bims-pideca 2020-02-09 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2020–02–09
thirty-one papers selected by
Ralitsa Radostinova Madsen, University College London

PI3K in stemness regulation: from development to cancer.
Glutamine and asparagine activate mTORC1 independently of Rag GTPases.
Oncogenic ERG represses PI3K signaling through down-regulation of IRS2.
Translational studies within the TAMRAD randomized GINECO trial: evidence for mTORC1 activation marker as a predictive factor for everolimus efficacy in advanced breast cancer.
Methylglyoxal Scavengers Resensitize KRAS-Mutated Colorectal Tumors to Cetuximab.
LATS suppresses mTORC1 activity to directly coordinate Hippo and mTORC1 pathways in growth control.
Incidence and time course of everolimus-related adverse events in postmenopausal women with hormone receptor-positive advanced breast cancer: insights from BOLERO-2.
The evolutionary history of 2,658 cancers.
IGF1-mediated human embryonic stem cell self-renewal recapitulates the embryonic niche.
Genomic basis for RNA alterations in cancer.
PIK3CA mutations, PTEN, and pHER2 expression and impact on outcome in HER2-positive early-stage breast cancer patients treated with adjuvant chemotherapy and trastuzumab.
Acetate supplementation restores chromatin accessibility and promotes tumor cell differentiation under hypoxia.
IL-8 dedifferentiates primary human luminal cells to multipotent stem cells.
Adverse event management in patients with advanced cancer receiving oral everolimus: focus on breast cancer.
Histone demethylase JMJD1C is phosphorylated by mTOR to activate de novo lipogenesis.
HSF1 phase transition mediates stress adaptation and cell fate decisions.
Long-Lived Mice with Reduced Growth Hormone Signaling Have a Constitutive Upregulation of Hepatic Chaperone-Mediated Autophagy.
The PI3K pathway impacts stem gene expression in a set of glioblastoma cell lines.
MK-2206 and Standard Neoadjuvant Chemotherapy Improves Response in Patients With Human Epidermal Growth Factor Receptor 2-Positive and/or Hormone Receptor-Negative Breast Cancers in the I-SPY 2 Trial.
Ras assemblies and signaling at the membrane.
Divergent mutational processes distinguish hypoxic and normoxic tumours.
Molecular subtype and tumor characteristics of breast cancer metastases as assessed by gene expression significantly influence patient post-relapse survival.
mTORC1 restrains adipocyte lipolysis to prevent systemic hyperlipidemia.
Phosphoinositides in cell proliferation and metabolism.
The IGF-II-Insulin Receptor Isoform-A Autocrine Signal in Cancer: Actionable Perspectives.
Genetic screens in isogenic mammalian cell lines without single cell cloning.
Crosstalk between autophagy and metabolic regulation of cancer stem cells.
Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations.
C/EBPɑ is crucial determinant of epithelial maintenance by preventing epithelial-to-mesenchymal transition.
Quantitative analysis of how Myc controls T cell proteomes and metabolic pathways during T cell activation.
Deregulation of ribosomal protein expression and translation promotes breast cancer metastasis.

Biochem Soc Trans. 2020 Feb 03. pii: BST20190778. [Epub ahead of print]

PI3K in stemness regulation: from development to cancer.

Ralitsa R Madsen.

  The PI3K/AKT pathway is a key target in oncology where most efforts are focussed on phenotypes such as cell proliferation and survival. Comparatively, little attention has been paid to PI3K in stemness regulation, despite the emerging link between acquisition of stem cell-like features and therapeutic failure in cancer. The aim of this review is to summarise current known and unknowns of PI3K-dependent stemness regulation, by integrating knowledge from the fields of developmental, signalling and cancer biology. Particular attention is given to the role of the PI3K pathway in pluripotent stem cells (PSCs) and the emerging parallels to dedifferentiated cancer cells with stem cell-like features. Compelling evidence suggests that PI3K/AKT signalling forms part of a 'core molecular stemness programme' in both mouse and human PSCs. In cancer, the oncogenic PIK3CAH1047R variant causes constitutive activation of the PI3K pathway and has recently been linked to increased stemness in a dose-dependent manner, similar to observations in mouse PSCs with heterozygous versus homozygous Pten loss. There is also evidence that the stemness phenotype may become 'locked' and thus independent of the original PI3K activation, posing limitations for the success of PI3K monotherapy in cancer. Ongoing therapeutic developments for PI3K-associated cancers may therefore benefit from a better understanding of the pathway's two-layered and highly context-dependent regulation of cell growth versus stemness.

Keywords:  PI3K signalling; PIK3CA; cancer; development; pluripotent stem cells; stemness

DOI:  https://doi.org/10.1042/BST20190778
J Biol Chem. 2020 Feb 04. pii: jbc.AC119.011578. [Epub ahead of print]

Glutamine and asparagine activate mTORC1 independently of Rag GTPases.

Delong Meng, Qianmei Yang, Huanyu Wang, Chase H Melick, Rishika Navlani, Anderson R Frank, Jenna L Jewell.

  Nutrient sensing by cells is crucial, and when this sensing mechanism is disturbed human disease can occur. mTOR complex 1 (mTORC1) senses amino acids to control cell growth, metabolism and autophagy. Leucine, arginine, and methionine signal to mTORC1 through the well-characterized Rag GTPase signaling pathway. In contrast, glutamine activates mTORC1 through a Rag GTPase-independent mechanism that requires ADP-ribosylation factor 1 (Arf1). Here, using several biochemical and genetic approaches, we show that eight amino acids filter through the Rag GTPase pathway. Like glutamine, asparagine signals to mTORC1 through Arf1 in the absence of the Rag GTPases. Both the Rag-dependent and Rag-independent pathways required the lysosome and lysosomal function for mTORC1 activation. Our results show that mTORC1 is differentially regulated by amino acids through two distinct pathways.

Keywords:  Arf1; Rag GTPase; amino acid; asparagine; glutamine; mTOR complex (mTORC); mTORC1; metabolism; signal transduction

DOI:  https://doi.org/10.1074/jbc.AC119.011578
Cancer Res. 2020 Feb 03. pii: canres.1394.2019. [Epub ahead of print]

Oncogenic ERG represses PI3K signaling through down-regulation of IRS2.

Ninghui Mao, Dong Gao, Wenhuo Hu, Sunyana Gadal, Haley Hieronymus, Shangqian Wang, Young Sun Lee, Patrick Sullivan, Zeda Zhang, Danielle Choi, Neal Rosen, Charles L Sawyers, Anuradha Gopalan, Yu Chen, Brett S Carver.

Genomic rearrangements leading to the aberrant expression of ERG are the most common early events in prostate cancer and are significantly enriched for the concomitant loss of PTEN. Genetically engineered mouse models reveal that ERG overexpression alone is not sufficient to induce tumorigenesis, but combined loss of PTEN results in an aggressive invasive phenotype. Here we show that oncogenic ERG repressed PI3K signaling though direct transcriptional suppression of IRS2 leading to reduced RTK levels and activity. In accordance with this finding, ERG positive human prostate cancers had a repressed AKT gene signature and transcriptional down-regulation of IRS2. While overexpression of IRS2 activated PI3K signaling, promoting cell migration in a PI3K dependent manner, this did not fully recapitulate the phenotype seen with loss of PTEN as PI3K signaling is not as robust as observed in the setting of loss of PTEN. Importantly, deletions of the PTEN locus, which promotes active PI3K signaling, were among the most significant copy number alterations that co-occurred with ERG genomic rearrangements. This work provides insight on how initiating oncogenic events may directly influence the selection of secondary concomitant alterations to promote oncogenic signaling during tumor evolution.

DOI: https://doi.org/10.1158/0008-5472.CAN-19-1394
Ann Oncol. 2015 Jan;pii: S0923-7534(19)31337-7. [Epub ahead of print]26(1): 120-125

Translational studies within the TAMRAD randomized GINECO trial: evidence for mTORC1 activation marker as a predictive factor for everolimus efficacy in advanced breast cancer.

I Treilleux, M Arnedos, C Cropet, Q Wang, J-M Ferrero, S Abadie-Lacourtoisie, C Levy, E Legouffe, A Lortholary, E Pujade-Lauraine, A-V Bourcier, J-C Eymard, D Spaeth, T Bachelot.

   BACKGROUND: Everolimus is an agent frequently associated with specific toxicities. Predictive markers of efficacy are needed to help define which patients could benefit from it. The goal of this exploratory study was to identify potential predictive biomarkers in the mammalian target of rapamycin (mTOR) complex 1 (mTORC1) activation pathway using primary tumor samples collected during the phase II tamoxifen plus everolimus (TAMRAD) trial.
PATIENTS AND METHODS: Tumor tissues were collected retrospectively from the TAMRAD trial. Immunohistochemistry was carried out using specific antibodies directed toward proteins that result in mTORC1 activation [canonical phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt)/mTOR or alternative pathways]. DNA was extracted from the tumor tissue; mutation screening in the PIK3CA gene (exons 9 and 20) and the KRAS gene (exons 2 and 3) was first carried out using Sanger direct sequencing, and then completed by next-generation sequencing for PIK3CA. An exploratory analysis of everolimus efficacy in terms of a time-to-progression (TTP) increase was carried out in each biomarker subgroup (high versus low expression referring to the median percentage of marked cells).
RESULTS: A total of 55 primary tumor samples from the TAMRAD trial-25 from the tamoxifen-alone group and 30 from the tamoxifen/everolimus group-were evaluated for biomarkers. The subgroups most likely to have an improvement in TTP with tamoxifen/everolimus therapy, compared with tamoxifen alone, were patients with high p4EBP1, low 4EBP1, low liver kinase B1, low pAkt, and low PI3K. Among the 45 samples screened for mutation status, nine samples (20%; 95% CI 9.6-34.6) had a PIK3CA mutation. KRAS mutation was observed in one patient.
CONCLUSIONS: A positive correlation between late effectors of mTORC1 activation, a positive correlation between Akt-independent mTORC1 activation, and an inverse correlation between canonical PI3K/Akt/mTOR pathway and everolimus efficacy were observed in this exploratory analysis. However, these correlations need to be validated in larger studies before applying the findings to routine clinical practice.

Keywords:  biomarkers; breast cancer; everolimus; mTORC1; tamoxifen

DOI:  https://doi.org/10.1093/annonc/mdu497
Cell Rep. 2020 Feb 04. pii: S2211-1247(20)30021-8. [Epub ahead of print]30(5): 1400-1416.e6

Methylglyoxal Scavengers Resensitize KRAS-Mutated Colorectal Tumors to Cetuximab.

Justine Bellier, Marie-Julie Nokin, Maurine Caprasse, Assia Tiamiou, Arnaud Blomme, Jean L Scheijen, Benjamin Koopmansch, Gillian M MacKay, Barbara Chiavarina, Brunella Costanza, Gilles Rademaker, Florence Durieux, Ferman Agirman, Naïma Maloujahmoum, Pino G Cusumano, Pierre Lovinfosse, Hing Y Leung, Frédéric Lambert, Vincent Bours, Casper G Schalkwijk, Roland Hustinx, Olivier Peulen, Vincent Castronovo, Akeila Bellahcène.

  The use of cetuximab anti-epidermal growth factor receptor (anti-EGFR) antibodies has opened the era of targeted and personalized therapy in colorectal cancer (CRC). Poor response rates have been unequivocally shown in mutant KRAS and are even observed in a majority of wild-type KRAS tumors. Therefore, patient selection based on mutational profiling remains problematic. We previously identified methylglyoxal (MGO), a by-product of glycolysis, as a metabolite promoting tumor growth and metastasis. Mutant KRAS cells under MGO stress show AKT-dependent survival when compared with wild-type KRAS isogenic CRC cells. MGO induces AKT activation through phosphatidylinositol 3-kinase (PI3K)/mammalian target of rapamycin 2 (mTORC2) and Hsp27 regulation. Importantly, the sole induction of MGO stress in sensitive wild-type KRAS cells renders them resistant to cetuximab. MGO scavengers inhibit AKT and resensitize KRAS-mutated CRC cells to cetuximab in vivo. This study establishes a link between MGO and AKT activation and pinpoints this oncometabolite as a potential target to tackle EGFR-targeted therapy resistance in CRC.

Keywords:  AKT signaling; EGFR-targeted therapy; Hsp27; KRAS mutation; aminoguanidine; carnosine; cetuximab; colorectal cancer; methylglyoxal

DOI:  https://doi.org/10.1016/j.celrep.2020.01.012
Nat Cell Biol. 2020 Feb;22(2): 246-256

LATS suppresses mTORC1 activity to directly coordinate Hippo and mTORC1 pathways in growth control.

Wenjian Gan, Xiaoming Dai, Xiangpeng Dai, Jun Xie, Shasha Yin, Junjie Zhu, Chen Wang, Yuchen Liu, Jianping Guo, Min Wang, Jing Liu, Jia Hu, Ryan J Quinton, Neil J Ganem, Pengda Liu, John M Asara, Pier Paolo Pandolfi, Yingzi Yang, Zhigang He, Guangping Gao, Wenyi Wei.

The Hippo and mammalian target of rapamycin complex 1 (mTORC1) pathways are the two predominant growth-control pathways that dictate proper organ development. We therefore explored potential crosstalk between these two functionally relevant pathways to coordinate their growth-control functions. We found that the LATS1 and LATS2 kinases, the core components of the Hippo pathway, phosphorylate S606 of Raptor, an essential component of mTORC1, to attenuate mTORC1 activation by impairing the interaction of Raptor with Rheb. The phosphomimetic Raptor-S606D knock-in mutant led to a reduction in cell size and proliferation. Compared with Raptor+/+ mice, RaptorD/D knock-in mice exhibited smaller livers and hearts, and a significant inhibition of elevation in mTORC1 signalling induced by Nf2 or Lats1 and Lats2 loss. Thus, our study reveals a direct link between the Hippo and mTORC1 pathways to fine-tune organ growth.

DOI: https://doi.org/10.1038/s41556-020-0463-6
Ann Oncol. 2014 Apr;pii: S0923-7534(19)36498-1. [Epub ahead of print]25(4): 808-815

Incidence and time course of everolimus-related adverse events in postmenopausal women with hormone receptor-positive advanced breast cancer: insights from BOLERO-2.

H S Rugo, K I Pritchard, M Gnant, S Noguchi, M Piccart, G Hortobagyi, J Baselga, A Perez, M Geberth, T Csoszi, E Chouinard, V Srimuninnimit, P Puttawibul, J Eakle, W Feng, H Bauly, M El-Hashimy, T Taran, H A Burris.

   BACKGROUND: In the BOLERO-2 trial, everolimus (EVE), an inhibitor of mammalian target of rapamycin, demonstrated significant clinical benefit with an acceptable safety profile when administered with exemestane (EXE) in postmenopausal women with hormone receptor-positive (HR+) advanced breast cancer. We report on the incidence, time course, severity, and resolution of treatment-emergent adverse events (AEs) as well as incidence of dose modifications during the extended follow-up of this study.
PATIENTS AND METHODS: Patients were randomized (2:1) to receive EVE 10 mg/day or placebo (PBO), with open-label EXE 25 mg/day (n = 724). The primary end point was progression-free survival. Secondary end points included overall survival, objective response rate, and safety. Safety evaluations included recording of AEs, laboratory values, dose interruptions/adjustments, and study drug discontinuations.
RESULTS: The safety population comprised 720 patients (EVE + EXE, 482; PBO + EXE, 238). The median follow-up was 18 months. Class-effect toxicities, including stomatitis, pneumonitis, and hyperglycemia, were generally of mild or moderate severity and occurred relatively early after treatment initiation (except pneumonitis); incidence tapered off thereafter. EVE dose reduction and interruption (360 and 705 events, respectively) required for AE management were independent of patient age. The median duration of dose interruption was 7 days. Discontinuation of both study drugs because of AEs was higher with EVE + EXE (9%) versus PBO + EXE (3%).
CONCLUSIONS: Most EVE-associated AEs occur soon after initiation of therapy, are typically of mild or moderate severity, and are generally manageable with dose reduction and interruption. Discontinuation due to toxicity was uncommon. Understanding the time course of class-effect AEs will help inform preventive and monitoring strategies as well as patient education.
TRIAL REGISTRATION NUMBER: NCT00863655.

Keywords:  advanced breast cancer; everolimus; mammalian target of rapamycin (mTOR); safety

DOI:  https://doi.org/10.1093/annonc/mdu009
Nature. 2020 02;578(7793): 122-128

The evolutionary history of 2,658 cancers.

PCAWG Evolution & Heterogeneity Working Group

Cancer develops through a process of somatic evolution1,2. Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of mutational processes3. Here, by whole-genome sequencing analysis of 2,658 cancers as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)4, we reconstruct the life history and evolution of mutational processes and driver mutation sequences of 38 types of cancer. Early oncogenesis is characterized by mutations in a constrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and isochromosome 17q in medulloblastoma. The mutational spectrum changes significantly throughout tumour evolution in 40% of samples. A nearly fourfold diversification of driver genes and increased genomic instability are features of later stages. Copy number alterations often occur in mitotic crises, and lead to simultaneous gains of chromosomal segments. Timing analyses suggest that driver mutations often precede diagnosis by many years, if not decades. Together, these results determine the evolutionary trajectories of cancer, and highlight opportunities for early cancer detection.

DOI: https://doi.org/10.1038/s41586-019-1907-7
Nat Commun. 2020 Feb 07. 11(1): 764

IGF1-mediated human embryonic stem cell self-renewal recapitulates the embryonic niche.

Sissy E Wamaitha, Katarzyna J Grybel, Gregorio Alanis-Lobato, Claudia Gerri, Sugako Ogushi, Afshan McCarthy, Shantha K Mahadevaiah, Lyn Healy, Rebecca A Lea, Miriam Molina-Arcas, Liani G Devito, Kay Elder, Phil Snell, Leila Christie, Julian Downward, James M A Turner, Kathy K Niakan.

Our understanding of the signalling pathways regulating early human development is limited, despite their fundamental biological importance. Here, we mine transcriptomics datasets to investigate signalling in the human embryo and identify expression for the insulin and insulin growth factor 1 (IGF1) receptors, along with IGF1 ligand. Consequently, we generate a minimal chemically-defined culture medium in which IGF1 together with Activin maintain self-renewal in the absence of fibroblast growth factor (FGF) signalling. Under these conditions, we derive several pluripotent stem cell lines that express pluripotency-associated genes, retain high viability and a normal karyotype, and can be genetically modified or differentiated into multiple cell lineages. We also identify active phosphoinositide 3-kinase (PI3K)/AKT/mTOR signalling in early human embryos, and in both primed and naïve pluripotent culture conditions. This demonstrates that signalling insights from human blastocysts can be used to define culture conditions that more closely recapitulate the embryonic niche.

DOI: https://doi.org/10.1038/s41467-020-14629-x
Nature. 2020 02;578(7793): 129-136

Genomic basis for RNA alterations in cancer.

PCAWG Transcriptome Core Group

Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.

DOI: https://doi.org/10.1038/s41586-020-1970-0
Ann Oncol. 2012 Aug;pii: S0923-7534(19)38088-3. [Epub ahead of print]23(8): 2034-2042

PIK3CA mutations, PTEN, and pHER2 expression and impact on outcome in HER2-positive early-stage breast cancer patients treated with adjuvant chemotherapy and trastuzumab.

J D Jensen, A Knoop, A V Laenkholm, M Grauslund, M B Jensen, E Santoni-Rugiu, M Andersson, M Ewertz.

   BACKGROUND: This study was conducted to determine the frequency of PIK3CA mutations and human epidermal growth factor receptor-2 (HER2) phosphorylation status (pHER2-Tyr1221/1222) and if PIK3CA, phosphatase and tensin homolog (PTEN), or pHER2 has an impact on outcome in HER2-positive early-stage breast cancer patients treated with adjuvant chemotherapy and trastuzumab.
PATIENTS AND METHODS: Two hundred and forty HER2-positive early-stage breast cancer patients receiving adjuvant treatment (cyclophosphamide 600 mg/m2, epirubicin 60 mg/m2, and fluorouracil 600 mg/m2) before administration of 1 year trastuzumab were assessable. PTEN and pHER2 expression were assessed by immunohistochemistry. PIK3CA mutations (exons 9 and 20) were determined by pyrosequencing.
RESULTS: Five-year overall survival (OS) and invasive disease-free survival were 87.8% and 81.0%, respectively. Twenty-six percent of patients had a PIK3CA mutation, 24% were PTEN low, 45% pHER2 high, and 47% patients had increased PI3K pathway activation (PTEN low and/or PIK3CA mutation). No significant correlations were observed between the clinicopathological variables and PIK3CA, PTEN, and pHER2 status. In both univariate and multivariate analyses, patients with PIK3CA mutations or high PI3K pathway activity had a significant worse OS [multivariate: hazard ratio (HR) 2.14, 95% confidence interval (CI) 1.01-4.51, P = 0.046; and HR 2.35, 95% CI 1.10-5.04, P = 0.03].
CONCLUSION: Patients with PIK3CA mutations or increased PI3K pathway activity had a significantly poorer survival despite adequate treatment with adjuvant chemotherapy and trastuzumab.

Keywords:  HER2-positive early-stage breast cancer; PI3K activity; PIK3CA mutations; PTEN; pHER2; trastuzumab resistance

DOI:  https://doi.org/10.1093/annonc/mdr546
Cell Death Dis. 2020 Feb 06. 11(2): 102

Acetate supplementation restores chromatin accessibility and promotes tumor cell differentiation under hypoxia.

Yang Li, Joshua J Gruber, Ulrike M Litzenburger, Yiren Zhou, Yu Rebecca Miao, Edward L LaGory, Albert M Li, Zhen Hu, Michaela Yip, Lori S Hart, John M Maris, Howard Y Chang, Amato J Giaccia, Jiangbin Ye.

Despite the fact that Otto H. Warburg discovered the Warburg effect almost one hundred years ago, why cancer cells waste most of the glucose carbon as lactate remains an enigma. Warburg proposed a connection between the Warburg effect and cell dedifferentiation. Hypoxia is a common tumor microenvironmental stress that induces the Warburg effect and blocks tumor cell differentiation. The underlying mechanism by which this occurs is poorly understood, and no effective therapeutic strategy has been developed to overcome this resistance to differentiation. Using a neuroblastoma differentiation model, we discovered that hypoxia repressed cell differentiation through reducing cellular acetyl-CoA levels, leading to reduction of global histone acetylation and chromatin accessibility. The metabolic switch triggering this global histone hypoacetylation was the induction of pyruvate dehydrogenase kinases (PDK1 and PDK3). Inhibition of PDKs using dichloroacetate (DCA) restored acetyl-CoA generation and histone acetylation under hypoxia. Knocking down PDK1 induced neuroblastoma cell differentiation, highlighting the critical role of PDK1 in cell fate control. Importantly, acetate or glycerol triacetate (GTA) supplementation restored differentiation markers expression and neuron differentiation under hypoxia. Moreover, ATAC-Seq analysis demonstrated that hypoxia treatment significantly reduced chromatin accessibility at RAR/RXR binding sites, which can be restored by acetate supplementation. In addition, hypoxia-induced histone hypermethylation by increasing 2-hydroxyglutarate (2HG) and reducing α-ketoglutarate (αKG). αKG supplementation reduced histone hypermethylation upon hypoxia, but did not restore histone acetylation or differentiation markers expression. Together, these findings suggest that diverting pyruvate flux away from acetyl-CoA generation to lactate production is the key mechanism that Warburg effect drives dedifferentiation and tumorigenesis. We propose that combining differentiation therapy with acetate/GTA supplementation might represent an effective therapy against neuroblastoma.

DOI: https://doi.org/10.1038/s41419-020-2303-9
Mol Cell Biol. 2020 Feb 03. pii: MCB.00508-19. [Epub ahead of print]

IL-8 dedifferentiates primary human luminal cells to multipotent stem cells.

Huda H Al-Khalaf, Hazem Ghebeh, Salma M Wakil, Falah Al-Mohanna, Abdelilah Aboussekhra.

During aging, cellular plasticity and senescence play important roles in tissue regeneration and the pathogenesis of different diseases including cancer. We have recently shown that senescent breast luminal cells can activate their adjacent stromal fibroblasts. In the present report, we present clear evidence that these senescence-related active fibroblasts can dedifferentiate proliferating primary human luminal cells to multipotent stem cells in an IL-8-dependent manner. This was confirmed using recombinant IL-8, while the truncated protein was not active. This IL-8-related dedifferentiation of luminal cells was mediated through STAT3-dependent down-regulation of p16INK4A and miR-141. Importantly, these in vitro-generated mammary stem cells exhibited high molecular and cellular similarities with human mammary stem cells. They have also shown long-term mammary gland reconstituting ability, and capacity to produce milk post-delivery. Thereby, these IL-8-generated mammary stem cells could be of great value for autologous cell therapy procedures, and also for biomedical research as well as drug development.

DOI: https://doi.org/10.1128/MCB.00508-19
Ann Oncol. 2014 Apr;pii: S0923-7534(19)36504-4. [Epub ahead of print]25(4): 763-773

Adverse event management in patients with advanced cancer receiving oral everolimus: focus on breast cancer.

M Aapro, F Andre, K Blackwell, E Calvo, M Jahanzeb, K Papazisis, C Porta, K Pritchard, A Ravaud.

   BACKGROUND: Everolimus, an orally administered rapamycin analogue, inhibits the mammalian target of rapamycin (mTOR), a highly conserved intracellular serine-threonine kinase that is a central node in a network of signaling pathways controlling cellular metabolism, growth, survival, proliferation, angiogenesis, and immune function. Everolimus has demonstrated substantial clinical benefit in randomized, controlled, phase III studies leading to approval for the treatment of advanced renal cell carcinoma, advanced neuroendocrine tumors of pancreatic origin, renal angiomyolipoma and subependymal giant-cell astrocytoma associated with tuberous sclerosis complex, as well as advanced hormone-receptor-positive (HR+) and human epidermal growth factor receptor-2-negative advanced breast cancer.
MATERIALS AND METHODS: We discuss clinically relevant everolimus-related adverse events from the phase III studies, including stomatitis, noninfectious pneumonitis, rash, selected metabolic abnormalities, and infections, with focus on appropriate clinical management of these events and specific considerations in patients with breast cancer.
RESULTS: The majority of adverse events experienced during everolimus therapy are of mild to moderate severity. The safety profile and protocols for toxicity management are well established. The class-effect adverse event profile observed with everolimus plus endocrine therapy in breast cancer is (as expected) distinct from that of endocrine therapy alone, but is similar to that observed with everolimus in other solid tumors. Information gained from the experience in other carcinomas on prompt diagnosis and treatments to optimize drug exposure, treatment outcomes, and patients' quality of life also applies to the patient population with advanced breast cancer.
CONCLUSIONS: As with all orally administered agents, education of both physicians and patients in the management of adverse events for patients receiving everolimus is critical to achieving optimal exposure and clinical benefit. Active monitoring for early identification of everolimus-related adverse events combined with aggressive and appropriate intervention should lead to a reduction in the severity and duration of the event.

Keywords:  everolimus; infections; metabolic abnormality; pneumonitis; rash; stomatitis

DOI:  https://doi.org/10.1093/annonc/mdu021
Nat Commun. 2020 Feb 07. 11(1): 796

Histone demethylase JMJD1C is phosphorylated by mTOR to activate de novo lipogenesis.

Jose A Viscarra, Yuhui Wang, Hai P Nguyen, Yoon Gi Choi, Hei Sook Sul.

Fatty acid and triglyceride synthesis increases greatly in response to feeding and insulin. This lipogenic induction involves coordinate transcriptional activation of various enzymes in lipogenic pathway, including fatty acid synthase and glycerol-3-phosphate acyltransferase. Here, we show that JMJD1C is a specific histone demethylase for lipogenic gene transcription in liver. In response to feeding/insulin, JMJD1C is phosphorylated at T505 by mTOR complex to allow direct interaction with USF-1 for recruitment to lipogenic promoter regions. Thus, by demethylating H3K9me2, JMJD1C alters chromatin accessibility to allow transcription. Consequently, JMJD1C promotes lipogenesis in vivo to increase hepatic and plasma triglyceride levels, showing its role in metabolic adaption for activation of the lipogenic program in response to feeding/insulin, and its contribution to development of hepatosteatosis resulting in insulin resistance.

DOI: https://doi.org/10.1038/s41467-020-14617-1
Nat Cell Biol. 2020 Feb;22(2): 151-158

HSF1 phase transition mediates stress adaptation and cell fate decisions.

Giorgio Gaglia, Rumana Rashid, Clarence Yapp, Gaurav N Joshi, Carmen G Li, Susan L Lindquist, Kristopher A Sarosiek, Luke Whitesell, Peter K Sorger, Sandro Santagata.

Under proteotoxic stress, some cells survive whereas others die. The mechanisms governing this heterogeneity in cell fate remain unknown. Here we report that condensation and phase transition of heat-shock factor 1 (HSF1), a transcriptional regulator of chaperones1,2, is integral to cell-fate decisions underlying survival or death. During stress, HSF1 drives chaperone expression but also accumulates separately in nuclear stress bodies called foci3-6. Foci formation has been regarded as a marker of cells actively upregulating chaperones3,6-10. Using multiplexed tissue imaging, we observed HSF1 foci in human tumours. Paradoxically, their presence inversely correlated with chaperone expression. By live-cell microscopy and single-cell analysis, we found that foci dissolution rather than formation promoted HSF1 activity and cell survival. During prolonged stress, the biophysical properties of HSF1 foci changed; small, fluid condensates enlarged into indissoluble gel-like arrangements with immobilized HSF1. Chaperone gene induction was reduced in such cells, which were prone to apoptosis. Quantitative analysis suggests that survival under stress results from competition between concurrent but opposing mechanisms. Foci may serve as sensors that tune cytoprotective responses, balancing rapid transient responses and irreversible outcomes.

DOI: https://doi.org/10.1038/s41556-019-0458-3
Autophagy. 2020 Feb 03.

Long-Lived Mice with Reduced Growth Hormone Signaling Have a Constitutive Upregulation of Hepatic Chaperone-Mediated Autophagy.

S Joseph Endicott, Dennis N Boynton, Logan J Beckmann, Richard A Miller.

  Chaperone-mediated autophagy (CMA) is a selective, vesicle-independent, lysosomal degradation pathway for intracellular proteins. CMA modulates proteomic organization through selective protein degradation, with targets including metabolic enzymes, regulators of cell growth, and neurodegeneration-related proteins. CMA activity is low in ad libitum-fed rodents but is increased by prolonged fasting (>16 h). AKT negatively regulates CMA activity at the lysosomal membrane by phosphorylating and inhibiting the CMA regulator GFAP. We have previously reported that long-lived Pou1f1/Pit1 mutant (Snell) mice and ghr (growth hormone receptor) knockout mice (ghr KO) have lower AKT activity when fed compared to littermate controls, suggesting the hypothesis that these mice have increased baseline CMA activity. Here, we report that liver lysosomes from fed Snell dwarf mice and ghr KO mice have decreased GFAP phosphorylation and increased CMA substrate uptake activity. Liver lysosomes isolated from fed Snell dwarf mice and ghr KO mice injected with the protease inhibitor leupeptin had increased accumulation of endogenous CMA substrates, compared to littermate controls, suggesting an increase in CMA in vivo. Mice with liver-specific ablation of GH (growth hormone) signaling did not have increased liver CMA, suggesting that a signaling effect resulting from a loss of growth hormone in another tissue causes enhanced CMA in Snell dwarf and ghr KO mice. Finally, we find Snell dwarf mice have decreased protein levels (in liver and kidney) of CIP2A, a well-characterized CMA target protein, without an associated change in Cip2a mRNA. Collectively, these data suggest that CMA is enhanced downstream of an endocrine change resulting from whole-body ablation of GH signaling.

Keywords:  Aging; chaperone-mediated autophagy; endocrine control of autophagy; endocrine signaling; growth hormone

DOI:  https://doi.org/10.1080/15548627.2020.1725378
J Cancer Res Clin Oncol. 2020 Feb 06.

The PI3K pathway impacts stem gene expression in a set of glioblastoma cell lines.

Eduardo Martinez, Neftali Vazquez, Alma Lopez, Victor Fanniel, Lilia Sanchez, Rebecca Marks, Leetoria Hinojosa, Victoria Cuello, Marisa Cuevas, Angelica Rodriguez, Cerin Tomson, Andrea Salinas, Mark Abad, Martin Holguin, Noel Garza, Abraham Arenas, Kevin Abraham, Luis Maldonado, Vivian Rojas, Alex Basdeo, Erin Schuenzel, Michael Persans, Wendy Innis-Whitehouse, Megan Keniry.

   BACKGROUND: The PI3K pathway controls diverse cellular processes including growth, survival, metabolism, and apoptosis. Nuclear FOXO factors were observed in cancers that harbor constitutively active PI3K pathway output and stem signatures. FOXO1 and FOXO3 were previously published to induce stem genes such as OCT4 in embryonic stem cells. Here, we investigated FOXO-driven stem gene expression in U87MG glioblastoma cells.
METHODS: PI3K-activated cancer cell lines were investigated for changes in gene expression, signal transduction, and clonogenicity under conditions with FOXO3 disruption or exogenous expression. The impact of PI3K pathway inhibition on stem gene expression was examined in a set of glioblastoma cell lines.
RESULTS: We found that CRISPR-Cas9-mediated FOXO3 disruption in U87MG cells caused decreased OCT4 and SOX2 gene expression, STAT3 phosphorylation on tyrosine 705 and clonogenicity. FOXO3 over expression led to increased OCT4 in numerous glioblastoma cancer cell lines. Strikingly, treatment of glioblastoma cells with NVP-BEZ235 (a dual inhibitor of PI3K and mTOR), which activates FOXO factors, led to robust increases OCT4 gene expression. Direct FOXO factor recruitment to the OCT4 promoter was detected by chromatin immunoprecipitation analyses using U87MG extracts.
DISCUSSION: We show for the first time that FOXO transcription factors promote stem gene expression glioblastoma cells. Treatment with PI3K inhibitor NVP-BEZ235 led to dramatic increases in stem genes in a set of glioblastoma cell lines.
CONCLUSION: Given that, PI3K inhibitors are actively investigated as targeted cancer therapies, the FOXO-mediated induction of stem genes observed in this study highlights a potential hazard to PI3K inhibition. Understanding the molecular underpinnings of stem signatures in cancer will allow refinements to therapeutic strategies. Targeting FOXO factors to reduce stem cell characteristics in concert with PI3K inhibition may prove therapeutically efficacious.

Keywords:  FOXO transcription factors; Glioblastoma; OCT4; PI3K inhibition; Stem genes

DOI:  https://doi.org/10.1007/s00432-020-03133-w
J Clin Oncol. 2019 Feb 07. JCO1901027

MK-2206 and Standard Neoadjuvant Chemotherapy Improves Response in Patients With Human Epidermal Growth Factor Receptor 2-Positive and/or Hormone Receptor-Negative Breast Cancers in the I-SPY 2 Trial.

I-SPY 2 Consortium

PURPOSE: The phosphatidylinositol 3-kinase/Akt/mammalian target of rapamycin is a key pathway of survival and therapeutic resistance in breast cancer. We evaluated the pan-Akt inhibitor MK-2206 in combination with standard therapy in patients with high-risk early-stage breast cancer.
PATIENTS AND METHODS: I-SPY 2 is a multicenter, phase II, open-label, adaptively randomized neoadjuvant platform trial that screens experimental therapies and efficiently identifies potential predictive biomarker signatures. Patients are categorized by human epidermal growth factor receptor 2 (HER2), hormone receptor (HR), and MammaPrint statuses in a 2 × 2 × 2 layout. Patients within each of these 8 biomarker subtypes are adaptively randomly assigned to one of several experimental therapies, including MK-2206, or control. Therapies are evaluated for 10 biomarker signatures, each of which is a combination of these subtypes. The primary end point is pathologic complete response (pCR). A therapy graduates with one or more of these signatures if and when it has an 85% Bayesian predictive probability of success in a hypothetical phase III trial, adjusting for biomarker covariates. Patients in the current report received standard taxane- and anthracycline-based neoadjuvant therapy without (control) or with oral MK-2206 135 mg/week.
RESULTS: MK-2206 graduated with 94 patients and 57 concurrently randomly assigned controls in 3 graduation signatures: HR-negative/HER2-positive, HR-negative, and HER2-positive. Respective Bayesian mean covariate-adjusted pCR rates and percentage probability that MK-2206 is superior to control were 0.48:0.29 (97%), 0.62:0.36 (99%), and 0.46:0.26 (94%). In exploratory analyses, MK-2206 evinced a numerical improvement in event-free survival in its graduating signatures. The most significant grade 3-4 toxicity was rash (14% maculopapular, 8.6% acneiform).
CONCLUSION: The Akt inhibitor MK-2206 combined with standard neoadjuvant therapy resulted in higher estimated pCR rates in HR-negative and HER2-positive breast cancer. Although MK-2206 is not being further developed at this time, this class of agents remains of clinical interest.

DOI: https://doi.org/10.1200/JCO.19.01027
Curr Opin Struct Biol. 2020 Feb 04. pii: S0959-440X(20)30009-9. [Epub ahead of print]62 140-148

Ras assemblies and signaling at the membrane.

Ruth Nussinov, Chung-Jung Tsai, Hyunbum Jang.

Here, we review mechanisms of Ras spatiotemporal clustering with PI3Kα and Raf at the membrane. The large RTK‒Ras‒PI3Kα lipid kinase assembly is at the membrane to generate signaling lipid PIP3. Raf, but not PI3Kα, has long linker extending from the membrane to the kinase domain. This disordered linker stretches into the cytoplasm where Raf's kinase domain side-to-side dimerization and activation is allosterically-driven by MEK under KSR dimers control. The cytoplasm, but not the crowded membrane surface, can accommodate the large Raf's activation and MAPK signaling assemblies, and Raf's disordered linker brings them there. Further, Raf's activation, but not PI3Kα's, requires kinase domain dimerization; Ras nanoclusters accomplishing this necessitate Raf's long linkers. Thus, biophysical and functional constraints shape Ras spatiotemporal assemblies.

DOI: https://doi.org/10.1016/j.sbi.2020.01.009
Nat Commun. 2020 Feb 05. 11(1): 737

Divergent mutational processes distinguish hypoxic and normoxic tumours.

PCAWG Consortium

Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.

DOI: https://doi.org/10.1038/s41467-019-14052-x
Ann Oncol. 2015 Jan;pii: S0923-7534(19)31338-9. [Epub ahead of print]26(1): 81-88

Molecular subtype and tumor characteristics of breast cancer metastases as assessed by gene expression significantly influence patient post-relapse survival.

TEX Trialists Group

   BACKGROUND: We and others have recently shown that tumor characteristics are altered throughout tumor progression. These findings emphasize the need for re-examination of tumor characteristics at relapse and have led to recommendations from ESMO and the Swedish Breast Cancer group. Here, we aim to determine whether tumor characteristics and molecular subtypes in breast cancer metastases confer clinically relevant prognostic information for patients.
PATIENTS AND METHODS: The translational aspect of the Swedish multicenter randomized trial called TEX included 111 patients with at least one biopsy from a morphologically confirmed locoregional or distant breast cancer metastasis diagnosed from December 2002 until June 2007. All patients had detailed clinical information, complete follow-up, and metastasis gene expression information (Affymetrix array GPL10379). We assessed the previously published gene expression modules describing biological processes [proliferation, apoptosis, human epidermal receptor 2 (HER2) and estrogen (ER) signaling, tumor invasion, immune response, and angiogenesis] and pathways (Ras, MAPK, PTEN, AKT-MTOR, PI3KCA, IGF1, Src, Myc, E2F3, and β-catenin) and the intrinsic subtypes (PAM50). Furthermore, by contrasting genes expressed in the metastases in relation to survival, we derived a poor metastasis survival signature.
RESULTS: A significant reduction in post-relapse breast cancer-specific survival was associated with low-ER receptor signaling and apoptosis gene module scores, and high AKT-MTOR, Ras, and β-catenin module scores. Similarly, intrinsic subtyping of the metastases provided statistically significant post-relapse survival information with the worst survival outcome in the basal-like [hazard ratio (HR) 3.7; 95% confidence interval (CI) 1.3-10.9] and HER2-enriched (HR 4.4; 95% CI 1.5-12.8) subtypes compared with the luminal A subtype. Overall, 25% of the metastases were basal-like, 32% HER2-enriched, 10% luminal A, 28% luminal B, and 5% normal-like.
CONCLUSIONS: We show that tumor characteristics and molecular subtypes of breast cancer metastases significantly influence post-relapse patient survival, emphasizing that molecular investigations at relapse provide prognostic and clinically relevant information. CLINICALTRIALS.GOV: This is the translational part of the Swedish multicenter and randomized trial TEX, clinicaltrials.gov identifier nct01433614 (http://www.clinicaltrials.gov/ct2/show/nct01433614).

Keywords:  TEX randomized trial; biopsy at relapse; breast cancer metastases; gene expression; gene modules; metastasis characteristics

DOI:  https://doi.org/10.1093/annonc/mdu498
Mol Metab. 2020 Feb;pii: S2212-8778(19)30954-8. [Epub ahead of print]32 136-147

mTORC1 restrains adipocyte lipolysis to prevent systemic hyperlipidemia.

Lauren M Paolella, Sarmistha Mukherjee, Cassie M Tran, Bruna Bellaver, Mindy Hugo, Timothy S Luongo, Swapnil V Shewale, Wenyun Lu, Karthikeyani Chellappa, Joseph A Baur.

   OBJECTIVE: Pharmacological agents targeting the mTOR complexes are used clinically as immunosuppressants and anticancer agents and can extend the lifespan of model organisms. An undesirable side effect of these drugs is hyperlipidemia. Although multiple roles have been described for mTOR complex 1 (mTORC1) in lipid metabolism, the etiology of hyperlipidemia remains incompletely understood. The objective of this study was to determine the influence of adipocyte mTORC1 signaling in systemic lipid homeostasis in vivo.
METHODS: We characterized systemic lipid metabolism in mice lacking the mTORC1 subunit Raptor (RaptoraKO), the key lipolytic enzyme ATGL (ATGLaKO), or both (ATGL-RaptoraKO) in their adipocytes.
RESULTS: Mice lacking mTORC1 activity in their adipocytes failed to completely suppress lipolysis in the fed state and displayed prominent hypertriglyceridemia and hypercholesterolemia. Blocking lipolysis in their adipose tissue restored normal levels of triglycerides and cholesterol in the fed state as well as the ability to clear triglycerides in an oral fat tolerance test.
CONCLUSIONS: Unsuppressed adipose lipolysis in the fed state interferes with triglyceride clearance and contributes to hyperlipidemia. Adipose tissue mTORC1 activity is necessary for appropriate suppression of lipolysis and for the maintenance of systemic lipid homeostasis.

Keywords:  Adipose tissue; Lipolysis; Rapamycin; Triglycerides; mTORC1

DOI:  https://doi.org/10.1016/j.molmet.2019.12.003
Adv Biol Regul. 2020 Jan 20. pii: S2212-4926(20)30004-X. [Epub ahead of print] 100693

Phosphoinositides in cell proliferation and metabolism.

Emilio Hirsch, Federico Gulluni, Miriam Martini.

  Phosphoinositides (PI) are key players in many trafficking and signaling pathways. Recent advances regarding the synthesis, location and functions of these lipids have improved our understanding of how and when these lipids are generated and what their roles are in physiology and disease. In particular, PI play a central role in the regulation of cell proliferation and metabolism. Here, we will review recent advances in our understanding of PI function, regulation, and importance in different aspects of proliferation and energy metabolism.

Keywords:  Cell metabolism; PI3K; Phosphoinositides; Proliferation; mTOR

DOI:  https://doi.org/10.1016/j.jbior.2020.100693
Cancers (Basel). 2020 Feb 05. pii: E366. [Epub ahead of print]12(2):

The IGF-II-Insulin Receptor Isoform-A Autocrine Signal in Cancer: Actionable Perspectives.

Pierluigi Scalia, Antonio Giordano, Stephen J Williams.

  Insulin receptor overexpression is a common event in human cancer. Its overexpression is associated with a relative increase in the expression of its isoform A (IRA), a shorter variant lacking 11 aa in the extracellular domain, conferring high affinity for the binding of IGF-II along with added intracellular signaling specificity for this ligand. Since IGF-II is secreted by the vast majority of malignant solid cancers, where it establishes autocrine stimuli, the co-expression of IGF-II and IRA in cancer provides specific advantages such as apoptosis escape, growth, and proliferation to those cancers bearing such a co-expression pattern. However, little is known about the exact role of this autocrine ligand-receptor system in sustaining cancer malignant features such as angiogenesis, invasion, and metastasis. The recent finding that the overexpression of angiogenic receptor kinase EphB4 along with VEGF-A is tightly dependent on the IGF-II/IRA autocrine system independently of IGFIR provided new perspectives for all malignant IGF2omas (those aggressive solid cancers secreting IGF-II). The present review provides an updated view of the IGF system in cancer, focusing on the biology of the autocrine IGF-II/IRA ligand-receptor axis and supporting its underscored role as a malignant-switch checkpoint target.

Keywords:  HIF; IGF binding protein; IGF(I/II/1R), Insulin-like Growth factor (1 or 2 or receptor); IGFBP; IRA/IR-A; ITN; M6PR; OCT; TF; Transferrin; VHL; VTN; Von Hippel-Lindau gene product; hypoxia-inducible factor; insulin receptor isoform A; integrin; mannose 6 phosphate receptor; off-context targeting; vitronectin

DOI:  https://doi.org/10.3390/cancers12020366
Nat Commun. 2020 Feb 06. 11(1): 752

Genetic screens in isogenic mammalian cell lines without single cell cloning.

Peter C DeWeirdt, Annabel K Sangree, Ruth E Hanna, Kendall R Sanson, Mudra Hegde, Christine Strand, Nicole S Persky, John G Doench.

Isogenic pairs of cell lines, which differ by a single genetic modification, are powerful tools for understanding gene function. Generating such pairs of mammalian cells, however, is labor-intensive, time-consuming, and, in some cell types, essentially impossible. Here, we present an approach to create isogenic pairs of cells that avoids single cell cloning, and screen these pairs with genome-wide CRISPR-Cas9 libraries to generate genetic interaction maps. We query the anti-apoptotic genes BCL2L1 and MCL1, and the DNA damage repair gene PARP1, identifying both expected and uncharacterized buffering and synthetic lethal interactions. Additionally, we compare acute CRISPR-based knockout, single cell clones, and small-molecule inhibition. We observe that, while the approaches provide largely overlapping information, differences emerge, highlighting an important consideration when employing genetic screens to identify and characterize potential drug targets. We anticipate that this methodology will be broadly useful to comprehensively study gene function across many contexts.

DOI: https://doi.org/10.1038/s41467-020-14620-6
Mol Cancer. 2020 Feb 06. 19(1): 27

Crosstalk between autophagy and metabolic regulation of cancer stem cells.

Mouradi El Hout, Emma Cosialls, Maryam Mehrpour, Ahmed Hamaï.

  Cancer is now considered as a heterogeneous ecosystem in which tumor cells collaborate with each other and with host cells in their microenvironment. As circumstances change, the ecosystem evolves to ensure the survival and growth of the cancer cells. In this ecosystem, metabolism is not only a key player but also drives stemness. In this review, we first summarize our current understanding of how autophagy influences cancer stem cell phenotype. We emphasize metabolic pathways in cancer stem cells and discuss how autophagy-mediated regulation metabolism is involved in their maintenance and proliferation. We then provide an update on the role of metabolic reprogramming and plasticity in cancer stem cells. Finally, we discuss how metabolic pathways in cancer stem cells could be therapeutically targeted.

Keywords:  Autophagy; Cancer stem cells; Lipid metabolism; Metabolic heterogeneity; Therapeutic target

DOI:  https://doi.org/10.1186/s12943-019-1126-8
Science. 2020 Feb 07. 367(6478): 643-652

Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations.

Stephan Wilmes, Maximillian Hafer, Joni Vuorio, Julie A Tucker, Hauke Winkelmann, Sara Löchte, Tess A Stanly, Katiuska D Pulgar Prieto, Chetan Poojari, Vivek Sharma, Christian P Richter, Rainer Kurre, Stevan R Hubbard, K Christopher Garcia, Ignacio Moraga, Ilpo Vattulainen, Ian S Hitchcock, Jacob Piehler.

Homodimeric class I cytokine receptors are assumed to exist as preformed dimers that are activated by ligand-induced conformational changes. We quantified the dimerization of three prototypic class I cytokine receptors in the plasma membrane of living cells by single-molecule fluorescence microscopy. Spatial and spatiotemporal correlation of individual receptor subunits showed ligand-induced dimerization and revealed that the associated Janus kinase 2 (JAK2) dimerizes through its pseudokinase domain. Oncogenic receptor and hyperactive JAK2 mutants promoted ligand-independent dimerization, highlighting the formation of receptor dimers as the switch responsible for signal activation. Atomistic modeling and molecular dynamics simulations based on a detailed energetic analysis of the interactions involved in dimerization yielded a mechanistic blueprint for homodimeric class I cytokine receptor activation and its dysregulation by individual mutations.

DOI: https://doi.org/10.1126/science.aaw3242
Nat Commun. 2020 Feb 07. 11(1): 785

C/EBPɑ is crucial determinant of epithelial maintenance by preventing epithelial-to-mesenchymal transition.

Ana Rita Lourenço, M Guy Roukens, Danielle Seinstra, Cynthia L Frederiks, Cornelieke E Pals, Stephin J Vervoort, Andreia S Margarido, Jacco van Rheenen, Paul J Coffer.

Extracellular signals such as TGF-β can induce epithelial-to-mesenchymal transition (EMT) in cancers of epithelial origin, promoting molecular and phenotypical changes resulting in pro-metastatic characteristics. We identified C/EBPα as one of the most TGF-β-mediated downregulated transcription factors in human mammary epithelial cells. C/EBPα expression prevents TGF-β-driven EMT by inhibiting expression of known EMT factors. Depletion of C/EBPα is sufficient to induce mesenchymal-like morphology and molecular features, while cells that had undergone TGF-β-induced EMT reverted to an epithelial-like state upon C/EBPα re-expression. In vivo, mice injected with C/EBPα-expressing breast tumor organoids display a dramatic reduction of metastatic lesions. Collectively, our results show that C/EBPα is required for maintaining epithelial homeostasis by repressing the expression of key mesenchymal markers, thereby preventing EMT-mediated tumorigenesis. These data suggest that C/EBPα is a master epithelial "gatekeeper" whose expression is required to prevent unwarranted mesenchymal transition, supporting an important role for EMT in mediating breast cancer metastasis.

DOI: https://doi.org/10.1038/s41467-020-14556-x
Elife. 2020 Feb 05. pii: e53725. [Epub ahead of print]9

Quantitative analysis of how Myc controls T cell proteomes and metabolic pathways during T cell activation.

Julia M Marchingo, Linda V Sinclair, Andrew Jm Howden, Doreen A Cantrell.

  T cell expansion and differentiation are critically dependent on the transcription factor c-Myc (Myc). Herein we use quantitative mass-spectrometry to reveal how Myc controls antigen receptor driven cell growth and proteome restructuring in murine T cells. Analysis of copy numbers per cell of >7000 proteins provides new understanding of the selective role of Myc in controlling the protein machinery that govern T cell fate. The data identify both Myc dependent and independent metabolic processes in immune activated T cells. We uncover that a primary function of Myc is to control expression of multiple amino acid transporters and that loss of a single Myc-controlled amino acid transporter effectively phenocopies the impact of Myc deletion. This study provides a comprehensive map of how Myc selectively shapes T cell phenotypes, revealing that Myc induction of amino acid transport is pivotal for subsequent bioenergetic and biosynthetic programs and licences T cell receptor driven proteome reprogramming.

Keywords:  immunology; inflammation; mouse

DOI:  https://doi.org/10.7554/eLife.53725
Science. 2020 Feb 06. pii: eaay0939. [Epub ahead of print]

Deregulation of ribosomal protein expression and translation promotes breast cancer metastasis.

Richard Y Ebright, Sooncheol Lee, Ben S Wittner, Kira L Niederhoffer, Benjamin T Nicholson, Aditya Bardia, Samuel Truesdell, Devon F Wiley, Benjamin Wesley, Selena Li, Andy Mai, Nicola Aceto, Nicole Vincent-Jordan, Annamaria Szabolcs, Brian Chirn, Johannes Kreuzer, Valentine Comaills, Mark Kalinich, Wilhelm Haas, David T Ting, Mehmet Toner, Shobha Vasudevan, Daniel A Haber, Shyamala Maheswaran, Douglas S Micalizzi.

Circulating tumor cells (CTCs) are shed into the bloodstream from primary tumors, but only a small subset generates metastases. We conducted an in vivo genome-wide CRISPR activation screen in breast cancer patient-derived CTCs to identify genes that promote their distant metastasis in mice. Genes coding for ribosomal proteins and regulators of translation were enriched in this screen. Overexpression of RPL15, which encodes a component of the large ribosomal subunit, increased metastatic growth in multiple organs and selectively enhanced translation of other ribosomal proteins and cell cycle regulators. RNA-sequencing of freshly-isolated CTCs from breast cancer patients revealed a subset with strong ribosome and protein synthesis signatures; these CTCs expressed proliferation and epithelial markers and correlated with poor clinical outcome. Therapies targeting this aggressive subset of CTCs may merit exploration as potential suppressors of metastatic progression.

DOI: https://doi.org/10.1126/science.aay0939