<> "The repository administrator has not yet configured an RDF license."^^ . <> . . "Profiling pathogenicity of Bovine Meat and Milk Factors in cancer by genome and transcriptome analysis"^^ . "Bovine Meat and Milk factors are circular DNA sequences isolated from bovine milk and serum \r\nsamples, which have been proposed to contribute to cancer development of different cancer \r\ntypes by inducing chronic inflammation in exposed tissues. While experimental analyses \r\nindicated the presence of certain BMMF sequences in different tumor types, only specific \r\nBMMF genomes and cancer types have been targeted in experiments so far. \r\nFor this reason, I screened multiple publicly available high-throughput sequencing data sets for \r\na comprehensive library of BMMF genomes using the D-ViSioN algorithm to fill this \r\nknowledge gap by in silico analysis. With this, I managed to prove the feasibility of BMMF \r\ndetection via computational tools in RNA, WGS and single cell sequencing data and developed \r\nprocessing steps to filter, normalize and characterize the BMMF signal. I screened WGS and \r\nRNA sequencing samples of 29 and 25 different cancer cohorts of the PCAWG project, RNA \r\nsequencing data of five cancer types provided by the TCGA project, as well as, 15 healthy tissue \r\ncohorts derived from healthy donors included in the GTEx project. Additionally, I analyzed cell \r\nline data of the DepMap project and a single cell data set of metastatic lung cancer. \r\nI detected BMMF sequences on the RNA and even stronger on the DNA level in tumor and \r\nnon-tumor samples of patients with a wide range of different cancer types as well as in samples \r\nof healthy donors. The detection of BMMF group 1 targets outnumbered the detection of \r\nBMMF group 2, 3 and 4 targets by far both on DNA and RNA level. The comparison of BMMF \r\ndetection in a set of cancer and tissue types across five different data sets revealed the highest \r\npercentage of BMMF positive samples for ovarian, stomach and uterine cancer in RNA \r\nsequencing data as well as for breast, kidney, lung, pancreas, prostate and stomach cancer in \r\nWGS data. For further subtyping of the reported BMMF hits, I defined in total 26 BMMF \r\nsubgroups spanning the four main BMMF groups. Detailed analysis of BMMF detection at \r\nsubgroup level showed that for a broad set of BMMF subgroups and a broad range of different \r\ncancer cohorts a lower BMMF signal was found in the RNA data of tumor samples compared \r\nto matched healthy tissue samples. These findings would indicate no increased cancer risk upon \r\ndetection of these BMMF types. On the contrary, BMMF subgroup 6 in acute myeloid leukemia \r\nand ovarian cancer, subgroup 5 in stomach cancer, subgroup 8 in uterine cancer and subgroup \r\n21 in acute myeloid leukemia were found to be increased in the case versus control comparison \r\nof RNA data, which are thus candidates for investigating potential high-risk patterns. While \r\nWGS data of early-onset prostate cancer patients exhibited a higher BMMF signal in non-tumor\r\nsamples than in tumor samples of the same patients, a kidney, lung, pancreatic and prostate \r\nII\r\ncancer cohort each included two or more BMMF subgroups with increased BMMF detection \r\nin tumor samples compared to non-tumor samples of the same patients. These analyses \r\nhighlighted the importance of BMMF subgroups 1, 5, 6, 7, 10 and 21, which frequently stood \r\nout in different data sets analyzed. In addition, I characterized the specific coverage of BMMF \r\nreads on the respective BMMF templates for the BMMF genomes C1MI.3M.1, H1MSB.1, \r\nC1MI.2 and C1HB.4, which showed that either the entire sequence or large parts of it are \r\ncovered by BMMF reads indicating a specific detection.\r\nWith these analyses, I identified new cancer types-of-interest as well as new target BMMF \r\ngenomes for further BMMF research. The definition and characterization of BMMF-positive \r\ncohorts and subgroups might help to understand the pathogenic phenotype of BMMFs and to \r\nestablish BMMF detection workflows helpful in diagnostic and therapeutic setup."^^ . "2025" . . . . . . . "Lisa Ruth"^^ . "Häfele"^^ . "Lisa Ruth Häfele"^^ . . . . . . "Profiling pathogenicity of Bovine Meat and Milk Factors in cancer by genome and transcriptome analysis (PDF)"^^ . . . "Profiling pathogenicity of Bovine Meat and Milk Factors in cancer by genome and transcriptome analysis (Other)"^^ . . . . . . "Profiling pathogenicity of Bovine Meat and Milk Factors in cancer by genome and transcriptome analysis (Other)"^^ . . . . . . "Profiling pathogenicity of Bovine Meat and Milk Factors in cancer by genome and transcriptome analysis (Other)"^^ . . . . . . "Profiling pathogenicity of Bovine Meat and Milk Factors in cancer by genome and transcriptome analysis (Other)"^^ . . . . . . "Profiling pathogenicity of Bovine Meat and Milk Factors in cancer by genome and transcriptome analysis (Other)"^^ . . . . . "HTML Summary of #35508 \n\nProfiling pathogenicity of Bovine Meat and Milk Factors in cancer by genome and transcriptome analysis\n\n" . "text/html" . .