Showing papers by "Jussi Taipale published in 2019"

Impact of constitutional TET2 haploinsufficiency on molecular and clinical phenotype in humans.

Abstract: Clonal hematopoiesis driven by somatic heterozygous TET2 loss is linked to malignant degeneration via consequent aberrant DNA methylation, and possibly to cardiovascular disease via increased cytokine and chemokine expression as reported in mice. Here, we discover a germline TET2 mutation in a lymphoma family. We observe neither unusual predisposition to atherosclerosis nor abnormal pro-inflammatory cytokine or chemokine expression. The latter finding is confirmed in cells from three additional unrelated TET2 germline mutation carriers. The TET2 defect elevates blood DNA methylation levels, especially at active enhancers and cell-type specific regulatory regions with binding sequences of master transcription factors involved in hematopoiesis. The regions display reduced methylation relative to all open chromatin regions in four DNMT3A germline mutation carriers, potentially due to TET2-mediated oxidation. Our findings provide insight into the interplay between epigenetic modulators and transcription factor activity in hematological neoplasia, but do not confirm the putative role of TET2 in atherosclerosis.

Gain-of-function CEBPE mutation causes noncanonical autoinflammatory inflammasomopathy

Abstract: Background CCAAT enhancer–binding protein epsilon (C/EBPe) is a transcription factor involved in late myeloid lineage differentiation and cellular function. The only previously known disorder linked to C/EBPe is autosomal recessive neutrophil-specific granule deficiency leading to severely impaired neutrophil function and early mortality. Objective The aim of this study was to molecularly characterize the effects of C/EBPe transcription factor Arg219His mutation identified in a Finnish family with previously genetically uncharacterized autoinflammatory and immunodeficiency syndrome. Methods Genetic analysis, proteomics, genome-wide transcriptional profiling by means of RNA-sequencing, chromatin immunoprecipitation (ChIP) sequencing, and assessment of the inflammasome function of primary macrophages were performed. Results Studies revealed a novel mechanism of genome-wide gain-of-function that dysregulated transcription of 464 genes. Mechanisms involved dysregulated noncanonical inflammasome activation caused by decreased association with transcriptional repressors, leading to increased chromatin occupancy and considerable changes in transcriptional activity, including increased expression of NLR family, pyrin domain-containing 3 protein (NLRP3) and constitutively expressed caspase-5 in macrophages. Conclusion We describe a novel autoinflammatory disease with defective neutrophil function caused by a homozygous Arg219His mutation in the transcription factor C/EBPe. Mutated C/EBPe acts as a regulator of both the inflammasome and interferome, and the Arg219His mutation causes the first human monogenic neomorphic and noncanonical inflammasomopathy/immunodeficiency. The mechanism, including widely dysregulated transcription, is likely not unique for C/EBPe. Similar multiomics approaches should also be used in studying other transcription factor–associated diseases.

Reply to “CRISPR screens are feasible in TP53 wild-type cells”

Abstract: Haapaniemi et al address the issues raised by Brown et al and discuss several differences between the analyses performed by the two groups.

Defining the molecular state of human cancer

Abstract: Cancer is the most complex genetic disease known, with mutations implicated in more than 250 genes. However, it is still elusive which specific mutations found in human patients lead to tumorigenesis. Here we show that a combination of oncogenes that is characteristic of liver cancer (CTNNB1, TERT, MYC) induces senescence in human fibroblasts and primary hepatocytes. However, reprogramming fibroblasts to a liver progenitor fate, induced hepatocytes (iHeps), makes them sensitive to transformation by the same oncogenes. The transformed iHeps are highly proliferative, tumorigenic in nude mice, and bear gene expression signatures of liver cancer. These results show that tumorigenesis is triggered by a combination of three elements: the set of driver mutations, the cellular lineage, and the state of differentiation of the cells along the lineage. Our results indicate that cell identity is a key determinant in transformation, and establish a paradigm for defining the molecular states of human cancer.

Direct conversion of human fibroblasts to liver cancer cells

Abstract: Cancer is the most complex genetic disease known, with mutations in more than 250 genes contributing to different forms of the disease. Most mutations are specific to particular types of cancer, suggesting that cancer genes interact with cell lineage-determining factors to drive the transformation process. To identify the factors necessary and sufficient to define a lineage-specific cancer type, we have reprogrammed and transformed normal human fibroblasts to liver cancer cells. We show that reprogramming human fibroblasts to induced hepatocytes (iHeps) makes the cells sensitive to transformation by a combination of oncogenes that is characteristic of liver cancer (CTNNB1, TERT and MYC). The transformed iHeps are highly proliferative, tumorigenic in nude mice, and bear gene expression signatures of liver cancer. Our results show that lineage-determining factors collaborate with oncogenes to drive tumorigenesis and establish a paradigm for defining the molecular states of distinct types of human cancer.