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Stem Cell Research

○ Elsevier BV

Preprints posted in the last 90 days, ranked by how well they match Stem Cell Research's content profile, based on 16 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

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Sustained 10% Oxygen Promotes Atrial Rather Than Ventricular Specification During Human iPSC-Cardiomyocyte Differentiation

Mathiesen, S. B.; Bjerre, F. A.; Terp, A. K. S.; Ellman, D. G.; Larsen, J. H.; Horn, P. B.; Svenningsen, P.; Poon, E. N.-Y.; Jensen, C. H.; Andersen, D. C.

2026-09-21 cell biology 10.64898/2026.09.16.750048 medRxiv
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Background: Induced pluripotent stem cell-derived ventricular cardiomyocytes (iPSC-vCMs) hold great promise for replacing ventricular cardiomyocytes lost after myocardial infarction. However, their immature phenotype limits successful engraftment by increasing the risk of post-transplant arrhythmias. In contrast to the atmospheric O2 used during most iPSC-vCM differentiations, O2 levels inside the developing heart remain low, but very little is known on the effect on O2 on iPSC-vCM differentiation. Methods: We used a GMP compliant Quad Physoxia glovebox platform providing continuous stable specified O2 tensions during all processes to simulate the in vivo O2 conditions more closely with the aim of improving iPSC-vCM maturation. Results: We demonstrate by single cell RNA sequencing, and data integration with datasets for human cardiomyocytes from the different heart chambers as well as cell morphology-, ploidy-, and functional studies, that sustained 10% O2 throughout iPSC-CM differentiation promotes atrial- instead of ventricular iPSC-CM subtype specification. Conclusions: While this rejects our original hypothesis and forces some concerns to iPSC-vCM manufacturing by sphere technology, these unexpected data may serve as an attractive and easy approach to refine atrial iPSC-CM specification to benefit their exponentially growing diagnostic-, cytotoxic-, and regenerative use.

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Human iPSCs and iPSC-Derived Endothelial Cells from PAD Patients and Healthy Donors Exhibit Comparable Characteristics and Potency: Implications for Autologous Cell Therapy in Peripheral Artery Disease

Bae, J. Y.; Lee, S.-J.; Bae, S.; Park, J.; Jung, J.; Han, J. W.; Jung, C.; Park, S.; Kim, Y.; Kim, J.; Kim, H.-K.; Lee, S.-J.; Ko, Y.-G.; Choi, D.; Kim, H. O.; Yoon, Y.-s.

2026-09-07 cell biology 10.64898/2026.09.04.749119 medRxiv
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BACKGROUND: Peripheral artery disease (PAD) can lead to amputation in advanced cases, making cell therapy using human induced pluripotent stem cells (hiPSCs) a promising therapeutic option. hiPSC-derived endothelial cells (hiPSC-ECs) have shown favorable effects in treating experimental ischemic cardiovascular disease. An autologous approach for PAD patients is preferable to avoid immunological reactions. However, it is yet unknown whether hiPSCs and hiPSC-ECs derived from PAD patients have similar characteristics and potency compared to those derived from non-PAD donors. Therefore, we explored whether there are significant differences in the characteristics and potency of hiPSCs and hiPSC-ECs between non-PAD donors and PAD patients. METHODS: We generated hiPSCs from the blood of non-PAD donors and patients with PAD. We determined the pluripotency of hiPSCs using qRT-PCR, flow cytometry, immunostaining, RNA-seq, and teratoma formation assay. The genetic stability of hiPSCs was confirmed by G-banding karyotyping. We then differentiated hiPSCs into endothelial cells (ECs) in a clinically compatible manner. We compared the characteristics and therapeutic potency of hiPSC-ECs derived from non-PAD and PAD groups using qRT-PCR, flow cytometry, immunostaining, and RNA-seq. In vitro endothelial functions were determined by nitric oxide (NO) production and capillary network formation. Therapeutic potency and incorporation of engrafted hiPSC-ECs were evaluated in a hindlimb ischemia model. RESULTS: We successfully generated hiPSCs from the blood of seven non-PAD donors and eight PAD patients. Both non-PAD and PAD-derived hiPSCs exhibited similar expression levels of pluripotency markers. All hiPSCs, regardless of the group, formed teratomas and showed normal karyotypes. RNA-seq analyses revealed similar gene expression profiles between the groups. hiPSC-ECs derived from both non-PAD and PAD donors exhibited similar expression levels of EC markers at both the gene and protein levels. RNA-seq analyses showed no significant overall differences in gene expression profiles between the groups. Functional analyses demonstrated similar endothelial characteristics and function in hiPSC-ECs from both groups. Both groups showed similar perfusion recovery, limb salvage, and vessel-forming capacity. Engrafted hiPSC-ECs from both groups also exhibited similar angiogenic and vessel-forming capabilities. CONCLUSIONS: Our study demonstrated no significant differences in hiPSCs and hiPSC-ECs derived from non-PAD donors and PAD patients in terms of molecular and cell biological characteristics, therapeutic effects, and vessel-forming capability. Our study indicates that hiPSCs and hiPSC-ECs derived from PAD patients can serve as a novel platform for autologous cell therapy.

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Poor survival after myocardial infarction in immune deficient NXG B2m mice is alleviated by transplantation of induced pluripotent stem cell derived cardiomyocytes (iPSC-CM) formulated as spheres, but not single cells

Terp, A. K. S.; Ellman, D. G.; Mathiesen, S. B.; Laursen, S. M.; Bjerre, F. A.; Ammentorp, B. a. G.; Willadsen, F. G.; Poon, E. N. Y.; Jensen, C. H.; Andersen, D. C.

2026-09-11 cell biology 10.64898/2026.09.08.748837 medRxiv
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The human heart lacks cardiac stem cells and the ability to reestablish the loss of ventricular cardiomyocytes (vCMs) after myocardial infarction (MI) resulting in heart dysfunction. vCM replacement using intracardiac transplantation of human induced pluripotent stem cell (iPSC) derived vCMs represent a promising strategy for targeting MI, but low engraftment remains a challenge. Herein, we investigated whether formulation of ventricular iPSC-CMs (iPSC-vCM) as spheres (iPSC-vCMSphere) improves cell retention and cardiac function as directly compared to single-cells (iPSC-vCMSC) after transplantation in a new severely immunocompromised mouse model with MI. Recipient survival immediately after MI and intervention was poor for both Vehicle (50%) and iPSC-vCMSC (36%) groups, whereas 92% of iPSC-vCMSphere treated mice survived, which is comparable to non-immune deficient C57bl/6 mice (91%). All surviving and engrafted animals retained iPSC-vCMs in the infarct border zone at 8-weeks, and heart function remained similar between groups, although minor improvements were observed for iPSC-vCMSphere animals. Surprisingly, iPSC-vCMSpheres were less mature than iPSC-vCMSCs. Thus, our data suggest that iPSC-vCM sphere formulation may offer some benefits for intracardiac delivery as compared with single cell formulated iPSC-vCMs, and thus remains a promising candidate for reestablishing the lost CMs after MI in the future.

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Derivation of primary fetal epithelial organoids from cryopreserved human amniotic fluid cells.

D'Ariano, G.; Zhang, G. J.; Cala, G.; Carrino, G. M.; Agarwal, A.; Mariani, A.; Marinaro, M.; Matias de Sousa, R.; Cenedese, G.; Camilli, C.; David, A. L.; Eaton, S.; Pellegata, A. F.; Pellegrini, M.; De Coppi, P.; Gerli, M. F. M.

2026-09-09 cell biology 10.64898/2026.09.07.749928 medRxiv
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Primary fetal human epithelial organoids are canonically derived from tissue samples obtained after termination of pregnancy. Recently, we have demonstrated that these organoids can be consistently generated from amniotic fluid cells isolated prenatally during diagnostic and interventional procedures. Amniotic Fluid-derived Organoids (AFOs) are promising fetal epithelial lung, kidney and small intestine tissue models that bypass some of the ethical and legal constraints associated with obtaining primary fetal tissue. Despite this, the widespread adoption of this technology is limited by the lack of standardised and accessible pipelines for the biobanking, culturing and distribution of organoid-forming amniotic fluid cells. To enable broader AFO use for research and clinical purposes, this work investigates two cryopreservation strategies to optimise AF cell recovery for organoid derivation. In Strategy 1, viable AF cells were sorted before freezing, while in Strategy 2 unsorted AF was frozen, and viable AF cells were sorted for viability after thawing. We present here a comprehensive evaluation of 5 commercially available GMP-compliant freezing media (FM1-5) alongside a standard lab-grade control (FM CT). AFOs were assessed for formation efficiency, morphological characteristics, proliferation capacity, epithelial identity, and tissue type. Our results demonstrate that organoid-forming AF cells can be successfully cryopreserved both pre- and post-sorting. Strategy 1 yielded higher organoid formation efficiency, with AFOs derived from cryopreserved and fresh cells exhibiting comparable expansion potential. Finally, FM4 provided minimal to no decline in survival rate, making it the most effective GMP-grade freezing medium tested. In conclusion, we present two viable cryopreservation strategies adaptable to different laboratory settings and identify optimal GMP-compliant freezing media, to support safe distribution and centralised processing, thereby facilitating scalability and collaborative work on the AFO technology.

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Minimizing time in culture: A prototypic autologous manufacturing workflow for monoclonal iPSC lines within seven weeks

Haberhausen, D.; Woehle, C.; Raab, C.; Ludwig, C.; Kuchler, T.; Barth, S.; Wuellner, U.; Bosio, A.; Johannsen, H.; Knoebel, S.

2026-08-10 cell biology 10.64898/2026.08.04.741960 medRxiv
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Induced pluripotent stem cells (iPSCs) hold great promise for both allogeneic and autologous cellular therapies. However, broad application and clinical translation is hindered by fragmented, complex and time-intensive workflows, resulting in high manufacturing costs, poor standardization and increased risk of genomic aberrations in derived iPSCs. In this study we developed a standardizable, automatable and time- efficient process for the derivation of monoclonal iPSC lines straight from skin including a comprehensive and cascaded OC strategy. We generated monoclonal iPSC lines derived from human skin punch biopsies of ten donors (age 49-81) via mRNA-based reprogramming that subsequently underwent comprehensive and thorough characterization of phenotypic and genetic properties. The use of a combined mechanical and enzymatic fibroblast isolation protocol and a transient non-integrative reprogramming technology allowed us to obtain 78 monoclonal iPSC lines, ready for banking, molecular characterization and further differentiation within seven weeks from initial sample processing to passage four iPSC lines. The phenotypical characterization via flow cytometry-based pluripotency marker expression and 2D-directed differentiation into the three germ layers showed low intra- and inter-donor variability over all generated lines. A combination of SNP array based CNV analysis followed by whole exome sequencing proved to be the most efficient approach for assessment of genomic integrity. Proof-of-concept experiments for closed system processing revealed that a substantial part of the most error-prone and technically demanding steps can be transferred to semi- automated, closed systems. In conclusion, the described protocol allows for time- efficient, standardizable and automatable generation of high-quality monoclonal iPSC lines from human skin punch biopsies within seven weeks, thus moving the field of autologous iPSC manufacturing one step further towards cost-efficient clinical implementation.

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Midbody inheritance predicts re-entry into quiescence, but not lineage potential, in mouse hematopoietic stem cells

Fukushima, T.; Wehling, A.; Shimamoto, R.; Asada, S.; Kawamura, S.; Fukuyama, T.; Goyama, S.; Schroeder, T.; Kitamura, T.; Tanaka, Y.

2026-07-29 cell biology 10.64898/2026.07.28.739739 medRxiv
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Hematopoietic stem cells (HSCs) give rise to all blood cell lineages and possess long-term self-renewal potential. HSCs undergo symmetric division for their expansion and asymmetric division to generate one HSCs and one progenitor cells which contribute to production of mature blood cells. The midbody is a structure which is formed in the center of the intercellular bridge during cytokinesis. However, the midbody is either asymmetrically inherited by one daughter cell or symmetrically released after cell division, whether these distinct patterns of midbody inheritance influence HSC fate remain poorly understood. In this study, we designed a fusion protein hmKO2 and MgcRacGAP which is a component of midbody. We then traced the midbody inheritance during cell division and the future cell fates of HSC daughters after division by time-lapse imaging. As a result, we found that the midbody release correlated with the delay of the time to the next division but not to the lineage potential of HSCs, indicating the possibility that midbody remnant plays some roles in cell cycle progression. HighlightHematopoietic stem cells exhibit a low frequency of midbody inheritance. Midbody inheritance does not affect the lineage potential of daughter cells. Midbody loss is associated with delayed entry into the next cell cycle.

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Prime Editing Corrects the HBB Codon 8/9 (+G) Mutation in Patient-Derived Induced Pluripotent Stem Cells and Restores β-Globin Expression in iPSC-Derived Erythroid Cells

hussain, i.; Mumtaz, K.; Javed, M.; Fatima, S.; Zahra, H.; Alam, A.; Jameel, M.; Malik, N. A.; Syed, F.; Rehman, F. U.; Kirmani, S.; Fatima, A.; Mian, A. A.

2026-09-24 cell biology 10.64898/2026.09.22.753453 medRxiv
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Homozygosity for the HBB codon 8/9 (+G) frameshift (c.27dup (p.Ser10ValfsTer14)) causes transfusion-dependent {beta}-thalassaemia and is common in South Asia. Prime editing can reverse this insertion without double-strand breaks or donor DNA, but its efficiency depends on pegRNA design. We derived Sendai-reprogrammed iPSCs from a homozygous patient, optimised PEmax editing (spacer, pegRNA extension, secondary nick, MLH1dn) and compared patient, PEmax-treated and control iPSC-derived erythroid cells by flow cytometry, colony assays, RT-qPCR, western blotting and cation-exchange HPLC. Patient iPSCs had a normal 46,XY karyotype, expressed pluripotency markers, formed all three germ layers and were Sendai-free by passage 15. A PAM-disrupting spacer with a +68 nicking sgRNA gave the highest intended-edit frequency 8.4%; MLH1dn added little. PEmax-treated cultures matured and formed colonies more like control than patient cultures, restored HBB transcript (about 4-fold control iPSC-derived cells) and detectable {beta}-globin protein, and contained an HPLC fraction consistent with HbA ( undetectable in patient cells). Fetal haemoglobin (about 80%) and embryonic globin remained predominant. Prime editing corrects HBB c.27dupG in patient iPSCs and restores {beta}-globin expression, with partial restoration of adult haemoglobin in a fetal/embryonic-type erythroid background. Validation in additional donors, haematopoietic stem cells and in vivo is required.

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Comparison of hiPSC-derived hepatic organoids and liver-on-a-chip systems reveal microenvironment-driven maturation

Tamargo Rubio, I.; Krempel, T.; Palasantzas, V. E. J. M.; Green, B.; Weijer, G. D. L.; Moerkens, R.; van der Woude, C.; van IJzendoorn, S.; Touw, D. J.; Hoogerland, J. A.; Withoff, S.; Fu, J.

2026-07-29 cell biology 10.64898/2026.07.28.741157 medRxiv
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Human liver organoids (HLOs) and liver-on-a-chip (LoC) systems are emerging as physiologically relevant human models for studying liver function, disease, and drug metabolism, often in combination with human induced pluripotent stem cell (hiPSC)-derived tissues. However, hiPSC-derived models often display batch-to-batch variation and incomplete maturation, and the contribution of microfluidic flow to hepatic maturation remains insufficiently characterized. Here, we developed a cryopreservable and scalable workflow to generate hiPSC-derived hepatic organoids that can be directly matured to either static HLOs or LoC systems, enabling matched comparison of both platforms. Transcriptomic and functional characterization revealed progressive hepatic maturation during organoid differentiation, including increased expression of liver-specific metabolic pathways, enhanced albumin secretion, and increased CYP3A4 activity. Compared to mature HLOs, LoCs exposed to continuous microfluidic flow exhibited transcriptomic profiles suggesting further maturation, with increased enrichment of pathways related to lipid metabolism, xenobiotic metabolism, transport, and tissue organization. These findings demonstrate that microfluidic perfusion promotes hepatic metabolic specialization compared to static organoid culture while maintaining donor-specific characteristics. Together, this study establishes a robust hiPSC-derived LoC platform and highlights the potential of flow-based systems for improved modeling of human liver physiology, disease mechanisms, and drug responses.

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Metabolic profiling of licensed mesenchymal stromal cells reveals a disconnect between glycolytic fitness and immunomodulatory responsiveness

Bilal, H.; DeGroot, B. T.; Braid, L.

2026-09-28 cell biology 10.64898/2026.09.27.754820 medRxiv
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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.

10
Phenotypes and Cellular Mechanics of Primary Human Aorta- and Pluripotent Stem Cell-derived Vascular Smooth Muscle Cells

Huang, C.-Y.; Wu, S. C. M.; Kissling, M.; Arking, A.; Chen, Y.-W.; Hall, F. D.; Sivarajan, S.; Yezzi, H.; Reich, D. H.; Boheler, K. R.

2026-10-02 cell biology 10.64898/2025.12.18.694995 medRxiv
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Aims: Mature, contractile vascular smooth muscle cells (vSMC) in muscular blood vessels can de-differentiate into synthetic vSMC, while human pluripotent stem cells (hPSC) differentiate into proliferating, fetal-like vSMC that can be induced to form contractile vSMC. Given the complicated embryonic origins and conflicting views on vSMC heterogeneity, our aim was to establish how closely hPSC-vSMC of a known germ layer lineage and defined phenotype are representative of vSMC obtained from aorta (AoSMC). Methods and Results: We generated paraxial mesoderm (PM)-derived synthetic and contractile vSMC from hPSC lines and performed phenotypic and mechanical comparisons with AoSMC. Synthetic hPSC-vSMC and cultured AoSMC are proliferative, sensitive to contact inhibition and exhibit phenotype switching. Contractile hPSC-vSMC are non-proliferative, capable of phenotype switching and have elevated levels of contractile proteins (CNN1, TAGLN, ACTA2). These contractile proteins also displayed density-dependent, cell-to-cell heterogeneity in both AoSMC and hPSC-vSMC. Single-cell traction force measurements on micropost array detectors (mPADs) yielded comparable forces per micropost in the nN range across cell types. Quantitative 3D force measurements on humanized smooth muscle cell microtissues (SMTs) developed similar forces per cell. Larger forces were generated by MEKi-treated hPSC-vSMC and AoSMC versus controls. Conclusions: We have systematically studied the properties of hPSC-vSMC and performed comprehensive phenotypic and mechanical comparisons with AoSMC. These results demonstrate that synthetic hPSC-vSMC generated in vitro and cultured AoSMC derived from tissues are comparable and mechanically similar, but results with hPSC-vSMC are more reproducible.

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Multi-scale electrophysiological characterization of human cardioids reveals progressive maturation

Vashanthakumar, V. K.; Naveed, M.; Wisnumurti, E.; Alerni, N.; Conrad, L.; Tissieres, V.; Tuchler, J.; Barozzi, I.; Ordog, B.; Horvath, A.; Osterwalder, M.; Odening, K. E.

2026-10-05 physiology 10.64898/2026.09.29.755336 medRxiv
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Background: Human induced pluripotent stem cell-derived cardiomyocytes are valuable for cardiac disease modelling and drug testing but remain limited by immature structural and electrophysiological properties in conventional two-dimensional cultures. Three-dimensional cardiac models, including cardioids, provide a more physiological environment through multicellular organization and enable tissue-level functional analysis. Their electrophysiological properties and maturation, however, remain incompletely characterized. Methods: We performed an integrated electrophysiological characterization of human cardioids over the first three weeks of maturation using sharp microelectrode recordings, calcium transient measurements, whole-cell patch clamp recordings, immunofluorescence, transcriptomic analysis, and pharmacological interventions. Results: During maturation, cardioids exhibited progressive electrophysiological maturation, characterized by more physiological resting membrane potentials (-54.0{+/-}3.1mV to -68.1{+/-}1.2mV), increased action potential amplitude (73.5{+/-}4.8mV to 101.7{+/-}2.1mV) and upstroke velocity (44.3{+/-}5mV/ms to 86.6{+/-}8.4mV/ms), and shorter action potential duration (178.9{+/-}8.7ms to 144.0{+/-}4.8ms at 1Hz stimulation). These changes were associated with progressively increased INa density and enhanced SCN5A mRNA and Nav1.5 protein expression, consistent with progressive maturation of cardiac excitability. IKr current and KCNH2/hERG expression were already present at early maturation stages and remained stable, as evidenced by preserved sensitivity to dofetilide-blockade. Pharmacological inhibition of barium- and HMR-sensitive currents altered resting membrane and/or action potential characteristics in intact cardioids, whereas in isolated cardiomyocytes classical IK1 remained undetectable and IKs was small, highlighting a certain degree of persisting immaturity of the model. Conclusions: These findings demonstrate that human cardioids undergo progressive electrophysiological maturation and provide complementary tissue- and cellular-level insights into cardiac function, establishing their suitability for investigating INa and IKr-related cardiac pathologies.

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iPS-CNM: an iPSC collection generated by base editing for centronuclear myopathy

Staecker, I.; Pommerenke, C.; Ellinghaus, A.; Steinkirchinger, I.; Hauer, V.; Kallnischkies, H.; Kaufmann, M.; Groebe, L.; Faehnrich, S.; Haake, J.; Steenpass, L.; Wang, H.

2026-09-21 genetics 10.64898/2026.09.15.751756 medRxiv
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Centronuclear myopathy (CNM) is a rare form of inherited diseases often caused by single base mutations. Modelling CNM is challenging due to the diversity of CNM mutations and genetic background of individual patient. To address this, we used base editing to introduce CNM mutations into an induced pluripotent stem cell (iPSC) line from a healthy donor, generating a collection of iPSC lines (iPS-CNM) carrying distinct CNM mutations. We found that the efficiency of base editing depended critically on selecting base editor (BE) variants and the target sequences. Optimization using different BE variant and sgRNA pair was required for each target site. Moreover, whole genome sequencing (WGS) was performed to confirm on-targets and detect off-targets in order to select iPSC clones for the collection. Our findings highlight the feasibility of base editing for generating an iPSC collection from one parental iPSC line combined with thorough evaluation of rare off-targets using WGS.

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DNA barcoding-based paired daughter cell analysis reveals division preferences of hematopoietic stem cells

Fukushima, T.; Nishiyama, A.; Koide, S.; Isobe, T.; Yabushita, T.; Asada, S.; Goyama, S.; Iwama, A.; Yamazaki, S.; Tamura, T.; Kitamura, T.; Suda, T.; Tanaka, Y.

2026-07-24 cell biology 10.64898/2026.07.24.739718 medRxiv
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Hematopoietic stem cells(HSCs) maintain their pools by stem-stem division and produce mature blood cells through stem-progenitor or progenitor-progenitor division. A paired daughter cell(PDC) assay combined with single cell transplantation is a powerful method to compare the lineage outputs of two HSC daughter cells. However, single-cell transplantation precludes large-scale analysis of daughter-cell pairs, as only one cell can be transplanted per recipient. Here, we developed a DNA barcoding-based PDC assay to overcome this limitation, enabling simultaneous analysis of 476 daughter pairs from individual HSC divisions and revealing that daughter-cell fates are coordinated and that HSC division patterns are biased toward stem-stem and progenitor-progenitor divisions rather than stem-progenitor divisions. These findings indicate that HSC fate outcomes are directed toward symmetric division outcomes. Integration of single-cell RNA sequencing with DNA barcoding revealed a continuum of HSC states--from balanced HSCs to myeloid-biased HSCs and ultimately to a low-output HSC subset--in which progressively reduced production of mature blood cells relative to stem cell expansion, a proxy for stem-stem division bias, exhibits distinct activities of transcription factors and signaling pathways. Overall, our analysis uncovers characteristic patterns of HSC division and links stem maintenance with distinct molecular features.

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Spectral Analysis of the T Cell Repertoire Recovery Following Allogeneic Stem Cell Transplantation

Toor, A. A.; Marinos-Velarde, A.; Qayyum, R.

2026-09-29 transplantation 10.64898/2026.09.28.26364185 medRxiv
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The human T cell repertoire is generated through recombination of a multitude of T cell receptor gene segments, yielding a complex array of T cell clones. T cell receptor beta (TRB) V gene segment defined, T cell clonal frequency when organized in correspondence with the respective V gene segment positions on the TRB genomic locus yields a periodic, undulating curve in the spatial domain. Using the genomic distance from the TRB-D1 segment to the TRB-V1-29 segments, spectral analysis was performed utilizing Lomb-Scargle periodogram (modified Fourier analysis) to obtain spectral power curves quantifying the TRB V clonal frequencies from 12 allogeneic stem cell transplant donors (baseline) and recipients (<100 days or b/w 100-365) using a variety of analytic software. Patients either underwent HLA matched related bone marrow or HLA matched unrelated blood stem cell transplantation, using PT-CY for the former and ATG for the latter. Spectral Power curves revealed dominant spectral peaks at wavelengths ranging from 113-335 millicycles/kb in the 12 donors, with consistent frequency domain spectral patterns, supporting similar use of V segments across healthy individuals. PT-CY recipients had power spectra closely corresponding to the respective donors, however the ATG recipients had relatively dispersed spectra, with spectral centroid shifted towards higher frequencies compared to donors and a reciprocal decline in the low frequency indices. Spectral power was concentrated in the <3 kb and 3-12 kb wavelengths in both groups, consistent with the periodicity observed in the relative V gene segment usage across the repertoire. The analyses reported here demonstrate that the healthy SCT donors have a spectral signature occupying short to intermediate wavelegnths in the frequency domain, PT CY recipients recover with donor-like spectra on the average, however ATG recipients tend to shift towards higher frequencies. These findings are consistent with a normal organized distribution of TRB V segment usage in healthy individuals, with PT-CY preserving this organization more consistently than ATG. Spectral (Fourier) analysis of TRB sequencing data provides a repertoire wide summary of T cell clonal distribution.

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Generation and characterization of a patient-specific human induced pluripotent stem cell line from a Skogholt syndrome patient (ASCFi003-A)

Przybyla, W.; Gupta, S.; Fjerdingstad, H. B.; Selnes, P.; Sharma, K.

2026-08-31 cell biology 10.64898/2026.08.29.747981 medRxiv
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We report the generation and characterization of a human induced pluripotent stem cell (iPSC) line derived from dermal fibroblasts of a patient with Skogholt disease, a rare maternally inherited neurodegenerative syndrome associated with choroid plexus dysfunction and impaired cerebrospinal fluid (CSF) homeostasis. Patient fibroblasts were reprogrammed using the non-integrating Repro-OSKGM kit. The resulting iPSC line exhibited typical pluripotent morphology, expressed canonical pluripotency markers, maintained a normal karyotype, retained the disease-associated genetic variant, was mycoplasma-free, and demonstrated trilineage differentiation potential. We also made choroid plexus (ChP) like organoids from the generated iPSCs. This patient-specific iPSC line provides a valuable resource for generating choroid plexus organoids and neurons to investigate disease mechanisms and develop therapeutic strategies.

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Communicating Ethically Relevant Practices of Patient Registries: An Interview Study on the Information Needs of People with Multiple Sclerosis

van den Akker, O.; Windfuhr, F.; Almeida, D.; De Vries, S.; Stark, S.

2026-09-08 medical ethics 10.64898/2026.09.05.26362329 medRxiv
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Patient registries play a key role in research on chronic conditions like multiple sclerosis (MS), but their success typically depends on patients' willingness to share data. Information provided about ethically relevant registry practices may strongly influence their willingness. This study explores what information about ethics practices people with MS consider important when deciding whether to contribute data to a patient registry, and how they prefer this information to be communicated. We conducted semi-structured online interviews with 21 people with MS and patient representatives from nine European countries. The interview guide first addressed general information needs and then seven predefined ethically relevant topics. The topics registry governance, registry funding, data handling, and use-and-access procedures were adapted from the literature, while communication, access, and rewards for contributing data provided contextual and practical insight. They also served as the initial coding categories for directed qualitative content analysis, after which categories were refined and reorganized during analysis, and subcategories were inductively developed. We found that trust emerged as a cross-cutting factor. Participants required less information about registry practices when they trusted the registry or associated parties and preferred registry communication through trusted intermediaries. When deciding whether to contribute data to a patient registry, participants emphasized the importance of clarity about how the data will be used, who would have access to it, and what privacy protections are in place, while information preferences for technical details regarding data use and access varied widely. Feedback on personal or aggregate results was highly valued and seen as types of personal and communal benefits for participating. In conclusion, patient registries should adopt flexible communication strategies that balance transparency and accessibility. Building and maintaining trust, potentially through trusted affiliates like universities or patient organizations, appears central to properly inform (potential) registry participants about ethically relevant registry practices.

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Evaluation of the Translational Readiness of Pluripotent Stem Cell-Derived Vascular Cell Therapy for Limb Ischemia: A Systematic Review and Meta-analysis

Shin, M.; Choi, H.; Kim, T.; Jeon, J. P.; Jung, S.; Cho, K.

2026-09-09 cell biology 10.64898/2026.09.02.749027 medRxiv
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Background: For the first time, pluripotent stem cell (PSC)-derived endothelial cells were administered to a human for peripheral artery disease (PAD), in August 2026. This translation is based on a large preclinical literature claiming that donor cells build blood vessels in animal models of limb ischemia, but whether it supports that claim has not been assessed systematically. Methods: In this systematic review and meta-analysis, we searched MEDLINE, Web of Science, Europe PMC, and Embase to August 2026 for studies of PSC-derived vascular cells in animal models of limb ischemia with an acellular control. Limb perfusion at each experiment's primary timepoint was pooled as Hedges' g in a three-level random-effects model with cluster-robust variance. Donor-cell fate and a seven-level ordinal of vascular contribution were graded for every study. This meta-analysis was registered on PROSPERO (CRD420261465308). Results: Sixty-eight studies in 69 reports met the criteria; 51 contributed 114 comparisons at primary timepoints. Cell therapy increased perfusion (Hedges' g 2.26, 95% CI 1.72-2.79; P=4.1x10-11; I2=87.5%; 95% prediction interval -1.47 to 5.98). No prespecified moderator survived Holm-Bonferroni adjustment, including the donor-cell fate grade (P=0.30). A donor cell was resolved in a vessel wall in 35 studies, and flow through such a vessel in 7. Small-study effects were strong (Egger t=6.25, P=9x10-8) but were not reproduced by a sample-size-based test (P=0.80); trim-and-fill moved the estimate to 1.15. On the natural scale, treated limbs recovered about twice the control perfusion (ratio of means 1.96, 95% CI 1.66-2.33). Limb preservation favored cell therapy in 11 studies with countable events (risk ratio 4.88, 95% CI 2.28-10.45), but 43 of 68 studies reported no functional outcome, and only 22 comparisons from 8 studies were both randomized and blindly assessed. In a post hoc analysis that did not survive multiplicity adjustment, effects were largest in studies whose images could not resolve their incorporation claims (g 3.23) versus those that resolved incorporation (g 2.33). Conclusions: PSC-derived vascular cell therapy improved limb perfusion in animal models, consistently across every sensitivity analysis, although the magnitude is uncertain given heterogeneity and small-study effects. Benefit was not associated with the degree of donor-cell incorporation across studies and was largest where incorporation was least resolvable, a pattern more consistent with reporting and measurement bias than with a true mechanistic effect. The first rigorous, blinded test of that benefit may come not from animals but from the patients now receiving these cells.

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Glutathione Protects Hematopoietic Stem Cells from Proteotoxic Stress

Paul, A.; Tom, H.; Merchant, S.; Phan, J.; Lemoff, A.; Mathews, T. P.; Karner, C. M.; Hoxaj, G.; Zhao, Z.; Morrison, S. J.

2026-10-06 cell biology 10.64898/2026.10.05.756790 medRxiv
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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.

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SOX9-mediated G1 elongation confers reserve stem cell-associated injury resistance in human intestinal stem cells

Burclaff, J.; Breau, K.; Chi, L. T.; DeLoach, W.; Amare, E. A.; Cooper, L.; Walcott, V.; Hinesley, C.; Dixit, M.; Chen, K.; Meyer, M.; Sweet, C.; Walker, D.; Bliton, R. J.; Tang, C. Y.; Magness, S. T.

2026-08-24 cell biology 10.64898/2026.08.21.745750 medRxiv
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Background & Aims Dynamic cell cycle control is critical for intestinal crypt maintenance and injury responses, yet genetic regulators driving these changes remain poorly defined. As reserve intestinal stem cells (rISCs) are often considered to be slowly-cycling and can resist replication-dependent injury, factors that restrain proliferation may confer cytoprotection. Here, we define SOX9 as a regulator of intestinal stem cell (ISC) cycling and injury resistance. Methods Primary human ISCs were engineered to tune SOX9 levels, visualize cell cycle state, and manipulate cell cycle regulators. Using this system, we tested how SOX9 dosage impacts stemness, differentiation, proliferative recovery after SOX9 washout, and survival after 5-FU-mediated injury. Transcriptional analyses identified candidate links between SOX9 levels and cell cycle control, which were functionally tested using inducible INK4A (CDKN2A) and Cyclin D2 (CCND2) ISC lines. Results SOX9 induction lengthens the cell cycle in a dose-dependent manner largely by elongating G1 phase through the INK4A-Rb pathway. The effects of high SOX9 levels repressing proliferation and stem cell activity are reversible. SOX9 induction protects against 5-FU toxicity. This protection is mimicked by INK4A overexpression or pharmacological G1 phase arrest and repressed by CCND2 induction. Conclusions These findings identify SOX9-mediated G1 elongation as a reversible cytoprotective program that confers key functional properties associated with rISCs: proliferative restraint, retained stem cell potential, and resistance to replication-dependent injury. This positions G1 length as a potential determinant of which crypt cells survive injury to act as reserve stem cells.

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A randomized trial of grant writing coaching groups: Qualitative interviews revealing key elements of intervention efficacy

Mendes, J.; Wood, C.; Jones, R.; Engler, J.; Weber-Main, A. M.; Jones, H.; Steiner, M.; Okuyemi, K.; McGee, R.

2026-09-22 scientific communication and education 10.64898/2026.09.17.752282 medRxiv
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Background Training in grant proposal writing is an essential component of professional development for academic scientists in the biomedical and behavioral sciences. Despite the expansion of inter- and intra-institutional grant writing coaching groups as an approach to honing these skills, specific features that enhance or limit coaching group effectiveness have not been rigorously studied. Methods Qualitative inerviews were conducted with a subset of early-career investigators (n=204 and coaches (n=36) engaged in a national, U.S. based, group-randomized trial of grant writing coaching groups to test the effects of two variables on submission and funding of national-level proposals: (1) coaching duration (regular/extended dose) and (2) mode of engaging a scientific advisor (someone with content-aligned expertise) in the coaching process. This report focuses on interviews conducted upon completion of the regular coaching dose - 5 months of biweekly, group-based coaching sessions to support active proposal writing. Interviews were designed to identify which coaching group elements were perceived to be the most critical. Transcribed interviews were analyzed using deductive (participants) or open (coaches) coding to identify themes. Results Triangulation of results from participant and coach interviews showed strong concordance that coaches, peers, and scientific advisors all played key roles in supporting intervention efficacy. Sufficient alignment of scientific fields and/or methodologies among group members was important, although breadth of perspectives was also valued. Other critical group features were skilled and well-organized coaches, detailed feedback, peer-to-peer support (technical and psychosocial), and clear expectations for group functioning. Factors attenuating impact included variation in participants' engagement and "readiness to write," within-group mismatches of expertise or grant mechanisms, and limited research support at some participants' home institutions. Conclusion This study identified key elements of successful grant writing coaching groups and potential barriers to their effectiveness, while yielding insights about tailoring this approach for individuals at different stages of proposal development.