prdm16 mouse  (Eurofins)

Journal: bioRxiv

Article Title: Abnormal ventricular wall patterning precedes and drives MYBPC3 hypertrophic cardiomyopathy

doi: 10.64898/2026.03.25.714341

Figure Lengend Snippet: ( A ) Gene set enrichment analysis (GSEA) analysis of ventricular RNA-seq datasets at E15.5, P1, P7 and adulthood comparing homozygous Mybpc3 p.Pro109Serfs*12 and Mybpc3 +/+ ventricular transcriptome against Hallmark and Reactome gene sets. The first 4 columns show comparisons between mutant and control samples at E15.5, P1, P7 and adult stages. Most significant processes seem to occur at P1 and P7. The mutation causes similar direction changes at P1 and P7 on cell cycle terms (increased in the mutants), but opposite changes in metabolism, NMD and metabolism/proteostasis terms (oxphos, translation) which are decreased at P1 mutants compared to control but increased in the mutants at P7. The last two columns represent the longitudinal comparisons between P1 and P7 in both control and mutant samples. The WT (control) P7-P1 column indicates the developmental change in the transition from P1 to P7 (red, up in P7). NMD and proteostasis (translation etc.) terms are decreased in the controls at P7, but in the mutants, these same processes are increased. Cell cycle terms maintain the same enrichment direction in the mutants but seem to be even more exacerbated at P7. ( B ) Left, bubble plot of differentially expressed genes at P7 in homozygous Mybpc3 p.Pro109Serfs*12 and Mybpc3+/+ hearts highlights upregulation of several genes and downregulation of Prdm16 within a hypertrophy-associated gene signature. Right, ISH for Nppa and Ankrd1 in control and homozygous Mybpc3 p.Pro109Serfs*12 P7 hearts. 250 μm. lv, left ventricle; rv, right ventricle. (( C ) Bar plot summarizing the normalized enrichment score (NES) and –log(padj) values for Mybpc3 P109Sfs*12 mutant vs. WT comparisons at E15.5, P1, P7, and Adult. Dotted line: p-value = 0.25. Dashed line: p -value = 0.01. D ) Bar plot summarizing the NES and –log(padj) values for P7 vs. P1 comparisons in control (WT) and Mybpc3 p.Pro109Serfs*12 (P109S) mutant. Dotted line: p -value = 0.25. Dashed line: p-value = 0.01. The NES represents the enrichment score after normalization, with higher scores (red) indicating positive enrichment and lower scores (blue) indicating negative enrichment. The adjusted p-value (padj) corresponds to p-values corrected for multiple testing using the Benjamini–Hochberg procedure, which controls the false discovery rate. ( E-F’’ ) IF for Prdm16 (green), Endomucin (red), and DAPI (blue) in in ventricular sections of E18.5 wild type ( E-E ’’) and homozygous Prdm16 Δ8 mutant hearts. Arrowheads in E’’ point to nuclear Prdm16 expression in trabecular cardiomyocytes. Scale bar 250 μm. Magnified views are shown in ( ’ ). Scale bar 50 μm. ( G-J’ ) IF for Prdm16 in ventricular sections at E16.5 ( G-H’ ) and P7 ( I-J’ ) reveals expanded Prdm16 signal in E16.5 Mybpc3 p.Pro109Serfs*12 mutant trabeculae (arrowheads, H’ , inset), and reduced Prdm16 expression at P7 in subendocardial myocardium of mutants ( J’ ). Scale bar, 250 μm. ( K ) Quantification of the ratio of trabecular (TM) to compact myocardium (CM) Prdm16 expression in E16.5 hearts (n=3, ≥3 sections per heart), and the ratio of inner myocardium (IM) to outter myocardium (OM) in P7 hearts. (n=4 control and n=3 Mybpc3 p.Pro109Serfs*12, ≥3 sections per heart). Data are represented as means ± SD. Statistical significance was determined by unpaired Student’s t-test (* p -value < 0.05).

Article Snippet: A full-length mouse Prdm16 cDNA cloned into pcDNA3.1 was obtained from addgene (#15503).

Techniques: RNA Sequencing, Mutagenesis, Control, Expressing

Journal: bioRxiv

Article Title: Abnormal ventricular wall patterning precedes and drives MYBPC3 hypertrophic cardiomyopathy

doi: 10.64898/2026.03.25.714341

Figure Lengend Snippet: ( A ) Whole-mount views of P7 control, Mybpc3 +/+ ;R26 Prdm16/+ ;Myh6 MerCreMer/+ , homozygous Mybpc3 p.Pro109Serfs*12 and Mybpc3 p.Pro109Serfs*12;R26 Prdm16/+ ;Myh6 MerCreMer/+ hearts. Right, Cre-mediated transgenic expression was induced upon Tamoxifen administration at P1. Scale bar, 250 μm. ( B ) Quantification of Heart weight/Body weight ratio (n=25 Mybpc3+/+, n=16 Mybpc3+/+;R26 Prdm16/+ ;Myh6 MerCreMer/+ , n=13 homozygous Mybpc3 p.Pro109Serfs*12 and n=14 Mybpc3 p.Pro109Serfs*12;R26 Prdm16/+ ;Myh6 MerCreMer/+ ), Septum thickness (μm), Left Ventricular Free Wall (LVFW) thickness (μm)(n=4 Mybpc3+/+, n=3 Mybpc3+/+;R26 Prdm16/+ ;Myh6 MerCreMer/+ , n=3 homozygous Mybpc3 p.Pro109Serfs*12 and n=5 Mybpc3 p.Pro109Serfs*12;R26 Prdm16/+ ;Myh6 MerCreMer ≥3 sections per heart), compact myocardium leght (CM) and trabecular myocardium leght (TM) (μm) (n=3 hearts per genotype, ≥3 sections per heart). Data are represented as means ± SD. Statistical significance was determined by unpaired Student’s t-test (ns, not significant; * p -value < 0.05; *** p -value < 0.001; **** p -value < 0.0001). ( C ) H&E images of representative hearts of the different genotypes. Scale bar, 250 μm. ( D ) ISH for Nppa in the different genotypes. Scale bar, 250 μm. ( E ) WGA (green) and DAPI (blue) fluorescence staining of P7 control, Mybpc3 +/+ ;R26 Prdm16/+ ;Myh6 MerCreMer/+ , Mybpc3 p.Pro109Serfs*12 and Mybpc3 p.Pro109Serfs*12;R26 Prdm16/+ ;Myh6 MerCreMer/+ heart sections. Scale bar, 10 μm. ( F ) Cardiomyocyte cross sectional area quantification of P7 hearts (n=3, ≥6 sections per heart). Data are represented as means ± SD. Statistical significance was determined by unpaired Student’s t-test (ns, not significant; * p -value < 0.05; ** p -value < 0.005). ( G ) Ventricular wall mispatterning drives MYBPC3-associated HCM that is attenuated by Prdm16 expression. Top, wild type: During late gestation (E18.5), compact (CM, Hey2⁺) and trabecular cardiomyocytes (TM, Hey2 - ) are spatially segregated and exhibit balanced proliferation, enabling ventricular compaction progression at birth (P1) and subsequent maturation. Postnatally, Prdm16 promotes cardiomyocyte maturation and restrains hypertrophy, resulting in normal ventricular architecture by P7. Middle, Mybpc3 P109Sfs*12 mutant. Mybpc3 loss disrupts ventricular wall patterning, leading to loss of compact–trabecular segregation, increased trabecular proliferation, and impaired compaction. This is accompanied by peak transcriptional dysregulation from P1 to P7. Abnormally reduced Prdm16 expression impairs maturation and contributes to pathological cardiomyocyte hypertrophy. Bottom, Mybpc3 P109Sfs*12; R26 Prdm16/+ ; Myh6 MerCreMer model. Tamoxifen-mediated Prdm16 expression at P1 attenuates hypertrophy despite persistent early patterning defects, promoting cardiomyocyte maturation and partially normalizing ventricular structure.

Article Snippet: A full-length mouse Prdm16 cDNA cloned into pcDNA3.1 was obtained from addgene (#15503).

Techniques: Control, Transgenic Assay, Expressing, Fluorescence, Staining, Mutagenesis

Journal: Cancer Research

Article Title: PRDM16 Regulates Prostate Cancer Cell Dormancy and Prevents Bone Metastatic Outgrowth

doi: 10.1158/0008-5472.CAN-24-4809

Figure Lengend Snippet: PRDM16 stalls cell division upon reawakening

Article Snippet: For Prdm16 ectopic expression, we purchased Lenti ORF viral particles for Prdm16 tagged with Myc-DDK (MR222596L3V, OriGene), with pLenti-C-Myc-DDK-P2A-Puro as nontargeting control (PS100092V, OriGene).

Techniques:

Journal: Cancer Research

Article Title: PRDM16 Regulates Prostate Cancer Cell Dormancy and Prevents Bone Metastatic Outgrowth

doi: 10.1158/0008-5472.CAN-24-4809

Figure Lengend Snippet: PRDM16 is upregulated in prostate cancer dormancy. A, Principal component (PC) analysis of the groups based on whole-transcriptome sequencing ( n = 3). B, Differential gene expression analysis in dormant vs. active groups based on the DESeq2 pipeline. C, Venn diagram based on differentially upregulated genes across cell lines from B . D, Heatmap of log 2 -fold change values for the 14 upregulated genes across cell lines from C . E, Disease-specific recurrence status of patients with primary prostate cancer ( n = 79) between PRDM16-high/low patients (based on median expression) from GSE25136 . A χ 2 test was used for statistical significance. F, RT-qPCR assessment of PRDM16-specific primers (total PRDM16, full length, and short form) in active and dormant 22Rv1 cells ( n = 3). G, Immunoblotting analysis of PRDM16 protein abundance in active and dormant 22Rv1 lysates. K562 lysate was used as the positive control ( n = 3). H, Immunoblotting analysis of PRDM16 localization in cell fractions taken from dormant RM1 and 22Rv1 cells. GAPDH was used as the indicator of fractionation efficiency ( n = 2). Chrom, chromatin; Cyto, cytoplasm; Memb, membrane; Nucl, nucleus. I, Immunofluorescence imaging of active, dormant, and reawakened groups from RM1 and 22Rv1 cell lines with PRDM16 (orange) and DAPI (blue; n ≥ 3). Magnification, ×20. J, Median fluorescence intensity (MFI) quantification of multiple regions of interest (from I ) in the groups ( n ≥ 3). An one-way ANOVA test was used to assess significance. A Student t test was used unless otherwise noted. ns, not significant.

Article Snippet: For Prdm16 ectopic expression, we purchased Lenti ORF viral particles for Prdm16 tagged with Myc-DDK (MR222596L3V, OriGene), with pLenti-C-Myc-DDK-P2A-Puro as nontargeting control (PS100092V, OriGene).

Techniques: Sequencing, Gene Expression, Expressing, Quantitative RT-PCR, Western Blot, Quantitative Proteomics, Positive Control, Fractionation, Membrane, Immunofluorescence, Imaging, Fluorescence

Journal: Cancer Research

Article Title: PRDM16 Regulates Prostate Cancer Cell Dormancy and Prevents Bone Metastatic Outgrowth

doi: 10.1158/0008-5472.CAN-24-4809

Figure Lengend Snippet: PRDM16 expression correlates with prostate cancer skeletal dormancy in vivo . A, Schematic of the intraprostate in vivo model to study orthotopic prostate cancer spontaneous bone metastasis. B, Bioluminescence in vivo (left) and ex vivo (right) imaging of luciferase-expressing RM1 cells. Top, prostate; bottom, bones ( n > 3). C, Immunofluorescence imaging of formalin-fixed, paraffin-embedded (FFPE) bone sections of mice ( n > 3) sacrificed at day 14 from A for PanCK and PRDM16. DAPI stains nuclei (blue). Top left insets show PRDM16 channel, and white arrows indicate PRDM16 + cells. Scale bar, 50 μm. D, Quantification of percentage of PRDM16 in all PanCK + cells in prostate orthotopic tumors and bone marrow–disseminated cells ( n ≥ 3). E, Schematic of the in vivo model to study prostate cancer metastatic bone colonization. F, Bioluminescence in vivo imaging of luciferase-expressing RM1 groups ( n > 3). G, Quantification of macrometastases (>20 cells) detected in histologic sections taken at endpoints from F ; black box above each sample indicates macrometastasis frequency in mice ( n > 3). H, Immunofluorescence imaging of FFPE bone sections of mice from E ( n = 4) sacrificed at day 5 for PanCK, Ki-67, CC3, and PRDM16. DAPI stains nuclei (blue). Top left insets show PRDM16 or CC3 channels. Scale bar, 20 μm. I–K, Quantification of sections in H . I, Quantification of Ki-67 positivity in all PanCK + cells ( n = 4). J, Quantification of %CC3 positivity in all PanCK + cells ( n ≥ 3). K, Quantification of %PRDM16 cells in all PanCK + cells ( n ≥ 3). For I–K quantification, multiple frames were aggregated and then presented as the average percentage per bone. L, Immunofluorescence imaging of FFPE bone sections based on E of mice ( n > 3) sacrificed at endpoint for PanCK, Ki-67, CC3, and PRDM16. DAPI stains nuclei (blue). Top left insets show PRDM16 or CC3 channels. Scale bar, 20 μm. M–O, Quantification of sections from L . M, Quantification of Ki-67 positivity in all PanCK + cells ( n = 4). N, Quantification of %CC3 positivity in all PanCK + cells ( n ≥ 3). O, Quantification of %PRDM16 + cells in all PanCK + cells ( n ≥ 3). For M–O , quantification was done using ILASTIK software; each frame is presented as one data point. A Student t test was used unless otherwise noted. ns, not significant. A and E, Created in BioRender. Nasr, M. (2025) https://BioRender.com/z3egiqu .

Article Snippet: For Prdm16 ectopic expression, we purchased Lenti ORF viral particles for Prdm16 tagged with Myc-DDK (MR222596L3V, OriGene), with pLenti-C-Myc-DDK-P2A-Puro as nontargeting control (PS100092V, OriGene).

Techniques: Expressing, In Vivo, Ex Vivo, Imaging, Luciferase, Immunofluorescence, Formalin-fixed Paraffin-Embedded, In Vivo Imaging, Software

Journal: Cancer Research

Article Title: PRDM16 Regulates Prostate Cancer Cell Dormancy and Prevents Bone Metastatic Outgrowth

doi: 10.1158/0008-5472.CAN-24-4809

Figure Lengend Snippet: PRDM16 promotes prostate cancer dormancy by stalling cell division. A and B, Total cell counts taken from active ( A ) or reawakened cells ( B ) using trypan blue staining, presented after normalizing to initial cell count ( n = 3). C, %Viability from A for active groups using trypan blue staining. D, Flow cytometry analysis of the percentage of DiD-high cells in live cells across time points in culture for active and dormant groups in 22Rv1 ( n ≥ 3). E, Breakdown of the percentage of DiD-high (no cell division), DiD-intermediate (some cell division), and DiD-low (high cell division) cells in active and dormant RM1 (day 3) and 22Rv1 (day 5) groups ( n ≥ 3). F, %DiD-high cells in live RM1 and 22Rv1 cells from E ( n ≥ 3). G, Flow cytometry analysis of cell-cycle phases in active and dormant groups of 22Rv1 cells using DAPI (DNA) and EdU (S-phase marker). G 0 /G 1 is defined as the G 1 EdU − population ( n = 3). H and I, Quantification of cell-cycle phases from G for the S-phase ( H ) and G 0 /G 1 -phase ( I ) presented as percentage of all live and DAPI single cells ( n = 3). A Student t test was used unless otherwise noted.

Article Snippet: For Prdm16 ectopic expression, we purchased Lenti ORF viral particles for Prdm16 tagged with Myc-DDK (MR222596L3V, OriGene), with pLenti-C-Myc-DDK-P2A-Puro as nontargeting control (PS100092V, OriGene).

Techniques: Staining, Cell Characterization, Flow Cytometry, Marker

Journal: Cancer Research

Article Title: PRDM16 Regulates Prostate Cancer Cell Dormancy and Prevents Bone Metastatic Outgrowth

doi: 10.1158/0008-5472.CAN-24-4809

Figure Lengend Snippet: PRDM16 inhibits prostate cancer metastatic outbreak in the bone microenvironment. A, Schematic of the intrailiac study with endpoint defined as 13 days. B, Immunofluorescence imaging for formalin-fixed, paraffin-embedded sections for PanCK, Ki-67, and DDK in the groups ( n ≥ 4). Scale bar, 20 μm. C, Quantification of the number of macrometastases (>20 cells) detected in sections from B in each mouse; black box above each sample indicates macrometastasis frequency in mice ( n ≥ 4). D and E, %Ki-67 + in all PanCK + cells in micrometastases (3–20 cells; D ) or single cells (1–2 cells; E ) aggregated and presented per mouse ( n ≥ 4). A Student t test was used unless otherwise noted. ns, not significant. A, Created in BioRender. Nasr, M. (2025) https://BioRender.com/z3egiqu .

Article Snippet: For Prdm16 ectopic expression, we purchased Lenti ORF viral particles for Prdm16 tagged with Myc-DDK (MR222596L3V, OriGene), with pLenti-C-Myc-DDK-P2A-Puro as nontargeting control (PS100092V, OriGene).

Techniques: Immunofluorescence, Imaging, Formalin-fixed Paraffin-Embedded

Journal: Cancer Research

Article Title: PRDM16 Regulates Prostate Cancer Cell Dormancy and Prevents Bone Metastatic Outgrowth

doi: 10.1158/0008-5472.CAN-24-4809

Figure Lengend Snippet: RB1 is a transcriptional target of PRDM16. A and B, Immunoblotting analysis of lysates generated from active or dormant (after 48 hours in A or 24 hours in B ) groups in RM1 and 22Rv1 cell lines ( n = 3). C, Schematic of ChIP primers designed upstream of RB1 TSS. D, RT-qPCR amplification of product 1 from C in the conditions shown for D-22Rv1 cells. Data presented as percentage of input sample ( n = 3). E, Immunofluorescence imaging of active, dormant, and reawakened groups from RM1 and 22Rv1 cell lines with pRB1 (S249/Th252; violet) and DAPI (blue; n = 3). Scale bar, 50 μm. F, Median fluorescence intensity (MFI) quantification of multiple regions of interest (from E ) in the groups ( n = 3). An one-way ANOVA test was used to assess significance. G, Immunofluorescence imaging of pRB1 (S249/Th252) under active conditions for RM1 and 22Rv1 groups ( n = 3). H, Quantification of pRB1 MFI signal from G . Each dot represents an area of interest ( n = 3). I, Immunofluorescence imaging of pRB1 (S249/Th252) under dormant conditions for RM1 and 22Rv1 groups ( n ≥ 3). J, Quantification of pRB1 MFI signal from I . Each dot represents a cluster of cells ( n ≥ 3). K, Immunofluorescence imaging of pRB1 (S249/Th252) under dormant conditions for RM1 groups ( n ≥ 3). L, Quantification of pRB1 MFI signal from K . Each dot represents a cluster of cells ( n ≥ 3). A Student t test was used unless otherwise noted. C, Created in BioRender. Nasr, M. (2025) https://BioRender.com/p03e209 .

Article Snippet: For Prdm16 ectopic expression, we purchased Lenti ORF viral particles for Prdm16 tagged with Myc-DDK (MR222596L3V, OriGene), with pLenti-C-Myc-DDK-P2A-Puro as nontargeting control (PS100092V, OriGene).

Techniques: Western Blot, Generated, Quantitative RT-PCR, Amplification, Immunofluorescence, Imaging, Fluorescence