Stem-cell niche articles within Nature Communications

Featured

• Article
  30 January 2026 | Open Access

  Ectopic cambia in wisteria vines are associated with the expression of conserved KNOX genes

  Here, using anatomy, transcriptomics, and functional assays, the authors reveal how Japanese wisteria climb using an unusual vascular architecture. Ectopic cambia arise from cortical cells and repurpose conserved cambium regulators, including KNOX genes.

  • Israel L. Cunha-Neto
  • , Anthony A. Snead
  •  & Joyce G. Onyenedum

• Article
  30 January 2026 | Open Access

  Mosaic partial epidermal reprogramming remodels neighbors and niches to refine skin homeostasis and repair

  Here, the authors show that transient, mosaic induction of Yamanaka factors in the epidermis can promote skin repair beyond reprogramming cells. They also influence neighboring epithelial cells and immune–mesenchymal niches by reshaping injury response programs.

  • Minjun Kwak
  • , Eunjun Choi
  •  & Sekyu Choi

• Article
  28 January 2026 | Open Access

  Impaired stem cell migration and divisions in Duchenne muscular dystrophy revealed by live imaging

  Using live-imaging in vivo and ex vivo, Sarde et al. show that dystrophic muscle stem cells have precocious differentiation through symmetric divisions and impaired migration, with differential impact of the myofibre niche upon cross-transplantation.

  • Liza Sarde
  • , Gaëlle Letort
  •  & Brendan Evano

• Article
  23 January 2026 | Open Access

  Endothelial stem cells of the retinal vasculature reside in the optic nerve

  This study finds stem-like endothelial cells in the optic nerve that supply and repair retinal blood vessels after injury, revealing a hierarchical repair system that may enable new treatments for blinding vascular eye diseases.

  • Susumu Sakimoto
  • , Toru Takigawa
  •  & Kohji Nishida

• Article
  28 November 2025 | Open Access

  A niche-dependent redox rheostat regulates epithelial stem cell fate

  Intracellular redox state orchestrates a self-reinforcing circuit connecting hypoxia inducible factor 1α-dependent signalling with post-translational regulation of the metabolic enzyme isocitrate dehydrogenase 1 to govern intestinal stem cell fate.

  • Xi Chen
  • , Krishnan Raghunathan
  •  & Jay R. Thiagarajah

• Article
  27 November 2025 | Open Access

  Autocrine ECM molecules establish MSC quiescence during incisor development by disrupting WNT ligand trafficking process

  This study identifies Smoc2 as a marker of mesenchymal stem cells in mouse incisors and shows that Smoc1/2 establishes stem cell quiescence by inhibiting Wnt signaling during development.

  • Zexi Chen
  • , Meilian Cai
  •  & Hu Zhao

• Article
  27 November 2025 | Open Access

  Lifting regenerative barriers promotes epithelial cell fate plasticity supporting lineage conversion

  This study established the HIF1a–SOX9 axis as a key regulatory barrier that limits epithelial cell fate plasticity, safeguarding against premature responses to incomplete or inadequate instructive cues during tissue repair.

  • Maria T. Bejar
  • , Paula Jimenez-Gomez
  •  & Maria P. Alcolea

• Article
  23 November 2025 | Open Access

  Disruption of Krox20-Notch1 signaling blocks meibomian gland development and homeostasis leading to dry eye disease

  Here they show that KROX20 marks a stem cell pool in the eyelid’s Meibomian glands whose development and homeostasis is regulated via Notch pathway signaling, thus offering a potential therapeutic target for dry eye disease.

  • Yumeng Zhang
  • , Edem Tchegnon
  •  & Lu Q. Le

• Article
  21 November 2025 | Open Access

  Epithelial-mesenchymal cell competition coordinates fate transitions across tissue compartments during lung development and fibrosis

  The authors discover a tissue-scale fitness sensing mechanism in the lung, where mesenchymal Yap antagonizes epithelial Yap to dictate epithelial cell fate. This inter-tissue cell competition orchestrates lung architecture and lung disease.

  • Kylie Klinkhammer
  • , Rachel Warren
  •  & Stijn P. De Langhe

• Article
  21 November 2025 | Open Access

  TGFβ-Smad3 signaling restores cell-autonomous Srsf1-mediated splicing of fibronectin in aged skeletal muscle stem cells

  Aging impairs the regenerative capacity of skeletal muscle stem cells. Here, the authors identify a stem cell-specific fibronectin splice variant and show that its cell-autonomous secretion through the TGFβ1-Smad3-Srsf1 pathway can be targeted to restore tissue repair in aged mice

  • Yuguo Liu
  • , Svenja C. Schüler
  •  & C. Florian Bentzinger

• Article
  21 November 2025 | Open Access

  Tripotent Lgr5 stem cells in the posterior tongue generate lingual, taste, and salivary gland lineages

  Here, the authors show that a single Lgr5 stem cell population in the posterior tongue produces taste buds, salivary glands, and epithelium, representing unified chemosensory units.

  • Laurens H. G. Verweij
  • , Seok-Young Kim
  •  & Hans Clevers

• Article
  19 November 2025 | Open Access

  Mesenchymal-to-epithelial transition of perivascular cells contributes to endometrial re-epithelialization

  Uterine perivascular cells were identified as progenitors for endometrial re-epithelialization via mesenchymal-to-epithelial transition, whereby cellular quiescence and activation were mediated via Notch signaling and estrogen, respectively.

  • Shu-Yun Li
  • , Sarah Whiteside
  •  & Tony DeFalco

• Article
  18 November 2025 | Open Access

  Inflammatory stromal and T cells mediate human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasia

  Clonal haematopoiesis of indeterminate potential is driven by somatic mutations in hematopoietic stem/progenitor cells and may progress to myelodysplastic syndromes (MDS). Here authors show that the two conditions share a similar pattern of bone marrow remodeling, characterized by the emergence of inflammatory mesenchymal stromal cells and IFN-responsive T cells, reinforcing their shared etio-pathology.

  • Karin D. Prummel
  • , Kevin Woods
  •  & Borhane Guezguez

• Article
  29 September 2025 | Open Access

  Contractile fibroblasts form a transient niche for the branching mammary epithelium

  Fibroblasts represent a heterogenous cell population but how their differences reflect their plasticity and origin is not fully understood. Here, the authors map the origin and fate of a transient contractile fibroblast population that forms a niche supporting pubertal mammary gland branching and growth.

  • Jakub Sumbal
  • , Robin P. Journot
  •  & Silvia Fre

• Article
  23 July 2025 | Open Access

  Dissecting the enhancer gene regulatory network in early Drosophila spermatogenesis

  Single-cell multi-omics in Drosophila testis reveals enhancer-driven gene regulatory networks and shows how Wnt signaling and key transcription factors orchestrate stem cell maintenance and lineage progression during early spermatogenesis.

  • Patrick van Nierop y Sanchez
  • , Pallavi Santhi Sekhar
  •  & Ingrid Lohmann

• Article
  01 July 2025 | Open Access

  Lipoic acid functions in Paneth cells to prevent human intestinal stem cell aging

  This study reveals that α-lipoic acid (ALA) is reduced in aged mouse and human intestine and ALA supplementation reduces aging hallmarks. Paneth cells play a role in the effects of ALA.

  • Zehong Zhang
  • , Qianyi Wan
  •  & Haiyang Chen

• Article
  03 June 2025 | Open Access

  Serotonergic neurons regulate the Drosophila vascular niche to control immune stress hematopoiesis

  While it is known that nerves are present in the hematopoietic niche, less is known about how they influence hematopoiesis. Here they show that serotonin signaling between the nervous system and vascular niche cells regulates Drosophila lymph gland stress hematopoiesis.

  • Xiaohui Liu
  • , Marianne Montemurro
  •  & Michèle Crozatier

• Article
  30 May 2025 | Open Access

  Human endothelial cells promote a human neural stem cell type B phenotype via Notch signaling

  Brain neural stem cell (NSC) and vessel-forming endothelial cell (EC) communication is vital. Here, the authors find that human ECs boost human adult NSCs (type B cells) via Notch, show EC-type B interaction in human brain, and identify human type B markers.

  • Brenda Gutierrez
  • , Tzu Chia Liu
  •  & Lisa A. Flanagan

• Article
  14 May 2025 | Open Access

  Embryonic macrophages orchestrate niche cell homeostasis for the establishment of the definitive hematopoietic stem cell pool

  Haematopoietic stem cells (HSC) are responsible for blood cell generation and reside in the bone marrow. Here, the authors show that macrophages in the bone marrow originate from embryonic or adult haematopoietic lineages and that embryo-derived macrophages are important for the establishment of the HSC pool.

  • Gülce Perçin
  • , Konstantin Riege
  •  & Claudia Waskow

• Article
  05 April 2025 | Open Access

  Colonic epithelial-derived FGF1 drives intestinal stem cell commitment toward goblet cells to suppress inflammatory bowel disease

  It is unclear which intestinal epithelial cell-derived cytokines can precisely regulate intestinal stem cell (ISC) commitment toward specific mature cells. Here, authors identify an epithelial-derived FGF1 driving ISC toward goblet cells.

  • Qian Lin
  • , Sudan Zhang
  •  & Jianlou Niu

• Article
  16 March 2025 | Open Access

  Drosophila ovarian stem cell niche ageing involves coordinated changes in transcription and alternative splicing

  Ageing is associated with alterations in gene expression and alternative splicing. Here, the authors show that ageing of the Drosophila ovarian stem cell niche involves coordinated changes in both expression and splicing, with distinct niche cells exhibiting specific ageing signatures.

  • Dilamm Even-Ros
  • , Judit Huertas-Romero
  •  & Acaimo González-Reyes

• Article
  21 February 2025 | Open Access

  Heparan sulfate regulates myofibroblast heterogeneity and function to mediate niche homeostasis during alveolar morphogenesis

  The alveoli of the lung are formed through the coordination of multiple cell types to yield a large surface area for gas exchange. Here they show that heparan sulfate plays essential roles in lung myofibroblasts to maintain MAPK signaling and the alveolar niche.

  • Hua He
  • , Chong Ma
  •  & Xinhua Lin

• Article
  03 February 2025 | Open Access

  Skeletal muscle stem cells modulate niche function in Duchenne muscular dystrophy mouse through YY1-CCL5 axis

  Li et al. demonstrate the critical role of skeletal muscle stem cells (MuSCs) in actively shaping their niche in dystrophic muscle through YY1-CCL5-CCR5 axis mediated cellular interaction with macrophages.

  • Yang Li
  • , Chuhan Li
  •  & Huating Wang

• Article
  06 January 2025 | Open Access

  Steroid hormone-induced wingless ligands tune female intestinal size in Drosophila

  Pregnancy induces a significant increase of intestinal epithelium to cope with metabolic demands. Here, Zipper et al. use Drosophila to show that the conserved Crooked legs/ZNF267 transcription factor relays steroidhormonal induction of Wnt-ligands to promote stem cell proliferation.

  • Lisa Zipper
  • , Bernat Corominas-Murtra
  •  & Tobias Reiff

• Article
  03 January 2025 | Open Access

  Long-range organization of intestinal 2D-crypts using exogenous Wnt3a micropatterning

  Through micropatterning of a soft basement membrane to control Wnt3a protein distribution, the authors demonstrate how the size, shape, and spatial arrangement of intestinal epithelial crypts can be precisely regulated, offering insights into tissue organization mechanisms.

  • Enara Larrañaga
  • , Miquel Marin-Riera
  •  & Elena Martinez

• Article
  31 August 2024 | Open Access

  Specific 3-O-sulfated heparan sulfate domains regulate salivary gland basement membrane metabolism and epithelial differentiation

  The use of heparan sulfate mimetics is an attractive target for organ regeneration. Here, the authors identify how highly 3-O-sulfated heparan sulfate domains regulate FGFR signaling and basement membrane metabolism to control epithelial differentiation.

  • Vaishali N. Patel
  • , Marit H. Aure
  •  & Matthew P. Hoffman

• Article
  22 April 2024 | Open Access

  LSD1 drives intestinal epithelial maturation and controls small intestinal immune cell composition independent of microbiota in a murine model

  Post birth the gastrointestinal tract undergoes development including the establishment of the microbiome, establishment of tolerance and maturation of the epithelium. Here the authors show a histone demethylase LSD1 is required for postnatal intestinal epithelium maturation and how this impacts local immune cell composition and gut homeostasis.

  • Alberto Díez-Sánchez
  • , Håvard T. Lindholm
  •  & Menno J. Oudhoff

• Article
  09 April 2024 | Open Access

  Decoding spatiotemporal transcriptional dynamics and epithelial fibroblast crosstalk during gastroesophageal junction development through single cell analysis

  Elucidating the gastroesophageal junction’s development is key to comprehending its disease susceptibility. Here, the authors mapped its development, uncovering cellular diversity and interaction dynamics using advanced spatiotemporal single-cell analysis.

  • Naveen Kumar
  • , Pon Ganish Prakash
  •  & Cindrilla Chumduri

• Article
  15 February 2024 | Open Access

  Neurofibromin 1 controls metabolic balance and Notch-dependent quiescence of murine juvenile myogenic progenitors

  The establishment of the postnatal skeletal muscle stem cell pool is not well understood. Here the authors show a requirement for Nf1 to coordinate muscle fiber growth and stem cell quiescence induction, and to prevent detrimental metabolic reprogramming with life-long consequences.

  • Xiaoyan Wei
  • , Angelos Rigopoulos
  •  & Sigmar Stricker

• Article
  07 February 2024 | Open Access

  Diffusible fraction of niche BMP ligand safeguards stem-cell differentiation

  The activity of Drosophila male germline stem cells is tightly regulated by a cluster of somatic niche cells. Here they find that Dpp induces opposed cellular responses in stem cells versus in differentiating descendants, thereby ensuring spatial control of the niche with a single factor.

  • Sharif M. Ridwan
  • , Autumn Twillie
  •  & Mayu Inaba

• Article
  02 January 2024 | Open Access

  Mcam inhibits macrophage-mediated development of mammary gland through non-canonical Wnt signaling

  Mammary epithelial cells act to continuously renew the mammary tissue and must balance differentiation and self-renewal. Here they show that Mcam, a non-canonical Wnt pathway member, regulates communication between macrophages and mammary epithelial cells, thereby maintaining self-renewal and subsequently promoting mammary ductal morphogenesis.

  • Xing Yang
  • , Haibo Xu
  •  & Baowei Jiao

• Article
  19 December 2023 | Open Access

  Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration

  Alveolar epithelial progenitors in the lungs can regenerate the epithelial surface after acute injury. Here they generate lung organoids that can be used to study lung regeneration after injury and identify Nkx2-1 as a key regulator of alveolar progenitor activation.

  • Andrea Toth
  • , Paranthaman Kannan
  •  & William J. Zacharias

• Article
  02 December 2023 | Open Access

  Role of PDGFRA⁺ cells and a CD55⁺ PDGFRA^Lo fraction in the gastric mesenchymal niche

  Digestive epithelia self-renew or differentiate in response to mesenchymal cues. Manieri et al. characterize gastric corpus and antral mesenchyme separately and identify PDGFRA^Lo CD55⁺ cells as those selectively supporting epithelial growth in vitro.

  • Elisa Manieri
  • , Guodong Tie
  •  & Ramesh A. Shivdasani

• Article
  20 November 2023 | Open Access

  Apoptotic dysregulation mediates stem cell competition and tissue regeneration

  The authors show that depletion of pro-apoptotic Bax protein bestows hair follicle stem cells with the capacity to eliminate viable neighboring cells by sequestration of TNFα, resulting in an increased stem cell pool, accelerated wound repair and de novo hair follicle regeneration.

  • Marianna Yusupova
  • , Roi Ankawa
  •  & Yaron Fuchs

• Article
  07 November 2023 | Open Access

  Proenkephalin-A secreted by renal proximal tubules functions as a brake in kidney regeneration

  The coordination of pro- and anti-regenerative factors is essential for organ regeneration. The authors show here that proenkephalin-A, secreted by proximal renal tubules in zebrafish, negatively regulates hydrogen peroxide production remodelling H3K4me3 in renal progenitor cells and controlling kidney regeneration strength.

  • Chi Liu
  • , Xiaoliang Liu
  •  & Jinghong Zhao

• Article
  25 October 2023 | Open Access

  Ebf3⁺ niche-derived CXCL12 is required for the localization and maintenance of hematopoietic stem cells

  CAR cells act as HSC niche cells. Here the authors show that CXCL12 ablation in half CAR cells attracts HSCs from affected CAR cells to intact CAR cells whereas CXCL12 ablation in all CAR cells depletes balanced HSCs producing B cells at high levels.

  • Taichi Nakatani
  • , Tatsuki Sugiyama
  •  & Takashi Nagasawa

• Article
  14 October 2023 | Open Access

  FGFR2 is essential for salivary gland duct homeostasis and MAPK-dependent seromucous acinar cell differentiation

  Restoring salivary acinar cells after gland damage is a major clinical challenge. Here, authors identify FGF7-FGFR2-MAPK signaling as a regenerative target, critical for myoepithelial-acinar crosstalk that regulates seromucous acinar differentiation.

  • Marit H. Aure
  • , Jennifer M. Symonds
  •  & Matthew P. Hoffman

• Article
  28 September 2023 | Open Access

  Perivascular niche cells sense thrombocytopenia and activate hematopoietic stem cells in an IL-1 dependent manner

  Hematopoietic stem cells (HSCs) replenish blood cells. Here, Luis et al., identify a feedback mechanism by which IL-1 secreted by activated platelets signals through niche Lepr+ cells to activate HSCs and restore platelet homeostasis.

  • Tiago C. Luis
  • , Nikolaos Barkas
  •  & Sten Eirik W. Jacobsen

• Article
  10 August 2023 | Open Access

  Hdac1 and Hdac2 regulate the quiescent state and survival of hair-follicle mesenchymal niche

  Cell division and stem cell maintenance are tightly linked. Here they show that in the hair follicle an epigenetic mechanism maintains mesenchymal niche dormancy in a highly proliferative microenvironment while repurposing mitogenic signaling to orchestrate the hair cycle clock.

  • Hadas Sibony-Benyamini
  • , Emil Aamar
  •  & David Enshell-Seijffers

• Article
  10 August 2023 | Open Access

  Single-cell analysis of lizard blastema fibroblasts reveals phagocyte-dependent activation of Hedgehog-responsive chondrogenesis

  Lizards are the closest known relatives of mammals capable of epimorphic tail regrowth. Here, single-cell analysis of regenerating lizard tails reveals a phagocyte-induced fibroblast population contributing to blastema formation and chondrogenesis.

  • Ariel C. Vonk
  • , Xiaofan Zhao
  •  & Thomas P. Lozito

• Article
  04 August 2023 | Open Access

  Cyclical dermal micro-niche switching governs the morphological infradian rhythm of mouse zigzag hair

  Biological rhythms influence physiology and morphogenesis, though how these influence periodic pattern formation remains unclear. Here the authors show that the infradian rhythm observed in zigzag hairs is regulated by hair progenitors and their micro-niche and influences hair shaft bending.

  • Makoto Takeo
  • , Koh-ei Toyoshima
  •  & Takashi Tsuji

• Article
  29 June 2023 | Open Access

  Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis

  Gastric progenitor cells are essential for tissue homeostasis of the stomach. Here, using single-cell RNA sequencing and gastric organoid experiments, the authors demonstrate that EGFR signaling promotes gastric progenitor cell differentiation.

  • Hitomi Takada
  • , Yohei Sasagawa
  •  & Akira Kurisaki

• Article
  24 June 2023 | Open Access

  Hedgehog signaling via its ligand DHH acts as cell fate determinant during skeletal muscle regeneration

  Successful skeletal muscle regeneration relies on the interplay of multiple cell populations. Here, the authors describe how ciliary Hedgehog signaling coordinates the intercellular crosstalk required to balance wound healing and fatty fibrosis.

  • Alessandra M. Norris
  • , Ambili Bai Appu
  •  & Daniel Kopinke

• Article
  17 May 2023 | Open Access

  Higher-order epistasis shapes natural variation in germ stem cell niche activity

  Stem cell niches regulate proliferation of stem cells, but variation in this control across natural populations has not been explored. Here they combine quantitative genetics and gene editing to show that natural variation in C. elegans germ stem cell niche activity is shaped by complex gene-gene interactions.

  • Sarah R. Fausett
  • , Asma Sandjak
  •  & Christian Braendle

• Article
  17 May 2023 | Open Access

  Cellular population dynamics shape the route to human pluripotency

  The contribution of cell-extrinsic factors during cellular reprogramming to human induced pluripotent stem cells has long been overlooked. Here, the authors show functional protein communication between reprogramming intermediates and the re-shaping of a permissive extracellular environment.

  • Francesco Panariello
  • , Onelia Gagliano
  •  & Nicola Elvassore

• Article
  14 February 2023 | Open Access

  A single-cell transcriptional atlas reveals resident progenitor cell niche functions in TMJ disc development and injury

  The transcriptional network in TMJ disc development and injury remains poorly characterized. Here they generate a scRNA-seq atlas of mouse TMJ disc, and identify the resident progenitor population and how its transcriptional reprogramming contributes to disc repair.

  • Ruiye Bi
  • , Qing Yin
  •  & Songsong Zhu

• Article
  30 January 2023 | Open Access

  Epigenetic control of cellular crosstalk defines gastrointestinal organ fate and function

  Mesenchymal-epithelial crosstalk plays a key role in gut development and stem cell homeostasis, though underlying mechanisms are still unclear. Here, the authors demonstrate that mesenchymal Polycomb Repressive Complex 2 controls niche signals for gut epithelial fate and growth.

  • Ryan J. Smith
  • , Minggao Liang
  •  & Tae-Hee Kim

• Article
  24 November 2022 | Open Access

  Integration of single-cell transcriptomes and biological function reveals distinct behavioral patterns in bone marrow endothelium

  Here Kim et al. show that primary BMECs can be maintained ex vivo as distinct sinusoidal- and arterial-like populations and that the presence of macrophages is critical to preserve their native transcriptomic profiles and functional heterogeneity.

  • Young-Woong Kim
  • , Greta Zara
  •  & Nadia Carlesso

• Article
  26 October 2022 | Open Access

  Eya-controlled affinity between cell lineages drives tissue self-organization during Drosophila oogenesis

  Oogenesis depends on close interaction between germ cells and the surrounding somatic niche. Here the authors demonstrate that Eya controls bilateral affinity at the germline-soma interface to generate self-organizing inter-lineage units that ensure oocyte maturation.

  • Vanessa Weichselberger
  • , Patrick Dondl
  •  & Anne-Kathrin Classen

• Article
  15 September 2022 | Open Access

  Murine fetal bone marrow does not support functional hematopoietic stem and progenitor cells until birth

  Relatively little is known about the first hematopoietic stem and progenitor cells to arrive in the fetal bone marrow. Here they characterize the frequency, function, and molecular identity of fetal BM HSPCs and their bone marrow niche, and show that most BM HSPCs have little hematopoietic function until birth.

  • Trent D. Hall
  • , Hyunjin Kim
  •  & Shannon McKinney-Freeman