Journal: Biosafety and Health

Article Title: Molecular phylogenomic analysis reveals a single origin of monkeypox virus transmission in Guangzhou, China in June 2023

doi: 10.1016/j.bsheal.2023.08.002

Figure Lengend Snippet: Phylogenetic analysis of monkeypox (mpox) virus sequences first reported in Guangzhou, China. A) The eight local sequences (red dot) in FASTA format were aligned by the BioEdit software 7.0.9 with the reference sequences of mpox viral clade IIb downloaded from GISAID (black dot) and NCBI (NC_063383.1, green dot, selected as the outgroup). The maximum likelihood (ML) phylogenetic tree of the full-length genome sequences of mpox virus was constructed with the MEGA software 11.0.11 using the General Time Reversible model with 500 bootstrap replicates. The scale bar represents the genetic distance. Bootstrap values >75% are presented at the corresponding nodes of the tree. Abbreviations: FASTA, Fast-All; GISAID, Global Initiative on Sharing Avian Influenza Data; NCBI, National Center For Biotechnology Information. B) The analysis of amino acid mutation of the eight local sequences compared to the reference Japan|EPI ISL 17692269|2023-04-28. In most cases, the mutation sites are mixed. Only the dominant amino acid is shown. “*” represents termination codon. As for this special site, the CAG (Q) codon accounts for 29.26% of all reads, but the TAG (stop) codon accounts for 70.74%. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: We then performed the amplicon-based mpox viral full-length genome sequencing of mpox virus using a newly developed method by MGI Tech Co., Ltd. (MGI), China.

Techniques: Virus, Software, Construct, Mutagenesis

Journal: Cancers

Article Title: MALINC1 an Immune-Related Long Non-Coding RNA Associated with Early-Stage Breast Cancer Progression

doi: 10.3390/cancers14122819

Figure Lengend Snippet: MALINC1 expression in normal, pre-invasive, and invasive breast samples. ( a ) In silico analysis of MALINC1 expression among normal, DCIS, and IDC samples obtained from three independent GEO datasets [ , , ]. MALINC1 expression (represented in log2 count per million (CPM) or log2 robust multi-array average values (RMA)) was significantly upregulated in DCIS samples compared with normal samples ( p = 0.0004 and p = 0.0335), whereas non-significant differences were observed between DCIS and IDC cases ( p = 0.619). ( b ) MALINC1 expression analysis of intrinsic subtypes among normal and DCIS samples obtained from GSE69994 dataset . Data are shown as means ±S.D. ( c ) Primary breast carcinomas were divided into MALINC1 low or high expression levels based on the StepMiner algorithm using TCGA RNA-seq datasets obtained from the UCSC Xena resource ( https://xenabrowser.net/ ) (accessed on 12 October 2021). ( d ) Percentage of cases with high or low MALINC1 expression among intrinsic subtypes showing a consistent upregulation in luminal-like tumors compared with basal-like and HER2 subtypes. ( e ) Kaplan-Meier survival analysis on data of 298 patients with luminal-like tumors obtained from the TCGA RNA-seq datasets. Breast cancer patients with high MALINC1 expression (red line) showed reduced overall survival compared to patients with low expression (blue line) (log-rank p = 0.027).

Article Snippet: The full-length sequence of MALINC1 (5090 bp spanning three exons, NCBI Entrez Gene: 100505636, Ensembl Gene ID: ENSG00000245146, Ensembl Transcript ID: ENST000004992037) was synthesized (Genscript, Piscataway, NJ, USA), sequence verified, and subsequently cloned into the pLOC lentiviral expression vector.

Techniques: Expressing, In Silico, RNA Sequencing

Journal: Cancers

Article Title: MALINC1 an Immune-Related Long Non-Coding RNA Associated with Early-Stage Breast Cancer Progression

doi: 10.3390/cancers14122819

Figure Lengend Snippet: Characterization of MALINC1 expression and subcellular localization in breast cancer cell lines. ( a ) MALINC1 expression levels in normal, DCIS, and breast cancer cell lines as determined by RT-qPCR. All assays were performed in triplicate and normalized to housekeeping gene GAPDH . Gene expression was expressed as relative units compared to MCF10A normal cell line. ( b ) Subcellular localization of MALINC1 in DCIS.COM, T47D and MCF7 cells. MALAT1 and MTRNR1 were analyzed as nuclear and cytoplasmic markers, respectively. Cellular homogenates were separated into nuclear and cytoplasmic fractions and relative MALINC1 expression was evaluated by RT-qPCR. T-test was used to compare MALINC1 expression among cell fractions. ( c ) MALINC1 expression induction in estrogen-stimulated MCF7 cells at various times post E2 treatment (1, 3, and 6 h). ANOVA with post-hoc Tukey HSD test was employed to compare the different time points. ( d ) Schematic representation of MALINC1 promoter region with the ESR2 transcription factor binding site (green boxes) predicted by the JASPAR resource ( https://jaspar.genereg.net ) (accessed on 1 September 2021). Arrows inside green boxes indicate the DNA strand of the mapped transcription factor binding sites.

Article Snippet: The full-length sequence of MALINC1 (5090 bp spanning three exons, NCBI Entrez Gene: 100505636, Ensembl Gene ID: ENSG00000245146, Ensembl Transcript ID: ENST000004992037) was synthesized (Genscript, Piscataway, NJ, USA), sequence verified, and subsequently cloned into the pLOC lentiviral expression vector.

Techniques: Expressing, Quantitative RT-PCR, Gene Expression, Binding Assay

Journal: Cancers

Article Title: MALINC1 an Immune-Related Long Non-Coding RNA Associated with Early-Stage Breast Cancer Progression

doi: 10.3390/cancers14122819

Figure Lengend Snippet: Transcriptomic analysis of MALINC1 -overexpressing cells. ( a ) Fold induction levels of MALINC1 expression in stably transduced MCF10A and DCIS.COM cell lines as determined by RNA-seq profiles (log2CPM) in pLOC- MALINC1 or pLOC-empty transfected cells ( p = 0.035 and p = 0.005, respectively). ( b ) Hierarchical clustering of MCF10A and DCIS.COM stably transduced cells with either vector control (pLOC-empty) or lentivirus expressing MALINC1 (pLOC- MALINC1 ) based on RNA-seq profiles. ( c ) Heat map representation of the differentially expressed genes (DEGs) obtained by RNA-seq analysis (FDR < 0.01; FC > 2). Red and green colors represent upregulated and downregulated genes, respectively. ( d ) Venn diagram of transcripts commonly modulated among MCF10 and DCIS.COM stably transduced cells. ( e ) Functional enrichment analysis of the transcription factor binding sites (TFBS) in the promoter region of the commonly modulated genes among normal and DCIS cells. Statistical significance was determined by the hypergeometric test. ( f , g ) Functional enrichment of bioprocesses identified as affected by the expression of MALINC1 in MCF10A and DCIS.COM cells. At the top, bioprocesses are enriched due MALINC1 overexpression in MCF10A cell lines. At the bottom, bioprocesses are enriched due MALINC1 overexpression in DCIS.COM cell lines. The red dotted line represents the basic significance level ( p < 0.05). ( h ) Pathway commonly affected among MCF10A and DCIS.COM MALINC1 stably transduced cells ( p < 0.05).

Article Snippet: The full-length sequence of MALINC1 (5090 bp spanning three exons, NCBI Entrez Gene: 100505636, Ensembl Gene ID: ENSG00000245146, Ensembl Transcript ID: ENST000004992037) was synthesized (Genscript, Piscataway, NJ, USA), sequence verified, and subsequently cloned into the pLOC lentiviral expression vector.

Techniques: Expressing, Stable Transfection, RNA Sequencing, Transfection, Plasmid Preparation, Control, Functional Assay, Binding Assay, Over Expression

Journal: Cancers

Article Title: MALINC1 an Immune-Related Long Non-Coding RNA Associated with Early-Stage Breast Cancer Progression

doi: 10.3390/cancers14122819

Figure Lengend Snippet: Stable MALINC1 overexpression effect in cell motility and migration of normal breast cells. ( a ) MCF10A-transduced cells with either vector control or lentivirus expressing MALINC1 were compared using the in vitro wound-healing assay. Forty-eight hours after the original scratch the area covered by migrating cells from the edges was compared. As can be observed in representative images, non-significant difference in cell motility was observed ( p = 0.483). Scale bar = 400 μm. ( b ) Transwell migration assay of MCF10A cells stably transduced with MALINC1 . On the left, comparative pictures of cells that migrated through the membrane; on the right, a box-and-whisker plot of numbers of cells per membrane ( p = 3.9 × 10 −5 ). Statistical significance was determined using the t -test.

Article Snippet: The full-length sequence of MALINC1 (5090 bp spanning three exons, NCBI Entrez Gene: 100505636, Ensembl Gene ID: ENSG00000245146, Ensembl Transcript ID: ENST000004992037) was synthesized (Genscript, Piscataway, NJ, USA), sequence verified, and subsequently cloned into the pLOC lentiviral expression vector.

Techniques: Over Expression, Migration, Plasmid Preparation, Control, Expressing, In Vitro, Wound Healing Assay, Transwell Migration Assay, Stable Transfection, Transduction, Membrane, Whisker Assay

Journal: Cancers

Article Title: MALINC1 an Immune-Related Long Non-Coding RNA Associated with Early-Stage Breast Cancer Progression

doi: 10.3390/cancers14122819

Figure Lengend Snippet: Pathway activity analysis in normal and DCIS MALINC1 -transduced cells. ( a ) Heatmap of integrated pathways activities (IPAs) differentially modulated in MALINC1 -overexpressing cells as predicted by PARADIGM using the normalized RNA-seq expression profiles (p-adj. < 0.01). ( b ) Circular bar plot of the top 10 most significantly activated IPAs in MCF10A and DCIS.COM MALINC1 -overexpressing cell lines. ( c , d ) Agarose gel of MALINC1 , FOS , and JUN RT-PCR amplicons in the T47D luminal-like breast cancer cell line. ( d ) Evaluation of MALINC1 , FOS , and JUN expression levels by RT-qPCR on breast normal and tumor samples. Gene expression levels were normalized to the RNA18S transcript and discretized in undetectable (negative in white boxes), low-, or high- MALINC1 -expressing samples (gray or black boxes, respectively).

Article Snippet: The full-length sequence of MALINC1 (5090 bp spanning three exons, NCBI Entrez Gene: 100505636, Ensembl Gene ID: ENSG00000245146, Ensembl Transcript ID: ENST000004992037) was synthesized (Genscript, Piscataway, NJ, USA), sequence verified, and subsequently cloned into the pLOC lentiviral expression vector.

Techniques: Activity Assay, RNA Sequencing, Expressing, Agarose Gel Electrophoresis, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Gene Expression

Journal: Cancers

Article Title: MALINC1 an Immune-Related Long Non-Coding RNA Associated with Early-Stage Breast Cancer Progression

doi: 10.3390/cancers14122819

Figure Lengend Snippet: Comparative immune profiling of high- and low- MALINC1 -expressing breast carcinomas. ( a ) Immune-cell fractions and PDL1 expression of high and low MALINC1 luminal-like tumors obtained from the TCGA-BRCA project as estimated by the quanTIseq deconvolution algorithm based on RNA-seq profiles. Statistical differences were determined using a Mann-Whitney-Wilcoxon test. ( b , c ) Waterfall plots of TIDE prediction scores across tumors with high or low MALINC1 expression in luminal-like and basal-like breast carcinomas. Breast cancer samples were sorted from high to low TIDE scores for their classification in non-responder (positive values in blue) and responder cases (negative values in red), as suggested by the TIDE resource.

Article Snippet: The full-length sequence of MALINC1 (5090 bp spanning three exons, NCBI Entrez Gene: 100505636, Ensembl Gene ID: ENSG00000245146, Ensembl Transcript ID: ENST000004992037) was synthesized (Genscript, Piscataway, NJ, USA), sequence verified, and subsequently cloned into the pLOC lentiviral expression vector.

Techniques: Expressing, RNA Sequencing, MANN-WHITNEY