Jiaqi Liu

CD146 as a new marker for an increased chondroprogenitor cell sub-population in the later stages of osteoarthritis.

Cartilage‐derived mesenchymal stem cells (MSCs) have been isolated with different methods. In this study lateral and medial femoral condyles were respectively collected from patients with late‐stage osteoarthritis during the total knee arthroplasty. After digestion of the cartilage tissues with type II collagenase and analysis by fluorescence‐activated cell sorting (FACS) with CD146, a chondroprogenitor cell sub‐population were isolated and purified. The expression of other MSC‐associated markers in the CD146+ chondroprogenitors was analyzed by flow cytometry. Multi‐lineage differentiation capacity of CD146+ chondroprogenitors was compared with that of unsorted chondrocytes and adipose‐derived MSCs (ADMSCs). Higher percentage of CD146+ chondroprogenitors isolated from the medial femoral condyles was observed than that from the lateral. CD146+ chondroprogenitors expressed high levels of MSC‐specific surface antigens, and showed higher chondrogenesis capacity than ADMSCs and unsorted chondrocytes in a 3D cell pellet culture model. Thus CD146 might be a new cell surface marker for cartilage progenitor cell population in the late‐stage osteoarthritis.

The involvement of ADAMTS-5 genetic polymorphisms in predisposition and diffusion tensor imaging alterations of lumbar disc degeneration

Purpose: Low back pain is a global health problem in which more than 40% is caused by lumbar intervertebral disc degeneration (LDD). ADAMTS‐5 (A disintegrin and metalloproteinase with thrombospondin motifs‐5) was shown to be involved in LDD by functional analyses. To identify whether there is an association between ADAMTS‐5 and LDD, and what is the contribution of ADAMTS‐5 genetic polymorphisms to MD (Mean diffusivity) changes in lumbar IVD (Intervertebral disc). We firstly genotyped selected ADAMTS‐5 SNPs (Single nucleotide polymorphisms) in a Chinese Han population. After the primary analyses of allelic, genotypic, and haplotypic association, we performed SNP–SNP interaction analysis. We subsequently genotyped another 50 participants and acquired the corresponding MD values from individual lumbar IVDs. The association analysis between the genotypic groups divided by the above positive SNPs and the corresponding MD values were also performed. Significant associations were identified in rs151058, rs229052, and rs162502. None of the 2‐SNP haplotypic analysis survived the 10,000 permutation test. The following interaction analysis demonstrated that rs151058 was strong associated with LDD when conditioning on rs162502. Significant difference of MD values between AA and G+ carriers was identified in rs162502. This is the first study indicating that the SNPs of ADAMTS‐5 may contribute to predisposition of LDD. An interaction between rs151058 and rs229052 may exist in ADAMTS‐5 with LDD. The rs162502 might be associated with altered MD values.

Comparison of Apparent Diffusion Coefficient and T2 Relaxation Time Variation Patterns in Assessment of Age and Disc Level Related Intervertebral Disc Changes

Purpose To compare the variation patterns of ADC and T2 values in different age and intervertebral disc (IVD) levels, thus to identify their sensitivities in assessing age and disc level related IVDs changes. Materials and Methods The T2 and ADC values were recorded from 345 IVDs of 69 volunteers. Kendalls correlation analysis was used to identify the relationship between age and T2/ADC mean values respectively. The one-way analysis of variance (ANOVA) with post hoc analysis was then applied to test the differences of T2 and ADC values among different IVD levels and age groups, followed by linear regression analysis between age (<45 and >45 years) and T2/ADC mean values. This study was approved by the Ethics Committee of the Chinese Academy of Medical Sciences and the Peking Union Medical College Hospital. Results Significant negative correlation was observed between age and T2/ADC mean values. The T2 and ADC values showed significant differences among IVD levels and among age groups except for T2 values in age group 1 (25–34 years) and group 2 (35–44 years), and for ADC values at L1–2 level. Both T2 and ADC values showed significant differences between young (age<45 years) and elderly group (age>45 years) at each IVD level. A linear relationship was observed between age and T2/ADC mean values in the elderly group as well as in the young group for the ADC mean values, while no such tendency was identified in the young group for the T2 mean values. Conclusions ADC values may be a more sensitive parameter than T2 in assessing age and disc level related intervertebral disc changes.

FusionCancer: a database of cancer fusion genes derived from RNA-seq data

BackgroundFusion genes are chimeric results originated from previous separate genes with aberrant functions. The resulting protein products may lead to abnormal status of expression levels, functions and action sites, which in return may cause the abnormal proliferation of cells and cancer development.ResultsWith the emergence of next-generation sequencing technology, RNA-seq has spurred gene fusion discovery in various cancer types. In this work, we compiled 591 recently published RNA-seq datasets in 15 kinds of human cancer, and the gene fusion events were comprehensively identified. Based on the results, a database was developed for gene fusion in cancers (FusionCancer), with the attempt to provide a user-friendly utility for the cancer research community. A flexible query engine has been developed for the acquisition of annotated information of cancer fusion genes, which would help users to determine the chimera events leading to functional changes. FusionCancer can be accessible at the following hyperlink website: http://donglab.ecnu.edu.cn/databases/FusionCancer/ConclusionTo the best of our knowledge, FusionCancer is the first comprehensive fusion gene database derived only from cancer RNA-seq data.

Downregulation of stathmin 1 in human gallbladder carcinoma inhibits tumor growth in vitro and in vivo

Gallbladder carcinoma (GBC) is a highly lethal malignancy of the gastrointestinal tract. Despite extensive research, the underlying molecular mechanism of GBC remains largely unclear. Stathmin 1 (STMN1) is an important cytosolic protein associated with microtubule stability that was reported to be involved in tumorigenesis. Up to our knowledge, its role in gallbladder carcinoma has not been analyzed. In this study, we found that STMN1 was significantly highly expressed in GBC by immunohistochemistry (IHC). Further research demonstrated that silencing of STMN1 inhibited cell growth in vitro. Moreover, knockdown of STMN1 induced apoptosis and delayed G2/M phase transformation in GBC cells. Our data support a rationale for further studies that the silencing of STMN1 may regulate the activity of p38 MAPK kinase and p53/p21 signal pathway. Besides, xenografted gallbladder carcinoma cells growth were significantly impaired after STMN1 was silenced in vivo. These results suggested that STMN1 played an important role in cell proliferation and migration. This provided a potential clue for investigating the therapeutic target in GBC.

Genetic Polymorphism of lbx1 is Associated with Adolescent Idiopathic Scoliosis in Northern Chinese Han Population

Study Design. A case-control association study was performed to investigate the relationship between ladybird homeobox (LBX1) and adolescent idiopathic scoliosis (AIS) in northern Chinese Han population. Objective. To explore the prevalence and functional importance of LBX1 polymorphisms in patients with AIS within the northern Chinese Han population. Summary of Background Data. AIS is the most common subtype of idiopathic scoliosis. Genetic factors such as LBX1 polymorphisms have been recently proved to be associated with AIS in some populations. In this study we explored the prevalence and functional importance of the polymorphisms around LBX1 in patients with AIS within the northern Chinese Han population. Methods. Five tag single nucleotide polymorphisms (SNPs) around or in LBX1 were genotyped in 180 patients with AIS and 182 controls. And the luciferase assay was performed to explore the functional importance of the most significant SNPs. Results. We replicated that rs11190870, previously reported as the most significantly associated SNP, was enriched in our AIS cohort. In addition, we found that the T allele of rs1322331 was associated with a novel risk allele (odds ratio = 3.349, 95% confidence interval 1.742–6.436). In the following luciferase assay, the TT-type promoter showed significantly reduced transcription activity in vitro. Conclusion. Two SNPs around LBX1, rs11190870 and rs1322331 are associated with AIS in northern Chinese Han population. The T allele of rs1322331 is a novel risk allele. We hypothesize that rs1322331 might increase patients’ susceptibility to AIS by reducing LBX1-AS1 transcription and thus upregulating the function of LBX1. Level of Evidence: 3

Progress and perspective of TBX6 gene in congenital vertebral malformations.

Congenital vertebral malformation is a series of significant health problems affecting a large number of populations. It may present as an isolated condition or as a part of an underlying syndromes occurring with other malformations and/or clinical features. Disruption of the genesis of paraxial mesoderm, somites or axial bones can result in spinal deformity. In the course of somitogenesis, the segmentation clock and the wavefront are the leading factors during the entire process in which TBX6 gene plays an important role. TBX6 is a member of the T-box gene family, and its important pathogenicity in spinal deformity has been confirmed. Several TBX6 gene variants and novel pathogenic mechanisms have been recently revealed, and will likely have significant impact in understanding the genetic basis for CVM. In this review, we describe the role which TBX6 plays during human spine development including its interaction with other key elements during the process of somitogenesis. We then systematically review the association between TBX6 gene variants and CVM associated phenotypes, highlighting an important and emerging role for TBX6 and human malformations.

Novel NTRK1 Frameshift Mutation in Congenital Insensitivity to Pain With Anhidrosis

Congenital insensitivity to pain with anhidrosis is a rare autosomal recessive disorder. It has been reported that the defect in the NTRK1 gene encoding tropomyosin-related kinase A (TrkA) can cause congenital insensitivity to pain with anhidrosis. Nerve growth factor (NGF), the product of NGFB, mediates biological effects by binding to and activating tropomyosin-related kinase A. In addition, necdin (encoded by NDN) is also essential in nerve growth factor–tropomyosin-related kinase A pathway. We performed mutation analysis in NTRK1, NGFB, and NDN genes in a Chinese Han 17-year-old female patient with congenital insensitivity to pain with anhidrosis and her healthy family members. As a result, the patient was found to have a novel insertion in exon 7 (c.727insT) of NTRK1, which causes premature termination, and a single nucleotide polymorphism (rs2192206 G>A) in NDN. Our findings imply that the genetic variations of the nerve growth factor–tropomyosin-related kinase A pathway play an important role in congenital insensitivity to pain with anhidrosis.

Association of LMX1A genetic polymorphisms with susceptibility to congenital scoliosis in Chinese Han population.

Study Design. A genetic association study of single nucleotide polymorphisms (SNPs) for the LMX1A gene with congenital scoliosis (CS) in the Chinese Han population. Objective. To determine whether LMX1A genetic polymorphisms are associated with susceptibility to CS. Summary of Background Data. CS is a lateral curvature of the spine due to congenital vertebral defects, whose exact genetic cause has not been well established. The LMX1A gene was suggested as a potential human candidate gene for CS. However, no genetic study of LMX1A in CS has ever been reported. Methods. We genotyped 13 SNPs of the LMX1A gene in 154 patients with CS and 144 controls with matched sex and age. After conducting the Hardy-Weinberg equilibrium test, the data of 13 SNPs were analyzed by the allelic and genotypic association with logistic regression analysis. Furthermore, the genotype-phenotype association and haplotype association analysis were also performed. Results. The 13 SNPs of the LMX1A gene met Hardy-Weinberg equilibrium in the controls, which was not in the cases. None of the allelic and genotypic frequencies of these SNPs showed significant difference between case and control groups (P > 0.05). However, the genotypic frequencies of rs1354510 and rs16841013 in the LMX1A gene were associated with CS predisposition in the unconditional logistic regression analysis (P = 0.02 and 0.018, respectively). Genotypic frequencies of 3 SNPs at rs6671290, rs1354510, and rs16841013 were found to exhibit significant differences between patients with CS with failure of formation and the healthy controls (P = 0.019, 0.007, and 0.006, respectively). Besides, in the model analysis by using unconditional logistic regression analysis, the optimized model for the 3 genotypic positive SNPs with failure of formation were rs6671290 (codominant; P = 0.025, Akaike information value = 316.6, Bayesian information criterion = 333.9), rs1354510 (overdominant; P = 0.0017, Akaike information value = 312.1, Bayesian information criterion = 325.9), and rsl6841013 (overdominant; P = 0.0016, Akaike information value = 311.1, Bayesian information criterion = 325), respectively. However, the haplotype distributions in the case group were not significantly different from those of the control group in the 3 haplotype blocks. Conclusion. To our knowledge, this is the first study to identify that the SNPs of the LMX1A gene might be associated with the susceptibility to CS and different clinical phenotypes of CS in the Chinese Han population. Level of Evidence: 4

Fusion Genes and their Detection through Next Generation Sequencing in Malignant Hematological Disease and Solid Tumors

Fusion genes are neoplasia-associated mutations, which play a particularly significant role in tumorgenesis and exhibits great importance for clinical applications in malignant hematological disease and solid tumors. Simultaneously with CNVs, gene fusions are resulting from balanced and unbalanced chromosomal rearrangements. Thus, understanding the mutagenesis and instability of CNV, as well as the underlying molecular mechanisms of chromosomal rearrangements will improve our comprehension of gene fusions. Recently, next generation sequencing (NGS), especially RNA-Seq, has become very useful tools to identify gene alterations in cancer and a powerful approach for investigating the tumorgenesis. While we are still faced with the challenge of minimizing false positives in RNA-seq result. WGS is also pervasively used for the fusion gene detection, which provides us a more comprehensive and integrative way to detect structural variants. And WGS may correct the false-negative results from RNA-seq. Additionally, many computational tools have also been developed for the detection of fusion transcripts using RNA-Seq data, while developing a more sensitivity and specificity fusion genes detection tools for NGS datas remains an important and open question. In future, multi-omics analysis, thirdgeneration sequencing and liquid biopsies technique all provides opportunities to comprehensively interpret gene fusions and understand the biology of cancer genomes.