Genomic breakpoint-specific monitoring of measurable residual disease in pediatric non-standard-risk acute myeloid leukemia.

Pediatric acute myeloid leukemia (AML) is a highly heterogeneous disease making standardized measurable residual disease (MRD) assessment challenging. Currently, patient-specific DNA-based assays are only rarely applied for MRD assessment in pediatric AML. We tested whether quantification of genomic breakpoint-specific sequences via quantitative polymerase chain reaction (gDNA-PCR) provides a reliable means of MRD quantification in children with non-standardrisk AML and compared its results to those obtained with state-of-the-art ten-color flow cytometry (FCM). Breakpointspecific gDNA-PCR assays were established according to Euro-MRD consortium guidelines. FCM-MRD assessment was performed according to the European Leukemia Network guidelines with adaptations for pediatric AML. Of 77 consecutively recruited non-standard-risk pediatric AML cases, 49 (64%) carried a chromosomal translocation potentially suitable for MRD quantification. Genomic breakpoint analysis returned a specific DNA sequence in 100% (41/41) of the cases submitted for investigation. MRD levels were evaluated using gDNA-PCR in 243 follow-up samples from 36 patients, achieving a quantitative range of at least 10-4 in 231/243 (95%) of samples. Comparing gDNA-PCR with FCM-MRD data for 183 bone marrow follow-up samples at various therapy timepoints showed a high concordance of 90.2%, considering a cut-off of ≥0.1%. Both methodologies outperformed morphological assessment. We conclude that MRD monitoring by gDNA-PCR is feasible in pediatric AML with traceable genetic rearrangements and correlates well with FCM-MRD in the currently applied clinically relevant range, while being more sensitive below that. The methodology should be evaluated in larger cohorts to pave the way for clinical application.

Identification and characterisation of novel Pichia pastoris promoters for heterologous protein production.

The number of available promoters for the protein production host Pichia pastoris is limited, and in most applications comprises the methanol inducible alcohol oxidase 1 (AOX1) promoter and the constitutive glyceraldehyde phosphate dehydrogenase (GAP) promoter. To close this gap, we identified 24 novel potential regulatory sequences and tested their applicability to drive the expression of both intracellular as well as secretory heterologous proteins. While more than 80% of the promoters derived from microarray data mining showed activity on all common carbon sources used for P. pastoris, the success rate of rationally selected promoters was lower. Many of the newly identified promoters showed a growth rate dependent behaviour, for example three ribosomal promoters as well as the promoters of two chaperones were much more active at early growth phase as compared to later phases. Fed batch cultivation of selected promoters expressing human serum albumin further strengthened the correlation of promoter activity (determined by HSA transcript levels) to specific growth rate. The promoter of the thiamine biosynthesis gene P(THI11) did not only show high transcript levels at low specific growth rate, but also exhibited interesting regulatory properties dependent on the availability of thiamine in the growth medium.

Directed gene copy number amplification in Pichia pastoris by vector integration into the ribosomal DNA locus.

The yeast Pichia pastoris is a widely used host organism for heterologous protein production. One of the basic steps for strain improvement is to ensure a sufficient level of transcription of the heterologous gene, based on promoter strength and gene copy number. To date, high-copy-number integrants of P. pastoris are achievable only by screening of random events or by cloning of gene concatemers. Methods for rapid and reliable multicopy integration of the expression cassette are therefore desirable. Here we present such a method based on vector integration into the rDNA locus and post-transformational vector amplification by repeated selection on increased antibiotic concentrations. Data are presented for two exemplary products: human serum albumin, which is secreted into the supernatant, and human superoxide dismutase, which is accumulated in the cytoplasm of the cells. The striking picture evolving is that intracellular protein production is tightly correlated with gene copy number, while use of the secretory pathway introduces a high clonal variability and the correlation with gene copy number is valid only for low gene copy numbers.