Identification of CXCL5 expression as a predictive biomarker associated with response and prognosis of immunotherapy in patients with non-small cell lung cancer.

BACKGROUND: The breakthrough of immunotherapy has revolutionized the treatment of non-small cell lung cancer (NSCLC). However, only a limited part of patients could derive clinical benefits. To study how immune microenvironment (IME) of patients could influence the therapeutic efficacy of immunotherapy, we evaluated the response patterns of NSCLC patients treated with PD-1 inhibitors and analyzed the molecules related to prognosis and efficacy of immunotherapy. METHODS: Tumor samples were collected from 47 NSCLC patients treated with PD-1 inhibitors. RNA expressions of tumor immune-related 289 genes were analyzed using NanoString nCounter. Immune infiltration and correlation between clinical information and expression of immune-related genes were assessed. RESULTS: Unsupervised clustering analysis revealed two groups infiltrated with different immune cells and differentially expressed genes (DEGs) including CXCL5, CXCL9, IDO1, and LAG3 were found between groups. Stratification based on DEGs indicated that the group with high expression of CXCL5 was characterized by neutrophils. Univariate and multivariate Cox analysis further demonstrated that CXCL5 mRNA expression was positively associated with worse progression free survival (PFS). Logistic analyses indicated high CXCL5 was associated with worse response to immunotherapy. CONCLUSIONS: CXCL5 may be a potential biomarker for prognosis and responsiveness to immunotherapy and may be a novel preventive and therapeutic target for NSCLC.

An improved genome assembly of the fluke Schistosoma japonicum.

BACKGROUND: Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery. FINDINGS: In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation. CONCLUSIONS: Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future.

RNA interference in vivo in Schistosoma japonicum: Establishing and optimization of RNAi mediated suppression of gene expression by long dsRNA in the intra-mammalian life stages of worms.

Schistosomes are parasitic platyhelminths that threaten over 600 million people globally. In recent years, RNA interference (RNAi) has been widely used as a molecular tool in research into the genomic function of parasites. We aim to develop effective protocols for application of RNAi technology in the intra-mammalian life stages of Schistosoma japonicum. In this work, the expression of the parasite gene encoding cathepsin B1 (SjCB1) was targeted by exposing the worms to 10 µg of long dsRNA dissolved in 0.1 ml of 0.7% NaCl injected into the tail vein of infected mice. This method was effective and specific for eliciting SjCB1 gene suppression in both male and female adult worms in vivo (>79.4% in male and >91.5% in female knockdown relative to control). In 60 cercaria infected mice, RNAi suppression of gene expression was best achieved by using 10 µg of target dsRNA for at least 4 days. The recommended procedure for interference producing long-term suppression was an injection of dsRNA on the first day of infection with booster injections administered every 4 days for up to 26 days. Long-term suppression of three published functional genes (peroxiredoxin-1, mago nashi, insulin receptor) in S. japonicum provided more information about the role of the expression of these genes in producing particular phenotypes. The protocols described here may be more convenient, economical and applicable, than currently available technology and have contributed to the observation of more phenotypes during worm development from schistosomula to adult. These approaches may promote and facilitate further studies into functional schistosome genomics.

Identification and characterization of the zinc finger protein SjZF in Schistosoma japonicum.

Schistosomiasis represents one of the most prevalent parasitic infections affecting over 249 million people worldwide. The pathological damage is mainly caused by the eggs laid by female schistosomes. Zinc finger proteins (ZFPs) usually play critical roles in many biological functions. In this study, we cloned, identified and characterized the zinc finger protein SjZF of Schistosoma japonicum. SjZF ortholog proteins were also identified in S. mansoni, S. haematobium, Opisthorchis viverrini and O. sinensis. Fluorescence localization showed that SjZF was particularly expressed in the worm gut of both genders and the vitelline glands of females. In vitro RNAi assay indicated that decreased expression of SjZF could affect the survival rate of adult worms. The immune protection assay indicated that rSjZF did partially protect mice with 54.8% reduction in the worm burden and 34.1% reduction in the liver eggs. Taken in concert, our preliminary results suggest that SjZF may be a potential vaccine candidate for schistosomiasis and may further provide evidence for a possible role of SjZF in the development of schistosomes.