378 results on '"Tobias, John W."'
Search Results
102. Hypoxia activates the cyclooxygenase-2–prostaglandin E synthase axis
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Lee, James J., primary, Natsuizaka, Mitsuteru, additional, Ohashi, Shinya, additional, Wong, Gabrielle S., additional, Takaoka, Munenori, additional, Michaylira, Carmen Z., additional, Budo, Daniela, additional, Tobias, John W., additional, Kanai, Michiyuki, additional, Shirakawa, Yasuhiro, additional, Naomoto, Yoshio, additional, Klein-Szanto, Andres J.P., additional, Haase, Volker H., additional, and Nakagawa, Hiroshi, additional
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- 2009
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103. Identification of a Putative Network of Actin-Associated Cytoskeletal Proteins in Glomerular Podocytes Defined by Co-Purified mRNAs
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Nabet, Behnam, primary, Tsai, Arthur, additional, Tobias, John W., additional, and Carstens, Russ P., additional
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- 2009
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104. Identification of Glial Cell Line-Derived Neurotrophic Factor-Regulated Genes Important for Spermatogonial Stem Cell Self-Renewal in the Rat1
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Schmidt, Jonathan A., primary, Avarbock, Mary R., additional, Tobias, John W., additional, and Brinster, Ralph L., additional
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- 2009
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105. Colony stimulating factor 1 is an extrinsic stimulator of mouse spermatogonial stem cell self-renewal
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Oatley, Jon M., primary, Oatley, Melissa J., additional, Avarbock, Mary R., additional, Tobias, John W., additional, and Brinster, Ralph L., additional
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- 2009
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106. Analysis of gene expression in pancreatic islets from diet-induced obese mice
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Imai, Yumi, primary, Patel, Hiral R., additional, Doliba, Nicolai M., additional, Matschinsky, Franz M., additional, Tobias, John W., additional, and Ahima, Rexford S., additional
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- 2008
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107. HFR1 Is Crucial for Transcriptome Regulation in the Cryptochrome 1-Mediated Early Response to Blue Light in Arabidopsis thaliana
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Zhang, Xiao-Ning, primary, Wu, Yingjie, additional, Tobias, John W., additional, Brunk, Brian P., additional, Deitzer, Gerald F., additional, and Liu, Dongmei, additional
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- 2008
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108. Cdx1 and c-Myc Foster the Initiation of Transdifferentiation of the Normal Esophageal Squamous Epithelium toward Barrett's Esophagus
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Stairs, Douglas B., primary, Nakagawa, Hiroshi, additional, Klein-Szanto, Andres, additional, Mitchell, Shukriyyah D., additional, Silberg, Debra G., additional, Tobias, John W., additional, Lynch, John P., additional, and Rustgi, Anil K., additional
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- 2008
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109. Activation of β-catenin signaling programs embryonic epidermis to hair follicle fate
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Zhang, Yuhang, primary, Andl, Thomas, additional, Yang, Steven H., additional, Teta, Monica, additional, Liu, Fei, additional, Seykora, John T., additional, Tobias, John W., additional, Piccolo, Stefano, additional, Schmidt-Ullrich, Ruth, additional, Nagy, Andras, additional, Taketo, Makoto M., additional, Dlugosz, Andrzej A., additional, and Millar, Sarah E., additional
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- 2008
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110. Differential Effects of Interleukin-2 and Interleukin-15 versus Interleukin-21 on CD4+ Cutaneous T-Cell Lymphoma Cells
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Marzec, Michal, primary, Halasa, Krzysztof, additional, Kasprzycka, Monika, additional, Wysocka, Maria, additional, Liu, Xiaobin, additional, Tobias, John W., additional, Baldwin, Donald, additional, Zhang, Qian, additional, Odum, Niels, additional, Rook, Alain H., additional, and Wasik, Mariusz A., additional
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- 2008
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111. Matrix Metalloproteinase 13 (MMP13) and Tissue Inhibitor of Matrix Metalloproteinase 1 (TIMP1), Regulated by the MAPK Pathway, Are Both Necessary for Madin-Darby Canine Kidney Tubulogenesis
- Author
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Hellman, Nathan E., primary, Spector, June, additional, Robinson, Jonathan, additional, Zuo, Xiaofeng, additional, Saunier, Sophie, additional, Antignac, Corinne, additional, Tobias, John W., additional, and Lipschutz, Joshua H., additional
- Published
- 2008
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112. Parvin-β Inhibits Breast Cancer Tumorigenicity and Promotes CDK9-Mediated Peroxisome Proliferator-Activated Receptor Gamma 1 Phosphorylation
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Johnstone, Cameron N., primary, Mongroo, Perry S., additional, Rich, A. Sophie, additional, Schupp, Michael, additional, Bowser, Mark J., additional, deLemos, Andrew S., additional, Tobias, John W., additional, Liu, Yingqiu, additional, Hannigan, Gregory E., additional, and Rustgi, Anil K., additional
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- 2008
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113. Two distinct activation states of plasmacytoid dendritic cells induced by influenza virus and CpG 1826 oligonucleotide
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Iparraguirre, Amaya, primary, Tobias, John W, additional, Hensley, Scott E, additional, Masek, Katherine S, additional, Cavanagh, Lois L, additional, Rendl, Michael, additional, Hunter, Christopher A, additional, Ertl, Hildegund C, additional, von Andrian, Ulrich H, additional, and Weninger, Wolfgang, additional
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- 2007
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114. Form-Deprivation Myopia in Chick Induces Limited Changes in Retinal Gene Expression
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McGlinn, Alice M., primary, Baldwin, Donald A., additional, Tobias, John W., additional, Budak, Murat T., additional, Khurana, Tejvir S., additional, and Stone, Richard A., additional
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- 2007
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115. Halothane Binding Proteome in Human Brain Cortex
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Pan, Jonathan Z., primary, Xi, Jin, additional, Tobias, John W., additional, Eckenhoff, Maryellen F., additional, and Eckenhoff, Roderic G., additional
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- 2006
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116. Differential Gene Expression in Mouse Sclera during Ocular Development
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Zhou, Jie, primary, Rappaport, Eric F., additional, Tobias, John W., additional, and Young, Terri L., additional
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- 2006
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117. The miRNA-Processing Enzyme Dicer Is Essential for the Morphogenesis and Maintenance of Hair Follicles
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Andl, Thomas, primary, Murchison, Elizabeth P., additional, Liu, Fei, additional, Zhang, Yuhang, additional, Yunta-Gonzalez, Monica, additional, Tobias, John W., additional, Andl, Claudia D., additional, Seykora, John T., additional, Hannon, Gregory J., additional, and Millar, Sarah E., additional
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- 2006
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118. Rat brain DNA transcript profile of halothane and isoflurane exposure
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Pan, Jonathan Z., primary, Wei, Huafeng, additional, Hecker, James G., additional, Tobias, John W., additional, Eckenhoff, Roderic G., additional, and Eckenhoff, Maryellen Fazen, additional
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- 2006
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119. Inactivation of Myc in Murine Two-Hit B lymphomas Causes Dormancy with Elevated Levels of Interleukin 10 Receptor and CD20: Implications for Adjuvant Therapies
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Yu, Duonan, primary, Dews, Michael, additional, Park, Andrea, additional, Tobias, John W., additional, and Thomas-Tikhonenko, Andrei, additional
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- 2005
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120. Novel MAPK-dependent and -independent tubulogenes identified via microarray analysis of 3D-cultured Madin-Darby canine kidney cells.
- Author
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Chacon-Heszele, Maria F., Xiaofeng Zuo, Hellman, Nathan E., McKenna, Sarah, Soo Young Choi, Liwei Huang, Tobias, John W., Park, Kwon Moo, and Lipschutz, Joshua H.
- Subjects
MITOGEN-activated protein kinases ,MICROARRAY technology ,KIDNEY cell culture ,HEPATOCYTE growth factor ,MATRIX metalloproteinases ,CANIDAE - Abstract
Cystogenesis and tubulogenesis are basic building blocks for many epithelial organs, including the kidney. Most researchers have used two-dimensional (2D) cell culture to investigate signaling pathways downstream of hepatocyte growth factor (HGF). We hypothesize that threedimensional (3D) collagen-grown Madin-Darby canine kidney (MDCK) cells, which form cysts and then tubulate in response to HGF, are a much more in vivo-like system for the identification of novel tubulogenes. With the use of a canine microarray containing over 20,000 genes, 2,417 genes were identified as potential tubulogenes that were differentially regulated, exclusively in 3D-grown MDCK cells. Among these, 840 were dependent on MAPK signaling. Importantly, this work shows that many putative tubulogenes, previously identified via microarray analysis of 2D cultures, including by us, do not change in 3D culture and vice versa. The use of a 3D-culture system allowed for the identification of novel MAPKdependent and -independent genes that regulate early renal tubulogenesis in vitro, e.g., matrix metalloproteinase 1 (MMP1). Knockdown of MMP1 led to defects in cystogenesis and tubulogenesis in 3D-grown MDCK cells, most likely due to problems establishing normal polarity. We suggest that data obtained from 2D cultures, even those using MDCK cells treated with HGF, should not be automatically extrapolated to factors important for cystogenesis and tubulogenesis. Instead, 3D culture, which more closely replicates the biological environment and is therefore a more accurate model for identifying tubulogenes, is preferred. Results from the present analysis will be used to build a more accurate model of the signaling pathways that control cystogenesis and tubulogenesis. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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121. MicroRNA-21 regulates the self-renewal of mouse spermatogonial stem cells.
- Author
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Zhiyv Niu, Goodyear, Shaun M., Shilpa Rao, Xin Wu, Tobias, John W., Avarbock, Mary R., and Brinster, Ralph L.
- Subjects
STEM cells ,GENE expression ,APOPTOSIS ,HOMEOSTASIS ,SOMATIC cells - Abstract
MicroRNAs (miRs) play a key role in the control of gene expression in a wide array of tissue systems, where their functions include the regulation of self-renewal, cellular differentiation, proliferation, and apoptosis. However, the functional importance of individual miRs in controlling spermatogonial stem cell (SSC) homeostasis has not been investigated. Using high-throughput sequencing, we profiled the expression of miRs in the Thy1+ testis cell population, which is highly enriched for SSCs, and the Thy1- cell population, composed primarily of testis somatic cells. In addition, we profiled the global expression of miRs in cultured germ cells, also enriched for SSCs. Our results demonstrate that miR-21, along with miR-34c, -182, -183, and -146a, are preferentially expressed in the Thy1+ SSC-enriched population, compared with Thy1- somatic cells. Importantly, we demonstrate that transient inhibition of miR-21 in SSC-enriched germ cell cultures increased the number of germ cells undergoing apoptosis and significantly reduced the number of donor-derived colonies of spermatogenesis formed from transplanted treated cells in recipient mouse testes, indicating that miR-21 is important in maintaining the SSC population. Moreover, we show that in SSC-enriched germ cell cultures, miR-21 is regulated by the transcription factor ETV5, known to be critical for SSC self-renewal. [ABSTRACT FROM AUTHOR]
- Published
- 2011
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122. Prepubertal human spermatogonia and mouse gonocytes share conserved gene expression of germline stem cell regulatory molecules.
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Xin Wua, Schmidt, Jonathan A., Avarbock, Mary R., Tobias, John W., Carlson, Claire A., Kolon, Thomas F., Ginsberg, Jill P., and Brinster, Ralph L.
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GENE expression ,STEM cells ,PUBERTY ,SOMATIC cells ,GERM cells ,TESTIS ,SPERMATOGENESIS in animals ,LABORATORY mice ,TRANSPLANTATION of organs, tissues, etc. - Abstract
In the human testis, beginning at ≈2 months of age, gonocytes are replaced by adult dark (Ad) and pale (Ap) spermatogonia that make up the spermatogonial stem cell (SSC) pool. In mice, the SSC pool arises from gonocytes ≈6 days after birth. During puberty in both species, complete spermatogenesis is established by cells that differentiate from SSCs. Essentially pure populations of prepubertal human spermatogonia and mouse gonocytes were selected from testis biopsies and validated by confirming the presence of specific marker proteins in cells. Stem cell potential of germ cells was demonstrated by transplantation to mouse testes, following which the cells migrated to the basement membrane of the seminiferous tubule and were maintained similar to SSCs. Differential gene expression profiles generated between germ cells and testis somatic cells demonstrated that expression of genes previously identified as SSC and spermatogonial-specific markers (e.g., zinc-finger and BTB-domain containing 16, ZBTB16) was greatly elevated in both human spermatogonia and mouse gonocytes compared to somatic cells. Several genes were expressed at significantly higher levels in germ cells of both species. Most importantly, genes known to be essential for mouse SSC self-renewal (e.g., Ret proto-oncogene, Ret GDNF-family receptor α1 Gfrα1; and B-cell CLL/lymphoma 6, member B, BcI6b) were more highly expressed in both prepubertal human spermatogonia and mouse gonocytes than in somatic cells. The results indicate remarkable conservation of gene expression, notably for self-renewal genes, in these prepubertal germline cells between two species that diverged phylogenetically ≈75 million years ago. [ABSTRACT FROM AUTHOR]
- Published
- 2009
123. Lack of TNFα expression protects anaplastic lymphoma kinase-positive T-cell lymphoma (ALK+ TCL) cells from apoptosis.
- Author
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Qian Zhang, Wang, Hong V., Bhutani, Gauri, Xiaobin Liu, Paessler, Michele, Tobias, John W., Baldwin, Donald, Swaminathan, Kunchithapadam, Milone, Michael C., and Wasik, Mariusz A.
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GENE expression ,LYMPHOMAS ,T-cell lymphoma ,APOPTOSIS ,CELL death ,PROMOTERS (Genetics) - Abstract
Here we report that T-cell lymphomas characterized by the expression of anaplastic lymphoma kinase (ALK+ TCL) fail to express the TNFa and frequently display DNA methylation of the TNFα gene promoter. While only a subset of the ALK+ TCL-derived cell lines showed a high degree of the promoter methylation, all 6 showed low to nondetectable expression of the TNFα mRNA, and none expressed the TNFα protein. All 14 ALK+ TCL tissue samples examined displayed some degree of the TNFα promoter methylation, which was the most prominent in the distal portion of the the promoter. Treatment with a DNA methyltransferase inhibitor, 5′-aza-2′-deoxy-cytidine (5-ADC), reversed the promoter methylation and led to the expression of TNFα mRNA and protein. Furthermore, in vitro DNA methylation of the promoter impaired its transcriptional activity in the luciferase reporter assay. This impairment was seen even if only either distal or proximal portion were methylated, with methylation of the former exerting a more profound inhibitory effect. Notably, the ALK+ TCL cell lines uniformly expressed the type 1 TNFα receptor (TNF-R1) protein known to transduce the TNFα-induced pro-apoptotic signals. Moreover, exogeneous TNFα-inhibited growth of the ALK+ TCL cell lines in a dose-dependent manner and induced activation of the members of the cell apoptotic pathway: Caspase 8 and caspase 3. These findings provide additional rationale for the therapeutic inhibition of DNA methyltransferases in ALK+ TCL. They also suggest that treatment with TNFa may be highly effective in this type of lymphoma. [ABSTRACT FROM AUTHOR]
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- 2009
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124. HFR1 Is Crucial for Transcriptome Regulation in the Cryptochrome 1-Mediated Early Response to Blue Light in Arabidopsis thaliana.
- Author
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Xiao-Ning Zhang, Yingjie Wu, Tobias, John W., Brunk, Brian P., Deitzer, Gerald F., and Dongmei Liu
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CRYPTOCHROMES ,ARABIDOPSIS thaliana ,PLANT photoreceptors ,GENES ,GENETIC testing ,GENE expression ,PLANTS ,PHENOTYPES ,PHOTOSYNTHESIS - Abstract
Cryptochromes are blue light photoreceptors involved in development and circadian clock regulation. They are found in both eukaryotes and prokaryotes as light sensors. Long Hypocotyl in Far-Red 1 (HFR1) has been identified as a positive regulator and a possible transcription factor in both blue and far-red light signaling in plants. However, the gene targets that are regulated by HFR1 in cryptochrome 1 (cry1)-mediated blue light signaling have not been globally addressed. We examined the transcriptome profiles in a cry1- and HFR1-dependent manner in response to 1 hour of blue light. Strikingly, more than 70% of the genes induced by blue light in an HFR1-dependent manner were dependent on cry1, and vice versa. High overrepresentation of W-boxes and OCS elements were found in these genes, indicating that this strong cry1 and HFR1 co-regulation on gene expression is possibly through these two cis-elements. We also found that cry1 was required for maintaining the HFR1 protein level in blue light, and that the HFR1 protein level is strongly correlated with the global gene expression pattern. In summary, HFR1, which is fine-tuned by cry1, is crucial for regulating global gene expression in cry1-mediated early blue light signaling, especially for the function of genes containing W-boxes and OCS elements. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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125. Orthogonal analysis of C/EBP β targets in vivo during liver proliferation.
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Friedman, Joshua R., Larris, Brian, Le, Phillip P., Peiris, T. Harshani, Arsenlis, Athanasios, Schug, Jonathan, Tobias, John W., Kaestner, Klaus H., and Greenbaum, Linda E.
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CARRIER proteins ,LEUCINE ,CHROMATIN ,TRANSCRIPTION factors ,LIVER ,PROTEINS - Abstract
CCAAT enhancer-binding protein β (C/EBPβ), a basic-leucine zipper transcription factor, is an important effector of signals in physiologic growth and cancer. The identification of direct C/EBPβ targets in vivo has been limited by functional compensation by other C/EBP family proteins and the low stringency of the consensus sequence. Here we use the combined power of expression profiling and high-throughput chromatin immunoprecipitation to identify direct and biologically relevant targets of C/EBPβ. We identified 25 potential C/EBPβ targets, of which 88% of those tested were confirmed as in vivo C/EBPβ-binding sites. Six of these genes also displayed differential expression in C/EBPβ livers. Computational analysis revealed that bona fide C/EBPβ target genes can be distinguished by the presence of binding motifs for specific additional transcription factors in the vicinity of the C/EBPβ site. This approach is generally applicable to the discovery of direct biologically relevant targets of mammalian transcription factors. [ABSTRACT FROM AUTHOR]
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- 2004
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126. In Vivo and In Vitro Aging Is Detrimental to Mouse Spermatogonial Stem Cell Function1
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Schmidt, Jonathan A., Abramowitz, Lara K., Kubota, Hiroshi, Wu, Xin, Niu, Zhiyv, Avarbock, Mary R., Tobias, John W., Bartolomei, Marisa S., and Brinster, Ralph L.
- Abstract
The development of techniques to maintain the spermatogonial stem cell (SSC) in vivo and in vitro for extended periods essentially allows for the indefinite continuation of an individual germline. Recent evidence indicates that the aging of male reproductive function is due to failure of the SSC niche. SSCs are routinely cultured for 6 mo, and no apparent effect of culture over this period has been observed. To determine the effects of SSC aging, we utilized an in vitro culture system, followed by quantitative transplantation experiments. After culture for 6 mo, SSCs that had been aged in vivo for 1500 days had a slower proliferation rate than SSCs that were aged in vivo to 8 or 300 days. Examination of methylation patterns revealed no apparent difference in DNA methylation between SSCs that were aged 8, 300, or 1500 days before culture. Long-term culture periods resulted in a loss of stem cell potential without an obvious change in the visual appearance of the culture. DNA microarray analysis of in vivo- and in vitro-aged SSCs identified the differential expression of several genes important for SSC function, including B-cell CLL/lymphoma 6, member B (Bcl6b), Lim homeobox protein 1 (Lhx1), and thymus cell antigen 1, theta (Thy1). Collectively, these data indicate that, although both in vitro and in vivo aging are detrimental to SSC function, in vitro aging results in greater loss of function, potentially due to a decrease in core SSC self-renewal gene expression and an increase in germ cell differentiation gene expression.
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- 2011
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127. Accelerated photo-oxidation of polyethylene. II. Further evaluation of selected additives.
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Taylor, Lynn J. and Tobias, John W.
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- 1981
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128. Accelerated photo-oxidation of polyethylene. I. Screening of degradation-sensitizing additives.
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Taylor, Lynn J. and Tobias, John W.
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- 1977
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129. Shrinkage behavior of oriented PVC by thermomechanical analysis.
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Tobias, John W. and Taylor, Lynn J.
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- 1975
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130. Two distinct activation states of plasmacytoid dendritic cells induced by influenza virus and CpG 1826 oligonucleotide
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Iparraguirre, Amaya, Tobias, John W., Hensley, Scott E., Masek, Katherine S., Cavanagh, Lois L., Rendl, Michael, Hunter, Christopher A., Ertl, Hildegund C., Andrian, Ulrich. H., and Weninger, Wolfgang
- Abstract
There is growing evidence that plasmacytoid dendritic cells (pDC) are involved in the innate recognition of various microbes. However, the precise consequences of pathogen recognition on pDC activation and function are incompletely understood. Using a novel transgenic mouse model that facilitates the isolation of highly pure pDC populations, we found that influenza virus PR/8, a TLR7 ligand, and CpG 1826 oligonucleotide, a TLR9 ligand, induced surprisingly divergent activation programs in these cells. pDC stimulated with PR/8 produced large amounts of type I IFNs, and CpG 1826‐stimulated pDC expressed higher levels of costimulatory molecules and proinflammatory cytokines and induced stronger proliferation of T cells. Transcriptome analysis uncovered the differential regulation in pDC of 178 and 1577 genes by PR/8 and CpG 1826, respectively. These differences may relate to the activation of discrete signaling pathways, as evidenced by distinct ERK1/2 and p38 MAPK phosphorylation kinetics. Finally, pDC isolated ex vivo during PR/8 infection or after i.v. CpG 1826 injection resembled their in vitro counterparts, corroborating that these cells can adopt specialized phenotypes in vivo. Thus, pDC display remarkable functional flexibility, which emphasizes their versatile functions in antimicrobial immunity and inflammatory processes.
- Published
- 2008
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131. Gene Expression Profiling to Predict Viridans Group Streptococcal and Invasive Fungal Infection in Pediatric Acute Myeloid Leukemia: A Brief Report from the Children's Oncology Group.
- Author
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Lee, Grace E., Sung, Lillian, Fisher, Brian T., Sullivan, Kathleen E., McWilliams, Tom, Tobias, John W., Meshinchi, Soheil, alonzo, Todd a., Gamis, alan, and aplenc, Richard
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GENE expression ,VIRIDANS strepotococci ,MYCOSES ,ACUTE myeloid leukemia in children ,PEDIATRIC therapy - Abstract
No abstract available [ABSTRACT FROM AUTHOR]
- Published
- 2014
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132. Molecular profiling of failed endochondral ossification in mucopolysaccharidosis VII.
- Author
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Peck, Sun H., Tobias, John W., Shore, Eileen M., Malhotra, Neil R., Haskins, Mark E., Casal, Margret L., and Smith, Lachlan J.
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ENDOCHONDRAL ossification , *BONE diseases , *CHONDROITIN sulfates , *BONE growth , *SKELETAL abnormalities - Abstract
Mucopolysaccharidosis (MPS) VII is a lysosomal storage disorder characterized by deficient activity of β-glucuronidase, leading to progressive accumulation of incompletely degraded heparan, dermatan, and chondroitin sulfate glycosaminoglycans (GAGs). Patients with MPS VII exhibit progressive skeletal deformity including kyphoscoliosis and joint dysplasia, which decrease quality of life and increase mortality. Previously, using the naturally-occurring canine model, we demonstrated that one of the earliest skeletal abnormalities to manifest in MPS VII is failed initiation of secondary ossification in vertebrae and long bones at the requisite postnatal developmental stage. The objective of this study was to obtain global insights into the molecular mechanisms underlying this failed initiation of secondary ossification. Epiphyseal tissue was isolated postmortem from the vertebrae of control and MPS VII-affected dogs at 9 and 14 days-of-age (n = 5 for each group). Differences in global gene expression across this developmental window for both cohorts were measured using whole-transcriptome sequencing (RNA-Seq). Principal Component Analysis revealed clustering of samples within each group, indicating clear effects of both age and disease state. At 9 days-of-age, 1375 genes were significantly differentially expressed between MPS VII and control, and by 14 days-of-age, this increased to 4719 genes. A targeted analysis focused on signaling pathways important in the regulation of endochondral ossification was performed, and a subset of gene expression differences were validated using qPCR. Osteoactivin (GPNMB) was the top upregulated gene in MPS VII at both ages. In control samples, temporal changes in gene expression from 9 to 14 days-of-age were consistent with chondrocyte maturation, cartilage resorption, and osteogenesis. In MPS VII samples, however, elements of key osteogenic pathways such as Wnt/β-catenin and BMP signaling were not upregulated during this same developmental window suggesting that important bone formation pathways are not activated. In conclusion, this study represents an important step towards identifying therapeutic targets and biomarkers for bone disease in MPS VII patients during postnatal growth. • Failed endochondral ossification in MPS VII is associated with broad dysregulation of osteogenic signaling pathways. • Dysregulated gene expression precedes tissue level abnormalities in MPS VII secondary ossification centers. • Wnt and BMP signaling pathways may represent druggable targets for normalizing bone formation in MPS VII patients. • Glycoprotein non-metastatic melanoma B (osteoactivin) may represent a biomarker of skeletal disease severity in MPS VII. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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133. Monocyte Adhesion to Subendothelial Components
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Tobias, John W., Bern, Murray M., Netland, Peter A., and Zetter, Bruce R.
- Abstract
Human monocytes have been shown to penetrate the endothelial layer of large blood vessels and to adhere to the subendothelial basement membrane. To determine the active components of this process, we have studied the ability of monocytes to adhere to isolated components of the subendothelial matrix. Using a quantitative dot-blot adhesion assay, we find that monocytes adhere preferen-tially to immobilized laminin and elastin. The monocytes adhere less well to fibronectin and bind poorly or not at all to collagen types I and IV, or to heparan sulfate. Monocyte binding to elastin requires an intact, crosslinked molecule as no binding was observed to soluble, acid-alcohol elastin extracts, to pepsin or elastase digests of elastin, to tropo-elastin monomer, or to desmosine/isodesmosine cross-links. Similar binding profiles to elastin, laminin, and fibron-ectin were seen with the established human leukocyte cell line U937. The promyelocyte cell line HL60 adhered equally well to laminin but showed slightly reduced adhesion to elastin when compared with the fresh monocytes or U937 cells. Freshly isolated human erythrocytes did not demon-strate significant adhesion to fibronectin, laminin, or elastin.
- Published
- 1987
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134. Menin Maintains Cholesterol Content in Colorectal Cancer via Repression of LXR-Mediated Transcription.
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Nyul, Thomas E., Beyries, Keely, Hojnacki, Taylor, Glynn, Rebecca, Paulosky, Kayla E., Gedela, Anitej, Majer, Ariana, Altman, Lily, Buckley, Kole H., Feng, Zijie, Sun, Kunfeng, Peng, Zhicheng, Tobias, John W., Hua, Xianxin, and Katona, Bryson W.
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PROTEIN metabolism , *IN vitro studies , *BIOCHEMISTRY , *REPRESSION (Psychology) , *IN vivo studies , *SEQUENCE analysis , *ANIMAL experimentation , *PHENOMENOLOGICAL biology , *COLORECTAL cancer , *CELLULAR signal transduction , *GENE expression , *COMPARATIVE studies , *DNA-binding proteins , *RESEARCH funding , *DESCRIPTIVE statistics , *CHALONES , *TRANSCRIPTION factors , *CELL lines , *CHOLESTEROL , *MICE - Abstract
Simple Summary: Colorectal cancer (CRC) is the leading cause of cancer-related death worldwide, and new therapeutic approaches are direly needed to improve the outcomes of metastatic disease. Herein, we uncover that menin, a nuclear scaffold protein that has a myriad of tissue-specific effects on gene transcription, serves as a novel regulator of cholesterol homeostasis in CRC cell lines in vitro and in the benign colonic epithelium in vivo. Specifically, we demonstrate that menin inhibits the transcription of LXR-regulated genes, including the cholesterol exporters ABCA1 and ABCG1, leading to increased cellular cholesterol content. Conversely, menin inhibition reduces total cellular cholesterol content and sensitizes CRC to small molecule EGFR inhibitors and lipid-poor conditions. These combined findings demonstrate that menin is a key regulator of cholesterol homeostasis in both CRC and the colonic epithelium, and targeting menin may be an effective route for improving therapies for CRC. Background and Aims: Menin is a nuclear scaffold protein that regulates gene transcription in an oftentimes tissue-specific manner. Our previous work showed that menin is over-expressed in colorectal cancer (CRC); however, the full spectrum of menin function in colonic neoplasia remains unclear. Herein, we aimed to uncover novel menin-regulated pathways important for colorectal carcinogenesis. Methods: RNA-Seq analysis identified that menin regulates LXR-target gene expressions in CRC cell lines. Isolated colonic epithelium from Men1f/f;Vil1-Cre and Men1f/f mice was used to validate the results in vivo. Cholesterol content was quantified via an enzymatic assay. Results: RNA-Seq analysis in the HT-29 CRC cell line identified that menin inhibition upregulated LXR-target genes, specifically ABCG1 and ABCA1, with protein products that promote cellular cholesterol efflux. Similar results were noted across other CRC cell lines and with different methods of menin inhibition. Consistent with ABCG1 and ABCA1 upregulation, and similarly to LXR agonists, menin inhibition reduced the total cellular cholesterol in both HT-29 and HCT-15 cells. To confirm the effects of menin inhibition in vivo, we assessed Men1f/f;Vil1-Cre mice lacking menin expression in the colonic epithelium. Men1f/f;Vil1-Cre mice were found to have no distinct baseline phenotype compared to control Men1f/f mice. However, similarly to CRC cell lines, Men1f/f;Vil1-Cre mice showed an upregulation of Abcg1 and a reduction in total cellular cholesterol. Promoting cholesterol efflux, either via menin inhibition or LXR activation, was found to synergistically suppress CRC cell growth under cholesterol-depleted conditions and when administered concomitantly with small molecule EGFR inhibitors. Conclusions: Menin represses the transcription of LXR-target genes, including ABCA1 and ABCG1 in the colonic epithelium and CRC. Menin inhibition conversely upregulates LXR-target genes and reduces total cellular cholesterol, demonstrating that menin inhibition may be an important mechanism for targeting cholesterol-dependent pathways in colorectal carcinogenesis. [ABSTRACT FROM AUTHOR]
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- 2023
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135. In Vivo and In Vitro Aging Is Detrimental to Mouse Spermatogonial Stem Cell Function1
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Schmidt, Jonathan A., Abramowitz, Lara K., Kubota, Hiroshi, Wu, Xin, Niu, Zhiyv, Avarbock, Mary R., Tobias, John W., Bartolomei, Marisa S., and Brinster, Ralph L.
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- 2010
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136. Activation of β-catenin signaling programs embryonic epidermis to hair follicle fate.
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Yuhang Zhang, Andl, Thomas, Yang, Steven H., Teta, Monica, Fei Liu, Seykora, John T., Tobias, John W., Piccolo, Stefano, Schmidt-Ullrich, Ruth, Nagy, Andras, Taketo, Makoto M., Dlugosz, Andrzej A., and Millar, Sarah E.
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EPIDERMIS ,HAIR follicles ,PLACODES ,CELL differentiation ,KERATIN ,PROTEINS - Abstract
β-Catenin signaling is required for hair follicle development, but it is unknown whether its activation is sufficient to globally program embryonic epidermis to hair follicle fate. To address this, we mutated endogenous epithelial β-catenin to a dominant-active form in vivo. Hair follicle placodes were expanded and induced prematurely in activated β-catenin mutant embryos, but failed to invaginate or form multilayered structures. Eventually, the entire epidermis adopted hair follicle fate, broadly expressing hair shaft keratins in place of epidermal stratification proteins. Mutant embryonic skin was precociously innervated, and displayed prenatal pigmentation, a phenomenon never observed in wild-type controls. Thus, β-catenin signaling programs the epidermis towards placode and hair shaft fate at the expense of epidermal differentiation, and activates signals directing pigmentation and innervation. In transcript profiling experiments, we identified elevated expression of Sp5, a direct β-catenin target and transcriptional repressor. We show that Sp5 normally localizes to hair follicle placodes and can suppress epidermal differentiation gene expression. We identified the pigmentation regulators Foxn1, Adamts20 and Kitl, and the neural guidance genes Sema4c, Sema3c, Unc5b and Unc5c, as potential mediators of the effects of β-catenin signaling on pigmentation and innervation. Our data provide evidence for a new paradigm in which, in addition to promoting hair follicle placode and hair shaft fate, β-catenin signaling actively suppresses epidermal differentiation and directs pigmentation and nerve fiber growth. Controlled downregulation of β-catenin signaling is required for normal placode patterning within embryonic ectoderm, hair follicle downgrowth, and adoption of the full range of follicular fates. [ABSTRACT FROM AUTHOR]
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- 2008
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137. TRIB1 regulates LDL metabolism through CEBPα-mediated effects on the LDL receptor in hepatocytes.
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Quiroz-Figueroa, Katherine, Vitali, Cecilia, Conlon, Donna M., Millar, John S., Tobias, John W., Bauer, Robert C., Hand, Nicholas J., and Rader, Daniel J.
- Abstract
Genetic variants near the TRIB1 gene are highly significantly associated with plasma lipid traits and coronary artery disease. While TRIB1 is likely causal of these associations, the molecular mechanisms are not well understood. Here we sought to investigate how TRIB1 influences low density lipoprotein cholesterol (LDL-C) levels in mice. Hepatocyte-specific deletion of Trib1 (Trib1Δhep) in mice increased plasma cholesterol and apoB and slowed the catabolism of LDL-apoB due to decreased levels of LDL receptor (LDLR) mRNA and protein. Simultaneous deletion of the transcription factor CCAAT/enhancer-binding protein alpha (CEBPα) with TRIB1 eliminated the effects of TRIB1 on hepatic LDLR regulation and LDL catabolism. Using RNA-seq, we found that activating transcription factor 3 (Atf3) was highly upregulated in the livers of Trib1Δhep but not Trib1Δhep CebpaΔhep mice. ATF3 has been shown to directly bind to the CEBPα protein, and to repress the expression of LDLR by binding its promoter. Blunting the increase of ATF3 in Trib1Δhep mice reduced the levels of plasma cholesterol and partially attenuated the effects on LDLR. Based on these data, we conclude that deletion of Trib1 leads to a posttranslational increase in CEBPα, which increases ATF3 levels, thereby contributing to the downregulation of LDLR and increased plasma LDL-C. [ABSTRACT FROM AUTHOR]
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- 2021
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138. Genome-wide analyses and functional profiling of human NK cell lines.
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Gunesch, Justin T., Angelo, Laura S., Mahapatra, Sanjana, Deering, Raquel P., Kowalko, Johanna E., Sleiman, Patrick, Tobias, John W., Monaco-Shawver, Linda, Orange, Jordan S., and Mace, Emily M.
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CELL lines , *FUNCTIONAL analysis , *KILLER cells - Abstract
• Found 557 genes with >50-fold difference in expression between at least 2 cell lines. • NK92 cells have a CD56bright-like phenotype while YTS cells are CD56dim-like. • Identified 417 genes differentially expressed between lytic and less lytic cell lines. Natural killer (NK) cell lines, including YTS, NK92, NK3.3, and NKL, represent excellent models for the study of human natural killer cells. While phenotypic and functional differences between these cell lines have been reported, a multi-parametric study, encompassing genomic, phenotypic, and functional assays, has not been performed. Here, using a combination of techniques including microarray and copy number analyses, flow cytometry, and functional assays, we provide in-depth genetic, functional, and phenotypic comparison of YTS, NK92, NK3.3, and NKL cell lines. Specifically, we found that while the cell lines shared similarities in enrichment of growth and survival pathways, they had differential expression of 557 genes, including genes related to NK cell development, survival, and function. In addition, we provide genetic and phenotypic analyses that demonstrate distinct developmental origins of NK92, YTS, and NKL cell lines. Specifically, NK92 has a phenotype associated with the CD56bright NK cell subset, while both YTS and NKL appear more CD56dim-like. Finally, by classifying cell lines based on their lytic potential, we identified genes differentially expressed between NK cell lines with high and low lytic function. Taken together, these data provide the first comprehensive genetic, phenotypic, and functional analyses of these commonly used NK cell lines and provides deeper understanding into their origins and function. This will ultimately improve their use as models for human NK cell biology. [ABSTRACT FROM AUTHOR]
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- 2019
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139. Tumor cell-intrinsic EPHA2 suppresses anti-tumor immunity by regulating PTGS2 (COX-2).
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Markosyan, Nune, Jinyang Li, Sun, Yu H., Richman, Lee P., Lin, Jeffrey H., Fangxue Yan, Quinones, Liz, Sela, Yogev, Taiji Yamazoe, Gordon, Naomi, Tobias, John W., Byrne, Katelyn T., Rech, Andrew J., FitzGerald, Garret A., Stanger, Ben Z., Vonderheide, Robert H., Li, Jinyang, Yan, Fangxue, and Yamazoe, Taiji
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T cells , *IMMUNITY , *TUMORS , *TUMOR microenvironment - Abstract
Resistance to immunotherapy is one of the biggest problems of current oncotherapeutics. WhileT cell abundance is essential for tumor responsiveness to immunotherapy, factors that define the T cell inflamed tumor microenvironment are not fully understood. We conducted an unbiased approach to identify tumor-intrinsic mechanisms shaping the immune tumor microenvironment(TME), focusing on pancreatic adenocarcinoma because it is refractory to immunotherapy and excludes T cells from the TME. From human tumors, we identified EPHA2 as a candidate tumor intrinsic driver of immunosuppression. Epha2 deletion reversed T cell exclusion and sensitized tumors to immunotherapy. We found that PTGS2, the gene encoding cyclooxygenase-2, lies downstream of EPHA2 signaling through TGFβ and is associated with poor patient survival. Ptgs2 deletion reversed T cell exclusion and sensitized tumors to immunotherapy; pharmacological inhibition of PTGS2 was similarly effective. Thus, EPHA2-PTGS2 signaling in tumor cells regulates tumor immune phenotypes; blockade may represent a novel therapeutic avenue for immunotherapy-refractory cancers. Our findings warrant clinical trials testing the effectiveness of therapies combining EPHA2-TGFβ-PTGS2 pathway inhibitors with anti-tumor immunotherapy, and may change the treatment of notoriously therapy-resistant pancreatic adenocarcinoma. [ABSTRACT FROM AUTHOR]
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- 2019
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140. Age-Associated B Cells Express a Diverse Repertoire of VH and Vκ Genes with Somatic Hypermutation.
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Knode, Lisa M. Russell, Naradikian, Martin S., Myles, Arpita, Scholz, Jean L., Yi Hao, Liu, Danya, Ford, Mandy L., Tobias, John W., Cancro, Michael P., and Gearhart, Patricia J.
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B cells , *LYMPHOID tissue , *PARASITIC diseases , *LABORATORY mice , *FLOW cytometry , *PHYSIOLOGY - Abstract
The origin and nature of age-associated B cells (ABCs) in mice are poorly understood. In this article, we show that their emergence required MHC class II and CD40/CD40L interactions. Young donor B cells were adoptively transferred into congenic recipients and allowed to remain for 1 mo in the absence of external Ag. B cells expressing the T-bet transcription factor, a marker for ABCs, were generated after multiple cell divisions from C57BL/6 donors but not from MHC class II- or CD40-deficient donors. Furthermore, old CD154 (CD40L)-deficient mice did not accrue ABCs, confirming that they arise primarily through T-dependent interactions. To determine what Igs ABCs express, we sequenced VH and Vκ rearranged genes from unimmunized 22-mo-old C57BL/6 mice and showed that they had a heterogeneous repertoire, which was comparable to that seen in old follicular and marginal zone B cell subsets. However, in contrast to the follicular and marginal zone cells, ABCs displayed significant somatic hypermutation. The mutation frequency was lower than found in germinal center cells after deliberate immunization, suggesting that ABCs have undergone mild stimulation from endogenous Ags over time. These observations show that quiescent ABCs are Ag-experienced cells that accumulate during T cell-dependent responses to diverse Ags during the life of an individual. [ABSTRACT FROM AUTHOR]
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- 2017
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141. Iron-induced Local Complement Component 3 (C3) Up-regulation via Non-canonical Transforming Growth Factor (TGF)-β Signaling in the Retinal Pigment Epithelium.
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Yafeng Li, Delu Song, Ying Song, Liangliang Zhao, Wolkow, Natalie, Tobias, John W., Wenchao Song, and Dunaief, Joshua L.
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TRANSFORMING growth factors-beta , *RETINAL degeneration , *IRON in the body , *RETINAL diseases , *RHODOPSIN , *EPITHELIUM - Abstract
Dysregulation of iron homeostasis may be a pathogenic factor in age-related macular degeneration (AMD). Meanwhile, the formation of complement-containing deposits under the retinal pigment epithelial (RPE) cell layer is a pathognomonic feature of AMD. In this study, we investigated the molecular mechanisms by which complement component 3 (C3), a central protein in the complement cascade, is up-regulated by iron in RPE cells. Modulation of TGF-β signaling, involving ERK1/2, SMAD3, and CCAAT/enhancer-binding protein-δ, is responsible for iron-induced C3 expression. The differential effects of spatially distinct SMAD3 phosphorylation sites at the linker region and at the C terminus determined the up-regulation of C3. Pharmacologic inhibition of either ERK1/2 or SMAD3 phosphorylation decreased iron-induced C3 expression levels. Knockdown of SMAD3 blocked the iron-induced up-regulation and nuclear accumulation of CCAAT/enhancer-binding protein-δ, a transcription factor that has been shown previously to bind the basic leucine zipper 1 domain in the C3 promoter. We show herein that mutation of this domain reduced iron-induced C3 promoter activity. In vivo studies support our in vitro finding of iron-induced C3 up-regulation. Mice with a mosaic pattern of RPE-specific iron overload demonstrated co-localization of iron-induced ferritin and C3d deposits. Humans with aceruloplasminemia causing RPE iron overload had increased RPE C3d deposition. The molecular events in the iron-C3 pathway represent therapeutic targets for AMD or other diseases exacerbated by iron-induced local complement dysregulation. [ABSTRACT FROM AUTHOR]
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- 2015
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142. Malignant Transformation of CD4+ T Lymphocytes Mediated by Oncogenic Kinase NPM/ALK Recapitulates IL-2-Induced Cell Signaling and Gene Expression Reprogramming.
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Marzec, Michal, Halasa, Krzysztof, Xiaobin Liu, Wang, Hong Y., Mangeng Cheng, Baldwin, Donald, Tobias, John W., Schuster, Stephen J., Woetmann, Anders, Qian Zhang, Turner, Suzanne D., Ødum, Niels, and Wasik, Mariusz A.
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LYMPHOCYTE metabolism , *T cells , *GENE expression , *ONCOGENIC proteins , *ANAPLASTIC lymphoma kinase , *NUCLEOPHOSMIN - Abstract
Anaplastic lymphoma kinase (ALK), physiologically expressed only by nervous system cells, displays a remarkable capacity to transform CD4+ T lymphocytes and other types of nonneural cells. In this study, we report that activity of nucleophosmin (NPM)/ALK chimeric protein, the dominant form of ALK expressed in T cell lymphomas (TCLs), closely resembles cell activation induced by IL-2, the key cytokine supporting growth and survival of normal CD4+ T lymphocytes. Direct comparison of gene expression by ALK+ TCL cells treated with an ALK inhibitor and IL-2-dependent ALK- TCL cells stimulated with the cytokine revealed a very similar, albeit inverse, gene-regulation pattern. Depending on the analysis method, up to 67% of the affected genes were modulated in common by NPM/ALK and IL-2. Based on the gene expression patterns, Jak/ STAT- and IL-2-signaling pathways topped the list of pathways identified as affected by both IL-2 and NPM/ALK. The expression dependence on NPM/ALK and IL-2 of the five selected genes--CD25 (IL-2Rα), Egr-1, Fosl-1, SOCS3, and Irf-4--was confirmed at the protein level. In both ALK+ TCL and IL-2-stimulated ALK- TCL cells, CD25, SOCS3, and Irf-4 genes were activated predominantly by the STAT5 and STAT3 transcription factors, whereas transcription of Egr-1 and Fosl-1 was induced by the MEK-ERK pathway. Finally, we found that Egr-1, a protein not associated previously with either IL-2 or ALK, contributes to the cell proliferation. These findings indicate that NPM/ALK transforms the target CD4+ T lymphocytes, at least in part, by using the pre-existing, IL-2-dependent signaling pathways. [ABSTRACT FROM AUTHOR]
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- 2013
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143. Matrix Metalloproteinase 13 (MMP1 3) and Tissue Inhibitor of Matrix Metalloproteinase 1 (TIMP1), Regulated by the MAPK Pathway, Are Both Necessary for Madin-Darby Canine Kidney Tubulogenesis.
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Hellman, Nathan E., Spector, June, Robinson, Jonathan, Xiaofeng Zuo, Saunier, Sophie, Antignac, Corinne, Tobias, John W., and Lipschutz, Joshua H.
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METALLOPROTEINASES , *HEPATOCYTE growth factor , *KIDNEY diseases , *EPITHELIAL cells , *MITOGENS - Abstract
A classic model of tubulogenesis utilizes Madin-Darby canine kidney (MDCK) cells. MDCK cells form monoclonal cysts in three-dimensional collagen and tubulate in response to hepatocyte growth factor, which activates multiple signaling pathways, including the mitogen-activated protein kinase (MAPK) pathway. It was shown previously that MAPK activation is necessary and sufficient to induce the first stage of tubulogenesis, the partial epithelial to mesenchymal transition (p-EMT), whereas matrix metalloproteinases (MMPs) are necessary for the second redifferentiation stage. To identify specific MMP genes, their regulators, tissue inhibitors of matrix metalloproteinases (TIMPs), and the molecular pathways by which they are activated, we used two distinct MAPK inhibitors and a technique we have termed subtraction pathway microarray analysis. Of the 19 MMPs and 3 TIMPs present on the Canine Genome 2.0 Array, MMP13 and TIMP1 were up-regulated 198- and 169-fold, respectively, via the MAPK pathway. This was confirmed by two-dimensional and three-dimensional real time PCR, as well as in MDCK cells inducible for the MAPK gene Raf Knockdown of MMP13 using short hairpin RNA prevented progression past the initial phase of p-EMT. Knockdown of TIMP1 prevented normal cystogenesis, although the initial phase of p-EMT did occasionally occur. The MMP13 knockdown phenotype is likely because of decreased collagenase activity, whereas the TIMP1 knockdown phenotype appears due to increased apoptosis. These data suggest a model, which may also be important for development of other branched organs, whereby the MAPK pathway controls both MDCK p-EMT and redifferentiation, in part by activating MMP13 and TIMP1. [ABSTRACT FROM AUTHOR]
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- 2008
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144. High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing
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Federico M. Giorgi, Steven Mulackal Thomas, Yanghee Woo, John W. Tobias, Antonia R. Sepulveda, Jorge L. Sepulveda, Andrea Califano, Jorge L Gutierrez-Pajares, Aesis M. Luna, Timothy C. Wang, Elena V. Komissarova, Yuan Yao, Sepulveda, Jorge L., Gutierrez-Pajares, Jorge L., Luna, Aesi, Yao, Yuan, Tobias, John W., Thomas, Steven, Woo, Yanghee, Giorgi, Federico, Komissarova, Elena V., Califano, Andrea, Wang, Timothy C., and Sepulveda, Antonia R.
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0301 basic medicine ,Pathology ,medicine.medical_specialty ,Prognosi ,Chronic gastritis ,Predictive Value of Test ,Biology ,Adenocarcinoma ,Pathology and Forensic Medicine ,Epigenesis, Genetic ,03 medical and health sciences ,0302 clinical medicine ,SGCE ,Predictive Value of Tests ,Stomach Neoplasms ,Gastrectomy ,Stomach Neoplasm ,Databases, Genetic ,medicine ,Gastric mucosa ,Biomarkers, Tumor ,Humans ,Genetic Predisposition to Disease ,Epigenetics ,Regulation of gene expression ,Metaplasia ,Gastriti ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Methylation ,Sequence Analysis, DNA ,DNA Methylation ,medicine.disease ,Prognosis ,digestive system diseases ,030104 developmental biology ,medicine.anatomical_structure ,Cell Transformation, Neoplastic ,Phenotype ,CpG site ,Gastric Mucosa ,030220 oncology & carcinogenesis ,Gastritis ,DNA methylation ,Disease Progression ,CpG Islands ,CpG Island ,Human - Abstract
Gastric cancers are the most frequent gastric malignancy and usually arise in the sequence of Helicobacter pylori-associated chronic gastritis. CpG methylation is a central mechanism of epigenetic gene regulation affecting cancer-related genes, and occurs early in gastric carcinogenesis. DNA samples from non-metaplastic gastric mucosa with variable levels of gastritis (non-metaplastic mucosa), intestinal metaplasia, or gastric cancer were screened with methylation arrays for CpG methylation of cancer-related genes and 30 gene targets were further characterized by high-definition bisulfite next-generation sequencing. In addition, data from The Cancer Genome Atlas were analyzed for correlation of methylation with gene expression. Overall, 13 genes had significantly increased CpG methylation in gastric cancer vs non-metaplastic mucosa (BRINP1, CDH11, CHFR, EPHA5, EPHA7, FGF2, FLI1, GALR1, HS3ST2, PDGFRA, SEZ6L, SGCE, and SNRPN). Further, most of these genes had corresponding reduced expression levels in gastric cancer compared with intestinal metaplasia, including novel hypermethylated genes in gastric cancer (FLI1, GALR1, SGCE, and SNRPN), suggesting that they may regulate neoplastic transformation from non-malignant intestinal metaplasia to cancer. Our data suggest a tumor-suppressor role for FLI1 in gastric cancer, consistent with recently reported data in breast cancer. For the genes with strongest methylation/expression correlation, namely FLI1, the expression was lowest in microsatellite-unstable tumors compared with other gastric cancer molecular subtypes. Importantly, reduced expression of hypermethylated BRINP1 and SGCE was significantly associated with favorable survival in gastric cancer. In summary, we report novel methylation gene targets that may have functional roles in discrete stages of gastric carcinogenesis and may serve as biomarkers for diagnosis and prognosis of gastric cancer.
- Published
- 2016
145. Pivotal roles for cancer cell-intrinsic mPGES-1 and autocrine EP4 signaling in suppressing anti-tumor immunity.
- Author
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Markosyan N, Kim IK, Arora C, Quinones-Ware L, Joshi N, Cheng NC, Schechter EY, Tobias JW, Hochberg JE, Corse E, Liu K, Rodriguez DiBlasi V, Chan LC, Smyth EM, Fitzgerald GA, Stanger BZ, and Vonderheide RH
- Abstract
Tumor cell-derived prostaglandin E2 (PGE2) is a tumor cell-intrinsic factor that supports immunosuppression in the tumor microenvironment (TME) by acting on the immune cells, but the impact of PGE2 signaling in tumor cells on immunosuppressive TME is unclear. We demonstrate that deleting the PGE2 synthesis enzyme or disrupting autocrine PGE2 signaling through EP4 receptors on tumor cells reverses the T cell-low, myeloid cell-rich TME, activates T cells, and suppresses tumor growth. Knockout (KO) of Ptges (the gene encoding PGE2 synthesis enzyme mPGES-1) or the EP4 receptor gene (Ptger4) in KPCY (KrasG12D/P53R172H/Yfp/CrePdx) pancreatic tumor cells abolished growth of implanted tumors in a T cell-dependent manner. Blockade of the EP4 receptor in combination with immunotherapy, but not immunotherapy alone, induced complete tumor regressions and immunological memory. Mechanistically, Ptges and Ptger4 KO tumor cells exhibited altered T and myeloid cell attractant chemokines, became more susceptible to TNF-α killing, and exhibited reduced adenosine synthesis. In hosts treated with an adenosine deaminase inhibitor, Ptger4 KO tumor cells accumulated adenosine and gave rise to tumors. These studies reveal an unexpected finding - a non-redundant role for the autocrine mPGES1-PGE2-EP4 signaling axis in pancreatic cancer cells - further nominating mPGES-1 inhibition and EP4 blockade as immune-sensitizing therapy in cancer.
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- 2024
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146. Telomeric DNA breaks in human induced pluripotent stem cells trigger ATR-mediated arrest and telomerase-independent telomere damage repair.
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Estep KN, Tobias JW, Fernandez RJ, Beveridge BM, and Johnson FB
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- Animals, Humans, Male, Mice, DNA Damage, Telomeric Repeat Binding Protein 1 metabolism, Telomeric Repeat Binding Protein 1 genetics, Ataxia Telangiectasia Mutated Proteins metabolism, Ataxia Telangiectasia Mutated Proteins genetics, DNA Breaks, Double-Stranded, DNA Repair, Induced Pluripotent Stem Cells metabolism, Induced Pluripotent Stem Cells cytology, Telomerase metabolism, Telomerase genetics, Telomere metabolism, Telomere genetics
- Abstract
Although mechanisms of telomere protection are well-defined in differentiated cells, how stem cells sense and respond to telomere dysfunction, in particular telomeric double-strand breaks (DSBs), is poorly characterized. Here, we report the DNA damage signaling, cell cycle, and transcriptome changes in human induced pluripotent stem cells (iPSCs) in response to telomere-internal DSBs. We engineer human iPSCs with an inducible TRF1-FokI fusion protein to acutely induce DSBs at telomeres. Using this model, we demonstrate that TRF1-FokI DSBs activate an ATR-dependent DNA damage response, which leads to p53-independent cell cycle arrest in G2. Using CRISPR-Cas9 to cripple the catalytic domain of telomerase reverse transcriptase, we show that telomerase is largely dispensable for survival and lengthening of TRF1-FokI-cleaved telomeres, which instead are effectively repaired by robust homologous recombination (HR). In contrast to HR-based telomere maintenance in mouse embryonic stem cells, where HR causes ZSCAN4-dependent extension of telomeres beyond their initial lengths, HR-based repair of telomeric breaks is sufficient to maintain iPSC telomeres at a normal length, which is compatible with sustained survival of the cells over several days of TRF1-FokI induction. Our findings suggest a previously unappreciated role for HR in telomere maintenance in telomerase-positive iPSCs and reveal distinct iPSC-specific responses to targeted telomeric DNA damage., (© The Author(s) (2023). Published by Oxford University Press on behalf of Journal of Molecular Cell Biology, CEMCS, CAS.)
- Published
- 2024
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147. Diurnal gene expression patterns in retina and choroid distinguish myopia progression from myopia onset.
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Stone RA, Tobias JW, Wei W, Carlstedt X, Zhang L, Iuvone PM, and Nickla DL
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- Animals, Humans, Disease Models, Animal, Gene Expression Regulation, Gene Expression Profiling, Choroid metabolism, Choroid pathology, Retina metabolism, Retina pathology, Myopia genetics, Myopia metabolism, Circadian Rhythm genetics, Disease Progression, Chickens genetics
- Abstract
The world-wide prevalence of myopia (nearsightedness) is increasing, but its pathogenesis is incompletely understood. Among many putative mechanisms, laboratory and clinical findings have implicated circadian biology in the etiology of myopia. Consistent with a circadian hypothesis, we recently reported a marked variability in diurnal patterns of gene expression in two crucial tissues controlling post-natal refractive development - the retina and choroid-at the onset of form-deprivation myopia in chick, a widely studied and validated model. To extend these observations, we assayed gene expression by RNA-Seq in retina and choroid during the progression of established unilateral form-deprivation myopia of chick. We assayed gene expression every 4 hours during a single day from myopic and contralateral control eyes. Retinal and choroidal gene expression in myopic vs. control eyes during myopia progression differed strikingly at discrete times during the day. Very few differentially expressed genes occurred at more than one time in either tissue during progressing myopia. Similarly, Gene Set Enrichment Analysis pathways varied markedly by time during the day. Some of the differentially expressed genes in progressing myopia coincided with candidate genes for human myopia, but only partially corresponded with genes previously identified at myopia onset. Considering other laboratory findings and human genetics and epidemiology, these results further link circadian biology to the pathogenesis of myopia; but they also point to important mechanistic differences between the onset of myopia and the progression of established myopia. Future laboratory and clinical investigations should systematically incorporate circadian mechanisms in studying the etiology of myopia and in seeking more effective treatments to normalize eye growth in children., Competing Interests: The authors have read the journal’s policy and have the following competing interests: RAS serves as an advisor to iView Therapeutics, Inc. (https://www.iviewtherapeutics.com/). PMI serves as an advisor to Spave Science, Inc. (https://www.spavescience.com/) and to NeuroRays, LLC (https://neurorays.com). This does not alter our adherence to PLOS ONE policies on sharing data and materials. There are no patents, products in development or marketed products associated with this research to declare., (Copyright: © 2024 Stone et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2024
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148. IL-12 drives the differentiation of human T follicular regulatory cells.
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Castaño D, Wang S, Atencio-Garcia S, Shields EJ, Rico MC, Sharpe H, Bustamante J, Feng A, Le Coz C, Romberg N, Tobias JW, Utz PJ, Henrickson SE, Casanova JL, Bonasio R, and Locci M
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- Humans, STAT4 Transcription Factor immunology, STAT4 Transcription Factor genetics, Receptors, Interleukin-12 immunology, Receptors, Interleukin-12 genetics, Female, Male, Interleukin-12 immunology, Cell Differentiation immunology, T-Lymphocytes, Regulatory immunology
- Abstract
T follicular regulatory (T
fr ) cells can counteract the B cell helper activity of T follicular helper (Tfh ) cells and hinder the production of antibodies against self-antigens or allergens. A mechanistic understanding of the cytokines initiating the differentiation of human regulatory T (Treg ) cells into Tfr cells is still missing. Herein, we report that low doses of the pro-Tfh cytokine interleukin-12 (IL-12) drive the induction of a Tfr cell program on activated human Treg cells while also preserving their regulatory function. Mechanistically, we found that IL-12 led to STAT4 (signal transducer and activator of transcription 4) phosphorylation and binding to IL-12-driven follicular signature genes. Patients with inborn errors of immunity in the IL12RB1 gene presented with a strong decrease in circulating Tfr cells and produced higher levels of anti-actin autoantibodies in vivo. Overall, this study unveils IL-12 as an inducer of Tfr cell differentiation in vivo and provides an approach for the in vitro generation of human Tfr -like cells.- Published
- 2024
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149. Plasticity-induced repression of Irf6 underlies acquired resistance to cancer immunotherapy in pancreatic ductal adenocarcinoma.
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Kim IK, Diamond MS, Yuan S, Kemp SB, Kahn BM, Li Q, Lin JH, Li J, Norgard RJ, Thomas SK, Merolle M, Katsuda T, Tobias JW, Baslan T, Politi K, Vonderheide RH, and Stanger BZ
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- Humans, Cell Line, Tumor, Neoplasm Recurrence, Local, Immunotherapy, Epithelial-Mesenchymal Transition genetics, Tumor Microenvironment, Carcinoma, Pancreatic Ductal genetics, Carcinoma, Pancreatic Ductal therapy, Carcinoma, Pancreatic Ductal metabolism, Pancreatic Neoplasms genetics, Pancreatic Neoplasms therapy, Pancreatic Neoplasms metabolism
- Abstract
Acquired resistance to immunotherapy remains a critical yet incompletely understood biological mechanism. Here, using a mouse model of pancreatic ductal adenocarcinoma (PDAC) to study tumor relapse following immunotherapy-induced responses, we find that resistance is reproducibly associated with an epithelial-to-mesenchymal transition (EMT), with EMT-transcription factors ZEB1 and SNAIL functioning as master genetic and epigenetic regulators of this effect. Acquired resistance in this model is not due to immunosuppression in the tumor immune microenvironment, disruptions in the antigen presentation machinery, or altered expression of immune checkpoints. Rather, resistance is due to a tumor cell-intrinsic defect in T-cell killing. Molecularly, EMT leads to the epigenetic and transcriptional silencing of interferon regulatory factor 6 (Irf6), rendering tumor cells less sensitive to the pro-apoptotic effects of TNF-α. These findings indicate that acquired resistance to immunotherapy may be mediated by programs distinct from those governing primary resistance, including plasticity programs that render tumor cells impervious to T-cell killing., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
150. Diurnal retinal and choroidal gene expression patterns support a role for circadian biology in myopia pathogenesis.
- Author
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Stone RA, Tobias JW, Wei W, Schug J, Wang X, Zhang L, Iuvone PM, and Nickla DL
- Subjects
- Humans, Animals, Choroid metabolism, Circadian Rhythm genetics, Gene Expression, Biology, Chickens genetics, Retina metabolism, Myopia genetics, Myopia metabolism
- Abstract
The prevalence of myopia (nearsightedness) is increasing to alarming levels, but its etiology remains poorly understood. Because both laboratory and clinical findings suggest an etiologic role for circadian rhythms in myopia development, we assayed gene expression by RNA-Seq in retina and choroid at the onset of unilateral experimental myopia in chick, isolating tissues every 4 h during a single 24-h period from myopic and contralateral control eyes. Occluded versus open eye gene expression differences varied considerably over the 24-h sampling period, with some occurring at multiple times of day but with others showing differences at only a single investigated timepoint. Some of the genes identified in retina or choroid of chick myopia were previously identified as candidate genes for common human myopia. Like differentially expressed genes, pathways identified by Gene Set Enrichment Analysis also varied dramatically by sampling time. Considered with other laboratory data, human genetic and epidemiology data, these findings further implicate circadian events in myopia pathogenesis. The present results emphasize a need to include time of day in mechanistic studies of myopia and to assess circadian biology directly in trying to understand better the origin of myopia and to develop more effective therapies., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
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