Papers by Rudolf Jaenisch
Proceedings of the National Academy of Sciences of the United States of America, Nov 13, 2002
The Mecp2 gene has been shown to be mutated in most cases of human Rett syndrome, and mouse model... more The Mecp2 gene has been shown to be mutated in most cases of human Rett syndrome, and mouse models deleted for the ortholog have been generated. Lineage-specific deletion of the gene indicated that the Rett-like phenotype is caused by Mecp2 deficiency in neurons. Biochemical evidence suggests that Mecp2 acts as a global transcriptional repressor, predicting that mutant mice should have genome-wide transcriptional deregulation. We tested this hypothesis by comparing global gene expression in wild-type and Mecp2 mutant mice. The results of numerous microarray analyses revealed no dramatic changes in transcription even in mice displaying overt disease symptoms, although statistical power analyses of the data indicated that even a small number of relatively subtle changes in transcription would have been detected if present. However, a classifier consisting of a combined small set of genes was able to distinguish between mutant and wild-type samples with high accuracy. This result suggests that Mecp2 deficiency leads to subtle gene expression changes in mutant brains which may be associated with the phenotypic changes observed. R ett syndrome (RTT) is a common, severe mental retardation disorder affecting mainly females (incidence 1͞20,000-1͞ 15,000; Online Mendelian Inheritance in Man no. 312750; ref. 1). Behavioral findings include developmental stagnation after 7-18 months, ataxia, stereotyped hand-wringing motions, and autism (2). Microcephaly of affected girls has been reported (2-5), and histological findings include reduced neuron size (6). Mutation of the MECP2 gene was found in most cases of RTT studied (7-10). The MECP2 gene encodes a methyl-CpGbinding protein which is thought to bind specifically to methylated CpG dinucleotides (11) and to act as a transcriptional repressor by virtue of its interaction with a histone deacetylase͞ Sin3 complex (12, 13). The involvement of the Mecp2 gene product in methylation-specific transcriptional repression suggests that RTT may be a result of misregulated gene expression. Because the prevailing model (based on biochemical evidence) suggests that Mecp2 acts as a global transcriptional repressor, it would predict that Mecp2 deficiency should result in widespread gene derepression. Mice deficient for Mecp2 were generated by targeted mutagenesis (14, 15) and found to exhibit phenotypic similarities to RTT. Importantly, the specific deletion of Mecp2 in the brain (by using a Nestin-Cre;Mecp2 2lox conditional allele) mimicked the germline loss of Mecp2 (14, 15), indicating that Mecp2 is exclusively required for proper central nervous system function. Furthermore, it was shown that deletion of Mecp2 in postmitotic neurons (using a calmodulin kinase promoter-driven Cre recombinase) also mirrored the Rett phenotype, although with later onset ( ). These results suggest that the Rett-like phenotype is not caused by a defect in early development, but rather is caused by dysfunction of postmitotic, differentiated neurons. In this work, we tested the hypothesis that Mecp2 deficiency results in a widespread alteration of transcription by performing global transcriptional profiling of brain tissue from Mecp2 wild-type and mutant (14) mice by using oligonucleotide microarrays. The goal was to identify genes associated with the disease state, and, possibly, to identify genes whose expression may be regulated directly by Mecp2. Our results suggest that Mecp2 deficiency does not lead to global alterations in transcription but instead leads to subtle changes of gene expression that are only detectable by sensitive statistical analysis of relatively large datasets.
Cell, Sep 1, 2005
The transcription factors OCT4, SOX2, and NANOG have essential roles in early development and are... more The transcription factors OCT4, SOX2, and NANOG have essential roles in early development and are required for the propagation of undifferentiated embryonic stem (ES) cells in culture. To gain insights into transcriptional regulation of human ES cells, we have identified OCT4, SOX2, and NANOG target genes using genome-scale location analysis. We found, surprisingly, that OCT4, SOX2, and NANOG co-occupy a substantial portion of their target genes. These target genes frequently encode transcription factors, many of which are developmentally important homeodomain proteins. Our data also indicate that OCT4, SOX2, and NANOG collaborate to form regulatory circuitry consisting of autoregulatory and feedforward loops. These results provide new insights into the transcriptional regulation of stem cells and reveal how OCT4, SOX2, and NANOG contribute to pluripotency and self-renewal.
Molecular and Cellular Biology, Oct 1, 1991
The Movl3 mouse strain carries a mutation in the otl(I) procollagen gene which is due to the inse... more The Movl3 mouse strain carries a mutation in the otl(I) procollagen gene which is due to the insertion of a Moloney murine leukemia provirus into the first intron. This insertion results in the de novo methylation of the provirus and flanking DNA, the alteration of chromatin structure, and the transcriptional inactivity of the collagen promoter. To address the mechanism of mutagenesis, we reintroduced a cloned and therefore demethylated version of the Movl3 mutant allele into mouse fibroblasts. The transfected gene was not transcribed, indicating that the transcriptional defect was not due to the hypermethylation. Rather, this result strongly suggests that the mutation is due to the displacement or disruption of cis-acting regulatory DNA sequences within the first intron. We also constructed a Movl3 variant allele containing a single long terminal repeat instead of the whole provirus. This construct also failed to express mRNA, indicating that the Movl3 mutation does not revert by provirus excision as has been observed for other retrovirus-induced mutations.
Frontiers in Immunology, Dec 7, 2023
Developing effective vaccines against viral infections have significant impacts on development, p... more Developing effective vaccines against viral infections have significant impacts on development, prosperity and well-being of human populations. Thus, successful vaccines such as smallpox and polio vaccines, have promoted global societal well-being. In contrast, ineffective vaccines may fuel arguments that retard scientific progress. We aim to stimulate a multilevel discussion on how to develop effective vaccines against recent and future pandemics by focusing on acquired immunodeficiency syndrome (AIDS), coronavirus disease (COVID) and other viral infections. We appeal to harnessing recent achievements in this field specifically towards a cure for current pandemics and prevention of the next pandemics. Among these, we propose to apply the HIV DNA in chromatin format an end product of aborted HIV integration in episomal forms, i.e., the chromatin vaccines (cVacc), to elicit the epigenetic silencing and memory that prevent viral replication and infection.
Cell, Apr 1, 2008
Pluripotent cells can be derived from fibroblasts by ectopic expression of defined transcription ... more Pluripotent cells can be derived from fibroblasts by ectopic expression of defined transcription factors. A fundamental unresolved question is whether terminally differentiated cells can be reprogrammed to pluripotency. We utilized transgenic and inducible expression of four transcription factors (Oct4, Sox2, Klf4, and c-Myc) to reprogram mouse B lymphocytes. These factors were sufficient to convert nonterminally differentiated B cells to a pluripotent state. However, reprogramming of mature B cells required additional interruption with the transcriptional state maintaining B cell identity by either ectopic expression of the myeloid transcription factor CCAAT/enhancer-binding-protein-a (C/EBPa) or specific knockdown of the B cell transcription factor Pax5. Multiple iPS lines were clonally derived from both nonfully and fully differentiated B lymphocytes, which gave rise to adult chimeras with germline contribution, and to late-term embryos when injected into tetraploid blastocysts. Our study provides definite proof for the direct nuclear reprogramming of terminally differentiated adult cells to pluripotency.
Journal of Visualized Experiments, Sep 30, 2010
Lymphocytes, such as T cells, undergo genetic V(D)J recombination, to generate a receptor with a ... more Lymphocytes, such as T cells, undergo genetic V(D)J recombination, to generate a receptor with a certain specificity 1. Mice transgenic for a rearranged antigen-specific T cell receptor (TCR) have been an indispensable tool to study T cell development and function. However, such TCRs are usually isolated from the relevant T cells after long-term culture often following repeated antigen stimulation, which unavoidably selects for T cells with high affinity. Random genomic integration of the TCR α-and β-chain and expression from non-endogenous promoters can lead to variations in expression level and kinetics. Epigenetic reprogramming via somatic cell nuclear transfer provides a tool to generate embryonic stem cells and mice from any cell of interest. Consequently, when SCNT is applied to T cells of known specificity, these genetic V(D)J rearrangements are transferred to the SCNT-embryonic stem cells (ESCs) and the mice derived from them, while epigenetic marks are reset. We have demonstrated that T cells with pre-defined specificities against Toxoplasma gondii can be used to generate mouse models that express the specific TCR from their endogenous loci, without experimentally introduced genetic modification. The relative ease and speed with which such transnuclear models can be obtained holds promise for the construction of other disease models.
Parkinson’s disease (PD) is characterized by the aggregation of α-synuclein into Lewy bodies and ... more Parkinson’s disease (PD) is characterized by the aggregation of α-synuclein into Lewy bodies and Lewy neurites in the brain. Microglia-driven neuroinflammation may contribute to neuronal death in PD, however the exact role of microglia remains unclear and has been understudied. The A53T mutation in the gene coding for α-synuclein has been linked to early-onset PD, and exposure to A53T-mutant human α-synuclein increases the potential for inflammation of murine microglia. To date, its effect has not been studied in human microglia. Here, we used 2-dimensional cultures of human iPSC-derived microglia and transplantation of these cells into the mouse brain to assess the effects of the A53T mutation on human microglia. We found that A53T-mutant human microglia had an intrinsically increased propensity towards pro-inflammatory activation upon inflammatory stimulus. Additionally, A53T mutant microglia showed a strong decrease in catalase expression in non-inflammatory conditions, and incre...
SummaryAlthough respiratory symptoms are the most prevalent disease manifestation of infection by... more SummaryAlthough respiratory symptoms are the most prevalent disease manifestation of infection by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), nearly 20% of hospitalized patients are at risk for thromboembolic events1. This prothrombotic state is considered a key factor in the increased risk of stroke, which has been observed clinically during both acute infection and long after symptoms have cleared2. Here we developed a model of SARS-CoV-2 infection using human-induced pluripotent stem cell-derived endothelial cells, pericytes, and smooth muscle cells to recapitulate the vascular pathology associated with SARS-CoV-2 exposure. Our results demonstrate that perivascular cells, particularly smooth muscle cells (SMCs), are a specifically susceptible vascular target for SARS-CoV-2 infection. Utilizing RNA sequencing, we characterized the transcriptomic changes accompanying SARS-CoV-2 infection of SMCs, and endothelial cells (ECs). We observed that infected human SMCs sh...
Studies on the function of Methyl CpG binding protein 2 (MECP2) and the consequence ofMECP2defici... more Studies on the function of Methyl CpG binding protein 2 (MECP2) and the consequence ofMECP2deficiency and duplication have largely focused on neurons. The function of MECP2 in human glia, along with the comprehensive understanding of glial function in neurodevelopmental disorders, is much less understood. Using female and male human embryonic stem cell (hESC) lines to modelMECP2loss-of-function (LOF) in Rett Syndrome (RTT) in the developing brain, we investigated the molecular underpinnings of astrocyte (AST) development and dysfunction, and the mechanisms by which AST contribute to neuronal activity. Here we show that hESC-derived RTT ASTs have fewer mitochondria yet similar levels of reactive oxygen species compared to isogenic controls (CTR). We identified significantly diminished mitochondrial respiration that was compensated by increased glycolysis, and that the molecular mechanism behind mitochondrial dysfunction were reduced key proteins around the tricarboxylic acid (TCA) cy...
ABSTRACTSARS-CoV-2 sequences can be reverse-transcribed and integrated into the genomes of virus-... more ABSTRACTSARS-CoV-2 sequences can be reverse-transcribed and integrated into the genomes of virus-infected cells by a LINE1-mediated retrotransposition mechanism. Whole genome sequencing (WGS) methods detected retrotransposed SARS-CoV-2 subgenomic sequences in virus-infected cells overexpressing LINE1, while an enrichment method (TagMap) identified retrotranspositions in cells that did not overexpress LINE1. LINE1 overexpression increased retrotranspositions about 1,000-fold as compared to non-overexpressing cells. Nanopore WGS can directly recover retrotransposed viral and flanking host sequences but its sensitivity depends on the depth of sequencing (a typical 20-fold sequencing depth would only examine 10 diploid cell equivalents). In contrast, TagMap enriches for the host-virus junctions and can interrogate up to 20,000 cells and is able to detect rare viral retrotranspositions in LINE1 non-overexpressing cells. Although Nanopore WGS is 10 – 20-fold more sensitive per tested cell...
Nature Communications
Insulin receptor (IR) signaling is central to normal metabolic control and is dysregulated in met... more Insulin receptor (IR) signaling is central to normal metabolic control and is dysregulated in metabolic diseases such as type 2 diabetes. We report here that IR is incorporated into dynamic clusters at the plasma membrane, in the cytoplasm and in the nucleus of human hepatocytes and adipocytes. Insulin stimulation promotes further incorporation of IR into these dynamic clusters in insulin-sensitive cells but not in insulin-resistant cells, where both IR accumulation and dynamic behavior are reduced. Treatment of insulin-resistant cells with metformin, a first-line drug used to treat type 2 diabetes, can rescue IR accumulation and the dynamic behavior of these clusters. This rescue is associated with metformin’s role in reducing reactive oxygen species that interfere with normal dynamics. These results indicate that changes in the physico-mechanical features of IR clusters contribute to insulin resistance and have implications for improved therapeutic approaches.
Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by loss-of-function heteroz... more Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by loss-of-function heterozygous mutations of Methyl CpG-binding Protein 2 (MECP2) on the X chromosome in girls. Reactivation of the silent wild-type MECP2 allele from the inactive X chromosome (Xi) represents a promising therapeutic opportunity for female patients with RTT. Here, we applied a multiplex epigenome editing approach to reactivate MECP2 from Xi in RTT human embryonic stem cells (hESCs) and derived neurons. Demethylation of the MECP2 promoter by dCas9-Tet1 with target sgRNA reactivated MECP2 from Xi in RTT hESCs without detectable off-target effects at the transcriptome level. Neurons derived from methylation-edited RTT hESCs maintained MECP2 reactivation and reversed the smaller soma size and electrophysiological abnormalities. In RTT neurons, insulation of the methylation edited MECP2 locus by dCpf1-CTCF with target CRISPR RNA enhanced MECP2 reactivation and rescued RTT-related neuronal defects, prov...
ABSTRACTIntracellular inclusions accompanying neurodegeneration are histopathologically and ultra... more ABSTRACTIntracellular inclusions accompanying neurodegeneration are histopathologically and ultrastructurally heterogeneous but the significance of this heterogeneity is unclear. iPSC models, while promising for disease modeling, do not form inclusions in a reasonable timeframe and suffer from limited tractability. Here, we developed an iPSC toolbox utilizing piggyBac-based or targeted transgenes to rapidly induce CNS cells with concomitant expression of aggregation-prone proteins. This system is amenable to screening and longitudinal tracking at single-cell and single-inclusion resolution. For proof-of-principle, cortical neuron α-synuclein “inclusionopathy” models were engineered to form inclusions through exogenous seeding or α-synuclein mutation. These models recapitulated known fibril- and lipid-rich inclusion subtypes, uncovering dynamic interactions between them, and refined the classification of inclusions in postmortem brain. Genetic-modifier and protein-interaction screens...
Frontiers in Virology
Coronaviruses have been responsible for severe outbreaks worldwide over the past 20 years. Most r... more Coronaviruses have been responsible for severe outbreaks worldwide over the past 20 years. Most recently, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus was responsible for a global pandemic leading to over 500 million documented cases and over 6 million deaths as of May 2022 (1). Although the primary symptoms of SARS-CoV-2 infection are associated with the respiratory system, there is increasing evidence that severe infection is also associated with neurological complications. Over one third of patients diagnosed with SAR-CoV-2 experience neurological symptoms including stroke, headache, fatigue, impairment of consciousness, myalgia, seizures, smell impairment and taste impairment (2-4). The cause of the neurological symptoms remains unknown. Damage to neuronal axons in the central nervous system (CNS) can cause headaches, fatigue, nausea, and disorientation (5, 6). In addition, axonal damage is associated with the development of several neurodegenerative diseases including multiple sclerosis (MS), Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's disease (7-9). The overlap in the symptoms of axonal damage and the neurological symptoms associated with severe SARS-CoV-2 infection led to the hypothesis that SARS-CoV-2 infection may result in axonal damage (10, 11). In support of this hypothesis serum levels of neurofilament light chain (NfL), a highly specific biomarker of axonal damage, are elevated in in SARS-CoV-2 infected patients. Coronaviruses, including Middle Eastern Respiratory (MERS), SARS-CoV and SARS-CoV-2, activate the cellular kinases p38-MAPK and Casein kinase 2 (CK2) (12-20). Inhibition of these kinases during infection reduces viral replication suggesting that these kinases are specifically targeted by the virus to promote infection (16, 19). Aberrant activation of both p38-MAPK and CK2 can induce axonal damage through the disruption of axonal transport (21-25). In this opinion piece we discuss a possible role Frontiers in Virology frontiersin.org 01
Adipocytes are key regulatory cells of human metabolism, and their dysfunction in insulin signali... more Adipocytes are key regulatory cells of human metabolism, and their dysfunction in insulin signaling is central to metabolic diseases such as type II diabetes mellitus (T2D). However, the progression of insulin resistance that leads to T2D is still poorly understood. This limited understanding is due, in part, to the dearth of suitable models of insulin signaling in human adipocytes. Traditionally, in vitro adipocyte models fail to recapitulate in vivo insulin signaling, possibly due to exposure to supraphysiological nutrient and hormone conditions. Here, we have developed a sensitization protocol for human pluripotent stem cell-derived adipocytes that uses physiologically relevant nutrient conditions to produce a potent signaling response comparable to in vivo adipocytes. After systematically optimizing conditions, this protocol allows for robust insulin-stimulated glucose uptake and transcriptional insulin response. Furthermore, exposure of these sensitized adipocytes to physiologi...
Genome Biology, 2021
Gurumurthy et al. [1] recently reported that a method developed by Yang et al. to generate floxed... more Gurumurthy et al. [1] recently reported that a method developed by Yang et al. to generate floxed allele (designated as "two donor method" by Gurumurthy et al.) [2] had poor reproducibility. They claimed that three centers could not reproduce our results on generating conditional alleles of the Mecp2 locus and that the "two-donor method" had very low success rate on other loci. Here, we provide our responses to these claims:
SUMMARYImmunotherapy for patients with neuroblastoma has met with limited success, partly due to ... more SUMMARYImmunotherapy for patients with neuroblastoma has met with limited success, partly due to an incomplete understanding of the mechanisms underlying immune responsiveness in this clinically and genetically heterogenic tumor. Here, we undertook an unbiased analysis using dimension reduction and UMAP visualization of transcriptional signatures derived from 498 primary neuroblastoma tumors. Four distinct clusters based on differentially expressed genes emerged, of which one, representing about 30% and comprising mainly of MYCN-nonamplified tumors, was notable for the high expression of genes associated with both immune response activation and suppression. This capacity to elicit a productive immune response resided exclusively in tumors with dominant populations of undifferentiated, neural crest-like or mesenchymal cells; by contrast, tumors comprising primarily of committed, adrenergic neuron-like cells were less immunogenic. Mesenchymal neuroblastoma cells were enriched for inna...
Development, 1991
The pigment cells of the skin are derived from melanoblasts which originate in the neural crest. ... more The pigment cells of the skin are derived from melanoblasts which originate in the neural crest. The dorsoventral migration of melanoblasts has been visualized in pigment stripes seen in aggregation chimeras, and the width of these bands has suggested that the entire pigmentation of the coat is derived from a small number of founder cells. We have generated mosaic mice by marking single melanoblasts in utero to gain information on the clonal history of pigment-forming cells. A retroviral vector carrying the human tyrosinase gene was constructed and microinjected into neurulating albino mouse embryos. Albino mice are devoid of pigmentation due to deficiency of tyrosinase. Thus, transduction of the wild-type gene into the otherwise normal melanoblasts should rescue the mutant phenotype, giving rise to patches of pigmentation, which correspond to the area colonized by the mitotic progeny of a marked clone. Mosaic animals derived from the injected embryos indeed showed pigmented bands w...
Development, 1996
A mutation was targeted to the murine α3 integrin gene. Homozygous mutant mice survived to birth,... more A mutation was targeted to the murine α3 integrin gene. Homozygous mutant mice survived to birth, but died during the neonatal period. The mutation caused abnormal kidney and lung development. Mutant kidneys displayed decreased branching of the medullary collecting ducts, although the number of nephrons was not altered. Proximal tubules exhibited two distinct subsets of abnormalities, with the epithelial cells either containing excess lysosomes or becoming microcystic. In addition, glomerular development was markedly affected. In mutant kidneys, the extent of branching of glomerular capillary loops was decreased, with capillary lumina being wider than normal. The glomerular basement membrane was disorganized and glomerular podocytes were unable to form mature foot processes. Branching of the bronchi in lungs of mutant mice was also decreased and the large bronchi extended to the periphery. These results indicate a role for integrin receptors in basement membrane organization and bra...
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Papers by Rudolf Jaenisch