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US-20260125755-A1 - METHOD OF IDENTIFYING A SUBJECT HAVING KAWASAKI DISEASE

US20260125755A1US 20260125755 A1US20260125755 A1US 20260125755A1US-20260125755-A1

Abstract

A method of identifying a subject having Kawasaki disease (KD), which includes discriminating the subject from a subject having another condition, for example other infectious and inflammatory conditions, such as those that present similar symptoms to KD. Also provided is a minimal gene signature employed in the method, as well as primers, probes and gene chips for use in the method.

Inventors

  • Jethro Herberg
  • Victoria Wright
  • Michael Levin
  • Clive Hoggart
  • Myrsini Kaforou
  • Jane Burns

Assignees

  • IMPERIAL COLLEGE INNOVATIONS LIMITED
  • THE REGENTS OF THE UNIVERSITY OF CALIFORNIA

Dates

Publication Date
20260507
Application Date
20250307
Priority Date
20180804

Claims (20)

  1. 1 . A method of identifying a subject having Kawasaki disease (KD) comprising detecting in a subject derived RNA sample the modulation in gene expression levels of a gene signature comprising at least 5 of the following genes: CACNA1E, DDIAS, KLHL2, PYROXD2, SMOX, ZNF185, LINC02035, CLIC3, S100P, IF127, HS.553068, CD163, and RTN1.
  2. 2 - 23 . (canceled)
  3. 24 . A method of treating a subject having Kawasaki disease (KD), comprising administering a treatment for KD to the subject, wherein the subject has been previously identified as having Kawasaki disease by detecting in a subject derived RNA sample the modulation in gene expression levels of a gene signature comprising at least 5 of the following genes: CACNA1E, DDIAS, KLHL2, PYROXD2, SMOX, ZNF185, LINC02035, CLIC3, S100P, IF127, HS.553068, CD163, and RTN1.
  4. 25 . The method according to claim 1 , wherein the gene signature comprises 6, 7, 8, 9, 10, 11, 12 or 13 of the genes.
  5. 26 . The method according to claim 1 , wherein the gene signature comprises at least one of the following genes: PYROXD2, SMOX, CACNA1E, CD163, DDIAS, CLIC3, KLHL2 and HS.553068, in particular at least one of PYROXD2, SMOX, CACNA1E and CD163.
  6. 27 . The method according to claim 1 , wherein the gene signature comprises PYROXD2.
  7. 28 . The method according to claim 1 , wherein the gene signature comprises CACNA1E.
  8. 29 . The method according to claim 1 , wherein the gene signature comprises SMOX.
  9. 30 . The method according to claim 1 , wherein the gene signature comprises CD163.
  10. 31 . The method according to claim 1 , wherein the gene signature comprises: (i) PYROXD2 and CACNA1E; (ii) PYROXD2 and SMOX; or (iii) PYROXD2, CACNA1E and SMOX.
  11. 32 . The method according to claim 1 , wherein the gene signature comprises or consists of any one of the following combinations of genes: (i) PYROXD2, CACNA1E, CD163, KLHL2 and SMOX; (ii) PYROXD2, CACNA1E, IF127, KLHL2 and SMOX; (iii) PYROXD2, CACNA1E, HS.553068, IF127 and SMOX; (iv) PYROXD2, DDIAS, CACNA1E, IF127 and SMOX; (v) PYROXD2, CACNA1E, CD163, KLHL2 and ZNF185; (vi) PYROXD2, DDIAS, CD163, KLHL2 and SMOX; (vii) PYROXD2, CACNA1E, CD163, IF127, KLHL2 and SMOX; (viii) PYROXD2, CACNA1E, CD163, KLHL2, LINC02035 and SMOX; (ix) PYROXD2, DDIAS, CACNA1E, CD163, IF127 and SMOX; (x) PYROXD2, CACNA1E, CD163, HS.553068, IF127 and SMOX; (xi) PYROXD2, CACNA1E, CD163, KLHL2, SMOX and ZNF185; (xii) PYROXD2, CACNA1E, IF127, KLHL2, RTN1 and SMOX; (xiii) PYROXD2, CACNA1E, CD163, CLIC3, KLHL2 and SMOX; (xiv) PYROXD2, CACNA1E, CLIC3, IF127, KLHL2 and SMOX; (xv) PYROXD2, DDIAS, CACNA1E, IF127, RTN1 and SMOX; (xvi) PYROXD2, DDIAS, CD163, IF127, KLHL2 and SMOX; (xvii) PYROXD2, CACNA1E, CD163, HS.553068, IF127, KLHL2 and SMOX; (xviii) PYROXD2, CACNA1E, CD163, CLIC3, IF127, KLHL2 and SMOX; (xix) PYROXD2, DDIAS, CACNA1E, CD163, IF127, KLHL2 and SMOX; (xx) PYROXD2, CACNA1E, CD163, IF127, KLHL2, RTN1 and SMOX; (xxi) PYROXD2, DDIAS, CACNA1E, CD163, HS.553068, IF127 and SMOX; (xxii) PYROXD2, DDIAS, CACNA1E, CD163, CLIC3, IF127, KLHL2 and SMOX; (xxiii) PYROXD2, CACNA1E, CD163, CLIC3, HS.553068, IF127, KLHL2 and SMOX; (xxiv) PYROXD2, CACNA1E, CD163, CLIC3, IF127, KLHL2, RTN1 and SMOX; (xxv) PYROXD2, CACNA1E, CD163, HS.553068, IF127, KLHL2, S100P and SMOX; (xxvi) PYROXD2, DDIAS, CACNA1E, CD163, CLIC3, HS.553068, IF127, KLHL2 and SMOX; (xxvii) PYROXD2, DDIAS, CACNA1E, CD163, CLIC3, IF127, KLHL2, RTN1 and SMOX; (xxviii) PYROXD2, CACNA1E, CD163, CLIC3, HS.553068, IF127, KLHL2, RTN1 and SMOX; (xxix) PYROXD2, DDIAS, CACNA1E, CD163, CLIC3, IF127, KLHL2, RTN1, S100P and SMOX; (xxx) PYROXD2, DDIAS, CACNA1E, CD163, CLIC3, HS.553068, IF127, KLHL2, RTN1 and SMOX; (xxxi) PYROXD2, DDIAS, CACNA1E, CD163, CLIC3, HS.553068, IF127, KLHL2, RTN1, S100P and SMOX; (xxxii) PYROXD2, DDIAS, CACNA1E, CD163, CLIC3, IF127, KLHL2, LINC02035, RTN1, S100P and SMOX; (xxxiii) PYROXD2, DDIAS, CACNA1E, CD163, CLIC3, IF127, KLHL2, RTN1, S100P, SMOX and ZNF185. (xxxiv) PYROXD2, DDIAS, CACNA1E, CD163, CLIC3, HS.553068, IF127, KLHL2, RTN1, S100P, SMOX and ZNF185; (xxxv) PYROXD2, DDIAS, CACNA1E, CD163, CLIC3, HS.553068, IF127, KLHL2, LINC02035, RTN1, S100P and SMOX; or (xxxvi) PYROXD2, DDIAS, CACNA1E, CD163, CLIC3, IF127, KLHL2, LINC02035, RTN1, S100P, SMOX and ZNF185.
  12. 33 . The method according to claim 1 , wherein the gene signature comprises or consists of CACNA1E, DDIAS, KLHL2, PYROXD2, SMOX, ZNF185, LINC02035, CLIC3, S100P, IF127, HS.553068, CD163, and RTN1.
  13. 34 . The method according to claim 1 , wherein the method further incorporates detecting the expression levels or one or more housekeeping genes, such as 1, 2, 3, 4 or 5 housekeeping genes, for example selected from actin, GAPDH, ubiquitin, 18s rRNA, RPII (POLR2A), TBP, PPIA, GUSB, HSPCB, YWHAZ, SDHA, RPS13, HPRT1 and B4GALT6.
  14. 35 . The method according to claim 1 , wherein the subject with KD was identified in the presence of or discriminated from a patient with one or more of the following: a bacterial infection, a viral infection and an inflammatory condition.
  15. 36 . The method according to claim 1 , wherein the subject is a child, for example where the child is in the age range 2 to 59 months.
  16. 37 . The method according to claim 1 , wherein the subject has a fever.
  17. 38 . The method according to claim 1 , wherein the analysis of gene expression modulation employs a microarray, a gene chip or PCR, such as RT-PCR, in particular a multiplex PCR.
  18. 39 . The method according to claim 1 , wherein the treatment is gamma globulin (IVIg), aspirin, or other anti-inflammatory agents, such as steroids and infliximab.
  19. 40 . A set of primers for use in a method of identifying a subject having Kawasaki disease (KD) comprising primers specific to a polynucleotide gene transcript from at least 5 of the following genes: CACNA1E, DDIAS, KLHL2, PYROXD2, SMOX, ZNF185, LINC02035, CLIC3, S100P, IF127, HS.553068, CD163, and RTN1.
  20. 41 . A gene chip consisting of probes that are specific to at least 5 of the following genes: CACNA1E, DDIAS, KLHL2, PYROXD2, SMOX, ZNF185, LINC02035, CLIC3, S100P, IF127, HS.553068, CD163, and RTN1.

Description

The present disclosure relates to a method of identifying a subject having Kawasaki disease (KD), which includes discriminating the subject from a subject having another condition, for example other infectious and inflammatory conditions, such as those that present similar symptoms to KD. The disclosure also relates to a minimal gene signature employed in the said method and to a bespoke gene chip for use in the method. The disclosure further extends to probes and/or primers specific to genes in a signature of the present disclosure. The disclosure further relates to use of known gene chips in the methods of the disclosure and kits comprising the elements required for performing the method. The disclosure also relates to use of the method to provide a composite expression score which can be used in the discrimination of a bacterial infection from a viral infection or inflammatory disease, particularly suitable for use in a low resource setting. BACKGROUND Kawasaki disease (KD) is an acute inflammatory disorder predominantly affecting young children. Since its initial description in Japan [1], the disease has emerged as the most common cause of acquired heart disease with an incidence in children under five ranging from 265/100,000 in Japan [2], 51-194/100,000 in other Asian countries [3-5], and 8-20/100,000 in Europe [6] and the USA [7] respectively. What has made KD of such concern is its association with vasculitis, affecting predominantly the coronary arteries, which results in coronary artery aneurysm (CAA) formation in up to 25% of untreated children [8]. Death from myocardial infarction may occur due to thrombotic occlusion of the aneurysms, or from the later development of stenotic lesions due to vascular remodelling in the damaged artery. Long-term outcome studies of children with giant CAA indicate a worrying prognosis with over 50% needing revascularization or suffering myocardial infarction within a 30-year period [9, 10]. Treatment with intravenous immunoglobulin (IVIG) and, for those who do not respond, the administration of additional IVIG [11] or other anti-inflammatory agents such as steroids and infliximab, is effective in abrogating the inflammatory process and reduces the risk of CAA to 5-10% [12]. As KD is difficult to distinguish from other common febrile conditions, many children with KD are not diagnosed and treated early enough in the course of the illness to prevent development of CAA [13]. Furthermore, patients who do not fulfil the clinical criteria for diagnosing KD (so called “incomplete KD”) may nonetheless suffer CAA. Delayed diagnosis is a consistent risk factor for development of CAA, and even in centres with considerable experience with KD, treatment is often commenced only when coronary dilatation is already demonstrated on echocardiography. CAA development is clinically silent and may be recognised only years later at the time of sudden death or myocardial infarction. The symptoms of KD are similar to those of several other childhood febrile illnesses, including staphylococcal and streptococcal toxic shock syndromes, measles and other viral illnesses such as adenovirus infection, Rocky Mountain spotted fever, and childhood inflammatory diseases, leading to diagnostic difficulty and thus delay in diagnosis and treatment. Guidelines have been developed to facilitate clinical diagnosis based on clinical signs and symptoms, echocardiography, and laboratory parameters [14]. However, there is no definitive diagnostic test for the disease. As the global incidence of KD is increasing, there is an urgent need for an accurate test to distinguish KD from other conditions causing prolonged fever in children. SUMMARY OF THE INVENTION In the era of precision medicine, diagnosis of many conditions previously based on clinical features alone is being replaced by diagnosis based on molecular pathology. Host blood gene expression signatures have been shown to distinguish a number of specific infectious and inflammatory diseases including tuberculosis [15], bacterial and viral infections [16], and systemic lupus erythematosus [17]. Support for a diagnostic approach for KD based on gene expression signatures comes from identification of microRNA biomarkers in KD [18, 19], though existing studies are limited by the range of comparator patient groups, or by the need to extract RNA from exosomes. Accordingly, the present inventors have explored the use of whole blood gene expression patterns to distinguish KD from other childhood infectious and inflammatory conditions. The present disclosure provides a gene expression signature, discovered and validated in independent patient groups, that distinguishes KD from a range of bacterial, viral and inflammatory illnesses. The present disclosure is summarised in the following paragraphs: 1. A method of identifying a subject having Kawasaki disease (KD) comprising detecting in a subject derived RNA sample the modulation in gene expression levels of a ge