Overview

The surfaces of cells are covered with a dense layer of glycoproteins, glycolipids, and proteoglycans, which together make up the glycocalyx. These glycoconjugates bind to growth factors, enzymes, and extracellular matrix proteins, and thereby participate in a wide variety of biological phenomena related to cell differentiation, proliferation and migration, morphogenesis, and normal and pathophysiology. To a large extent these interactions are determined by the structure of the polysaccharide chains (glycans) that distinguish the various subclasses of glycoconjugates. The assembly of these molecules involves many enzymes, substrates and cofactors and differs from the assembly of nucleic acids and proteins in not requiring a template. Understanding how cells organize the assembly process to bring about cell-type specific glycan expression and biological responses is a major problem in modern cell biology.

Research in the Esko lab utilizes a combination of chemistry, cell biology and genetics to understand the structure, assembly and function of sulfated glycosaminoglycans found on proteoglycans. The glycosaminoglycans include hyaluronan, heparan sulfate, chondroitin/dermatan sulfate, and keratan sulfate. Studies of mutant cell lines and mice bearing conditional and systemic mutations allow us to analyze glycan function in normal physiology and disease. Current work arranged by systems include:

Proteoglycan Metabolism: We have an ongoing program to characterize mouse strains lacking specific sulfotransferases and glycosyltransferases involved in heparan and chondroitin/dermatan sulfate assembly. We are also interested in lysosomal catabolism of glycosaminoglycans and the development of methods to restore homeostasis in tissues through enzyme replacement and substrate deprivation. Part of these studies involve collaborations with companies and family foundations with interest in lysosomal storage disorders.

Proteoglycans and Infectious Disease: A major effort in the lab focuses on the impact of heparan sulfate and chondroitin/dermatan sulfate on infectious disease. These studies involve assessment of the vascular glycoproteome remodeling after bacterial challenge. Another set of studies focus on altering heparan sulfate in endothelial cells and myeloid cells to determine how these changes affect infection and inflammation. A third area concerns the impact of natural variation in heparan sulfate content and composition on infection.

Proteoglycans and Cancer Biology: Projects in this area involve studies of proteoglycans in cancer cells using genome wide methods to alter glycosaminoglycan structure and function and studies of an unusual form of heparan sulfate in pancreatic adenocarcinoma.

The lab currently consists of 2 postdoc researchers, 1 graduate student, 3 technicians, and 3 undergraduates, and Chris Toomey, a Professor of Ophthalmology at UCSD. We have lab meeting every week (Thursdays at 8:00 am), a joint meeting with Professor Philip Gordts lab (every other Tuesday at 8:00 am), a journal club focused on Current Literature in Glycobiology (BIOM 246 , weekly on Friday), and weekly submeetings to coordinate projects with collaborators on and off campus. Trainees receive classical training in the chemistry and biochemistry of glycans and modern training in genetics, cell biology and physiology. My door is always open

Metabolism

Virtually all animal cells carry proteoglycans on their plasma membrane and secrete them into the surrounding extracellular matrix. Proteoglycans consist of a protein core and one or more glycosaminoglycan chains, such as heparan sulfate (which is related in structure to the anticoagulant heparin) or chondroitin sulfate/dermatan sulfate. During their biosynthesis, a large family of enzymes install sulfate groups at various positions along the chains, creating binding sites for proteins, such as growth factors, proteases and their inhibitors, lipolytic enzymes and plasma apolipoproteins, and extracellular matrix proteins. The importance of these interactions is exemplified by the profound pathophysiological phenotypes in mice and humans bearing mutations in the core proteins or the biosynthetic enzymes responsible for assembly of the chains.

Ongoing projects include creation of conditional mutants in mice to study the function of heparan sulfate and chondroitin sulfate proteoglycans and their binding proteins. We are also interested in the process of assembly, in particular how cells regulate the formation of ligand binding sites in the chains. Towards this end, we have performed genome wide CRISPR-Cas9 screenings to look for novel genes involved in assembly. These studies have led to the identification of unexpected factors that regulate the biosynthetic pathway, including transcription factors, chromatin remodeling genes, and components of several signaling pathways.

We are also interested in lysosomal catabolism of glycosaminoglycans and inherited diseases that alter their natural turnover. We work with TEGA Therapeutics towards the development of therapeutic forms of heparan sulfate and heparin and enzyme replacement therapies.

Relevant Papers

Poli, M., Anower-E-Khuda, F., Asperti, M., Ruzzenenti, P., Gryzik, M., Gordts, P.L.S.M., Arosio, P. and Esko, J.D. (2019) Hepatic heparan sulfate regulates hepcidin expression in human hepatocytes and mice. J. Biol. Chem. 294:13292-13303. PMID:31315930

Weiss, R.J., Spahn, P.N., Chiang, A.W.T., Li , J., Kellman, B.P., Benner, C., Glass, C.K., Gordts, P.L.S.M., Lewis, N.E. and Esko, J.D. (2020) ZNF263 is a novel transcriptional regulator of heparin biosynthesis. Proc. Natl. Acad. Sci. 117:9311-9317. PMID: 32277030

Sandoval, D.R., Toledo, A., Painter, C.D., Tota, E.M., Sheikh, M.O., West, A.M.V., Frank, M.M., Wells, L., Xu, D., Bicknell, R., Corbett, K.D. and Esko, J.D. (2020) Proteomics-based screening of the endothelial heparan sulfate interactome reveals that C-type lectin 14a (CLEC14A) is a heparin binding protein. J. Biol. Chem. 295:2804-2821. PMID:31964714. PMCID:7049958. Selected for a special virtual issue.

Spliid ,C.B., Toledo, A.G., Salanti, A., Esko, J.D. and Clausen, T.M. (2021) Beware, commercial chondroitinases vary in activity and substrate specificity. Glycobiology 31:103-115. PMID:32573715

Trabszo, C., Ramms, B., Chopra, P., Lüllmann-Rauch, R., Stroobants, S., Sproß, J., Jeschke, A., Schinke, T., Boons, G.-J., Esko, J.D., Lübke, T. and Dierks, T. Arylsulfatase K inactivation causes mucopolysaccharidosis due to deficient glucuronate desulfation of heparan and chondroitin sulfate Biochem. J. (2020) 477:3433–3451. PMID:32856704

Weiss, R.J., Spahn, P.N., Chiang, A.W.T., Liu, Q., Li , J., Hamill, K.M., Rother, S., Clausen, T.M., Hoeksema, M.A., Timm, B.M., Godula, K., Glass, C.K., Tor, Y., Gordts, P.S.L.M., Lewis, N.E. and Esko, J.D. (2021) Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate. Nat. Chem. Biol. 17:684-692. PMID: 33846619

Thacker, B.E., Thorne, K.J., Cartwright, C., Park, J., Glass, K., Chea, A., Kellman, B.P., Lewis, N.E., Wang, Z., Di Nardo, A., Sharfstein, S.T., Jeske, W., Walenga, J., Hogwood, J., Gray, E., Mulloy, B., Esko, J.D., and Glass, C.A. (2022) Multiplex Genome Editing of Mammalian Cells for Producing Recombinant Heparin. Metab. Eng. 70:155-165. PMID:35038554

Tillo, M., Lamanna, W.C., Dwyer, C.A., Sandoval, D.R., Pessentheiner, A.R., Al-Azzam, N., Sarrazin, S., Gonzales, J.C., Kan, S.H., Andreyev, A.Y., Schultheis, N., Thacker, B.E., Glass, C.A., Dickson, P.I., Wang, R.Y., Selleck, S.B., Esko, J.D. and Gordts, P.L.S.M. Impaired Mitophagy in Sanfilippo A mice Causes Hypertriglyceridemia and Brown Adipose Tissue Activation. (2022) J Biol Chem. 21:102159. PMID: 35750212 PMCID:9364035

Sørensen, D., Büll, C., Madsen, T., Lira-Navarrete, E., Clausen, T., Clark, A., Garretson, A., Karlsson, R., Pijnenborg, J., Yin, X., Miller, R., Chanda, S., Boltje, T., Schjoldager, K., Vakhrushev, S., Halim, A., Esko, J.D., Carlin, A., Hurtado-Guerrero, R., Weigert, R., Clausen, H. and Narimatsu, Y. (2023) Identification of global inhibitors of cellular glycosylation. Nat. Commun. 14:948. PMID:36804936 PMCID:9941569

Infectious Disease

A major effort in the lab is focused on the impact of heparan sulfate and chondroitin/dermatan sulfate on infection. We developed a vascular tagging method to measure how the endothelial proteome and glycoproteome change after bacterial challenge. A striking remodeling of the vascular proteome occurs in a temporally regulated and organotypic manner. These studies have uncovered a previously uncharacterized acute phase protein generated by the liver that is present at very high levels of the plasma of septic patients. Mechanistic studies revealed that this acute phase protein modulates the coagulation pathway, presumably to reduce the coagulopathy associated with sepsis. Ongoing studies include analysis of the origin and function of vascular biomarkers in plasma, their stratification according to infectious agent, and species-specific alterations in the vascular glycoproteome.

Recently, we have become interested in the role of heparan sulfate in modulating the complement system, our first line of defense against pathogens. It turns out that many of the complement regulatory factors, such as Factor H and the Factor H related proteins, bind to heparan sulfate, but the functional significance of this interaction is unclear. Biochemical and genetic studies are underway to address this problem.

We have continued interest in other infectious agents as well. For example, we showed during the pandemic that SARS-CoV-2 infection depends on both heparan sulfate and ACE2 receptors. This observation, which has been substantiated by genome-wide screens and molecular modeling studies, led to studies that revealed enormous variation of heparan sulfate in human saliva and various organs. We hope to answer whether these differences correlate with susceptibility to infection and to idiopathic diseases in humans.

Relevant Papers

Pimienta, G., Heithoff, D.M., Rosa-Campos, A., Tran, M., Esko, J.D., Mahan, M.J., Marth, J.D., and Smith, J.W. (2019) Plasma proteome signature of sepsis: a functionally connected protein network. Proteomics 19:1800389-98. PMID:30706660 PMCID:6447370

Toledo, A.G., Golden, G., Campos, A.R., Cuello, H., Sorrentino, J., Lewis, N., Varki, N., Nizet, V., Smith, J.W. and Esko, J.D. (2019) Proteomic atlas of organ vasculopathies triggered by Staphylococcus aureus sepsis. Nat. Commun. 10:4656. PMID:31604940 PMCID:6789120

Clausen, T.M., Sandoval, D.R., Spliid, C.B., Pihl, J., Painter, C.D., Thacker, B.E., Glass, C.A., Narayanan, A., Majowicz, S.A., Zhang, Y., Torres, J.L., Golden, G.J., Porell, R., Garretson, A.F., Laubach, L., Feldman, J., Yin, X., Pu, Y., Hauser, B., Caradonna, T.M., Kellman, B.P., Martino, C., Gordts, P.L.S.M., Leibel, S.L., Chanda, S.K., Schmidt, A.G., Godula, K., Jose, J., Corbett, K.D., Ward, A.B., Carlin, A.F. and Esko, J.D. (2020) SARS-CoV-2 infection depends on cellular heparan sulfate and ACE2. Cell 83:1043-1057. PMID: 32699853

Marki, A., Buscher, K., Lorenzini, C., Meyer, M., Saigusa, R., Fan, Z., Yeh, Y.T., Hartmann, N., Dan, J.M., Kiosses, W.B., Golden, G.J., Ganesan, R., Winkels, H., Orecchioni, M., McArdle, S., Mikulski, Z., Altman, Y., Bui, J., Kronenberg, M., Chien, S., Esko, J.D., Nizet, V., Smalley, D., Roth, J. and Ley, K. (2021) Elongated neutrophil-derived structures are blood-borne microparticles formed by rolling neutrophils during sepsis. J. Exp. Med. 218:e20200551. PMID:33275138

Golden, G.J., Toledo, A.G., Marki, A., Sorrentino, J.T., Morris, C., Riley, R.J., Spliid, C., Chen, Q., Cornax, I., Lewis, N.E., Varki, N., Le, D., Malmström, J., Karlsson, C., Ley, K., Nizet, V. and Esko, J.D.. (2021) Endothelial heparan sulfate mediates hepatic neutrophil trafficking and injury during Staphylococcus aureus sepsis. mBio 12:e0118121. PMID:34544271 PMCID:PMC8546592

Toledo, A.G., Sorrentino, J.T., Sandoval, D.R., Malmström, J., Lewis, N.E. and Esko, J.D. (2021) A systems view of the heparan sulfate interactome. J. Histol. Histochem. 69:105-119. PMID: 33494649

Sorrentino, J.T., Golden, G.J., Morris, C., Painter, C., Nizet, V., Campos, A.R., Smith, J.W., Karlsson, C., Malmström, J., Lewis, N.E., Esko, J.D. and Toledo, A.G. (2022) Vascular proteome responses precede organ dysfunction in a murine model of Staphylococcus aureus bacteremia (2022) mSystems 7:e0039522. PMID:35913192 PMCID:9426442

SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling (2022) Biering, S.B., Gomes de Sousa, F.T., Tjang, L.V., Pahmeier, F., Zhu, C., Ruan, R., Blanc, S.F., Patel, T.S., Worthington, C.M., Glasner, D.R., Castillo-Rojas, B., Servellita, V., Lo, N.T.N., Wong, M.P., Warnes, C.M., Sandoval, D.R., Clausen, T.M., Santos, Y.A., Fox, D.M., Ortega, V., Näär, A.M., Baric, R.S., Stanley, S,A., Aguilar, H.C., Esko, J.D., Chiu, C.Y., Pak, J.E., Beatty, P.R. and Harris, E. Nat. Commun. 13:7630. PMID:36494335 PMCID:PMC9734751

Aguilar-Calvo, P., Malik, A., Sandoval, D.R., Barback, C., Orrù, C.D., Standke, H.G., Thomas, O.R., Dwyer, C.A., Pizzo, D.P., Bapat, J., Soldau, K., Ogawa, R., Riley, M.B., Nilsson, K.P.R., Kraus, A., Caughey, B., Iliff, J.J., Vera, D.R., Esko, J.D. and Sigurdson, C.J. (2023) Neuronal Ndst1 depletion accelerates prion protein clearance and slows neurodegeneration in prion infection. PLoS Pathog. 19:e1011487. PMID:37747931

Toledo, A.G., Bratanis, E., Velásquez, E., Chowdhury, S., Olofsson, B., Sorrentino, J.T., Karlsson, C., Lewis, N.E., Esko, J.D., Collin, M., Shannon, O., Malmström, J. (2023) Pathogen-driven degradation of endogenous and therapeutic antibodies during streptococcal infections. Nat. Commun. 14:6693. PMID:37872209

Cancer Biology

We remain interested in the role of proteoglycans in tumor formation, angiogenesis and metastasis. We were the first group to show that tumor formation depends on heparan sulfate in CHO cells, which has been subsequently confirmed in other types of cancer. We also showed that endothelial heparan sulfate was crucial in pathological tumor angiogenesis. Ongoing studies focus on a novel form of heparan sulfate produced by pancreatic adenocarcinoma that is present in basement membranes and in the plasma in mice and humans with pancreatic cancer. Studies show a surprising correlation of these biomarkers and survival in patients. Efforts are underway to determine its utility as a biomarker for early diagnosis and its functional significance in terms of tumor growth, invasion and metastasis. We also collaborate with other labs that specialize in cancer research to address the role of glycosylation in various aspects of tumor biology, including dormancy.

Relevant Papers

Esko, J.D., Rostand, K.S., and Weinke, J.L. (1988) Tumor formation dependent on proteoglycan biosynthesis. Science 241:1092-1096. PMID:3137658

Belting, M, Borsig, L., Fuster, M., Brown, JR, Persson, L., Fransson, L.-Å., and Esko, J.D. (2002) Tumor attenuation by combined heparan sulfate and polyamine depletion. Proc. Natl. Acad. Sci USA 99:371-376. PMID:11752393 PMCID:117567

Fuster, M.M., Brown, J.R., Wang, L, and Esko, J.D. (2003) A disaccharide precursor of sialyl Lewis X inhibits metastatic potential of tumor cells. Cancer Res. 63:2775-2781. PMID:12782582

Stickens, D., Zak, B.M., Rougier, N., Esko, J.D., Werb, Z. (2005) Mice deficient in Ext2 lack heparan sulfate and develop exostoses. Development 132:5055-5068. PMID:16236767, PMCID:2767329

Zak, B.M., Schuksz, M., Koyama, E., Mundy, C., Wells, D.E., Yamaguchi, Y., Pacifici, M., and Esko, J.D. (2011) Compound heterozygous loss of Ext1 and Ext2 is sufficient for formation of multiple exostoses in mouse ribs and long bones. Bone 48:979-987. PMID:21310272 PMCID:3335264

Spinler, K., Bajaj, J., Ito, T., Zimdahl, B., Hamilton, M., Ahmadi, A., Koechlein, C., Lytle, N., Kwon, H.Y., Anower-E-Khuda, F., Sun, H., Blevins, A., Weeks, J., Kritzik, M., Karlseder, J., Park, P.W., Ginsberg, M., Esko, J.D. and Reya, T. (2020) A stem cell reporter based platform to identify and target drug resistant stem cells in myeloid leukemia. Nat. Comm. 11:5998. PMID:33243988

Spliid, C.B., Toledo, A.G., Sanderson, P., Mao, Y., Gatto, F., Gustavsson, T., Choudhary, S., Saldanha, A.L., Vogelsang, R.P., Gögenur, I., Theander, T.G., Leach, F.E. 3rd, Amster, I.J., Esko, J.D., Salanti, A., Clausen, T.M. (2021) The specificity of the malarial VAR2CSA protein for chondroitin sulfate depends on 4-O-sulfation and ligand accessibility. J. Biol. Chem. 297(6):101391. PMID:34762909

Oo, H.Z., Lohinai, Z., Khazamipour, N., Lo, J., Kumar, G., Pihl, J., Adomat, H., Nabavi, N., Behmanesh, H., Zhai, B., Dagil, R., Choudhary, S., Gustavsson, T., Clausen, T.M., Esko, J.D., Allen, J.W., Thompson, M.A., Tran, N.L., Moldvay, J., Dome, B., Salanti, A., Al-Nakouzi, N., Weiss, G.J., Daugaard, M. (2021) Oncofetal chondroitin sulfate is a highly expressed therapeutic target in non-small cell lung cancer. Cancers (Basel) 3:4489. PMID:34503301

Al Nakouzi, N., Wang, C., Oo, H.Z., Nelepcu, I., Lallous, N., Spliid, C., Khazamipour, N., Lo, J., Truong, S., Collins, C., Hui, D., Esfandnia, S., Adomat, H., Mandel-Clausen, T., Gustavsson, T., Choudhary, S., Dagil, R., Corey, E., Wang, Y., Chauchereau, A., Fazli, L., Esko, J., Salanti, A., Nelson, P., Gleave, M. and Daugaard, M. (2022) Reformation of the chondroitin sulfate glycocalyx enables progression of AR-independent prostate cancer Nat. Commun. 13:4760. PMID:35963852 PMCID:9376089

Wang, X., Ramos, R., Phan, A.Q., Yamaga, K., Flesher, J.L., Jiang, S., Oh, J.W., Jin, S., Jahid, S., Kuan, C.H., Nguyen, T.K., Liang, H.Y., Shettigar. N.U., Hou, R., Tran, K.H., Nguyen, A., Vu, K.N., Phung, J.L., Ingal, J.P., Levitt, K.M., Cao, X., Liu, Y., Deng, Z., Taguchi, N., Scarfone, V.M., Wang, G., Paolilli, K.N., Wang, X., Guerrero-Juarez, C.F., Davis, R.T., Greenberg, E.N., Ruiz-Vega, R., Vasudeva, P., Murad, R., Widyastuti, L.H.P., Lee, H.L., McElwee, K.J., Gadeau, A.P., Lawson, D.A., Andersen, B., Mortazavi, A., Yu, Z., Nie, Q., Kunisada, T., Karin, M., Tuckermann, J., Esko, J.D., Ganesan, A.K., Li, J. and Plikus, M.V. (2023) Signalling by senescent melanocytes hyperactivates hair growth Nature 618:808-817. PMID: 37344645

Sreekumar, A., Lu, M., Choudhury, B., Pan, T.C., Pant, D.K., Lawrence-Paul, M.R., Sterner, C.J., Belka, G.K., Toriumi, T., Benz, B.A., Escobar-Aguirre, M., Marino, F.E., Esko, J.D. and Chodosh. L.A. (2023) B3GALT6 promotes dormant breast cancer cell survival and recurrence by enabling heparan sulfate-mediated FGF signaling. Cancer Cell. S1535-6108(23)00399-9. PMID: 38065100