bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2021‒12‒19
twenty-two papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute
  1. Phosphoinositide 3-kinase signalling in the nucleolus.
  2. Non-synaptic Cell-Autonomous Mechanisms Underlie Neuronal Hyperactivity in a Genetic Model of PIK3CA-Driven Intractable Epilepsy.
  3. p53-mediated AKT and mTOR inhibition requires RFX7 and DDIT4 and depends on nutrient abundance.
  4. Targeting Phosphoinositide 3-Kinase - Five Decades of Chemical Space Exploration.
  5. Can Improved Use of Biomarkers Alter the Fate of PI3K Pathway Inhibitors in the Clinic?
  6. Capillary Endothelial Insulin Transport: The Rate Limiting Step for Insulin-stimulated Glucose Uptake.
  7. Circulating PIK3CA mutation detection at diagnosis in non-metastatic inflammatory breast cancer patients.
  8. How Compensatory Mechanisms and Adaptive Rewiring Have Shaped Our Understanding of Therapeutic Resistance in Cancer.
  9. Molecular design of dual inhibitors of PI3K and potential molecular target of cancer for its treatment: A review.
  10. TOX4, an insulin receptor-independent regulator of hepatic glucose production, is activated in diabetic liver.
  11. Smurf1 silencing restores PTEN expression that ameliorates progression of human glioblastoma and sensitizes tumor cells to mTORC1/C2 inhibitor Torin1.
  12. Patient-Centered Diabetes Care of Cancer Patients.
  13. Functional Mapping of AKT Signaling and Biomarkers of Response From the FAIRLANE Trial of Neoadjuvant Ipatasertib Plus Paclitaxel for Triple-Negative Breast Cancer.
  14. Metabolic drug survey highlights cancer cell dependencies and vulnerabilities.
  15. Sima, a Drosophila homolog of HIF-1α, in fat body tissue inhibits larval body growth by inducing Tribbles gene expression.
  16. scNetViz: from single cells to networks using Cytoscape.
  17. Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data.
  18. What is the most appropriate covariate in ANCOVA when analysing metabolic rate?
  19. KRAS mutation-independent downregulation of MAPK/PI3K signaling in colorectal cancer.
  20. Lymphatic endothelial cell fate specification in the mammalian embryo: An historical perspective.
  21. Mass Spectrometry-Based Analytical Strategy for Single-Cell Proteomics.
  22. The onset of circulation triggers a metabolic switch required for endothelial to hematopoietic transition.
  1. Adv Biol Regul. 2021 Dec 10. pii: S2212-4926(21)00059-2. [Epub ahead of print] 100843
    Phosphoinositide 3-kinase signalling in the nucleolus.
    Andrea Papdiné Morovicz, Fatemeh Mazloumi Gavgani, Rhîan G Jacobsen, Malene Skuseth Slinning, Diana C Turcu, Aurélia E Lewis.
      The phosphoinositide 3-kinase (PI3K) signalling pathway plays key roles in many cellular processes and is altered in many diseases. The function and mode of action of the pathway have mostly been elucidated in the cytoplasm. However, many of the components of the PI3K pathway are also present in the nucleus at specific sub-nuclear sites including nuclear speckles, nuclear lipid islets and the nucleolus. Nucleoli are membrane-less subnuclear structures where ribosome biogenesis occurs. Processes leading to ribosome biogenesis are tightly regulated to maintain protein translation capacity of cells. This review focuses on nucleolar PI3K signalling and how it regulates rRNA synthesis, as well as on the identification of downstream phosphatidylinositol (3,4,5)trisphosphate effector proteins.
    Keywords:  EBP1; Nucleolus; Nucleophosmin; PI3K; Phosphoinositide 3-kinase; p110β; phosphatidylinositol(3,4,5)trisphosphate; rRNA
    DOI:  https://doi.org/10.1016/j.jbior.2021.100843
  2. Front Mol Neurosci. 2021 ;14 772847
    Non-synaptic Cell-Autonomous Mechanisms Underlie Neuronal Hyperactivity in a Genetic Model of PIK3CA-Driven Intractable Epilepsy.
    Achira Roy, Victor Z Han, Angela M Bard, Devin T Wehle, Stephen E P Smith, Jan-Marino Ramirez, Franck Kalume, Kathleen J Millen.
      Patients harboring mutations in the PI3K-AKT-MTOR pathway-encoding genes often develop a spectrum of neurodevelopmental disorders including epilepsy. A significant proportion remains unresponsive to conventional anti-seizure medications. Understanding mutation-specific pathophysiology is thus critical for molecularly targeted therapies. We previously determined that mouse models expressing a patient-related activating mutation in PIK3CA, encoding the p110α catalytic subunit of phosphoinositide-3-kinase (PI3K), are epileptic and acutely treatable by PI3K inhibition, irrespective of dysmorphology. Here we report the physiological mechanisms underlying this dysregulated neuronal excitability. In vivo, we demonstrate epileptiform events in the Pik3ca mutant hippocampus. By ex vivo analyses, we show that Pik3ca-driven hyperactivation of hippocampal pyramidal neurons is mediated by changes in multiple non-synaptic, cell-intrinsic properties. Finally, we report that acute inhibition of PI3K or AKT, but not MTOR activity, suppresses the intrinsic hyperactivity of the mutant neurons. These acute mechanisms are distinct from those causing neuronal hyperactivity in other AKT-MTOR epileptic models and define parameters to facilitate the development of new molecularly rational therapeutic interventions for intractable epilepsy.
    Keywords:  AZD5363 (PubChem CID: 25227436); BKM120 (buparlisib); PI3K; RAD001 (everolimus); electrophysiology; epilepsy; hippocampus; mouse model
    DOI:  https://doi.org/10.3389/fnmol.2021.772847
  3. Oncogene. 2021 Dec 14.
    p53-mediated AKT and mTOR inhibition requires RFX7 and DDIT4 and depends on nutrient abundance.
    Luis Coronel, David Häckes, Katjana Schwab, Konstantin Riege, Steve Hoffmann, Martin Fischer.
      In recent years the tumor suppressor p53 has been increasingly recognized as a potent regulator of the cell metabolism and for its ability to inhibit the critical pro-survival kinases AKT and mTOR. The mechanisms through which p53 controls AKT and mTOR, however, are largely unclear. Here, we demonstrate that p53 activates the metabolic regulator DDIT4 indirectly through the regulatory factor X 7 (RFX7). We provide evidence that DDIT4 is required for p53 to inhibit mTOR complex 2 (mTORC2)-dependent AKT activation. Most strikingly, we also find that the DDIT4 regulator RFX7 is required for p53-mediated inhibition of mTORC1 and AKT. Our results suggest that AMPK activation plays no role and p53-mediated AKT inhibition is not critical for p53-mediated mTORC1 inhibition. Moreover, using recently developed physiological cell culture media we uncover that basal p53 and RFX7 activity can play a critical role in restricting mTORC1 activity under physiological nutrient conditions, and we propose a nutrient-dependent model for p53-RFX7-mediated mTORC1 inhibition. These results establish RFX7 and its downstream target DDIT4 as essential effectors in metabolic control elicited by p53.
    DOI:  https://doi.org/10.1038/s41388-021-02147-z
  4. Chimia (Aarau). 2021 Dec 22. 75(12): 1037-1044
    Targeting Phosphoinositide 3-Kinase - Five Decades of Chemical Space Exploration.
    Chiara Borsari, Matthias P Wymann.
      Phosphoinositide 3-kinase (PI3K) plays a key role in a plethora of physiologic processes and controls cell growth, metabolism, immunity, cardiovascular and neurological function, and more. The discovery of wort-mannin as the first potent PI3K inhibitor (PI3Ki) in the 1990s provided rapid identification of PI3K-dependent processes, which drove the discovery of the PI3K/protein kinase B (PKB/Akt)/target of rapamycin (mTOR) pathway. Genetic mouse models and first PI3K isoform-specific inhibitors pinpointed putative therapeutic applications. The recognition of PI3K as target for cancer therapy drove subsequently drug development. Here we provide a brief journey through the emerging roles of PI3K to the development of preclinical and clinical PI3Ki candidates.
    DOI:  https://doi.org/10.2533/chimia.2021.1037
  5. Cancer Res. 2021 Dec 15. 81(24): 6083-6086
    Can Improved Use of Biomarkers Alter the Fate of PI3K Pathway Inhibitors in the Clinic?
    Emily C Erickson, Alex Toker.
      The high frequency of PI3K pathway alterations in cancer has motivated numerous efforts to develop drugs targeting this network. Although many potent and selective inhibitors have been developed and evaluated in preclinical models, their progress to clinical approval has been limited. Here we discuss the pressing need to develop improved biomarker strategies to guide patient selection and improve assessment of patient responses to PI3K pathway inhibitors to address unresolved issues surrounding the efficacy and tolerability of these compounds in patients with cancer.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-2035
  6. Endocrinology. 2021 Dec 15. pii: bqab252. [Epub ahead of print]
    Capillary Endothelial Insulin Transport: The Rate Limiting Step for Insulin-stimulated Glucose Uptake.
    Ian M Williams, David H Wasserman.
      The rate limiting step for skeletal muscle glucose uptake is transport from microcirculation to muscle interstitium. Capillary endothelium poses a barrier that delays the onset of muscle insulin action. Defining physiological barriers that control insulin access to interstitial space is difficult due to technical challenges that confront study of microscopic events in an integrated physiological system. Two physiological variables determine muscle insulin access. These are the number of perfused capillaries and the permeability of capillary walls to insulin. Disease states associated with capillary rarefaction are closely linked to insulin resistance. Insulin permeability through high resistant capillary walls of muscle poses a significant barrier to insulin access. Insulin may traverse the endothelium through narrow intercellular junctions or vesicular trafficking across the endothelial cell. Insulin is large compared to intercellular junctions making this an unlikely route. Transport by endothelial vesicular trafficking is likely the primary route of transit. Studies in vivo show movement of insulin is not insulin receptor-dependent. This aligns with single cell transcriptomics that show the insulin receptor is not expressed in muscle capillaries. Work in cultured endothelial cell lines suggest that insulin receptor activation is necessary for endothelial insulin transit. Controversies remain in the understanding of trans-endothelial insulin transit to muscle. These controversies closely align with experimental approaches. Control of circulating insulin accessibility to skeletal muscle is an area that remains ripe for discovery. Factors that impede insulin access to muscle may contribute to disease and factors that accelerate access may be of therapeutic value for insulin resistance.
    Keywords:  capillary; endothelial cell; insulin; interstitium; skeletal muscle; transport
    DOI:  https://doi.org/10.1210/endocr/bqab252
  7. Sci Rep. 2021 Dec 15. 11(1): 24041
    Circulating PIK3CA mutation detection at diagnosis in non-metastatic inflammatory breast cancer patients.
    Violette Allouchery, Anne Perdrix, Céline Calbrix, Anca Berghian, Justine Lequesne, Maxime Fontanilles, Marianne Leheurteur, Pascaline Etancelin, Nasrin Sarafan-Vasseur, Frédéric Di Fiore, Florian Clatot.
      Inflammatory breast cancer (IBC) is an aggressive BC subtype with poor outcomes. A targetable somatic PIK3CA mutation is reported in 30% of IBC, allowing for treatment by PI3Kα-specific inhibitors, such as alpelisib. The aim of this study was to evaluate the detection rate of circulating PIK3CA mutation in locally-advanced IBC (LAIBC) patients harbouring a PIK3CA mutation on initial biopsy. This monocentric retrospective study was based on available stored plasma samples and tumour biopsies at diagnosis from all LAIBC patients treated with neo-adjuvant chemotherapy (NCT) between 2008 and 2018 at the Centre Henri Becquerel. PIK3CA mutations (E542K, E545K, H1047R/L) were assessed by droplet digital PCR (ddPCR) in plasma samples and tumoral tissue at diagnosis. A total of 55 patients were included. Overall, 14/55 patients (25%) had a PIK3CA mutation identified on baseline biopsy (H1047R = 8; H1047L = 3; E545K = 2; E542K = 1). Among them, 11 (79%) patients had enough DNA for circulating DNA analyses, and corresponding circulating PIK3CA mutations were found in 6/11 (55%). Among the 41 patients without PIK3CA mutations on biopsy, 32 (78%) had enough DNA for circulating DNA analysis, and no circulating PIK3CA mutation was identified. Our results revealed no prognostic or predictive value of PIK3CA mutations at the diagnosis of non-metastatic IBC but highlighted the prognostic value of the cfDNA rate at diagnosis. Our study showed that a corresponding circulating PIK3CA mutation was identified in 55% of LAIBC patients with PIK3CA-mutated tumours, while no circulating mutation was found among patients with PI3KCA wild-type tumours.
    DOI:  https://doi.org/10.1038/s41598-021-02643-y
  8. Cancer Res. 2021 Dec 15. 81(24): 6074-6077
    How Compensatory Mechanisms and Adaptive Rewiring Have Shaped Our Understanding of Therapeutic Resistance in Cancer.
    Johann S Bergholz, Jean J Zhao.
      Therapeutic resistance to targeted therapies by tumor cells is a common and serious problem in the clinic. Increased understanding of the molecular mechanisms that underly resistance is necessary for the rational design and improvement of effective pharmacologic treatment strategies. The landmark study by O'Reilly and colleagues published in Cancer Research in 2006 provided valuable insights into nongenomic adaptive rewiring and compensatory mechanisms responsible for mediating resistance to targeted inhibition of the PI3K-AKT-mTOR pathway, and how tumor cells regulate signaling pathways via negative feedback loops. These findings have proven fundamental for guiding current efforts to develop effective combination treatments and provided a blueprint for research studies aimed at understanding the intricacies of cellular signaling.See related article by O'Reilly and colleagues, Cancer Res 2006;66:1500-8.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-3605
  9. Eur J Med Chem. 2021 Dec 04. pii: S0223-5234(21)00888-6. [Epub ahead of print]228 114039
    Molecular design of dual inhibitors of PI3K and potential molecular target of cancer for its treatment: A review.
    Yuanze Wang, Micky Tortorella.
      Aberrant activation of the phosphoinositide 3-kinase (PI3K) signaling network is a key event in many human cancers and therefore enormous efforts have been made in the development of PI3K inhibitors. However, due to intrinsic and acquired resistance as well as poor drug tolerance, limited therapeutic efficacy has been achieved with these agents. In view of the fact that PI3K inhibitors can show synergistic antitumor effects with other cancer agents, namely mammalian target of rapamycin (mTOR) inhibitors, histone deacetylase (HDAC) inhibitors and mitogen-activated protein kinase (MEK) inhibitors, dual inhibition of both targets by a single-molecule is regarded as a promising complementary or alternative therapeutic strategy to overcome the drawbacks of just PI3K monotherapy. In this review, we discuss the theoretical foundation for designing PI3K-based dual-target inhibitors and summarize the structure-activity relationships and clinical progress of these dual-binding agents.
    Keywords:  Anticancer; Dual-target inhibitors; HDAC; MEK; PI3K; mTOR
    DOI:  https://doi.org/10.1016/j.ejmech.2021.114039
  10. Cell Metab. 2021 Dec 09. pii: S1550-4131(21)00541-6. [Epub ahead of print]
    TOX4, an insulin receptor-independent regulator of hepatic glucose production, is activated in diabetic liver.
    Liheng Wang, Junjie Yu, Qiuzhong Zhou, Xiaobo Wang, Maria Mukhanova, Wen Du, Lei Sun, Utpal B Pajvani, Domenico Accili.
      Increased hepatic glucose production (HGP) contributes to hyperglycemia in type 2 diabetes. Hormonal regulation of this process is primarily, but not exclusively, mediated by the AKT-FoxO1 pathway. Here, we show that cAMP and dexamethasone regulate the high-mobility group superfamily member TOX4 to mediate HGP, independent of the insulin receptor/FoxO1 pathway. TOX4 inhibition decreases glucose production in primary hepatocytes and liver and increases glucose tolerance. Combined genetic ablation of TOX4 and FoxO1 in liver has additive effects on glucose tolerance and gluconeogenesis. Moreover, TOX4 ablation fails to reverse the metabolic derangement brought by insulin receptor knockout. TOX4 expression is increased in livers of patients with steatosis and diabetes and in diet-induced obese and db/db mice. In the latter two murine models, knockdown Tox4 decreases glycemia and improves glucose tolerance. We conclude that TOX4 is an insulin receptor-independent regulator of HGP and a candidate contributor to the pathophysiology of diabetes.
    Keywords:  TOX2, transcription regulation, HGP, type 2 diabetes
    DOI:  https://doi.org/10.1016/j.cmet.2021.11.013
  11. iScience. 2021 Dec 17. 24(12): 103528
    Smurf1 silencing restores PTEN expression that ameliorates progression of human glioblastoma and sensitizes tumor cells to mTORC1/C2 inhibitor Torin1.
    Qin Xia, Wenxuan Li, Sakhawat Ali, Mengchuan Xu, Yang Li, Shengzhen Li, Xinyi Meng, Liqun Liu, Lei Dong.
      Amplification of ubiquitin E3 ligase Smurf1 promotes degradation of PTEN leading to hyperactivation of the Akt/mTORC1 pathway. However, inhibitors of this pathway have not hitherto yielded promising results in clinical studies because of strong drug resistance. Here, we investigated Smurf1 expression in various glioblastoma (GB) cell lines and patient tissues. The therapeutic efficacy of Smurf1 silencing and Torin1 treatment was assessed in GB cells and orthotopic mouse model. We found Smurf1 loss elevates PTEN levels that interrupt the epidermal growth factor receptor pathway activity. Cotreatment with Smurf1 silencing and mTORC1/C2 inhibitor Torin1 remarkably decreased phosphorylation of Akt, and mTORC1 downstream targets 4EBP1 and S6K resulting in synergistic inhibitory effects. Smurf1 knockdown in orthotopic GB mouse model impaired tumor growth and enhanced cytotoxicity of Torin1. Together, these findings suggest a rational combination of Smurf1 inhibition and Torin1 as a promising new avenue to circumvent PI3K/Akt pathway-driven tumor progression and drug resistance.
    Keywords:  Molecular biology; Oncology
    DOI:  https://doi.org/10.1016/j.isci.2021.103528
  12. Curr Diab Rep. 2021 Dec 13. 21(12): 62
    Patient-Centered Diabetes Care of Cancer Patients.
    Anupam Kotwal, Yee-Ming M Cheung, Grace Cromwell, Andjela Drincic, Houry Leblebjian, Zoe Quandt, Robert J Rushakoff, Marie E McDonnell.
      PURPOSE OF REVIEW: There is a bidirectional relationship between cancer and diabetes, with one condition influencing the prognosis of the other. Multiple cancer therapies cause diabetes including well-established medications such as glucocorticoids and novel cancer therapies such as immune checkpoint inhibitors (CPIs) and phosphoinositide 3-kinase (PI3K) inhibitors.RECENT FINDINGS: The nature and severity of diabetes caused by each therapy differ, with some predominantly mediated by insulin resistance, such as PI3K inhibitors and glucocorticoids, while others by insulin deficiency, such as CPIs. Studies have demonstrated diabetes from CPIs to be more rapidly progressing than conventional type 1 diabetes. There remains a scarcity of published guidance for the screening, diagnosis, and management of hyperglycemia and diabetes from these therapies. The need for such guidance is critical because diabetes management in the cancer patient is complex, individualized, and requires inter-disciplinary care. In the present narrative review, we synthesize and summarize the most relevant literature pertaining to diabetes and hyperglycemia in the setting of these cancer therapies and provide an updated patient-centered framework for their evaluation and management.
    Keywords:  Diabetes mellitus; Glucocorticoid; Hyperglycemia; Immune checkpoint inhibitor; PI3 kinase inhibitor
    DOI:  https://doi.org/10.1007/s11892-021-01435-y
  13. Clin Cancer Res. 2021 Dec 14. pii: clincanres.2498.2021. [Epub ahead of print]
    Functional Mapping of AKT Signaling and Biomarkers of Response From the FAIRLANE Trial of Neoadjuvant Ipatasertib Plus Paclitaxel for Triple-Negative Breast Cancer.
    Zhen Shi, Julia Wulfkuhle, Malgorzata Nowicka, Rosa I Gallagher, Cristina Saura, Paolo G Nuciforo, Isabel Calvo, Jay Andersen, José Luis Passos-Coelho, Miguel J Gil-Gil, Begoña Bermejo, Debra A Pratt, Eva M Ciruelos, Patricia Villagrasa, Matthew J Wongchenko, Emanuel F Petricoin, Mafalda Oliveira, Steven J Isakoff.
      PURPOSE: Despite extensive genomic and transcriptomic profiling, it remains unknown how signaling pathways are differentially activated and how tumors are differentially sensitized to certain perturbations. Here, we aim to characterize AKT signaling activity and its association with other genomic or immunohistochemistry-based PI3K/AKT pathway biomarkers as well as the clinical activity of ipatasertib (AKT inhibitor) in the FAIRLANE trial.EXPERIMENTAL DESIGN: In FAIRLANE, 151 patients with early triple-negative breast cancer were randomized 1:1 to receive paclitaxel with ipatasertib or placebo for 12 weeks prior to surgery. Adding ipatasertib did not increase pathologic complete response rate and numerically improved overall response rate by magnetic resonance imaging (MRI). We used reverse-phase protein microarrays (RPPA) to examine the total level and/or phosphorylation states of over 100 proteins in various signaling or cell processes including PI3K/AKT and mTOR signaling. 125 baseline and 127 on-treatment samples were evaluable by RPPA, with 110 paired samples at both time points.
    RESULTS: Tumors with genomic/protein alterations in PIK3CA/AKT1/PTEN were associated with higher levels of AKT phosphorylation. In addition, phosphorylated(p)AKT levels exhibited a significant association with enriched clinical benefit of ipatasertib, and identified patients who received benefit in the absence of PIK3CA/AKT1/PTEN alterations. Ipatasertib treatment led to a down-regulation of AKT/mTORC1 signaling, which was more pronounced among the tumors with PIK3CA/AKT1/PTEN alterations or among the responders to the treatment.
    CONCLUSIONS: We showed that the high baseline pAKT levels are associated with the alterations of PI3K/AKT pathway components and enriched benefit of ipatasertib in TNBC.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-21-2498
  14. Nat Commun. 2021 Dec 14. 12(1): 7190
    Metabolic drug survey highlights cancer cell dependencies and vulnerabilities.
    Tea Pemovska, Johannes W Bigenzahn, Ismet Srndic, Alexander Lercher, Andreas Bergthaler, Adrián César-Razquin, Felix Kartnig, Christoph Kornauth, Peter Valent, Philipp B Staber, Giulio Superti-Furga.
      Interrogation of cellular metabolism with high-throughput screening approaches can unravel contextual biology and identify cancer-specific metabolic vulnerabilities. To systematically study the consequences of distinct metabolic perturbations, we assemble a comprehensive metabolic drug library (CeMM Library of Metabolic Drugs; CLIMET) covering 243 compounds. We, next, characterize it phenotypically in a diverse panel of myeloid leukemia cell lines and primary patient cells. Analysis of the drug response profiles reveals that 77 drugs affect cell viability, with the top effective compounds targeting nucleic acid synthesis, oxidative stress, and the PI3K/mTOR pathway. Clustering of individual drug response profiles stratifies the cell lines into five functional groups, which link to specific molecular and metabolic features. Mechanistic characterization of selective responses to the PI3K inhibitor pictilisib, the fatty acid synthase inhibitor GSK2194069, and the SLC16A1 inhibitor AZD3965, bring forth biomarkers of drug response. Phenotypic screening using CLIMET represents a valuable tool to probe cellular metabolism and identify metabolic dependencies at large.
    DOI:  https://doi.org/10.1038/s41467-021-27329-x
  15. Genes Cells. 2021 Dec 16.
    Sima, a Drosophila homolog of HIF-1α, in fat body tissue inhibits larval body growth by inducing Tribbles gene expression.
    Koji Noguchi, Kyosuke Yokozeki, Yuko Tanaka, Yasuhiro Suzuki, Kazuki Nakajima, Takashi Nishimura, Nobuhito Goda.
      Limited oxygen availability impairs normal body growth, although the underlying mechanisms are not fully understood. In Drosophila, hypoxic responses in the larval fat body (FB) disturb the secretion of insulin-like peptides from the brain, inhibiting body growth. However, the cell-autonomous effects of hypoxia on the insulin signaling pathway in larval FB have been underexplored. In this study, we aimed to examine the effects of overexpression of Sima, a Drosophila hypoxia inducible factor-1 (HIF-1) α homolog and a key component of HIF-1 transcription factor essential for hypoxic adaptation, on the insulin signaling pathway in larval FB. Forced expression of Sima in FB reduced the larval body growth with reduced Akt phosphorylation levels in FB cells and increased hemolymph sugar levels. Sima-mediated growth inhibition was reversed by overexpression of TOR or suppression of FOXO. After Sima overexpression, larvae showed higher expression levels of Tribbles, a negative regulator of Akt activity, and a simultaneous knockdown of Tribbles completely abolished the effects of Sima on larval body growth. Furthermore, a reporter analysis revealed Tribbles as a direct target gene of Sima. These results suggest that Sima in FB evokes Tribbles-mediated insulin resistance and consequently protects against aberrant insulin-dependent larval body growth under hypoxia.
    Keywords:   Tribbles ; HIF-1; fat body; insulin signaling; larval body growth
    DOI:  https://doi.org/10.1111/gtc.12913
  16. F1000Res. 2021 ;pii: ISCB Comm J-448. [Epub ahead of print]10
    scNetViz: from single cells to networks using Cytoscape.
    Krishna Choudhary, Elaine C Meng, J Javier Diaz-Mejia, Gary D Bader, Alexander R Pico, John H Morris.
      Single-cell RNA-sequencing (scRNA-seq) has revolutionized molecular biology and medicine by enabling high-throughput studies of cellular heterogeneity in diverse tissues. Applying network biology approaches to scRNA-seq data can provide useful insights into genes driving heterogeneous cell-type compositions of tissues. Here, we present scNetViz -  a Cytoscape app to aid biological interpretation of cell clusters in scRNA-seq data using network analysis. scNetViz calculates the differential expression of each gene across clusters and then creates a cluster-specific gene functional interaction network between the significantly differentially expressed genes for further analysis, such as pathway enrichment analysis. To automate a complete data analysis workflow, scNetViz integrates parts of the Scanpy software, which is a popular Python package for scRNA-seq data analysis, with Cytoscape apps such as stringApp, cyPlot, and enhancedGraphics. We describe our implementation of methods for accessing data from public single cell atlas projects, differential expression analysis, visualization, and automation. scNetViz enables users to analyze data from public atlases or their own experiments, which we illustrate with two use cases. Analysis can be performed via the Cytoscape GUI or CyREST programming interface using R (RCy3) or Python (py4cytoscape).
    Keywords:  App; Cytoscape; Expression analysis; Network biology; Single cell; scRNA-seq
    DOI:  https://doi.org/10.12688/f1000research.52460.1
  17. Genome Med. 2021 Dec 16. 13(1): 187
    Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data.
    Coral Fustero-Torre, María José Jiménez-Santos, Santiago García-Martín, Carlos Carretero-Puche, Luis García-Jimeno, Vadym Ivanchuk, Tomás Di Domenico, Gonzalo Gómez-López, Fátima Al-Shahrour.
      We present Beyondcell, a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments. Our method calculates an enrichment score in a collection of drug signatures, delineating therapeutic clusters (TCs) within cellular populations. Additionally, Beyondcell determines the therapeutic differences among cell populations and generates a prioritised sensitivity-based ranking in order to guide drug selection. We performed Beyondcell analysis in five single-cell datasets and demonstrated that TCs can be exploited to target malignant cells both in cancer cell lines and tumour patients. Beyondcell is available at: https://gitlab.com/bu_cnio/beyondcell .
    Keywords:  Drug repositioning; Intratumoural heterogeneity; Personalised therapy; Single-cell RNA-seq; Therapeutic clusters
    DOI:  https://doi.org/10.1186/s13073-021-01001-x
  18. Nat Metab. 2021 Dec 13.
    What is the most appropriate covariate in ANCOVA when analysing metabolic rate?
    Sam Virtue, Christopher J Lelliott, Antonio Vidal-Puig.
      
    DOI:  https://doi.org/10.1038/s42255-021-00505-5
  19. Mol Oncol. 2021 Dec 17.
    KRAS mutation-independent downregulation of MAPK/PI3K signaling in colorectal cancer.
    Kuen Kuen Lam, Choong Leong Tang, Emile Tan, Siew Heng Wong, Peh Yean Cheah.
      KRAS is a gatekeeper gene in human colorectal tumorigenesis. KRAS is "undruggable", hence efforts have been diverted to inhibit downstream RAF/MEK/ERK and PI3K/Akt signaling. Nevertheless, none of these inhibitors has progressed to clinical use despite extensive trials. We examined levels of phospho-ERK1/2(T202/Y204) and phospho-Akt1/2/3(S473) in human colorectal tumor compared to matched mucosa with semi-quantitative near-infrared western blot and confocal fluorescence immunohistochemistry imaging. Surprisingly, 75.5% (25/33) of tumors had lower or equivalent phospho-ERK1/2 and 96.9% (31/32) of tumors had lower phospho-Akt1/2/3 compared to matched mucosa, irrespective of KRAS mutation status. In contrast, we discovered KRAS-dependent SOX9 upregulation in 28 of the 31 (90.3%) tumors. These observations were substantiated by analysis of the public domain transcriptomics The Cancer Genome Atlas (TCGA) and NCBI Gene Expression Omnibus (GEO) datasets and proteomics Clinical Proteomic Tumor Analysis Consortium (CPTAC) dataset. These data suggest that RAF/MEK/ERK and PI3K/Akt signaling are unlikely to be activated in most human colorectal cancer.
    Keywords:  CPTAC; KRAS signaling; MAPK/PI3K; SOX9; TCGA; colorectal tumorigenesis
    DOI:  https://doi.org/10.1002/1878-0261.13163
  20. Dev Biol. 2021 Dec 13. pii: S0012-1606(21)00250-5. [Epub ahead of print]
    Lymphatic endothelial cell fate specification in the mammalian embryo: An historical perspective.
    Guillermo Oliver.
      Development of the mammalian lymphatic vasculature is a stepwise process requiring the specification of lymphatic endothelial cell progenitors in the embryonic veins, and their subsequent budding to give rise to most of the mature lymphatic vasculature. In mice, formation of the lymphatic vascular network starts inside the cardinal vein at around E9.5 when a subpopulation of venous endothelial cells gets committed into the lymphatic lineage by their acquisition of Prox1 expression. Identification of critical genes regulating lymphatic development facilitated the detailed cellular and molecular characterization of some of the cellular and molecular mechanisms regulating the early steps leading to the formation of the mammalian lymphatic vasculature. A better understanding of basic aspects of early lymphatic development, and the availability of novel tools and animal models has been instrumental in the identification of important novel functional roles of this vasculature network.
    Keywords:  Embryo; Lymphatic endothelial cell; Lymphatic progenitor; Lymphatic progenitors; Lymphatics; Mouse; Prox1; Vegfr3
    DOI:  https://doi.org/10.1016/j.ydbio.2021.12.005
  21. Methods Mol Biol. 2022 ;2420 63-72
    Mass Spectrometry-Based Analytical Strategy for Single-Cell Proteomics.
    Ákos Végvári.
      Single-cell proteomics is a novel application area of bioanalysis aiming to characterize proteomes of isolated single cells, which in contrast to bulk cell analysis has the potential to reveal a more detailed heterogeneity of cell populations. Although several antibody-based targeted approaches have been readily available for single-cell analysis, so far only the mass spectrometry methodology can offer unbiased proteome profiling. While this strategy has only recently emerged, it has already demonstrated unparalleled analytical power quantifying >1000 proteins in single cells. Several applications of a general isobaric labeling scheme for multiplexed sample preparation and data acquisition have been outlined using various cell types and instrumentation. This chapter provides a typical example of mass spectrometry-based single-cell proteomics workflow with details about the critical steps of analysis and alternative methods useful for optimization purposes.
    Keywords:  Clean sample preparation; Isobaric labeling; Mass spectrometry; Single-cell proteomics
    DOI:  https://doi.org/10.1007/978-1-0716-1936-0_6
  22. Cell Rep. 2021 Dec 14. pii: S2211-1247(21)01597-7. [Epub ahead of print]37(11): 110103
    The onset of circulation triggers a metabolic switch required for endothelial to hematopoietic transition.
    Emanuele Azzoni, Vincent Frontera, Giorgio Anselmi, Christina Rode, Chela James, Elitza M Deltcheva, Atanasiu S Demian, John Brown, Cristiana Barone, Arianna Patelli, Joe R Harman, Matthew Nicholls, Simon J Conway, Edward Morrissey, Sten Eirik W Jacobsen, Duncan B Sparrow, Adrian L Harris, Tariq Enver, Marella F T R de Bruijn.
      Hematopoietic stem cells (HSCs) emerge during development from the vascular wall of the main embryonic arteries. The onset of circulation triggers several processes that provide critical external factors for HSC generation. Nevertheless, it is not fully understood how and when the onset of circulation affects HSC emergence. Here we show that in Ncx1-/- mouse embryos devoid of circulation the HSC lineage develops until the phenotypic pro-HSC stage. However, these cells reside in an abnormal microenvironment, fail to activate the hematopoietic program downstream of Runx1, and are functionally impaired. Single-cell transcriptomics shows that during the endothelial-to-hematopoietic transition, Ncx1-/- cells fail to undergo a glycolysis to oxidative phosphorylation metabolic switch present in wild-type cells. Interestingly, experimental activation of glycolysis results in decreased intraembryonic hematopoiesis. Our results suggest that the onset of circulation triggers metabolic changes that allow HSC generation to proceed.
    DOI:  https://doi.org/10.1016/j.celrep.2021.110103
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