3d collagen models  (Thermo Fisher)

Journal: iScience

Article Title: Optimized alveolar epithelial cell model for chronic Pseudomonas aeruginosa and Staphylococcus aureus coinfections

doi: 10.1016/j.isci.2025.113620

Figure Lengend Snippet: Pro-inflammatory cytokine production in collagen coating and 3D c ollagen models (A) IL-6 (pg/mL) and (B) IL-8 levels (pg/mL) in cell culture supernatants at 30 h post-infection. The different strains are indicated as follows: P. aeruginosa PAET1 (PAET1) and Staphylococcus aureus Newman (SA). Values are represented as mean ± SD. Data were compared by a two-way ANOVA analysis with a Tukey’s multiple comparisons test. Statistical significance denoting differences between non-infected (black bars) and infected cells, or between coinfection and single-species infections are indicated by asterisks (∗∗∗, p < 0.001; ∗∗∗∗, p ≤ 0.0001).

Article Snippet: For 3D collagen models, 200 μL of collagenase I (800 -1000 units/mL; Thermo Fisher Scientific) in DMEM/F12 was added, whereas for the 3D VitroGel model, 200 μL of VitroGel cell recovery solution (Tebubio) was used instead.

Techniques: Cell Culture, Infection

Journal: iScience

Article Title: Optimized alveolar epithelial cell model for chronic Pseudomonas aeruginosa and Staphylococcus aureus coinfections

doi: 10.1016/j.isci.2025.113620

Figure Lengend Snippet: Expression of virulence ( exoS , toxA , and vgrG ) and biofilm-related ( wspR , bfiR , and pelA ) genes Fold changes are expressed in comparison to their control (stationary planktonic bacteria in a non-infecting state, without the presence of A549 cells) obtained by RT‒qPCR analysis. 2D refers to the c ollagen coating model, while 3D to the 3D collagen model. The different strains are indicated as follows: P. aeruginosa PAO1 (PAO1) and P. aeruginosa PAET1 (PAET1). Data are presented as mean ± SD. Data between models was compared by one-way ANOVA analysis with a Tukey’s multiple comparisons test (represented in dashed lines). In addition, each gene was compared to its own control with an unpaired t test (∗∗, p ≤ 0.01; ∗∗∗, p < 0.001; ∗∗∗∗, p ≤ 0.0001).

Article Snippet: For 3D collagen models, 200 μL of collagenase I (800 -1000 units/mL; Thermo Fisher Scientific) in DMEM/F12 was added, whereas for the 3D VitroGel model, 200 μL of VitroGel cell recovery solution (Tebubio) was used instead.

Techniques: Expressing, Comparison, Control, Bacteria

Journal: Cells

Article Title: Growing Role of 3D In Vitro Cell Cultures in the Study of Cellular and Molecular Mechanisms: Short Focus on Breast Cancer, Endometriosis, Liver and Infectious Diseases

doi: 10.3390/cells13121054

Figure Lengend Snippet: ( a ) In 2D adherent cultures, cells grow as a monolayer on a flat surface, allowing unrestricted access to a similar number of nutrients and growth factors in the culture medium, resulting in homogeneous growth and proliferation. Cell–cell interactions and the extracellular environment are absent. The 3D model recapitulates the characteristics of the tumour microenvironment. Adequate cell–cell and extracellular environment interactions are allowed. A variable availability of oxygen, nutrients, metabolites and signalling molecules is established (adapted from under the terms and conditions of the Creative Commons Attribution (CC-BY) license (CC-BY 4.0)). ( b – d ) Schematic representation of different culture conditions ( b ), expression of CCL5 receptors (CCR1 and CCR5) in mono- and co-culture spheroids of ASCs and MDA-MB-231 or MCF-7 compared to indirect and direct 2D cultures ( c , d ). * indicates statistically significant differences ( p < 0.05) between culture systems; Δ indicates statistically significant differences ( p < 0.05) to corresponding monocultures (adapted from under the terms of the CC-BY 4.0 publishing license). ( e , f ) Images of HCC1954 spheroids stiffened by different concentrations of ribose (0.50 and 200 mM). ( e ) Fixed samples show the distribution of ERK (green) and F-actin (magenta), with counterstained nuclei in blue. Scale bars, 20 μm. ( f ) Spheroids embedded in a 3D collagen structure show the localization of YAP (green); nuclei are stained blue. Scale bars, 20 μm (adapted from under the terms of the CC-BY 4.0 publishing license). ( g ) Box representation of doxorubicin effects in the MDA-MB-231 cell line cultured within the 3D biomimetic collagen scaffold, indicating the most significantly altered pathways implicated in DOX resistance (green = up-regulation; red = down-regulation) (adapted from under the terms of the CC-BY 4.0 publishing license).

Article Snippet: Specifically, they engineered a 3D model based on biomimetic collagen scaffolds, revealed the involvement of hypoxia in doxorubicin resistance in MDA-MB-231 and also made it possible to identify the most significantly altered pathways involved in drug resistance ( g).

Techniques: Expressing, Co-Culture Assay, Staining, Cell Culture

Journal: Cells

Article Title: Growing Role of 3D In Vitro Cell Cultures in the Study of Cellular and Molecular Mechanisms: Short Focus on Breast Cancer, Endometriosis, Liver and Infectious Diseases

doi: 10.3390/cells13121054

Figure Lengend Snippet: Summary of some recent findings on BC using 3D cell cultures.

Article Snippet: Specifically, they engineered a 3D model based on biomimetic collagen scaffolds, revealed the involvement of hypoxia in doxorubicin resistance in MDA-MB-231 and also made it possible to identify the most significantly altered pathways involved in drug resistance ( g).

Techniques: Expressing, Binding Assay, Gene Expression, Activity Assay, Concentration Assay, Formulation, Phospho-proteomics, Cell Culture, Over Expression, RNA Sequencing, Injection, Knockdown

Journal: Cells

Article Title: Growing Role of 3D In Vitro Cell Cultures in the Study of Cellular and Molecular Mechanisms: Short Focus on Breast Cancer, Endometriosis, Liver and Infectious Diseases

doi: 10.3390/cells13121054

Figure Lengend Snippet: Examples of 3D in vitro models for the study of host–microbe interactions.

Article Snippet: Specifically, they engineered a 3D model based on biomimetic collagen scaffolds, revealed the involvement of hypoxia in doxorubicin resistance in MDA-MB-231 and also made it possible to identify the most significantly altered pathways involved in drug resistance ( g).

Techniques: In Vitro, Over Expression, Protein-Protein interactions, Homologous Recombination, Expressing, Gene Expression, Translocation Assay, Cell Culture, Chemotaxis Assay

Journal: Cells

Article Title: Growing Role of 3D In Vitro Cell Cultures in the Study of Cellular and Molecular Mechanisms: Short Focus on Breast Cancer, Endometriosis, Liver and Infectious Diseases

doi: 10.3390/cells13121054

Figure Lengend Snippet: Infection in 3D culture models. ( a ) Human intestinal enteroids (HIE) monolayers were infected with wild-type (WT) Shigella and the avirulent CSF100 strain. The panel shows host gene expression (as log 2 -fold change) after three hours of Shigella infection (adapted from with permission from Copyright American Society for Microbiology-License number 1494825-1). Statistical significance is expressed as p < 0.05, *. ( b , c ) Salmonella infection in LSMMG and in control culture conditions (adapted from under the terms of a CC-BY 4.0 publishing license). The analyzed strains were the wild-type (WT) and the mutant delta-hfq strains. ( b ) Bacterial genes that were up- and down-regulated, in red and blue, respectively, were associated with Salmonella Pathogenic Islands (SPI) 1, 2, motility and chemotaxis. The expression was reported as the mean log 2 fold change. ( c ) Plots illustrating the up- (red dots) and down-regulation (blue dots) of genes expressed by host cells infected at 24 h post-infection (hpi) by WT (left panel) and delta-hfq (right panel) strains in LSMMG conditions. Expression reported as the logFC (logged fold change) as a function of the FDR (false discovery rate) < 0.05. ( d ) Label of a section of a skin 3D model after 48 h of infection with MRSA bacterial strains (ST8, ST30, ST59, ST22, ST45, ST239). Each line composed of i, ii, iii and iv represents a bacterial strain. The white dashed line marks the dermal epidermal barrier between the stratum basale and the collagen gel containing fibroblasts. Specifically, (i) shows HaCaT keratinocytes nuclei, at the strata basale and spinosum (yellow line), marked in blue with Hoechst stain. (ii) shows MRSA bacteria labeled with an anti- S. aureus antibody and Alexa Fluor ® 568 conjugated secondary antibody. Those indicated by yellow arrows are in the collagen gel. (iii) shows the Click-iT ® TUNEL Alexa Fluor ® 488 cell for the detection of damaged DNA. Finally, (iv) is an overlay where bacteria and apoptosis/DNA damage are co-localized in keratinocytes in the stratum spinosum. The yellow circles in (iv) depict the model’s skin being exfoliated. Scale Bar (i–iv) of 50 µm (adapted from under the terms of a CC-BY 4.0 publishing license).

Article Snippet: Specifically, they engineered a 3D model based on biomimetic collagen scaffolds, revealed the involvement of hypoxia in doxorubicin resistance in MDA-MB-231 and also made it possible to identify the most significantly altered pathways involved in drug resistance ( g).

Techniques: Infection, Gene Expression, Control, Mutagenesis, Chemotaxis Assay, Expressing, Staining, Bacteria, Labeling, TUNEL Assay

Journal: Pharmaceutics

Article Title: Microfluidic Liver-on-a-Chip for Preclinical Drug Discovery

doi: 10.3390/pharmaceutics15041300

Figure Lengend Snippet: Summary of the application of LoC in drug development.

Article Snippet: Drug toxicity , collagen-based 3D model, integrated biomimetic array chip, cell–extracellular matrix interaction , PHHs , 122 clinical drugs evaluated for liver toxicity , large-scale hepatotoxicity screening , [ ] .

Techniques: In Vitro, High Throughput Screening Assay