Journal: bioRxiv

Article Title: Chemotherapy-Induced Oral Mucosal Injury Is Defined by p53 Activation, Cell Cycle Arrest and Diverse Epithelial Progenitor Dynamics

doi: 10.64898/2026.04.06.716752

Figure Lengend Snippet: (A) Heatmaps showing differentially expressed p53 targets in tongue and intestine in 5-FU-treated mice compared to PBS as determined via bulk RNA sequencing. Only genes with log2 fold-change (log2FC) > 1 or < –1 and adjusted p values < 0.05 are shown. (B-C) Representative micrographs and quantification of KI67 staining indicating proliferative cells in tongue mucosa (B) and small intestine (C) of PBS– and 5-FU-treated mice. (D) Western blot of total and cleaved Caspase-3 protein in tongue tissue lysates of PBS– and 5-FU-treated mice. Positive control (PC) is Jurkat cells treated with 1 μM staurosporine, and Negative control (NC) is untreated Jurkat cells. (E) Representative micrographs of sections corresponding to tongue lesion areas in mice treated with 5-FU and sacrificed at day 4 showing H&E staining and immunohistochemistry for detection of KI67 and cleaved Caspase 3 protein (Scale bar = 50 µm). Data in B and C are presented as mean±SD; *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001, as determined via ANOVA with Tukey post hoc analysis.

Article Snippet: Slides were incubated with an anti-cleaved Caspase-3 (Asp175) antibody (Cell Signaling Technology, Danvers, MA, USA; Cat# 9661, RRID:AB_2341188) at 1:150 or an anti-KI67 antibody (R&D Systems, Minneapolis, MN, USA; Cat# MAB7617) at 1:125 for 20 min followed by Rabbit Envision (Dako, Carpinteria, CA, USA; Cat# K4003) for 30 min. Diaminobenzidine (DAB) was applied for 10 minutes for visualization.

Techniques: RNA Sequencing, Staining, Western Blot, Positive Control, Negative Control, Immunohistochemistry

Journal: Cell Reports Medicine

Article Title: Neoadjuvant Fc-enhanced anti-CTLA-4 targets Tregs to augment androgen deprivation in high-risk prostate cancer: A randomized phase I trial

doi: 10.1016/j.xcrm.2026.102638

Figure Lengend Snippet: Phenotypic modulation of T cells and enhanced priming by anti-CTLA4-NF (A) PaCMAP plot of NeoRED-P patient tumor-infiltrating CD8 T cells by CyTOF. Clusters were derived from FlowSOM. (B) Pseudocolor density plots of CD8 T cells in PaCMAP space stratified by treatment group. (C) Expression of CD39 and 4-1BB by geometric MI on CD8 T cells as represented by color mapping on PaCMAP plot. (D) Violin plot representing frequency of manually gated CD39 + 4-1BB + CD8 T cells as a percentage of all CD8 T cells stratified by treatment group. Untreated, n = 7; ADT, n = 8; ADT + anti-CTLA4-NF, n = 8. Single patient with MSI hi status called out in plot. For this and all violin plots to follow, solid lines denote group medians, while dashed lines denote quartiles. (E) PaCMAP plot of NeoRED-P patient tumor-infiltrating CD4 + FoxP3 - Tconv cells by CyTOF. Clusters were derived from FlowSOM. (F) Pseudocolor density plots of CD4 Tconv cells in PaCMAP space stratified by treatment group. (G) Expression of CD39 and 4-1BB by geometric MI on CD4 Tconv as represented by color mapping on PaCMAP plot. (H) Violin plot representing frequency of manually gated CD39 + 4-1BB + CD4 Tconv cells as a percentage of all CD8 T cells stratified by treatment group. Untreated, n = 7; ADT, n = 8; ADT + anti-CTLA4-NF, n = 8. Single patient with MSI hi status called out in plot. (I) PaCMAP plot of MycCaP-infiltrating CD8 T cells by 45-parameter flow cytometry in response to ADT, ADT + anti-CTLA4 (ND), or ADT + anti-CTLA4 (D). Clusters were derived from FlowSOM. (J) Pseudocolor density plots of CD8 T cells in PaCMAP space stratified by treatment group. (K) Expression of CD39 and 4-1BB by geometric MFI on CD8 T cells as represented by color mapping on PaCMAP plot. (L) Violin plot representing frequency of manually gated CD39 + 4-1BB + CD8 T cells as a percentage of all CD8 T cells stratified by treatment group. (M) Biaxial plots representing expression of CD44 and Ki67 on CD8 T cells in tumor-draining lymph nodes of mice shown in (I–L). (N) Biaxial plots representing expression of CD44 and Ki67 on CD4 + FoxP3 − Tconv cells in tumor-draining lymph nodes of mice shown in (L–O). (O) Violin plots representing frequencies of CD44 + Ki67 + CD8 and CD4 Tconv cells as a percentage of parent populations stratified by treatment group. Two-tailed Welch’s t test was used to assess statistical significance. All murine data shown are n = 7 per group and representative of two independent experiments each for survival and immune profiling studies.

Article Snippet: Anti-Human Ki67 (B56) 172Yb , Standard BioTools , Cat# 3172024B.

Techniques: Derivative Assay, Expressing, Flow Cytometry, Two Tailed Test

Journal: Cells

Article Title: From Patient Liver Tissue to Organoids: Establishment of a Translational Platform Using Healthy, Steatotic, and Cirrhotic Tissue Sources

doi: 10.3390/cells15050432

Figure Lengend Snippet: Immunofluorescence imaging of patient-derived organoid culture. ( A ) ( a ) Overlay of all markers, ( b ) DAPI (blue, nuclear staining), ( c ) Ki-67 (cyan, proliferation marker), ( d ) Albumin (green, hepatocyte marker), ( e ) HNF4α (yellow, hepatocyte marker), ( f ) CK 19 (red, cholangiocyte marker), ( g ) LGR5 (pink, liver-specific stem-cell marker). ( B ) Healthy patients’ organoids ( a ) Overlay of all markers, ( b ) Collagen I (green, collagen marker), ( c ) SMA (red, hepatic stellate cells and myofibroblasts). ( C ) Cirrhotic patients organoids ( a ) Overlay of all markers, ( b ) Collagen I (green), ( c ) SMA (red). Scale bars: 200 µm.

Article Snippet: The human HNF4a qPCR primer pair (# HP200437 , NM_000457 , Origene), human MKI67 (# HP206104 , NM_002417.5 , Origene), human LGR5 ( NM_001277226.2 , [ ]), and human ALB ( NM_000477.7 , [ ]) were used.

Techniques: Immunofluorescence, Imaging, Derivative Assay, Staining, Marker

Journal: Cells

Article Title: From Patient Liver Tissue to Organoids: Establishment of a Translational Platform Using Healthy, Steatotic, and Cirrhotic Tissue Sources

doi: 10.3390/cells15050432

Figure Lengend Snippet: Analysis of antibody distribution in liver organoids derived from healthy, steatotic, and cirrhotic patients. The antibodies used were Ki-67, Albumin, HNF4α, CK19, Collagen I, and SMA. The bars in the figure represent the mean ± SD from three technical replicates (N = 3). An ordinary one-way ANOVA was conducted for statistical analysis (ns: non-significant, * p < 0.05).

Article Snippet: The human HNF4a qPCR primer pair (# HP200437 , NM_000457 , Origene), human MKI67 (# HP206104 , NM_002417.5 , Origene), human LGR5 ( NM_001277226.2 , [ ]), and human ALB ( NM_000477.7 , [ ]) were used.

Techniques: Derivative Assay

Journal: Cells

Article Title: From Patient Liver Tissue to Organoids: Establishment of a Translational Platform Using Healthy, Steatotic, and Cirrhotic Tissue Sources

doi: 10.3390/cells15050432

Figure Lengend Snippet: Relative expression of HNF4A , MKI67 , LGR5 , and ALB in human organoids as determined by qPCR. The bars represent the mean ± SD (N = 3). An ordinary one-way ANOVA was conducted for statistical analysis (* p < 0.05, ** p < 0.01, *** p < 0.001, and **** p < 0.0001).

Article Snippet: The human HNF4a qPCR primer pair (# HP200437 , NM_000457 , Origene), human MKI67 (# HP206104 , NM_002417.5 , Origene), human LGR5 ( NM_001277226.2 , [ ]), and human ALB ( NM_000477.7 , [ ]) were used.

Techniques: Expressing

Journal: Nature Communications

Article Title: Tissue-resident macrophage survival depends on mitochondrial function regulated by SerpinB2 in chronic inflammation

doi: 10.1038/s41467-026-69196-4

Figure Lengend Snippet: A Flowcytometric analysis of the macrophage subsets in visceral adipose tissue of CX 3 CR1 +/GFP mice which express GFP under the CX 3 CR1promoter. B tdTomato + (CX 3 CR1 high ) macrophages were quantified at day 7 after a single i.p injection of tamoxifen in CX 3 CR 1 CreER/+ ROSA tdTomato/+ mice that express YFP under the CX 3 CR1 promoter and tdTomato in CX 3 CR1-expressing cells upon tamoxifen injection using intravital microscopy (n = 6/group). C Parabiosis between C57BL/6 and CX 3 CR1 GFP/+ mice was performed. Flow cytometry was conducted to enumerate chimerism in the macrophage subsets in the C57BL/6 mice six months after parabiosis. (n = 5 for CX 3 CR1 − and 6 for CX 3 CR1 + ). D Heatmap displaying the genes with at least a two-fold difference between the VAT macrophage subsets and with FDR < 0.01 (n = 3/group). E – G Heatmaps displaying the expression of the genes using bulk RNA sequencing comparing CX 3 CR1 + CCR2 + and CX 3 CR1 − CCR2 − macrophages (n = 3/group) and CD206 − and CD206 + macrophage subsets of VAT (n = 3/group). H q-PCR quantification of the genes associated with glycemia and diabetes in CX 3 CR1 + CCR2 + and CX 3 CR1 − CCR2 − macrophages sorted from VAT of lean mice (n = 6–12/group). I Bar graph representing the frequency of CX 3 CR1 + CCR2 + and CX 3 CR1 − CCR2 − VAT macrophages enriched in the insulin sensitivity and resistance genes shown in ( G , H ) (n = 3-6 /group). J PCA plot showing the relations among the genes responsible for insulin sensitivity, survival, resident macrophage (ATM) markers, inflammation, insulin resistance, and monocyte-derived macrophages (MDM) markers in the VAT macrophage subsets using bulk RNA sequencing. K , L Frequencies of CCR2 + and CCR2 − macrophage subsets in human VAT as measured by flow cytometry ( K ) (n = 5/group) and confocal microscopy ( L ) (n = 15 for lean and 13 for obese). M – O Quantification of the VAT macrophage subsets in HFD-fed mice by flow cytometry (n = 4/group) ( M ) and serial intravital microscopy (Scale bar = 10 µm) ( N , O ) was performed in lean and obese CX 3 CR1 CreER/+ ROSA tdTomato/+ mice (n = 3 for CD, 4 for HFD 2 months, and 5 for HFD 4 months). P – R Apoptosis in VAT resident and monocyte-derived macrophages in lean and obese mice was examined using annexin V by flow cytometry ( P ) (n = 4/group), and caspase 3 staining by flow cytometry ( Q ) (n = 5 for CD and 4 for HFD/group) and confocal microscopy ( R ) (n = 14/group). S Quantification of the VAT macrophage subsets in lean and obese CX 3 CR1 creER/+ ROSA tdTomato mice before and after removal of HFD (n = 7/group). T Evaluation of Ki-67 + VAT resident macrophages after HFD withdrawal (n = 10/group). Mean ± s.e.m. * P < 0.05, ** P < 0.01, *** P < 0.001. The Mann–Whitney test (two-tailed) was used to determine the significance between two groups. One-way ANOVA with Bonferoni’s post hoc correction test was performed to determine differences among data obtained from more than two groups (Fig. 1O and S).

Article Snippet: Tissues were incubated for 48 hours with the primary antibodies against proteins like F4/80 (Invitrogen, #MAI-91124), cleaved caspase 3 (Abcam, #ab13847), CD11b (Abcam, #ab133357), CX 3 CR1 (Abcam, #ab8021), CCR2 (Bio-Rad, #AAM72), Ki67 , , , CD68 (ThermoFisher Scientifics, # 14-0688-82), and SerpinB2 (Invitrogen, #PA5-27857) followed by washing with PBS and incubation for 24 hours at 4 °C with Alexa fluor 488, 594 and 647-conjugated secondary antibodies.

Techniques: Injection, Expressing, Intravital Microscopy, Flow Cytometry, RNA Sequencing, Derivative Assay, Confocal Microscopy, Staining, MANN-WHITNEY, Two Tailed Test