PDK1 Research Articles

Insilico design of an allosteric modulator targeting the protein-protein interaction site of3 Phosphoinositide dependent Kinase-1: design, synthesis and biological activity.

The online version contains supplementary material available at 10.1007/s40203-023-00160-6.

A pure de novo 16p13.3 duplication and amplification in a patient with femoral hypoplasia, psychomotor retardation, heart defect, and facial dysmorphism—a case report and literature review of the partial 16p13.3 trisomy syndrome

Partial 16p trisomy syndrome is a rare disorder typically characterized by psychomotor retardation, prenatal and postnatal growth deficiency, cleft palate, and facial dysmorphism, with some patients also presenting with heart defects and urogenital anomalies. Pure 16p13.3 duplications usually occur de novo, while those duplications that associate with partial monosomy result rather from parental chromosomal translocations. Due to the large size of the aberrations, the majority of patients are identified by standard chromosome analysis. In all published cases, the minimal-causative duplicated region encompasses the CREBBP gene. Here, we report on the patient presenting with psychomotor retardation, femoral hypoplasia, and some features of the partial 16p trisomy syndrome, who carries a complex de novo terminal 16p13.3 microduplication with an overlapping region of amplification without translocation or associated monosomy. In contrast to the previously reported cases, the duplicated region of the patient does not involve CREBBP and other neighboring genes; still, the observed pattern of dysmorphic features of the index is characteristic of the described syndrome. Based on the animal studies and other published cases, we discuss the possible role of the PDK1 and IGFALS genes in the development of limb anomalies, while IFT140 could contribute both to the observed femoral phenotype and heart abnormalities in the patient. To the best of our knowledge, we present a proband harboring the smallest terminal 16p13.3 duplication of the size below 3 Mb. Therefore, our proband with her detailed phenotypic description may be helpful for clinicians who consult patients with this syndrome.

Insulin resistance in adipose tissue and metabolic diseases.

Adipose tissue regulates systemic energy metabolism through adipokine production as well as energy storage and energy supply to other organs in response to changes in energy status. Adipose tissue dysfunction is therefore thought to be a key contributor to the pathogenesis of a variety of metabolic disorders including nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH). Given that insulin plays a central role in the regulation of many aspects of adipocyte function, insulin resistance in adipose tissue is implicated in the pathogenesis of metabolic disorders as a cause of adipose tissue dysfunction. The concept of metabolic dysfunction-associated fatty liver disease (MAFLD) has recently been proposed for liver disease associated with metabolic disorders in both obese and nonobese individuals, with insulin resistance in adipose tissue likely being an important factor in its pathogenesis. This review outlines the relation between insulin resistance in adipose tissue and metabolic disorders, with a focus on the physiological relevance and mechanism of action of 3'-phosphoinositide-dependent kinase 1 (PDK1), a key kinase in insulin signaling, and its downstream transcription factor FoxO1 in adipocytes.

Serum and glucocorticoid-regulated kinase 1: Structure, biological functions, and its inhibitors.

Serum and glucocorticoid-regulated kinase 1 (SGK1) is a serine/threonine kinase belonging to the protein kinase A, G, and C (AGC) family. Upon initiation of the phosphoinositide 3-kinase (PI3K) signaling pathway, mammalian target of rapamycin complex 2 (mTORC2) and phosphoinositide-dependent protein kinase 1 (PDK1) phosphorylate the hydrophobic motif and kinase domain of SGK1, respectively, inducing SGK1 activation. SGK1 modulates essential cellular processes such as proliferation, survival, and apoptosis. Hence, dysregulated SGK1 expression can result in multiple diseases, including hypertension, cancer, autoimmunity, and neurodegenerative disorders. This review provides a current understanding of SGK1, particularly in sodium transport, cancer progression, and autoimmunity. In addition, we summarize the developmental status of SGK1 inhibitors, their structures, and respective potencies evaluated in pre-clinical experimental settings. Collectively, this review highlights the significance of SGK1 and proposes SGK1 inhibitors as potential drugs for treatment of clinically relevant diseases.

De Novo Transcriptome Assembly and Analysis of Longevity Genes Using Subterranean Termite (Reticulitermes chinensis) Castes.

The longevity phenomenon is entirely controlled by the insulin signaling pathway (IIS-pathway). Both vertebrates and invertebrates have IIS-pathways that are comparable to one another, though no one has previously described de novo transcriptome assembly of IIS-pathway-associated genes in termites. In this research, we analyzed the transcriptomes of both reproductive (primary kings “PK” and queens “PQ”, secondary worker reproductive kings “SWRK” and queens “SWRQ”) and non-reproductive (male “WM” and female “WF” workers) castes of the subterranean termite Reticulitermes chinensis. The goal was to identify the genes responsible for longevity in the reproductive and non-reproductive castes. Through transcriptome analysis, we annotated 103,589,264 sequence reads and 184,436 (7G) unigenes were assembled, GC performance was measured at 43.02%, and 64,046 sequences were reported as CDs sequences. Of which 35 IIS-pathway-associated genes were identified, among 35 genes, we focused on the phosphoinositide-dependent kinase-1 (Pdk1), protein kinase B2 (akt2-a), tuberous sclerosis-2 (Tsc2), mammalian target of rapamycin (mTOR), eukaryotic translation initiation factor 4E (EIF4E) and ribosomal protein S6 (RPS6) genes. Previously these genes (Pdk1, akt2-a, mTOR, EIF4E, and RPS6) were investigated in various organisms, that regulate physiological effects, growth factors, protein translation, cell survival, proliferation, protein synthesis, cell metabolism and survival, autophagy, fecundity rate, egg size, and follicle number, although the critical reason for longevity is still unclear in the termite castes. However, based on transcriptome profiling, the IIS-pathway-associated genes could prolong the reproductive caste lifespan and health span. Therefore, the transcriptomic shreds of evidence related to IIS-pathway genes provide new insights into the maintenance and relationships between biomolecular homeostasis and remarkable longevity. Finally, we propose a strategy for future research to decrypt the hidden costs associated with termite aging in reproductive and non-reproductive castes.

Cell-impermeable staurosporine analog targets extracellular kinases to inhibit HSV and SARS-CoV-2

Herpes simplex virus (HSV) receptor engagement activates phospholipid scramblase triggering Akt translocation to the outer leaflet of the plasma membrane where its subsequent phosphorylation promotes viral entry. We hypothesize that this previously unrecognized outside-inside signaling pathway is employed by other viruses and that cell-impermeable kinase inhibitors could provide novel antivirals. We synthesized a cell-impermeable analog of staurosporine, CIMSS, which inhibited outer membrane HSV-induced Akt phosphorylation and blocked viral entry without inducing apoptosis. CIMSS also blocked the phosphorylation of 3-phosphoinositide dependent protein kinase 1 and phospholipase C gamma, which were both detected at the outer leaflet following HSV exposure. Moreover, vesicular stomatitis virus pseudotyped with SARS-CoV-2 spike protein (VSV-S), but not native VSV or VSV pseudotyped with Ebola virus glycoprotein, triggered this scramblase-Akt outer membrane signaling pathway. VSV-S and native SARS-CoV-2 infection were inhibited by CIMSS. Thus, CIMSS uncovered unique extracellular kinase processes linked to HSV and SARS-CoV-2 entry.

RNA-seq transcriptome profiling of liver regeneration in mice identifies the miR-34b-5p/phosphoinositide-dependent protein kinase 1 axis as a potential target for hepatocyte proliferation

Characterized by compensatory hyperplasia dependent on hepatocyte proliferation, the liver will initiate regeneration after partial hepatectomy (PH) and acute or chronic injuries. A variety of genes and noncoding RNAs play pivotal roles in these cell proliferation and growth processes. However, it is still unclear how competition endogenous RNAs (ceRNAs) modulate cellular activities during each phase of liver regeneration, and the specific mechanisms of posttranscriptional gene expression regulation in hepatocyte proliferation remain to be elucidated. To investigate the mechanism of liver regeneration through RNA-seq profiling and to determine the role of miR-34b-5p/PDK1 on hepatocyte proliferation, we established a 2/3 PH mouse model for whole transcriptome profiling based on high-throughput sequencing techniques. We subsequently constructed a lncRNA-miRNA-mRNA ceRNA regulatory network through integrative analyses of RNA interactions. Finally, plasmid transfection in NCTC 1469 cells, dual luciferase reporter gene assay, quantitative real-time PCR, western blotting, Cell Counting Kit-8, and EdU-DNA synthesis cell proliferation assay were used to demonstrate the role of the miR-34b-5p/PDK1 axis in hepatocyte proliferation in vitro. A total of 1443 mRNAs (962 up, 481 down), 48 miRNAs (35 up, 13 down), and 1955 lncRNAs (986 up, 969 down) were identified as significantly differentially expressed. We then successfully constructed a ceRNA regulatory network consisting of 7 lncRNAs, 15 miRNAs, and 347 mRNAs based on the predicted inverse interactions among ceRNAs. Additionally, miR-34b-5p/PDK1 was predicted to be closely related to hepatocyte proliferation. We further demonstrated that miR-34b-5p could bind specifically to the 3′-untranslated region (3′-UTR) of PDK1 using the dual luciferase reporter assay. Ectopic overexpression of miR-34b-5p significantly reduced the mRNA and protein expression of PDK1, while it markedly inhibited the proliferation of mouse NCTC 1469 cells in vitro. In contrast, knocking down miR-34b-5p exhibited the inverse effects on PDK1 expression and hepatocyte proliferation. Through analyzing the ceRNA network during mouse liver regeneration, this study reveals that miR-34b-5p can inhibit hepatocyte proliferation through negatively regulating PDK1 and may be a potential pharmacological intervention target.

Inhibition of TLR4 Suppresses the Inflammatory Response in Inflammatory Bowel Disease (IBD) by Modulating the PDK1-Induced Metabolism Reprogramming via a m6A-Denpendent Manner.

Objective To investigate the role of TLR4 and PDK1 genes in IBD. Methods The DSS mouse model was established by inducing BALB/C with 5% DSS solution. The behavior of DSS mice was detected, and the m6A modification was detected by m6A methylation chip. At the same time, the expressions of TLR and PDK1 were detected by fluorescence real-time quantitative PCR. Results The results showed that the model of dextran sodium sulfate colitis in mice was successful, and the colon membrane of mice had obvious naked eye inflammation. Through comparison, it was found that there were differences in m6A modification between the blank group and the model group, and compared with the blank group, the expression of PKD1 in DSS group was significantly reduced and the expression of TLR4 was significantly increased. Conclusion TLR4 inhibition inhibits the inflammatory response in inflammatory bowel disease (IBD) in a m6A-dependent manner by regulating PDK1-induced metabolic reprogramming.

KARDIOMIOPATIA ROZSTRZENIOWA U PSA DOMOWEGO – ANALIZA IN SILICO WYBRANYCH GENÓW

Dilated cardiomyopathy (DCM) is a progressive loss of contractility of the heart muscle as the disease progresses. It causes a decrease in the heart’s minute capacity, i.e. the volume of blood pumped by the heart into the blood vessels in one minute. DCM leads to congestive heart failure and sudden death. The aim of this study was to identify in silico genes within which mutations have occurred that may cause DCM in the domestic dog (Canis lupus familiaris), to identify dog breeds at risk, and to propose breed-specific diagnostic molecular tests. For bioinformatic analyses of sequences retrieved from GenBank (NC_006587.3 – FGGY, NC_006583.3 – DCC and CM023383.1 – PDE3B) and from scientific publications (PDK4 – from patent publication number US 2011/0307965 A1 and STRN – Meurs et al. 2010), the following programs were used: Primer3 v. 0.4.0, NEBcutter v. 2.0 and BLAST. Based on literature data, domestic dog breeds such as Doberman Pinscher, Boxer, Portuguese Water Dog, Newfoundland, Irish Wolfhound and Great Dane were found to be among the breeds with the highest risk of DCM. In order to identify relevant mutations in the genes studied (FGGY, DCC, PDE3B, PDK4 and STRN) that may cause the occurrence of dilated cardiomyopathy, the use of specific restriction enzymes has been proposed in molecular diagnostic tests: BmiI for mutations in the PDK4 gene and Tth111I for SNPs in the FGGY gene (Doberman Pinscher) and TaqI for SNPs in the DCC gene and HinfI for SNPs in the PDE3B gene (Irish Wolfhound). This work, may serve as a prelude to analysis for targeted genetic testing to enable correct diagnosis of DCM in asymptomatic dogs

Terpenoid-Rich Extract of Dillenia indica L. Bark Displays Antidiabetic Action in Insulin-Resistant C2C12 Cells and STZ-Induced Diabetic Mice by Attenuation of Oxidative Stress.

Insulin resistance (IR) plays a key role in the pathogenesis and clinical outcome of patients with multiple diseases and diabetes. In this study, we examined the antidiabetic effects of a terpenoid-rich extract from Dillenia indica L. bark (TRDI) in palmitic acid-induced insulin resistance (PA-IR) in C2C12 myotube and a streptozotocin (STZ)-induced diabetic mice model and explored the possible underlying mechanism. TRDI showed potential DPPH- and ABTS-radical scavenging effects with a half-maximal inhibitory concentration (IC50) value of 9.76 ± 0.50 µg/mL and 17.47 ± 1.31 µg/mL, respectively. Furthermore, TRDI strongly mitigated α-glucosidase activity with an IC50 value of 3.03 ± 1.01 µg/mL, which was 92-fold higher than the positive control, acarbose (IC50 = 279.49 ± µg/mL). TRDI stimulated the insulin receptor substrarte-1 (INS-1), downregulated phosphoinositide-dependent kinase-1 (PDK1) and protein kinase B (Akt) in both normal and PA-IR C2C12 cells as well as in STZ-induced diabetic mice, enhanced glucose transporter 4 (GLUT4) translocation to the plasma membrane (PM), and increased glucose absorption. Furthermore, TRDI administration significantly reduced PA-induced reactive oxygen species (ROS) formation in C2C12 cells and increased the protein level of numerous antioxidant enzymes such as superoxide dismutase 1 (SOD1), catalase (CAT), glutathione peroxidase-1 (GPx-1) and thioredoxin reductase (TrxR) both in vitro and in vivo. Furthermore, TRDI facilitated nuclear factor erythroid 2 related factor 2 (Nrf2) nuclear translocation and increased HO-1 expression in PA-IR C2C12 cells and STZ-induced diabetic mice. However, for the inhibition of Nrf2, TRDI failed to resist the effects of IR. Thus, this study provides new evidence to support the use of TRDI for diabetes treatment.

Abstract 2569: Development of potent dual PDK1/AurA kinase inhibitors for Ewing sarcoma therapy

Abstract Background. It has been estimated that more than 50% of cancers are related to the dysregulation of the PI3K-PDK1-Akt signaling axis. Within this pathway, phosphoinositide-dependent kinase-1 (PDK1) and Aurora kinase A (AurA) have key roles. PDK1 is a phosphorylation-mediated activator of Akt, the main apoptotic regulator, thereby acting at the crossroads of several oncogenic pathways. Overexpression and/or aberrant activation of AurA have been functionally linked to neoplastic transformation principally through the development of centrosome amplification and chromosomal instability. In this study, the molecular mechanisms involved in the dual inhibitory capacity of PDK1- and AurA-targeting OXID-pyridonyl compounds were explored in a panel of tumor cell lines carrying PI3KCA, K-RAS, PTEN, RB-1, EGFR and/or TP53 mutations Materials and Methods. To evaluate the enzymatic inhibitory activity, the oxindole-based derivatives were subjected to FRET-based Z′-Lyte assay (Invitrogen™) against PDK1 and AurA. All in vitro assays for ADME-Tox profiling were performed as published previously[1]. Anti-proliferative effects of OXID-pyridonyl compounds (SA16, IB35, VI8, VI18) were assessed by soft agar clonogenic formation and MTT assays after 72-h exposures with increasing concentrations (from 0.014 to 30 µM) in a panel of 15 cell lines. Protein levels were analyzed by Western Blot using commercial antibodies. OSU-03012 (PDK-1 inhibitor) and MK-5108 (AurA inhibitor) were used as reference compounds. Results. Among the four evaluated compounds, SA16 displayed nanomolar inhibitory potency against both PDK1 and AurA. In vitro, drugs SA16 and VI8 showed to exert anti-tumor activity in the 6647, TC71, SKNMC Ewing sarcoma (ES) cells lines and in the HCT116 colon carcinoma-derived cells (IC50s values between 2.6 and 25 µM after 72-h exposures), when tested in a panel of 15 cancer cell lines. These results were confirmed by the evaluation of 3D-clonogenic capacity in soft agar. The effect of 1 µM SA16 at the protein level was evaluated after 5 to 120 min exposure in the ES cell line SKNMC. No modulation of Aur-A protein or PDK-1 phosphorylation (Ser241) were observed in SKNMC cells, whereas a decrease of downstream PDK1 targets such as p-AKT, p-RSK2, and p-p44/42 MAPK was observed after 30 min of exposure. In addition, SA16 displayed acceptable in vitro ADME-Tox properties. Our results on structural insights into the mode of binding[2], in vitro drug-intake kinetics and in vivo PK appear to indicate that SA16 presents adequate features as a scaffold for the design of PDK1/AurA dual-target molecules. Conclusion. We report the synthesis of novel first-in-class 2-oxindole-based derivatives as dual PDK1-AurA kinase inhibitors as a novel scaffold for the design and synthesis of a new multitarget strategy for Ewing sarcoma.[1] Runfola M. et al. Data Brief 29 (2020) 105206.[2] Sistito S. et al. Eu J Med Chem 226 (2021) 11389. Citation Format: Maria Eugenia Riveiro, Samuel Huguet, Ramiro Vazquez, Roberta Frapolli, Guido Puricelli, Simona Sestito, Olivier Madar, Keyvan Rezai, Gianpiero Garau, Simona Rapposelli. Development of potent dual PDK1/AurA kinase inhibitors for Ewing sarcoma therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2569.

NCAPD3 enhances Warburg effect through c-myc and E2F1 and promotes the occurrence and progression of colorectal cancer

BackgroundNCAPD3 is one of the three non-SMC subunits of condensin II complex, which plays an important role in the chromosome condensation and segregation during mitosis. Notably, elevated levels of NCAPD3 are found in many somatic cancers. However, the clinical role, biological functions of NCAPD3 in cancers especially in colorectal cancer (CRC) and the underlying molecular mechanisms remain poorly elucidated.MethodsClinical CRC and adjacent normal tissues were used to confirm the expression of NCAPD3. The association of NCAPD3 expression with clinicopathological characteristics and patient outcomes were analyzed by using online database. In vivo subcutaneous tumor xenograft model, NCAPD3 gene knockout following azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced tumor mouse model, Co-IP, western blot, qRT-PCR, IHC, ChIP assays and cell functional assays were used to investigate the biological functions of NCAPD3 in CRC and the underlying molecular mechanisms.ResultsNCAPD3 was overexpressed in CRC tissues and positively correlated with poor prognosis of CRC patients. NCAPD3 knockout suppressed CRC development in AOM/DSS induced and xenograft mice models. Moreover, we found that NCAPD3 promoted aerobic glycolysis in CRC. Mechanistically, NCAPD3 up-regulated the level of c-Myc and interacted with c-Myc to recruit more c-Myc to the gene promoter of its downstream glycolytic regulators GLUT1, HK2, ENO1, PKM2 and LDHA, and finally enhanced cellular aerobic glycolysis. Also, NCAPD3 increased the level of E2F1 and interacted with E2F1 to recruit more E2F1 to the promoter regions of PDK1 and PDK3 genes, which resulted in the inhibition of PDH activity and TCA cycle.ConclusionsOur data demonstrated that NCAPD3 promoted glucose metabolism reprogramming and enhanced Warburg effect in colorectal tumorigenesis and CRC progression. These findings reveal a novel mechanism underlying NCAPD3 mediated CRC cell growth and provide new targets for CRC treatment.

Aristolone in Nardostachys jatamansi DC. induces mesenteric vasodilation and ameliorates hypertension via activation of the KATP channel and PDK1-Akt-eNOS pathway

BackgroundNardostachys jatamansi DC. is a common medicinal herb used to treat cardiovascular diseases, particularly hypertension. Previously, our lab characterized the chemical compounds of N. jatamansi. However, the bioactive compounds of N. jatamansi and their mechanisms of action on blood pressure and blood vessels are unknown. PurposeThe vasorelaxant effects of the methanolic extract (MeOH ext.) of the roots and rhizomes of N. jatamansi, its main compounds, and their underlying mode of action, were investigated. MethodsThe main compounds of N. jatamansi were isolated and identified using UHPLC-TOF MS. The antihypertensive effect of N. jatamansi extracts and (-)-aristolone were determined using spontaneously hypertensive rats. The extracts, fractions, and compounds were also evaluated for their vasorelaxant effects on U46619 contractile responses in isolated thoracic aortic and mesenteric arterial rings. The endothelial-dependent relaxation, as well as the regulatory pathways and targets of (-)-aristolone, were studied in-vitro and ex-vivo. Molecular docking and biophysical characterization (Surface plasmon resonance) studies were utilized to investigate the molecular interaction between (-)-aristolone and the target protein. ResultsMeOH ext. (200 mg/kg) reduces the systolic and diastolic blood pressure in spontaneously hypertensive rats. MeOH ext. and its ethyl acetate fraction (EtOAc Fr.), but not the H2O fraction, had a significant relaxing effect on the thoracic aorta. (-)-aristolone and kanshone H from EtOAc Fr. induced vasorelaxation of the thoracic aorta and mesenteric artery. In human umbilical vein endothelial cells, (-)-aristolone treatment upregulated phosphorylation of Akt (T308) and eNOS. Molecular docking and surface plasmon resonance experiments revealed an interaction between (-)-aristolone and phosphoinositide-dependent protein kinase 1 (PDK1), an upstream protein kinase that phosphorylates Akt at T308. Treatment with PDK1 inhibitor PHT-427 and eNOS inhibitor L-NAME consistently inhibited (-)-aristolone-induced vasorelaxation. In addition, KATP channel inhibitor glibenclamide dramatically inhibited the vasorelaxant effects of (-)-aristolone and kanshone H in the endothelium-denuded thoracic aorta. Finally, (-)-aristolone lowers hypertensive rats' systolic and diastolic blood pressure. ConclusionsThe extracts of N. jatamansi promote vasorelaxation and alleviate hypertension. The essential chemicals responsible for producing vasorelaxation effects are (-)-aristolone and kanshone H, which activate the PDK1-Akt-eNOS-NO relaxing pathway and stimulate the opening of the KATP channel. These findings point to N. jatamansi and aristolone as possible antihypertensive agents.

Reducing PDK1/Akt Activity: An Effective Therapeutic Target in the Treatment of Alzheimer's Disease.

Alzheimer’s disease (AD) is a common age-related neurodegenerative disease that leads to memory loss and cognitive function damage due to intracerebral neurofibrillary tangles (NFTs) and amyloid-β (Aβ) protein deposition. The phosphoinositide-dependent protein kinase (PDK1)/protein kinase B (Akt) signaling pathway plays a significant role in neuronal differentiation, synaptic plasticity, neuronal survival, and neurotransmission via the axon–dendrite axis. The phosphorylation of PDK1 and Akt rises in the brain, resulting in phosphorylation of the TNF-α-converting enzyme (TACE) at its cytoplasmic tail (the C-terminal end), changing its internalization as well as its trafficking. The current review aimed to explain the mechanisms of the PDK1/Akt/TACE signaling axis that exerts its modulatory effect on AD physiopathology. We provide an overview of the neuropathological features, genetics, Aβ aggregation, Tau protein hyperphosphorylation, neuroinflammation, and aging in the AD brain. Additionally, we summarized the phosphoinositide 3-kinase (PI3K)/PDK1/Akt pathway-related features and its molecular mechanism that is dependent on TACE in the pathogenesis of AD. This study reviewed the relationship between the PDK1/Akt signaling pathway and AD, and discussed the role of PDK1/Akt in resisting neuronal toxicity by suppressing TACE expression in the cell membrane. This work also provides a perspective for developing new therapeutics targeting PDK1/Akt and TACE for the treatment of AD.

Unique mutations in mitochondrial DNA and associated pathways involved in high altitude pulmonary edema susceptibility in Indian lowlanders

High altitude pulmonary edema (HAPE) is a life threatening non-cardiogenic pulmonary edema that occurs in an otherwise healthy individuals travelling to altitude above 2500 m. Earlier studies have reported association of mutations in nuclear (nDNA) and mitochondrial DNA (mtDNA) with HAPE susceptibility. However, the molecular mechanisms involved in the pathobiology of HAPE have not been fully understood. The present study investigates the genetic predisposition to HAPE by analyzing the mtDNA mutations in HAPE susceptibles (n = 23) and acclimatized controls (n = 23) using next generation sequencing. Structural analysis of mutations was done using SWISS Model server and stability was determined using ΔΔG values. Meta-analysis of GSE52209 dataset was done to identify differentially expressed genes (DEGs) in HAPE susceptibles and acclimatized controls. Fourteen non-synonymous, conserved and pathogenic mutations were predicted using SIFT and PolyPhen scoring in protein coding genes, whereas six mutations in mt-tRNA genes showed association with HAPE (p ≤ 0.05). The structural analysis of these mutations revealed conformational changes in critical regions in Complexes I–V which are involved in subunit assembly and proton pumping activity. The protein–protein interaction network analysis of DEGs showed that HIF1α, EGLN2, EGLN3, PDK1, TFAM, PPARGC1α and NRF1 genes form highly interconnected cluster. Further, pathway enrichment analysis using DAVID revealed that “HIF-1 signaling”, “oxidative phosphorylation” and “Metabolic pathways” had strong association with HAPE. Based on the findings it appears that the identified mtDNA mutations may be a potential risk factor in development of HAPE with the associated pathways providing mechanistic insight into the understanding of pathobiology of HAPE and sites for development of therapeutic targets. Communicated by Ramaswamy H. Sarma

Conservation of Ilp4, Pdk1 and HDAC4 Across Drosophila Species

The degree of gene conservation is influenced by many factors including relative expression levels and number of interactions of the gene and its protein product. In collaboration with the Genomics Education Project, the conservation of several insulin signaling pathway genes and their protein products within Drosophila has been investigated. Insulin‐like peptide 4 (Ilp4) functions in the insulin signaling pathway by binding to the insulin receptor, thus triggering the phosphatidylinositol 3‐kinase pathway, which involves Phosphoinositide‐dependent kinase 1 (Pdk1). Another player in the insulin‐signaling pathway investigated in this work is Histone deacetylase 4 (HDAC4), which catalyzes the removal of acetyl functional groups from histone proteins, ultimately decreasing the expression of associated genes. Predicting the relative conservation of these genes is not trivial. For example, Ilp4 is at the beginning of the pathway and has one contact according to the Flybase physical interaction network. This might indicate the potential for greater evolutionary change over time, but contradicting this hypothesis is this insulin‐like peptide’s importance as a ligand in the pathway. Pdk1 also shows one contact on Flybase, but is located towards the beginning of the pathway, suggesting a relatively higher evolutionary rate. HDAC4 plays a role in many other cellular processes and so should be well conserved. To evaluate conservation, we first used BLAST to identify orthologs of these three genes across several Drosophilaspecies. We then evaluated conservation in terms of amino acid identity, exon length, number of exons, and degree of synteny using genomic sequences, BLAST, and evidence such as gene prediction tracks and RNA expression data available on the UCSC Genome Browser. Thus far, Pdk1 has demonstrated the greatest similarity over multiple species, with less conservation being observed in Ilp4 and HDAC4. This suggests the complexity in determining the interplay between number of protein contacts and pathway position on evolutionary rate.

Network based identification of Potential Key Genes associated with Alzheimer’s disease and Type 2 Diabetes using mTOR signalling

mTOR is involved in various signalling pathways, including TSC1/TSC2/Rheb, PI3K/Akt, LKBL/AMPK, VAM6/Rag GTPase etc. and dysregulation of the mTOR pathway has been related with cancer, neurological diseases and type 2 diabetes. In the present work, we created a comprehensive network of mTOR signalling that consisted of 255 nodes (proteins/genes) and 592 edges (interactions) using the Cytoscape 3.6 editor and its plugins for analysis. The experimental design included retrieving gene expression profiles for two diseases, namely Alzheimer's disease (AD) and type 2 diabetes (T2D), from the Gene Expression Omnibus (NCBI GEO) and performing pre-processing and normalisation using R and Bioconductor. The ExprEssence plugin was used to identify differentially expressed genes (DEGs) across gene expression samples using network condensation. GO (Gene Ontology) analysis was performed using PANTHER along with Venn plot for identification of overlapping proteins/genes between two microarray datasets of AD and T2D. PDK1 (3-Phosphoinositidedependent kinase 1) was identified as a common upregulated DEG between both the disease conditions (AD and T2D). The Schrödinger TM Suite was employed for ligand and protein preparation, docking investigations and pharmacophore development. Based on docking score, phase screen score and site of interaction, two compounds namely (2R,3R,4S,5S,6R)‐ 4,5‐dihydroxy‐2‐methyl‐6‐{[(2S,3R,4R,5S,6R)‐3,4,5‐tr ihydroxy‐6‐{[5 ‐hydroxy‐6‐methoxy‐2‐(4‐methoxyp henyl)‐4‐oxo‐4H‐chromen‐7‐yl]oxy}oxan‐2‐yl]methox y}oxan‐3‐yl aceta te and 5‐hydroxy‐6‐methoxy‐2‐(4‐ methoxyphenyl)‐7‐{[(2R,3S,4R,5R,6S)‐ 3,4,5‐trihydrox y‐6‐({[(2R,3S,4R, 5R,6R)‐3,4,5‐trihydroxy‐6‐methylox an‐2‐yl]oxy} methyl)oxan‐2‐yl]oxy}‐4H‐chromen‐4‐ one) were identified as potential inhibitors of PDK1.

Melatonin treatment improves human umbilical cord mesenchymal stem cell therapy in a mouse model of type II diabetes mellitus via the PI3K/AKT signaling pathway

BackgroundMesenchymal stem cells (MSCs) are promising candidates for tissue regeneration and disease treatment. However, long-term in vitro passaging leads to stemness loss of MSCs, resulting in failure of MSC therapy. This study investigated whether the combination of melatonin and human umbilical cord mesenchymal stem cells (hUC-MSCs) was superior to hUC-MSCs alone in ameliorating high-fat diet and streptozocin (STZ)-induced type II diabetes mellitus (T2DM) in a mouse model.MethodsMice were divided into four groups: normal control (NC) group; T2DM group; hUC-MSCs treatment alone (UCMSC) group and pretreatment of hUC-MSCs with melatonin (UCMSC/Mel) group.ResultsRNA sequence analysis showed that certain pathways, including the signaling pathway involved in the regulation of cell proliferation signaling pathway, were regulated by melatonin. The blood glucose levels of the mice in the UCMSC and UCMSC/Mel treatment groups were significantly reduced compared with the T2DM group without treatment (P < 0.05). Furthermore, hUC-MSCs enhance the key factor in the activation of the PI3K/Akt pathway in T2DM mouse hepatocytes.ConclusionThe pretreatment of hUC-MSCs with melatonin partly boosted cell efficiency and thereby alleviated impaired glycemic control and insulin resistance. This study provides a practical strategy to improve the application of hUC-MSCs in diabetes mellitus and cytotherapy.Graphical abstractOverview of the PI3K/AKT signaling pathway. (A) Underlying mechanism of UCMSC/Mel inhibition of hyperglycemia and insulin resistance T2DM mice via regulation of PI3K/AKT pathway. hUC-MSCs stimulates glucose uptake and improves insulin action thus should inhibition the clinical signs of T2DM, through activation of the p-PI3K/Akt signaling pathway and then regulates glucose transport through activating AS160. UCMSC/Mel increases p53-dependent expression of BCL2, and inhibit BAX and Capase3 protein activation. Leading to the decrease in apoptosis. (B) Melatonin modulated PI3K/AKT signaling pathway. Melatonin activated PI3K/AKT response pathway through binding to MT1and MT2 receptor. Leading to the increase in hUC-MSCs proliferation, migration and differentiation. → (Direct stimulatory modification); ┴ ( Direct Inhibitory modification); → ┤ (Multistep inhibitory modification); ↑ (Up regulate); ↓ (Down regulate); PI3K (Phosphoinositide 3-Kinase); AKT ( protein kinase B); PDK1 (Phosphoinositide-dependent protein kinase 1); IR, insulin receptor; GLUT4 ( glucose transporter type 4); ROS (reactive oxygen species); BCL-2 (B-cell lymphoma-2); PDK1 (phosphoinositide-dependent kinase 1) BAX (B-cell lymphoma-2-associated X protein); PCNA (Proliferating cell nuclear antigen); Cell cycle-associated proteins (KI67, cyclin A, cyclin E)

Analysis of the epidermal growth factor receptor/phosphoinositide-dependent protein kinase-1 axis in tumor of the external auditory canal in response to epidermal growth factor stimulation.

ObjectivesThe epidermal growth factor receptor (EGFR) is related to the invasion and metastasis of external auditory canal (EAC) squamous cell carcinoma (SCC). The phosphoinositide‐dependent protein kinase‐1 (PDPK1) accelerates tumor cell growth through anti‐apoptotic signaling under the influence of downstream EGFR‐mediated signaling pathways. In this study, we investigated the EGFR/PDPK1 axis in the EAC under EGF stimulation.MethodsWe confirmed EGFR and PDPK1 expression in human EACSCC specimens immunohistochemically. We next transfected the EGF expression vector in the mouse EAC and then conducted a PDPK1 inhibitory experiment. Immunohistochemical analysis was performed in the mouse EAC, using anti‐EGF, anti‐EGFR, anti‐PDPK1, and anti‐Ki67 antibodies. Immunohistochemical analysis of cleaved caspase‐3 and terminal deoxy(d)‐UTP nick end labeling (TUNEL) detection assays were also performed for the assessment of apoptosis in the inhibitory experiment.ResultsImmunohistochemical analysis revealed overexpression and colocalization of EGFR and PDPK1 in human EACSCC specimens. The growth of a protuberant tumor was observed in the mouse EAC in which EGF expression vector was transfected, and EGF, EGFR, PDPK1, and Ki67 labeling indexes (LIs) were significantly increased. PDPK1 inhibition then induced normal epithelial appearance in the EAC. Moreover, EGF, EGFR, PDPK1, and Ki67 LIs were decreased, and cleaved caspase‐3 and TUNEL LIs were increased in the EAC.ConclusionWe demonstrated the possibility that PDPK1 plays an important role in EACSCC.Level of Evidence: NA.

Mechanism of Porphyromonas gingivalis-lipopolysaccharide in regulating the insulin signaling pathway in adipocytes via X-box binding protein 1.

This study aims to investigate the effect of X-box binding protein 1 (XBP1), a key signal molecule of ERS, on the insulin signaling pathway in adipocytes stimulated by Porphyromonas gingivalis (P. gingivalis)-lipopolysaccharide (LPS), a pathogenic bacterium of periodontitis. Primary cultured rat adipocytes were stimulated by P. gingivalis-LPS (100 ng·mL-1) for 4, 8, 12, and 24 h. The protein expression levels of insulin receptor substrate-1 (IRS-1), phosphoinositide dependent protein kinase (p-PDK-1), and protein kinase B (p-AKT-1) in the insulin signaling pathway were detected by Western blot analysis. pLVX-NC1, pLVX-XBP1, pLVX-NC2, and pLVX-XBP1-RNAi were transfected into adipocytes, respectively. The transfected rat adipocytes were stimulated by P. gingivalis-LPS, and the protein expression of the insulin signaling pathway was detected by Western blot. The Western Blot showed decreased protein expression of the insulin signaling pathway in rat adipocytes stimulated with P. gingivalis-LPS compared with the control, and the difference was statistically significant (P<0.05). The protein expression levels of IRS-1, p-PDK-1, and p-AKT in the rat adipocytes of pLVX-XBP1 were significantly higher than those in pLVX-NC1 at 8 and 12 h after P. gingivalis-LPS stimulation (P<0.05). The protein expression levels of IRS-1, p-PDK-1, and p-AKT in the rat adipocytes of pLVX-XBP1-RNAi were significantly lower than those in pLVX-NC2 at 4, 8, 12, and 24 h after P. gingivalis-LPS stimulation (P<0.05). P. gingivalis-LPS regulates the insulin signaling pathway in adipocytes th-rough XBP1.