576 Genetik und Evolution
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Quantitative estimates for the global impact of COVID-19 on the diagnosis and management of patients with inborn errors of metabolism (IEM) are lacking. We collected relevant data from 16 specialized medical centers treating IEM patients in Europe, Asia and Africa. The median decline of reported IEM related services in March 1st-May 31st 2020 compared to the same period in 2019 were as high as 60-80% with a profound impact on patient management and care for this vulnerable patient group. More representative data along with outcome data and guidelines for managing IEM disorders under such extraordinary circumstances are needed.
In forensic DNA profiling, the occurrence of complex mixed profiles is currently a common issue. Cases involving intimate swabs or skin flake tape liftings are prone to mixed profiles, because of more than one donor contributing to a DNA sample. By DNA profiling of single spermatozoa and skin flakes, problems associated with mixed profile could ideally be overcome. However, PCR is not a sensitive enough method to generate DNA profiles by STRs on single cells. Moreover, high quality intact DNA is required, but is not always available in skin flakes due to degradation. Additionally, single skin flakes are difficult to discriminate from other similar looking particles on tape liftings used to secure DNA samples from evidence. The main purpose of this study was to develop a method that enables DNA profiling of single sperm cells and skin flakes. After studying multiple whole genome amplification (WGA) protocols, REPLI-g Single Cell WGA was selected due to its suitability in the pre-amplification step of template DNA. Micromanipulation was used to isolate single spermatozoa. Furthermore, micromanipulation in combination with REPLI-g Single Cell WGA resulted in successful DNA profiling of single spermatozoa by using autosomal STRs as well as X- and Y-chromosomal STRs. The single spermatozoa DNA profiling method described in this thesis was successfully used to identify male contributors from mock intimate swabs with a mixture of semen from multiple male contributors. Different dyes were analysed to develop a staining method to discriminate skin flakes from other particles including particles such as those from hair cosmetic products. From all dyes tested, Orange G was the only dye which successfully discriminated skin flakes from hair product particles. Also, an alkaline based lysis protocol was developed that allowed PCR to be carried out directly on the lysates of single skin flakes. Furthermore, REPLI-g Single Cell WGA was tested on single skin flakes. In contrast to the single spermatozoa, REPLI-g Single Cell WGA was not successful in DNA profiling of single skin flakes. The single skin flake DNA profiling method described in this thesis was successfully used in correctly identifying contributors from mock mixed DNA evidence. Additionally, a small amplicon-based NGS method was tested on single skin flakes. Compared to the PCR and CE approach, the small amplicon-based NGS method improved DNA profiling of single skin flakes, giving a significant increase in allele recovery. In conclusion, this study shows circumventing mixtures is possible by DNA profiling of single spermatozoa, using micromanipulation and WGA. Furthermore, DNA profiling of single skin flakes has been improved by the staining of tape liftings methodology with Orange G, alkaline lysis, direct-PCR and a small amplicon-based NGS approach. Nonetheless, future work is required to assess the performance of the single spermatozoa method on mock swabs with more diluted semen. Also, commercially available NGS kits should be tested with single skin flakes and compared with the in-house NGS method.
Survival of patients with pediatric acute lymphoblastic leukemia (ALL) after allogeneic hematopoietic stem cell transplantation (allo-SCT) is mainly compromised by leukemia relapse, carrying dismal prognosis. As novel individualized therapeutic approaches are urgently needed, we performed whole-exome sequencing of leukemic blasts of 10 children with post–allo-SCT relapses with the aim of thoroughly characterizing the mutational landscape and identifying druggable mutations. We found that post–allo-SCT ALL relapses display highly diverse and mostly patient-individual genetic lesions. Moreover, mutational cluster analysis showed substantial clonal dynamics during leukemia progression from initial diagnosis to relapse after allo-SCT. Only very few alterations stayed constant over time. This dynamic clonality was exemplified by the detection of thiopurine resistance-mediating mutations in the nucleotidase NT5C2 in 3 patients’ first relapses, which disappeared in the post–allo-SCT relapses on relief of selective pressure of maintenance chemotherapy. Moreover, we identified TP53 mutations in 4 of 10 patients after allo-SCT, reflecting acquired chemoresistance associated with selective pressure of prior antineoplastic treatment. Finally, in 9 of 10 children’s post–allo-SCT relapse, we found alterations in genes for which targeted therapies with novel agents are readily available. We could show efficient targeting of leukemic blasts by APR-246 in 2 patients carrying TP53 mutations. Our findings shed light on the genetic basis of post–allo-SCT relapse and may pave the way for unraveling novel therapeutic strategies in this challenging situation.
Die Diskussion über Nutzen und Risiken der Biound Gentechnik beherrschte die Jahre von 1998 bis 2001. Die „grüne Gentechnik“ kämpfte auch 1997 gegen wachsende Widerstände. Erst als sich im Jahr 2001 die Medien mit der „roten“ Gentechnik befassten, sank der Anteil kritischer Vorbehalte und stieg die Akzeptanz gegenüber gentechnisch herstellten Medikamenten in der Bevölkerung. Die Entschlüsselung der menschlichen Erbanlage und die Diskussion um das Klonen von Menschen sowie die Forschung mit embryonalen Stammzellen führte neue Aspekte in die öffentliche Diskussion ein. Die Debatte findet seither auf allen politischen Ebenen statt. Im Zusammenhang mit der Genforschung werden in den Medien immer häufiger Moral und Ökonomie gegenübergestellt und gegeneinander abgewogen. In diesem Wirrwarr von unterschiedlichen und häufig auch widerstreitenden Interessen ist es nicht einfach, sich zurechtzufinden und schließlich zu einer eigenen Position zu gelangen. Umso wichtiger ist daher eine nüchterne Darstellung der Sachverhalte.
Mutations in SELENBP1, encoding a novel human methanethiol oxidase, cause extraoral halitosis
(2017)
Selenium-binding protein 1 (SELENBP1) has been associated with several cancers, although its exact role is unknown. We show that SELENBP1 is a methanethiol oxidase (MTO), related to the MTO in methylotrophic bacteria, that converts methanethiol to H2O2, formaldehyde, and H2S, an activity not previously known to exist in humans. We identified mutations in SELENBP1 in five patients with cabbage-like breath odor. The malodor was attributable to high levels of methanethiol and dimethylsulfide, the main odorous compounds in their breath. Elevated urinary excretion of dimethylsulfoxide was associated with MTO deficiency. Patient fibroblasts had low SELENBP1 protein levels and were deficient in MTO enzymatic activity; these effects were reversed by lentivirus-mediated expression of wild-type SELENBP1. Selenbp1-knockout mice showed biochemical characteristics similar to those in humans. Our data reveal a potentially frequent inborn error of metabolism that results from MTO deficiency and leads to a malodor syndrome.
Nutrigenomics and nutrigenetics are receiving growing attention from a diverse range of stakeholders including health care professionals, citizens, governments, insurers and industry. Currently there is special focus on research on how our food influences us and might cause discomfort or even symptoms of disease, but also the fact that several food intolerances are caused by genetic alterations. The strong interest expressed by certain segments of the general population for predictive and preventive diagnostic testing in relation to diet and ways in which this can improve overall health led to a fast growing market of nutrigenetic based tests. This puts pressures and challenges on governments and insurers for how best to reimburse new genetic tests. These discussions are best informed by a sound understanding of nutrigenetics science and technology, its promises and challenges, which are addressed in this paper. For example, some of the most common food intolerances caused by genetic variations are lactose intolerance, inherited fructose intolerance, congenital sucrase isomaltase deficiency (sucrose intolerance), celiac disease, glucose-6-phosphate deficiency (favism), alcohol intolerance and hemochromatosis. The increasing understanding of molecular mechanisms associated with these conditions is stimulating the development of a broad range of diagnostics allowing any person with adequate resources to have their genetic predispositions determined. However, many of the currently available tests cover only one of the above mentioned diseases or a small set of responsible mutations, which is in strong contrast to the evolution of medicine towards a more holistic approach as, for example, P4 medicine. Additionally, available tests are often not based on evidence or other guidelines for genetic test development as recommended by the ACCE evidentiary framework. In this paper we discuss the most common nutrigenetic diseases and their potential and demonstrated impacts on public health, as well as ways to devise personalized diet informed by human genomics variation in the future.
TCF3-HLF-positive acute lymphoblastic leukemia (ALL) is currently incurable. Using an integrated approach, we uncovered distinct mutation, gene expression and drug response profiles in TCF3-HLF-positive and treatment-responsive TCF3-PBX1-positive ALL. We identified recurrent intragenic deletions of PAX5 or VPREB1 in constellation with the fusion of TCF3 and HLF. Moreover somatic mutations in the non-translocated allele of TCF3 and a reduction of PAX5 gene dosage in TCF3-HLF ALL suggest cooperation within a restricted genetic context. The enrichment for stem cell and myeloid features in the TCF3-HLF signature may reflect reprogramming by TCF3-HLF of a lymphoid-committed cell of origin toward a hybrid, drug-resistant hematopoietic state. Drug response profiling of matched patient-derived xenografts revealed a distinct profile for TCF3-HLF ALL with resistance to conventional chemotherapeutics but sensitivity to glucocorticoids, anthracyclines and agents in clinical development. Striking on-target sensitivity was achieved with the BCL2-specific inhibitor venetoclax (ABT-199). This integrated approach thus provides alternative treatment options for this deadly disease.
Alpha-aminoadipic and alpha-ketoadipic aciduria is an autosomal recessive inborn error of lysine, hydroxylysine, and tryptophan degradation. To date, DHTKD1 mutations have been reported in two alpha-aminoadipic and alpha-ketoadipic aciduria patients. We have now sequenced DHTKD1 in nine patients diagnosed with alpha-aminoadipic and alpha-ketoadipic aciduria as well as one patient with isolated alpha-aminoadipic aciduria, and identified causal mutations in eight. We report nine novel mutations, including three missense mutations, two nonsense mutations, two splice donor mutations, one duplication, and one deletion and insertion. Two missense mutations, one of which was reported before, were observed in the majority of cases. The clinical presentation of this group of patients was inhomogeneous. Our results confirm that alpha-aminoadipic and alpha-ketoadipic aciduria is caused by mutations in DHTKD1, and further establish that DHTKD1 encodes the E1 subunit of the alpha-ketoadipic acid dehydrogenase complex.
Abstract Mitochondrial DNA depletion syndromes (MDDS) are severe pediatric diseases with diverse clinical manifestations. Gene mutations that underlie MDDS have been associated with alterations in the mitochondrial DNA (mtDNA) replication machinery or in mitochondrial deoxyribonucleoside triphosphate pools. However, the nuclear gene MPV17, whose mutated forms are associated with hepatocerebral MDDS in humans, plays a so-far unknown role in mtDNA maintenance. A high degree of conservation has been determined between MPV17 and its mouse (Mpv17), zebrafish (tra) and yeast (SYM1) homologs, respectively, whereby mutants in these cause very different phenotypes. While dysfunction in this gene in humans causes fatal liver disease, kidney pathology is induced in mice. Moreover, in zebrafish inactivation of the Mpv17 homolog was detected as a viable dyscolouration mutant. Knock out of the yeast ortholog results in a temperature-sensitive metabolic growth phenotype. Detailed analyses on common denominators between these different phenotypes strengthen the hypothesis that the Mpv17 protein forms a channel in the inner mitochondrial membrane, allowing small molecules - in vertebrates probably nucleotides, and in yeast probably intermediates of the tricarboxylic acid cycle - to pass. Moreover, a function modifying the pathologic manifestations of MPV17-related disease in mice has been identified. This signaling pathway remarkably involves the non-mitochondrial catalytic subunit of DNA-dependent protein kinase (PRKDC), important in double-strand break repair resistance against reactive oxygen-induced genotoxic stress.
DNA Sequencing
(2011)
Isolation of DNA and RNA
(2011)
