Cathy Browne

Efficient, Long Term Production of Monocyte-Derived Macrophages from Human Pluripotent Stem Cells under Partly-Defined and Fully-Defined Conditions

Human macrophages are specialised hosts for HIV-1, dengue virus, Leishmania and Mycobacterium tuberculosis. Yet macrophage research is hampered by lack of appropriate cell models for modelling infection by these human pathogens, because available myeloid cell lines are, by definition, not terminally differentiated like tissue macrophages. We describe here a method for deriving monocytes and macrophages from human Pluripotent Stem Cells which improves on previously published protocols in that it uses entirely defined, feeder- and serum-free culture conditions and produces very consistent, pure, high yields across both human Embryonic Stem Cell (hESC) and multiple human induced Pluripotent Stem Cell (hiPSC) lines over time periods of up to one year. Cumulatively, up to ∼3×107 monocytes can be harvested per 6-well plate. The monocytes produced are most closely similar to the major blood monocyte (CD14+, CD16low, CD163+). Differentiation with M-CSF produces macrophages that are highly phagocytic, HIV-1-infectable, and upon activation produce a pro-inflammatory cytokine profile similar to blood monocyte-derived macrophages. Macrophages are notoriously hard to genetically manipulate, as they recognise foreign nucleic acids; the lentivector system described here overcomes this, as pluripotent stem cells can be relatively simply genetically manipulated for efficient transgene expression in the differentiated cells, surmounting issues of transgene silencing. Overall, the method we describe here is an efficient, effective, scalable system for the reproducible production and genetic modification of human macrophages, facilitating the interrogation of human macrophage biology.

C9orf72 Hexanucleotide Expansions Are Associated with Altered Endoplasmic Reticulum Calcium Homeostasis and Stress Granule Formation in Induced Pluripotent Stem Cell-Derived Neurons from Patients with Amyotrophic Lateral Sclerosis and Frontotemporal Dementia.

An expanded hexanucleotide repeat in a noncoding region of the C9orf72 gene is a major cause of amyotrophic lateral sclerosis (ALS), accounting for up to 40% of familial cases and 7% of sporadic ALS in European populations. We have generated induced pluripotent stem cells (iPSCs) from fibroblasts of patients carrying C9orf72 hexanucleotide expansions, differentiated these to functional motor and cortical neurons, and performed an extensive phenotypic characterization. In C9orf72 iPSC‐derived motor neurons, decreased cell survival is correlated with dysfunction in Ca2+ homeostasis, reduced levels of the antiapoptotic protein Bcl‐2, increased endoplasmic reticulum (ER) stress, and reduced mitochondrial membrane potential. Furthermore, C9orf72 motor neurons, and also cortical neurons, show evidence of abnormal protein aggregation and stress granule formation. This study is an extensive characterization of iPSC‐derived motor neurons as cellular models of ALS carrying C9orf72 hexanucleotide repeats, which describes a novel pathogenic link between C9orf72 mutations, dysregulation of calcium signaling, and altered proteostasis and provides a potential pharmacological target for the treatment of ALS and the related neurodegenerative disease frontotemporal dementia. Stem Cells 2016;34:2063–2078

Derivation and Functional Analysis of Patient-Specific Induced Pluripotent Stem Cells as an In Vitro Model of Chronic Granulomatous Disease†‡§

Chronic granulomatous disease (CGD) is an inherited disorder of phagocytes in which NADPH oxidase is defective in generating reactive oxygen species. In this study, we reprogrammed three normal unrelated patients fibroblasts (p47phox and gp91phox) to pluripotency by lentiviral transduction with defined pluripotency factors. These induced pluripotent stem cells (iPSC) share the morphological features of human embryonic stem cells, express the key pluripotency factors, and possess high telomerase activity. Furthermore, all the iPSC lines formed embryoid bodies in vitro containing cells originating from all three germ layers and were capable of teratoma formation in vivo. They were isogenic with the original patient fibroblasts, exhibited normal karyotype, and retained the p47phox or gp91phox mutations found in the patient fibroblasts. We further demonstrated that these iPSC could be differentiated into monocytes and macrophages with a similar cytokine profile to blood‐derived macrophages under resting conditions. Most importantly, CGD‐patient‐specific iPSC‐derived macrophages showed normal phagocytic properties but lacked reactive oxygen species production, which correlates with clinical diagnosis of CGD in the patients. Together these results suggest that CGD‐patient‐specific iPSC lines represent an important tool for modeling CGD disease phenotypes, screening candidate drugs, and the development of gene therapy. STEM CELLS 2012; 30:599–611

C9orf72 Hexanucleotide Expansions are Associated with Altered ER Calcium Homeostasis and Stress Granule Formation in iPSC-Derived Neurons from Patients with Amyotrophic Lateral Sclerosis and Frontotemporal Dementia.

An expanded hexanucleotide repeat in a noncoding region of the C9orf72 gene is a major cause of amyotrophic lateral sclerosis (ALS), accounting for up to 40% of familial cases and 7% of sporadic ALS in European populations. We have generated induced pluripotent stem cells (iPSCs) from fibroblasts of patients carrying C9orf72 hexanucleotide expansions, differentiated these to functional motor and cortical neurons, and performed an extensive phenotypic characterization. In C9orf72 iPSC‐derived motor neurons, decreased cell survival is correlated with dysfunction in Ca2+ homeostasis, reduced levels of the antiapoptotic protein Bcl‐2, increased endoplasmic reticulum (ER) stress, and reduced mitochondrial membrane potential. Furthermore, C9orf72 motor neurons, and also cortical neurons, show evidence of abnormal protein aggregation and stress granule formation. This study is an extensive characterization of iPSC‐derived motor neurons as cellular models of ALS carrying C9orf72 hexanucleotide repeats, which describes a novel pathogenic link between C9orf72 mutations, dysregulation of calcium signaling, and altered proteostasis and provides a potential pharmacological target for the treatment of ALS and the related neurodegenerative disease frontotemporal dementia. Stem Cells 2016;34:2063–2078

Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3′-end-seq

Despite the many advantages of Caenorhabditis elegans, biochemical approaches to study tissue-specific gene expression in post-embryonic stages are challenging. Here, we report a novel experimental approach for efficient determination of tissue-specific transcriptomes involving the rapid release and purification of nuclei from major tissues of post-embryonic animals by fluorescence-activated nuclei sorting (FANS), followed by deep sequencing of linearly amplified 3′-end regions of transcripts (3′-end-seq). We employed these approaches to compile the transcriptome of the developed C. elegans intestine and used this to analyse tissue-specific cleavage and polyadenylation. In agreement with intestinal-specific gene expression, highly expressed genes have enriched GATA-elements in their promoter regions and their functional properties are associated with processes that are characteristic for the intestine. We systematically mapped pre-mRNA cleavage and polyadenylation sites, or polyA sites, including more than 3000 sites that have previously not been identified. The detailed analysis of the 3′-ends of the nuclear mRNA revealed widespread alternative polyA site use (APA) in intestinally expressed genes. Importantly, we found that intestinal polyA sites that undergo APA tend to have U-rich and/or A-rich upstream auxiliary elements that may contribute to the regulation of 3′-end formation in the intestine.

The 5'-3' exoribonuclease pacman is required for epithelial sheet sealing in Drosophila and genetically interacts with the phosphatase puckered

Background information. Ribonucleases have been well studied in yeast and bacteria, but their biological significance to developmental processes in multicellular organisms is not well understood. However, there is increasing evidence that specific timed transcript degradation is critical for regulation of many cellular processes, including translational repression, nonsense‐mediated decay and RNA interference. The Drosophila gene pacman is highly homologous to the major yeast exoribonuclease XRN1 and is the only known cytoplasmic 5′–3′ exoribonuclease in eukaryotes. To determine the effects of this exoribonuclease in development we have constructed a number of mutations in pacman by P‐element excision and characterized the resulting phenotypes.

Regulation of transcription termination in the nematode Caenorhabditis elegans

The current predicted mechanisms that describe RNA polymerase II (pol II) transcription termination downstream of protein expressing genes fail to adequately explain, how premature termination is prevented in eukaryotes that possess operon-like structures. Here we address this issue by analysing transcription termination at the end of single protein expressing genes and genes located within operons in the nematode Caenorhabditis elegans. By using a combination of RT-PCR and ChIP analysis we found that pol II generally transcribes up to 1 kb past the poly(A) sites into the 3′ flanking regions of the nematode genes before it terminates. We also show that pol II does not terminate after transcription of internal poly(A) sites in operons. We provide experimental evidence that five randomly chosen C. elegans operons are transcribed as polycistronic pre-mRNAs. Furthermore, we show that cis-splicing of the first intron located in downstream positioned genes in these polycistronic pre-mRNAs is critical for their expression and may play a role in preventing premature pol II transcription termination.

Variant U1 snRNAs are implicated in human pluripotent stem cell maintenance and neuromuscular disease

The U1 small nuclear (sn)RNA (U1) is a multifunctional ncRNA, known for its pivotal role in pre-mRNA splicing and regulation of RNA 3′ end processing events. We recently demonstrated that a new class of human U1-like snRNAs, the variant (v)U1 snRNAs (vU1s), also participate in pre-mRNA processing events. In this study, we show that several human vU1 genes are specifically upregulated in stem cells and participate in the regulation of cell fate decisions. Significantly, ectopic expression of vU1 genes in human skin fibroblasts leads to increases in levels of key pluripotent stem cell mRNA markers, including NANOG and SOX2. These results reveal an important role for vU1s in the control of key regulatory networks orchestrating the transitions between stem cell maintenance and differentiation. Moreover, vU1 expression varies inversely with U1 expression during differentiation and cell re-programming and this pattern of expression is specifically de-regulated in iPSC-derived motor neurons from Spinal Muscular Atrophy (SMA) type 1 patients. Accordingly, we suggest that an imbalance in the vU1/U1 ratio, rather than an overall reduction in Uridyl-rich (U)-snRNAs, may contribute to the specific neuromuscular disease phenotype associated with SMA.

Stem Cell modeling of Mitochondrial Parkinsonism reveals key functions of OPA1.

Defective mitochondrial function attributed to optic atrophy 1 (OPA1) mutations causes primarily optic atrophy and, less commonly, neurodegenerative syndromes. The pathomechanism by which OPA1 mutations trigger diffuse loss of neurons in some, but not all, patients is unknown. Here, we used a tractable induced pluripotent stem cell (iPSC)‐based model to capture the biology of OPA1 haploinsufficiency in cases presenting with classic eye disease versus syndromic parkinsonism.

DERIVATION AND FUNCTIONAL ANALYSIS OF PATIENT SPECIFIC INDUCED PLURIPOTENT STEM CELLS (IPSCS) AS AN IN VITRO MODEL OF CHRONIC GRANULOMATOUS DISEASE

Continued B) In homozygous IGHG diplotypes only one of the two alternative allotypes is expressed, which result in restricted qualities of IgG molecules and B cells. IGHG gene frequencies and the allotypic IgG subclass levels, the activity of the genes, are available for children and adults of healthy Caucasians (Fig. 4). IGHG genes have impact on disease and immunotherapy. The function of IgG is related to the constant part of the heavy γ chains the Fcγ part of the molecule in parallel with the variable adaptive antibody binding site. Different effects of polysaccharide and protein vaccines, with different amounts of specific antibodies were recorded for different IGHG genes. They are also associated to different severity of bacterial and viral infections and can be used as predisposing, prognostic and sometimes carrier markers. The IgG molecules of IGHG genes are differently affected by viruses acting as FcγRs modifying the disease. Suscepetibility/resistence of various infections both bacterial and viral, allergens and tumour antigens are influenced by IGHG genes. The IGHG genes are associated with different phenotypes of allergic, autoimmune, infectious, immunodeficiency and malignt disorders. In treatments with IVIG, the levels of foreign allelic IgG subclasses are recognized and can be followed. This is the ultimate evidence of that the allelic IgG subclasses are unique. IGHG genes and allotypic IgG subclasses are predisposing or prognostic genetic markers in various infections, immunodeficiencies, different phenotypes of allergic disease, autoimmune disorders and malignant diseases. Fig.1Fig. 2Fig.3Fig. 4 29 IMMUNOPHENOTYPING OF B LYMPHOCYTES IN PATIENTS WITH COMMON VARIABLE IMMUNODEFICIENCY (CVID) F. Mazzi, G. Patuzzo, A. Vella, R. Ortolani, A. Barbieri, A. Puccetti, E. Tinazzi, G. Marchi, O.M. Codella, R. Beri, C. Lunardi Department of Medicine, Unit of Autoimmune Diseases, University of Verona, Department of Pathology and Diagnosis, Section of Immunology, University of Verona, Verona, Immunopathology, Institute G. Gaslini and University of Genova, Genova, Italy Introduction: CVID is a primary immunodeficiency characterized by failure of B lymphocytes to differentiate in plasma cells, with deficient immunoglobulin secretion. The identified genetic defects account only for a minority of cases. Objective: The importance of B cells immunophenotyping in the classification of CVID is well known. This procedure can identify some alterations on cell surface molecule expression that could explain the immunological disorder at the basis of CVID. Moreover, some immunophenotipical aspects can correlate with clinical features, severity and prognosis of the disease. Aim: We studied a cohort of 16 patients affected by CVID, to identify alterations of B cells and to find correlations with clinical features. Methods: We studied circulating B cells in patients and controls by flow-cytometry, using a specific panel of antibodies for B cells. Conclusion: We compared the population of “switched memory” IgD-CD27+B lymphocytes, used in the Friburg classification, with the population of IgM-IgDCD23-CD27+B cells, we have analysed. IgM-IgDCD23-CD27+B cells were reduced in patients compared to healthy controls and in patients they were lower than IgD-CD27+B cells. The reduction of these lymphocytes was correlated more tightly than IgDCD27+B cells to lymphoadenopathy, splenomegaly, J Clin Immunol (2012) 32 (Suppl 1):S1–S379