Transcriptional and proteomic analysis

Unintended effects of gene edit crops may pose safety issues. Omics is a useful tool for researchers to evaluate these unexpected effects. Transcriptome and proteomics analyses were performed for two gene editors, CRISPR-Cas9 and adenine base editor (ABE) gene edit rice, as well as corresponding wild-type plants (Nipponbare). Transcriptome revealed 520 and 566 rice differentially expressed genes (DEGs) in the Cas9/Nip and ABE/Nip comparisons, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that most DEGs participated in metabolism of terpenoids and polyketones, plant–pathogen interactions, and plant signal transduction. It mainly belongs to environmental adaptation. Proteomics revealed 298 and 54 rice differentially expressed proteins (DEPs) in the Cas9/Nip and ABE/Nip comparisons, respectively. KEGG pathway enrichment analysis showed that most DEPs participated in the biosynthesis of secondary metabolite and metabolic pathways. According to integrated transcriptomes and proteomics analysis, the results showed that no newly generated genes were identified as new transcripts of these differentially expressed genes, and gene edit tools had little effect on rice transcription levels and no new proteins were generated in the gene-edited rice.</p

Additional file 3: Figure S2. of PD-1 axis expression in musculoskeletal tumors and antitumor effect of nivolumab in osteosarcoma model of humanized mouse

PD-L1, PD-L2 and PD-1 expressions in osteosarcoma. (DOCX 1426 kb

Additional file 2: Figure S1. of PD-1 axis expression in musculoskeletal tumors and antitumor effect of nivolumab in osteosarcoma model of humanized mouse

Representative images of the assessment of the human CD45 positivity cell rate in humanized mice and immunofluorescence assay for PD-L1/PD-1 and PD-L2/PD-1 in osteosarcoma. (DOCX 1962 kb

Additional file 2: of Novel oncogene COPS3 interacts with Beclin1 and Raf-1 to regulate metastasis of osteosarcoma through autophagy

Figure S2. COPS3 downregulation did not significantly affect tumorigenesis of osteosarcoma cells. (a) 143B-shCtrl and 143B-shCOPS3 cells were subcutaneously injected to BALB/c nude mice. The xenografts were collected four weeks later. (b) the tumor weights were compared between 143B-shCtrl and 143B-shCOPS3 group. (mean ± SD, n = 4). The ns was short for no significant. (PDF 172 kb

Additional file 1: of Novel oncogene COPS3 interacts with Beclin1 and Raf-1 to regulate metastasis of osteosarcoma through autophagy

Figure S1. Knockdown of COPS3 reduces the migratory and invasive abilities of osteosarcoma cells through ERK/RSK. (a and b) HOS cells stably transfected with shCOPS3 or shCtrl were treated with or without MAPK/ERK inhibitor U0126 (1 μM) for 24 h. Migratory and invasive abilities were evaluated by transwell assay and Wound-healing assay. (c and d) HOS cells were exposed to 5 μM or 10 μM RSK inhibitor BI-D1870 for 24 h. Transwell assay and wound-healing assay were performed to assess migratory and invasive abilities. The data are presented as mean ± S.D. from three independent experiments. Scale bars: 100 μm. **P < 0.01 vs. shCtrl group (a and b) or the control group (c and d). (PDF 1338 kb

Additional file 1 of Effects of bone marrow sparing radiotherapy on acute hematologic toxicity for patients with locoregionally advanced cervical cancer: a prospective phase II randomized controlled study

Supplementary Material