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University of Exeter Medical School

Dr Matthew Johnson

Dr Matthew Johnson

Independent Research Fellow

 +44 (0)1392 408277

 RILD Building 03.01


University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK


I have a background in biology and completed my PhD in molecular genetics 2017, where I primarily studied patients with autoimmune forms of neonatal diabetes (diagnosed in the first 6 months of life). Before starting my PhD I worked in a diagnostic genetics laboratory and was involved in the development and implementation of Next Generation Sequencing tests (targeted and whole exome) for NHS patients.

My current research focusses on early-onset autoimmune diabetes. This includes identifying novel monogenic causes and characterising known monogenic forms, as well as understanding the mechansisms and genetics underpinning extreme-ly early onset type 1 diabetes (diagnosed in the first 12 months of life). 


  • BSc (hons) (University of Birmingham, 2011)
  • PhD (University of Exeter, 2017)


2013-2014 - NHS Genetic Technologist

2014-2017 - PhD student

2017-2019 - Postdoctoral researcher

2019-2023 - Independent research fellow (personal fellowship)


Research group links

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Research interests

I continues to study patients with extreme forms of diabetes including rare genetic forms and type 1 diabetes diagnosed in the first year of life. The long-term goal of this is to identify the genetic and physiological pathways that lead to the development of type 1 diabetes, opening up new targets for prevention and treatment. I am also passionate about the translation of research into clinical practice and work closely with the diagnostic molecular genetics lab in Exeter to achieve this.

During  my current fellowship, I am using whole genome sequencing and new and emerging genetics technologies to study patients with autoimmune diabetes, including DNA based immune phenotyping and transcriptomic studies to understand the consequences of mutations and the phenotype of type 1 diabetes diagnosed in the first year of life.  

Research projects

Current Projects:

  • Improving diagnosis in monogenic disorders of insulin secretion
  • Gene discovery in monogenic autoimmunity
  • Characterization of Extremely early-onset type 1 diabetes
  • Uncovering low-level somatic mutations in monogenic diseases
  • Immune profiling and phenotyping in rare forms of autoimmunity

Research grants

  • 2023 Diabetes UK
    Diabetes UK and JDRF RD Lawrence Fellowship
  • 2021 Helmsley Charitable Trust
    Extreme autoimmune type 1 diabetes study Phase 2
  • 2021 Diabetes UK
    Identifying new subtypes of syndromic diabetes to provide novel insights into diabetes
  • 2019 Diabetes Research and Wellness Foundation
    New insights into extreme forms of autoimmune diabetes
  • 2019 Research England
    Exeter Diabetes Centre of Excellence Independent Research Fellowship “new insights into extreme forms of autoimmune diabetes”
  • 2018 Northcott Devon Medical Research Foundation
    Whole genome sequencing in monogenic forms of autoimmune diabetes
  • 2018 Diabetes UK
    Using state-of-the-art genetic technologies to identify low-level mosaic mutations and provide new diagnoses in monogenic diabetes
  • 2018 European Association for the Study of Diabetes
    Travel Grant
  • 2017 European Association for the Study of Diabetes
    Travel Grant
  • 2016 The Genetics Society
    Travel Grant
  • 2015 Pacific Biosciences
    Pilot Study Grant
  • 0 Helmsley Charitable Trust
    Uncovering new genetic mechanisms underlying extreme early-onset type 1 diabetes


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Journal articles

Wakeling M, Owens NDL, Hopkinson JR, Johnson MB, Houghton JAL, Dastamani A, Flaxman CS, Wyatt RC, Hewat TI, Hopkins JJ, et al (In Press). A novel disease mechanism leading to the expression of a disallowed gene in the pancreatic beta-cell identified by non-coding, regulatory mutations controlling HK1. Nature Genetics Abstract.
Hewat TI, Johnson M, Flanagan S (In Press). Congenital hyperinsulinism: current laboratory-based approaches to the genetic diagnosis of a heterogeneous disease. Frontiers in Endocrinology
De Franco E, Caswell R, Johnson M, Wakeling M, Zung A, Dũng VC, Bích Ngọc CT, Goonetilleke R, Vivanco Jury M, El- Khateeb M, et al (In Press). De novo mutations in EIF2B1 affecting eIF2 signaling cause neonatal/early onset diabetes and transient hepatic dysfunction. Diabetes
Hopkins J, Childs A, Houghton J, Hewat T, Atapattu N, Johnson M, Patel K, Laver T, Flanagan S (In Press). Hyperinsulinaemic hypoglycaemia diagnosed in childhood can be monogenic. The Journal of Clinical Endocrinology & Metabolism Abstract.
Hewat TI, Laver T, Houghton J, Mannisto J, Alvi S, Brearey S, Cody D, Dastamani A, de los Santos la Torre M, Murphy N, et al (In Press). Increased referrals for congenital hyperinsulinism genetic testing in children with trisomy 21 reflects the high burden of non-genetic risk factors in this group. Pediatric Diabetes
De Franco E, Flanagan S, Johnson M (In Press). Neonatal and early onset diabetes in Ukraine: atypical features and mortality. Diabetic Medicine
De Franco E, Owens N, Hattersley A, Flanagan S, Wakeling M, Johnson M, Wright C (In Press). Primate-specific ZNF808 is essential for pancreatic development in humans. Nature Genetics
Johnson MB, De Franco E, Lango-Allen H, Al Senani A, Elbarbary N, Siklar Z, Berberoglu M, Imane Z, Haghighi A, Ullah I, et al (In Press). Recessively inherited LRBA mutations cause autoimmunity presenting as neonatal diabetes. Diabetes
Johnson M, Patel K, De Franco E, McDonald T, Hudson M, Dobbs R, Ellard S, Flanagan S, Hattersley A, Oram R, et al (In Press). Type 1 Diabetes can present before the age of 6 months and is characterised by autoimmunity and rapid loss of beta-cells. Diabetologia
Johnson MB, Ogishi M, Domingo-Vila C, De Franco E, Wakeling MN, Imane Z, Resnick B, Williams E, Galão RP, Caswell R, et al (2024). Human inherited PD-L1 deficiency is clinically and immunologically less severe than PD-1 deficiency. The Journal of experimental medicine, 221(6). Abstract.
Narula M, Lakshmanan U, Borna S, Schulze JJ, Holmes TH, Harre N, Kirkey M, Ramachandran A, Tagi VM, Barzaghi F, et al (2023). Epigenetic and immunological indicators of IPEX disease in subjects with FOXP3 gene mutation. Journal of Allergy and Clinical Immunology, 151(1), 233-246.e10. Abstract.
Wyatt RC, Olek S, De Franco E, Samans B, Patel K, Houghton J, Walter S, Schulze J, Bacchetta R, Hattersley AT, et al (2023). FOXP3 TSDR Measurement Could Assist Variant Classification and Diagnosis of IPEX Syndrome. J Clin Immunol, 43(3), 662-669. Abstract.  Author URL.
Hopkins JJ, Wakeling MN, Johnson MB, Flanagan SE, Laver TW (2023). REVEL is Better at Predicting Pathogenicity of Loss-of-Function than Gain-of-Function Variants. Human Mutation, 2023, 1-6. Abstract.
Russ-Silsby J, Patel KA, Laver TW, Hawkes G, Johnson MB, Wakeling MN, Patil PP, Hattersley AT, Flanagan SE, Weedon MN, et al (2023). The Role of ONECUT1 Variants in Monogenic and Type 2 Diabetes Mellitus. Diabetes, 72(11), 1729-1734. Abstract.  Author URL.
Wyatt RC, Hagopian WA, Roep BO, Patel KA, Resnick B, Dobbs R, Hudson M, EXE-T1D Consortium, De Franco E, Ellard S, et al (2022). Congenital beta cell defects are not associated with markers of islet autoimmunity, even in the context of high genetic risk for type 1 diabetes. Diabetologia, 65(7), 1179-1184. Abstract.  Author URL.
Laver TW, De Franco E, Johnson MB, Patel KA, Ellard S, Weedon MN, Flanagan SE, Wakeling MN (2022). SavvyCNV: Genome-wide CNV calling from off-target reads. PLOS Computational Biology, 18(3), e1009940-e1009940. Abstract.
Patel KA, Ozbek MN, Yildiz M, Guran T, Kocyigit C, Acar S, Siklar Z, Atar M, Colclough K, Houghton J, et al (2022). Systematic genetic testing for recessively inherited monogenic diabetes: a cross-sectional study in paediatric diabetes clinics. Diabetologia, 65(2), 336-342. Abstract.  Author URL.
Johnson MB, Hattersley AT, Patel KA (2021). More on STAT1 Gain of Function, Type 1 Diabetes, and JAK Inhibition. N Engl J Med, 384(1).  Author URL.
Meshaal S, El Hawary R, Adel R, Abd Elaziz D, Erfan A, Lotfy S, Hafez M, Hassan M, Johnson M, Rojas-Restrepo J, et al (2020). Clinical Phenotypes and Immunological Characteristics of 18 Egyptian LRBA Deficiency Patients. Journal of Clinical Immunology, 40(6), 820-832. Abstract.
Musa SA, Ibrahim AA, Hassan SS, Johnson MB, Basheer AT, Arabi AM, Abdullah MA (2020). Fanconi Bickel syndrome: clinical phenotypes and genetics in a cohort of Sudanese children. Int J Pediatr Endocrinol, 2020(1). Abstract.  Author URL.
Wegehaupt O, Muckenhaupt T, Johnson MB, Schwab KO, Speckmann C (2020). Ruxolitinib Controls Lymphoproliferation and Diabetes in a STAT3-GOF Patient. Journal of Clinical Immunology, 40(8), 1207-1210.
De Franco E, Lytrivi M, Ibrahim H, Montaser H, Wakeling M, Fantuzzi F, Patel K, Demarez C, Cai Y, Igoillo-Esteve M, et al (2020). YIPF5 mutations cause neonatal diabetes and microcephaly through endoplasmic reticulum stress. Journal of Clinical Investigation, 130
Johnson MB, Cerosaletti K, Flanagan SE, Buckner JH (2019). Genetic Mechanisms Highlight Shared Pathways for the Pathogenesis of Polygenic Type 1 Diabetes and Monogenic Autoimmune Diabetes. Curr Diab Rep, 19(5). Abstract.  Author URL.
Laver TW, De Franco E, Johnson MB, Patel K, Ellard S, Weedon MN, Flanagan SE, Wakeling MN (2019). SavvyCNV: genome-wide CNV calling from off-target reads. Abstract.
Strakova V, Elblova L, Johnson MB, Dusatkova P, Obermannova B, Petruzelkova L, Kolouskova S, Snajderova M, Fronkova E, Svaton M, et al (2019). Screening of monogenic autoimmune diabetes among children with type 1 diabetes and multiple autoimmune diseases: is it worth doing?. J Pediatr Endocrinol Metab, 32(10), 1147-1153. Abstract.  Author URL.
Johnson MBJ, De Franco E, Atma W Greeley S, Letourneau LR, Gillespie K, Wakeling MN, Ellard S, Flanagan SE, Patel K, Hattersley AT, et al (2019). Trisomy 21 is a Cause of Permanent Neonatal Diabetes that is Autoimmune but not HLA Associated. Diabetes
Iacovazzo D, Flanagan S, Walker E, Quezado R, Antonio de Sousa F, Caswell R, Johnson MBJ, Wakeling M, Brandle M, Guo M, et al (2018). A MAFA missense mutation causes familial insulinomatosis and diabetes mellitus. Proceedings of the National Academy of Sciences
Johnson MBJ, Patel K, De Franco E, Houghton J, McDonald T, Ellard S, Flanagan S, Hattersley A (2018). A Type 1 diabetes genetic risk score can discriminate monogenic autoimmunity with diabetes from early onset clustering of polygenic autoimmunity with diabetes. Diabetologia
Johnson MB, De Franco E, Lango Allen H, Al Senani A, Elbarbary N, Siklar Z, Berberoglu M, Imane Z, Haghighi A, Razavi Z, et al (2018). Erratum. Recessively Inherited LRBA Mutations Cause Autoimmunity Presenting as Neonatal Diabetes. Diabetes 2017;66:2316-2322. Diabetes, 67(3).  Author URL.
Al Senani A, Hamza N, Al Azkawi H, Al Kharusi M, Al Sukaiti N, Al Badi M, Al Yahyai M, Johnson M, De Franco E, Flanagan S, et al (2018). Genetic mutations associated with neonatal diabetes mellitus in Omani patients. J Pediatr Endocrinol Metab, 31(2), 195-204. Abstract.  Author URL.
Şıklar Z, de Franco E, Johnson MB, Flanagan SE, Ellard S, Ceylaner S, Boztuğ K, Doğu F, İkincioğulları A, Kuloğlu Z, et al (2018). Monogenic Diabetes Not Caused By Mutations in Mody Genes: a Very Heterogenous Group of Diabetes. Exp Clin Endocrinol Diabetes, 126(10), 612-618. Abstract.  Author URL.
Flanagan SE, Vairo F, Johnson MB, Caswell R, Laver TW, Lango Allen H, Hussain K, Ellard S (2017). A CACNA1D mutation in a patient with persistent hyperinsulinaemic hypoglycaemia, heart defects, and severe hypotonia. Pediatr Diabetes, 18(4), 320-323. Abstract.  Author URL.
Han B, Mohamed Z, Estebanez MS, Craigie RJ, Newbould M, Cheesman E, Padidela R, Skae M, Johnson M, Flanagan S, et al (2017). Atypical Forms of Congenital Hyperinsulinism in Infancy Are Associated with Mosaic Patterns of Immature Islet Cells. JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, 102(9), 3261-3267.  Author URL.
De Franco E, Flanagan SE, Yagi T, Abreu D, Mahadevan J, Johnson MB, Jones G, Acosta F, Mulaudzi M, Lek N, et al (2017). Dominant ER Stress-Inducing WFS1 Mutations Underlie a Genetic Syndrome of Neonatal/Infancy-Onset Diabetes, Congenital Sensorineural Deafness, and Congenital Cataracts. Diabetes, 66(7), 2044-2053. Abstract.  Author URL.
Patel KA, Kettunen J, Laakso M, Stančáková A, Laver TW, Colclough K, Johnson MB, Abramowicz M, Groop L, Miettinen PJ, et al (2017). Heterozygous <i>RFX6</i> protein truncating variants are associated with Maturity-Onset Diabetes of the Young (MODY) with reduced penetrance. Abstract.
Patel KA, Kettunen J, Laakso M, Stančáková A, Laver TW, Colclough K, Johnson MB, Abramowicz M, Groop L, Miettinen PJ, et al (2017). Heterozygous RFX6 protein truncating variants are associated with MODY with reduced penetrance. Nat Commun, 8(1). Abstract.  Author URL.
Cabezas OR, Flanagan SE, Stanescu H, García-Martínez E, Caswell R, Lango-Allen H, Antón-Gamero M, Argente J, Bussell A-M, Brandli A, et al (2017). Polycystic Kidney Disease with Hyperinsulinemic Hypoglycemia Caused by a Promoter Mutation in Phosphomannomutase 2. J Am Soc Nephrol, 28(8), 2529-2539. Abstract.  Author URL.
Johnson MB, Flanagan SE, Martins TB, Hill HR, Hattersley AT, McDonald TJ (2016). Low IgE is a Useful Tool to Identify STAT3 Gain-of-Function Mutations. Clin Chem, 62(11), 1536-1538.  Author URL.
Johnson MB, Hattersley AT, Flanagan SE (2016). Monogenic autoimmune diseases of the endocrine system. Lancet Diabetes Endocrinol, 4(10), 862-872. Abstract.  Author URL.
Laver TW, Caswell RC, Moore KA, Poschmann J, Johnson MB, Owens MM, Ellard S, Paszkiewicz KH, Weedon MN (2016). Pitfalls of haplotype phasing from amplicon-based long-read sequencing. Sci Rep, 6 Abstract.  Author URL.
Devall M, Burrage J, Caswell R, Johnson M, Troakes C, Al-Sarraj S, Jeffries AR, Mill J, Lunnon K (2015). A comparison of mitochondrial DNA isolation methods in frozen post-mortem human brain tissue--applications for studies of mitochondrial genetics in brain disorders. Biotechniques, 59(4), 241-246. Abstract.  Author URL.
Ellard S, Kivuva E, Turnpenny P, Stals K, Johnson M, Xie W, Caswell R, Lango Allen H (2015). An exome sequencing strategy to diagnose lethal autosomal recessive disorders. European Journal of Human Genetics, 23(3), 401-404. Abstract.
Ellard S, Kivuva E, Turnpenny P, Stals K, Johnson M, Xie W, Caswell R, Lango Allen H (2015). An exome sequencing strategy to diagnose lethal autosomal recessive disorders. Eur J Hum Genet, 23(3), 401-404. Abstract.  Author URL.
Habeb AM, Deeb A, Johnson M, Abdullah M, Abdulrasoul M, Al-Awneh H, Al-Maghamsi MSF, Al-Murshedi F, Al-Saif R, Al-Sinani S, et al (2015). Liver disease and other comorbidities in Wolcott-Rallison syndrome: Different phenotype and variable associations in a large cohort. Hormone Research in Paediatrics, 83(3), 190-197. Abstract.


De Franco E, Johnson MB (2023). Classification of Neonatal Diabetes. In  (Ed) Neonatal and Early Onset Diabetes Mellitus, Springer Nature, 39-61.

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External Engagement and Impact


  • European Association for the Study of Diabetes 'Rising Star Award' 2022.
  • Awarded ‘Best Oral Presentation’ at the EASD Study Group on the Genetics of Diabetes conference (Leiden, NL, May ’17)

Invited lectures

  • 2021: International Society for Paediatric & Adolescent Diabetes Virtual Conference
  • 2021: Keystone Virtual Symposia; Diabetes: Many Faces of the Disease. Vancouver, Canada
  • 2019: MRC GW4 alliance, Universities of Bath, Bristol, Cardiff & Exeter. Infection, Immunity, Repair symposia. Exeter, UK
  • 2019: EASD: Genetics of Diabetes study group conference. Prague, Czech Republic
  • 2019: Bulgarian Paediatric Endocrine Society meeting. Varna, Bulgaria
  • 2017: Association of Clinical Biochemists in Ireland conference. Galway, Ireland

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  • University of Exeter Medical School – supervision of MSc research projects
  • Royal Devon and Exeter NHS foundation trust – Molecular genetics 
  • University of Exeter Medical School - Genetic Diabetes Nurses
  • University of Exeter (Biosciences) – Laboratory demonstrator

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Office Hours:

Mon - Fri 8.00-16.30

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