Dr Rachel Simmonds FRSB


Senior Lecturer in Immunopathogenesis
B.Sc. (Manchester), PhD (Imperial)

Academic and research departments

School of Biosciences and Medicine.

Biography

University roles and responsibilities

  • Director of Post-Graduate Research for the Department of Microbial Sciences

    Academic networks

      Research

      Research interests

      Research collaborations

      Indicators of esteem

      • Member of the Wellcome Trust Expert Review Group on Pathogen Biology

      • Editorial board of Tuberculosis

      • Member of the Biochemical Society's Awards Committee

      • Visiting Research Fellow at University of Southampton

      • Visiting Lecturer at the University of Ghana

      Supervision

      Postgraduate research supervision

      My teaching

      Courses I teach on

      Undergraduate

      Postgraduate taught

      Postgraduate research

      Biosciences and Medicine MD

      My publications

      Publications

      Daniel Klionsky, Amal Kamal Abdel-Aziz, Sara Abdelfatah, Mahmoud Abdellatif, Asghar Abdoli, Steffen Abel, Hagai Abeliovich, Marie Abildgaard, Yakubu Princely Abudu, Abraham Acevedo-Arozena, Iannis Adamopoulos, Khosrow Adeli, Timon Adolph, Annagrazia Adornetto, Elma Aflaki, Galila Agam, Anupam Agarwal, Bharat Aggarwal, Maria Agnello, Patrizia Agostinis, Javed Agrewala, Alexander Agrotis, Patricia Aguilar, S Tariq Ahmad, Zubair Ahmed, Ulises Ahumada-Castro, Sonja Aits, Shu Aizawa, Yunus Akkoc, Tonia Akoumianaki, Hafize Aysin Akpinar, Ahmed Al-Abd, Lina Al-Akra, Abeer Al-Gharaibeh, Moulay Alaoui-Jamali, Simon Alberti, Elísabet Alcocer-Gómez, Cristiano Alessandri, Muhammad Ali, M Abdul Alim Al-Bari, Saeb Aliwaini, Javad Alizadeh, Eugènia Almacellas, Alexandru Almasan, Alicia Alonso, Guillermo D Alonso, Nihal Altan-Bonnet, Dario C Altieri, Élida M. C Álvarez, Sara Alves, Cristine Alves Da Costa, Mazen Alzaharna, Marialaura Amadio, Consuelo Amantini, Cristina Amaral, Susanna Ambrosio, Amal Amer, Veena Ammanathan, Zhenyi An, Stig Andersen, Shaida Andrabi, Magaiver Andrade-Silva, Allen Andres, Sabrina Angelini, David Ann, Uche Anozie, Mohammad Ansari, Pedro Antas, Adam Antebi, Zuriñe Antón, Tahira Anwar, Lionel Apetoh, Nadezda Apostolova, Toshiyuki Araki, Yasuhiro Araki, Kohei Arasaki, Wagner Araújo, Jun Araya, Catherine Arden, Maria-Angeles Arévalo, Sandro Arguelles, Esperanza Arias, Jyothi Arikkath, Hirokazu Arimoto, Aileen Ariosa, Darius Armstrong-James, Laetitia Arnauné-Pelloquin, Angeles Aroca, Daniela Arroyo, Ivica Arsov, Rubén Artero, Dalia Maria Lucia Asaro, Michael Aschner, Milad Ashrafizadeh, Osnat Ashur-Fabian, Atanas Atanasov, Alicia Au, Patrick Auberger, Holger Auner, RACHEL SIMMONDS, Laure Aurelian (2021)Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition), In: Autophagy17(1)pp. 1-382 Taylor & Francis
      In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
      M McKenna, Rachel Simmonds, S High (2017)Mycolactone reveals substrate-driven complexity of Sec61-dependent transmembrane protein biogenesis, In: Journal of Cell Science130pp. 1307-1320 Company of Biologists
      Mycolactone is the exotoxin virulence factor produced by Mycobacterium ulcerans, the pathogen responsible for Buruli ulcer. The skin lesions and immunosuppression characteristic of this disease result from the action of mycolactone, which targets the Sec61 complex and inhibits the co-translational translocation of secretory proteins into the endoplasmic reticulum. In this study, we investigate the effect of mycolactone on the Sec61-dependent biogenesis of different classes of transmembrane protein (TMP). Our data suggest that the effect of mycolactone on TMP biogenesis depends on how the nascent chain initially engages the Sec61 complex. For example, translocation of TMP lumenal domains driven by an N-terminal, cleavable signal sequence is efficiently inhibited by mycolactone. In contrast, the effect of mycolactone on protein translocation driven solely by a non-cleavable signal anchor/transmembrane domain depends on which flanking region is translocated. For example, while translocation of the region N-terminal to a signal anchor/transmembrane domain is refractive to mycolactone, C-terminal translocation is efficiently inhibited. Our findings highlight the diversity of Sec61-dependent translocation and provide a molecular basis for understanding the effect of mycolactone on the biogenesis of different TMPs.
      Mycolactone is a polyketide macrolide lipid-like secondary metabolite synthesized by Mycobacterium ulcerans, the causative agent of BU (Buruli ulcer), and is the only virulence factor for this pathogen identified to date. Prolonged exposure to high concentrations of mycolactone is cytotoxic to diverse mammalian cells (albeit with varying efficiency), whereas at lower doses it has a spectrum of immunosuppressive activities. Combined, these pleiotropic properties have a powerful influence on local and systemic cellular function that should explain the pathophysiology of BU disease. The last decade has seen significant advances in our understanding of the molecular mechanisms underlying these effects in a range of different cell types. The present review focuses on the current state of our knowledge of mycolactone function, and its molecular and cellular targets, and seeks to identify commonalities between the different functional and cellular systems. Since mycolactone influences fundamental cellular processes (cell division, cell death and inflammation), getting to the root of how mycolactone achieves this could have a profound impact on our understanding of eukaryotic cell biology.
      BS Hall, R Simmonds, ME Benbow, L Mosi, S Roberts, H Williamso Jordan (2015)Mycobacterium ulcerans and Buruli Ulcer, In: Human Emerging and Re-emerging Infections: Viral and Parasitic Infections, Volume I1(44) John Wiley and Sons
      Buruli Ulcer (BU) is the third most common mycobacterium disease following only tuberculosis and leprosy. Though BU is thought to be associated with large-and small-scale disturbances to the landscape and bodies of water frequented by human populations, primary prevention of BU is difficult because the mode of transmission is not known. This chapter reviews the most common environmental risk factors for BU and recent research into understanding its transmission. It is predicted that the proteins affected by mycolactone may share an underlying mechanism of production that could explain their co-regulation. Early work on the mechanism of suppression by mycolac-tone was carried out in Jurkat T cells using ASLs and focused on the suppression of IL-2 production. A multidisciplinary approach to treatment and patient care is essential for optimizing treatment outcomes. Physiotherapy is paramount minimizing and/or preventing disabilities.
      M McKenna, RE Simmonds, S High (2016)Mechanistic insights into the inhibition of Sec61-dependent co- and post-translational translocation by mycolactone., In: Journal of Cell Science129 The Company of Biologists
      The virulence factor mycolactone is responsible for the immunosuppression and tissue necrosis that characterise Buruli ulcer, a disease caused by infection with Mycobacterium ulcerans. In this study, we confirm that Sec61, the protein-conducting channel that coordinates entry of secretory proteins into the endoplasmic reticulum, is a primary target of mycolactone, and characterise the nature of its inhibitory effect. We conclude that mycolactone constrains the ribosome-nascent chain-Sec61 complex, consistent with its broad-ranging perturbation of the co-translational translocation of classical secretory proteins. In contrast, the effect of mycolactone on the post-translational, ribosome-independent translocation of short secretory proteins through the Sec61 complex is dependent on both signal sequence hydrophobicity and the translocation competence of the mature domain. Changes to protease sensitivity strongly suggest that mycolactone acts by inducing a conformational change in the pore-forming Sec61α subunit. These findings establish that mycolactone inhibits Sec61-mediated protein translocation and highlight differences between the co- and post-translational routes that the Sec61 complex mediates. We propose that mycolactone also provides a useful tool for further delineating the molecular mechanisms of Sec61-dependent protein translocation.
      SM Rezende, DA Lane, B Zoller, B Mille-Baker, M Laffan, B Dahlback, RE Simmonds (2002)Genetic and phenotypic variability between families with hereditary protein S deficiency, In: THROMBOSIS AND HAEMOSTASIS87(2)pp. 258-265 SCHATTAUER GMBH-VERLAG MEDIZIN NATURWISSENSCHAFTEN
      Joy Ogbechi, Belinda Hall, Thomas Sbarrato, Jack Taunton, Anne E. Willis, Ronald C. Wek, Rachel Simmonds (2018)Inhibition of Sec61-dependent translocation by mycolactone uncouples the integrated stress response from ER stress, driving cytotoxicity via translational activation of ATF4, In: Cell Death & Disease9397 Nature Publishing Group
      Mycolactone is the exotoxin virulence factor of Mycobacterium ulcerans that causes the neglected tropical disease Buruli ulcer. We recently showed it to be a broad spectrum inhibitor of Sec61-dependent co-translational translocation of proteins into the endoplasmic reticulum (ER). An outstanding question is the molecular pathway linking this to its known cytotoxicity. We have now used translational profiling to better understand the reprogramming that occurs in cells exposed to mycolactone. Gene ontology identified enrichment in genes involved in cellular response to stress, and apoptosis signalling amongst those showing enhanced translation. Validation of these results supports a mechanism by which mycolactone activates an integrated stress response meditated by phosphorylation of eIF2α via multiple kinases (PERK, GCN, PKR) without activation of the ER stress sensors IRE1 or ATF6. The response therefore uncouples the integrated stress response from ER stress, and features translational and transcription modes of genes expression that feature the key regulatory transcription factor ATF4. Emphasizing the importance of this uncoupled response in cytotoxicity, downstream activation of this pathway is abolished in cells expressing mycolactone-resistant Sec61α variants. Using multiple genetic and biochemical approaches, we demonstrate that eIF2α phosphorylation is responsible for mycolactone-dependent translation attenuation, which initially protects cells from cell death. However, chronic activation without stress remediation enhances autophagy and apoptosis of cells by a pathway facilitated by ATF4 and CHOP. Our findings demonstrate that priming events at the ER can result in the sensing of stress within different cellular compartments.
      RE Simmonds, H Ireland, G Kunz, DA Lane, M Bhavnani, G Castaman, H Hambley, M Laffan, N OConnor, G Sas, CJ Tew, ID Walker (1996)Identification of 19 protein S gene mutations in patients with phenotypic protein S deficiency and thrombosis, In: BLOOD88(11)pp. 4195-4204 W B SAUNDERS CO
      S Gandrille, D Borgel, H Ireland, DA Lane, R Simmonds, PH Reitsma, C Mannhalter, I Pabinger, H Saito, K Suzuki, C Formstone, DN Cooper, Y Espinosa, N Sala, F Bernardi, M Alach (1997)Protein S deficiency: A database of mutations - For the Plasma Coagulation Inhibitors Subcommittee of the Scientific and Standardization Committee of the International Society on Thrombosis and Haemostasis, In: THROMBOSIS AND HAEMOSTASIS77(6)pp. 1201-1214
      Background: The innate immune response is a tightly regulated process that reacts rapidly in response to pathogen-associated molecular patterns(PAMPs) such as lipopolysaccharide (LPS). Evidence is accumulating thatmicroRNAs contribute to this, although few studies have examined the earlyevents that constitute the “primary” response. LPS-dependent changes to miRNA expression were studied inMethods:primary human monocyte-derived macrophages (1°MDMs). An unbiasedscreen by microarray was validated by qPCR and a method for the absolutequantitation of miRNAs was also developed, utilising 5’ phosphorylatedRNA oligonucleotide templates. RNA immunoprecipitation was performedto explore incorporation of miRNAs into the RNA-induced silencingcomplex (RISC). The effect of miRNA functional inhibition on TNFexpression (mRNA and secretion) was investigated. Of the 197 miRNAs expressed in 1°MDMs, only five were inducedResults:>1.5-fold. The most strongly induced was miR-155-3p, the partner strand tomiR-155-5p, which are both derived from the MIR155HG/BIC gene(pri-miR-155). The abundance of miR-155-3p was induced transiently~250-fold at 2-4hrs and then returned towards baseline, mirroringpri-miR-155. Other PAMPs, IL-1β, and TNF caused similar responses.IL-10, NF-κB, and JNK inhibition reduced these responses,unlike cytokine-suppressing mycolactone. Absolute quantitation revealedthat miRNA abundance varies widely from donor-to-donor, and showed thatmiR-155-3p abundance is substantially less than miR-155-5p inunstimulated cells. However, at its peak there were 446-1,113 copies/cell,and miR-155-3p was incorporated into the RISC with an efficiency similar tomiR-16-5p and miR-155-5p. Inhibition of neither miRNA affected TNFsecretion after 2hrs in 1°MDMs, but technical challenges here are noted. Dynamic regulation of miRNAs during the primary responseConclusions:is rare, with the exception of miR-155-3p. Further work is required toestablish whether its low abundance, even at the transient peak, issufficient for biological activity and to determine whether there are specificmechanisms determining its biogenesis from miR-155 precursor.
      RE Simmonds, J Hermida, SM Rezende, DA Lane (2001)Haemostatic genetic risk factors in arterial thrombosis, In: THROMBOSIS AND HAEMOSTASIS86(1)pp. 374-385
      SM Rezende, DA Lane, B Mille-Baker, MM Samama, J Conard, RE Simmonds (2002)Protein S Gla-domain mutations causing impaired Ca2+-induced phospholipid binding and severe functional protein S deficiency, In: BLOOD100(8)pp. 2812-2819 AMER SOC HEMATOLOGY
      RE Simmonds, DA Lane (2001)The endothelial cell protein C receptor: A candidate genetic risk factor for thrombosis, In: THROMBOSIS AND HAEMOSTASIS86(4)pp. 939-941 F K SCHATTAUER VERLAG GMBH
      JB Rance, GA Follows, PN Cockerill, C Bonifer, DA Lane, RE Simmonds (2003)Regulation of the human endothelial cell protein C receptor gene promoter by multiple Sp1 binding sites, In: BLOOD101(11)pp. 4393-4401 AMER SOC HEMATOLOGY
      S Gandrille, D Borgel, N Sala, Y Espinosa-Parrilla, R Simmonds, S Rezende, B Lind, C Mannhalter, I Pabinger, PH Reitsma, C Formstone, DN Cooper, H Saito, K Suzuki, F Bernardi, M Aiach (2000)Protein S deficiency: A database of mutations - Summary of the first update, In: THROMBOSIS AND HAEMOSTASIS84(5)pp. 918-918 F K SCHATTAUER VERLAG GMBH
      SM Rezende, RE Simmonds, B Zoller, B Dahlback, DA Lane (1999)The molecular basis of type I/III protein S deficiency, In: THROMBOSIS AND HAEMOSTASISpp. 426-427 F K SCHATTAUER VERLAG GMBH
      J Ogbechi, MT Ruf, BS Hall, K Bodman-Smith, M Vogel, HL Wu, A Stainer, CT Esmon, J Ahnström, G Pluschke, RE Simmonds (2015)Mycolactone-Dependent Depletion of Endothelial Cell Thrombomodulin Is Strongly Associated with Fibrin Deposition in Buruli Ulcer Lesions., In: PLoS Pathog11(7) PLoS
      A well-known histopathological feature of diseased skin in Buruli ulcer (BU) is coagulative necrosis caused by the Mycobacterium ulcerans macrolide exotoxin mycolactone. Since the underlying mechanism is not known, we have investigated the effect of mycolactone on endothelial cells, focussing on the expression of surface anticoagulant molecules involved in the protein C anticoagulant pathway. Congenital deficiencies in this natural anticoagulant pathway are known to induce thrombotic complications such as purpura fulimans and spontaneous necrosis. Mycolactone profoundly decreased thrombomodulin (TM) expression on the surface of human dermal microvascular endothelial cells (HDMVEC) at doses as low as 2ng/ml and as early as 8hrs after exposure. TM activates protein C by altering thrombin's substrate specificity, and exposure of HDMVEC to mycolactone for 24 hours resulted in an almost complete loss of the cells' ability to produce activated protein C. Loss of TM was shown to be due to a previously described mechanism involving mycolactone-dependent blockade of Sec61 translocation that results in proteasome-dependent degradation of newly synthesised ER-transiting proteins. Indeed, depletion from cells determined by live-cell imaging of cells stably expressing a recombinant TM-GFP fusion protein occurred at the known turnover rate. In order to determine the relevance of these findings to BU disease, immunohistochemistry of punch biopsies from 40 BU lesions (31 ulcers, nine plaques) was performed. TM abundance was profoundly reduced in the subcutis of 78% of biopsies. Furthermore, it was confirmed that fibrin deposition is a common feature of BU lesions, particularly in the necrotic areas. These findings indicate that there is decreased ability to control thrombin generation in BU skin. Mycolactone's effects on normal endothelial cell function, including its ability to activate the protein C anticoagulant pathway are strongly associated with this. Fibrin-driven tissue ischemia could contribute to the development of the tissue necrosis seen in BU lesions.
      RE Simmonds, H Ireland, DA Lane, B Zoller, PG de Frutos, B Dahlback (1998)Clarification of the risk for venous thrombosis associated with hereditary protein S deficiency by investigation of a large kindred with a characterized gene defect, In: ANNALS OF INTERNAL MEDICINE128(1)pp. 8-+ AMER COLL PHYSICIANS
      E Biguzzi, C Razzari, DA Lane, G Castaman, A Cappellari, P Bucciarelli, G Fontana, M Margaglione, G D'Andrea, RE Simmonds, SM Rezende, R Preston, D Prisco, EM Faioni (2005)Molecular diversity and thrombotic risk in Protein S deficiency: The PROSIT study, In: HUMAN MUTATION25(3)pp. 259-269 WILEY-LISS
      RE Simmonds, FV Lali, T Smallie, PLC Small, BM Foxwell (2009)Mycolactone Inhibits Monocyte Cytokine Production by a Posttranscriptional Mechanism, In: JOURNAL OF IMMUNOLOGY182(4)pp. 2194-2202 AMER ASSOC IMMUNOLOGISTS
      B Mille-Baker, SM Rezende, RE Simmonds, PJ Mason, DA Lane, MA Laffan (2003)Deletion or replacement of the second EGF-hke domain of protein S results in loss of APC cofactor activity, In: BLOOD101(4)pp. 1416-1418 AMER SOC HEMATOLOGY
      Guanghui Zong, Zhijian Hu, Sarah O’Keefe, Dale Tranter, Michael J. Iannotti, Ludivine Baron, Belinda Hall, Katherine Corfield, Anja O. Paatero, Mark J. Henderson, Peristera Roboti, Jianhong Zhou, Xianwei Sun, Mugunthan Govindarajan, Jason M. Rohde, Nicolas Blanchard, Rachel Simmonds, James Inglese, Yuchun Du, Caroline Demangel, Stephen High, Ville O. Paavilainen, Wei Q. Shi (2019)Ipomoeassin F Binds Sec61α to Inhibit Protein Translocation, In: Journal of the American Chemical Society141(21)pp. 8450-8461 American Chemical Society
      Ipomoeassin F is a potent natural cytotoxin that inhibits growth of many tumor cell lines with single-digit nanomolar potency. However, its biological and pharmacological properties have remained largely unexplored. Building upon our earlier achievements in total synthesis and medicinal chemistry, we used chemical proteomics to identify Sec61α (protein transport protein Sec61 subunit alpha isoform 1), the pore-forming subunit of the Sec61 protein translocon, as a direct binding partner of ipomoeassin F in living cells. The interaction is specific and strong enough to survive lysis conditions, enabling a biotin analogue of ipomoeassin F to pull down Sec61α from live cells, yet it is also reversible, as judged by several experiments including fluorescent streptavidin staining, delayed competition in affinity pulldown, and inhibition of TNF biogenesis after washout. Sec61α forms the central subunit of the ER protein translocation complex, and the binding of ipomoeassin F results in a substantial, yet selective, inhibition of protein translocation in vitro and a broad ranging inhibition of protein secretion in live cells. Lastly, the unique resistance profile demonstrated by specific amino acid single-point mutations in Sec61α provides compelling evidence that Sec61α is the primary molecular target of ipomoeassin F and strongly suggests that the binding of this natural product to Sec61α is distinctive. Therefore, ipomoeassin F represents the first plant-derived, carbohydrate-based member of a novel structural class that offers new opportunities to explore Sec61α function and to further investigate its potential as a therapeutic target for drug discovery.
      N Moyo, D Westcott, R Simmonds, F Steinbach (2012)Equine arteritis virus replication in monocytic cells suppresses differentiation and function of dendritic cells, In: IMMUNOLOGY137pp. 625-625

      Additional publications