Defined Cell Culture Highlights

Immunocompetent Organoids, Stem Cell Secretomics, & Bioprocess Monitoring

October 5-11, 2026

New research in lung organoids, iPSC secretome analysis, hematopoietic stem cell maintenance, mesenchymal stem cell culture, and large-scale bioprocess monitoring showed how culture conditions shape both biological function and analytical performance. These studies highlighted the importance of preserving multicellular complexity, controlling sample collection conditions, maintaining stem cell potency, and measuring culture behavior throughout production.

Lung organoids preserve tissue-resident immune responses

A Nature study published October 7 developed long-term adult human lung organoids that retain epithelial, stromal, and immune populations from the original tissue.

The researchers placed intact distal lung fragments from more than 220 donors into a three-dimensional air-liquid interface culture. The organoids could be maintained for several months while preserving endogenous T cells, B cells, natural killer cells, and myeloid cells. Resident T cells retained memory markers and T cell receptor repertoires resembling those in the corresponding fresh tissue.

When infected with SARS-CoV-2, the organoids produced inflammatory signals and virus-specific tissue-resident T cell responses. Pre-exposure to SARS-CoV-2 peptide pools strengthened the local immune response and reduced subsequent infection.

Many organoid workflows emphasize epithelial expansion but lose immune and stromal populations during tissue processing. This study shows that culture architecture can preserve a more complete tissue environment, enabling epithelial infection and local immune memory to be studied in the same system. Maintaining that complexity over several months will require careful control of media, gas exchange, tissue geometry, and culture stability.

Read the study here.

Culture conditions determine the quality of iPSC secretome measurements

A Journal of Proteome Research paper published October 7 introduced an optimized workflow for analyzing proteins secreted by human iPSCs.

Secretome analysis is particularly difficult in pluripotent stem cells because serum starvation or growth factor withdrawal can disrupt cell state. At the same time, proteins already present in the culture medium can obscure lower-abundance proteins released by the cells.

The researchers systematically evaluated medium composition, conditioned medium collection time, plating density, sample clarification, mass spectrometry acquisition, and data analysis. The best-performing workflow used full-strength maintenance medium, cultures at approximately 80% confluence, a 48-hour collection period, two-step centrifugation, and data-independent acquisition mass spectrometry.

The workflow was then applied to isogenic progranulin-deficient iPSCs. The extracellular proteome showed a coordinated reduction in lysosomal hydrolases even though intracellular proteomic changes were comparatively modest, suggesting altered lysosomal trafficking or secretion.

The study demonstrates that conditioned medium measurements are inseparable from the culture process used to generate the samples. Cell density, collection duration, medium composition, and sample handling all need to be standardized before secretome profiles can be compared reliably.

You can find the paper here.

Activated protein C helps preserve hematopoietic stem cell function

An EMBO Molecular Medicine study published October 9 examined how activated protein C influences human CD34-positive hematopoietic stem and progenitor cells during ex vivo culture.

Activated protein C and thrombin can both signal through the EPCR-PAR1 pathway, but researchers found that they produced different cell state outcomes. Thrombin increased calcium signaling, ERK activation, glycolysis, and differentiation, while activated protein C instead activated CREB and AKT without causing the same metabolic shift.

Brief exposure to activated protein C reduced differentiation, enhanced clonogenic potential, and counteracted the proliferation induced by interleukin-1 alpha. Treated cells also showed improved short-term serial engraftment and multilineage reconstitution in immunodeficient mice.

Ex vivo manipulation can cause hematopoietic stem cells to leave quiescence and lose engraftment capacity. These results suggest that selectively controlling EPCR-PAR1 signaling could help maintain functional potency during culture. The distinction between activated protein C and thrombin also illustrates how related signaling inputs can produce opposing outcomes through the same receptor system.

Read the study here.

Three-dimensional scaffolds support extended MSC secretome production

A European Journal of Medical Research paper published October 6 described a scalable three-dimensional culture platform for producing conditioned medium from human umbilical cord-derived mesenchymal stem cells.

The researchers cultured the cells at high density on clinical-grade gelatin sponge scaffolds. The system maintained cell viability for at least 15 days, and the conditioned medium was collected and concentrated by lyophilization.

The resulting material promoted dermal papilla cell migration and proliferation in vitro. In a mouse model, it accelerated the transition of hair follicles into the active growth phase and increased hair follicle density.

Although the scaffold was not animal-free, the study demonstrates how moving from a flat culture surface to a porous three-dimensional structure can increase cell density and support longer production periods. For cell-derived secretome or extracellular vesicle manufacturing, scaffold composition, nutrient transport, harvest timing, and downstream concentration methods can all influence the final product.

Learn more here.

Benchtop NMR tracks multiple parameters in industrial cell culture

A Journal of Pharmaceutical Innovation study published October 9 evaluated benchtop proton NMR combined with machine learning as an analytical tool for large-scale CHO cell culture.

Researchers analyzed 128 samples collected from eight 1,500-liter production batches. Models were trained to predict 36 metabolites, six metal ions, viable cell density, viability, and antibody titer using spectra from an 80 MHz benchtop instrument.

Lasso and partial least squares models predicted the measured metabolites with performance comparable to results from a 600 MHz system. The models also estimated properties that were not directly detected by NMR, including viable cell density and antibody titer. For antibody titer, the benchtop Lasso model achieved an R-squared value of 0.959 in the test batches.

While focused on CHO cell culture rather than the typical stem cell-based methods we usually cover, this study shows how information-rich measurements can be converted into practical culture monitoring tools, with clear applications across cell types. Similar approaches could support media optimization, batch comparison, early deviation detection, and feed decisions in other mammalian cell processes, including stem cell manufacturing.

Read the paper here.

Medium adaptation simplifies suspension-based virus production

A Biotechnology Progress study published October 11 investigated whether suspension-adapted Vero cells could be transferred from a proprietary formulation into a commercially available serum-free culture system.

The researchers transitioned the cells into a commercial base medium with additional readily available supplements and then evaluated production of an attenuated mumps vaccine strain. A key variable was dextran sulfate, which is commonly included to reduce aggregation but can interfere with infection by some viruses.

In this system, dextran sulfate unexpectedly increased culture longevity and infectious virus titers. Its presence may eliminate the need to exchange the growth medium before infection, simplifying the production process.

This work illustrates how media requirements can change between cell expansion and product formation. A component that supports suspension growth may inhibit, enhance, or otherwise alter viral production. Evaluating both phases together can reveal opportunities to reduce handling steps and develop more scalable manufacturing workflows.

You can find the study here.

The week’s takeaway

Long-term lung organoids preserved resident immune populations and local antiviral memory. Standardized culture and collection conditions improved the reliability of iPSC secretome measurements. Activated protein C helped human hematopoietic progenitors retain quiescence and engraftment potential, while three-dimensional scaffolds supported extended mesenchymal stem cell culture and conditioned medium production. At manufacturing scale, benchtop NMR and machine learning extracted multiple culture parameters from a single analytical platform. Suspension Vero culture showed that media components must be evaluated for their effects on both cell expansion and downstream production. Across these studies, medium composition, tissue organization, cell density, scaffold structure, collection timing, and analytical strategy all affected the biological or manufacturing outcome.

Whether you are developing a PSC, organoid, cell therapy, or disease modeling workflow, reducing variability starts with well-characterized media and supplements. Defined Bioscience provides animal-free solutions and custom media development. Explore our products or contact us to discuss your workflow.