bims-pideca 2021-01-03 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2021‒01‒03
eighteen papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute

mTORC2 Assembly Is Regulated by USP9X-Mediated Deubiquitination of RICTOR.
The Organoid Cell Atlas.
Sustained mTORC1 activity during palbociclib-induced growth arrest triggers senescence in ER+ breast cancer cells.
Menstrual disorders associated with sirolimus treatment.
Structure-Based Drug Design and Synthesis of PI3Kα-Selective Inhibitor (PF-06843195).
Dis3L2 regulates cell proliferation and tissue growth though a conserved mechanism.
Phosphoinositide Signaling and Mechanotransduction in Cardiovascular Biology and Disease.
Active integrins regulate white adipose tissue insulin sensitivity and brown fat thermogenesis.
Increased demand for NAD+ relative to ATP drives aerobic glycolysis.
Targeting the mutant PIK3CA gene by DNA-alkylating pyrrole imidazole polyamide in cervical cancer.
Microenvironmental Determinants of Breast Cancer Metastasis: Focus on the Crucial Interplay Between Estrogen and Insulin/Insulin-Like Growth Factor Signaling.
The crosstalk of hedgehog, PI3K and Wnt pathways in diabetes.
CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy.
PIK3CA somatic alterations in invasive breast cancers: different spectrum from Caucasians to Chinese detected by next generation sequencing.
Driver versus navigator causation in biology: the case of insulin and fasting glucose.
Vascular Tumor Recapitulated in Endothelial Cells from hiPSCs Engineered to Express the SERPINE1-FOSB Translocation.
An AKT2-specific nanobody that targets the hydrophobic motif induces cell cycle arrest, autophagy and loss of focal adhesions in MDA-MB-231 cells.
"Treasure Your Exceptions"-Studying Human Extreme Phenotypes to Illuminate Metabolic Health and Disease: The 2019 Banting Medal for Scientific Achievement Lecture.

Cell Rep. 2020 Dec 29. pii: S2211-1247(20)31553-9. [Epub ahead of print]33(13): 108564

mTORC2 Assembly Is Regulated by USP9X-Mediated Deubiquitination of RICTOR.

Lidia Wrobel, Farah H Siddiqi, Sandra M Hill, Sung Min Son, Cansu Karabiyik, Hyunjeong Kim, David C Rubinsztein.

  The mechanistic target of rapamycin complex 2 (mTORC2) controls cell metabolism and survival in response to environmental inputs. Dysregulation of mTORC2 signaling has been linked to diverse human diseases, including cancer and metabolic disorders, highlighting the importance of a tightly controlled mTORC2. While mTORC2 assembly is a critical determinant of its activity, the factors regulating this event are not well understood, and it is unclear whether this process is regulated by growth factors. Here, we present data, from human cell lines and mice, describing a mechanism by which growth factors regulate ubiquitin-specific protease 9X (USP9X) deubiquitinase to stimulate mTORC2 assembly and activity. USP9X removes Lys63-linked ubiquitin from RICTOR to promote its interaction with mTOR, thereby facilitating mTORC2 signaling. As mTORC2 is central for cellular homeostasis, understanding the mechanisms regulating mTORC2 activation toward its downstream targets is vital for our understanding of physiological processes and for developing new therapeutic strategies in pathology.

Keywords:  RICTOR; USP9X; growth factor signaling; mTORC2; mechanistic target of rapamycin complex 2; posttranslational modification; ubiquitin-specific protease 9X

DOI:  https://doi.org/10.1016/j.celrep.2020.108564
Nat Biotechnol. 2020 Dec 31.

The Organoid Cell Atlas.

Christoph Bock, Michael Boutros, J Gray Camp, Laura Clarke, Hans Clevers, Juergen A Knoblich, Prisca Liberali, Aviv Regev, Anne C Rios, Oliver Stegle, Hendrik G Stunnenberg, Sarah A Teichmann, Barbara Treutlein, Robert G J Vries, .

DOI: https://doi.org/10.1038/s41587-020-00762-x
Cell Cycle. 2020 Dec 28. 1-16

Sustained mTORC1 activity during palbociclib-induced growth arrest triggers senescence in ER+ breast cancer cells.

Reeja S Maskey, Fang Wang, Elyssa Lehman, Yiqun Wang, Natasha Emmanuel, Wenyan Zhong, Guixian Jin, Robert T Abraham, Kim T Arndt, Jeremy S Myers, Anthony Mazurek.

  Palbociclib, a selective CDK4/6 kinase inhibitor, is approved in combination with endocrine therapies for the treatment of advanced estrogen receptor positive (ER+) breast cancer. In pre-clinical cancer models, CDK4/6 inhibitors act primarily as cytostatic agents. In two commonly studied ER+ breast cancer cell lines (MCF7 and T47D), CDK4/6 inhibition drives G1-phase arrest and the acquisition of a senescent-like phenotype, both of which are reversible upon palbociclib withdrawal (incomplete senescence). Here we identify an ER+ breast cancer cell line, CAMA1, in which palbociclib treatment induces irreversible cell cycle arrest and senescence (complete senescence). In stark contrast to T47D and MCF7 cells, mTORC1 activity is not stably suppressed in CAMA1 cells during palbociclib treatment. Importantly, inhibition of mTORC1 signaling either by the mTORC1 inhibitor rapamycin or by knockdown of Raptor, a unique component of mTORC1, during palbociclib treatment of CAMA1 cells blocks the induction of complete senescence. These results indicate that sustained mTORC1 activity promotes complete senescence in ER+ breast cancer cells during CDK4/6 inhibitor-induced cell cycle arrest. Consistent with this mechanism, genetic depletion of TSC2, a negative regulator of mTORC1, in MCF7 cells resulted in sustained mTORC1 activity during palbociclib treatment and evoked a complete senescence response. These findings demonstrate that persistent mTORC1 signaling during palbociclib-induced G1 arrest is a potential liability for ER+ breast cancer cells, and suggest a strategy for novel drug combinations with palbociclib.

Keywords:  Palbociclib; cdk4/6; er+ Breast Cancer; mTORC1; senescence

DOI:  https://doi.org/10.1080/15384101.2020.1859195
Pediatr Blood Cancer. 2020 Dec 27. e28867

Menstrual disorders associated with sirolimus treatment.

Paloma Triana, Juan Carlos López-Gutierrez.

  INTRODUCTION: Sirolimus has become a pillar in the treatment of vascular anomalies due to its inhibition of the mammalian target of rapamycin (mTOR). Adverse effects include metabolic and hematologic disorders among others, although menstrual disorders have not been well described.MATERIALS AND METHODS: Retrospective review of patients with vascular anomalies on sirolimus treatment was performed. Patients presenting menstrual alterations were included.
MAIN RESULTS: One hundred and thirty-six patients with vascular anomalies on treatment with sirolimus were reviewed, finding seven women out of 74 (9.4%) who presented menstrual alterations attributable to the treatment. These seven patients presented with different vascular malformations and three showed pathogenic variants in phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) in affected tissue. Partial response in six and stability in one patient was obtained after treatment, administered for an average of 27.5 months (6-48). Five patients have completed treatment and two patients continue on after 12 and 15 months, respectively. All patients reported regular menstrual cycles prior to sirolimus treatment. One patient presented with amenorrhea for 4 months after treatment initiation that later spontaneously resolved. The other six patients presented with hypermenorrhea, four of them associating metrorrhagia. Most patients presented with mild menstrual alterations, without needing dose reduction or withdrawal, although one discontinued sirolimus due to hypermenorrhea, metrorrhagia, and hematuria. After sirolimus withdrawal, regular menstrual cycles were restored in five patients.
CONCLUSION: Sirolimus treatment can produce menstrual disorders as adverse effects. Although mild and reversible upon dose reduction or cessation of treatment, patients and physicians should be aware on this potential side effect.

Keywords:  amenorrhea; menstrual disorders; metrorrhagia; rapamycin; sirolimus; vascular anomalies

DOI:  https://doi.org/10.1002/pbc.28867
J Med Chem. 2020 Dec 24.

Structure-Based Drug Design and Synthesis of PI3Kα-Selective Inhibitor (PF-06843195).

Hengmiao Cheng, Suvi T M Orr, Simon Bailey, Alexei Brooun, Ping Chen, Judith G Deal, Yali L Deng, Martin P Edwards, Gary M Gallego, Neil Grodsky, Buwen Huang, Mehran Jalaie, Stephen Kaiser, Robert S Kania, Susan E Kephart, Jennifer Lafontaine, Martha A Ornelas, Mason Pairish, Simon Planken, Hong Shen, Scott Sutton, Luke Zehnder, Chau D Almaden, Shubha Bagrodia, Matthew D Falk, Hovhannes J Gukasyan, Caroline Ho, Xiaolin Kang, Rachel E Kosa, Ling Liu, Mary E Spilker, Sergei Timofeevski, Ravi Visswanathan, Zhenxiong Wang, Fanxiu Meng, Shijian Ren, Li Shao, Feng Xu, John C Kath.

The phosphoinositide 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) signaling pathway is a frequently dysregulated pathway in human cancer, and PI3Kα is one of the most frequently mutated kinases in human cancer. A PI3Kα-selective inhibitor may provide the opportunity to spare patients the side effects associated with broader inhibition of the class I PI3K family. Here, we describe our efforts to discover a PI3Kα-selective inhibitor by applying structure-based drug design (SBDD) and computational analysis. A novel series of compounds, exemplified by 2,2-difluoroethyl (3S)-3-{[2'-amino-5-fluoro-2-(morpholin-4-yl)-4,5'-bipyrimidin-6-yl]amino}-3-(hydroxymethyl)pyrrolidine-1-carboxylate (1) (PF-06843195), with high PI3Kα potency and unique PI3K isoform and mTOR selectivity were discovered. We describe here the details of the design and synthesis program that lead to the discovery of 1.

DOI: https://doi.org/10.1021/acs.jmedchem.0c01652
PLoS Genet. 2020 Dec 28. 16(12): e1009297

Dis3L2 regulates cell proliferation and tissue growth though a conserved mechanism.

Benjamin P Towler, Amy L Pashler, Hope J Haime, Katarzyna M Przybyl, Sandra C Viegas, Rute G Matos, Simon J Morley, Cecilia M Arraiano, Sarah F Newbury.

Dis3L2 is a highly conserved 3'-5' exoribonuclease which is mutated in the human overgrowth disorders Perlman syndrome and Wilms' tumour of the kidney. Using Drosophila melanogaster as a model system, we have generated a new dis3L2 null mutant together with wild-type and nuclease-dead genetic lines in Drosophila to demonstrate that the catalytic activity of Dis3L2 is required to control cell proliferation. To understand the cellular pathways regulated by Dis3L2 to control proliferation, we used RNA-seq on dis3L2 mutant wing discs to show that the imaginal disc growth factor Idgf2 is responsible for driving the wing overgrowth. IDGFs are conserved proteins homologous to human chitinase-like proteins such as CHI3L1/YKL-40 which are implicated in tissue regeneration as well as cancers including colon cancer and non-small cell lung cancer. We also demonstrate that loss of DIS3L2 in human kidney HEK-293T cells results in cell proliferation, illustrating the conservation of this important cell proliferation pathway. Using these human cells, we show that loss of DIS3L2 results in an increase in the PI3-Kinase/AKT signalling pathway, which we subsequently show to contribute towards the proliferation phenotype in Drosophila. Our work therefore provides the first mechanistic explanation for DIS3L2-induced overgrowth in humans and flies and identifies an ancient proliferation pathway controlled by Dis3L2 to regulate cell proliferation and tissue growth.

DOI: https://doi.org/10.1371/journal.pgen.1009297
Front Cell Dev Biol. 2020 ;8 595849

Phosphoinositide Signaling and Mechanotransduction in Cardiovascular Biology and Disease.

Amanda Krajnik, Joseph A Brazzo, Kalyanaraman Vaidyanathan, Tuhin Das, Javier Redondo-Muñoz, Yongho Bae.

  Phosphoinositides, which are membrane-bound phospholipids, are critical signaling molecules located at the interface between the extracellular matrix, cell membrane, and cytoskeleton. Phosphoinositides are essential regulators of many biological and cellular processes, including but not limited to cell migration, proliferation, survival, and differentiation, as well as cytoskeletal rearrangements and actin dynamics. Over the years, a multitude of studies have uniquely implicated phosphoinositide signaling as being crucial in cardiovascular biology and a dominant force in the development of cardiovascular disease and its progression. Independently, the cellular transduction of mechanical forces or mechanotransduction in cardiovascular cells is widely accepted to be critical to their homeostasis and can drive aberrant cellular phenotypes and resultant cardiovascular disease. Given the versatility and diversity of phosphoinositide signaling in the cardiovascular system and the dominant regulation of cardiovascular cell functions by mechanotransduction, the molecular mechanistic overlap and extent to which these two major signaling modalities converge in cardiovascular cells remain unclear. In this review, we discuss and synthesize recent findings that rightfully connect phosphoinositide signaling to cellular mechanotransduction in the context of cardiovascular biology and disease, and we specifically focus on phosphatidylinositol-4,5-phosphate, phosphatidylinositol-4-phosphate 5-kinase, phosphatidylinositol-3,4,5-phosphate, and phosphatidylinositol 3-kinase. Throughout the review, we discuss how specific phosphoinositide subspecies have been shown to mediate biomechanically sensitive cytoskeletal remodeling in cardiovascular cells. Additionally, we discuss the direct interaction of phosphoinositides with mechanically sensitive membrane-bound ion channels in response to mechanical stimuli. Furthermore, we explore the role of phosphoinositide subspecies in association with critical downstream effectors of mechanical signaling in cardiovascular biology and disease.

Keywords:  PI3K; PIP2; PIP3; actin cytoskeleton; cardiovascular mechanotransduction; focal adhesion; ion channel; phosphoinositides

DOI:  https://doi.org/10.3389/fcell.2020.595849
Mol Metab. 2020 Dec 21. pii: S2212-8778(20)30221-0. [Epub ahead of print] 101147

Active integrins regulate white adipose tissue insulin sensitivity and brown fat thermogenesis.

Francisco Javier Ruiz-Ojeda, Jiefu Wang, Theresa Bäcker, Martin Krueger, Samira Zamani, Simon Rosowski, Tim Gruber, Yasuhiro Onogi, Annette Feuchtinger, Tim J Schulz, Reinhard Fässler, Timo D Müller, Cristina García-Cáceres, Matthias Meier, Matthias Blüher, Siegfried Ussar.

  OBJECTIVE: Reorganization of the extracellular matrix is a prerequisite for healthy adipose tissue expansion, whereas fibrosis is a key feature of adipose dysfunction and inflammation. However, very little is known about the direct effects of impaired cell-matrix interaction in adipocyte function and insulin sensitivity. The objective of this study was to determine whether integrin activity can regulate insulin sensitivity in adipocytes and thereby systemic metabolism.METHODS: We characterized integrin activity in adipose tissue and its consequences on whole body metabolism using adipose selective deletion of β1 integrin (Itgb1adipo-cre) and Kindlin-2 (Kind2adipo-cre) in mice.
RESULTS: We demonstrate that integrin signaling regulates white adipocyte insulin action and systemic metabolism. Consequently, loss of adipose integrin activity, similar to loss of adipose insulin receptors, results in a lipodystrophy-like phenotype and systemic insulin resistance. However, brown adipose tissue of Kind2adipo-cre and Itgb1adipo-cre mice is chronically hyperactivated, and has increased substrate delivery, reduced endothelial basement membrane thickness, and increased endothelial vesicular transport.
CONCLUSION: Thus, we establish integrin-extracellular matrix interactions as key regulators of white and brown adipose tissue function and whole body metabolism.

Keywords:  Integrins; Kindlin-2; adipose tissue; brown fat; insulin receptor; insulin resistance; lipodystrophy; obesity

DOI:  https://doi.org/10.1016/j.molmet.2020.101147
Mol Cell. 2020 Dec 22. pii: S1097-2765(20)30904-7. [Epub ahead of print]

Increased demand for NAD+ relative to ATP drives aerobic glycolysis.

Alba Luengo, Zhaoqi Li, Dan Y Gui, Lucas B Sullivan, Maria Zagorulya, Brian T Do, Raphael Ferreira, Adi Naamati, Ahmed Ali, Caroline A Lewis, Craig J Thomas, Stefani Spranger, Nicholas J Matheson, Matthew G Vander Heiden.

  Aerobic glycolysis, or preferential fermentation of glucose-derived pyruvate to lactate despite available oxygen, is associated with proliferation across many organisms and conditions. To better understand that association, we examined the metabolic consequence of activating the pyruvate dehydrogenase complex (PDH) to increase pyruvate oxidation at the expense of fermentation. We find that increasing PDH activity impairs cell proliferation by reducing the NAD+/NADH ratio. This change in NAD+/NADH is caused by increased mitochondrial membrane potential that impairs mitochondrial electron transport and NAD+ regeneration. Uncoupling respiration from ATP synthesis or increasing ATP hydrolysis restores NAD+/NADH homeostasis and proliferation even when glucose oxidation is increased. These data suggest that when demand for NAD+ to support oxidation reactions exceeds the rate of ATP turnover in cells, NAD+ regeneration by mitochondrial respiration becomes constrained, promoting fermentation, despite available oxygen. This argues that cells engage in aerobic glycolysis when the demand for NAD+ is in excess of the demand for ATP.

Keywords:  Aerobic Glycolysis; Cell Metabolism; Fermentation; NAD+; PDK; Warburg Effect

DOI:  https://doi.org/10.1016/j.molcel.2020.12.012
Cancer Sci. 2020 Dec 29.

Targeting the mutant PIK3CA gene by DNA-alkylating pyrrole imidazole polyamide in cervical cancer.

Sakthisri Krishnamurthy, Hiroyuki Yoda, Kiriko Hiraoka, Takahiro Inoue, Jason Lin, Yoshinao Shinozaki, Takayoshi Watanabe, Nobuko Koshikawa, Atsushi Takatori, Hiroki Nagase.

  PIK3CA is the most frequently mutated oncogene in cervical cancer, and somatic mutations in the PIK3CA gene result in increased activity of PI3K. In cervical cancer, the E545K mutation in PIK3CA leads to the elevated cell proliferation and reduced apoptosis. In the present study, we designed and synthesized a novel pyrrole-imidazole polyamide-seco-CBI conjugate, P3AE5K, to target the PIK3CA gene bearing E545K mutation, rendered possible by nuclear access and unique sequence specificity of pyrrole-imidazole polyamides. P3AE5K interacted with double-strand DNA of the coding region containing the E545K mutation. When compared to conventional PI3K inhibitors, P3AE5K demonstrated strong cytotoxicity in E545K-positive cervical cancer cells at lower concentrations. PIK3CA mutant cells exposed to P3AE5K exhibited reduced expression levels of PIK3CA mRNA and protein, and subsequent apoptotic cell death. Moreover, P3AE5K significantly decreased tumor growth in mouse xenograft models derived from PIK3CA mutant cells. Overall, the present data strongly suggest that the alkylating pyrrole-imidazole polyamide P3AE5K should be a promising new drug candidate targeting a constitutively activating mutation of PIK3CA in cervical cancer.

Keywords:  E545K mutation; PI3K inhibitor; PIK3CA gene; cervical cancer; pyrrole-imidazole polyamide-seco-CBI

DOI:  https://doi.org/10.1111/cas.14785
Front Cell Dev Biol. 2020 ;8 608412

Microenvironmental Determinants of Breast Cancer Metastasis: Focus on the Crucial Interplay Between Estrogen and Insulin/Insulin-Like Growth Factor Signaling.

Veronica Vella, Ernestina Marianna De Francesco, Rosamaria Lappano, Maria Grazia Muoio, Livia Manzella, Marcello Maggiolini, Antonino Belfiore.

  The development and progression of the great majority of breast cancers (BCs) are mainly dependent on the biological action elicited by estrogens through the classical estrogen receptor (ER), as well as the alternate receptor named G-protein-coupled estrogen receptor (GPER). In addition to estrogens, other hormones and growth factors, including the insulin and insulin-like growth factor system (IIGFs), play a role in BC. IIGFs cooperates with estrogen signaling to generate a multilevel cross-communication that ultimately facilitates the transition toward aggressive and life-threatening BC phenotypes. In this regard, the majority of BC deaths are correlated with the formation of metastatic lesions at distant sites. A thorough scrutiny of the biological and biochemical events orchestrating metastasis formation and dissemination has shown that virtually all cell types within the tumor microenvironment work closely with BC cells to seed cancerous units at distant sites. By establishing an intricate scheme of paracrine interactions that lead to the expression of genes involved in metastasis initiation, progression, and virulence, the cross-talk between BC cells and the surrounding microenvironmental components does dictate tumor fate and patients' prognosis. Following (i) a description of the main microenvironmental events prompting BC metastases and (ii) a concise overview of estrogen and the IIGFs signaling and their major regulatory functions in BC, here we provide a comprehensive analysis of the most recent findings on the role of these transduction pathways toward metastatic dissemination. In particular, we focused our attention on the main microenvironmental targets of the estrogen-IIGFs interplay, and we recapitulated relevant molecular nodes that orientate shared biological responses fostering the metastatic program. On the basis of available studies, we propose that a functional cross-talk between estrogens and IIGFs, by affecting the BC microenvironment, may contribute to the metastatic process and may be regarded as a novel target for combination therapies aimed at preventing the metastatic evolution.

Keywords:  GPER; breast cancer; estrogen receptor; insulin/IGF signaling; metastasis; targeted therapies; tumor microenvionment

DOI:  https://doi.org/10.3389/fcell.2020.608412
Arch Biochem Biophys. 2020 Dec 29. pii: S0003-9861(20)30751-7. [Epub ahead of print]698 108743

The crosstalk of hedgehog, PI3K and Wnt pathways in diabetes.

Khaled Benchoula, Ishwar S Parhar, Eng Hwa Wong.

  Hyperglycaemia causes pancreatic β-cells to release insulin that then attaches to a specific expression of receptor isoform and reverses high glucose concentrations. It is well known that insulin is capable of initiating insulin-receptor substrate (IRS)/phosphatidylinositol 3-kinase (PI3K)/protein kinase B (PKB) signaling pathways in target cells; such as liver, adipose tissues, and muscles. However, recent discoveries indicate that many other pathways, such as the Hedgehog (Hh) and growth factor-stimulating Wingless-related integration (Wnt) signaling pathways; are activated in hyperglycaemia as well. Although these two pathways are traditionally thought to have a decisive role in cellular growth and differentiation only, recent reports show that they are involved in regulating cellular homeostasis and energy balance. While insulin-activated IRS/PI3K/PKB pathway cascades are primarily known to reduce glucose production, it was recently discovered to increase the Hh signaling pathway's stability, thereby activating the PI3K/PKB/mammalian target of rapamycin complex 2 (mTORC2) signaling pathway. The Hh signaling pathway not only plays a role in lipid metabolism, insulin sensitivity, inflammatory response, diabetes-related complications, but crosstalks with the Wnt signaling pathway resulting in improved insulin sensitivity and decrease inflammatory response in diabetes.

Keywords:  Diabetes; Hedgehog pathway; PI3K pathway; Wnt pathway

DOI:  https://doi.org/10.1016/j.abb.2020.108743
Cell Syst. 2020 Dec 21. pii: S2405-4712(20)30464-6. [Epub ahead of print]

CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy.

Bo Yuan, Ciyue Shen, Augustin Luna, Anil Korkut, Debora S Marks, John Ingraham, Chris Sander.

  Systematic perturbation of cells followed by comprehensive measurements of molecular and phenotypic responses provides informative data resources for constructing computational models of cell biology. Models that generalize well beyond training data can be used to identify combinatorial perturbations of potential therapeutic interest. Major challenges for machine learning on large biological datasets are to find global optima in a complex multidimensional space and mechanistically interpret the solutions. To address these challenges, we introduce a hybrid approach that combines explicit mathematical models of cell dynamics with a machine-learning framework, implemented in TensorFlow. We tested the modeling framework on a perturbation-response dataset of a melanoma cell line after drug treatments. The models can be efficiently trained to describe cellular behavior accurately. Even though completely data driven and independent of prior knowledge, the resulting de novo network models recapitulate some known interactions. The approach is readily applicable to various kinetic models of cell biology. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.

Keywords:  cancer; cell dynamics; combinatorial therapy; dynamical systems; interpretability; machine learning; network pharmacology; perturbation biology; systems biology

DOI:  https://doi.org/10.1016/j.cels.2020.11.013
Breast Cancer. 2021 Jan 01.

PIK3CA somatic alterations in invasive breast cancers: different spectrum from Caucasians to Chinese detected by next generation sequencing.

Minghan Jia, Ning Liao, Bo Chen, Guochun Zhang, Yulei Wang, Xuerui Li, Li Cao, Hsiaopei Mok, Chongyang Ren, Kai Li, Cheukfai Li, Lingzhu Wen, Jiali Lin, Guangnan Wei, Charles M Balch.

  PURPOSE: Somatic alteration of phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) is a crucial therapeutic target in breast cancer (BC) and PI3Kα-specific inhibitor Alpelisib has been used in clinics. This study investigates the PIK3CA alterations in Chinese and Caucasians BC patients for the purpose of selecting anti-PI3K therapy.METHODS: The molecular profile of the PIK3CA gene was analyzed in 412 Chinese patients with untreated invasive BC using a 540 gene next-generation sequencing panel. The results were compared with data of the Caucasian BC patients in The Cancer Genome Atlas (TCGA-white).
RESULTS: PIK3CA alterations were frequently found in BC of estrogen receptor (ER) positive (49.3%, p = 0.024), low ki67 proliferation index (58.3%, p = 0.007) and low pathological grade (grade I/II/III 80%, 53.4%, 35.9%, p < 0.001). Compared to TCGA-white, Chinese BC patients had a higher alteration frequency (45.6% vs. 34.7%, p < 0.001) with larger proportion of p.H1047R mutation among three common mutation sites (p.E545K, p.E542K and p.H1047R) (66.1% vs. 43.7%, p = 0.01). Across four molecular subtypes, ER + /human epidermal growth factor receptor 2 positive (HER2 +) tumors harbored the most PIK3CA alterations (51.6%), while ER-/HER2- harbored the least alteration (30.0%) but the most copy number amplification (19.05%).
CONCLUSION: PIK3CA alterations prevail in Chinese BC patients and have different molecular features compared to that of Caucasians. The results provide precise annotations of PIK3CA genomic alterations of Chinese in the context of application of PIK3CA inhibitor.

Keywords:  Breast cancer; PIK3CA; Sequencing; Somatic alteration; TCGA

DOI:  https://doi.org/10.1007/s12282-020-01199-5
PeerJ. 2020 ;8 e10396

Driver versus navigator causation in biology: the case of insulin and fasting glucose.

Manawa Diwekar-Joshi, Milind Watve.

  Background: In biomedicine, inferring causal relation from experimental intervention or perturbation is believed to be a more reliable approach than inferring causation from cross-sectional correlation. However, we point out here that even in interventional inference there are logical traps. In homeostatic systems, causality in a steady state can be qualitatively different from that in a perturbed state. On a broader scale there is a need to differentiate driver causality from navigator causality. A driver is essential for reaching a destination but may not have any role in deciding the destination. A navigator on the other hand has a role in deciding the destination and the path but may not be able to drive the system to the destination. The failure to differentiate between types of causalities is likely to have resulted into many misinterpretations in physiology and biomedicine.Methods: We illustrate this by critically re-examining a specific case of the causal role of insulin in glucose homeostasis using five different approaches (1) Systematic review of tissue specific insulin receptor knock-outs, (2) Systematic review of insulin suppression and insulin enhancement experiments, (3) Differentiating steady state and post-meal state glucose levels in streptozotocin treated rats in primary experiments, (4) Mathematical and theoretical considerations and (5) Glucose-insulin relationship in human epidemiological data.
Results: All the approaches converge on the inference that although insulin action hastens the return to a steady state after a glucose load, there is no evidence that insulin action determines the steady state level of glucose. Insulin, unlike the popular belief in medicine, appears to be a driver but not a navigator for steady state glucose level. It is quite likely therefore that the current line of clinical action in the field of type 2 diabetes has limited success largely because it is based on a misinterpretation of glucose-insulin relationship. The insulin-glucose example suggests that we may have to carefully re-examine causal inferences from perturbation experiments and set up revised norms for experimental design for causal inference.

Keywords:  Causality; Glucose homeostasis; Physiology; Steady state

DOI:  https://doi.org/10.7717/peerj.10396
Cell Rep Med. 2020 Dec 22. 1(9): 100153

Vascular Tumor Recapitulated in Endothelial Cells from hiPSCs Engineered to Express the SERPINE1-FOSB Translocation.

David G P van IJzendoorn, Daniela C F Salvatori, Xu Cao, Francijna van den Hil, Inge H Briaire-de Bruijn, Danielle de Jong, Hailiang Mei, Christine L Mummery, Karoly Szuhai, Judith V M G Bovée, Valeria V Orlova.

  Chromosomal translocations are prevalent among soft tissue tumors, including those of the vasculature such as pseudomyogenic hemangioendothelioma (PHE). PHE shows endothelial cell (EC) features and has a tumor-specific t(7;19)(q22;q13) SERPINE1-FOSB translocation, but is difficult to study as no primary tumor cell lines have yet been derived. Here, we engineer the PHE chromosomal translocation into human induced pluripotent stem cells (hiPSCs) using CRISPR/Cas9 and differentiate these into ECs (hiPSC-ECs) to address this. Comparison of parental with PHE hiPSC-ECs shows (1) elevated expression of FOSB, (2) higher proliferation and more tube formation but lower endothelial barrier function, (3) invasive growth and abnormal vessel formation in mice after transplantation, and (4) specific transcriptome alterations reflecting PHE and indicating PI3K-Akt and MAPK signaling pathways as possible therapeutic targets. The modified hiPSC-ECs thus recapitulate functional features of PHE and demonstrate how these translocation models can be used to understand tumorigenic mechanisms and identify therapeutic targets.

Keywords:  CRISPR/Cas9-mediated gene targeting; PHE; chromosomal translocation; endothelial cell differentiation; gene fusion; hiPSC-ECs; hiPSC-derived ECs; hiPSCs; human induced pluripotent stem cells; pseudomyogenic hemangioendothelioma; t(7;19)(q22;q13) SERPINE1-FOSB chromosomal translocation; tumor model; vascular tumor

DOI:  https://doi.org/10.1016/j.xcrm.2020.100153
Biomed Pharmacother. 2021 Jan;pii: S0753-3322(20)31247-6. [Epub ahead of print]133 111055

An AKT2-specific nanobody that targets the hydrophobic motif induces cell cycle arrest, autophagy and loss of focal adhesions in MDA-MB-231 cells.

Tijs Merckaert, Olivier Zwaenepoel, Kris Gevaert, Jan Gettemans.

  The AKT kinase family is a high-profile target for cancer therapy. Despite their high degree of homology the three AKT isoforms (AKT1, AKT2 and AKT3) are non-redundant and can even have opposing functions. Small-molecule AKT inhibitors affect all three isoforms which severely limits their usefulness as research tool or therapeutic. Using AKT2-specific nanobodies we examined the function of endogenous AKT2 in breast cancer cells. Two AKT2 nanobodies (Nb8 and Nb9) modulate AKT2 and reduce MDA-MB-231 cell viability/proliferation. Nb8 binds the AKT2 hydrophobic motif and reduces IGF-1-induced phosphorylation of this site. This nanobody also affects the phosphorylation and/or expression levels of a wide range of proteins downstream of AKT, resulting in a G0/G1 cell cycle arrest, the induction of autophagy, a reduction in focal adhesion count and loss of stress fibers. While cell cycle progression is likely to be regulated by more than one isoform, our results indicate that both the effects on autophagy and the cytoskeleton are specific to AKT2. By using an isoform-specific nanobody we were able to map a part of the AKT2 pathway. Our results confirm AKT2 and the hydrophobic motif as targets for cancer therapy. Nb8 can be used as a research tool to study AKT2 signalling events and aid in the design of an AKT2-specific inhibitor.

Keywords:  AKT2; Autophagy; Cell cycle; Cytoskeleton; Intrabody; Nanobody

DOI:  https://doi.org/10.1016/j.biopha.2020.111055
Diabetes. 2021 Jan;70(1): 29-38

"Treasure Your Exceptions"-Studying Human Extreme Phenotypes to Illuminate Metabolic Health and Disease: The 2019 Banting Medal for Scientific Achievement Lecture.

Stephen O'Rahilly.

The study of humans with genetic mutations which lead to a substantial disturbance of physiological processes has made a contribution to biomedical science that is disproportionate to the rarity of affected individuals. In this lecture, I discuss examples of where such studies have helped to illuminate two areas of human metabolism. First, the control of insulin sensitivity and its disruption in states of insulin resistance and second, the regulation of energy balance and its disturbances in obesity.

DOI: https://doi.org/10.2337/dbi19-0037