Research output
ResearchGate Profile
See my ResearchGate profile for the most up to date list of my research outputs
Preprints
Christina Gkantsinikoudi, Joshua P Dignam, Raju Kumar, Elliot Jokl, Wenhao Li, Maryna Samus, Stephanie Landi, Varinder S Athwal, Timothy J Kendall, Antal Rot, Jonathan A Fallowfield, Karen Piper Hanley, William Alazawi, Neil P Dufton
bioRxiv 2026 doi: 10.64898/2026.03.12.710459
Spartan: activation-aware framework for spatial domain and variable gene discovery
Mohammad Faiz Iqbal Faiz, Elliot Jokl, Rachel Jennings, Karen Piper Hanley, Andrew Sharrocks, Mudassar Iqbal, Syed Murtuza Baker
bioRxiv 2026 doi:10.64898/2026.02.18.706570
Laurence Pearmain, Elliot Jokl, Kara Simpson, Lindsay Birchall, Yaqing Ou, Craig Lawless, Angela Simpson, Lizzie Mann, Nick Scott, Rajesh Shah, Rajamiyer Venkateswaran, Stefan Stanel, Conal Hayton, Pilar Rivera-Ortega, Phil Hansbro, Neil A Hanley, John F Blaikley, Karen Piper Hanley
bioRxiv 2024 doi:10.1101/2024.01.21.576509
This study showed that the inability to express SOX9 has stage-dependent impacts on lung disease progression, identifying severity associated markers in acute injury and fibrotic stages of bleomycin induced injury altered in response to SOX9 loss. Several of these show a predictive ability for poor outcomes in the time course of COVID-19 infection and pulmonary fibrosis in human patients.
Papers
Kim Su*, Elliot Jokl*, Alice Costain*, Kara Simpson, Antonn Cheeseman, Alexander Phythian-Adams, Kevin N. Couper, Andrew S. MacDonald, Karen Piper Hanley *joint first authors
PLOS Pathogens 21(6): e1012928 (2025) doi:10.1371/journal.ppat.1012928
Here we demonstrated that the inability to express the Sox9 gene led to a more disorganised granuloma in response to Schistosomiasis infection in the liver. Though extracellular matrix deposition was less intense around eggs, these "leaky" granulomas led to more diffuse fibrotic damage throughout the tissue.
Spatial gene regulatory networks driving cell state transitions during human liver disease
Nigel L Hammond, Syed Murtuza Baker, Sokratia Georgaka, Ali Al-Anbaki, Elliot Jokl, Kara Simpson, Rosa Sanchez-Alvarez, Varinder S Athwal, Huw Purssell, Ajith K Siriwardena, Harry V M Spiers, Mike J Dixon, Leoma D Bere, Adam P Jones, Michael J Haley, Kevin N Couper, Nicoletta Bobola, Andrew D Sharrocks, Neil A Hanley, Magnus Rattray & Karen Piper Hanley
EMBO Mol Med 17, 1452–1474 (2025) doi:10.1038/s44321-025-00230-6
In this study we generated spatial transcriptomic and single nuclear RNA and ATAC seq data of fibrotic livers to develop a profile of diseased hepatocyte states forming in response to the scar microenvironment, developing an understanding of the gene regulatory networks underpinning a transition into disease.
Elliot Jokl*, Aoibheann F Mullan*, Kara Simpson, Lindsay Birchall, Laurence Pearmain, Katherine Martin, James Pritchett, Sayyid Raza, Rajesh Shah, Nigel W Hodson, Craig J Williams, Elizabeth Camacho, Leo Zeef, Ian Donaldson, Varinder S Athwal, Neil A Hanley, Karen Piper Hanley *joint first authors
Cell Reports Nov 2023 doi: 10.1016/j.celrep.2023.113414
This paper explored how the nuclei and chromatin organsiation of hepatic stellate cells, the main mediators of excessive extracellular matrix deposition in fibrotic liver disease, changes as they activate in stiffer environments. We showed that the mechanical forces influence hepatic stellate cell gene expression and that the loss of PAK1 interferes with this process, highlighting this as a potential therapeutic target to limit fibrosis.
Elliot Jokl*, Jessica Llewellyn*, Kara Simpson, Oluwatobi Adegboye, James Pritchett, Leo Zeef, Ian Donaldson, Varinder S. Athwal, Huw Purssell, Oliver Street, Lucy Bennett, Indra Neil Guha, Neil A. Hanley, Qing-Jun Meng, Karen Piper Hanley on behalf of the ID LIVER consortium *joint first authors
Cells 12, no. 12: 1582. doi: 10.3390/cells12121582
This work examined the impact of circadian rhythm disruption on the activation of hepatic stellate cells, showing that this leads to a primed state that worsens fibrotic injury in mice. We leveraged the genes that had altered expression in this primed state as potential biomarkers, using the ID LIVER cohort to show elevated levels of AOC3 in patients with evidence of fibrosis or high risk of liver disease.
Sayyid Raza*, Elliot Jokl*, James Pritchett, Katherine Martin, Kim Su, Kara Simpson, Aoibheann F Mullan, Varinder Athwal, Daniel T Doherty, Leo Zeef, Neil C Henderson, Philip A Kalra, Neil A Hanley, Karen Piper Hanley * Joint first authors
Sci Signal . 2021 Mar 2;14(672):eabb4282. doi: 10.1126/scisignal.abb4282.
This study explored the role of SOX9 in kidney fibrosis using the unilateral ureteral obstruction model with or without repression of SOX9 expression, demonstrating that markers of fibrosis are significantly reduced in the absence of SOX9. RNAseq and relative gene expression analyses identified Neural Navigator 3 (NAV3) as a novel, SOX9-dependent marker of fibrosis. Inhibiting Nav3 in cultured kidney pericytes and HEK fibroblasts impaired migration, cytoskeletal stability and mechanotransduction.
Genetic Contribution to Non-alcoholic Fatty Liver Disease and Prognostic Implications
Katherine Martin , Anas Hatab, Varinder S Athwal, Elliot Jokl, Karen Piper Hanley
Curr Diab Rep . 2021 Feb 5;21(3):8. doi: 10.1007/s11892-021-01377-5.
Elliot J. Jokl, Gideon L. Hughes, Tobias Cracknell, Mary E. Pownall, Gonzalo Blanco
Disease Models & Mechanisms 2018 11: dmm033225 doi: 10.1242/dmm.033225 Published 6 July 2018
In this paper, based on my PhD project, we showed that the absence of the cytoskeletal protein KY results in the apparent upregulation of the chaperone BAG3. In this project I generated in vitro myoblast and in vivo zebrafish models of KY deficiency using CRISPR/Cas9 and explored common hallmarks with the established ky/ky mouse model. My work suggests that the absence of KY leads to a baseline of elevated cell stress and a failure to further upregulate this in response to mechanical stimulation.
Disrupted autophagy undermines skeletal muscle adaptation and integrity
Elliot J. Jokl and Gonzalo Blanco
Mamm Genome. 2016; doi: 10.1007/s00335-016-9659-2 Published online 2 Aug 2016
This review explored the critical role of autophagy in skeletal muscle and the myopathies resulting from mutations or disruption to autophagy components.
Presented Conference Abstracts
Multiomic analyses demonstrate hepatocyte SOX9 loss exacerbates fibrosis and HCC development in the DEN-CCl4 mouse model
Oral presentation; 2nd International Conference of Liver Pathobiology: From Bench to Bedside 2025, Crete (Travel Award Recipient)
Elliot Jokl, Syed Murtuza Baker, Sokratia Georgaka, Kara Simpson, Rosa Sanchez-Alvarez, Nigel Hammond, Chris Mysko, Varinder Athwal, Richard Hubner, Karen Piper Hanley
Multiomic analyses demonstrate hepatocyte SOX9 loss exacerbates fibrosis and HCC development in the DEN-CCl4 mouse model
Oral presentation; HCC UK 2025, Manchester, UK
Elliot Jokl, Syed Murtuza Baker, Sokratia Georgaka, Kara Simpson, Rosa Sanchez-Alvarez, Nigel Hammond, Chris Mysko, Varinder Athwal, Richard Hubner, Karen Piper Hanley
CLOCKΔ19 circadian disruption primes myofibroblasts for accelerated activation and fibrotic progression
Oral presentation; EASL ILC 2023, Vienna, Austria
Elliot Jokl, Jessica Llewelyn, Kara Simpson, Oluwatobi Adegboye, James Pritchett, Leo Zeef, Qing-Jun Meng, Karen Piper Hanley
SOX9 is required for fibrosis in multiple organs and regulates NAV3 to control myofibroblast function
Poster presentation; Keystone Symposia: Fibrosis and Tissue Repair 2020, Victoria, Canada
Elliot J Jokl, Sayyid Raza, James Pritchett, Katherine Martin, Kim Su, Kara Simpson, Aoibheann F Mullan, Varinder S Athwal, Daniel T Doherty, Leo Zeef, Neil Henderson, Philip A Kalra, Neil A Hanley, Karen Piper Hanley
Mechanotransduction at the z-disc of skeletal muscle
Oral and poster presentation; White Rose Mechanistic Biology DTP Annual Research Symposium 2016
Elliot Jokl, Mary E Pownall, Gonzalo Blanco
No recycling = no growth? Insights from the ky/ky mouse
Poster presentation; 44th European Muscle Conference 2015, Warsaw, Poland
Elliot Jokl, Mary E Pownall, Gonzalo Blanco
Mechanotransduction at the z-disc of skeletal muscle
Poster presentation; London Myology Forum December 2013, London, UK
Elliot Jokl, Mary E Pownall, Gonzalo Blanco