TY  - JOUR
A1  - Flunkert, Julia
A1  - Maierhofer, Anna
A1  - Dittrich, Marcus
A1  - Müller, Tobias
A1  - Horvath, Steve
A1  - Nanda, Indrajit
A1  - Haaf, Thomas
T1  - Genetic and epigenetic changes in clonal descendants of irradiated human fibroblasts
JF  - Experimental Cell Research
N2  - To study delayed genetic and epigenetic radiation effects, which may trigger radiation-induced carcinogenesis, we have established single-cell clones from irradiated and non-irradiated primary human fibroblasts. Stable clones were endowed with the same karyotype in all analyzed metaphases after 20 population doublings (PDs), whereas unstable clones displayed mosaics of normal and abnormal karyotypes. To account for variation in radiation sensitivity, all experiments were performed with two different fibroblast strains. After a single X-ray dose of 2 Gy more than half of the irradiated clones exhibited radiation-induced genome instability (RIGI). Irradiated clones displayed an increased rate of loss of chromosome Y (LOY) and copy number variations (CNVs), compared to controls. CNV breakpoints clustered in specific chromosome regions, in particular 3p14.2 and 7q11.21, coinciding with common fragile sites. CNVs affecting the FHIT gene in FRA3B were observed in independent unstable clones and may drive RIGI. Bisulfite pyrosequencing of control clones and the respective primary culture revealed global hypomethylation of ALU, LINE-1, and alpha-satellite repeats as well as rDNA hypermethylation during in vitro ageing. Irradiated clones showed further reduced ALU and alpha-satellite methylation and increased rDNA methylation, compared to controls. Methylation arrays identified several hundred differentially methylated genes and several enriched pathways associated with in vitro ageing. Methylation changes in 259 genes and the MAP kinase signaling pathway were associated with delayed radiation effects (after 20 PDs). Collectively, our results suggest that both genetic (LOY and CNVs) and epigenetic changes occur in the progeny of exposed cells that were not damaged directly by irradiation, likely contributing to radiation-induced carcinogenesis. We did not observe epigenetic differences between stable and unstable irradiated clones. The fact that the DNA methylation (DNAm) age of clones derived from the same primary culture varied greatly suggests that DNAm age of a single cell (represented by a clone) can be quite different from the DNAm age of a tissue. We propose that DNAm age reflects the emergent property of a large number of individual cells whose respective DNAm ages can be highly variable.
KW  - copy number variation (CNV)
KW  - delayed radiation effects
KW  - DNA methylation (DNAm) age
KW  - global DNA methylation
KW  - loss of chromosome Y (LOY);
KW  - methylation array analysis
KW  - radiation-induced genome instability (RIGI)
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-228177
VL  - 370
ER  - 
TY  - JOUR
A1  - Hofrichter, Michaela A. H.
A1  - Doll, Julia
A1  - Habibi, Haleh
A1  - Enayati, Samaneh
A1  - Mehrjardi, Mohammad Yahya Vahidi
A1  - Müller, Tobias
A1  - Dittrich, Marcus
A1  - Haaf, Thomas
A1  - Vona, Barbara
T1  - Exome-wide copy number variation analysis identifies a COL9A1 in frame deletion that is associated with hearing loss
JF  - European Journal of Medical Genetics
N2  - Pathogenic variants in COL9A1 are primarily associated with autosomal recessive Stickler syndrome. Patients with COL9A1-associated Stickler syndrome (STL) present hearing loss (HL), ophthalmic manifestations and skeletal abnormalities. However, the clinical spectrum of patients with COL9A1 variants can also include multiple epiphyseal dysplasia, as well as non-syndromic HL that was observed in one previously reported proband. Exome sequencing was performed on the genomic DNA of an Iranian patient and his affected brother who both report non-syndromic HL. A 44.6 kb homozygous in-frame deletion spanning exons 6 to 33 of COL9A1 was detected via exome-based copy number variation analysis. The deleted exons were confirmed by PCR in the patient and his affected brother, who both have non-syndromic HL. Segregation analysis via qPCR confirmed the parents as heterozygous deletion carriers. Breakpoint analysis mapped the homozygous deletion spanning introns 5 to 33 (g.70,948,188_70,997,277del, NM_001851.4(COL9A1):c.697–3754_2112+769del, p.(Phe233_Ser704del), with an additional 67 bp of inserted intronic sequence that may have originated due to a fork stalling and template switching/microhomology-mediated break-induced replication (FoSTeS/MMBIR) mechanism. This mechanism has not been previously implicated in HL or STL. This is also the first reported copy number variation in COL9A1 that was identified through an exome data set in an Iranian family with apparent non-syndromic HL. The present study emphasizes the importance of exome-wide copy number variation analysis in molecular diagnosis and provides supporting evidence to associate COL9A1 with autosomal recessive non-syndromic HL.
KW  - COL9A1
KW  - copy number variation
KW  - FoSTeS/MMBIR mechanism
KW  - non-syndromic hearing loss
KW  - Stickler syndrome
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-322008
VL  - 62
ER  - 
TY  - JOUR
A1  - Luther, Christian H.
A1  - Brandt, Philipp
A1  - Vylkova, Slavena
A1  - Dandekar, Thomas
A1  - Müller, Tobias
A1  - Dittrich, Marcus
T1  - Integrated analysis of SR-like protein kinases Sky1 and Sky2 links signaling networks with transcriptional regulation in Candida albicans
JF  - Frontiers in Cellular and Infection Microbiology
N2  - Fungal infections are a major global health burden where Candida albicans is among the most common fungal pathogen in humans and is a common cause of invasive candidiasis. Fungal phenotypes, such as those related to morphology, proliferation and virulence are mainly driven by gene expression, which is primarily regulated by kinase signaling cascades. Serine-arginine (SR) protein kinases are highly conserved among eukaryotes and are involved in major transcriptional processes in human and S. cerevisiae. Candida albicans harbors two SR protein kinases, while Sky2 is important for metabolic adaptation, Sky1 has similar functions as in S. cerevisiae. To investigate the role of these SR kinases for the regulation of transcriptional responses in C. albicans, we performed RNA sequencing of sky1Δ and sky2Δ and integrated a comprehensive phosphoproteome dataset of these mutants. Using a Systems Biology approach, we study transcriptional regulation in the context of kinase signaling networks. Transcriptomic enrichment analysis indicates that pathways involved in the regulation of gene expression are downregulated and mitochondrial processes are upregulated in sky1Δ. In sky2Δ, primarily metabolic processes are affected, especially for arginine, and we observed that arginine-induced hyphae formation is impaired in sky2Δ. In addition, our analysis identifies several transcription factors as potential drivers of the transcriptional response. Among these, a core set is shared between both kinase knockouts, but it appears to regulate different subsets of target genes. To elucidate these diverse regulatory patterns, we created network modules by integrating the data of site-specific protein phosphorylation and gene expression with kinase-substrate predictions and protein-protein interactions. These integrated signaling modules reveal shared parts but also highlight specific patterns characteristic for each kinase. Interestingly, the modules contain many proteins involved in fungal morphogenesis and stress response. Accordingly, experimental phenotyping shows a higher resistance to Hygromycin B for sky1Δ. Thus, our study demonstrates that a combination of computational approaches with integration of experimental data can offer a new systems biological perspective on the complex network of signaling and transcription. With that, the investigation of the interface between signaling and transcriptional regulation in C. albicans provides a deeper insight into how cellular mechanisms can shape the phenotype.
KW  - sky kinases
KW  - kinase signaling
KW  - network analysis
KW  - transcriptome
KW  - transcriptional regulation
KW  - phosphoproteome
KW  - Candida albicans
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-311771
SN  - 2235-2988
VL  - 13
ER  - 
TY  - JOUR
A1  - Conrad, David
A1  - Kehl, Alexandra
A1  - Müller, Tobias
A1  - Klopfleisch, Robert
A1  - Aupperle-Lellbach, Heike
T1  - Immunohistochemical and molecular genetic analysis of canine digital mast cell tumours
JF  - Animals
N2  - Grading, immunohistochemistry and c-kit mutation status are criteria for assessing the prognosis and therapeutic options of canine cutaneous mast cell tumours (MCTs). As a subset, canine digital MCTs have rarely been explored in this context. Therefore, in this retrospective study, 68 paraffin-embedded canine digital MCTs were analysed, and histological grading was assessed according to Patnaik and Kiupel. The immunohistochemical markers KIT and Ki67 were used, as well as polymerase chain reaction (PCR) for mutational screening in c-kit exons 8, 9, 11 and 14. Patnaik grading resulted in 22.1% grade I, 67.6% grade II and 10.3% grade III tumours. Some 86.8% of the digital MCTs were Kiupel low-grade. Aberrant KIT staining patterns II and III were found in 58.8%, and a count of more than 23 Ki67-positive cells in 52.3% of the cases. Both parameters were significantly associated with an internal tandem duplication (ITD) in c-kit exon 11 (12.7%). French Bulldogs, which tend to form well-differentiated cutaneous MCTs, had a higher proportion of digital high-grade MCTs and ITD in c-kit exon 11 compared with mongrels. Due to its retrospective nature, this study did not allow for an analysis of survival data. Nevertheless, it may contribute to the targeted characterisation of digital MCTs.
KW  - dog
KW  - digit
KW  - toe
KW  - CD117
KW  - Ki67
KW  - KIT
KW  - grading
KW  - PCR
KW  - sequencing
KW  - c-kit
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-319199
SN  - 2076-2615
VL  - 13
IS  - 10
ER  - 
TY  - JOUR
A1  - Aupperle-Lellbach, Heike
A1  - Heidrich, Daniela
A1  - Kehl, Alexandra
A1  - Conrad, David
A1  - Brockmann, Maria
A1  - Törner, Katrin
A1  - Beitzinger, Christoph
A1  - Müller, Tobias
T1  - KITLG copy number germline variations in schnauzer breeds and their relevance in digital squamous cell carcinoma in black giant schnauzers
JF  - Veterinary Sciences
N2  - Copy number variations (CNVs) of the KITLG gene seem to be involved in the oncogenesis of digital squamous cell carcinoma (dSCC). The aims of this study were (1) to investigate KITLG CNV in giant (GS), standard (SS), and miniature (MS) schnauzers and (2) to compare KITLG CNV between black GS with and without dSCC. Blood samples from black GS (22 with and 17 without dSCC), black SS (18 with and 4 without dSSC; 5 unknown), and 50 MS (unknown dSSC status and coat colour) were analysed by digital droplet PCR. The results are that (1) most dogs had a copy number (CN) value > 4 (range 2.5–7.6) with no significant differences between GS, SS, and MS, and (2) the CN value in black GS with dSCC was significantly higher than in those without dSCC (p = 0.02). CN values > 5.8 indicate a significantly increased risk for dSCC, while CN values < 4.7 suggest a reduced risk for dSCC (grey area: 4.7–5.8). Diagnostic testing for KITLG CNV may sensitise owners to the individual risk of their black GS for dSCC. Further studies should investigate the relevance of KITLG CNV in SS and the protective effects in MS, who rarely suffer from dSCC.
KW  - tumour
KW  - toe
KW  - miniature schnauzer
KW  - standard schnauzer
KW  - CNV
KW  - ddPCR
KW  - breed predisposition
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-303913
SN  - 2306-7381
VL  - 10
IS  - 2
ER  - 
TY  - JOUR
A1  - Cerezo-Echevarria, Argiñe
A1  - Kehl, Alexandra
A1  - Beitzinger, Christoph
A1  - Müller, Tobias
A1  - Klopfleisch, Robert
A1  - Aupperle-Lellbach, Heike
T1  - Evaluating the histologic grade of digital squamous cell carcinomas in dogs and copy number variation of KIT Ligand — a correlation study
JF  - Veterinary Sciences
N2  - Dark-haired dogs are predisposed to the development of digital squamous cell carcinoma (DSCC). This may potentially suggest an underlying genetic predisposition not yet completely elucidated. Some authors have suggested a potential correlation between the number of copies KIT Ligand (KITLG) and the predisposition of dogs to DSCC, containing a higher number of copies in those affected by the neoplasm. In this study, the aim was to evaluate a potential correlation between the number of copies of the KITLG and the histological grade of malignancy in dogs with DSCC. For this, 72 paraffin-embedded DSCCs with paired whole blood samples of 70 different dogs were included and grouped according to their haircoat color as follow: Group 0/unknown haircoat color (n = 11); Group 1.a/black non-Schnauzers (n = 15); group 1.b/black Schnauzers (n = 33); group 1.c/black and tan dogs (n = 7); group 2/tan animals (n = 4). The DSCCs were histologically graded. Additionally, KITLG Copy Number Variation (CNV) was determined by ddPCR. A significant correlation was observed between KITLG copy number and the histological grade and score value. This finding may suggest a possible factor for the development of canine DSCC, thus potentially having an impact on personalized veterinary oncological strategies and breeding programs.
KW  - canine
KW  - cancer
KW  - toe
KW  - grading
KW  - haircoat
KW  - color
KW  - genetics
KW  - gene
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-304824
SN  - 2306-7381
VL  - 10
IS  - 2
ER  - 
TY  - JOUR
A1  - Floren, Andreas
A1  - Linsenmair, Karl Eduard
A1  - Müller, Tobias
T1  - Diversity and functional relevance of canopy arthropods in Central Europe
JF  - Diversity
N2  - Although much is known about the ecology and functional importance of canopy arthropods in temperate forests, few studies have tried to assess the overall diversity and investigate the composition and dynamics of tree-specific communities. This has impeded a deeper understanding of the functioning of forests, and of how to maintain system services. Here, we present the first comprehensive data of whole arthropod communities, collected by insecticidal knockdown (fogging) from 1159 trees in 18 study areas in Central Europe during the last 25 years. The data includes 3,253,591 arthropods from 32 taxa (order, suborder, family) collected on 24 tree species from 18 genera. Fogging collects free-living, ectophytic arthropods in approximately the same number as they occur in the trees. To our knowledge, these are the most comprehensive data available today on the taxonomic composition of arboreal fauna. Assigning all arthropods to their feeding guild provided a proxy of their functional importance. The data showed that the canopy communities were regularly structured, with a clear dominance hierarchy comprised of eight ‘major taxa’ that represented 87% of all arthropods. Despite significant differences in the proportions of taxa on deciduous and coniferous trees, the composition of the guilds was very similar. The individual tree genera, on the other hand, showed significant differences in guild composition, especially when different study areas and years were compared, whereas tree-specific traits, such as tree height, girth in breast height or leaf cover, explained little of the overall variance. On the ordinal level, guild composition also differed significantly between managed and primary forests, with a simultaneous low within-group variability, indicating that management is a key factor determining the distribution of biodiversity and guild composition.
KW  - temperate forests
KW  - insecticidal knockdown
KW  - community structure
KW  - functional diversity
KW  - guild constancy
KW  - forest management
KW  - pristine forests
KW  - Bialowieza
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-285924
SN  - 1424-2818
VL  - 14
IS  - 8
ER  - 
TY  - JOUR
A1  - Doll, Julia
A1  - Kolb, Susanne
A1  - Schnapp, Linda
A1  - Rad, Aboulfazl
A1  - Rüschendorf, Franz
A1  - Khan, Imran
A1  - Adli, Abolfazl
A1  - Hasanzadeh, Atefeh
A1  - Liedtke, Daniel
A1  - Knaup, Sabine
A1  - Hofrichter, Michaela AH
A1  - Müller, Tobias
A1  - Dittrich, Marcus
A1  - Kong, Il-Keun
A1  - Kim, Hyung-Goo
A1  - Haaf, Thomas
A1  - Vona, Barbara
T1  - Novel loss-of-function variants in CDC14A are associated with recessive sensorineural hearing loss in Iranian and Pakistani patients
JF  - International Journal of Molecular Sciences
N2  - CDC14A encodes the Cell Division Cycle 14A protein and has been associated with autosomal recessive non-syndromic hearing loss (DFNB32), as well as hearing impairment and infertile male syndrome (HIIMS) since 2016. To date, only nine variants have been associated in patients whose initial symptoms included moderate-to-profound hearing impairment. Exome analysis of Iranian and Pakistani probands who both showed bilateral, sensorineural hearing loss revealed a novel splice site variant (c.1421+2T>C, p.?) that disrupts the splice donor site and a novel frameshift variant (c.1041dup, p.Ser348Glnfs*2) in the gene CDC14A, respectively. To evaluate the pathogenicity of both loss-of-function variants, we analyzed the effects of both variants on the RNA-level. The splice variant was characterized using a minigene assay. Altered expression levels due to the c.1041dup variant were assessed using RT-qPCR. In summary, cDNA analysis confirmed that the c.1421+2T>C variant activates a cryptic splice site, resulting in a truncated transcript (c.1414_1421del, p.Val472Leufs*20) and the c.1041dup variant results in a defective transcript that is likely degraded by nonsense-mediated mRNA decay. The present study functionally characterizes two variants and provides further confirmatory evidence that CDC14A is associated with a rare form of hereditary hearing loss.
KW  - CDC14A
KW  - DFNB32
KW  - autosomal recessive hearing loss
KW  - exome sequencing
KW  - splicing
KW  - frameshift
KW  - non-sense mediated mRNA decay
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-285142
SN  - 1422-0067
VL  - 21
IS  - 1
ER  - 
TY  - JOUR
A1  - Floren, Andreas
A1  - Horchler, Peter J.
A1  - Müller, Tobias
T1  - The impact of the neophyte tree Fraxinus pennsylvanica [Marshall] on beetle diversity under climate change
JF  - Sustainability
N2  - We studied the impact of the neophyte tree Fraxinus pennsylvanica on the diversity of beetles in floodplain forests along the river Elbe in Germany in 2016, 2017 and in 2020, where 80% of all Fraxinus excelsior trees had died following severe droughts. Beetles were collected by insecticidal knock-down from 121 trees (64 F. excelsior and 57 F. pennsylvanica) and identified to 547 species in 15,214 specimens. The trees sampled in 2016 and 2017 showed no signs of drought stress or ash dieback and serve as a reference for the comparison with the 2020 fauna. The data proved that F. excelsior harbours the most diverse beetle community, which differed also significantly in guild composition from F. pennsylvanica. Triggered by extremely dry and long summer seasons, the 2020 ash dieback had profound and forest-wide impacts. Several endangered, red-listed beetle species of Saxonia Anhalt had increased in numbers and became secondary pests on F. excelsior. Diversity decreased whilst numbers of xylobionts increased on all trees, reaching 78% on F. excelsior. Proportions of xylobionts remained constant on F. pennsylvanica. Phytophages were almost absent from all trees, but mycetophages increased on F. pennsylvanica. Our data suggest that as a result of the dieback of F. excelsior the neophyte F. pennsylvanica might become a rescue species for the European Ash fauna, as it provides the second-best habitat. We show how difficult it is to assess the dynamics and the ecological impact of neophytes, especially under conditions similar to those projected by climate change models. The diversity and abundance of canopy arthropods demonstrates their importance in understanding forest functions and maintenance of ecosystem services, illustrating that their consideration is essential for forest adaptation to climate change.
KW  - forest conversion
KW  - neophyte trees
KW  - ash dieback
KW  - beetle communities
KW  - ecosystem function
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-262223
SN  - 2071-1050
VL  - 14
IS  - 3
ER  - 
TY  - JOUR
A1  - Grassinger, Julia Maria
A1  - Floren, Andreas
A1  - Müller, Tobias
A1  - Cerezo-Echevarria, Argiñe
A1  - Beitzinger, Christoph
A1  - Conrad, David
A1  - Törner, Katrin
A1  - Staudacher, Marlies
A1  - Aupperle-Lellbach, Heike
T1  - Digital lesions in dogs: a statistical breed analysis of 2912 cases
JF  - Veterinary Sciences
N2  - Breed predispositions to canine digital neoplasms are well known. However, there is currently no statistical analysis identifying the least affected breeds. To this end, 2912 canine amputated digits submitted from 2014–2019 to the Laboklin GmbH & Co. KG for routine diagnostics were statistically analyzed. The study population consisted of 155 different breeds (most common: 634 Mongrels, 411 Schnauzers, 197 Labrador Retrievers, 93 Golden Retrievers). Non-neoplastic processes were present in 1246 (43%), tumor-like lesions in 138 (5%), and neoplasms in 1528 cases (52%). Benign tumors (n = 335) were characterized by 217 subungual keratoacanthomas, 36 histiocytomas, 35 plasmacytomas, 16 papillomas, 12 melanocytomas, 9 sebaceous gland tumors, 6 lipomas, and 4 bone tumors. Malignant neoplasms (n = 1193) included 758 squamous cell carcinomas (SCC), 196 malignant melanomas (MM), 76 soft tissue sarcomas, 52 mast cell tumors, 37 non-specified sarcomas, 29 anaplastic neoplasms, 24 carcinomas, 20 bone tumors, and 1 histiocytic sarcoma. Predisposed breeds for SCC included the Schnauzer (log OR = 2.61), Briard (log OR = 1.78), Rottweiler (log OR = 1.54), Poodle (log OR = 1.40), and Dachshund (log OR = 1.30). Jack Russell Terriers (log OR = −2.95) were significantly less affected by SCC than Mongrels. Acral MM were significantly more frequent in Rottweilers (log OR = 1.88) and Labrador Retrievers (log OR = 1.09). In contrast, Dachshunds (log OR = −2.17), Jack Russell Terriers (log OR = −1.88), and Rhodesian Ridgebacks (log OR = −1.88) were rarely affected. This contrasted with the well-known predisposition of Dachshunds and Rhodesian Ridgebacks to oral and cutaneous melanocytic neoplasms. Further studies are needed to explain the underlying reasons for breed predisposition or “resistance” to the development of specific acral tumors and/or other sites.
KW  - canine
KW  - subungual
KW  - toe
KW  - tumor
KW  - inflammation
KW  - breed predisposition
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-242690
SN  - 2306-7381
VL  - 8
IS  - 7
ER  -