SEC23A Inhibit Melanoma Metastatic through Secretory PF4 Cooperation with SPARC to Inhibit MAPK Signaling Pathway

Metastasis of melanoma to the distant organs is a multistep process in which the tumor microenvironment (TME) may play an important role. However, the relationship between metastatic progression and TME is intricate. In the present study, using melanoma derivative cell lines OL (oligometastatic) and POL (polymetastatic) that differ in their metastatic colonization capability, we have elucidated a new mechanism involving “SEC23A-PF4-MAPK/ERK axis” in which PF4 transported by COPII hinders metastasis through inhibition of MAPK/ERK signaling pathway. Furthermore, SPARC can act cooperatively to enhance the inhibition of Pf4 on ERK phosphorylation and melanoma cell metastasis. Our findings show the possibility of targeting cancer cell secretome for therapeutic development.     

Hybrid assembly of ultra-long Nanopore reads augmented with 10x-Genomics contigs: Demonstrated with a human genome

The 3rd generation of sequencing (3GS) technologies generate ultra-long reads (up to 1 Mb), which makes it possible to eliminate gaps and effectively resolve repeats in genome assembly. However, the 3GS technologies suffer from the high base-level error rates (15%–40%) and high sequencing costs. To address these issues, the hybrid assembly strategy, which utilizes both 3GS reads and inexpensive NGS (next generation sequencing) short reads, was invented. Here, we use 10×-Genomics® technology, which integrates a novel bar-coding strategy with Illumina® NGS with an advantage of revealing long-range sequence information, to replace common NGS short reads for hybrid assembly of long erroneous 3GS reads. We demonstrate the feasibility of integrating the 3GS with 10×-Genomics technologies for a new strategy of hybrid de novo genome assembly by utilizing DBG2OLC and Sparc software packages, previously developed by the authors for regular hybrid assembly. Using a human genome as an example, we show that with only 7× coverage of ultra-long Nanopore® reads, augmented with 10× reads, our approach achieved nearly the same level of quality, compared with non-hybrid assembly with 35× coverage of Nanopore reads. Compared with the assembly with 10×-Genomics reads alone, our assembly is gapless with slightly high cost. These results suggest that our new hybrid assembly with ultra-long 3GS reads augmented with 10×-Genomics reads offers a low-cost (less than ¼ the cost of the non-hybrid assembly) and computationally light-weighted (only took 109 calendar hours with peak memory-usage = 61GB on a dual-CPU office workstation) solution for extending the wide applications of the 3GS technologies.     

Sparc基因的克隆及其在HEK293细胞中的表达

目的：为探讨SPARC（secreted protein acidic and rich in cysteine）在人恶性肿瘤发生、发展中的作用及其分子机制,进一步明确SPARC发挥作用的方式及其与肿瘤发生类型的关系。方法：我们首先提取了人乳腺癌细胞系MCF-7的总RNA,在对总RNA进行纯度与定量检测后,利用RT-PCR的方法,以该总RNA为模板,将其反转录为cDNA;再设计引物,以该cDNA为模板,利用PCR扩增出包含Sparc编码区的DNA片段,将该产物纯化后通过T-A克隆连接入pMD20-T载体,利用菌落PCR及DNA测序进行鉴定。以pMD20-T-Sparc为模板,我们设计了特异的针对Sparc全长编码区的引物,并在引物5＇端分别加入BamHI、HindIII酶切位点,通过PCR将Sparc编码区扩增出来,经纯化及双酶切后与真核表达载体pcDNA3.1myc-his（-）相连,再经菌落PCR和DNA测序进行鉴定。通过瞬时转染的方法,利用脂质体将所构建的重组SPARC真核表达载体转染HEK293细胞,48h后裂解所培养的细胞,使用western blot检测有无SPARC的表达。结果：测序证实所克隆的Sparc编码区cDNA正确地插入pcDNA3.1myc-his（-）中,western blot检测证实其在HEK293细胞中得到表达,而空载体转染的细胞则无表达,说明所构建的pcDNA3.1myc-his（-）-Sparc能够成功表达。结论：我们成功克隆了人Sparc cDNA,构建了其真核表达载体,并在HEK293细胞中得到有效表达,从而为进一步研究人SPARC的功能及其与肿瘤的关系奠定了基础。     

Sparc (Osteonectin) functions in morphogenesis of the pharyngeal skeleton and inner ear

Sparc (Osteonectin), a matricellular glycoprotein expressed by many differentiated cells, is a major non-collagenous constituent of vertebrate bones. Recent studies indicate that Sparc expression appears early in development, although its function and regulation during embryogenesis are largely unknown. We cloned zebrafish sparc and investigated its role during development, using a mo rpholino antisense oligonucleotide-based knockdown approach. Consistent with its strong expression in the otic vesicle and developing pharyngeal cartilages, knockdown of Sparc function resulted in specific inner ear and cartilage defects that are highlighted by changes in gene expression, morphology and behavior. We rescued the knockdown phenotypes by co-injecting sparc mRNA, providing evidence that the knockdown phenotype is due specifically to impairment of Sparc function. A comparison of the phenotypes of Sparc knockdown and known zebrafish mutants with similar defects places Sparc downstream of sox9 in the genetic network that regulates development of the pharyngeal skeleton and inner ear of vertebrates.