Identification of an HLA-A2-Restricted Epitope Peptide Derived from Hypoxia-Inducible Protein 2 (HIG2)

We herein report the identification of an HLA-A2 supertype-restricted epitope peptide derived from hypoxia-inducible protein 2 (HIG2), which is known to be a diagnostic marker and a potential therapeutic target for renal cell carcinoma. Among several candidate peptides predicted by the HLA-binding prediction algorithm, HIG2-9-4 peptide (VLNLYLLGV) was able to effectively induce peptide-specific cytotoxic T lymphocytes (CTLs). The established HIG2-9-4 peptide-specific CTL clone produced interferon-γ (IFN-γ) in response to HIG2-9-4 peptide-pulsed HLA-A*02:01-positive cells, as well as to cells in which HLA-A*02:01 and HIG2 were exogenously introduced. Moreover, the HIG2-9-4 peptide-specific CTL clone exerted cytotoxic activity against HIG2-expressing HLA-A*02:01-positive renal cancer cells, thus suggesting that the HIG2-9-4 peptide is naturally presented on HLA-A*02:01 of HIG-2-expressing cancer cells and is recognized by CTLs. Furthermore, we found that the HIG2-9-4 peptide could also induce CTLs under HLA-A*02:06 restriction. Taken together, these findings indicate that the HIG2-9-4 peptide is a novel HLA-A2 supertype-restricted epitope peptide that could be useful for peptide-based immunotherapy against cancer cells with HIG2 expression.     

Predicting MoRFs in protein sequences using HMM profiles

Background

Intrinsically Disordered Proteins (IDPs) lack an ordered three-dimensional structure and are enriched in various biological processes. The Molecular Recognition Features (MoRFs) are functional regions within IDPs that undergo a disorder-to-order transition on binding to a partner protein. Identifying MoRFs in IDPs using computational methods is a challenging task.

Methods

In this study, we introduce hidden Markov model (HMM) profiles to accurately identify the location of MoRFs in disordered protein sequences. Using windowing technique, HMM profiles are utilised to extract features from protein sequences and support vector machines (SVM) are used to calculate a propensity score for each residue. Two different SVM kernels with high noise tolerance are evaluated with a varying window size and the scores of the SVM models are combined to generate the final propensity score to predict MoRF residues. The SVM models are designed to extract maximal information between MoRF residues, its neighboring regions (Flanks) and the remainder of the sequence (Others).

Results

To evaluate the proposed method, its performance was compared to that of other MoRF predictors; MoRFpred and ANCHOR. The results show that the proposed method outperforms these two predictors.

Conclusions

Using HMM profile as a source of feature extraction, the proposed method indicates improvement in predicting MoRFs in disordered protein sequences.

     

Eph receptor A10 has a potential as a target for a prostate cancer therapy

We recently identified Eph receptor A10 (EphA10) as a novel breast cancer-specific protein. Moreover, we also showed that an in-house developed anti-EphA10 monoclonal antibody (mAb) significantly inhibited proliferation of breast cancer cells, suggesting EphA10 as a promising target for breast cancer therapy. However, the only other known report for EphA10 was its expression in the testis at the mRNA level. Therefore, the potency of EphA10 as a drug target against cancers other than the breast is not known. The expression of EphA10 in a wide variety of cancer cells was studied and the potential of EphA10 as a drug target was evaluated. Screening of EphA10 mRNA expression showed that EphA10 was overexpressed in breast cancer cell lines as well as in prostate and colon cancer cell lines. Thus, we focused on prostate cancers in which EphA10 expression was equivalent to that in breast cancers. As a result, EphA10 expression was clearly shown in clinical prostate tumor tissues as well as in cell lines at the mRNA and protein levels. In order to evaluate the potential of EphA10 as a drug target, we analyzed complement-dependent cytotoxicity effects of anti-EphA10 mAb and found that significant cytotoxicity was mediated by the expression of EphA10. Therefore, the idea was conceived that the overexpression of EphA10 in prostate cancers might have a potential as a target for prostate cancer therapy, and formed the basis for the studies reported here.     

Interactive effects of soil nutrient heterogeneity and belowground herbivory on the growth of plants with different root foraging traits

Aims

Plants with precise root foraging patterns can proliferate roots preferentially in nutrient-rich soil patches. When nutrients are distributed heterogeneously, this trait is often competitively advantageous in pot experiments but not field experiments. We hypothesized that this difference is due to belowground herbivory under field conditions.

Methods

We performed pot experiments using seedlings of Lolium perenne (a more precise root foraging species) and Plantago lanceolata (a less precise root foraging species). The experiment had a two-way factorial randomized block design, with nutrient distribution pattern (homogeneous or heterogeneous) and belowground herbivore (present or absent) as the two factors. Each pot contained one seedling of each species.

Results

With no herbivore present, plant biomass was smaller in the heterogeneous nutrient treatment than in the homogeneous treatment in P. lanceolata, but not in L. perenne. Under homogeneous nutrient distribution, plant biomass was lower in both species with a herbivore present than with no herbivore. Under heterogeneous nutrient distribution, biomass reduction due to herbivory occurred only in L. perenne.

Conclusions

Roots of the precise root foraging species were grazed more under the heterogeneous nutrient distribution, suggesting that the herbivore more efficiently foraged for roots in nutrient-rich soil patches.     

ZFAT is an antiapoptotic molecule and critical for cell survival in MOLT-4 cells

ZFAT (also known as ZNF406), originally identified as a candidate gene for autoimmune thyroid disease, encodes a zinc-finger protein, however, its function has not been elucidated. Here, we report that human ZFAT protein is expressed in peripheral B and T lymphocytes and a human acute T lymphoblastic leukaemia cell line, MOLT-4 cells. Intriguing is that mouse ZFAT expression in CD4⁺ lymphocytes is increased during blast formation. Furthermore, ZFAT-knockdown in MOLT-4 induces apoptosis via activation of caspases. These results suggested that ZFAT protein is a critical regulator involved in apoptosis and cell survival for immune-related cells.     

Two Complementary Enzymes for Threonylation of tRNA in Crenarchaeota: Crystal Structure of Aeropyrum pernix Threonyl-tRNA Synthetase Lacking a cis-Editing Domain

In protein synthesis, threonyl-tRNA synthetase (ThrRS) must recognize threonine (Thr) from the 20 kinds of amino acids and the cognate tRNA^Thr from different tRNAs in order to generate Thr-tRNA^Thr. In general, an organism possesses one kind of gene corresponding to ThrRS. However, it has been recently found that some organisms have two different genes for ThrRS in the genome, suggesting that their proteins ThrRS-1 and ThrRS-2 function separately and complement each other in the threonylation of tRNA^Thr, one for catalysis and the other for trans-editing of misacylated Ser-tRNA^Thr. In order to clarify their three-dimensional structures, we performed X-ray analyses of two putatively assigned ThrRSs from Aeropyrum pernix (ApThrRS-1 and ApThrRS-2). These proteins were overexpressed in Escherichia coli, purified, and crystallized. The crystal structure of ApThrRS-1 has been successfully determined at 2.3 Å resolution. ApThrRS-1 is a dimeric enzyme composed of two identical subunits, each containing two domains for the catalytic reaction and for anticodon binding. The essential editing domain is completely missing as expected. These structural features reveal that ThrRS-1 catalyzes only the aminoacylation of the cognate tRNA, suggesting the necessity of the second enzyme ThrRS-2 for trans-editing. Since the N-terminal sequence of ApThrRS-2 is similar to the sequence of the editing domain of ThrRS from Pyrococcus abyssi, ApThrRS-2 has been expected to catalyze deaminoacylation of a misacylated serine moiety at the CCA terminus.     

Effects of low-load resistance training with vascular occlusion on the mechanical properties of muscle and tendon

The present study aimed to investigate the effects of low-load resistance training with vascular occlusion on the specific tension and tendon properties by comparing with those of high-load training. Nine participants completed 12 weeks (3 days/week) of a unilateral isotonic training program on knee extensors. One leg was trained using low load (20% of 1 RM) with vascular occlusion (LLO) and other leg using high load (80% of 1 RM) without vascular occlusion (HL). Before and after training, maximal isometric knee extension torque (MVC) and muscle volume were measured. Specific tension of vastus lateralis muscle (VL) was calculated from MVC, muscle volume, and muscle architecture measurements. Stiffness of tendon-aponeurosis complex in VL was measured using ultrasonography during isometric knee extension. Both protocols significantly increased MVC and muscle volume of quadriceps femoris muscle. Specific tension of VL increased significantly 5.5% for HL, but not for LLO. The LLO protocol did not alter the stiffness of tendon-aponeurosis complex in knee extensors, while the HL protocol increased it significantly. The present study demonstrated that the specific tension and tendon properties were found to remain following low-load resistance training with vascular occlusion, whereas they increased significantly after high-load training.     

Efficient solid-phase synthesis of oligodeoxynucleotides having a 5′-terminal 2,2,7-trimethylguanosine pyrophosphate linkage

A 5′-terminal 2,2,7-trimethylguanosine (TMG) cap structure plays an important role in transport of TMG-capped snRNAs from the cytoplasm to the nucleus in living cells. This property can be expected to be used for carrying artificial nucleic acids into the nucleus in gene therapy. In this paper, a new TMG-capping reagent 1 was developed and used for the synthesis of oligodeoxynucleotides having a 5′-terminal TMG-capped pyrophosphate linkage (m₃^2,2,7G^5′pp-DNA) lacking one phosphate group using a silyl-type linker on polymer supports.     

Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one

The incorporation of the bicyclic cytosine analogue 7,8-dihydropyrido[2,3-d]pyrimidin-2-one (X) into DNA duplexes results in a significant enhancement of their stability (3–4 K per modification). To establish the effects of X on the local hydrogen-bonding and base stacking interactions and the overall DNA conformation, and to obtain insights into the correlation between the structure and stability of X-containing DNA duplexes, the crystal structures of [d(CGCGAATT-X-GCG)]₂ and [d(CGCGAAT-X-CGCG)]₂ have been determined at 1.9–2.9 Å resolutions. In all of the structures, the analogue X base pairs with the purine bases on the opposite strands through Watson–Crick and/or wobble type hydrogen bonds. The additional ring of the X base is stacked on the thymine bases at the 5′-side and overall exhibits greatly enhanced stacking interactions suggesting that this is a major contribution to duplex stabilization.