Additional file 4: of Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis

Rekha Narasimhan (5594711)
Roxana Coras (5594714)
Sara Rosenthal (5594717)
Shannon Sweeney (5594720)
Alessia Lodi (256296)
Stefano Tiziani (256302)
David Boyle (221745)
Arthur Kavanaugh (2683)
Monica Guma (814502)

Open link

Publication date

August 2018

DOI

10.6084/m9.figshare.6933785.v1

Abstract

Figure S3. Correlation between serum metabolites and synovial CD19, CD79A, and IgGHC. (TIFF 14826 kb

Extracted data

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Data Protection

Additional file 4: of Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis

Rekha Narasimhan (5594711)
Roxana Coras (5594714)
Sara Rosenthal (5594717)
Shannon Sweeney (5594720)
Alessia Lodi (256296)
Stefano Tiziani (256302)
David Boyle (221745)
Arthur Kavanaugh (2683)
Monica Guma (814502)

Open link

Publication date

August 2018

DOI

10.6084/m9.figshare.6933785.v1

Abstract

Figure S3. Correlation between serum metabolites and synovial CD19, CD79A, and IgGHC. (TIFF 14826 kb

Extracted data

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

July 2016

Illustration of the distribution of patients in this observational study. (PDF 223 kb

Additional file 1: of Higher expression of TNFα-induced genes in the synovium of patients with early rheumatoid arthritis correlates with disease activity, and predicts absence of response to first line therapy

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Patients’ characteristics (immunohistochemistry studies on needle arthroscopic biopsies). Characteri...

Additional file 10: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

July 2016

Correlation matrixes of signature scores of core genes for TCZ (a) and ABT (b). (PDF 297 kb

Additional file 5: of Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis

Rekha Narasimhan (5594711)
Roxana Coras (5594714)
Sara Rosenthal (5594717)
Shannon Sweeney (5594720)
Alessia Lodi (256296)
Stefano Tiziani (256302)
David Boyle (221745)
Arthur Kavanaugh (2683)
Monica Guma (814502)

August 2018

Figure S4. Correlation between serum metabolites and synovial APRIL, CD138, SDF1, IgKappa, and IgMHC...

Additional file 2: of Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis

Rekha Narasimhan (5594711)
Roxana Coras (5594714)
Sara Rosenthal (5594717)
Shannon Sweeney (5594720)
Alessia Lodi (256296)
Stefano Tiziani (256302)
David Boyle (221745)
Arthur Kavanaugh (2683)
Monica Guma (814502)

August 2018

Figure S1. Correlation between synovial markers and serum metabolites. (TIFF 14826 kb

Additional file 7: of Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis

Rekha Narasimhan (5594711)
Roxana Coras (5594714)
Sara Rosenthal (5594717)
Shannon Sweeney (5594720)
Alessia Lodi (256296)
Stefano Tiziani (256302)
David Boyle (221745)
Arthur Kavanaugh (2683)
Monica Guma (814502)

August 2018

Figure S6. Correlation between serum metabolites and synovial IL-1Î˛ and IL-8. (TIFF 14826 kb

Additional file 6: of Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis

Rekha Narasimhan (5594711)
Roxana Coras (5594714)
Sara Rosenthal (5594717)
Shannon Sweeney (5594720)
Alessia Lodi (256296)
Stefano Tiziani (256302)
David Boyle (221745)
Arthur Kavanaugh (2683)
Monica Guma (814502)

August 2018

Figure S5. Correlation between serum metabolites and synovial MMP1, MMP3, and IL-6. (TIFF 14826 kb

Additional file 4: of Higher expression of TNFα-induced genes in the synovium of patients with early rheumatoid arthritis correlates with disease activity, and predicts absence of response to first line therapy

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Genes over-expressed in poor responders to therapy at baseline. Lists of probe sets differentially e...

Additional file 2: of Differential synovial tissue biomarkers among psoriatic arthritis and rheumatoid factor/anti-citrulline antibody-negative rheumatoid arthritis

Stefano Alivernini (204814)
Dario Bruno (6687539)
Barbara Tolusso (146649)
Laura Bui (5475797)
Luca Petricca (5475788)
Maria Gigante (6687542)
Domenico Birra (6687545)
Anna Fedele (3432314)
Giusy Peluso (3432311)
Francesco Federico (487943)
Gianfranco Ferraccioli (146644)
Elisa Gremese (146657)

May 2019

Table S1. Inter-rater agreement coefficients for CD68, CD21, CD20, CD3, CD117, CD138, and CD31 IHC s...

Additional file 3: of Higher expression of TNFα-induced genes in the synovium of patients with early rheumatoid arthritis correlates with disease activity, and predicts absence of response to first line therapy

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Numbers of probe sets displaying a positive correlation with global disease activity indices and eac...

Additional file 1: of S100A8/A9, a potent serum and molecular imaging biomarker for synovial inflammation and joint destruction in seronegative experimental arthritis

Edwin Geven (3469427)
Martijn van den Bosch (3469424)
Irene Di Ceglie (3454922)
Giuliana Ascone (3469421)
Shahla Abdollahi-Roodsaz (531410)
Annet Sloetjes (3469430)
Sven Hermann (1613419)
Michael SchĂ¤fers (3469433)
Fons van de Loo (3436691)
Peter van der Kraan (3436700)
Marije Koenders (3436682)
Dirk Foell (249589)
Johannes Roth (125060)
Thomas Vogl (125044)
Peter van Lent (383542)

October 2016

(A) Serum S100A8/A9 as a positive marker to predict joint swelling (macroscopic score >0.5) at week ...

Additional file 2: of S100A8/A9, a potent serum and molecular imaging biomarker for synovial inflammation and joint destruction in seronegative experimental arthritis

Edwin Geven (3469427)
Martijn van den Bosch (3469424)
Irene Di Ceglie (3454922)
Giuliana Ascone (3469421)
Shahla Abdollahi-Roodsaz (531410)
Annet Sloetjes (3469430)
Sven Hermann (1613419)
Michael Schäfers (199804)
Fons van de Loo (3436691)
Peter van der Kraan (3436700)
Marije Koenders (3436682)
Dirk Foell (249589)
Johannes Roth (125060)
Thomas Vogl (125044)
Peter van Lent (383542)

October 2016

(A). Serum levels of the cytokines IL-17, IL-4, and IFN-γ did not correlate with the combined macros...

Additional file 1: of Baseline metabolic profiles of early rheumatoid arthritis patients achieving sustained drug-free remission after initiating treat-to-target tocilizumab, methotrexate, or the combination: insights from systems biology

Xavier Teitsma (3514304)
Wei Yang (109917)
Johannes Jacobs (3514301)
Attila PethĂś-Schramm (4262896)
Michelle Borm (4262875)
Amy Harms (3007857)
Thomas Hankemeier (135670)
Jacob van Laar (213989)
Johannes Bijlsma (3424766)
Floris Lafeber (2301085)

October 2018

Additional information regarding the metabolite profiling on the three platforms. (DOCX 15 kb

Additional file 3: Table S1. of Circulating DNA in rheumatoid arthritis: pathological changes and association with clinically used serological markers

Elena Rykova (1298229)
Aleksey Sizikov (3994805)
Dirk Roggenbuck (407723)
Oksana Antonenko (3994799)
Leonid Bryzgalov (3601136)
Evgeniy Morozkin (3994796)
Kseniya Skvortsova (3994790)
Valentin Vlassov (503649)
Pavel Laktionov (3994793)
Vladimir Kozlov (3994802)

May 2017

Comparison of cir-nDNA, m-cirDNA, n-csbDNA, and m-csbDNA concentration in the blood from patients wi...

Additional file 9: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

July 2016

qRT-PCR results of five core genes of each signature identified from GSEA. (PDF 317 kb

Additional file 1: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

July 2016

Illustration of the distribution of patients in this observational study. (PDF 223 kb

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Patients’ characteristics (immunohistochemistry studies on needle arthroscopic biopsies). Characteri...

Additional file 10: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

July 2016

Correlation matrixes of signature scores of core genes for TCZ (a) and ABT (b). (PDF 297 kb

Additional file 5: of Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis

Rekha Narasimhan (5594711)
Roxana Coras (5594714)
Sara Rosenthal (5594717)
Shannon Sweeney (5594720)
Alessia Lodi (256296)
Stefano Tiziani (256302)
David Boyle (221745)
Arthur Kavanaugh (2683)
Monica Guma (814502)

August 2018

Figure S4. Correlation between serum metabolites and synovial APRIL, CD138, SDF1, IgKappa, and IgMHC...

Additional file 2: of Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis

Rekha Narasimhan (5594711)
Roxana Coras (5594714)
Sara Rosenthal (5594717)
Shannon Sweeney (5594720)
Alessia Lodi (256296)
Stefano Tiziani (256302)
David Boyle (221745)
Arthur Kavanaugh (2683)
Monica Guma (814502)

August 2018

Figure S1. Correlation between synovial markers and serum metabolites. (TIFF 14826 kb

Additional file 7: of Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis

Rekha Narasimhan (5594711)
Roxana Coras (5594714)
Sara Rosenthal (5594717)
Shannon Sweeney (5594720)
Alessia Lodi (256296)
Stefano Tiziani (256302)
David Boyle (221745)
Arthur Kavanaugh (2683)
Monica Guma (814502)

August 2018

Figure S6. Correlation between serum metabolites and synovial IL-1Î˛ and IL-8. (TIFF 14826 kb

Additional file 6: of Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis

Rekha Narasimhan (5594711)
Roxana Coras (5594714)
Sara Rosenthal (5594717)
Shannon Sweeney (5594720)
Alessia Lodi (256296)
Stefano Tiziani (256302)
David Boyle (221745)
Arthur Kavanaugh (2683)
Monica Guma (814502)

August 2018

Figure S5. Correlation between serum metabolites and synovial MMP1, MMP3, and IL-6. (TIFF 14826 kb

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Genes over-expressed in poor responders to therapy at baseline. Lists of probe sets differentially e...

Additional file 2: of Differential synovial tissue biomarkers among psoriatic arthritis and rheumatoid factor/anti-citrulline antibody-negative rheumatoid arthritis

Stefano Alivernini (204814)
Dario Bruno (6687539)
Barbara Tolusso (146649)
Laura Bui (5475797)
Luca Petricca (5475788)
Maria Gigante (6687542)
Domenico Birra (6687545)
Anna Fedele (3432314)
Giusy Peluso (3432311)
Francesco Federico (487943)
Gianfranco Ferraccioli (146644)
Elisa Gremese (146657)

May 2019

Table S1. Inter-rater agreement coefficients for CD68, CD21, CD20, CD3, CD117, CD138, and CD31 IHC s...

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Numbers of probe sets displaying a positive correlation with global disease activity indices and eac...

Additional file 1: of S100A8/A9, a potent serum and molecular imaging biomarker for synovial inflammation and joint destruction in seronegative experimental arthritis

Edwin Geven (3469427)
Martijn van den Bosch (3469424)
Irene Di Ceglie (3454922)
Giuliana Ascone (3469421)
Shahla Abdollahi-Roodsaz (531410)
Annet Sloetjes (3469430)
Sven Hermann (1613419)
Michael SchĂ¤fers (3469433)
Fons van de Loo (3436691)
Peter van der Kraan (3436700)
Marije Koenders (3436682)
Dirk Foell (249589)
Johannes Roth (125060)
Thomas Vogl (125044)
Peter van Lent (383542)

October 2016

(A) Serum S100A8/A9 as a positive marker to predict joint swelling (macroscopic score >0.5) at week ...

Additional file 2: of S100A8/A9, a potent serum and molecular imaging biomarker for synovial inflammation and joint destruction in seronegative experimental arthritis

Edwin Geven (3469427)
Martijn van den Bosch (3469424)
Irene Di Ceglie (3454922)
Giuliana Ascone (3469421)
Shahla Abdollahi-Roodsaz (531410)
Annet Sloetjes (3469430)
Sven Hermann (1613419)
Michael Schäfers (199804)
Fons van de Loo (3436691)
Peter van der Kraan (3436700)
Marije Koenders (3436682)
Dirk Foell (249589)
Johannes Roth (125060)
Thomas Vogl (125044)
Peter van Lent (383542)

October 2016

(A). Serum levels of the cytokines IL-17, IL-4, and IFN-γ did not correlate with the combined macros...

Xavier Teitsma (3514304)
Wei Yang (109917)
Johannes Jacobs (3514301)
Attila PethĂś-Schramm (4262896)
Michelle Borm (4262875)
Amy Harms (3007857)
Thomas Hankemeier (135670)
Jacob van Laar (213989)
Johannes Bijlsma (3424766)
Floris Lafeber (2301085)

October 2018

Additional information regarding the metabolite profiling on the three platforms. (DOCX 15 kb

Additional file 3: Table S1. of Circulating DNA in rheumatoid arthritis: pathological changes and association with clinically used serological markers

Elena Rykova (1298229)
Aleksey Sizikov (3994805)
Dirk Roggenbuck (407723)
Oksana Antonenko (3994799)
Leonid Bryzgalov (3601136)
Evgeniy Morozkin (3994796)
Kseniya Skvortsova (3994790)
Valentin Vlassov (503649)
Pavel Laktionov (3994793)
Vladimir Kozlov (3994802)

May 2017

Comparison of cir-nDNA, m-cirDNA, n-csbDNA, and m-csbDNA concentration in the blood from patients wi...

Additional file 9: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

July 2016

qRT-PCR results of five core genes of each signature identified from GSEA. (PDF 317 kb

Additional file 1: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

July 2016

Illustration of the distribution of patients in this observational study. (PDF 223 kb

Aurélie De Groof (3581453)
Julie Ducreux (732980)
Frances Humby (84694)
Adrien Nzeusseu Toukap (732984)
Valérie Badot (3581456)
Costantino Pitzalis (23531)
Frédéric Houssiau (3581450)
Patrick Durez (11540)
Bernard Lauwerys (3462587)

January 2016

Patients’ characteristics (immunohistochemistry studies on needle arthroscopic biopsies). Characteri...

Additional file 10: of Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Seiji Nakamura (126240)
Katsuya Suzuki (1786093)
Hiroshi Iijima (3399872)
Yuko Hata (428188)
Chun Lim (3399875)
Yohei Ishizawa (3399869)
Hideto Kameda (3399878)
Koichi Amano (2543410)
Kenichi Matsubara (22850)
Ryo Matoba (1609)
Tsutomu Takeuchi (163145)

July 2016

Correlation matrixes of signature scores of core genes for TCZ (a) and ABT (b). (PDF 297 kb

Additional file 4: of Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis

Abstract

Extracted data

Additional file 4: of Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis

Abstract

Extracted data

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