Prognostic alternative splicing regulatory network of splicing events in acute myeloid leukemia patients based on SpliceSeq data from 136 cases

This study aimed to create prognostic signatures to predict AML patients' survival using alternative splicing (AS) events. The AS data, RNA sequencing data, and the survival statistics of 136 AML patients were obtained from The Cancer Genome Atlas (TCGA) and TCGA SpliceSeq databases. Total 34,984 AS events generated from 8,656 genes, 2,583 of which were survival-associated AS events, were identified using univariate Cox regression. The prognostic models constructed using independent survival-associated AS events revealed that low-risk splicing better predicted patients' survival. ROC analysis indicated that the predictive efficacy of the alternate terminator model was best in the area under the curve at 0.781. Enrichment analysis revealed several important genes (TP53, BCL2, AURKB, PPP2R1B, FOS, and BIRC5) and pathways, such as the protein processing pathway in the endoplasmic reticulum, RNA transport pathway, and HTLV-I infection pathway. The splicing network of splicing events and factors revealed interesting interactions, such as the positive correlation between HNRNPH3 and CALHM2-13010-AT, which may indicate the potential splicing regulatory mechanism. Taken together, survival-associated splicing events and the prognostic signatures for predicting survival can help provide an overview of splicing in AML patients and facilitate clinical practice. The splicing regulatory network may improve the understanding of spliceosomes in AML.

Lymphocytic HLA-A mRNA is a reliable indicator of acute rejection in renal transplantation

BACKGROUND

Rejection in renal transplantation is the most frequent event causing transplant failure. It is important to identify parameters to predict rejection, which are helpful in a timely fashion.

METHODS

Fifty-nine renal transplant recipients were divided into two groups: group 1 (stable renal function) and group 2 (acute rejection episodes). The levels of HLA-A mRNA in peripheral blood lymphocytes (both pre- and posttransplantation) were measured by reverse transcriptase-polymerase chain reaction (RT-PCR) with glucose-6-phosphate dehydrogenase (G6PDH) as an internal reference. The TEST software was used to analyze the relative expressions of HLA-A mRNA.

RESULTS

There was no statistical significance between features of the two groups pretransplant versus normal controls. Posttransplant, the HLA-A mRNA levels decreased significantly compared to those of pretransplant and normal control individuals. The levels of HLA-A mRNA among the 10 patients with acute rejection episodes were significantly increased. There was no significant change in the lymphocyte populations in the early stage of an acute rejection episode compared with the prerejection value.

CONCLUSION

HLA-A mRNA expression was strongly correlated with immune status. The HLA-A mRNA levels may provide an effective and reliable indicator to predict acute rejection episodes in renal transplantation.

Physical and functional interaction of Runt-related protein 1 with hypoxia-inducible factor-1alpha

Angiogenesis and hematopoiesis are closely linked and interactive with each other, but few studies were given to identify possible links between angiogenesis-promoting proteins and hematopoiesis-related transcription factors. Here we investigated the potential relationship of oxygen-sensitive alpha-subunit of angiogenesis-related hypoxia-inducible factor-1alpha (HIF-1alpha) with Runt-related protein 1 (Runx1, also known as acute myeloid leukemia-1, AML-1), an important hematopoietic transcription factor. The results demonstrated that Runx1 and HIF-1alpha proteins directly interacted with each other to a degree, in which Runt homology domain of Runx1 was mainly involved. Leukemia-related abnormal Runx1 fusion protein AML1-ETO, which fuses the N-terminal 177 amino acid residues of the Runx1 protein in frame to ETO (eight-twenty-one) protein, also interacted with HIF-1alpha protein with greater ability than Runx1 itself. More intriguingly, Runx1 overexpression inhibited DNA-binding and transcriptional activity of HIF-1 protein with reduced expression of HIF-1-targeted genes such as vascular endothelial growth factor, while silence of Runx1 expression by specific small interfering RNA significantly increased transcriptional activity of HIF-1 protein, suggesting that Runx1 inhibited transcription-dependent function of HIF-1. Vice versa, HIF-1alpha increased DNA-binding ability and transcriptional activity of Runx1 protein. All these data would shed new insight to understanding Runx1 and HIF-1alpha-related hematopoietic cell differentiation and angiogenesis.

Selective and sequential adsorption of bovine serum albumin and lysozyme from a binary mixture on nanosized magnetic particles

Magnetic particles about 10 nm in size were prepared by chemical precipitation under nitrogen and used for the selective and sequential adsorption of bovine serum albumin (BSA) (pI = 4.7) and lysozyme (LSZ) (pI = 1.1) under different conditions, such as pH and initial protein concentration. The separation ratio of BSA over LSZ at pH 4.6 is about 5, which is about 1.5 times the separation ratio of LSZ over BSA at pH 11.0. Only 10% of the preadsorbed BSA could be displaced by the sequential adsorption of LSZ at pH 11.0. On the other hand, 60% of the preadsorbed LSZ was desorbed due to the sequential adsorption of BSA at pH 4.6. Over 50% desorption of BSA or LSZ could be achieved either by 0.5 M Na(2)HPO(4) or 0.5 M NaH(2)PO(4) after 2 h. Over 80% of the enzymatic activity of LSZ was preserved when it was desorbed from magnetic particles.

Adsorption and desorption of lysozyme on nano-sized magnetic particles and its conformational changes

Adsorption and desorption of lysozyme on nano-sized magnetic particles and its conformational change were studied in this work. Adsorption of lysozyme on nano-sized magnetic particles (Fe(3)O(4)) was carried out at different pH. Maximum adsorption of lysozyme (4.65 mg/m2) occurred at its isoelectric point (pI = 11.1). Differential scanning calorimetry (DSC) results show that the lysozyme adsorbed on magnetic particles did not show any thermal transition over the range 20-100 degrees C. High desorption of lysozyme from magnetic particles was achieved using NaH(2)PO(4) (pH 4.0) (90%) and NaSCN (pH 6.0) (97%) as desorbents. The conformational change of the lysozyme desorbed by NaH(2)PO(4) was small, while the lysozyme desorbed by NaSCN underwent a significant conformational change as measured by the intrinsic fluorescence. Eighty-eight and 82% activity was retained in the desorbed enzyme for desorption by NaH(2)PO(4) and NaSCN, respectively.

Adsorption of bovine serum albumin on nanosized magnetic particles

Adsorption of bovine serum albumin (BSA) on nanosized magnetic particles (Fe(3)O(4)) was carried out in the presence of carbodiimide. The equilibrium and kinetics of the adsorption process were studied. Nanosized magnetic particles (Fe(3)O(4)) were prepared by the chemical precipitation method using Fe2+, Fe3+ salts, and ammonium hydroxide under a nitrogen atmosphere. Characterizations of magnetic particles were carried out using transmission electron microscopy (TEM) and a vibrating sample magnetometer (VSM). Fourier-transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) were used to confirm the attachment of BSA on magnetic particles. Effects of pH and salt concentrations were investigated on the adsorption process. The experimental results show that the adsorption of BSA on magnetic particles was affected greatly by the pH, while the effect of salt concentrations was insignificant at a low concentration range. The adsorption equilibrium isotherm was fitted well by the Langmuir model. The maximum adsorption of BSA on magnetic particles occurred at the isoelectric point of BSA. Adsorption kinetics was analyzed by a linear driving force mass-transfer model. BSA was desorbed from magnetic particles under alkaline conditions, which was confirmed by SDS-PAGE electrophoresis and FTIR results.

Molecular cloning, sequence analysis and mRNA expression of human ADP-ribosylation factor

The ADP-ribosylation factor (ARF) is the small (21 kb) GTP-binding protein required for the efficient cholera toxin-catalyzed ADP-ribosylation of purified Gs, the stimulating regulatory component of adenylate cyclase. Human ARF cDNA clones were obtained from a human cDNA library by cross-species hybridization with bovine ARF1, and the nucleotide and deduced amino acid sequences were determined. Comparison of the sequences of human and bovine ARF1 showed 90% identity at the nucleotide level and 100% identity at the amino acid level, demonstrating the highly conserved nature of the ARF protein. Using human ARF cDNA as the probe, we have detected ARF messenger RNA (approximately 2.2-2.3 kb) in a wide variety of human tissues and tumor cell lines.

A simple and rapid nucleotide sequencing strategy and its application in analyzing a rice histone 3 gene

An improved rapid method for sequencing a target DNA is described. A new plasmid, pAA-PZ1, which contains the origin of replication from phage M13 and a portion of the Tn9 transposon was constructed. A long fragment of target DNA cloned into this vector is progressively shortened in vivo from one end by transposon-mediated deletions. The plasmids carrying different lengths of target DNA are then made into single-stranded DNA in the same host upon infection with an M13 phage and their sequence is determined using the dideoxynucleotide chain-termination method. This method bypasses the in vitro enzymatic manipulations for progressive deletions and requires no subcloning. Using this strategy, we sequenced 1.3 kb of rice DNA containing a histone 3 gene within three weeks.