The combination of tandem spectrometry and database searching is one of the most popular technologies for protein identification.However,only those proteins in the searching database could be identified,and current database is far from completeness.So it is necessary to mining the MS/MS data comprehensively,in which novel protein identification is the most important one.The definition of novel protein could be divided into three levels according to their annotations of sequences and functions.As a part of protein identification,the main approaches used to identify novel protein are basing on the following two different ways:de novo sequencing combined with similarity search and searching against nucleotide acid databases such as EST or genome databases.Several mature or newly developed methods and techniques were summarized,and the problems and strategies discussed here would be helpful for the related researches.

AIM: To investigate the effects of alanyl - glutamine ( Ala -Gln) on expression of iNOS and TNF- α in injured intestinal mucosa induced by oral tacrolimus (FK506). METHODS: Twenty -four BALB/c mice were randomized to receive orally 0.2 mL of normal saline solution ( group Ⅰ ), 0.2 mL of FK506 in a dose of 0.1 mg/kg ( group Ⅱ ) or 1.0 mg/kg (group Ⅲ), and orally high -dose FK506 (0.2 mL, 1.0 mg/kg) plus intraperitoneal injection of Ala -Gln (0.5 g/kg )(group Ⅳ ),respectively. Damages of intestinal mucosa were determined by pathological examination.Intestinal mucosal permeability was analysed by FITC - dextran fluorescence assay. Expression of iNOS and TNF - α in intestine was detected by RT - PCR and Western blotting. RESULTS: Severe damage on the villi and increased intestinal permeability were observed in high - dose FK506 treated mice according to scanning electron microscopy and FITC - dextran flux respectively. The erosion and increased intestinal permeability were significantly alleviated by Ala - Gln treatment. Transcription of iNOS mRNA and TNF - α mRNA, which was up - regulated in high - dose FK506 treated group,was also markedly down- regulated in mice combined with Ala- Gln- treatment. A significantly increased expression of iNOS and TNF - α protein was found in the high - dose FK506 treated mice, while small amounts of these proteins were identified in the Ala - Gln - treated group. CONCLUSION: FK506 could induce a significant impairment of intestinal mucosa morphologically, which might be associated with up - regulated expression of iNOS and TNF - α in small intestinal mucosa. Subsequently, the intestinal permeability is increased. Ala - Gln has a strong protective effect on FK506 - induced intestinal barrier dysfunction, probably relates to the down - regulation of iNOS and TNF - α expression.

Data analysis poses a significant challenge to the large-scale proteomics studies. Based on the structured and controlled vocabularies-Gene Ontology (GO), and the GO annotation from related databases, a strategy composed of several programs and local databases is developed to identify the functional distribution and the significantly enriched functional categories of the proteomic expression profile. It would be helpful for understanding the overall functions of these identified proteins and supply the fundamental information for further bioinformatics exploration. This strategy has been successfully used in the Human Fetal Liver (HFL) proteomic research, which is available online at http://www.hupo.org.cn/GOfact/.

More and more DNA sequences have been obtained since the start-up of human genome project. Powerful system is badly needed for data mining on these DNA sequences. Based on a personal computer and Linux operating system, the Phred/Phrap/Consed software and Blast software were used to construct a platform for batch analysis of the sequences, including identifying raw DNA sequence from chromatogram file, vector sequence removing, contig analysis (sequence assembly), repeat sequence identifying and sequence similarity analysis. Result demonstrated that this robust platform could accelerate data analysis for large-scale DNA sequencing.

AIM: To investigate the effects of alanyl-glutamine (Ala-Gln) on expression of iNOS and TNF-? in injured intestinal mucosa induced by oral tacrolimus(FK506). METHODS: Twenty-four BALB/c mice were randomized to receive orally 0.2 mL of normal saline solution ( groupⅠ), 0.2 mL of FK506 in a dose of 0.1 mg/kg (groupⅡ) or 1.0 mg/kg (groupⅢ), and orally high-dose FK506 (0.2 mL, 1.0 mg/kg) plus intraperitoneal injection of Ala-Gln (0.5 g/kg )(groupⅣ),respectively. Damages of intestinal mucosa were determined by pathological examination. Intestinal mucosal permeability was analysed by FITC-dextran fluorescence assay. Expression of iNOS and TNF-? in intestine was detected by RT-PCR and Western blotting.RESULTS: Severe damage on the villi and increased intestinal permeability were observed in high-dose FK506 treated mice according to scanning electron microscopy and FITC-dextran flux respectively. The erosion and increased intestinal permeability were significantly alleviated by Ala-Gln treatment. Transcription of iNOS mRNA and TNF-? mRNA, which was up-regulated in high-dose FK506 treated group, was also markedly down-regulated in mice combined with Ala-Gln-treatment. A significantly increased expression of iNOS and TNF-? protein was found in the high-dose FK506 treated mice, while small amounts of these proteins were identified in the Ala-Gln-treated group.CONCLUSION: FK506 could induce a significant impairment of intestinal mucosa morphologically, which might be associated with up-regulated expression of iNOS and TNF-? in small intestinal mucosa. Subsequently, the intestinal permeability is increased. Ala-Gln has a strong protective effect on FK506-induced intestinal barrier dysfunction, probably relates to the down-regulation of iNOS and TNF-? expression.

Immunotherapy combined with targeted therapy can benefit the survival of patients with unresectable hepatocellular carcinoma. Atezolizumab combined with bevacizumab has achieved remarkable efficacy in patients with advanced hepatocellular carcinoma, but the efficacy of conversion therapy in patients with unresectable hepatocellular carcinoma still needs more evidences. The authors report the clinical efficacy of a case of unresectable hepatocellular carcinoma with hepatitis B virus related liver cirrhosis who was treated with immunotherapy plus targeted therapy combined with local treatment. Results show a good effect in patient without tumor recurrence after postoperative 9 months.

Cancer is a heterogeneous disease with complex mechanisms that requires targeted precision medicine strategies. The growth of precision medicine is indispensable from the rapid development of genomics. However, genomics has certain limitations in molecular phenotype analysis, proteogenomics thus arose at the right time. Proteogenomics is the merging of proteomics and genomics. This review describes the limitations of genomic analysis and highlights the importance of proteogenomics to re-understand precision oncology from a proteogenomic perspective. In addition, the application of proteogenomics in precision oncology is briefly introduced, the related public data projects are described, and finally, the challenges that need to be addressed at this stage are proposed.
Humans ; Proteogenomics ; Precision Medicine ; Neoplasms/genetics* ; Proteomics ; Genomics

Objective:To investigate the role and molecular mechanism of sensory neuron-derived exosomes (nExo) in mediating intervertebral disc degeneration (IDD).Methods:A rat IDD model was constructed, with nExo injected into the intervertebral disc. After 4 weeks, the degenerative grades of operated discs were evaluated using histological staining, while the senescent phenotype of nucleus pulposus stem cells (NPSC) in the tissue was evaluated using immunofluorescence staining. For in vitro experiments, 24 hours after the treatment of nExo to NPSC, immunoblotting, flow cytometry, or senescence-associated β-galactosidase staining was applied to evaluate the senescent phenotype of NPSC. Transcriptomics analysis was applied to identify the key molecules that mediate nExo-induced cells senescence. After 4 weeks of injecting nExo and TXN into the rat tail disc degeneration model.Results:nExo increased the degenerative grades of IDD and increased the proportion of TEK +p16 + and TEK +p21 + cells (from 36.32% ±4.04%, 33.69% ±4.56% in IDD group to 56.41% ±5.26%, 50.14% ±8.49% in IDD+nExo group, respectively; t=7.420, P<0.001; t=4.184, P<0.0019, respectively) in the disc tissue. Besides, nExo promoted the expression of p16 and p21 in NPSC and increased the percentage of cells with positive senescence-associated β-galactosidase staining (from 7.32%±1.73% to 58.22%±11.38%, t=7.658, P=0.002), while the percentage of G2/M cells was downregulated (from 18.10%±1.32% to 1.60%±0.67%, t=19.290, P<0.001). Transcriptomic analysis showed that the differential genes of CTRL vs. nExo were closely related to cell senescence, and TXN was screened by intersecting the differential gene set with the cellular senescence gene sets from the published database. Furthermore, we verified that nExo decreased the content of TXN in NPSC, while exogenous TXN downregulated the expression of p16 and p21 in NPSC, reduced the positive cell rate of senescence-associated β-galactosidase staining (from 58.84%±3.99% to 21.68%±8.16%, t=7.048, P=0.021), increased the percentage of G2/M cells (from 1.21%±0.34% to 15.26%±2.60%, t=9.259, P=0.001). TXN significantly reduced the grade of disc tissue degeneration (histological score: 14.33±0.82 in the nExo group; 8.17±1.17 in the nExo+TXN group, t=10.590, P<0.001), significantly increased the content of extracellular matrix (from 10.94±4.35 μg/mg to 50.55±12.16 μg/mg, t=7.512, P<0.001), and reduced the proportion of TEK +p16 + and TEK +p21 + double-positive cells (from 54.92%±4.21% and 60.31%±9.02% to 27.93%±3.26% and 33.75%±8.07%, respectively; t=12.430, P<0.001; t=5.375, P<0.001, respectively). Conclusion:nExo promotes cell senescence and IDD by downregulating TXN in NPSC.