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18 results on '"Montemayor, Casandra"'

1. Genetic effects on liver chromatin accessibility identify disease regulatory variants

Author

Barnabas, Beatrice B., Black, Sean, Bouffard, Gerard G., Brooks, Shelise Y., Coleman, Holly, Dekhtyar, Lyudmila, Han, Joel, Ho, Shi-ling, Kim, Juyun, Legaspi, Richelle, Maduro, Quino L., Masiello, Catherine A., McDowell, Jennifer C., Montemayor, Casandra, Mullikin, James C., Park, Morgan, Riebow, Nancy L., Schandler, Karen, Schmidt, Brian, Sison, Christina, Stantripop, Sirintorn, Thomas, James W., Thomas, Pamela J., Vemulapalli, Meghana, Young, Alice C., Currin, Kevin W., Erdos, Michael R., Narisu, Narisu, Rai, Vivek, Vadlamudi, Swarooparani, Perrin, Hannah J., Idol, Jacqueline R., Yan, Tingfen, Albanus, Ricardo D’Oliveira, Broadaway, K. Alaine, Etheridge, Amy S., Bonnycastle, Lori L., Orchard, Peter, Didion, John P., Chaudhry, Amarjit S., Innocenti, Federico, Schuetz, Erin G., Scott, Laura J., Parker, Stephen C.J., Collins, Francis S., and Mohlke, Karen L.

Published
2021
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2. Evaluation of Recipients of Positive and Negative Secondary Findings Evaluations in a Hybrid CLIA-Research Sequencing Pilot

Author

Barnabas, Beatrice B., Bouffard, Gerard G., Brooks, Shelise Y., Coleman, Holly, Dekhtyar, Lyudmila, Guan, Xiaobin, Han, Joel, Ho, Shi-ling, Legaspi, Richelle, Maduro, Quino L., Masiello, Catherine A., McDowell, Jennifer C., Montemayor, Casandra, Park, Morgan, Riebow, Nancy L., Schandler, Karen, Scharer, Chanthra, Schmidt, Brian, Sison, Christina, Stantripop, Sirintorn, Thomas, James W., Thomas, Pamela J., Vemulapalli, Meghana, Young, Alice C., Sapp, Julie C., Johnston, Jennifer J., Driscoll, Kate, Heidlebaugh, Alexis R., Miren Sagardia, Ane, Dogbe, D. Nadine, Umstead, Kendall L., Turbitt, Erin, Alevizos, Ilias, Baron, Jeffrey, Bönnemann, Carsten, Brooks, Brian, Donkervoort, Sandra, Jee, Youn Hee, Linehan, W. Marston, McMahon, Francis J., Moss, Joel, Mullikin, James C., Nielsen, Deborah, Pelayo, Eileen, Remaley, Alan T., Siegel, Richard, Su, Helen, Zarate, Carlos, Manolio, Teri A., Biesecker, Barbara B., and Biesecker, Leslie G.

Published
2018
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3. A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope

Author

Benjamin, Betty, Blakesley, Robert, Bouffard, Gerry, Brooks, Shelise, Coleman, Holly, Dekhtyar, Mila, Gregory, Michael, Guan, Xiaobin, Gupta, Jyoti, Han, Joel, Hargrove, April, Ho, Shiling, Legaspi, Richelle, Maduro, Quino, Masiello, Cathy, Maskeri, Baishali, McDowell, Jenny, Montemayor, Casandra, Mullikin, James, Park, Morgan, Riebow, Nancy, Schandler, Karen, Schmidt, Brian, Sison, Christina, Stantripop, Mal, Thomas, James, Thomas, Pam, Vemulapalli, Meg, Young, Alice, Zhou, Tongqing, Zheng, Anqi, Baxa, Ulrich, Chuang, Gwo-Yu, Georgiev, Ivelin S., Kong, Rui, O’Dell, Sijy, Shahzad-ul-Hussan, Syed, Shen, Chen-Hsiang, Tsybovsky, Yaroslav, Bailer, Robert T., Gift, Syna K., Louder, Mark K., McKee, Krisha, Rawi, Reda, Stevenson, Catherine H., Stewart-Jones, Guillaume B.E., Taft, Justin D., Waltari, Eric, Yang, Yongping, Zhang, Baoshan, Shivatare, Sachin S., Shivatare, Vidya S., Lee, Chang-Chun D., Wu, Chung-Yi, Mullikin, James C., Bewley, Carole A., Burton, Dennis R., Polonis, Victoria R., Shapiro, Lawrence, Wong, Chi-Huey, Mascola, John R., Kwong, Peter D., and Wu, Xueling

Published
2018
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4. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma

Author

Gartner, Jared J, Parker, Stephen CJ, Prickett, Todd D, Dutton-Regester, Ken, Stitzel, Michael L, Lin, Jimmy C, Davis, Sean, Simhadri, Vijaya L, Jha, Sujata, Katagiri, Nobuko, Gotea, Valer, Teer, Jamie K, Wei, Xiaomu, Morken, Mario A, Bhanot, Umesh K, Chen, Guo, Elnitski, Laura L, Davies, Michael A, Gershenwald, Jeffrey E, Carter, Hannah, Karchin, Rachel, Robinson, William, Robinson, Steven, Rosenberg, Steven A, Collins, Francis S, Parmigiani, Giovanni, Komar, Anton A, Kimchi-Sarfaty, Chava, Hayward, Nicholas K, Margulies, Elliott H, Samuels, Yardena, Becker, Jesse, Benjamin, Betty, Blakesley, Robert, Bouffard, Gerry, Brooks, Shelise, Coleman, Holly, Dekhtyar, Mila, Gregory, Michael, Guan, Xiaobin, Gupta, Jyoti, Han, Joel, Hargrove, April, Ho, Shi-ling, Johnson, Taccara, Legaspi, Richelle, Lovett, Sean, Maduro, Quino, Masiello, Cathy, Maskeri, Baishali, McDowell, Jenny, Montemayor, Casandra, Mullikin, James, Park, Morgan, Riebow, Nancy, Schandler, Karen, Schmidt, Brian, Sison, Christina, Stantripop, Mal, Thomas, James, Thomas, Pam, Vemulapalli, Meg, and Young, Alice

Subjects
Biotechnology, Human Genome, Genetics, Cancer, Prevention, 1.1 Normal biological development and functioning, Underpinning research, 2.1 Biological and endogenous factors, Aetiology, Generic health relevance, Apoptosis, Base Sequence, Blotting, Western, DNA Primers, Exome, Gene Expression Regulation, Genetic Vectors, Genome, Human, HEK293 Cells, Humans, Immunoprecipitation, Lentivirus, Melanoma, MicroRNAs, Molecular Sequence Data, Muscle Proteins, Mutation, Polymorphism, Single Nucleotide, Proto-Oncogene Proteins c-bcl-2, RNA, Small Interfering, Real-Time Polymerase Chain Reaction, Sequence Analysis, DNA, Tumor Suppressor Protein p53, NISC Comparative Sequencing Program
Abstract

Synonymous mutations, which do not alter the protein sequence, have been shown to affect protein function [Sauna ZE, Kimchi-Sarfaty C (2011) Nat Rev Genet 12(10):683-691]. However, synonymous mutations are rarely investigated in the cancer genomics field. We used whole-genome and -exome sequencing to identify somatic mutations in 29 melanoma samples. Validation of one synonymous somatic mutation in BCL2L12 in 285 samples identified 12 cases that harbored the recurrent F17F mutation. This mutation led to increased BCL2L12 mRNA and protein levels because of differential targeting of WT and mutant BCL2L12 by hsa-miR-671-5p. Protein made from mutant BCL2L12 transcript bound p53, inhibited UV-induced apoptosis more efficiently than WT BCL2L12, and reduced endogenous p53 target gene transcription. This report shows selection of a recurrent somatic synonymous mutation in cancer. Our data indicate that silent alterations have a role to play in human cancer, emphasizing the importance of their investigation in future cancer genome studies.

Published
2013

5. Expanded microbiome niches of RAG-deficient patients

Author

Blaustein, Ryan A., primary, Shen, Zeyang, additional, Kashaf, Sara Saheb, additional, Lee-Lin, ShihQueen, additional, Conlan, Sean, additional, Bosticardo, Marita, additional, Delmonte, Ottavia M., additional, Holmes, Cassandra J., additional, Taylor, Monica E., additional, Banania, Glenna, additional, Nagao, Keisuke, additional, Dimitrova, Dimana, additional, Kanakry, Jennifer A., additional, Su, Helen, additional, Holland, Steven M., additional, Bergerson, Jenna R.E., additional, Freeman, Alexandra F., additional, Notarangelo, Luigi D., additional, Kong, Heidi H., additional, Segre, Julia A., additional, Thomas, Jim, additional, Mullikin, James, additional, Young, Alice, additional, Bouffard, Gerry, additional, Barnabas, Betty, additional, Brooks, Shelise, additional, Buchter, Chloe, additional, Crawford, Juyun, additional, Han, Joel, additional, Ho, Shi-ling, additional, Legaspi, Richelle, additional, Maduro, Quino, additional, Marfani, Holly, additional, Montemayor, Casandra, additional, Schandler, Karen, additional, Schmidt, Brian, additional, Sison, Christina, additional, Stantripop, Mal, additional, Black, Sean, additional, Dekhtyar, Mila, additional, Masiello, Cathy, additional, McDowell, Jenny, additional, Park, Morgan, additional, Thomas, Pam, additional, and Vemulapalli, Meg, additional

Published
2023
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6. Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection

Author

Benjamin, Betty, Blakesley, Robert, Bouffard, Gerry, Brooks, Shelise, Coleman, Holly, Dekhtyar, Mila, Gregory, Michael, Guan, Xiaobin, Gupta, Jyoti, Han, Joel, Hargrove, April, Ho, Shi-ling, Legaspi, Richelle, Maduro, Quino, Masiello, Cathy, Maskeri, Baishali, McDowell, Jenny, Montemayor, Casandra, Park, Morgan, Riebow, Nancy, Schandler, Karen, Schmidt, Brian, Sison, Christina, Stantripop, Mal, Thomas, James, Thomas, Pam, Vemulapalli, Meg, Young, Alice, Wu, Xueling, Zhang, Zhenhai, Schramm, Chaim A., Joyce, M. Gordon, Do Kwon, Young, Zhou, Tongqing, Sheng, Zizhang, Zhang, Baoshan, O’Dell, Sijy, McKee, Krisha, Georgiev, Ivelin S., Chuang, Gwo-Yu, Longo, Nancy S., Lynch, Rebecca M., Saunders, Kevin O., Soto, Cinque, Srivatsan, Sanjay, Yang, Yongping, Bailer, Robert T., Louder, Mark K., Mullikin, James C., Connors, Mark, Kwong, Peter D., Mascola, John R., and Shapiro, Lawrence

Published
2015
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7. Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group.

Author

Tisza, Michael J., Smith, Derek D. N., Clark, Andrew E., Youn, Jung-Ho, Barnabas, Beatrice B., Black, Sean, Bouffard, Gerard G., Brooks, Shelise Y., Crawford, Juyun, Marfani, Holly, Dekhtyar, Lyudmila, Han, Joel, Ho, Shi-Ling, Legaspi, Richelle, Maduro, Quino L., Masiello, Catherine A., McDowell, Jennifer C., Montemayor, Casandra, Mullikin, James C., and Park, Morgan

Subjects
BACTEROIDES fragilis, METHYLTRANSFERASES, BACTERIAL genomes, ANAEROBIC infections, EPIGENETICS, EPIGENOMICS, CATECHOL-O-methyltransferase, DNA methyltransferases
Abstract

Three types of DNA methyl modifications have been detected in bacterial genomes, and mechanistic studies have demonstrated roles for DNA methylation in physiological functions ranging from phage defense to transcriptional control of virulence and host-pathogen interactions. Despite the ubiquity of methyltransferases and the immense variety of possible methylation patterns, epigenomic diversity remains unexplored for most bacterial species. Members of the Bacteroides fragilis group (BFG) reside in the human gastrointestinal tract as key players in symbiotic communities but also can establish anaerobic infections that are increasingly multi-drug resistant. In this work, we utilize long-read sequencing technologies to perform pangenomic (n = 383) and panepigenomic (n = 268) analysis of clinical BFG isolates cultured from infections seen at the NIH Clinical Center over four decades. Our analysis reveals that single BFG species harbor hundreds of DNA methylation motifs, with most individual motif combinations occurring uniquely in single isolates, implying immense unsampled methylation diversity within BFG epigenomes. Mining of BFG genomes identified more than 6000 methyltransferase genes, approximately 1000 of which were associated with intact prophages. Network analysis revealed substantial gene flow among disparate phage genomes, implying a role for genetic exchange between BFG phages as one of the ultimate sources driving BFG epigenome diversity. Here, Tisza, Dekker, and colleagues perform large scale analysis of genome methylation in the gut commensal and pathogen, Bacteroides fragilis group, revealing immense methyl motif diversity and evidence of widespread methyltransferase exchange among phages. [ABSTRACT FROM AUTHOR]

Published
2023
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8. Biogeography and individuality shape function in the human skin metagenome

Author

Oh, Julia, Byrd, Allyson L., Deming, Clay, Conlan, Sean, Barnabas, Betty, Blakesley, Robert, Bouffard, Gerry, Brooks, Shelise, Coleman, Holly, Dekhtyar, Mila, Gregory, Michael, Guan, Xiaobin, Gupta, Jyoti, Han, Joel, Ho, Shi-ling, Legaspi, Richelle, Maduro, Quino, Masiello, Cathy, Maskeri, Baishali, McDowell, Jenny, Montemayor, Casandra, Mullikin, James, Park, Morgan, Riebow, Nancy, Schandler, Karen, Schmidt, Brian, Sison, Christina, Stantripop, Mal, Thomas, James, Thomas, Pamela, Vemulapalli, Meg, Young, Alice, Kong, Heidi H., and Segre, Julia A.

Published
2014
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9. Genetic effects on liver chromatin accessibility identify disease regulatory variants

Author

Currin, Kevin W., primary, Erdos, Michael R., additional, Narisu, Narisu, additional, Rai, Vivek, additional, Vadlamudi, Swarooparani, additional, Perrin, Hannah J., additional, Idol, Jacqueline R., additional, Yan, Tingfen, additional, Albanus, Ricardo D’Oliveira, additional, Broadaway, K. Alaine, additional, Etheridge, Amy S., additional, Bonnycastle, Lori L., additional, Orchard, Peter, additional, Didion, John P., additional, Chaudhry, Amarjit S., additional, Innocenti, Federico, additional, Schuetz, Erin G., additional, Scott, Laura J., additional, Parker, Stephen C.J., additional, Collins, Francis S., additional, Mohlke, Karen L., additional, Barnabas, Beatrice B., additional, Black, Sean, additional, Bouffard, Gerard G., additional, Brooks, Shelise Y., additional, Coleman, Holly, additional, Dekhtyar, Lyudmila, additional, Han, Joel, additional, Ho, Shi-ling, additional, Kim, Juyun, additional, Legaspi, Richelle, additional, Maduro, Quino L., additional, Masiello, Catherine A., additional, McDowell, Jennifer C., additional, Montemayor, Casandra, additional, Mullikin, James C., additional, Park, Morgan, additional, Riebow, Nancy L., additional, Schandler, Karen, additional, Schmidt, Brian, additional, Sison, Christina, additional, Stantripop, Sirintorn, additional, Thomas, James W., additional, Thomas, Pamela J., additional, Vemulapalli, Meghana, additional, and Young, Alice C., additional

Published
2021
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10. Topographic diversity of fungal and bacterial communities in human skin

Author

Findley, Keisha, Oh, Julia, Yang, Joy, Conlan, Sean, Deming, Clayton, Meyer, Jennifer A., Schoenfeld, Deborah, Nomicos, Effie, Park, Morgan, Becker, Jesse, Benjamin, Betty, Blakesley, Robert, Bouffard, Gerry, Brooks, Shelise, Coleman, Holly, Dekhtyar, Mila, Gregory, Michael, Guan, Xiaobin, Gupta, Jyoti, Han, Joel, Hargrove, April, Ho, Shi-ling, Johnson, Taccara, Legaspi, Richelle, Lovett, Sean, Maduro, Quino, Masiello, Cathy, Maskeri, Baishali, McDowell, Jenny, Montemayor, Casandra, Mullikin, James, Park, Morgan, Riebow, Nancy, Schandler, Karen, Schmidt, Brian, Sison, Christina, Stantripop, Mal, Thomas, James, Thomas, Pam, Vemulapalli, Meg, Young, Alice, Kong, Heidi H., and Segre, Julia A.

Published
2013
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11. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

Author

Liao, Hua-Xin, Lynch, Rebecca, Zhou, Tongqing, Gao, Feng, Alam, S. Munir, Boyd, Scott D., Fire, Andrew Z., Roskin, Krishna M., Schramm, Chaim A., Zhang, Zhenhai, Zhu, Jiang, Shapiro, Lawrence, Becker, Jesse, Benjamin, Betty, Blakesley, Robert, Bouffard, Gerry, Brooks, Shelise, Coleman, Holly, Dekhtyar, Mila, Gregory, Michael, Guan, Xiaobin, Gupta, Jyoti, Han, Joel, Hargrove, April, Ho, Shi-ling, Johnson, Taccara, Legaspi, Richelle, Lovett, Sean, Maduro, Quino, Masiello, Cathy, Maskeri, Baishali, McDowell, Jenny, Montemayor, Casandra, Mullikin, James, Park, Morgan, Riebow, Nancy, Schandler, Karen, Schmidt, Brian, Sison, Christina, Stantripop, Mal, Thomas, James, Thomas, Pam, Vemulapalli, Meg, Young, Alice, Mullikin, James C., Gnanakaran, S., Hraber, Peter, Wiehe, Kevin, Kelsoe, Garnett, Yang, Guang, Xia, Shi-Mao, Montefiori, David C., Parks, Robert, Lloyd, Krissey E., Scearce, Richard M., Soderberg, Kelly A., Cohen, Myron, Kamanga, Gift, Louder, Mark K., Tran, Lillian M., Chen, Yue, Cai, Fangping, Chen, Sheri, Moquin, Stephanie, Du, Xiulian, Joyce, M. Gordon, Srivatsan, Sanjay, Zhang, Baoshan, Zheng, Anqi, Shaw, George M., Hahn, Beatrice H., Kepler, Thomas B., Korber, Bette T. M., Kwong, Peter D., Mascola, John R., and Haynes, Barton F.

Published
2013
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12. Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies

Author

Doria-Rose, Nicole A., Schramm, Chaim A., Gorman, Jason, Moore, Penny L., Bhiman, Jinal N., Dekosky, Brandon J., Ernandes, Michael J., Georgiev, Ivelin S., Kim, Helen J., Pancera, Marie, Staupe, Ryan P., Altae-Tran, Han R., Bailer, Robert T., Crooks, Ema T., Cupo, Albert, Druz, Aliaksandr, Garrett, Nigel J., Hoi, Kam H., Kong, Rui, Louder, Mark K., Longo, Nancy S., McKee, Krisha, Nonyane, Molati, O'Dell, Sijy, Roark, Ryan S., Rudicell, Rebecca S., Schmidt, Stephen D., Sheward, Daniel J., Soto, Cinque, Wibmer, Constantinos Kurt, Yang, Yongping, Zhang, Zhenhai, Mullikin, James C., Binley, James M., Sanders, Rogier W., Wilson, Ian A., Moore, John P., Ward, Andrew B., Georgiou, George, Williamson, Carolyn, Abdool Karim, Salim S., Morris, Lynn, Kwong, Peter D., Shapiro, Lawrence, Mascola, John R., Becker, Jesse, Benjamin, Betty, Blakesley, Robert, Bouffard, Gerry, Brooks, Shelise, Coleman, Holly, Dekhtyar, Mila, Gregory, Michael, Guan, Xiaobin, Gupta, Jyoti, Han, Joel, Hargrove, April, Ho, Shi-ling, Johnson, Taccara, Legaspi, Richelle, Lovett, Sean, Maduro, Quino, Masiello, Cathy, Maskeri, Baishali, McDowell, Jenny, Montemayor, Casandra, Mullikin, James, Park, Morgan, Riebow, Nancy, Schandler, Karen, Schmidt, Brian, Sison, Christina, Stantripop, Mal, Thomas, James, Thomas, Pam, Vemulapalli, Meg, Young, Alice, AII - Amsterdam institute for Infection and Immunity, and Medical Microbiology and Infection Prevention

Subjects
Models, Molecular, Molecular Sequence Data, Population, Antibody Affinity, Somatic hypermutation, HIV Infections, Complementarity determining region, HIV Antibodies, Article, Epitope, Virus, HIV Envelope Protein gp160, Evolution, Molecular, Affinity maturation, Neutralization Tests, Humans, Cell Lineage, Amino Acid Sequence, education, AIDS Vaccines, B-Lymphocytes, education.field_of_study, Binding Sites, Multidisciplinary, biology, Antibodies, Neutralizing, Complementarity Determining Regions, Virology, Protein Structure, Tertiary, Epitope mapping, CD4 Antigens, Immunology, HIV-1, biology.protein, Epitopes, B-Lymphocyte, Somatic Hypermutation, Immunoglobulin, Antibody, Epitope Mapping
Abstract

Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental pathway by which such antibodies are generated and acquire the requisite molecular characteristics for neutralization. Twelve somatically related neutralizing antibodies (CAP256-VRC26.01–12) were isolated from donor CAP256 (from the Centre for the AIDS Programme of Research in South Africa (CAPRISA)); each antibody contained the protruding tyrosine-sulphated, anionic antigen-binding loop (complementarity-determining region (CDR) H3) characteristic of this category of antibodies. Their unmutated ancestor emerged between weeks 30–38 post-infection with a 35-residue CDR H3, and neutralized the virus that superinfected this individual 15 weeks after initial infection. Improved neutralization breadth and potency occurred by week 59 with modest affinity maturation, and was preceded by extensive diversification of the virus population. HIV-1 V1V2-directed neutralizing antibodies can thus develop relatively rapidly through initial selection of B cells with a long CDR H3, and limited subsequent somatic hypermutation. These data provide important insights relevant to HIV-1 vaccine development. A longitudinal study of an individual patient developing neutralizing antibodies against HIV-1 (targeting the V1V2 region of gp120) reveals how such neutralizing antibodies develop and evolve over time, providing important insights relevant to vaccine development. A better understanding of how HIV-1-neutralizing antibodies are generated could be a useful contribution to the design of improved AIDS vaccines. John Mascola and colleagues have now elucidated the immunological pathway of an important category of HIV-1-neutralizing antibody — those that target the variable V1V2 region of the viral envelope. These antibodies are more frequently elicited than CD4-binding site antibodies in the early stages of HIV infection and feature modest affinity maturation, a process that favours mutations in antibody variable domains that enhance antigen binding.

Published
2014
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13. Evaluation of Recipients of Positive and Negative Secondary Findings Evaluations in a Hybrid CLIA-Research Sequencing Pilot

Author

Sapp, Julie C., primary, Johnston, Jennifer J., additional, Driscoll, Kate, additional, Heidlebaugh, Alexis R., additional, Miren Sagardia, Ane, additional, Dogbe, D. Nadine, additional, Umstead, Kendall L., additional, Turbitt, Erin, additional, Alevizos, Ilias, additional, Baron, Jeffrey, additional, Bönnemann, Carsten, additional, Brooks, Brian, additional, Donkervoort, Sandra, additional, Jee, Youn Hee, additional, Linehan, W. Marston, additional, McMahon, Francis J., additional, Moss, Joel, additional, Mullikin, James C., additional, Nielsen, Deborah, additional, Pelayo, Eileen, additional, Remaley, Alan T., additional, Siegel, Richard, additional, Su, Helen, additional, Zarate, Carlos, additional, Manolio, Teri A., additional, Biesecker, Barbara B., additional, Biesecker, Leslie G., additional, Barnabas, Beatrice B., additional, Bouffard, Gerard G., additional, Brooks, Shelise Y., additional, Coleman, Holly, additional, Dekhtyar, Lyudmila, additional, Guan, Xiaobin, additional, Han, Joel, additional, Ho, Shi-ling, additional, Legaspi, Richelle, additional, Maduro, Quino L., additional, Masiello, Catherine A., additional, McDowell, Jennifer C., additional, Montemayor, Casandra, additional, Park, Morgan, additional, Riebow, Nancy L., additional, Schandler, Karen, additional, Scharer, Chanthra, additional, Schmidt, Brian, additional, Sison, Christina, additional, Stantripop, Sirintorn, additional, Thomas, James W., additional, Thomas, Pamela J., additional, Vemulapalli, Meghana, additional, and Young, Alice C., additional

Published
2018
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14. A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope

Author

Zhou, Tongqing, primary, Zheng, Anqi, additional, Baxa, Ulrich, additional, Chuang, Gwo-Yu, additional, Georgiev, Ivelin S., additional, Kong, Rui, additional, O’Dell, Sijy, additional, Shahzad-ul-Hussan, Syed, additional, Shen, Chen-Hsiang, additional, Tsybovsky, Yaroslav, additional, Bailer, Robert T., additional, Gift, Syna K., additional, Louder, Mark K., additional, McKee, Krisha, additional, Rawi, Reda, additional, Stevenson, Catherine H., additional, Stewart-Jones, Guillaume B.E., additional, Taft, Justin D., additional, Waltari, Eric, additional, Yang, Yongping, additional, Zhang, Baoshan, additional, Shivatare, Sachin S., additional, Shivatare, Vidya S., additional, Lee, Chang-Chun D., additional, Wu, Chung-Yi, additional, Mullikin, James C., additional, Bewley, Carole A., additional, Burton, Dennis R., additional, Polonis, Victoria R., additional, Shapiro, Lawrence, additional, Wong, Chi-Huey, additional, Mascola, John R., additional, Kwong, Peter D., additional, Wu, Xueling, additional, Benjamin, Betty, additional, Blakesley, Robert, additional, Bouffard, Gerry, additional, Brooks, Shelise, additional, Coleman, Holly, additional, Dekhtyar, Mila, additional, Gregory, Michael, additional, Guan, Xiaobin, additional, Gupta, Jyoti, additional, Han, Joel, additional, Hargrove, April, additional, Ho, Shiling, additional, Legaspi, Richelle, additional, Maduro, Quino, additional, Masiello, Cathy, additional, Maskeri, Baishali, additional, McDowell, Jenny, additional, Montemayor, Casandra, additional, Mullikin, James, additional, Park, Morgan, additional, Riebow, Nancy, additional, Schandler, Karen, additional, Schmidt, Brian, additional, Sison, Christina, additional, Stantripop, Mal, additional, Thomas, James, additional, Thomas, Pam, additional, Vemulapalli, Meg, additional, and Young, Alice, additional

Published
2018
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15. Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response

Author

Grice, Elizabeth A., Snitkin, Evan S., Yockey, Laura J., Bermudez, Dustin M., Liechty, Kenneth W., Segre, Julia A., Mullikin, Jim, Blakesley, Robert, Young, Alice, Chu, Grace, Ramsahoye, Colleen, Lovett, Sean, Han, Joel, Legaspi, Richelle, Fuksenko, Tatyana, Reddix-Dugue, Natalie, Sison, Christina, Gregory, Michael, Montemayor, Casandra, Gestole, Marie, Hargrove, April, Johnson, Taccara, Myrick, Jerlil, Riebow, Nancy, Schmidt, Brian, Novotny, Betsy, Gupti, Jyoti, Benjamin, Betty, Brooks, Shelise, Coleman, Holly, Ho, Shi-ling, Schandler, Karen, Smith, Lauren, Stantripop, Mal, Maduro, Quino, Bouffard, Gerry, Dekhtyar, Mila, Guan, Xiaobin, Masiello, Cathy, Maskeri, Baishali, McDowell, Jenny, Park, Morgan, and Jacques Thomas, Pamela

Subjects
Time Factors, Staphylococcus, Molecular Sequence Data, Population Dynamics, Biology, Microbiology, Mice, Immune system, Diabetes mellitus, RNA, Ribosomal, 16S, Gene expression, medicine, Animals, Cluster Analysis, Microbiome, Gene, Skin, Mice, Knockout, Wound Healing, Multidisciplinary, Innate immune system, Bacteria, Gene Expression Profiling, Bacterial Infections, Biodiversity, Sequence Analysis, DNA, Biological Sciences, medicine.disease, Gene expression profiling, Diabetes Mellitus, Type 2, Immunology, Host-Pathogen Interactions, Metagenome, Receptors, Leptin, Female, Wound healing
Abstract

Diabetics frequently suffer from chronic, nonhealing wounds. Although bacterial colonization and/or infection are generally acknowledged to negatively impact wound healing, the precise relationship between the microbial community and impaired wound healing remains unclear. Because the host cutaneous defense response is proposed to play a key role in modulating microbial colonization, we longitudinally examined the diabetic wound microbiome in tandem with host tissue gene expression. By sequencing 16S ribosomal RNA genes, we show that a longitudinal selective shift in wound microbiota coincides with impaired healing in diabetic mice ( Lepr db/db ; db/db). We demonstrate a parallel shift in longitudinal gene expression that occurs in a cluster of genes related to the immune response. Further, we establish a correlation between relative abundance of Staphylococcus spp. and the expression of cutaneous defense response genes. Our data demonstrate that integrating two types of global datasets lends a better understanding to the dynamics governing host–microbe interactions.

Published
2010

16. Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection

Author

Wu, Xueling, primary, Zhang, Zhenhai, additional, Schramm, Chaim A., additional, Joyce, M. Gordon, additional, Do Kwon, Young, additional, Zhou, Tongqing, additional, Sheng, Zizhang, additional, Zhang, Baoshan, additional, O’Dell, Sijy, additional, McKee, Krisha, additional, Georgiev, Ivelin S., additional, Chuang, Gwo-Yu, additional, Longo, Nancy S., additional, Lynch, Rebecca M., additional, Saunders, Kevin O., additional, Soto, Cinque, additional, Srivatsan, Sanjay, additional, Yang, Yongping, additional, Bailer, Robert T., additional, Louder, Mark K., additional, Mullikin, James C., additional, Connors, Mark, additional, Kwong, Peter D., additional, Mascola, John R., additional, Shapiro, Lawrence, additional, Benjamin, Betty, additional, Blakesley, Robert, additional, Bouffard, Gerry, additional, Brooks, Shelise, additional, Coleman, Holly, additional, Dekhtyar, Mila, additional, Gregory, Michael, additional, Guan, Xiaobin, additional, Gupta, Jyoti, additional, Han, Joel, additional, Hargrove, April, additional, Ho, Shi-ling, additional, Legaspi, Richelle, additional, Maduro, Quino, additional, Masiello, Cathy, additional, Maskeri, Baishali, additional, McDowell, Jenny, additional, Montemayor, Casandra, additional, Park, Morgan, additional, Riebow, Nancy, additional, Schandler, Karen, additional, Schmidt, Brian, additional, Sison, Christina, additional, Stantripop, Mal, additional, Thomas, James, additional, Thomas, Pam, additional, Vemulapalli, Meg, additional, and Young, Alice, additional

Published
2015
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17. Hypoxia-induced HIF1 α targets in melanocytes reveal a molecular profile associated with poor melanoma prognosis.

Author

Loftus, Stacie K., Baxter, Laura L., Cronin, Julia C., Fufa, Temesgen D., Pavan, William J., Barnabas, Beatrice B., Bouffard, Gerard G., Brooks, Shelise Y., Coleman, Holly, Dekhtyar, Lyudmila, Guan, Xiaobin, Han, Joel, Ho, Shi ‐ ling, Legaspi, Richelle, Maduro, Quino L., Masiello, Catherine A., McDowell, Jennifer C., Montemayor, Casandra, Mullikin, James C., and Park, Morgan

Subjects
MELANOMA prognosis, HYPOXIA-inducible factors, MELANOCYTES, CANCER invasiveness, METASTASIS
Abstract

Hypoxia and HIF1 α signaling direct tissue-specific gene responses regulating tumor progression, invasion, and metastasis. By integrating HIF1 α knockdown and hypoxia-induced gene expression changes, this study identifies a melanocyte-specific, HIF1 α-dependent/hypoxia-responsive gene expression signature. Integration of these gene expression changes with HIF1 α Ch IP-Seq analysis identifies 81 HIF1 α direct target genes in melanocytes. The expression levels for 10 of the HIF1 α direct targets - GAPDH, PKM, PPAT, DARS, DTWD1, SEH1L, ZNF292, RLF, AGTRAP, and GPC6 - are significantly correlated with reduced time of disease-free status in melanoma by logistic regression (P -value = 0.0013) and ROC curve analysis ( AUC = 0.826, P-value < 0.0001). This HIF1 α-regulated profile defines a melanocyte-specific response under hypoxia, and demonstrates the role of HIF1 α as an invasive cell state gatekeeper in regulating cellular metabolism, chromatin and transcriptional regulation, vascularization, and invasion. [ABSTRACT FROM AUTHOR]

Published
2017
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18. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma

Author

Gartner, Jared J., Parker, Stephen C. J., Prickett, Todd D., Dutton-Regester, Kenneth Adam, Stitzel, Michael L., Lin, Jimmy C., Davis, Sean, Simhadri, Vijaya L., Jha, Sujata, Katagiri, Nobuko, Gotea, Valer, Teer, Jamie K., Wei, Xiaomu, Morken, Mario A., Bhanot, Umesh K., Chen, Guo, Elnitski, Laura L., Davies, Michael A., Gershenwald, Jeffrey E., Carter, Hannah, Karchin, Rachel, Robinson, William, Robinson, Steven, Rosenberg, Steven A., Collins, Francis S., Parmigiani, Giovanni, Komar, Anton A., Kimchi-Sarfaty, Chava, Hayward, Nicholas K., Margulies, Elliott H., Samuels, Yardena, Becker, Jesse, Benjamin, Betty, Blakesley, Robert, Bouffard, Gerry, Brooks, Shelise, Coleman, Holly, Dekhtyar, Mila, Gregory, Michael, Guan, Xiaobin, Gupta, Jyoti, Han, Joel, Hargrove, April, Ho, Shi-ling, Johnson, Taccara, Legaspi, Richelle, Lovett, Sean, Maduro, Quino, Masiello, Cathy, Maskeri, Baishali, McDowell, Jenny, Montemayor, Casandra, Mullikin, James, Park, Morgan, Riebow, Nancy, Schandler, Karen, Schmidt, Brian, Sison, Christina, Stantripop, Mal, Thomas, James, Thomas, Pam, Vemulapalli, Meg, and Young, Alice

Abstract

Synonymous mutations, which do not alter the protein sequence, have been shown to affect protein function [Sauna ZE, Kimchi-Sarfaty C (2011) Nat Rev Genet 12(10):683–691]. However, synonymous mutations are rarely investigated in the cancer genomics field. We used whole-genome and -exome sequencing to identify somatic mutations in 29 melanoma samples. Validation of one synonymous somatic mutation in BCL2L12 in 285 samples identified 12 cases that harbored the recurrent F17F mutation. This mutation led to increased BCL2L12 mRNA and protein levels because of differential targeting of WT and mutant BCL2L12 by hsa-miR-671–5p. Protein made from mutant BCL2L12 transcript bound p53, inhibited UV-induced apoptosis more efficiently than WT BCL2L12, and reduced endogenous p53 target gene transcription. This report shows selection of a recurrent somatic synonymous mutation in cancer. Our data indicate that silent alterations have a role to play in human cancer, emphasizing the importance of their investigation in future cancer genome studies.

Published
2013
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