Targeted enrichment and novel DNA sequencing strategies for the molecular analysis of fanconi anemia genes

Fanconi-Anämie (FA) ist, mit Ausnahme von Mutationen in FANCR/RAD51, eine autosomal-rezessive oder X-chromosomal vererbte Krankheit, die sich durch eine ausgesprochene klinische als auch genetische Heterogenität auszeichnet. Neben einem fortschreitenden Knochenmarksversagen zählen zu den typischen Merkmalen eine Vielzahl an angeborenen Fehlbildungen, wie beispielsweise Radialstrahlanomalien, Minderwuchs oder Pigmentierungsstörungen. Zudem besteht für FA-Patienten ein überdurchschnittlich hohes Risiko bereits in jungen Jahren an akuter myeloischer Leukämie oder soliden Tumoren zu erkranken. Bislang konnten in 21 FA-Genen (FANCA, -B, -C, - D1, -D2, -E, -F, -G, -I, -J, -L, -M, -N, -O, -P, -Q, -R, -S, -T, -U oder -V) krankheitsverursachende Mutationen identifiziert werden, deren Proteinprodukte maßgeblich an der Aufrechterhaltung der Genomstabilität beteiligt sind und Komponenten des FA/BRCA-DNA-Reparaturweges darstellen. In der klassischen FA-Mutationsanalyse kommen meist Sanger-Sequenzierungen sowie MLPA- und Immunblot-Analysen zum Einsatz. Da im Wesentlichen keine Genotyp-Phänotyp-Korrelation besteht, gestaltet sich, gerade bei seltenen FA-Komplementationsgruppen, der Nachweis von krankheitsverursachenden Mutationen oftmals sehr zeit- und kostenintensiv. Während der letzten Jahre wurden verschiedene Strategien zur Anreicherung und Sequenzierung entwickelt, welche die parallele Sequenzanalyse einzelner ausgewählter Gene, ganzer Exome oder sogar des gesamten Genoms und somit eine kosten- und zeiteffiziente Mutationsanalyse ermöglichen. In der vorliegenden Arbeit wurden unterschiedliche Anreicherungsmethoden mit anschließender Hochdurchsatzsequenzierung auf ihre Anwendbarkeit in der molekulargenetischen FA-Diagnostik getestet, um klassische Mutationsanalyse-Methoden zu ergänzen oder möglicherweise sogar ganz ersetzen zu können. Der erste Teil der Arbeit befasste sich mit der Etablierung eines FA-spezifischen Genpanels zur Genotypisierung von FA-Patienten. Nachdem die Methode zunächst anhand von FA-Patienten mit bekannten Mutationen optimiert werden musste, erwies sie sich als effizienter Ansatz zum Nachweis krankheitsverursachender Mutationen bei FA-Patienten unbekannter Komplementationsgruppe. Durch die FA-Panelanalyse konnten 37 von 47 unklassifizierten Patienten einer FA-Komplementationsgruppe zugeordnet werden, indem deren kausalen Mutationen bestimmt wurden. In einem weiteren Ansatz sollte die Anwendbarkeit eines kommerziellen Anreicherungspanels zur FA-Diagnostik untersucht werden. Auch hier konnte ein Großteil der krankheitsverursachenden Mutationen von fünf bekannten wie auch 13 nicht zugeordneten FA-Patienten detektiert und somit eine molekulargenetische Diagnose bei neun weiteren, zuvor unklassifizierten FA-Patienten, gestellt werden. Ferner wurden sechs ausgewählte Patienten, zusätzlich zur Panelanreicherung, per Exomanalyse untersucht. Zum einen konnten Mutationen in bekannten FA-Genen bestätigt oder neu identifiziert werden. Zum anderen wurden auch potentiell pathogene Mutationen in DNA-Reparaturgenen außerhalb des FA/BRCA-Signalweges bei zwei Patienten mit unbestätigter Verdachtsdiagnose FA verifiziert. So wurde bei mehreren Mitgliedern einer Familie mit unterschiedlichen Tumorerkrankungen eine zuvor unbeschriebene homozygote Nonsense-Mutation in der BER-Glykosylase NTHL1 nachgewiesen, für welche bislang erst zwei pathogene Mutationen als Auslöser eines neuen Krebssyndroms bekannt sind. Bei einem weiteren Patienten wurden compound-heterozygote Mutationen in RPA1 detektiert, ein Gen für das bislang noch kein Krankheitsbild bekannt ist. Mit Hilfe der drei verschiedenen Anreicherungsstrategien konnten insgesamt 47 von 60 unklassifizierten FA-Patienten 13 verschiedenen Komplementationsgruppen eindeutig zugeordnet werden. Es zeigte sich dabei ein breites Spektrum an neuen, bislang unbeschriebenen FA-Mutationen. Den größten Anteil an der Gesamtzahl der nachgewiesenen Mutationen hatten Spleißmutationen, die auf eine Auswirkung auf das kanonische Spleißmuster untersucht wurden, um einen pathogenen Effekt nachweisen zu können. Weiterhin schloss die Arbeit die Charakterisierung einzelner FA-Patienten bzw. Komplementationsgruppen mit ein. Dazu zählen die seltenen Untergruppen FA-T und FA-Q, für die jeweils ein neuer Patient identifiziert werden konnte. Durch die funktionelle Charakterisierung der dritten jemals beschriebenen FA-Q-Patientin konnten Einblicke in das Zusammenspiel der Reparatur von DNA-Quervernetzungen und der Nukleotidexzisionsreparatur gewonnen und die phänotypische Variabilität von FA durch die subjektive als auch zelluläre UV-Sensitivität der Patientin ergänzt werden. Darüber hinaus konnte das Mutationsspektrum in FA-I sowie FA-D2 erweitert werden. Eine genauere Untersuchung der Pseudogenregionen von FANCD2 ermöglichte dabei die gezielte Mutationsanalyse des Gens. Insgesamt konnten die Ergebnisse dieser Arbeit dazu beitragen, das Mutationsspektrum in FA zu erweitern und durch die Identifizierung und Charakterisierung einzelner Patienten neue Einblicke in verschiedene Komponenten des FA/BRCA-Signalweges zu erhalten. Es zeigte sich, dass neue DNA-Sequenzierungsstrategien in der FA-Diagnostik eingesetzt werden können, um eine effiziente Mutationsanalyse zu gewährleisten und klassische Methoden in Teilbereichen zu ersetzen.Fanconi anemia (FA) is, with the exception of mutations in FANCR/RAD51, an autosomal recessive or X-linked inherited disease that is characterized by a remarkable clinical and genetic heterogeneity. In addition to progressive bone marrow failure, typical features include a multitude of developmental malformations, such as radial ray anomalies, growth retardation or cutaneous pigment displacement. Additionally, FA patients have a higher risk for developing acute myelogenous leukemia or solid tumors early in life. To date, pathogenic mutations have been identified in 21 FA genes (FANCA, -B, -C, - D1, -D2, -E, -F, -G, -I, -J, -L, -M, -N, -O, -P, -Q, -R, -S, -T, -U or -V) whose protein products are responsible for maintaining genomic integrity and constitute components of the FA/BRCA DNA repair pathway. Typical methods for FA mutation analysis comprise Sanger sequencing as well as MLPA and immunoblot analyses. As no definite genotype-phenotype correlation exists, pathogenic mutation detection in rare subgroups is often quite time-consuming and cost-intensive. Within the last few years, distinct strategies for both enrichment and sequencing of a subset of genes, whole exomes or even the whole genome have been developed that facilitate a cost-effective and time-saving mutation analysis. In the present work different target-enrichment strategies followed by high-throughput sequencing were tested for their applicability in molecular genetic diagnostics of FA in order to complement or even replace classic strategies for mutation analysis. The first part of this work addressed the establishment of an FA-specific gene panel for genotyping FA patients. After optimizing this method by means of FA patients with known mutations, this proved to be an efficient approach for detecting pathogenic mutations in FA patients of unknown complementation groups. Due to FA gene panel analysis, 37 of 47 unclassified FA patients were assigned to a complementation group based on the identification of their causative mutations. In another approach, a commercial enrichment panel was tested for its application in FA diagnostics. Again, most pathogenic mutations of five classified and 13 unclassified FA patients were detected, enabling a molecular diagnosis for nine previously unclassified FA patients. Moreover, six selected patients were studied by exome analysis in addition to panel enrichment. This allowed for mutations in known FA complementation groups to be confirmed or newly identified. Additionally, potentially pathogenic variants in DNA-repair genes outside the FA/BRCA pathway were verified in two patients with an unconfirmed suspected diagnosis of FA. One previously undescribed homozygous nonsense mutation in the BER glycosylase NTHL1 was detected in several members of one family with various tumors. For this gene, only two distinct pathogenic mutations were previously described to cause a novel cancer syndrome. In another patient, compound heterozygous mutations in RPA1 were detected, a gene for which no disease pattern is yet known. By means of the three different enrichment strategies a total of 47 of 60 unclassified FA patients were definitely assigned to 13 diverse complementation groups. In this context, a broad spectrum of previously undescribed mutations was identified. The majority of all verified mutations were splice mutations that were examined for an effect on the canonical splicing pattern in order to verify a pathogenic effect. Additionally, this work also included the characterization of individual FA patients and complementation groups, respectively. These include the rare subgroups FA-T and FA-Q, for each of which one new patient was identified. Functional characterization of the third ever described FA-Q patient allowed new insights into the interplay of DNA interstrand-crosslink and nucleotide excision repair and broadened the spectrum of phenotypic variability of FA by the subjective and cellular UV sensitivity of this patient. Furthermore, the mutation spectrum in both FA-I and FA-D2 was expanded. Here, a closer investigation of the pseudogene regions of FANCD2 facilitated a precise mutation screening of the gene. Overall, the results of this work broadened the mutation spectrum of FA and allowed new insights into diverse components of the FA/BRCA pathway by identifying and characterizing individual patients. It became apparent that novel strategies for DNA sequencing can be applied in FA diagnostics to ensure an efficient mutation analysis, as well as to replace some parts of classical approaches

A Novel MCPH1 Isoform Complements the Defective Chromosome Condensation of Human MCPH1-Deficient Cells

Biallelic mutations in MCPH1 cause primary microcephaly (MCPH) with the cellular phenotype of defective chromosome condensation. MCPH1 encodes a multifunctional protein that notably is involved in brain development, regulation of chromosome condensation, and DNA damage response. In the present studies, we detected that MCPH1 encodes several distinct transcripts, including two major forms: full-length MCPH1 (MCPH1-FL) and a second transcript lacking the six 39 exons (MCPH1De9–14). Both variants show comparable tissue-specific expression patterns, demonstrate nuclear localization that is mediated independently via separate NLS motifs, and are more abundant in certain fetal than adult organs. In addition, the expression of either isoform complements the chromosome condensation defect found in genetically MCPH1-deficient or MCPH1 siRNA-depleted cells, demonstrating a redundancy of both MCPH1 isoforms for the regulation of chromosome condensation. Strikingly however, both transcripts are regulated antagonistically during cell-cycle progression and there are functional differences between the isoforms with regard to the DNA damage response; MCPH1-FL localizes to phosphorylated H2AX repair foci following ionizing irradiation, while MCPH1De9–14 was evenly distributed in the nucleus. In summary, our results demonstrate here that MCPH1 encodes different isoforms that are differentially regulated at the transcript level and have different functions at the protein level

Expression of GFP-tagged MCPH1 isoforms in MCPH1-deficient 562T fibroblasts.

<p>(A) Cells were transduced with GFP-tagged coding sequence of full-length MCPH1 cDNA in a conditional, doxycycline (DOX)-dependent construct with a second regulatory construct trKRAB. Cultures were exposed to increasing DOX concentrations as indicated. Whole-cell extracts were prepared 72 h later and analyzed for the expression of MCPH1 using immunoblotting with an antibody against GFP. (B) The graph shows MCPH1 band intensity relative to the loading control p84 plotted against DOX concentrations. Data represent means ± one S.D. of three independent assays. (C) Immunoblot analysis of whole-cell extracts from non-transduced (NT) 562T cells (lane 1), 562T cells transduced with the regulatory construct only (lane 2), with GFP alone (30 kDa, lane 3) or with GFP fused to MCPH1-FL (120 kDa, lane 4), MCPH1Δe9–14 (94 kDa, lane 5), MCPH1Δe8 (78 kDa, lane 6), or MCPH1Δe1–7 (96 kDa, lane 7) with an antibody against GFP.. Nuclear matrix protein p84 served as the loading control.</p

Cell cycle-dependent regulation of MCPH1 transcripts.

<p>(A) HeLa cells were arrested in G1 phase by double thymidine block. Cultures harvested at various time points after release were analyzed using flow cytometry. (B) Plots represent numbers of cells as a function of their DNA content. A total of 90% of the cells synchronously progressed into S phase (0–4 h), entered G2 phase (4–6 h), started passing through mitosis after 7 h, and were completely in G1 phase after 12 h. (C) Levels of MCPH1-FL (diamonds, solid line), MCPH1Δe9–14 (squares, dotted line), and MCPH1Δe8 (circles, dashed line) mRNA. Data represent means ± S.E.M. of three independent experiments and are normalized to the expression levels of <i>GAPDH</i> and <i>B2M</i>.</p

Intracellular distribution of MCPH1 isoforms.

<p>(A) MCPH1-deficient fibroblasts expressing GFP alone or the specified GFP-MCPH1 fusion proteins were fractionated and cytoplasmic (Cyt) and nuclear (Nuc) protein extracts were analyzed using immunoblotting with an antibody against GFP. The nuclear matrix protein p84 and GAPDH were used as index proteins and loading controls. (B) Cells indicated in A stained with an anti-GFP antibody (green), counterstained with DAPI (blue) and analyzed using fluorescence microscopy. Arrows indicate the prophase-like nuclei. Scale bar = 10 µm. All MCPH1 isoforms exhibit unambiguous nuclear localization.</p

Colocalization of MCPH1 and γH2AX in ionizing irradiation-induced nuclear foci.

<p>(A) Non-transduced (NT) MCPH1-deficient 562T cells and 562T stably expressing GFP alone or the specified GFP-MCPH1 fusion proteins were fixed 2 h after irradiation with 10 Gy and co-stained with antibodies against γH2AX (red) and GFP (green). Nuclei were counterstained with DAPI (blue). Rectangles frame areas, which are shown enlarged in the bottom row. MCPH1 focus formation was observed for MCPH1 isoforms containing the C-terminal BRCT tandem. (B) Quantification of cells expressing foci containing γH2AX and/or (C) MCPH1. Error bars indicate the S.D. of three different measurements, counting approximately 300 nuclei. * <i>p</i>≤0.05 vs. NT as calculated using the Student's <i>t</i>-test.</p

The human <i>MCPH1</i> gene, its transcripts and predicted polypeptides.

<p>(A) Exon (filled boxes) and intron (open boxes) organization of the 241 906-bp encompassing <i>MCPH1</i> gene locus. Red arrows indicate the positions of the regular and of the alternative (*) polyadenylation sites (polyA). (B) The full-length (FL) and the alternative transcripts Δe9–14, Δe1–3, and Δe8: numbered boxes indicate exons, black filled areas illustrate the entire coding regions (CDS), and colored areas show untranslated regions (UTR) as indicated. (C) Predicted polypeptides representing MCPH1 isoforms: blue boxes depict the positions of BRCT domains, while green boxes represent the site of the canonical nuclear localization signal sequence (NLS). Two additional amino acids, S and M, are included into MCPH1Δe9–14 prior to premature termination (#). (D) Expression of MCPH1 transcript variants. Columns represent the levels of MCPH1 transcripts in indicated adult and fetal tissues determined using quantitative real-time PCR. Data represent means ± one S.D. of three independent experiments and are normalized to the geometric mean levels of <i>UBC</i>, <i>GAPDH</i>, <i>B2M</i>, and <i>HPRT1</i> cDNA.</p

Complementation of PCC in patient fibroblasts.

<p>Cells are derived from patient with homozygous truncating mutation c.427dupA (p.T143NfsX5) in <i>MCPH1</i>. Chromosome preparations from (A) non-transduced cells and (B) cells expressing GFP only, or GFP fusions with (C) full-length, (D) Δe9–14, (E) Δe8, or (F) Δe1–7 MCPH1. Arrows indicate nuclei of prophase-like cells (PLCs). (G) Mean rates of PLCs (filled columns) of slides from A-F. Open columns represent mean mitotic indices. Error bars denote the S.D. of counts of approximately 1000 cells each from three independent experiments.</p

Nuclear localization signals (NLSs) in human MCPH1.

<p>(A) The positions of the putative NLS motifs and their amino acid sequences are highlighted in the diagram of the full-length MCPH1. (B) Subcellular distribution of GFP-tagged wild-type (wt) MCPH1 and mutants with deleted NLSs as indicated were transiently expressed in HeLa cells. Cytoplasmic (Cyt) and nuclear (Nuc) protein extracts were immunoblotted with an antibody against GFP (left panel). GAPDH (center panel) and the nuclear matrix protein p84 (right panel) served as index proteins and loading controls. (C) Ratios of relative GFP band intensity in the cytoplasmic (Cyt) vs. nuclear (Nuc) fractions. Absolute numbers were assessed using densitometry and normalized to the loading controls. Columns designate means, and error bars represent the S.D. from three different experiments. Significant differences to wt MCPH1 are indicated by asterisks denoting <i>p</i><0.05 (Student's <i>t</i>-test). Scale bar = 10 µm.</p