Journal: bioRxiv

Article Title: Pinpointing the tumor-specific T-cells via TCR clusters

doi: 10.1101/2022.01.30.478375

Figure Lengend Snippet: a,b . Normalized counts of cluster-related TCRβ clonotypes from metastatic melanoma samples before and after anti-PD-1 therapy from datasets published in (a) Ref. 36 and (b) Ref. 37. c . Cumulative frequency of VDJdb-matched TAA-specific clonotypes within the whole repertoire (in bulk) and within cluster-related clonotypes (ALICE hits) of patients with at least one VDJdb-matched cluster (N = 8 patients) from the two published datasets. d . TCRβ clusters from patient pt44 (Ref. 36). VDJdb-matched TAA-specific clonotypes are colored in red. e, f . Number and size of clusters before and after therapy for each patient from (e) Ref. 36 and (f) Ref. 37, one point corresponds to one cluster. VDJdb-matched TAA-specific clusters are colored in red. N = number of biological replicates in each group. Data in (a) were analyzed with paired t-test; b, c were analyzed with the Wilcoxon test.

Article Snippet: On the fourth day of cultivation, the medium was renewed, and dendritic cells were loaded with the mix of melanoma TAA peptides (PepTivator Melan-A/MART-1, gp100/Pmel, and MAGE-A3 human; Miltenyi Biotec) at a concentration of 600 nM each.

Techniques:

Journal: bioRxiv

Article Title: Pinpointing the tumor-specific T-cells via TCR clusters

doi: 10.1101/2022.01.30.478375

Figure Lengend Snippet: a . The experimental workflow. b - g . TCRβ repertoire analysis for CD8 + (b, d, f) and CD4 + (c, e, g) DP and non-DP TIL subsets sorted from metastatic lymph nodes of eight melanoma patients. Panels show repertoire clonality calculated as [1-Normalized Shannon-Wiener index] (b, c), normalized counts (d, e) and cumulative frequency of cluster-related clonotypes (f, g). Paired t-test. h . TCRβ clusters identified in repertoires obtained from fresh-frozen tumor samples (FFT), and sorted CD8 + DP and non-DP TILs for HLA-A*02 patient mp26. VDJdb-matched TAA-specific clusters are colored in red. i,j . Cumulative frequency of (i) VDJdb-matched TAA-specific clonotypes and (j) VDJdb-matched TAA-specific cluster-related clonotypes within CD8 + DP, CD8 + non-DP, and FFT TCRβ repertoires of patient mp26. One-way ANOVA, Bonferroni multiple comparisons correction. k,l . Proportion of CD137 + cells among CD8 + T cells (k) and proportion of VDJdb-matched TAA-specific clonotypes in sorted CD137 + CD8 + T cells (l) in DP and non-DP TILs from patient mp26 that were cultured and re-stimulated with TAA-loaded or control dendritic cells.

Article Snippet: On the fourth day of cultivation, the medium was renewed, and dendritic cells were loaded with the mix of melanoma TAA peptides (PepTivator Melan-A/MART-1, gp100/Pmel, and MAGE-A3 human; Miltenyi Biotec) at a concentration of 600 nM each.

Techniques: Cell Culture, Control

Journal:

Article Title: Gene-expression signature of benign monoclonal gammopathy evident in multiple myeloma is linked to good prognosis

doi: 10.1182/blood-2006-07-037077

Figure Lengend Snippet: Fifty-two SAM-defined genes are differentially expressed in NPC, MGUS, and MM

Article Snippet: 2.05 1.55 3.18 1.36 212038_s_at VDAC1 Ion channel for cytochrome c 2.62 1.56 3.17 1.42 208308_s_at GPI Energy metabolism 1.97 1.48 3.17 1.48 201013_s_at PA1CS DNA synthesis 2.81 1.43 3.17 1.45 202708_s_at HIST2H2BE Chromosome organization and biogenesis 2.35 1.71 3.14 2.11 215071_s_at HIST1H2AC Chromosome organization and biogenesis 3.47 3.62 3.13 1.97 225361_x_at LOC159090 Unknown 3.43 1.68 3.11 1.53 219366_at AVEN Antiapoptosis 2.63 1.76 3.10 1.47 209398_at H1ST1H1C Chromosome organization and biogenesis 5.39 5.53 3.09 2.02 221652_s_at C12orf11 Unknown; sarcoma antigen NY-SAR-95 2.07 1.37 3.06 1.57 225028_at LOC550643 Unknown 3.83 2.01 3.03 1.45 214214_s_at C1QBP Immunity 2.64 1.45 3.03 1.47 201577_at NME1 Nucleotide biosynthesis 3.57 1.62 2.99 1.58 218280_x_at H1ST2H2AA Chromosome organization and biogenesis 4.24 4.76 2.95 1.92 201479_at DKC1 Telomere maintenance 2.24 1.42 2.92 1.43 208864_s_at TXN Redox reactions 2.90 1.68 2.91 1.51 212297_at ATP13A3 Cation transport 2.64 1.42 2.88 1.54 222825_at OTUD6B Unknown 2.66 1.35 2.88 1.40 209267_s_at SLC39A8 Ion transport 3.41 1.86 2.88 1.56 217898_at C15orf24 Unknown 2.35 1.70 2.83 1.33 210275_s_at ZA20D2 Unknown 2.27 1.36 2.81 1.37 213485_s_at ABCC10 ATP-dependent efflux pump; multidrug resistance pump 3.17 1.51 2.76 1.34 200994_at IPO7 Nuclear trafficking 2.08 1.46 2.72 1.37 222428_s_at LARS Protein synthesis 3.64 1.68 2.71 1.32 202591_s_at SSBP1 Mitochondrial DNA replication 2.22 1.42 2.69 1.35 204244_s_at ASK Cell cycle 3.25 1.77 2.67 1.37 225916_at ZNF131 Gene transcription 2.47 1.39 2.63 1.36 202396_at TCERG1 Gene transcription 3.85 1.62 2.63 1.32 213340_s_at K1AA0495 Unknown −2.40 0.78 −2.52 0.75 206150_at TNFRSF7 Immune cell signaling −3.82 0.55 −2.56 0.75 228139_at RIPK3 Cell signaling −2.63 0.74 −2.59 0.77 220066_at CARD15 Antiapoptosis −4.02 0.50 −2.66 0.62 210347_s_at BCL11A Gene transcription 3.48 2.04 −2.67 0.64 232511_at RANBP2L1 Nuclear import 2.07 1.54 −2.71 0.64 214041_x_at RPL37A Ribosomal protein 2.22 1.80 −3.09 0.60 219371_s_at KLF2 Gene transcription 3.81 1.78 −3.11 0.66 202724_s_at FOXO1A Gene transcription 2.49 1.55 −3.27 0.64 215671_at PDE4B Drug metabolism 2.07 1.53 −3.30 0.59 219675_s_at UXS1 Glycosaminoglycan biosynthesis −2.33 0.76 2.97 1.35 Open in a separate window Genes are ordered based on the SAM score in the MM vs MGUS comparison.

Techniques: Binding Assay, DNA Synthesis

Journal: Scientific Reports

Article Title: Retarding breast tumor growth with nanoparticle-facilitated intravenous delivery of BRCA1 and BRCA2 tumor suppressor genes

doi: 10.1038/s41598-022-25511-9

Figure Lengend Snippet: (a) Size and (b) zeta potential measurement. NPs, BRCA1 + NPs, and BRCA2 + NPs formed with addition of 4 mM of exogeneous Ca 2+ in 1 mL DMEM medium with 1 µg of BRCA1 or BRCA2 plasmid DNA, followed by incubation for 30 min at 37 °C. Each of the measurements was performed three times and mean and standard deviation were calculated.

Article Snippet: The plasmids encoding BRCA1 (catalog no. 61586) and BRCA2 (catalog no. 16245) tumor suppressor genes were ordered from ‘Addgene’ (USA), where pc BRCA1-385 was a gift from Lawrence Brody and p CIN BRCA2 WT was a gift from Mien-Chie Hung , .

Techniques: Zeta Potential Analyzer, Plasmid Preparation, Incubation, Standard Deviation

Journal: Scientific Reports

Article Title: Retarding breast tumor growth with nanoparticle-facilitated intravenous delivery of BRCA1 and BRCA2 tumor suppressor genes

doi: 10.1038/s41598-022-25511-9

Figure Lengend Snippet: Cell viability assessment of BRCA1 and BRCA2 plasmid delivery in (a) MCF-7 (b) MDA-MB-231 and (c) 4T1 cells treated with BRCA1 + NP, and BRCA2 + NP formulations for 48 h. The experiments were performed three times in each of the cell lines and values were presented as mean ± SD of triplicates in MTT assay. * indicated p < 0.05 compared to NPs control.

Article Snippet: The plasmids encoding BRCA1 (catalog no. 61586) and BRCA2 (catalog no. 16245) tumor suppressor genes were ordered from ‘Addgene’ (USA), where pc BRCA1-385 was a gift from Lawrence Brody and p CIN BRCA2 WT was a gift from Mien-Chie Hung , .

Techniques: Plasmid Preparation, MTT Assay, Control

Journal: Scientific Reports

Article Title: Retarding breast tumor growth with nanoparticle-facilitated intravenous delivery of BRCA1 and BRCA2 tumor suppressor genes

doi: 10.1038/s41598-022-25511-9

Figure Lengend Snippet: Cytotoxicity imposed by BRCA1 + NP and BRCA2 + NP formulations in three breast cancer cell lines.

Article Snippet: The plasmids encoding BRCA1 (catalog no. 61586) and BRCA2 (catalog no. 16245) tumor suppressor genes were ordered from ‘Addgene’ (USA), where pc BRCA1-385 was a gift from Lawrence Brody and p CIN BRCA2 WT was a gift from Mien-Chie Hung , .

Techniques:

Journal: Scientific Reports

Article Title: Retarding breast tumor growth with nanoparticle-facilitated intravenous delivery of BRCA1 and BRCA2 tumor suppressor genes

doi: 10.1038/s41598-022-25511-9

Figure Lengend Snippet: Light microscopic images of two different cell lines following treatment with NP, BRCA1 + NP and BRCA2 + NP. Cells treated with BRCA1 + NP and BRCA2 + NP, revealed decrease in cellular density in MCF-7 (upper panel) and 4T1 (lower panel) cell line, compared to the untreated control cells (concentrated).

Article Snippet: The plasmids encoding BRCA1 (catalog no. 61586) and BRCA2 (catalog no. 16245) tumor suppressor genes were ordered from ‘Addgene’ (USA), where pc BRCA1-385 was a gift from Lawrence Brody and p CIN BRCA2 WT was a gift from Mien-Chie Hung , .

Techniques: Control

Journal: Scientific Reports

Article Title: Retarding breast tumor growth with nanoparticle-facilitated intravenous delivery of BRCA1 and BRCA2 tumor suppressor genes

doi: 10.1038/s41598-022-25511-9

Figure Lengend Snippet: (a) Western Blot image following intracellular delivery of BRCA1 + NP and BRCA2 + NP in MCF-7 cell line. Cells were incubated with NPs with loaded BRCA1 and BRCA2 plasmids for 48 h prior to cell lysis for protein extraction and Western blotting analysis. Detection of P-MAPK, T-MAPK and GAPDH (housekeeping protein) was performed using respective primary antibodies. (b) Densitometry analysis showing ratio of P-MAPK/total MAPK expression. * indicates p < 0.05, with significant change in protein expression profile.

Article Snippet: The plasmids encoding BRCA1 (catalog no. 61586) and BRCA2 (catalog no. 16245) tumor suppressor genes were ordered from ‘Addgene’ (USA), where pc BRCA1-385 was a gift from Lawrence Brody and p CIN BRCA2 WT was a gift from Mien-Chie Hung , .

Techniques: Western Blot, Incubation, Lysis, Protein Extraction, Expressing

Journal: Scientific Reports

Article Title: Retarding breast tumor growth with nanoparticle-facilitated intravenous delivery of BRCA1 and BRCA2 tumor suppressor genes

doi: 10.1038/s41598-022-25511-9

Figure Lengend Snippet: Tumor regression study following intravenous delivery of NP, BRCA1 + NP, and BRCA2 + NP in 4T1 cells-induced tumor mouse model. 4T1 cells were inoculated subcutaneously on the mammary pad of mice. On day 8, as the tumor reached an approximate volume of ~ 25 mm 3 , mice were treated intravenously through tail-vein injection with 100 μL of NP (8 M Ca 2+ ), BRCA1 + NP (40 µg of plasmid) and BRCA2 + NP (40 µg of plasmid); followed by the 2nd dose at day 10. The tumor outgrowth was monitored until day 22. Five mice were used per group and data were represented as mean ± SD. Compared to NP control group, statistical analysis was significant, * when p < 0.05. (* p < 0.05 (NP control and BRCA1 + NP), * p < 0.05 (NP control and BRCA2 + NP).

Article Snippet: The plasmids encoding BRCA1 (catalog no. 61586) and BRCA2 (catalog no. 16245) tumor suppressor genes were ordered from ‘Addgene’ (USA), where pc BRCA1-385 was a gift from Lawrence Brody and p CIN BRCA2 WT was a gift from Mien-Chie Hung , .

Techniques: Injection, Plasmid Preparation, Control

Journal: Scientific Reports

Article Title: Retarding breast tumor growth with nanoparticle-facilitated intravenous delivery of BRCA1 and BRCA2 tumor suppressor genes

doi: 10.1038/s41598-022-25511-9

Figure Lengend Snippet: Transgene delivery of BRCA1 + NP and BRCA2 + NP in 4T1-induced tumor mouse model inhibited tumor growth. ( a ) Tumor images captured following sacrifice at day 22. ( b ) Quantitation of tumor volumes in NP control, BRCA1 plasmid-treated mice and BRCA2 plasmid-treated mice. ( c ) Quantitation of tumor weights. Statistical analysis was found significant compared to NP control group, * when p < 0.05.

Article Snippet: The plasmids encoding BRCA1 (catalog no. 61586) and BRCA2 (catalog no. 16245) tumor suppressor genes were ordered from ‘Addgene’ (USA), where pc BRCA1-385 was a gift from Lawrence Brody and p CIN BRCA2 WT was a gift from Mien-Chie Hung , .

Techniques: Quantitation Assay, Control, Plasmid Preparation