Stem Cell Reports

Human pluripotent stem cells (hPSCs) are increasingly expanded in 3D suspension culture to support scalable cell culturing, yet how the transition from 2D to 3D cultures affects hPSCs remains poorly understood. Here, we compare hPSCs in 2D and 3D cultures using transcriptomics, proteomics, spent medium analysis, and stable-isotope tracing. hPSCs maintained pluripotency in both formats, although suspension culture showed altered growth dynamics and increased initial cell loss. Multi-omics analysis identified culture format as the dominant driver of molecular variation and revealed changes in adhesion, cytoskeletal organization, glycolysis, and oxidative phosphorylation. Functional analyses showed increased lactate production from glucose and stable-isotope tracing revealed increased glucose-derived pyruvate formation and altered partitioning of glucose-derived carbon within the TCA cycle in 3D suspension cultures. Glutamine contribution to the TCA cycle was reduced, whereas relative reductive carboxylation was increased in 3D suspension cultures. Together, these findings show that transition from 2D to 3D suspension culture induces metabolic rewiring in hPSCs.

Midbrain dopaminergic (mDA) neurons comprise molecularly and functionally distinct subtypes with differential vulnerability in neurodegenerative and psychiatric disorders. However, the mechanisms specifying subtype identity remain poorly understood, and protocols for the selective derivation of human mDA subtypes are lacking. Here we establish a strategy to derive substantia nigra (A9) and ventral tegmental area (A10) mDA neurons from human pluripotent stem cells (hPSCs). A9 identity is specified by dual-SMAD activation through Activin A and BMP7 at the midbrain floor-plate progenitor stage, whereas A10 identity is promoted by BMP inhibition. A9 mDA neurons are purified based on ALDH1A1 expression, and subtype identity is maintained by continued TGF-{beta} modulation and ESRRB activation in vitro and upon transplantation in vivo. Single-cell RNA sequencing and biochemical analyses demonstrate that hPSC-derived A9 neurons exhibit increased oxidative phosphorylation, neuromelanin-like pigmentation, elevated dopamine synthesis and release, and electrophysiological properties characteristic of A9 mDA neurons in vivo. Integration with human fetal midbrain datasets confirms strong transcriptional concordance between in vitro-derived and in vivo mDA subtypes. Neuromelanin-like structures produced by hPSC-derived A9 neurons trigger pro-inflammatory cytokine secretion from hPSC-derived microglia, and A9 neurons are primed to upregulate MHC-I genes in response to interferon-{gamma}, features which may contribute to the selective vulnerability of A9 neurons. Together, these results establish a robust in vitro platform to interrogate human mDA subtype development, function, and selective vulnerability, enabling mechanistic studies relevant to Parkinson's disease and the development of cell-based therapies.

Neuronal loss resulting from brain injury and neurodegenerative diseases currently lacks effective regenerative therapies. While neurogenic compounds and cell transplantation hold promise, clinical translation is hindered by poor graft integration and limited cell survival. Here, we developed a novel organoid-to-organoid transplantation model using human pluripotent stem cell-derived cortical organoids (hCOs) to evaluate a dual cell transplantation and pro-neurogenic strategy for brain repair. We demonstrate that pro-neurogenic treatment with ER272 stimulates early-stage hCO growth and enhances neurogenesis through a PKC- and Notch-dependent pathway. Mechanistically, ER272 upregulates genes associated with extracellular matrix, cell adhesion and growth factor signaling. Notably, combining early-stage hCO transplantation with ER272 treatment significantly enhanced graft integration and improved neuronal repair in an ischemic-like model of late-stage host hCOs. This novel human organoid-to-organoid platform offers a robust translational tool to test regenerative therapies and highlight the potential of combining cell transplantation with pro-neurogenic stimulation for the treatment of neurological conditions associated with neuronal loss.

Achieving near-single-cell precision in the prospective identification of long-term engrafting hematopoietic stem cells (LT-HSCs) remains challenging, likely because current static, point-in-time single-cell phenotyping technologies do not capture the dynamic nature of cell fate decisions. Here, we overcome this barrier by longitudinally tracking individual hematopoietic stem and progenitor cells (HSPCs) in ex vivo niche cultures using live imaging, coupled with downstream immunophenotyping, single-cell transcriptomics, and transplant assays. Deep learning analysis of live imaging data achieved 98.5% average precision in predicting serially-engrafting LT-HSC (serial-LT-HSC) identity from the behaviorome (the totality of observed behaviors) of each cell, outperforming currently available technologies. Serial-LT-HSCs exhibited lower motility among HSPC populations, which was associated with reduced Activin signaling activity and elevated expression of cell adhesion genes. Correspondingly, antagonizing Activin signaling by Inhibin-A treatment in ex vivo niche cultures suppressed HSPC motility while increasing the frequency of post-expansion serial-LT-HSCs, revealing a novel role for Activin signaling in HSPC behavior and fate determination. Collectively, this study establishes a broadly applicable framework that connects behavioromic analysis and single-cell transcriptomics to enable near-single-cell precision in predicting stem cell fate and uncover molecular mechanisms governing behavior-fate relationships.

Stem cell-derived (SC) islets hold promise as a transformative therapy for type 1 diabetes (T1D). To enhance graft uniformity, SC-islet organoids are often dissociated and reaggregated into standardized sizes. However, how endocrine cell composition varies with islet size in native human islets remains largely unknown. Defining this relationship is essential for establishing physiological benchmarks for islet engineering for transplantation. In this study, we examined the relationships among islet size, endocrine cell composition, and spatial distribution throughout whole pancreata from 10 age-matched, non-diabetic male subjects. Insulin-, glucagon-, and somatostatin-positive endocrine cells were identified as single-, double-, and triple-hormone populations ranging from non-islet single endocrine cells and small clusters (niSSCs) to large islets. Approximately 80% of the total endocrine area was contained in islets positive for all three hormones. Islet size strongly correlated with endocrine composition. Specifically, larger islets had increased alpha-cell fractions and reduced beta-cell fractions, while delta-cell fractions were consistent across sizes. Spatial analysis revealed that niSSCs, mono-, and tri-hormone islets frequently exhibit a clustered distribution. Additionally, tri-hormone islets were positioned near the core of the pancreas, whereas mono-somatostatin islets were often localized in the periphery. These findings were consistent across all three pancreatic regions (head, body and tail).

Retinal organoids (ROs) model human retinogenesis but remain avascular and lack immune components, limiting their utility for studying vascular retinopathies. We generated vascular organoids (VOrs) from human pluripotent stem cells and evaluated their integration into developing ROs. Dissociated VOr cells (day 12 or day 30) were seeded onto 2D retinal neuroepithelium before 3D transition, followed by long-term culture to day 210. VOr derived cells migrated into ROs and transiently persisted. V30 ROs preserved retinal lamination, major neuronal subtypes and light evoked retinal ganglion cell responses comparable to non vascularised controls, whereas media-only ROs cultured in proangiogenic conditions showed structural disorganisation and reduced neuronal survival. Single-cell RNA sequencing revealed an endogenous, inflammatory endothelial-like population with partial endothelial-to-mesenchymal features and a perivascular fibroblast-like cluster in pro-angiogenic media only RO controls. The endothelial-like cell cluster was significantly enriched for genes upregulated in human retinal endothelial cells exposed to high glucose, indicating a diabetic retinopathy like transcriptional state. Microglia like and border associated macrophage populations were present across all conditions, with developmental shifts in morphology and marker expression. Our findings define conditions under which vascular cells can be incorporated into human ROs without disrupting retinal architecture, while uncovering an intrinsic capacity for inflammatory endothelial activation that partially recapitulates diabetic retinopathy. This work advances the engineering of vascularised, immunocompetent retinal models and highlights endogenous vascular immune programmes that must be considered when modelling retinal disease in vitro.

Microglia, the immune cells of the brain parenchyma, play a pivotal role in neurodevelopment and neuroprotection. Human stem cell-derived microglia-like cells (MGL) offer a valuable, human-relevant system to study microglia in vitro. However, their cell states and intercellular interactions within complex 3-dimensional (3D) tissue contexts in vitro remain underexplored. Here, we analyze the gene expression profiles of MGL generated by two differentiation protocols in conventional 2D cultures. We show that co-culture with neural organoids promotes a more mature, in vivo-like MGL phenotype but this signature is lost during long-term co-culture. By varying media compositions, we modulate 2D MGL states toward more active or more homeostatic identities, which may enhance the similarity to primary microglia identities upon subsequent co-culture. Moreover, forced expression of the microglial lineage regulator SALL1 shifts MGL away from a general myeloid state toward a more defined pre-microglial fate. SALL1 overexpression within a 3D neural organoid environment further amplifies the shift toward a homeostatic developmental microglia population. Collectively, our transcriptomic analysis delineates human MGL states in 2D and 3D contexts, refines existing differentiation protocols toward more authentic MGL, and establishes a framework to investigate the intricate microglia-neural tissue interplay.

Glutathione is a redox buffer, best known for preventing oxidative stress and ferroptosis, but rarely studied in stem cells. We studied glutathione function in hematopoietic stem cells (HSCs) by deleting the glutamate-cysteine ligase catalytic subunit (GCLC), which synthesizes glutathione, or glutathione peroxidase 4 (GPX4), which employs glutathione to prevent ferroptosis. GCLC deficiency eliminated glutathione from hematopoietic cells, severely impairing HSC function and hematopoiesis. In contrast, GPX4 deficiency did not affect HSC function and had little effect on hematopoiesis, even after vitamin E depletion, suggesting glutathione has ferroptosis-independent functions in HSCs. Consistent with this, GCLC deficiency increased reactive oxygen species levels in hematopoietic cells. But treatment with antioxidants or ferroptosis inhibitors gave little or no rescue of HSC function despite reducing ROS levels. Rather, GCLC-deficient, but not GPX4-deficient, HSCs exhibited unfolded protein accumulation, proteostatic stress, and cell death marked by elevated p53 levels and Annexin V staining. Deficiency for p53 prolonged the function of GCLC-deficient HSCs after transplantation. Glutathione is thus necessary in HSCs for proteostasis but may be dispensable for ferroptosis inhibition in vivo.

In silico perturbation (ISP) enables virtual genetic screens, prioritizing candidate regulators before costly wet-lab experiments. However, applying foundation models requires programming expertise. Here, we present the ISP Platform, that automates ISP powered by Geneformer without code execution. The platform enables cross-species analyses by independently selecting input species and human or mouse Geneformer models. The platform also implements sequential multi-gene ISP, in which each perturbation chains from the cell state produced by the preceding step. Using induced pluripotent stem cell (iPSC) datasets, the platform successfully performed cross-species analysis of human and mouse single cell-RNA (scRNA)-seq data. Screening all 24 permutations of the Yamanaka factors identified an optimal overexpression sequence that produced the highest shift toward the pluripotent state. Genome-wide knockdown screens prioritized key pluripotency regulators but revealed an asymmetric cross-species concordance. The human model effectively captured mouse pluripotency programs, whereas applying the mouse model to human cells yielded predominantly translation-related terms. Furthermore, a targeted pairwise overexpression screen nominated candidate modulators of the primed-to-naive transition beyond the conventional NANOG and KLF2 benchmark. Together, the ISP Platform provides a unified, accessible framework for three dimensions of in silico perturbation (cross-species, sequential, and multi-gene) to guide focused experimental validation and reduce exploratory animal use.

During embryogenesis, the cortical and medullary compartments of the adrenal gland emerge from two distinct sources: intermediate mesoderm-derived steroidogenic progenitors that comprise the cortex, and migratory neural crest-derived catecholaminergic progenitors that give rise to the medulla. The distinct cellular origins and paracrine signaling environments that foster induction, differentiation, and/or migration of cortical and medullary layers present challenges to recapitulating their co-emergence and incorporation in a human pluripotent stem cell (hPSC) based system. To address this, we developed an approach for modeling the adreno-gonadal primordium (AGP) in compound organoids that are organized along a gradient of NR5A1 expression and which unexpectedly incorporate SOX10-expressing Schwann cell precursors that ultimately generate chromaffin cells. Deconstruction of paracrine signaling within AGP-like organoids (AGPLOs) identified a fibroblast growth factor 9 (FGF9)-driven mechanism that expands bridge cell-like chromaffin progenitors and correlates to paracrine signaling cues encountered by physiological correlates along their migration corridor to the cortex in vivo. Combination of NR5A1-expressing cells with chromaffin cell clusters generated corticomedullar-like assembloids (CMLAs) that generated steroids and catecholamines and were responsive to adrenocorticotropic hormone. This work establishes a platform for modeling the reciprocal signaling relationships that drive adrenal gland development and function in health and disease and provides an approach for generating hPSC-derived adrenal cells/tissues that can be applied therapeutically.

Lack of robustness and high variability in cardiomyocyte (CM) differentiation from human induced pluripotent stem cells (hiPSCs) remain critical challenges for cardiac regenerative medicine and biological research. Guided by developmental principles of lineage specification, we investigated whether early WNT inhibition could expand the process window of CM differentiation and thereby improve robustness. To test this, we compared early WNT inhibition from days 1--5 with standard inhibition from days 3--5 following a 1-day CHIR99021 (CHIR) treatment for WNT activation. Focusing on CHIR concentration as a critical parameter, we found that early WNT inhibition substantially broadened the concentration window yielding [≥]80% differentiation efficiency across distinct hiPSC lines. Extending the analysis to a two-dimensional parameter space incorporating cell density revealed a markedly expanded [≥]80% process window. Temporal analysis of lineage-specific transcription factor expression showed that early WNT inhibition suppressed paraxial mesoderm (PM) specification, likely through MSGN1 suppression, in the range of high initial WNT activation that otherwise favored PM fate, thereby extending the process window. It also suppressed definitive endoderm (DE) specification within the expanded window, promoting a more favorable lateral plate mesoderm/cardiac fate. We further demonstrated substantially reduced variability under parameter perturbations and across wells and batches, accompanied by higher differentiation efficiency, without compromising CM phenotypes. These findings demonstrate early WNT inhibition as an effective strategy for expanding the process window of CM differentiation and improving robustness, while exemplifying the process engineering principle that a broader window can support more robust differentiation, with potential relevance to stem cell--based bioprocesses.

Transplantation is limited by how long organs survive outside the body. Existing preservation methods slow metabolism or sustain physiological support, but neither eliminates ischemia-reperfusion injury (IRI), which shortens storage and drives organ discard. Embryonic diapause and hibernation show that mammalian cells retain a latent capacity for reversible metabolic arrest. Screening the PI3K-mTOR axis, we identified a dual inhibitor that pauses embryonic stem cells reversibly at ambient oxygen and holds intact mouse embryos in arrest for 11 days. Combined with a mitochondria-targeted hydrogen sulfide donor, this yields TorPause: a two-component flush pairing metabolic pausing with mitochondrial protection, compatible with existing preservation protocols. In a rat liver transplantation model, TorPause reduced structural injury and improved recipient survival after severe warm ischemic storage, potentially expanding the usable donor pool.

Leukodystrophies (LKD) comprise mostly inherited white matter disorders whose developmental origins and underlying pathomechanisms remain poorly understood. Progress has been limited by restricted access to human primary tissue and by the inability of animal models to fully recapitulate human neurodevelopment. Human induced pluripotent stem cell-derived neural organoids provide an alternative approach, but most culture systems do not capture later, glia-rich developmental stages relevant to these diseases. Recent studies have shown that appropriate patterning cues and long in vitro differentiation can generate neuroglial spheroids comprising multiple neuronal and macroglial populations, including mature oligodendrocytes. Here, we adapt the human oligodendrocyte (hOLS) spheroid platform to establish 3D models of globoid cell leukodystrophy (GLD), 4H leukodystrophy (4H), and Canavan disease (CD). Here we adapt this organoid platform to establish 3D models of globoid cell leukodystrophy (GLD), 4H leukodystrophy (4H), and Canavan disease (CD). Across 150 days of differentiation, hOLS from different genetic backgrounds displayed largely comparable growth kinetics and developmental trajectories, comprising multiple neuroglial cell types with predominantly ventral forebrain and midbrain identities. Comparison of LKD and control hOLS revealed both shared and disease-specific alterations, with prominent transcriptional changes in lysosomal, metabolic, and stress-response pathways. Lineage-resolved pathway analysis further identified signatures across individual LKDs, including mitochondrial and translational stress in GLD glial lineages, disruption of RNA metabolic and cell-cycle pathways in 4H, and prominent astrocyte-centered metabolic dysregulation in CD. Our results establish hOLS as a human 3D in vitro platform for studying the impact of LKD-associated genetic variants on early neural development and for dissecting lineage-specific disease vulnerability.

Hematopoietic stem and progenitor cells (HSPC) depend on interactions with nearby stromal cells to support their homeostatic functions and mount responses to perturbations. The murine bone marrow (BM) niche can be profiled using single-cell RNA sequencing (scRNA-seq), but there is considerable inconsistency in cell type identification, and uncertainty over how populations can be isolated prospectively by flow cytometry. Here, we produced new scRNA-seq reference datasets using purified populations of murine BM stromal cells, which we used to create a bespoke classifier for stromal cells. Our NicheScribe approach is consistent, accurate, and generalizable to query datasets irrespective of methods used for cell isolation. Moreover, consistent annotation permits comparative analyses of the same stromal cells across different bone types and perturbations like inflammation, neoplasia, and aging. Our work provides new tools for consistent cell type annotation in the murine BM niche and new insights for combined molecular and functional analyses.

Definitive hematopoietic stem cells (HSCs) emerge predominantly along the ventral surface of the dorsal aorta in the embryonic aorta-gonad-mesonephros (AGM) region, yet the spatial organization of the niche underlying this developmental asymmetry remains poorly understood. Defining the native niche of pre-HSCs has also been hindered by their rarity, transient nature and lack of a single definitive marker for their identification in situ. Here, we integrated single-cell and spatial transcriptomics to construct a spatiotemporal atlas of the niche in the AGM. Neural cells and chondrogenic mesenchyme predominated dorsally, whereas N-cadherin mesenchymal stromal cells (N-cad+ MSCs) formed a ventral layer between the aortic endothelium and mesonephric cells. BMP and SHH signaling showed overall dorsal enrichment, whereas WNT, NOTCH and KIT signaling were enriched ventrally, with these cellular and signaling patterns dynamically remodeled across HSC ontogeny. Imaging-based spatial transcriptomics validated the findings and further enabled the identification of individual pre-HSCs in situ and revealed a multicellular niche comprising endothelial cells, N-cad+ MSCs, intra-aortic hematopoietic cluster cells and macrophages. TGF{beta} and NOTCH signals were primarily supplied locally, whereas major sources of BMP and WNT were more distant. Functional perturbation identified niche-derived CD200 as an immune-regulatory signal promoting HSC development, validating a spatially predicted niche interaction. Together, our findings link tissue-scale spatial organization with the local multicellular niche supporting the preferential development of HSCs along the ventral aorta.

Animal-derived surface coatings present the gold standard in stem cell culture. However, they come with major drawbacks such as lot-to-lot inconsistency and an ethically problematic production. Approaches to develop synthetic coating alternatives have largely failed to recapitulate biological functions essential to PSC-self renewal and differentiation. In this study, we have investigated the suitability of a fully synthetic, chemically defined extracellular matrix-mimicking coating named BIOINSTRUCT for hiPSC culture. BIOINSTRUCT was employed during maintenance culture of IMR90-4 cells, as well as directed differentiation of HIHCNi008-A, ACTN2-GFP, and UKKI-011-A cells. BIOINSTRUCT preserved hiPSC characteristics over the experimental period of 10 passages similar to Matrigel. Spontaneous differentiation resulted in the formation of ectodermal, mesodermal and endodermal derivatives, confirming the retention of pluripotency. Directed differentiation on BIOINSTRUCT enabled the generation of neuronal, cardiac and pancreatic endocrine cells. Altogether, our data underscore BIOINSTRUCT as a promising alternative to animal-derived extracellular matrix coatings.

Mesenchymal stromal cells (MSCs) are promising cell therapeutics, but their development as off-the-shelf products requires cryopreservation, which impairs cell function after thaw. Inflammatory licensing enhances MSC therapeutic attributes, yet protocols vary considerably and little is known about how these variables affect MSC metabolism or post-thaw recovery. We characterized mitochondrial and glycolytic flux in umbilical cord (UC) and bone marrow (BM) MSCs licensed with interferon-{gamma} (IFN-{gamma}), tumor necrosis factor- (TNF-), or both. Brief exposure to either cytokine shifted MSC metabolism toward glycolysis and reduced mitochondrial respiration, whereas prolonged exposure led to heterogeneous responses. Conversely, combined IFN-{gamma} and TNF- increased glycolytic flux and respiratory capacity in most donors, with responses detectable after 2 hours and at concentrations below those conventionally used. Cryopreservation impaired aerobic metabolism, followed by donor-dependent recovery. Preconditioning with combined IFN-{gamma} and TNF- partially improved post-thaw metabolism, particularly in BM MSCs, and enhanced early responsiveness to inflammatory challenge, particularly in UC MSCs, as detected by IDO and candidate biomarkers CTSS and C1S. However, donors with improved post-thaw metabolism did not consistently show increased biomarker responses. These findings demonstrate that metabolic fitness and inducible biomarkers capture complementary aspects of post-thaw MSC quality and may inform preconditioning strategies for cryopreserved MSC products.

Background: The ability to repopulate all lineages of blood cells from a single hematopoietic stem cell (HSC) requires a constant balancing between maintenance of quiescence/self-renewal and the need for differentiation and adoption of specific lineage phenotypes. A classical interpretation suggests that during homeostasis, long- and then short-term HSCs differentiate into multipotent progenitors (MPPs), which then lack self-renewal capacity but can still differentiate into all downstream lineages. While much is known about the intrinsic and extrinsic regulators that promote HSC homeostasis, less is known about factors which influence HSC behavior following significant bone marrow (BM) injury, such as sublethal irradiation (SLI). Methods: Conditional knock-out of follistatin-like 1 (FSTL-1) was achieved by breeding mice with floxed Fstl1 sites to mice expressing CreERT2 under control of the ROSA locus, followed by systemic tamoxifen administration. ELISA and RT-PCR quantitated protein and RNA level loss of FSTL-1, respectively. HSC populations were assessed by flow cytometry under multiple conditions. Sublethal irradiation induced BM injury and blocking polyclonal FSTL-1 antibodies were used to recapitulate results seen with genetic ablation. Finally, single cell RNA sequencing defined both cell-specific expression of Fstl1 within the BM compartment, but also identified transcripts and pathways upregulated in the absence of FSTL-1. Results: These studies delineate a novel role for FSTL-1 in regulating HSC biology. In addition to selective expression of Fstl1 within HSCs, genetic deletion of Fstl1 increases Lineage negative;Sca-1+c-Kit+ (LSK) cell number and alters HSC homeostasis. These findings are further amplified in the BM in the context of recovery from sublethal irradiation. Importantly, the post-irradiation increase in BM cellularity seen with Fstl1 deletion is replicated by treatment with anti-FSTL-1 polyclonal antibodies. Finally, single cell RNA sequencing reveals distinct Fstl1 expression in specific LSK subpopulations, including HSCs and proliferating cells, and identifies a novel relationship between decreased FSTL-1 levels and enrichment of canonical metabolic pathways including oxidative phosphorylation, fatty acid metabolism, and glycolysis. Conclusions: Taken together, these results highlight a novel role for FSTL-1 in promoting HSC homeostasis. They also unlock an innovative way to promote HSPC recovery following BM injury, knowledge predicted to be of significant therapeutic value.

Intervertebral disc (IVD) degeneration, a major cause of low back pain, is driven by the disruption of nucleus pulposus (NP) tissue homeostasis. The NP arises from embryonic notochord cells that differentiate and adapt to the hypoxic, matrix-rich environment of the developing disc. Recapitulating the developmental trajectory from notochordal progenitors to NP-like cells in vitro remains challenging, as most protocols bypass early specification steps and fail to capture this understudied lineage. Here, using a three-dimensional (3D) system, we reconstruct this developmental path from human pluripotent stem cells into mesendoderm progenitor cells (MEPCs), notochord-like cells (NLCs), and NP-like cells, guided by single-cell transcriptomics and spatial profiling. We identify MEPCs as a distinct progenitor population with a unique gene signature and conserved regulatory networks (GSC, KLF8, LHX1, MIXL1) shared with early organizer and mesendodermal cells. Self-organization in MEPCs-derived aggregates induced spontaneous expression of NOTO, a key transcription factor orchestrating notochordal identity, and enhanced commitment to notochordal fate. Long-term culture in a medium containing TGF-{beta}1 and GDF-5 promoted maturation into SOX9+, KRT8+, CD109+ NP-like cells exhibiting robust matrix deposition and prominent LAMP1-positive intracytoplasmic vacuoles. This scalable, physiologically relevant model enables fundamental studies of human disc biology and early degenerative processes, while advancing regenerative strategies.

Metabolism and mitochondrial remodelling are increasingly recognised as key regulators of stem cell identity, governing the balance between self-renewal and differentiation. Here we compared mitochondrial and metabolic properties of stem and progenitor cells from the male germline using transmission electron microscopy, quantitative proteomics and extracellular flux analysis. While the stem cell-to-progenitor transition was accompanied by increased mitochondrial abundance and cristae density, our analyses unveiled a remarkable and unexpected capacity for spermatogonial stem cells (SSCs) to engage oxidative phosphorylation. When oxygen availability was unrestricted, SSCs displayed markedly greater maximal and spare respiratory capacity than progenitors, despite comparable glycolytic flux. SSCs were also enriched for glutathione-dependent antioxidant enzymes and maintained lower basal mitochondrial superoxide levels than progenitors. Collectively, these findings challenge the view that SSCs are predominantly glycolytic and instead identify metabolic plasticity, marked by latent oxidative capacity and enhanced redox control, as a hallmark of the stem cell state.