Journal: EMBO Molecular Medicine
Article Title: Non‐invasive lung cancer diagnosis by detection of GATA6 and NKX2‐1 isoforms in exhaled breath condensate
Figure Lengend Snippet: Optimization of EBC ‐based expression analysis for LC diagnosis RTube is suitable for RNA isolation. Two main EBC collection devices, RTube and TurboDECCS, were compared for the total RNA yield ( y ‐axis, ng) obtained using the QIAGEN RNeasy Micro kit and 500 μl EBC as starting material. Triangles and rhombuses are used to denote RNA yield of each individual sample using EBCs collected from the different EBC collection devices. Data are represented as mean ± s.e.m.; n = 6. P ‐values after one‐way ANOVA. 500 μl of EBC is optimal for RNA isolation. Total RNA isolation with the RNeasy Micro kit was performed using 200, 350, 500, or 1,000 μl EBC as starting material. Data are represented as mean ± s.e.m.; n = 4. The High Capacity cDNA Reverse Transcriptase kit is more efficient than EpiScript Reverse Transcriptase. Two RT kits were tested for qRT–PCR‐based analysis of GATA6 Ad. CT values were plotted. Each dot represents the CT value for a technical triplicate. Data are represented as mean ± s.e.m.; n = 3. Serial dilution of cDNA template to determine the linear range of detection of GATA6 Ad. cDNA from control EBC was serially diluted and used as template for qRT–PCR‐based expression analysis of GATA6 Ad. Each dot represents the CT value for a technical triplicate. Data are represented as mean ± s.e.m.; n = 3. Delayed snap‐freezing of EBC after collection compromises mRNA integrity. Top, schematic representation of the precursor mRNAs from GAPDH (E) and HPRT1 (F) showing exons (boxes), introns (lines), and location of primer pairs (arrowheads) used for qRT–PCR‐based expression analysis. Bottom, EBCs were collected and incubated on ice for 0, 5, and 15 min prior to snap‐freezing in liquid nitrogen. Expression of GAPDH and HPRT1 was determined in the EBCs using the indicated primers, and the expression ratios (5′/3′) of each gene were calculated as indicators of mRNA integrity. RNA purified from EBCs with expression ratios of GAPDH and HPRT1 between 0.75 and 1.5 (dashed lines) was considered as acceptable for further analysis. Data are represented as mean ± s.e.m.; n = 3. Each colored triangle represents one individual. EBCs should be thawed on ice, for a maximum of 15 min, before further processing. EBCs, that were stored at −80°C, were thawed on ice (green line) or 25°C (red dashed line) for 15, 30, and 60 min. GAPDH 5′/3′ expression ratios were determined as in (E) as indicators of mRNA integrity. Each triangle refers to the 5′/3′ expression ratio for GAPDH of one sample. Each sample was measured in triplicates and the mean was used for the calculation of the ratio. Long‐term storage at −80°C or transportation on dry ice did not compromise mRNA integrity. EBCs were collected either in Germany (GER, green line) or in Mexico (MEX, red dashed line) and subsequently transported to Germany on dry ice. EBCs were stored at −80°C for 7, 30, or 365 days before they were thawed on ice and further processed in less than 15 min. GAPDH 5′/3′ expression ratios were determined as in (E) as indicators of mRNA integrity.
Article Snippet: Exosome pellets were lysed in 350 μl RLT Plus Buffer (RNeasy Micro Kit, Qiagen), and 200 ng of 16S‐ and 23S‐ribosomal Spike‐In RNA (Roche) was added to the lysate.
Techniques: Expressing, Isolation, Quantitative RT-PCR, Serial Dilution, Incubation, Purification