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Riordan JD, Nadeau JH. From Peas to Disease: Modifier Genes, Network Resilience, and the Genetics of Health. Am J Hum Genet 2017; 101:177-191. [PMID: 28777930 PMCID: PMC5544383 DOI: 10.1016/j.ajhg.2017.06.004] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Phenotypes are rarely consistent across genetic backgrounds and environments, but instead vary in many ways depending on allelic variants, unlinked genes, epigenetic factors, and environmental exposures. In the extreme, individuals carrying the same causal DNA sequence variant but on different backgrounds can be classified as having distinct conditions. Similarly, some individuals that carry disease alleles are nevertheless healthy despite affected family members in the same environment. These genetic background effects often result from the action of so-called "modifier genes" that modulate the phenotypic manifestation of target genes in an epistatic manner. While complicating the prospects for gene discovery and the feasibility of mechanistic studies, such effects are opportunities to gain a deeper understanding of gene interaction networks that provide organismal form and function as well as resilience to perturbation. Here, we review the principles of modifier genetics and assess progress in studies of modifier genes and their targets in both simple and complex traits. We propose that modifier effects emerge from gene interaction networks whose structure and function vary with genetic background and argue that these effects can be exploited as safe and effective ways to prevent, stabilize, and reverse disease and dysfunction.
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Review |
8 |
100 |
2
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Lim L, Balakrishnan A, Huskey N, Jones KD, Jodari M, Ng R, Song G, Riordan J, Anderton B, Cheung ST, Willenbring H, Dupuy A, Chen X, Brown D, Chang AN, Goga A. MicroRNA-494 within an oncogenic microRNA megacluster regulates G1/S transition in liver tumorigenesis through suppression of mutated in colorectal cancer. Hepatology 2014; 59:202-15. [PMID: 23913442 PMCID: PMC3877416 DOI: 10.1002/hep.26662] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 07/26/2013] [Indexed: 12/30/2022]
Abstract
UNLABELLED Hepatocellular carcinoma (HCC) is associated with poor survival for patients and few effective treatment options, raising the need for novel therapeutic strategies. MicroRNAs (miRNAs) play important roles in tumor development and show deregulated patterns of expression in HCC. Because of the liver's unique affinity for small nucleic acids, miRNA-based therapy has been proposed in the treatment of liver disease. Thus, there is an urgent need to identify and characterize aberrantly expressed miRNAs in HCC. In our study, we profiled miRNA expression changes in de novo liver tumors driven by MYC and/or RAS, two canonical oncogenes activated in a majority of human HCCs. We identified an up-regulated miRNA megacluster comprised of 53 miRNAs on mouse chromosome 12qF1 (human homolog 14q32). This miRNA megacluster is up-regulated in all three transgenic liver models and in a subset of human HCCs. An unbiased functional analysis of all miRNAs within this cluster was performed. We found that miR-494 is overexpressed in human HCC and aids in transformation by regulating the G1 /S cell cycle transition through targeting of the Mutated in Colorectal Cancer tumor suppressor. miR-494 inhibition in human HCC cell lines decreases cellular transformation, and anti-miR-494 treatment of primary MYC-driven liver tumor formation significantly diminishes tumor size. CONCLUSION Our findings identify a new therapeutic target (miR-494) for the treatment of HCC.
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research-article |
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100 |
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Doering CR, Horsthemke W, Riordan J. Nonequilibrium fluctuation-induced transport. PHYSICAL REVIEW LETTERS 1994; 72:2984-2987. [PMID: 10056038 DOI: 10.1103/physrevlett.72.2984] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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31 |
96 |
4
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Riordan J, Gross A, Angeron J, Krumwiede B, Melin J. The effect of labor pain relief medication on neonatal suckling and breastfeeding duration. J Hum Lact 2000; 16:7-12. [PMID: 11138228 DOI: 10.1177/089033440001600103] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We examined the relationship of labor pain relief medications with neonatal suckling and breastfeeding duration in 129 mothers delivering vaginally. Suckling was measured using the Infant Breastfeeding Assessment Tool (IBFAT). Controlling for infant age, birthweight, and gender, infants of unmedicated mothers had higher IBFAT suckling scores than those of medicated mothers (x = 11.1 vs. x = 8.2 respectively, P = .001). IBFAT suckling scores for intravenous and epidural groups were similar (x = 8.5) while those who received a combination of both intravenous and epidural medications were lower (x = 6.4 +/- 2.96, P = .001). Mothers evaluated their breastfeeding similarly to nurse evaluators (Z = 9.39, P = .001). Breastfeeding duration did not differ between unmedicated and medicated groups; however, dyads with low IBFAT scores weaned earlier than those with medium or high scores. Labor pain relief medications diminish early suckling but are not associated with duration of breastfeeding through 6 weeks postpartum.
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68 |
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Riordan J, Bibb D, Miller M, Rawlins T. Predicting breastfeeding duration using the LATCH breastfeeding assessment tool. J Hum Lact 2001; 17:20-3. [PMID: 11847847 DOI: 10.1177/089033440101700105] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The authors tested the validity of the LATCH breastfeeding assessment tool, controlling for intervening variables in 133 dyads. LATCH scores, mother's evaluation of an index feed, and intended duration of breastfeeding were assessed postpartum and followed 6 weeks. Women breastfeeding at 6 weeks postpartum had higher LATCH scores (mean +/- SD = 9.3 +/- 0.9) than those who weaned (mean +/- SD = 8.7 +/- 1.0), due to only one measure, breast/nipple comfort. Women who weaned before 6 weeks reported lower breast/nipple comfort (1.5 +/- 0.5) than those who were still breastfeeding at 6 weeks (1.7 +/- 0.5, P < .05). Total LATCH scores accounted for 7.3% of variance in breastfeeding duration. Total LATCH scores positively correlated with duration of breastfeeding (n = 128; r = .26, P = .003) and to mothers' scores (n = 132; r = .58, P = .001). Correlations among LATCH measures ranged from .02 to .51. The LATCH tool is a useful identifies the need for follow-up with breastfeeding mothers at risk for early weaning because of sore nipples.
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Validation Study |
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DeZwaan-McCabe D, Riordan JD, Arensdorf AM, Icardi MS, Dupuy AJ, Rutkowski DT. The stress-regulated transcription factor CHOP promotes hepatic inflammatory gene expression, fibrosis, and oncogenesis. PLoS Genet 2013; 9:e1003937. [PMID: 24367269 PMCID: PMC3868529 DOI: 10.1371/journal.pgen.1003937] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/18/2013] [Indexed: 12/13/2022] Open
Abstract
Viral hepatitis, obesity, and alcoholism all represent major risk factors for hepatocellular carcinoma (HCC). Although these conditions also lead to integrated stress response (ISR) or unfolded protein response (UPR) activation, the extent to which these stress pathways influence the pathogenesis of HCC has not been tested. Here we provide multiple lines of evidence demonstrating that the ISR-regulated transcription factor CHOP promotes liver cancer. We show that CHOP expression is up-regulated in liver tumors in human HCC and two mouse models thereof. Chop-null mice are resistant to chemical hepatocarcinogenesis, and these mice exhibit attenuation of both apoptosis and cellular proliferation. Chop-null mice are also resistant to fibrosis, which is a key risk factor for HCC. Global gene expression profiling suggests that deletion of CHOP reduces the levels of basal inflammatory signaling in the liver. Our results are consistent with a model whereby CHOP contributes to hepatic carcinogenesis by promoting inflammation, fibrosis, cell death, and compensatory proliferation. They implicate CHOP as a common contributing factor in the development of HCC in a variety of chronic liver diseases. Liver cancer is the third most common cause of cancer death worldwide. It is most commonly caused by viral hepatitis, alcoholism, or obesity, all of which activate cellular stress responses in the liver. However, the contribution of these responses to disease pathogenesis was unknown. We found that expression of the stress-regulated transcription factor CHOP—widely thought to be anti-oncogenic because of its cell death-promoting properties—was associated with both human liver cancer and two mouse models thereof. In response to challenge with a tumor-causing agent, mice lacking CHOP developed fewer tumors, exhibited less cell death, compensatory cellular proliferation, and liver scarring (fibrosis), and showed lower expression of immune and inflammatory genes. These findings establish CHOP as a biomarker for liver cancer and demonstrate its importance in promoting liver tumor formation. They raise the possibility that promotion of tumorigenesis by CHOP is a common feature of liver cancer caused by viral infection, alcoholism, and obesity.
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Research Support, Non-U.S. Gov't |
12 |
60 |
7
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Keng VW, Sia D, Sarver AL, Tschida BR, Fan D, Alsinet C, Solé M, Lee WL, Kuka TP, Moriarity BS, Villanueva A, Dupuy AJ, Riordan JD, Bell JB, Silverstein KA, Llovet JM, Largaespada DA. Sex bias occurrence of hepatocellular carcinoma in Poly7 molecular subclass is associated with EGFR. Hepatology 2013; 57:120-30. [PMID: 22899566 PMCID: PMC3511635 DOI: 10.1002/hep.26004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 07/08/2012] [Indexed: 12/15/2022]
Abstract
UNLABELLED Hepatocellular carcinoma (HCC) is one of the deadliest solid cancers and is the third leading cause of cancer-related death. There is a universal estimated male/female ratio of 2.5, but the reason for this is not well understood. The Sleeping Beauty (SB) transposon system was used to elucidate candidate oncogenic drivers of HCC in a forward genetics screening approach. Sex bias occurrence was conserved in our model, with male experimental mice developing liver tumors at reduced latency and higher tumor penetrance. In parallel, we explored sex differences regarding genomic aberrations in 235 HCC patients. Liver cancer candidate genes were identified from both sexes and genotypes. Interestingly, transposon insertions in the epidermal growth factor receptor (Egfr) gene were common in SB-induced liver tumors from male mice (10/10, 100%) but infrequent in female mice (2/9, 22%). Human single-nucleotide polymorphism data confirmed that polysomy of chromosome 7, locus of EGFR, was more frequent in males (26/62, 41%) than females (2/27, 7%) (P = 0.001). Gene expression-based Poly7 subclass patients were predominantly male (9/9) compared with 67% males (55/82) in other HCC subclasses (P = 0.02), and this subclass was accompanied by EGFR overexpression (P < 0.001). CONCLUSION Sex bias occurrence of HCC associated with EGFR was confirmed in experimental animals using the SB transposon system in a reverse genetic approach. This study provides evidence for the role of EGFR in sex bias occurrences of liver cancer and as the driver mutational gene in the Poly7 molecular subclass of human HCC.
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research-article |
12 |
48 |
8
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Blanc V, Riordan JD, Soleymanjahi S, Nadeau JH, Nalbantoglu ILK, Xie Y, Molitor EA, Madison BB, Brunt EM, Mills JC, Rubin DC, Ng IO, Ha Y, Roberts LR, Davidson NO. Apobec1 complementation factor overexpression promotes hepatic steatosis, fibrosis, and hepatocellular cancer. J Clin Invest 2021; 131:138699. [PMID: 33445170 DOI: 10.1172/jci138699] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 09/10/2020] [Indexed: 12/11/2022] Open
Abstract
The RNA-binding protein Apobec1 complementation factor (A1CF) regulates posttranscriptional ApoB mRNA editing, but the range of RNA targets and the long-term effect of altered A1CF expression on liver function are unknown. Here we studied hepatocyte-specific A1cf-transgenic (A1cf+/Tg), A1cf+/Tg Apobec1-/-, and A1cf-/- mice fed chow or high-fat/high-fructose diets using RNA-Seq, RNA CLIP-Seq, and tissue microarrays from human hepatocellular cancer (HCC). A1cf+/Tg mice exhibited increased hepatic proliferation and steatosis, with increased lipogenic gene expression (Mogat1, Mogat2, Cidea, Cd36) associated with shifts in polysomal RNA distribution. Aged A1cf+/Tg mice developed spontaneous fibrosis, dysplasia, and HCC, and this development was accelerated on a high-fat/high-fructose diet and was independent of Apobec1. RNA-Seq revealed increased expression of mRNAs involved in oxidative stress (Gstm3, Gpx3, Cbr3), inflammatory response (Il19, Cxcl14, Tnfα, Ly6c), extracellular matrix organization (Mmp2, Col1a1, Col4a1), and proliferation (Kif20a, Mcm2, Mcm4, Mcm6), and a subset of mRNAs (including Sox4, Sox9, Cdh1) were identified in RNA CLIP-Seq. Increased A1CF expression in human HCC correlated with advanced fibrosis and with reduced survival in a subset with nonalcoholic fatty liver disease. In conclusion, we show that hepatic A1CF overexpression selectively alters polysomal distribution and mRNA expression, promoting lipogenic, proliferative, and inflammatory pathways leading to HCC.
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Research Support, Non-U.S. Gov't |
4 |
38 |
9
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Blanc V, Xie Y, Kennedy S, Riordan JD, Rubin DC, Madison BB, Mills JC, Nadeau JH, Davidson NO. Apobec1 complementation factor (A1CF) and RBM47 interact in tissue-specific regulation of C to U RNA editing in mouse intestine and liver. RNA (NEW YORK, N.Y.) 2019; 25:70-81. [PMID: 30309881 PMCID: PMC6298562 DOI: 10.1261/rna.068395.118] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/07/2018] [Indexed: 05/05/2023]
Abstract
Mammalian C to U RNA is mediated by APOBEC1, the catalytic deaminase, together with RNA binding cofactors (including A1CF and RBM47) whose relative physiological requirements are unresolved. Although A1CF complements APOBEC1 for in vitro RNA editing, A1cf-/- mice exhibited no change in apolipoproteinB (apoB) RNA editing, while Rbm47 mutant mice exhibited impaired intestinal RNA editing of apoB as well as other targets. Here we examined the role of A1CF and RBM47 in adult mouse liver and intestine, following deletion of either one or both gene products and also following forced (liver or intestinal) transgenic A1CF expression. There were minimal changes in hepatic and intestinal apoB RNA editing in A1cf-/- mice and no changes in either liver- or intestine-specific A1CF transgenic mice. Rbm47 liver-specific knockout (Rbm47LKO ) mice demonstrated reduced editing in a subset (11 of 20) of RNA targets, including apoB. By contrast, apoB RNA editing was virtually eliminated (<6% activity) in intestine-specific (Rbm47IKO ) mice with only five of 53 targets exhibiting C-to-U RNA editing. Double knockout of A1cf and Rbm47 in liver (ARLKO ) eliminated apoB RNA editing and reduced editing in the majority of other targets, with no changes following adenoviral APOBEC1 administration. Intestinal double knockout mice (ARIKO ) demonstrated further reduced editing (<10% activity) in four of five of the residual APOBEC1 targets identified in ARIKO mice. These data suggest that A1CF and RBM47 each function independently, yet interact in a tissue-specific manner, to regulate the activity and site selection of APOBEC1 dependent C-to-U RNA editing.
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Research Support, N.I.H., Extramural |
6 |
37 |
10
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Tschida BR, Temiz NA, Kuka TP, Lee LA, Riordan JD, Tierrablanca CA, Hullsiek R, Wagner S, Hudson WA, Linden MA, Amin K, Beckmann PJ, Heuer RA, Sarver AL, Yang JD, Roberts LR, Nadeau JH, Dupuy AJ, Keng VW, Largaespada DA. Sleeping Beauty Insertional Mutagenesis in Mice Identifies Drivers of Steatosis-Associated Hepatic Tumors. Cancer Res 2017; 77:6576-6588. [PMID: 28993411 DOI: 10.1158/0008-5472.can-17-2281] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/11/2017] [Accepted: 09/27/2017] [Indexed: 12/24/2022]
Abstract
Hepatic steatosis is a strong risk factor for the development of hepatocellular carcinoma (HCC), yet little is known about the molecular pathology associated with this factor. In this study, we performed a forward genetic screen using Sleeping Beauty (SB) transposon insertional mutagenesis in mice treated to induce hepatic steatosis and compared the results to human HCC data. In humans, we determined that steatosis increased the proportion of female HCC patients, a pattern also reflected in mice. Our genetic screen identified 203 candidate steatosis-associated HCC genes, many of which are altered in human HCC and are members of established HCC-driving signaling pathways. The protein kinase A/cyclic AMP signaling pathway was altered frequently in mouse and human steatosis-associated HCC. We found that activated PKA expression drove steatosis-specific liver tumorigenesis in a mouse model. Another candidate HCC driver, the N-acetyltransferase NAT10, which we found to be overexpressed in human steatosis-associated HCC and associated with decreased survival in human HCC, also drove liver tumorigenesis in a steatotic mouse model. This study identifies genes and pathways promoting HCC that may represent novel targets for prevention and treatment in the context of hepatic steatosis, an area of rapidly growing clinical significance. Cancer Res; 77(23); 6576-88. ©2017 AACR.
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Journal Article |
8 |
35 |
11
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Abstract
Cognitive deficits in schizophrenia are reported to be more consistent with a static encephalopathy than a dementing disorder. This study investigates memory and intellectual decline in 62 chronic schizophrenic subjects using the Wechsler Adult Intelligence Scale-Revised (WAIS-R), the Rivermead Behavioural Memory Test and the National Adult Reading Test (NART) in a cross-sectional study using five age cohorts (18-29, 30-39, 40-49, 50-59 and 60-69 years of age) and then by two cohorts (young: 18-39; older: 40-69). A second method of investigating intellectual decline was implemented by estimating the discrepancy score between WAIS-R (current IQ) and NART (premorbid IQ) for each subject. No significant differences were found in WAIS-R Full Scale. Verbal and Performance IQ and memory functioning across the five age cohorts (and when using two age groups). A significant difference in test scores was found using the Picture Completion and Digit Symbol subtests of the WAIS-R. The differences were not related to age or duration of illness. No significant difference in scores were evident in the remaining WAIS-R subtests. These results support previous findings that schizophrenia is more consistent with a static encephalopathy than a dementing disorder and that intellectual and memory function does not markedly decline with age.
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28 |
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12
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Riordan JD, Feddersen CR, Tschida BR, Jackson P, Keng VW, Linden MA, Amin K, Stipp CS, Largaespada DA, Dupuy AJ. Chronic liver injury alters driver mutation profiles in hepatocellular carcinoma in mice. Hepatology 2018; 67:924-939. [PMID: 28961327 PMCID: PMC5826818 DOI: 10.1002/hep.29565] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/31/2017] [Accepted: 09/27/2017] [Indexed: 02/06/2023]
Abstract
Most hepatocellular carcinomas (HCCs) develop in a chronically injured liver, yet the extent to which this microenvironment promotes neoplastic transformation or influences selective pressures for genetic drivers of HCC remains unclear. We sought to determine the impact of hepatic injury in an established mouse model of HCC induced by Sleeping Beauty transposon mutagenesis. Chemically induced chronic liver injury dramatically increased tumor penetrance and significantly altered driver mutation profiles, likely reflecting distinct selective pressures. In addition to established human HCC genes and pathways, we identified several injury-associated candidates that represent promising loci for further study. Among them, we found that FIGN is overexpressed in human HCC and promotes hepatocyte invasion. We also validated Gli2's oncogenic potential in vivo, providing direct evidence that Hedgehog signaling can drive liver tumorigenesis in the context of chronic injury. Finally, we show that a subset of injury-associated candidate genes identifies two distinct classes of human HCCs. Further analysis of these two subclasses revealed significant trends among common molecular classification schemes of HCC. The genes and mechanisms identified here provide functional insights into the origin of HCC in a chronic liver damage environment. CONCLUSION A chronically damaged liver microenvironment influences the genetic mechanisms that drive hepatocarcinogenesis. (Hepatology 2018;67:924-939).
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Research Support, N.I.H., Extramural |
7 |
32 |
13
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Zanesi N, Balatti V, Riordan J, Burch A, Rizzotto L, Palamarchuk A, Cascione L, Lagana A, Dupuy AJ, Croce CM, Pekarsky Y. A Sleeping Beauty screen reveals NF-kB activation in CLL mouse model. Blood 2013; 121:4355-8. [PMID: 23591791 PMCID: PMC3663428 DOI: 10.1182/blood-2013-02-486035] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 04/14/2013] [Indexed: 11/20/2022] Open
Abstract
TCL1 oncogene is overexpressed in aggressive form of human chronic lymphocytic leukemia (CLL) and its dysregulation in mouse B cells causes a CD5-positive leukemia similar to the aggressive form of human CLLs. To identify oncogenes that cooperate with Tcl1, we performed genetic screen in Eμ-TCL1 mice using Sleeping Beauty transposon-mediated mutagenesis. Analysis of transposon common insertion sites identified 7 genes activated by transposon insertions. Overexpression of these genes in mouse CLL was confirmed by real time reverse transcription-polymerase chain reaction. Interestingly, the main known function of 4 of 7 genes (Nfkb1, Tab2, Map3K14, and Nfkbid) is participation in or activation of the nuclear factor-kB (NF-kB) pathway. In addition, activation of the NF-kB is 1 of main functions of Akt2, also identified in the screen. These findings demonstrate cooperation of Tcl1 and the NF-kB pathway in the pathogenesis of aggressive CLL. Identification cooperating cancer genes will result in the development of combinatorial therapies to treat CLL.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Disease Models, Animal
- Gene Expression Regulation, Leukemic/physiology
- Genetic Testing/methods
- Kaplan-Meier Estimate
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Mice
- Mice, Transgenic
- Mutagenesis, Insertional/methods
- NF-kappa B p50 Subunit/genetics
- NF-kappa B p50 Subunit/metabolism
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Signal Transduction/physiology
- Transposases/genetics
- NF-kappaB-Inducing Kinase
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Research Support, N.I.H., Extramural |
12 |
26 |
14
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Temiz NA, Moriarity BS, Wolf NK, Riordan JD, Dupuy AJ, Largaespada DA, Sarver AL. RNA sequencing of Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens. Genome Res 2015; 26:119-29. [PMID: 26553456 PMCID: PMC4691744 DOI: 10.1101/gr.188649.114] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 11/04/2015] [Indexed: 11/24/2022]
Abstract
Forward genetic screens using Sleeping Beauty (SB)-mobilized T2/Onc transposons have been used to identify common insertion sites (CISs) associated with tumor formation. Recurrent sites of transposon insertion are commonly identified using ligation-mediated PCR (LM-PCR). Here, we use RNA sequencing (RNA-seq) data to directly identify transcriptional events mediated by T2/Onc. Surprisingly, the majority (∼80%) of LM-PCR identified junction fragments do not lead to observable changes in RNA transcripts. However, in CIS regions, direct transcriptional effects of transposon insertions are observed. We developed an automated method to systematically identify T2/Onc-genome RNA fusion sequences in RNA-seq data. RNA fusion-based CISs were identified corresponding to both DNA-based CISs (Cdkn2a, Mycl1, Nf2, Pten, Sema6d, and Rere) and additional regions strongly associated with cancer that were not observed by LM-PCR (Myc, Akt1, Pth, Csf1r, Fgfr2, Wisp1, Map3k5, and Map4k3). In addition to calculating recurrent CISs, we also present complementary methods to identify potential driver events via determination of strongly supported fusions and fusions with large transcript level changes in the absence of multitumor recurrence. These methods independently identify CIS regions and also point to cancer-associated genes like Braf. We anticipate RNA-seq analyses of tumors from forward genetic screens will become an efficient tool to identify causal events.
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Research Support, Non-U.S. Gov't |
10 |
25 |
15
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Abstract
Although the number and diversity of minority women in the United States is growing, breastfeeding rates remain low. Nurses can increase breastfeeding rates in minority populations if they are aware of and appreciate cultural differences. Following an overview of culture's effect on breastfeeding, this article focuses on practical aspects of caring for breastfeeding mothers in various cultural groups. Breastfeeding educational programs are effective when they are culturally sensitive and emerge from the culture itself.
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Review |
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16
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Riordan JD, Drury LJ, Smith RP, Brett BT, Rogers LM, Scheetz TE, Dupuy AJ. Sequencing methods and datasets to improve functional interpretation of sleeping beauty mutagenesis screens. BMC Genomics 2014; 15:1150. [PMID: 25526783 PMCID: PMC4378557 DOI: 10.1186/1471-2164-15-1150] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Animal models of cancer are useful to generate complementary datasets for comparison to human tumor data. Insertional mutagenesis screens, such as those utilizing the Sleeping Beauty (SB) transposon system, provide a model that recapitulates the spontaneous development and progression of human disease. This approach has been widely used to model a variety of cancers in mice. Comprehensive mutation profiles are generated for individual tumors through amplification of transposon insertion sites followed by high-throughput sequencing. Subsequent statistical analyses identify common insertion sites (CISs), which are predicted to be functionally involved in tumorigenesis. Current methods utilized for SB insertion site analysis have some significant limitations. For one, they do not account for transposon footprints - a class of mutation generated following transposon remobilization. Existing methods also discard quantitative sequence data due to uncertainty regarding the extent to which it accurately reflects mutation abundance within a heterogeneous tumor. Additionally, computational analyses generally assume that all potential insertion sites have an equal probability of being detected under non-selective conditions, an assumption without sufficient relevant data. The goal of our study was to address these potential confounding factors in order to enhance functional interpretation of insertion site data from tumors. RESULTS We describe here a novel method to detect footprints generated by transposon remobilization, which revealed minimal evidence of positive selection in tumors. We also present extensive characterization data demonstrating an ability to reproducibly assign semi-quantitative information to individual insertion sites within a tumor sample. Finally, we identify apparent biases for detection of inserted transposons in several genomic regions that may lead to the identification of false positive CISs. CONCLUSION The information we provide can be used to refine analyses of data from insertional mutagenesis screens, improving functional interpretation of results and facilitating the identification of genes important in cancer development and progression.
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Research Support, N.I.H., Extramural |
11 |
20 |
17
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Sinasac DS, Riordan JD, Spiezio SH, Yandell BS, Croniger CM, Nadeau JH. Genetic control of obesity, glucose homeostasis, dyslipidemia and fatty liver in a mouse model of diet-induced metabolic syndrome. Int J Obes (Lond) 2015; 40:346-55. [PMID: 26381349 DOI: 10.1038/ijo.2015.184] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/24/2015] [Accepted: 08/19/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND/OBJECTIVES Both genetic and dietary factors contribute to the metabolic syndrome (MetS) in humans and animal models. Characterizing their individual roles as well as relationships among these factors is critical for understanding MetS pathogenesis and developing effective therapies. By studying phenotypic responsiveness to high-risk versus control diet in two inbred mouse strains and their derivatives, we estimated the relative contributions of diet and genetic background to MetS, characterized strain-specific combinations of MetS conditions, and tested genetic and phenotypic complexity on a single substituted chromosome. METHODS Ten measures of metabolic health were assessed in susceptible C57BL/6 J and resistant A/J male mice fed either a control or a high-fat, high-sucrose (HFHS) diet, permitting estimates of the relative influences of strain, diet and strain-diet interactions for each trait. The same traits were measured in a panel of C57BL/6 J (B6)-Chr(A/J) chromosome substitution strains (CSSs) fed the HFHS diet, followed by characterization of interstrain relationships, covariation among metabolic traits and quantitative trait loci (QTLs) on Chromosome 10. RESULTS We identified significant genetic contributions to nine of ten metabolic traits and significant dietary influence on eight. Significant strain-diet interaction effects were detected for four traits. Although a range of HFHS-induced phenotypes were observed among the CSSs, significant associations were detected among all traits but one. Strains were grouped into three clusters based on overall phenotype and specific CSSs were identified with distinct and reproducible trait combinations. Finally, several Chr10 regions were shown to control the severity of MetS conditions. CONCLUSIONS Generally strong genetic and dietary effects validate these CSSs as a multifactorial model of MetS. Although traits tended to segregate together, considerable phenotypic heterogeneity suggests that underlying genetic factors influence their co-occurrence and severity. Identification of multiple QTLs within and among strains highlights both the complexity of genetically regulated, diet-induced MetS and the ability of CSSs to prioritize candidate loci for mechanistic studies.
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Research Support, N.I.H., Extramural |
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Riordan J, Doering CR, ben-Avraham D. Fluctuations and stability of fisher waves. PHYSICAL REVIEW LETTERS 1995; 75:565-568. [PMID: 10060053 DOI: 10.1103/physrevlett.75.565] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Riordan J. Predicting breastfeeding problems. These tools may--or may not--help assess high-risk mother-baby couples. AWHONN LIFELINES 1998; 2:31-3. [PMID: 9934021 DOI: 10.1111/j.1552-6356.1998.tb01049.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Review |
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Smith RP, Riordan JD, Feddersen CR, Dupuy AJ. A Hybrid Adenoviral Vector System Achieves Efficient Long-Term Gene Expression in the Liver via piggyBac Transposition. Hum Gene Ther 2016; 26:377-85. [PMID: 25808258 DOI: 10.1089/hum.2014.123] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Much research has gone into the development of hybrid gene delivery systems that combine the broad tropism and efficient transduction of adenoviral vectors with the ability to achieve stable expression of cargo genes. In addition to gene therapy applications, such a system has considerable advantages for studies of gene function in vivo, permitting fine-tuned genetic manipulation with higher throughput than can be achieved using standard transgenic and DNA targeting techniques. Existing strategies are limited, however, by low integration efficiencies, small cargo capacity, and/or a dependence on target cell division. The utility of this approach could be enhanced by a system that provides all of the following: (1) efficient delivery, (2) stable expression in a high percentage of target cells (whether mitotic or not), (3) large cargo capacity, (4) flexibility to use with a wide range of additional experimental conditions, and (5) simple experimental technique. Here we report the initial characterization of a hybrid system that meets these criteria by utilizing piggyBac (PB) transposition to achieve genomic integration from adenoviral vectors. We demonstrate stable expression of an adenovirus (Ad)-PB-delivered reporter gene in ∼20-40% of hepatocytes following standard tail vein injection. Its high efficiency and flexibility relative to existing hybrid adenoviral gene delivery approaches indicate a considerable potential utility of the Ad-PB system for therapeutic gene delivery and in vivo studies of gene function.
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Feddersen CR, Schillo JL, Varzavand A, Vaughn HR, Wadsworth LS, Voigt AP, Zhu EY, Jennings BM, Mullen SA, Bobera J, Riordan JD, Stipp CS, Dupuy AJ. Src-Dependent DBL Family Members Drive Resistance to Vemurafenib in Human Melanoma. Cancer Res 2019; 79:5074-5087. [PMID: 31416844 PMCID: PMC6774858 DOI: 10.1158/0008-5472.can-19-0244] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/05/2019] [Accepted: 08/06/2019] [Indexed: 12/25/2022]
Abstract
The use of selective BRAF inhibitors (BRAFi) has produced remarkable outcomes for patients with advanced cutaneous melanoma harboring a BRAFV600E mutation. Unfortunately, the majority of patients eventually develop drug-resistant disease. We employed a genetic screening approach to identify gain-of-function mechanisms of BRAFi resistance in two independent melanoma cell lines. Our screens identified both known and unappreciated drivers of BRAFi resistance, including multiple members of the DBL family. Mechanistic studies identified a DBL/RAC1/PAK signaling axis capable of driving resistance to both current and next-generation BRAFis. However, we show that the SRC inhibitor, saracatinib, can block the DBL-driven resistance. Our work highlights the utility of our straightforward genetic screening method in identifying new drug combinations to combat acquired BRAFi resistance. SIGNIFICANCE: A simple, rapid, and flexible genetic screening approach identifies genes that drive resistance to MAPK inhibitors when overexpressed in human melanoma cells.
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research-article |
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Riordan JD, Dupuy AJ. Domesticated transposable element gene products in human cancer. Mob Genet Elements 2013; 3:e26693. [PMID: 24251072 DOI: 10.4161/mge.26693] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/24/2013] [Accepted: 10/03/2013] [Indexed: 11/19/2022] Open
Abstract
The adaptation of transposable elements inserted within the genome to serve novel functions in a host cell, a process known as molecular domestication, is a widespread phenomenon in nature. Around fifty protein-coding genes in humans have arisen through this mechanism. Functional characterization of these domesticated genes has revealed involvement in a multitude of diverse cellular processes. Some of these functions are related to cellular activities and pathways known to be involved in cancer development. In this mini-review we discuss such roles of domesticated genes that may be aberrantly regulated in human cancer, as well as studies that have identified disrupted expression in tumors. We also describe studies that have provided definitive experimental evidence for transposable element-derived gene products in promoting tumorigenesis.
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Mockler D, Riordan J, Murphy M. Psychosocial factors associated with the use/non-use of mental health services by primary carers of individuals with dementia. Int J Geriatr Psychiatry 1998; 13:310-4. [PMID: 9658263 DOI: 10.1002/(sici)1099-1166(199805)13:5<310::aid-gps765>3.0.co;2-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The study investigated psychosocial factors associated with the use/non-use of services by primary carers of people with dementia (caring for relative/friend with dementia). The factors considered were individual differences, health, stress, family/social support, years of caring, age of carers/person with dementia, gender and level of behavioural disturbance presented by the person with dementia. The participants were referred to the study by health services, social services representatives and GPs. The carers (N = 50) were divided into two groups (service user/non-user). The findings indicated that primary carers in the non-user service group scored significantly higher on a measure (sense of coherence; SOC) estimating an individual's ability to deal with stressful situations. The individual's ability to deal with caring responsibilities was associated with a reduction in the level of diagnosable psychiatric disorder or 'caseness' and the non-use of services. None of the other factors considered were found to be significantly different between the two career groups. However, a significant inverse association between health, stress and individual ability to deal with stressful situations was found when the two career groups were combined.
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Abstract
By examining and predicting dimensions of job satisfaction of community-based nurses, this study sought to provide information for recruiting and retaining community nurses. Data were collected from a sample of 104 community health, school health, and home health nurses. Prestige had the highest positive correlation with and was the single significant predictor of job satisfaction. Three other subscales, autonomy, social interaction, and organizational requirements, correlated with job satisfaction as moderately positive. Weak positive relationships were found with years of work, years on the job, age, and years of education. Pay was not associated with job satisfaction for these nurses.
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