bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2022–03–27
thirty papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Comprehensive characterization of PTEN mutational profile in a series of 34,129 colorectal cancers.
  2. PI3K Inhibitors for the Treatment of Chronic Lymphocytic Leukemia: Current Status and Future Perspectives.
  3. S6K1-mediated phosphorylation of PDK1 impairs AKT kinase activity and oncogenic functions.
  4. The central moTOR of metabolism.
  5. Zebrafish mutants in vegfab can affect endothelial cell proliferation without altering ERK phosphorylation and are phenocopied by loss of PI3K signaling.
  6. BYL719 (alpelisib) for the treatment of PIK3CA-mutated, recurrent/advanced cervical cancer.
  7. Clathrin coated pits as signaling platforms for Akt signaling.
  8. Endosomal phosphatidylinositol 3-phosphate controls synaptic vesicle cycling and neurotransmission.
  9. Telomerase RNA TERC and the PI3K-AKT pathway form a positive feedback loop to regulate cell proliferation independent of telomerase activity.
  10. A non-dividing cell population with high pyruvate dehydrogenase kinase activity regulates metabolic heterogeneity and tumorigenesis in the intestine.
  11. What cancer survivors can teach cancer researchers.
  12. Integrating mutational and nonmutational mechanisms of acquired therapy resistance within the Darwinian paradigm.
  13. Hemogenic and aortic endothelium arise from a common hemogenic angioblast precursor and are specified by the Etv2 dosage.
  14. Impact of baseline culture conditions of cancer organoids when determining therapeutic response and tumor heterogeneity.
  15. Hepatic IRF3 fuels dysglycemia in obesity through direct regulation of Ppp2r1b.
  16. A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens.
  17. The role of ARID1A in the non-estrogenic modulation of IGF-1 signaling.
  18. Temporal control of the integrated stress response by a stochastic molecular switch.
  19. Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro.
  20. Harnessing DSB repair to promote efficient homology-dependent and -independent prime editing.
  21. Neddylation is essential for β-catenin degradation in Wnt signaling pathway.
  22. The glucocorticoid receptor associates with RAS complexes to inhibit cell proliferation and tumor growth.
  23. Targeting Myc-driven stress vulnerability in mutant KRAS colorectal cancer.
  24. Extracellular matrix remodeling facilitates obesity-associated cancer progression.
  25. R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue.
  26. Proper migration of lymphatic endothelial cells requires survival and guidance cues from arterial mural cells.
  27. Measurement of activity of developmental signal transduction pathways to quantify stem cell pluripotency and phenotypically characterize differentiated cells.
  28. Integrating mechanical signals into cellular identity.
  29. DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update).
  30. Large scale, single-cell FRET-based glucose uptake measurements within heterogeneous populations.
  1. Nat Commun. 2022 Mar 25. 13(1): 1618
    Comprehensive characterization of PTEN mutational profile in a series of 34,129 colorectal cancers.
    Ilya G Serebriiskii, Valery Pavlov, Rossella Tricarico, Grigorii Andrianov, Emmanuelle Nicolas, Mitchell I Parker, Justin Newberg, Garrett Frampton, Joshua E Meyer, Erica A Golemis.
      Loss of expression or activity of the tumor suppressor PTEN acts similarly to an activating mutation in the oncogene PIK3CA in elevating intracellular levels of phosphatidylinositol (3,4,5)-trisphosphate (PIP3), inducing signaling by AKT and other pro-tumorigenic signaling proteins. Here, we analyze sequence data for 34,129 colorectal cancer (CRC) patients, capturing 3,434 PTEN mutations. We identify specific patterns of PTEN mutation associated with microsatellite stability/instability (MSS/MSI), tumor mutational burden (TMB), patient age, and tumor location. Within groups separated by MSS/MSI status, this identifies distinct profiles of nucleotide hotspots, and suggests differing profiles of protein-damaging effects of mutations. Moreover, discrete categories of PTEN mutations display non-identical patterns of co-occurrence with mutations in other genes important in CRC pathogenesis, including KRAS, APC, TP53, and PIK3CA. These data provide context for clinical targeting of proteins upstream and downstream of PTEN in distinct CRC cohorts.
    DOI:  https://doi.org/10.1038/s41467-022-29227-2
  2. Cancers (Basel). 2022 Mar 18. pii: 1571. [Epub ahead of print]14(6):
    PI3K Inhibitors for the Treatment of Chronic Lymphocytic Leukemia: Current Status and Future Perspectives.
    Iwona Hus, Bartosz Puła, Tadeusz Robak.
      Phosphoinositide 3-kinases (PI3Ks) signaling regulates key cellular processes, such as growth, survival and apoptosis. Among the three classes of PI3K, class I is the most important for the development, differentiation and activation of B and T cells. Four isoforms are distinguished within class I (PI3Kα, PI3Kβ, PI3Kδ and PI3Kγ). PI3Kδ expression is limited mainly to the B cells and their precursors, and blocking PI3K has been found to promote apoptosis of chronic lymphocytic leukemia (CLL) cells. Idelalisib, a selective PI3Kδ inhibitor, was the first-in-class PI3Ki introduced into CLL treatment. It showed efficacy in patients with del(17p)/TP53 mutation, unmutated IGHV status and refractory/relapsed disease. However, its side effects, such as autoimmune-mediated pneumonitis and colitis, infections and skin changes, limited its widespread use. The dual PI3Kδ/γ inhibitor duvelisib is approved for use in CLL patients but with similar toxicities to idelalisib. Umbralisib, a highly selective inhibitor of PI3Kδ and casein kinase-1ε (CK1ε), was found to be efficient and safe in monotherapy and in combination regimens in phase 3 trials in patients with CLL. Novel PI3Kis are under evaluation in early phase clinical trials. In this paper we present the mechanism of action, efficacy and toxicities of PI3Ki approved in the treatment of CLL and developed in clinical trials.
    Keywords:  BGB-10188; PI3-kinase inhibitors; chronic lymphocytic leukemia; copanlisib; duvelisib; idelalisib; parsaclisib; safety; treatment; umbralisib; zandelisib
    DOI:  https://doi.org/10.3390/cancers14061571
  3. Nat Commun. 2022 Mar 22. 13(1): 1548
    S6K1-mediated phosphorylation of PDK1 impairs AKT kinase activity and oncogenic functions.
    Qiwei Jiang, Xiaomei Zhang, Xiaoming Dai, Shiyao Han, Xueji Wu, Lei Wang, Wenyi Wei, Ning Zhang, Wei Xie, Jianping Guo.
      Functioning as a master kinase, 3-phosphoinositide-dependent protein kinase 1 (PDK1) plays a fundamental role in phosphorylating and activating protein kinases A, B and C (AGC) family kinases, including AKT. However, upstream regulation of PDK1 remains largely elusive. Here we report that ribosomal protein S6 kinase beta 1 (S6K1), a member of AGC kinases and downstream target of mechanistic target of rapamycin complex 1 (mTORC1), directly phosphorylates PDK1 at its pleckstrin homology (PH) domain, and impairs PDK1 interaction with and activation of AKT. Mechanistically, S6K1-mediated phosphorylation of PDK1 augments its interaction with 14-3-3 adaptor protein and homo-dimerization, subsequently dissociating PDK1 from phosphatidylinositol 3,4,5 triphosphate (PIP3) and retarding its interaction with AKT. Pathologically, tumor patient-associated PDK1 mutations, either attenuating S6K1-mediated PDK1 phosphorylation or impairing PDK1 interaction with 14-3-3, result in elevated AKT kinase activity and oncogenic functions. Taken together, our findings not only unravel a delicate feedback regulation of AKT signaling via S6K1-mediated PDK1 phosphorylation, but also highlight the potential strategy to combat mutant PDK1-driven cancers.
    DOI:  https://doi.org/10.1038/s41467-022-28910-8
  4. Dev Cell. 2022 Mar 15. pii: S1534-5807(22)00126-5. [Epub ahead of print]
    The central moTOR of metabolism.
    Judith Simcox, Dudley W Lamming.
      The protein kinase mechanistic target of rapamycin (mTOR) functions as a central regulator of metabolism, integrating diverse nutritional and hormonal cues to control anabolic processes, organismal physiology, and even aging. This review discusses the current state of knowledge regarding the regulation of mTOR signaling and the metabolic regulation of the four macromolecular building blocks of the cell: carbohydrate, nucleic acid, lipid, and protein by mTOR. We review the role of mTOR in the control of organismal physiology and aging through its action in key tissues and discuss the potential for clinical translation of mTOR inhibition for the treatment and prevention of diseases of aging.
    Keywords:  amino acids; lipids; mTOR; mTORC1; mTORC2; metabolism; protein; rapamycin
    DOI:  https://doi.org/10.1016/j.devcel.2022.02.024
  5. Dev Biol. 2022 Mar 22. pii: S0012-1606(22)00049-5. [Epub ahead of print]
    Zebrafish mutants in vegfab can affect endothelial cell proliferation without altering ERK phosphorylation and are phenocopied by loss of PI3K signaling.
    Martin Lange, Nils Ohnesorge, Dennis Hoffmann, Susana F Rocha, Rui Benedito, Arndt F Siekmann.
      The formation of appropriately patterned blood vessel networks requires endothelial cell migration and proliferation. Signaling through the Vascular Endothelial Growth Factor A (VEGFA) pathway is instrumental in coordinating these processes. mRNA splicing generates short (diffusible) and long (extracellular matrix bound) Vegfa isoforms. The differences between these isoforms in controlling cellular functions are not understood. In zebrafish, vegfaa generates short and long isoforms, while vegfab only generates long isoforms. We found that mutations in vegfaa had an impact on endothelial cell (EC) migration and proliferation. Surprisingly, mutations in vegfab more strongly affected EC proliferation in distinct blood vessels, such as intersegmental blood vessels in the zebrafish trunk and central arteries in the head. Analysis of downstream signaling pathways revealed no change in MAPK (ERK) activation, while inhibiting PI3 kinase signaling phenocopied vegfab mutant phenotypes in affected blood vessels. Together, these results suggest that extracellular matrix bound Vegfa might act through PI3K signaling to control EC proliferation in a distinct set of blood vessels during angiogenesis.
    Keywords:  Angiogenesis; Endothelial cell proliferation; PI3 kinase signaling; Vegf signaling; Zebrafish
    DOI:  https://doi.org/10.1016/j.ydbio.2022.03.006
  6. Tumori. 2022 Mar 20. 3008916211073621
    BYL719 (alpelisib) for the treatment of PIK3CA-mutated, recurrent/advanced cervical cancer.
    Giorgio Bogani, Valentina Chiappa, Marta Bini, Dominique Ronzulli, Alice Indini, Elena Conca, Francesco Raspagliesi.
       PURPOSE: Advanced/recurrent cervical cancer has limited therapeutic options, with a median progression-free survival after the failure of systemic treatments ranging between 3.5 and 4.5 months. Here, we reported our preliminary experience in the use of BYL719 (alpelisib) in advanced/recurrent cervical cancer after failure of at least 2 lines of treatment. The Istituto Nazionale dei Tumori di Milano approved this investigation.
    METHODS: From April 2020 to September 2020, 17 consecutive patients with recurrent cervical cancer had Next Generation Sequencing (NGS). Of these, six patients harboring the PIK3CA mutation were included in the study. All patients had been treated with at least 2 previous lines of systemic treatment: 3 patients received >2 prior lines of treatment in the recurrent or metastatic setting; 60% had received prior bevacizumab in combination with chemotherapy. All patients started alpelisib at the daily dosage of 300 mg.
    RESULTS: Investigator-assessed confirmed objective response rate (ORR) was 33%. The disease control rate (DCR) was 100%. According to RECIST 1.1, two patients had a partial response (PR), and four patients had stable disease (SD). No complete response was observed. The mean duration of response (DOR) was 11.5 (SD 3.75) months; five patients had PR lasting for >9 months. One patient stopped the treatment at 0.82 months due to the onset of a grade 2 adverse event (AE) (skin rash). Grade 3 treatment-related AEs included: lymphoedema (n = 1, 17%) and rash (n = 1, 17%). No treatment-related grade 4-5 AEs occurred.
    CONCLUSIONS: Our preliminary data highlighted a high level of efficacy in this setting of patients. Further trials are needed to assess the safety and effectiveness of alpelisib in PIK3CA-mutated recurrent/advanced cervical cancer.
    Keywords:  Alpelisib; PIK3CA; cervical cancer; metastatic cervical cancer
    DOI:  https://doi.org/10.1177/03008916211073621
  7. J Cell Biol. 2022 Apr 04. pii: e202203026. [Epub ahead of print]221(4):
    Clathrin coated pits as signaling platforms for Akt signaling.
    Elizabeth Smythe.
      Signaling by the activated epidermal growth factor receptor (EGFR) results in diverse cell fates. In this issue, Cabral-Dias et al. (2022. J. Cell Biol.https://doi.org/10.1083/jcb.201808181) demonstrate how plasma membrane clathrin coated pits can act as a signaling platform for one branch of EGFR downstream signaling.
    DOI:  https://doi.org/10.1083/jcb.202203026
  8. EMBO J. 2022 Mar 22. e109352
    Endosomal phosphatidylinositol 3-phosphate controls synaptic vesicle cycling and neurotransmission.
    Guan-Ting Liu, Gaga Kochlamazashvili, Dmytro Puchkov, Rainer Müller, Carsten Schultz, Albert I Mackintosh, Dennis Vollweiter, Volker Haucke, Tolga Soykan.
      Neural circuit function requires mechanisms for controlling neurotransmitter release and the activity of neuronal networks, including modulation by synaptic contacts, synaptic plasticity, and homeostatic scaling. However, how neurons intrinsically monitor and feedback control presynaptic neurotransmitter release and synaptic vesicle (SV) recycling to restrict neuronal network activity remains poorly understood at the molecular level. Here, we investigated the reciprocal interplay between neuronal endosomes, organelles of central importance for the function of synapses, and synaptic activity. We show that elevated neuronal activity represses the synthesis of endosomal lipid phosphatidylinositol 3-phosphate [PI(3)P] by the lipid kinase VPS34. Neuronal activity in turn is regulated by endosomal PI(3)P, the depletion of which reduces neurotransmission as a consequence of perturbed SV endocytosis. We find that this mechanism involves Calpain 2-mediated hyperactivation of Cdk5 downstream of receptor- and activity-dependent calcium influx. Our results unravel an unexpected function for PI(3)P-containing neuronal endosomes in the control of presynaptic vesicle cycling and neurotransmission, which may explain the involvement of the PI(3)P-producing VPS34 kinase in neurological disease and neurodegeneration.
    Keywords:  endocytosis; endosomes; neurotransmission; phosphatidylinositol 3-phosphate; synaptic vesicle
    DOI:  https://doi.org/10.15252/embj.2021109352
  9. Nucleic Acids Res. 2022 Mar 22. pii: gkac179. [Epub ahead of print]
    Telomerase RNA TERC and the PI3K-AKT pathway form a positive feedback loop to regulate cell proliferation independent of telomerase activity.
    Shu Wu, Yuanlong Ge, Kaixuan Lin, Qianqian Liu, Haoxian Zhou, Qian Hu, Yong Zhao, Weifeng He, Zhenyu Ju.
      The core catalytic unit of telomerase comprises telomerase reverse transcriptase (TERT) and telomerase RNA (TERC). Unlike TERT, which is predominantly expressed in cancer and stem cells, TERC is ubiquitously expressed in normal somatic cells without telomerase activity. However, the functions of TERC in these telomerase-negative cells remain elusive. Here, we reported positive feedback regulation between TERC and the PI3K-AKT pathway that controlled cell proliferation independent of telomerase activity in human fibroblasts. Mechanistically, we revealed that TERC activated the transcription of target genes from the PI3K-AKT pathway, such as PDPK1, by targeting their promoters. Overexpression of PDPK1 partially rescued the deficiency of AKT activation caused by TERC depletion. Furthermore, we found that FOXO1, a transcription factor negatively regulated by the PI3K-AKT pathway, bound to TERC promoter and suppressed its expression. Intriguingly, TERC-induced activation of the PI3K-AKT pathway also played a critical role in the proliferation of activated CD4+ T cells. Collectively, our findings identify a novel function of TERC that regulates the PI3K-AKT pathway via positive feedback to elevate cell proliferation independent of telomerase activity and provide a potential strategy to promote CD4+ T cells expansion that is responsible for enhancing adaptive immune reactions to defend against pathogens and tumor cells.
    DOI:  https://doi.org/10.1093/nar/gkac179
  10. Nat Commun. 2022 Mar 21. 13(1): 1503
    A non-dividing cell population with high pyruvate dehydrogenase kinase activity regulates metabolic heterogeneity and tumorigenesis in the intestine.
    Carlos Sebastian, Christina Ferrer, Maria Serra, Jee-Eun Choi, Nadia Ducano, Alessia Mira, Manasvi S Shah, Sylwia A Stopka, Andrew J Perciaccante, Claudio Isella, Daniel Moya-Rull, Marianela Vara-Messler, Silvia Giordano, Elena Maldi, Niyati Desai, Diane E Capen, Enzo Medico, Murat Cetinbas, Ruslan I Sadreyev, Dennis Brown, Miguel N Rivera, Anna Sapino, David T Breault, Nathalie Y R Agar, Raul Mostoslavsky.
      Although reprogramming of cellular metabolism is a hallmark of cancer, little is known about how metabolic reprogramming contributes to early stages of transformation. Here, we show that the histone deacetylase SIRT6 regulates tumor initiation during intestinal cancer by controlling glucose metabolism. Loss of SIRT6 results in an increase in the number of intestinal stem cells (ISCs), which translates into enhanced tumor initiating potential in APCmin mice. By tracking down the connection between glucose metabolism and tumor initiation, we find a metabolic compartmentalization within the intestinal epithelium and adenomas, where a rare population of cells exhibit features of Warburg-like metabolism characterized by high pyruvate dehydrogenase kinase (PDK) activity. Our results show that these cells are quiescent cells expressing +4 ISCs and enteroendocrine markers. Active glycolysis in these cells suppresses ROS accumulation and enhances their stem cell and tumorigenic potential. Our studies reveal that aerobic glycolysis represents a heterogeneous feature of cancer, and indicate that this metabolic adaptation can occur in non-dividing cells, suggesting a role for the Warburg effect beyond biomass production in tumors.
    DOI:  https://doi.org/10.1038/s41467-022-29085-y
  11. Nat Rev Cancer. 2022 Mar 23.
    What cancer survivors can teach cancer researchers.
    Victoria J Forster.
      
    DOI:  https://doi.org/10.1038/s41568-022-00468-z
  12. Trends Cancer. 2022 Mar 17. pii: S2405-8033(22)00040-1. [Epub ahead of print]
    Integrating mutational and nonmutational mechanisms of acquired therapy resistance within the Darwinian paradigm.
    Robert Vander Velde, Sydney Shaffer, Andriy Marusyk.
      Mutational processes and nongenetic phenotypic state transitions represent distinct paradigms for understanding acquired resistance to targeted therapies. While ample empirical evidence supports both paradigms, they are typically viewed as mutually exclusive. However, a growing body of evidence points to the multifactorial nature of resistance, where resistant tumor cell phenotypes integrate the influence of multiple mutational and epigenetic changes. This leads to growing calls for a conceptual framework capable of incorporating the effects of genetic and nongenetic mechanisms. Here, we argue that the original Darwinian paradigm centered on the concept of natural selection, rather than its mutation-centric reinterpretation, might provide the optimal backbone for a much-needed synthesis.
    Keywords:  Darwinian evolution; acquired resistance; cellular reprogramming; targeted therapy
    DOI:  https://doi.org/10.1016/j.trecan.2022.02.004
  13. Proc Natl Acad Sci U S A. 2022 Mar 29. 119(13): e2119051119
    Hemogenic and aortic endothelium arise from a common hemogenic angioblast precursor and are specified by the Etv2 dosage.
    Shizheng Zhao, Shachuan Feng, Ye Tian, Zilong Wen.
      SignificanceHematopoietic stem cells (HSCs) are generated from specialized endothelial cells, called hemogenic endothelial cells (HECs). It has been debated whether HECs and non-HSC-forming conventional endothelial cells (cECs) arise from a common precursor or represent distinct lineages. Moreover, the molecular basis underlying their distinct fate determination is poorly understood. We use photoconvertible labeling, time-lapse imaging, and single-cell RNA-sequencing analysis to trace the lineage of HECs. We discovered that HECs and cECs arise from a common hemogenic angioblast precursor, and their distinct fate is determined by high or low dosage of Etv2, respectively. Our results illuminate the lineage origin and a mechanism on the fate determination of HECs, which may enhance the understanding on the ontogeny of HECs in vertebrates.
    Keywords:  endothelium; fate determination; hemogenic endothelium; lineage origin
    DOI:  https://doi.org/10.1073/pnas.2119051119
  14. Sci Rep. 2022 Mar 25. 12(1): 5205
    Impact of baseline culture conditions of cancer organoids when determining therapeutic response and tumor heterogeneity.
    Rebecca A DeStefanis, Jeremy D Kratz, Autumn M Olson, Aishwarya Sunil, Alyssa K DeZeeuw, Amani A Gillette, Gioia C Sha, Katherine A Johnson, Cheri A Pasch, Linda Clipson, Melissa C Skala, Dustin A Deming.
      Representative models are needed to screen new therapies for patients with cancer. Cancer organoids are a leap forward as a culture model that faithfully represents the disease. Mouse-derived cancer organoids (MDCOs) are becoming increasingly popular, however there has yet to be a standardized method to assess therapeutic response and identify subpopulation heterogeneity. There are multiple factors unique to organoid culture that could affect how therapeutic response and MDCO heterogeneity are assessed. Here we describe an analysis of nearly 3500 individual MDCOs where individual organoid morphologic tracking was performed. Change in MDCO diameter was assessed in the presence of control media or targeted therapies. Individual organoid tracking was identified to be more sensitive to treatment response than well-level assessment. The impact of different generations of mice of the same genotype, different regions of the colon, and organoid specific characteristics including baseline size, passage number, plating density, and location within the matrix were examined. Only the starting size of the MDCO altered the subsequent growth. These results were corroborated using ~ 1700 patient-derived cancer organoids (PDCOs) isolated from 19 patients. Here we establish organoid culture parameters for individual organoid morphologic tracking to determine therapeutic response and growth/response heterogeneity for translational studies.
    DOI:  https://doi.org/10.1038/s41598-022-08937-z
  15. Sci Transl Med. 2022 Mar 23. 14(637): eabh3831
    Hepatic IRF3 fuels dysglycemia in obesity through direct regulation of Ppp2r1b.
    Suraj J Patel, Nan Liu, Sam Piaker, Anton Gulko, Maynara L Andrade, Frankie D Heyward, Tyler Sermersheim, Nufar Edinger, Harini Srinivasan, Margo P Emont, Gregory P Westcott, Jay Luther, Raymond T Chung, Shuai Yan, Manju Kumari, Reeby Thomas, Yann Deleye, André Tchernof, Phillip J White, Guido A Baselli, Marica Meroni, Dario F De Jesus, Rasheed Ahmad, Rohit N Kulkarni, Luca Valenti, Linus Tsai, Evan D Rosen.
      Inflammation has profound but poorly understood effects on metabolism, especially in the context of obesity and nonalcoholic fatty liver disease (NAFLD). Here, we report that hepatic interferon regulatory factor 3 (IRF3) is a direct transcriptional regulator of glucose homeostasis through induction of Ppp2r1b, a component of serine/threonine phosphatase PP2A, and subsequent suppression of glucose production. Global ablation of IRF3 in mice on a high-fat diet protected against both steatosis and dysglycemia, whereas hepatocyte-specific loss of IRF3 affects only dysglycemia. Integration of the IRF3-dependent transcriptome and cistrome in mouse hepatocytes identifies Ppp2r1b as a direct IRF3 target responsible for mediating its metabolic actions on glucose homeostasis. IRF3-mediated induction of Ppp2r1b amplified PP2A activity, with subsequent dephosphorylation of AMPKα and AKT. Furthermore, suppression of hepatic Irf3 expression with antisense oligonucleotides reversed obesity-induced insulin resistance and restored glucose homeostasis in obese mice. Obese humans with NAFLD displayed enhanced activation of liver IRF3, with reversion after bariatric surgery. Hepatic PPP2R1B expression correlated with HgbA1C and was elevated in obese humans with impaired fasting glucose. We therefore identify the hepatic IRF3-PPP2R1B axis as a causal link between obesity-induced inflammation and dysglycemia and suggest an approach for limiting the metabolic dysfunction accompanying obesity-associated NAFLD.
    DOI:  https://doi.org/10.1126/scitranslmed.abh3831
  16. Cell Syst. 2022 Mar 16. pii: S2405-4712(22)00084-9. [Epub ahead of print]
    A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens.
    Takamasa Kudo, Keara Lane, Markus W Covert.
      Pooled genetic libraries have improved screening throughput for mapping genotypes to phenotypes. However, selectable phenotypes are limited, restricting screening to outcomes with a low spatiotemporal resolution. Here, we integrated live-cell imaging with pooled library-based screening. To enable intracellular multiplexing, we developed a method called EPICode that uses a combination of short epitopes, which can also appear in various subcellular locations. EPICode thus enables the use of live-cell microscopy to characterize a phenotype of interest over time, including after sequential stimulatory/inhibitory manipulations, and directly connects behavior to the cellular genotype. To test EPICode's capacity against an important milestone-engineering and optimizing dynamic, live-cell reporters-we developed a live-cell PKA kinase translocation reporter with improved sensitivity and specificity. The use of epitopes as fluorescent barcodes introduces a scalable strategy for high-throughput screening broadly applicable to protein engineering and drug discovery settings where image-based phenotyping is desired.
    Keywords:  epitope barcodes; fluorescent reporters; in situ genotyping; pooled screen; spatial multiplexing
    DOI:  https://doi.org/10.1016/j.cels.2022.02.006
  17. Mol Cancer Res. 2022 Mar 23. pii: molcanres.0961.2021. [Epub ahead of print]
    The role of ARID1A in the non-estrogenic modulation of IGF-1 signaling.
    Sham Jdeed, Edina Erdos, Balint Laszlo Balint, Ivan P Uray.
      Gaining pharmacologic access to the potential of ARID1A, a tumor suppressor protein, to mediate transcriptional control over cancer gene expression is an unresolved challenge. Retinoid X receptor ligands are pleiotropic, incompletely understood tools that regulate breast epithelial cell proliferation and differentiation. We found that low-dose bexarotene (Bex) combined with the non-selective beta-blocker carvedilol (Carv) reduces proliferation of MCF10DCIS.com cells and markedly suppresses ARID1A levels. Similarly, carvedilol synergized with Bex in MCF-7 cells to suppress cell growth. ChIP-seq analysis revealed that under non-estrogenic conditions Bex+Carv alters the concerted genomic distribution of the chromatin remodeler ARID1A and acetylated histone H3K27, at sites related to insulin-like growth factor (IGF) signaling. Several distinct sites of ARID1A enrichment were identified in the IGF-1 receptor and IRS1 genes, associated with a suppression of both proteins. The knock-down of ARID1A increased IGF-1R levels, prevented IGF-1R and IRS1 suppression upon Bex+Carv and stimulated proliferation. In vitro IGF-1 receptor neutralizing antibody suppressed cell growth, while elevated IGF-1R or IRS1 expression was associated with poor survival of ER-negative breast cancer patients. Our study demonstrates direct impact of ARID1A redistribution on the expression and growth regulation of IGF1-related genes, induced by repurposed clinical drugs under non-estrogenic conditions. Implications: This study underscores the possibility of the pharmacologic modulation of the ARID1A factor to down-regulate pro-tumorigenic IGF-1 activity in postmenopausal breast cancer patients undergoing aromatase inhibitor treatment.
    DOI:  https://doi.org/10.1158/1541-7786.MCR-21-0961
  18. Sci Adv. 2022 Mar 25. 8(12): eabk2022
    Temporal control of the integrated stress response by a stochastic molecular switch.
    Philipp Klein, Stefan M Kallenberger, Hanna Roth, Karsten Roth, Thi Bach Nga Ly-Hartig, Vera Magg, Janez Aleš, Soheil Rastgou Talemi, Yu Qiang, Steffen Wolf, Olga Oleksiuk, Roma Kurilov, Barbara Di Ventura, Ralf Bartenschlager, Roland Eils, Karl Rohr, Fred A Hamprecht, Thomas Höfer, Oliver T Fackler, Georg Stoecklin, Alessia Ruggieri.
      Stress granules (SGs) are formed in the cytosol as an acute response to environmental cues and activation of the integrated stress response (ISR), a central signaling pathway controlling protein synthesis. Using chronic virus infection as stress model, we previously uncovered a unique temporal control of the ISR resulting in recurrent phases of SG assembly and disassembly. Here, we elucidate the molecular network generating this fluctuating stress response by integrating quantitative experiments with mathematical modeling and find that the ISR operates as a stochastic switch. Key elements controlling this switch are the cooperative activation of the stress-sensing kinase PKR, the ultrasensitive response of SG formation to the phosphorylation of the translation initiation factor eIF2α, and negative feedback via GADD34, a stress-induced subunit of protein phosphatase 1. We identify GADD34 messenger RNA levels as the molecular memory of the ISR that plays a central role in cell adaptation to acute and chronic stress.
    DOI:  https://doi.org/10.1126/sciadv.abk2022
  19. Nat Biotechnol. 2022 Mar 24.
    Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro.
    Bingjie Zhang, Avi Srivastava, Eleni Mimitou, Tim Stuart, Ivan Raimondi, Yuhan Hao, Peter Smibert, Rahul Satija.
      Technologies that profile chromatin modifications at single-cell resolution offer enormous promise for functional genomic characterization, but the sparsity of the measurements and integrating multiple binding maps represent substantial challenges. Here we introduce single-cell (sc)CUT&Tag-pro, a multimodal assay for profiling protein-DNA interactions coupled with the abundance of surface proteins in single cells. In addition, we introduce single-cell ChromHMM, which integrates data from multiple experiments to infer and annotate chromatin states based on combinatorial histone modification patterns. We apply these tools to perform an integrated analysis across nine different molecular modalities in circulating human immune cells. We demonstrate how these two approaches can characterize dynamic changes in the function of individual genomic elements across both discrete cell states and continuous developmental trajectories, nominate associated motifs and regulators that establish chromatin states and identify extensive and cell-type-specific regulatory priming. Finally, we demonstrate how our integrated reference can serve as a scaffold to map and improve the interpretation of additional scCUT&Tag datasets.
    DOI:  https://doi.org/10.1038/s41587-022-01250-0
  20. Nat Commun. 2022 Mar 24. 13(1): 1240
    Harnessing DSB repair to promote efficient homology-dependent and -independent prime editing.
    Martin Peterka, Nina Akrap, Songyuan Li, Sandra Wimberger, Pei-Pei Hsieh, Dmitrii Degtev, Burcu Bestas, Jack Barr, Stijn van de Plassche, Patricia Mendoza-Garcia, Saša Šviković, Grzegorz Sienski, Mike Firth, Marcello Maresca.
      Prime editing recently emerged as a next-generation approach for precise genome editing. Here we exploit DNA double-strand break (DSB) repair to develop two strategies that install precise genomic insertions using an SpCas9 nuclease-based prime editor (PEn). We first demonstrate that PEn coupled to a regular prime editing guide RNA (pegRNA) efficiently promotes short genomic insertions through a homology-dependent DSB repair mechanism. While PEn editing leads to increased levels of by-products, it can rescue pegRNAs that perform poorly with a nickase-based prime editor. We also present a small molecule approach that yields increased product purity of PEn editing. Next, we develop a homology-independent PEn editing strategy, which installs genomic insertions at DSBs through the non-homologous end joining pathway (NHEJ). Lastly, we show that PEn-mediated insertions at DSBs prevent Cas9-induced large chromosomal deletions and provide evidence that continuous Cas9-mediated cutting is one of the mechanisms by which Cas9-induced large deletions arise. Altogether, this work expands the current prime editing toolbox by leveraging distinct DNA repair mechanisms including NHEJ, which represents the primary pathway of DSB repair in mammalian cells.
    DOI:  https://doi.org/10.1038/s41467-022-28771-1
  21. Cell Rep. 2022 Mar 22. pii: S2211-1247(22)00279-0. [Epub ahead of print]38(12): 110538
    Neddylation is essential for β-catenin degradation in Wnt signaling pathway.
    Bojun Wang, Tiantian Wang, Huimin Zhu, Rong Yan, Xinru Li, Chengqian Zhang, Wanyu Tao, Xisong Ke, Piliang Hao, Yi Qu.
      β-Catenin is a central component in the Wnt signaling pathway; its degradation has been tightly connected to ubiquitylation, but it is rarely examined by loss-of-function assays. Here we observe that endogenous β-catenin is not stabilized upon ubiquitylation depletion by a ubiquitylation inhibitor, TAK-243. We demonstrate that N-terminal phosphorylated β-catenin is quickly and strongly stabilized by a specific neddylation inhibitor, MLN4924, in all examined cell types, and that β-catenin and TCF4 interaction is strongly enhanced by inhibition of neddylation but not ubiquitylation. We also confirm that the E3 ligase β-TrCP2, but not β-TrCP1, is associated with neddylation and destruction of β-catenin. GSK3β and adenomatous polyposis coli (APC) are not required for β-catenin neddylation but essential for its subsequent degradation. Our findings not only clarify the process of β-catenin modification and degradation in the Wnt signaling pathway but also highlight the importance of reassessing previously identified ubiquitylation substrates.
    Keywords:  CP; CP: Molecular Biology; Molecular Biology; Wnt signaling pathway; neddylation; stabilization; ubiquitylation; β-TrCP2; β-catenin
    DOI:  https://doi.org/10.1016/j.celrep.2022.110538
  22. Sci Signal. 2022 Mar 22. 15(726): eabm4452
    The glucocorticoid receptor associates with RAS complexes to inhibit cell proliferation and tumor growth.
    Bozhena Caratti, Miray Fidan, Giorgio Caratti, Kristina Breitenecker, Melanie Engler, Naser Kazemitash, Rebecca Traut, Rainer Wittig, Emilio Casanova, Mohammad Reza Ahmadian, Jan P Tuckermann, Herwig P Moll, Ion Cristian Cirstea.
      Mutations that activate members of the RAS family of GTPases are associated with various cancers and drive tumor growth. The glucocorticoid receptor (GR), a member of the nuclear receptor family, has been proposed to interact with and inhibit the activation of components of the PI3K-AKT and MAPK pathways downstream of RAS. In the absence of activating ligands, we found that GR was present in cytoplasmic KRAS-containing complexes and inhibited the activation of wild-type and oncogenic KRAS in mouse embryonic fibroblasts and human lung cancer A549 cells. The DNA binding domain of GR was involved in the interaction with KRAS, but GR-dependent inhibition of RAS activation did not depend on the nuclear translocation of GR. The addition of ligand released GR-dependent inhibition of RAS, AKT, the MAPK p38, and the MAPKK MEK. CRISPR-Cas9-mediated deletion of GR in A549 cells enhanced tumor growth in xenografts in mice. Patient samples of non-small cell lung carcinomas showed lower expression of NR3C1, the gene encoding GR, compared to adjacent normal tissues and lower NR3C1 expression correlated with a worse disease outcome. These results suggest that glucocorticoids prevent the ability of GR to limit tumor growth by inhibiting RAS activation, which has potential implications for the use of glucocorticoids in patients with cancer.
    DOI:  https://doi.org/10.1126/scisignal.abm4452
  23. Mol Biomed. 2022 Mar 21. 3(1): 10
    Targeting Myc-driven stress vulnerability in mutant KRAS colorectal cancer.
    Hang Ruan, Brian J Leibowitz, Yingpeng Peng, Lin Shen, Lujia Chen, Charlie Kuang, Robert E Schoen, Xinghua Lu, Lin Zhang, Jian Yu.
      Mutant KRAS is a key driver in colorectal cancer (CRC) and promotes Myc translation and Myc-dependent stress adaptation and proliferation. Here, we report that the combination of two FDA-approved drugs Bortezomib and Everolimus (RAD001) (BR) is highly efficacious against mutant KRAS CRC cells. Mechanistically, the combination, not single agent, rapidly depletes Myc protein, not mRNA, and leads to GCN2- and p-eIF2α-dependent cell death through the activation of extrinsic and intrinsic apoptotic pathways. Cell death is selectively induced in mutant KRAS CRC cells with elevated basal Myc and p-eIF2α and is characterized by CHOP induction and transcriptional signatures in proteotoxicity, oxidative stress, metabolic inhibition, and immune activation. BR-induced p-GCN2/p-eIF2α elevation and cell death are strongly attenuated by MYC knockdown and enhanced by MYC overexpression. The BR combination is efficacious against mutant KRAS patient derived organoids (PDO) and xenografts (PDX) by inducing p-eIF2α/CHOP and cell death. Interestingly, an elevated four-gene (DDIT3, GADD45B, CRYBA4 and HSPA1L) stress signature is linked to shortened overall survival in CRC patients. These data support that Myc-dependent stress adaptation drives the progression of mutant KRAS CRC and serves as a therapeutic vulnerability, which can be targeted using dual translational inhibitors.
    Keywords:  Bortezomib; Colorectal cancer; Everolimus; Mutant KRAS; Myc; eIF2α
    DOI:  https://doi.org/10.1186/s43556-022-00070-7
  24. Trends Cell Biol. 2022 Mar 17. pii: S0962-8924(22)00059-9. [Epub ahead of print]
    Extracellular matrix remodeling facilitates obesity-associated cancer progression.
    Min Kim, Changhu Lee, Jiyoung Park.
      Obesity, a global public health concern, is an important risk factor for metabolic diseases and several cancers. Fibro-inflammation in adipose tissues (ATs) is tightly associated with the pathologies of obesity; excessive or uncontrolled extracellular matrix (ECM) production in AT has a crucial role in this pathogenesis. The ECM is a critical and functional component of various tissues, providing a mechanical and chemical network of proteins that controls cell survival, development, and tissue repair. The ECM is tightly regulated and dynamically remodeled; this is an important factor for AT expansion and can result in modifications to the physical shape and biological function of AT. Here, we focus on ECM remodeling in AT and how it affects obesity-related cancer progression.
    Keywords:  extracellular matrix remodeling; fibro-inflammation; obesity; obesity-associated cancer
    DOI:  https://doi.org/10.1016/j.tcb.2022.02.008
  25. Sci Data. 2022 Mar 23. 9(1): 96
    R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue.
    Yunshun Chen, Bhupinder Pal, Geoffrey J Lindeman, Jane E Visvader, Gordon K Smyth.
      Breast cancer is a common and highly heterogeneous disease. Understanding cellular diversity in the mammary gland and its surrounding micro-environment across different states can provide insight into cancer development in the human breast. Recently, we published a large-scale single-cell RNA expression atlas of the human breast spanning normal, preneoplastic and tumorigenic states. Single-cell expression profiles of nearly 430,000 cells were obtained from 69 distinct surgical tissue specimens from 55 patients. This article extends the study by providing quality filtering thresholds, downstream processed R data objects, complete cell annotation and R code to reproduce all the analyses. Data quality assessment measures are presented and details are provided for all the bioinformatic analyses that produced results described in the study.
    DOI:  https://doi.org/10.1038/s41597-022-01236-2
  26. Elife. 2022 Mar 22. pii: e74094. [Epub ahead of print]11
    Proper migration of lymphatic endothelial cells requires survival and guidance cues from arterial mural cells.
    Di Peng, Koji Ando, Melina Hußmann, Marleen Gloger, Renae Skoczylas, Naoki Mochizuki, Christer Betsholtz, Shigetomo Fukuhara, Stefan Schulte-Merker, Nathan D Lawson, Katarzyna Koltowska.
      The migration of lymphatic endothelial cells (LECs) is key for the development of the complex and vast lymphatic vascular network that pervades most tissues in an organism. In zebrafish, arterial intersegmental vessels together with chemokines have been shown to promote lymphatic cell migration from the horizontal myoseptum (HM). We observed that emergence of mural cells around the intersegmental arteries coincides with lymphatic departure from HM which raised the possibility that arterial mural cells promote LEC migration. Our live imaging and cell ablation experiments revealed that LECs migrate slower and fail to establish the lymphatic vascular network in the absence of arterial mural cells. We determined that mural cells are a source for the C-X-C motif chemokine 12 (Cxcl12a and Cxcl12b), Vascular endothelial growth factor C (Vegfc) and Collagen and calcium-binding EGF domain-containing protein 1 (Ccbe1). We showed that chemokine and growth factor signalling function cooperatively to induce robust LEC migration. Specifically, Vegfc-Vegfr3 signalling, but not chemokines, induces extracellular signal-regulated kinase (ERK) activation in LECs, and has an additional pro-survival role in LECs during the migration. Together, the identification of mural cells as a source for signals that guide LEC migration and survival will be important in the future design for rebuilding lymphatic vessels in disease contexts.
    Keywords:  developmental biology; zebrafish
    DOI:  https://doi.org/10.7554/eLife.74094
  27. Stem Cell Res. 2022 Mar 14. pii: S1873-5061(22)00097-6. [Epub ahead of print]61 102748
    Measurement of activity of developmental signal transduction pathways to quantify stem cell pluripotency and phenotypically characterize differentiated cells.
    Laurent Holtzer, Yvonne Wesseling-Rozendaal, Wim Verhaegh, Anja van de Stolpe.
      Important challenges in stem cell research and regenerative medicine are reliable assessment of pluripotency state and purity of differentiated cell populations. Pluripotency and differentiation are regulated and determined by activity of developmental signal transduction pathways (STPs). To date activity of these STPs could not be directly measured on a cell sample. Here we validate a novel assay platform for measurement of activity of developmental STPs (STP) for use in stem cells and stem cell derivatives. In addition to previously developed STP assays, we report development of an additional STP assay for the MAPK-AP1 pathway. Subsequently, activity of Notch, Hedgehog, TGFβ, Wnt, PI3K, MAPK-AP1, and NFκB signaling pathways was calculated from Affymetrix transcriptome data of human pluripotent embryonic (hES) and iPS cell lines under different culture conditions, organ-derived multipotent stem cells, and differentiated cell types, to generate quantitative STP activity profiles. Results show that the STP assay technology enables reliable and quantitative measurement of multiple STP activities simultaneously on any individual cell sample. Using the technology, we found that culture conditions dominantly influence the pluripotent stem cell STP activity profile, while the origin of the stem cell line was a minor variable. A pluripotency STP activity profile (Pluripotency qPAP) was defined (active PI3K, MAPK, Hedgehog, Notch, TGFβ, and NFκB pathway, inactive Wnt pathway). Differentiation of hES cells to intestinal progenitor cells resulted in an STP activity profile characterized by active PI3K, Wnt and Notch pathways, comparable to the STP activity profile measured on primary intestinal crypt stem cells. Quantitative STP activity measurement is expected to improve experimental reproducibility and standardization of pluripotent and multipotent stem cell culture/differentiation, and enable controlled manipulation of pluripotency/differentiation state using pathway targeting compounds.
    DOI:  https://doi.org/10.1016/j.scr.2022.102748
  28. Trends Cell Biol. 2022 Mar 22. pii: S0962-8924(22)00039-3. [Epub ahead of print]
    Integrating mechanical signals into cellular identity.
    Emma Carley, Megan C King, Shangqin Guo.
      The large arrays of cell types in a multicellular organism are defined by their stereotypic size and/or morphology, and, for cells in vivo, by their anatomic positions. Historically, this identity-structure-function correlation was conceptualized as arising from distinct gene expression programs that dictate how cells appear and behave. However, a growing number of studies suggest that a cell's mechanical state is also an important determinant of its identity, both in lineage-committed cells and in pluripotent stem cells. Defining the mechanism by which mechanical inputs influence complex cellular programs remains an area of ongoing investigation. Here, we discuss how the cytoskeleton actively participates in instructing the response of the nucleus and genome to integrate mechanical and biochemical inputs, with a primary focus on the role of the actomyosin-LINC (linker of nucleoskeleton and cytoskeleton) complex axis.
    Keywords:  LINC complex; actomyosin cytoskeleton; cell identity; chromatin; mechanotransduction; reprogramming
    DOI:  https://doi.org/10.1016/j.tcb.2022.02.006
  29. Nucleic Acids Res. 2022 Mar 23. pii: gkac194. [Epub ahead of print]
    DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update).
    Brad T Sherman, Ming Hao, Ju Qiu, Xiaoli Jiao, Michael W Baseler, H Clifford Lane, Tomozumi Imamichi, Weizhong Chang.
      DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis tools. Here, we report all updates made in 2021. The DAVID Gene system was rebuilt to gain coverage of more organisms, which increased the taxonomy coverage from 17 399 to 55 464. All existing annotation types have been updated, if available, based on the new DAVID Gene system. Compared with the last version, the number of gene-term records for most annotation types within the updated Knowledgebase have significantly increased. Moreover, we have incorporated new annotations in the Knowledgebase including small molecule-gene interactions from PubChem, drug-gene interactions from DrugBank, tissue expression information from the Human Protein Atlas, disease information from DisGeNET, and pathways from WikiPathways and PathBank. Eight of ten subgroups split from Uniprot Keyword annotation were assigned to specific types. Finally, we added a species parameter for uploading a list of gene symbols to minimize the ambiguity between species, which increases the efficiency of the list upload and eliminates confusion for users. These current updates have significantly expanded the Knowledgebase and enhanced the discovery power of DAVID.
    DOI:  https://doi.org/10.1093/nar/gkac194
  30. iScience. 2022 Apr 15. 25(4): 104023
    Large scale, single-cell FRET-based glucose uptake measurements within heterogeneous populations.
    Adam J M Wollman, Dimitrios Kioumourtzoglou, Rebecca Ward, Gwyn W Gould, Nia J Bryant.
      Fluorescent biosensors are powerful tools allowing the concentration of metabolites and small molecules, and other properties such as pH and molecular crowding to be measured inside live single cells. The technology has been hampered by lack of simple software to identify cells and quantify biosensor signals in single cells. We have developed a new software package, FRETzel, to address this gap and demonstrate its use by measuring insulin-stimulated glucose uptake in individual fat cells of varying sizes for the first time. Our results support the long-standing hypothesis that larger fat cells are less sensitive to insulin than smaller ones, a finding that has important implications for the battle against type 2 diabetes. FRETzel has been optimized using the messy and crowded environment of cultured adipocytes, demonstrating its utility for quantification of FRET biosensors in a wide range of other cell types, including fibroblasts and yeast via a simple user-friendly quantitative interface.
    Keywords:  Biocomputational method; Bioinformatics; Biological sciences; Cell biology; Optical imaging
    DOI:  https://doi.org/10.1016/j.isci.2022.104023
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