pde8a Search Results


90
Thermo Fisher gene exp pde8a mm01315378 m1
Gene Exp Pde8a Mm01315378 M1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Proteintech anti pde8a
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Santa Cruz Biotechnology anti pde8a antibody
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Santa Cruz Biotechnology lentiviral particles expressing pde8a shrna
Lentiviral Particles Expressing Pde8a Shrna, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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OriGene pde8a overexpression
Figure 1. <t>PDE8A</t> expression during macrophage differentiation and polarisation. (A) PDE8A mRNA expression in freshly isolated monocytes and macrophages cultured for 7 days from 32 donors. (B) PDE8A mRNA expression in freshly isolated monocytes and macrophages from 4 donors cultured in the absence or presence of IFN-a (250 U/ml), IFN-b (250 U/ml), IFN-c (2501U/ml), IL-4 (10 ng/ml), or IL-10 (100 U/ml) for 7 days. Statistical differences were analyzed using a paired T test: *p,0.05, **p,0.01, ***p,0.001. doi:10.1371/journal.pone.0109673.g001
Pde8a Overexpression, supplied by OriGene, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Atlas Antibodies anti pde8a
Figure 1. <t>PDE8A</t> expression during macrophage differentiation and polarisation. (A) PDE8A mRNA expression in freshly isolated monocytes and macrophages cultured for 7 days from 32 donors. (B) PDE8A mRNA expression in freshly isolated monocytes and macrophages from 4 donors cultured in the absence or presence of IFN-a (250 U/ml), IFN-b (250 U/ml), IFN-c (2501U/ml), IL-4 (10 ng/ml), or IL-10 (100 U/ml) for 7 days. Statistical differences were analyzed using a paired T test: *p,0.05, **p,0.01, ***p,0.001. doi:10.1371/journal.pone.0109673.g001
Anti Pde8a, supplied by Atlas Antibodies, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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OriGene myc tagged pde8a
Fig. 2. Schematic overview of the five different <t>PDE8A</t> transcript variants, including 3′ UTR and a 2 kb region upstream of the ATG start codon containing the promoter and 5′ UTR. Exons are depicted as gray boxes, UTR (thick border) and promoter (thin border) as white boxes. SNPs in moderate to high LD (r2N0.6) with rs2304418 or rs12909130 that affect possible human transcription factor binding sites (#) or microsatellites (*) are shown, as well as the SNP identified in the promoter region of PDE8A. SNPs rs12909130 and rs12900078 were used for genotyping since they are perfect proxies for SNP rs2304418 and the promoter SNP rs11689332 respectively. All other SNPs in LD (r2N0.6) with rs12909130 or rs2304418 can be found in Table S3. LD, linkage disequilibrium.
Myc Tagged Pde8a, supplied by OriGene, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Thermo Fisher gene exp pde8a hs01079617 m1
Fig. 2. Schematic overview of the five different <t>PDE8A</t> transcript variants, including 3′ UTR and a 2 kb region upstream of the ATG start codon containing the promoter and 5′ UTR. Exons are depicted as gray boxes, UTR (thick border) and promoter (thin border) as white boxes. SNPs in moderate to high LD (r2N0.6) with rs2304418 or rs12909130 that affect possible human transcription factor binding sites (#) or microsatellites (*) are shown, as well as the SNP identified in the promoter region of PDE8A. SNPs rs12909130 and rs12900078 were used for genotyping since they are perfect proxies for SNP rs2304418 and the promoter SNP rs11689332 respectively. All other SNPs in LD (r2N0.6) with rs12909130 or rs2304418 can be found in Table S3. LD, linkage disequilibrium.
Gene Exp Pde8a Hs01079617 M1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Thermo Fisher gene exp pde8a hs00400174 m1
Fig. 2. Schematic overview of the five different <t>PDE8A</t> transcript variants, including 3′ UTR and a 2 kb region upstream of the ATG start codon containing the promoter and 5′ UTR. Exons are depicted as gray boxes, UTR (thick border) and promoter (thin border) as white boxes. SNPs in moderate to high LD (r2N0.6) with rs2304418 or rs12909130 that affect possible human transcription factor binding sites (#) or microsatellites (*) are shown, as well as the SNP identified in the promoter region of PDE8A. SNPs rs12909130 and rs12900078 were used for genotyping since they are perfect proxies for SNP rs2304418 and the promoter SNP rs11689332 respectively. All other SNPs in LD (r2N0.6) with rs12909130 or rs2304418 can be found in Table S3. LD, linkage disequilibrium.
Gene Exp Pde8a Hs00400174 M1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Thermo Fisher copy number variation pde8a hs03902365 cn
Detailed list of the identified CNVs affecting genes potentially related to female fertility.
Copy Number Variation Pde8a Hs03902365 Cn, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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BPS Bioscience camp for pde8a
Detailed list of the identified CNVs affecting genes potentially related to female fertility.
Camp For Pde8a, supplied by BPS Bioscience, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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GenScript corporation pde8a – c-raf disrupter
Effects of PPL008 conjugates on pERK levels and rate of cell proliferation. Normalised phospho-ERK (mean ± SEM) following treatment with DMSO (lane 1), PLX4032 B-Raf inhibitor (lane 2), PPL008 conjugates (lanes 11–14) or PLX co-treatments with <t>PDE8A</t> – C-Raf peptide disrupters (original stearylated ‘disrupter’ lane 3, or scrambled control, lane 4) or PPL-008 conjugates (lanes 7–10) in: a MM415 (NRAS Q61L) and ( b ) A375 (BRAF V600E) human malignant melanoma cell lines. Respective pERK and GAPDH immunoblot examples shown below ( N ≥ 3, * P < 0.05, ** P < 0.01 ). c Real-time cell analyses (xCELLigence platform) of MM415 cell proliferation following treatments described above. Treatments occurred at 21 h and the slope of normalised cell index (mean ± STDEV) was measured between 21 and 39 h, with (ii) representing DMSO vs. peptide disrupter treatments only (10 μM) and (iii) representing PLX (1 μM) vs. co-treatments of peptide disrupters and PLX4032 ( n = 3, *** P < 0.001) . D, stearylated disrupter; S, stearylated scrambled; N, PPL-008 N; C, PPL-008C; NSS, PPL-008NSS; CSS, PPL-008CSS
Pde8a – C Raf Disrupter, supplied by GenScript corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


Figure 1. PDE8A expression during macrophage differentiation and polarisation. (A) PDE8A mRNA expression in freshly isolated monocytes and macrophages cultured for 7 days from 32 donors. (B) PDE8A mRNA expression in freshly isolated monocytes and macrophages from 4 donors cultured in the absence or presence of IFN-a (250 U/ml), IFN-b (250 U/ml), IFN-c (2501U/ml), IL-4 (10 ng/ml), or IL-10 (100 U/ml) for 7 days. Statistical differences were analyzed using a paired T test: *p,0.05, **p,0.01, ***p,0.001. doi:10.1371/journal.pone.0109673.g001

Journal: PloS one

Article Title: Phosphodiesterase 8a supports HIV-1 replication in macrophages at the level of reverse transcription.

doi: 10.1371/journal.pone.0109673

Figure Lengend Snippet: Figure 1. PDE8A expression during macrophage differentiation and polarisation. (A) PDE8A mRNA expression in freshly isolated monocytes and macrophages cultured for 7 days from 32 donors. (B) PDE8A mRNA expression in freshly isolated monocytes and macrophages from 4 donors cultured in the absence or presence of IFN-a (250 U/ml), IFN-b (250 U/ml), IFN-c (2501U/ml), IL-4 (10 ng/ml), or IL-10 (100 U/ml) for 7 days. Statistical differences were analyzed using a paired T test: *p,0.05, **p,0.01, ***p,0.001. doi:10.1371/journal.pone.0109673.g001

Article Snippet: Plasmids For PDE8A overexpression and testing knockdown efficiency of the shRNAs targeting PDE8A, a vector expressing a MYC-tagged PDE8A under the control of the CMV promotor (Origene, Rockville, MD, USA) was used.

Techniques: Expressing, Isolation, Cell Culture

Figure 2. Regulation of PDE8A expression by miR-145-5p during differentiation of monocytes into macrophages. Confirmation of PDE8A mRNA (A) and miR-145-5p (B) expression during differentiation of monocytes into macrophages obtained from 8 donors. PDE8A mRNA or miR- 145-5p expression during differentiation was compared with the expression at day 0 by using a paired T test: *p,0.05, **p,0.01, ***p,0.001. (C) Schematic overview of the PDE8A mRNA transcript 1 including the miR-145-5p binding site between base pair 3412 and 3435. (D) Expression levels of miR-145-5p determined by qPCR in HEK293T cells 2 days after transfection with an empty vector control or a vector containing a miR-145-5p expression cassette (n = 2, mean and SD). (E) Direct interaction between miR-145-5p and its target sequence in the PDE8A mRNA transcript was tested by co-transfection of p-hEF1a-miR-145-5p or an empty vector control and p-hEF1a-Luc-39UTR PDE8A. Luciferase activity was measured 2 days post- transfection (n = 3, mean and SD). Statistical differences were analyzed using an un-paired T test: *p,0.05, **p,0.01, ***p,0.001. doi:10.1371/journal.pone.0109673.g002

Journal: PloS one

Article Title: Phosphodiesterase 8a supports HIV-1 replication in macrophages at the level of reverse transcription.

doi: 10.1371/journal.pone.0109673

Figure Lengend Snippet: Figure 2. Regulation of PDE8A expression by miR-145-5p during differentiation of monocytes into macrophages. Confirmation of PDE8A mRNA (A) and miR-145-5p (B) expression during differentiation of monocytes into macrophages obtained from 8 donors. PDE8A mRNA or miR- 145-5p expression during differentiation was compared with the expression at day 0 by using a paired T test: *p,0.05, **p,0.01, ***p,0.001. (C) Schematic overview of the PDE8A mRNA transcript 1 including the miR-145-5p binding site between base pair 3412 and 3435. (D) Expression levels of miR-145-5p determined by qPCR in HEK293T cells 2 days after transfection with an empty vector control or a vector containing a miR-145-5p expression cassette (n = 2, mean and SD). (E) Direct interaction between miR-145-5p and its target sequence in the PDE8A mRNA transcript was tested by co-transfection of p-hEF1a-miR-145-5p or an empty vector control and p-hEF1a-Luc-39UTR PDE8A. Luciferase activity was measured 2 days post- transfection (n = 3, mean and SD). Statistical differences were analyzed using an un-paired T test: *p,0.05, **p,0.01, ***p,0.001. doi:10.1371/journal.pone.0109673.g002

Article Snippet: Plasmids For PDE8A overexpression and testing knockdown efficiency of the shRNAs targeting PDE8A, a vector expressing a MYC-tagged PDE8A under the control of the CMV promotor (Origene, Rockville, MD, USA) was used.

Techniques: Expressing, Binding Assay, Transfection, Plasmid Preparation, Control, Sequencing, Cotransfection, Luciferase, Activity Assay

Figure 3. PDE8A supports HIV-1 replication at the level of reverse transcription. (A) HEK293T cells were transfected with different concentrations of pCMV6-PDE8A or an empty vector control. PDE8A expression was analyzed forty-eight hours after transfection by western blot. (B) HEK293T cells were transfected with different concentrations of pCMV6-PDE8A or an empty vector control and infected with VSV-G/NL4-3.Luc 48 hours after transfection. Luciferase activity was measured 2 days after infection (n = 3, mean and SD). (C) HEK293T cells were transfected with different concentrations of pCMV6-PDE8A or an empty vector control and infected with VSV-G/NL4-3-Ba-L 48 hours after transfection. Proviral DNA levels were analyzed forty-eight hours after infection by qPCR. Proviral DNA levels are expressed relative to the control after correction for b-actin levels in the same sample (n = 3, mean and SD). (D) HEK293T cells were transfected with 1 mg of pCMV6-PDE8A or 1 mg of empty vector control and infected with VSV-G/NL4-3-Ba-L 48 hours after transfection. R/U5 and Pol proviral DNA levels were analyzed by qPCR during 48 hours post-infection. R/U5 and Pol levels are expressed as the ratio of the expression in cells transfected with pCMV-PDE8A divided by the expression in cells that were transfected with the empty vector control and corrected for b-actin levels (n = 2, mean and SD). (E) HEK293T cells were transfected with 1 mg of pCMV6-PDE8A or 1 mg of the empty vector control and infected with VSV-G/NL4-3-Ba-L 48 hours after transfection. Integrated HIV-1 copies were determined 48 hours post infection by Alu-PCR and expressed relative to the control after correction for b-actin levels in the same sample (n = 2, mean and SD). Statistical differences were analyzed using an un-paired T test: *p,0.05, **p,0.01, ***p,0.001. doi:10.1371/journal.pone.0109673.g003

Journal: PloS one

Article Title: Phosphodiesterase 8a supports HIV-1 replication in macrophages at the level of reverse transcription.

doi: 10.1371/journal.pone.0109673

Figure Lengend Snippet: Figure 3. PDE8A supports HIV-1 replication at the level of reverse transcription. (A) HEK293T cells were transfected with different concentrations of pCMV6-PDE8A or an empty vector control. PDE8A expression was analyzed forty-eight hours after transfection by western blot. (B) HEK293T cells were transfected with different concentrations of pCMV6-PDE8A or an empty vector control and infected with VSV-G/NL4-3.Luc 48 hours after transfection. Luciferase activity was measured 2 days after infection (n = 3, mean and SD). (C) HEK293T cells were transfected with different concentrations of pCMV6-PDE8A or an empty vector control and infected with VSV-G/NL4-3-Ba-L 48 hours after transfection. Proviral DNA levels were analyzed forty-eight hours after infection by qPCR. Proviral DNA levels are expressed relative to the control after correction for b-actin levels in the same sample (n = 3, mean and SD). (D) HEK293T cells were transfected with 1 mg of pCMV6-PDE8A or 1 mg of empty vector control and infected with VSV-G/NL4-3-Ba-L 48 hours after transfection. R/U5 and Pol proviral DNA levels were analyzed by qPCR during 48 hours post-infection. R/U5 and Pol levels are expressed as the ratio of the expression in cells transfected with pCMV-PDE8A divided by the expression in cells that were transfected with the empty vector control and corrected for b-actin levels (n = 2, mean and SD). (E) HEK293T cells were transfected with 1 mg of pCMV6-PDE8A or 1 mg of the empty vector control and infected with VSV-G/NL4-3-Ba-L 48 hours after transfection. Integrated HIV-1 copies were determined 48 hours post infection by Alu-PCR and expressed relative to the control after correction for b-actin levels in the same sample (n = 2, mean and SD). Statistical differences were analyzed using an un-paired T test: *p,0.05, **p,0.01, ***p,0.001. doi:10.1371/journal.pone.0109673.g003

Article Snippet: Plasmids For PDE8A overexpression and testing knockdown efficiency of the shRNAs targeting PDE8A, a vector expressing a MYC-tagged PDE8A under the control of the CMV promotor (Origene, Rockville, MD, USA) was used.

Techniques: Reverse Transcription, Transfection, Plasmid Preparation, Control, Expressing, Western Blot, Infection, Luciferase, Activity Assay

Figure 4. The effect of PDE8A knockdown on HIV-1 replication in macrophages. (A) To analyze the effect of PDE8A knockdown on HIV-1 replication in macrophages, monocytes from 4 donors were cultured for 5 days and transduced with lentiviral vectors expressing shRNA control or two shRNA’s targeting PDE8A. Forty-eight hours after the lentiviral transduction, macrophages were infected with VSV-G/NL4-3.Luc and luciferase activity was measured at day 2 after infection. The results are given as the mean fold luciferase expression from 4 donors, relative to the medium control. UT: Untransduced control. Statistical differences were analyzed by mixed linear model, repeated covariance: diagonal (IBM SPSS Statistics 20). (B) To determine the effect of PDE8A knockdown on Pol proviral DNA levels, monocytes in which PDE8A was downregulated by lentiviral transduction were infected with VSV-G/NL4-3-Ba-L. Pol proviral DNA levels were analyzed by qPCR during 48 hours post-infection and expressed relative to b-actin. Results are given as mean and sd from 2 donors. (C) Monocytes in which PDE8A was downregulated by lentiviral transduction were infected with VSV-G/NL4-3-Ba-L. Two days post-infection, proviral DNA levels were analyzed by qPCR for Pol. Proviral DNA levels are expressed relative to the control after correction to b-actin for input. Results shown are representative for 3 donors. Inact.: Inactivated virus. Statistical differences were analyzed using a paired T test: *p,0.05, **p,0.01, ***p,0.001. doi:10.1371/journal.pone.0109673.g004

Journal: PloS one

Article Title: Phosphodiesterase 8a supports HIV-1 replication in macrophages at the level of reverse transcription.

doi: 10.1371/journal.pone.0109673

Figure Lengend Snippet: Figure 4. The effect of PDE8A knockdown on HIV-1 replication in macrophages. (A) To analyze the effect of PDE8A knockdown on HIV-1 replication in macrophages, monocytes from 4 donors were cultured for 5 days and transduced with lentiviral vectors expressing shRNA control or two shRNA’s targeting PDE8A. Forty-eight hours after the lentiviral transduction, macrophages were infected with VSV-G/NL4-3.Luc and luciferase activity was measured at day 2 after infection. The results are given as the mean fold luciferase expression from 4 donors, relative to the medium control. UT: Untransduced control. Statistical differences were analyzed by mixed linear model, repeated covariance: diagonal (IBM SPSS Statistics 20). (B) To determine the effect of PDE8A knockdown on Pol proviral DNA levels, monocytes in which PDE8A was downregulated by lentiviral transduction were infected with VSV-G/NL4-3-Ba-L. Pol proviral DNA levels were analyzed by qPCR during 48 hours post-infection and expressed relative to b-actin. Results are given as mean and sd from 2 donors. (C) Monocytes in which PDE8A was downregulated by lentiviral transduction were infected with VSV-G/NL4-3-Ba-L. Two days post-infection, proviral DNA levels were analyzed by qPCR for Pol. Proviral DNA levels are expressed relative to the control after correction to b-actin for input. Results shown are representative for 3 donors. Inact.: Inactivated virus. Statistical differences were analyzed using a paired T test: *p,0.05, **p,0.01, ***p,0.001. doi:10.1371/journal.pone.0109673.g004

Article Snippet: Plasmids For PDE8A overexpression and testing knockdown efficiency of the shRNAs targeting PDE8A, a vector expressing a MYC-tagged PDE8A under the control of the CMV promotor (Origene, Rockville, MD, USA) was used.

Techniques: Knockdown, Cell Culture, Transduction, Expressing, shRNA, Control, Infection, Luciferase, Activity Assay, Virus

Fig. 2. Schematic overview of the five different PDE8A transcript variants, including 3′ UTR and a 2 kb region upstream of the ATG start codon containing the promoter and 5′ UTR. Exons are depicted as gray boxes, UTR (thick border) and promoter (thin border) as white boxes. SNPs in moderate to high LD (r2N0.6) with rs2304418 or rs12909130 that affect possible human transcription factor binding sites (#) or microsatellites (*) are shown, as well as the SNP identified in the promoter region of PDE8A. SNPs rs12909130 and rs12900078 were used for genotyping since they are perfect proxies for SNP rs2304418 and the promoter SNP rs11689332 respectively. All other SNPs in LD (r2N0.6) with rs12909130 or rs2304418 can be found in Table S3. LD, linkage disequilibrium.

Journal: Virology

Article Title: Polymorphism in HIV-1 dependency factor PDE8A affects mRNA level and HIV-1 replication in primary macrophages.

doi: 10.1016/j.virol.2011.08.013

Figure Lengend Snippet: Fig. 2. Schematic overview of the five different PDE8A transcript variants, including 3′ UTR and a 2 kb region upstream of the ATG start codon containing the promoter and 5′ UTR. Exons are depicted as gray boxes, UTR (thick border) and promoter (thin border) as white boxes. SNPs in moderate to high LD (r2N0.6) with rs2304418 or rs12909130 that affect possible human transcription factor binding sites (#) or microsatellites (*) are shown, as well as the SNP identified in the promoter region of PDE8A. SNPs rs12909130 and rs12900078 were used for genotyping since they are perfect proxies for SNP rs2304418 and the promoter SNP rs11689332 respectively. All other SNPs in LD (r2N0.6) with rs12909130 or rs2304418 can be found in Table S3. LD, linkage disequilibrium.

Article Snippet: For PDE8A overexpression and knock-down the pCMV6-entry expressing a MYC-tagged PDE8A (Origene, Rockville, MD, USA) and pLKO.1 constructs expressing shRNA candidates from the MISSIONTM TRC-Hs 1.0 library (PDE8A TRCN48874, PDE8A TRCN48875, PDE8A TRCN48876 and empty vector SHC001; Sigma-Aldrich St. Louis, MO, USA) (Root et al., 2006) were used.

Techniques: Binding Assay

Fig. 3. Top: schematic alignment of the 5 different PDE8A transcript variants. Primers (arrows) were designed to allow for the unique detection of each splice variant. Vertical lines represent start or stop codon. Bottom: PCR products confirming the presence of multiple different PDE8A transcripts in monocyte-derived macrophages. The similarity in PCR re- sults between MAJ, HZ and MIN donors suggests that SNP rs2304418 in PDE8A does not affect splicing of the PDE8A pre-mRNA. For transcript variant 5, additional nonspecific ampli- cons were seen for some donors. MAJ, homozygous for the major allele; HZ, heterozygous; MIN, homozygous for the minor allele; 100 bp, 100 base pair DNA marker.

Journal: Virology

Article Title: Polymorphism in HIV-1 dependency factor PDE8A affects mRNA level and HIV-1 replication in primary macrophages.

doi: 10.1016/j.virol.2011.08.013

Figure Lengend Snippet: Fig. 3. Top: schematic alignment of the 5 different PDE8A transcript variants. Primers (arrows) were designed to allow for the unique detection of each splice variant. Vertical lines represent start or stop codon. Bottom: PCR products confirming the presence of multiple different PDE8A transcripts in monocyte-derived macrophages. The similarity in PCR re- sults between MAJ, HZ and MIN donors suggests that SNP rs2304418 in PDE8A does not affect splicing of the PDE8A pre-mRNA. For transcript variant 5, additional nonspecific ampli- cons were seen for some donors. MAJ, homozygous for the major allele; HZ, heterozygous; MIN, homozygous for the minor allele; 100 bp, 100 base pair DNA marker.

Article Snippet: For PDE8A overexpression and knock-down the pCMV6-entry expressing a MYC-tagged PDE8A (Origene, Rockville, MD, USA) and pLKO.1 constructs expressing shRNA candidates from the MISSIONTM TRC-Hs 1.0 library (PDE8A TRCN48874, PDE8A TRCN48875, PDE8A TRCN48876 and empty vector SHC001; Sigma-Aldrich St. Louis, MO, USA) (Root et al., 2006) were used.

Techniques: Variant Assay, Derivative Assay, Marker

Fig. 4. Western blot demonstrating PDE8A expression in monocyte-derived macro- phages derived from 2 healthy individuals. The bands correspond with PDE8A isoforms 1 (93 kDa), 2 (88 kDa), 3 (51 kDa), and isoforms 4 and 5 (both 66 kDa).

Journal: Virology

Article Title: Polymorphism in HIV-1 dependency factor PDE8A affects mRNA level and HIV-1 replication in primary macrophages.

doi: 10.1016/j.virol.2011.08.013

Figure Lengend Snippet: Fig. 4. Western blot demonstrating PDE8A expression in monocyte-derived macro- phages derived from 2 healthy individuals. The bands correspond with PDE8A isoforms 1 (93 kDa), 2 (88 kDa), 3 (51 kDa), and isoforms 4 and 5 (both 66 kDa).

Article Snippet: For PDE8A overexpression and knock-down the pCMV6-entry expressing a MYC-tagged PDE8A (Origene, Rockville, MD, USA) and pLKO.1 constructs expressing shRNA candidates from the MISSIONTM TRC-Hs 1.0 library (PDE8A TRCN48874, PDE8A TRCN48875, PDE8A TRCN48876 and empty vector SHC001; Sigma-Aldrich St. Louis, MO, USA) (Root et al., 2006) were used.

Techniques: Western Blot, Expressing, Derivative Assay

Fig. 5. SNP in PDE8A associated with messenger levels in monocyte-derived macrophages (MDM). (A) Quantitative PCR on MDM cDNA from 69 individuals showed a significant association between SNP rs12909130 (as a perfect proxy for rs2304418) genotype and PDE8A transcript 1 mRNA levels. GAPDH was used as reference gene; similar results were obtained when ACTB was used. Results are representative for transcript variants 1–4 (no data for transcript variant 5, since additional nonspecific amplicons were seen for some donors, Fig. 3) and multiple independent experiments. Filled circles represent samples used for resequencing. (B) When tested for association between transcript levels and SNP rs12900078 genotype (near perfect proxy for promoter SNP rs116893322), we again found a significant association. (C) PDE8A-promoter driven expression of luciferase did not differ between the variant containing the major (MAJ) or minor (MIN) allele of SNPs rs116893322. Bars represent the average measured value for one experiment and the standard deviation. Results are representative for multiple experiments, and different concentrations of PDE8A-promoter DNA used for the transfections (25, 50, 100 and 200 ng/well). (D) Trend towards association between SNP rs116893322 in the PDE8A promoter and HIV-1 replication as measured by normalized Gag p24 levels, tested for all donors (n=393). MAJ, homozygous for the major allele; HZ, heterozygous; MIN, homozygous for the minor allele.

Journal: Virology

Article Title: Polymorphism in HIV-1 dependency factor PDE8A affects mRNA level and HIV-1 replication in primary macrophages.

doi: 10.1016/j.virol.2011.08.013

Figure Lengend Snippet: Fig. 5. SNP in PDE8A associated with messenger levels in monocyte-derived macrophages (MDM). (A) Quantitative PCR on MDM cDNA from 69 individuals showed a significant association between SNP rs12909130 (as a perfect proxy for rs2304418) genotype and PDE8A transcript 1 mRNA levels. GAPDH was used as reference gene; similar results were obtained when ACTB was used. Results are representative for transcript variants 1–4 (no data for transcript variant 5, since additional nonspecific amplicons were seen for some donors, Fig. 3) and multiple independent experiments. Filled circles represent samples used for resequencing. (B) When tested for association between transcript levels and SNP rs12900078 genotype (near perfect proxy for promoter SNP rs116893322), we again found a significant association. (C) PDE8A-promoter driven expression of luciferase did not differ between the variant containing the major (MAJ) or minor (MIN) allele of SNPs rs116893322. Bars represent the average measured value for one experiment and the standard deviation. Results are representative for multiple experiments, and different concentrations of PDE8A-promoter DNA used for the transfections (25, 50, 100 and 200 ng/well). (D) Trend towards association between SNP rs116893322 in the PDE8A promoter and HIV-1 replication as measured by normalized Gag p24 levels, tested for all donors (n=393). MAJ, homozygous for the major allele; HZ, heterozygous; MIN, homozygous for the minor allele.

Article Snippet: For PDE8A overexpression and knock-down the pCMV6-entry expressing a MYC-tagged PDE8A (Origene, Rockville, MD, USA) and pLKO.1 constructs expressing shRNA candidates from the MISSIONTM TRC-Hs 1.0 library (PDE8A TRCN48874, PDE8A TRCN48875, PDE8A TRCN48876 and empty vector SHC001; Sigma-Aldrich St. Louis, MO, USA) (Root et al., 2006) were used.

Techniques: Derivative Assay, Real-time Polymerase Chain Reaction, Variant Assay, Expressing, Luciferase, Standard Deviation, Transfection

Fig. 6. Correlation between PDE8A mRNA levels and HIV-1 replication. SNP rs12909130 (perfect proxy for rs2304418) associated with (A) HIV-1 replication (measured as p24 ng/ ml, corrected for the number of monocyte-derived macrophages per well) and (B) PDE8A mRNA levels. (C) PDE8A1 mRNA levels are correlated with HIV-1 replication. MAJ, homo- zygous for the major allele; HZ, heterozygous; MIN, homozygous for the minor allele.

Journal: Virology

Article Title: Polymorphism in HIV-1 dependency factor PDE8A affects mRNA level and HIV-1 replication in primary macrophages.

doi: 10.1016/j.virol.2011.08.013

Figure Lengend Snippet: Fig. 6. Correlation between PDE8A mRNA levels and HIV-1 replication. SNP rs12909130 (perfect proxy for rs2304418) associated with (A) HIV-1 replication (measured as p24 ng/ ml, corrected for the number of monocyte-derived macrophages per well) and (B) PDE8A mRNA levels. (C) PDE8A1 mRNA levels are correlated with HIV-1 replication. MAJ, homo- zygous for the major allele; HZ, heterozygous; MIN, homozygous for the minor allele.

Article Snippet: For PDE8A overexpression and knock-down the pCMV6-entry expressing a MYC-tagged PDE8A (Origene, Rockville, MD, USA) and pLKO.1 constructs expressing shRNA candidates from the MISSIONTM TRC-Hs 1.0 library (PDE8A TRCN48874, PDE8A TRCN48875, PDE8A TRCN48876 and empty vector SHC001; Sigma-Aldrich St. Louis, MO, USA) (Root et al., 2006) were used.

Techniques: Derivative Assay

Fig. 7. PDE8A supports HIV-1 replication in HEK293T cells. (A) HEK293T cells were transfected with pCMV6-PDE8A and after 24 h infected with VSV-G-pseudotyped luciferase re- porter virus. Luciferase activity was measured 2 days after infection. (B) HEK293T cells were co-transfected with pCMV6-PDE8A (1 μg) and constructs expressing shRNA's targeting PDE8A (1 μg). Twenty-four hours after transfection, the cells were infected with VSV-G-pseudotyped luciferase reporter virus and luciferase activity was measured at day 2 after infection. Combined results of 3 independent overexpression and knock-down experiments are shown. Western analysis demonstrating (C) dose-dependent overexpression of PDE8A and (D) knock-down of PDE8A by three different shRNA's in HEK293T cells. Results are representative for 2 independent experiments performed.

Journal: Virology

Article Title: Polymorphism in HIV-1 dependency factor PDE8A affects mRNA level and HIV-1 replication in primary macrophages.

doi: 10.1016/j.virol.2011.08.013

Figure Lengend Snippet: Fig. 7. PDE8A supports HIV-1 replication in HEK293T cells. (A) HEK293T cells were transfected with pCMV6-PDE8A and after 24 h infected with VSV-G-pseudotyped luciferase re- porter virus. Luciferase activity was measured 2 days after infection. (B) HEK293T cells were co-transfected with pCMV6-PDE8A (1 μg) and constructs expressing shRNA's targeting PDE8A (1 μg). Twenty-four hours after transfection, the cells were infected with VSV-G-pseudotyped luciferase reporter virus and luciferase activity was measured at day 2 after infection. Combined results of 3 independent overexpression and knock-down experiments are shown. Western analysis demonstrating (C) dose-dependent overexpression of PDE8A and (D) knock-down of PDE8A by three different shRNA's in HEK293T cells. Results are representative for 2 independent experiments performed.

Article Snippet: For PDE8A overexpression and knock-down the pCMV6-entry expressing a MYC-tagged PDE8A (Origene, Rockville, MD, USA) and pLKO.1 constructs expressing shRNA candidates from the MISSIONTM TRC-Hs 1.0 library (PDE8A TRCN48874, PDE8A TRCN48875, PDE8A TRCN48876 and empty vector SHC001; Sigma-Aldrich St. Louis, MO, USA) (Root et al., 2006) were used.

Techniques: Transfection, Infection, Luciferase, Virus, Activity Assay, Construct, Expressing, shRNA, Over Expression, Knockdown, Western Blot

Detailed list of the identified CNVs affecting genes potentially related to female fertility.

Journal: Human Reproduction (Oxford, England)

Article Title: Gene dosage as a relevant mechanism contributing to the determination of ovarian function in Turner syndrome

doi: 10.1093/humrep/det436

Figure Lengend Snippet: Detailed list of the identified CNVs affecting genes potentially related to female fertility.

Article Snippet: The target TaqMan Copy Number mixes were chosen to detect: exon 8 (Hs01858886_cn) of the GYG2 gene (MIM *300198, at Xp22.3); exon 1 (Hs01299108_cn) and exon 2 (HS00957878_cn) of the BMP15 gene (MIM *300247, at Xp11.22); exon 10 (Hs05613398_cn) of the SMARCA1 gene (MIM *300012, at Xq26.1); exon 2 (Hs02373345_cn) and exon 7 (Hs01648393_cn) of the PAPPA gene (MIM *176385, at 9q33.1); intron 2 (Hs03902365) and exon 21 (Hs03005502_cn) of the PDE8A gene (MIM *602972, at 15q25.3); and exon 9 (Hs02909158_cn) of the PRKX gene (MIM *300083, at Xp22.33).

Techniques:

Detection of copy number variations. High-resolution aCGH analysis 244 K Agilent identified in patient PA5 a deletion of at least 216 kb at 9q33.1 (chr9:118971743-119187538, hg19), which interrupts the PAPPA gene coding region ( A ), in patient PA4 a duplication of at least 75 kb at 15q25.3 (chr15:85591615-85666309, hg19), which includes part of the PDE8A gene coding region ( B ), and in patient SM1 a duplication of at least 554 kb at Xp11.22 (chrX:50400649-50955142, hg19,), which contains the entire BMP15 gene ( C ). In addition, a mosaic deletion of at least 2 Mb at Xp22.33-p22.32 (chrX:2700316-4739185, hg19), which includes the entire PRKX gene, was detected in patient PA4 ( D ). The most important genes involved in the identified microrearrangements are highlighted in light blue.

Journal: Human Reproduction (Oxford, England)

Article Title: Gene dosage as a relevant mechanism contributing to the determination of ovarian function in Turner syndrome

doi: 10.1093/humrep/det436

Figure Lengend Snippet: Detection of copy number variations. High-resolution aCGH analysis 244 K Agilent identified in patient PA5 a deletion of at least 216 kb at 9q33.1 (chr9:118971743-119187538, hg19), which interrupts the PAPPA gene coding region ( A ), in patient PA4 a duplication of at least 75 kb at 15q25.3 (chr15:85591615-85666309, hg19), which includes part of the PDE8A gene coding region ( B ), and in patient SM1 a duplication of at least 554 kb at Xp11.22 (chrX:50400649-50955142, hg19,), which contains the entire BMP15 gene ( C ). In addition, a mosaic deletion of at least 2 Mb at Xp22.33-p22.32 (chrX:2700316-4739185, hg19), which includes the entire PRKX gene, was detected in patient PA4 ( D ). The most important genes involved in the identified microrearrangements are highlighted in light blue.

Article Snippet: The target TaqMan Copy Number mixes were chosen to detect: exon 8 (Hs01858886_cn) of the GYG2 gene (MIM *300198, at Xp22.3); exon 1 (Hs01299108_cn) and exon 2 (HS00957878_cn) of the BMP15 gene (MIM *300247, at Xp11.22); exon 10 (Hs05613398_cn) of the SMARCA1 gene (MIM *300012, at Xq26.1); exon 2 (Hs02373345_cn) and exon 7 (Hs01648393_cn) of the PAPPA gene (MIM *176385, at 9q33.1); intron 2 (Hs03902365) and exon 21 (Hs03005502_cn) of the PDE8A gene (MIM *602972, at 15q25.3); and exon 9 (Hs02909158_cn) of the PRKX gene (MIM *300083, at Xp22.33).

Techniques:

Validation and structural characterization of the identified CNVs. ( A ) iFISH analysis performed on 100 nuclei from patient SM1 characterized the rearrangement involving BMP15 earlier identified by array-CGH analysis as a tandem duplication (thin arrow). In the 9% of the cells an additional smaller signal was identified (big arrow) which represents the low-level mosaic euploid cell line carrying a ring(X) chromosome as seen in the patient's metaphases ( B) . The BAC probe CTD-2004N6, specific for BMP15 , is shown in red and the CEP6 probe (locus D6Z1) is in green. ( C and D ) Multi-colour FISH analysis on metaphases from patient PA4 identified both the 45,X (C) and the 46,XX (D) cell lineages, and confirmed the presence of a heterozygous Xp terminal deletion in the euploid cell lineage (D), as demonstrated by the loss of the expected subtelomeric Xp signal (arrowhead) compared with the conserved X chromosome (arrow). The TelVysion 1p probe is shown in green, the TelVysion 1q is in red, the TelVysion Xp/Yp is in yellow (red + green merged) and CEPX (locus DXZ1) is in blue. ( E ) Real-time quantitative PCR on gDNAs from patients PA4 and PA5. PA4's copy number (CN) profile for both the PRKX and GYG2 genes, located at Xp22.32, showed only one copy of both genes (predicted CN = 1n), and confirmed the heterozygous duplication of part of the PDE8A gene, located at 15q25.3, by comparing the regions within (dark orange bar, 3n) and outside the duplication (light orange bar, 2n). The CN profile of patient PN5 identified the heterozygous deletion interrupting the PAPPA gene, located at 9q33.1, by comparing the region not affected (light purple bar, 2n) with the deleted one (dark purple bar, 1n). All samples were also compared with 46,XX control (calibrator) gDNA. *The CN profile of the interested regions has been previously tested by array-CGH analysis. Calculated mean CNs are shown on the left-axis, while predicted CNs are displayed on the top of each bar. SD, standard deviation, is represented by the error bars (CN means of the calibrator have been calculated as 2n by the analysis software and therefore no SD values are shown).

Journal: Human Reproduction (Oxford, England)

Article Title: Gene dosage as a relevant mechanism contributing to the determination of ovarian function in Turner syndrome

doi: 10.1093/humrep/det436

Figure Lengend Snippet: Validation and structural characterization of the identified CNVs. ( A ) iFISH analysis performed on 100 nuclei from patient SM1 characterized the rearrangement involving BMP15 earlier identified by array-CGH analysis as a tandem duplication (thin arrow). In the 9% of the cells an additional smaller signal was identified (big arrow) which represents the low-level mosaic euploid cell line carrying a ring(X) chromosome as seen in the patient's metaphases ( B) . The BAC probe CTD-2004N6, specific for BMP15 , is shown in red and the CEP6 probe (locus D6Z1) is in green. ( C and D ) Multi-colour FISH analysis on metaphases from patient PA4 identified both the 45,X (C) and the 46,XX (D) cell lineages, and confirmed the presence of a heterozygous Xp terminal deletion in the euploid cell lineage (D), as demonstrated by the loss of the expected subtelomeric Xp signal (arrowhead) compared with the conserved X chromosome (arrow). The TelVysion 1p probe is shown in green, the TelVysion 1q is in red, the TelVysion Xp/Yp is in yellow (red + green merged) and CEPX (locus DXZ1) is in blue. ( E ) Real-time quantitative PCR on gDNAs from patients PA4 and PA5. PA4's copy number (CN) profile for both the PRKX and GYG2 genes, located at Xp22.32, showed only one copy of both genes (predicted CN = 1n), and confirmed the heterozygous duplication of part of the PDE8A gene, located at 15q25.3, by comparing the regions within (dark orange bar, 3n) and outside the duplication (light orange bar, 2n). The CN profile of patient PN5 identified the heterozygous deletion interrupting the PAPPA gene, located at 9q33.1, by comparing the region not affected (light purple bar, 2n) with the deleted one (dark purple bar, 1n). All samples were also compared with 46,XX control (calibrator) gDNA. *The CN profile of the interested regions has been previously tested by array-CGH analysis. Calculated mean CNs are shown on the left-axis, while predicted CNs are displayed on the top of each bar. SD, standard deviation, is represented by the error bars (CN means of the calibrator have been calculated as 2n by the analysis software and therefore no SD values are shown).

Article Snippet: The target TaqMan Copy Number mixes were chosen to detect: exon 8 (Hs01858886_cn) of the GYG2 gene (MIM *300198, at Xp22.3); exon 1 (Hs01299108_cn) and exon 2 (HS00957878_cn) of the BMP15 gene (MIM *300247, at Xp11.22); exon 10 (Hs05613398_cn) of the SMARCA1 gene (MIM *300012, at Xq26.1); exon 2 (Hs02373345_cn) and exon 7 (Hs01648393_cn) of the PAPPA gene (MIM *176385, at 9q33.1); intron 2 (Hs03902365) and exon 21 (Hs03005502_cn) of the PDE8A gene (MIM *602972, at 15q25.3); and exon 9 (Hs02909158_cn) of the PRKX gene (MIM *300083, at Xp22.33).

Techniques: Biomarker Discovery, Real-time Polymerase Chain Reaction, Control, Standard Deviation, Software

Effects of PPL008 conjugates on pERK levels and rate of cell proliferation. Normalised phospho-ERK (mean ± SEM) following treatment with DMSO (lane 1), PLX4032 B-Raf inhibitor (lane 2), PPL008 conjugates (lanes 11–14) or PLX co-treatments with PDE8A – C-Raf peptide disrupters (original stearylated ‘disrupter’ lane 3, or scrambled control, lane 4) or PPL-008 conjugates (lanes 7–10) in: a MM415 (NRAS Q61L) and ( b ) A375 (BRAF V600E) human malignant melanoma cell lines. Respective pERK and GAPDH immunoblot examples shown below ( N ≥ 3, * P < 0.05, ** P < 0.01 ). c Real-time cell analyses (xCELLigence platform) of MM415 cell proliferation following treatments described above. Treatments occurred at 21 h and the slope of normalised cell index (mean ± STDEV) was measured between 21 and 39 h, with (ii) representing DMSO vs. peptide disrupter treatments only (10 μM) and (iii) representing PLX (1 μM) vs. co-treatments of peptide disrupters and PLX4032 ( n = 3, *** P < 0.001) . D, stearylated disrupter; S, stearylated scrambled; N, PPL-008 N; C, PPL-008C; NSS, PPL-008NSS; CSS, PPL-008CSS

Journal: BMC Cancer

Article Title: Targeting B-Raf inhibitor resistant melanoma with novel cell penetrating peptide disrupters of PDE8A – C-Raf

doi: 10.1186/s12885-019-5489-4

Figure Lengend Snippet: Effects of PPL008 conjugates on pERK levels and rate of cell proliferation. Normalised phospho-ERK (mean ± SEM) following treatment with DMSO (lane 1), PLX4032 B-Raf inhibitor (lane 2), PPL008 conjugates (lanes 11–14) or PLX co-treatments with PDE8A – C-Raf peptide disrupters (original stearylated ‘disrupter’ lane 3, or scrambled control, lane 4) or PPL-008 conjugates (lanes 7–10) in: a MM415 (NRAS Q61L) and ( b ) A375 (BRAF V600E) human malignant melanoma cell lines. Respective pERK and GAPDH immunoblot examples shown below ( N ≥ 3, * P < 0.05, ** P < 0.01 ). c Real-time cell analyses (xCELLigence platform) of MM415 cell proliferation following treatments described above. Treatments occurred at 21 h and the slope of normalised cell index (mean ± STDEV) was measured between 21 and 39 h, with (ii) representing DMSO vs. peptide disrupter treatments only (10 μM) and (iii) representing PLX (1 μM) vs. co-treatments of peptide disrupters and PLX4032 ( n = 3, *** P < 0.001) . D, stearylated disrupter; S, stearylated scrambled; N, PPL-008 N; C, PPL-008C; NSS, PPL-008NSS; CSS, PPL-008CSS

Article Snippet: The original PDE8A – C-Raf disrupter, and its scrambled isoform, were synthesised with a C-terminal stearic acid group [CH3(CH2)16COOH] (GenScript) [ ].

Techniques: Control, Western Blot

Dual inhibition of B-Raf and C-Raf inhibits melanoma tumour progression. a B-Raf inhibition leads to the Ras negative feedback mechanism switching to C-Raf driven tumourigenesis via potentiation of the Raf/MEK/ERK signalling axis. b PPL-008 (PDE8A – C-Raf disrupter peptide) binds to C-Raf, preventing PDE8A localisation within the C-Raf cAMP microdomain and exposing serine 259 – C-Raf to inhibitory phosphorylation by PKA. Co-treatment with B-Raf inhibitor and PPL-008 blocks onco-Ras driven tumour progression via inhibition of the Raf/MEK/ERK axis

Journal: BMC Cancer

Article Title: Targeting B-Raf inhibitor resistant melanoma with novel cell penetrating peptide disrupters of PDE8A – C-Raf

doi: 10.1186/s12885-019-5489-4

Figure Lengend Snippet: Dual inhibition of B-Raf and C-Raf inhibits melanoma tumour progression. a B-Raf inhibition leads to the Ras negative feedback mechanism switching to C-Raf driven tumourigenesis via potentiation of the Raf/MEK/ERK signalling axis. b PPL-008 (PDE8A – C-Raf disrupter peptide) binds to C-Raf, preventing PDE8A localisation within the C-Raf cAMP microdomain and exposing serine 259 – C-Raf to inhibitory phosphorylation by PKA. Co-treatment with B-Raf inhibitor and PPL-008 blocks onco-Ras driven tumour progression via inhibition of the Raf/MEK/ERK axis

Article Snippet: The original PDE8A – C-Raf disrupter, and its scrambled isoform, were synthesised with a C-terminal stearic acid group [CH3(CH2)16COOH] (GenScript) [ ].

Techniques: Inhibition, Phospho-proteomics