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Article ; Online: CD40 expression in renal cell carcinoma is associated with tumor apoptosis, CD8(+) T cell frequency and patient survival.

Weiss, Jonathan M / Gregory Alvord, W / Quiñones, Octavio A / Stauffer, Jimmy K / Wiltrout, Robert H

2014 Volume 75, Issue 7, Page(s) 614–620

Abstract: The co-stimulatory molecule, CD40, is expressed in renal cell carcinoma (RCC) and a variety of inflammatory diseases in the kidney. We investigated the relationship between tumor-associated CD40 expression, immune milieu of the tumor microenvironment, ... ...

Abstract	The co-stimulatory molecule, CD40, is expressed in renal cell carcinoma (RCC) and a variety of inflammatory diseases in the kidney. We investigated the relationship between tumor-associated CD40 expression, immune milieu of the tumor microenvironment, tumor stage and survival of patients with RCC. The expression of CD40, TUNEL and CD8 in human renal cell carcinomas was analyzed by immunohistochemistry performed on tissue samples obtained at the time of surgery. Computer-assisted quantitation of protein expression was used to analyze results in connection with patient survival and tumor stage. We show for the first time that tumor-associated CD40 expression is associated with prolonged survival in RCC patients. Tumor apoptosis (TUNEL) and CD8 immunostaining were also associated with patient survival. No relation was observed between CD40 expression and tumor stage. Our results suggest CD40 may be a prognostic biomarker indicative of prolonged RCC patient survival. Strategies that up-regulate CD40 expression in some RCC patients may thus improve survival, supporting further studies of agonistic CD40 antibodies in RCC.
MeSH term(s)	Apoptosis ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; CD40 Antigens/genetics ; CD40 Antigens/metabolism ; CD8-Positive T-Lymphocytes/metabolism ; CD8-Positive T-Lymphocytes/pathology ; Carcinoma, Renal Cell/genetics ; Carcinoma, Renal Cell/metabolism ; Carcinoma, Renal Cell/mortality ; Carcinoma, Renal Cell/pathology ; Female ; Follow-Up Studies ; Gene Expression ; Humans ; In Situ Nick-End Labeling ; Kidney/metabolism ; Kidney/pathology ; Kidney Neoplasms/genetics ; Kidney Neoplasms/metabolism ; Kidney Neoplasms/mortality ; Kidney Neoplasms/pathology ; Lymphocyte Count ; Male ; Middle Aged ; Neoplasm Staging ; Prognosis ; Survival Analysis ; Tumor Microenvironment/genetics
Chemical Substances	Biomarkers, Tumor ; CD40 Antigens
Language	English
Publishing date	2014-05-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	801524-7
ISSN	1879-1166 ; 0198-8859
ISSN (online)	1879-1166
ISSN	0198-8859
DOI	10.1016/j.humimm.2014.04.018
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Article ; Online: C/EBPγ Is a Critical Regulator of Cellular Stress Response Networks through Heterodimerization with ATF4

Huggins, Christopher J. / Mayekar, Manasi K. / Martin, Nancy / Saylor, Karen L. / Gonit, Mesfin / Jailwala, Parthav / Kasoji, Manjula / Haines, Diana C. / Quiñones, Octavio A. / Johnson, Peter F.

Molecular and Cellular Biology. 2016 Mar. 1, v. 36, no. 5 p.693-713

2016

Abstract: The integrated stress response (ISR) controls cellular adaptations to nutrient deprivation, redox imbalances, and endoplasmic reticulum (ER) stress. ISR genes are upregulated in stressed cells, primarily by the bZIP transcription factor ATF4 through its ... ...

Abstract	The integrated stress response (ISR) controls cellular adaptations to nutrient deprivation, redox imbalances, and endoplasmic reticulum (ER) stress. ISR genes are upregulated in stressed cells, primarily by the bZIP transcription factor ATF4 through its recruitment to cis-regulatory C/EBP:ATF response elements (CAREs) together with a dimeric partner of uncertain identity. Here, we show that C/EBPγ:ATF4 heterodimers, but not C/EBPβ:ATF4 dimers, are the predominant CARE-binding species in stressed cells. C/EBPγ and ATF4 associate with genomic CAREs in a mutually dependent manner and coregulate many ISR genes. In contrast, the C/EBP family members C/EBPβ and C/EBP homologous protein (CHOP) were largely dispensable for induction of stress genes. Cebpg ⁻/⁻ mouse embryonic fibroblasts (MEFs) proliferate poorly and exhibit oxidative stress due to reduced glutathione levels and impaired expression of several glutathione biosynthesis pathway genes. Cebpg ⁻/⁻ mice (C57BL/6 background) display reduced body size and microphthalmia, similar to ATF4-null animals. In addition, C/EBPγ-deficient newborns die from atelectasis and respiratory failure, which can be mitigated by in utero exposure to the antioxidant, N-acetyl-cysteine. Cebpg ⁻/⁻ mice on a mixed strain background showed improved viability but, upon aging, developed significantly fewer malignant solid tumors than WT animals. Our findings identify C/EBPγ as a novel antioxidant regulator and an obligatory ATF4 partner that controls redox homeostasis in normal and cancerous cells.
Keywords	antioxidants ; biosynthesis ; body size ; dimerization ; endoplasmic reticulum ; fibroblasts ; genomics ; glutathione ; homeostasis ; maternal exposure ; mice ; oxidative stress ; stress response ; transcription factors ; viability
Language	English
Dates of publication	2016-0301
Size	p. 693-713.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/MCB.00911-15
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Pharmacological analysis of Drosophila melanogaster gamma-secretase with respect to differential proteolysis of Notch and APP.

Groth, Casper / Alvord, W Gregory / Quiñones, Octavio A / Fortini, Mark E

Molecular pharmacology

2010 Volume 77, Issue 4, Page(s) 567–574

Abstract: The gamma-secretase aspartyl protease is responsible for the cleavage of numerous type I integral membrane proteins, including amyloid precursor protein (APP) and Notch. APP cleavage contributes to the generation of toxic amyloid beta peptides in ... ...

Abstract	The gamma-secretase aspartyl protease is responsible for the cleavage of numerous type I integral membrane proteins, including amyloid precursor protein (APP) and Notch. APP cleavage contributes to the generation of toxic amyloid beta peptides in Alzheimer's disease, whereas cleavage of the Notch receptor is required for normal physiological signaling between differentiating cells. Mutagenesis studies as well as in vivo analyses of Notch and APP activity in the presence of pharmacological inhibitors indicate that these substrates can be differentially modulated by inhibition of mammalian gamma-secretase, although some biochemical studies instead show nearly identical dose-response inhibitor effects on Notch and APP cleavages. Here, we examine the dose-response effects of several inhibitors on Notch and APP in Drosophila melanogaster cells, which possess a homogeneous form of gamma-secretase. Four different inhibitors that target different domains of gamma-secretase exhibit similar dose-response effects for both substrates, including rank order of inhibitor potencies and effective concentration ranges. For two inhibitors, modest differences in inhibitor dose responses toward Notch and APP were detected, suggesting that inhibitors might be identified that possess some discrimination in their ability to target alternative gamma-secretase substrates. These findings also indicate that despite an overall conservation in inhibitor potencies toward different gamma-secretase substrates, quantitative differences might exist that could be relevant for the development of therapeutically valuable substrate-specific inhibitors.
MeSH term(s)	Amyloid Precursor Protein Secretases/antagonists & inhibitors ; Amyloid Precursor Protein Secretases/physiology ; Animals ; Dose-Response Relationship, Drug ; Drosophila Proteins/metabolism ; Drosophila melanogaster ; Membrane Proteins/metabolism ; Nerve Tissue Proteins/metabolism ; Protease Inhibitors/pharmacology ; Receptors, Notch/metabolism
Chemical Substances	Appl protein, Drosophila ; Drosophila Proteins ; Membrane Proteins ; N protein, Drosophila ; Nerve Tissue Proteins ; Protease Inhibitors ; Receptors, Notch ; Amyloid Precursor Protein Secretases (EC 3.4.-)
Language	English
Publishing date	2010-01-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	124034-1
ISSN	1521-0111 ; 0026-895X
ISSN (online)	1521-0111
ISSN	0026-895X
DOI	10.1124/mol.109.062471
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Article: Chr 19A/J modifies tumor resistance in a sex- and parent-of-origin-specific manner

Walrath, Jessica C / Fox, Kristi / Truffer, Erika / Gregory Alvord, W / Quiñones, Octavio A / Reilly, Karlyne M

Mammalian genome official journal of the International Mammalian Genome Society. 2009 Apr., v. 20, no. 4

2009

Abstract: Neurofibromatosis type 1 (NF1) is one of the most common human genetic diseases affecting the nervous system and predisposes individuals to cancer, including peripheral nerve sheath tumors (PNSTs) and astrocytomas. Modifiers in the genetic background ... ...

Abstract	Neurofibromatosis type 1 (NF1) is one of the most common human genetic diseases affecting the nervous system and predisposes individuals to cancer, including peripheral nerve sheath tumors (PNSTs) and astrocytomas. Modifiers in the genetic background affect the severity of the disease and we have previously mapped two modifier loci, Nstr1 and Nstr2, that influence resistance to PNSTs in the Nf1-/+;Trp53-/+cis mouse model of NF1. We report here the analysis of Nstr1 in isolation from other epistatic loci using a chromosome substitution strain, and further show that a modifier locus (or loci) on chromosome 19 influences resistance to both PNSTs and astrocytomas. This modifier locus interacts with sex, resulting in sex-specific modification of tumors. Allele variability on chromosome 19 affects both the timing and the penetrance of the growth of different tumor types associated with NF1, specifically PNSTs and astrocytoma. These results indicate that modifiers of cancer susceptibility interact and affect tumorigenesis under different genetic conditions and demonstrate the power of chromosome substitution strains to study genetic modifiers.
Keywords	alleles ; animal models ; carcinogenesis ; chromosome substitution ; disease severity ; epistasis ; genetic background ; genetic disorders ; humans ; loci ; neoplasms ; nerve tissue ; penetrance
Language	English
Dates of publication	2009-04
Size	p. 214-223.
Publisher	Springer-Verlag
Publishing place	New York
Document type	Article
ZDB-ID	1058547-3
ISSN	1432-1777 ; 0938-8990
ISSN (online)	1432-1777
ISSN	0938-8990
DOI	10.1007/s00335-009-9179-4
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: C/EBPγ Is a Critical Regulator of Cellular Stress Response Networks through Heterodimerization with ATF4.

Huggins, Christopher J / Mayekar, Manasi K / Martin, Nancy / Saylor, Karen L / Gonit, Mesfin / Jailwala, Parthav / Kasoji, Manjula / Haines, Diana C / Quiñones, Octavio A / Johnson, Peter F

Molecular and cellular biology

2015 Volume 36, Issue 5, Page(s) 693–713

Abstract	The integrated stress response (ISR) controls cellular adaptations to nutrient deprivation, redox imbalances, and endoplasmic reticulum (ER) stress. ISR genes are upregulated in stressed cells, primarily by the bZIP transcription factor ATF4 through its recruitment to cis-regulatory C/EBP:ATF response elements (CAREs) together with a dimeric partner of uncertain identity. Here, we show that C/EBPγ:ATF4 heterodimers, but not C/EBPβ:ATF4 dimers, are the predominant CARE-binding species in stressed cells. C/EBPγ and ATF4 associate with genomic CAREs in a mutually dependent manner and coregulate many ISR genes. In contrast, the C/EBP family members C/EBPβ and C/EBP homologous protein (CHOP) were largely dispensable for induction of stress genes. Cebpg(-/-) mouse embryonic fibroblasts (MEFs) proliferate poorly and exhibit oxidative stress due to reduced glutathione levels and impaired expression of several glutathione biosynthesis pathway genes. Cebpg(-/-) mice (C57BL/6 background) display reduced body size and microphthalmia, similar to ATF4-null animals. In addition, C/EBPγ-deficient newborns die from atelectasis and respiratory failure, which can be mitigated by in utero exposure to the antioxidant, N-acetyl-cysteine. Cebpg(-/-) mice on a mixed strain background showed improved viability but, upon aging, developed significantly fewer malignant solid tumors than WT animals. Our findings identify C/EBPγ as a novel antioxidant regulator and an obligatory ATF4 partner that controls redox homeostasis in normal and cancerous cells.
MeSH term(s)	Activating Transcription Factor 4/analysis ; Activating Transcription Factor 4/genetics ; Activating Transcription Factor 4/metabolism ; Animals ; CCAAT-Enhancer-Binding Proteins/analysis ; CCAAT-Enhancer-Binding Proteins/genetics ; CCAAT-Enhancer-Binding Proteins/metabolism ; Cell Line ; Female ; Fetus/abnormalities ; Fetus/metabolism ; Gene Deletion ; Gene Expression Regulation ; Glutathione/metabolism ; Humans ; Male ; Mice, Inbred C57BL ; Neoplasms/genetics ; Neoplasms/metabolism ; Oxidative Stress ; Protein Multimerization ; Response Elements ; Transcription Factor CHOP/metabolism
Chemical Substances	CCAAT-Enhancer-Binding Proteins ; Ddit3 protein, mouse ; Cebpg protein, mouse (136958-00-4) ; Activating Transcription Factor 4 (145891-90-3) ; Transcription Factor CHOP (147336-12-7) ; Glutathione (GAN16C9B8O)
Language	English
Publishing date	2015-12-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/MCB.00911-15
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Article ; Online: A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R.

Gregory Alvord, W / Roayaei, Jean A / Quiñones, Octavio A / Schneider, Katherine T

Briefings in bioinformatics

2007 Volume 8, Issue 6, Page(s) 415–431

Abstract: This article describes specific procedures for conducting quality assessment of Affymetrix GeneChip(R) soybean genome data and for performing analyses to determine differential gene expression using the open-source R programming environment in ... ...

Abstract	This article describes specific procedures for conducting quality assessment of Affymetrix GeneChip(R) soybean genome data and for performing analyses to determine differential gene expression using the open-source R programming environment in conjunction with the open-source Bioconductor software. We describe procedures for extracting those Affymetrix probe set IDs related specifically to the soybean genome on the Affymetrix soybean chip and demonstrate the use of exploratory plots including images of raw probe-level data, boxplots, density plots and M versus A plots. RNA degradation and recommended procedures from Affymetrix for quality control are discussed. An appropriate probe-level model provides an excellent quality assessment tool. To demonstrate this, we discuss and display chip pseudo-images of weights, residuals and signed residuals and additional probe-level modeling plots that may be used to identify aberrant chips. The Robust Multichip Averaging (RMA) procedure was used for background correction, normalization and summarization of the AffyBatch probe-level data to obtain expression level data and to discover differentially expressed genes. Examples of boxplots and MA plots are presented for the expression level data. Volcano plots and heatmaps are used to demonstrate the use of (log) fold changes in conjunction with ordinary and moderated t-statistics for determining interesting genes. We show, with real data, how implementation of functions in R and Bioconductor successfully identified differentially expressed genes that may play a role in soybean resistance to a fungal pathogen, Phakopsora pachyrhizi. Complete source code for performing all quality assessment and statistical procedures may be downloaded from our web source: http://css.ncifcrf.gov/services/download/MicroarraySoybean.zip.
MeSH term(s)	Gene Expression Profiling/methods ; Genome, Plant/genetics ; Oligonucleotide Array Sequence Analysis/methods ; Plant Proteins/genetics ; Programming Languages ; Proteome/genetics ; Software ; Glycine max/physiology
Chemical Substances	Plant Proteins ; Proteome
Language	English
Publishing date	2007-09-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbm043
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Article ; Online: C/EBPγ Suppresses Senescence and Inflammatory Gene Expression by Heterodimerizing with C/EBPβ

Huggins, Christopher J. / Malik, Radek / Lee, Sook / Salotti, Jacqueline / Thomas, Sara / Martin, Nancy / Quiñones, Octavio A. / Alvord, W. Gregory / Olanich, Mary E. / Keller, Jonathan R. / Johnson, Peter F.

Molecular and Cellular Biology. 2013 Aug. 1, v. 33, no. 16 p.3242-3258

2013

Abstract: C/EBPβ is an important regulator of oncogene-induced senescence (OIS). Here, we show that C/EBPγ, a heterodimeric partner of C/EBPβ whose biological functions are not well understood, inhibits cellular senescence. Cebpg ⁻/⁻ mouse embryonic fibroblasts ( ... ...

Abstract	C/EBPβ is an important regulator of oncogene-induced senescence (OIS). Here, we show that C/EBPγ, a heterodimeric partner of C/EBPβ whose biological functions are not well understood, inhibits cellular senescence. Cebpg ⁻/⁻ mouse embryonic fibroblasts (MEFs) proliferated poorly, entered senescence prematurely, and expressed a proinflammatory gene signature, including elevated levels of senescence-associated secretory phenotype (SASP) genes whose induction by oncogenic stress requires C/EBPβ. The senescence-suppressing activity of C/EBPγ required its ability to heterodimerize with C/EBPβ. Covalently linked C/EBPβ homodimers (β∼β) inhibited the proliferation and tumorigenicity of Rasⱽ¹²-transformed NIH 3T3 cells, activated SASP gene expression, and recruited the CBP coactivator in a Ras-dependent manner, whereas γ∼β heterodimers lacked these capabilities and efficiently rescued proliferation of Cebpg ⁻/⁻ MEFs. C/EBPβ depletion partially restored growth of C/EBPγ-deficient cells, indicating that the increased levels of C/EBPβ homodimers in Cebpg ⁻/⁻ MEFs inhibit proliferation. The proliferative functions of C/EBPγ are not restricted to fibroblasts, as hematopoietic progenitors from Cebpg ⁻/⁻ bone marrow also displayed impaired growth. Furthermore, high CEBPG expression correlated with poorer clinical prognoses in several human cancers, and C/EBPγ depletion decreased proliferation and induced senescence in lung tumor cells. Our findings demonstrate that C/EBPγ neutralizes the cytostatic activity of C/EBPβ through heterodimerization, which prevents senescence and suppresses basal transcription of SASP genes.
Keywords	bone marrow ; cell senescence ; chemical bonding ; dimerization ; fibroblasts ; gene expression ; genes ; humans ; lung neoplasms ; mice ; phenotype
Language	English
Dates of publication	2013-0801
Size	p. 3242-3258.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/MCB.01674-12
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: C/EBPγ suppresses senescence and inflammatory gene expression by heterodimerizing with C/EBPβ.

Huggins, Christopher J / Malik, Radek / Lee, Sook / Salotti, Jacqueline / Thomas, Sara / Martin, Nancy / Quiñones, Octavio A / Alvord, W Gregory / Olanich, Mary E / Keller, Jonathan R / Johnson, Peter F

Molecular and cellular biology

2013 Volume 33, Issue 16, Page(s) 3242–3258

Abstract	C/EBPβ is an important regulator of oncogene-induced senescence (OIS). Here, we show that C/EBPγ, a heterodimeric partner of C/EBPβ whose biological functions are not well understood, inhibits cellular senescence. Cebpg(-/-) mouse embryonic fibroblasts (MEFs) proliferated poorly, entered senescence prematurely, and expressed a proinflammatory gene signature, including elevated levels of senescence-associated secretory phenotype (SASP) genes whose induction by oncogenic stress requires C/EBPβ. The senescence-suppressing activity of C/EBPγ required its ability to heterodimerize with C/EBPβ. Covalently linked C/EBPβ homodimers (β∼β) inhibited the proliferation and tumorigenicity of Ras(V12)-transformed NIH 3T3 cells, activated SASP gene expression, and recruited the CBP coactivator in a Ras-dependent manner, whereas γ∼β heterodimers lacked these capabilities and efficiently rescued proliferation of Cebpg(-/-) MEFs. C/EBPβ depletion partially restored growth of C/EBPγ-deficient cells, indicating that the increased levels of C/EBPβ homodimers in Cebpg(-/-) MEFs inhibit proliferation. The proliferative functions of C/EBPγ are not restricted to fibroblasts, as hematopoietic progenitors from Cebpg(-/-) bone marrow also displayed impaired growth. Furthermore, high CEBPG expression correlated with poorer clinical prognoses in several human cancers, and C/EBPγ depletion decreased proliferation and induced senescence in lung tumor cells. Our findings demonstrate that C/EBPγ neutralizes the cytostatic activity of C/EBPβ through heterodimerization, which prevents senescence and suppresses basal transcription of SASP genes.
MeSH term(s)	Animals ; CCAAT-Enhancer-Binding Protein-beta/metabolism ; CCAAT-Enhancer-Binding Proteins/genetics ; CCAAT-Enhancer-Binding Proteins/metabolism ; Cell Cycle ; Cell Line ; Cell Line, Tumor ; Cell Proliferation ; Cells, Cultured ; Cellular Senescence ; Fibroblasts/cytology ; Fibroblasts/metabolism ; Gene Deletion ; Gene Expression Regulation ; Gene Expression Regulation, Neoplastic ; Hematopoiesis ; Hematopoietic Stem Cells/cytology ; Hematopoietic Stem Cells/metabolism ; Humans ; Inflammation/genetics ; Inflammation/metabolism ; Mice ; Mice, Inbred C57BL ; NIH 3T3 Cells ; Neoplasms/genetics ; Neoplasms/metabolism ; Protein Multimerization
Chemical Substances	CCAAT-Enhancer-Binding Protein-beta ; CCAAT-Enhancer-Binding Proteins ; CCAAT-enhancer-binding protein-gamma
Language	English
Publishing date	2013-06-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/MCB.01674-12
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Article ; Online: Chr 19(A/J) modifies tumor resistance in a sex- and parent-of-origin-specific manner.

Walrath, Jessica C / Fox, Kristi / Truffer, Erika / Gregory Alvord, W / Quiñones, Octavio A / Reilly, Karlyne M

Mammalian genome : official journal of the International Mammalian Genome Society

2009 Volume 20, Issue 4, Page(s) 214–223

Abstract	Neurofibromatosis type 1 (NF1) is one of the most common human genetic diseases affecting the nervous system and predisposes individuals to cancer, including peripheral nerve sheath tumors (PNSTs) and astrocytomas. Modifiers in the genetic background affect the severity of the disease and we have previously mapped two modifier loci, Nstr1 and Nstr2, that influence resistance to PNSTs in the Nf1-/+;Trp53-/+cis mouse model of NF1. We report here the analysis of Nstr1 in isolation from other epistatic loci using a chromosome substitution strain, and further show that a modifier locus (or loci) on chromosome 19 influences resistance to both PNSTs and astrocytomas. This modifier locus interacts with sex, resulting in sex-specific modification of tumors. Allele variability on chromosome 19 affects both the timing and the penetrance of the growth of different tumor types associated with NF1, specifically PNSTs and astrocytoma. These results indicate that modifiers of cancer susceptibility interact and affect tumorigenesis under different genetic conditions and demonstrate the power of chromosome substitution strains to study genetic modifiers.
MeSH term(s)	Animals ; Astrocytoma/genetics ; Chromosomes, Human, Pair 19/genetics ; Disease Models, Animal ; Female ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Nerve Sheath Neoplasms/genetics ; Neurofibromatosis 1/genetics ; Sex Factors
Language	English
Publishing date	2009-04-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	1058547-3
ISSN	1432-1777 ; 0938-8990
ISSN (online)	1432-1777
ISSN	0938-8990
DOI	10.1007/s00335-009-9179-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Molecularly tagged simian immunodeficiency virus SIVmac239 synthetic swarm for tracking independent infection events.

Del Prete, Gregory Q / Park, Haesun / Fennessey, Christine M / Reid, Carolyn / Lipkey, Leslie / Newman, Laura / Oswald, Kelli / Kahl, Christoph / Piatak, Michael / Quiñones, Octavio A / Alvord, W Gregory / Smedley, Jeremy / Estes, Jacob D / Lifson, Jeffrey D / Picker, Louis J / Keele, Brandon F

Journal of virology

2014 Volume 88, Issue 14, Page(s) 8077–8090

Abstract: Following mucosal human immunodeficiency virus type 1 transmission, systemic infection is established by one or only a few viral variants. Modeling single-variant, mucosal transmission in nonhuman primates using limiting-dose inoculations with a diverse ... ...

Abstract	Following mucosal human immunodeficiency virus type 1 transmission, systemic infection is established by one or only a few viral variants. Modeling single-variant, mucosal transmission in nonhuman primates using limiting-dose inoculations with a diverse simian immunodeficiency virus isolate stock may increase variability between animals since individual variants within the stock may have substantial functional differences. To decrease variability between animals while retaining the ability to enumerate transmitted/founder variants by sequence analysis, we modified the SIVmac239 clone to generate 10 unique clones that differ by two or three synonymous mutations (molecular tags). Transfection- and infection-derived virus stocks containing all 10 variants showed limited phenotypic differences in 9 of the 10 clones. Twenty-nine rhesus macaques were challenged intrarectally or intravenously with either a single dose or repeated, limiting doses of either stock. The proportion of each variant within each inoculum and in plasma from infected animals was determined by using a novel real-time single-genome amplification assay. Each animal was infected with one to five variants, the number correlating with the dose. Longitudinal sequence analysis revealed that the molecular tags are highly stable with no reversion to the parental sequence detected in >2 years of follow-up. Overall, the viral stocks are functional and mucosally transmissible and the number of variants is conveniently discernible by sequence analysis of a small amplicon. This approach should be useful for tracking individual infection events in preclinical vaccine evaluations, long-term viral reservoir establishment/clearance research, and transmission/early-event studies. Importance: Human immunodeficiency virus type 1 transmission is established by one or only a few viral variants. Modeling of limited variant transmission in nonhuman primates with a diverse simian immunodeficiency virus isolate stock may increase the variability between animals because of functional differences in the individual variants within the stock. To decrease such variability while retaining the ability to distinguish and enumerate transmitted/founder variants by sequence analysis, we generated a viral stock with 10 sequence-identifiable but otherwise genetically identical variants. This virus was characterized in vitro and in vivo and shown to allow discrimination of distinct transmission events. This approach provides a novel nonhuman primate challenge system for the study of viral transmission, evaluation of vaccines and other prevention approaches, and characterization of viral reservoirs and strategies to target them.
MeSH term(s)	Animals ; Disease Models, Animal ; Genetic Variation ; Genotype ; Longitudinal Studies ; Macaca mulatta ; Plasma/virology ; RNA, Viral/genetics ; Sequence Analysis, DNA ; Simian Acquired Immunodeficiency Syndrome/virology ; Simian Immunodeficiency Virus/classification ; Simian Immunodeficiency Virus/genetics ; Simian Immunodeficiency Virus/isolation & purification
Chemical Substances	RNA, Viral
Language	English
Publishing date	2014-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.01026-14
Database	MEDical Literature Analysis and Retrieval System OnLINE

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