Journal: Frontiers in Medicine

Article Title: Validation of ITPR2 , DPF3 , EPAS1 , and PVT1 -associated SNPs as biomarkers for RCC in an independent case-control cohort

doi: 10.3389/fmed.2026.1734511

Figure Lengend Snippet: Overall survival analysis according to SNP genotypes and metastatic status in RCC patients. (A) Forest plot from the Cox proportional hazards regression model (dominant model). (B) Adjusted survival curves derived from the Cox proportional hazards model comparing overall survival between ITPR2 rs1049380 genotypes (T/T vs. G/T + G/G). (C) Kaplan–Meier survival curves based on observed data for ITPR2 rs1049380, stratified by metastasis status, showing survival probability, cumulative events, and cumulative hazard curves.

Article Snippet: Quantitative polymerase chain reaction (qPCR) was performed with TaqMan TM gene expression assays (Thermo Fisher Scientific, Waltham, MA, United States) for: ITPR2 (Assay ID: Hs00181916_m1), ZEB2 (Assay ID: Hs00207691_m1), MYC (Assay ID: Hs00153408_m1) and PVT1 (Assay ID: Hs00413039_m1). qPCR reactions were performed as follows: 95 °C during 10 min for enzyme activation; followed by 45 cycles of 15 s at 95 °C and 1 min at 60 °C for denaturing and annealing/extension.

Techniques: Derivative Assay

Journal: Frontiers in Medicine

Article Title: Validation of ITPR2 , DPF3 , EPAS1 , and PVT1 -associated SNPs as biomarkers for RCC in an independent case-control cohort

doi: 10.3389/fmed.2026.1734511

Figure Lengend Snippet: Five-year overall survival analysis according to SNPs genotypes and metastatic status in RCC patients. (A) Forest plot from the Cox proportional hazards regression model (dominant model). (B) Adjusted survival curves derived from the Cox proportional hazards model comparing five-years overall survival between ITPR2 rs1049380 and PVT1 rs35252396 genotypes. (C) Kaplan–Meier survival curves based on observed data for ITPR2 rs1049380 and PVT1 rs35252396 stratified by metastasis status, showing survival probability, cumulative events, and cumulative hazard curves.

Article Snippet: Quantitative polymerase chain reaction (qPCR) was performed with TaqMan TM gene expression assays (Thermo Fisher Scientific, Waltham, MA, United States) for: ITPR2 (Assay ID: Hs00181916_m1), ZEB2 (Assay ID: Hs00207691_m1), MYC (Assay ID: Hs00153408_m1) and PVT1 (Assay ID: Hs00413039_m1). qPCR reactions were performed as follows: 95 °C during 10 min for enzyme activation; followed by 45 cycles of 15 s at 95 °C and 1 min at 60 °C for denaturing and annealing/extension.

Techniques: Derivative Assay

Journal: Frontiers in Medicine

Article Title: Validation of ITPR2 , DPF3 , EPAS1 , and PVT1 -associated SNPs as biomarkers for RCC in an independent case-control cohort

doi: 10.3389/fmed.2026.1734511

Figure Lengend Snippet: Expression levels of ITPR2 , PVT1 , and MYC genes by genetic model in tumor and adjacent healthy FFPE tissues.

Article Snippet: Quantitative polymerase chain reaction (qPCR) was performed with TaqMan TM gene expression assays (Thermo Fisher Scientific, Waltham, MA, United States) for: ITPR2 (Assay ID: Hs00181916_m1), ZEB2 (Assay ID: Hs00207691_m1), MYC (Assay ID: Hs00153408_m1) and PVT1 (Assay ID: Hs00413039_m1). qPCR reactions were performed as follows: 95 °C during 10 min for enzyme activation; followed by 45 cycles of 15 s at 95 °C and 1 min at 60 °C for denaturing and annealing/extension.

Techniques: Expressing

Journal: bioRxiv

Article Title: Astrocyte Store-Released Calcium Modulates Visual Cortex Synapse Development and Circuit Function

doi: 10.1101/2025.07.20.665758

Figure Lengend Snippet: See also Fig. S6. A. Schematic of the strategy to express fluorescent reporter in astrocytes. P1 mouse pups were injected icv with AAV to express membrane tethered eGFP (Lck-eGFP) under astrocyte specific promoter GfaABC1D. Tissue is collected 2 weeks following injection, sectioned and imaged using Airyscan super resolution confocal microscope. B-E. Astrocytic volume is reduced in IP3R2 KO mice compared to WT. Example images of Lck-eGFP (green) expressing astrocytes ( D ) and 3D rendering of volume using Imaris ( E ) for each genotype is shown as labeled. B-C. Quantification shows reduced total volume and area of IP3R2 KO astrocytes in L1 VC. Graphs show mean ± s.e.m. Black circles above each bar are average of signal in each mouse, colored open circles are data for each astrocyte. Number of mice/ group (N) N=5, number of astrocytes = 25-27. Scale bar = 10 μm. **P<0.01 by t-test.

Article Snippet: The following primary antibodies were used: Rb anti IP3R2 (Alomone labs #ACC-116, 1:250), Gp anti-VGLUT1 (Millipore #AB5905, 1:1000), Gp anti-VGLUT2 (Millipore #AB2251 1:1000), Rb anti-PSD95 (Fisher #516900 1:250), Gp anti-VGAT (Synaptic Systems #131004 1:250), Rb anti-Gephyrin (Synaptic Systems #147008 1:500), Rb anti-Nf200 (Millipore Sigma #N4142 1:400), Chk anti-GFP (Invitrogen A10262 1:1000), Rb anti-S100β (Abcam #AB52642, 1:100).

Techniques: Injection, Membrane, Microscopy, Expressing, Labeling

Journal: bioRxiv

Article Title: Astrocyte Store-Released Calcium Modulates Visual Cortex Synapse Development and Circuit Function

doi: 10.1101/2025.07.20.665758

Figure Lengend Snippet: See also Fig S1. A. Schematic of experiment: Brain tissue is collected from WT and KO mice at P7, P14 and P28 corresponding to stages of synapse development; IHC to quantify synapses as indicated is performed in Layer 1 of the VC for VGLUT1-containing cortico-cortical synapses, and VGLUT2-containing thalamo-cortical synapses. B. Validation of IP3R2 KO by IHC and WB (top right panel). Example images of IP3R2 (cyan), astrocyte marker S100ꞵ (magenta) and neuronal marker Neun (blue) in the VC at P14 as labeled. Graph on the right is quantification of colocalized signal with each cell marker. IP3R2 signal is highly colocalized with astrocytes and not with neurons and is downregulated in KO VC. WB shows IP3R2 band (∼250KDa) and GAPDH (loading control, ∼36 KDa) in WT and KO at P14 as labeled. Numbers indicate samples from individual animals. See also Fig. S1A-D. C-G. Cortico-cortical VGLUT1-containing, synapses are reduced in IP3R2 KO VC at P14 and P28 but not P7. Example images of the presynaptic VGLUT1, postsynaptic PSD95 and merged (synapses) in each age and genotype as labeled ( C-D ) and quantification of individual synaptic proteins and synapse number per mm 3 represented as colocalization between VGLUT1 and PSD95 for both genotypes ( E-F ) are shown. Single channel grayscale images on the left, merged images on the right. The number of VGLUT1 puncta and VGLUT1-containing synapses is reduced in KO ( E, G ), while PSD95 numbers are unaltered ( F ). H-J. Thalamo-cortical VGLUT2-containing synapses are reduced in IP3R2 KO VC at P14 and P28 but not P7. Quantification of individual synaptic proteins and synapse number per mm 3 represented as colocalization between VGLUT2 and PSD95 for both genotypes are shown (see also Fig. S1E-F). The number of VGLUT2 puncta and VGLUT2-containing synapses is reduced in KO ( H, J ), while PSD95 numbers are unaltered ( I ). Plots show mean ± s.e.m. Squares and circles above each bar are average of signal in each mouse. Number of mice/ group (N) N=5. Scale bar = 5 μm. Arrowheads mark representative colocalized puncta. #,*P<0.05, ##, **P<0.01, ###, ***P<0.001. # indicates comparing age groups within each genotype by one-way ANOVA. Within each age, WT and KO comparison by t-test indicated by *. ns denotes Non-significant results (P>0.05).

Article Snippet: The following primary antibodies were used: Rb anti IP3R2 (Alomone labs #ACC-116, 1:250), Gp anti-VGLUT1 (Millipore #AB5905, 1:1000), Gp anti-VGLUT2 (Millipore #AB2251 1:1000), Rb anti-PSD95 (Fisher #516900 1:250), Gp anti-VGAT (Synaptic Systems #131004 1:250), Rb anti-Gephyrin (Synaptic Systems #147008 1:500), Rb anti-Nf200 (Millipore Sigma #N4142 1:400), Chk anti-GFP (Invitrogen A10262 1:1000), Rb anti-S100β (Abcam #AB52642, 1:100).

Techniques: Biomarker Discovery, Marker, Labeling, Control, Comparison

Journal: bioRxiv

Article Title: Astrocyte Store-Released Calcium Modulates Visual Cortex Synapse Development and Circuit Function

doi: 10.1101/2025.07.20.665758

Figure Lengend Snippet: See also Fig. S4. A. Schematic of experimental paradigm. Following 4 hours of dark exposure (ZT12 marks lights off), mice were exposed to 20-minute light pulse, tissue collected immediately after for IHC analysis of c-FOS expression. B, E. Light evoked c-FOS levels are diminished in IP3R2 KO mice VC. Example images of c-FOS (green) and nuclear marker DAPI (blue) in each genotype as labeled in the dark or light exposed groups. Neuronal cortical layers are labeled on the right E. Quantification of B represented as c-FOS positive cell numbers per area. Light exposure produced a strong increase in the number of c-FOS positive cells in the WT, but not in the KO. C-G. Same as B, E, but for the dorsal lateral geniculate nucleus of the thalamus (dLGN; C, F) and the superior colliculus (SC; D, G). In both regions, light exposure produced a strong increase in the number of c-FOS positive cells in the WT, but to a lesser extent in the KO. Graphs show mean ± s.e.m. Squares and circles above each bar are average of signal in each mouse. Number of mice/ group (N) N=5. Scale bar in B = 100 μm; in C-D = 20 μm. *P<0.05, **P<0.01, ***P<0.001 by one-way ANOVA. ns denotes non-significant results (P>0.05).

Article Snippet: The following primary antibodies were used: Rb anti IP3R2 (Alomone labs #ACC-116, 1:250), Gp anti-VGLUT1 (Millipore #AB5905, 1:1000), Gp anti-VGLUT2 (Millipore #AB2251 1:1000), Rb anti-PSD95 (Fisher #516900 1:250), Gp anti-VGAT (Synaptic Systems #131004 1:250), Rb anti-Gephyrin (Synaptic Systems #147008 1:500), Rb anti-Nf200 (Millipore Sigma #N4142 1:400), Chk anti-GFP (Invitrogen A10262 1:1000), Rb anti-S100β (Abcam #AB52642, 1:100).

Techniques: Expressing, Marker, Labeling, Produced

Journal: bioRxiv

Article Title: Astrocyte Store-Released Calcium Modulates Visual Cortex Synapse Development and Circuit Function

doi: 10.1101/2025.07.20.665758

Figure Lengend Snippet: A. Diagram depicting inhibitory neurons within the VC analyzed. B-F. GABAergic synapse numbers are not altered in IP3R2 KO VC at P14. Example images of the presynaptic VGAT, postsynaptic Gephyrin and merged (synapses) in each genotype as labeled ( B ) and quantification of individual synaptic proteins and synapse number per mm 3 represented as colocalization between VGAT and Gephyrin for both genotypes ( C-E ) are shown. Single channel grayscale images on the left, merged images on the right. No difference is observed in any of the parameters compared. F. Cumulative distributions of volumes from 3D rendered images for VGAT per genotype as labeled. Bar graphs show mean ± s.e.m. Squares and circles above each bar are average of signal in each mouse. Number of mice/ group (N) N=5. Scale bar = 5 μm. Arrowheads mark representative colocalized puncta. ns denotes non-significant results (P>0.05) by t-test in C-E, and Kolmogorov-Smirnov test in F, comparing WT and KO groups.

Article Snippet: The following primary antibodies were used: Rb anti IP3R2 (Alomone labs #ACC-116, 1:250), Gp anti-VGLUT1 (Millipore #AB5905, 1:1000), Gp anti-VGLUT2 (Millipore #AB2251 1:1000), Rb anti-PSD95 (Fisher #516900 1:250), Gp anti-VGAT (Synaptic Systems #131004 1:250), Rb anti-Gephyrin (Synaptic Systems #147008 1:500), Rb anti-Nf200 (Millipore Sigma #N4142 1:400), Chk anti-GFP (Invitrogen A10262 1:1000), Rb anti-S100β (Abcam #AB52642, 1:100).

Techniques: Labeling

Journal: eLife

Article Title: Circadian regulation of endoplasmic reticulum calcium response in cultured mouse astrocytes

doi: 10.7554/eLife.96357

Figure Lengend Snippet: ( A–I ) Cultured astrocytes were co-transfected with 20 μM non-targeting (CTRL) siRNA or Herp siRNA together with G-CEPIA1er ( A–C ), R-GECO1 ( D–F ) or mito-R-GECO1 ( G–I ). At 48 hr post transfection, cultured astrocytes were treated with 100 µM ATP and Ca 2+ imaging analysis was performed. Images were acquired every 3 seconds. ( A, D, G ) Representative time-lapse images of each Ca 2+ indicator. ( B, E, H ) ΔF/F 0 values over time following ATP application. ( C, F, I ) Area above or area under the curve values, calculated from panels B, E, and H. ( A–C ) CTRL siRNA, n=19; Herp siRNA, n=22. ( D–F ) CTRL siRNA, n=20; Herp siRNA, n=25. ( G–I ) CTRL siRNA, n=16; Herp siRNA, n=16. ( J–M ) Cultured astrocytes were transfected with the indicated siRNA (20 nM) and processed for Western blot analysis 48 hr post transfection. Vinculin and GAPDH served as loading control for ITPRs and HERP, respectively. ( J ) Representative western blot images from twelve independent experiments are shown. NS, non-specific band ( K ) Densitometric quantification of western blot data showing relative levels of ITPR1 in Herp siRNA-transfected astrocytes compared to CTRL siRNA transfected astrocytes. ( L ) Representative Western blot images from five independent experiments. ( M ) Densitometric quantification of western blot data showing relative levels of ITPR2 in Herp siRNA-transfected astrocytes compared to Control astrocytes. Values are mean ± SEM (*p<0.05, * * p<0.005, ** * p<0.0005, *** * p<0.00005; t -test). ( N–P ) Cultured astrocytes were treated with 10 μM Xestospongin C (XesC), an IP3R inhibitor, for 30 min before live imaging. Cells were then treated with 100 μM ATP, and images were captured every 3 s. ( N ) Representative time-lapse images of ER Ca 2+ indicator. ( O ) ΔF/F 0 values over time following ATP application. ( P ) Area above the curve values were calculated from panel O. CTRL siRNA + Mock, n=9; Herp siRNA + Mock, n=9; CTRL siRNA + XesC, n=8; Herp siRNA + XesC, n=14. Values are means ± SEM (*p<0.05, * * p<0.005, ** * p<0.0005, *** * p<0.00005; one-way ANOVA). Figure 3—source data 1. PDF file containing original western blot for , indicating the relevant bands and treatments. Figure 3—source data 2. Original files for western blot analysis displayed in . Figure 3—source data 3. PDF file containing original western blot for , indicating the relevant bands and treatments. Figure 3—source data 4. Original files for western blot analysis displayed in .

Article Snippet: Membranes were blocked with 5% skim milk and incubated overnight at 4°C with primary antibodies: anti-BMAL1 (Abcam (UK), ab93806), 1:2000; anti-HERP (Abcam, ab150424), 1:1000; anti-ITPR1 (Alomone Labs, Israel, ACC-019), 1:1000; anti-ITPR2 (Alomone Labs, ACC-116), 1:1000; anti-CX43 (Sigma, C6219), 1:5000; anti-pCX43 (Ser368; CST, USA, 3511), 1:1000; anti-GAPDH (Novus, USA, NB100-56875), 1:5000; anti-Vinculin (Sigma-Aldrich, V4505), 1:5000; and anti-total ERK (CST, 9102), 1:5000.

Techniques: Cell Culture, Transfection, Imaging, Western Blot, Control

Journal: eLife

Article Title: Circadian regulation of endoplasmic reticulum calcium response in cultured mouse astrocytes

doi: 10.7554/eLife.96357

Figure Lengend Snippet: ( A ) Schematic diagram of the experimental scheme from transfection to live-cell Ca 2+ imaging at different times. ( B–M ) Cultured astrocytes were transfected with G-CEPIA1er ( B–D, K–M ), R-GECO1 ( E–G ), or mito-R-GECO1 ( H–J ) compartment-specific Ca 2+ indicators (denoted at left) and then their circadian rhythm was synchronized by SS. ( K–M ) The indicated siRNA was co-transfected with the ER Ca 2+ indicator. After transfection, cells were allowed 48 hr for the siRNA to take effect and stabilize before synchronization by serum shock. At the indicated times, astrocytes were treated with 100 µM ATP and Ca 2+ imaging was performed. ( B, E, H, K ) Representative time-lapse images of each Ca 2+ indicator. ( C, F, I, L ) ΔF/F 0 values over time following ATP application. ( D, G, J, M ) Area above or area under the curve values, calculated from panels C, F, I, and L. ( B–D ) 30 hr post sync, n=24; 42 hr post sync, n=19. ( E–G ) 30 hr post sync, n=33; 42 hr post sync, n=38. ( H–J ) 30 hr post sync, n=50; 42 hr post sync, n=54. ( K–M ) CTRL siRNA, 30 hr post sync, n=5; CTRL siRNA, 42 hr post sync, n=4; Herp siRNA, 30 hr post sync, n=11; Herp siRNA, 42 hr post sync, n=5. Values in graphs are mean ± SEM (*p<0.05, *** * p<0.00005); ( D, G, J ) t -test, ( M ) one-way ANOVA. ( N–O ) Cells were harvested at the indicated times and processed for western blot analysis. Vinculin and GAPDH served as loading controls for ITPR and BMAL1, respectively. ( N ) Representative western blot images from six independent experiments. ( O ) Densitometric quantification of western blot data showing relative levels of ITPR1 and ITPR2 at different times. Values in graphs are mean ± SEMs (*p<0.05, *** * p<0.00005; t -test). Panel A was created with BioRender.com . Figure 4—source data 1. PDF file containing original western blot for , indicating the relevant bands and treatments. Figure 4—source data 2. Original files for western blot analysis displayed in .

Article Snippet: Membranes were blocked with 5% skim milk and incubated overnight at 4°C with primary antibodies: anti-BMAL1 (Abcam (UK), ab93806), 1:2000; anti-HERP (Abcam, ab150424), 1:1000; anti-ITPR1 (Alomone Labs, Israel, ACC-019), 1:1000; anti-ITPR2 (Alomone Labs, ACC-116), 1:1000; anti-CX43 (Sigma, C6219), 1:5000; anti-pCX43 (Ser368; CST, USA, 3511), 1:1000; anti-GAPDH (Novus, USA, NB100-56875), 1:5000; anti-Vinculin (Sigma-Aldrich, V4505), 1:5000; and anti-total ERK (CST, 9102), 1:5000.

Techniques: Transfection, Imaging, Cell Culture, Western Blot

Journal: eLife

Article Title: Circadian regulation of endoplasmic reticulum calcium response in cultured mouse astrocytes

doi: 10.7554/eLife.96357

Figure Lengend Snippet:

Article Snippet: Membranes were blocked with 5% skim milk and incubated overnight at 4°C with primary antibodies: anti-BMAL1 (Abcam (UK), ab93806), 1:2000; anti-HERP (Abcam, ab150424), 1:1000; anti-ITPR1 (Alomone Labs, Israel, ACC-019), 1:1000; anti-ITPR2 (Alomone Labs, ACC-116), 1:1000; anti-CX43 (Sigma, C6219), 1:5000; anti-pCX43 (Ser368; CST, USA, 3511), 1:1000; anti-GAPDH (Novus, USA, NB100-56875), 1:5000; anti-Vinculin (Sigma-Aldrich, V4505), 1:5000; and anti-total ERK (CST, 9102), 1:5000.

Techniques: Transfection, Construct, Plasmid Preparation, Sequencing, Negative Control, Software, Microscopy