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Karolinska institutet
Karolinska universitetssjukhuset

Eduardo Villablanca Group


Our lab that lies at the interface of immunology, human health, biological engineering, and systems biology, is seeking to define the complex dynamics of host-environment interactions required to sustain intestinal homeostasis, how breakdown in these interactions may lead to intestinal inflammatory disorders, and how we can promote mucosal healing to reverse the intestinal damage caused by inflammation. The main focus of our lab is to gain insights into the mechanisms that underlie the initiation and resolution of inflammatory bowel disease (IBD) to eventually develop therapeutics to treat intestinal autoimmune diseases.

To accomplish these goals, we have built an interdisciplinary research program that combines the generation of novel experimental models of IBD (zebrafish and mouse), traditional molecular and cellular approaches (e.g. ex vivoimmune cell- intestinal organoid co-culture), cutting-edge technologies (scRNA-seq and spatial transcriptomics), systems biology, and the use of clinical samples. Thus, we are working to provide insights that may lead to novel, rational-based strategies to prevent the initiation of IBD by intervening during its preclinical phase and/or to accelerate and promote tissue regeneration upon damage.

Research projects

Interrogate the effects of genetic and environmental crosstalk in the maintenance and breakdown of intestinal homeostasis

The functional annotation of IBD risk-associated noncoding variants has been limited by their reduced penetrance, which results in subtle or immeasurable effects under steady-state conditions, suggesting that measurable effects might appear only upon exposure to environmental stressors. In particular we are working on:

– Develop novel models of intestinal inflammation.

– Generate IBD reporter zebrafish lines to investigate the function of coding and non-coding IBD risk variants.

– Identify then environmental factors and mechanism by which aberrant intestinal immune responses are triggered in genetically susceptible hosts.

– Characterize the initiation and progression of adaptive commensal-specific T cell responses.

Identify novel cellular and molecular mechanisms of tissue regeneration following injury

Using unbiased analysis of the immune cell composition, microbiota and transcriptomics during intestinal inflammation and regeneration, we have identified specific immune cells, bugs and pathways that might promote tissue regeneration upon damage. In particular we are working on:

– Characterize and validate candidate genes/pathways and/or cell types with respect to their potential role(s) in tissue regeneration.

– Identify pathways that promote colorectal cancer.

– Further characterize the crosstalk between lymphocytes and the epithelium that modulate intestinal regeneration.

– Gain mechanistic insights into how lymphocytes may support barrier functions.

Identifying novel mechanisms of intestinal inflammation and resolution using zebrafish

It is widely accepted that the etiology of Inflammatory bowel disease (IBD) lies on the complex crosstalk between genetics, environmental factors, microbiota, and host immune responses. However, the identification of which and how these variables interplay to trigger IBD is limited by the lack of tools and models that allows the cost- and time-effective screening of hundreds of relevant compounds from the environment and microbiota, are genetically tractable, and recapitulate the in vivo intestinal context. In recent years, zebrafish (Danio rerio) have emerged as an attractive model to study human diseases, due to their significant genetic and physiological conservation with humans. In addition, the zebrafish embryo offers unique advantages such as

  1. i) transparency, which enables non-invasive intravital imaging in fluorescently-tagged reporter lines;
  2. ii) external fertilization, that facilitates transient genetic manipulation of fertilized eggs;

iii) large numbers of individuals (~200 embryos/mating pair), iv) small size, allowing their growth in 96-well plates;

  1. v) amenability to test molecules/compounds, as they can be added directly to the immersion water;
  2. vi) compatibility with high-throughput screenings.

By using zebrafish, our lab has identified new environmental risk factors exacerbating intestinal inflammation (Diaz et al., Dis Model Mech. 2021) and new functions of IBD-risk genes in the intestine (Kaya et al., Cell Rep. 2020; Morales et al., Mucosal Immunol. 2022). We are currently developing new zebrafish models of intestinal damage/inflammation and using state-of-the-art transcriptomic technologies to identify novel modulators of intestinal inflammation and resolution, which will be further validated in mouse and humans.

The role of B cells in mucosal healing and tumorigenesis

Inflammatory bowel disease (IBD) is a chronic intestinal disorder characterized by a disrupted intestinal barrier that is continually attempting to heal. The constant need for tissue regeneration leads to an elevated risk for the development of intestinal tumors. Attempts to identify cellular and molecular signaling pathways that promote tissue regeneration but not oncogenic transformation have been largely unsuccessful.

A number of recent studies suggest that the accumulation of B cells and tertiary lymphoid structures in the tumor microenvironment correlates positively with improved disease prognosis and response to immune checkpoint blockade (ICB) therapy in various cancer types. However, it is still largely unknown how B cells and tertiary lymphoid structures (TLS) influence intestinal tumorigenesis.

Through a comparative longitudinal transcriptome analysis between intestinal regeneration and tumorigenesis, we have identified new potential targets that separate intestinal regeneration from tumorigenesis. Among other discoveries, we have found B cell gene signatures involved as potential unlikers of intestinal regeneration and tumorigenesis.

In this regard, we recently identified a novel detrimental role of B cells in the healing colon upon acute intestinal injury and showed that expansion of an IFN-induced B cell subset hinders the stromal-epithelial crosstalk required during mucosal healing, thereby slowing intestinal tissue regeneration (Frede A., Czarnewski P., Monasterio G., et al, Immunity, 2022).

Furthermore, we recently found that activation of specific nuclear receptors associated with elevated colonic B cell and TLS emergence in the colon lead to reduced tumor development and dramatic prolongation of survival in pre-clinical models, highlighting the link between a potential anti-tumorigenic role of B cells.

Based on our recent findings, we aim to further:

– Integrate scRNAseq and spatial transcriptomics to enable spatial positioning of clinically relevant pathways

– Investigate the mechanistic and functional involvement of B cells during acute and chronic intestinal inflammation and tumorigenesis

– To characterize cell circuitry and heterogeneity of tertiary lymphoid structures during tumorigenesis

– To investigate whether B cells/TLS modulate response to ICB therapy

To determine the heterogeneity of UC

Ulcerative Colitis (UC) is a chronic inflammatory bowel disease (IBD) that is usually confined to the colon. UC is highly heterogeneous, encompassing a wide range of patterns associated with behavior, location, and response to treatment. Despite this heterogeneity, patient classification criteria for tailored therapies are currently lacking. It is vital to characterize the heterogeneity of UC patients to correctly predict if they will respond or not to available treatments and to eventually move towards precision medicine in IBD. Our lab has recently developed an unbiased stratification of UC patients (Czarnewski P. et al., Nat Communications, 2019.) based on their transcriptomic profiles: UC1 patients, which are characterized by a low response (~10%) to biological therapies (infliximab/vedolizumab) and an increased expression of genes associated with neutrophil degranulation and cytokine signaling. While UC2 patients have a higher responsiveness to biological therapy (~60%), and low expression of genes associated with lack of response to anti-TNF treatment. However, to consolidate this novel classification for clinical practice, further characterization is needed. Using multi-omics approaches, such as single cell and spatial transcriptomics, we aim to deeply characterize the immune cell composition and molecular pathways underpinning different UC subsets. This project will provide potential new mechanistic insights into the etiology of IBD and UC therapy management. Therefore we are still working to:

– Further characterize UC1 patients and identify therapeutic targets to either promote remission or make them responders (e.g. conversion into UC2).

– Generate an affordable diagnostic tool that can be used to identify UC1 and UC2 patients.

– Further characterize UC1 and UC2 patients using other “omic” approaches (e.g. microbiome, CyTOFF, etc).

– To perform cross-species comparisons of different processes associated with IBD, such as acute intestinal inflammation and mucosal healing.

Group Leader

Eduardo Villablanca, PhD, Associate professor


The breakdown of intestinal immune homeostasis may lead to diseases such as IBD, a currently incurable disorder that affects millions of individuals worldwide. The large numbers of patients that fail to respond to available therapies and the high cost of biologic agents highlight an urgent need for alternative treatments, such as those that prevent the disease or promote intestinal regeneration upon injury. My lab exploits competencies in experimental immunology, the versatility of zebrafish models, ex vivo intestinal organoid co-cultures, transcriptomics (bulk, single-cell and spatial level), and translational research to identify mechanisms that modulate the initiation and resolution of IBD.

Group members

Das Srustidhar, PhD, Postdoc, srustidhar.das@ki.se

Rodrigo Morales, PhD, Postdoc, rodrigo.morales@ki.se

Gustavo Monasterio, PhD Postdoc, gustavo.monasterio@ki.se

Jennifer Fransson, PhD, Postdoc, jennifer.fransson@ki.se

Katja Selin, PhD student, katja.selin@ki.se

Xinxin Luo, PhD student, xinxin.luo@ki.se

Francisca Castillo, PhD student, francisca.castillo@ki.se

Bianca Kern, PhD student, bianca.kern@ki.se

Ali Okhovat, PhD student, mohammad.ali.okhovat@ki.se

Ning He, PhD student, ning.he@ki.se

Selected publications


Metagenomic and single-cell RNA-Seq survey of the Helicobacter pylori-infected stomach in asymptomatic individuals. Sorini C, Tripathi KP, Wu S, Higdon SM, Wang J, Cheng L, Banerjee S, Reinhardt A, Kreslavsky T, Thorell A, Engstrand L, Du J, Villablanca EJ. JCI Insight. 2023, Feb 22;8(4):e161042.

B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing. Frede, A., Czarnewski, P., Monasterio, G., Tripathi, K. P., Bejarano, D. A., Ramirez Flores, R. O., Sorini, C., Larsson, L., Luo, X., Geerlings, L., Novella-Rausell, C., Zagami, C., Kuiper, R., Morales, R. A., Castillo, F., Hunt, M., Mariano, L. L., Hu, Y. O. O., Engblom, C., Lennon-Duménil, AM., Mittenzwei, R., Westendorf, A.M., Hövelmeyer, N., Lundeberg, J., Saez-Rodriguez, J., Schlitzer, A., Das, S., Villablanca EJ. Immunity. 2022 Dec 13;55(12):2336-2351.e12

Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH. Borm, L. E., Mossi Albiach, A., Mannens, C. C. A., Janusauskas, J., Özgün, C., Fernández-García, D., Hodge, R., Castillo, F., Hedin, C. R. H., Villablanca EJ, Uhlén, P., Lein, E. S., Codeluppi, S., & Linnarsson, S. Nat Biotechnol. 2023 Feb;41(2):222-231

Interleukin-10 regulates goblet cell numbers through Notch signaling in the developing zebrafish intestine. Morales, R. A., Rabahi, S., Diaz, O. E., Salloum, Y., Kern, B. C., Westling, M., Luo, X., Parigi, S. M., Monasterio, G., Das, S., Hernández, P. P., & Villablanca EJ. Mucosal Immunol. 2022 May;15(5):940-951.

Epithelial GPR35 protects from Citrobacter rodentium infection by preserving goblet cells and mucosal barrier integrity. Melhem H., Kaya B., Kaymak T., Wuggening P., Flint E., Roux J., Oost KC, Weder CC., Balmer ML., Wasler JC., Morales RA., Riedel CU., Liberali P., Villablanca EJ  & Niess JH. Mucosal Immunol. 2022 Mar;15(3):443-458

The spatial transcriptomic landscape of the healing mouse intestine following damage. Parigi SM., Larsson L, Das S, Ramirez-Flores RO, Frede A, Tripathi KP, Diaz OE, Selin K, Morales R, Luo X, Monasterio G., Engblom C., Gagliani N., Saez-Rodriguez J., Lundeberg J. & Villablanca EJ Nat Commun. 2022 Feb 11;13(1):828.

Mechanisms of mucosal healing: treating inflammatory bowel disease without immunosuppression?  Villablanca EJ, Selin K., & Hedin CRH. Nat Rev Gastroenterol Hepatol. 2022 Aug;19(8):493-507.

Type 2 immunity in in intestinal homeostasis and inflammatory bowel diseases. Luo X. & Villablanca EJBiochem Soc Trans. 2021 Nov 1;49(5):2371-2380.

Cell trafficking in the intestinal mucosa in the healthy and inflamed gut. Monasterio G., Castillo F. & Villablanca EJ. Chapter in book “Cell movement in health and disease”. Elsevier Book Chapter. In press

Intestinal helminth infection transforms the CD4+ T cell composition of the skin. Classon C., Li M, Clavero AL, Ma J, Feng X, Tibbitt C, Stark JM, Cardoso R, Rinqvist E, Boon L., Villablanca EJ, Rothfuchs A., Eidsmo L., Coquet J, & Nylen S.  Mucosal Immunol. 2022 Feb;15(2):257-267.

Perfluorooctanesulfonic acid modulates barrier function and systemic T cell homeostasis during intestinal inflammation. Diaz OE, Sorini C, Morales RA, Luo X, Frede A, Krais AM, Chávez MN, Wincent E, Das S., & Villablanca EJ.  Dis Model Mech.. 2021 Dec 1;14(12):dmm049104.    

Epithelial colonization promotes the functional diversification of gut dendritic cells. Rivera C., Randrian V., Richer W., Gerber Y., Delgado MG., Chikinia A., Frede A., Sorini C., Mauring M., Parigi SM., Goudot C., Krndija D., Cabeza-Cabrerizo M., Baulande S., Lameiras S., Guermonprez P., Reis e Sousa C., Lecuit M., Moreau HD., Helft J., Vignjevic DM., Villablanca EJ, AM Lennon-Dumenil.  Immunity. 2022 Jan 11;55(1):129-144.e8.

ILC damage, and I’ll repair it. Sorini C. & Villablanca EJ Immunity. 2021, Jun 8;54(6):1097-1099.

Immunological networks defining the heterogeneity of inflammatory bowel diseases. Selin K., Hedin C. & Villablanca EJ.  J Crohns Colitis. 2021, Nov 8;15(11):1959-1973.

Mapping the monocytic origin of lung macrophages identifies new pathways of human macrophage ontogeny. Evren E, Ringqvist E., Tripathi KP., Sleiers N., Rives IC, Alisjahbana A, Gao Y, Sarhan D, Halle T, Sorini C, Lepzien R, Marquardt N, Michaëlsson J, Smed-Sörensen A, Botling J, Karlsson M, Villablanca EJ, Willinger T.  Immunity. 2020, Feb 9;54(2):259-275.e7

Selenization of S. cerevisiae increases its protective potential in experimental autoimmune encephalomyelitis by triggering an intestinal immunomodulatory loop. Fraga-Silva TFC, Nishiyama-Mimura LA, Cardoso de Oliveira LR, dos Santos Toledo JH, Borim PA, Zorzella-Pezavento SFG, Peres Alonso D, Martins Ribolla PE, Ferreira de Oliveira CA, Morais da Fonseca D, Villablanca EJ, Sartori A.  Sci Rep. 2020, Dec 17;10(1):22190.

O-polysaccharide Plays a Major Role on the Virulence and Immunostimulatory Potential of Aggregatibacter actinomycetemcomitans During Periodontal Infection. Monasterio G., Castillo F., Astorga J., Hoare A., Terraza-Aguirre C., Cafferata EA., Villablanca EJ, Vernal R.  Front Immunol. 2020, Oct 30:11:591240.

Liver X receptor regulates Th17 and RORgt+ Treg cells by distinct mechanisms. Parigi SM, Das S, Frede A, Cardoso RF, Tripathi KP, Doñas C, Yue OO, Antonson P, Engstrand L, Gustafsson JA, & Villablanca EJ.   Mucosal Immunol. 2021, Mar;14(2):411-419.

Cytokines regulate the antigen-presenting characteristics of human circulating and tissue-resident intestinal ILCs. Rao A, Strauss O, Kokkinou E, Bruchard M, Tripathi K, Schlums H, Carrasco A, Mazzurana L, Konya V, Villablanca EJ, Björkström N, Lindforss U, Spits H, & Mjösberg J. Nat Commun. 2020, Apr 27;11(1):2049.

Lysophosphatidic acid-mediated GPR35 signaling in CX3CR1+ macrophages regulates the intestinal cytokine milieu. Kaya B, Doñas C, Wuggenig P, Diaz O, Morales R, Melhem H, Swiss IBD Cohort, Hernández PP, Kaymak T, Das S, Hruz P, Ayata CK, Villablanca EJ*, Niess JH*.  Cell Rep. 2020, Aug 4;32(5):107979.

Neutrophilic HGF-MET signaling exacerbates intestinal inflammation. Stakenborg M., Verstockt B, Meroni E, Goverse G, Verstockt S, Di Matteo M, Czarnewski P, Villablanca EJ, Ferrante M, Boeckxstaens GE, Mazzone M., Vermeire S., Matteoli G. J Crohns Colitis. 2020, Dec 2;14(12):1748-1758.

The cell circuitry of Ulcerative Colitis, a new view for a highly complex disease. Perez-Jeldres T., Alvarez-Lobos M., Rivera-Nieves J. & Villablanca EJ. Gastroenterology. 2020, Apr;158(5):1506-1508.

Cytokines regulate the antigen-presenting characteristics of human circulating and tissue-resident intestinal ILCs. Rao A., Strauss O., Kokkinou E, Bruchard M., Tripathi K., Schlums H, Carrasco A., Mazzurana L., Konya V, Villablanca EJ, Bjorkstrom N., Lindforss U., Spits H., and Mjosberg J. Nat Commun2020, Apr 27;11(1):2049.

Retinoic acid induced cytokines are selectively modulated by liver X receptor in zebrafish. Diaz OE., Xue S., Luo X., Nava J., Appelblom A., Morales RA., Das, S. & Villablanca EJReprod Toxicol. 2020, Apr:93:163-168.

Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses. Phad GE, Pushparaj P, Tran K, Dubrovskaya V, Àdori M, Martinez-Murillo P, Vázquez Bernat N, Singh S, Dionne G, O’Dell S, Bhullar K, Narang S, Sorini C, Villablanca EJ, Sundling C, Murrell B, Mascola JR, Shapiro L, Pancera M, Martin M, Corcoran M, Wyatt RT, Karlsson Hedestam GB. J Exp Med.2020, Feb 3;217(2):e20191155.

Experimental Models of Intestinal Inflammation: Lessons from Mouse and Zebrafish. Diaz O.E., Morales R.A., Das S., Villablanca EJMolecular Genetics of Inflammatory Bowel Disease. Springer, Cham. Book Chapter., 2020.

Dietary Habits and Intestinal Immunity: From Food Intake to CD4+ T H Cells. Siracusa F, Schaltenberg N, Villablanca EJ, Huber S, Gagliani N. Front Immunol.2019, Jan 15:9:3177.

Conserved transcriptomic profile between mouse and humans allows temporal dynamic visualization of IBD-risk genes and unsupervised patient stratification. Czarnewski P, Parigi SM, Sorini C, Diaz OE, Das D, Gagliani N, Villablanca EJ. Nat. Commun. 2019, Jun 28;10(1):2892.

Multi-faceted inhibition of dendritic cell function by CD4+Foxp4+ regulatory T cells. Seitz C, Liu S, Klocke K, Joly AL, Czarnewski P, Tibbitt CA, Parigi SM, Westerberg LS, Coquet JM, Villablanca EJ, Wing K, Andersson J. J Autoimmun.2019,  Mar:98:86-94.

About CMM

The Center for Molecular Medicine (CMM) is a foundation instituted by the Stockholm County Council (Region Stockholm). CMM is at the heart of a close partnership with the Karolinska University Hospital and Karolinska Institutet, fueling advancements in biomedical and clinical research.


Center for Molecular Medicine Foundation, org. nr. 815201-3689

Karolinska University Hospital L8:05

Visionsgatan 18

171 76 Stockholm, Sweden


Karolinska institutet
Karolinska universitetssjukhuset