bims-pideca 2022-02-13 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2022–02–13
fifteen papers selected by
Ralitsa Radostinova Madsen, University College London

Alpelisib to treat CLOVES syndrome, a member of the PIK3CA-related overgrowth syndrome spectrum.
Response to Alpelisib in Clinically Distinct Pediatric Patients With PIK3CA-related Disorders.
Phase II Study of Copanlisib in Patients With Tumors With PIK3CA Mutations: Results From the NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocol Z1F.
Phase II Study of Taselisib in PIK3CA-Mutated Solid Tumors Other Than Breast and Squamous Lung Cancer: Results From the NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocol I.
GLUT4 On the move.
dCas9-based gene editing for cleavage-free genomic knock-in of long sequences.
Structural mechanism of allosteric activation of TRPML1 by PI(3,5)P2 and rapamycin.
CRAF dimerization with ARAF regulates KRAS-driven tumor growth.
Phase 1b Clinical Trial with Alpelisib plus Olaparib for Patients with Advanced Triple-Negative Breast Cancer.
Beta-cell specific Insr deletion promotes insulin hypersecretion and improves glucose tolerance prior to global insulin resistance.
Experimental manipulation of phosphoinositide lipids: from cells to organisms.
Autoreactive antibodies control blood glucose by regulating insulin homeostasis.
Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types.
Phosphoinositide-binding protein TIPE1 promotes alternative activation of macrophages and tumor progression via PIP3/Akt/TGF-β axis.
Glioblastoma mutations alter EGFR dimer structure to prevent ligand bias.

Br J Clin Pharmacol. 2022 Feb 10.

Alpelisib to treat CLOVES syndrome, a member of the PIK3CA-related overgrowth syndrome spectrum.

Gemma Garreta Fontelles, Júlia Pardo Pastor, Carme Grande Moreillo.

  CLOVES syndrome is a rare congenital overgrowth disorder caused by mutations in the phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) gene. It is part of the PIK3CA-related overgrowth syndrome (PROS) spectrum and its treatment is challenging. PROS malformations have traditionally been treated by surgery, but research into pharmacological treatments capable of blocking the PIK/AKT/mTOR pathway has increased over the past decade. The results have been promising and suggest that compassionate use of these treatments in patients with PROS disorders could have clinical benefits. Another promising drug is alpelisib (BYL719), which is a selective inhibitor that competitively binds to the p110a subunit of PIK3 in the intracellular PI3K/AKT signaling pathway. Compassionate use of low-dose alpelisib had striking effects in an uncontrolled case series of 19 PROS patients, several with life-threatening complications. Moreover, there were few adverse effects and the treatment did not impair linear growth, despite the young age of many of the patients. We present the case of a patient with CLOVES syndrome who was started on compassionate treatment with alpelisib after surgical debulking of a cystic lymphangioma and treatment with sirolimus. This promising drug significantly reduced the size of the lymphangioma and prevented progression of the tissue overgrowth in the gluteal region. This case suggests that low-dose PI3K inhibition may provide collateral benefits that extend beyond mitigation of disease-specific features of PROS.

Keywords:  Clinical Pharmacology; Congenital Disorders; Genetic Diseases; Genetics and Pharmacogenetics; Molecular Biology; Molecular Pharmacology; Paediatrics; Patient safety; Pharmacotherapy

DOI:  https://doi.org/10.1111/bcp.15270
J Pediatr Hematol Oncol. 2022 Feb 04.

Response to Alpelisib in Clinically Distinct Pediatric Patients With PIK3CA-related Disorders.

Elysha Kolitz, Neil J Fernandes, Nnenna G Agim, Kathleen Ludwigl.

PIK3CA-related disorders include vascular malformations, potential overgrowth of various tissues, limb abnormalities, disordered soft tissue, and/or fatty hyperplasia that often leads to significant morbidity. Alpelisib, a targeted inhibitor of p110α, an enzyme encoded by the PIK3CA gene, has demonstrated success in a cohort of patients with PIK3CA-driven overgrowth syndromes. We describe the clinical course of 2 pediatric patients treated with alpelisib under the Novartis Managed Access Program. Both patients, though clinically distinct, demonstrate improvements in overgrowth volumes/extent, function of their affected limb, and quality of life, without significant adverse effects after prolonged treatment.

DOI: https://doi.org/10.1097/MPH.0000000000002418
J Clin Oncol. 2022 Feb 08. JCO2101648

Phase II Study of Copanlisib in Patients With Tumors With PIK3CA Mutations: Results From the NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocol Z1F.

Senthil Damodaran, Fengmin Zhao, Dustin A Deming, Edith P Mitchell, John J Wright, Robert J Gray, Victoria Wang, Lisa M McShane, Larry V Rubinstein, David R Patton, P Mickey Williams, Stanley R Hamilton, Jennifer M Suga, Barbara A Conley, Carlos L Arteaga, Lyndsay N Harris, Peter J O'Dwyer, Alice P Chen, Keith T Flaherty.

PURPOSE: Activating mutations in PIK3CA are observed across multiple tumor types. The NCI-MATCH (EAY131) is a tumor-agnostic platform trial that enrolls patients to targeted therapies on the basis of matching genomic alterations. Arm Z1F evaluated copanlisib, an α and δ isoform-specific phosphoinositide 3-kinase (PI3K) inhibitor, in patients with PIK3CA mutations (with or without PTEN loss).
PATIENTS AND METHODS: Patients received copanlisib (60 mg intravenous) once weekly on days 1, 8, and 15 in 28-day cycles until progression or toxicity. Patients with KRAS mutations, human epidermal growth factor receptor 2-positive breast cancers, and lymphomas were excluded. The primary end point was centrally assessed objective response rate (ORR); secondary end points included progression-free survival, 6-month progression-free survival, and overall survival.
RESULTS: Thirty-five patients were enrolled, and 25 patients were included in the primary efficacy analysis as prespecified in the protocol. Multiple histologies were enrolled, with gynecologic (n = 6) and gastrointestinal (n = 6) being the most common. Sixty-eight percent of patients had ≥ 3 lines of prior therapy. The ORR was 16% (4 of 25, 90% CI, 6 to 33) with P = .0341 against a null rate of 5%. The most common reason for protocol discontinuation was disease progression (n = 17, 68%). Grade 3/4 toxicities observed were consistent with reported toxicities for PI3K pathway inhibition. Sixteen patients (53%) had grade 3 toxicities, and one patient (3%) had grade 4 toxicity (CTCAE v5.0). Most common toxicities include hyperglycemia (n = 19), fatigue (n = 12), diarrhea (n = 11), hypertension (n = 10), and nausea (n = 10).
CONCLUSION: The study met its primary end point with an ORR of 16% (P = .0341) with copanlisib showing clinical activity in select tumors with PIK3CA mutation in the refractory setting.

DOI: https://doi.org/10.1200/JCO.21.01648
JCO Precis Oncol. 2022 Feb;6 e2100424

Phase II Study of Taselisib in PIK3CA-Mutated Solid Tumors Other Than Breast and Squamous Lung Cancer: Results From the NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocol I.

Ian E Krop, Opeyemi A Jegede, Juneko E Grilley-Olson, Josh D Lauring, Edith P Mitchell, James A Zwiebel, Robert J Gray, Victoria Wang, Lisa M McShane, Larry V Rubinstein, David Patton, P Mickey Williams, Stanley R Hamilton, Scott A Kono, James M Ford, Agustin A Garcia, Xingwei D Sui, Robert D Siegel, Brian M Slomovitz, Barbara A Conley, Carlos L Arteaga, Lyndsay N Harris, Peter J O'Dwyer, Alice P Chen, Keith T Flaherty.

PURPOSE: PIK3CA mutations frequently contribute to oncogenesis in solid tumors. Taselisib, a potent and selective inhibitor of phosphoinositide 3-kinase, has demonstrated clinical activity in PIK3CA-mutant breast cancer. Whether PIK3CA mutations predict sensitivity to taselisib in other cancer types is unknown. National Cancer Institute-Molecular Analysis for Therapy Choice Arm EAY131-I is a single-arm, phase II study of the safety and efficacy of taselisib in patients with advanced cancers.
METHODS: Eligible patients had tumors with an activating PIK3CA mutation. Patients with breast or squamous cell lung carcinoma, or whose cancer had KRAS or PTEN mutations, were excluded. Patients received taselisib 4 mg, orally once daily continuously, until disease progression or unacceptable toxicity. The primary end point was objective response rate. Secondary end points included progression-free survival (PFS), 6-month PFS, overall survival (OS), and identification of predictive biomarkers.
RESULTS: Seventy patients were enrolled, and 61 were eligible and initiated protocol therapy. Types of PIK3CA mutations included helical 41 of 61 (67%), kinase 11 of 61 (18%), and other 9 of 61 (15%). With a median follow-up of 35.7 months, there were no complete or partial responses. Six-month PFS was 19.9% (90% CI, 12.0 to 29.3) and median PFS was 3.1 months (90% CI, 1.8 to 3.7). Six-month OS was 60.7% (90% CI, 49.6 to 70.0) and median OS was 7.2 months (90% CI, 5.9 to 10.0). Individual comutations were too heterogeneous to correlate with clinical outcome. Fatigue, diarrhea, nausea, and hyperglycemia were the most common toxicities, and most were grade 1 and 2.
CONCLUSION: In this study, taselisib monotherapy had very limited activity in a heterogeneous cohort of heavily pretreated cancer patients with PIK3CA-mutated tumors; the presence of a PIK3CA mutation alone does not appear to be a sufficient predictor of taselisib activity.

DOI: https://doi.org/10.1200/PO.21.00424
Biochem J. 2022 Feb 11. 479(3): 445-462

GLUT4 On the move.

Daniel J Fazakerley, Francoise Koumanov, Geoffrey D Holman.

  Insulin rapidly stimulates GLUT4 translocation and glucose transport in fat and muscle cells. Signals from the occupied insulin receptor are translated into downstream signalling changes in serine/threonine kinases within timescales of seconds, and this is followed by delivery and accumulation of the glucose transporter GLUT4 at the plasma membrane. Kinetic studies have led to realisation that there are distinct phases of this stimulation by insulin. There is a rapid initial burst of GLUT4 delivered to the cell surface from a subcellular reservoir compartment and this is followed by a steady-state level of continuing stimulation in which GLUT4 recycles through a large itinerary of subcellular locations. Here, we provide an overview of the phases of insulin stimulation of GLUT4 translocation and the molecules that are currently considered to activate these trafficking steps. Furthermore, we suggest how use of new experimental approaches together with phospho-proteomic data may help to further identify mechanisms for activation of these trafficking processes.

Keywords:  GLUT4; glucose transport; insulin; membrane traffic; membrane trafficking kinetics; signal transduction

DOI:  https://doi.org/10.1042/BCJ20210073
Nat Cell Biol. 2022 Feb 10.

dCas9-based gene editing for cleavage-free genomic knock-in of long sequences.

Chengkun Wang, Yuanhao Qu, Jason K W Cheng, Nicholas W Hughes, Qianhe Zhang, Mengdi Wang, Le Cong.

Gene editing is a powerful tool for genome and cell engineering. Exemplified by CRISPR-Cas, gene editing could cause DNA damage and trigger DNA repair processes that are often error-prone. Such unwanted mutations and safety concerns can be exacerbated when altering long sequences. Here we couple microbial single-strand annealing proteins (SSAPs) with catalytically inactive dCas9 for gene editing. This cleavage-free gene editor, dCas9-SSAP, promotes the knock-in of long sequences in mammalian cells. The dCas9-SSAP editor has low on-target errors and minimal off-target effects, showing higher accuracy than canonical Cas9 methods. It is effective for inserting kilobase-scale sequences, with an efficiency of up to approximately 20% and robust performance across donor designs and cell types, including human stem cells. We show that dCas9-SSAP is less sensitive to inhibition of DNA repair enzymes than Cas9 references. We further performed truncation and aptamer engineering to minimize its size to fit into a single adeno-associated-virus vector for future application. Together, this tool opens opportunities towards safer long-sequence genome engineering.

DOI: https://doi.org/10.1038/s41556-021-00836-1
Proc Natl Acad Sci U S A. 2022 Feb 15. pii: e2120404119. [Epub ahead of print]119(7):

Structural mechanism of allosteric activation of TRPML1 by PI(3,5)P2 and rapamycin.

Ninghai Gan, Yan Han, Weizhong Zeng, Yan Wang, Jing Xue, Youxing Jiang.

  Transient receptor potential mucolipin 1 (TRPML1) is a Ca2+-permeable, nonselective cation channel ubiquitously expressed in the endolysosomes of mammalian cells and its loss-of-function mutations are the direct cause of type IV mucolipidosis (MLIV), an autosomal recessive lysosomal storage disease. TRPML1 is a ligand-gated channel that can be activated by phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2] as well as some synthetic small-molecule agonists. Recently, rapamycin has also been shown to directly bind and activate TRPML1. Interestingly, both PI(3,5)P2 and rapamycin have low efficacy in channel activation individually but together they work cooperatively and activate the channel with high potency. To reveal the structural basis underlying the synergistic activation of TRPML1 by PI(3,5)P2 and rapamycin, we determined the high-resolution cryoelectron microscopy (cryo-EM) structures of the mouse TRPML1 channel in various states, including apo closed, PI(3,5)P2-bound closed, and PI(3,5)P2/temsirolimus (a rapamycin analog)-bound open states. These structures, combined with electrophysiology, elucidate the molecular details of ligand binding and provide structural insight into how the TRPML1 channel integrates two distantly bound ligand stimuli and facilitates channel opening.

Keywords:  PI(3,5)P2; TRPML1; lysosomal channel; rapamycin

DOI:  https://doi.org/10.1073/pnas.2120404119
Cell Rep. 2022 Feb 08. pii: S2211-1247(22)00067-5. [Epub ahead of print]38(6): 110351

CRAF dimerization with ARAF regulates KRAS-driven tumor growth.

Avinashnarayan Venkatanarayan, Jason Liang, Ivana Yen, Frances Shanahan, Benjamin Haley, Lilian Phu, Erik Verschueren, Trent B Hinkle, David Kan, Ehud Segal, Jason E Long, Tony Lima, Nicholas P D Liau, Jawahar Sudhamsu, Jason Li, Christiaan Klijn, Robert Piskol, Melissa R Junttila, Andrey S Shaw, Mark Merchant, Matthew T Chang, Donald S Kirkpatrick, Shiva Malek.

  KRAS, which is mutated in ∼30% of all cancers, activates the RAF-MEK-ERK signaling cascade. CRAF is required for growth of KRAS mutant lung tumors, but the requirement for CRAF kinase activity is unknown. Here, we show that subsets of KRAS mutant tumors are dependent on CRAF for growth. Kinase-dead but not dimer-defective CRAF rescues growth inhibition, suggesting that dimerization but not kinase activity is required. Quantitative proteomics demonstrates increased levels of CRAF:ARAF dimers in KRAS mutant cells, and depletion of both CRAF and ARAF rescues the CRAF-loss phenotype. Mechanistically, CRAF depletion causes sustained ERK activation and induction of cell-cycle arrest, while treatment with low-dose MEK or ERK inhibitor rescues the CRAF-loss phenotype. Our studies highlight the role of CRAF in regulating MAPK signal intensity to promote tumorigenesis downstream of mutant KRAS and suggest that disrupting CRAF dimerization or degrading CRAF may have therapeutic benefit.

Keywords:  ARAF; BRAF; CRAF; ERK; KRAS; MAPK; MEK; cancer; dimerization; kinase

DOI:  https://doi.org/10.1016/j.celrep.2022.110351
Clin Cancer Res. 2022 Feb 11. pii: clincanres.3045.2021. [Epub ahead of print]

Phase 1b Clinical Trial with Alpelisib plus Olaparib for Patients with Advanced Triple-Negative Breast Cancer.

Felipe Batalini, Niya Xiong, Nabihah Tayob, Madeline Polak, Julia Eismann, Lewis C Cantley, Geoffrey I Shapiro, Viktor Adalsteinsson, Eric P Winer, Panagiotis A Konstantinopoulos, Alan D D'Andrea, Elizabeth M Swisher, Ursula A Matulonis, Gerburg M Wulf, Erica L Mayer.

PURPOSE: We had previously reported on the safety and the recommended phase 2 dose (RP2D) of olaparib in combination with the PI3Kα-specific inhibitor alpelisib in patients with high-grade serous ovarian cancer as studied in a phase 1b trial (NCT01623349). Here we report on the breast cancer cohort from that study.
EXPERIMENTAL DESIGN: Eligible patients had recurrent triple-negative breast cancer (TNBC), or recurrent breast cancer of any subtype with a germline BRCA mutation and were enrolled to a dose escalation or expansion cohort. After definition of the RP2D, secondary end points included safety and objective response rate (ORR). Exploratory analyses were performed using circulating free DNA (cfDNA).
RESULTS: 17 patients with TNBC were enrolled with a median of 3 prior lines of chemotherapy. The most common treatment-related grade 3-4 adverse events were hyperglycemia (18%) and rash (12%). The ORR was 18% (23% for patients treated at the RP2D) and 59% had disease control. The median duration of response was 7.4 months. Analysis of cfDNA tumor fractions (TFx) revealed that patients with TFx<15% after completion of the first cycle had a longer progression-free survival compared to those with TFx>15% (6.0 months vs 0.9 months, p=0.0001).
CONCLUSIONS: Alpelisib in combination with olaparib is tolerable in patients with pre-treated TNBC, with evidence of activity in non-BRCA carriers. CfDNA provided important prognostic information. Results highlight potential synergistic use of a PI3Ki to sensitize HR-proficient (BRCA wild-type) TNBC to PARPi and suggest the potential to expand the use of PARPi beyond BRCA-mutant tumors.

DOI: https://doi.org/10.1158/1078-0432.CCR-21-3045
Nat Commun. 2022 Feb 08. 13(1): 735

Beta-cell specific Insr deletion promotes insulin hypersecretion and improves glucose tolerance prior to global insulin resistance.

Søs Skovsø, Evgeniy Panzhinskiy, Jelena Kolic, Haoning Howard Cen, Derek A Dionne, Xiao-Qing Dai, Rohit B Sharma, Lynda Elghazi, Cara E Ellis, Katharine Faulkner, Stephanie A M Marcil, Peter Overby, Nilou Noursadeghi, Daria Hutchinson, Xiaoke Hu, Hong Li, Honey Modi, Jennifer S Wildi, J Diego Botezelli, Hye Lim Noh, Sujin Suk, Brian Gablaski, Austin Bautista, Ryekjang Kim, Corentin Cras-Méneur, Stephane Flibotte, Sunita Sinha, Dan S Luciani, Corey Nislow, Elizabeth J Rideout, Eric N Cytrynbaum, Jason K Kim, Ernesto Bernal-Mizrachi, Laura C Alonso, Patrick E MacDonald, James D Johnson.

Insulin receptor (Insr) protein is present at higher levels in pancreatic β-cells than in most other tissues, but the consequences of β-cell insulin resistance remain enigmatic. Here, we use an Ins1cre knock-in allele to delete Insr specifically in β-cells of both female and male mice. We compare experimental mice to Ins1cre-containing littermate controls at multiple ages and on multiple diets. RNA-seq of purified recombined β-cells reveals transcriptomic consequences of Insr loss, which differ between female and male mice. Action potential and calcium oscillation frequencies are increased in Insr knockout β-cells from female, but not male mice, whereas only male βInsrKO islets have reduced ATP-coupled oxygen consumption rate and reduced expression of genes involved in ATP synthesis. Female βInsrKO and βInsrHET mice exhibit elevated insulin release in ex vivo perifusion experiments, during hyperglycemic clamps, and following i.p. glucose challenge. Deletion of Insr does not alter β-cell area up to 9 months of age, nor does it impair hyperglycemia-induced proliferation. Based on our data, we adapt a mathematical model to include β-cell insulin resistance, which predicts that β-cell Insr knockout improves glucose tolerance depending on the degree of whole-body insulin resistance. Indeed, glucose tolerance is significantly improved in female βInsrKO and βInsrHET mice compared to controls at 9, 21 and 39 weeks, and also in insulin-sensitive 4-week old males. We observe no improved glucose tolerance in older male mice or in high fat diet-fed mice, corroborating the prediction that global insulin resistance obscures the effects of β-cell specific insulin resistance. The propensity for hyperinsulinemia is associated with mildly reduced fasting glucose and increased body weight. We further validate our main in vivo findings using an Ins1-CreERT transgenic line and find that male mice have improved glucose tolerance 4 weeks after tamoxifen-mediated Insr deletion. Collectively, our data show that β-cell insulin resistance in the form of reduced β-cell Insr contributes to hyperinsulinemia in the context of glucose stimulation, thereby improving glucose homeostasis in otherwise insulin sensitive sex, dietary and age contexts.

DOI: https://doi.org/10.1038/s41467-022-28039-8
Trends Cell Biol. 2022 Feb 05. pii: S0962-8924(22)00024-1. [Epub ahead of print]

Experimental manipulation of phosphoinositide lipids: from cells to organisms.

Mehdi Doumane, Marie-Cécile Caillaud, Yvon Jaillais.

  Phosphoinositides (PIs) have critical roles in various cellular, physiological, developmental, pathological, and infectious processes. They are signaling phospholipids that can affect every aspect of membrane biology, including protein function (e.g., recruitment and activity), membrane physicochemical properties (e.g., curvature, surface charges, and packing), and the generation of secondary messengers. PIs act at precise locations within the cell in a dose-dependent manner, and their local concentration can vary drastically during signaling and trafficking. Thus, techniques able to manipulate PI amounts acutely and with subcellular accuracy are paramount to understanding the role of these lipids in vivo. Here, we review these methods and emphasize approaches recently developed to perturb PI levels in multicellular organisms.

Keywords:  lipid; membrane; model organism; optogenetics; targeted manipulation

DOI:  https://doi.org/10.1016/j.tcb.2022.01.009
Proc Natl Acad Sci U S A. 2022 Feb 08. pii: e2115695119. [Epub ahead of print]119(6):

Autoreactive antibodies control blood glucose by regulating insulin homeostasis.

Timm Amendt, Gabriele Allies, Antonella Nicolò, Omar El Ayoubi, Marc Young, Tamás Röszer, Corinna S Setz, Klaus Warnatz, Hassan Jumaa.

  Homeostasis of metabolism by hormone production is crucial for maintaining physiological integrity, as disbalance can cause severe metabolic disorders such as diabetes mellitus. Here, we show that antibody-deficient mice and immunodeficiency patients have subphysiological blood glucose concentrations. Restoring blood glucose physiology required total IgG injections and insulin-specific IgG antibodies detected in total IgG preparations and in the serum of healthy individuals. In addition to the insulin-neutralizing anti-insulin IgG, we identified two fractions of anti-insulin IgM in the serum of healthy individuals. These autoreactive IgM fractions differ in their affinity to insulin. Interestingly, the low-affinity IgM fraction (anti-insulin IgMlow) neutralizes insulin and leads to increased blood glucose, whereas the high-affinity IgM fraction (anti-insulin IgMhigh) protects insulin from neutralization by anti-insulin IgG, thereby preventing blood glucose dysregulation. To demonstrate that anti-insulin IgMhigh acts as a protector of insulin and counteracts insulin neutralization by anti-insulin IgG, we expressed the variable regions of a high-affinity anti-insulin antibody as IgG and IgM. Remarkably, the recombinant anti-insulin IgMhigh normalized insulin function and prevented IgG-mediated insulin neutralization. These results suggest that autoreactive antibodies recognizing insulin are key regulators of blood glucose and metabolism, as they control the concentration of insulin in the blood. Moreover, our data suggest that preventing autoimmune damage and maintaining physiological homeostasis requires adaptive tolerance mechanisms generating high-affinity autoreactive IgM antibodies during memory responses.

Keywords:  B cells; IgG; IgM; aging; autoimmunity

DOI:  https://doi.org/10.1073/pnas.2115695119
Elife. 2022 02 10. pii: e71361. [Epub ahead of print]11

Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types.

Katherine Rhodes, Kenneth A Barr, Joshua M Popp, Benjamin J Strober, Alexis Battle, Yoav Gilad.

  Practically all studies of gene expression in humans to date have been performed in a relatively small number of adult tissues. Gene regulation is highly dynamic and context-dependent. In order to better understand the connection between gene regulation and complex phenotypes, including disease, we need to be able to study gene expression in more cell types, tissues, and states that are relevant to human phenotypes. In particular, we need to characterize gene expression in early development cell types, as mutations that affect developmental processes may be of particular relevance to complex traits. To address this challenge, we propose to use embryoid bodies (EBs), which are organoids that contain a multitude of cell types in dynamic states. EBs provide a system in which one can study dynamic regulatory processes at an unprecedentedly high resolution. To explore the utility of EBs, we systematically explored cellular and gene expression heterogeneity in EBs from multiple individuals. We characterized the various cell types that arise from EBs, the extent to which they recapitulate gene expression in vivo, and the relative contribution of technical and biological factors to variability in gene expression, cell composition, and differentiation efficiency. Our results highlight the utility of EBs as a new model system for mapping dynamic inter-individual regulatory differences in a large variety of cell types.

Keywords:  embryoid bodies; genetics; genomics; human; iPSC; scRNA-seq; single cell

DOI:  https://doi.org/10.7554/eLife.71361
Cancer Res. 2022 Feb 08. pii: canres.0003.2021. [Epub ahead of print]

Phosphoinositide-binding protein TIPE1 promotes alternative activation of macrophages and tumor progression via PIP3/Akt/TGF-β axis.

Yang Cheng, Fuxiang Bai, Xiaolei Ren, Renhui Sun, Xiaowei Guo, Wen Liu, Bo Wang, Yongheng Yang, Xiaolu Zhang, Yong Xu, Chunyang Li, Xiaoyun Yang, Lifen Gao, Chunhong Ma, Xueen Li, Xiaohong Liang.

Macrophages perform key and distinct functions in maintaining tissue homeostasis by finely tuning their activation state. Within the tumor microenvironment, macrophages are reshaped to drive tumor progression. Here we report that tumor necrosis factor α-induced protein 8-like 1 (TIPE1) is highly expressed in macrophages, and that depletion of TIPE1 impedes alternative activation of macrophages. TIPE1 enhanced activation of the PI3K/Akt pathway in macrophages by directly binding with and regulating the metabolism of phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylinositol 3,4,5-trisphosphate (PIP3). Accordingly, inhibition of the PI3K/Akt pathway significantly attenuated the effect of TIPE1 on macrophage alternative activation. Tumor-associated macrophages (TAM) in human liver cancer and melanoma tissues showed significantly upregulated TIPE1 expression that negatively correlated with patient survival. In vitro and in vivo, TIPE1 knockdown in macrophages retarded the growth and metastasis of liver cancer and melanoma. Furthermore, blockade or depletion of TGF-β signaling in macrophages abrogated the effects of TIPE1 on tumor cell growth and migration. Together, these results highlight that the phosphoinositide-related signaling pathway involves reprogramming tumor-associated macrophages to optimize the microenvironment for cancer progression.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-0003
Nature. 2022 Feb 09.

Glioblastoma mutations alter EGFR dimer structure to prevent ligand bias.

Chun Hu, Carlos A Leche, Anatoly Kiyatkin, Zhaolong Yu, Steven E Stayrook, Kathryn M Ferguson, Mark A Lemmon.

The epidermal growth factor receptor (EGFR) is frequently mutated in human cancer1,2, and is an important therapeutic target. EGFR inhibitors have been successful in lung cancer, where mutations in the intracellular tyrosine kinase domain activate the receptor1, but not in glioblastoma multiforme (GBM)3, where mutations occur exclusively in the extracellular region. Here we show that common extracellular GBM mutations prevent EGFR from discriminating between its activating ligands4. Different growth factor ligands stabilize distinct EGFR dimer structures5 that signal with different kinetics to specify or bias outcome5,6. EGF itself induces strong symmetric dimers that signal transiently to promote proliferation. Epiregulin (EREG) induces much weaker asymmetric dimers that drive sustained signalling and differentiation5. GBM mutations reduce the ability of EGFR to distinguish EREG from EGF in cellular assays, and allow EGFR to form strong (EGF-like) dimers in response to EREG and other low-affinity ligands. Using X-ray crystallography, we further show that the R84K GBM mutation symmetrizes EREG-driven extracellular dimers so that they resemble dimers normally seen with EGF. By contrast, a second GBM mutation, A265V, remodels key dimerization contacts to strengthen asymmetric EREG-driven dimers. Our results argue for an important role of altered ligand discrimination by EGFR in GBM, with potential implications for therapeutic targeting.

DOI: https://doi.org/10.1038/s41586-021-04393-3