Journal: PLoS ONE

Article Title: Expression of Novel Alzheimer’s Disease Risk Genes in Control and Alzheimer’s Disease Brains

doi: 10.1371/journal.pone.0050976

Figure Lengend Snippet: Gene expression is associated with AD pathology.

Article Snippet: Taqman real-time PCR assays were utilized to quantify expression for the following genes: ABCA7 (ABI: Hs01105094_m1), AIF1 (ABI: Hs00610419_g1), BIN1 (ABI: Hs00184913_m1), BIN1 n (ABI : Hs01120896_m1), CD2AP (ABI: Hs00961451_m1), CD33 (ABI: Hs00233544_m1), CLU 1 (ABI: Hs00156548_m1), CLU 2 (ABI: Hs00971653_m1), CR1 (ABI: Hs00559342_m1), EPHA1 (ABI: Hs00178313_m1), GAPDH (ABI: Hs02758991_g1 (VIC) and Hs99999905_m1 (FAM)), GFAP (ABI: Hs00909233_m1), MAP2 (ABI: Hs00258900_m1), MS4A6A (ABI: Hs00223521_m1), PICALM (ABI: Hs00200318_m1).

Techniques: Gene Expression

Journal: PLoS ONE

Article Title: Expression of Novel Alzheimer’s Disease Risk Genes in Control and Alzheimer’s Disease Brains

doi: 10.1371/journal.pone.0050976

Figure Lengend Snippet: AD GWAS SNPs do not modify gene expression in the parietal lobe of human brains.

Article Snippet: Taqman real-time PCR assays were utilized to quantify expression for the following genes: ABCA7 (ABI: Hs01105094_m1), AIF1 (ABI: Hs00610419_g1), BIN1 (ABI: Hs00184913_m1), BIN1 n (ABI : Hs01120896_m1), CD2AP (ABI: Hs00961451_m1), CD33 (ABI: Hs00233544_m1), CLU 1 (ABI: Hs00156548_m1), CLU 2 (ABI: Hs00971653_m1), CR1 (ABI: Hs00559342_m1), EPHA1 (ABI: Hs00178313_m1), GAPDH (ABI: Hs02758991_g1 (VIC) and Hs99999905_m1 (FAM)), GFAP (ABI: Hs00909233_m1), MAP2 (ABI: Hs00258900_m1), MS4A6A (ABI: Hs00223521_m1), PICALM (ABI: Hs00200318_m1).

Techniques: Gene Expression

Journal: PLoS ONE

Article Title: Expression of Novel Alzheimer’s Disease Risk Genes in Control and Alzheimer’s Disease Brains

doi: 10.1371/journal.pone.0050976

Figure Lengend Snippet: Gene SNPs do not significantly influence AD brain pathology.

Article Snippet: Taqman real-time PCR assays were utilized to quantify expression for the following genes: ABCA7 (ABI: Hs01105094_m1), AIF1 (ABI: Hs00610419_g1), BIN1 (ABI: Hs00184913_m1), BIN1 n (ABI : Hs01120896_m1), CD2AP (ABI: Hs00961451_m1), CD33 (ABI: Hs00233544_m1), CLU 1 (ABI: Hs00156548_m1), CLU 2 (ABI: Hs00971653_m1), CR1 (ABI: Hs00559342_m1), EPHA1 (ABI: Hs00178313_m1), GAPDH (ABI: Hs02758991_g1 (VIC) and Hs99999905_m1 (FAM)), GFAP (ABI: Hs00909233_m1), MAP2 (ABI: Hs00258900_m1), MS4A6A (ABI: Hs00223521_m1), PICALM (ABI: Hs00200318_m1).

Techniques:

Journal: International immunopharmacology

Article Title: Minnelide combined with Angptl3 knockout completely protects mice with adriamycin nephropathy via suppression of TGF-β1-Smad2 and p53 pathways.

doi: 10.1016/j.intimp.2022.109656

Figure Lengend Snippet: Fig. 2. Minnelide alleviates podocyte injury in Angptl3 knockout mice with adriamycin nephropathy. (A) Immunofluorescence of nephrin, podocin, and cd2ap in kidney tissues of three groups of mice. (B and C) The protein expression levels of nephrin, podocin, and cd2ap in kidney tissues of three groups of mice were measured by western blot. n = 3, ****P < 0.0001 vs Angptl3-/- group; #P < 0.05, ##P < 0.01 and ####P < 0.0001 vs ADR + Angptl3-/- group.

Article Snippet: The membrane was incubated overnight at 4 ◦C with the following primary antibodies: nephrin (1:500, Invitrogen, PA5-106921), podocin (1:500, Proteintech, 20384–1-AP), cd2ap (1:500, Invitrogen, PA5-51894), α-SMA (1:1000, Servicebio, GB111364), TGF-β1 (1:500, Servicebio, GB111876), pSmad2 (1:500, Servicebio, GB11343), pp53 (1:500, Servicebio, B. Ji et al. International Immunopharmacology 115 (2023) 109656 GB114061), p53 (1:500, Proteintech, 10442–1-AP), Bax (1:500, Abcam, ab216494), Bcl-2 (1:500, Abcam, ab196495), and Cleaved-caspase3 (1:500, Servicebio, GB11532).

Techniques: Knock-Out, Immunofluorescence, Expressing, Western Blot

Journal: International immunopharmacology

Article Title: Minnelide combined with Angptl3 knockout completely protects mice with adriamycin nephropathy via suppression of TGF-β1-Smad2 and p53 pathways.

doi: 10.1016/j.intimp.2022.109656

Figure Lengend Snippet: Fig. 8. Triptolide attenuates podocyte injury in Angptl3 knockout primary podocytes. (A) Immunofluorescence of nephrin, podocin, and cd2ap in Angptl3 knockout primary podocytes. (B) The expression of podocin and cd2ap proteins in Angptl3 knockout primary podocytes was measured by western blot. n = 3. ****P < 0.0001 vs Angptl3-/- group; ##P < 0.01 and ####P < 0.0001 vs ADR + Angptl3-/- group.

Article Snippet: The membrane was incubated overnight at 4 ◦C with the following primary antibodies: nephrin (1:500, Invitrogen, PA5-106921), podocin (1:500, Proteintech, 20384–1-AP), cd2ap (1:500, Invitrogen, PA5-51894), α-SMA (1:1000, Servicebio, GB111364), TGF-β1 (1:500, Servicebio, GB111876), pSmad2 (1:500, Servicebio, GB11343), pp53 (1:500, Servicebio, B. Ji et al. International Immunopharmacology 115 (2023) 109656 GB114061), p53 (1:500, Proteintech, 10442–1-AP), Bax (1:500, Abcam, ab216494), Bcl-2 (1:500, Abcam, ab196495), and Cleaved-caspase3 (1:500, Servicebio, GB11532).

Techniques: Knock-Out, Immunofluorescence, Expressing, Western Blot

Journal: Journal of the American Society of Nephrology : JASN

Article Title: TRPC6 Binds to and Activates Calpain, Independent of Its Channel Activity, and Regulates Podocyte Cytoskeleton, Cell Adhesion, and Motility

doi: 10.1681/ASN.2018070729

Figure Lengend Snippet: A GFP tagged TRPC6 construct is functional when expressed in a TRPC6 KO podocyte cell line. (A) Podocyte markers CD2-associated protein (CD2AP), synaptopodin, Wills tumor protein 1 (WT1), podocin, and nephrin are expressed in TRPC6 knockout (T6K) cells. TRPC6 is not expressed. (B) A TRPC6 construct with an extracellular green fluorescent protein (GFP) tag at amino acid 561 was generated and reintroduced to the T6K cells. This is demonstrated by western blotting and immunofluorescence (magenta, actin; GFP, green; DAPI, blue). Disease-causing and DN forms of the GFP-tagged TRPC6 construct were also generated and introduced to T6K cells. (C and D) Biotinylation and TIRF microscopy demonstrating that WT TRPC6-GFP was able to traffic to the plasma membrane. CD99 is a membrane protein and was used as a control in both experiments. (E) Patch clamp analysis of channel function. Pooled data of change in Ihold caused by 6-minute 1 μM AngII perfusion. AngII perfusion causes a rapid change in Ihold in WT (−36.2±10.5 pA at 8-minute timepoint, open symbols, n=5) but not the null mutant (8.7±3.4 pA at 8-minute timepoint, closed symbols, n=4) or T6K (−3.5±4.3 pA at 8-minute timepoint, triangle symbols, n=4) cells. Gray vertical bar represents perfusion of AngII. All symbols represent the mean±SEM. (F) Summary box plot (boxes, 25th–75th percentile; lines, median) showing changes in Ihold caused by 1 μM AngII perfusion at the 8-minute timepoint in (E). *P<0.05, unpaired t test. Con, control.

Article Snippet: CD2AP , Cell Signaling #5478.

Techniques: Construct, Functional Assay, Knock-Out, Generated, Western Blot, Immunofluorescence, Microscopy, Clinical Proteomics, Membrane, Control, Patch Clamp, Mutagenesis

Journal: Journal of the American Society of Nephrology : JASN

Article Title: TRPC6 Binds to and Activates Calpain, Independent of Its Channel Activity, and Regulates Podocyte Cytoskeleton, Cell Adhesion, and Motility

doi: 10.1681/ASN.2018070729

Figure Lengend Snippet: Antibodies Used

Article Snippet: CD2AP , Cell Signaling #5478.

Techniques:

Journal: Neurobiology of aging

Article Title: Translating Alzheimer’s disease-associated polymorphisms into functional candidates: a survey of IGAP genes and SNPs

doi: 10.1016/j.neurobiolaging.2018.10.017

Figure Lengend Snippet: Significant association of the IGAP SNPs with brain gene expression in NABEC and UKBEC

Article Snippet: In UKBEC, the risk allele of rs4147929 in ABCA7 , the risk allele of rs10948363 in CD2AP , and the protective allele of rs3865444 in CD33 were associated with increased EID2B expression in FCTX, increased AK9 expression in FCTX, and decreased IER2 expression in TCTX, respectively. table ft1 table-wrap mode="anchored" t5 Table 3. caption a7 IGAP SNP Closest gene Probe set ID a Gene expression Brain region β ^ P-value b NABEC rs8093731 DSG2 ILMN_23 80779 DLGAP1 FCTX 0.770 1.36×10 −8 ILMN_1783168 NETO1 FCTX 0.706 1.11×10 −5 UKBEC rs4147929 ABCA7 t3862068 EID2B FCTX 0.259 3.94×10 −6 rs10948363 CD2AP t2969159 AK9 FCTX 0.343 1.64×10 −5 rs3865444 CD33 t3822216 IER2 TCTX -0.255 1.96×10 −5 Open in a separate window a Probe set IDs on HumanHT-12_v3 Expression BeadChips in NABEC (platform = {"type":"entrez-geo","attrs":{"text":"GPL6947","term_id":"6947"}} GPL6947 ) and on Affymetrix Exon 1.0 ST Arrays in UKBEC (platform = {"type":"entrez-geo","attrs":{"text":"GPL5175","term_id":"5175"}} GPL5175 ) b P-values less than significance level after false discovery rate adjustment are displayed.

Techniques: Gene Expression

Journal: Neurobiology of aging

Article Title: Translating Alzheimer’s disease-associated polymorphisms into functional candidates: a survey of IGAP genes and SNPs

doi: 10.1016/j.neurobiolaging.2018.10.017

Figure Lengend Snippet: Associations between gene expressions identified in NABEC and UKBEC and Alzheimer’s disease status in the merged dataset

Article Snippet: In UKBEC, the risk allele of rs4147929 in ABCA7 , the risk allele of rs10948363 in CD2AP , and the protective allele of rs3865444 in CD33 were associated with increased EID2B expression in FCTX, increased AK9 expression in FCTX, and decreased IER2 expression in TCTX, respectively. table ft1 table-wrap mode="anchored" t5 Table 3. caption a7 IGAP SNP Closest gene Probe set ID a Gene expression Brain region β ^ P-value b NABEC rs8093731 DSG2 ILMN_23 80779 DLGAP1 FCTX 0.770 1.36×10 −8 ILMN_1783168 NETO1 FCTX 0.706 1.11×10 −5 UKBEC rs4147929 ABCA7 t3862068 EID2B FCTX 0.259 3.94×10 −6 rs10948363 CD2AP t2969159 AK9 FCTX 0.343 1.64×10 −5 rs3865444 CD33 t3822216 IER2 TCTX -0.255 1.96×10 −5 Open in a separate window a Probe set IDs on HumanHT-12_v3 Expression BeadChips in NABEC (platform = {"type":"entrez-geo","attrs":{"text":"GPL6947","term_id":"6947"}} GPL6947 ) and on Affymetrix Exon 1.0 ST Arrays in UKBEC (platform = {"type":"entrez-geo","attrs":{"text":"GPL5175","term_id":"5175"}} GPL5175 ) b P-values less than significance level after false discovery rate adjustment are displayed.

Techniques:

Journal: Frontiers in Pharmacology

Article Title: Shensu IV maintains the integrity of the glomerular filtration barrier and exerts renal protective effects by regulating endogenous hydrogen sulfide levels

doi: 10.3389/fphar.2024.1447249

Figure Lengend Snippet: FIGURE 6 Shensu IV regulates the PI3K/AKT signaling pathway through H2S. (A) The effects of Shensu IV and NaHS on the mRNA expression of CD2AP, nephrin, CBS, CSE, NOX4, PI3K, and AKT in renal tissue of PAN rats were analyzed by RT-qPCR. (B) Western blot analysis of the effects of Shensu IV and NaHS on the protein levels of CD2AP, nephrin, CBS, CSE, NOX4, PI3K, p-PI3K,AKT,p-AKT in renal tissue of PAN rats. *P< 0.05, **P< 0.01, ***P< 0.001. Abbreviations: CD2AP, CD2-associated protein; CBS, Cystathionine β-synthase; CSE, Cystathionine γ-lyase; PI3K, Phosphoinositide 3-Kinase; AKT, Protein Kinase B.

Article Snippet: Membranes were blocked with 5% skim milk (Solarbio) to prevent nonspecific binding and then incubated with primary antibodies against CD2AP (1:2000; A01756-2, BOSTER, Wuhan, China), nephrin (1:2000; A01756-2, BOSTER), CBS (1: 10,000; 14787-1-AP, Proteintech, Wuhan, China), CSE (1: 4,000; 12217-1-AP, Proteintech), PI3K (1:2000; 60225-1-Ig, Proteintech), p-PI3K (1:2000; bs-3332R, BOSTER), AKT (1:10,000; 60203-2-Ig, Proteintech), p-AKT (1: 10,000; 66,444-1-lg, Proteintech), NOX4 (1: 8,000; 14347-1-AP, Proteintech), and GAPDH (1:40,000; 60004-1- Ig, Proteintech).

Techniques: Expressing, Quantitative RT-PCR, Western Blot

Journal: Frontiers in Pharmacology

Article Title: Shensu IV maintains the integrity of the glomerular filtration barrier and exerts renal protective effects by regulating endogenous hydrogen sulfide levels

doi: 10.3389/fphar.2024.1447249

Figure Lengend Snippet: FIGURE 8 Shensu IV regulates the PI3K/AKT signaling pathway through H2S in podocytes. (A) The effects of Shensu IV and NaHS on the mRNA expression of CD2AP, nephrin, CBS, CSE, NOX4, PI3K, and AKT in podocytes were analyzed by RT-qPCR. (B) Western blot analysis of the effects of Shensu IV and NaHS on the protein levels of CD2AP, nephrin, CBS, CSE, NOX4, PI3K, p-PI3K,AKT,p-AKT in PAN-induced podocyocytes. *P< 0.05, **P< 0.01, ***P< 0.001. Abbreviations: CD2AP, CD2-associated protein; CBS, Cystathionine β-synthase; CSE, Cystathionine γ-lyase; PI3K, Phosphoinositide 3-Kinase; AKT, Protein Kinase B.

Article Snippet: Membranes were blocked with 5% skim milk (Solarbio) to prevent nonspecific binding and then incubated with primary antibodies against CD2AP (1:2000; A01756-2, BOSTER, Wuhan, China), nephrin (1:2000; A01756-2, BOSTER), CBS (1: 10,000; 14787-1-AP, Proteintech, Wuhan, China), CSE (1: 4,000; 12217-1-AP, Proteintech), PI3K (1:2000; 60225-1-Ig, Proteintech), p-PI3K (1:2000; bs-3332R, BOSTER), AKT (1:10,000; 60203-2-Ig, Proteintech), p-AKT (1: 10,000; 66,444-1-lg, Proteintech), NOX4 (1: 8,000; 14347-1-AP, Proteintech), and GAPDH (1:40,000; 60004-1- Ig, Proteintech).

Techniques: Expressing, Quantitative RT-PCR, Western Blot