title: A blood RNA signature for tuberculosis disease risk: a prospective cohort study.
abstract: BACKGROUND
  Identification of blood biomarkers that prospectively predict progression of Mycobacterium tuberculosis infection to tuberculosis disease might lead to interventions that combat the tuberculosis epidemic. We aimed to assess whether global gene expression measured in whole blood of healthy people allowed identification of prospective signatures of risk of active tuberculosis disease.
  
  
  METHODS
  In this prospective cohort study, we followed up healthy, South African adolescents aged 12-18 years from the adolescent cohort study (ACS) who were infected with M tuberculosis for 2 years. We collected blood samples from study participants every 6 months and monitored the adolescents for progression to tuberculosis disease. A prospective signature of risk was derived from whole blood RNA sequencing data by comparing participants who developed active tuberculosis disease (progressors) with those who remained healthy (matched controls). After adaptation to multiplex quantitative real-time PCR (qRT-PCR), the signature was used to predict tuberculosis disease in untouched adolescent samples and in samples from independent cohorts of South African and Gambian adult progressors and controls. Participants of the independent cohorts were household contacts of adults with active pulmonary tuberculosis disease.
  
  
  RESULTS
  Between July 6, 2005, and April 23, 2007, we enrolled 6363 participants from the ACS study and 4466 from independent South African and Gambian cohorts. 46 progressors and 107 matched controls were identified in the ACS cohort. A 16 gene signature of risk was identified. The signature predicted tuberculosis progression with a sensitivity of 66·1% (95% CI 63·2-68·9) and a specificity of 80·6% (79·2-82·0) in the 12 months preceding tuberculosis diagnosis. The risk signature was validated in an untouched group of adolescents (p=0·018 for RNA sequencing and p=0·0095 for qRT-PCR) and in the independent South African and Gambian cohorts (p values <0·0001 by qRT-PCR) with a sensitivity of 53·7% (42·6-64·3) and a specificity of 82·8% (76·7-86) in the 12 months preceding tuberculosis.
  
  
  CONCLUSIONS
  The whole blood tuberculosis risk signature prospectively identified people at risk of developing active tuberculosis, opening the possibility for targeted intervention to prevent the disease.
  
  
  BACKGROUND
  Bill & Melinda Gates Foundation, the National Institutes of Health, Aeras, the European Union, and the South African Medical Research Council.
authors.affiliation: The Center for Infectious Disease Research, Seattle, WA, USA.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Zak
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Adam
authors.initials: A
authors.lastname: Penn-Nicholson
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Scriba
authors.affiliation: The Center for Infectious Disease Research, Seattle, WA, USA.
authors.forename: Ethan
authors.initials: E
authors.lastname: Thompson
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Sara
authors.initials: S
authors.lastname: Suliman
authors.affiliation: The Center for Infectious Disease Research, Seattle, WA, USA.
authors.forename: Lynn M
authors.initials: LM
authors.lastname: Amon
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Hassan
authors.initials: H
authors.lastname: Mahomed
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Mzwandile
authors.initials: M
authors.lastname: Erasmus
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Wendy
authors.initials: W
authors.lastname: Whatney
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Hussey
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Deborah
authors.initials: D
authors.lastname: Abrahams
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Fazlin
authors.initials: F
authors.lastname: Kafaar
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Tony
authors.initials: T
authors.lastname: Hawkridge
authors.affiliation: KNCV Tuberculosis Foundation, The Hague, Netherlands.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Verver
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: E Jane
authors.initials: EJ
authors.lastname: Hughes
authors.affiliation: Vaccines & Immunity, Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Martin
authors.initials: M
authors.lastname: Ota
authors.affiliation: Vaccines & Immunity, Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Jayne
authors.initials: J
authors.lastname: Sutherland
authors.affiliation: Immunology Unit, Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
authors.forename: Rawleigh
authors.initials: R
authors.lastname: Howe
authors.affiliation: Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK.
authors.forename: Hazel M
authors.initials: HM
authors.lastname: Dockrell
authors.affiliation: Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH, USA.
authors.forename: W Henry
authors.initials: WH
authors.lastname: Boom
authors.affiliation: Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH, USA.
authors.forename: Bonnie
authors.initials: B
authors.lastname: Thiel
authors.affiliation: Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands.
authors.forename: Tom H M
authors.initials: THM
authors.lastname: Ottenhoff
authors.affiliation: Department of Medicine and Department of Microbiology, Makerere University, Kampala, Uganda.
authors.forename: Harriet
authors.initials: H
authors.lastname: Mayanja-Kizza
authors.affiliation: Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK; Karonga Prevention Study, Chilumba, Malawi.
authors.forename: Amelia C
authors.initials: AC
authors.lastname: Crampin
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Katrina
authors.initials: K
authors.lastname: Downing
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
authors.forename: Mark
authors.initials: M
authors.lastname: Hatherill
authors.affiliation: The Center for Infectious Disease Research, Seattle, WA, USA.
authors.forename: Joe
authors.initials: J
authors.lastname: Valvo
authors.affiliation: The Center for Infectious Disease Research, Seattle, WA, USA.
authors.forename: Smitha
authors.initials: S
authors.lastname: Shankar
authors.affiliation: Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany.
authors.forename: Shreemanta K
authors.initials: SK
authors.lastname: Parida
authors.affiliation: Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany.
authors.forename: Stefan H E
authors.initials: SHE
authors.lastname: Kaufmann
authors.affiliation: DST/NRF Centre of Excellence for Biomedical TB Research and MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Walzl
authors.affiliation: The Center for Infectious Disease Research, Seattle, WA, USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Aderem
authors.affiliation: South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa. Electronic address: willem.hanekom@gatesfoundation.org.
authors.forename: Willem A
authors.initials: WA
authors.lastname: Hanekom
mesh_terms: D000293:Adolescent; D000328:Adult; D016022:Case-Control Studies; D002648:Child; D015870:Gene Expression; D006801:Humans; D008875:Middle Aged; D009169:Mycobacterium tuberculosis / Q000235:genetics; D011446:Prospective Studies; D012329:RNA, Bacterial / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D018570:Risk Assessment; D012307:Risk Factors; D014376:Tuberculosis / Q000097:blood / Q000175:diagnosis* / Q000235:genetics; D055815:Young Adult
chemical_list: D012329:RNA, Bacterial