Unravelling the transcriptome of the human tuberculosis lesion and its clinical implications

Tuberculosis (TB) disease causes up to 1.5 million deaths every year and represents an important problem of public health at worldwide level. Here, we quantified the gene expression signatures of granuloma biopsies across human TB pulmonary lesions, and validated the best gene candidates using NanoString technology, profiling 157 samples from 40 TB patients who underwent surgery. We characterised the transcriptional profile of the TB granuloma in comparison to healthy tissue, described an 11-gene signature and measured 7 proteins in plasma associated with it. We demonstrated a gradient of immune-related transcript abundance across the granuloma substructure and evidenced metabolically-active Mycobacterium tuberculosis in the lesions. Patients who converted to sputum negative after two months of starting treatment, showed enriched inflammatory pathways in the lesion several months after, supporting use of sputum culture conversion (SCC) as a prognostic biomarker during clinical management and as a factor to prioritise patients when considering lung surgery. ### Competing Interest Statement F.M-T has received honoraria from GSK group of companies, Pfizer Inc, Sanofi Pasteur, MSD, Seqirus, Biofabri and Janssen for taking part in advisory boards and expert meetings and for acting as a speaker in congresses outside the scope of the submitted work. F.M-T has also acted as principal investigator in randomized controlled trials of the above-mentioned companies as well as Ablynx, Gilead, Regeneron, Roche, Abbott, Novavax, and MedImmune, with honoraria paid to his institution. C.V salary is covered by ISCIII (CPII18/00031) and Fundacio Institut d’Investigació en Ciencies de la Salut Germans Trias I Pujol (IGTP). IGTP is the applicant of the patent EP3880702A1, which inventors are: MR Sarrias Fornes, G Aran Canals, E Téllez Caballero, C Vilaplana Massaguer and FE Borràs Serres. The patent relates to method and kit for the diagnosis and/or prognosis of inflammatory conditions based on analysing the levels of CD5L in a sample and it has entered into National Phase. In the present manuscript, we found CD5L under-expressed in the granuloma compared with the healthy tissue, as well as lower CD5L plasma levels in patients requiring surgery compared to those who didn’t. Consequently, CD5L was included both in the TB lesion 11-gene signature and in the 6-plasma protein TB signature described in the present manuscript. C.V is an unpaid board member of the following non-profit organizations: the FUITB foundation and the ACTMON foundation. Neither the ISCIII, the IGTP, the FUITB nor ACTMON have had any role in the conceptualization, design, data collection, analysis, decision to publish, or preparation of the manuscript. ### Clinical Protocols ### Funding Statement This work was supported by: 1) the Plan Nacional I + D + I co-financed by ISCIII-Subdirección General de Evaluación and Fondo-EU de Desarrollo Regional (FEDER) through PI16/01511, PI20/01424, CP13/00174, CPII18/00031 and CB06/06/0031. 2) The European Union’s Horizon 2020 research and innovation program under grant agreement No 847762. 3) The Catalan Agency for Management of University and Research Grants (AGAUR) through 2017SGR500 and 2017 FI\_B\_00797. 4) The ‘Spanish Society of Pneumology and Thoracic Surgery’ (SEPAR) (16/023). 5) The Wellcome Trust, the Medical Research Foundation grants (206508/Z/17/Z and MRF-160-0008-ELP-KAFO-C0801) and the NIHR Imperial College BRC to M.K. 6). N.G., registered in the EMJMD LIVE (Erasmus+ Mundus Joint Master Degree Leading International Vaccinology Education), co-funded by the EACEA (Education, Audiovisual and Culture Executive Agency, award 2018-1484) of the European Commission, receives a scholarship from the EACEA. 7). Wellcome Trust (204538/Z/16/Z) and National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs) (NC/R001669/1) grants to S.J.W. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committees/IRBs of the National Center for Tuberculosis and Lung Disease (IRB00007705 NCTLD Georgia #1, IORG0006411) and the Germans Trias i Pujol Hospital (EC: PI-16-171 and CEI PI-17-064) gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All metadata and sequencing data from this manuscript have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) Database and will be released after manuscript acceptance in a peer-reviewed scientific journal.