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1.  Polymorphisms Near TBX5 and GDF7 Are Associated With Increased Risk for Barrett’s Esophagus 
Palles, Claire | Chegwidden, Laura | Li, Xinzhong | Findlay, John M. | Farnham, Garry | Castro Giner, Francesc | Peppelenbosch, Maikel P. | Kovac, Michal | Adams, Claire L. | Prenen, Hans | Briggs, Sarah | Harrison, Rebecca | Sanders, Scott | MacDonald, David | Haigh, Chris | Tucker, Art | Love, Sharon | Nanji, Manoj | deCaestecker, John | Ferry, David | Rathbone, Barrie | Hapeshi, Julie | Barr, Hugh | Moayyedi, Paul | Watson, Peter | Zietek, Barbara | Maroo, Neera | Gay, Laura | Underwood, Tim | Boulter, Lisa | McMurtry, Hugh | Monk, David | Patel, Praful | Ragunath, Krish | Al Dulaimi, David | Murray, Iain | Koss, Konrad | Veitch, Andrew | Trudgill, Nigel | Nwokolo, Chuka | Rembacken, Bjorn | Atherfold, Paul | Green, Elaine | Ang, Yeng | Kuipers, Ernst J. | Chow, Wu | Paterson, Stuart | Kadri, Sudarshan | Beales, Ian | Grimley, Charles | Mullins, Paul | Beckett, Conrad | Farrant, Mark | Dixon, Andrew | Kelly, Sean | Johnson, Matthew | Wajed, Shahjehan | Dhar, Anjan | Sawyer, Elinor | Roylance, Rebecca | Onstad, Lynn | Gammon, Marilie D. | Corley, Douglas A. | Shaheen, Nicholas J. | Bird, Nigel C. | Hardie, Laura J. | Reid, Brian J. | Ye, Weimin | Liu, Geoffrey | Romero, Yvonne | Bernstein, Leslie | Wu, Anna H. | Casson, Alan G. | Fitzgerald, Rebecca | Whiteman, David C. | Risch, Harvey A. | Levine, David M. | Vaughan, Tom L. | Verhaar, Auke P. | van den Brande, Jan | Toxopeus, Eelke L. | Spaander, Manon C. | Wijnhoven, Bas P.L. | van der Laan, Luc J.W. | Krishnadath, Kausilia | Wijmenga, Cisca | Trynka, Gosia | McManus, Ross | Reynolds, John V. | O’Sullivan, Jacintha | MacMathuna, Padraic | McGarrigle, Sarah A. | Kelleher, Dermot | Vermeire, Severine | Cleynen, Isabelle | Bisschops, Raf | Tomlinson, Ian | Jankowski, Janusz
Gastroenterology  2015;148(2):367-378.
Background & Aims
Barrett's esophagus (BE) increases the risk of esophageal adenocarcinoma (EAC). We found the risk to be BE has been associated with single nucleotide polymorphisms (SNPs) on chromosome 6p21 (within the HLA region) and on 16q23, where the closest protein-coding gene is FOXF1. Subsequently, the Barrett's and Esophageal Adenocarcinoma Consortium (BEACON) identified risk loci for BE and esophageal adenocarcinoma near CRTC1 and BARX1, and within 100 kb of FOXP1. We aimed to identify further SNPs that increased BE risk and to validate previously reported associations.
Methods
We performed a genome-wide association study (GWAS) to identify variants associated with BE and further analyzed promising variants identified by BEACON by genotyping 10,158 patients with BE and 21,062 controls.
Results
We identified 2 SNPs not previously associated with BE: rs3072 (2p24.1; odds ratio [OR] = 1.14; 95% CI: 1.09–1.18; P = 1.8 × 10−11) and rs2701108 (12q24.21; OR = 0.90; 95% CI: 0.86–0.93; P = 7.5 × 10−9). The closest protein-coding genes were respectively GDF7 (rs3072), which encodes a ligand in the bone morphogenetic protein pathway, and TBX5 (rs2701108), which encodes a transcription factor that regulates esophageal and cardiac development. Our data also supported in BE cases 3 risk SNPs identified by BEACON (rs2687201, rs11789015, and rs10423674). Meta-analysis of all data identified another SNP associated with BE and esophageal adenocarcinoma: rs3784262, within ALDH1A2 (OR = 0.90; 95% CI: 0.87–0.93; P = 3.72 × 10−9).
Conclusions
We identified 2 loci associated with risk of BE and provided data to support a further locus. The genes we found to be associated with risk for BE encode transcription factors involved in thoracic, diaphragmatic, and esophageal development or proteins involved in the inflammatory response.
doi:10.1053/j.gastro.2014.10.041
PMCID: PMC4315134  PMID: 25447851
EAC; Intestinal Metaplasia; Susceptibility; Cancer; ASE, allele-specific expression; BE, Barrett’s esophagus; BEACON, Barrett's and Esophageal Adenocarcinoma Consortium; CI, confidence interval; EAC, esophageal adenocarcinoma; eQTL, expression quantitative trait locus; GWAS, genome-wide association study; LD, linkage disequilibrium; OR, odds ratio; PC, principal component; SNP, single nucleotide polymorphism; TCGA, The Cancer Genome Atlas
2.  Long-Term Culture of Genome-Stable Bipotent Stem Cells from Adult Human Liver 
Cell  2015;160(1-2):299-312.
Summary
Despite the enormous replication potential of the human liver, there are currently no culture systems available that sustain hepatocyte replication and/or function in vitro. We have shown previously that single mouse Lgr5+ liver stem cells can be expanded as epithelial organoids in vitro and can be differentiated into functional hepatocytes in vitro and in vivo. We now describe conditions allowing long-term expansion of adult bile duct-derived bipotent progenitor cells from human liver. The expanded cells are highly stable at the chromosome and structural level, while single base changes occur at very low rates. The cells can readily be converted into functional hepatocytes in vitro and upon transplantation in vivo. Organoids from α1-antitrypsin deficiency and Alagille syndrome patients mirror the in vivo pathology. Clonal long-term expansion of primary adult liver stem cells opens up experimental avenues for disease modeling, toxicology studies, regenerative medicine, and gene therapy.
Graphical Abstract
Highlights
•Establishment of a long-term human liver organoid culture•Human liver stem cells retain genetic stability after long-term expansion•Liver organoid cultures differentiate to functional hepatocytes in vitro and in vivo•Organoids derived from patients with genetic disorders model liver disease in vitro
A culture system that allows long-term expansion of human liver can be used to model and study various human diseases.
doi:10.1016/j.cell.2014.11.050
PMCID: PMC4313365  PMID: 25533785
3.  Tumor promotion through the mesenchymal stem cell compartment in human hepatocellular carcinoma 
Carcinogenesis  2013;34(10):2330-2340.
Although the infiltration of mesenchymal stem (stromal) cells (MSCs) into different tumors is widely recognized in animal models, the question whether these MSCs have a positive or negative effect on disease progression remains unanswered. The aim of this study is to investigate whether human hepatocellular carcinoma (HCC) harbors MSCs and whether these MSCs affect tumor growth. We observed that cells capable of differentiation into both adipocyte and osteocyte lineages and expressing MSC markers can be cultured from surgically resected HCC tissues. In situ staining of human HCC tissues with a STRO-1 antibody showed that the tumor and tumor-stromal region are significantly enriched with candidate MSCs compared with adjacent tissue (n = 12, P < 0.01). In mice, coengraftment of a human HCC cell line (Huh7) with MSCs resulted in substantially larger tumors compared with paired engraftment of Huh7 alone (n = 8, P < 0.01). Consistently, coculturing Huh7 with irradiated MSCs significantly increased the number and the size of colonies formed. This enhancement of Huh7 colony formation was also observed by treatment of MSC-conditioned medium (MSC-CM), suggesting that secreted trophic factors contribute to the growth-promoting effects. Genome-wide gene expression array and pathway analysis confirmed the upregulation of cell growth and proliferation-related processes and downregulation of cell death-related pathways by treatment of MSC-CM in Huh7 cells. In conclusion, these results show that MSCs are enriched in human HCC tumor compartment and could exert trophic effects on tumor cells. Thus, targeting of HCC tumor MSCs may represent a new avenue for therapeutic intervention.
doi:10.1093/carcin/bgt210
PMCID: PMC3786382  PMID: 23740837
4.  Detailed Kinetics of the Direct Allo-Response in Human Liver Transplant Recipients: New Insights from an Optimized Assay 
PLoS ONE  2010;5(12):e14452.
Conventional assays for quantification of allo-reactive T-cell precursor frequencies (PF) are relatively insensitive. We present a robust assay for quantification of PF of T-cells with direct donor-specificity, and establish the kinetics of circulating donor-specific T cells after liver transplantation (LTx). B cells from donor splenocytes were differentiated into professional antigen-presenting cells by CD40-engagement (CD40-B cells). CFSE-labelled PBMC from LTx-recipients obtained before and at several time points after LTx, were stimulated with donor-derived or 3rd party CD40-B cells. PF of donor-specific T cells were calculated from CFSE-dilution patterns, and intracellular IFN-γ was determined after re-stimulation with CD40-B cells. Compared to splenocytes, stimulations with CD40-B cells resulted in 3 to 5-fold higher responding T-cell PF. Memory and naïve T-cell subsets responded equally to allogeneic CD40-B cell stimulation. Donor-specific CD4+ and CD8+ T-cell PF ranged from 0.5 to 19% (median: 5.2%). One week after LTx, PF of circulating donor-specific CD4+ and CD8+ T cells increased significantly, while only a minor increase in numbers of T cells reacting to 3rd party allo-antigens was observed. One year after LTx numbers of CD4+ and CD8+ T cells reacting to donor antigens, as well as those reacting to 3rd party allo-antigens, were slightly lower compared to pre-transplant values. Moreover, CD4+ and CD8+ T cells responding to donor-derived, as well as those reacting to 3rd party CD40-B cells, produced less IFN-γ. In conclusion, our alternative approach enables detection of allo-reactive human T cells at high frequencies, and after application we conclude that donor-specific T-cell PF increase immediately after LTx. However, no evidence for a specific loss of circulating T-cells recognizing donor allo-antigens via the direct pathway up to 1 year after LTx was obtained, underscoring the relative insensitiveness of previous assays.
doi:10.1371/journal.pone.0014452
PMCID: PMC3012075  PMID: 21206923
5.  Combined antiviral activity of interferon-α and RNA interference directed against hepatitis C without affecting vector delivery and gene silencing 
The current standard interferon-alpha (IFN-α)-based therapy for chronic hepatitis C virus (HCV) infection is only effective in approximately half of the patients, prompting the need for alternative treatments. RNA interference (RNAi) represents novel approach to combat HCV by sequence-specific targeting of viral or host factors involved in infection. Monotherapy of RNAi, however, may lead to therapeutic resistance by mutational escape of the virus. Here, we proposed that combining lentiviral vector-mediated RNAi and IFN-α could be more effective and avoid therapeutic resistance. In this study, we found that IFN-α treatment did not interfere with RNAi-mediated gene silencing. RNAi and IFN-α act independently on HCV replication showing combined antiviral activity when used simultaneously or sequentially. Transduction of mouse hepatocytes in vivo and in vitro was not effected by IFN-α treatment. In conclusion, RNAi and IFN-α can be effectively combined without cross-interference and may represent a promising combinational strategy for the treatment of hepatitis C.
doi:10.1007/s00109-009-0470-3
PMCID: PMC2700866  PMID: 19404587
RNAi; IFN-α; Gene therapy; Lentiviral vector; HCV
6.  Porcine Endogenous Retrovirus Infects but Does Not Replicate in Nonhuman Primate Primary Cells and Cell Lines 
Journal of Virology  2002;76(22):11312-11320.
Porcine endogenous retroviruses (PERV) can infect human cell lines in vitro; hence, there is a presumed risk of viral exposure to a recipient when pig cells are transplanted into humans (xenotransplantation). Nonhuman primates (NHP) are considered a potential permissive animal model to study the risk of in vivo infection of PERV after xenotransplantation. We set out to determine whether PERV can infect and replicate in NHP primary cells or established cell lines from African green monkey, rhesus macaque, and baboon. We confirm that the NHP cell lines under investigation were infected with PERV as measured by detection of viral DNA and RNA by PCR and reverse transcription (RT)-PCR, respectively, indicating that a functional receptor must be present on the cell surface. However, the load of detectable viral DNA in infected NHP cells declined over time, and the cells never had detectable reverse transcriptase activity. Utilizing quantitative real-time TaqMan PCR we found detectable levels of unintegrated DNA intermediates, but the levels were approximately 100-fold lower compared to HEK 293 cells infected with PERV. Virions released from infected NHP cells could productively infect naïve human cell lines, HEK 293 and HeLa, as shown by RT-PCR and RT assay. However, naïve NHP cells remained negative in RT-PCR and RT assay after exposure to virions from infected NHP cells. Together our data demonstrate that NHP cells are not permissive to productive replication by PERV, presumably due to inefficient cell entry and replication. In light of these observations, the appropriateness of NHP as suitable animal models to study PERV infection in vivo needs to be reevaluated.
doi:10.1128/JVI.76.22.11312-11320.2002
PMCID: PMC136785  PMID: 12388691

Results 1-6 (6)