bims-pideca 2022-10-23 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2022‒10‒23
forty-two papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute

Class I PI3K Biology.
PI3K and AKT at the Interface of Signaling and Metabolism.
Long noncoding RNA-mediated activation of PROTOR1/PRR5-AKT signaling shunt downstream of PI3K in triple-negative breast cancer.
PTEN in Immunity.
Evaluation of the pan-class I phosphoinositide 3-kinase (PI3K) inhibitor copanlisib in the Pediatric Preclinical Testing Consortium in vivo models of osteosarcoma.
PI3K Isoforms in Cell Signalling and Innate Immune Cell Responses.
An Overview of Class II Phosphoinositide 3-Kinases.
PI3K Isoforms in B Cells.
PI3K Isoform Immunotherapy for Solid Tumours.
Control of CD4+ T Cell Differentiation and Function by PI3K Isoforms.
Inhibiting glutamine utilization creates a synthetic lethality for suppression of ATP citrate lyase in KRas-driven cancer cells.
PI3K Targeting in Non-solid Cancer.
AKT Isoforms as a Target in Cancer and Immunotherapy.
Genetic Causes of Vascular Malformations and Common Signaling Pathways Involved in Their Formation.
PI3K Isoforms in CD8+ T Cell Development and Function.
SZT2 maintains hematopoietic stem cell homeostasis via nutrient-mediated mTORC1 regulation.
AKT Isoforms in Macrophage Activation, Polarization, and Survival.
Claudin-3 inhibits tumor-induced lymphangiogenesis via regulating the PI3K signaling pathway in lymphatic endothelial cells.
The Role of PI3K Isoforms in Autoimmune Disease.
Methylglyoxal induces multiple serine phosphorylation in insulin receptor substrate 1 via the TAK1-p38-mTORC1 signaling axis in adipocytes.
PI3K Isoform Signalling in Platelets.
Class III PI3K Biology.
A path to translation: How 3D patient tumor avatars enable next generation precision oncology.
p53 mutation in normal esophagus promotes multiple stages of carcinogenesis but is constrained by clonal competition.
Case report: Alpelisib-induced Stevens-Johnson syndrome.
AKT Isoforms in the Immune Response in Cancer.
Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail.
Glutamine synthetase limits b-catenin-mutated liver cancer growth by maintaining nitrogen homeostasis and suppressing mTORC1.
Cutaneous kinase activity correlates with treatment outcomes following PI3K delta inhibition in mice with experimental pemphigoid diseases.
TSC22D4 interacts with Akt1 to regulate glucose metabolism.
Spatial modeling reveals nuclear phosphorylation and subcellular shuttling of YAP upon drug-induced liver injury.
14-3-3τ drives estrogen receptor loss via ERα36 induction and GATA3 inhibition in breast cancer.
Sublinear scaling of the cellular proteome with ploidy.
Tumor-produced and aging-associated oncometabolite methylmalonic acid promotes cancer-associated fibroblast activation to drive metastatic progression.
PI3K Isoforms in Vascular Biology, A Focus on the Vascular System-Immune Response Connection.
Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing.
How to smuggle a drug into cells: add a lipid 'tail'.
Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space.
Landscape of epithelial mesenchymal plasticity as an emergent property of coordinated teams in regulatory networks.
Resistance exercise enhances long-term mTORC1 sensitivity to leucine.
Tugs-of-war in science.
ShareLoc - an open platform for sharing localization microscopy data.

Curr Top Microbiol Immunol. 2022 ;436 3-49

Class I PI3K Biology.

Tihitina Y Aytenfisu, Hannah M Campbell, Mayukh Chakrabarti, L Mario Amzel, Sandra B Gabelli.

  This chapter is an introduction to phosphoinositide 3-kinases (PI3K), with class I PI3Ks as the central focus. First, the various PI3K isoforms in class I are presented with emphasis on their overall structure, subunits, subunit constitutive domains, domain-domain interactions, and functional relevance. This structural analysis is followed by a comprehensive history of seminal investigations into PI3K activity. Next, we highlight the divergent roles of the isoforms: PI3Kα, PI3Kβ, PI3Kδ, and PI3Kγ. This section details signaling pathways in which these PI3K isoforms are involved, including the key upstream regulators of PI3K activity and some downstream cellular effects. Nodes of the PI3K pathway are also presented. Inhibitors of some isoforms are discussed to give an overview of the basis of some immunotherapies that are being used to target cell signaling. Finally, the chapter ends with a discussion of the dysregulation of PI3Ks in diseases including APDS, asthma, arthritis, and oncogenic mutations.

Keywords:  APDS; Arthritis; Asthma; B-cell signaling; Chronic inflammation; Class I PI3Ks; Oncogenic mutation; PI3K; Phosphoinositide-3-kinase; RTK signaling; Ras signaling; T-cell signaling; p101; p110β; p110γ; p110δ; p84; pl10α

DOI:  https://doi.org/10.1007/978-3-031-06566-8_1
Curr Top Microbiol Immunol. 2022 ;436 311-336

PI3K and AKT at the Interface of Signaling and Metabolism.

Giovanni Solinas, Barbara Becattini.

  The PI3K/AKT signaling module is recruited by several receptors implicated in maintaining tissue and metabolic homeostasis and signaling pathways controlling immune responses. Constitutive activation of PI3K/AKT signaling leads to tissue overgrowth and is frequently observed in cancer cells, whereas reduced PI3K/AKT signaling is associated with diabetes and growth defects. Thus, a critical roadblock to effective PI3K-targeted therapy comes from the crucial role of PI3K/AKT signaling in systemic metabolic homeostasis. This chapter describes the role of PI3K/AKT in insulin signaling and metabolic homeostasis and the interplay between insulin action and metabolic feedback loops that cause resistance to PI3K-targeted therapies. Furthermore, we provide examples of insulin-independent roles for PI3K/AKT in metabolic homeostasis, and some generalizations on the action of PI3K/AKT signaling at the interface of signaling and metabolism are derived. Finally, the specific roles for different class I PI3K isoforms in controlling systemic metabolic homeostasis and energy balance are discussed. We conclude that defining the functional specificities and redundancies of different class I PI3K isoforms in pathways driving disease and controlling metabolic homeostasis is fundamental to develop novel PI3K-targeted therapies.

Keywords:  Cancer; Diabetes; Growth; Immunometabolism; Insulin; Metabolic Inflammation; Obesity

DOI:  https://doi.org/10.1007/978-3-031-06566-8_13
Proc Natl Acad Sci U S A. 2022 Oct 25. 119(43): e2203180119

Long noncoding RNA-mediated activation of PROTOR1/PRR5-AKT signaling shunt downstream of PI3K in triple-negative breast cancer.

Zhenbo Tu, Yi Hu, Devesh Raizada, Mahmoud A Bassal, Daniel G Tenen, Antoine E Karnoub.

  The phosphoinositide 3-kinase (PI3K) pathway represents the most hyperactivated oncogenic pathway in triple-negative breast cancer (TNBC), a highly aggressive tumor subtype encompassing ∼15% of breast cancers and which possesses no targeted therapeutics. Despite critical contributions of its signaling arms to disease pathogenesis, PI3K pathway inhibitors have not achieved expected clinical responses in TNBC, owing largely to a still-incomplete understanding of the compensatory cascades that operate downstream of PI3K. Here, we investigated the contributions of long noncoding RNAs (lncRNAs) to PI3K activities in clinical and experimental TNBC and discovered a prominent role for LINC01133 as a PI3K-AKT signaling effector. We found that LINC01133 exerted protumorigenic roles in TNBC and that it governed a previously undescribed mTOR Complex 2 (mTORC2)-dependent pathway that activated AKT in a PI3K-independent manner. Mechanistically, LINC01133 induced the expression of the mTORC2 component PROTOR1/PRR5 by competitively coupling away its negative messenger RNA (mRNA) regulator, the heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2B1). PROTOR1/PRR5 in turn was sufficient and necessary for LINC01133-triggered functions, casting previously unappreciated roles for this Rictor-binding protein in cellular signaling and growth. Notably, LINC01133 antagonism undermined cellular growth, and we show that the LINC01133-PROTOR1/PRR5 pathway was tightly associated with TNBC poor patient survival. Altogether, our findings uncovered a lncRNA-driven signaling shunt that acts as a critical determinant of malignancy downstream of the PI3K pathway and as a potential RNA therapeutic target in clinical TNBC management.

Keywords:  AKT; LINC01133; PROTOR1; TNBC; hnRNPA2B1

DOI:  https://doi.org/10.1073/pnas.2203180119
Curr Top Microbiol Immunol. 2022 ;436 95-115

PTEN in Immunity.

Antonella Papa, Pier Paolo Pandolfi.

  The tumor suppressor PTEN (Phosphatase and Tensin homolog deleted on Chromosome 10) executes critical biological functions that limit cellular growth and proliferation. PTEN inhibits activation of the proto-oncogenic PI3K pathway and is required during embryogenesis and to suppress tumor formation and cancer progression throughout life. The critical role that PTEN plays in restraining cellular growth has been validated through the generation of a number of animal models whereby PTEN inactivation invariably leads to tumor formation in a cell-autonomous fashion. However, the increasing understanding of the mechanisms through which the immune system contributes to suppressing tumor progression has highlighted how, in a cell non-autonomous fashion, cancer-associated mutations can indirectly enhance oncogenesis by evading immune cell recognition. Here, in light of the essential role of PTEN in the regulation of immune cell development and function, and based on recent findings showing that PTEN loss can promote resistance to immune checkpoint inhibitors in various tumor types, we re-evaluate our understanding of the mechanisms through which PTEN functions as a tumor suppressor and postulate that this task is achieved through a combination of cell autonomous and non-autonomous effects. We highlight some of the critical studies that have delineated the functional role of PTEN in immune cell development and blood malignancies and propose new strategies for the treatment of PTEN loss-driven diseases.

Keywords:  Cancer resistance; Immune cell development; Immunotherapy; PTEN; Tumor suppression

DOI:  https://doi.org/10.1007/978-3-031-06566-8_4
Pediatr Blood Cancer. 2022 Oct 17. e30017

Evaluation of the pan-class I phosphoinositide 3-kinase (PI3K) inhibitor copanlisib in the Pediatric Preclinical Testing Consortium in vivo models of osteosarcoma.

Douglas Harrison, Jonathan Gill, Michael Roth, Pooja Hingorani, Wendong Zhang, Beverly Teicher, Eric Earley, Stephen Erickson, Gregory Gatto, Raushan Kumasheva, Peter Houghton, Malcolm Smith, E Anders Kolb, Richard Gorlick.

Copanlisib is a pan-class I phosphoinositide 3-kinase (PI3K) inhibitor, with activity against all four PI3K class I isoforms (PI3Kα, PI3Kβ, PI3Kγ, and PI3Kδ). Whole-genome and RNA sequencing data have revealed several PI3K aberrations in osteosarcoma tumor samples. The in vivo anticancer effects of copanlisib were assessed in a panel of six osteosarcoma models. Copanlisib induced prolonged event-free survival in five of six osteosarcoma models; however, all models demonstrated progressive disease suggesting minimal activity. While copanlisib did not result in tumor regression, more data are needed to fully explore the role of the PI3K pathway in the pathogenesis of osteosarcoma.

DOI: https://doi.org/10.1002/pbc.30017
Curr Top Microbiol Immunol. 2022 ;436 147-164

PI3K Isoforms in Cell Signalling and Innate Immune Cell Responses.

Izabela Galvão, Lirlândia P Sousa, Mauro M Teixeira, Vanessa Pinho.

  Phosphoinositide-3-kinases (PI3Ks) are enzymes involved in signalling and modification of the function of all mammalian cells. These enzymes phosphorylate the 3-hydroxyl group of the inositol ring of phosphatidylinositol, resulting in lipid products that act as second messengers responsible for coordinating many cellular functions, including activation, chemotaxis, proliferation and survival. The identification of the functions that are mediated by a specific PI3K isoform is complex and depends on the specific cell type and inflammatory context. In this chapter we will focus on the role of PI3K isoforms in the context of innate immunity, focusing on the mechanisms by which PI3K signalling regulates phagocytosis, the activation of immunoglobulin, chemokine and cytokines receptors, production of ROS and cell migration, and how PI3K signalling plays a central role in host defence against infections and tissue injury.

Keywords:  Inflammation; Innate immune response; Neutrophil activation; Neutrophil migration; Neutrophil survival; PI3K isoforms

DOI:  https://doi.org/10.1007/978-3-031-06566-8_6
Curr Top Microbiol Immunol. 2022 ;436 51-68

An Overview of Class II Phosphoinositide 3-Kinases.

Emily Yan Zhi Heng, Tania Maffucci.

  Phosphoinositide 3-kinases (PI3Ks) catalyse the synthesis of specific members of the family of lipids collectively known as 'phosphoinositides'. These PI3Ks products can in turn modulate activation of many downstream proteins, ultimately regulating several cellular processes. Mammalian cells possess eight PI3Ks which are grouped into three classes based on their structure and substrate specificity. While class I and III PI3Ks have been extensively investigated, our understanding of the three class II members has only improved in most recent years. This chapter will summarise some of the available information on mammalian class II PI3Ks and their physiological roles.

Keywords:  PI3K-C2α; PI3K-C2β; PI3K-C2γ; Phosphoinositide 3-kinases; Trafficking

DOI:  https://doi.org/10.1007/978-3-031-06566-8_2
Curr Top Microbiol Immunol. 2022 ;436 235-254

PI3K Isoforms in B Cells.

Elissa K Deenick, Julia Bier, Anthony Lau.

  Phosphatidylinositol-3-kinases (PI3K) control many aspects of cellular activation and differentiation and play an important role in B cells biology. Three different classes of PI3K have been described, all of which are expressed in B cells. However, it is the class IA PI3Ks, and the p110δ catalytic subunit in particular, which seem to play the most critical role in B cells. Here we discuss the important role that class IA PI3K plays in B cell development, activation and differentiation, as well as examine what is known about the other classes of PI3Ks in B cells.

Keywords:  Antibody production; B cell development; B cells; Humoral immunity; PI3K

DOI:  https://doi.org/10.1007/978-3-031-06566-8_10
Curr Top Microbiol Immunol. 2022 ;436 369-392

PI3K Isoform Immunotherapy for Solid Tumours.

Jake Scott, Lauren Rees, Awen Gallimore, Sarah N Lauder.

  Improving the anti-tumour T cell response as a consequence of immunotherapy can result in eradication of tumour burden, however, the majority of patients fail with current treatment regimens and so novel immunotherapies with greater efficacy and improved tolerability are needed. The phosphoinositide-3-kinase (PI3K) family members that are directly involved in cell signalling comprise PI3Kα, PI3Kβ, PI3Kδ and PI3Kγ, with the latter two isoforms expressed primarily by leukocytes. The survival and optimal function of regulatory T cells (Treg) and myeloid-derived suppressor cells (MDSCs) is dependent on PI3Kδ, whereas tumour-associated macrophages (TAMs), use PI3Kγ. Blocking these signalling isoforms can boost development of effective anti-cancer immune responses and result in control of tumour burden. The dependence on different PI3K isoforms in immune cells makes targeting this pathway an attractive approach for tumour immunotherapy. Herein, we discuss how inhibiting specific PI3K isoforms in pro-tumoural Tregs, MDSCS and TAMs can unleash a powerful anti-tumour immune response, driven by CD8+ T cells, capable of controlling tumour burden and consider how the immune response to therapy needs careful investigation, to identify both the correlates of successful treatment and those that impede the generation of robust anti-tumour responses. Furthermore, we review how combination immunotherapy approaches with both PI3K inhibitors and subsequent immune checkpoint blockade can potentiate the efficacy of monotherapy. Finally, we discuss the recent advances in the use of PI3K isoform-specific inhibitors as an immunotherapy for solid tumours in clinical trials.

Keywords:  CD8+ T cell; Immunotherapy; Myeloid-derived suppressor cell; Regulatory T cell; Tumour; Tumour-associated macrophage

DOI:  https://doi.org/10.1007/978-3-031-06566-8_16
Curr Top Microbiol Immunol. 2022 ;436 197-216

Control of CD4+ T Cell Differentiation and Function by PI3K Isoforms.

Benjamin Cameron, Syed Aymaan Zaheer, Margarita Dominguez-Villar.

  The phosphoinositide-3-kinase (PI3K) pathway is a highly conserved intracellular signaling pathway involving numerous key effectors which, in response to diverse extracellular stimuli, modulate the phenotype and function of most mammalian cell types in a pleiotropic manner. PI3K signaling plays a critical role in the development, activation, and differentiation of lymphocytes. In particular, the PI3Kδ and PI3Kγ isoforms have been shown to carry out essential, non-redundant roles in T cells, and therefore, tight regulation of the PI3K pathway is important to maintain the balance between immune tolerance and inflammation. Recent and ongoing efforts to manipulate the biology of T helper cell subsets in the treatment of autoimmune conditions, inflammatory disorders, as well as cancer have shown promising results, and targeting the PI3K pathway may be beneficial in these contexts. However, more insight as to the precise function of individual PI3K isoforms in pathogenic and protective immune cell subsets is still required, and how exactly PI3K signaling is regulated and integrated with classical immune pathways. This chapter provides an overview of the role of PI3K isoforms in the differentiation and function of T helper cell subsets, within the broader context of targeting this pathway to potentially alleviate immunopathology.

Keywords:  Autoimmunity; CD4+ T cells; Differentiation; Helper T cells; Inflammation; PI3K isoforms; Phosphoinositide-3-kinase; mTOR

DOI:  https://doi.org/10.1007/978-3-031-06566-8_8
PLoS One. 2022 ;17(10): e0276579

Inhibiting glutamine utilization creates a synthetic lethality for suppression of ATP citrate lyase in KRas-driven cancer cells.

Ahmet Hatipoglu, Deepak Menon, Talia Levy, Maria A Frias, David A Foster.

Metabolic reprogramming is now considered a hallmark of cancer cells. KRas-driven cancer cells use glutaminolysis to generate the tricarboxylic acid cycle intermediate α-ketoglutarate via a transamination reaction between glutamate and oxaloacetate. We reported previously that exogenously supplied unsaturated fatty acids could be used to synthesize phosphatidic acid-a lipid second messenger that activates both mammalian target of rapamycin (mTOR) complex 1 (mTORC1) and mTOR complex 2 (mTORC2). A key target of mTORC2 is Akt-a kinase that promotes survival and regulates cell metabolism. We report here that mono-unsaturated oleic acid stimulates the phosphorylation of ATP citrate lyase (ACLY) at the Akt phosphorylation site at S455 in an mTORC2 dependent manner. Inhibition of ACLY in KRas-driven cancer cells in the absence of serum resulted in loss of cell viability. We examined the impact of glutamine (Gln) deprivation in combination with inhibition of ACLY on the viability of KRas-driven cancer cells. While Gln deprivation was somewhat toxic to KRas-driven cancer cells by itself, addition of the ACLY inhibitor SB-204990 increased the loss of cell viability. However, the transaminase inhibitor aminooxyacetate was minimally toxic and the combination of SB-204990 and aminooxtacetate led to significant loss of cell viability and strong cleavage of poly-ADP ribose polymerase-indicating apoptotic cell death. This effect was not observed in MCF7 breast cancer cells that do not have a KRas mutation or in BJ-hTERT human fibroblasts which have no oncogenic mutation. These data reveal a synthetic lethality between inhibition of glutamate oxaloacetate transaminase and ACLY inhibition that is specific for KRas-driven cancer cells and the apparent metabolic reprogramming induced by activating mutations to KRas.

DOI: https://doi.org/10.1371/journal.pone.0276579
Curr Top Microbiol Immunol. 2022 ;436 393-407

PI3K Targeting in Non-solid Cancer.

Hye Na Kim, Heather Ogana, Vanessa Sanchez, Cydney Nichols, Yong-Mi Kim.

  Despite the therapeutic progress, relapse remains a major problem in the treatment of acute lymphoblastic leukemia (ALL). Most leukemia cells that survive chemotherapy are found in the bone marrow (BM), thus resistance to chemotherapy and other treatments may be partially attributed to pro-survival signaling to leukemic cells mediated by leukemia cell-microenvironment interactions. Adhesion of leukemia cells to BM stromal cells may lead to cell adhesion-mediated drug resistance (CAM-DR) mediating intracellular signaling changes that support survival of leukemia cells. In ALL and chronic lymphocytic leukemia (CLL), adhesion-mediated activation of the PI3K/AKT signaling pathway has been shown to be critical in CAM-DR. PI3K targeting inhibitors have been approved for CLL and have been evaluated preclinically in ALL. However, PI3K inhibition has yet to be approved for clinical use in ALL. Here, we review the role of PI3K signaling for normal hematopoietic and leukemia cells and summarize preclinical inhibitors of PI3K in ALL.

Keywords:  Acute lymphoblastic leukemia (ALL); Cell adhesion mediated drug resistance (CAM-DR); PI3K/AKT; PI3Kγ; PI3Kδ

DOI:  https://doi.org/10.1007/978-3-031-06566-8_17
Curr Top Microbiol Immunol. 2022 ;436 409-436

AKT Isoforms as a Target in Cancer and Immunotherapy.

Daniel J Smit, Manfred Jücker.

  Over the past years, targeted therapies have received tremendous attention in cancer therapy. One of the most frequently targeted pathways is the PI3K/AKT/mTOR signaling pathway that regulates crucial cellular processes including proliferation, survival, and migration. In a wide variety of cancer entities, the PI3K/AKT/mTOR signaling pathway was found to be a critical driver of disease progression, indicating a noteworthy target in cancer therapy. This chapter focuses on targeted therapies against AKT, which is a key enzyme within the PI3K/AKT/mTOR pathway. Although the three different isoforms of AKT, namely AKT1, AKT2, and AKT3, have a high homology, the isoforms exhibit different biological functions. Recently, direct inhibitors against all AKT isoforms as well as selective inhibitors against specific AKT isoforms have been extensively investigated in preclinical work as well as in clinical trials to attenuate proliferation of cancer cells. While no AKT inhibitor has been approved by the FDA for cancer therapy to date, AKT still plays a crucial role in a variety of treatment strategies including immune checkpoint inhibition. In this chapter, we summarize the status of AKT inhibitors either targeting all or specific AKT isoforms. Furthermore, we explain the role of AKT signaling in direct inhibition of tumor cell growth as well as in immune cells and immune checkpoint inhibition.

Keywords:  AKT; CTLA-4; Cancer therapy; Immune checkpoint inhibition; Immune escape; PD1 signaling; PI3K/AKT/mTOR signaling pathway; Targeted therapy

DOI:  https://doi.org/10.1007/978-3-031-06566-8_18
Dermatol Clin. 2022 Oct;pii: S0733-8635(22)00054-7. [Epub ahead of print]40(4): 449-459

Genetic Causes of Vascular Malformations and Common Signaling Pathways Involved in Their Formation.

Aubrey L Rose, Sara S Cathey.

  The identification of the genetic cause of vascular malformations is improving understanding of pathogenesis of these lesions and also informing potential opportunities for treatment. Somatic activating mutations affecting RAS/MAPK and PIK3/AKT/mTor pathways are implicated in all types of vascular malformations. Pathogenic variants associated with vascular lesions may be germline or somatic. Next-generation sequencing technologies allow identification of lower level mosaic mutations than was achievable with standard Sanger sequencing. Best practice strategies to identify underlying genetic mutations in vascular malformations are influenced by the tissues involved and the type of vascular lesion.

Keywords:  AVM; Capillary; Germline; Lymphatic; PI3K-AKT-mTOR; Somatic; Vascular; Venous

DOI:  https://doi.org/10.1016/j.det.2022.07.002
Curr Top Microbiol Immunol. 2022 ;436 217-234

PI3K Isoforms in CD8+ T Cell Development and Function.

Pankaj Gaur, Mikayel Mkrtichyan, Vivek Verma, Nazli Jafarzadeh, Mariana Hattar, Seema Gupta, Samir N Khleif.

  CD8+ T cells are an essential part of the immune system and play a vital role in defending against tumors and infections. The phosphoinositide-3-kinase (PI3K), especially class I, is involved in numerous interrelated signaling pathways which control CD8+ T cell development, maturation, migration, activation, and differentiation. While CD8+ T lymphocytes express all class I PI3K isoforms (PI3Kα, PI3Kβ, PI3Kδ, and PI3Kγ), isoform-specific functions, especially for PI3Kα and PI3Kβ have not been fully elucidated. A few studies suggest the important role of p110δ and p110γ in CD8+ T cell activation, signaling, chemotaxis and function and several clinical trials are currently testing the effect of isoform-specific inhibitors in various types of cancers, including Indolent Non-Hodgkin Lymphoma, Peripheral T cell Lymphoma, Chronic Lymphocytic Leukemia, Small Lymphocytic Lymphoma, non-small cell lung carcinoma (NSCLC), head & neck cancer, and breast cancer. This chapter summarizes current knowledge of the roles of various PI3K isoforms and downstream signaling pathways in regulating CD8+ T cell fate, including cell proliferation, migration, and memory generation. We also discuss certain clinical trials employing PI3K inhibitors for cancer therapy, their limitations, and future perspectives.

Keywords:  CD8+ T cell; Memory; Migration; PI3K signaling; PI3Kγ; PI3Kδ; Survival

DOI:  https://doi.org/10.1007/978-3-031-06566-8_9
J Clin Invest. 2022 Oct 17. pii: e146272. [Epub ahead of print]132(20):

SZT2 maintains hematopoietic stem cell homeostasis via nutrient-mediated mTORC1 regulation.

Na Yin, Gang Jin, Yuying Ma, Hanfei Zhao, Guangyue Zhang, Ming O Li, Min Peng.

  The mTORC1 pathway coordinates nutrient and growth factor signals to maintain organismal homeostasis. Whether nutrient signaling to mTORC1 regulates stem cell function remains unknown. Here, we show that SZT2 - a protein required for mTORC1 downregulation upon nutrient deprivation - is critical for hematopoietic stem cell (HSC) homeostasis. Ablation of SZT2 in HSCs decreased the reserve and impaired the repopulating capacity of HSCs. Furthermore, ablation of both SZT2 and TSC1 - 2 repressors of mTORC1 on the nutrient and growth factor arms, respectively - led to rapid HSC depletion, pancytopenia, and premature death of the mice. Mechanistically, loss of either SZT2 or TSC1 in HSCs led to only mild elevation of mTORC1 activity and reactive oxygen species (ROS) production. Loss of both SZT2 and TSC1, on the other hand, simultaneously produced a dramatic synergistic effect, with an approximately 10-fold increase of mTORC1 activity and approximately 100-fold increase of ROS production, which rapidly depleted HSCs. These data demonstrate a critical role of nutrient mTORC1 signaling in HSC homeostasis and uncover a strong synergistic effect between nutrient- and growth factor-mediated mTORC1 regulation in stem cells.

Keywords:  Amino acid metabolism; Bone marrow transplantation; Hematology; Hematopoietic stem cells; Metabolism

DOI:  https://doi.org/10.1172/JCI146272
Curr Top Microbiol Immunol. 2022 ;436 165-196

AKT Isoforms in Macrophage Activation, Polarization, and Survival.

Ioanna Lapi, Maria G Daskalaki, Konstantinos Axarlis, Eleni Paflioti, Philip N Tsichlis, Eleni Vergadi, Christos Tsatsanis.

Macrophages display an array of activation phenotypes depending on the activation signal and the cellular microenvironment. The type and magnitude of the response depend on signaling molecules as well as on the epigenetic and metabolic status of the cells at the time of activation. The AKT family of kinases consists of three isoforms encoded by independent genes possessing similar functions and structures. Generation of research tools such as isoform-specific gene deletion mutant mice and cells and isoform-specific antibodies has allowed us to understand the role of each kinase isoform in macrophage activation and homeostasis. This chapter discusses the current evidence on the role of AKT kinases in macrophage activation, polarization, and homeostasis, highlighting the gaps in knowledge and future challenges in the field.

DOI: https://doi.org/10.1007/978-3-031-06566-8_7
Sci Rep. 2022 Oct 19. 12(1): 17440

Claudin-3 inhibits tumor-induced lymphangiogenesis via regulating the PI3K signaling pathway in lymphatic endothelial cells.

Ningjing Lei, Yanru Cheng, Jiajia Wan, Rosel Blasig, Anqi Li, Yueyue Bai, Reiner F Haseloff, Ingolf E Blasig, Linyu Zhu, Zhihai Qin.

Claudin-3 is a tight junction protein that has often been associated with the progression and metastasis of various tumors. Here, the role of claudin-3 in tumor-induced lymphangiogenesis is investigated. We found an increased lymphangiogenesis in the B16F10 tumor in claudin-3 knockout mice, accompanied by augmented melanoma cell metastasis into sentinel lymph nodes. In vitro, the overexpression of claudin-3 on lymphatic endothelial cells inhibited tube formation by suppressing cell migration, resulting in restricted lymphangiogenesis. Further experiments showed that claudin-3 inhibited lymphatic endothelial cell migration by regulating the PI3K signaling pathway. Interestingly, the expression of claudin-3 in lymphatic endothelial cells is down-regulated by vascular endothelial growth factor C that is often present in the tumor microenvironment. This study indicates that claudin-3 plays an important role as a signaling molecule in lymphatic endothelial cell activity associated with tumor lymphangiogenesis, which may further contribute to melanoma metastasis.

DOI: https://doi.org/10.1038/s41598-022-22156-6
Curr Top Microbiol Immunol. 2022 ;436 337-347

The Role of PI3K Isoforms in Autoimmune Disease.

Stephen G Ward.

  Aberrant overactivation of the immune system can give rise to chronic and persistent self-attack, culminating in autoimmune disease. This is currently managed therapeutically using potent immunosuppressive and anti-inflammatory drugs. Class I phosphoinositide-3-kinases (PI3Ks) have been identified as ideal therapeutic targets for autoimmune diseases given their wide-ranging roles in immunological processes. Although progress has been hampered by issues such as poor drug tolerance and drug resistance, several PI3K inhibitors have now received regulatory approval with many others in development, including several intended to suppress the immune response in autoimmune and inflammatory diseases. This chapter reviews the evidence for contribution of aberrant PI3K activity to a range of autoimmune diseases (rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis and type I diabetes) and possible therapeutic application of isoform-specific PI3K inhibitors as immunosuppressive drugs.

Keywords:  Arthritis; Autoimmune; Diabetes; Inhibitors; Leukocytes; Lupus; Multiple Sclerosis; PI3K

DOI:  https://doi.org/10.1007/978-3-031-06566-8_14
Biochem J. 2022 Oct 18. pii: BCJ20220271. [Epub ahead of print]

Methylglyoxal induces multiple serine phosphorylation in insulin receptor substrate 1 via the TAK1-p38-mTORC1 signaling axis in adipocytes.

Su-Ping Ng, Wataru Nomura, Haruya Takahashi, Kazuo Inoue, Teruo Kawada, Tsuyoshi Goto, Yoshiharu Inoue.

  Certain metabolic intermediates produced during metabolism are known to regulate a wide range of cellular processes. Methylglyoxal (MG), a natural metabolite derived from glycolysis, has been shown to negatively influences systemic metabolism by inducing glucose intolerance, insulin resistance, and diabetic complications. MG plays a functional role as a signaling molecule that initiates signal transduction. However, the specific relationship between MG-induced activation of signal transduction and its negative effects on metabolism remains unclear. Here, we found that MG activated mammalian target of rapamycin complex 1 (mTORC1) signaling via p38 mitogen-activated protein kinase in adipocytes, and that the transforming growth factor-b-activated kinase 1 (TAK1) is needed to activate p38-mTORC1 signaling following treatment with MG. We also found that MG increased the phosphorylation levels of serine residues in insulin receptor substrate (IRS)-1, which is involved in its negative regulation, thereby attenuating insulin-stimulated tyrosine phosphorylation in IRS-1. The negative effect of MG on insulin-stimulated IRS-1 tyrosine phosphorylation was exerted due to the MG-induced activation of the TAK1-p38-mTORC1 signaling axis. The involvement of the TAK1-p38-mTORC1 signaling axis in the induction of IRS-1 multiple serine phosphorylation was not unique to MG, as the proinflammatory cytokine, tumor necrosis factor-α, also activated the same signaling axis. Therefore, our findings suggest that MG-induced activation of the TAK1-p38-mTORC1 signaling axis caused multiple serine phosphorylation on IRS-1, potentially contributing to insulin resistance.

Keywords:  TAK1; adipocytes; insulin signalling; mTOR; methylglyoxal; signalling

DOI:  https://doi.org/10.1042/BCJ20220271
Curr Top Microbiol Immunol. 2022 ;436 255-285

PI3K Isoform Signalling in Platelets.

Waltraud C Schrottmaier, Marion Mussbacher, Manuel Salzmann, Julia B Kral-Pointner, Alice Assinger.

  Platelets are unique anucleated blood cells that constantly patrol the vasculature to seal and prevent injuries in a process termed haemostasis. Thereby they rapidly adhere to the subendothelial matrix and recruit further platelets, resulting in platelet aggregates. Apart from their central role in haemostasis, they also kept some of their features inherited by their evolutionary ancestor-the haemocyte, which was also involved in immune defences. Together with leukocytes, platelets fight pathogenic invaders and guide many immune processes. In addition, they rely on several signalling pathways which are also relevant to immune cells. Among these, one of the central signalling hubs is the PI3K pathway. Signalling processes in platelets are unique as they lack a nucleus and therefore transcriptional regulation is absent. As a result, PI3K subclasses fulfil distinct roles in platelets compared to other cells. In contrast to leukocytes, the central PI3K subclass in platelet signalling is PI3K class Iβ, which underlines the uniqueness of this cell type and opens new ways for potential platelet-specific pharmacologic inhibition. An overview of platelet function and signalling with emphasis on PI3K subclasses and their respective inhibitors is given in this chapter.

Keywords:  Haemostasis; Inflammation; Phosphoinositide-3-kinase; Platelets; Thrombosis

DOI:  https://doi.org/10.1007/978-3-031-06566-8_11
Curr Top Microbiol Immunol. 2022 ;436 69-93

Class III PI3K Biology.

Manuella Caux, Gaetan Chicanne, Sonia Severin.

  Highly conserved from yeast to mammals, vacuolar protein sorting 34 (Vps34) is the sole member of the third class of the phosphoinositide 3-kinase (PI3K) family. By producing phosphatidylinositol-3-monophosphate (PtdIns3P) through its scaffolding function essential for the catalytic lipid activity, Vps34 regulates endosomal trafficking, autophagy, phagocytosis, and nutrient-sensing signaling. The development of genetically modified mouse models and specific inhibitors has largely contributed over the past ten years to a better understanding of Vps34 functions in biological and physiological processes in mammals and, ultimately, its potential implications and targeting in human diseases. This chapter will summarize the current knowledge of the structure and regulation of Vps34 as well as its cellular and organismal functions.

Keywords:  Autophagy; PhosphatIdylinositol-3-monophosphate; Signaling; Vesicular trafficking; Vps34

DOI:  https://doi.org/10.1007/978-3-031-06566-8_3
Cancer Cell. 2022 Oct 18. pii: S1535-6108(22)00475-5. [Epub ahead of print]

A path to translation: How 3D patient tumor avatars enable next generation precision oncology.

Shree Bose

3D patient tumor avatars (3D-PTAs) hold promise for next-generation precision medicine. Here, we describe the benefits and challenges of 3D-PTA technologies and necessary future steps to realize their potential for clinical decision making. 3D-PTAs require standardization criteria and prospective trials to establish clinical benefits. Innovative trial designs that combine omics and 3D-PTA readouts may lead to more accurate clinical predictors, and an integrated platform that combines diagnostic and therapeutic development will accelerate new treatments for patients with refractory disease.

DOI: https://doi.org/10.1016/j.ccell.2022.09.017
Nat Commun. 2022 Oct 20. 13(1): 6206

p53 mutation in normal esophagus promotes multiple stages of carcinogenesis but is constrained by clonal competition.

Kasumi Murai, Stefan Dentro, Swee Hoe Ong, Roshan Sood, David Fernandez-Antoran, Albert Herms, Vasiliki Kostiou, Irina Abnizova, Benjamin A Hall, Moritz Gerstung, Philip H Jones.

Aging normal human oesophagus accumulates TP53 mutant clones. These are the origin of most oesophageal squamous carcinomas, in which biallelic TP53 disruption is almost universal. However, how p53 mutant clones expand and contribute to cancer development is unclear. Here we show that inducing the p53R245W mutant in single oesophageal progenitor cells in transgenic mice confers a proliferative advantage and clonal expansion but does not disrupt normal epithelial structure. Loss of the remaining p53 allele in mutant cells results in genomically unstable p53R245W/null epithelium with giant polyaneuploid cells and copy number altered clones. In carcinogenesis, p53 mutation does not initiate tumour formation, but tumours developing from areas with p53 mutation and LOH are larger and show extensive chromosomal instability compared to lesions arising in wild type epithelium. We conclude that p53 has distinct functions at different stages of carcinogenesis and that LOH within p53 mutant clones in normal epithelium is a critical step in malignant transformation.

DOI: https://doi.org/10.1038/s41467-022-33945-y
Front Oncol. 2022 ;12 954027

Case report: Alpelisib-induced Stevens-Johnson syndrome.

Christine Jane Kurian, Akshay Desai, William Rafferty, Ahmed Kamel Abou Hussein.

  Background: Alpelisib is a recently approved treatment for hormone receptor-positive, HER2-negative, PIK3CA-mutated advanced breast cancer. It has been associated with alopecia and rash, but there are no documented cases of Stevens-Johnson Syndrome (SJS) associated with this drug. Here, we detail the first case of SJS associated with alpelisib.Case description: Our patient is a 60-year-old woman with a past medical history of metastatic hormone receptor-positive (ER+ 80% and PR+ 1%), HER2-negative metastatic breast cancer who presented with acute odynophagia, fevers, and diffuse body rash after receiving her first doses of alpelisib and fulvestrant in the preceding days. She presented to the emergency department after developing a whole-body rash and severe ulceration of her buccal mucosa. She was started on methylprednisolone with remarkable improvement in symptoms.
Conclusion: This case report details the only report of SJS following alpelisib treatment. Immediate cessation of drugs and initiation of steroids are the cornerstone of treatment. Patients who experience such side effects will have to be monitored closely for long-term sequelae associated with SJS, including cutaneous, ocular, and oral sequelae, all of which can profoundly affect the quality of life for cancer patients.

Keywords:  Stevens Johnson Syndrome; Stevens Johnson syndrome (SJS); alpelisib; breast cancer; metastatic breast cancer

DOI:  https://doi.org/10.3389/fonc.2022.954027
Curr Top Microbiol Immunol. 2022 ;436 349-366

AKT Isoforms in the Immune Response in Cancer.

Zayd Ahmad, Payaningal R Somanath.

  AKT is a protein kinase that exists in three isoforms: AKT1, AKT2, and AKT3. Though similar in structure, these isoforms display different effects. AKT is activated downstream of PI3K, and together, this signaling pathway helps regulate cellular processes including cell growth, proliferation, metabolism, survival, and apoptosis. Disruption in these pathways has been associated with disorders including cardiovascular diseases, developmental disorders, inflammatory responses, autoimmune diseases, neurologic disorders, type 2 diabetes, and several cancers. In cancer, deregulation in the PI3K/AKT pathway can be manifested as tumorigenesis, pathological angiogenesis, and metastasis. Increased activity has been correlated with tumor progression and resistance to cancer treatments. Recent studies have suggested that inhibition of the PI3K/AKT pathway plays a significant role in the development, expansion, and proliferation of cells of the immune system. Additionally, AKT has been found to play an important role in differentiating regulatory T cells, activating B cells, and augmenting tumor immunosurveillance. This emphasizes AKT as a potential target for inhibition in cancer therapy. This chapter reviews AKT structure and regulation, its different isoforms, its role in immune cells, and its modulation in oncotherapy.

Keywords:  AKT1; AKT2; AKT3; Cancer; Immunology; Protein kinase B

DOI:  https://doi.org/10.1007/978-3-031-06566-8_15
Nat Protoc. 2022 Oct 19.

Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail.

Carlos A Tristan, Hyenjong Hong, Yogita Jethmalani, Yu Chen, Claire Weber, Pei-Hsuan Chu, Seungmi Ryu, Vukasin M Jovanovic, Inae Hur, Ty C Voss, Anton Simeonov, Ilyas Singeç.

Human pluripotent stem cells (hPSCs) are inherently sensitive cells. Single-cell dissociation and the establishment of clonal cell lines have been long-standing challenges. This inefficiency of cell cloning represents a major obstacle for the standardization and streamlining of gene editing in induced pluripotent stem cells for basic and translational research. Here we describe a chemically defined protocol for robust single-cell cloning using microfluidics-based cell sorting in combination with the CEPT small-molecule cocktail. This advanced strategy promotes the viability and cell fitness of self-renewing stem cells. The use of low-pressure microfluidic cell dispensing ensures gentle and rapid dispensing of single cells into 96- and 384-well plates, while the fast-acting CEPT cocktail minimizes cellular stress and maintains cell structure and function immediately after cell dissociation. The protocol also facilitates clone picking and produces genetically stable clonal cell lines from hPSCs in a safe and cost-efficient fashion. Depending on the proliferation rate of the clone derived from a single cell, this protocol can be completed in 7-14 d and requires experience with aseptic cell culture techniques. Altogether, the relative ease, scalability and robustness of this workflow should boost gene editing in hPSCs and leverage a wide range of applications, including cell line development (e.g., reporter and isogenic cell lines), disease modeling and applications in regenerative medicine.

DOI: https://doi.org/10.1038/s41596-022-00753-z
J Clin Invest. 2022 Oct 18. pii: e161408. [Epub ahead of print]

Glutamine synthetase limits b-catenin-mutated liver cancer growth by maintaining nitrogen homeostasis and suppressing mTORC1.

Weiwei Dai, Jianliang Shen, Junrong Yan, Alex J Bott, Sara Maimouni, Heineken Q Daguplo, Yujue Wang, Khoosheh Khayati, Jessie Yanxiang Guo, Lanjing Zhang, Yongbo Wang, Alexander Valvezan, Wen-Xing Ding, Xin Chen, Xiaoyang Su, Shenglan Gao, Wei-Xing Zong.

  Glutamine synthetase (GS) catalyzes de novo synthesis of glutamine that facilitates cancer cell growth. In the liver, GS functions next to the urea cycle to remove ammonia waste. As dysregulated urea cycle is implicated in cancer development, the impact of GS' ammonia clearance function has not been explored in cancer. Here we show that, oncogenic activation of beta-catenin led to decreased urea cycle and elevated ammonia waste burden. While beta-catenin induced the expression of GS, which is thought to be cancer-promoting, surprisingly, genetic ablation of hepatic GS accelerated the onset of liver tumors in several mouse models that involved β-catenin activation. Mechanistically, GS ablation exacerbated hyperammonemia and facilitated the production of glutamate-derived non-essential amino acids (NEAAs), which subsequently stimulated mTORC1. Pharmacological and genetic inhibition of mTORC1 and glutamic transaminases suppressed tumorigenesis facilitated by GS ablation. While HCC patients, especially those with CTNNB1 mutations, have an overall defective urea cycle and increased expression of GS, there exists a subset of patients with low GS expression that is associated with mTORC1 hyperactivation. Therefore, GS-mediated ammonia clearance serves as a tumor-suppressing mechanism in livers that harbor β-catenin activation mutations and a compromised urea cycle.

Keywords:  Hepatology; Liver cancer; Metabolism

DOI:  https://doi.org/10.1172/JCI161408
Front Immunol. 2022 ;13 865241

Cutaneous kinase activity correlates with treatment outcomes following PI3K delta inhibition in mice with experimental pemphigoid diseases.

Saeedeh Ghorbanalipoor, Shirin Emtenani, Melissa Parker, Mayumi Kamaguchi, Colin Osterloh, Manuela Pigors, Natalie Gross, Stanislav Khil'chenko, Anika Kasprick, Sabrina Patzelt, Diana Wortmann, Ibrahim O Ibrahim, Kentaro Izumi, Stephanie Goletz, Katharina Boch, Kathrin Kalies, Katja Bieber, Paul Smith, Enno Schmidt, Ralf J Ludwig.

  Chronic blistering at the skin and/or mucous membranes, accompanied by a varying degree of inflammation, is the clinical hallmark of pemphigoid diseases that impose a major medical burden. Pemphigoid diseases are caused by autoantibodies targeting structural proteins of the epithelial basement membrane. One major pathogenic pathway of skin blistering and inflammation is activation of myeloid cells following Fc gamma receptor-dependent binding to the skin-bound immune complexes. This process requires activation of specific kinases, such as PI3Kδ, which have emerged as potential targets for the treatment of pemphigoid diseases. Yet, it is unknown if global cutaneous kinase activity present in lesional pemphigoid disease correlates with therapeutic effects following treatment with a given target-selective kinase inhibitor. To address this, we here first determined the kinase activity in three different mouse models of pemphigoid diseases: Antibody transfer-induced mucous membrane pemphigoid (MMP), antibody transfer-induced epidermolysis bullosa acquisita (EBA) and immunization-induced EBA. Interestingly, the kinome signatures were different among the three models. More specifically, PI3Kδ was within the kinome activation network of antibody transfer-induced MMP and immunization-induced EBA, but not in antibody transfer-induced EBA. Next, the therapeutic impact of the PI3Kδ-selective inhibitor parsaclisib was evaluated in the three model systems. In line with the kinome signatures, parsaclisib had therapeutic effects in antibody transfer-induced MMP and immunization-induced EBA, but not in autoantibody-induced EBA. In conclusion, kinase activation signatures of inflamed skin, herein exemplified by pemphigoid diseases, correlate with the therapeutic outcomes following kinase inhibition, demonstrated here by the PI3Kδ inhibitor parsaclisib.

Keywords:  animal model; autoimmunity; epidermolysis bullosa acquisita; mucous membrane pemphigoid; neutrophils; pemphigoid; phosphatidylinositol 3-kinase (P13k); signal transduction

DOI:  https://doi.org/10.3389/fimmu.2022.865241
Sci Adv. 2022 Oct 21. 8(42): eabo5555

TSC22D4 interacts with Akt1 to regulate glucose metabolism.

Sevgican Demir, Gretchen Wolff, Annika Wieder, Adriano Maida, Lea Bühler, Maik Brune, Oksana Hautzinger, Annette Feuchtinger, Tanja Poth, Julia Szendroedi, Stephan Herzig, Bilgen Ekim Üstünel.

Maladaptive insulin signaling is a key feature in the pathogenesis of severe metabolic disorders, including obesity and diabetes. Enhancing insulin sensitivity represents a major goal in the treatment of patients affected by diabetes. Here, we identify transforming growth factor-β1 stimulated clone 22 D4 (TSC22D4) as a novel interaction partner for protein kinase B/Akt1, a critical mediator of insulin/phosphatidylinositol 3-kinase signaling pathway. While energy deprivation and oxidative stress promote the TSC22D4-Akt1 interaction, refeeding mice or exposing cells to glucose and insulin impairs this interaction, which relies on an intrinsically disordered region (D2 domain) within TSC22D4. Functionally, the interaction with TSC22D4 reduces basal phosphorylation of Akt and its downstream targets during starvation, thereby promoting insulin sensitivity. Genetic, liver-specific reconstitution experiments in mice demonstrate that the interaction between TSC22D4 and Akt1 improves glucose handling and insulin sensitivity. Overall, our findings postulate a model whereby TSC22D4 acts as an environmental sensor and interacts with Akt1 to regulate insulin signaling and glucose metabolism.

DOI: https://doi.org/10.1126/sciadv.abo5555
Elife. 2022 Oct 18. pii: e78540. [Epub ahead of print]11

Spatial modeling reveals nuclear phosphorylation and subcellular shuttling of YAP upon drug-induced liver injury.

Lilija Wehling, Liam Keegan, Paula Fernández-Palanca, Reham Hassan, Ahmed Ghallab, Jennifer Schmitt, Yingyue Tang, Maxime Le Marois, Stephanie Roessler, Peter Schirmacher, Ursula Kummer, Jan G Hengstler, Sven Sahle, Kai Breuhahn.

  The Hippo signaling pathway controls cell proliferation and tissue regeneration via its transcriptional effectors yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ). The canonical pathway topology is characterized by sequential phosphorylation of kinases in the cytoplasm that defines the subcellular localization of YAP and TAZ. However, the molecular mechanisms controlling the nuclear/cytoplasmic shuttling dynamics of both factors under physiological and tissue-damaging conditions are poorly understood. By implementing experimental in vitro data, partial differential equation modeling, as well as automated image analysis, we demonstrate that nuclear phosphorylation contributes to differences between YAP and TAZ localization in the nucleus and cytoplasm. Treatment of hepatocyte-derived cells with hepatotoxic acetaminophen (APAP) induces a biphasic protein phosphorylation eventually leading to nuclear protein enrichment of YAP but not TAZ. APAP-dependent regulation of nuclear/cytoplasmic YAP shuttling is not an unspecific cellular response but relies on the sequential induction of reactive oxygen species (ROS), RAC-alpha serine/threonine-protein kinase (AKT, synonym: protein kinase B), as well as elevated nuclear interaction between YAP and AKT. Mouse experiments confirm this sequence of events illustrated by the expression of ROS-, AKT-, and YAP-specific gene signatures upon APAP administration. In summary, our data illustrate the importance of nuclear processes in the regulation of Hippo pathway activity. YAP and TAZ exhibit different shuttling dynamics, which explains distinct cellular responses of both factors under physiological and tissue-damaging conditions.

Keywords:  DILI; Hippo pathway; TAZ; acetaminophen; computational biology; human; medicine; mouse; partial differential equations; systems biology

DOI:  https://doi.org/10.7554/eLife.78540
Proc Natl Acad Sci U S A. 2022 Oct 25. 119(43): e2209211119

14-3-3τ drives estrogen receptor loss via ERα36 induction and GATA3 inhibition in breast cancer.

Lidija A Wilhelms Garan, Yang Xiao, Weei-Chin Lin.

  About one-fourth of recurrent estrogen receptor-positive (ER+) breast cancers lose ER expression, leading to endocrine therapy failure. However, the mechanisms underlying ER loss remain to be fully explored. We now show that 14-3-3τ, up-regulated in ∼60% of breast cancer, drives the conversion of ER+ to ER- and epithelial-to-mesenchymal transition (EMT). We identify ERα36, an isoform of ERα66, as a downstream effector of 14-3-3τ. Overexpression of 14-3-3τ induces ERα36 in xenografts and tumor spheroids. The regulation is further supported by a positive correlation between ERα36 and 14-3-3τ expression in human breast cancers. ERα36 can antagonize ERα66 and inhibit ERα66 expression. Isoform-specific depletion of ERα36 blocks the ER conversion and EMT induced by 14-3-3τ overexpression in tumor spheroids, thus establishing ERα36 as a key mediator in 14-3-3τ-driven ER loss and EMT. ERα36 promoter is repressed by GATA3, which can be phosphorylated by AKT at consensus binding sites for 14-3-3. Upon AKT activation, 14-3-3τ binds phosphorylated GATA3 and facilitates the degradation of GATA3 causing GATA3 to lose transcriptional control over its target genes ERα66 and ERα36. We also demonstrate a role for the collaboration between 14-3-3τ and AKT in ERα36 induction and endocrine therapy resistance by three-dimensional spheroid and tamoxifen treatment models in MCF7 and T47D ER+ breast cancer cells. Thus, the 14-3-3τ-ERα36 regulation provides a previously unrecognized mechanism for ER loss and endocrine therapy failure.

Keywords:  14-3-3τ; 3D tumor spheroid model; ERα36; GATA3; estrogen receptor

DOI:  https://doi.org/10.1073/pnas.2209211119
Nat Commun. 2022 Oct 19. 13(1): 6182

Sublinear scaling of the cellular proteome with ploidy.

G Yahya, P Menges, P S Amponsah, D A Ngandiri, D Schulz, A Wallek, N Kulak, M Mann, P Cramer, V Savage, M Räschle, Z Storchova.

Ploidy changes are frequent in nature and contribute to evolution, functional specialization and tumorigenesis. Analysis of model organisms of different ploidies revealed that increased ploidy leads to an increase in cell and nuclear volume, reduced proliferation, metabolic changes, lower fitness, and increased genomic instability, but the underlying mechanisms remain poorly understood. To investigate how gene expression changes with cellular ploidy, we analyzed isogenic series of budding yeasts from 1N to 4N. We show that mRNA and protein abundance scales allometrically with ploidy, with tetraploid cells showing only threefold increase in protein abundance compared to haploids. This ploidy-dependent sublinear scaling occurs via decreased rRNA and ribosomal protein abundance and reduced translation. We demonstrate that the activity of Tor1 is reduced with increasing ploidy, which leads to diminished rRNA gene repression via a Tor1-Sch9-Tup1 signaling pathway. mTORC1 and S6K activity are also reduced in human tetraploid cells and the concomitant increase of the Tup1 homolog Tle1 downregulates the rDNA transcription. Our results suggest that the mTORC1-Sch9/S6K-Tup1/TLE1 pathway ensures proteome remodeling in response to increased ploidy.

DOI: https://doi.org/10.1038/s41467-022-33904-7
Nat Commun. 2022 Oct 20. 13(1): 6239

Tumor-produced and aging-associated oncometabolite methylmalonic acid promotes cancer-associated fibroblast activation to drive metastatic progression.

Zhongchi Li, Vivien Low, Valbona Luga, Janet Sun, Ethan Earlie, Bobak Parang, Kripa Shobana Ganesh, Sungyun Cho, Jennifer Endress, Tanya Schild, Mengying Hu, David Lyden, Wenbing Jin, Chunjun Guo, Noah Dephoure, Lewis C Cantley, Ashley M Laughney, John Blenis.

The systemic metabolic shifts that occur during aging and the local metabolic alterations of a tumor, its stroma and their communication cooperate to establish a unique tumor microenvironment (TME) fostering cancer progression. Here, we show that methylmalonic acid (MMA), an aging-increased oncometabolite also produced by aggressive cancer cells, activates fibroblasts in the TME, which reciprocally secrete IL-6 loaded extracellular vesicles (EVs) that drive cancer progression, drug resistance and metastasis. The cancer-associated fibroblast (CAF)-released EV cargo is modified as a result of reactive oxygen species (ROS) generation and activation of the canonical and noncanonical TGFβ signaling pathways. EV-associated IL-6 functions as a stroma-tumor messenger, activating the JAK/STAT3 and TGFβ signaling pathways in tumor cells and promoting pro-aggressive behaviors. Our findings define the role of MMA in CAF activation to drive metastatic reprogramming, unveiling potential therapeutic avenues to target MMA at the nexus of aging, the tumor microenvironment and metastasis.

DOI: https://doi.org/10.1038/s41467-022-33862-0
Curr Top Microbiol Immunol. 2022 ;436 289-309

PI3K Isoforms in Vascular Biology, A Focus on the Vascular System-Immune Response Connection.

Daniela Carnevale, Giuseppe Lembo, Sara Perrotta.

  Cardiovascular diseases are the most common cause of death around the world. Hypertension and atherosclerosis, along with their sequalae and consequent target organ damage, constitute the main vascular risk factors contributing to the onset of cardiovascular disease. Disturbances in the homeostatic relationship established among the various components of the vascular milieu-namely endothelial and smooth muscle cells, adventitia, immune cells, and fibers of the autonomic nervous system-trigger the development of these arterial pathologies. In terms of molecular targets involved in vascular dysfunction and appealing for therapeutic purposes, the multitude of functions that phosphoinositide-3-kinases (PI3K) perform has become an attractive area of investigation in the field of arterial diseases. Composed of eight members arranged in III different classes based on their structure and substrate specificity, PI3Ks are characterized by their shared capability to produce phosphoinositides but, at the same time, they provide specificity and non-redundancy, owing to differences in expression levels of each member in different cell components of the vascular environment, different activation mechanisms and specific subcellular locations. This chapter aims at providing an overview of the functions of the different PI3K isoforms identified thus far in the vasculature, focusing on the emerging relationship established by components of the vascular and immune systems, at the steady-state and during pathology.

Keywords:  Atherosclerosis; Endothelial cells; Hypertension; Immune cells; Phosphoinositide-3-kinases; Smooth muscle cells; Vascular function

DOI:  https://doi.org/10.1007/978-3-031-06566-8_12
Sci Adv. 2022 Oct 21. 8(42): eabo7676

Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing.

So Hyun Park, Mingming Cao, Yidan Pan, Timothy H Davis, Lavanya Saxena, Harshavardhan Deshmukh, Yilei Fu, Todd Treangen, Vivien A Sheehan, Gang Bao.

Most genome editing analyses to date are based on quantifying small insertions and deletions. Here, we show that CRISPR-Cas9 genome editing can induce large gene modifications, such as deletions, insertions, and complex local rearrangements in different primary cells and cell lines. We analyzed large deletion events in hematopoietic stem and progenitor cells (HSPCs) using different methods, including clonal genotyping, droplet digital polymerase chain reaction, single-molecule real-time sequencing with unique molecular identifier, and long-amplicon sequencing assay. Our results show that large deletions of up to several thousand bases occur with high frequencies at the Cas9 on-target cut sites on the HBB (11.7 to 35.4%), HBG (14.3%), and BCL11A (13.2%) genes in HSPCs and the PD-1 (15.2%) gene in T cells. Our findings have important implications to advancing genome editing technologies for treating human diseases, because unintended large gene modifications may persist, thus altering the biological functions and reducing the available therapeutic alleles.

DOI: https://doi.org/10.1126/sciadv.abo7676
Nature. 2022 Oct 20.

How to smuggle a drug into cells: add a lipid 'tail'.



Keywords:  Chemical biology

DOI:  https://doi.org/10.1038/d41586-022-03282-7
Nat Commun. 2022 Oct 17. 13(1): 6118

Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space.

Lei Xiong, Kang Tian, Yuzhe Li, Weixi Ning, Xin Gao, Qiangfeng Cliff Zhang.

Computational tools for integrative analyses of diverse single-cell experiments are facing formidable new challenges including dramatic increases in data scale, sample heterogeneity, and the need to informatively cross-reference new data with foundational datasets. Here, we present SCALEX, a deep-learning method that integrates single-cell data by projecting cells into a batch-invariant, common cell-embedding space in a truly online manner (i.e., without retraining the model). SCALEX substantially outperforms online iNMF and other state-of-the-art non-online integration methods on benchmark single-cell datasets of diverse modalities, (e.g., single-cell RNA sequencing, scRNA-seq, single-cell assay for transposase-accessible chromatin use sequencing, scATAC-seq), especially for datasets with partial overlaps, accurately aligning similar cell populations while retaining true biological differences. We showcase SCALEX's advantages by constructing continuously expandable single-cell atlases for human, mouse, and COVID-19 patients, each assembled from diverse data sources and growing with every new data. The online data integration capacity and superior performance makes SCALEX particularly appropriate for large-scale single-cell applications to build upon previous scientific insights.

DOI: https://doi.org/10.1038/s41467-022-33758-z
Elife. 2022 Oct 21. pii: e76535. [Epub ahead of print]11

Landscape of epithelial mesenchymal plasticity as an emergent property of coordinated teams in regulatory networks.

Kishore Hari, Varun Ullanat, Archana Balasubramanian, Aditi Gopalan, Mohit Kumar Jolly.

  Elucidating the design principles of regulatory networks driving cellular decision-making has fundamental implications in mapping and eventually controlling cell-fate decisions. Despite being complex, these regulatory networks often only give rise to a few phenotypes. Previously, we identified two 'teams' of nodes in a small cell lung cancer regulatory network that constrained the phenotypic repertoire and aligned strongly with the dominant phenotypes obtained from network simulations (Chauhan et al., 2021). However, it remained elusive whether these 'teams' exist in other networks, and how do they shape the phenotypic landscape. Here, we demonstrate that five different networks of varying sizes governing epithelial-mesenchymal plasticity comprised of two 'teams' of players - one comprised of canonical drivers of epithelial phenotype and the other containing the mesenchymal inducers. These 'teams' are specific to the topology of these regulatory networks and orchestrate a bimodal phenotypic landscape with the epithelial and mesenchymal phenotypes being more frequent and dynamically robust to perturbations, relative to the intermediary/hybrid epithelial/ mesenchymal ones. Our analysis reveals that network topology alone can contain information about corresponding phenotypic distributions, thus obviating the need to simulate them. We propose 'teams' of nodes as a network design principle that can drive cell-fate canalization in diverse decision-making processes.

Keywords:  computational biology; none; physics of living systems; systems biology

DOI:  https://doi.org/10.7554/eLife.76535
Mol Metab. 2022 Oct 14. pii: S2212-8778(22)00184-3. [Epub ahead of print] 101615

Resistance exercise enhances long-term mTORC1 sensitivity to leucine.

Gommaar D'Hulst, Evi Masschelein, Katrien De Bock.

  OBJECTIVE: Exercise enhances the sensitivity of mammalian target of rapamycin complex 1 (mTORC1) to amino acids, in particular leucine. How long this enhanced sensitivity lasts, and which mechanisms control enhanced leucine-mediated mTORC1 activation following exercise is currently unknown.METHODS: C57BL/6J mice were exercised for one night in a resistance-braked running wheel after a 12-day acclimatization period. Mice were gavaged with a submaximal dose of L-leucine or saline acutely or 48 hours after exercise cessation, following 3 h food withdrawal. Muscles were excised 30 min after leucine administration. To study the contribution of mTORC1, we repeated those experiments but blocked mTORC1 activation using rapamycin immediately before the overnight running bout and one hour before the first dose of leucine. mTORC1 signaling, muscle protein synthesis and amino acid sensing machinery were assessed using immunoblot and qPCR. Leucine uptake was measured using L-[14C(U)]-leucine tracer labeling.
RESULTS: When compared to sedentary conditions, leucine supplementation more potently activated mTORC1 and protein synthesis in acutely exercised muscle. This effect was observed in m. soleus but not in m. tibialis anterior nor m. plantaris. The synergistic effect in m. soleus was long-lasting as key downstream markers of mTORC1 as well as protein synthesis remained higher when leucine was administered 48 h after exercise. We found that exercise enhanced the expression of amino acid transporters and promoted uptake of leucine into the muscle, leading to higher free intramuscular leucine levels. This coincided with increased expression of activating transcription factor 4 (ATF4), a main transcriptional regulator of amino acid uptake and metabolism, and downstream activation of amino acid genes as well as leucyl-tRNA synthetase (LARS), a putative leucine sensor. Finally, blocking mTORC1 using rapamycin did not reduce expression and activation of ATF4, suggesting that the latter does not act downstream of mTORC1. Rather, we found a robust increase in eukaryotic initiation factor 2α (eIF2α) phosphorylation, suggesting that the integrated stress response pathway, rather than exercise-induced mTORC1 activation, drives long-term ATF4 expression in skeletal muscle after exercise.
CONCLUSIONS: The enhanced sensitivity of mTORC1 to leucine is maintained at least 48 h after exercise. This shows that the anabolic window of opportunity for protein ingestion is not restricted to the first hours immediately following exercise. Increased mTORC1 sensitivity to leucine coincided with enhanced leucine influx into muscle and higher expression of genes involved in leucine sensing and amino acid metabolism. Also, exercise induced an increase in ATF4 protein expression. Altogether, these data suggest that muscular contractions switch on a coordinated program to enhance amino acid uptake as well as intramuscular sensing of key amino acids involved in mTORC1 activation and the stimulation of muscle protein synthesis.

Keywords:  ATF4; exercise; leucine; mTOR; sensitivity

DOI:  https://doi.org/10.1016/j.molmet.2022.101615
J Clin Invest. 2022 10 17. pii: e165312. [Epub ahead of print]132(20):

Tugs-of-war in science.

Mitchell A Lazar.

DOI: https://doi.org/10.1172/JCI165312
Nat Methods. 2022 Oct 21.

ShareLoc - an open platform for sharing localization microscopy data.

Wei Ouyang, Jiachuan Bai, Manish Kumar Singh, Christophe Leterrier, Paul Barthelemy, Samuel F H Barnett, Teresa Klein, Markus Sauer, Pakorn Kanchanawong, Nicolas Bourg, Mickael M Cohen, Benoît Lelandais, Christophe Zimmer.

DOI: https://doi.org/10.1038/s41592-022-01659-0