Institute of Clinical Molecular Biology

Kiel, Germany

Institute of Clinical Molecular Biology

Kiel, Germany
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Geismann C.,University of Kiel | Grohmann F.,University of Kiel | Sebens S.,2Institute for Experimental Medicine | Wirths G.,University of Kiel | And 11 more authors.
Cell Death and Disease | Year: 2014

Pancreatic ductal adenocarcinoma (PDAC) represents one of the deadliest malignancies with an overall life expectancy of 6 months despite current therapies. NF-?B signalling has been shown to be critical for this profound cell-autonomous resistance against chemotherapeutic drugs and death receptor-induced apoptosis, but little is known about the role of the c-Rel subunit in solid cancer and PDAC apoptosis control. In the present study, by analysis of genome-wide patterns of c-Rel-dependent gene expression, we were able to establish c-Rel as a critical regulator of tumour necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis in PDAC. TRAIL-resistant cells exhibited a strong TRAIL-inducible NF-?B activity, whereas TRAIL-sensitive cells displayed only a small increase in NF-?B-binding activity. Transfection with siRNA against c-Rel sensitized the TRAIL-resistant cells in a manner comparable to siRNA targeting the p65/RelA subunit. Gel-shift analysis revealed that c-Rel is part of the TRAIL-inducible NF-?B complex in PDAC. Array analysis identified NFATc2 as a c-Rel target gene among the 12 strongest TRAIL-inducible genes in apoptosis-resistant cells. In line, siRNA targeting c-Rel strongly reduced TRAIL-induced NFATc2 activity in TRAIL-resistant PDAC cells. Furthermore, siRNA targeting NFATc2 sensitized these PDAC cells against TRAILinduced apoptosis. Finally, TRAIL-induced expression of COX-2 was diminished through siRNA targeting c-Rel or NFATc2 and pharmacologic inhibition of COX-2 with celecoxib or siRNA targeting COX-2, enhanced TRAIL apoptosis. In conclusion, we were able to delineate a novel c-Rel-, NFATc2- and COX-2-dependent antiapoptotic signalling pathway in PDAC with broad clinical implications for pharmaceutical intervention strategies. © 2014 Macmillan Publishers Limited. All rights reserved.

PubMed | University of Turku, University of Maryland Baltimore County, New York University, University of Bordeaux Segalen and 38 more.
Type: Journal Article | Journal: Kidney international | Year: 2015

Genome-wide association studies (GWASs) have identified multiple loci associated with cross-sectional eGFR, but a systematic genetic analysis of kidney function decline over time is missing. Here we conducted a GWAS meta-analysis among 63,558 participants of European descent, initially from 16 cohorts with serial kidney function measurements within the CKDGen Consortium, followed by independent replication among additional participants from 13 cohorts. In stage 1 GWAS meta-analysis, single-nucleotide polymorphisms (SNPs) at MEOX2, GALNT11, IL1RAP, NPPA, HPCAL1, and CDH23 showed the strongest associations for at least one trait, in addition to the known UMOD locus, which showed genome-wide significance with an annual change in eGFR. In stage 2 meta-analysis, the significant association at UMOD was replicated. Associations at GALNT11 with Rapid Decline (annual eGFR decline of 3ml/min per 1.73m(2) or more), and CDH23 with eGFR change among those with CKD showed significant suggestive evidence of replication. Combined stage 1 and 2 meta-analyses showed significance for UMOD, GALNT11, and CDH23. Morpholino knockdowns of galnt11 and cdh23 in zebrafish embryos each had signs of severe edema 72h after gentamicin treatment compared with controls, but no gross morphological renal abnormalities before gentamicin administration. Thus, our results suggest a role in the deterioration of kidney function for the loci GALNT11 and CDH23, and show that the UMOD locus is significantly associated with kidney function decline.

Basova L.,Saint Petersburg State University | Begum S.,Khulna University | Strahl J.,Alfred Wegener Institute for Polar and Marine Research | Sukhotin A.,Russian Academy of Sciences | And 3 more authors.
Aquatic Biology | Year: 2012

Environmental factors such as temperature and salinity regimes shape lifespan in marine ectotherms. We investigated whether the effect occurs through modification of metabolic reactive oxygen species (ROS)-producing processes and is thus in line with the rate of living-free radical theory of aging. We compared 6 biogeographically and climatically distinct populations of the extremely long-lived ocean quahog Arctica islandica for age-dependent differences in metabolic rates and antioxidant capacities (superoxide dismutase, catalase activity and total glutathione concentration). The temperature and salinity ranges covered by the sampling locations (Norwegian coast, White Sea, Iceland, Kattegat, Kiel Bay and German Bight) were 3.7 to 9.3°C and 20 to 35 ppt. Bivalve shells were used as age recorders by counting annual growth bands. Maximum determined age in different populations varied between 29 and 192 yr. Extreme longevity observed in some North Atlantic A. islandica populations seems to be based on their very low lifetime mass-specific respiration, in combination with stable maintenance of antioxidant protection throughout life in mature specimens. While the antioxidant capacity was similar among all populations, the shorter-lived populations exhibited the highest metabolic rates and showed no metabolic response (Q 10) when warmed to higher temperature. Low and fluctuating salinity in the Baltic may further exert stress, which enhances respiration rates and reduces longevity in the Baltic Sea population. The exceptionally long lifespan of A. islandica cannot be exclusively explained by a well-established antioxidant defense system, and the long lifespan of some populations may rather be a function of low ROS formation (low metabolic rate) and high damage repair/removal capacities. © Inter-Research 2012.

Begum S.,Alfred Wegener Institute for Polar and Marine Research | Basova L.,Saint Petersburg State University | Heilmayer O.,German Aerospace Center | Philipp E.E.R.,Institute of Clinical Molecular Biology | And 2 more authors.
Journal of Shellfish Research | Year: 2010

We compared lifetime and population energy budgets of the extraordinary long-lived ocean quahog Arctica islandica from 6 different sitesthe Norwegian coast, Kattegat, Kiel Bay, White Sea, German Bight, and off northeast Icelandcovering a temperature and salinity gradient of 4-10°C (annual mean) and 2534, respectively. Based on von Bertalanffy growth models and sizemass relationships, we computed organic matter production of body (PSB) and of shell (Pss), whereas gonad production (PG) was estimated from the seasonal cycle in mass. Respiration (R) was computed by a model driven by body mass, temperature, and site. A. islandica populations differed distinctly in maximum life span (40 y in Kiel Bay to 197 y in Iceland), but less in growth performance (φ ranged from 2.41 in the White Sea to 2.65 in Kattegat). Individual lifetime energy throughput, as approximated by assimilation, was highest in Iceland (43,730 kJ) and lowest in the White Sea (313 kJ). Net growth efficiency ranged between 0.251 and 0.348, whereas lifetime energy investment distinctly shifted from somatic to gonad production with increasing life span; Ps/PG decreased from 0.362 (Kiel Bay, 40 y) to 0.031 (Iceland, 197 y). Population annual energy budgets were derived from individual budgets and estimates of population mortality rate (0.035/y in Iceland to 0.173/y in Kiel Bay). Relationships between budget ratios were similar on the population level, albeit with more emphasis on somatic production; Ps/PG/ a ranged from 0.196 (Iceland) to 2.728 (White Sea), and P/B ranged from 0.2030.285/y. Life span is the principal determinant of the relationship between budget parameters, whereas temperature affects net growth efficiency only. In the White Sea population, both growth performance and net growth efficiency of A. islandica were lowest. We presume that low temperature combined with low salinity represent a particularly stressful environment for this species.

News Article | December 21, 2016

Nicholas Volker first developed the symptoms of inflammatory bowel disease (IBD) shortly before his second birthday. Childhood cases of this gut disease are often severe, but even by this standard Nicholas's case was extreme. Over the next three years, his parents and doctors watched, helpless, as wounds opened up on his abdomen and leaked faeces. The doctors could do nothing as treatment after treatment failed, and Nicholas endured sepsis, excruciating pain and more than 100 surgical procedures. In 2009, geneticist Howard Jacob, then at the Medical College of Wisconsin in Milwaukee, and his team sequenced Nicholas's genome in a last-ditch effort to find the cause of his symptoms and, they hoped, save his life. The team discovered that Nicholas had a mutation in the gene XIAP, which had previously been linked to immune deficiency. Doctors performed a cord-blood transplant, giving Nicholas a complement of stem cells that form immune cells with an intact XIAP, and his gut symptoms soon went into remission. His case is frequently touted as the first example of a person cured of any condition as a result of DNA sequencing. Paediatric IBD is thought to be predominantly due to genetic factors. Researchers have identified around 50 genes that, when mutated, can each cause IBD symptoms in young children. Many of these, like XIAP, have also been linked to immune deficiency. In a large number of the youngest patients, IBD can be thought of as a rare, single-gene disorder. In adults, the picture is much more complex — a clean fix is not an option. Over the past 15 years, research into the genetics of IBD has identified around 200 genomic hotspots that influence the risk of Crohn's disease or ulcerative colitis, the two major forms of IBD (see page S98). But so far, this information has had little clinical impact. “These are flags waving towards different regions of the genome,” says Sarah Ennis, who leads the Genomics Informatics Group at the University of Southampton, UK. “But they're not very useful for a consultant sitting with a patient in front of him or her.” These genetic flags have provided clues to the underlying mechanisms of IBD, and revealed surprising subgroups within the IBD spectrum, connections with other conditions and possible drug targets. The challenge now, researchers such as Ennis say, is to apply this knowledge to improve the lives of patients. This challenge is hard to meet, however. In adults, IBD results from a complex mixture of environmental risk factors, which are themselves not fully understood, and genetic factors that have varying impact (see page S100). A clear pattern that has emerged is that the strongest genetic risk factors tend to be specific to either Crohn's disease or ulcerative colitis. These differences provide clues to the mechanisms behind each disease and will hopefully inform new treatment approaches. The biggest player in Crohn's disease is a gene called NOD2, an important part of the innate immune system — the set of non-specific mechanisms that provide the body's first line of defence against infection. NOD2's role was uncovered in 2001, when two independent groups of researchers traced the inheritance of gut problems in families affected by the disease1, 2. “That was the first major insight that came from gene discovery, and that really spurred the next decade of immunological research into Crohn's disease,” says Charlie Lees, a gastroenterologist at the University of Edinburgh, UK. The advance also sparked a surge of research into the genetics of IBD more broadly. Subsequent research confirmed the link between NOD2 and Crohn's disease, but found only a weak association with ulcerative colitis. Autophagy, the process by which cells process and degrade intracellular bacteria and cellular components, has also been implicated only in Crohn's disease. These findings suggest that this condition could be due to an abnormal immune response to microbiota, the community of bacteria that inhabits our guts. For ulcerative colitis, the link seems to be with variations to genes involved in maintaining the integrity and function of the digestive-tract lining, suggesting that this disease might be caused by an inadequate barrier or 'leaky gut'. Variations within a set of genes from the human leukocyte antigen gene family (HLA class II) — which are involved in fine-tuning the immune system and helping it to recognize proteins made by foreign invaders — also make a major contribution to ulcerative-colitis risk, but are only weakly linked with Crohn's disease. This suggests that there might be an external trigger for ulcerative colitis, similar to the role that gluten has in coeliac disease, says Andre Franke, director of the Institute of Clinical Molecular Biology at the University of Kiel in Germany. Genetic investigations are also challenging the idea that IBD can be divided into two main diseases — Crohn's that can affect any part of the digestive tract and ulcerative colitis, which affects only the colon. In January, Lees and colleagues reported that certain genes determine where in the gut IBD causes inflammation, and that the genetic distinction provided a different way to classify IBD3. “What we found was that this disease location separated out IBD much more naturally into three main disease types, rather than just two,” Lees says. “Small-bowel Crohn's disease was as distinct from colonic Crohn's disease as it was from ulcerative colitis.” Curiously, the three-disease classification is how doctors thought of IBD half a century ago, but rather than that system being superseded by an advance in biological understanding, it seems to have steadily drifted out of favour, Lees says. There's still substantial genetic overlap between the three groups, so the analysis is not immediately clinically applicable. But the findings do suggest that simply sorting people into either those with Crohn's disease or those with ulcerative colitis may not be enough to determine the best treatment for them. Because so many genes linked with the immune system have been implicated in IBD, researchers are looking for genetic connections with other inflammatory and autoimmune diseases. About 70% of the genetic loci that contribute to IBD susceptibility are thought to be shared with other complex diseases such as ankylosing spondylitis. Perhaps the most surprising link that genetic studies have thrown up is that between IBD and susceptibility to mycobacteria — a group that includes the pathogens that cause tuberculosis and leprosy. NOD2 and roughly a dozen other genetic factors associated with IBD, particularly Crohn's disease, are also associated with susceptibility to tuberculosis and leprosy. There are two main ideas about the biological mechanisms behind this link. It is possible that certain genetic variants increase susceptibility to leprosy while also increasing the risk of Crohn's disease. “I believe that Crohn's disease is an immunodeficiency,” Franke says. In people who are susceptible to leprosy, the immune system overlooks the bacterium and enables the infection to become established. Similarly, Franke explains, this deficient immune response may permit normal gut bacteria to penetrate the intestinal wall and trigger the inflammation seen in Crohn's disease. Or, the link could run the other way around: some genetic variants might confer resistance to leprosy, but by coincidence increase the risk of Crohn's disease. Support for this hypothesis comes from the fact that some of the variants that increase IBD susceptibility are so widespread — present in 20–50% of people in certain populations — that many scientists think that they must have conferred some evolutionary advantage in the past. Many of these genetic insights into IBD have come from genome-wide association studies (GWAS), which scan the genomes of large numbers of people with the disease and compare certain genetic markers to those of controls. GWAS have been unusually successful in IBD, partly because of the uncommonly large and well-coordinated International Inflammatory Bowel Disease Genetics Consortium. “Around the globe we've got probably hundreds of clinicians contributing their own data sets and samples and patients into these studies,” says Miles Parkes, a gastroenterologist at the University of Cambridge, UK, and a member of the consortium. Some of the largest analyses have involved more than 75,000 patients. GWAS are a powerful approach — a practical way of finding markers for disease risk across the vast human genome — but they do have their downsides. For one, the gene chips (slides containing known sequences that are used to rapidly scan DNA for variations) are based on European genetics. But different ethnic groups are thought to have separate suites of genes that put them at risk. NOD2 variants seem to have little involvement in Japanese and Korean people with Crohn's disease, for instance. And a study of more than 2,300 African Americans with IBD found 2 genetic markers linked to ulcerative colitis that have not been seen in people of European ancestry4. The European chips have complicated efforts to identify the genes that are most important in various ethnic groups. And GWAS for IBD have so far involved a disproportionate number of individuals of European ancestry. Moreover, GWAS simply identify loci — positions in the genome — not the genes themselves, nor the precise mutations involved. On their own, GWAS don't directly illuminate the biological mechanisms behind the disease that might translate into clinical applications. Researchers are making progress in identifying the specific genes that increase the risk of IBD. The pro-inflammatory molecule interleukin-23 (IL-23) and other proteins in its signalling pathway, for example, repeatedly pop up as players in both Crohn's disease and ulcerative colitis. Indeed, several pharmaceutical companies have drug candidates in clinical trials that target the IL-23 pathway. Many of the most promising IBD treatments in the pipeline involve biochemical pathways highlighted by genetics studies, says Parkes. Still, a more comprehensive picture of the specific genes and variants involved is needed to move new treatments for IBD forward. And that picture may be about to develop. The International Inflammatory Bowel Disease Genetics Consortium has recently completed a three-year 'fine-mapping' effort that has pinpointed 45 specific genetic variants that contribute to the disease. The data suggest that some of these variants lie outside the coding and regulatory regions of genes — in parts of the genome that have no known function5. Working out how these variations contribute to disease will be a major challenge, but an exciting one. “There's clearly a huge amount of new biology waiting to be discovered,” Parkes says.

Rivas M.A.,Massachusetts General Hospital | Rivas M.A.,The Broad Institute of MIT and Harvard | Rivas M.A.,University of Oxford | Beaudoin M.,Montreal Heart Institute | And 43 more authors.
Nature Genetics | Year: 2011

More than 1,000 susceptibility loci have been identified through genome-wide association studies (GWAS) of common variants; however, the specific genes and full allelic spectrum of causal variants underlying these findings have not yet been defined. Here we used pooled next-generation sequencing to study 56 genes from regions associated with Crohn's disease in 350 cases and 350 controls. Through follow-up genotyping of 70 rare and low-frequency protein-altering variants in nine independent case-control series (16,054 Crohn's disease cases, 12,153 ulcerative colitis cases and 17,575 healthy controls), we identified four additional independent risk factors in NOD2, two additional protective variants in IL23R, a highly significant association with a protective splice variant in CARD9 (P < 1 × 10 -16, odds ratio ≈ 0.29) and additional associations with coding variants in IL18RAP, CUL2, C1orf106, PTPN22 and MUC19. We extend the results of successful GWAS by identifying new, rare and probably functional variants that could aid functional experiments and predictive models. © 2011 Nature America, Inc. All rights reserved.

Arlt A.,Laboratory of Molecular Gastroenterology and Hepatology | Sebens S.,Institute of Experimental Medicine | Krebs S.,Laboratory of Molecular Gastroenterology and Hepatology | Geismann C.,Laboratory of Molecular Gastroenterology and Hepatology | And 5 more authors.
Oncogene | Year: 2013

Evidence accumulates that the transcription factor nuclear factor E2-related factor 2 (Nrf2) has an essential role in cancer development and chemoresistance, thus pointing to its potential as an anticancer target and undermining its suitability in chemoprevention. Through the induction of cytoprotective and proteasomal genes, Nrf2 confers apoptosis protection in tumor cells, and inhibiting Nrf2 would therefore be an efficient strategy in anticancer therapy. In the present study, pancreatic carcinoma cell lines (Panc1, Colo357 and MiaPaca2) and H6c7 pancreatic duct cells were analyzed for the Nrf2-inhibitory effect of the coffee alkaloid trigonelline (trig), as well as for its impact on Nrf2-dependent proteasome activity and resistance to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and anticancer drug-induced apoptosis. Chemoresistant Panc1 and Colo357 cells exhibit high constitutive Nrf2 activity, whereas chemosensitive MiaPaca2 and H6c7 cells display little basal but strong tert-butylhydroquinone (tBHQ)-inducible Nrf2 activity and drug resistance. Trig efficiently decreased basal and tBHQ-induced Nrf2 activity in all cell lines, an effect relying on a reduced nuclear accumulation of the Nrf2 protein. Along with Nrf2 inhibition, trig blocked the Nrf2-dependent expression of proteasomal genes (for example, s5a/psmd4 and α5/psma5) and reduced proteasome activity in all cell lines tested. These blocking effects were absent after treatment with Nrf2 siRNA, a condition in which proteasomal gene expression and proteasome activity were already decreased, whereas siRNA against the related transcription factor Nrf1 did not affect proteasome activity and the inhibitory effect of trig. Depending on both Nrf2 and proteasomal gene expression, the sensitivity of all cell lines to anticancer drugs and TRAIL-induced apoptosis was enhanced by trig. Moreover, greater antitumor responses toward anticancer drug treatment were observed in tumor-bearing mice when receiving trig. In conclusion, representing an efficient Nrf2 inhibitor capable of blocking Nrf2-dependent proteasome activity and thereby apoptosis protection in pancreatic cancer cells, trig might be beneficial in improving anticancer therapy. © 2013 Macmillan Publishers Limited All rights reserved 0950-9232/13.

Sina C.,Institute of Clinical Molecular Biology | Arlt A.,Laboratory of Molecular Gastroenterology and Hepatology | Gavrilova O.,Institute of Clinical Molecular Biology | Midtling E.,Institute of Clinical Molecular Biology | And 7 more authors.
Inflammatory Bowel Diseases | Year: 2010

Background: Inflammatory bowel diseases (IBDs) result from environmental and genetic factors and are characterized by an imbalanced immune response in the gut and deregulated activation of the transcription factor NF-kB. Addressing the potential role of gly96/iex-1 in the regulation of NF-kB in IBD, we used the dextran sodium sulfate (DSS) colitis model in mice in which the gly96/iex-1 gene had been deleted. Methods: C57BL/6 mice of gly96/iex-1-/- or gly96/iex-1+/+ genotype were treated continuously with 4% DSS (5 days) and repeatedly with 2% DSS (28 days) for inducing acute and chronic colitis, respectively. In addition to clinical and histological exploration, colon organ culture and bone marrow-derived cells (BMCs) were analyzed for chemo/cytokine expression and NF-kB activation. Results: Compared to wildtype littermates, gly96/iex-1-/- mice exhibited an aggravated phenotype of both acute and chronic colitis, along with a greater loss of body weight and colon length. Colonic endoscopy revealed a higher degree of hyperemia, edema, and bleeding in gly96/iex-1-/- mice, and immunohistochemistry detected massive mucosal infiltration of leukocytes and marked histological changes. The expression of proinflammatory chemoand cytokines was higher in the colon of DSS-treated gly96/iex-1-/- mice, and the NF-jB activation was enhanced particularly in the distal colon. In cultured BMCs from gly96/iex-1-/- mice, Pam3Cys4 treatment induced expression of proinflammatory mediators to a higher degree than in gly96/iex-1+/+ BMCs, along with greater NF-kB activation. Conclusions: Based on the observation that genetic ablation of gly96/iex-1 triggers intestinal inflammation in mice, we demonstrate for the first time that gly96/iex-1 exerts strong antiinflammatory activity via its NF-kB-counterregulatory effect. Copyright © 2009 Crohn's & Colitis Foundation of America, Inc.

PubMed | Okinawa Institute of Science and Technology, Leibniz Institute of Marine Science, Genoscope Center National Of Sequencage, Institute of Clinical Molecular Biology and 3 more.
Type: | Journal: eLife | Year: 2015

Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable arsenal of TRGs.

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