<> "The repository administrator has not yet configured an RDF license."^^ . <> . . "Intra-clonal gene expression heterogeneity in human \r\ncolorectal cancer"^^ . "Colorectal cancer (CRC) harbors heterogeneous subclonal cell populations that contribute to \r\ntumor progression, metastasis and therapy resistance. Subclonal heterogeneity arises not only \r\nfrom genetic and epigenetic differences, but also from functional heterogeneity of subclones \r\nsharing homogeneous genetic features. Genetic barcoding approaches have shown that \r\nsubclones with long-term tumor-initiating cell (LT-TIC) activity are capable of fueling CRC \r\nexpansion to metastasis and that CRC subclones can enter a drug tolerant persister state to \r\ntolerate chemotherapy. Nevertheless, subclonal transcriptional features which characterize \r\nfunctional states, such as treatment response and metastasis, are underexplored. Characterizing \r\nhow subclonal gene expression contributes to functional states of CRC enhances understanding\r\nthe dynamics of tumor progression. Here, I describe subclonal dynamics in addition to associated \r\nsingle cell transcriptomics of treatment response and metastasis in barcoded CRC patient-derived \r\norganoids (PDOs) and xenografts, respectively. \r\nTo study subclonal gene expression heterogeneity in metastatic and therapy resistant populations, \r\nI transduced three CRC PDOs with a genetic RNA-expressed barcoding library for unique single \r\ncell marking. Barcoded PDOs were either orthotopically serially transplanted into NOD.Cg-Prkdc \r\nscid Il2rg tm1Wjl /SzJ (NSG) mice or treated with chemotherapy to study clonal and transcriptional \r\ndynamics in tumor progression to metastasis and in treatment response. I performed single cell \r\nRNA (scRNA) sequencing in addition to target barcode DNA sequencing on cells harvested from \r\nxenografts or treated PDOs to analyze clonal dynamics and subclonal gene expression programs. \r\nI found that combined scRNA data from more than 3.5x10E5 cells in xenografts demonstrated a \r\ndrop in the number of clones by which 0.05-1% of detected clones formed the majority of cancer \r\ncells in serial transplantations of tumor, liver and lung metastasis, with an enrichment of few \r\nindividual clones that drive tumor progression. The frequency of these enriched clones varied \r\nacross serial transplantations of different tumor locations such as the tumor and metastases, \r\nsuggesting a dynamic subclonal expansion in different microenvironments. Subclonal cell \r\npopulations in both tumor and liver or lung metastases reflected distinct gene expression profiles \r\nof differentiated and undifferentiated intestinal cells. Differentiated epithelial profiles were \r\nreminiscent of epithelial intestinal cells such as absorptive enterocytes and secretory cells while \r\nundifferentiated cells shared transcriptional features of invasive and fetal/embryonic cell states. \r\nIndividual metastatic subclones of liver metastasis showed higher expression of particular genes \r\nsuch as SOX4, VEGFA and PLCG2 which were enriched in the invasive fetal cell phenotype. Lung \r\nmetastasis cells of the same subclones demonstrated higher expression of S100A11, ANXA1 and \r\nKRT19, which were elevated in the differentiated epithelial cell phenotype. In addition, clones \r\nwhich represent more than 25% of the tumor or metastasis cell population did not show \r\nreproducible gene expression differences in comparison to smaller clones forming less than 5% \r\nof the cell population. Upon chemotherapy treatment and recovery of PDOs, the frequency of \r\nindividual clones was marginally affected in comparison to control DMSO treated cells, without a \r\nstrong selection of particular clones. In response to treatment, cells reflected abundant pre-existing \r\ngene expression profiles reminiscent to those of intestinal enterocytes, undifferentiated cycling \r\nand progenitor cells and a low frequency of transcriptional profiles related to proliferative and \r\nsecretory cells. One week after drug washout, stem cell transcriptional clusters, in addition to \r\ntranscriptional clusters abundant in treatment response, were enriched. The functional relevance \r\nof 181 marker genes of treatment response-associated transcriptional clusters was assessed \r\nthrough a custom clustered regularly interspaced palindromic repeats interference (CRISPRi)\r\nscreen, which demonstrated the depletion of 43 out of 52 significantly affected genes after \r\nchemotherapy treatment. Further, transposase-accessible chromatin single cell (scATAC)\r\nsequencing data from two PDOs treated with 5-Fluorouracil (5-FU) showed an open chromatin \r\nstatus in the region of genes detected to be differentially expressed in response-associated \r\ntranscriptional clusters identified in scRNA data, thus linking gene transcription to epigenetic \r\nchromatin regulation.\r\nOverall, this study links clonal dynamics to transcriptional states, thereby dissecting gene \r\nexpression of subclonal functional states of tumor progression. This analysis reveals that gene \r\nexpression states and marker genes associated with metastasis and treatment response could be \r\nimplemented in further development and validation of innovative treatment strategies in CRC."^^ . "2025" . . . . . . . "Mhd Haidar"^^ . "Kasem"^^ . "Mhd Haidar Kasem"^^ . . . . . . "Intra-clonal gene expression heterogeneity in human \r\ncolorectal cancer (Other)"^^ . . . . . . "Intra-clonal gene expression heterogeneity in human \r\ncolorectal cancer (Other)"^^ . . . . . . "Intra-clonal gene expression heterogeneity in human \r\ncolorectal cancer (Other)"^^ . . . . . . "Intra-clonal gene expression heterogeneity in human \r\ncolorectal cancer (Other)"^^ . . . . . . "Intra-clonal gene expression heterogeneity in human \r\ncolorectal cancer (Other)"^^ . . . . . . "Intra-clonal gene expression heterogeneity in human \r\ncolorectal cancer (PDF)"^^ . . "HTML Summary of #34798 \n\nIntra-clonal gene expression heterogeneity in human \ncolorectal cancer\n\n" . "text/html" . . . "500 Naturwissenschaften und Mathematik"@de . "500 Natural sciences and mathematics"@en . . . "570 Biowissenschaften, Biologie"@de . "570 Life sciences"@en . .