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4. Subsets of ILC3−ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues

Author

Cella, Marina, Gamini, Ramya, Sécca, Cristiane, Collins, Patrick L., Zhao, Shanrong, Peng, Vincent, Robinette, Michelle L., Schettini, Jorge, Zaitsev, Konstantin, Gordon, William, Bando, Jennifer K., Yomogida, Kentaro, Cortez, Victor, Fronick, Catrina, Fulton, Robert, Lin, Lih-Ling, Gilfillan, Susan, Flavell, Richard A., Shan, Liang, Artyomov, Maxim N., Bowman, Michael, Oltz, Eugene M., Jelinsky, Scott A., and Colonna, Marco

Published
2019
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5. Transcriptional changes associated with breast cancer occur as normal human mammary epithelial cells overcome senescence barriers and become immortalized

Author

Li, Yizheng, Pan, Jing, Li, Jian-Liang, Lee, Jee Hyung, Tunkey, Chris, Saraf, Katie, Garbe, James C, Whitley, Maryann Z, Jelinsky, Scott A, Stampfer, Martha R, and Haney, Steven A

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Breast Cancer, Cancer, Biotechnology, Genetics, Aging, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Generic health relevance, Breast Neoplasms, Cell Nucleus, Cluster Analysis, Epithelial Cells, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Humans, Mammary Glands, Human, Polymerase Chain Reaction, Promoter Regions, Genetic, Receptor, ErbB-2, Regulatory Elements, Transcriptional, Transcription, Genetic, Tumor Cells, Cultured, Tumor Suppressor Protein p53, Receptor, erbB-2, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

BackgroundHuman mammary epithelial cells (HMEC) overcome two well-characterized genetic and epigenetic barriers as they progress from primary cells to fully immortalized cell lines in vitro. Finite lifespan HMEC overcome an Rb-mediated stress-associated senescence barrier (stasis), and a stringent, telomere-length dependent, barrier (agonescence or crisis, depending on p53 status). HMEC that have overcome the second senescence barrier are immortalized.MethodsWe have characterized pre-stasis, post-selection (post-stasis, with p16 silenced), and fully immortalized HMEC by transcription profiling and RT-PCR. Four pre-stasis and seven post-selection HMEC samples, along with 10 representatives of fully immortalized breast epithelial cell lines, were profiled using Affymetrix U133A/B chips and compared using both supervised and unsupervised clustering. Datasets were validated by RT-PCR for a select set of genes. Quantitative immunofluorescence was used to assess changes in transcriptional regulators associated with the gene expression changes.ResultsThe most dramatic and uniform changes we observed were in a set of about 30 genes that are characterized as a "cancer proliferation cluster," which includes genes expressed during mitosis (CDC2, CDC25, MCM2, PLK1) and following DNA damage. The increased expression of these genes was particularly concordant in the fully immortalized lines. Additional changes were observed in IFN-regulated genes in some post-selection and fully immortalized cultures. Nuclear localization was observed for several transcriptional regulators associated with expression of these genes in post-selection and immortalized HMEC, including Rb, Myc, BRCA1, HDAC3 and SP1.ConclusionGene expression profiles and cytological changes in related transcriptional regulators indicate that immortalized HMEC resemble non-invasive breast cancers, such as ductal and lobular carcinomas in situ, and are strikingly distinct from finite-lifespan HMEC, particularly with regard to genes involved in proliferation, cell cycle regulation, chromosome structure and the DNA damage response. The comparison of HMEC profiles with lines harboring oncogenic changes (e.g. overexpression of Her-2neu, loss of p53 expression) identifies genes involved in tissue remodeling as well as proinflamatory cytokines and S100 proteins. Studies on carcinogenesis using immortalized cell lines as starting points or "normal" controls need to account for the significant pre-existing genetic and epigenetic changes inherent in such lines before results can be broadly interpreted.

Published
2007

7. High-dimensional immune phenotyping and transcriptional analyses reveal robust recovery of viable human immune and epithelial cells from frozen gastrointestinal tissue

Author

Konnikova, Liza, Boschetti, Gilles, Rahman, Adeeb, Mitsialis, Vanessa, Lord, James, Richmond, Camilla, Tomov, Vesselin T., Gordon, Will, Jelinsky, Scott, Canavan, James, Liss, Andrew, Wall, Sarah, Field, Michael, Zhou, Fanny, Goldsmith, Jeffery D., Bewtra, Meenakshi, Breault, David T., Merad, Miriam, and Snapper, Scott B.

Published
2018
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8. Supplementary Table 2 from Comparison of Human and Rat Uterine Leiomyomata: Identification of a Dysregulated Mammalian Target of Rapamycin Pathway

Author

Crabtree, Judy S., primary, Jelinsky, Scott A., primary, Harris, Heather A., primary, Choe, Sung E., primary, Cotreau, Monette M., primary, Kimberland, Michelle L., primary, Wilson, Ewa, primary, Saraf, Kathryn A., primary, Liu, Wei, primary, McCampbell, Adrienne S., primary, Dave, Bhuvanesh, primary, Broaddus, Russell R., primary, Brown, Eugene L., primary, Kao, Wenling, primary, Skotnicki, Jerauld S., primary, Abou-Gharbia, Magid, primary, Winneker, Richard C., primary, and Walker, Cheryl L., primary

Published
2023
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9. Supplementary Methods from Comparison of Human and Rat Uterine Leiomyomata: Identification of a Dysregulated Mammalian Target of Rapamycin Pathway

Author

Crabtree, Judy S., primary, Jelinsky, Scott A., primary, Harris, Heather A., primary, Choe, Sung E., primary, Cotreau, Monette M., primary, Kimberland, Michelle L., primary, Wilson, Ewa, primary, Saraf, Kathryn A., primary, Liu, Wei, primary, McCampbell, Adrienne S., primary, Dave, Bhuvanesh, primary, Broaddus, Russell R., primary, Brown, Eugene L., primary, Kao, Wenling, primary, Skotnicki, Jerauld S., primary, Abou-Gharbia, Magid, primary, Winneker, Richard C., primary, and Walker, Cheryl L., primary

Published
2023
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10. Supplementary Table 1 from Comparison of Human and Rat Uterine Leiomyomata: Identification of a Dysregulated Mammalian Target of Rapamycin Pathway

Author

Crabtree, Judy S., primary, Jelinsky, Scott A., primary, Harris, Heather A., primary, Choe, Sung E., primary, Cotreau, Monette M., primary, Kimberland, Michelle L., primary, Wilson, Ewa, primary, Saraf, Kathryn A., primary, Liu, Wei, primary, McCampbell, Adrienne S., primary, Dave, Bhuvanesh, primary, Broaddus, Russell R., primary, Brown, Eugene L., primary, Kao, Wenling, primary, Skotnicki, Jerauld S., primary, Abou-Gharbia, Magid, primary, Winneker, Richard C., primary, and Walker, Cheryl L., primary

Published
2023
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11. Data from Comparison of Human and Rat Uterine Leiomyomata: Identification of a Dysregulated Mammalian Target of Rapamycin Pathway

Author

Crabtree, Judy S., primary, Jelinsky, Scott A., primary, Harris, Heather A., primary, Choe, Sung E., primary, Cotreau, Monette M., primary, Kimberland, Michelle L., primary, Wilson, Ewa, primary, Saraf, Kathryn A., primary, Liu, Wei, primary, McCampbell, Adrienne S., primary, Dave, Bhuvanesh, primary, Broaddus, Russell R., primary, Brown, Eugene L., primary, Kao, Wenling, primary, Skotnicki, Jerauld S., primary, Abou-Gharbia, Magid, primary, Winneker, Richard C., primary, and Walker, Cheryl L., primary

Published
2023
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12. Supplementary Table 4 from Comparison of Human and Rat Uterine Leiomyomata: Identification of a Dysregulated Mammalian Target of Rapamycin Pathway

Author

Crabtree, Judy S., primary, Jelinsky, Scott A., primary, Harris, Heather A., primary, Choe, Sung E., primary, Cotreau, Monette M., primary, Kimberland, Michelle L., primary, Wilson, Ewa, primary, Saraf, Kathryn A., primary, Liu, Wei, primary, McCampbell, Adrienne S., primary, Dave, Bhuvanesh, primary, Broaddus, Russell R., primary, Brown, Eugene L., primary, Kao, Wenling, primary, Skotnicki, Jerauld S., primary, Abou-Gharbia, Magid, primary, Winneker, Richard C., primary, and Walker, Cheryl L., primary

Published
2023
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13. Supplementary Table 3 from Comparison of Human and Rat Uterine Leiomyomata: Identification of a Dysregulated Mammalian Target of Rapamycin Pathway

Author

Crabtree, Judy S., primary, Jelinsky, Scott A., primary, Harris, Heather A., primary, Choe, Sung E., primary, Cotreau, Monette M., primary, Kimberland, Michelle L., primary, Wilson, Ewa, primary, Saraf, Kathryn A., primary, Liu, Wei, primary, McCampbell, Adrienne S., primary, Dave, Bhuvanesh, primary, Broaddus, Russell R., primary, Brown, Eugene L., primary, Kao, Wenling, primary, Skotnicki, Jerauld S., primary, Abou-Gharbia, Magid, primary, Winneker, Richard C., primary, and Walker, Cheryl L., primary

Published
2023
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14. Supplementary Figures 1-3 from Comparison of Human and Rat Uterine Leiomyomata: Identification of a Dysregulated Mammalian Target of Rapamycin Pathway

Author

Crabtree, Judy S., primary, Jelinsky, Scott A., primary, Harris, Heather A., primary, Choe, Sung E., primary, Cotreau, Monette M., primary, Kimberland, Michelle L., primary, Wilson, Ewa, primary, Saraf, Kathryn A., primary, Liu, Wei, primary, McCampbell, Adrienne S., primary, Dave, Bhuvanesh, primary, Broaddus, Russell R., primary, Brown, Eugene L., primary, Kao, Wenling, primary, Skotnicki, Jerauld S., primary, Abou-Gharbia, Magid, primary, Winneker, Richard C., primary, and Walker, Cheryl L., primary

Published
2023
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15. Supplementary Figure Legends 1-3 from Comparison of Human and Rat Uterine Leiomyomata: Identification of a Dysregulated Mammalian Target of Rapamycin Pathway

Author

Crabtree, Judy S., primary, Jelinsky, Scott A., primary, Harris, Heather A., primary, Choe, Sung E., primary, Cotreau, Monette M., primary, Kimberland, Michelle L., primary, Wilson, Ewa, primary, Saraf, Kathryn A., primary, Liu, Wei, primary, McCampbell, Adrienne S., primary, Dave, Bhuvanesh, primary, Broaddus, Russell R., primary, Brown, Eugene L., primary, Kao, Wenling, primary, Skotnicki, Jerauld S., primary, Abou-Gharbia, Magid, primary, Winneker, Richard C., primary, and Walker, Cheryl L., primary

Published
2023
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16. Molecular signature of methotrexate response among rheumatoid arthritis patients

Author

Brynedal, Boel, primary, Yoosuf, Niyaz, additional, Ulfarsdottir, Tinna Bjorg, additional, Ziemek, Daniel, additional, Maciejewski, Mateusz, additional, Folkersen, Lasse, additional, Westerlind, Helga, additional, Müller, Malin, additional, Sahlström, Peter, additional, Jelinsky, Scott A., additional, Hensvold, Aase, additional, Padyukov, Leonid, additional, Pomiano, Nancy Vivar, additional, Catrina, Anca, additional, Klareskog, Lars, additional, and Berg, Louise, additional

Published
2023
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17. Molecular and Functional Characterization of Human Intestinal Organoids and Monolayers for Modeling Epithelial Barrier

Author

MS MDL 1, Infection & Immunity, Jelinsky, Scott A, Derksen, Merel, Bauman, Eric, Verissimo, Carla S, van Dooremalen, Wies T M, Roos, Jamie Lee, Higuera Barón, Celia, Caballero-Franco, Celia, Johnson, Bryce G, Rooks, Michelle G, Pott, Johanna, Oldenburg, Bas, Vries, Robert G J, Boj, Sylvia F, Kasaian, Marion T, Pourfarzad, Farzin, Rosadini, Charles V, MS MDL 1, Infection & Immunity, Jelinsky, Scott A, Derksen, Merel, Bauman, Eric, Verissimo, Carla S, van Dooremalen, Wies T M, Roos, Jamie Lee, Higuera Barón, Celia, Caballero-Franco, Celia, Johnson, Bryce G, Rooks, Michelle G, Pott, Johanna, Oldenburg, Bas, Vries, Robert G J, Boj, Sylvia F, Kasaian, Marion T, Pourfarzad, Farzin, and Rosadini, Charles V

Published
2023

18. Molecular and Functional Characterization of Human Intestinal Organoids and Monolayers for Modeling Epithelial Barrier

Author

Jelinsky, Scott A, primary, Derksen, Merel, additional, Bauman, Eric, additional, Verissimo, Carla S, additional, van Dooremalen, Wies T M, additional, Roos, Jamie Lee, additional, Higuera Barón, Celia, additional, Caballero-Franco, Celia, additional, Johnson, Bryce G, additional, Rooks, Michelle G, additional, Pott, Johanna, additional, Oldenburg, Bas, additional, Vries, Robert G J, additional, Boj, Sylvia F, additional, Kasaian, Marion T, additional, Pourfarzad, Farzin, additional, and Rosadini, Charles V, additional

Published
2022
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19. RA-MAP, molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients

Author

Isaacs, John D., Brockbank, Sarah, Pedersen, Ayako Wakatsuki, Hilkens, Catharien, Anderson, Amy, Stocks, Philip, Lendrem, Dennis, Tarn, Jessica, Smith, Graham R., Allen, Ben, Casement, John, Diboll, Julie, Harry, Rachel, Cooles, Faye A. H., Cope, Andrew P., Simpson, Gemma, Toward, Ruth, Noble, Hayley, Parke, Angela, Wu, Wing, Clarke, Fiona, Scott, David, Scott, Ian C., Galloway, James, Lempp, Heidi, Ibrahim, Fowzia, Schwank, Samana, Molyneux, Gemma, Lazarov, Tomi, Geissmann, Frederic, Goodyear, Carl S., McInnes, Iain B., Donnelly, Iona, Gilmour, Ashley, Virlan, Aysin Tulunay, Porter, Duncan, Ponchel, Frederique, Emery, Paul, El-Jawhari, Jehan, Parmar, Rekha, McDermott, Michael F., Fisher, Benjamin A., Young, Steve P., Jones, Philip, Raza, Karim, Filer, Andrew, Pitzalis, Costantino, Barnes, Michael R., Watson, David S., Henkin, Rafael, Thorborn, Georgina, Fossati-Jimack, Liliane, Kelly, Stephen, Humby, Frances, Bombardieri, Michele, Rana, Sharmila, Jia, Zhilong, Goldmann, Katriona, Lewis, Myles, Ng, Sandra, Barbosa-Silva, Adriano, Tzanis, Evan, Gallagher-Syed, Amaya, John, Christopher R., Ehrenstein, Michael R., Altobelli, Gioia, Martins, Sandra, Nguyen, Dao, Ali, Humayara, Ciurtin, Coziana, Buch, Maya, Symmons, Deborah, Worthington, Jane, Bruce, Ian N., Sergeant, Jamie C., Verstappen, Suzanne M. M., Stirling, Fiona, Hughes-Morley, Adwoa, Tom, Brian, Farewell, Vernon, Zhong, Yujie, Taylor, Peter C., Buckley, Christopher D., Keidel, Sarah, Cuff, Carolyn, Levesque, Marc, Long, Andrew, Liu, Zheng, Lipsky, Samantha, Harvey, Bohdan, Macoritto, Michael, Hong, Feng, Kaymakcalan, Sukru, Tsuji, Wayne, Sabin, Tony, Ward, Neil, Talbot, Susan, Padhji, Desmond, Sleeman, Matthew, Finch, Donna, Herath, Athula, Lindholm, Catharina, Jenkins, Martin, Ho, Meilien, Hollis, Sally, Marshall, Chris, Parker, Gerry, Page, Matt, Edwards, Hannah, Cuza, Alexandru, Gozzard, Neil, Pandis, Ioannis, Rowe, Anthony, Capdevila, Francisco Bonachela, Loza, Matthew J., Curran, Mark, Verbeeck, Denny, Dan Baker, Mela, Christopher M., Vranic, Ivana, Mela, Catherine T., Wright, Stephen, Rowell, Lucy, Vernon, Emma, Joseph, Nina, Payne, Neil, Rao, Ravi, Binks, Michael, Belson, Alexandra, Ludbrook, Valerie, Hicks, Kirsty, Tipney, Hannah, Ellis, Joanne, Hasan, Samiul, Didierlaurent, Arnaud, Burny, Wivine, Haynes, Andrea, Larminie, Chris, Harris, Ray, Dastros-Pitei, Daniela, Carini, Claudio, Kola, Blerina, Jelinsky, Scott, Hodge, Martin, Maciejewski, Mateusz, Ziemek, Daniel, Schulz-Knappe, Peter, Zucht, Hans-Dieter, Budde, Petra, Coles, Mark, Butler, James A., Read, Simon, and Consortium, The RA-MAP

Subjects
Arthritis, Rheumatoid, Proteomics, Statistics and Probability, Vaccines, Humans, Library and Information Sciences, Statistics, Probability and Uncertainty, Monocytes, Autoantibodies, Biological Specimen Banks, Computer Science Applications, Education, Information Systems
Abstract

Rheumatoid arthritis (RA) is a chronic inflammatory disorder with poorly defined aetiology characterised by synovial inflammation with variable disease severity and drug responsiveness. To investigate the peripheral blood immune cell landscape of early, drug naive RA, we performed comprehensive clinical and molecular profiling of 267 RA patients and 52 healthy vaccine recipients for up to 18 months to establish a high quality sample biobank including plasma, serum, peripheral blood cells, urine, genomic DNA, RNA from whole blood, lymphocyte and monocyte subsets. We have performed extensive multi-omic immune phenotyping, including genomic, metabolomic, proteomic, transcriptomic and autoantibody profiling. We anticipate that these detailed clinical and molecular data will serve as a fundamental resource offering insights into immune-mediated disease pathogenesis, progression and therapeutic response, ultimately contributing to the development and application of targeted therapies for RA.

Published
2022

20. Publisher Correction: Subsets of ILC3−ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues

Author

Cella, Marina, Gamini, Ramya, Sécca, Cristiane, Collins, Patrick L., Zhao, Shanrong, Peng, Vincent, Robinette, Michelle L., Schettini, Jorge, Zaitsev, Konstantin, Gordon, William, Bando, Jennifer K., Yomogida, Kentaro, Cortez, Victor, Fronick, Catrina, Fulton, Robert, Lin, Lih-Ling, Gilfillan, Susan, Flavell, Richard A., Shan, Liang, Artyomov, Maxim N., Bowman, Michael, Oltz, Eugene M., Jelinsky, Scott A., and Colonna, Marco

Published
2019
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22. Peripheral blood cellular dynamics of Rheumatoid arthritis treatment informs about efficacy of response to disease modifying drugs

Author

Jelinsky, Scott A., primary, Hedman, Åsa K., additional, Winter, Eitan, additional, Yoosuf, Niyaz, additional, Benita, Yair, additional, Berg, Louise, additional, Brynedal, Boel, additional, Folkersen, Lasse, additional, Klareskog, Lars, additional, Maciejewski, Mateusz, additional, Sirota-Madi, Alexandra, additional, Spector, Yael, additional, Ziemek, Daniel, additional, Padyukov, Leonid, additional, and Shen-Orr, Shai S., additional

Published
2022
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24. Ageing and interferon gamma response drive the phenotype of neutrophils in the inflamed joint

Author

Grieshaber-Bouyer, Ricardo, primary, Exner, Tarik, additional, Hackert, Nicolaj S, additional, Radtke, Felix A, additional, Jelinsky, Scott A, additional, Halyabar, Olha, additional, Wactor, Alexandra, additional, Karimizadeh, Elham, additional, Brennan, Joseph, additional, Schettini, Jorge, additional, Jonsson, Helena, additional, Rao, Deepak A, additional, Henderson, Lauren A, additional, Müller-Tidow, Carsten, additional, Lorenz, Hanns-Martin, additional, Wabnitz, Guido, additional, Lederer, James A, additional, Hadjipanayis, Angela, additional, and Nigrovic, Peter A, additional

Published
2022
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26. Aging and interferon gamma response drive the phenotype of neutrophils in the inflamed joint

Author

Grieshaber-Bouyer, Ricardo, primary, Exner, Tarik, additional, Hackert, Nicolaj S., additional, Radtke, Felix A., additional, Jelinsky, Scott A., additional, Halyabar, Olha, additional, Wactor, Alexandra, additional, Karimizadeh, Elham, additional, Schettini, Jorge, additional, Jonsson, A. Helena, additional, Rao, Deepak A., additional, Henderson, Lauren A., additional, Müller-Tidow, Carsten, additional, Lorenz, Hanns-Martin, additional, Wabnitz, Guido, additional, Lederer, James A., additional, Hadjipanayis, Angela, additional, and Nigrovic, Peter A., additional

Published
2021
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27. Early prediction of clinical response to anti-TNF treatment using multi-omics and machine learning in rheumatoid arthritis

Author

Yoosuf, Niyaz, primary, Maciejewski, Mateusz, additional, Ziemek, Daniel, additional, Jelinsky, Scott A, additional, Folkersen, Lasse, additional, Müller, Malin, additional, Sahlström, Peter, additional, Vivar, Nancy, additional, Catrina, Anca, additional, Berg, Louise, additional, Klareskog, Lars, additional, Padyukov, Leonid, additional, and Brynedal, Boel, additional

Published
2021
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31. Heterogeneity of human intestinal intraepithelial T cells and their abnormal distribution in Crohn’s disease revealed at high resolution

Author

Jaeger, Natalia, primary, Gamini, Ramya, additional, Cella, Marina, additional, Schettini, Jorge L., additional, Bugatti, Mattia, additional, Zhao, Shanrong, additional, Rosadini, Charles V., additional, Esaulova, Ekaterina, additional, Di Luccia, Blanda, additional, Kinnett, Baylee, additional, Vermi, Willam, additional, Artyomov, Maxim N., additional, Wynn, Thomas A, additional, Xavier, Ramnik J, additional, Jelinsky, Scott A., additional, and Colonna, Marco, additional

Published
2021
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32. Myod1 and GR coordinate myofiber-specific transcriptional enhancers

Author

Rovito, Daniela, primary, Rerra, Anna-Isavella, additional, Ueberschlag-Pitiot, Vanessa, additional, Joshi, Shilpy, additional, Karasu, Nezih, additional, Dacleu-Siewe, Vanessa, additional, Rayana, Khalil Ben, additional, Ghaibour, Kamar, additional, Parisotto, Maxime, additional, Ferry, Arnaud, additional, Jelinsky, Scott A, additional, Laverny, Gilles, additional, Klaholz, Bruno P, additional, Sexton, Tom, additional, Billas, Isabelle M L, additional, Duteil, Delphine, additional, and Metzger, Daniel, additional

Published
2021
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34. Early prediction of clinical response to anti-TNF treatment using multi-omics and machine learning in rheumatoid arthritis.

Author

Yoosuf, Niyaz, Maciejewski, Mateusz, Ziemek, Daniel, Jelinsky, Scott A, Folkersen, Lasse, Müller, Malin, Sahlström, Peter, Vivar, Nancy, Catrina, Anca, Berg, Louise, Klareskog, Lars, Padyukov, Leonid, and Brynedal, Boel

Subjects
BIOMARKERS, FLOW cytometry, PROTEINS, ANTI-inflammatory agents, MACHINE learning, TREATMENT effectiveness, METHOTREXATE, GENE expression, RHEUMATOID arthritis, MULTIOMICS, PREDICTION models, LONGITUDINAL method
Abstract

Objectives Advances in immunotherapy by blocking TNF have remarkably improved treatment outcomes for Rheumatoid arthritis (RA) patients. Although treatment specifically targets TNF, the downstream mechanisms of immune suppression are not completely understood. The aim of this study was to detect biomarkers and expression signatures of treatment response to TNF inhibition. Methods Peripheral blood mononuclear cells (PBMCs) from 39 female patients were collected before anti-TNF treatment initiation (day 0) and after 3 months. The study cohort included patients previously treated with MTX who failed to respond adequately. Response to treatment was defined based on the EULAR criteria and classified 23 patients as responders and 16 as non-responders. We investigated differences in gene expression in PBMCs, the proportion of cell types and cell phenotypes in peripheral blood using flow cytometry and the level of proteins in plasma. Finally, we used machine learning models to predict non-response to anti-TNF treatment. Results The gene expression analysis in baseline samples revealed notably higher expression of the gene EPPK1 in future responders. We detected the suppression of genes and proteins following treatment, including suppressed expression of the T cell inhibitor gene CHI3L1 and its protein YKL-40. The gene expression results were replicated in an independent cohort. Finally, machine learning models mainly based on transcriptomic data showed high predictive utility in classifying non-response to anti-TNF treatment in RA. Conclusions Our integrative multi-omics analyses identified new biomarkers for the prediction of response, found pathways influenced by treatment and suggested new predictive models of anti-TNF treatment in RA patients. [ABSTRACT FROM AUTHOR]

Published
2022
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37. Molecular Biomarkers of Anti-TNF Response in Patients with Rheumatoid Arthritis

Author

Yoosuf, Niyaz, primary, Maciejewski, Mateusz, additional, Ziemek, Daniel, additional, Jelinsky, Scott, additional, Folkersen, Lasse, additional, Müller, Malin, additional, Sahlström, Peter, additional, Vivar, Nancy, additional, Catrina, Anca, additional, Berg, Louise, additional, Klareskog, Lars, additional, Padyukov, Leonid, additional, and Brynedal, Boel, additional

Published
2020
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38. Aiolos and T-bet cooperate to repress the ILC3 transcriptional program in human innate lymphocytes

Author

da Silva, Cristiane Sécca, primary, Cella, Marina, additional, Gamini, Ramya, additional, Collins, Patrick, additional, Zhao, Shanrong, additional, Peng, Vincent, additional, Robinette, Michelle, additional, Schettini, Jorge, additional, Zaitsev, Konstantin, additional, Gordon, Willian, additional, Bando, Jennifer K., additional, Yomogida, Kentaro, additional, Cortez, Victor, additional, Fronick, Catrina, additional, Fulton, Robert, additional, Lih, Ling Lin, additional, Gilfillan, Susan, additional, Flavell, Richard A, additional, Shan, Liang, additional, Artyomov, Maxim N., additional, Bowman, Michael, additional, Oltz, Eugene M, additional, Jelinsky, Scott, additional, and Colonna, Marco, additional

Published
2020
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47. How stereochemistry affects mutagenesis by N2-deoxyguanosine adducts of 7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene: configuration of the adduct bond is more important than those of the hydroxyl groups

Author

Shukla, Rajiv, Jelinsky, Scott, Liu, Tongming, Geacintov, Nicholas E., and Loechler, Edward L.

Subjects
Stereochemistry -- Research, Mutagenesis -- Research, Biological sciences, Chemistry
Abstract

A study was conducted on the relationship between stereochemistry and mutagenesis by N2-deoxyguanosine adducts. The results indicate that anti-B[a]P-N2-dG adduct mutagenesis depends more on the stereochemistry of the adduct bond than on the stereochemistry of the hyudroxyl groups. Moreover, different stereochemically distinct adducts can induce different mutations in different sequence contexts.

Published
1997

48. The major, N2-Gua adduct of the (+)-anti-benzo(a)pyrene diol epoxide is capable of inducing G->A and G->C, in addition to G->T, mutations

Author

Jelinsky, Scott A., Liu, Tongming, Geacintov, Nicholas E., and Loechler, Edward L.

Subjects
Mutation (Biology) -- Research, Epoxy compounds -- Analysis, Escherichia coli -- Research, Biological sciences, Chemistry
Abstract

The N2-Gua adduct of the (+)-anti-B(a)PDE, (+)-anti-B(a)P-N2-Gua, is capable of inducing G->A, G->C and G->T mutations and the DNA sequence context affect the qualitative pattern of mutations due to (+)-anti-B(a)P-N2-Gua. G->A, G->C mutations became more dominant when the mutations in the supF gene of the E. coli plasmid pUB3 were heated at 80 degree C and subsequently cooled to 0 degree C. Prior to heating only G->T mutations were obtained. The most likely model to explain the variation in mutations is that heating induces a change towards stable conformation which results in G->T,A, and C mutations.

Published
1995

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