bims-pideca 2022-04-10 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2022‒04‒10
29 papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute

Activation of the essential kinase PDK1 by phosphoinositide-driven trans-autophosphorylation.
Roles for 3' Phosphoinositides in Macropinocytosis.
A suspension technique for efficient large-scale cancer organoid culturing and perturbation screens.
Somatic activating BRAF variants cause isolated lymphatic malformations.
Circling back to PTEN: Fumarate inhibits canonical tumor suppressor.
Systemic Deficiency of PTEN Accelerates Breast Cancer Growth and Metastasis.
The Small GTPase RHOA Links SLP65 Activation to PTEN Function in Pre B Cells and Is Essential for the Generation and Survival of Normal and Malignant B Cells.
Targeting mTOR in the context of diet and whole-body metabolism.
Prostaglandin E2-Induced AKT Activation Regulates the Life Span of Short-Lived Plasma Cells by Attenuating IRE1α Hyperactivation.
The Amoebal Model for Macropinocytosis.
Signaling Pathways that Regulate Macropinocytosis in Mammalian Cells.
A Comprehensive Survey of Genomic Mutations in Breast Cancer Reveals Recurrent Neoantigens as Potential Therapeutic Targets.
Single-molecule, quantitative detection of low-abundance somatic mutations by high-throughput sequencing.
acorde unravels functionally interpretable networks of isoform co-usage from single cell data.
Brain charts for the human lifespan.
A split prime editor with untethered reverse transcriptase and circular RNA template.
Studying extrachromosomal DNA with the ecTag method.
Genome-wide analysis of somatic noncoding mutation patterns in cancer.
The hexosamine pathway and coat complex II promote malignant adaptation to nutrient scarcity.
Opposite physiological and pathological mTORC1-mediated roles of the CB1 receptor in regulating renal tubular function.
Pulsatile Basal Insulin Secretion is Driven by Glycolytic Oscillations.
Pan-cancer analysis on the role of PIK3R1 and PIK3R2 in human tumors.
Mapping the energetic and allosteric landscapes of protein binding domains.
Quantitative live-cell imaging of GPCR downstream signaling dynamics.
Compartmentalized metabolism supports midgestation mammalian development.
Physical and functional interactome atlas of human receptor tyrosine kinases.
NRASQ61R mutation in human endothelial cells causes vascular malformations.
An amino acid-defined diet impairs tumour growth in mice by promoting endoplasmic reticulum stress and mTOR inhibition.
A small-molecule cocktail promotes mammalian cardiomyocyte proliferation and heart regeneration.

Nat Commun. 2022 Apr 06. 13(1): 1874

Activation of the essential kinase PDK1 by phosphoinositide-driven trans-autophosphorylation.

Aleksandra Levina, Kaelin D Fleming, John E Burke, Thomas A Leonard.

3-phosphoinositide-dependent kinase 1 (PDK1) is an essential serine/threonine protein kinase, which plays a crucial role in cell growth and proliferation. It is often referred to as a 'master' kinase due to its ability to activate at least 23 downstream protein kinases implicated in various signaling pathways. In this study, we have elucidated the mechanism of phosphoinositide-driven PDK1 auto-activation. We show that PDK1 trans-autophosphorylation is mediated by a PIP3-mediated face-to-face dimer. We report regulatory motifs in the kinase-PH interdomain linker that allosterically activate PDK1 autophosphorylation via a linker-swapped dimer mechanism. Finally, we show that PDK1 is autoinhibited by its PH domain and that positive cooperativity of PIP3 binding drives switch-like activation of PDK1. These results imply that the PDK1-mediated activation of effector kinases, including Akt, PKC, Sgk, S6K and RSK, many of whom are not directly regulated by phosphoinositides, is also likely to be dependent on PIP3 or PI(3,4)P2.

DOI: https://doi.org/10.1038/s41467-022-29368-4
Subcell Biochem. 2022 ;98 119-141

Roles for 3' Phosphoinositides in Macropinocytosis.

Joel A Swanson, Nobukazu Araki.

  The distinct movements of macropinosome formation and maturation have corresponding biochemical activities which occur in a defined sequence of stages and transitions between those stages. Each stage in the process is regulated by variously phosphorylated derivatives of phosphatidylinositol (PtdIns) which reside in the cytoplasmic face of the membrane lipid bilayer. PtdIns derivatives phosphorylated at the 3' position of the inositol moiety, called 3' phosphoinositides (3'PIs), regulate different stages of the sequence. 3'PIs are synthesized by numerous phosphoinositide 3'-kinases (PI3K) and other lipid kinases and phosphatases, which are themselves regulated by small GTPases of the Ras superfamily. The combined actions of these enzymes localize four principal species of 3'PI to distinct domains of the plasma membrane or to discrete organelles, with distinct biochemical activities confined to those domains. Phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3) and phosphatidylinositol (3,4)-bisphosphate (PtdIns(3,4)P2) regulate the early stages of macropinosome formation, which include cell surface ruffling and constrictions of circular ruffles which close into macropinosomes. Phosphatidylinositol 3-phosphate (PtdIns3P) regulates macropinosome fusion with other macropinosomes and early endocytic organelles. Phosphatidylinositol (3,5)-bisphosphate (PtdIns(3,5)P2) mediates macropinosome maturation and shrinkage, through loss of ions and water, and subsequent traffic to lysosomes. The different characteristic rates of macropinocytosis in different cell types indicate levels of regulation which may be governed by the cell's capacity to generate 3'PIs.

Keywords:  Macrophage; Macropinosome closure; Phosphatidylinositol 3-kinase; Ruffling

DOI:  https://doi.org/10.1007/978-3-030-94004-1_7
Sci Rep. 2022 Apr 02. 12(1): 5571

A suspension technique for efficient large-scale cancer organoid culturing and perturbation screens.

Stacey Price, Shriram Bhosle, Emanuel Gonçalves, Xiaodun Li, Dylan P McClurg, Syd Barthorpe, Alex Beck, Caitlin Hall, Howard Lightfoot, Luke Farrow, Rizwan Ansari, David A Jackson, Laura Allen, Kirsty Roberts, Charlotte Beaver, Hayley E Francies, Mathew J Garnett.

Organoid cell culture methodologies are enabling the generation of cell models from healthy and diseased tissue. Patient-derived cancer organoids that recapitulate the genetic and histopathological diversity of patient tumours are being systematically generated, providing an opportunity to investigate new cancer biology and therapeutic approaches. The use of organoid cultures for many applications, including genetic and chemical perturbation screens, is limited due to the technical demands and cost associated with their handling and propagation. Here we report and benchmark a suspension culture technique for cancer organoids which allows for the expansion of models to tens of millions of cells with increased efficiency in comparison to standard organoid culturing protocols. Using whole-genome DNA and RNA sequencing analyses, as well as medium-throughput drug sensitivity testing and genome-wide CRISPR-Cas9 screening, we demonstrate that cancer organoids grown as a suspension culture are genetically and phenotypically similar to their counterparts grown in standard conditions. This culture technique simplifies organoid cell culture and extends the range of organoid applications, including for routine use in large-scale perturbation screens.

DOI: https://doi.org/10.1038/s41598-022-09508-y
HGG Adv. 2022 Apr 14. 3(2): 100101

Somatic activating BRAF variants cause isolated lymphatic malformations.

Kaitlyn Zenner, Dana M Jensen, Victoria Dmyterko, Giridhar M Shivaram, Candace T Myers, Cate R Paschal, Erin R Rudzinski, Minh-Hang M Pham, V Chi Cheng, Scott C Manning, Randall A Bly, Sheila Ganti, Jonathan A Perkins, James T Bennett.

  Somatic activating variants in PIK3CA, the gene that encodes the p110α catalytic subunit of phosphatidylinositol 3-kinase (PI3K), have been previously detected in ∼80% of lymphatic malformations (LMs).1 , 2 We report the presence of somatic activating variants in BRAF in individuals with LMs that do not possess pathogenic PIK3CA variants. The BRAF substitution p.Val600Glu (c.1799T>A), one of the most common driver mutations in cancer, was detected in multiple individuals with LMs. Histology revealed abnormal lymphatic channels with immunopositivity for BRAFV600E in endothelial cells that was otherwise indistinguishable from PIK3CA-positive LM. The finding that BRAF variants contribute to low-flow LMs increases the complexity of prior models associating low-flow vascular malformations (LM and venous malformations) with mutations in the PI3K-AKT-MTOR and high-flow vascular malformations (arteriovenous malformations) with mutations in the RAS-mitogen-activated protein kinase (MAPK) pathway.3 In addition, this work highlights the importance of genetic diagnosis prior to initiating medical therapy as more studies examine therapeutics for individuals with vascular malformations.

Keywords:  BRAF; PIK3CA; VANSeq; clinical diagnostics; ddPCR; endothelium; lymphatic malformation; mosaicism; post-zygotic; vascular

DOI:  https://doi.org/10.1016/j.xhgg.2022.100101
Mol Cell. 2022 Apr 07. pii: S1097-2765(22)00222-2. [Epub ahead of print]82(7): 1244-1245

Circling back to PTEN: Fumarate inhibits canonical tumor suppressor.

Sally E Claridge, Benjamin D Hopkins.

Ge et al. (2022) describes an inhibitory, post-translational modification of PTEN at C211 by fumarate, which offers new insight into the integration of PI3K signaling and metabolism via a potential feedforward regulatory mechanism involving a PI3K-glucose-fumarate-PTEN axis.

DOI: https://doi.org/10.1016/j.molcel.2022.03.013
Front Oncol. 2022 ;12 825484

Systemic Deficiency of PTEN Accelerates Breast Cancer Growth and Metastasis.

Jing Chen, Jingjing Sun, Qunfeng Wang, Yanze Du, Jie Cheng, Juan Yi, Bei Xie, Suya Jin, Gang Chen, Lina Wang, Xiaoyuan Wang, Hulai Wei.

  Mutation or loss of the tumor suppressor gene PTEN or its functional status in tumor stromal cells may affect tumor occurrence, development, invasion, and metastasis, in which, however, the role of overall low PTEN expression, mutation, or deletion in the tumor-bearing host has rarely been reported. Breast cancer is a common highly invasive metastatic tumor. We therefore treated mouse breast cancer 4T1 cells with the specific PTEN inhibitor VO-OHpic to study the effects of PTEN suppression or deletion on malignant behavior in vivo and in vitro. VO-OHpic effectively inhibited PTEN gene/protein expression in 4T1 cells, accelerated cell proliferation, and enhanced cell migration and invasion. We also transplanted 4T1 cells with VO-OHpic-inhibited PTEN into mice to create orthotopic and metastatic breast cancer models. The proliferation of 4T1 cells in mouse mammary gland was increased and distant metastasis was enhanced, with metastatic foci in the lung, liver, and intestinal tract. In addition, injection of mice with VO-OHpic to inhibit PTEN in the overall microenvironment accelerated the proliferation of transplanted 4T1 cells and enhanced distant metastasis and the formation of metastatic tumors. Metastatic foci formed in the lung, liver, intestine, thymus, and brain, and PTEN levels in the organ/tissues were negatively associated with the formation of metastatic foci. Similarly, inoculation of PTEN-deficient 4T1 cells into systemic PTEN-inhibited mice further enhanced the orthotopic growth and distant metastasis of 4T1 breast cancer. VO-OHpic inhibition of PTEN in 4T1 cells was also associated with significantly increased phosphorylation of Akt and phosphoinositide 3-kinase (PI3K), suggesting that inhibition of PTEN could activate the PI3K-Akt pathway, as a key signaling pathway regulating cell proliferation and death. These results confirmed that functional loss or deletion of the tumor suppressor gene PTEN significantly enhanced the proliferation, invasion, and metastasis of 4T1 cells. Systemic decrease or deletion of PTEN in the organism or organ/tissue microenvironment was conducive to the proliferation of breast cancer cells in situ and distant metastasis. These results suggest that, as well the PTEN in cancer cells the systemic microenvironment PTEN intensely mediates the proliferation, invasion and metastasis of mouse breast cancer cells via regulating the PI3K-Akt signaling pathway.

Keywords:  4T1 cell; PTEN; invasion; metastasis; multiplication

DOI:  https://doi.org/10.3389/fonc.2022.825484
Front Immunol. 2022 ;13 842340

The Small GTPase RHOA Links SLP65 Activation to PTEN Function in Pre B Cells and Is Essential for the Generation and Survival of Normal and Malignant B Cells.

Anila Vadakumchery, Hemin Faraidun, Omar El Ayoubi, Issame Outaleb, Vera Schmid, Hend Abdelrasoul, Timm Amendt, Ahmad Khadour, Corinna Setz, Katharina Göhring, Karoline Lodd, Christoffer Hitzing, Alabbas Alkhatib, Mayas Bilal, Julian Benckendorff, Abdul Kader Al Shugri, Cord Herbert Brakebusch, Niklas Engels, Moumita Datta, Elias Hobeika, Ameera Alsadeq, Hassan Jumaa.

  The generation, differentiation, survival and activation of B cells are coordinated by signals emerging from the B cell antigen receptor (BCR) or its precursor, the pre-BCR. The adaptor protein SLP65 (also known as BLNK) is an important signaling factor that controls pre-B cell differentiation by down-regulation of PI3K signaling. Here, we investigated the mechanism by which SLP65 interferes with PI3K signaling. We found that SLP65 induces the activity of the small GTPase RHOA, which activates PTEN, a negative regulator of PI3K signaling, by enabling its translocation to the plasma membrane. The essential role of RHOA is confirmed by the complete block in early B cell development in conditional RhoA-deficient mice. The RhoA-deficient progenitor B cells showed defects in activation of immunoglobulin gene rearrangement and fail to survive both in vitro and in vivo. Reconstituting the RhoA-deficient cells with RhoA or Foxo1, a transcription factor repressed by PI3K signaling and activated by PTEN, completely restores the survival defect. However, the defect in differentiation can only be restored by RhoA suggesting a unique role for RHOA in B cell generation and selection. In full agreement, conditional RhoA-deficient mice develop increased amounts of autoreactive antibodies with age. RHOA function is also required at later stage, as inactivation of RhoA in peripheral B cells or in a transformed mature B cell line resulted in cell loss. Together, these data show that RHOA is the key signaling factor for B cell development and function by providing a crucial SLP65-activated link between BCR signaling and activation of PTEN. Moreover, the identified essential role of RHOA for the survival of transformed B cells offers the opportunity for targeting B cell malignancies by blocking RHOA function.

Keywords:  BCR-ABL; CLL; PI3K signaling; PTEN; RHOA; SLP65

DOI:  https://doi.org/10.3389/fimmu.2022.842340
Endocrinology. 2022 Apr 02. pii: bqac041. [Epub ahead of print]

Targeting mTOR in the context of diet and whole-body metabolism.

Nikos Koundouros, John Blenis.

  The mechanistic target of rapamycin (mTOR) signaling pathway is the central regulator of cell growth and proliferation by integrating growth factor and nutrient availability. Under healthy physiological conditions, this process is tightly coordinated and essential to maintain whole-body homeostasis. Not surprisingly, dysregulated mTOR signaling underpins several diseases with increasing incidence worldwide, including obesity, diabetes and cancer. Consequently, there is significant clinical interest in developing therapeutic strategies that effectively target this pathway. The transition of mTOR inhibitors from the bench to bedside, however, has largely been marked with challenges and shortcomings, such as the development of therapy resistance and adverse side effects in patients. In this review, we discuss the current status of first, second and third generation mTOR inhibitors as a cancer therapy in both pre-clinical and clinical settings, with a particular emphasis on the mechanisms of drug resistance. We focus especially on the emerging role of diet as an important environmental determinant of therapy response, and posit a conceptual framework that links nutrient availability and whole-body metabolic states such as obesity with many of the previously defined processes that drive resistance to mTOR-targeted therapies. Given the role of mTOR as a central integrator of cell metabolism and function, we propose that modulating nutrient inputs through dietary interventions may influence the signaling dynamics of this pathway and compensatory nodes. In doing so, new opportunities for exploiting diet/drug synergies are highlighted that may unlock the therapeutic potential of mTOR inhibitors as a cancer treatment.

Keywords:  diet; drug resistance; mTOR; metabolism

DOI:  https://doi.org/10.1210/endocr/bqac041
J Immunol. 2022 Apr 04. pii: ji2100466. [Epub ahead of print]

Prostaglandin E2-Induced AKT Activation Regulates the Life Span of Short-Lived Plasma Cells by Attenuating IRE1α Hyperactivation.

Wei Wang, Xiaodan Qin, Liang Lin, Jia Wu, Xiuyuan Sun, Ye Zhao, Yurong Ju, Ziheng Zhao, Liwei Ren, Xuewen Pang, Youfei Guan, Yu Zhang.

The mechanism regulating the life span of short-lived plasma cells (SLPCs) remains poorly understood. Here we demonstrated that the EP4-mediated activation of AKT by PGE2 was required for the proper control of inositol-requiring transmembrane kinase endoribonuclease-1α (IRE1α) hyperactivation and hence the endoplasmic reticulum (ER) homeostasis in IgM-producing SLPCs. Disruption of the PGE2-EP4-AKT signaling pathway resulted in IRE1α-induced activation of JNK, leading to accelerated death of SLPCs. Consequently, Ptger4-deficient mice (C57BL/6) exhibited a markedly impaired IgM response to T-independent Ags and increased susceptibility to Streptococcus pneumoniae infection. This study reveals a highly selective impact of the PGE2-EP4 signal on the humoral immunity and provides a link between ER stress response and the life span of SLPCs.

DOI: https://doi.org/10.4049/jimmunol.2100466
Subcell Biochem. 2022 ;98 41-59

The Amoebal Model for Macropinocytosis.

Robert R Kay, Josiah Lutton, Helena Coker, Peggy Paschke, Jason S King, Till Bretschneider.

  Macropinocytosis is a relatively unexplored form of large-scale endocytosis driven by the actin cytoskeleton. Dictyostelium amoebae form macropinosomes from cups extended from the plasma membrane, then digest their contents and absorb the nutrients in the endo-lysosomal system. They use macropinocytosis for feeding, maintaining a high rate of fluid uptake that makes assay and experimentation easy. Mutants collected over the years identify cytoskeletal and signalling proteins required for macropinocytosis. Cups are organized around plasma membrane domains of intense PIP3, Ras and Rac signalling, proper formation of which also depends on the RasGAPs NF1 and RGBARG, PTEN, the PIP3-regulated protein kinases Akt and SGK and their activators PDK1 and TORC2, Rho proteins, plus other components yet to be identified. This PIP3 domain directs dendritic actin polymerization to the extending lip of macropinocytic cups by recruiting a ring of the SCAR/WAVE complex around itself and thus activating the Arp2/3 complex. The dynamics of PIP3 domains are proposed to shape macropinocytic cups from start to finish. The role of the Ras-PI3-kinase module in organizing feeding structures in unicellular organisms most likely predates its adoption into growth factor signalling, suggesting an evolutionary origin for growth factor signalling.

Keywords:  Dictyostelium discoideum; Endocytosis; Macropinocytosis; NF1; PI3-kinase; PIP3; Ras; SCAR/WAVE

DOI:  https://doi.org/10.1007/978-3-030-94004-1_3
Subcell Biochem. 2022 ;98 143-167

Signaling Pathways that Regulate Macropinocytosis in Mammalian Cells.

Wilhelm Palm.

  Macropinocytosis is an evolutionarily conserved endocytic pathway that mediates non-selective uptake of extracellular fluid in bulk. Macropinocytosis is initiated by localized polymerization of the actin cytoskeleton, which generates plasma membrane protrusions that enclose part of the environment into large endocytic vesicles. From amoebae to mammalian cells, the actin dynamics that drive macropinosome formation are regulated by a conserved set of intracellular signaling proteins including Ras superfamily GTPases and PI3-kinases. In mammalian cells, multiple upstream signaling pathways control activity of these core regulators in response to cell-extrinsic and cell-intrinsic stimuli. Growth factor signaling pathways play a central role in macropinocytosis induction. In addition, an increasing number of functionally diverse processes has been identified as macropinocytosis regulators, including several nutrient-sensing and developmental signaling pathways. Many of these signaling pathways have proto-oncogenic properties, and their dysregulation drives the high macropinocytic activity that is commonly observed in cancer cells. These regulatory principles illustrate how macropinocytosis is controlled by complex upstream inputs to exert diverse cellular functions in physiological and pathological contexts.

Keywords:  AMPK; Macropinocytosis; PI3-kinase; Ras GTPase; developmental signaling; growth factor signaling; mTORC1; nutrient-sensing; oncogenic signaling

DOI:  https://doi.org/10.1007/978-3-030-94004-1_8
Front Oncol. 2022 ;12 786438

A Comprehensive Survey of Genomic Mutations in Breast Cancer Reveals Recurrent Neoantigens as Potential Therapeutic Targets.

Si Zhou, Songming Liu, Lijian Zhao, Hai-Xi Sun.

  Neoantigens are mutated antigens specifically generated by cancer cells but absent in normal cells. With high specificity and immunogenicity, neoantigens are considered as an ideal target for immunotherapy. This study was aimed to investigate the signature of neoantigens in breast cancer. Somatic mutations, including SNVs and indels, were obtained from cBioPortal of 5991 breast cancer patients. 738 non-silent somatic variants present in at least 3 patients for neoantigen prediction were selected. PIK3CA (38%), the highly mutated gene in breast cancer, could produce the highest number of neoantigens per gene. Some pan-cancer hotspot mutations, such as PIK3CA E545K (6.93%), could be recognized by at least one HLA molecule. Since there are more SNVs than indels in breast cancer, SNVs are the major source of neoantigens. Patients with hormone receptor-positive or HER2 negative are more competent to produce neoantigens. Age, but not the clinical stage, is a significant contributory factor of neoantigen production. We believe a detailed description of breast cancer neoantigen signatures could contribute to neoantigen-based immunotherapy development.

Keywords:  PIK3CA; SNVs; breast cancer; immunotherapy; neoantigens

DOI:  https://doi.org/10.3389/fonc.2022.786438
Sci Adv. 2022 Apr 08. 8(14): eabm3259

Single-molecule, quantitative detection of low-abundance somatic mutations by high-throughput sequencing.

Alexander Y Maslov, Sergey Makhortov, Shixiang Sun, Johanna Heid, Xiao Dong, Moonsook Lee, Jan Vijg.

Postzygotic somatic mutations have been found associated with human disease, including diseases other than cancer. Most information on somatic mutations has come from studying clonally amplified mutant cells, based on a growth advantage or genetic drift. However, almost all somatic mutations are unique for each cell, and the quantitative analysis of these low-abundance mutations in normal tissues remains a major challenge in biology. Here, we introduce single-molecule mutation sequencing (SMM-seq), a novel approach for quantitative identification of point mutations in normal cells and tissues.

DOI: https://doi.org/10.1126/sciadv.abm3259
Nat Commun. 2022 Apr 05. 13(1): 1828

acorde unravels functionally interpretable networks of isoform co-usage from single cell data.

Angeles Arzalluz-Luque, Pedro Salguero, Sonia Tarazona, Ana Conesa.

Alternative splicing (AS) is a highly-regulated post-transcriptional mechanism known to modulate isoform expression within genes and contribute to cell-type identity. However, the extent to which alternative isoforms establish co-expression networks that may be relevant in cellular function has not been explored yet. Here, we present acorde, a pipeline that successfully leverages bulk long reads and single-cell data to confidently detect alternative isoform co-expression relationships. To achieve this, we develop and validate percentile correlations, an innovative approach that overcomes data sparsity and yields accurate co-expression estimates from single-cell data. Next, acorde uses correlations to cluster co-expressed isoforms into a network, unraveling cell type-specific alternative isoform usage patterns. By selecting same-gene isoforms between these clusters, we subsequently detect and characterize genes with co-differential isoform usage (coDIU) across cell types. Finally, we predict functional elements from long read-defined isoforms and provide insight into biological processes, motifs, and domains potentially controlled by the coordination of post-transcriptional regulation. The code for acorde is available at https://github.com/ConesaLab/acorde .

DOI: https://doi.org/10.1038/s41467-022-29497-w
Nature. 2022 Apr 06.

Brain charts for the human lifespan.

3R-BRAIN

Over the past few decades, neuroimaging has become a ubiquitous tool in basic research and clinical studies of the human brain. However, no reference standards currently exist to quantify individual differences in neuroimaging metrics over time, in contrast to growth charts for anthropometric traits such as height and weight1. Here we assemble an interactive open resource to benchmark brain morphology derived from any current or future sample of MRI data ( http://www.brainchart.io/ ). With the goal of basing these reference charts on the largest and most inclusive dataset available, acknowledging limitations due to known biases of MRI studies relative to the diversity of the global population, we aggregated 123,984 MRI scans, across more than 100 primary studies, from 101,457 human participants between 115 days post-conception to 100 years of age. MRI metrics were quantified by centile scores, relative to non-linear trajectories2 of brain structural changes, and rates of change, over the lifespan. Brain charts identified previously unreported neurodevelopmental milestones3, showed high stability of individuals across longitudinal assessments, and demonstrated robustness to technical and methodological differences between primary studies. Centile scores showed increased heritability compared with non-centiled MRI phenotypes, and provided a standardized measure of atypical brain structure that revealed patterns of neuroanatomical variation across neurological and psychiatric disorders. In summary, brain charts are an essential step towards robust quantification of individual variation benchmarked to normative trajectories in multiple, commonly used neuroimaging phenotypes.

DOI: https://doi.org/10.1038/s41586-022-04554-y
Nat Biotechnol. 2022 Apr 04.

A split prime editor with untethered reverse transcriptase and circular RNA template.

Bin Liu, Xiaolong Dong, Haoyang Cheng, Chunwei Zheng, Zexiang Chen, Tomás C Rodríguez, Shun-Qing Liang, Wen Xue, Erik J Sontheimer.

Delivery and optimization of prime editors (PEs) have been hampered by their large size and complexity. Although split versions of genome-editing tools can reduce construct size, they require special engineering to tether the binding and catalytic domains. Here we report a split PE (sPE) in which the Cas9 nickase (nCas9) remains untethered from the reverse transcriptase (RT). The sPE showed similar efficiencies in installing precise edits as the parental unsplit PE3 and no increase in insertion-deletion (indel) byproducts. Delivery of sPE to the mouse liver with hydrodynamic injection to modify β-catenin drove tumor formation with similar efficiency as PE3. Delivery with two adeno-associated virus (AAV) vectors corrected the disease-causing mutation in a mouse model of type I tyrosinemia. Similarly, prime editing guide RNAs (pegRNAs) can be split into a single guide RNA (sgRNA) and a circular RNA RT template to increase flexibility and stability. Compared to previous sPEs, ours lacks inteins, protein-protein affinity modules and nuclease-sensitive pegRNA extensions, which increase construct complexity and might reduce efficiency. Our modular system will facilitate the delivery and optimization of PEs.

DOI: https://doi.org/10.1038/s41587-022-01255-9
Nat Rev Cancer. 2022 Apr 04.

Studying extrachromosomal DNA with the ecTag method.

Eunhee Yi.

DOI: https://doi.org/10.1038/s41568-022-00474-1
Science. 2022 Apr 08. 376(6589): eabg5601

Genome-wide analysis of somatic noncoding mutation patterns in cancer.

Felix Dietlein, Alex B Wang, Christian Fagre, Anran Tang, Nicolle J M Besselink, Edwin Cuppen, Chunliang Li, Shamil R Sunyaev, James T Neal, Eliezer M Van Allen.

We established a genome-wide compendium of somatic mutation events in 3949 whole cancer genomes representing 19 tumor types. Protein-coding events captured well-established drivers. Noncoding events near tissue-specific genes, such as ALB in the liver or KLK3 in the prostate, characterized localized passenger mutation patterns and may reflect tumor-cell-of-origin imprinting. Noncoding events in regulatory promoter and enhancer regions frequently involved cancer-relevant genes such as BCL6, FGFR2, RAD51B, SMC6, TERT, and XBP1 and represent possible drivers. Unlike most noncoding regulatory events, XBP1 mutations primarily accumulated outside the gene's promoter, and we validated their effect on gene expression using CRISPR-interference screening and luciferase reporter assays. Broadly, our study provides a blueprint for capturing mutation events across the entire genome to guide advances in biological discovery, therapies, and diagnostics.

DOI: https://doi.org/10.1126/science.abg5601
Life Sci Alliance. 2022 Jul;pii: e202101334. [Epub ahead of print]5(7):

The hexosamine pathway and coat complex II promote malignant adaptation to nutrient scarcity.

Helena Dragic, Audrey Barthelaix, Cédric Duret, Simon Le Goupil, Hadrien Laprade, Sophie Martin, Sabine Brugière, Yohann Couté, Christelle Machon, Jerome Guitton, Justine Rudewicz, Paul Hofman, Serge Lebecque, Cedric Chaveroux, Carole Ferraro-Peyret, Toufic Renno, Serge N Manié.

The glucose-requiring hexosamine biosynthetic pathway (HBP), which produces UDP-N-acetylglucosamine for glycosylation reactions, promotes lung adenocarcinoma (LUAD) progression. However, lung tumor cells often reside in low-nutrient microenvironments, and whether the HBP is involved in the adaptation of LUAD to nutrient stress is unknown. Here, we show that the HBP and the coat complex II (COPII) play a key role in cell survival during glucose shortage. HBP up-regulation withstood low glucose-induced production of proteins bearing truncated N-glycans, in the endoplasmic reticulum. This function for the HBP, alongside COPII up-regulation, rescued cell surface expression of a subset of glycoproteins. Those included the epidermal growth factor receptor (EGFR), allowing an EGFR-dependent cell survival under low glucose in anchorage-independent growth. Accordingly, high expression of the HBP rate-limiting enzyme GFAT1 was associated with wild-type EGFR activation in LUAD patient samples. Notably, HBP and COPII up-regulation distinguished LUAD from the lung squamous-cell carcinoma subtype, thus uncovering adaptive mechanisms of LUAD to their harsh microenvironment.

DOI: https://doi.org/10.26508/lsa.202101334
Nat Commun. 2022 Apr 04. 13(1): 1783

Opposite physiological and pathological mTORC1-mediated roles of the CB1 receptor in regulating renal tubular function.

Liad Hinden, Majdoleen Ahmad, Sharleen Hamad, Alina Nemirovski, Gergő Szanda, Sandra Glasmacher, Aviram Kogot-Levin, Rinat Abramovitch, Bernard Thorens, Jürg Gertsch, Gil Leibowitz, Joseph Tam.

Activation of the cannabinoid-1 receptor (CB1R) and the mammalian target of rapamycin complex 1 (mTORC1) in the renal proximal tubular cells (RPTCs) contributes to the development of diabetic kidney disease (DKD). However, the CB1R/mTORC1 signaling axis in the kidney has not been described yet. We show here that hyperglycemia-induced endocannabinoid/CB1R stimulation increased mTORC1 activity, enhancing the transcription of the facilitative glucose transporter 2 (GLUT2) and leading to the development of DKD in mice; this effect was ameliorated by specific RPTCs ablation of GLUT2. Conversely, CB1R maintained the normal activity of mTORC1 by preventing the cellular excess of amino acids during normoglycemia. Our findings highlight a novel molecular mechanism by which the activation of mTORC1 in RPTCs is tightly controlled by CB1R, either by enhancing the reabsorption of glucose and inducing kidney dysfunction in diabetes or by preventing amino acid uptake and maintaining normal kidney function in healthy conditions.

DOI: https://doi.org/10.1038/s41467-022-29124-8
Physiology (Bethesda). 2022 Apr 04.

Pulsatile Basal Insulin Secretion is Driven by Glycolytic Oscillations.

Patrick Allen Fletcher, Isabella Marinelli, Richard Bertam, Leslie S Satin, Arthur Sherman.

  In fasted and fed states, blood insulin levels are oscillatory. While this phenomenon is well studied at high glucose levels, comparatively little is known about its origin under basal conditions. We propose a possible mechanism for basal insulin oscillations based on oscillations in glycolysis, demonstrated using an established mathematical model. At high glucose, this is superseded by a calcium-dependent mechanism.

Keywords:  bursting electrical activity; calcium; metabolism; pulsatile insulin secretion

DOI:  https://doi.org/10.1152/physiol.00044.2021
Sci Rep. 2022 Apr 08. 12(1): 5924

Pan-cancer analysis on the role of PIK3R1 and PIK3R2 in human tumors.

Yane Liu, Duo Wang, Zhijun Li, Xinwei Li, Mengdi Jin, Ningning Jia, Xingyao Cui, Guoyan Hu, Tongyu Tang, Qiong Yu.

Phosphoinositide-3-Kinase Regulatory Subunit 1 (PIK3R1) is believed to function as a tumor suppressor, while Phosphoinositide-3-Kinase Regulatory Subunit 2 (PIK3R2) as a tumor driver. However, there is no systematic pan-cancer analysis of them. The pan-cancer study comprehensively investigated the gene expression, genetic alteration, DNA methylation, and prognostic significance of PIK3R1 and PIK3R2 in 33 different tumors based on the TIMER, GEPIA, UALCAN, HPA, cBioPortal, and Kaplan-Meier Plotter database. The results indicated that PIK3R1 is lowly expressed in most tumors while PIK3R2 is highly expressed in most tumors, and abnormal gene expression may be related to promoter methylation. Moreover, not only mutations, downregulation of PIK3R1 and upregulation of PIK3R2 were found to be detrimental to the survival of most cancer patients as well. Furthermore, the expression of both PIK3R1 and PIK3R2 was associated with the level of immune infiltration in multiple tumors, such as breast invasive carcinoma. Our study conducted a comparatively comprehensive analysis of the role of PIK3R1 and PIK3R2 in a variety of cancers, contributing to further study of their potential mechanisms in cancer occurrence and progression. Our findings suggested that PIK3R1 and PIK3R2 could serve as prognostic markers for several cancers.

DOI: https://doi.org/10.1038/s41598-022-09889-0
Nature. 2022 Apr;604(7904): 175-183

Mapping the energetic and allosteric landscapes of protein binding domains.

Andre J Faure, Júlia Domingo, Jörn M Schmiedel, Cristina Hidalgo-Carcedo, Guillaume Diss, Ben Lehner.

Allosteric communication between distant sites in proteins is central to biological regulation but still poorly characterized, limiting understanding, engineering and drug development1-6. An important reason for this is the lack of methods to comprehensively quantify allostery in diverse proteins. Here we address this shortcoming and present a method that uses deep mutational scanning to globally map allostery. The approach uses an efficient experimental design to infer en masse the causal biophysical effects of mutations by quantifying multiple molecular phenotypes-here we examine binding and protein abundance-in multiple genetic backgrounds and fitting thermodynamic models using neural networks. We apply the approach to two of the most common protein interaction domains found in humans, an SH3 domain and a PDZ domain, to produce comprehensive atlases of allosteric communication. Allosteric mutations are abundant, with a large mutational target space of network-altering 'edgetic' variants. Mutations are more likely to be allosteric closer to binding interfaces, at glycine residues and at specific residues connecting to an opposite surface within the PDZ domain. This general approach of quantifying mutational effects for multiple molecular phenotypes and in multiple genetic backgrounds should enable the energetic and allosteric landscapes of many proteins to be rapidly and comprehensively mapped.

DOI: https://doi.org/10.1038/s41586-022-04586-4
Biochem J. 2022 Apr 06. pii: BCJ20220021. [Epub ahead of print]

Quantitative live-cell imaging of GPCR downstream signaling dynamics.

Ryosuke Tany, Yuhei Goto, Yohei Kondo, Kazuhiro Aoki.

  G-protein-coupled receptors (GPCRs) play an important role in sensing various extracellular stimuli, such as neurotransmitters, hormones, and tastants, and transducing the input information into the cell. While the human genome encodes more than 800 GPCR genes, only four Gα-proteins (Gαs, Gαi/o, Gαq/11, and Gα12/13) are known to couple with GPCRs. It remains unclear how such divergent GPCR information is translated into the downstream G-protein signaling dynamics. To answer this question, we report a live-cell fluorescence imaging system for monitoring GPCR downstream signaling dynamics. Genetically encoded biosensors for cAMP, Ca2+, RhoA, and ERK were selected as markers for GPCR downstream signaling, and were stably expressed in HeLa cells. GPCR was further transiently overexpressed in the cells. As a proof-of-concept, we visualized GPCR signaling dynamics of 5 dopamine receptors and 12 serotonin receptors, and found heterogeneity between GPCRs and between cells. Even when the same Gα proteins were known to be coupled, the patterns of dynamics in GPCR downstream signaling, including the signal strength and duration, were substantially distinct among GPCRs. These results suggest the importance of dynamical encoding in GPCR signaling.

Keywords:  G-protein-coupled receptors; dopamine; fluorescence resonance energy transfer; serotonin

DOI:  https://doi.org/10.1042/BCJ20220021
Nature. 2022 Apr 06.

Compartmentalized metabolism supports midgestation mammalian development.

Ashley Solmonson, Brandon Faubert, Wen Gu, Aparna Rao, Mitzy A Cowdin, Ivan Menendez-Montes, Sherwin Kelekar, Thomas J Rogers, Chunxiao Pan, Gerardo Guevara, Amy Tarangelo, Lauren G Zacharias, Misty S Martin-Sandoval, Duyen Do, Panayotis Pachnis, Dennis Dumesnil, Thomas P Mathews, Alpaslan Tasdogan, An Pham, Ling Cai, Zhiyu Zhao, Min Ni, Ondine Cleaver, Hesham A Sadek, Sean J Morrison, Ralph J DeBerardinis.

Mammalian embryogenesis requires rapid growth and proper metabolic regulation1. Midgestation features increasing oxygen and nutrient availability concomitant with fetal organ development2,3. Understanding how metabolism supports development requires approaches to observe metabolism directly in model organisms in utero. Here we used isotope tracing and metabolomics to identify evolving metabolic programmes in the placenta and embryo during midgestation in mice. These tissues differ metabolically throughout midgestation, but we pinpointed gestational days (GD) 10.5-11.5 as a transition period for both placenta and embryo. Isotope tracing revealed differences in carbohydrate metabolism between the tissues and rapid glucose-dependent purine synthesis, especially in the embryo. Glucose's contribution to the tricarboxylic acid (TCA) cycle rises throughout midgestation in the embryo but not in the placenta. By GD12.5, compartmentalized metabolic programmes are apparent within the embryo, including different nutrient contributions to the TCA cycle in different organs. To contextualize developmental anomalies associated with Mendelian metabolic defects, we analysed mice deficient in LIPT1, the enzyme that activates 2-ketoacid dehydrogenases related to the TCA cycle4,5. LIPT1 deficiency suppresses TCA cycle metabolism during the GD10.5-GD11.5 transition, perturbs brain, heart and erythrocyte development and leads to embryonic demise by GD11.5. These data document individualized metabolic programmes in developing organs in utero.

DOI: https://doi.org/10.1038/s41586-022-04557-9
EMBO Rep. 2022 Apr 05. e54041

Physical and functional interactome atlas of human receptor tyrosine kinases.

Kari Salokas, Xiaonan Liu, Tiina Öhman, Iftekhar Chowdhury, Lisa Gawriyski, Salla Keskitalo, Markku Varjosalo.

  Much cell-to-cell communication is facilitated by cell surface receptor tyrosine kinases (RTKs). These proteins phosphorylate their downstream cytoplasmic substrates in response to stimuli such as growth factors. Despite their central roles, the functions of many RTKs are still poorly understood. To resolve the lack of systematic knowledge, we apply three complementary methods to map the molecular context and substrate profiles of RTKs. We use affinity purification coupled to mass spectrometry (AP-MS) to characterize stable binding partners and RTK-protein complexes, proximity-dependent biotin identification (BioID) to identify transient and proximal interactions, and an in vitro kinase assay to identify RTK substrates. To identify how kinase interactions depend on kinase activity, we also use kinase-deficient mutants. Our data represent a comprehensive, systemic mapping of RTK interactions and substrates. This resource adds information regarding well-studied RTKs, offers insights into the functions of less well-studied RTKs, and highlights RTK-RTK interactions and shared signaling pathways.

Keywords:  RTK; interaction proteomics; phosphoproteomics; receptor tyrosine kinase; systems biology

DOI:  https://doi.org/10.15252/embr.202154041
Angiogenesis. 2022 Apr 07.

NRASQ61R mutation in human endothelial cells causes vascular malformations.

Elisa Boscolo, Patricia Pastura, Sandra Schrenk, Jillian Goines, Rachael Kang, Devin Pillis, Punam Malik, Timothy D Le Cras.

  Somatic mutations in NRAS drive the pathogenesis of melanoma and other cancers but their role in vascular anomalies and specifically human endothelial cells is unclear. The goals of this study were to determine whether the somatic-activating NRASQ61R mutation in human endothelial cells induces abnormal angiogenesis and to develop in vitro and in vivo models to identify disease-causing pathways and test inhibitors. Here, we used mutant NRASQ61R and wild-type NRAS (NRASWT) expressing human endothelial cells in in vitro and in vivo angiogenesis models. These studies demonstrated that expression of NRASQ61R in human endothelial cells caused a shift to an abnormal spindle-shaped morphology, increased proliferation, and migration. NRASQ61R endothelial cells had increased phosphorylation of ERK compared to NRASWT cells indicating hyperactivation of MAPK/ERK pathways. NRASQ61R mutant endothelial cells generated abnormal enlarged vascular channels in a 3D fibrin gel model and in vivo, in xenografts in nude mice. These studies demonstrate that NRASQ61R can drive abnormal angiogenesis in human endothelial cells. Treatment with MAP kinase inhibitor U0126 prevented the change to a spindle-shaped morphology in NRASQ61R endothelial cells, whereas mTOR inhibitor rapamycin did not.

Keywords:  Kaposiform lymphangiomatosis; Lymphatic anomaly; RASopathies; Vascular Anomaly; Vascular Malformation

DOI:  https://doi.org/10.1007/s10456-022-09836-7
Mol Metab. 2022 Mar 30. pii: S2212-8778(22)00047-3. [Epub ahead of print] 101478

An amino acid-defined diet impairs tumour growth in mice by promoting endoplasmic reticulum stress and mTOR inhibition.

Maurizio Ragni, Chiara Ruocco, Laura Tedesco, Michele O Carruba, Alessandra Valerio, Enzo Nisoli.

  OBJECTIVE: Profound metabolic alterations characterize cancer development and, beyond glucose addiction, amino acid (AA) dependency is now recognized as a hallmark of tumour growth. Therefore, targeting the metabolic addiction of tumours by reprogramming their substrate utilization is an attractive therapeutic strategy. We hypothesized that a dietary approach targeted to stimulate oxidative metabolism could reverse the metabolic inflexibility of tumours and represent a proper adjuvant therapy.METHODS: We measured tumour development in xenografted mice fed with a designer, casein-deprived diet enriched in free essential amino acids (EAAs; SFA-EAA diet), or two control isocaloric, isolipidic, and isonitrogenous diets, identical to the SFA-EAA diet except for casein presence (SFA diet), or casein replacement by the free AA mixture designed on the AA profile of casein (SFA-CAA diet). Moreover, we investigated the metabolic, biochemical, and molecular effects of two mixtures that reproduce the AA composition of the SFA-EAA diet (i.e., EAAm) and SFA-CAA diet (i.e., CAAm) in diverse cancer and non-cancer cells.
RESULTS: The SFA-EAA diet reduced tumour growth in vivo, promoted endoplasmic reticulum (ER) stress, and inhibited mechanistic/mammalian target of rapamycin (mTOR) activity in the tumours. Accordingly, in culture, the EAAm, but not the CAAm, activated apoptotic cell death in cancer cells without affecting the survival and proliferation of non-cancer cells. The EAAm increased branched-chain amino acid (BCAA) oxidation and decreased glycolysis, ATP levels, redox potential, and intracellular content of selective non-essential amino acids (NEAA) in cancer cells. The EAAm-induced NEAA starvation activated the GCN2-ATF4 stress pathway, leading to ER stress, mTOR inactivation, and apoptosis in cancer cells, unlike non-cancer cells.
CONCLUSION: Together, these results confirm the efficacy of specific EAA mixtures in promoting cancer cells' death and suggest that manipulation of dietary EAA content and profile could be a valuable support to the standard chemotherapy for specific cancers.

Keywords:  Branched-chain amino acids; Cancer metabolism; Essential amino acids; Glycolysis; Mechanistic/mammalian target of rapamycin; Mitochondria

DOI:  https://doi.org/10.1016/j.molmet.2022.101478
Cell Stem Cell. 2022 Apr 07. pii: S1934-5909(22)00107-2. [Epub ahead of print]29(4): 545-558.e13

A small-molecule cocktail promotes mammalian cardiomyocyte proliferation and heart regeneration.

Jianyong Du, Lixia Zheng, Peng Gao, Hang Yang, Wan-Jie Yang, Fusheng Guo, Ruqi Liang, Mengying Feng, Zihao Wang, Zongwang Zhang, Linlu Bai, Ye Bu, Shijia Xing, Wen Zheng, Xuelian Wang, Li Quan, Xinli Hu, Haosen Wu, Zhixing Chen, Liangyi Chen, Ke Wei, Zhe Zhang, Xiaojun Zhu, Xiaolin Zhang, Qiang Tu, Shi-Min Zhao, Xiaoguang Lei, Jing-Wei Xiong.

  Zebrafish and mammalian neonates possess robust cardiac regeneration via the induction of endogenous cardiomyocyte (CM) proliferation, but adult mammalian hearts have very limited regenerative potential. Developing small molecules for inducing adult mammalian heart regeneration has had limited success. We report a chemical cocktail of five small molecules (5SM) that promote adult CM proliferation and heart regeneration. A high-content chemical screen, along with an algorithm-aided prediction of small-molecule interactions, identified 5SM that efficiently induced CM cell cycle re-entry and cytokinesis. Intraperitoneal delivery of 5SM reversed the loss of heart function, induced CM proliferation, and decreased cardiac fibrosis after rat myocardial infarction. Mechanistically, 5SM potentially targets α1 adrenergic receptor, JAK1, DYRKs, PTEN, and MCT1 and is connected to lactate-LacRS2 signaling, leading to CM metabolic switching toward glycolysis/biosynthesis and CM de-differentiation before entering the cell-cycle. Our work sheds lights on the understanding CM regenerative mechanisms and opens therapeutic avenues for repairing the heart.

Keywords:  cardiomyocyte cytokinesis; cardiomyocyte proliferation; heart regeneration; high-content screen; lactate signaling; rats; small-molecule compounds

DOI:  https://doi.org/10.1016/j.stem.2022.03.009