Dominant Transcripts Research Articles

Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediment benthic flux denitrification efficiency.

Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus. In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated with Nitrosopumilus nitric oxide nitrite reduction (nirK). The environmental conditions close to organic nitrogen inputs that select for increased transcription in Nitrosopumilus (amoCAB, nirK, nirS, nmo, hcp) additionally selected for increased transcription of bacterial nitrite reduction (nxrB) and transcripts associated with anammox (hzo) but not denitrification (bacterial nirS/nirk). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction (nosZ) and changes in nosZ transcript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community-level nitrification-denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaeal nirK transcripts were site- and season-specific. This study indicates that the transcription of archaeal nirK in response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling.

CpG Site-Specific Methylation-Modulated Divergent Expression of PRSS3 Transcript Variants Facilitates Nongenetic Intratumor Heterogeneity in Human Hepatocellular Carcinoma.

BackgroundHepatocellular carcinoma (HCC) is one of the most lethal human tumors with extensive intratumor heterogeneity (ITH). Serine protease 3 (PRSS3) is an indispensable member of the trypsin family and has been implicated in the pathogenesis of several malignancies, including HCC. However, the paradoxical effects of PRSS3 on carcinogenesis due to an unclear molecular basis impede the utilization of its biomarker potential. We hereby explored the contribution of PRSS3 transcripts to tumor functional heterogeneity by systematically dissecting the expression of four known splice variants of PRSS3 (PRSS3-SVs, V1~V4) and their functional relevance to HCC.MethodsThe expression and DNA methylation of PRSS3 transcripts and their associated clinical relevance in HCC were analyzed using several publicly available datasets and validated using qPCR-based assays. Functional experiments were performed in gain- and loss-of-function cell models, in which PRSS3 transcript constructs were separately transfected after deleting PRSS3 expression by CRISPR/Cas9 editing.Results PRSS3 was aberrantly differentially expressed toward bipolarity from very low (PRSS3Low ) to very high (PRSS3High ) expression across HCC cell lines and tissues. This was attributable to the disruption of PRSS3-SVs, in which PRSS3-V2 and/or PRSS3-V1 were dominant transcripts leading to PRSS3 expression, whereas PRSS3-V3 and -V4 were rarely or minimally expressed. The expression of PRSS3-V2 or -V1 was inversely associated with site-specific CpG methylation at the PRSS3 promoter region that distinguished HCC cells and tissues phenotypically between hypermethylated low-expression (mPRSS3-SVLow ) and hypomethylated high-expression (umPRSS3-SVHigh ) groups. PRSS3-SVs displayed distinct functions from oncogenic PRSS3-V2 to tumor-suppressive PRSS3-V1, -V3 or PRSS3-V4 in HCC cells. Clinically, aberrant expression of PRSS3-SVs was translated into divergent relevance in patients with HCC, in which significant epigenetic downregulation of PRSS3-V2 was seen in early HCC and was associated with favorable patient outcome.ConclusionsThese results provide the first evidence for the transcriptional and functional characterization of PRSS3 transcripts in HCC. Aberrant expression of divergent PRSS3-SVs disrupted by site-specific CpG methylation may integrate the effects of oncogenic PRSS3-V2 and tumor-suppressive PRSS3-V1, resulting in the molecular diversity and functional plasticity of PRSS3 in HCC. Dysregulated expression of PRSS3-V2 by site-specific CpG methylation may have potential diagnostic value for patients with early HCC.

A case report of pediatric acute lymphoblastic leukemia with e8a2 BCR/ABL1 fusion transcript

BackgroundAcute lymphoblastic leukemia is the most common type of cancer in children. Most often it affects the age group between 2 and 5 years of age. Studies have shown an improvement in general survivability, more than 90% 5-year overall survival (OS). Current treatment protocols for acute lymphoblastic leukemia require verification of the presence of favorable and unfavorable genetic abnormalities, which help qualify patients to the appropriate risk group and select a more suitable treatment. The presence of the BCR/ABL1 fusion gene stratifies the patient into a high-risk group and requires special treatment with tyrosine kinase inhibitors (TKI). The three dominant mRNA transcripts are e1a2, e13a2, and e14a2. Nevertheless, cases of atypical BCR/ABL1 transcripts have also been reported.Case presentationThis paper presents the case of a pediatric patient with Ph + B-cell precursor acute lymphoblastic leukemia with rare atypical e8a2 BCR/ABL1 fusion transcript. Our patient achieved complete remission after 33 days of treatment. Molecular and cytogenetic studies in TP1 did not reveal the presence of the BCR/ABL1 transcript. The PCR-MRD test in TP1b was negative, the patient did not require hematopoietic stem cell transplantation.ConclusionGenetic evaluation of the bone marrow sample is crucial in the initial stage of the diagnosis. Fluorescent in situ hybridization and reverse transcriptase polymerase chain reaction with Sanger sequencing are the appropriate methods used in the detection of rare variants of BCR/ABL1 transcripts.

Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O2 Cyanobacterial Mat Community.

ABSTRACTCyanobacterial mats profoundly influenced Earth’s biological and geochemical evolution and still play important ecological roles in the modern world. However, the biogeochemical functioning of cyanobacterial mats under persistent low-O2 conditions, which dominated their evolutionary history, is not well understood. To investigate how different metabolic and biogeochemical functions are partitioned among community members, we conducted metagenomics and metatranscriptomics on cyanobacterial mats in the low-O2, sulfidic Middle Island sinkhole (MIS) in Lake Huron. Metagenomic assembly and binning yielded 144 draft metagenome assembled genomes, including 61 of medium quality or better, and the dominant cyanobacteria and numerous Proteobacteria involved in sulfur cycling. Strains of a Phormidium autumnale-like cyanobacterium dominated the metagenome and metatranscriptome. Transcripts for the photosynthetic reaction core genes psaA and psbA were abundant in both day and night. Multiple types of psbA genes were expressed from each cyanobacterium, and the dominant psbA transcripts were from an atypical microaerobic type of D1 protein from Phormidium. Further, cyanobacterial transcripts for photosystem I genes were more abundant than those for photosystem II, and two types of Phormidium sulfide quinone reductase were recovered, consistent with anoxygenic photosynthesis via photosystem I in the presence of sulfide. Transcripts indicate active sulfur oxidation and reduction within the cyanobacterial mat, predominately by Gammaproteobacteria and Deltaproteobacteria, respectively. Overall, these genomic and transcriptomic results link specific microbial groups to metabolic processes that underpin primary production and biogeochemical cycling in a low-O2 cyanobacterial mat and suggest mechanisms for tightly coupled cycling of oxygen and sulfur compounds in the mat ecosystem.IMPORTANCE Cyanobacterial mats are dense communities of microorganisms that contain photosynthetic cyanobacteria along with a host of other bacterial species that play important yet still poorly understood roles in this ecosystem. Although such cyanobacterial mats were critical agents of Earth’s biological and chemical evolution through geological time, little is known about how they function under the low-oxygen conditions that characterized most of their natural history. Here, we performed sequencing of the DNA and RNA of modern cyanobacterial mat communities under low-oxygen and sulfur-rich conditions from the Middle Island sinkhole in Lake Huron. The results reveal the organisms and metabolic pathways that are responsible for both oxygen-producing and non-oxygen-producing photosynthesis as well as interconversions of sulfur that likely shape how much O2 is produced in such ecosystems. These findings indicate tight metabolic reactions between community members that help to explain the limited the amount of O2 produced in cyanobacterial mat ecosystems.

PD37-11 TROPOMYOSIN ISOFORM SWITCHING IN UROTHELIAL BLADDER CANCER AS A DIAGNOSTIC BIOMARKER

You have accessJournal of UrologyBladder Cancer: Basic Research & Pathophysiology I (PD37)1 Sep 2021PD37-11 TROPOMYOSIN ISOFORM SWITCHING IN UROTHELIAL BLADDER CANCER AS A DIAGNOSTIC BIOMARKER Nada Humayun-Zakaria, Douglas Ward, Ben Abbotts, Maurice Zeegers, KK Cheng, Nick James, Richard Bryan, and Roland Arnold Nada Humayun-ZakariaNada Humayun-Zakaria More articles by this author , Douglas WardDouglas Ward More articles by this author , Ben AbbottsBen Abbotts More articles by this author , Maurice ZeegersMaurice Zeegers More articles by this author , KK ChengKK Cheng More articles by this author , Nick JamesNick James More articles by this author , Richard BryanRichard Bryan More articles by this author , and Roland ArnoldRoland Arnold More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002047.11AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: The urgent unmet need for biomarker discovery for the early detection and surveillance of bladder cancer in parallel with advancements in high throughput sequencing has fuelled understanding of molecular biology and pathology, paving the way for ‘precision medicine’. Transcriptomic analyses of Tropomyosin (TPM) have revealed differential expression of isoforms with ‘isoform switching’ in the presence of urothelial bladder cancer (UBC) making them promising candidates as diagnostic biomarkers. METHODS: RNA-sequence quantification was performed on 3 cancer datasets (Cancer Cell Line Encyclopaedia (CCLE), The Cancer Genome Atlas (TCGA) and West Midland’s Bladder Cancer Prognosis Program (BCPP)) and one non-cancer dataset (GEO Accession number GSE133624) using a bespoke bioinformatics pipeline – ‘IsoTPM’. Wilcoxon rank sum determined p-values for pairwise-comparison of isoform expression in cancer vs non-cancer. Subsequent qPCR analysis with isoform-specific primers was performed on in-house CCLE cell lines followed by Sanger sequencing. Evaluation of TPM isoform expression at protein level was achieved using mass spectrometry (MS) on CCLE and BCPP samples to delineate peptides of interest. RESULTS: The differential expression (DE) of two TPM1 isoforms, TPM1-201 and TPM1-206, appeared as dominant transcripts in non-cancer and cancer datasets, respectively. TPM4 analyses revealed high abundance of TPM4-218 in cancer datasets in comparison to TPM4-221 found exclusively in non-cancer. Additionally, TPM4-205 was expressed in non-muscle-invasive tumours (BCPP). qPCR analysis showed the relative expressions of TPM1-206 and TPM4-218 in a range of cell lines. MS revealed ∼20 peptides, including splice-junction exons from TPM4-218 and TPM1-206, from both cancer datasets (BCPP and CCLE). CONCLUSIONS: Comparative analysis of non-cancer and cancer datasets demonstrates that TPM1-201 isoform switching to TPM1-206 accompanies early bladder tumorigenesis and/or epithelial-mesenchymal-transition (EMT). TPM4-218 is upregulated in all cancer datasets accompanied by downregulation of TPM4-221 also suggesting an association with bladder tumorigenesis. Source of Funding: QEHB charities funded NH-Z's research © 2021 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 206Issue Supplement 3September 2021Page: e659-e660 Advertisement Copyright & Permissions© 2021 by American Urological Association Education and Research, Inc.MetricsAuthor Information Nada Humayun-Zakaria More articles by this author Douglas Ward More articles by this author Ben Abbotts More articles by this author Maurice Zeegers More articles by this author KK Cheng More articles by this author Nick James More articles by this author Richard Bryan More articles by this author Roland Arnold More articles by this author Expand All Advertisement Loading ...

An overlapping lncRNA antisense to coding arachidonate 12‐lipoxygenase gene is ubiquitously expressed and exhibited cell‐type‐specific subcellular localization

The arachidonate 12-lipoxygenase (ALOX12) gene encodes an enzyme that acts on polyunsaturated fatty acid substrates and generates bioactive lipid mediators regulating a variety of biological processes associated with various disease pathologies. The human genome assembly (version GRCh38/hg38) revealed that the ALOX12 gene is overlapped by a previously uncharacterized antisense long non-coding RNA (lncRNA) designated as ALOX12-antisense 1 (ALOX12-AS1) indicating a possibility of antisense-sense regulation of the coding ALOX12. Furthermore, based on expressed sequence tag (EST) mapping, the Ensemble database revealed the existence of multiple transcriptional isoforms of ALOX12-AS1. Nine transcripts successively numbered as 201-209 are supported by at least one EST. Therefore, the objective of this study was to characterize human tissue and cell-type-specific expression as well as intracellular localization of ALOX12-AS1 lncRNA isoforms. Reverse transcription polymerase chain reaction and northern blotting-based studies revealed that ALOX12-AS1-201 and -202 are the dominant transcripts expressed in a variety of adult primary human tissues including adipose, artery, bone marrow, cerebellum, cortex, intestine, liver, smooth muscle, and skin tissues. Furthermore, RNA fluorescence in situ hybridization using primary adult human tissues as well as five transformed human cell lines (A431: skin epithelial, EA.hy926: endothelial, THP-1: monocytic, HEK293: embryonic kidney-derived, and HepG2: hepatoma-derived) revealed cell-type-specific expression and intracellular localization of the lncRNA. ALOX12-AS1-201 and -202 isoforms were differentially localized in the cytosol, nucleoplasm, as well as nucleoli, and the subcellular distribution exhibited variation depending on the cell-type and cell division state. The tissue and cell-type-specificity of ALOX12-AS1 lncRNA isoforms indicate that the isoforms might be involved in cell-type-specific regulation of ALOX12. This has been further reinforced by the overlapping nature of specific antisense-sense sequence elements involving both genes. Future studies are warranted to unravel the details of potential antisense-sense regulatory mechanism which is beyond the scope of the present study. Overall, this study provided a starting point to unravel a lncRNA-mediated regulation of ALOX12 that may underlie the generation of potent bioactive lipid mediators associated with disease pathogenesis.

Identification of Dominant Transcripts in Oxidative Stress Response by a Full-Length Transcriptome Analysis.

Our body responds to environmental stress by changing the expression levels of a series of cytoprotective enzymes/proteins through multilayered regulatory mechanisms, including the KEAP1-NRF2 system. While NRF2 upregulates the expression of many cytoprotective genes, there are fundamental limitations in short-read RNA sequencing (RNA-Seq), resulting in confusion regarding interpreting the effectiveness of cytoprotective gene induction at the transcript level. To precisely delineate isoform usage in the stress response, we conducted independent full-length transcriptome profiling (isoform sequencing; Iso-Seq) analyses of lymphoblastoid cells from three volunteers under normal and electrophilic stress-induced conditions. We first determined the first exon usage in KEAP1 and NFE2L2 (encoding NRF2) and found the presence of transcript diversity. We then examined changes in isoform usage of NRF2 target genes under stress conditions and identified a few isoforms dominantly expressed in the majority of NRF2 target genes. The expression levels of isoforms determined by Iso-Seq analyses showed striking differences from those determined by short-read RNA-Seq; the latter could be misleading concerning the abundance of transcripts. These results support that transcript usage is tightly regulated to produce functional proteins under electrophilic stress. Our present study strongly argues that there are important benefits that can be achieved by long-read transcriptome sequencing.

Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network

Under normal conditions, cells of almost all tissue types express the same predominant canonical transcript isoform at each gene locus. In cancer, however, splicing regulation is often disturbed, leading to cancer-specific switches in the most dominant transcripts (MDT). To address the pathogenic impact of these switches, we have analyzed isoform-specific protein–protein interaction disruptions in 1,209 cancer samples covering 27 different cancer types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project of the International Cancer Genomics Consortium (ICGC). Our study revealed large variations in the number of cancer-specific MDT (cMDT) with the highest frequency in cancers of female reproductive organs. Interestingly, in contrast to the mutational load, cancers arising from the same primary tissue had a similar number of cMDT. Some cMDT were found in 100% of all samples in a cancer type, making them candidates for diagnostic biomarkers. cMDT tend to be located at densely populated network regions where they disrupted protein interactions in the proximity of pathogenic cancer genes. A gene ontology enrichment analysis showed that these disruptions occurred mostly in protein translation and RNA splicing pathways. Interestingly, samples with mutations in the spliceosomal complex tend to have higher number of cMDT, while other transcript expressions correlated with mutations in non-coding splice-site and promoter regions of their genes. This work demonstrates for the first time the large extent of cancer-specific alterations in alternative splicing for 27 different cancer types. It highlights distinct and common patterns of cMDT and suggests novel pathogenic transcripts and markers that induce large network disruptions in cancers.

FBXW7γ is a tumor-suppressive and prognosis-related FBXW7 transcript isoform in ovarian serous cystadenocarcinoma.

Aim: To explore FBXW7 protein-coding transcript isoform (α, β and γ) expression, their functions and prognostic value in ovarian serous cystadenocarcinoma (OSC). Materials & methods: FBXW7 transcript data were collected from The Cancer Genome Atlas and the Genotype-Tissue Expression project. IOSE, A2780 and SKOV3 cells were used for in vitro and in vivo studies. Results: FBXW7α and FBXW7γ are dominant protein-coding transcripts that were downregulated in OSC. FBXW7γ overexpression reduced the protein expression of c-Myc, Notch1 and Yap1 and suppressed OSC cell growth in vitro and in vivo. FBXW7γ expression was an independent indicator of longer disease-specific survival (HR: 0.588; 95% CI: 0.449-0.770) and progression-free survival (HR: 0.708; 95% CI: 0.562-0.892). Conclusion: FBXW7γ is a tumor-suppressive and might be the only prognosis-related FBXW7 transcript in OSC.

ANXA4 Activates JAK-STAT3 Signaling by Interacting with ANXA1 in Basal-Like Breast Cancer.

Annexin A4 (encoded by the ANXA4 gene) is a calcium ion (Ca2+)- and phospholipid-binding protein of the Annexin family. In this study, we checked the expression profile of ANXA4 in basal-like breast cancer (BLBC) and its association with survival outcomes using pan-cancer data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. Then, using MDA-MB-231 and MDA-MB-468 cells, we explored the functional role of ANXA4 in regulating a cancer-related signaling pathway and identified potential partners of ANXA4. The results showed that expression of total ANXA4 and the two dominant ANXA4 protein-coding transcripts (ENST00000409920.5 and ENST00000394295.4) was consistently upregulated in tumor tissues compared with normal breast tissues. BLBC patients with high ANXA4 expression had significantly worse overall survival, progression-free survival, and disease-free survival than those with low ANXA4 expression. ANXA4 could positively modulate cyclin D1 expression and G1/S progression in the two cell lines. An in vivo tumor model showed that ANXA4 inhibition significantly slowed the growth of tumors derived from the two BLBC cell lines. ANXA4 could increase JAK1 expression and STAT3 phosphorylation (Y705). ANXA4 colocalized with ANXA1 in some MDA-MB-231 cells. A co-immunoprecipitation assay confirmed direct binding between ANXA4 and ANXA1. Knockdown of ANXA1 reduced JAK1 expression and STAT3 phosphorylation and impaired ANXA4-induced upregulation of JAK1 and p-STAT3. In conclusion, this study revealed that aberrant ANXA4 upregulation is associated with poor survival in BLBC. ANXA4 could activate JAK-STAT3 signaling by elevating the expression of JAK1 and p-STAT3, which was mediated by direct interaction with ANXA1.

Differential Accumulation of Innate- and Adaptive-Immune-Response-Derived Transcripts during Antagonism between Papaya Ringspot Virus and Papaya Mosaic Virus.

Papaya ringspot virus (PRSV), a common potyvirus infecting papaya plants worldwide, can lead to either antagonism or synergism in mixed infections with Papaya mosaic virus (PapMV), a potexvirus. These two unrelated viruses produce antagonism or synergism depending on their order of infection in the plant. When PRSV is inoculated first or at the same time as PapMV, the viral interaction is synergistic. However, an antagonistic response is observed when PapMV is inoculated before PRSV. In the antagonistic condition, PRSV is deterred from the plant and its drastic effects are overcome. Here, we examine differences in gene expression by high-throughput RNA sequencing, focused on immune system pathways. We present the transcriptomic expression of single and mixed inoculations of PRSV and PapMV leading to synergism and antagonism. Upregulation of dominant and hormone-mediated resistance transcripts suggests that the innate immune system participates in synergism. In antagonism, in addition to innate immunity, upregulation of RNA interference-mediated resistance transcripts suggests that adaptive immunity is involved.

Of Cyberliberation and Forbidden Fornication: Hidden Transcripts of Autonomous Mobility in Finland

While autonomous mobility technology is developing, comparatively less is known about how a sociotechnical system of autonomous mobility may impact our urban living conditions. Using Finland as a case study, this research aims to identify the possible implications of changing power relations created by autonomous mobility technology. This study uses a theoretical and conceptual approach grounded in the planning research tradition of Aristotelian practical judgement (phronesis). Drawing from political theory of technology, it investigates the social relations that may be afforded by autonomous mobility technology. Adapting a concept drawn from geography of power, it examines how power is expressed in terms of transcripts of dominant technological agency and hidden social context. 31 interviews of extended users in the transition (intermediaries) revealed three dominant transcripts of technological agency associated with the philosophy of cyberlibertarianism (liberation of the driver, safety of the driver and customer accessibility), and four hidden transcripts of social context (restrictions on sharing street space, loss of social safety, vulnerability of passengers, and loss of privacy). The phronetic research tradition that was used in the study revealed several things. The impact of autonomous mobility technology goes beyond the purely systemic, affecting the very fabric of our connection with place and society. Failure to consider autonomous mobility technology as a sociotechnical system that will restructure society unperceptively (technological somnambulism) may bring profound societal changes.

Metatranscriptomics profile of the gill microbial community during Bathymodiolus azoricus aquarium acclimatization at atmospheric pressure.

BackgroundThe deep-sea mussels Bathymodiolus azoricus (Bivalvia: Mytilidae) are the dominant macrofauna subsisting at the hydrothermal vents site Menez Gwen in the Mid-Atlantic Ridge (MAR). Their adaptive success in such challenging environments is largely due to their gill symbiotic association with chemosynthetic bacteria. We examined the response of vent mussels as they adapt to sea-level environmental conditions, through an assessment of the relative abundance of host-symbiont related RNA transcripts to better understand how the gill microbiome may drive host-symbiont interactions in vent mussels during hypothetical venting inactivity.ResultsThe metatranscriptome of B. azoricus was sequenced from gill tissues sampled at different time-points during a five-week acclimatization experiment, using Next-Generation-Sequencing. After Illumina sequencing, a total of 181,985,262 paired-end reads of 150 bp were generated with an average of 16,544,115 read per sample. Metatranscriptome analysis confirmed that experimental acclimatization in aquaria accounted for global gill transcript variation. Additionally, the analysis of 16S and 18S rRNA sequences data allowed for a comprehensive characterization of host-symbiont interactions, which included the gradual loss of gill endosymbionts and signaling pathways, associated with stress responses and energy metabolism, under experimental acclimatization. Dominant active transcripts were assigned to the following KEGG categories: “Ribosome”, “Oxidative phosphorylation” and “Chaperones and folding catalysts” suggesting specific metabolic responses to physiological adaptations in aquarium environment.ConclusionsGill metagenomics analyses highlighted microbial diversity shifts and a clear pattern of varying mRNA transcript abundancies and expression during acclimatization to aquarium conditions which indicate change in bacterial community activity. This approach holds potential for the discovery of new host-symbiont associations, evidencing new functional transcripts and a clearer picture of methane metabolism during loss of endosymbionts. Towards the end of acclimatization, we observed trends in three major functional subsystems, as evidenced by an increment of transcripts related to genetic information processes; the decrease of chaperone and folding catalysts and oxidative phosphorylation transcripts; but no change in transcripts of gluconeogenesis and co-factors-vitamins.

Salivary gland transcripts of the kissing bug, Panstrongylus chinai, a vector of Chagas disease

The saliva of hematophagous arthropods injected during blood feeding contains potent pharmacologically active components to counteract the host hemostatic and inflammatory systems. In the present study, dominant salivary gland transcripts of Panstrongylus chinai, a vector of Chagas disease, were analyzed by sequencing randomly selected clones of the salivary gland cDNA library. This analysis showed that 56.5% of the isolated transcripts coded for putative secreted proteins, of which 73.7% coded for proteins belonging to the lipocalin family. The most abundant transcript of lipocalin family proteins was a homologue of pallidipin 2, an inhibitor of collagen-induced platelet aggregation of Triatoma pallidipennis. In addition, homologues of triafestin, an inhibitor of the kallikrein-kinin system of T. infestans, were identified as the dominant transcript. Other salivary transcripts encoding lipocalin family proteins had homology to triplatin (an inhibitor of platelet aggregation) and others with unknown function. Other than lipocalin family proteins, homologues of a Kazal-type serine protease inhibitor (putative anticoagulant), a hemolysin-like protein (unknown function), inositol polyphosphate 5-related protein (a regulator of membrane phosphoinositide), antigen 5-related protein (unknown function) and apyrase (platelet aggregation inhibitor) were identified.

Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing

Variable surface antigens of Plasmodium falciparum have been a major research focus since they facilitate parasite sequestration and give rise to deadly malaria complications. Coupled with its potential use as a vaccine candidate, the recent suggestion that the repetitive interspersed families of polypeptides (RIFINs) mediate blood group A rosetting and influence blood group distribution has raised the research profile of these adhesins. Nevertheless, detailed investigations into the functions of this highly diverse multigene family remain hampered by the limited number of validated reagents. In this study, we assess the specificities of three promising polyclonal anti-RIFIN antibodies that were IgG-purified from sera of immunized animals. Their epitope regions were mapped using a 175,000-peptide microarray holding overlapping peptides of the P. falciparum variable surface antigens. Through immunoblotting and immunofluorescence imaging, we show that different antibodies give varying results in different applications/assays. Finally, we authenticate the antibody-based detection of RIFINs in two previously uncharacterized non-rosetting parasite lines by identifying the dominant rif transcripts using RNA sequencing.

Strengthening the remaining synapses.

Neuroscience Working memory depends in part on the proper activation of neural circuits in a brain area called the dorsolateral prefrontal cortex (DLPFC). In primates, DLPFC performance during working memory tasks improves through adolescence. Synaptic pruning eliminates unwanted or imprecise connections and strengthens the remaining connections. Chung et al. found that the excitatory synapses on a crucial subgroup of interneurons in the monkey DLPFC also undergo pruning during adolescence. Such synapses are partially regulated by an enzyme called ErbB4. This enzyme exists in alternative splice variants. During development, there is a shift in the dominant alternative splice transcripts, which is accompanied by fewer but stronger excitatory synapses. Shifts in ErbB4 splicing thus modulate the pruning of excitatory synapses on these interneurons during maturation. Proc. Natl. Acad. Sci. U.S.A. 10.1073/pnas.1610077114 (2017).

Spontaneous Ca(2+) transients in interstitial cells of Cajal located within the deep muscular plexus of the murine small intestine.

Interstitial cells of Cajal at the level of the deep muscular plexus (ICC-DMP) in the small intestine generate spontaneous Ca(2+) transients that consist of localized Ca(2+) events and limited propagating Ca(2+) waves. Ca(2+) transients in ICC-DMP display variable characteristics: from discrete, highly localized Ca(2+) transients to regionalized Ca(2+) waves with variable rates of occurrence, amplitude, duration and spatial spread. Ca(2+) transients fired stochastically, with no cellular or multicellular rhythmic activity being observed. No correlation was found between the firing sites in adjacent cells. Ca(2+) transients in ICC-DMP are suppressed by the ongoing release of inhibitory neurotransmitter(s). Functional intracellular Ca(2+) stores are essential for spontaneous Ca(2+) transients, and the sarco/endoplasmic reticulum Ca(2+) -ATPase (SERCA) pump is necessary for maintenance of spontaneity. Ca(2+) release mechanisms involve both ryanodine receptors (RyRs) and inositol triphosphate receptors (InsP3 Rs). Release from these channels is interdependent. ICC express transcripts of multiple RyRs and InsP3 Rs, with Itpr1 and Ryr2 subtypes displaying the highest expression. Interstitial cells of Cajal in the deep muscular plexus of the small intestine (ICC-DMP) are closely associated with varicosities of enteric motor neurons and generate responses contributing to neural regulation of intestinal motility. Responses of ICC-DMP are mediated by activation of Ca(2+) -activated Cl(-) channels; thus, Ca(2+) signalling is central to the behaviours of these cells. Confocal imaging was used to characterize the nature and mechanisms of Ca(2+) transients in ICC-DMP within intact jejunal muscles expressing a genetically encoded Ca(2+) indicator (GCaMP3) selectively in ICC. ICC-DMP displayed spontaneous Ca(2+) transients that ranged from discrete, localized events to waves that propagated over variable distances. The occurrence of Ca(2+) transients was highly variable, and it was determined that firing was stochastic in nature. Ca(2+) transients were tabulated in multiple cells within fields of view, and no correlation was found between the events in adjacent cells. TTX (1μm) significantly increased the occurrence of Ca(2+) transients, suggesting that ICC-DMP contributes to the tonic inhibition conveyed by ongoing activity of inhibitory motor neurons. Ca(2+) transients were minimally affected after 12min in Ca(2+) free solution, indicating these events do not depend immediately upon Ca(2+) influx. However, inhibitors of sarco/endoplasmic reticulum Ca(2+) -ATPase (SERCA) pump and blockers of inositol triphosphate receptor (InsP3 R) and ryanodine receptor (RyR) channels blocked ICC Ca(2+) transients. These data suggest an interdependence between RyR and InsP3 R in the generation of Ca(2+) transients. Itpr1 and Ryr2 were the dominant transcripts expressed by ICC. These findings provide the first high-resolution recording of the subcellular Ca(2+) dynamics that control the behaviour of ICC-DMP in situ.

Intrathecal BCR transcriptome in multiple sclerosis versus other neuroinflammation: Equally diverse and compartmentalized, but more mutated, biased and overlapping with the proteome

The mechanisms driving the intrathecal synthesis of IgG in multiple sclerosis (MS) are unknown. We combined high-throughput sequencing of transcribed immunoglobulin heavy-chain variable (IGHV) genes and mass spectrometry to chart the diversity and compartmentalization of IgG-producing B cells in the cerebrospinal fluid (CSF) of MS patients and controls with other neuroinflammatory diseases. In both groups, a few clones dominated the intrathecal IGHV transcriptome. In most MS patients and some controls, dominant transcripts matched the CSF IgG. The IGHV transcripts in CSF of MS patients frequently carried IGHV4 genes and had more replacement mutations compared to controls. In both groups, dominant IGHV transcripts were identified within clusters of clonally related B cells that had identical or related IGHV transcripts in the blood. These findings suggest more pronounced affinity maturation, but an equal degree of diversity and compartmentalization of the intrathecal B-cell response in MS compared to other neuroinflammatory diseases.

Expression of Tropomyosin 1 Gene Isoforms in Human Breast Cancer Cell Lines.

Nine malignant breast epithelial cell lines and 3 normal breast cell lines were examined for stress fiber formation and expression of TPM1 isoform-specific RNAs and proteins. Stress fiber formation was strong (++++) in the normal cell lines and varied among the malignant cell lines (negative to +++). Although TPM1γ and TPM1δ were the dominant transcripts of TPM1, there was no clear evidence for TPM1δ protein expression. Four novel human TPM1 gene RNA isoforms were discovered (λ, μ, ν, and ξ), which were not identified in adult and fetal human cardiac tissues. TPM1λ was the most frequent isoform expressed in the malignant breast cell lines, and it was absent in normal breast epithelial cell lines. By western blotting, we were unable to distinguish between TPM1γ, λ, and ν protein expression, which were the only TPM1 gene protein isoforms potentially expressed. Some malignant cell lines demonstrated increased or decreased expression of these isoforms relative to the normal breast cell lines. Stress fiber formation did not correlate with TPM1γ RNA expression but significantly and inversely correlated with TPM1δ and TPM1λ expression, respectively. The exact differences in expression of these novel isoforms and their functional properties in breast epithelial cells will require further study.

E6-associated transcription patterns in human papilloma virus 16-positive cervical tissues.

The change in transcription pattern induced by post-transcriptional RNA splicing is an important mechanism in the regulation of the early gene expression of human papilloma virus (HPV). The present study was conducted to establish a method to specifically amplify HPV-16 E6-associated transcripts. The E6-related transcripts from 63 HPV-16-positive cervical tumor tissue samples were amplified, consisting of eight cases of low-risk intraepithelial lesions, 38 cases of high-risk intraepithelial lesions and 17 cases of cervical cancer (CxCa). The appropriate amplified segments were recovered following agarose gel electrophoresis, and subjected to further sequencing and sequence alignment analysis. Six groups of E6 transcription patterns were identified from HPV-16-positive cervical tumor tissue, including five newly-discovered transcripts. Different HPV-16 E6-associated transcription patterns were detected during the development of CxCa. Over the course of the progression of the low-grade squamous intraepithelial lesions to CxCa, the specific HPV-16 E6-associated transcription patterns and the dominant transcripts were all different. As indicated by this study, the transcription pattern of the E6 early gene of HPV-16 was closely associated with the stages of cervical carcinogenesis, and may also be involved in the development of CxCa.