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Cytotherapy

○ Elsevier BV

Preprints posted in the last 30 days, ranked by how well they match Cytotherapy's content profile, based on 15 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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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.

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Enhancing the hyaline cartilage regenerative potential of induced pluripotent stem cell-derived chondrocyte cell sheets

Takahashi, T.; Uchiyama, R.; Toyoda, E.; Maehara, M.; Takahashi, Y.; Wasai, S.; Oomura, H.; Ogawa, M.; Yamashita, A.; Watanabe, M.; Tsumaki, N.; Sato, M.

2026-09-28 bioengineering 10.64898/2026.09.25.754531 medRxiv
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Introduction Autologous and allogeneic chondrocyte cell sheet transplantation has shown safety and potential efficacy for cartilage defects associated with knee osteoarthritis. Although polydactyly-derived chondrocyte (PDC) cell sheets have been used clinically for allogeneic transplantation, a scalable and reliable alternative cell source is needed. This study aimed to establish a proof-of-concept protocol for generating chondrocyte cell sheets from clinical-grade human induced pluripotent stem cells (iPS cells). Methods Cartilaginous tissue was generated from human iPS cells, and isolated chondrocytes were used to fabricate iPS cell-derived chondrocyte sheets. In Phase 1, sheets were produced in high-serum medium under normoxic, hypoxic, or hypoxic/high-seeding-density conditions and compared with PDC sheets using a three-dimensional in vitro model and xenogeneic orthotopic transplantation in an immunodeficient rat model. In Phase 2, sheets were produced in low-serum medium under hypoxic/high-seeding-density conditions and evaluated for cartilage-related gene expression, secreted factors, cell surface marker expression, and in vivo cartilage repair. Results In Phase 1, hypoxic/high-seeding-density culture enhanced in vitro chondrogenic properties. However, after transplantation, iPS cell-derived chondrocyte sheets formed fibrotic repair tissue, whereas PDC sheets generated hyaline-like cartilage. In Phase 2, low-serum culture increased expression of cartilage-related genes, including collagen type II alpha 1 (COL2A1) and SRY-box transcription factor 9 (SOX9), enhanced secretion of transforming growth factor beta 1 and melanoma inhibitory activity, and upregulated CD9, CD26, CD56, CD201, CD227, and GD2. Low-serum iPS cell-derived chondrocyte sheets regenerated hyaline cartilage at 4 weeks, and the repair tissue was maintained at 12 weeks without bone formation. Conclusions A robust fabrication protocol enabled human iPS cell-derived chondrocyte sheets to regenerate hyaline-like cartilage in vivo. These findings support their potential as a scalable cell source for clinical cartilage repair.

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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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Engineering robust cardiomyocyte differentiation from iPSCs through WNT-mediated process window expansion

Akiyama, H.; Kobayashi, R.; Nakamura, S.; Yasui, T.; Shimizu, K.; Honda, H.

2026-09-30 bioengineering 10.64898/2026.09.29.755404 medRxiv
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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.

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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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Benchmarking cartilage regeneration across ten chondrogenic cell sources using native tissue references

Ponta, S.; Pecina, V.; Airoldi, M.; Simmen, D.; Novoa Olivares, E.; Linder, T.; Laurent, A. E.; Applegate, L. A.; Salzmann, G.; Bruhin, V.; Stoddart, M.; Zenobi-Wong, M.; Fisch, P.

2026-10-06 bioengineering 10.64898/2026.10.05.756631 medRxiv
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A persistent challenge in cartilage tissue engineering is identifying cell sources capable of regenerating cartilage with native-like properties. Variability in chondrogenic potential among human- and animal-derived cells complicates graft development and disease modeling. Here we benchmarked ten chondrogenic cell sources under standardized culture conditions using hyaluronan-alginate biomaterials and implementing a functionality index combining histological and mechanical metrics referenced to native tissue. Mesenchymal stem cells and fetal chondroprogenitors demonstrated superior regenerative capacity, achieving 103% and 95% of native cartilage functionality, respectively. In contrast, adult articular chondrocytes from healthy and osteoarthritic donors produced fibrocartilaginous tissue with functionality scores below 50%. These findings provide a quantitative framework to guide cell source selection and optimize cartilage graft standardization for clinical applications and physiologically relevant disease models, addressing regulatory demands for product characterization.

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HLA-A*11:01-Restricted T Cell Receptors Targeting Mutant NPM1 for Adoptive Cell Therapy in Acute Myeloid Leukemia

Pursley, A. J.; Kirmani, U.; Chen, A. L.; Yu, Z.; Hanada, K.-I.; Ade, C. M.; Chien, C. D.; Cha, N.; Flegel, W. A.; Aplan, P. D.; Carroll, M.; Taylor, N. N.; Yang, J. C.; Pavletic, S. Z.; Pai, S.-Y.; Leko, V.

2026-10-01 immunology 10.64898/2026.09.25.754423 medRxiv
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Acute myeloid leukemia (AML) is an aggressive hematologic malignancy associated with a poor prognosis and an unmet need for more effective treatment options, particularly after relapse. One potential approach to address this need, which has been used successfully in solid tumors, is adoptive transfer of T cells engineered to express specific T cell receptors (TCRs). Particularly attractive are TCRs that can target epitopes derived from oncogenes on which cancer cells depend while sparing normal cells that do not harbor the mutation. One promising oncogenic target in AML is mutated nucleophosmin 1 (mtNPM1), present in up to 30% of AML cases. Most NPM1 mutations result in a common frameshifted sequence that generates peptides presented by several class I human leukocyte antigens (HLAs), such as HLA-A*11:01. In this study, we vaccinated HLA-A*11:01-transgenic mice with the mtNPM1 peptide AVEEVSLRK and isolated six functional TCRs from mtNPM1-reactive lymphocytes. When engineered into human T cells, two of these TCRs consistently mediated robust and specific lysis of an AML cell line and primary AML cells co-expressing HLA-A*11:01 and mtNPM1. Neither TCR recognized related human peptides, HLA-A*11:01-expressing normal peripheral blood mononuclear cells or stem/progenitor cells, or cells expressing diverse allogeneic HLAs, suggesting a low risk of cross-reactivity and alloreactivity. In an AML xenograft model, both TCRs controlled AML in hematopoietic organs, although extramedullary tumors emerged during treatment, potentially reflecting the aggressive behavior of the model that may not be representative of AML in patients. Together, these data suggest that the two TCRs represent strong candidates for further preclinical development in adoptive T cell therapy for NPM1-mutated, HLA-A*11:01-positive AML. These results also support the use of HLA-transgenic mice as a platform for generating TCRs targeting oncogene-derived epitopes in hematologic malignancies.

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Enhanced 3D Osteogenic Differentiation of Encapsulated Human MSCs in Hyaluronic Acid Core Alginate Shell Capsules under Dynamic Culture Conditions

Dreger, J.; Contreras-Perez, D. A.; Keck, M.; Egger, D.

2026-09-29 bioengineering 10.64898/2026.09.29.755283 medRxiv
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The growing demand for three-dimensional (3D) in vitro models that accurately replicate human tissue to investigate disease mechanisms, enable tissue replacement, and support drug testing is driving the need for more advanced manufacturing platforms. Mesenchymal stem/stromal cells (MSCs) are promising candidates for tissue engineering and stem cell therapies due to their regenerative potential and ethical advantages. However, the reproducible and scalable production of 3D models that truly mimic the human complexity and function poses a major challenge. To address these challenges, we have developed a scalable and semi-automated 3D differentiation process for generating osteogenic microtissue derived from MSCs encapsulated in core-shell capsules (CSCs). To validate material-dependent, osteo-inductive effects of hyaluronic acid (HA), we systematically characterised our encapsulation process with regard to CSC integrity, spheroid formation and viability, as well as diffusion and shear thinning properties. Osteogenic differentiation was performed in static and dynamic culture, using either conventional 6-well plate format or a rotating wall vessel bioreactor. HA-CSCs were compared with inert carboxymethyl cellulose (CMC)-CSCs. In addition, hypoxic culture condition and the implementation of human platelet lysate (hPL) further supported physiological relevance. HA led to the formation of larger spheroids with high cell viability and increased metabolic activity compared to CMC. Calcium phosphate deposition within the extracellular matrix (ECM) and elevated ALP activity confirmed successful osteogenesis in all conditions. Furthermore, both HA and dynamic culture promote osteogenesis, and when combined, synergistically enhance the osteogenic differentiation. In conclusion, we present a semi-automated, high-throughput and xeno-free platform process for the 3D differentiation of MSCs towards osteogenic lineage. By integrating HA, hypoxia and dynamic culture conditions, this capsule-based system enhances the physiological relevance, enabling advanced in vitro disease modelling, drug testing, and scalable microtissue generation while reducing reliance on animal models.

9
Fed-batch production of antiviral OP7 chimera defective interfering influenza A particles

Holste, W.; Kupke, S. Y.; Seitz, C.; Reichl, U.; Ziehr, H.

2026-10-01 bioengineering 10.64898/2026.09.30.755589 medRxiv
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Influenza A virus (IAV) defective interfering particles (DIPs) are regarded as promising broad-spectrum antivirals due to their high efficacy demonstrated in animal trials. Previously, an OP7 chimera DIP was generated that showed markedly enhanced antiviral efficacy compared to conventional IAV DIPs. In addition, a high-yield cell culture-based production process for OP7 chimera DIPs was established in perfusion mode. However, due to the technical complexity of this technology, we aimed to combine the advantages of perfusion in terms of yield with that of a simple and less complex batch process. In the present work, we established a fed-batch production process for OP7 chimera DIPs that allows a more straightforward implementation into existing production facilities. Using a feeding regime that was able to overcome the cell density effect, we achieved productive virus infection in stirred tank reactors until a cell density of 10E+6 cells/mL. Furthermore, we obtained a high virus titer of 3.8 log10(HAU/100 uL), corresponding to a 3.4-fold increase compared to a reference batch production. Moreover, the produced material demonstrated a significantly increased interfering bioactivity shown by an in vitro potency assay. Interestingly, this efficacy was similarly high as compared to OP7 chimera DIP material previously produced in perfusion mode, despite twofold lower virus titers. Finally, we demonstrate robustness of OP7 chimera DIP seed virus trains, which is significant step towards later pharmaceutical production. Further, corresponding GMP MDCK-PB2(sus) cell and OP7 chimera virus banks are now available for later biomanufacturing further use. In conclusion, the established fed-batch process offers a valid n additional option for pharmaceutical grade OP7 chimera DIP GMP manufacturing production under GMP conditions required for subsequent clinical testing and for later large-scale manufacturing.

10
Low-Cost Tissue Expansion Using a Saline-Based Device Shows Comparable Histological Outcomes in a Rat Model

Rosa, T. G.; da Silva, L. C. K.; de Abreu, T. Z.; Neto, J. S.; Ribas Filho, J. M.

2026-10-06 bioengineering 10.64898/2026.10.05.756788 medRxiv
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Tissue expansion is an established technique for the reconstruction of skin defects, but the cost of conventional silicone expanders may limit its application in contexts with lower resource availability. This study evaluated, in an experimental model, whether a container for storing saline solution could act as a low-cost alternative device for tissue expansion. An experimental, prospective, controlled and randomized study was carried out with 10 Wistar rats, distributed in two groups: conventional silicone expander and saline storage container. Both underwent the same surgical and expansion protocol. Abdominal circumference gain, final expanded skin length, histological and histomorphometric aspects of the skin, including collagen types I and III, as well as exploratory cost analysis, were analyzed. The conventional expander produced a greater gain in abdominal circumference, but the final length of the expanded skin was similar between the groups. Microscopic evaluation showed preservation of the cutaneous architecture, intact epidermis, cellularized dermis, and collagen deposition in both groups. There was no significant difference in the proportion of type I or type III collagen. The saline solution container had a substantially lower cost per centimeter of expanded skin than the conventional expander. These findings suggest that the saline container can produce experimental skin expansion with final length and collagen composition similar to the conventional method, at a lower cost, although additional studies are needed before clinical application.

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Enriching microlaser-labelled cells by commercial flow cytometry-based cell sorting systems

Koenig, M.; Plaskocinski, T. T.; Popczyk, A.; Titze, V. M.; Gaedke, F.; Germer, M.; Schumacher, A.-L.; Schmidt, A. M.; Schubert, M.; Gather, M. C.

2026-10-05 bioengineering 10.64898/2026.10.02.756078 medRxiv
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Microlasers based on whispering-gallery modes (WGMs) provide bright, spectrally narrow emission, making them ideal optical probes for high-resolution cellular tagging, single-cell tracking, and biosensing. To reproducibly apply WGM microlasers in biomedical or tissue-engineering contexts, control over the number of lasers in a cell population is highly desirable. Here we use a commercial instrument for flow cytometry-based cell sorting to obtain HEK293T cell populations with a controlled number of polystyrene laser particles (LPs). By modifying the particle surface with poly(ethyleneimine) (PEI) or lipofectamine, we enhance LP-association to cells. We demonstrate that our sorting procedure yields viable cells showing unchanged proliferation rates. Manufacturer-dependent differences in particle-cell interactions were observed and investigated by scanning and transmission electron microscopy (SEM/TEM) and flow cytometry. Finally, we show that the same sorting approach enables the generation of multi-cellular spheroids with a defined ratio of LP-containing and LP-free cells. This work lays the foundation for larger tissue engineering studies with defined LP populations and control over LP-placement with respect to the cell.

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Patient-Derived Melanoma Organoids Preserve Tumor-Immune Heterogeneity and Reveal Context-Dependent Responses to Immune Checkpoint Blockade

Serasanambati, M.; Chadokiya, J.; Nakano, M.; Julve, M.; Funchain, P.; Sharma, S.; Wagner, E.; Singh, P.; Kuo, C.; Betof, A.; Kirane, A. R.

2026-09-29 immunology 10.64898/2026.09.23.753873 medRxiv
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Abstract Background: Experimental models that retain endogenous tumor immune complexity are needed to investigate heterogeneous responses to immune checkpoint inhibitors (ICIs) in melanoma. We established patient-derived melanoma organoids (PDMOs) to examine retention of parental tumor cellular components and investigate patient-specific and context-dependent responses to checkpoint blockade. Methods: Fresh melanoma specimens (n=50), including primary tumors, neoadjuvant-treated tumors and tumor-infiltrating lymphocyte (TIL) associated samples were processed for Matrigel-embedded culture of patient-derived melanoma organoids (PDMOs). Characterization and functional studies were performed in subsets of established cultures. Immunofluorescence assessed tumor, stromal, immune, and checkpoint-marker expression in PDMOs and matched parental tissues. NGFR expression was evaluated in relation to organoid establishment and growth. Responses to anti PD1 alone or combined with anti-LAG3 or anti-CTLA4 therapies were evaluated using viability and morphological analyses, with selected models undergoing immune phenotyping and multiplex cytokine profiling. Available clinical outcomes were used for exploratory comparison. PDMOs and matched two-dimensional cultures were evaluated under 21% and 5% oxygen conditions. Results: PDMOs were established from 30 of 50 specimens (60%) and retained melanoma, stromal, lymphoid, and myeloid components identified in matched parental tissues during early culture, together with immune checkpoint expression. Higher NGFR (CD271) expression was associated with greater organoid-forming capacity in an exploratory subset. Responses to checkpoint blockade varied across patient-derived models and regimens, with combination blockade not uniformly producing lower viability than PD1 monotherapy. Ex vivo responses showed parallels with available clinical outcomes, with discordant cases also observed. In three selected PDMOs, divergent PD-1 responses were accompanied by differences in T-cell and myeloid representation, MHCII and AXL expression, and inflammatory versus immunoregulatory cytokine profiles. Under normoxic conditions, PDMOs and matched two-dimensional cultures exhibited divergent treatment sensitivities, including clinically responding cases in which sensitivity was retained in PDMOs but attenuated in monolayers. Changing oxygen tension further altered checkpoint sensitivity within individual PDMOs, with the direction and magnitude of the observed shifts varying by model and regimen. Conclusions: Early passage PDMOs retain key endogenous tumor, immune, and stromal components and support functional investigation of patient-derived melanoma biology. Their heterogenous responses across checkpoint regimens and oxygen conditions provide a platform for investigating how tumor-immune composition and environmental context influence treatment sensitivity.

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A synthetic xeno-free extracellular matrix surrogate supports robust human induced pluripotent stem cell maintenance and multilineage differentiation

Berger, C.; Wiora, L.; Holmes, T. L.; Walz, F.; Sauter, C.; Baraban, L.; Schwebler, J.; Beer, G.; Lauke, S.; Keller, J.; Kraft, M.; Schelling, Y.; Cheung, K.; Nurnberg, E.; Al Muthafer, S.; Segeletz, S.; Neser, C.; Smith, J. G. W.; Hauser, S.; Zdzieblo, D.

2026-10-09 cell biology 10.64898/2026.10.07.757018 medRxiv
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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.

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Toward Digital-Twin-Enabled Bioprocess Monitoring: Fault-Inclusive Soft Sensing of Penicillin Concentration Under Process Deviations

Behlim, A. B.; Tilewale, A.; Patel, D.

2026-09-23 bioengineering 10.64898/2026.09.21.753176 medRxiv
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Data-driven soft sensors can estimate fermentation product concentrations from routinely recorded process variables, but strong performance during normal operation does not establish reliability during process deviations. This study evaluated current-time penicillin-concentration estimation using 100 simulated IndPenSim batches comprising 90 normal-operation batches and ten documented deviation batches, with 113,935 observations in total. Initial normal-trained models and five follow-up experiments examined complete-batch validation, dependence on batch-progress features, phase-specific error, model-family comparisons, early out-of-distribution warnings and empirical prediction ranges. These analyses motivated a matched comparison between normal-only and fault-inclusive HistGradientBoosting regressors using 36 current and causal history-based inputs. Normal performance was evaluated in five regime-balanced complete-batch folds, and deviation performance by leave-one-fault-batch-out evaluation; every tested deviation batch was excluded from its own model fit. Batch-balanced sample weights were used, with a factor of three assigned to permitted deviation batches in fault-inclusive fitting. On held-out deviation batches, pooled RMSE decreased from 3.195 to 2.564 g/L, a reduction of 19.73%, while MAE decreased from 2.076 to 1.441 g/L and R2 increased from 0.8580 to 0.9085. Normal-operation RMSE was nearly unchanged at 1.981 and 1.983 g/L. Eight of ten deviation batches improved. The mean paired fault-batch RMSE difference was -0.7063 g/L, with a descriptive 95% batch-bootstrap interval of -1.2844 to -0.2194 g/L. Improvement was largest within the first-to-last recorded fault-reference window, but late-stage errors persisted. Batch 100 remained poorly predicted, with fault-inclusive RMSE of 6.631 g/L and R2 of -2.4837. A fault-risk classifier, Isolation Forest OOD detector and empirical error ranges offered incomplete reliability information. Fault-inclusive training therefore improved this benchmark on average, but did not establish generalization to unseen fault mechanisms, calibrated safety warnings or deployment in physical fermentation.

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TorPause: Efficient Static Organ Preservation for Transplants

Bhadury, J.; Tajima, T.; Suchy, F. P.; Masaki, H.; Zhang, J.; Rivera, M.; Nishimura, T.; Charlesworth, C. T.; Esquivel, C. O.; Nakauchi, H.

2026-10-09 developmental biology 10.64898/2026.10.08.755167 medRxiv
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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.

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CD19 CAR Engineered T Regulatory Cells Promote Durable Immune Tolerance in Experimental Systemic Lupus Erythematosus

Drow, T.; Doglio, M.; Grimm, A.; DeVault-Nelson, V.; Hoover, M.; McKinney, B.; Tripathi, S. K.; Mellen, J.; Milazewski, M.; Zarin, P.; Burgess, A.; Moore, C. L.; Carulli, P.; Ugolini, A.; Bercher, C.; Vakil, A.; Dahl, N. P.; Ponnan, S. M.; Mungra, N.; Akilesh, S.; Chen, Y.; Knebusch, P.; Jackson, S. W.; Patel, C.; Chen, T.; Del Rio-Espinola, A.; Bonini, C.; Wickham, T.; Cook, P. J.; Rawlings, D. J.

2026-10-11 immunology 10.64898/2026.10.05.756761 medRxiv
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While the immune reset induced by CD19 CAR T therapies has shown striking promise in systemic lupus erythematosus (SLE), the nature and duration of benefit mediated by B cell depletion remains unclear. Loss of tolerance in SLE is driven by extrafollicular and germinal center interactions between dendritic cells and self-reactive T and B cells. We hypothesized that CD19 CAR-engineered regulatory T cells (CAR19 EngTreg), capable of suppressing multiple autoimmune effector cell types, might promote long-term tolerance without producing high-levels of inflammatory mediators. To generate CAR19 EngTreg, we combined CD19 CAR delivery with homology directed repair at the FOXP3 locus to drive constitutive, stable FOXP3 expression in CD4 T cells. CAR19 EngTreg expressed canonical Treg markers; exhibited minimal inflammatory cytokine production; and blocked human B cell differentiation into antibody secreting plasma cells. In humanized mouse models, transfer of CAR19 EngTreg led to a reduction in B cell numbers with low inflammatory cytokine production relative to CD19 CAR Teff, and reduced tissue inflammation. In a short-term, in vivo imiquimod-induced inflammatory model, murine CAR19 EngTreg reduced skin pathology, spleen size, and inflammatory cytokines. Finally, in two distinct mouse models of lupus, CAR19 EngTreg persisted for >4 months leading to reduced autoimmune T and B effector populations, sustained reduction in multiple autoantibodies and improved renal function and histopathology. Thus, CAR19 EngTreg may offer a promising and durable therapeutic avenue for B cell-mediated autoimmune disorders capable of long-term regulation of both autoreactive B and T cells.

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Scalable generation of human stem cell-derived ureteric bud and collecting duct organoids in stirred bioreactors

Wolf, K. J.; Rubins, J.; van Gaal, R.; Stevens, K.; Klaus, A.; Nair, P.; Lewis, J. A.

2026-09-28 bioengineering 10.64898/2026.09.27.754790 medRxiv
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Emerging efforts to engineer multicellular kidney tissues for drug discovery, disease modeling, and therapeutic repair require scalable generation of kidney organoids derived from human induced pluripotent stem cells (hiPSCs). Here, we report a method for generating kidney ureteric bud and collecting duct epithelial organoids in stirred tank bioreactors. We demonstrate that extracellular matrix microcarriers facilitate organoid expansion and are compatible with suspension bioreactor methods. The combination of cell-coated matrix microcarriers with stirred bioreactors promotes maturation marker expression compared to static controls comprising matrix-embedded organoids. Our method offers promise for generating epithelial organoids that serve as multicellular models and organ building blocks for scalable biofabrication.

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Venous Angiogenesis and Dermal Fibroblast Augmentation of Decellularized Dermis: Towards Transplantable Dermal Substitutes

Lau, S. W.; Zhang, Y. L.; Xie, D.; Makhoul, N.; Jaloux, C.; Barralet, J.

2026-10-02 bioengineering 10.64898/2026.09.30.755543 medRxiv
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The ability to generate vascularized tissue constructs supplied by surgically accessible vessels remains a major limitation in reconstructive tissue engineering. Previous work demonstrated that positioning porous biomaterials around a vein can induce extensive vascular sprouting and generate a vascularized tissue volume without creation of an arteriovenous loop. However, this phenomenon has principally been demonstrated using rigid calcium-phosphate scaffolds, limiting its direct relevance to soft-tissue reconstruction. Here, we investigated whether a flexible decellularized dermal matrix could similarly be vascularized around a single unmodified vein and whether autologous dermal fibroblasts could further enhance this response. Decellularized rat dermis, with or without autologous dermal fibroblast seeding, was implanted either subcutaneously in the dorsal region or around the femoral vein for 8 weeks. Following Microfil perfusion, three-dimensional micro-CT demonstrated an extensive branching vascular network within perivenous constructs. Vessel volume relative to tissue volume was 0.2 +/- 0.1% in subcutaneous constructs without fibroblasts (n = 11) and 0.6 +/- 0.2% with fibroblasts (n = 9), compared with 6.+/- 1.4 % in perivenous constructs without fibroblasts (n = 10) and 7.3+/- 1.2% with fibroblasts (n = 10). Histology and immunohistochemistry similarly showed greater cellular repopulation and substantially higher CD31- and -SMA-positive vessel densities following perivenous implantation. Integrated two-way ANOVA of the same 8-week data confirmed a dominant effect of implantation site across the vascular outcomes, while fibroblast seeding significantly affected vascular volume, dermal remodeling, and nuclear density. The effect of fibroblast seeding on vascular volume was site dependent, with a significant implantation site fibroblast interaction. At 8 weeks, the vascularized dermal construct was completely dissected free from the surrounding tissues while maintaining its connection to the femoral vein. A small superficial incision into the isolated dermis produced visible bleeding, supporting an acute functional connection of the intradermal vascular network to the host circulation while the femoral venous connection was preserved. After flap elevation, perivenous constructs retained substantially greater vascular volume and showed more complete surface healing and organized skin architecture than subcutaneous constructs. Fibroblast seeding accelerated wound closure, while its effect on post-elevation vascular volume depended on implantation site: VV/TV decreased in subcutaneous constructs but increased in perivenous constructs. These findings show that single-vein vascularization can extend from rigid calcium-phosphate biomaterials to a compliant biological extracellular-matrix scaffold and may provide a simplified axial vascularization strategy without arterialization or incorporation of an arterial vessel.

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Bioreactor cultures of brain endothelial cells produce extracellular vesicles with comparable characteristics as that of batch cultures

Govindaswamy, B.; Lu, C.-C.; Achanta, N.; Chen, E. Y.; Rebeles, K.; Pinky, P. P.; Basudkar, V.; Parween, F.; Soundara Manickam, D.

2026-10-06 bioengineering 10.64898/2026.10.05.756840 medRxiv
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Our prior works have demonstrated the therapeutic potential extracellular vesicles (EVs) derived from batch cultures of brain endothelial cells (BECs) owing to their ability to transfer mitochondria to injured recipient cells. However, conventional batch/flask cultures limit scalable and reproducible production of EVs. Here, we evaluated a CELLine AD1000 bioreactor as a platform for sustained production of EVs from mouse b.End3 BECs and compared bioreactor-derived (BR) EVs with EVs obtained conventional batch cultures (BT). Large EVs (lEVs) and small (sEVs) were isolated using a sequential centrifugation protocol and were characterized using dynamic light scattering, nanoparticle tracking analysis, microBCA assay, western blotting, proteomics analysis, and their ability to rescue bioenergetics in oxygen-glucose deprived (OGD) BECs. Bioreactor cultures maintained high cell viabilities (~90%) for up to eight weeks and produced approximately three- to four-fold greater EV protein yields than batch cultures. BR EVs showed reproducible particle characteristics consistent with EV subtypes derived from BT cultures. CD63, CD9 and Arf6 were detected in EV fractions, whereas the mitochondrial outer-membrane protein TOMM20 was enriched in lEVs. Proteomic analyses revealed that bioreactor-derived lEVs retained the mitochondrial cargo signature observed in batch-derived lEVs. Both bioreactor and batch EVs restored relative ATP levels in ODG-exposed BECs. These findings suggest that bioreactor BEC cultures are a scalable approach for generating functionally active BEC-EVs for downstream characterization and therapeutic development.

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TGFB1-Engineered Induced Mesenchymal Stromal Cells Exhibit High Immunomodulatory Potency and Durably Reprogram Synovial Macrophages in Osteoarthritis

Fan, K.; Rasti, M.; Khan, R.; Ziyaeyan, A.; Barazandeh, A. F.; Low, R.; Garcia, J.; Safara, S.; Nouri, S.; Robb, K. P.; Gandhi, R.; Viswanathan, S.

2026-09-29 immunology 10.64898/2026.09.24.753893 medRxiv
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Clinical translation of mesenchymal stromal cell (MSC) therapies derived from primary tissue sources is limited by manufacturing inconsistencies driven by donor-to-donor variability, which reduces predictability of clinical response. Induced pluripotent stem cell (iPSC)-derived MSCs (iMSCs) offer a promising donor-independent, clonal alternative strategy that is also more amenable to engineering, but whether engineered iMSCs reproduce the potency attributes of primary MSCs remains unclear. Here, we benchmarked a doxycycline-inducible, hTERT-immortalized iMSC line engineered to overexpress TGFB1 (TGFB1-iMSCs), a key regulator of macrophage polarization, against multiple adipose tissue-derived MSC (MSC(AT)) donors across predefined immunomodulatory and angiogenic potency attributes. TGFB1-iMSCs were smaller and more circular with comparable or higher proliferative rates than primary MSC(AT) donors. Interestingly, they had a distinct angiogenic signature (EDIL3, EDN1, PDGFA), and nine differentially expressed microRNAs were predicted to target secretory trafficking and growth factor receptor signalling. Functionally, however, TGFB1-iMSCs secreted less VEGF and showed intermediate HUVEC tube formation, but matched or exceeded all primary MSC(AT) donors in a monocyte-macrophage transwell immunomodulatory assay. Notably, in a murine destabilization of the medial meniscus (DMM) model of post-traumatic osteoarthritis, a single intra-articular injection of TGFB1-iMSCs, but not MSC(AT), reduced total synovial macrophage numbers and lowered the MHCII/CD206 ratio at eight weeks, although it did not reduce cartilage degeneration, synovitis, or fibrosis. Together, these findings show that TGFB1-engineered iMSCs have a macrophage-directed potency profile distinct from that of primary MSC(AT). Immortalized iMSCs therefore provide a reproducible platform for mechanistically dissecting engineered MSC potency and its effects on the immune environment.