Publications: Stem cells and Regenerative Medicine

Liver X receptor unlinks intestinal regeneration and tumorigenesis.
Das S, Parigi SM, Luo X, Fransson J, Kern BC, Okhovat A, Diaz OE, Sorini C, Czarnewski P, Webb AT, Morales RA, Lebon S, Monasterio G, Castillo F, Tripathi KP, He N, Pelczar P, Schaltenberg N, De la Fuente M, López-Köstner F, Nylén S, Larsen HL, Kuiper R, Antonson P, Hermoso MA, Huber S, Biton M, Scharaw S, Gustafsson JÅ, Katajisto P, Villablanca EJ
Nature 2025 Jan;637(8048):1198-1206

A comprehensive human embryo reference tool using single-cell RNA-sequencing data.
Zhao C, Plaza Reyes A, Schell JP, Weltner J, Ortega NM, Zheng Y, Björklund ÅK, Baqué-Vidal L, Sokka J, Trokovic R, Cox B, Rossant J, Fu J, Petropoulos S, Lanner F
Nat Methods 2025 Jan;22(1):193-206

A Latent Cardiomyocyte Regeneration Potential in Human Heart Disease.
Derks W, Rode J, Collin S, Rost F, Heinke P, Hariharan A, Pickel L, Simonova I, Lázár E, Graham E, Jashari R, Andrä M, Jeppsson A, Salehpour M, Alkass K, Druid H, Kyriakopoulos CP, Taleb I, Shankar TS, Selzman CH, Sadek H, Jovinge S, Brusch L, Frisén J, Drakos S, Bergmann O
Circulation 2025 Jan;151(3):245-256

Spatiotemporal single-cell roadmap of human skin wound healing.
Liu Z, Bian X, Luo L, Björklund ÅK, Li L, Zhang L, Chen Y, Guo L, Gao J, Cao C, Wang J, He W, Xiao Y, Zhu L, Annusver K, Gopee NH, Basurto-Lozada D, Horsfall D, Bennett CL, Kasper M, Haniffa M, Sommar P, Li D, Landén NX
Cell Stem Cell 2024 Dec;():

Cancer-associated fibroblast subtypes modulate the tumor-immune microenvironment and are associated with skin cancer malignancy.
Forsthuber A, Aschenbrenner B, Korosec A, Jacob T, Annusver K, Krajic N, Kholodniuk D, Frech S, Zhu S, Purkhauser K, Lipp K, Werner F, Nguyen V, Griss J, Bauer W, Soler Cardona A, Weber B, Weninger W, Gesslbauer B, Staud C, Nedomansky J, Radtke C, Wagner SN, Petzelbauer P, Kasper M, Lichtenberger BM
Nat Commun 2024 Nov;15(1):9678

Whole-brain spatial transcriptional analysis at cellular resolution.
Kanatani S, Kreutzmann JC, Li Y, West Z, Larsen LL, Nikou DV, Eidhof I, Walton A, Zhang S, Rodríguez-Kirby LR, Skytte JL, Salinas CG, Takamatsu K, Li X, Tanaka DH, Kaczynska D, Fukumoto K, Karamzadeh R, Xiang Y, Uesaka N, Tanabe T, Adner M, Hartman J, Miyakawa A, Sundström E, Castelo-Branco G, Roostalu U, Hecksher-Sørensen J, Uhlén P
Science 2024 Nov;386(6724):907-915

Aging is associated with functional and molecular changes in distinct hematopoietic stem cell subsets.
Su TY, Hauenstein J, Somuncular E, Dumral Ö, Leonard E, Gustafsson C, Tzortzis E, Forlani A, Johansson AS, Qian H, Månsson R, Luc S
Nat Commun 2024 Sep;15(1):7966

Microglia depletion and repopulation do not alter the effects of cranial irradiation on hippocampal neurogenesis.
Zhou K, Zisiadis GA, Havermans M, Fragkopoulou A, Dominguez C, Ohshima M, Osman AM, Rodrigues CFD, Blomgren K
Brain Behav Immun 2025 Jan;123():57-63

Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors.
Bian X, Piipponen M, Liu Z, Luo L, Geara J, Chen Y, Sangsuwan T, Maselli M, Diaz C, Bain CA, Eenjes E, Genander M, Crichton M, Cash JL, Archambault L, Haghdoost S, Fradette J, Sommar P, Halle M, Xu Landén N
Nat Commun 2024 Oct;15(1):9286

An atlas of small non-coding RNAs in human preimplantation development.
Russell SJ, Zhao C, Biondic S, Menezes K, Hagemann-Jensen M, Librach CL, Petropoulos S
Nat Commun 2024 Oct;15(1):8634

The lncRNA SNHG26 drives the inflammatory-to-proliferative state transition of keratinocyte progenitor cells during wound healing.
Li D, Liu Z, Zhang L, Bian X, Wu J, Li L, Chen Y, Luo L, Pan L, Kong L, Xiao Y, Wang J, Zhang X, Wang W, Toma M, Piipponen M, Sommar P, Xu Landén N
Nat Commun 2024 Oct;15(1):8637

Adipose stem cells are sexually dimorphic cells with dual roles as preadipocytes and resident fibroblasts.
Uhrbom M, Muhl L, Genové G, Liu J, Palmgren H, Alexandersson I, Karlsson F, Zhou AX, Lunnerdal S, Gustafsson S, Buyandelger B, Petkevicius K, Ahlstedt I, Karlsson D, Aasehaug L, He L, Jeansson M, Betsholtz C, Peng XR
Nat Commun 2024 Sep;15(1):7643

In-depth analysis of transcriptomes in ovarian cortical follicles from children and adults reveals interfollicular heterogeneity.
Rooda I, Hassan J, Hao J, Wagner M, Moussaud-Lamodière E, Jääger K, Otala M, Knuus K, Lindskog C, Papaikonomou K, Gidlöf S, Langenskiöld C, Vogt H, Frisk P, Malmros J, Tuuri T, Salumets A, Jahnukainen K, Velthut-Meikas A, Damdimopoulou P
Nat Commun 2024 Aug;15(1):6989

Patient-Specific Measurable Residual Disease Markers Predict Outcome in Patients With Myelodysplastic Syndrome and Related Diseases After Hematopoietic Stem-Cell Transplantation.
Tobiasson M, Pandzic T, Illman J, Nilsson L, Weström S, Ejerblad E, Olesen G, Björklund A, Olsnes Kittang A, Werlenius O, Lorentz F, Rasmussen B, Cammenga J, Weber D, Lindholm C, Wiggh J, Dimitriou M, Moen AE, Yip Lundström L, von Bahr L, Baltzer-Sollander K, Jädersten M, Kytölä S, Walldin G, Ljungman P, Groenbaek K, Mielke S, Jacobsen SEW, Ebeling F, Cavelier L, Smidstrup Friis L, Dybedal I, Hellström-Lindberg E
J Clin Oncol 2024 Apr;42(12):1378-1390

Distinct origin and region-dependent contribution of stromal fibroblasts to fibrosis following traumatic injury in mice.
Holl D, Hau WF, Julien A, Banitalebi S, Kalkitsas J, Savant S, Llorens-Bobadilla E, Herault Y, Pavlovic G, Amiry-Moghaddam M, Dias DO, Göritz C
Nat Neurosci 2024 Jul;27(7):1285-1298

Extracellular vesicles originating from melanoma cells promote dysregulation in haematopoiesis as a component of cancer immunoediting.
Mamand DR, Bazaz S, Mohammad DK, Liang X, Pavlova S, Mim C, Gabrielsson S, Nordin JZ, Wiklander OPB, Abedi-Valugerdi M, El-Andaloussi S
J Extracell Vesicles 2024 Jul;13(7):e12471

Dissecting the Impact of Maternal Androgen Exposure on Developmental Programming through Targeting the Androgen Receptor.
Lu H, Jiang H, Li C, Derisoud E, Zhao A, Eriksson G, Lindgren E, Pui HP, Risal S, Pei Y, Maxian T, Ohlsson C, Benrick A, Haider S, Stener-Victorin E, Deng Q
Adv Sci (Weinh) 2024 Sep;11(36):e2309429

Inferring clonal somatic mutations directed by X chromosome inactivation status in single cells.
Demirci I, Larsson AJM, Chen X, Hartman J, Sandberg R, Frisén J
Genome Biol 2024 Aug;25(1):214

Corpora cavernosa fibroblasts mediate penile erection.
Guimaraes EL, Dias DO, Hau WF, Julien A, Holl D, Garcia-Collado M, Savant S, Vågesjö E, Phillipson M, Jakobsson L, Göritz C
Science 2024 Feb;383(6683):eade8064

Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics.
Engblom C, Thrane K, Lin Q, Andersson A, Toosi H, Chen X, Steiner E, Lu C, Mantovani G, Hagemann-Jensen M, Saarenpää S, Jangard M, Saez-Rodriguez J, Michaëlsson J, Hartman J, Lagergren J, Mold JE, Lundeberg J, Frisén J
Science 2023 Dec;382(6675):eadf8486

Loss of endothelial membrane KIT ligand affects systemic KIT ligand levels but not bone marrow hematopoietic stem cells.
Matsuoka S, Facchini R, Luis TC, Carrelha J, Woll PS, Mizukami T, Wu B, Boukarabila H, Buono M, Norfo R, Arai F, Suda T, Mead AJ, Nerlov C, Jacobsen SEW
Blood 2023 Nov;142(19):1622-1632

Skin mesenchymal niches maintain and protect AML-initiating stem cells.
Sandhow L, Cai H, Leonard E, Xiao P, Tomaipitinca L, Månsson A, Kondo M, Sun X, Johansson AS, Tryggvason K, Kasper M, Järås M, Qian H
J Exp Med 2023 Oct;220(10):

Placental growth factor exerts a dual function for cardiomyogenesis and vasculogenesis during heart development.
Witman N, Zhou C, Häneke T, Xiao Y, Huang X, Rohner E, Sohlmér J, Grote Beverborg N, Lehtinen ML, Chien KR, Sahara M
Nat Commun 2023 Sep;14(1):5435

Perivascular niche cells sense thrombocytopenia and activate hematopoietic stem cells in an IL-1 dependent manner.
Luis TC, Barkas N, Carrelha J, Giustacchini A, Mazzi S, Norfo R, Wu B, Aliouat A, Guerrero JA, Rodriguez-Meira A, Bouriez-Jones T, Macaulay IC, Jasztal M, Zhu G, Ni H, Robson MJ, Blakely RD, Mead AJ, Nerlov C, Ghevaert C, Jacobsen SEW
Nat Commun 2023 Sep;14(1):6062

Injury prevents Ras mutant cell expansion in mosaic skin.
Gallini S, Annusver K, Rahman NT, Gonzalez DG, Yun S, Matte-Martone C, Xin T, Lathrop E, Suozzi KC, Kasper M, Greco V
Nature 2023 Jul;619(7968):167-175

Human skin-resident CD8+ T cells require RUNX2 and RUNX3 for induction of cytotoxicity and expression of the integrin CD49a.
Zitti B, Hoffer E, Zheng W, Pandey RV, Schlums H, Perinetti Casoni G, Fusi I, Nguyen L, Kärner J, Kokkinou E, Carrasco A, Gahm J, Ehrström M, Happaniemi S, Keita ÅV, Hedin CRH, Mjösberg J, Eidsmo L, Bryceson YT
Immunity 2023 Jun;56(6):1285-1302.e7

Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag.
Bartosovic M, Castelo-Branco G
Nat Biotechnol 2023 Jun;41(6):794-805

Delivery of gene therapy through a cerebrospinal fluid conduit to rescue hearing in adult mice.
Mathiesen BK, Miyakoshi LM, Cederroth CR, Tserga E, Versteegh C, Bork PAR, Hauglund NL, Gomolka RS, Mori Y, Edvall NK, Rouse S, Møllgård K, Holt JR, Nedergaard M, Canlon B
Sci Transl Med 2023 Jun;15(702):eabq3916

Inhibition of VEGF-B signaling prevents non-alcoholic fatty liver disease development by targeting lipolysis in the white adipose tissue.
Falkevall A, Mehlem A, Folestad E, Ning FC, Osorio-Conles Ó, Radmann R, de Hollanda A, Wright SD, Scotney P, Nash A, Eriksson U
J Hepatol 2023 May;78(5):901-913

Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.
Li X, Andrusivova Z, Czarnewski P, Langseth CM, Andersson A, Liu Y, Gyllborg D, Braun E, Larsson L, Hu L, Alekseenko Z, Lee H, Avenel C, Kallner HK, Åkesson E, Adameyko I, Nilsson M, Linnarsson S, Lundeberg J, Sundström E
Nat Neurosci 2023 May;26(5):891-901

Targeting long non-coding RNA NUDT6 enhances smooth muscle cell survival and limits vascular disease progression.
Winter H, Winski G, Busch A, Chernogubova E, Fasolo F, Wu Z, Bäcklund A, Khomtchouk BB, Van Booven DJ, Sachs N, Eckstein HH, Wittig I, Boon RA, Jin H, Maegdefessel L
Mol Ther 2023 Jun;31(6):1775-1790

Perivascular localized cells commit erythropoiesis in PDGF-B-expressing solid tumors.
Hosaka K, Wang C, Zhang S, Lv X, Seki T, Zhang Y, Jing X, Wu J, Du Q, He X, Fan Y, Li X, Kondo M, Yoshihara M, Qian H, Shi L, Zhu P, Xu Y, Yang Y, Cheng T, Cao Y
Cancer Commun (Lond) 2023 Jun;43(6):637-660

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

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

Spatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases.
Schäbitz A, Hillig C, Mubarak M, Jargosch M, Farnoud A, Scala E, Kurzen N, Pilz AC, Bhalla N, Thomas J, Stahle M, Biedermann T, Schmidt-Weber CB, Theis F, Garzorz-Stark N, Eyerich K, Menden MP, Eyerich S
Nat Commun 2022 Dec;13(1):7729

Polycomb repressive complex 2 shields naïve human pluripotent cells from trophectoderm differentiation.
Kumar B, Navarro C, Winblad N, Schell JP, Zhao C, Weltner J, Baqué-Vidal L, Salazar Mantero A, Petropoulos S, Lanner F, Elsässer SJ
Nat Cell Biol 2022 Jun;24(6):845-857

Elastic dosage compensation by X-chromosome upregulation.
Lentini A, Cheng H, Noble JC, Papanicolaou N, Coucoravas C, Andrews N, Deng Q, Enge M, Reinius B
Nat Commun 2022 Apr;13(1):1854

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

Spidroin N-terminal domain forms amyloid-like fibril based hydrogels and provides a protein immobilization platform.
Arndt T, Jaudzems K, Shilkova O, Francis J, Johansson M, Laity PR, Sahin C, Chatterjee U, Kronqvist N, Barajas-Ledesma E, Kumar R, Chen G, Strömberg R, Abelein A, Langton M, Landreh M, Barth A, Holland C, Johansson J, Rising A
Nat Commun 2022 Aug;13(1):4695

Single-cell RNA-sequencing analysis of the developing mouse inner ear identifies molecular logic of auditory neuron diversification.
Petitpré C, Faure L, Uhl P, Fontanet P, Filova I, Pavlinkova G, Adameyko I, Hadjab S, Lallemend F
Nat Commun 2022 Jul;13(1):3878

Transient expression of an adenine base editor corrects the Hutchinson-Gilford progeria syndrome mutation and improves the skin phenotype in mice.
Whisenant D, Lim K, Revêchon G, Yao H, Bergo MO, Machtel P, Kim JS, Eriksson M
Nat Commun 2022 Jun;13(1):3068

Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility.
Meijer M, Agirre E, Kabbe M, van Tuijn CA, Heskol A, Zheng C, Mendanha Falcão A, Bartosovic M, Kirby L, Calini D, Johnson MR, Corces MR, Montine TJ, Chen X, Chang HY, Malhotra D, Castelo-Branco G
Neuron 2022 Apr;110(7):1193-1210.e13

Transcriptional kinetics and molecular functions of long noncoding RNAs.
Johnsson P, Ziegenhain C, Hartmanis L, Hendriks GJ, Hagemann-Jensen M, Reinius B, Sandberg R
Nat Genet 2022 Mar;54(3):306-317

Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.
Ratz M, von Berlin L, Larsson L, Martin M, Westholm JO, La Manno G, Lundeberg J, Frisén J
Nat Neurosci 2022 Mar;25(3):285-294

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 RA, Luo X, Monasterio G, Engblom C, Gagliani N, Saez-Rodriguez J, Lundeberg J, Villablanca EJ
Nat Commun 2022 Feb;13(1):828