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4. The Transcription Factor Encyclopedia

Author

Yusuf, Dimas, Butland, Stefanie L, Swanson, Magdalena I, Bolotin, Eugene, Ticoll, Amy, Cheung, Warren A, Cindy Zhang, Xiao, Dickman, Christopher TD, Fulton, Debra L, Lim, Jonathan S, Schnabl, Jake M, Ramos, Oscar HP, Vasseur-Cognet, Mireille, de Leeuw, Charles N, Simpson, Elizabeth M, Ryffel, Gerhart U, Lam, Eric W-F, Kist, Ralf, Wilson, Miranda SC, Marco-Ferreres, Raquel, Brosens, Jan J, Beccari, Leonardo L, Bovolenta, Paola, Benayoun, Bérénice A, Monteiro, Lara J, Schwenen, Helma DC, Grontved, Lars, Wederell, Elizabeth, Mandrup, Susanne, Veitia, Reiner A, Chakravarthy, Harini, Hoodless, Pamela A, Mancarelli, M Michela, Torbett, Bruce E, Banham, Alison H, Reddy, Sekhar P, Cullum, Rebecca L, Liedtke, Michaela, Tschan, Mario P, Vaz, Michelle, Rizzino, Angie, Zannini, Mariastella, Frietze, Seth, Farnham, Peggy J, Eijkelenboom, Astrid, Brown, Philip J, Laperrière, David, Leprince, Dominique, de Cristofaro, Tiziana, Prince, Kelly L, Putker, Marrit, del Peso, Luis, Camenisch, Gieri, Wenger, Roland H, Mikula, Michal, Rozendaal, Marieke, Mader, Sylvie, Ostrowski, Jerzy, Rhodes, Simon J, Van Rechem, Capucine, Boulay, Gaylor, Olechnowicz, Sam WZ, Breslin, Mary B, Lan, Michael S, Nanan, Kyster K, Wegner, Michael, Hou, Juan, Mullen, Rachel D, Colvin, Stephanie C, Noy, Peter, Webb, Carol F, Witek, Matthew E, Ferrell, Scott, Daniel, Juliet M, Park, Jason, Waldman, Scott A, Peet, Daniel J, Taggart, Michael, Jayaraman, Padma-Sheela, Karrich, Julien J, Blom, Bianca, Vesuna, Farhad, O'Geen, Henriette, Sun, Yunfu, Gronostajski, Richard M, Woodcroft, Mark W, Hough, Margaret R, Chen, Edwin, Europe-Finner, G Nicholas, Karolczak-Bayatti, Magdalena, Bailey, Jarrod, Hankinson, Oliver, Raman, Venu, LeBrun, David P, Biswal, Shyam, Harvey, Christopher J, DeBruyne, Jason P, Hogenesch, John B, Hevner, Robert F, and Héligon, Christophe

Abstract

Abstract Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe.

Published
2012

5. Supplementary Figures 1 - 11 from The Twist Box Domain Is Required for Twist1-induced Prostate Cancer Metastasis

Author

Gajula, Rajendra P., primary, Chettiar, Sivarajan T., primary, Williams, Russell D., primary, Thiyagarajan, Saravanan, primary, Kato, Yoshinori, primary, Aziz, Khaled, primary, Wang, Ruoqi, primary, Gandhi, Nishant, primary, Wild, Aaron T., primary, Vesuna, Farhad, primary, Ma, Jinfang, primary, Salih, Tarek, primary, Cades, Jessica, primary, Fertig, Elana, primary, Biswal, Shyam, primary, Burns, Timothy F., primary, Chung, Christine H., primary, Rudin, Charles M., primary, Herman, Joseph M., primary, Hales, Russell K., primary, Raman, Venu, primary, An, Steven S., primary, and Tran, Phuoc T., primary

Published
2023
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6. Data from The Twist Box Domain Is Required for Twist1-induced Prostate Cancer Metastasis

Author

Gajula, Rajendra P., primary, Chettiar, Sivarajan T., primary, Williams, Russell D., primary, Thiyagarajan, Saravanan, primary, Kato, Yoshinori, primary, Aziz, Khaled, primary, Wang, Ruoqi, primary, Gandhi, Nishant, primary, Wild, Aaron T., primary, Vesuna, Farhad, primary, Ma, Jinfang, primary, Salih, Tarek, primary, Cades, Jessica, primary, Fertig, Elana, primary, Biswal, Shyam, primary, Burns, Timothy F., primary, Chung, Christine H., primary, Rudin, Charles M., primary, Herman, Joseph M., primary, Hales, Russell K., primary, Raman, Venu, primary, An, Steven S., primary, and Tran, Phuoc T., primary

Published
2023
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7. Supplementary Table 2 from The Twist Box Domain Is Required for Twist1-induced Prostate Cancer Metastasis

Author

Gajula, Rajendra P., primary, Chettiar, Sivarajan T., primary, Williams, Russell D., primary, Thiyagarajan, Saravanan, primary, Kato, Yoshinori, primary, Aziz, Khaled, primary, Wang, Ruoqi, primary, Gandhi, Nishant, primary, Wild, Aaron T., primary, Vesuna, Farhad, primary, Ma, Jinfang, primary, Salih, Tarek, primary, Cades, Jessica, primary, Fertig, Elana, primary, Biswal, Shyam, primary, Burns, Timothy F., primary, Chung, Christine H., primary, Rudin, Charles M., primary, Herman, Joseph M., primary, Hales, Russell K., primary, Raman, Venu, primary, An, Steven S., primary, and Tran, Phuoc T., primary

Published
2023
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8. Supplementary Table 1 from The Twist Box Domain Is Required for Twist1-induced Prostate Cancer Metastasis

Author

Gajula, Rajendra P., primary, Chettiar, Sivarajan T., primary, Williams, Russell D., primary, Thiyagarajan, Saravanan, primary, Kato, Yoshinori, primary, Aziz, Khaled, primary, Wang, Ruoqi, primary, Gandhi, Nishant, primary, Wild, Aaron T., primary, Vesuna, Farhad, primary, Ma, Jinfang, primary, Salih, Tarek, primary, Cades, Jessica, primary, Fertig, Elana, primary, Biswal, Shyam, primary, Burns, Timothy F., primary, Chung, Christine H., primary, Rudin, Charles M., primary, Herman, Joseph M., primary, Hales, Russell K., primary, Raman, Venu, primary, An, Steven S., primary, and Tran, Phuoc T., primary

Published
2023
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18. Supplementary Figure 2 from Twist Overexpression Induces In vivo Angiogenesis and Correlates with Chromosomal Instability in Breast Cancer

Author

Mironchik, Yelena, primary, Winnard, Paul T., primary, Vesuna, Farhad, primary, Kato, Yoshinori, primary, Wildes, Flonne, primary, Pathak, Arvind P., primary, Kominsky, Scott, primary, Artemov, Dmitri, primary, Bhujwalla, Zaver, primary, Van Diest, Paul, primary, Burger, Horst, primary, Glackin, Carlotta, primary, and Raman, Venu, primary

Published
2023
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19. Supplementary Figure 1 from Twist Overexpression Induces In vivo Angiogenesis and Correlates with Chromosomal Instability in Breast Cancer

Author

Mironchik, Yelena, primary, Winnard, Paul T., primary, Vesuna, Farhad, primary, Kato, Yoshinori, primary, Wildes, Flonne, primary, Pathak, Arvind P., primary, Kominsky, Scott, primary, Artemov, Dmitri, primary, Bhujwalla, Zaver, primary, Van Diest, Paul, primary, Burger, Horst, primary, Glackin, Carlotta, primary, and Raman, Venu, primary

Published
2023
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20. Supplementary Figure Legends from Twist Overexpression Induces In vivo Angiogenesis and Correlates with Chromosomal Instability in Breast Cancer

Author

Mironchik, Yelena, primary, Winnard, Paul T., primary, Vesuna, Farhad, primary, Kato, Yoshinori, primary, Wildes, Flonne, primary, Pathak, Arvind P., primary, Kominsky, Scott, primary, Artemov, Dmitri, primary, Bhujwalla, Zaver, primary, Van Diest, Paul, primary, Burger, Horst, primary, Glackin, Carlotta, primary, and Raman, Venu, primary

Published
2023
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21. Data from Twist Overexpression Induces In vivo Angiogenesis and Correlates with Chromosomal Instability in Breast Cancer

Author

Mironchik, Yelena, primary, Winnard, Paul T., primary, Vesuna, Farhad, primary, Kato, Yoshinori, primary, Wildes, Flonne, primary, Pathak, Arvind P., primary, Kominsky, Scott, primary, Artemov, Dmitri, primary, Bhujwalla, Zaver, primary, Van Diest, Paul, primary, Burger, Horst, primary, Glackin, Carlotta, primary, and Raman, Venu, primary

Published
2023
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25. RK-33, a small molecule inhibitor of host RNA helicase DDX3, suppresses multiple variants of SARS-CoV-2

Author

Vesuna, Farhad, Akhrymuk, Ivan, Smith, Amy, Winnard Jr, Paul T., Lin, Shih-Chao, Panny, Lauren, Scharpf, Robert, Kehn-Hall, Kylene, and Raman, Venu

Subjects
RNA helicase, SARS-CoV-2, host-targeted antiviral, DDX3 inhibitor, viral isolates, TMPRSS2, RK-33
Abstract

SARS-CoV-2, the virus behind the deadly COVID-19 pandemic, continues to spread globally even as vaccine strategies are proving effective in preventing hospitalizations and deaths. However, evolving variants of the virus appear to be more transmissive and vaccine efficacy toward them is waning. As a result, SARS-CoV-2 will continue to have a deadly impact on public health into the foreseeable future. One strategy to bypass the continuing problem of newer variants is to target host proteins required for viral replication. We have used this host-targeted antiviral (HTA) strategy that targets DDX3X (DDX3), a host DEAD-box RNA helicase that is usurped by SARS-CoV-2 for virus production. We demonstrated that targeting DDX3 with RK-33, a small molecule inhibitor, reduced the viral load in four isolates of SARS-CoV-2 (Lineage A, and Lineage B Alpha, Beta, and Delta variants) by one to three log orders in Calu-3 cells. Furthermore, proteomics and RNA-seq analyses indicated that most SARS-CoV-2 genes were downregulated by RK-33 treatment. Also, we show that the use of RK-33 decreases TMPRSS2 expression, which may be due to DDX3s ability to unwind G-quadraplex structures present in the TMPRSS2 promoter. The data presented support the use of RK-33 as an HTA strategy to control SARS-CoV-2 infection, irrespective of its mutational status, in humans. Published version

Published
2022

27. Targeting DDX3 with a small molecule inhibitor for lung cancer therapy

Author

Bol, Guus M, Vesuna, Farhad, Xie, Min, Zeng, Jing, Aziz, Khaled, Gandhi, Nishant, Levine, Anne, Irving, Ashley, Korz, Dorian, Tantravedi, Saritha, Heerma van Voss, Marise R, Gabrielson, Kathleen, Bordt, Evan A, Polster, Brian M, Cope, Leslie, van der Groep, Petra, Kondaskar, Atul, Rudek, Michelle A, Hosmane, Ramachandra S, van der Wall, Elsken, van Diest, Paul J, Tran, Phuoc T, and Raman, Venu

Published
2015
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31. Targeting DDX3 in Medulloblastoma Using the Small Molecule Inhibitor RK-33

Author

Tantravedi, Saritha, Vesuna, Farhad, Winnard, Paul T., Martin, Allison, Lim, Michael, Eberhart, Charles G., Berlinicke, Cynthia, Raabe, Eric, van Diest, Paul J., Raman, Venu, Tantravedi, Saritha, Vesuna, Farhad, Winnard, Paul T., Martin, Allison, Lim, Michael, Eberhart, Charles G., Berlinicke, Cynthia, Raabe, Eric, van Diest, Paul J., and Raman, Venu

Published
2019

32. Targeting DDX3 in Medulloblastoma Using the Small Molecule Inhibitor RK-33

Author

Secretariaat Medische Oncologie, Pathologie mortuarium en obductie, Pathologie, Cancer, Tantravedi, Saritha, Vesuna, Farhad, Winnard, Paul T., Martin, Allison, Lim, Michael, Eberhart, Charles G., Berlinicke, Cynthia, Raabe, Eric, van Diest, Paul J., Raman, Venu, Secretariaat Medische Oncologie, Pathologie mortuarium en obductie, Pathologie, Cancer, Tantravedi, Saritha, Vesuna, Farhad, Winnard, Paul T., Martin, Allison, Lim, Michael, Eberhart, Charles G., Berlinicke, Cynthia, Raabe, Eric, van Diest, Paul J., and Raman, Venu

Published
2019

36. Global Effects of DDX3 Inhibition on Cell Cycle Regulation Identified by a Combined Phosphoproteomics and Single Cell Tracking Approach

Author

Heerma van Voss, Marise R., Kammers, Kai, Vesuna, Farhad, Brilliant, Justin, Bergman, Yehudit, Tantravedi, Saritha, Wu, Xinyan, Cole, Robert N., Holland, Andrew, van Diest, Paul J., Raman, Venu, Heerma van Voss, Marise R., Kammers, Kai, Vesuna, Farhad, Brilliant, Justin, Bergman, Yehudit, Tantravedi, Saritha, Wu, Xinyan, Cole, Robert N., Holland, Andrew, van Diest, Paul J., and Raman, Venu

Published
2018

37. Global Effects of DDX3 Inhibition on Cell Cycle Regulation Identified by a Combined Phosphoproteomics and Single Cell Tracking Approach

Author

Pathologie Stafondersteuning, Cancer, Hoofd-Hals Chirurgische Oncologie, Pathologie, Heerma van Voss, Marise R., Kammers, Kai, Vesuna, Farhad, Brilliant, Justin, Bergman, Yehudit, Tantravedi, Saritha, Wu, Xinyan, Cole, Robert N., Holland, Andrew, van Diest, Paul J., Raman, Venu, Pathologie Stafondersteuning, Cancer, Hoofd-Hals Chirurgische Oncologie, Pathologie, Heerma van Voss, Marise R., Kammers, Kai, Vesuna, Farhad, Brilliant, Justin, Bergman, Yehudit, Tantravedi, Saritha, Wu, Xinyan, Cole, Robert N., Holland, Andrew, van Diest, Paul J., and Raman, Venu

Published
2018

41. Global Effects of DDX3 Inhibition on Cell Cycle Regulation Identified by a Combined Phosphoproteomics and Single Cell Tracking Approach

Author

Heerma van Voss, Marise R., primary, Kammers, Kai, additional, Vesuna, Farhad, additional, Brilliant, Justin, additional, Bergman, Yehudit, additional, Tantravedi, Saritha, additional, Wu, Xinyan, additional, Cole, Robert N., additional, Holland, Andrew, additional, van Diest, Paul J., additional, and Raman, Venu, additional

Published
2018
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44. Role of DDX3 in the pathogenesis of inflammatory bowel disease

Author

Tantravedi, Saritha, Vesuna, Farhad, Winnard, Paul T., van Voss, Marise R.Heerma, van Diest, Paul J., Raman, Venu, Tantravedi, Saritha, Vesuna, Farhad, Winnard, Paul T., van Voss, Marise R.Heerma, van Diest, Paul J., and Raman, Venu

Published
2017

45. Nuclear DDX3 expression predicts poor outcome in colorectal and breast cancer

Author

Heerma Van Voss, Marise R., Vesuna, Farhad, Bol, Guus M., Meeldijk, Jan, Raman, Ana, Offerhaus, G. Johan, Buerger, Horst, Patel, Arvind H., Van Der Wall, Elsken, Van Diest, Paul J., Raman, Venu, Heerma Van Voss, Marise R., Vesuna, Farhad, Bol, Guus M., Meeldijk, Jan, Raman, Ana, Offerhaus, G. Johan, Buerger, Horst, Patel, Arvind H., Van Der Wall, Elsken, Van Diest, Paul J., and Raman, Venu

Published
2017

47. Role of DDX3 in the pathogenesis of inflammatory bowel disease

Author

Cancer, Pathologie Groep Van Diest, Pathologie, Pathologie mortuarium en obductie, Tantravedi, Saritha, Vesuna, Farhad, Winnard, Paul T., van Voss, Marise R.Heerma, van Diest, Paul J., Raman, Venu, Cancer, Pathologie Groep Van Diest, Pathologie, Pathologie mortuarium en obductie, Tantravedi, Saritha, Vesuna, Farhad, Winnard, Paul T., van Voss, Marise R.Heerma, van Diest, Paul J., and Raman, Venu

Published
2017

48. Nuclear DDX3 expression predicts poor outcome in colorectal and breast cancer

Author

Pathologie patiënten zorg, Cancer, Pathologie Groep Van Diest, Unit Opleiding Aios, Cancer Center, Medisch Oncologische Disciplines, Heerma Van Voss, Marise R., Vesuna, Farhad, Bol, Guus M., Meeldijk, Jan, Raman, Ana, Offerhaus, G. Johan, Buerger, Horst, Patel, Arvind H., Van Der Wall, Elsken, Van Diest, Paul J., Raman, Venu, Pathologie patiënten zorg, Cancer, Pathologie Groep Van Diest, Unit Opleiding Aios, Cancer Center, Medisch Oncologische Disciplines, Heerma Van Voss, Marise R., Vesuna, Farhad, Bol, Guus M., Meeldijk, Jan, Raman, Ana, Offerhaus, G. Johan, Buerger, Horst, Patel, Arvind H., Van Der Wall, Elsken, Van Diest, Paul J., and Raman, Venu

Published
2017

49. Combination treatment using DDX3 and PARP inhibitors induces synthetic lethality in BRCA1-proficient breast cancer

Author

Pathologie patiënten zorg, Cancer, Pathologie Groep Van Diest, Unit Opleiding Aios, Cancer Center, Medisch Oncologische Disciplines, Heerma van Voss, Marise R., Brilliant, Justin D., Vesuna, Farhad, Bol, Guus M., van der Wall, Elsken, van Diest, Paul J., Raman, Venu, Pathologie patiënten zorg, Cancer, Pathologie Groep Van Diest, Unit Opleiding Aios, Cancer Center, Medisch Oncologische Disciplines, Heerma van Voss, Marise R., Brilliant, Justin D., Vesuna, Farhad, Bol, Guus M., van der Wall, Elsken, van Diest, Paul J., and Raman, Venu

Published
2017

50. Organ-specific isogenic metastatic breast cancer cell lines exhibit distinct Raman spectral signatures and metabolomes

Author

Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Laser Biomedical Research Center, Kang, Jeon Woong, Dasari, Ramachandra Rao, Winnard Jr., Paul T., Zhang, Chi, Vesuna, Farhad, Garry, Jonah, Barman, Ishan, Raman, Venu, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Laser Biomedical Research Center, Kang, Jeon Woong, Dasari, Ramachandra Rao, Winnard Jr., Paul T., Zhang, Chi, Vesuna, Farhad, Garry, Jonah, Barman, Ishan, and Raman, Venu

Abstract

Molecular characterization of organ-specific metastatic lesions, which distinguish them from the primary tumor, will provide a better understanding of tissue specific adaptations that regulate metastatic progression. Using an orthotopic xenograft model, we have isolated isogenic metastatic human breast cancer cell lines directly from organ explants that are phenotypically distinct from the primary tumor cell line. Label-free Raman spectroscopy was used and informative spectral bands were ascertained as differentiators of organ-specific metastases as opposed to the presence of a single universal marker. Decision algorithms derived from the Raman spectra unambiguously identified these isogenic cell lines as unique biological entities – a finding reinforced through metabolomic analyses that indicated tissue of origin metabolite distinctions between the cell lines. Notably, complementarity of the metabolomics and Raman datasets was found. Our findings provide evidence that metastatic spread generates tissue-specific adaptations at the molecular level within cancer cells, which can be differentiated with Raman spectroscopy., National Institute of Biomedical Imaging and Bioengineering (U.S.) (9P41EB015871-26A1)

Published
2017

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