bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2020–02–23
eightteen papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Filamin A inhibition reduces seizure activity in a mouse model of focal cortical malformations.
  2. Estrogen activates pyruvate kinase M2 and increases the growth of TSC2-deficient cells.
  3. Macroautophagy is repressed during mitosis - seeing is believing.
  4. Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies.
  5. Recent advances in human stem cell-based modeling of Tuberous Sclerosis Complex.
  6. The acute effects of growth hormone in adipose tissue is associated with suppression of antilipolytic signals.
  7. Rationale for the advancement of PI3K pathway inhibitors for personalized chordoma therapy.
  8. Alterations and molecular targeting of the GSK-3 regulator, PI3K, in head and neck cancer.
  9. AMPK activation does not enhance autophagy in neurons in contrast to MTORC1 inhibition: different impact on β-amyloid clearance.
  10. High-intensity muscle contraction-mediated increases in Akt1 and Akt2 phosphorylation do not contribute to mTORC1 activation and muscle protein synthesis.
  11. A CINful way to overcome addiction: how chromosomal instability enables cancer to overcome its oncogene addiction.
  12. A framework for transcriptome-wide association studies in breast cancer in diverse study populations.
  13. Mechanistic Links between Obesity, Insulin, and Cancer.
  14. Cell-type-specific signaling networks in heterocellular organoids.
  15. Gene expression and cell identity controlled by anaphase-promoting complex.
  16. Novel insights into adiponectin action in breast cancer: Evidence of its mechanistic effects mediated by ERα expression.
  17. A census of pathway maps in cancer systems biology.
  18. Tracing tumorigenesis in a solid tumor model at single-cell resolution.
  1. Sci Transl Med. 2020 Feb 19. pii: eaay0289. [Epub ahead of print]12(531):
    Filamin A inhibition reduces seizure activity in a mouse model of focal cortical malformations.
    Longbo Zhang, Tianxiang Huang, Shannon Teaw, Lena H Nguyen, Lawrence S Hsieh, Xuan Gong, Lindsay H Burns, Angélique Bordey.
      Epilepsy treatments for patients with mechanistic target of rapamycin (mTOR) disorders, such as tuberous sclerosis complex (TSC) or focal cortical dysplasia type II (FCDII), are urgently needed. In these patients, the presence of focal cortical malformations is associated with the occurrence of lifelong epilepsy, leading to severe neurological comorbidities. Here, we show that the expression of the actin cross-linking protein filamin A (FLNA) is increased in resected cortical tissue that is responsible for seizures in patients with FCDII and in mice modeling TSC and FCDII with mutations in phosphoinositide 3-kinase (PI3K)-ras homolog enriched in brain (Rheb) pathway genes. Normalizing FLNA expression in these mice through genetic knockdown limited cell misplacement and neuronal dysmorphogenesis, two hallmarks of focal cortical malformations. In addition, Flna knockdown reduced seizure frequency independently of mTOR signaling. Treating mice with a small molecule targeting FLNA, PTI-125, before the onset of seizures alleviated neuronal abnormalities and reduced seizure frequency compared to vehicle-treated mice. In addition, the treatment was also effective when injected after seizure onset in juvenile and adult mice. These data suggest that targeting FLNA with either short hairpin RNAs or the small molecule PTI-125 might be effective in reducing seizures in patients with TSC and FCDII bearing mutations in PI3K-Rheb pathway genes.
    DOI:  https://doi.org/10.1126/scitranslmed.aay0289
  2. PLoS One. 2020 ;15(2): e0228894
    Estrogen activates pyruvate kinase M2 and increases the growth of TSC2-deficient cells.
    Yiyang Lu, Xiaolei Liu, Erik Zhang, Elizabeth J Kopras, Eric P Smith, Aristotelis Astreinidis, Chenggang Li, Yuet-Kin Leung, Shuk-Mei Ho, Jane J Yu.
      Lymphangioleiomyomatosis (LAM) is a devastating lung disease caused by inactivating gene mutations in either TSC1 or TSC2 that result in hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1). As LAM occurs predominantly in women during their reproductive age and is exacerbated by pregnancy, the female hormonal environment, and in particular estrogen, is implicated in LAM pathogenesis and progression. However, detailed underlying molecular mechanisms are not well understood. In this study, utilizing human pulmonary LAM specimens and cell culture models of TSC2-deficient LAM patient-derived and rat uterine leiomyoma-derived cells, we tested the hypothesis that estrogen promotes the growth of mTORC1-hyperactive cells through pyruvate kinase M2 (PKM2). Estrogen increased the phosphorylation of PKM2 at Ser37 and induced the nuclear translocation of phospho-PKM2. The estrogen receptor antagonist Faslodex reversed these effects. Restoration of TSC2 inhibited the phosphorylation of PKM2 in an mTORC1 inhibitor-insensitive manner. Finally, accumulation of phosphorylated PKM2 was evident in pulmonary nodule from LAM patients. Together, our data suggest that female predominance of LAM might be at least in part attributed to estrogen stimulation of PKM2-mediated cellular metabolic alterations. Targeting metabolic regulators of PKM2 might have therapeutic benefits for women with LAM and other female-specific neoplasms.
    DOI:  https://doi.org/10.1371/journal.pone.0228894
  3. Autophagy. 2020 Feb 20. 1-2
    Macroautophagy is repressed during mitosis - seeing is believing.
    Richard I Odle, Simon J Cook.
      For the last two decades there has been wide ranging debate about the status of macroautophagy during mitosis. Because metazoan cells undergo an "open" mitosis in which the nuclear envelope breaks down, it has been proposed that macroautophagy must be inhibited to maintain genome integrity. While many studies have agreed that the number of autophagosomes is greatly reduced in cells undergoing mitosis, there has been no consensus on whether this reflects decreased autophagosome synthesis or increased autophagosome degradation. Reviewing the literature we were concerned that many studies relied too heavily on autophagy assays that were simply not appropriate for a relatively brief event such as mitosis. Using highly dynamic omegasome markers we have recently shown unequivocally that autophagosome synthesis is repressed at the onset of mitosis and is restored once cell division is complete. This is accomplished by CDK1, the master regulator of mitosis, taking over the function of MTORC1, to ensure autophagy is repressed during mitosis.
    Keywords:  ATG13 (autophagy related 13); Autophagy; CDK1 (cyclin dependent kinase 1); MTOR (mechanistic target of rapamycin kinase); MTORC1 (MTOR complex 1); RPTOR/RAPTOR (regulatory associated protein of MTOR complex 1); ULK1 (unc-51 like autophagy activating kinase 1); mitosis; omegasome
    DOI:  https://doi.org/10.1080/15548627.2020.1725405
  4. Mol Syst Biol. 2020 Feb;16(2): e8664
    Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies.
    Federica Eduati, Patricia Jaaks, Jessica Wappler, Thorsten Cramer, Christoph A Merten, Mathew J Garnett, Julio Saez-Rodriguez.
      Mechanistic modeling of signaling pathways mediating patient-specific response to therapy can help to unveil resistance mechanisms and improve therapeutic strategies. Yet, creating such models for patients, in particular for solid malignancies, is challenging. A major hurdle to build these models is the limited material available that precludes the generation of large-scale perturbation data. Here, we present an approach that couples ex vivo high-throughput screenings of cancer biopsies using microfluidics with logic-based modeling to generate patient-specific dynamic models of extrinsic and intrinsic apoptosis signaling pathways. We used the resulting models to investigate heterogeneity in pancreatic cancer patients, showing dissimilarities especially in the PI3K-Akt pathway. Variation in model parameters reflected well the different tumor stages. Finally, we used our dynamic models to efficaciously predict new personalized combinatorial treatments. Our results suggest that our combination of microfluidic experiments and mathematical model can be a novel tool toward cancer precision medicine.
    Keywords:  drug combinations; logic modeling; patient-specific models; precision oncology; signaling pathways
    DOI:  https://doi.org/10.15252/msb.20188664
  5. Mol Autism. 2020 Feb 19. 11(1): 16
    Recent advances in human stem cell-based modeling of Tuberous Sclerosis Complex.
    Wardiya Afshar Saber, Mustafa Sahin.
      Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by epilepsy, intellectual disability, and benign tumors of the brain, heart, skin, and kidney. Animal models have contributed to our understanding of normal and abnormal human brain development, but the construction of models that accurately recapitulate a human pathology remains challenging. Recent advances in stem cell biology with the derivation of human-induced pluripotent stem cells (hiPSCs) from somatic cells from patients have opened new avenues to the study of TSC. This approach combined with gene-editing tools such as CRISPR/Cas9 offers the advantage of preserving patient-specific genetic background and the ability to generate isogenic controls by correcting a specific mutation. The patient cell line and the isogenic control can be differentiated into the cell type of interest to model various aspects of TSC. In this review, we discuss the remarkable capacity of these cells to be used as a model for TSC in two- and three-dimensional cultures, the potential variability in iPSC models, and highlight differences between findings reported to date.
    Keywords:  Astrocytes; Autism; Brain organoids; CRISPR/Cas9; Cortical tuber; Human pluripotent stem cells; Neurons; Purkinje neurons; Tuberous sclerosis complex
    DOI:  https://doi.org/10.1186/s13229-020-0320-2
  6. Physiol Rep. 2020 Feb;8(3): e14373
    The acute effects of growth hormone in adipose tissue is associated with suppression of antilipolytic signals.
    Katrine L Høyer, Morten L Høgild, Edward O List, Kevin Y Lee, Emily Kissinger, Rita Sharma, Nils Erik Magnusson, Vishwajeet Puri, John J Kopchick, Jens O L Jørgensen, Niels Jessen.
       AIM: Since GH stimulates lipolysis in vivo after a 2-hr lag phase, we studied whether this involves GH signaling and gene expression in adipose tissue (AT).
    METHODS: Human subjects (n = 9) each underwent intravenous exposure to GH versus saline with measurement of serum FFA, and GH signaling, gene array, and protein in AT biopsies after 30-120 min. Human data were corroborated in adipose-specific GH receptor knockout (FaGHRKO) mice versus wild-type mice. Expression of candidate genes identified in the array were investigated in 3T3-L1 adipocytes.
    RESULTS: GH increased serum FFA and AT phosphorylation of STAT5b in human subjects. This was replicated in wild-type mice, but not in FaGHRKO mice. The array identified 53 GH-regulated genes, and Ingenuity Pathway analysis showed downregulation of PDE3b, an insulin-dependent antilipolytic signal, upregulation of PTEN that inhibits insulin-dependent antilipolysis, and downregulation of G0S2 and RASD1, both encoding antilipolytic proteins. This was confirmed in 3T3-L1 adipocytes, except for PDE3B, including reciprocal effects of GH and insulin on mRNA expression of PTEN, RASD1, and G0S2.
    CONCLUSION: (a) GH directly stimulates AT lipolysis in a GHR-dependent manner, (b) this involves suppression of antilipolytic signals at the level of gene expression, (c) the underlying GH signaling pathways remain to be defined.
    Keywords:  clinical studies; fatty acid/metabolism; gene expression; growth hormone; hormones; lipase/hormone sensitive
    DOI:  https://doi.org/10.14814/phy2.14373
  7. J Neurooncol. 2020 Feb 17.
    Rationale for the advancement of PI3K pathway inhibitors for personalized chordoma therapy.
    N L Michmerhuizen, J H Owen, M E Heft Neal, J E Mann, E Leonard, J Wang, J Zhai, H Jiang, J B McHugh, J C Brenner, M E P Prince.
       PURPOSE: Chordomas are rare and serious tumors with few effective treatments outside of aggressive surgery and radiation. Targeted therapies may present a more effective option for a subset of patients with lesions possessing certain genetic biomarkers.
    METHODS: A small molecule inhibitor library was tested in patient-derived UM-Chor1 cells to identify targeted therapies with potential efficacy. Targeted exome sequencing of UM-Chor1 and UM-Chor2 cells was performed to investigate genetic aberrations in relevant pathways. Chordoma cell lines were treated with inhibitors of the phosphotidylinositol 3-kinase (PI3K), epidermal growth factor receptor (EGFR), and cyclin dependent kinase (CDK) pathways, and responses were determined using resazurin cell viability assays, Annexin V apoptosis assays, and western blotting. Pan-PI3K inhibitor BKM120 was also tested in five chordoma xenograft models.
    RESULTS: Unbiased small molecule profiling nominated PI3K-AKT-mTOR pathway inhibitors as a promising therapy in chordoma, and genetic analyses of UM-Chor1 and UM-Chor2 cell lines revealed aberrations in PTEN, EGFR, and CDKN2A. Treatment of UM-Chor1 and UM-Chor2 with targeted PI3K, EGFR, and CDK inhibitors inhibited growth and proliferation and induced apoptosis more robustly than imatinib, a currently used chordoma therapy. Furthermore, BKM120 significantly inhibited tumor growth in a subset of the xenograft models tested.
    CONCLUSION: Targeted therapies, especially those inhibiting PI3K, display promising effects in multiple chordoma cell line and xenograft models. Nevertheless, the limited effects of PI3K, EGFR, and CDK targeting agents in other models reveal the presence of resistance mechanisms, which motivates future research to both identify biomarkers of response and develop combination therapies.
    Keywords:  AKT; Chordoma; PI3K; PTEN; Personalized medicine
    DOI:  https://doi.org/10.1007/s11060-020-03418-7
  8. Biochim Biophys Acta Mol Cell Res. 2020 Feb 12. pii: S0167-4889(20)30037-9. [Epub ahead of print] 118679
    Alterations and molecular targeting of the GSK-3 regulator, PI3K, in head and neck cancer.
    Michelle Lee, Nan Jin, Jennifer R Grandis, Daniel E Johnson.
      Head and neck squamous cell carcinoma (HNSCC) is a highly morbid, genetically unstable disease derived from the mucoepithelium of the upper aerodigestive tract. Recent characterization of this disease has implicated the PI3K-Akt-mTOR pathway as one of the most frequently dysregulated pathways. As such, there are several classes of PI3K inhibitors currently undergoing clinical trials. In this article, we review the PI3K pathway, mutations of this pathway in HNSCC, drugs that target PI3K, the impact of these agents on the PI3K and GSK-3 signaling axes, ongoing clinical trials evaluating PI3K inhibitors, and the challenges of using these drugs in the clinic. This article is part of a Special Issue entitled: GSK-3 and related kinases in cancer, neurological and other disorders edited by James McCubrey, Agnieszka Gizak and Dariusz Rakus.
    Keywords:  GSK-3; HNSCC; Head and neck squamous cell carcinoma; PI3K; PIK3CA
    DOI:  https://doi.org/10.1016/j.bbamcr.2020.118679
  9. Autophagy. 2020 Feb 20. 1-16
    AMPK activation does not enhance autophagy in neurons in contrast to MTORC1 inhibition: different impact on β-amyloid clearance.
    Irene Benito-Cuesta, Lara Ordóñez-Gutiérrez, Francisco Wandosell.
      The physiological AKT-MTORC1 and AMPK signaling pathways are considered key nodes in the regulation of anabolism-catabolism, and particularly of macroautophagy/autophagy. Indeed, it is reported that these are altered processes in neurodegenerative proteinopathies such as Alzheimer disease (AD), mainly characterized by deposits of β-amyloid (Aβ) and hyperphosphorylated MAPT. These accumulations disrupt the optimal neuronal proteostasis, and hence, the recovery/enhancement of autophagy has been proposed as a therapeutic approach against these proteinopathies. The purpose of the present study was to characterize the modulation of autophagy by MTORC1 and AMPK signaling pathways in the highly specialized neurons, as well as their repercussions on Aβ production. Using a double transgenic mice model of AD, we demonstrated that MTORC1 inhibition, either in vivo or ex vivo (primary neuronal cultures), was able to reduce amyloid secretion through moderate autophagy induction in neurons. The pharmacological prevention of autophagy in neurons augmented the Aβ secretion and reversed the effect of rapamycin, confirming the anti-amyloidogenic effects of autophagy in neurons. Inhibition of AMPK with compound C generated the expected decrease in autophagy induction, though surprisingly did not increase the Aβ secretion. In contrast, increased activity of AMPK with metformin, AICAR, 2DG, or by gene overexpression did not enhance autophagy but had different effects on Aβ secretion: whereas metformin and 2DG diminished the secreted Aβ levels, AICAR and PRKAA1/AMPK gene overexpression increased them. We conclude that AMPK has a significantly different role in primary neurons than in other reported cells, lacking a direct effect on autophagy-dependent amyloidosis.Abbreviations: 2DG: 2-deoxy-D-glucose; Aβ: β-amyloid; ACACA: acetyl-CoA carboxylase alpha; ACTB: actin beta; AD: Alzheimer disease; AICAR: 5-aminoimidazole-4-carboxamide-1-β-riboside; AKT: AKT kinases group (AKT1 [AKT serine/threonine kinase 1], AKT2 and AKT3); AMPK: adenosine 5'-monophosphate (AMP)-activated protein kinase; APP: amyloid beta precursor protein; APP/PSEN1: B6.Cg-Tg (APPSwe, PSEN1dE9) 85Dbo/J; ATG: autophagy related; ATP: adenosine triphosphate; BafA1: bafilomycin A1; CA: constitutively active; CGN: cerebellar granule neuron; CoC/compound C: dorsommorphin dihydrochloride; ELISA: enzyme-linked immunosorbent assay; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; Gmax: GlutaMAX™; IN1: PIK3C3/VPS34-IN1; KI: kinase-inactive; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3; MAPT/TAU: microtubule associated protein tau; Metf: metformin; MRT: MRT68921; MTORC1: mechanistic target of rapamycin kinase complex 1; NBR1: NBR1 autophagy cargo receptor; PRKAA: 5'-AMP-activated protein kinase catalytic subunit alpha; PtdIns3K: phosphatidylinositol 3-kinase; Rapa: rapamycin; RPS6KB1/S6K: ribosomal protein S6 (RPS6) kinase polypeptide 1; SCR: scramble; SQSTM1/p62: sequestosome 1; ULK1/2: unc-51 like autophagy activating kinase 1/2; WT: wild type.
    Keywords:  2-deoxy-D-glucose; aicar; alzheimer; amyloid accumulation; bafilomycin A1; cultured cerebellar granule neuron; dorsomorphin; metformin; rapamycin; sh-SY5Y
    DOI:  https://doi.org/10.1080/15548627.2020.1728095
  10. J Appl Physiol (1985). 2020 Feb 20.
    High-intensity muscle contraction-mediated increases in Akt1 and Akt2 phosphorylation do not contribute to mTORC1 activation and muscle protein synthesis.
    Yuki Maruyama, Chisaki Ikeda, Koki Wakabayashi, Satoru Ato, Riki Ogasawara.
      High-intensity muscle contraction (HiMC) is known to induce muscle protein synthesis, a process in which mechanistic target of rapamycin (mTOR) was reported to play a critical role. However, the mechanistic details have not been completely elucidated. Here, we investigated whether Akt plays a role in regulating HiMC-induced mTORC1 activation and muscle protein synthesis using a rodent model of resistance exercise and MK2206 (an Akt kinase inhibitor). The right gastrocnemius muscle of male C57BL/6J mice aged 10 weeks was isometrically contracted via percutaneous electrical stimulation (100 Hz, 5 sets of ten 3 s contractions, 7 s rest between contractions, 3 min rest between sets), while the left gastrocnemius muscle served as a control. Vehicle or MK2206 was injected intraperitoneally 6 h before contraction. MK2206 inhibited both resting and HiMC-induced phosphorylation of Akt1 and Akt2. MK2206 also inhibited the resting phosphorylation of p70S6K and 4E-BP1, which are downstream targets of mTORC1; however, it did not inhibit the HiMC-induced increase in phosphorylation of these targets. Similarly, MK2206 inhibited the resting, but not the resistance exercise-induced muscle protein synthesis. Based on these observations, we conclude that although Akt2 regulates resting mTORC1 activity and muscle protein synthesis, HiMC-induced increases in mTORC1 activity and muscle protein synthesis are Akt-independent processes.
    Keywords:  Akt; MK2206; contraction; mTOR; skeletal muscle
    DOI:  https://doi.org/10.1152/japplphysiol.00578.2019
  11. EMBO Mol Med. 2020 Feb 18. e12017
    A CINful way to overcome addiction: how chromosomal instability enables cancer to overcome its oncogene addiction.
    Daniel Bronder, Samuel F Bakhoum.
      Oncogene-addicted tumors present a valuable target for therapeutic intervention and an opportunity to achieve a wide therapeutic window. Nonetheless, resistance to targeted therapies is frequently observed and it arises through multiple mechanisms, including mutations in the target gene. Chromosomal instability, a defining feature of human cancer, has been linked to targeted therapy resistance, but the mechanism underlying this association is poorly understood. In the current issue of EMBO Molecular Medicine, Salgueiro et al show that chromosomal instability can lead to the generation of alternative oncogenic drivers, thereby providing the ability for cancer cells to overcome the oncogene withdrawal bottleneck. Importantly, this study shows that, by generating de novo genomic diversity, chromosomal instability serves as an adaptive response to therapeutic insult.
    DOI:  https://doi.org/10.15252/emmm.202012017
  12. Genome Biol. 2020 Feb 20. 21(1): 42
    A framework for transcriptome-wide association studies in breast cancer in diverse study populations.
    Arjun Bhattacharya, Montserrat García-Closas, Andrew F Olshan, Charles M Perou, Melissa A Troester, Michael I Love.
       BACKGROUND: The relationship between germline genetic variation and breast cancer survival is largely unknown, especially in understudied minority populations who often have poorer survival. Genome-wide association studies (GWAS) have interrogated breast cancer survival but often are underpowered due to subtype heterogeneity and clinical covariates and detect loci in non-coding regions that are difficult to interpret. Transcriptome-wide association studies (TWAS) show increased power in detecting functionally relevant loci by leveraging expression quantitative trait loci (eQTLs) from external reference panels in relevant tissues. However, ancestry- or race-specific reference panels may be needed to draw correct inference in ancestrally diverse cohorts. Such panels for breast cancer are lacking.
    RESULTS: We provide a framework for TWAS for breast cancer in diverse populations, using data from the Carolina Breast Cancer Study (CBCS), a population-based cohort that oversampled black women. We perform eQTL analysis for 406 breast cancer-related genes to train race-stratified predictive models of tumor expression from germline genotypes. Using these models, we impute expression in independent data from CBCS and TCGA, accounting for sampling variability in assessing performance. These models are not applicable across race, and their predictive performance varies across tumor subtype. Within CBCS (N = 3,828), at a false discovery-adjusted significance of 0.10 and stratifying for race, we identify associations in black women near AURKA, CAPN13, PIK3CA, and SERPINB5 via TWAS that are underpowered in GWAS.
    CONCLUSIONS: We show that carefully implemented and thoroughly validated TWAS is an efficient approach for understanding the genetics underpinning breast cancer outcomes in diverse populations.
    Keywords:  Breast cancer; Expression quantitative trait loci (eQTL); Polygenic traits; Survival; Transcriptome-wide analysis (TWAS)
    DOI:  https://doi.org/10.1186/s13059-020-1942-6
  13. Trends Cancer. 2020 Feb;pii: S2405-8033(19)30261-4. [Epub ahead of print]6(2): 75-78
    Mechanistic Links between Obesity, Insulin, and Cancer.
    Rachel J Perry, Gerald I Shulman.
      Obesity and type 2 diabetes (T2D) increase the prevalence and worsen the prognosis of more than a dozen tumor types; however, the mechanism for this association remains hotly debated. Here we discuss a potential role for insulin as the key hormonal mediator of tumor metabolism and growth in obesity-associated insulin resistance.
    Keywords:  diabetes; insulin resistance; metabolism; obesity
    DOI:  https://doi.org/10.1016/j.trecan.2019.12.003
  14. Nat Methods. 2020 Feb 17.
    Cell-type-specific signaling networks in heterocellular organoids.
    Xiao Qin, Jahangir Sufi, Petra Vlckova, Pelagia Kyriakidou, Sophie E Acton, Vivian S W Li, Mark Nitz, Christopher J Tape.
      Despite the widespread adoption of organoids as biomimetic tissue models, methods to comprehensively analyze cell-type-specific post-translational modification (PTM) signaling networks in organoids are absent. Here, we report multivariate single-cell analysis of such networks in organoids and organoid cocultures. Simultaneous analysis by mass cytometry of 28 PTMs in >1 million single cells derived from small intestinal organoids reveals cell-type- and cell-state-specific signaling networks in stem, Paneth, enteroendocrine, tuft and goblet cells, as well as enterocytes. Integrating single-cell PTM analysis with thiol-reactive organoid barcoding in situ (TOBis) enables high-throughput comparison of signaling networks between organoid cultures. Cell-type-specific PTM analysis of colorectal cancer organoid cocultures reveals that shApc, KrasG12D and Trp53R172H cell-autonomously mimic signaling states normally induced by stromal fibroblasts and macrophages. These results demonstrate how standard mass cytometry workflows can be modified to perform high-throughput multivariate cell-type-specific signaling analysis of healthy and cancerous organoids.
    DOI:  https://doi.org/10.1038/s41592-020-0737-8
  15. Nature. 2020 Feb 19.
    Gene expression and cell identity controlled by anaphase-promoting complex.
    Eugene Oh, Kevin G Mark, Annamaria Mocciaro, Edmond R Watson, J Rajan Prabu, Denny D Cha, Martin Kampmann, Nathan Gamarra, Coral Y Zhou, Michael Rape.
      Metazoan development requires the robust proliferation of progenitor cells, the identities of which are established by tightly controlled transcriptional networks1. As gene expression is globally inhibited during mitosis, the transcriptional programs that define cell identity must be restarted in each cell cycle2-5 but how this is accomplished is poorly understood. Here we identify a ubiquitin-dependent mechanism that integrates gene expression with cell division to preserve cell identity. We found that WDR5 and TBP, which bind active interphase promoters6,7, recruit the anaphase-promoting complex (APC/C) to specific transcription start sites during mitosis. This allows APC/C to decorate histones with ubiquitin chains branched at Lys11 and Lys48 (K11/K48-branched ubiquitin chains) that recruit p97 (also known as VCP) and the proteasome, which ensures the rapid expression of pluripotency genes in the next cell cycle. Mitotic exit and the re-initiation of transcription are thus controlled by a single regulator (APC/C), which provides a robust mechanism for maintaining cell identity throughout cell division.
    DOI:  https://doi.org/10.1038/s41586-020-2034-1
  16. Obes Rev. 2020 Feb 17.
    Novel insights into adiponectin action in breast cancer: Evidence of its mechanistic effects mediated by ERα expression.
    Sebastiano Andò, Giuseppina Daniela Naimo, Luca Gelsomino, Stefania Catalano, Loredana Mauro.
      This review describes the multifaceted effects of adiponectin on breast cancer cell signalling, tumour metabolism, and microenvironment. It is largely documented that low adiponectin levels are associated with an increased risk of breast cancer. However, it needs to be still clarified what are the extents of the decrease of local/intra-tumoural adiponectin concentrations, which promote breast tumour malignancy. Most of the anti-proliferative and pro-apoptotic effects induced by adiponectin have been obtained in breast cancer cells not expressing estrogen receptor alpha (ERα). Here, we will highlight recent findings demonstrating the mechanistic effects through which adiponectin is able to fuel genomic and non-genomic estrogen signalling, inhibiting LKB1/AMPK/mTOR/S6K pathway and switching energy balance. Therefore, it emerges that the reduced adiponectin levels in patients with obesity work to sustain tumour growth and progression in ERα-positive breast cancer cells. All this may contribute to remove the misleading paradigm that adiponectin univocally inhibits breast cancer cell growth and progression independently on ERα status. The latter concept, here clearly provided by pre-clinical studies, may have translational relevance adopting adiponectin as a potential therapeutic tool. Indeed, the interfering role of ERα on adiponectin action addresses how a separate assessment of adiponectin treatment needs to be considered in novel therapeutic strategies for ERα-positive and ERα-negative breast cancer.
    Keywords:  adiponectin; breast cancer; estrogen receptor alpha; obesity
    DOI:  https://doi.org/10.1111/obr.13004
  17. Nat Rev Cancer. 2020 Feb 17.
    A census of pathway maps in cancer systems biology.
    Brent M Kuenzi, Trey Ideker.
      A key goal of cancer systems biology is to use big data to elucidate the molecular networks by which cancer develops. However, to date there has been no systematic evaluation of how far these efforts have progressed. In this Analysis, we survey six major systems biology approaches for mapping and modelling cancer pathways with attention to how well their resulting network maps cover and enhance current knowledge. Our sample of 2,070 systems biology maps captures all literature-curated cancer pathways with significant enrichment, although the strong tendency is for these maps to recover isolated mechanisms rather than entire integrated processes. Systems biology maps also identify previously underappreciated functions, such as a potential role for human papillomavirus-induced chromosomal alterations in ovarian tumorigenesis, and they add new genes to known cancer pathways, such as those related to metabolism, Hippo signalling and immunity. Notably, we find that many cancer networks have been provided only in journal figures and not for programmatic access, underscoring the need to deposit network maps in community databases to ensure they can be readily accessed. Finally, few of these findings have yet been clinically translated, leaving ample opportunity for future translational studies. Periodic surveys of cancer pathway maps, such as the one reported here, are critical to assess progress in the field and identify underserved areas of methodology and cancer biology.
    DOI:  https://doi.org/10.1038/s41568-020-0240-7
  18. Nat Commun. 2020 Feb 20. 11(1): 991
    Tracing tumorigenesis in a solid tumor model at single-cell resolution.
    Samantha D Praktiknjo, Benedikt Obermayer, Qionghua Zhu, Liang Fang, Haiyue Liu, Hazel Quinn, Marlon Stoeckius, Christine Kocks, Walter Birchmeier, Nikolaus Rajewsky.
      Characterizing the complex composition of solid tumors is fundamental for understanding tumor initiation, progression and metastasis. While patient-derived samples provide valuable insight, they are heterogeneous on multiple molecular levels, and often originate from advanced tumor stages. Here, we use single-cell transcriptome and epitope profiling together with pathway and lineage analyses to study tumorigenesis from a developmental perspective in a mouse model of salivary gland squamous cell carcinoma. We provide a comprehensive cell atlas and characterize tumor-specific cells. We find that these cells are connected along a reproducible developmental trajectory: initiated in basal cells exhibiting an epithelial-to-mesenchymal transition signature, tumorigenesis proceeds through Wnt-differential cancer stem cell-like subpopulations before differentiating into luminal-like cells. Our work provides unbiased insights into tumor-specific cellular identities in a whole tissue environment, and emphasizes the power of using defined genetic model systems.
    DOI:  https://doi.org/10.1038/s41467-020-14777-0
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