Life Sciences Research for Lifelong Health

Jonathan Clark

Jonathan studied Biological Chemistry at the University of Leicester and then obtained a PhD in new synthetic methods towards the synthesis of Taxol. After a postdoctoral position in the Pharmaceutical Science Department at the University of Nottingham, he moved to Cambridge to work in the local biotechnology industry for the next 11 years. He then took up a position with Babraham Bioscience Technologies to provide chemical services to the local biotechnology industry and to help commercialise and develop science originating from the Babraham Institute. He has now taken up a position within the Institute to provide biological chemistry support to the Institute. His group carry out chemical research focused on Institute science and ageing.

Latest Publications

PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K.
Malek M, Kielkowska A, Chessa T, Anderson KE, Barneda D, Pir P, Nakanishi H, Eguchi S, Koizumi A, Sasaki J, Juvin V, Kiselev VY, Niewczas I, Gray A, Valayer A, Spensberger D, Imbert M, Felisbino S, Habuchi T, Beinke S, Cosulich S, Le Novère N, Sasaki T, Clark J, Hawkins PT, Stephens LR

The PI3K signaling pathway regulates cell growth and movement and is heavily mutated in cancer. Class I PI3Ks synthesize the lipid messenger PI(3,4,5)P3. PI(3,4,5)P3 can be dephosphorylated by 3- or 5-phosphatases, the latter producing PI(3,4)P2. The PTEN tumor suppressor is thought to function primarily as a PI(3,4,5)P3 3-phosphatase, limiting activation of this pathway. Here we show that PTEN also functions as a PI(3,4)P2 3-phosphatase, both in vitro and in vivo. PTEN is a major PI(3,4)P2 phosphatase in Mcf10a cytosol, and loss of PTEN and INPP4B, a known PI(3,4)P2 4-phosphatase, leads to synergistic accumulation of PI(3,4)P2, which correlated with increased invadopodia in epidermal growth factor (EGF)-stimulated cells. PTEN deletion increased PI(3,4)P2 levels in a mouse model of prostate cancer, and it inversely correlated with PI(3,4)P2 levels across several EGF-stimulated prostate and breast cancer lines. These results point to a role for PI(3,4)P2 in the phenotype caused by loss-of-function mutations or deletions in PTEN.

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Molecular cell, , 1097-4164, , 2017

PMID: 29056325

Insulin resistance uncoupled from dyslipidemia due to C-terminal PIK3R1 mutations.
Huang-Doran I, Tomlinson P, Payne F, Gast A, Sleigh A, Bottomley W, Harris J, Daly A, Rocha N, Rudge S, Clark J, Kwok A, Romeo S, McCann E, Müksch B, Dattani M, Zucchini S, Wakelam M, Foukas LC, Savage DB, Murphy R, O'Rahilly S, Barroso I, Semple RK

Obesity-related insulin resistance is associated with fatty liver, dyslipidemia, and low plasma adiponectin. Insulin resistance due to insulin receptor (INSR) dysfunction is associated with none of these, but when due to dysfunction of the downstream kinase AKT2 phenocopies obesity-related insulin resistance. We report 5 patients with SHORT syndrome and C-terminal mutations in PIK3R1, encoding the p85α/p55α/p50α subunits of PI3K, which act between INSR and AKT in insulin signaling. Four of 5 patients had extreme insulin resistance without dyslipidemia or hepatic steatosis. In 3 of these 4, plasma adiponectin was preserved, as in insulin receptor dysfunction. The fourth patient and her healthy mother had low plasma adiponectin associated with a potentially novel mutation, p.Asp231Ala, in adiponectin itself. Cells studied from one patient with the p.Tyr657X PIK3R1 mutation expressed abundant truncated PIK3R1 products and showed severely reduced insulin-stimulated association of mutant but not WT p85α with IRS1, but normal downstream signaling. In 3T3-L1 preadipocytes, mutant p85α overexpression attenuated insulin-induced AKT phosphorylation and adipocyte differentiation. Thus, PIK3R1 C-terminal mutations impair insulin signaling only in some cellular contexts and produce a subphenotype of insulin resistance resembling INSR dysfunction but unlike AKT2 dysfunction, implicating PI3K in the pathogenesis of key components of the metabolic syndrome.

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JCI insight, 1, , e88766, 2016

PMID: 27766312

Dynamics of mTORC1 activation in response to amino acids.
Manifava M, Smith M, Rotondo S, Walker S, Niewczas I, Zoncu R, Clark J, Ktistakis NT

Amino acids are essential activators of mTORC1 via a complex containing RAG GTPases, RAGULATOR and the vacuolar ATPase. Sensing of amino acids causes translocation of mTORC1 to lysosomes, an obligate step for activation. To examine the spatial and temporal dynamics of this translocation, we used live imaging of the mTORC1 component RAPTOR and a cell permeant fluorescent analogue of di-leucine methyl ester. Translocation to lysosomes is a transient event, occurring within 2 min of aa addition and peaking within 5 min. It is temporally coupled with fluorescent leucine appearance in lysosomes and is sustained in comparison to aa stimulation. Sestrin2 and the vacuolar ATPase are negative and positive regulators of mTORC1 activity in our experimental system. Of note, phosphorylation of canonical mTORC1 targets is delayed compared to lysosomal translocation suggesting a dynamic and transient passage of mTORC1 from the lysosomal surface before targetting its substrates elsewhere.

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eLife, 5, 2050-084X, , 2016

PMID: 27725083

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Latest Publications

PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K.

Malek M, Kielkowska A, Chessa T

Molecular cell
1097-4164: (2017)

PMID: 29056325

Insulin resistance uncoupled from dyslipidemia due to C-terminal PIK3R1 mutations.

Huang-Doran I, Tomlinson P, Payne F

JCI insight
1 :e88766 (2016)

PMID: 27766312

Dynamics of mTORC1 activation in response to amino acids.

Manifava M, Smith M, Rotondo S

eLife
5 2050-084X: (2016)

PMID: 27725083

Tumor cells with KRAS or BRAF mutations or ERK5/MAPK7 amplification are not addicted to ERK5 activity for cell proliferation.

Lochhead PA, Clark J, Wang LZ

Cell cycle (Georgetown, Tex.)
15 1551-4005:506-18 (2016)

PMID: 26959608

The inositol-3-phosphate synthase biosynthetic enzyme has distinct catalytic and metabolic roles.

Frej AD, Clark J, Roy CL

Molecular and cellular biology
1098-5549: (2016)

PMID: 26951199

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).

Klionsky DJ, Abdelmohsen K, Abe A

Autophagy
12 1554-8635:1-222 (2016)

PMID: 26799652

Investigating the effect of arachidonate supplementation on the phosphoinositide content of MCF10a breast epithelial cells.

Anderson KE, Juvin V, Clark J

Advances in biological regulation
2212-4934: (2015)

PMID: 26639089

Dictyostelium uses ether-linked inositol phospholipids for intracellular signalling.

Clark J,Kay RR,Kielkowska A,Niewczas I,Fets L,Oxley D,Stephens LR,Hawkins PT

The EMBO journal
1460-2075: (2014)

PMID: 25180230

A new approach to measuring phosphoinositides in cells by mass spectrometry.

Kielkowska A, Niewczas I, Anderson KE

Advances in biological regulation
54 2212-4934:131-41 (2014)

PMID: 24120934

Two distinct functions for PI3-kinases in macropinocytosis.

O Hoeller, P Bolourani, J Clark

Journal of cell science
126 Pt 18:4296-307 (2013)

DOI: 10.1242/jcs.134015

PMID: 23843627