Journal: American Journal of Cancer Research

Article Title: Novel mutations in BRCA2 intron 11 and overexpression of COX-2 and BIRC3 mediate cellular resistance to PARP inhibitors

doi:

Figure Lengend Snippet: BRCA2-deficient Capan-1 cells develop drug resistance to PARPi, independent of PARP activation and PARP1-DNA trapping. (A) Schematic representation of the generation of PARPi-resistant cells. BRCA2-deficient pancreatic cancer Capan-1 cells were separately exposed to increasing concentrations of simmiparib (SP), olaparib (OP) and talazoparib (TP), and the resistant monoclones were denoted Capan-1/SP (/SP), Capan-1/OP (/OP), and Capan-1/TP (/TP), respectively. (B and C) Cells were treated with simmiparib (B) or olaparib (C) for 7 days and subjected to SRB assays. (D) Cross-resistance of PARPi-resistant variants. Cells were exposed to olaparib (OP), talazoparib (TP), simmiparib (SP), niraparib (NP) or rucaparib (RP) for 7 days and assessed by SRB assays. The resistance factor was calculated as the ratio of the averaged IC50 value of the indicated PARPi in the given resistant cells to that of the same PARPi in the parental Capan-1 cells. (E and F) Protein levels of the drug transporters P-gp, BCRP (E) and PARP1, PARP2, PARP3 (F) detected by Western blotting in PARPi-resistant variants and parental Capan-1 cells. A stable vincristine (VCR)- resistant variant (KB/VCR) was a positive control of P-gp. (G and H) Cell lysates were analyzed by Western blotting to determine PAR formation (G) and chromatin-bound PARP1 (H) triggered by MMS. Histone 3 was used as the positive control for the chromatin-bound fractions. TP, talazoparib. MMS, methyl methanesulfonate. (I and J) Simmiparib reduced H2O2-triggered PAR formation in both Capan-1/SP and Capan-1 cells. (I) Representative images of PAR formation. Nuclei were stained with DAPI. Scale bar, 100 μm. (J) Inhibitory curves and IC50 values of PAR formation inhibited by simmiparib in Capan-1/SP and Capan-1 cells. Data are presented as the mean ± SD from three independent experiments.

Article Snippet: The anti-PARP3 antibody (NBP2-49523) was from Novus (Novus Biologicals, CO, USA).

Techniques: Activation Assay, Western Blot, Variant Assay, Positive Control, Staining

Journal: bioRxiv

Article Title: Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex

doi: 10.1101/2022.06.10.495637

Figure Lengend Snippet: ( A ) The distribution of homoplasy scores for 834,981 SNVs and 46,306 INDELs. 0.49% of SNVs have a homoplasy score ≥ 5 ( P < 0.002) and 3.01% of INDELs have a homoplasy score ≥ 5. ( B ) Proportion of INDELs with Hs ≥ x for varying values of x , split into sets according to whether INDEL occurs within HT, SSR or other region of the genome. ( C - D ) Homoplasy score (Hs) for 1,525 SNVs and 655 INDELs with homoplasy score ≥ 5 and minor (SNVs)/alternate (INDELs) allele frequency > 0.1% among 31,428 isolates, plotted against position on the genome. Bubble size corresponds to Hs. ( C ) INDELs broken down by whether they occur within an HT, SSR or other region of the genome. HTs with a cumulative Hs score > 45 (across INDELs occurring within HT) are indicted by blue bars. ( D ) Variants colored in green occur within loci that have been associated with Antibiotic Resistance.

Article Snippet: A homopolymer frameshifting reporter was constructed from a hygromycin resistant pDE43- MCtH vector, which is a version of pDE43-MCK with a swapped antibiotic marker (Addgene plasmid #49523; ( )).

Techniques:

Journal: bioRxiv

Article Title: Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex

doi: 10.1101/2022.06.10.495637

Figure Lengend Snippet: ( A-B ) The distribution of the ratio of (homoplasy score) to (# of isolates harboring the minor allele) for 1,208/1,525 SNVs that occur in coding regions. ( C ) Breaking these SNV recency ratios down by gene category reveals higher ratios overall for antibiotic resistance genes when compared to other gene categories. ( D-E ) The distribution of the ratio of (homoplasy score) to (# of isolates harboring the alternate allele) for 100/655 INDELs that occur in HT and coding regions. ( F ) Breaking these INDEL ratios down by gene category reveals higher ratios overall for antibiotic resistance genes when compared to other gene categories, however the only two INDELs in this gene category were found in the HT of glpK . N = number of alleles, M = median RcR

Article Snippet: A homopolymer frameshifting reporter was constructed from a hygromycin resistant pDE43- MCtH vector, which is a version of pDE43-MCK with a swapped antibiotic marker (Addgene plasmid #49523; ( )).

Techniques:

Journal: bioRxiv

Article Title: Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex

doi: 10.1101/2022.06.10.495637

Figure Lengend Snippet: ( A-B ) The distribution of the ratio of (homoplasy score) to (# of isolates harboring the alternate allele) for 388/655 INDELs that occur in non-HT (SSR & other) and coding regions. ( C ) Breaking these INDEL ratios down by gene category reveals higher ratios overall for antibiotic resistance genes when compared to other gene categories. N = number of alleles, M = median RcR

Article Snippet: A homopolymer frameshifting reporter was constructed from a hygromycin resistant pDE43- MCtH vector, which is a version of pDE43-MCK with a swapped antibiotic marker (Addgene plasmid #49523; ( )).

Techniques: