Journal: bioRxiv

Article Title: Kinetic proofreading as a mechanism for transcriptional specificity in living human cells

doi: 10.64898/2026.03.17.711757

Figure Lengend Snippet: (A) Schematic for transcriptional regulation by ligand-inducible nuclear receptors. (B) Experimental designs for either 2 or 4h activation of GR, RXR, RARa, and PPARy nuclear receptors using synthetic ligands in human bronchial epithelial cells. (C) Volcano plots showing differentially expressed genes by RNA-seq after activation of nuclear receptors 2h post-treatment (dashed lines indicate adj p-val threshold of 0.05). (D-E) RNA-seq genome browser tracks (D) and read count values (E) at the ERRFI1 and MYH9 loci at the indicated ligand treatments. (F) GR-ChIP and H3K27ac-ChIP genome browser tracks at ERRFI1 in the absence and presence of Dex. (G) Summary of GR transcription factor acting as a specific transcription factor for ERRFI1 and non-specific transcription factor for MYH9 gene.

Article Snippet: Cells were cultured in Airway Epithelial Cell Basal Medium (ATCC, PCS-300-030) supplemented with 1% penicillin/streptomycin and Bronchial Epithelial Cell Growth Kit (ATCC, PCS-300-040) containing HLL Supplement, L-glutamine, Extract P, and Airway Epithelial Cell Supplement (“complete medium”).

Techniques: Activation Assay, RNA Sequencing

Journal: bioRxiv

Article Title: The Joubert syndrome protein CSPP1 is a conserved regulator of vertebrate multiciliogenesis and motile cilia function

doi: 10.64898/2026.03.20.713242

Figure Lengend Snippet: (A) Schematic illustration of multiciliated cell (MCC) differentiation in mouse tracheal epithelial cells (MTECs) and Xenopus embryonic epidermis. Key stages include cell cycle exit, centriole amplification (fibrous granules and deuterosomes), basal body docking, and ciliary axoneme elongation. ( B–F) CSPP1 localization in Mouse Tracheal Epithelial Cells (MTECs). Representative immunofluorescence images of MTECs at different air-liquid interface (ALI) culture days. Scale bars: 5 μm. (B) Centrioles. Cells were stained for CSPP1 (green), Centrin (magenta; centrioles), and ZO-1 (yellow; tight junctions) across differentiation stages. (C) Fibrous granules. MTECs at ALI2 (amplification) stained for CSPP1 (green), PCM1 (magenta; fibrous granules), and Centrin (yellow). (D) Deuterosomes. At ALI2, CSPP1 (green) associates with deuterosome cores marked by DEUP1 (magenta), surrounded by Centrin-positive nascent centrioles (yellow). Inset in ALI2 is 2.5X zoom. (E) Proximal-distal orientation at the centrioles. Top (ALI2) and Bottom (ALI8): CSPP1 (green) localizes relative to ODF2 (magenta; mother centriole appendage) and gamma-tubulin (yellow). Cyan arrowheads indicate the mother centriole (MC); DC indicates daughter centriole. Inset in ciliary plane is 2.5X zoom. (F) Basal bodies and cilia (ALI8). Orthogonal views show CSPP1 (green) localizing to the basal body plane (co-stained with Centrin, yellow) and extending into the ciliary plane (co-stained with Acetylated Tubulin, magenta). Inset in ciliary plane is 3X zoom. (G–J) Cspp1–mCherry localization in Xenopus epidermal MCCs. Representative immunofluorescence images of Xenopus MCCs at different differentiation stages. Scale bars: 10 μm (main panels), 0.1 μm (insets). (G) Fibrous granules. During early amplification, Cspp1–mCherry (magenta) co-localizes with PCM1 (green) and Centrin (yellow) within fibrous granules. Intercalating cell is outlined by dashed lines. Insets are 10X zoom. (H) Deuterosomes. During active amplification, Cspp1–mCherry (magenta) associates with deuterosomes marked by Deup1 (top, green) and PCNT (bottom, green), surrounded by Centrin-positive nascent centrioles (yellow). Intercalating cells are outlined by dashed lines. Inset is 10X zoom. (I) Basal bodies. In differentiated MCCs, Cspp1–mCherry (magenta) localizes to basal bodies marked by PCNT (top, green) and gamma-tubulin (bottom, green), occupying a region partially distinct from the Centrin core (yellow). Inset is 10X zoom. (J) Cilia. Cspp1–mCherry (magenta) localizes to the ciliary axoneme marked by Acetylated Tubulin (green) with enrichment at the distal tips, while maintaining basal body localization (bottom panels; Centrin in yellow).

Article Snippet: Cryopreserved human bronchial epithelial cells (HBEpC, C-12640, PromoCell, maximum passage 3) were thawed in T75 flasks in complete PneumaCult-Ex Plus medium and cultured at 37°C with 5% CO2.

Techniques: Amplification, Immunofluorescence, Staining

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: Cell viability ( A ) and cell proliferation ( B ) induced by nicotine in HBEpC and/or si-mRNA-α7-HBEpC viability. ( A ): For cell viability, 7500 cells/cm 2 are plated in T25 flask (total cell number 187,000) and treated with nicotine 1 × 10 −7 M, after 1 h cells are washed three times in PBS Ca 2+ and Mg 2+ free and then incubated in drug-free medium for additionally 48 h. Then, cells (detached or floating) are counted after staining with trypan blue dye. ( B ): For cell proliferation 7500 cells/cm 2 are plated in T25 flask and treated with nicotine every 48 h. Cells are detached and viable cells are counted every 12 h. Experiments are performed at least two times in triplicate. Statistical significance is analyzed with one-way ANOVA with multiple-comparison and post hoc test with Bonferroni correction.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques: Incubation, Staining, Comparison

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: Expression of Ki67 induced by nicotine in HBEpC and/or si-mRNA-α7-HBEpC. ( A ): ELISA experiments; ( B ): regression equation linearity, performed with Prism; ( C ): Western blotting, ( D ): densitometric analysis. Statistical significance is analyzed with one-way ANOVA with multiple-comparison and post hoc test with Bonferroni correction. Experiments are performed at least two times in triplicate. In the , raw data of Western blotting are reported.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques: Expressing, Enzyme-linked Immunosorbent Assay, Western Blot, Comparison

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: SA-β-Gal in HBEpC exposed continuously to nicotine. Experiments are performed at least two times in triplicate.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques:

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: Evaluation of intracellular Ca 2+ after exposure to nicotine for 48 h in HBEpC and/or si-mRNA-α7-HBEpC. ( A ): ELISA experiments; ( B ): regression equation linearity, performed with Prism. Statistical significance is analyzed with one-way ANOVA with multiple-comparison and post hoc test with Bonferroni correction. Experiments are performed at least two times in triplicate.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques: Enzyme-linked Immunosorbent Assay, Comparison

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: Evaluation of intracellular ATP after exposure to nicotine for 48 h in HBEpC. ( A ): ELISA experiments; ( B ): regression equation linearity, performed with Prism. Experiments are performed at least two times in triplicate.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques: Enzyme-linked Immunosorbent Assay

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: Expression of EGF and p-EGFR after exposure to nicotine for 48 h in HBEpC. ( A ): ELISA experiments for EGFR; ( B ): regression equation linearity for EGFR, performed with Prism; ( C ): ELISA experiments for p-EGFR; ( D ): regression equation linearity for p-EGFR, performed with Prism. Statistical significance is analyzed with one-way ANOVA with multiple-comparison and post hoc test with Bonferroni correction. Experiments are performed at least two times in triplicate.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques: Expressing, Enzyme-linked Immunosorbent Assay, Comparison

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: Induction of p53 and phospho-p53 induced by nicotine in HBEpC. ( A ): ELISA assay. ( B ): Western blotting experiments, ( C ): densometric analysis. Experiments are performed at least two times in triplicate. Statistical significance is analyzed with one-way ANOVA with multiple-comparison and post hoc test with Bonferroni correction. In the , raw data of Western blotting are reported.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques: Enzyme-linked Immunosorbent Assay, Western Blot, Comparison

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: Induction of phospho-p38 and p38 by nicotine in HBEpC. ( A ): ELISA experiments; ( B ): regression equation linearity for phosphor-p38; ( C ): regression equation linearity for phosphor-p38performed with Prism. Statistical significance is analyzed with one-way ANOVA with multiple-comparison and post hoc test with Bonferroni correction. Experiments are performed at least two times in triplicate.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques: Enzyme-linked Immunosorbent Assay, Comparison

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: EMT induced by nicotine in HBEpC. ( A ): Western blotting; ( B ): densitometric analysis. Statistical significance is analyzed with one-way ANOVA with multiple-comparison and post hoc test with Bonferroni correction. Experiments are performed at least two times in triplicate. In the , raw data of Western blotting are reported.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques: Western Blot, Comparison

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: Cell migration to nicotine for 48 h in HBEpC and/or si-mRNA-α7-HBEpC. HeLa cells are positive control. ( A ) HeLa positive control. ( B ): Cell migration h in HBEpC and/or si-mRNA-α7-HBEpC. Statistical significance is analyzed with one-way ANOVA with multiple-comparison and post hoc test with Bonferroni correction. Experiments are performed at least two times in triplicate.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques: Migration, Positive Control, Comparison

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: Induction of VEGF by nicotine in HBEpC and/or si-mRNA-α7-HBEpC. ( A ): ELISA experiments; ( B ) regression equation linearity for VEGFR. Statistical significance is analyzed with one-way AOVA with multiple-comparison and post hoc test with Bonferroni correction. Experiments are performed at least two times in triplicate.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques: Enzyme-linked Immunosorbent Assay, Comparison

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: Anchorage-independent growth induced by nicotine in HBEpC. HeLa cells are positive control and NIH3T3 the negative. ( A ): Representative picture of HBEpC cloned on soft agar. ( B ): Cloned cells. Statistical significance is analyzed with one-way ANOVA with multiple-comparison and post hoc test with Bonferroni correction. Experiments are performed at least two times in triplicate.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques: Positive Control, Clone Assay, Comparison

Journal: Molecules

Article Title: Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity

doi: 10.3390/molecules26010101

Figure Lengend Snippet: Effects induced by nicotine on different pathways in human airway epithelial cells (results obtained in this work and in literature) and comparison with effects caused by SARS-CoV-2, SARS-CoV, MERS-CoV and by non-tumorigenic virus infection on the same pathways.

Article Snippet: Human Bronchial Epithelial Cells (HBEpC) were obtained from Cell Applications Inc. ( www.cellapplications.com/product no. 502K-05a) and cultured in complete Bronchial/Tracheal Epithelial Cell Growth Medium ( www.cellapplications.com/product ) as described previously [ ]. si-mRNA-α7-HBEpC were obtained as described previously [ ].

Techniques: Comparison, Virus, Infection, Expressing, Concentration Assay, In Vitro, Activation Assay, Activity Assay, Knockdown, Control, Migration

Journal: Cancers

Article Title: Niclosamide and Palbociclib Act Synergistically to Reduce Cholangiocarcinoma Cell Viability In Vitro and Inhibit Tumour Growth in a Mouse Model

doi: 10.3390/cancers17223721

Figure Lengend Snippet: Drug screening and validation of Niclosamide using CCA cell lines and primary biliary epithelial cells. ( A ) A library of 104 off-patent drugs was screened using the CCLP CCA cell line. CCLP cells were plated at 1 × 10 4 cells per well in a 96 well plate and treated with each drug at its clinically relevant peak serum concentration for 96 h. Cell viability was then determined using an MTT assay and normalised to cells treated with the corresponding vehicle control for each drug. N = 3 biological repeats with a paired, two-tailed T-test followed by Benjamini–Hochberg multiple corrections. The inhibition of viability (%) is plotted against the reciprocal of the p value for each drug and Niclosamide is labelled. ( B – E ) Niclosamide dose–response curves for CCA cell lines (CCLP, RBE, and KKU-M055) and primary biliary epithelial cells (BECs) plated as in ( A ) and treated with Niclosamide [10 nM–100 μM] or vehicle control for 72 h. Cell viability was measured using an MTT assay and normalised to vehicle control. N = 3 biological repeats each performed in triplicate. Error bars represent SEM. When error bars cannot be seen they are smaller than the symbols. ( F ) The graph shows the relative EC50 values for each cell type calculated using GraphPad Prism. Error bars represent SEM (* = p < 0.05 unpaired t -test). The inserted Western blot shows PRH levels in the CCA cell lines prior to treatment and with β-actin as a loading control.

Article Snippet: Primary Biliary Epithelial Cells (BECs) obtained from healthy human liver tissue (Innoprot, Elexalde Derio, Spain) were grown in Epithelial Cell Media (Innoprot, P60106 , Elexalde Derio, Spain) supplemented with 2% FBS and 1% Epithelial Growth Supplement, as per the supplier’s protocol for a maximum of ten passages.

Techniques: Drug discovery, Biomarker Discovery, Concentration Assay, MTT Assay, Control, Two Tailed Test, Inhibition, Western Blot

Journal: Cancers

Article Title: Niclosamide and Palbociclib Act Synergistically to Reduce Cholangiocarcinoma Cell Viability In Vitro and Inhibit Tumour Growth in a Mouse Model

doi: 10.3390/cancers17223721

Figure Lengend Snippet: Palbociclib decreases the viability of CCA cells but has less effect on primary biliary epithelial cells. CCA cell lines (CCLP ( A ), RBE ( B ), KKU-M055 ( C ), or primary BECs ( D )) were plated at 1 × 10 4 cells per well in a 96-well plate and treated with increasing concentrations of Palbociclib for 96 h. Cell viability was then measured using an MTT assay and normalised to the vehicle control. Three biological repeats (five for CCLP cells) each performed in triplicate. Error bars represent SEM. When error bars cannot be seen, they are smaller than the symbols. ( E ) The graph shows the relative EC50 values calculated using GraphPad Prism. Error bars represent SEM (** = p < 0.01 *** = p < 0.001 unpaired t -test).

Article Snippet: Primary Biliary Epithelial Cells (BECs) obtained from healthy human liver tissue (Innoprot, Elexalde Derio, Spain) were grown in Epithelial Cell Media (Innoprot, P60106 , Elexalde Derio, Spain) supplemented with 2% FBS and 1% Epithelial Growth Supplement, as per the supplier’s protocol for a maximum of ten passages.

Techniques: MTT Assay, Control

Journal: Cancers

Article Title: Niclosamide and Palbociclib Act Synergistically to Reduce Cholangiocarcinoma Cell Viability In Vitro and Inhibit Tumour Growth in a Mouse Model

doi: 10.3390/cancers17223721

Figure Lengend Snippet: Niclosamide and Pablociclib act synergistically to reduce CCA cell viability. ( A ) CCLP cells were plated at 1 × 10 4 cells per well in a 96-well plate before treatment with Niclosamide (NIC), Palbociclib (PAL), or both drugs in combination (COM) at the concentrations shown and for 72 h. Cell viability was then measured using an MTT assay. N = 3 biological experiments each performed in triplicate. Error bars represent SEM (* = p < 0.05, ** = p < 0.01, ns = not significant) two-tailed paired t -test. ( B ) From the data shown in ( A ) combination index (CI), values were calculated and plotted against the corresponding response (Fa) values in a CI plot. CI < 1 indicates synergism. ( C ) CCLP cells were treated with 0.5 μM Niclosamide (NIC), 1 μM Palbociclib (PAL), or both drugs in combination (COM) for 24 h, then proteins were extracted for Western blot. ( D ) CCLP cells and BECs were grown as spheroids for 5 days before treatment with 0.5 μM Niclosamide, 1 μM Palbociclib, or both drugs in combination for a further 72 h. Images were taken using a Nikon brightfield microscope, and spheroid size was calculated using ImageJ. N = 3 biological repeats. Error bars represent SEM (* = p < 0.05, ** = p < 0.01, *** = p < 0.001, **** = p < 0.0001) two-tailed paired t -test. ( E ) Cell viability was measured in the spheroids from ( D ) using a PrestoBlue assay. Original western blots are presented in .

Article Snippet: Primary Biliary Epithelial Cells (BECs) obtained from healthy human liver tissue (Innoprot, Elexalde Derio, Spain) were grown in Epithelial Cell Media (Innoprot, P60106 , Elexalde Derio, Spain) supplemented with 2% FBS and 1% Epithelial Growth Supplement, as per the supplier’s protocol for a maximum of ten passages.

Techniques: MTT Assay, Two Tailed Test, Western Blot, Microscopy, Prestoblue Assay