Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site

p38 Molecular Targeting for Next-Generation Multiple Myeloma Therapy

Resistance to therapy and disease progression are the main causes of mortality in most cancers. In particular, the development of resistance is an important limitation affecting the efficacy of therapeutic alternatives for cancer, including chemotherapy, radiotherapy, and immunotherapy. Signaling pathways are largely responsible for the mechanisms of resistance to cancer treatment and progression, and multiple myeloma is no exception. p38 mitogen-activated protein kinase (p38) is downstream of several signaling pathways specific to treatment resistance and progression. Therefore, in recent years, developing therapeutic alternatives directed at p38 has been of great interest, in order to reverse chemotherapy resistance and prevent progression. In this review, we discuss recent findings on the role of p38, including recent advances in our understanding of its expression and activity as well as its isoforms, and its possible clinical role based on the mechanisms of resistance and progression in multiple myeloma.

Identification of rat Vstm1 with conservative anti-inflammatory effect between rat and human homologs

Human VSTM1 (also known as SIRL1) is an inhibitory immune checkpoint receptor involved in leukocyte activation. Identification of the homologous genes in other species, such as mice and rats, will undoubtedly contribute to functional studies and clinical applications. Here, we successfully cloned the Vstm1 gene in rats, as supported by high-throughput sequencing data. However, Vstm1 is degenerated to a pseudogene in the mouse genome. Rat Vstm1 mRNA contains a complete open reading frame (ORF) of 630 nucleotides encoding 209 amino acids. Rat Vstm1 is highly expressed in bone marrow, especially in granulocytes. The expression levels of Vstm1 gradually increase with the development of granulocytes in bone marrow but are downregulated in response to inflammatory stimuli. Rat VSTM1 does not have an immunoreceptor tyrosine-based inhibitory motif (ITIM), however, it shows a conservative function of inflammatory inhibition with human VSTM1, and both are anti-correlated with many inflammatory cytokines, such as IL-1α and TNF-α. In bone marrow-derived macrophages (BMDMs), either rat or human VSTM1 suppressed the secretion of inflammatory cytokines in response to LPS stimulation. Further analysis in lung cancer microenvironment revealed that VSTM1 is mainly expressed in myeloid cells, anti-correlated with inflammatory cytokines and associated with tumor development and metastasis.

Identification and functional analysis of a novel splice variant of AC3-33 in breast cancer

Alternative RNA splicing plays a key role in regulating gene function and influencing protein expression diversity. In the present study, an AC-33 transcript variant (NCBI Reference Sequence: NM_001308229.1), splice variant (sv)AC3-33, was successfully cloned from the MCF-7 breast cancer cell line by reverse transcription PCR using primers based on expressed sequence tags. The aim of the present study was to investigate the structure and function of svAC3-33. svAC3-33 has an open reading frame of 1,825 base pairs, lacks AC3-33 exon 2 and is encoded by 294 amino acids. svAC3-33 is localized within the cytoplasm. The Cell Counting Kit-8 and EdU detection of cell proliferation assays showed that svAC3-33 inhibited MCF-7 cell proliferation. Similarly, svAC3-33 knockdown by RNA interference was shown to have the opposite effect by repressing the cell cycle progression of breast cancer cells. Furthermore, the data indicated that svAC3-33 may upregulate the expression of p21. The present study provides evidence that the increased expression of svAC3-33 may inhibit the activity of the transcription factor AP-1. The luciferase reporter gene assay detected a downregulation of the expression of c-Jun, but not c-Fos, which in turn affected cell proliferation. In conclusion, these results indicated a function for svAC3-33 in inhibiting the cell proliferation of MCF-7 cells by regulating the AP-1 signaling pathway.

A Case Study on the Keap1 Interaction with Peptide Sequence Epitopes Selected by the Peptidomic mRNA Display

Many protein-protein and peptide-protein interactions (PPIs) play key roles in the regulation of biological functions, and therefore, the modulation of PPIs has become an attractive target of new drug development. Although a number of PPIs have already been identified, over 100 000 unknown PPIs are predicted to exist. To uncover such unknown PPIs, it is important to devise a conceptually distinct method from that of currently available methods. Herein, an mRNA display by using a total RNA library derived from various human tissues, which serves as a unique method to physically isolate peptide epitopes that potentially bind to a target protein of interest, is reported. In this study, selection was performed against Kelch-like ECH-associated protein (Keap1) as a model target protein, leading to a peptide epitope originating from astrotactin-1 (ASTN1). It turned out that this ASTN1 peptide was able to interact with Keap1 more strongly than that with a known peptide derived from Nrf2; a well-known, naturally occurring Keap1 binder. This case study demonstrates the applicability of peptidomic mRNA display for the rapid exploration of consensus binding peptide motifs and the potential for the discovery of unknown PPIs with other proteins of interest.

ImmuSort, a database on gene plasticity and electronic sorting for immune cells

Gene expression is highly dynamic and plastic. We present a new immunological database, ImmuSort. Unlike other gene expression databases, ImmuSort provides a convenient way to view global differential gene expression data across thousands of experimental conditions in immune cells. It enables electronic sorting, which is a bioinformatics process to retrieve cell states associated with specific experimental conditions that are mainly based on gene expression intensity. A comparison of gene expression profiles reveals other applications, such as the evaluation of immune cell biomarkers and cell subsets, identification of cell specific and/or disease-associated genes or transcripts, comparison of gene expression in different transcript variants and probe set quality evaluation. A plasticity score is introduced to measure gene plasticity. Average rank and marker evaluation scores are used to evaluate biomarkers. The current version includes 31 human and 17 mouse immune cell groups, comprising 10,422 and 3,929 microarrays derived from public databases, respectively. A total of 20,283 human and 20,963 mouse genes are available to query in the database. Examples show the distinct advantages of the database. The database URL is http://202.85.212.211/Account/ImmuSort.html.

ImmuCo: a database of gene co-expression in immune cells

Current gene co-expression databases and correlation networks do not support cell-specific analysis. Gene co-expression and expression correlation are subtly different phenomena, although both are likely to be functionally significant. Here, we report a new database, ImmuCo (http://immuco.bjmu.edu.cn), which is a cell-specific database that contains information about gene co-expression in immune cells, identifying co-expression and correlation between any two genes. The strength of co-expression of queried genes is indicated by signal values and detection calls, whereas expression correlation and strength are reflected by Pearson correlation coefficients. A scatter plot of the signal values is provided to directly illustrate the extent of co-expression and correlation. In addition, the database allows the analysis of cell-specific gene expression profile across multiple experimental conditions and can generate a list of genes that are highly correlated with the queried genes. Currently, the database covers 18 human cell groups and 10 mouse cell groups, including 20 283 human genes and 20 963 mouse genes. More than 8.6 × 10⁸ and 7.4 × 10⁸ probe set combinations are provided for querying each human and mouse cell group, respectively. Sample applications support the distinctive advantages of the database.

PIAS1 negatively modulates virus triggered type I IFN signaling by blocking the DNA binding activity of IRF3

During viral infection, production of proinflammatory cytokines including type I interferons (IFNs) is under stringent control to avoid detrimental overreaction. The protein inhibitor of activated STAT (PIAS) family proteins have been recognized as anti-inflammatory molecules by restraining type I IFN induced amplifying signaling. Here we identified PIAS1 as an important negative regulator of virus-triggered type I IFN signaling. Overexpression of PIAS1 repressed virus-or RIG-I like receptor stimulated type I IFN transcription, whereas knockdown of PIAS1 expression augmented virus-induced production of type I IFNs. PIAS1 with a mutation in the SAP domain retained the inhibitory function in virus-induced IFN transcription, but abolished the inhibition in IFN-stimulated signaling. SUMO E3 ligase activity dead mutant PIAS1/C350S still had the comparable inhibitory function with WT PIAS1. Further study indicated that PIAS1 interacted with IRF3 and inhibited the DNA binding activity of IRF3. The C-terminal region of PIAS1 around a cluster of acidic amino acids is critical for the interaction with IRF3 and the inhibitory functions of PIAS1. Therefore, these results unveil PIAS1 functions both at the virus-induced early signaling stage and IFN stimulated amplifying stage with distinct mechanisms. PIAS1 is important in maintaining proper amounts of type I IFNs and restrains its magnitude when the antiviral response intensifies.

Beta catenin and cytokine pathway dysregulation in patients with manifestations of the "PTEN hamartoma tumor syndrome"

Background

The "PTEN hamartoma tumor syndrome" (PHTS) includes a group of syndromes caused by germline mutations within the tumor suppressor gene "phosphatase and tensin homolog deleted on chromosome ten" (PTEN), characterized by multiple polyps in the gastrointestinal tract and by a highly increased risk of developing malignant tumours in many tissues.

The current work clarifies the molecular basis of PHTS in three unrelated Italian patients, and sheds light on molecular pathway disregulation constitutively associated to PTEN alteration.

Methods

We performed a combination of RT-PCR, PCR, sequencing of the amplified fragments, Real Time PCR and western blot techniques.

Results

Our data provide the first evidence of β-catenin accumulation in blood cells of patients with hereditary cancer syndrome caused by germ-line PTEN alteration. In addition, for the first time we show, in all PHTS patients analysed, alterations in the expression of TNFα, its receptors and IL-10. Importantly, the isoform of TNFRI that lacks the DEATH domain (TNFRSF1β) was found to be overexpressed.

Conclusion

In light of our findings, we suggest that the PTEN pathway disregulation could determine, in non-neoplastic cells of PHTS patients, cell survival and pro-inflammatory stimulation, mediated by the expression of molecules such as β-catenin, TNFα and TNFα receptors, which could predispose these patients to the development of multiple cancers.

Novel transcript variants of TRAIL show different activities in activation of NF-κB and apoptosis

AIMS

Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) has many transcript variants, but whether they possess distinct function is not completely known. In the present study, we compared the function of these TRAIL variants.

MAIN METHODS

A bioinformatics analysis was performed to examine potential TRAIL variants. For the functional study, over-expression of TRAIL isoforms was used to examine their NF-κB inducing and apoptotic activities in both cancer and normal cells. Moreover, soluble TRAIL E4 variant protein was expressed and purified in prokaryotic cells, and was used for apoptotic assay.

KEY FINDINGS

We cloned seven truncated TRAIL variants, designated as AK, E2, E3, E4, DA, BX424, and BX439. In comparison with the wild type TRAIL protein expressed from full-length RefSeq, over-expression of all these TRAIL variants activated NF-κB and its targeting genes in human cells at varying degrees. Some isoforms including BX424, DA and E4 even showed NF-κB, IL8, CCL4 and CCL20 promoter activating activity stronger than the wild type protein. All truncated variant proteins had no toxicity to normal human cells, similar to the wild type protein; however, they all failed to induce apoptosis in cancer cells that are sensitive to TRAIL. Recombinant soluble TRAIL E4 protein also failed to antagonize TRAIL-induced apoptosis in cancer cells.

SIGNIFICANCE

Truncated TRAIL variant proteins lost apoptotic activity but retained or even enhanced the NF-κB activating potentials, these results suggest that TRAIL variants may play roles in non-apoptotic cellular processes that are more important than we previously thought.

Human sphingomyelin synthase 1 gene (SMS1): organization, multiple mRNA splice variants and expression in adult tissues

We have previously characterized the structure of the human MOB gene (TMEM23), which encodes a hypothetical transmembrane protein (Vladychenskaya et al., 2002, 2004). The primary structure of the peptide that we predicted coincided completely with the amino acid sequence of the later identified sphingomyelin synthase 1 protein (SMS1), which catalyses the transfer of a phosphorylcholine moiety from phosphatidylcholine to ceramide, producing sphingomyelin and diacylglycerol (Huitema et al., 2004; Yamaoka et al., 2004). The gene we found was the SMS1 gene. The combination of in silico and RT-PCR data helped us identify and characterize numerous new transcripts of the human SMS1 gene. We identified mRNA isoforms that vary in the 5'-untranslated region (UTR) and encode the full-length protein, and transcripts resulting from alternative combinations of the exons in the coding region of the gene and the 3'-UTR. Comparison of the discovered transcripts' structures with the sequence of human chromosome 10 showed that the human SMS1 gene comprises at least 24 exons. RT-PCR and real-time PCR data showed that the expression patterns of the alternative SMS1 transcripts are tissue specific. Our results indicate that the regulation of SMS1 expression is complex and occurs at the transcriptional, post-transcriptional and translational levels.

Molecular cloning and characterization of novel human JNK2 (MAPK9) transcript variants that show different stimulation activities on AP-1

The c-Jun NH(2)-terminal kinase (JNK) signaling pathway participates in many physiological functions. In the current study we reported the cloning and characterization of five novel JNK2 transcript variants, which were designated as JNK2α3, JNK2α4, JNK2β3, JNK2γ1 and JNK2γ2, respectively. Among them, JNK2α4 and JNK2γ2 are potential non-coding RNA because they contain pre-mature stop codons. Both JNK2α3 and JNK2β3 contain an intact kinase domain, and both encode a protein product of 46 kDa, the same as those of JNK2α1 and JNK2β1. JNK2γ1 contains a disrupted kinase domain and it showed a disable function. When over-expressed in mammalian cells, JNK2α3 showed higher activity on AP-1 than that of JNK2β3 and JNK2γ1. Furthermore, JNK2α3 and JNK2β3 showed different levels of substrate phosphorylation, although they both could promote the proliferation of 293T cells. Our results further demonstrate that JNK2 isoforms preferentially target different substrates and may regulate the expression of various target genes.