes were investigated by direct sequencing of environmental DNA and mRNA. The corresponding datasets comprised more than 500 million sequences across all samples. Metatranscriptomic data sets were mapped on representative genomes of abundant marine groups present in the samples and on assembled metagenomic and metatranscriptomic datasets. Differences in gene expression profiles between non-bloom and bloom samples were recorded. The genome-wide gene expression level of Planktomarina temperata, an abundant member of the Roseobacter RCA cluster, was higher inside the bloom. Genes that were differently expressed included transposases, which showed increased expression levels inside the bloom. This might contribute to the adaptation of this organism toward environmental stresses through genome reorganization. In addition, several genes affiliated to the SAR92 clade were significantly upregulated inside the bloom including genes encoding for proteins involved in isoleucine and leucine incorporation. Obtained results provide novel insights into compositional and functional variations of marine bacterioplankton communities as response to a phytoplankton bloom.

Abstract 793: Preclinical study of efficacy and specificity of p53-reactivating drugs in multiple myeloma, identification of biomarkers.

Abstract In this study, the efficacy of RITA (Reactivating p53 and Inducing Tumor Apoptosis) to kill multiple myeloma (MM) cells was evaluated in comparison to that of nutlin3a (MDM2 inhibitor) and in relation to the TP53 status of 32 human myeloma cell lines (HMCLs, 9 wt, 15 mutated, 6 truncated, 2 KO) and primary samples (n=19). This panel of HMCLs is representative of the molecular diversity of patients for both the chromosomal abnormalities (14q32 translocation) and the TP53 status, and thus allows us to perform an accurate evaluation of both the specificity and efficacy of molecules. TP53 status of HMCLs was established by direct sequencing of TP53 mRNA while that of primary cells was evaluated by the presence of chromosome 17p deletion (del17p), which is strong adverse prognostic value for patients with MM. Both drugs induced the apoptosis of MM cells, as shown by the loss of CD138 expression (a marker of viability for myeloma cells), Apo2.7 staining, appearance of a subG1 peak and activation of caspases 3 and 9. RITA induced cell death in about one third of HMCLs and primary samples. The apoptosis induced by RITA was not related to the t(14q32) or TP53 status of HMCLs or primary samples (p=0.52 and p=0.96, respectively). RITA failed to increase the expression level of p53 or of p53 targets i.e., Noxa, p21, Bax or DR5 in sensitive cells. In primary samples, RITA slightly increased DR5 expression in resistant samples without del17p and decreased it in sensitive samples with or without del17p. RITA failed to modulate p53 re-localization to the mitochondria or nucleus in sensitive cells. Finally, silencing of p53 in two highly sensitive TP53mutated HMCLs failed to inhibit apoptosis induced by RITA, confirming that the RITA-induced apoptosis in myeloma cells was p53 independent. In contrast, the apoptosis induced by nutlin3a was directly linked to the TP53 status of HMCLs and primary samples (p&amp;lt;0.001 and p=0.026, respectively) and nutlin3a increased the level of both p53 and p53 targets in a p53-dependent manner. Moreover, nutlin3a increased p53 localization to the mitochondria and nucleus only in TP53wt HMCLs in good agreement with cell death response. In primary cells, we further showed that a nutlin3a-induced DR5 increase (≥1.2 fold increase) was a specific and sensitive marker (p=0.0001) of a weak incidence of del17p within the samples, and thus a biomarker of a functional p53 pathway. These data show that 1) RITA effectively induced apoptosis in a subset of MM cells independently of p53 and 14q32 heterogeneity, and could be of interest for patients with del17p, who are resistant to current therapies; 2) nutlin3a was effective in myeloma cells retaining a functional p53 pathway. The efficacy and specificity of other p53-reactivating small molecules i.e., PRIMA-1met and CP-31398, are currently under evaluation. Citation Format: Sylvanie Surget, Géraldine Descamps, Carole Brosseau, Philippe Moreau, Steven Le Gouill, Martine Amiot, Catherine Pellat-Deceunynck. Preclinical study of efficacy and specificity of p53-reactivating drugs in multiple myeloma, identification of biomarkers. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 793. doi:10.1158/1538-7445.AM2013-793

Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein.

Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. Expression analyses by RT-PCR and direct mRNA-sequencing showed that both rhodopsins and the complete β-carotene pathway necessary for retinal production are transcribed in PRO95. Proton translocation measurements showed enhanced proton pump activity in response to light, supporting that one or both rhodopsins are functional. Genomic information and carbon source respiration data were used to develop a defined cultivation medium for PRO95, but reproducible growth always required small amounts of yeast extract. Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations. Starvation or stress conditions might be needed to observe the physiological effect of light induced energy acquisition.

Increased antiprotease activity of the SERPINB3 polymorphic variant SCCA-PD

SERPINB3 has been found in chronic liver damage and hepatocellular carcinoma, but not in normal liver. By direct mRNA sequencing, a new SERPINB3 polymorphism (SCCA-PD) has been identified, presenting the substitution Gly351Ala in the reactive center loop of the protein. The prevalence of the SCCA-PD isoform has been found to be significantly higher in patients with cirrhosis than in patients with chronic liver disease and in normal subjects. The aim of this study was to investigate the biological and functional activity of SERPINB3 isoforms using in vitro models. HepG2 and Huh7 cells lines were transfected with plasmid vectors containing wild-type SERPINB3 or its polymorphic variant SCCA-PD and their expression at transcriptional and protein level was determined. To assess the functional activity, both recombinant proteins were produced and kinetic analysis was carried out using papain and cathepsin-L as target proteases. In addition, the inhibition of JNK kinase activity by SERPINB3 isoforms was assessed. The crystal structure of wild-type SERPINB3 at 2.7 Å resolution was used for preparation of refined 3D models of the two isoforms. The results showed that transcriptional activity and protein expression of the two isoforms were similar in both transfected cell lines. Both SERPINB3 preparations exerted a dose-dependent protease inhibitory activity, but the effect of SCCA-PD was higher than that of the wild-type isoform. This result was supported by 3D modelling, where increased hydrophobic profile of the SCCA-PD isoform, introduced by the G351A mutation, was detected. In addition, at high protein concentration, SCCA-PD revealed a 16% higher inhibitory effect on c-Jun phosphorylation by JNK1, compared with wild-type SERPINB3. In conclusion, the single amino acid substitution in the SERPINB3 reactive site loop improves the functional activity of SCCA-PD isoform. This different antiprotease activity might favor disease progression in patients carrying this polymorphism.

Splice Variant JAK2 Transcript Deleting Exon 14 in Patients with Chronic Myeloproliferative Neoplasms.

Abstract 2161Poster Board II-138The JAK2 V617F mutation in exon 14 is the most common mutation in chronic myeloproliferative neoplasms (MPNs). While other point mutations and small deletions and insertions in exons 12, 13, and 14 have been reported in the JAK2 JH2 domain, deletion of the entire exon 14 is rarely detected in patients with MPNs. In a series of >10,000 samples from patients with suspected MPNs tested for JAK2 mutations by direct sequencing of mRNA, we detected a complete exon 14 (88 bp) deletion mutation in <1% of those with JAK2 mutation. This appears to be an alternative splicing mutation, not detectable with DNA-based testing, leading to a frameshift deletion in the JAK2 JH2 domain and the expression of a truncated protein (S593I fsX8). Although this mutation was present at detectable levels (>15% of total JAK2 transcript) in a small proportion of MPN cases, we decided to investigate the possibility it may be expressed at low levels (<15% of JAK2 transcript) in patients with MPNs. Using a sensitive reverse transcription-PCR—based fluorescent fragment analysis method to quantify the percentage of truncated (minus exon 14) JAK2 mRNA as compared to wild-type, we tested 61 patients with confirmed MPN; 183 patients with suspected MPNs (93 V617F positive, 90 V617F negative); and 46 healthy normal control subjects. The wild-type PCR product was 273 bp, while the exon 14 splice mutant displayed a 185-bp peak. All samples with a splicing mutant expression to wild-type ratio >15% were confirmed by direct sequencing. The JAK2 exon 14 splice mutation was detected at low levels in 9 of the 61 MPN patients (15%), accounting for 3.96% to 33.85% (mean=12.04%) of JAK2 transcript in these individuals. Among the 183 suspected MPN patients, the exon 14 splice variant was detected in 20 of the 93 (21.5%) with V617F (mean expression level relative to wild type=5.41%, range=2.13%-26.22%) and 31 of the 90 (34.4%) without V617F (mean expression=3.88%; range=2.08%-12.22%). All 46 normal individuals were considered negative for the alternatively spliced transcript. In conclusion, the expression of an alternatively spliced JAK2 mRNA with deletion of exon 14, leading to a truncated JAK2 protein, is a common abnormality in patients with MPNs. This alternatively spliced transcript is more common in MPN patients without V617F mutation and might contribute to the leukemogenesis in these patients. Low levels of JAK2 exon 14 splice mutation may also contribute to the effects of the V617F mutation in patients with MPNs. However, this mutation is missed if DNA and not the RNA is used for testing for JAK2 mutations. Disclosures:No relevant conflicts of interest to declare.

Gene expression in bovine seminal vesicles: Genexpression in der Bullenbläschendrüse

Seminal vesicle secretion contributes significantly to the proteins of bovine seminal plasma. The following proteins from bull seminal vesicle were isolated and characterized: major protein (PDC 109), the basic proteins BUSI II, RNAse BS1, protein P6 and seminal antimicrobial protein (SAP). Using antibodies against the proteins BUSI II, RNAse BS1, SAP and major protein, the seminal vesicle epithelium was identified as the source of the respective antigens. The biosynthesis of bovine seminal vesicle secretory proteins was studied by cell free translation of poly (A)-RNA from seminal vesicles and the respective mRNAs were characterized by cDNA cloning. Recombinant clones (103) of a cDNA library of bull seminal vesicle poly (A) + RNA were screened by colony hybridisation using radioactively labelled synthetic probes. The respective clone containing the longest cDNA insert was sequenced. In case of major protein the Mr of the 134 amino acid residue precursor polypeptide was 15,480 as deduced from direct mRNA sequencing. The precursor sequence of 25 amino acid residues has a hydrophobic character and very likely constitutes a signal peptide, directing the protein towards the secretory pathway. The deduced amino acid sequence contained no consensus sequence indicative of N-glycosylation.

Dasatinib Efficacy in Patients with Chronic Myeloid Leukemia in Chronic Phase (CML-CP) and Pre-Existing BCR-ABL Mutations

Dasatinib (SPRYCEL®) is an effective BCR-ABL inhibitor that is 325-fold more potent than imatinib and 16-fold more potent than nilotinib in vitro against unmutated BCR-ABL. Across a series of phase II and III trials, dasatinib has demonstrated durable efficacy in patients with CML following resistance, suboptimal response, or intolerance to imatinib. BCR-ABL mutations are an important cause of imatinib failure and suboptimal response. Here, the efficacy of dasatinib in patients with CML-CP who had baseline BCR-ABL mutations following imatinib treatment was analyzed using data from three trials (CA180-013, -017, and -034). Mutational assessment of the BCR-ABL kinase domain was performed using RT-PCR and direct sequencing of peripheral blood cell mRNA. Hematologic, cytogenetic, and molecular response rates were reported after ≥24 mos of follow-up. Duration of response, progression-free survival (PFS), and overall survival (OS; in 013/034) were calculated using Kaplan-Meier analysis, and rates were estimated at the 24-mo time point. Of 1,150 patients with CML-CP who received dasatinib, 1,043 had a baseline mutational assessment and were analyzed further. Of these, 402 patients (39%) had a BCR-ABL mutation, including 8% of 238 imatinib-intolerant and 48% of 805 imatinib-resistant patients. Excluding known polymorphisms, 64 different BCR-ABL mutations were detected affecting 49 amino acids, with G250 (n=61), M351 (n=54), M244 (n=46), F359 (n=42), H396 (n=37), Y253 (n=26), and E255 (n=25) most frequently affected. Dasatinib treatment in patients with or without a baseline BCR-ABL mutation, respectively, resulted in high rates of major cytogenetic response (MCyR; 56% vs 65%), complete cytogenetic response (CCyR; 44% vs 56%), major molecular response (MMR; 33% vs 45%); PFS (70% vs 83%), and OS (89% vs 94%) (Table). After 24 mos, CCyRs in patients with or without a BCR-ABL mutation had been maintained by 84% vs 85%, respectively, of those achieving this response. Among patients with mutations who received dasatinib 100 mg once daily, which has a more favorable clinical safety profile, efficacy and durability were similar (MCyR: 55%; CCyR: 41%; MMR: 36%; PFS: 73%; OS: 90%). In general, high response rates and durable responses were observed in patients with different mutation types, including highly imatinib-resistant mutations in amino acids L248, Y253, E255, F359, and H396. When responses were analyzed according to dasatinib cellular IC50 for individual BCR-ABL mutations, dasatinib efficacy was observed in 44 patients who had any of 5 imatinib-resistant mutations with a dasatinib cellular IC50 >3 nM (Q252H, E255K/V, V299L, and F317L, excluding T315I), including MCyR in 34%, CCyR in 25%, MMR in 18%, PFS in 48%, and OS in 81%. Among patients whose mutations had a dasatinib IC50 ≤3 nM (n=254) or unknown IC50 (n=83), responses and durability were comparable to patients with no BCR-ABL mutation. As expected, few patients with a T315I mutation (IC50 >200 nM; n=21) achieved a response. Among 70 patients with >1 mutation, a MCyR was achieved in 53% and a CCyR in 37%. Among patients with mutational analysis at last follow-up (n=162), 42 (26%) retained a BCR-ABL mutation (20 retained a mutation with IC50 >3 nM), 42 (26%) lost a mutation (5 lost a mutation with IC50 >3 nM), and 44 (27%) developed a new mutation (39 developed a mutation with IC50 >3 nM), with some patients counted in more than one category. Overall, this analysis demonstrates that dasatinib has broad efficacy against all BCR-ABL mutations except for T315l. For patients with BCR-ABL mutations, dasatinib treatment is associated with durable responses and favorable long-term outcomes.TableAnalysis by dasatinib IC50No BCR-ABL mutationBCR-ABL mutationBCR-ABL mutation treated with 100 mg QD>3 nM (excl. T315I)3 nM*Unknown IC50**Patients, n641402494425483Response rates (≥24 mos of follow-up), %CHR939090829496MCyR655655345873CCyR564441254754MMR453336183443Median time to MCyR, mos2.82.92.85.72.92.8Median time to CcyR, mos3.05.33.05.75.43.424-mo PFS (95% CI), %83 (79.8–86.5)70 (65.3–75.2)73 (60.1–86.3)48 (31.2–64.7)73 (66.6–78.9)89 (82.3–96.3)24-mo OS (95% CI), %94 (91.4– 95.7)89 (85.1– 92.1)90 (81.2– 98.3)81 (68.8– 93.8)90 (85.8– 94.2)96 (91.2–100)Some patients had >1 mutation. *Excluding patients with a concurrent mutation with dasatinib IC50 >3 nM. **Excluding patients with a concurrent mutation with known dasatinib IC50.

Clinicopathological characteristics of colorectal cancers with loss of imprinting of insulin‐like growth factor 2

Loss of imprinting (LOI), the biallelic expression of an imprinting gene, of insulin-like growth factor 2 (IGF2) has been reported to be associated with colorectal carcinogenesis because of its high prevalence in normal colorectal mucosa as well as cancerous tissue in patients with colorectal cancer. However, the characteristics of colorectal cancer associated with IGF2 LOI have not been clearly demonstrated. In this study, we investigated the IGF2 LOI status of tumor and normal mucosa in 255 consecutive patients with colorectal cancer. Of these, 95 were informative for IGF2 LOI, by direct sequencing of mRNA of IGF2. Regarding the LOI status in each patient, the prevalence of LOI in nontumorus normal mucosa was significantly higher in cases with LOI-positive cancer than in those with LOI-negative cancer (p < 0.001). Concerning the clinicopathological characteristics of LOI-positive cancer, the prevalence of poorly differentiated or mucinous carcinoma (p = 0.016) and of right-sided locations (p = 0.009) were significantly higher than those of LOI-negative cancer. Contrary to past reports that revealed a significant correlation between microsatellite instability (MSI) and IGF2 LOI in a relatively small series of noncohort patients, our study did not find a statistically significant difference in LOI-positive rate between MSI-positive and -negative cases. Our results suggested the presence of a particular type of colorectal cancer associated with the proximal colon and poor differentiation, but independent of MSI. These results may contribute to clarification of the mechanism of colorectal tumorigenesis and to determining an appropriate screening strategy for colorectal carcinoma.

Deletion of 11 amino acids in p90(rsk-mo-1) abolishes kinase activity.

p90(rsk) is a distal member of the mitogen-activated protein kinase signaling pathway. It has been cloned from a variety of species including Xenopus laevis, mouse, chicken, rat, and human. The clone p90(rsk-mo-1), isolated by others from a mouse library, contains a unique 33-nucleotide deletion not found in the p90(rsk) clones from any other species that have been examined. When p90(rsk-mo-1) was expressed in Cos-7 cells that were subsequently stimulated with epidermal growth factor, the immunoprecipitated p90(rsk-mo-1) protein showed no measurable kinase activity toward the ribosomal protein S6 peptide. By comparison, expression of rat p90(rsk-1) resulted in significant kinase activity. Deletion of the 33-nucleotide region missing in the p90(rsk-mo-1) clone from the p90(rsk-rat-1) cDNA abolished kinase activity in the resulting protein. When these 33 nucleotides were introduced into the p90(rsk-mo-1) cDNA, the expressed protein showed significant kinase activity. Reverse transcription-PCR and direct sequencing of mRNA isolated from several mouse tissues indicated the presence of the full-length form of p90(rsk-1) in the mouse and showed no conclusive evidence for a deletion-containing form. This study indicates the presence of a full-length p90(rsk-1) mRNA in mouse tissues that is homologous to that identified in other species and suggests that the deletion in p90(rsk-mo-1) may be a cloning artifact. The findings provide additional support for the conclusion that the first catalytic domain of p90(rsk) is responsible for its enzymatic activity toward ribosomal protein S6.

Molecular characterization of the mineralocorticoid receptor in pseudohypoaldosteronism

Pseudohypoaldosteronism (PHA) is characterized by salt-wasting and failure to thrive in the newborn, accompanied by high urinary levels of sodium despite hyponatremia, hyperkalemia and metabolic acidosis, elevation of plasma renin activity, and high plasma aldosterone levels. PHA patients are resistant to mineralocorticoid administration, but their symptoms ameliorate after a period of sodium supplementation, which can be discontinued in older subjects. Binding studies performed on mononuclear leukocytes of the family members affected by the disease have shown the absence of binding of [ 3H]aldosterone to the mineralocorticoid receptor (MR) in mononuclear leukocytes in two siblings and a marked reduction in another sibling and the father, suggesting either the absence of MR or a defect in the ligand binding domain of the MR in these patients. Molecular analysis of the MR in the members of this family did not reveal any major rearrangement or deletion of the MR gene. In addition, no mutation was found in the entire MR coding sequence by RT-PCR and direct sequencing of MR mRNA, and the semiquantitative RT-PCR analysis of the MR mRNA of one affected patient failed to show any quantitative abnormality in MR expression. These results do not exclude a molecular abnormality present in the MR gene being responsible for PHA. However, they indicate that in this family PHA is not related to a modification of the MR primary structure or to a major abnormality in MR expression.

Metabolic compartmentation of vertebrate glutamine synthetase: putative mitochondrial targeting signal in avian liver glutamine synthetase.

The evolution of uricoteley as a mechanism for hepatic ammonia detoxication in vertebrates required targeting of glutamine synthetase (GS) to liver mitochondria in the sauropsid line of descent leading to the squamate reptiles and archosaurs. Previous studies have shown that in birds and crocodilians, sole survivors of the archosaurian line, hepatic GS is translated without a transient, N-terminal targeting signal common to other mitochondrial matrix proteins. To identify a putative internal targeting sequence in the avian enzyme, the amino acid sequence of chicken liver GS was derived by a combination of sequencing of cloned cDNA, direct sequencing of mRNA, and sequencing of polymerase chain reaction (PCR) products amplified from reverse-transcribed mRNA. Analysis of the first 20 or so N-terminal amino acids of the derived sequence for the chicken enzyme shows that they are devoid of acidic amino acids, contain several hydroxy amino acids, and can be predicted to form a positively charged, amphipathic helix, all of which are characteristic properties of mitochondrial targeting signals. A comparison of the N-terminus of chicken GS with the N-termini of cytosolic mammalian GSs indicates that at least three amino acid replacements may have been responsible for converting the N-terminus of the cytosolic mammalian enzyme into a mitochondrial targeting signal. Two of these, His15 and Lys19, result in additional positive charges, as well as in changes in hydrophilicity. Both could have resulted from third-base-codon substitutions. A third replacement, Ala12, may contribute to the helicity of the N-terminus of the chicken enzyme. The N-terminus of the cytosolic chicken brain GS (positions 1-36) was found to be identical to that of the liver enzyme. The complete sequence of chicken retinal GS is also identical to that of the liver enzyme. GS is coded by a single gene in birds, so these sequence data suggest that, unlike the situation in other tissue-specific compartmental isozymes, differential targeting of avian GS to the mitochondrial or cytosolic compartments is not dependent on the sequence of the primary translation product of its mRNA but may involve some other tissue-specific factor(s).