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1.
Nature ; 630(8015): 198-205, 2024 Jun.
Article En | MEDLINE | ID: mdl-38720074

Phosphoinositide-3-kinase-γ (PI3Kγ) is implicated as a target to repolarize tumour-associated macrophages and promote antitumour immune responses in solid cancers1-4. However, cancer cell-intrinsic roles of PI3Kγ are unclear. Here, by integrating unbiased genome-wide CRISPR interference screening with functional analyses across acute leukaemias, we define a selective dependency on the PI3Kγ complex in a high-risk subset that includes myeloid, lymphoid and dendritic lineages. This dependency is characterized by innate inflammatory signalling and activation of phosphoinositide 3-kinase regulatory subunit 5 (PIK3R5), which encodes a regulatory subunit of PI3Kγ5 and stabilizes the active enzymatic complex. We identify p21 (RAC1)-activated kinase 1 (PAK1) as a noncanonical substrate of PI3Kγ that mediates this cell-intrinsic dependency and find that dephosphorylation of PAK1 by PI3Kγ inhibition impairs mitochondrial oxidative phosphorylation. Treatment with the selective PI3Kγ inhibitor eganelisib is effective in leukaemias with activated PIK3R5. In addition, the combination of eganelisib and cytarabine prolongs survival over either agent alone, even in patient-derived leukaemia xenografts with low baseline PIK3R5 expression, as residual leukaemia cells after cytarabine treatment have elevated G protein-coupled purinergic receptor activity and PAK1 phosphorylation. Together, our study reveals a targetable dependency on PI3Kγ-PAK1 signalling that is amenable to near-term evaluation in patients with acute leukaemia.


Class Ib Phosphatidylinositol 3-Kinase , Signal Transduction , p21-Activated Kinases , Humans , Class Ib Phosphatidylinositol 3-Kinase/metabolism , Class Ib Phosphatidylinositol 3-Kinase/genetics , p21-Activated Kinases/metabolism , p21-Activated Kinases/antagonists & inhibitors , p21-Activated Kinases/genetics , Mice , Animals , Female , Leukemia/genetics , Leukemia/enzymology , Leukemia/pathology , Leukemia/metabolism , Phosphorylation , Cell Line, Tumor , Mitochondria/metabolism , Male
2.
Blood ; 143(19): 1965-1979, 2024 May 09.
Article En | MEDLINE | ID: mdl-38271660

ABSTRACT: Acute myeloid leukemia (AML) is an aggressive hematological malignancy originating from transformed hematopoietic stem or progenitor cells. AML prognosis remains poor owing to resistance and relapse driven by leukemia stem cells (LSCs). Targeting molecules essential for LSC function is a promising therapeutic approach. The phosphatidylinositol 3-kinase (PI3K)/AKT pathway is often dysregulated in AML. We found that although PI3Kγ is highly enriched in LSCs and critical for self-renewal, it was dispensable for normal hematopoietic stem cells. Mechanistically, PI3Kγ-AKT signaling promotes nuclear factor erythroid 2-related factor 2 (NRF2) nuclear accumulation, which induces 6-phosphogluconate dehydrogenase (PGD) and the pentose phosphate pathway, thereby maintaining LSC stemness. Importantly, genetic or pharmacological inhibition of PI3Kγ impaired expansion and stemness of murine and human AML cells in vitro and in vivo. Together, our findings reveal a key role for PI3Kγ in selectively maintaining LSC function by regulating AKT-NRF2-PGD metabolic pathway. Targeting the PI3Kγ pathway may, therefore, eliminate LSCs without damaging normal hematopoiesis, providing a promising therapeutic strategy for AML.


Class Ib Phosphatidylinositol 3-Kinase , Leukemia, Myeloid, Acute , Neoplastic Stem Cells , Pentose Phosphate Pathway , Leukemia, Myeloid, Acute/pathology , Leukemia, Myeloid, Acute/metabolism , Leukemia, Myeloid, Acute/genetics , Neoplastic Stem Cells/metabolism , Neoplastic Stem Cells/pathology , Animals , Humans , Mice , Class Ib Phosphatidylinositol 3-Kinase/metabolism , Class Ib Phosphatidylinositol 3-Kinase/genetics , Cell Self Renewal , NF-E2-Related Factor 2/metabolism , NF-E2-Related Factor 2/genetics , Signal Transduction , Proto-Oncogene Proteins c-akt/metabolism , Proto-Oncogene Proteins c-akt/genetics
3.
Immunobiology ; 227(5): 152242, 2022 09.
Article En | MEDLINE | ID: mdl-35870262

Single nucleotide polymorphisms (SNPs) that do not change the composition of amino acids and cause synonymous mutations (sSNPs) were previously considered to lack any functional roles. However, sSNPs have recently been shown to interfere with protein expression owing to a myriad of factors related to the regulation of transcription, mRNA stability, and protein translation processes. In patients with Chagas disease, the presence of the synonymous mutation rs1129293 in phosphatidylinositol-4,5-bisphosphate 3-kinase gamma (PIK3CG) gene contributes to the development of the chronic Chagas cardiomyopathy (CCC), instead of the digestive or asymptomatic forms. In this study, we aimed to investigate whether rs1129293 is associated with the transcription of PIK3CG mRNA and its activity by quantifying AKT phosphorylation in the heart samples of 26 chagasic patients with CCC. Our results showed an association between rs1129293 and decreased PIK3CG mRNA expression levels in the cardiac tissues of patients with CCC. The phosphorylation levels of AKT, the protein target of PI3K, were also reduced in patients with this mutation, but were not correlated with PI3KCG mRNA expression levels. Moreover, bioinformatics analysis showed that rs1129293 and other SNPs in linkage disequilibrium (LD) were associated with the transcriptional regulatory elements, post-transcriptional modifications, and cell-specific splicing expression of PIK3CG mRNA. Therefore, our data demonstrates that the synonymous SNP rs1129293 is capable of affecting the PIK3CG mRNA expression and PI3Kγ activation.


Chagas Cardiomyopathy , Chagas Cardiomyopathy/genetics , Class Ib Phosphatidylinositol 3-Kinase/genetics , Humans , Phosphatidylinositol 3-Kinases , Polymorphism, Single Nucleotide , Proto-Oncogene Proteins c-akt , RNA, Messenger/genetics , RNA, Messenger/metabolism , Silent Mutation
4.
Bioengineered ; 13(1): 1491-1506, 2022 01.
Article En | MEDLINE | ID: mdl-34986757

This paper probes the mechanisms underlying miR-142-3p's modulation of hepatocellular carcinoma (HCC) invasion and apoptosis. Quantitative real-time PCR and Western blot monitored the miR-142-3p profile in HCC tissues and non-tumor tissues. The correlation between miR-142-3p expression and HCC patients' clinicopathological indicators was analyzed. miR-142-3p overexpression and knockdown models were established in HCC cell lines. Cell proliferation was gauged by the colony formation assay and BrdU staining. For measuring apoptosis, flow cytometry and Western blot were implemented. Transwell assay tested cell migration and invasion. miR-142-3p mimics or inhibitors were transfected in Huh7 and HCCLM3 cells. The targeting association between miR-142-3p and PIK3CG was predicted through bioinformatics and further verified by related experiments. The influence of PIK3CG overexpression on miR-142-3p's role in HCC was assayed. A xenografted tumor model was built in mice to validate miR-142-3p knockdown's influence on HCC in vivo. As a result, miR-142-3p exhibited a decreased profile in HCC tissues and cells. Overexpressing miR-142-3p accelerated apoptosis and suppressed the PI3K/AKT/HIF-1α signal. Knocking down miR-142-3p presented opposite effects. PIK3CG overexpression dampened the anti-tumor effect of miR-142-3p. miR-142-3p repressed HCC invasion and intensified apoptosis to restrain HCC by abating the PIK3CG-mediated PI3K/AKT/HIF-1α pathway.


Carcinoma, Hepatocellular/drug therapy , Class Ib Phosphatidylinositol 3-Kinase/genetics , Liver Neoplasms/drug therapy , MicroRNAs/genetics , RNA, Small Interfering/administration & dosage , Animals , Apoptosis , Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/pathology , Cell Line, Tumor , Cell Movement , Cell Proliferation , Class Ib Phosphatidylinositol 3-Kinase/drug effects , Female , Gene Expression Regulation, Neoplastic/drug effects , Gene Knockdown Techniques , Humans , Liver Neoplasms/genetics , Liver Neoplasms/pathology , Male , Mice , RNA, Small Interfering/pharmacology , Xenograft Model Antitumor Assays
5.
Cells ; 10(10)2021 09 24.
Article En | MEDLINE | ID: mdl-34685514

(1) Background: Rapid microglial proliferation contributes to the complex responses of the innate immune system in the brain to various neuroinflammatory stimuli. Here, we investigated the regulatory function of phosphoinositide 3-kinase γ (PI3Kγ) and reactive oxygen species (ROS) for rapid proliferation of murine microglia induced by LPS and ATP. (2) Methods: PI3Kγ knockout mice (PI3Kγ KO), mice expressing catalytically inactive PI3Kγ (PI3Kγ KD) and wild-type mice were assessed for microglial proliferation using an in vivo wound healing assay. Additionally, primary microglia derived from newborn wild-type, PI3Kγ KO and PI3Kγ KD mice were used to analyze PI3Kγ effects on proliferation and cell viability, senescence and cellular and mitochondrial ROS production; the consequences of ROS production for proliferation and cell viability after LPS or ATP stimulation were studied using genetic and pharmacologic approaches. (3) Results: Mice with a loss of lipid kinase activity showed impaired proliferation of microglia. The prerequisite of induced microglial proliferation and cell viability appeared to be PI3Kγ-mediated induction of ROS production. (4) Conclusions: The lipid kinase activity of PI3Kγ plays a crucial role for microglial proliferation and cell viability after acute inflammatory activation.


Cell Proliferation/physiology , Cell Survival/physiology , Class Ib Phosphatidylinositol 3-Kinase/metabolism , Microglia/metabolism , Animals , Brain/metabolism , Cell Proliferation/genetics , Cell Survival/genetics , Class Ib Phosphatidylinositol 3-Kinase/genetics , Cyclic AMP/metabolism , Mice, Knockout , Neurogenesis/physiology , Reactive Oxygen Species/metabolism
6.
Elife ; 102021 03 04.
Article En | MEDLINE | ID: mdl-33661099

Class I Phosphoinositide 3-kinases (PI3Ks) are master regulators of cellular functions, with the class IB PI3K catalytic subunit (p110γ) playing key roles in immune signalling. p110γ is a key factor in inflammatory diseases and has been identified as a therapeutic target for cancers due to its immunomodulatory role. Using a combined biochemical/biophysical approach, we have revealed insight into regulation of kinase activity, specifically defining how immunodeficiency and oncogenic mutations of R1021 in the C-terminus can inactivate or activate enzyme activity. Screening of inhibitors using HDX-MS revealed that activation loop-binding inhibitors induce allosteric conformational changes that mimic those in the R1021C mutant. Structural analysis of advanced PI3K inhibitors in clinical development revealed novel binding pockets that can be exploited for further therapeutic development. Overall, this work provides unique insights into regulatory mechanisms that control PI3Kγ kinase activity and shows a framework for the design of PI3K isoform and mutant selective inhibitors.


Class Ib Phosphatidylinositol 3-Kinase/genetics , Immunologic Deficiency Syndromes/genetics , Mutation , Class Ib Phosphatidylinositol 3-Kinase/chemistry , Class Ib Phosphatidylinositol 3-Kinase/metabolism , Humans
7.
J Mol Biol ; 433(8): 166838, 2021 04 16.
Article En | MEDLINE | ID: mdl-33539876

Phosphatidylinositol-3-kinases (PI3Ks) are lipid kinases that phosphorylate phosphatidylinositol 4,5-bisphosphate to generate a key lipid second messenger, phosphatidylinositol 3,4,5-bisphosphate. PI3Kα and PI3Kγ require activation by RAS proteins to stimulate signaling pathways that control cellular growth, differentiation, motility and survival. Intriguingly, RAS binding to PI3K isoforms likely differ, as RAS mutations have been identified that discriminate between PI3Kα and PI3Kγ, consistent with low sequence homology (23%) between their RAS binding domains (RBDs). As disruption of the RAS/PI3Kα interaction reduces tumor growth in mice with RAS- and epidermal growth factor receptor driven skin and lung cancers, compounds that interfere with this key interaction may prove useful as anti-cancer agents. However, a structure of PI3Kα bound to RAS is lacking, limiting drug discovery efforts. Expression of full-length PI3K isoforms in insect cells has resulted in low yield and variable activity, limiting biophysical and structural studies of RAS/PI3K interactions. This led us to generate the first RBDs from PI3Kα and PI3Kγ that can be expressed at high yield in bacteria and bind to RAS with similar affinity to full-length PI3K. We also solved a 2.31 Å X-ray crystal structure of the PI3Kα-RBD, which aligns well to full-length PI3Kα. Structural differences between the PI3Kα and PI3Kγ RBDs are consistent with differences in thermal stability and may underly differential RAS recognition and RAS-mediated PI3K activation. These high expression, functional PI3K RBDs will aid in interrogating RAS interactions and could aid in identifying inhibitors of this key interaction.


Class Ib Phosphatidylinositol 3-Kinase/chemistry , Class Ib Phosphatidylinositol 3-Kinase/metabolism , Phosphatidylinositol 3-Kinases/chemistry , Phosphatidylinositol 3-Kinases/metabolism , Protein Interaction Domains and Motifs , Animals , Antineoplastic Agents/pharmacology , Class I Phosphatidylinositol 3-Kinases , Class Ib Phosphatidylinositol 3-Kinase/drug effects , Class Ib Phosphatidylinositol 3-Kinase/genetics , Drug Discovery , Humans , Mice , Mutation , Phosphatidylinositol 3-Kinases/drug effects , Phosphatidylinositol 3-Kinases/genetics , Phosphorylation , Protein Binding , Protein Conformation , Protein Isoforms , Sequence Alignment , Signal Transduction , ras Proteins/chemistry , ras Proteins/genetics , ras Proteins/metabolism
8.
J Biol Chem ; 296: 100325, 2021.
Article En | MEDLINE | ID: mdl-33493514

The Golgi apparatus (GA) is a cellular organelle that plays a critical role in the processing of proteins for secretion. Activation of G protein-coupled receptors at the plasma membrane (PM) induces the translocation of G protein ßγ dimers to the GA. However, the functional significance of this translocation is largely unknown. Here, we study PM-GA translocation of all 12 Gγ subunits in response to chemokine receptor CXCR4 activation and demonstrate that Gγ9 is a unique Golgi-translocating Gγ subunit. CRISPR-Cas9-mediated knockout of Gγ9 abolishes activation of extracellular signal-regulated kinase 1 and 2 (ERK1/2), two members of the mitogen-activated protein kinase family, by CXCR4. We show that chemically induced recruitment to the GA of Gßγ dimers containing different Gγ subunits activates ERK1/2, whereas recruitment to the PM is ineffective. We also demonstrate that pharmacological inhibition of phosphoinositide 3-kinase γ (PI3Kγ) and depletion of its subunits p110γ and p101 abrogate ERK1/2 activation by CXCR4 and Gßγ recruitment to the GA. Knockout of either Gγ9 or PI3Kγ significantly suppresses prostate cancer PC3 cell migration, invasion, and metastasis. Collectively, our data demonstrate a novel function for Gßγ translocation to the GA, via activating PI3Kγ heterodimers p110γ-p101, to spatiotemporally regulate mitogen-activated protein kinase activation by G protein-coupled receptors and ultimately control tumor progression.


Class Ib Phosphatidylinositol 3-Kinase/genetics , GTP-Binding Protein beta Subunits/genetics , GTP-Binding Protein gamma Subunits/genetics , Golgi Apparatus/genetics , Receptors, CXCR4/genetics , Cell Membrane/genetics , Dimerization , HEK293 Cells , Humans , Mitogen-Activated Protein Kinase Kinases/genetics , Phosphatidylinositol 3-Kinases/genetics , Protein Transport/genetics , Receptors, G-Protein-Coupled/genetics , Signal Transduction/genetics
9.
Infect Genet Evol ; 88: 104671, 2021 03.
Article En | MEDLINE | ID: mdl-33301989

Chagas disease is caused by the protozoan parasite Trypanosoma cruzi. During the chronic phase of disease, while most infected people do not present symptoms, characterizing the asymptomatic form, some patients develop the cardiac form or chronic chagasic cardiomyopathy, which is considered the most severe manifestation of this disease. Considering that the activation of the PI3Kγ signaling pathway is essential for an efficient immune response against T. cruzi infection, we evaluated the PIK3CG C > T (rs1129293) polymorphism in exon 3 of this gene, which encodes the catalytic subunit of PI3Kγ. The PIK3CG CT and TT genotypes were found to be associated with an increased risk of developing the cardiac form of the disease rather than the asymptomatic or digestive forms. In conclusion, the presence of the T allele at single or double doses may differentiate the cardiac from other clinical manifestations of Chagas disease. This finding should help in further studies to evaluate the mechanisms underlying the differential association of PIK3CG in Chagas disease.


Catalytic Domain/genetics , Chagas Cardiomyopathy/genetics , Chagas Disease/genetics , Chagas Disease/parasitology , Class Ib Phosphatidylinositol 3-Kinase/genetics , Polymorphism, Single Nucleotide , Trypanosoma cruzi , Chagas Cardiomyopathy/parasitology , Class Ib Phosphatidylinositol 3-Kinase/metabolism , Genetic Variation , Genotype , Heart/parasitology , Host-Parasite Interactions , Humans , Neglected Diseases/genetics , Neglected Diseases/parasitology , Signal Transduction
10.
Eur Rev Med Pharmacol Sci ; 24(20): 10366-10374, 2020 10.
Article En | MEDLINE | ID: mdl-33155192

OBJECTIVE: RBBP6 is identified to be a cancer-associated gene by bioinformatics analysis. This study aims to explore the role of RBBP6 in regulating proliferation and metastasis in ovarian cancer, thus providing theoretical references for ovarian cancer treatment. PATIENTS AND METHODS: Differential expressions of RBBP6 in ovarian cancer and normal ones were detected by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). The relationship between RBBP6 and prognosis in ovarian cancer patients was analyzed. The interaction between RBBP6 and PIK3R6 was detected by bioinformatics analysis and Dual-Luciferase reporter assay. Moreover, regulatory effects of RBBP6 and PIK3R6 on proliferative and migratory potentials in A2780 and CAOV3 cells were examined by Cell Counting Kit-8 (CCK-8) and transwell assay, respectively. Finally, tumorigenicity assay was conducted in nude mice to illustrate the in vivo regulations of PBBP6 and PIK3R6 on ovarian cancer growth. RESULTS: RBBP6 was upregulated in ovarian cancer tissues than normal ones. RBBP6 was irrelevant to age, tumor size and tumor node metastasis (TNM) staging in ovarian cancer patients, but correlated to lymphatic metastasis and distant metastasis. RBBP6 was abundantly expressed in ovarian cancer cells, and among the tested cell lines, CAOV3 and A2780 expressed the highest level of RBBP6. Knockdown of RBBP6 attenuated in vitro proliferative and migratory potentials in CAOV3 and A2780 cells. PIK3R6 was the target gene binding RBBP6, which was positively regulated by RBBP6. Overexpression of PIK3R6 could abolish the inhibited proliferative and migratory potentials in ovarian cancer cells with RBBP6 knockdown. In addition, the knockdown of RBBP6 slowed the in vivo growth of ovarian cancer in nude mice, and the alleviated cancer progression was reversed by overexpression of PIK3R6. CONCLUSIONS: RBBP6 is highly expressed in ovarian cancer cases, which stimulates proliferative and migratory potentials by targeting PIK3R6. RBBP6 may be a novel therapeutic target for ovarian cancer.


Class Ib Phosphatidylinositol 3-Kinase/metabolism , DNA-Binding Proteins/metabolism , Ovarian Neoplasms/metabolism , Ubiquitin-Protein Ligases/metabolism , Animals , Cell Line , Cell Movement , Cell Proliferation , Class Ib Phosphatidylinositol 3-Kinase/genetics , DNA-Binding Proteins/genetics , Female , Humans , Male , Mice , Mice, Nude , Neoplasms, Experimental/metabolism , Neoplasms, Experimental/pathology , Ovarian Neoplasms/pathology , Ubiquitin-Protein Ligases/genetics
11.
Sci Signal ; 13(656)2020 11 03.
Article En | MEDLINE | ID: mdl-33144519

The PI3Kγ isoform is activated by Gi-coupled GPCRs in myeloid cells, but the extent to which the two endogenous complexes of PI3Kγ, p101/p110γ and p84/p110γ, receive direct regulation through Gßγ or indirect regulation through RAS and the sufficiency of those inputs is controversial or unclear. We generated mice with point mutations that prevent Gßγ binding to p110γ (RK552DD) or to p101 (VVKR777AAAA) and investigated the effects of these mutations in primary neutrophils and in mouse models of neutrophilic inflammation. Loss of Gßγ binding to p110γ substantially reduced the activation of both p101/p110γ and p84/p110γ in neutrophils by various GPCR agonists. Loss of Gßγ binding to p101 caused more variable effects, depending on both the agonist and cellular response, with the biggest reductions seen in PIP3 production by primary neutrophils in response to LTB4 and MIP-2 and in the migration of neutrophils during thioglycolate-induced peritonitis or MIP2-induced ear pouch inflammation. We also observed that p101VVKR777AAAA neutrophils showed enhanced p84-dependent ROS responses to fMLP and C5a, suggesting that competition may exist between p101/p110γ and p84/p110γ for Gßγ subunits downstream of GPCR activation. GPCRs did not activate p110γ in neutrophils from mice lacking both the p101 and p84 regulatory subunits, indicating that RAS binding to p110γ is insufficient to support GPCR activation in this cell type. These findings define a direct role for Gßγ subunits in activating both of the endogenous PI3Kγ complexes and indicate that the regulatory PI3Kγ subunit biases activation toward different GPCRs.


Class Ib Phosphatidylinositol 3-Kinase/metabolism , GTP-Binding Protein beta Subunits/metabolism , GTP-Binding Protein gamma Subunits/metabolism , Multienzyme Complexes/metabolism , Neutrophils/enzymology , Signal Transduction , Animals , Class Ib Phosphatidylinositol 3-Kinase/genetics , GTP-Binding Protein beta Subunits/genetics , GTP-Binding Protein gamma Subunits/genetics , Mice , Mice, Knockout , Multienzyme Complexes/genetics
12.
J Mol Biol ; 432(22): 5849-5859, 2020 11 06.
Article En | MEDLINE | ID: mdl-32918948

PI3K lipid kinases signal through the PI3K/Akt pathway, regulating cell growth and proliferation. While the structural features that distinguish between the active and inactive states of protein kinases are well established, that has not been the case for lipid kinases, and neither was the structural mechanism controlling the switch between the two states. Class I PI3Ks are obligate heterodimers with catalytic and regulatory subunits. Here, we analyze PI3K crystal structures. Structures with the nSH2 (inactive state) are featured by collapsed activation loop (a-loop) and an IN kinase domain helix 11 (kα11). In the active state, the a-loop is extended and kα11 in the OUT conformation. Our analysis suggests that the nSH2 domain in the regulatory subunit regulates activation, catalysis and autoinhibition through the a-loop. Inhibition, activation and catalytic scenarios are shared by class IA PI3Ks; the activation is mimicked by oncogenic mutations and the inhibition offers an allosteric inhibitor strategy.


Lipids/chemistry , Phosphatidylinositol 3-Kinases/chemistry , Phosphatidylinositol 3-Kinases/metabolism , Animals , Class I Phosphatidylinositol 3-Kinases/chemistry , Class I Phosphatidylinositol 3-Kinases/genetics , Class I Phosphatidylinositol 3-Kinases/metabolism , Class Ib Phosphatidylinositol 3-Kinase/chemistry , Class Ib Phosphatidylinositol 3-Kinase/genetics , Class Ib Phosphatidylinositol 3-Kinase/metabolism , Enzyme Activation , Humans , Mice , Models, Molecular , Phosphatidylinositol 3-Kinase/chemistry , Phosphatidylinositol 3-Kinase/genetics , Phosphatidylinositol 3-Kinase/metabolism , Phosphatidylinositol 3-Kinases/genetics , Protein Binding , Protein Conformation , Protein Domains , Protein Kinases/metabolism
13.
Genome Res ; 30(11): 1655-1666, 2020 11.
Article En | MEDLINE | ID: mdl-32958497

Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by joint analysis of large collections of RNA-seq data sets has emerged as one such analysis. Current methods for transcript discovery rely on a '2-Step' approach where the first step encompasses building transcripts from individual data sets, followed by the second step that merges predicted transcripts across data sets. To increase the power of transcript discovery from large collections of RNA-seq data sets, we developed a novel '1-Step' approach named Pooling RNA-seq and Assembling Models (PRAM) that builds transcript models from pooled RNA-seq data sets. We demonstrate in a computational benchmark that 1-Step outperforms 2-Step approaches in predicting overall transcript structures and individual splice junctions, while performing competitively in detecting exonic nucleotides. Applying PRAM to 30 human ENCODE RNA-seq data sets identified unannotated transcripts with epigenetic and RAMPAGE signatures similar to those of recently annotated transcripts. In a case study, we discovered and experimentally validated new transcripts through the application of PRAM to mouse hematopoietic RNA-seq data sets. We uncovered new transcripts that share a differential expression pattern with a neighboring gene Pik3cg implicated in human hematopoietic phenotypes, and we provided evidence for the conservation of this relationship in human. PRAM is implemented as an R/Bioconductor package.


RNA-Seq/methods , Animals , Class Ib Phosphatidylinositol 3-Kinase/genetics , DNA, Intergenic , Genomics , Hematopoietic Stem Cells/metabolism , Humans , Mice , RNA/metabolism , Software
14.
Am J Pathol ; 190(11): 2194-2202, 2020 11.
Article En | MEDLINE | ID: mdl-32805234

The prostate epithelium consists of predominantly luminal cells that express androgen receptor and require androgens for growth. As a consequence, the depletion of testicular androgens in patients with prostate cancer results in tumor regression. However, it eventually leads to a castration-resistant disease that is highly metastatic. In this report, a mouse model of metastatic prostate cancer was generated through the deletion of the tumor-suppressor gene Trp53 in conjunction with oncogenic activation of the proto-oncogene Kras. These mice developed early-onset metastatic prostate cancer with complete penetrance. Tumors from these mice were poorly differentiated adenocarcinoma, characterized by extensive epithelial-mesenchymal transition. With no or a very low level of androgen receptor expression, the tumor cells were resistant to androgen receptor inhibition. Pik3cg, encoding phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit γ (Pi3kγ), was highly expressed in these tumors, and pharmacologic inhibition of Pi3kγ blocked tumor cell growth in vitro, reversed epithelial-mesenchymal transition, and abated tumor metastasis in vivo. Immunohistochemistry analysis in human prostate cancer specimens showed that the expression of PIK3CG was significantly associated with advanced clinical stages. Taken together, these results suggest that PIK3CG plays an important role in the progression and metastasis of prostate cancer, and may represent a new therapeutic target in the metastatic castration-resistant prostate cancer.


Class Ib Phosphatidylinositol 3-Kinase/metabolism , Neoplasm Proteins/metabolism , Prostatic Neoplasms/metabolism , Receptors, Androgen/metabolism , Animals , Class Ib Phosphatidylinositol 3-Kinase/genetics , Male , Mice , Mice, Transgenic , Neoplasm Metastasis , Neoplasm Proteins/genetics , Prostatic Neoplasms/genetics , Prostatic Neoplasms/pathology , Proto-Oncogene Mas , Receptors, Androgen/genetics
15.
Neuropharmacology ; 176: 108156, 2020 10 01.
Article En | MEDLINE | ID: mdl-32574650

The phosphatidylinositol 3-kinase (PI3K)/protein kinase B (PKB/Akt)/mechanistic target of rapamycin (mTOR) signaling pathway has been associated with several pathologies in the central nervous system (CNS), including epilepsy. There is evidence supporting the hypothesis that the PI3Kγ signaling pathway may mediate the powerful anticonvulsant properties associated with the cannabinoidergic system. This work aims to investigate if the anticonvulsant and neuroprotective effects of cannabidiol (CBD) are mediated by PI3Kγ. In vitro and in vivo experiments were performed on C57Bl/6 wild-type (WT) and PI3Kγ-/- mice. Behavioral seizures were induced by bilateral intra-hippocampal pilocarpine microinjection. Twenty-four hours after the first behavioral seizure, animals were perfused and their brains removed and processed, for histological analysis of neurodegeneration, microgliosis and astrocytosis. Primary cultures of hippocampal neurons were used for glutamate-induced cell death assay. CDB increased latency and reduced the severity of pilocarpine-induced behavioral seizures, as well as prevented postictal changes, such as neurodegeneration, microgliosis and astrocytosis, in WT animals, but not in PI3Kγ-/-. CBD in vivo effects were abolished by pharmacological inhibition of cannabinoid receptor or mTOR. In vitro, PI3Kγ inhibition or deficiency also changed CBD protection observed in glutamate-induced cell death assay. Thus, we suggest that the modulation of PI3K/mTOR signaling pathway is involved in the anticonvulsant and neuroprotective effects of CBD. These findings are important not only for the elucidation of the mechanisms of action of CBD, which are currently poorly understood, but also to allow the prediction of therapeutic and side effects, ensuring efficacy and safety in the treatment of patients with epilepsy.


Anticonvulsants/pharmacology , Cannabidiol/pharmacology , Class Ib Phosphatidylinositol 3-Kinase/metabolism , Seizures/metabolism , Seizures/prevention & control , Animals , Anticonvulsants/therapeutic use , Cannabidiol/therapeutic use , Cells, Cultured , Class Ib Phosphatidylinositol 3-Kinase/deficiency , Class Ib Phosphatidylinositol 3-Kinase/genetics , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Pilocarpine/toxicity , Receptor, Cannabinoid, CB1/agonists , Receptor, Cannabinoid, CB1/metabolism , Seizures/chemically induced , Treatment Outcome
16.
Commun Biol ; 3(1): 267, 2020 05 27.
Article En | MEDLINE | ID: mdl-32461675

Development of novel PI3K inhibitors is an important strategy to overcome their resistance and poor tolerability in clinical trials. The quassinoid family member Brusatol shows specific inhibitory activity against hematologic malignancies. However, the mechanism of its anti-cancer activity is unknown. We investigated the anti-cancer activity of Brusatol on multiple hematologic malignancies derived cell lines. The results demonstrated that the PI3Kγ isoform was identified as a direct target of Brusatol, and inhibition was dramatically reduced on cells with lower PI3Kγ levels. Novel synthetic analogs were also developed and tested in vitro and in vivo. They shared comparable or superior potency in their ability to inhibit malignant hematologic cell lines, and in a xenograft transplant mouse model. One unique analog had minimal toxicity to normal human cells and in a mouse model. These new analogs have enhanced potential for development as a new class of PI3K inhibitors for treatment of hematologic malignancies.


Class Ib Phosphatidylinositol 3-Kinase/genetics , Hematologic Neoplasms/drug therapy , Quassins/pharmacology , Animals , Class Ib Phosphatidylinositol 3-Kinase/chemistry , Hematologic Neoplasms/genetics , Heterografts , Isoenzymes , Male , Mice , Mice, Inbred NOD , Transplantation, Heterologous
17.
J Immunol ; 205(1): 78-89, 2020 07 01.
Article En | MEDLINE | ID: mdl-32414808

Class I PI3K enzymes are critical for the maintenance of effective immunity. In T cells, PI3Kα and PI3Kδ are activated by the TCR and costimulatory receptors, whereas PI3Kγ is activated by G protein-coupled chemokine receptors. PI3Kδ is a key regulator of regulatory T (Treg) cell function. PI3K isoform-selective inhibitors are in development for the treatment of diseases associated with immune dysregulation, including chronic inflammatory conditions, cancer, and autoimmune diseases. Idelalisib (PI3Kδ), alpelisib (PI3Kα), duvelisib (PI3Kδ/γ), and copanlisib (pan-PI3K) have recently been approved for use in cancer treatment. Although effective, these therapies often have severe side effects associated with immune dysregulation and, in particular, loss of Treg cells. Therefore, it is important to gain a better understanding of the relative contribution of different PI3K isoforms under homeostatic and inflammatory conditions. Experimental autoimmune encephalitis is a mouse model of T cell-driven CNS inflammation, in which Treg cells play a key protective role. In this study, we show that PI3Kδ is required to maintain normal Treg cell development and phenotype under homeostatic conditions but that loss of PI3Kδ alone in Treg cells does not lead to autoimmunity. However, combined loss of PI3Kα and PI3Kδ signaling resulted in increased experimental autoimmune encephalitis disease severity. Moreover, mice lacking PI3Kα and PI3Kδ in Treg cells developed spontaneous peripheral nerve inflammation. These results show a key role for PI3K signaling in Treg cell-mediated protection against CNS inflammation.


Class I Phosphatidylinositol 3-Kinases/metabolism , Class Ib Phosphatidylinositol 3-Kinase/metabolism , Encephalomyelitis, Autoimmune, Experimental/immunology , Peripheral Nerves/immunology , T-Lymphocytes, Regulatory/immunology , Animals , Autoimmunity/genetics , Class I Phosphatidylinositol 3-Kinases/genetics , Class Ib Phosphatidylinositol 3-Kinase/genetics , Encephalomyelitis, Autoimmune, Experimental/blood , Encephalomyelitis, Autoimmune, Experimental/diagnosis , Encephalomyelitis, Autoimmune, Experimental/pathology , Female , Humans , Male , Mice , Mice, Transgenic , Myelin-Oligodendrocyte Glycoprotein/administration & dosage , Myelin-Oligodendrocyte Glycoprotein/immunology , Peptide Fragments/administration & dosage , Peptide Fragments/immunology , Peripheral Nerves/pathology , Severity of Illness Index , Signal Transduction/genetics , Signal Transduction/immunology , T-Lymphocytes, Regulatory/metabolism
18.
Int Immunopharmacol ; 79: 105901, 2020 Feb.
Article En | MEDLINE | ID: mdl-31896510

Lipopolysaccharide stimulates the intestinal microbiome to activate phosphoinositide 3 kinase (PI3K) signaling via several pathways; however, the direct effect that PI3K has on the intestinal bacterial community remains unclear. Herein, we investigate changes in the colonic microbiome of colitis PI3Kγ-knockout (PI3Kγ-/-) mice. Additionally, the effect of anal administration of colonic irrigation fluid from control mice to those with colitis was examined. Microbial 16S rRNA genes from the colonic mucosa of PI3Kγ-/- and WT mice were sequenced using Illumina MiSeq platform, and colonic IgA, IL-2, IL-10, and IL-17A production was quantified by western blot analysis. Myeloperoxidase (MPO) activity was detected by absorbance via colorimetric analysis. From the results, two new indices were derived by dividing the bacterial community into invading taxa, common taxa, and vanishing taxa. These indices were used to estimate the degree of microbiome disorder in chronic experimental colitis models. PI3Kγ-/- mice showed slower remission of inflammation as assessed by the disease activity index,pathological score, IL-2, IL-17, IL-10, IgA expression and MPO activity. The unique and common taxa of wild-type and PI3Kγ-/- mice increased as colitis symptoms regressed. Continuous loss of commensal bacteria happened with the continuous invasion of exogenous bacteria in the intestinal mucosa of PI3Kγ--/- mice after colitis begin to aggravate. However, transplantation of normal intestinal microbiota to PI3Kγ-/- mice promoted remission of inflammation; while the microbial dysbiosis observed during PI3Kγ dysfunction aggravated the intestinal microbiome disorder and impeded colitis recovery. Thus, the PI3Kγ signaling pathway may regulate microbial community composition in the colon.


Class Ib Phosphatidylinositol 3-Kinase/metabolism , Colitis/immunology , Colon/microbiology , Inflammatory Bowel Diseases/immunology , RNA, Ribosomal, 16S/genetics , Animals , Class Ib Phosphatidylinositol 3-Kinase/genetics , Colitis/chemically induced , Colitis/microbiology , Colon/immunology , Cytokines/metabolism , Disease Models, Animal , Female , Humans , Mice , Mice, Inbred BALB C , Mice, Knockout , Microbiota , Signal Transduction , Trinitrobenzenesulfonic Acid
19.
Cardiovasc Res ; 116(2): 438-449, 2020 02 01.
Article En | MEDLINE | ID: mdl-31106375

AIMS: Defects in efficient endothelial healing have been associated with complication of atherosclerosis such as post-angioplasty neoatherosclerosis and plaque erosion leading to thrombus formation. However, current preventive strategies do not consider re-endothelialization in their design. Here, we investigate mechanisms linking immune processes and defect in re-endothelialization. We especially evaluate if targeting phosphoinositide 3-kinase γ immune processes could restore endothelial healing and identify immune mediators responsible for these defects. METHODS AND RESULTS: Using in vivo model of endovascular injury, we showed that both ubiquitous genetic inactivation of PI3Kγ and hematopoietic cell-specific PI3Kγ deletion improved re-endothelialization and that CD4+ T-cell population drives this effect. Accordingly, absence of PI3Kγ activity correlates with a decrease in local IFNγ secretion and its downstream interferon-inducible chemokine CXCL10. CXCL10 neutralization promoted re-endothelialization in vivo as the same level than those observed in absence of PI3Kγ suggesting a role of CXCL10 in re-endothelialization defect. Using a new established ex vivo model of carotid re-endothelialization, we showed that blocking CXCL10 restore the IFNγ-induced inhibition of endothelial healing and identify smooth muscle cells as the source of CXCL10 secretion in response to Th1 cytokine. CONCLUSION: Altogether, these findings expose an unforeseen cellular cross-talk within the arterial wall whereby a PI3Kγ-dependent T-cell response leads to CXCL10 production by smooth muscle cells which in turn inhibits endothelial healing. Therefore, both PI3Kγ and the IFNγ/CXCL10 axis provide novel strategies to promote endothelial healing.


CD4-Positive T-Lymphocytes/enzymology , Carotid Artery Injuries/enzymology , Chemokine CXCL10/metabolism , Class Ib Phosphatidylinositol 3-Kinase/metabolism , Endothelial Cells/metabolism , Muscle, Smooth, Vascular/metabolism , Myocytes, Smooth Muscle/metabolism , Wound Healing , Animals , CD4-Positive T-Lymphocytes/immunology , Carotid Artery Injuries/genetics , Carotid Artery Injuries/immunology , Carotid Artery Injuries/pathology , Cell Proliferation , Cells, Cultured , Class Ib Phosphatidylinositol 3-Kinase/deficiency , Class Ib Phosphatidylinositol 3-Kinase/genetics , Disease Models, Animal , Endothelial Cells/pathology , Human Umbilical Vein Endothelial Cells/metabolism , Humans , Interferon-gamma/metabolism , Mice, Inbred C57BL , Mice, Knockout , Muscle, Smooth, Vascular/immunology , Muscle, Smooth, Vascular/pathology , Myocytes, Smooth Muscle/immunology , Myocytes, Smooth Muscle/pathology , Paracrine Communication , Re-Epithelialization , Signal Transduction
20.
Sci Signal ; 12(607)2019 11 12.
Article En | MEDLINE | ID: mdl-31719171

Myofibroblasts are key contributors to pathological fibrotic conditions of several major organs. The transdifferentiation of fibroblasts into myofibroblasts requires both a mechanical signal and transforming growth factor-ß (TGF-ß) signaling. The cation channel transient receptor potential vanilloid 4 (TRPV4) is a critical mediator of myofibroblast transdifferentiation and in vivo fibrosis through its mechanosensitivity to extracellular matrix stiffness. Here, we showed that TRPV4 promoted the transdifferentiation of human and mouse lung fibroblasts through its interaction with phosphoinositide 3-kinase γ (PI3Kγ), forming nanomolar-affinity, intracellular TRPV4-PI3Kγ complexes. TGF-ß induced the recruitment of TRPV4-PI3Kγ complexes to the plasma membrane and increased the activities of both TRPV4 and PI3Kγ. Using gain- and loss-of-function approaches, we showed that both TRPV4 and PI3Kγ were required for myofibroblast transdifferentiation as assessed by the increased production of α-smooth muscle actin and its incorporation into stress fibers, cytoskeletal changes, collagen-1 production, and contractile force. Expression of various mutant forms of the PI3Kγ catalytic subunit (p110γ) in cells lacking PI3Kγ revealed that only the noncatalytic, amino-terminal domain of p110γ was necessary and sufficient for TGF-ß-induced TRPV4 plasma membrane recruitment and myofibroblast transdifferentiation. These data suggest that TGF-ß stimulates a noncanonical scaffolding action of PI3Kγ, which recruits TRPV4-PI3Kγ complexes to the plasma membrane, thereby increasing myofibroblast transdifferentiation. Given that both TRPV4 and PI3Kγ have pleiotropic actions, targeting the interaction between them could provide a specific therapeutic approach for inhibiting myofibroblast transdifferentiation.


Cell Membrane/metabolism , Cell Transdifferentiation , Class Ib Phosphatidylinositol 3-Kinase/metabolism , Myofibroblasts/metabolism , TRPV Cation Channels/metabolism , Animals , Cell Line , Cell Membrane/genetics , Cell Membrane/pathology , Class Ib Phosphatidylinositol 3-Kinase/genetics , Humans , Lung/metabolism , Lung/pathology , Mice , Myofibroblasts/pathology , Pulmonary Fibrosis/genetics , Pulmonary Fibrosis/metabolism , Pulmonary Fibrosis/pathology , TRPV Cation Channels/genetics , Transforming Growth Factor beta/genetics , Transforming Growth Factor beta/metabolism
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