Publications

Montano, C., Covarrubias, S., Malekos, E., Katzman, S., & Carpenter, S. (2024). Identification and functional characterization of lncRNAs involved in human monocyte-to-macrophage differentiation. RNA Biology, 21(1), 39–51. https://doi.org/10.1080/15476286.2024.2417155

Eric Malekos, Christy Montano, Susan Carpenter. bioRxiv 2024.06.18.599405 

doi: https://doi.org/10.1101/2024.06.18.599405

Halasz, H. et al. CRISPRi screens identify the lncRNA, LOUP, as a multifunctional locus regulating macrophage differentiation and inflammatory signaling. Proc. Natl. Acad. Sci.121, e2322524121 (2024).

doi: 10.1073/pnas.2322524121

Salih MM, Robinson EK, Malekos E, Perez E, Capili A, Kim K, Zhang WK, Cloonan SM and Carpenter S. LincRNA-Cox2 Regulates Smoke-induced Inflammation in Murine Macrophages. Am J Respir Cell Mol Biol. 2023 Jan 19. 

doi: 10.1165/rcmb.2022-0413OC.

Malekos E and Carpenter S. Short open reading frame genes in innate immunity: from discovery to characterization

Trends Immunol. 2022 Sep;43(9):741-756. 

doi: 10.1016/j.it.2022.07.005. Epub 2022 Aug 11.

Salih MM, Robinson EK, Malekos E, Perez E, Capili A, Kim K, Zhang WK, Cloonan SM and Carpenter S. BioRxiv. 2022 July 30 doi: https://doi.org/10.1101/2022.07.28.501765

Robinson EK, Worthington A, Poscablo D, Shapleigh B, Salih MM, Halasz H, Seninge L, Mosqueira B, Smaily V, Forsberg EC and Carpenter S. J Immunol. 2022 Apr 15;208(8):1886-1900. doi: 10.4049/jimmunol.2100743. Epub 2022 Apr 1.

Halasz, H and Carpenter, S. Challenges and Future Directions for lncRNAs and Inflammation. Adv Exp Med Biol 2022;1363:179-183. doi: 10.1007/978-3-030-92034-0_10.

Vollmers, A and Carpenter, S. Introduction and Overview. Adv Exp Med Biol 2022;1363:3-8. doi: 10.1007/978-3-030-92034-0_1.

Carpenter, S. Long noncoding RNA: Mechanistic insights and roles in inflammation

Mohammed Salih, M., Carpenter, S. What sequencing technologies can teach us about Innate Immunity. Immunol Rev 2021 Nov 7.

Robinson, E. K., Jagannatha, P., Covarrubias, S., Cattle, M., Safavi, R., Song, R., Viswanathan, K., Shapleigh, B., Abu-Shumays, R., Jain, M., Cloonan, S. M., Wakeland, E.,  Akeson, M., Brooks, A. N., & Carpenter, S. Inflammation Drives Alternative First Exon usage to Regulate Immune Genes including a Novel Iron Regulated Isoform of Aim2. biorxiv, (2020).

Vollmers, A. C., Mekonen, H. E., Campos, S., Carpenter, S., Vollmers, C. Isoform-level transcriptome Atlas of Macrophage Activation. biorxiv, (2020).

Robinson, E. K., Covarrubias, S., Zhou, S., & Carpenter, S. Generation and utilization of a HEK-293T murine GM-CSF expressing cell line. biorxiv, (2020).

Vollmers, A., Covarrubias, S., Kuang, D., Shulkin, A., Iwuagwu, J., Katzman, S., Song, R., Viswanathan, K., Vollmers, C., Wakeland, E. and Carpenter, S., 2021. A conserved long noncoding RNA, GAPLINC, modulates the immune response during endotoxic shock. Proceedings of the National Academy of Sciences, 118(7), p.e2016648118

Covarrubias, S., Vollmers, A. C., Capili, A., Boettcher, M., Shulkin, A., Correa, M. R., Halasz, H., Robinson, E. K., O'Briain, L., Vollmers, C., Blau, J., Katzman, S., McManus, M. T., and Carpenter, S.(2020). High-Throughput CRISPR Screening Identifies Genes Involved in Macrophage Viability and Inflammatory Pathways. Cell Rep. 33, 108541

Robinson, E. K., Covarrubias, S. & Carpenter, S. The how and why of lncRNA function: An innate immune perspective. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1863, 194419 (2019). 

Galván-Peña, S., Carroll, R. G., Newman, C., Hinchy E. C., Palsson-McDermott, E., Robinson E. K., Covarrubias, S., Nadin, A., James, A. M., Haneklaus, M., Carpenter, S. et al. Malonylation of GAPDH is an inflammatory signal in macrophages. Nature Communications 10, 1–11 (2019). 

Hennessy, E.J., van Solingen, C., Scacalossi, K.R. Ouimet M., Afonso, M. S., Prins, J., Koelwyn, G. J., Sharma, M., Ramkhelawon, B., Carpenter, S. et al. The long noncoding RNA CHROME regulates cholesterol homeostasis in primates. Nat Metab 1, 98–110 (2019). 

Elling R., Robinson, E. K., Shapleigh, B., Liapis, S. C., Covarrubias, S., Katzman, S., Groff, A. F., Jiang, Z., Agarwal, S., Motwani, M., Chan, J., Sharma, S., Hennessy, E. J., FitzGerald, G. A., McManus, M. T., Rinn, J. L., Fitzgerald, K. A., Carpenter, S. Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2. Cell Rep. 25, 1511–1524 (2018). 

Covarrubias, S., Robinson, E. K., Shapleigh, B., Vollmers, A., Katzman, S., Hanley, N., Fong, N., McManus, M. T., Carpenter, S. CRISPR/Cas-based screening of long non-coding RNAs (lncRNAs) in macrophages with an NF-κB reporter. J. Biol. Chem. 292, 20911–20920 (2017).

Ghosh, S., Wallerath, C., Covarrubias, S., Hornung, V., Carpenter, S., Fitzgerald, K. A. The PYHIN Protein p205 Regulates the Inflammasome by Controlling Asc Expression. J. Immunol. 199, 3249–3260 (2017). 

Carpenter, S. & Fitzgerald, K. A. Cytokines and Long Noncoding RNAs. Cold Spring Harb Perspect Biol 10, (2018). 

Akula, M., Shi, M., Jiang, Z., Foster, C. E., Miao, D., Li A. S., Zhang, X., Gavin, R. M., Forde, S. D., Germain, G., Carpenter, S. et al. Control of the innate immune response by the mevalonate pathway. Nat Immunol 17, 922–929 (2016). 

Carpenter, S. Long noncoding RNA: Novel links between gene expression and innate immunity. Virus Research 212, 137–145 (2016). 

Carpenter, S. Determining the Function of Long Noncoding RNA in Innate Immunity. in Toll-Like Receptors: Practice and Methods (ed. McCoy, C. E.) 183–195 (Springer, 2016).

Carpenter, S. Editorial: Functions of Non-Coding RNA in Innate Immunity. Front. Immunol. 6, (2015). 

Chan, J. Atianand, M., Jiang, Z., Carpenter, S., Aiello, D., Elling, R., Fitzgerald, K. A., Caffrey, D. R. Cutting Edge: A Natural Antisense Transcript, AS-IL1α, Controls Inducible Transcription of the Proinflammatory Cytokine IL-1α. The Journal of Immunology 195, 1359–1363 (2015).

Baum, R. Sharma, S., Carpenter, S., Li, Q., Fitzgerald, K. A., Marshak-Rothstein, A., Gravallese, E. M. Cutting Edge: AIM2 and Endosomal TLRs Differentially Regulate Arthritis and Autoantibody Production in DNase II–Deficient Mice. The Journal of Immunology 194, 873–877 (2015). 

Carpenter, S., & Fitzgerald, K. A. Transcription of Inflammatory genes; long noncoding RNA and beyond. J. Interferon Cytokine Res. 35, 79–88 (2015).

Wochal, P., Rathinam, V., Dunne, A., Carlson, T., Kuang, W., Seidl, K. J., Hall, J. P., Lin, L., Collins, M., Schattgen, S. A., MacKay C. R., Fagundes, C. T., Carpenter, S.*, Fitzgerald, K. A., and O’Neill L. A. J. TRIL is Essential for Cytokine Production in Brain Following Escherichia coli Infection. J Immunol. 193, 1911–1919 (2014).

Thompson, M. R., Sharma, S., Atianand, M., Jensen, S. B., Carpenter, S., Knipe, D. M., Fitzgerald K. A., Kurt-Jones, E. A. Interferon γ-inducible Protein (IFI) 16 Transcriptionally Regulates Type I Interferons and Other Interferon-stimulated Genes and Controls the Interferon Response to both DNA and RNA Viruses. J. Biol. Chem. 289, 23568–23581 (2014). 

Carpenter, S., Ricci, E. P., Mercier, B. C., Moore, M. J. & Fitzgerald, K. A. Post-transcriptional regulation of gene expression in innate immunity. Nature Reviews Immunology 14, 361–376 (2014).

Hangauer, M. J., Carpenter, S. & McManus, M. T. Discovering the complexity of the metazoan transcriptome. Genome Biology 15, 112 (2014). 

Carpenter, S. et al. A Long Noncoding RNA Mediates Both Activation and Repression of Immune Response Genes. Science 341, 789–792 (2013). 

Doyle, S. L., Shirey, K. A., McGettrick, A. F., Kenny, E. F., Carpenter, S. et al. Nuclear Factor κB2 p52 Protein Has a Role in Antiviral Immunity through IκB Kinase ϵ-dependent Induction of Sp1 Protein and Interleukin 15. J. Biol. Chem. 288, 25066–25075 (2013).

Sheedy, F. J., Grebe, A., Rayner, K. J., Kalantari, P., Ramkhelawon, B., Carpenter, S. B. et al. CD36 coordinates NLRP3 inflammasome activation by facilitating intracellular nucleation of soluble ligands into particulate ligands in sterile inflammation. Nature Immunology 14, 812–820 (2013). 

Scharfe-Nugent, A., Corr, S. C., Carpenter, S. B., Keogh, L. et al. TLR9 Provokes Inflammation in Response to Fetal DNA: Mechanism for Fetal Loss in Preterm Birth and Preeclampsia. The Journal of Immunology 188, 5706–5712 (2012).

Carpenter, S.*, Wochal, P. *, Dunne, A., & O'Neill, L. A. Toll-like Receptor 3 (TLR3) Signaling Requires TLR4 Interactor with Leucine-rich Repeats (TRIL). J. Biol. Chem. 286, 38795–38804 (2011). 

Madden, S. F., Carpenter, S. B., Jeffery, I. B., Bjorkbacka, H., Fitzgerald, K. A., O'Neill, L. A., et al. Detecting microRNA activity from gene expression data. BMC Bioinf. 257, 11 (2010).

Dunne, A.*, Carpenter, S.* et al. IRAK1 and IRAK4 promote phosphorylation, ubiquitination, and degradation of MyD88 adaptor-like (Mal). J. Biol. Chem. 291, 24802–24802 (2010).

Carpenter, S. et al. TRIL, a Functional Component of the TLR4 Signaling Complex, Highly Expressed in Brain. The Journal of Immunology 183, 3989–3995 (2009).

Carpenter, S. & O’Neill, L. A. J. Recent insights into the structure of Toll-like receptors and post-translational modifications of their associated signalling proteins. Biochem J 422, 1–10 (2009). 

McCoy, C. E., Carpenter, S., Pålsson-McDermott, E. M., Gearing, L. J. & O’Neill, L. A. J. Glucocorticoids Inhibit IRF3 Phosphorylation in Response to Toll-like Receptor-3 and -4 by Targeting TBK1 Activation. J. Biol. Chem. 283, 14277–14285 (2008). 

Carpenter S., & O'Neill, L. A. J. How important are Toll-like receptors for antimicrobial responses? Cell. Microbiol. 9, 1891–1901 (2007).