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870 results on '"Brown, Patrick O."'

1. Depot-specific mRNA expression programs in human adipocytes suggest physiological specialization via distinct developmental programs.

Author

Clemons, Heather J., Hogan, Daniel J., and Brown, Patrick O.

Subjects
DNA microarrays, PROGENITOR cells, DEVELOPMENTAL programs, STEM cell culture, HUMAN body, ADIPOSE tissues, FAT cells
Abstract

Adipose tissue is distributed in diverse locations throughout the human body. Not much is known about the extent to which anatomically distinct adipose depots are functionally distinct, specialized organs, nor whether depot-specific characteristics result from intrinsic developmental programs, as opposed to reversible physiological responses to differences in tissue microenvironment. We used DNA microarrays to compare mRNA expression patterns of isolated human adipocytes and cultured adipose stem cells, before and after ex vivo adipocyte differentiation, from seven anatomically diverse adipose tissue depots. Adipocytes from different depots display distinct gene expression programs, which are most closely shared with anatomically related depots. mRNAs whose expression differs between anatomically diverse groups of depots (e.g., subcutaneous vs. internal) suggest important functional specializations. These depot-specific differences in gene expression were recapitulated when adipocyte progenitor cells from each site were differentiated ex vivo, suggesting that progenitor cells from specific anatomic sites are deterministically programmed to differentiate into depot-specific adipocytes. Many developmental transcription factors show striking depot-specific patterns of expression, suggesting that adipocytes in each anatomic depot are programmed during early development in concert with anatomically related tissues and organs. Our results support the hypothesis that adipocytes from different depots are functionally distinct and that their depot-specific specialization reflects distinct developmental programs. [ABSTRACT FROM AUTHOR]

Published
2024
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2. Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments.

Author

Lareau, Liana F, Hite, Dustin H, Hogan, Gregory J, and Brown, Patrick O

Subjects
Ribosomes, Saccharomyces cerevisiae, RNA, Messenger, Peptide Chain Elongation, Translational, High-Throughput Nucleotide Sequencing, ribosome, ribosome profiling, translation, RNA, Messenger, Peptide Chain Elongation, Translational, Biochemistry and Cell Biology
Abstract

During translation elongation, the ribosome ratchets along its mRNA template, incorporating each new amino acid and translocating from one codon to the next. The elongation cycle requires dramatic structural rearrangements of the ribosome. We show here that deep sequencing of ribosome-protected mRNA fragments reveals not only the position of each ribosome but also, unexpectedly, its particular stage of the elongation cycle. Sequencing reveals two distinct populations of ribosome footprints, 28-30 nucleotides and 20-22 nucleotides long, representing translating ribosomes in distinct states, differentially stabilized by specific elongation inhibitors. We find that the balance of small and large footprints varies by codon and is correlated with translation speed. The ability to visualize conformational changes in the ribosome during elongation, at single-codon resolution, provides a new way to study the detailed kinetics of translation and a new probe with which to identify the factors that affect each step in the elongation cycle.DOI: http://dx.doi.org/10.7554/eLife.01257.001.

Published
2014

36. Diversity of Gene Expression in Adenocarcinoma of the Lung

Author

Garber, Mitchell E., Troyanskaya, Olga G., Schluens, Karsten, Petersen, Simone, Thaesler, Zsuzsanna, Pacyna-Gengelbach, Manuela, van de Rijn, Matt, Rosen, Glenn D., Perou, Charles M., Whyte, Richard I., Altman, Russ B., Brown, Patrick O., Botstein, David, and Petersen, Iver

Published
2001

38. Delineating Developmental and Metabolic Pathways in vivo by Expression Profiling Using the RIKEN Set of 18,816 Full-Length Enriched Mouse cDNA Arrays

Author

Miki, Rika, Kadota, Koji, Bono, Hidemasa, Mizuno, Yosuke, Tomaru, Yasuhiro, Carninci, Piero, Itoh, Masayoshi, Shibata, Kazuhiro, Kawai, Jun, Konno, Hideaki, Watanabe, Sachihiko, Sato, Kenjiro, Tokusumi, Yumiko, Kikuchi, Noriko, Ishii, Yoshiyuki, Hamaguchi, Yohei, Nishizuka, Itaru, Goto, Hitoshi, Nitanda, Hiroyuki, Satomi, Susumu, Yoshiki, Atsushi, Kusakabe, Moriaki, DeRisi, Joseph L., Eisen, Michael B., Iyer, Vishwnath R., Brown, Patrick O., Muramatsu, Masami, Shimada, Hiroshi, Okazaki, Yasushi, and Hayashizaki, Yoshihide

Published
2001

39. Predicting a local recurrence after breast-conserving therapy by gene expression profiling

Author

Nuyten, Dimitry SA, Kreike, Bas, Hart, Augustinus AM, Chi, Jen-Tsan Ashley, Sneddon, Julie B, Wessels, Lodewyk FA, Peterse, Hans J, Bartelink, Harry, Brown, Patrick O, Chang, Howard Y, and van de Vijver, Marc J

Subjects
Breast Cancer, Clinical Research, Cancer, Genetics, 4.2 Evaluation of markers and technologies, Detection, screening and diagnosis, Adult, Breast Neoplasms, Carcinoma, Ductal, Breast, Carcinoma, Intraductal, Noninfiltrating, Female, Gene Expression Profiling, Humans, Mastectomy, Segmental, Middle Aged, Neoplasm Recurrence, Local, Neoplasm Staging, Oligonucleotide Array Sequence Analysis, Predictive Value of Tests, Radiotherapy, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

IntroductionTo tailor local treatment in breast cancer patients there is a need for predicting ipsilateral recurrences after breast-conserving therapy. After adequate treatment (excision with free margins and radiotherapy), young age and incompletely excised extensive intraductal component are predictors for local recurrence, but many local recurrences can still not be predicted. Here we have used gene expression profiling by microarray analysis to identify gene expression profiles that can help to predict local recurrence in individual patients.MethodsBy using previously established gene expression profiles with proven value in predicting metastasis-free and overall survival (wound-response signature, 70-gene prognosis profile and hypoxia-induced profile) and training towards an optimal prediction of local recurrences in a training series, we establish a classifier for local recurrence after breast-conserving therapy.ResultsValidation of the different gene lists shows that the wound-response signature is able to separate patients with a high (29%) or low (5%) risk of a local recurrence at 10 years (sensitivity 87.5%, specificity 75%). In multivariable analysis the classifier is an independent predictor for local recurrence.ConclusionOur findings indicate that gene expression profiling can identify subgroups of patients at increased risk of developing a local recurrence after breast-conserving therapy.

Published
2006

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