bims-cagime 2021-06-27 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2021–06–27
thirty papers selected by
Kıvanç Görgülü, Technical University of Munich

The soluble reticulophagy receptor CALCOCO1 is also a Golgiphagy receptor.
Mitochondrial-derived vesicles compensate for loss of LC3-mediated mitophagy.
TNF-α induces endothelial-mesenchymal transition promoting stromal development of pancreatic adenocarcinoma.
Mechanisms of Selective Autophagy.
Investigating Tumor Heterogeneity in Mouse Models.
Fever supports CD8+ effector T cell responses by promoting mitochondrial translation.
Kras activation in endometrial organoids drives cellular transformation and epithelial-mesenchymal transition.
Identification of autophagy-related genes as targets for senescence induction using a customizable CRISPR-based suicide switch screen.
PGC1α-Mediated Metabolic Reprogramming Drives the Stemness of Pancreatic Precursor Lesions.
Hepcidin sequesters iron to sustain nucleotide metabolism and mitochondrial function in colorectal cancer epithelial cells.
Central nervous system regulation of organismal energy and glucose homeostasis.
Glucagon regulates the stability of REV-ERBα to modulate hepatic glucose production in a model of lung cancer-associated cachexia.
Evolution of fibroblasts in the lung metastatic microenvironment is driven by stage-specific transcriptional plasticity.
Mitochondrial metabolism regulates macrophage biology.
Autophagy in stromal fibroblasts promotes tumor desmoplasia and mammary tumorigenesis.
Systemic and cellular metabolism: the cause of and remedy for disease?
Identification and functional validation of FDA-approved positive and negative modulators of the mitochondrial calcium uniporter.
SOX9 is a critical regulator of TSPAN8-mediated metastasis in pancreatic cancer.
Phase separation drives aberrant chromatin looping and cancer development.
LINC00842 inactivates transcription co-regulator PGC-1α to promote pancreatic cancer malignancy through metabolic remodelling.
Mitochondrial STAT5A promotes metabolic remodeling and the Warburg effect by inactivating the pyruvate dehydrogenase complex.
Lineage tracing reveals metastatic dynamics.
Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism.
Biophysical interactions between components of the tumor microenvironment promote metastasis.
Mechanical compartmentalization of the intestinal organoid enables crypt folding and collective cell migration.
Clicking of organelle-enriched probes for fluorogenic imaging of autophagic and endocytic fluxes.
A single-cell-resolution fate map of endoderm reveals demarcation of pancreatic progenitors by cell cycle.
KDM1A and KDM3A promote tumor growth by upregulating cell cycle-associated genes in pancreatic cancer.
PARP14 regulates cyclin D1 expression to promote cell-cycle progression.
Analysis of multispectral imaging with the AstroPath platform informs efficacy of PD-1 blockade.

Autophagy. 2021 Jun 24. 1-2

The soluble reticulophagy receptor CALCOCO1 is also a Golgiphagy receptor.

Thaddaeus Mutugi Nthiga, Birendra Kumar Shrestha, Trond Lamark, Terje Johansen.

  Cellular stress response mechanisms typically increase organellar quantity and volume. To restore cellular homeostasis and organellar integrity, the surplus organelles are cleared by macroautophagy/autophagy, an intracellular process that shuttles cytoplasmic material to the lysosomes for degradation. The degradation is mediated by autophagy receptors that selectively link the degradable cargo to the autophagy machinery. Studies have identified receptors for the degradation of mitochondria, endoplasmic reticulum, lysosomes, and peroxisomes. The autophagic degradation of the Golgi, named Golgiphagy, however, has remained undefined. The Golgi is essential for the processing, sorting and trafficking of proteins and lipids in the secretory pathway. In a recent study, we identified CALCOCO1 as a Golgiphagy receptor in response to nutrient deprivation. CALCOCO1 interacts with Golgi membranes by binding to cytoplasmic Ankyrin repeat (AR) domains of Golgi resident ZDHHC17 and ZDHHC13 palmitoyltransferases (PATs) via a defined zDHHC-AR-binding motif (zDABM) to recruit autophagy machinery. Lack of CALCOCO1 in cells causes an impaired Golgiphagy and expansion of the Golgi.

Keywords:  Autophagy receptor; CALCOCO1; Golgi; Golgiphagy; Golgiphagy receptor; ZDHHC17; zDABM motif

DOI:  https://doi.org/10.1080/15548627.2021.1940610
Dev Cell. 2021 Jun 24. pii: S1534-5807(21)00481-0. [Epub ahead of print]

Mitochondrial-derived vesicles compensate for loss of LC3-mediated mitophagy.

Christina G Towers, Darya K Wodetzki, Jacqueline Thorburn, Katharine R Smith, M Cecilia Caino, Andrew Thorburn.

  Mitochondria are critical metabolic and signaling hubs, and dysregulated mitochondrial homeostasis is implicated in many diseases. Degradation of damaged mitochondria by selective GABARAP/LC3-dependent macro-autophagy (mitophagy) is critical for maintaining mitochondrial homeostasis. To identify alternate forms of mitochondrial quality control that functionally compensate if mitophagy is inactive, we selected for autophagy-dependent cancer cells that survived loss of LC3-dependent autophagosome formation caused by inactivation of ATG7 or RB1CC1/FIP200. We discovered rare surviving autophagy-deficient clones that adapted to maintain mitochondrial homeostasis after gene inactivation and identified two enhanced mechanisms affecting mitochondria including mitochondrial dynamics and mitochondrial-derived vesicles (MDVs). To further understand these mechanisms, we quantified MDVs via flow cytometry and confirmed an SNX9-mediated mechanism necessary for flux of MDVs to lysosomes. We show that the autophagy-dependent cells acquire unique dependencies on these processes, indicating that these alternate forms of mitochondrial homeostasis compensate for loss of autophagy to maintain mitochondrial health.

Keywords:  ATG7; FIP200; SNX9; autophagy; cancer; late endosomes; mitochondria; mitochondrial dynamics; mitochondrial-derived vesicles; mitophagy

DOI:  https://doi.org/10.1016/j.devcel.2021.06.003
Cell Death Dis. 2021 Jun 25. 12(7): 649

TNF-α induces endothelial-mesenchymal transition promoting stromal development of pancreatic adenocarcinoma.

Marjorie Adjuto-Saccone, Philippe Soubeyran, Julie Garcia, Stéphane Audebert, Luc Camoin, Marion Rubis, Julie Roques, Bernard Binétruy, Juan Lucio Iovanna, Roselyne Tournaire.

Endothelial-mesenchymal transition (EndMT) is an important source of cancer-associated fibroblasts (CAFs), which facilitates tumour progression. PDAC is characterised by abundant CAFs and tumour necrosis factor-α (TNF-α). Here, we show that TNF-α strongly induces human endothelial cells to undergo EndMT. Interestingly, TNF-α strongly downregulates the expression of the endothelial receptor TIE1, and reciprocally TIE1 overexpression partially prevents TNF-α-induced EndMT, suggesting that TNF-α acts, at least partially, through TIE1 regulation in this process. We also show that TNF-α-induced EndMT is reversible. Furthermore, TNF-α treatment of orthotopic mice resulted in an important increase in the stroma, including CAFs. Finally, secretome analysis identified TNFSF12, as a regulator that is also present in PDAC patients. With the aim of restoring normal angiogenesis and better access to drugs, our results support the development of therapies targeting CAFs or inducing the EndMT reversion process in PDAC.

DOI: https://doi.org/10.1038/s41419-021-03920-4
Annu Rev Cell Dev Biol. 2021 Jun 21.

Mechanisms of Selective Autophagy.

Trond Lamark, Terje Johansen.

Selective autophagy is the lysosomal degradation of specific intracellular components sequestered into autophagosomes, late endosomes, or lysosomes through the activity of selective autophagy receptors (SARs). SARs interact with autophagy-related (ATG)8 family proteins via sequence motifs called LC3-interacting region (LIR) motifs in vertebrates and Atg8-interacting motifs (AIMs) in yeast and plants. SARs can be divided into two broad groups: soluble or membrane bound. Cargo or substrate selection may be independent or dependent of ubiquitin labeling of the cargo. In this review, we discuss mechanisms of mammalian selective autophagy with a focus on the unifying principles employed in substrate recognition, interaction with the forming autophagosome via LIR-ATG8 interactions, and the recruitment of core autophagy components for efficient autophagosome formation on the substrate. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-cellbio-120219-035530
Annu Rev Cancer Biol. 2020 Mar;4(1): 99-119

Investigating Tumor Heterogeneity in Mouse Models.

Tuomas Tammela, Julien Sage.

  Cancer arises from a single cell through a series of acquired mutations and epigenetic alterations. Tumors gradually develop into a complex tissue comprised of phenotypically heterogeneous cancer cell populations, as well as noncancer cells that make up the tumor microenvironment. The phenotype, or state, of each cancer and stromal cell is influenced by a plethora of cell-intrinsic and cell-extrinsic factors. The diversity of these cellular states promotes tumor progression, enables metastasis, and poses a challenge for effective cancer treatments. Thus, the identification of strategies for the therapeutic manipulation of tumor heterogeneity would have significant clinical implications. A major barrier in the field is the difficulty in functionally investigating heterogeneity in tumors in cancer patients. Here we review how mouse models of human cancer can be leveraged to interrogate tumor heterogeneity and to help design better therapeutic strategies.

Keywords:  cancer stem cells; epigenetics; genetics; mouse models; tumor heterogeneity; tumor microenvironment

DOI:  https://doi.org/10.1146/annurev-cancerbio-030419-033413
Proc Natl Acad Sci U S A. 2021 Jun 22. pii: e2023752118. [Epub ahead of print]118(25):

Fever supports CD8+ effector T cell responses by promoting mitochondrial translation.

David O'Sullivan, Michal A Stanczak, Matteo Villa, Franziska M Uhl, Mauro Corrado, Ramon I Klein Geltink, David E Sanin, Petya Apostolova, Nisha Rana, Joy Edwards-Hicks, Katarzyna M Grzes, Agnieszka M Kabat, Ryan L Kyle, Mario Fabri, Jonathan D Curtis, Michael D Buck, Annette E Patterson, Annamaria Regina, Cameron S Field, Francesc Baixauli, Daniel J Puleston, Edward J Pearce, Robert Zeiser, Erika L Pearce.

  Fever can provide a survival advantage during infection. Metabolic processes are sensitive to environmental conditions, but the effect of fever on T cell metabolism is not well characterized. We show that in activated CD8+ T cells, exposure to febrile temperature (39 °C) augmented metabolic activity and T cell effector functions, despite having a limited effect on proliferation or activation marker expression. Transcriptional profiling revealed an up-regulation of mitochondrial pathways, which was consistent with increased mass and metabolism observed in T cells exposed to 39 °C. Through in vitro and in vivo models, we determined that mitochondrial translation is integral to the enhanced metabolic activity and function of CD8+ T cells exposed to febrile temperature. Transiently exposing donor lymphocytes to 39 °C prior to infusion in a myeloid leukemia mouse model conferred enhanced therapeutic efficacy, raising the possibility that exposure of T cells to febrile temperatures could have clinical potential.

Keywords:  T cell; fever; immunology; metabolism; mitochondria

DOI:  https://doi.org/10.1073/pnas.2023752118
Oncogenesis. 2021 Jun 25. 10(6): 46

Kras activation in endometrial organoids drives cellular transformation and epithelial-mesenchymal transition.

Yoshiaki Maru, Naotake Tanaka, Yasutoshi Tatsumi, Yuki Nakamura, Makiko Itami, Yoshitaka Hippo.

KRAS, an oncogene, is frequently activated by mutations in many cancers. Kras-driven adenocarcinoma development in the lung, pancreas, and biliary tract has been extensively studied using gene targeting in mice. By taking the organoid- and allograft-based genetic approach to these organs, essentially the same results as in vivo models were obtained in terms of tumor development. To verify the applicability of this approach to other organs, we investigated whether the combination of Kras activation and Pten inactivation, which gives rise to endometrial tumors in mice, could transform murine endometrial organoids in the subcutis of immunodeficient mice. We found that in KrasG12D-expressing endometrial organoids, Pten knockdown did not confer tumorigenicity, but Cdkn2a knockdown or Trp53 deletion led to the development of carcinosarcoma (CS), a rare, aggressive tumor comprising both carcinoma and sarcoma. Although they originated from epithelial cells, some CS cells expressed both epithelial and mesenchymal markers. Upon inoculation in immunodeficient mice, tumor-derived round organoids developed carcinoma or CS, whereas spindle-shaped organoids formed monophasic sarcoma only, suggesting an irreversible epithelial-mesenchymal transition during the transformation of endometrial cells and progression. As commonly observed in mutant Kras-driven tumors, the deletion of the wild-type Kras allele was identified in most induced tumors, whereas some epithelial cells in CS-derived organoids were unexpectedly negative for KrasG12D. Collectively, we showed that the oncogenic potential of KrasG12D and the histological features of derived tumors are context-dependent and varies according to the organ type and experimental settings. Our findings provide novel insights into the mechanisms underlying tissue-specific Kras-driven tumorigenesis.

DOI: https://doi.org/10.1038/s41389-021-00337-8
Mol Cancer Res. 2021 Jun 22. pii: molcanres.0146.2021. [Epub ahead of print]

Identification of autophagy-related genes as targets for senescence induction using a customizable CRISPR-based suicide switch screen.

Arnout Schepers, Fleur Jochems, Cor Lieftink, Liqin Wang, Ziva Pogacar, Rodrigo Leite de Oliveira, Giulia De Conti, Roderick L Beijersbergen, Rene Bernards.

Pro-senescence therapies are increasingly being considered for the treatment of cancer. Identifying additional targets to induce senescence in cancer cells could further enable such therapies. However, screening for targets whose suppression induces senescence on a genome-wide scale is challenging, as senescent cells become growth arrested, and senescence-associated features can take 1-2 weeks to develop. For a screen with a whole-genome CRISPR library, this would result in billions of undesirable proliferating cells by the time the senescent features emerge in the growth arrested cells. Here, we present a suicide switch system that allows genome-wide CRISPR screening in growth-arrested subpopulations by eliminating the proliferating cells during the screen through activation of a suicide switch in proliferating cells. Using this system, we identify in a genome-scale CRISPR screen several autophagy related proteins as targets for senescence induction. We show that inhibiting macroautophagy with a small molecule ULK1 inhibitor can induce senescence in cancer cell lines of different origin. Finally, we show that combining ULK1 inhibition with the senolytic drug ABT-263 leads to apoptosis in a panel of cancer cell lines. Implications: Our suicide switch approach allows for genome-scale identification of pro-senescence targets, and can be adapted to simplify other screens depending on the nature of the promoter used to drive the switch.

DOI: https://doi.org/10.1158/1541-7786.MCR-21-0146
Clin Cancer Res. 2021 Jun 25. pii: clincanres.5020.2020. [Epub ahead of print]

PGC1α-Mediated Metabolic Reprogramming Drives the Stemness of Pancreatic Precursor Lesions.

Rama Krishna Nimmakayala, Sanchita Rauth, Ramakanth Chirravuri Venkata, Saravanakumar Marimuthu, Palanisamy Nallasamy, Raghupathy Vengoji, Subodh M Lele, Satyanarayana Rachagani, Kavita Mallya, Mokenge P Malafa, Moorthy P Ponnusamy, Surinder K Batra.

PURPOSE: Metabolic reprogramming and cancer stem cells (CSCs) drive the aggressiveness of pancreatic ductal adenocarcinoma (PDAC). However, the metabolic and stemness programs of pancreatic precursor lesions (PPLs), considered early PDAC development events, have not been thoroughly explored.
EXPERIMENTAL DESIGN: Meta-analyses using gene expression profile data from NCBI GEO and immunohistochemistry on tissue microarrays (TMAs) were performed. The following animal and cellular models were used: cerulean-induced KrasG12D; Pdx1 Cre (KC) acinar-to-ductal metaplasia (ADM) mice, KrasG12D; Smad4Loss; Pdx-1 Cre (KCSmad4-) intraductal papillary mucinous neoplasm (IPMN) mice, LGKC1 cell line derived from the doxycycline-inducible Gnas IPMN model, and human IPMN organoids. Flow cytometry, Seahorse extracellular flux analyzer, qRT-PCR, and sphere assay were used to analyze metabolic and stemness features. SR18292 was used to inhibit PGC1α, and shRNA was used to knockdown (KD) PGC1α.
RESULTS: The meta-analysis revealed a significant upregulation of specific stemness genes in ADM-mediated pancreatic intraepithelial neoplasms (PanINs) and IPMN. Meta- and TMA analyses followed by in vitro and in vivo validation revealed that ADM/PanIN exhibit increased PGC1α and oxidative phosphorylation (OXPhos) but reduced CPT1A. IPMN showed elevated PGC1α, fatty acid β-oxidation (FAO) gene expression, and FAO-OXPhos. PGC1α was co-overexpressed with its coactivator NRF1 in ADM/PanINs and with PPARγ in IPMN. PGC1α KD or SR18292 inhibited the specific metabolic and stemness features of PPLs and repressed IPMN organoid growth.
CONCLUSIONS: ADM/PanINs and IPMNs show specific stemness signatures with unique metabolisms. Inhibition of PGC1α using SR18292 diminishes the specific stemness by targeting FAO-independent and FAO-dependent OXPhos of ADM/PanINs and IPMNs, respectively.

DOI: https://doi.org/10.1158/1078-0432.CCR-20-5020
Nat Metab. 2021 Jun 21.

Hepcidin sequesters iron to sustain nucleotide metabolism and mitochondrial function in colorectal cancer epithelial cells.

Andrew J Schwartz, Joshua W Goyert, Sumeet Solanki, Samuel A Kerk, Brandon Chen, Cristina Castillo, Peggy P Hsu, Brian T Do, Rashi Singhal, Michael K Dame, Ho-Joon Lee, Jason R Spence, Samira Lakhal-Littleton, Matthew G Vander Heiden, Costas A Lyssiotis, Xiang Xue, Yatrik M Shah.

Colorectal cancer (CRC) requires massive iron stores, but the complete mechanisms by which CRC modulates local iron handling are poorly understood. Here, we demonstrate that hepcidin is activated ectopically in CRC. Mice deficient in hepcidin specifically in the colon tumour epithelium, compared with wild-type littermates, exhibit significantly diminished tumour number, burden and size in a sporadic model of CRC, whereas accumulation of intracellular iron by deletion of the iron exporter ferroportin exacerbates these tumour parameters. Metabolomic analysis of three-dimensional patient-derived CRC tumour enteroids indicates a prioritization of iron in CRC for the production of nucleotides, which is recapitulated in our hepcidin/ferroportin mouse CRC models. Mechanistically, our data suggest that iron chelation decreases mitochondrial function, thereby altering nucleotide synthesis, whereas exogenous supplementation of nucleosides or aspartate partially rescues tumour growth in patient-derived enteroids and CRC cell lines in the presence of an iron chelator. Collectively, these data suggest that ectopic hepcidin in the tumour epithelium establishes an axis to sequester iron in order to maintain the nucleotide pool and sustain proliferation in colorectal tumours.

DOI: https://doi.org/10.1038/s42255-021-00406-7
Nat Metab. 2021 Jun;3(6): 737-750

Central nervous system regulation of organismal energy and glucose homeostasis.

Martin G Myers, Alison H Refined, Nicole Richardson, Michael W Schwartz.

Growing evidence implicates the brain in the regulation of both immediate fuel availability (for example, circulating glucose) and long-term energy stores (that is, adipose tissue mass). Rather than viewing the adipose tissue and glucose control systems separately, we suggest that the brain systems that control them are components of a larger, highly integrated, 'fuel homeostasis' control system. This conceptual framework, along with new insights into the organization and function of distinct neuronal systems, provides a context within which to understand how metabolic homeostasis is achieved in both basal and postprandial states. We also review evidence that dysfunction of the central fuel homeostasis system contributes to the close association between obesity and type 2 diabetes, with the goal of identifying more effective treatment options for these common metabolic disorders.

DOI: https://doi.org/10.1038/s42255-021-00408-5
Sci Adv. 2021 Jun;pii: eabf3885. [Epub ahead of print]7(26):

Glucagon regulates the stability of REV-ERBα to modulate hepatic glucose production in a model of lung cancer-associated cachexia.

Amandine Verlande, Sung Kook Chun, Maggie O Goodson, Bridget M Fortin, Hosung Bae, Cholsoon Jang, Selma Masri.

Lung adenocarcinoma is associated with cachexia, which manifests as an inflammatory response that causes wasting of adipose tissue and skeletal muscle. We previously reported that lung tumor-bearing (TB) mice exhibit alterations in inflammatory and hormonal signaling that deregulate circadian pathways governing glucose and lipid metabolism in the liver. Here, we define the molecular mechanism of how de novo glucose production in the liver is enhanced in a model of lung adenocarcinoma. We found that elevation of serum glucagon levels stimulates cyclic adenosine monophosphate production and activates hepatic protein kinase A (PKA) signaling in TB mice. In turn, we found that PKA targets and destabilizes the circadian protein REV-ERBα, a negative transcriptional regulator of gluconeogenic genes, resulting in heightened de novo glucose production. Together, we identified that glucagon-activated PKA signaling regulates REV-ERBα stability to control hepatic glucose production in a model of lung cancer-associated cachexia.

DOI: https://doi.org/10.1126/sciadv.abf3885
Elife. 2021 Jun 25. pii: e60745. [Epub ahead of print]10

Evolution of fibroblasts in the lung metastatic microenvironment is driven by stage-specific transcriptional plasticity.

Ophir Shani, Yael Raz, Lea Monteran, Ye'ela Scharff, Oshrat Levi-Galibov, Or Megides, Hila Shacham, Noam Cohen, Dana Silverbush, Camilla Avivi, Roded Sharan, Asaf Madi, Ruth Scherz-Shouval, Iris Barshack, Ilan Tsarfaty, Neta Erez.

  Mortality from breast cancer is almost exclusively a result of tumor metastasis, and lungs are one of the main metastatic sites. Cancer-associated fibroblasts (CAFs) are prominent players in the microenvironment of breast cancer. However, their role in the metastatic niche is largely unknown. In this study, we profiled the transcriptional co-evolution of lung fibroblasts isolated from transgenic mice at defined stage-specific time points of metastases formation. Employing multiple knowledge-based platforms of data analysis provided powerful insights on functional and temporal regulation of the transcriptome of fibroblasts. We demonstrate that fibroblasts in lung metastases are transcriptionally dynamic and plastic, and reveal stage-specific gene signatures that imply functional tasks, including extracellular matrix remodeling, stress response and shaping the inflammatory microenvironment. Furthermore, we identified Myc as a central regulator of fibroblast rewiring and found that stromal upregulation of Myc transcriptional networks is associated with disease progression in human breast cancer.

Keywords:  cancer biology; mouse

DOI:  https://doi.org/10.7554/eLife.60745
J Biol Chem. 2021 Jun 19. pii: S0021-9258(21)00704-3. [Epub ahead of print] 100904

Mitochondrial metabolism regulates macrophage biology.

Yafang Wang, Na Li, Xin Zhang, Tiffany Horng.

  Mitochondria are critical for regulation of the activation, differentiation, and survival of macrophages and other immune cells. In response to various extracellular signals, such as microbial or viral infection, changes to mitochondrial metabolism and physiology could underlie the corresponding state of macrophage activation. These changes include alterations of oxidative metabolism, mitochondrial membrane potential, and tricarboxylic acid (TCA) cycling, as well as the release of mitochondrial reactive oxygen species (mtROS) and mitochondrial DNA (mtDNA) and transformation of the mitochondrial ultrastructure. Here, we provide an updated review of how changes in mitochondrial metabolism and various metabolites such as fumarate, succinate, and itaconate coordinate to guide macrophage activation to distinct cellular states, thus clarifying the vital link between mitochondria metabolism and immunity. We also discuss how in disease settings, mitochondrial dysfunction and oxidative stress contribute to dysregulation of the inflammatory response. Therefore, mitochondria are a vital source of dynamic signals that regulate macrophage biology to fine-tune immune responses.

Keywords:  macrophage activation; macrophage biology; mitochondrial dysfunction; mitochondrial metabolism; oxidative stress

DOI:  https://doi.org/10.1016/j.jbc.2021.100904
Genes Dev. 2021 Jun 24.

Autophagy in stromal fibroblasts promotes tumor desmoplasia and mammary tumorigenesis.

Jenny A Rudnick, Teresa Monkkonen, Florie A Mar, James M Barnes, Hanna Starobinets, Juliet Goldsmith, Srirupa Roy, Sofía Bustamante Eguiguren, Valerie M Weaver, Jayanta Debnath.

  Autophagy inhibitors are currently being evaluated in clinical trials for the treatment of diverse cancers, largely due to their ability to impede tumor cell survival and metabolic adaptation. More recently, there is growing interest in whether and how modulating autophagy in the host stroma influences tumorigenesis. Fibroblasts play prominent roles in cancer initiation and progression, including depositing type 1 collagen and other extracellular matrix (ECM) components, thereby stiffening the surrounding tissue to enhance tumor cell proliferation and survival, as well as secreting cytokines that modulate angiogenesis and the immune microenvironment. This constellation of phenotypes, pathologically termed desmoplasia, heralds poor prognosis and reduces patient survival. Using mouse mammary cancer models and syngeneic transplantation assays, we demonstrate that genetic ablation of stromal fibroblast autophagy significantly impedes fundamental elements of the stromal desmoplastic response, including collagen and proinflammatory cytokine secretion, extracellular matrix stiffening, and neoangiogenesis. As a result, autophagy in stromal fibroblasts is required for mammary tumor growth in vivo, even when the cancer cells themselves remain autophagy-competent . We propose the efficacy of autophagy inhibition is shaped by this ability of host stromal fibroblast autophagy to support tumor desmoplasia.

Keywords:  autophagy; breast cancer; cancer-associated fibroblasts; collagen; tumor microenvironment

DOI:  https://doi.org/10.1101/gad.345629.120
FEBS J. 2021 Jun;288(12): 3624-3627

Systemic and cellular metabolism: the cause of and remedy for disease?

Colin Adrain.

  The word 'metabolism' is derived from the Greek word μεταβολή (metabolē), denoting 'change'. True to this definition, it is now appreciated that a cell or tissue cannot change its behaviour without altering its metabolism. Hence, most key cell decision-making processes are tightly coupled to metabolic change. Conversely, perturbations in metabolite abundance or flux can alter cellular (and whole-body) function profoundly, giving rise to disease. This Special Issue on Systemic and Cellular Metabolism and Disease provides an integrative perspective on the importance of metabolism for health and disease alike. Spanning several orders of scale (from metabolites, proteins, organelles, organs/tissues and whole-body physiology), these review articles cover a breadth of topics, including the importance of metabolites as signalling regulators, metabolic disease, immunity, organelle function/dysfunction, ageing and neurodegenerative disease. One of the emergent themes is that just as metabolism is the fulcrum of biology, metabolic perturbances underpin most forms of acute, chronic, infectious and non-infectious human disease; ageing and senescence could be similarly viewed. Arguably most diseases are metabolic diseases; hence, modulating metabolism may help to 'change' disease outcomes.

Keywords:  adipose tissue; disease; energy homeostasis; immunity; metabolism; metabolites; organelles

DOI:  https://doi.org/10.1111/febs.16033
Cell Rep. 2021 Jun 22. pii: S2211-1247(21)00642-2. [Epub ahead of print]35(12): 109275

Identification and functional validation of FDA-approved positive and negative modulators of the mitochondrial calcium uniporter.

Agnese De Mario, Anna Tosatto, Julia Marie Hill, Janos Kriston-Vizi, Robin Ketteler, Denis Vecellio Reane, Gino Cortopassi, Gyorgy Szabadkai, Rosario Rizzuto, Cristina Mammucari.

  The mitochondrial calcium uniporter (MCU), the highly selective channel responsible for mitochondrial Ca2+ entry, plays important roles in physiology and pathology. However, only few pharmacological compounds directly and selectively modulate its activity. Here, we perform high-throughput screening on a US Food and Drug Administration (FDA)-approved drug library comprising 1,600 compounds to identify molecules modulating mitochondrial Ca2+ uptake. We find amorolfine and benzethonium to be positive and negative MCU modulators, respectively. In agreement with the positive effect of MCU in muscle trophism, amorolfine increases muscle size, and MCU silencing is sufficient to blunt amorolfine-induced hypertrophy. Conversely, in the triple-negative breast cancer cell line MDA-MB-231, benzethonium delays cell growth and migration in an MCU-dependent manner and protects from ceramide-induced apoptosis, in line with the role of mitochondrial Ca2+ uptake in cancer progression. Overall, we identify amorolfine and benzethonium as effective MCU-targeting drugs applicable to a wide array of experimental and disease conditions.

Keywords:  FDA-approved drugs; MCU; amorolfine; benzethonium; high-throughput screening; mitochondrial Ca(2+) uptake; mitochondrial calcium uniporter; skeletal muscle hypertrophy; triple-negative breast cancer

DOI:  https://doi.org/10.1016/j.celrep.2021.109275
Oncogene. 2021 Jun 23.

SOX9 is a critical regulator of TSPAN8-mediated metastasis in pancreatic cancer.

Junjian Li, Xiaoliang Chen, Liqun Zhu, Zhenghong Lao, Tianhao Zhou, Lijuan Zang, Weiyu Ge, Mengyi Jiang, Jingxuan Xu, Yuan Cao, Shaoqian Du, Yue Yu, Guangjian Fan, Hongxia Wang.

Pancreatic ductal adenocarcinoma (PDAC) is the deadliest cancer mainly owing to its proclivity to early metastasis and the lack of effective targeted therapeutic drugs. Hence, understanding the molecular mechanisms underlying early invasion and metastasis by PDAC is imperative for improving patient outcomes. The present study identified that upregulation of TSPAN8 expression in PDAC facilitates metastasis in vivo and in vitro. We found SOX9 as a key transcriptional regulator of TSPAN8 expression in response to EGF stimulation. SOX9 modulation was sufficient to positively regulate endogenous expression of TSPAN8, with concomitant in vitro phenotypic changes such as loss of cell-matrix adherence and increased invasion. Moreover, increased SOX9 and TSPAN8 levels were shown to correlate in human pancreatic cancer specimens and downregulated in vitro by EGFR tyrosine kinase inhibitors. High expression of SOX9 and TSPAN8 has been associated with tumor stage, poor prognosis and poor patient survival in PDAC. In conclusion, this study highlights the importance of the EGF-SOX9-TSPAN8 signaling cascade in the control of PDAC invasion and implies that TSPAN8 may be a promising novel therapeutic target for the treatment of PDAC.

DOI: https://doi.org/10.1038/s41388-021-01864-9
Nature. 2021 Jun 23.

Phase separation drives aberrant chromatin looping and cancer development.

Jeong Hyun Ahn, Eric S Davis, Timothy A Daugird, Shuai Zhao, Ivana Yoseli Quiroga, Hidetaka Uryu, Jie Li, Aaron J Storey, Yi-Hsuan Tsai, Daniel P Keeley, Samuel G Mackintosh, Ricky D Edmondson, Stephanie D Byrum, Ling Cai, Alan J Tackett, Deyou Zheng, Wesley R Legant, Douglas H Phanstiel, Gang Greg Wang.

The development of cancer is intimately associated with genetic abnormalities that target proteins with intrinsically disordered regions (IDRs). In human haematological malignancies, recurrent chromosomal translocation of nucleoporin (NUP98 or NUP214) generates an aberrant chimera that invariably retains the nucleoporin IDR-tandemly dispersed repeats of phenylalanine and glycine residues1,2. However, how unstructured IDRs contribute to oncogenesis remains unclear. Here we show that IDRs contained within NUP98-HOXA9, a homeodomain-containing transcription factor chimera recurrently detected in leukaemias1,2, are essential for establishing liquid-liquid phase separation (LLPS) puncta of chimera and for inducing leukaemic transformation. Notably, LLPS of NUP98-HOXA9 not only promotes chromatin occupancy of chimera transcription factors, but also is required for the formation of a broad 'super-enhancer'-like binding pattern typically seen at leukaemogenic genes, which potentiates transcriptional activation. An artificial HOX chimera, created by replacing the phenylalanine and glycine repeats of NUP98 with an unrelated LLPS-forming IDR of the FUS protein3,4, had similar enhancing effects on the genome-wide binding and target gene activation of the chimera. Deeply sequenced Hi-C revealed that phase-separated NUP98-HOXA9 induces CTCF-independent chromatin loops that are enriched at proto-oncogenes. Together, this report describes a proof-of-principle example in which cancer acquires mutation to establish oncogenic transcription factor condensates via phase separation, which simultaneously enhances their genomic targeting and induces organization of aberrant three-dimensional chromatin structure during tumourous transformation. As LLPS-competent molecules are frequently implicated in diseases1,2,4-7, this mechanism can potentially be generalized to many malignant and pathological settings.

DOI: https://doi.org/10.1038/s41586-021-03662-5
Nat Commun. 2021 06 22. 12(1): 3830

LINC00842 inactivates transcription co-regulator PGC-1α to promote pancreatic cancer malignancy through metabolic remodelling.

Xudong Huang, Ling Pan, Zhixiang Zuo, Mei Li, Lingxing Zeng, Rui Li, Ying Ye, Jialiang Zhang, Guandi Wu, Ruihong Bai, Lisha Zhuang, Lusheng Wei, Yanfen Zheng, Jiachun Su, Junge Deng, Shuang Deng, Shaoping Zhang, Shihao Zhu, Xu Che, Chengfeng Wang, Chen Wu, Rufu Chen, Dongxin Lin, Jian Zheng.

The molecular mechanism underlying pancreatic ductal adenocarcinoma (PDAC) malignancy remains unclear. Here, we characterize a long intergenic non-coding RNA LINC00842 that plays a role in PDAC progression. LINC00842 expression is upregulated in PDAC and induced by high concentration of glucose via transcription factor YY1. LINC00842 binds to and prevents acetylated PGC-1α from deacetylation by deacetylase SIRT1 to form PGC-1α, an important transcription co-factor in regulating cellular metabolism. LINC00842 overexpression causes metabolic switch from mitochondrial oxidative catabolic process to fatty acid synthesis, enhancing the malignant phenotypes of PDAC cells. High LINC00842 levels are correlated with elevated acetylated- PGC-1α levels in PDAC and poor patient survival. Decreasing LINC00842 level and inhibiting fatty acid synthase activity significantly repress PDAC growth and invasiveness in mouse pancreatic xenograft or patient-derived xenograft models. These results demonstrate that LINC00842 plays a role in promoting PDAC malignancy and thus might serve as a druggable target.

DOI: https://doi.org/10.1038/s41467-021-23904-4
Cell Death Dis. 2021 Jun 19. 12(7): 634

Mitochondrial STAT5A promotes metabolic remodeling and the Warburg effect by inactivating the pyruvate dehydrogenase complex.

Liang Zhang, Jianong Zhang, Yan Liu, Pingzhao Zhang, Ji Nie, Rui Zhao, Qin Shi, Huiru Sun, Dongyue Jiao, Yingji Chen, Xiaying Zhao, Yan Huang, Yao Li, Jian-Yuan Zhao, Wei Xu, Shi-Min Zhao, Chenji Wang.

Signal transducer and activator 5a (STAT5A) is a classical transcription factor that plays pivotal roles in various biological processes, including tumor initiation and progression. A fraction of STAT5A is localized in the mitochondria, but the biological functions of mitochondrial STAT5A remain obscure. Here, we show that STAT5A interacts with pyruvate dehydrogenase complex (PDC), a mitochondrial gatekeeper enzyme connecting two key metabolic pathways, glycolysis and the tricarboxylic acid cycle. Mitochondrial STAT5A disrupts PDC integrity, thereby inhibiting PDC activity and remodeling cellular glycolysis and oxidative phosphorylation. Mitochondrial translocation of STAT5A is increased under hypoxic conditions. This strengthens the Warburg effect in cancer cells and promotes in vitro cell growth under hypoxia and in vivo tumor growth. Our findings indicate distinct pro-oncogenic roles of STAT5A in energy metabolism, which is different from its classical function as a transcription factor.

DOI: https://doi.org/10.1038/s41419-021-03908-0
Cancer Cell. 2021 Jun 19. pii: S1535-6108(21)00326-3. [Epub ahead of print]

Lineage tracing reveals metastatic dynamics.

Eunmi Lee, Yibin Kang.

Combining single-cell lineage tracing with RNA sequencing has provided unprecedented opportunities to prospectively explore metastatic dynamics in vivo. In this issue of Cancer Cell, Simeonov et al. developed the macsGESTALT lineage recording system to reveal that hybrid EMT states and S100 expression are associated with elevated metastatic abilities in a pancreatic cancer model.

DOI: https://doi.org/10.1016/j.ccell.2021.06.005
EMBO Rep. 2021 Jun 23. e52774

Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism.

Sandra Nitsch, Lara Zorro Shahidian, Robert Schneider.

  In eukaryotic cells, DNA is tightly packed with the help of histone proteins into chromatin. Chromatin architecture can be modified by various post-translational modifications of histone proteins. For almost 60 years now, studies on histone lysine acetylation have unraveled the contribution of this acylation to an open chromatin state with increased DNA accessibility, permissive for gene expression. Additional complexity emerged from the discovery of other types of histone lysine acylations. The acyl group donors are products of cellular metabolism, and distinct histone acylations can link the metabolic state of a cell with chromatin architecture and contribute to cellular adaptation through changes in gene expression. Currently, various technical challenges limit our full understanding of the actual impact of most histone acylations on chromatin dynamics and of their biological relevance. In this review, we summarize the state of the art and provide an overview of approaches to overcome these challenges. We further discuss the concept of subnuclear metabolic niches that could regulate local CoA availability and thus couple cellular metabolisms with the epigenome.

Keywords:  acylation; chromatin; histones; metabolism; microdomains

DOI:  https://doi.org/10.15252/embr.202152774
Biophys Rev. 2021 Jun;13(3): 339-357

Biophysical interactions between components of the tumor microenvironment promote metastasis.

Dimitra Vasilaki, Athina Bakopoulou, Alexandros Tsouknidas, Elaine Johnstone, Konstantinos Michalakis.

  During metastasis, tumor cells need to adapt to their dynamic microenvironment and modify their mechanical properties in response to both chemical and mechanical stimulation. Physical interactions occur between cancer cells and the surrounding matrix including cell movements and cell shape alterations through the process of mechanotransduction. The latter describes the translation of external mechanical cues into intracellular biochemical signaling. Reorganization of both the cytoskeleton and the extracellular matrix (ECM) plays a critical role in these spreading steps. Migrating tumor cells show increased motility in order to cross the tumor microenvironment, migrate through ECM and reach the bloodstream to the metastatic site. There are specific factors affecting these processes, as well as the survival of circulating tumor cells (CTC) in the blood flow until they finally invade the secondary tissue to form metastasis. This review aims to study the mechanisms of metastasis from a biomechanical perspective and investigate cell migration, with a focus on the alterations in the cytoskeleton through this journey and the effect of biologic fluids on metastasis. Understanding of the biophysical mechanisms that promote tumor metastasis may contribute successful therapeutic approaches in the fight against cancer.

Keywords:  Actomyosin contractility; Cell mechanics; Circulating tumor cells; Cytoskeleton; Metastasis; Shear stress

DOI:  https://doi.org/10.1007/s12551-021-00811-y
Nat Cell Biol. 2021 Jun 21.

Mechanical compartmentalization of the intestinal organoid enables crypt folding and collective cell migration.

Carlos Pérez-González, Gerardo Ceada, Francesco Greco, Marija Matejčić, Manuel Gómez-González, Natalia Castro, Anghara Menendez, Sohan Kale, Denis Krndija, Andrew G Clark, Venkata Ram Gannavarapu, Adrián Álvarez-Varela, Pere Roca-Cusachs, Eduard Batlle, Danijela Matic Vignjevic, Marino Arroyo, Xavier Trepat.

Intestinal organoids capture essential features of the intestinal epithelium such as crypt folding, cellular compartmentalization and collective movements. Each of these processes and their coordination require patterned forces that are at present unknown. Here we map three-dimensional cellular forces in mouse intestinal organoids grown on soft hydrogels. We show that these organoids exhibit a non-monotonic stress distribution that defines mechanical and functional compartments. The stem cell compartment pushes the extracellular matrix and folds through apical constriction, whereas the transit amplifying zone pulls the extracellular matrix and elongates through basal constriction. The size of the stem cell compartment depends on the extracellular-matrix stiffness and endogenous cellular forces. Computational modelling reveals that crypt shape and force distribution rely on cell surface tensions following cortical actomyosin density. Finally, cells are pulled out of the crypt along a gradient of increasing tension. Our study unveils how patterned forces enable compartmentalization, folding and collective migration in the intestinal epithelium.

DOI: https://doi.org/10.1038/s41556-021-00699-6
Chem Sci. 2021 Mar 19. 12(16): 5834-5842

Clicking of organelle-enriched probes for fluorogenic imaging of autophagic and endocytic fluxes.

Xianjun Liu, Mei-Hao Xiang, Wen-Jing Zhou, Fenglin Wang, Xia Chu, Jian-Hui Jiang.

Autophagy and endocytosis are essential in regulating cellular homeostasis and cancer immunotherapeutic responses. Existing methods for autophagy and endocytosis imaging are susceptible to cellular micro-environmental changes, and direct fluorogenic visualization of their fluxes remains challenging. We develop a novel strategy via clicking of organelle-enriched probes (COP), which comprises a pair of trans-cyclooctenol (TCO) and tetrazine probes separately enriched in lysosomes and mitochondria (in autophagy) or plasma membrane (in endocytosis). These paired probes are merged and boost a fluorogenic click reaction in response to autophagic or endocytic flux that ultimately fuses mitochondria or plasma membrane into lysosomes. We demonstrate that this strategy enables direct visualization of autophagic and endocytic fluxes, and confer insight into correlation of autophagic or endocytic flux to cell surface expression of immunotherapeutic targets such as MHC-I and PD-L1. The COP strategy provides a new paradigm for imaging autophagic and endocytic fluxes, and affords potential for improved cancer immunotherapy using autophagy or endocytosis inhibitors.

DOI: https://doi.org/10.1039/d0sc07057b
Proc Natl Acad Sci U S A. 2021 Jun 22. pii: e2025793118. [Epub ahead of print]118(25):

A single-cell-resolution fate map of endoderm reveals demarcation of pancreatic progenitors by cell cycle.

Yun Yang, Hao Wang, Jia He, Wenchao Shi, Zhanmei Jiang, Lina Gao, Yan Jiang, Rui Ni, Qifen Yang, Lingfei Luo.

  A progenitor cell could generate a certain type or multiple types of descendant cells during embryonic development. To make all the descendant cell types and developmental trajectories of every single progenitor cell clear remains an ultimate goal in developmental biology. Characterizations of descendant cells produced by each uncommitted progenitor for a full germ layer represent a big step toward the goal. Here, we focus on early foregut endoderm, which generates foregut digestive organs, including the pancreas, liver, foregut, and ductal system, through distinct lineages. Using unbiased single-cell labeling techniques, we label every individual zebrafish foregut endodermal progenitor cell out of 216 cells to visibly trace the distribution and number of their descendant cells. Hence, single-cell-resolution fate and proliferation maps of early foregut endoderm are established, in which progenitor regions of each foregut digestive organ are precisely demarcated. The maps indicate that the pancreatic endocrine progenitors are featured by a cell cycle state with a long G1 phase. Manipulating durations of the G1 phase modulates pancreatic progenitor populations. This study illustrates foregut endodermal progenitor cell fate at single-cell resolution, precisely demarcates different progenitor populations, and sheds light on mechanistic insights into pancreatic fate determination.

Keywords:  cell cycle; endoderm; fate map; pancreatic fate; single-cell labeling and tracing

DOI:  https://doi.org/10.1073/pnas.2025793118
Exp Biol Med (Maywood). 2021 Jun 25. 15353702211023473

KDM1A and KDM3A promote tumor growth by upregulating cell cycle-associated genes in pancreatic cancer.

Xuyang Hou, Qiuguo Li, Leping Yang, Zhulin Yang, Jun He, Qinglong Li, Daming Li.

  Pancreatic cancer is a highly malignant cancer of the pancreas with a very poor prognosis. Methylation of histone lysine residues is essential for regulating cancer physiology and pathophysiology, mediated by a set of methyltransferases (KMTs) and demethylases (KDMs). This study surveyed the expression of methylation regulators functioning at lysine 9 of histone 3 (H3K9) in pancreatic lesions and explored the underlying mechanisms. We analyzed KDM1A and KDM3A expression in clinical samples by immunohistochemical staining and searching the TCGA PAAD program and GEO datasets. Next, we identified the variation in tumor growth in vitro and in vivo after knockdown of KDM1A or KDM3A and explored the downstream regulators of KDM1A and KDM3A via RNA-seq, and gain- and loss-of-function assays. Eleven H3K9 methylation regulators were highly expressed in pancreatic cancer, and only KDM1A and KDM3A expression positively correlated with the clinicopathological characteristics in pancreatic cancer. High expression of KDM1A or KDM3A positively correlated with pathological grade, lymphatic metastasis, invasion, and clinical stage. Kaplan-Meier analysis indicated that a higher level of KDM1A or KDM3A led to a shorter survival period. Knockdown of KDM1A or KDM3A led to markedly impaired tumor growth in vitro and in vivo. Mechanistically, CCNA2, a cell cycle-associated gene was partially responsible for KDM1A knockdown-mediated effect and CDK6, also a cell cycle-associated gene was partially responsible for KDM3A knockdown-mediated effect on pancreatic cancer cells. Our study demonstrates that KDM1A and KDM3A are highly expressed in pancreatic cancer and are intimately correlated with clinicopathological factors and prognosis. The mechanism of action of KDM1A or KDM3A was both linked to the regulation of cell cycle-associated genes, such as CCNA2 or CDK6, respectively, by an H3K9-dependent pathway.

Keywords:  KDM1A; KDM3A; Pancreatic cancer; cell cycle; methylation

DOI:  https://doi.org/10.1177/15353702211023473
Oncogene. 2021 Jun 22.

PARP14 regulates cyclin D1 expression to promote cell-cycle progression.

Michael J O'Connor, Tanay Thakar, Claudia M Nicolae, George-Lucian Moldovan.

Cyclin D1 is an essential regulator of the G1-S cell-cycle transition and is overexpressed in many cancers. Expression of cyclin D1 is under tight cellular regulation that is controlled by many signaling pathways. Here we report that PARP14, a member of the poly(ADP-ribose) polymerase (PARP) family, is a regulator of cyclin D1 expression. Depletion of PARP14 leads to decreased cyclin D1 protein levels. In cells with a functional retinoblastoma (RB) protein pathway, this results in G1 cell-cycle arrest and reduced proliferation. Mechanistically, we found that PARP14 controls cyclin D1 mRNA levels. Using luciferase assays, we show that PARP14 specifically regulates cyclin D1 3'UTR mRNA stability. Finally, we also provide evidence that G1 arrest in PARP14-depleted cells is dependent on an intact p53-p21 pathway. Our work uncovers a new role for PARP14 in promoting cell-cycle progression through both cyclin D1 and the p53 pathway.

DOI: https://doi.org/10.1038/s41388-021-01881-8
Science. 2021 06 11. pii: eaba2609. [Epub ahead of print]372(6547):

Analysis of multispectral imaging with the AstroPath platform informs efficacy of PD-1 blockade.

Sneha Berry, Nicolas A Giraldo, Benjamin F Green, Tricia R Cottrell, Julie E Stein, Elizabeth L Engle, Haiying Xu, Aleksandra Ogurtsova, Charles Roberts, Daphne Wang, Peter Nguyen, Qingfeng Zhu, Sigfredo Soto-Diaz, Jose Loyola, Inbal B Sander, Pok Fai Wong, Shlomit Jessel, Joshua Doyle, Danielle Signer, Richard Wilton, Jeffrey S Roskes, Margaret Eminizer, Seyoun Park, Joel C Sunshine, Elizabeth M Jaffee, Alexander Baras, Angelo M De Marzo, Suzanne L Topalian, Harriet Kluger, Leslie Cope, Evan J Lipson, Ludmila Danilova, Robert A Anders, David L Rimm, Drew M Pardoll, Alexander S Szalay, Janis M Taube.

Next-generation tissue-based biomarkers for immunotherapy will likely include the simultaneous analysis of multiple cell types and their spatial interactions, as well as distinct expression patterns of immunoregulatory molecules. Here, we introduce a comprehensive platform for multispectral imaging and mapping of multiple parameters in tumor tissue sections with high-fidelity single-cell resolution. Image analysis and data handling components were drawn from the field of astronomy. Using this "AstroPath" whole-slide platform and only six markers, we identified key features in pretreatment melanoma specimens that predicted response to anti-programmed cell death-1 (PD-1)-based therapy, including CD163+PD-L1- myeloid cells and CD8+FoxP3+PD-1low/mid T cells. These features were combined to stratify long-term survival after anti-PD-1 blockade. This signature was validated in an independent cohort of patients with melanoma from a different institution.

DOI: https://doi.org/10.1126/science.aba2609