bims-camemi 2021-08-01 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2021–08–01
39 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit

Mitochondrial regulation of ferroptosis.
Hepatic mTORC1 signaling activates ATF4 as part of its metabolic response to feeding and insulin.
MDVs to the rescue: How autophagy-deficient cancer cells adapt to defective mitophagy.
Move it to lose it: Mitocytosis expels damaged mitochondria.
Host autophagy mediates organ wasting and nutrient mobilization for tumor growth.
UDP-glucose pyrophosphorylase 2, a regulator of glycogen synthesis and glycosylation, is critical for pancreatic cancer growth.
Super-resolution microscopy reveals the arrangement of inner membrane protein complexes in mammalian mitochondria.
MCU-Dependent mROS Generation Regulates Cell Metabolism and Cell Death Modulated by the AMPK/PGC-1α/SIRT3 Signaling Pathway.
Loss of the mitochondrial phosphate carrier SLC25A3 induces remodeling of the cardiac mitochondrial protein acylome.
Mitochondrial fusion and fission are required for proper mitochondrial function and cell proliferation in fission yeast.
Diverse mitochondrial abnormalities in a new cellular model of TAFFAZZIN deficiency are remediated by Cardiolipin-interacting small molecules.
EVI1 activates tumor-promoting transcriptional enhancers in pancreatic cancer.
Two transition states of the glycogen shunt and two steady states of gene expression support metabolic flexibility and the Warburg effect in cancer.
Dysregulated oxalate metabolism is a driver and therapeutic target in atherosclerosis.
Mutational signatures: emerging concepts, caveats and clinical applications.
TRIM8 modulates the EWS/FLI oncoprotein to promote survival in Ewing sarcoma.
The p53 transcriptional response across tumor types reveals core and senescence-specific signatures modulated by long noncoding RNAs.
PRMT1-dependent regulation of RNA metabolism and DNA damage response sustains pancreatic ductal adenocarcinoma.
In vivo isotope tracing reveals the versatility of glucose as a brown adipose tissue substrate.
CXCL10/CXCR3 signaling contributes to an inflammatory microenvironment and its blockade enhances progression of murine pancreatic precancerous lesions.
Fatty acid mobilization from adipose tissue is mediated by CD36 post-translational modifications and intracellular trafficking.
Anterograde regulation of mitochondrial genes and FGF21 signaling by hepatic LSD1.
A novel tool for detecting lysosomal membrane permeabilization by high-throughput fluorescence microscopy.
The immunological and metabolic landscape in primary and metastatic liver cancer.
Integration of transcriptional and metabolic control in macrophage activation.
The small Cajal body-specific RNA 15 (SCARNA15) directs p53 and redox homeostasis via selective splicing in cancer cells.
Sirtuin 5 depletion impairs mitochondrial function in human proximal tubular epithelial cells.
miR-1 coordinately regulates lysosomal v-ATPase and biogenesis to impact proteotoxicity and muscle function during aging.
The relevance of mitochondrial DNA variants fluctuation during reprogramming and neuronal differentiation of human iPSCs.
Tumour microenvironment 3D-modelling: simplicity to complexity and back again.
Interaction between Ras and Src clones causes interdependent tumor malignancy via Notch signaling in Drosophila.
Sequential oncogenic mutations influence cell competition.
Mutant IDH1 inhibitors activate pSTAT3-Y705 leading to an increase in BCAT1 and YKL-40 levels in mutant IDH1-expressing cells.
The Cancer SENESCopedia: A delineation of cancer cell senescence.
In silico saturation mutagenesis of cancer genes.
NAD+ metabolism and cardiometabolic health: the human evidence.
Calcium signaling induces a partial EMT.
An enzymatic activation of formaldehyde for nucleotide methylation.
Nrf2 deficiency decreases NADPH from impaired IDH shuttle and pentose phosphate pathway in retinal pigmented epithelial cells to magnify oxidative stress-induced mitochondrial dysfunction.

J Cell Biol. 2021 Sep 06. pii: e202105043. [Epub ahead of print]220(9):

Mitochondrial regulation of ferroptosis.

Boyi Gan.

Ferroptosis is a form of iron-dependent regulated cell death driven by uncontrolled lipid peroxidation. Mitochondria are double-membrane organelles that have essential roles in energy production, cellular metabolism, and cell death regulation. However, their role in ferroptosis has been unclear and somewhat controversial. In this Perspective, I summarize the diverse metabolic processes in mitochondria that actively drive ferroptosis, discuss recently discovered mitochondria-localized defense systems that detoxify mitochondrial lipid peroxides and protect against ferroptosis, present new evidence for the roles of mitochondria in regulating ferroptosis, and outline outstanding questions on this fascinating topic for future investigations. An in-depth understanding of mitochondria functions in ferroptosis will have important implications for both fundamental cell biology and disease treatment.

DOI: https://doi.org/10.1083/jcb.202105043
Mol Metab. 2021 Jul 22. pii: S2212-8778(21)00156-3. [Epub ahead of print] 101309

Hepatic mTORC1 signaling activates ATF4 as part of its metabolic response to feeding and insulin.

Vanessa Byles, Yann Cormerais, Krystle Kalafut, Victor Barrera, James E Hughes Hallett, Shannan Ho Sui, John M Asara, Christopher M Adams, Gerta Hoxhaj, Issam Ben-Sahra, Brendan D Manning.

   OBJECTIVE: The mechanistic target of rapamycin complex 1 (mTORC1) is dynamically regulated by fasting and feeding cycles in the liver to promote protein and lipid synthesis while suppressing autophagy. However, beyond these functions, the metabolic response of the liver to feeding and insulin signaling orchestrated by mTORC1 remains poorly defined. Here, we determine whether ATF4, a stress responsive transcription factor recently found to be independently regulated by mTORC1 signaling in proliferating cells, is responsive to hepatic mTORC1 signaling to alter hepatocyte metabolism.
METHODS: ATF4 protein levels and expression of canonical gene targets were analyzed in the liver following fasting and physiological feeding in the presence or absence of the mTORC1 inhibitor rapamycin. Primary hepatocytes from wild-type or liver-specific Atf4 knockout (LAtf4KO) mice were used to characterize the effects of insulin-stimulated mTORC1-ATF4 function on hepatocyte gene expression and metabolism. Both unbiased steady-state metabolomics and stable-isotope tracing methods were employed to define mTORC1 and ATF4-dependent metabolic changes. RNA-sequencing was used to determine global changes in feeding-induced transcripts in the livers of wild-type versus LAtf4KO mice.
RESULTS: We demonstrate that ATF4 and its metabolic gene targets are stimulated by mTORC1 signaling in the liver in response to feeding and in a hepatocyte-intrinsic manner by insulin. While we demonstrate that de novo purine and pyrimidine synthesis is stimulated by insulin through mTORC1 signaling in primary hepatocytes, this regulation was independent of ATF4. Metabolomics and metabolite tracing studies revealed that insulin-mTORC1-ATF4 signaling stimulates pathways of non-essential amino acid synthesis in primary hepatocytes, including those of alanine, aspartate, methionine, and cysteine, but not serine.
CONCLUSION: The results demonstrate that ATF4 is a novel metabolic effector of mTORC1 in liver, extending the molecular consequences of feeding and insulin-induced mTORC1 signaling in this key metabolic tissue to the control of amino acid metabolism.

Keywords:  ATF4; feeding; insulin; liver; mTORC1; methionine metabolism

DOI:  https://doi.org/10.1016/j.molmet.2021.101309
Dev Cell. 2021 Jul 26. pii: S1534-5807(21)00529-3. [Epub ahead of print]56(14): 2010-2012

MDVs to the rescue: How autophagy-deficient cancer cells adapt to defective mitophagy.

Laura Poillet-Perez, Eileen White.

Cancers are dependent on mitochondria, the powerhouse of the cell, and autophagy, the mechanism to preserve mitochondrial quality and function. In this issue of Developmental Cell, Towers et al. identify mitochondria-derived vesicles (MDVs) as a new adaptive mechanism enabling cancer cells to compensate for autophagy loss and to maintain mitochondrial function.

DOI: https://doi.org/10.1016/j.devcel.2021.06.022
Dev Cell. 2021 Jul 26. pii: S1534-5807(21)00546-3. [Epub ahead of print]56(14): 2014-2015

Move it to lose it: Mitocytosis expels damaged mitochondria.

Chahat Mehra, Lena Pernas.

Mechanisms by which cells remove damaged mitochondria extracellularly are unclear. Recent work by Jiao and colleagues in Cell shows that migrating cells expel dysfunctional mitochondria in membrane-bound structures called migrasomes to maintain mitochondrial homeostasis.

DOI: https://doi.org/10.1016/j.devcel.2021.07.001
EMBO J. 2021 Jul 26. e107336

Host autophagy mediates organ wasting and nutrient mobilization for tumor growth.

Rojyar Khezri, Petter Holland, Todd Andrew Schoborg, Ifat Abramovich, Szabolcs Takáts, Caroline Dillard, Ashish Jain, Fergal O'Farrell, Sebastian Wolfgang Schultz, William M Hagopian, Eduardo Martin Quintana, Rachel Ng, Nadja Sandra Katheder, Mohammed Mahidur Rahman, José Gerardo Teles Reis, Andreas Brech, Heinrich Jasper, Nasser M Rusan, Anne Hope Jahren, Eyal Gottlieb, Tor Erik Rusten.

  During tumor growth-when nutrient and anabolic demands are high-autophagy supports tumor metabolism and growth through lysosomal organelle turnover and nutrient recycling. Ras-driven tumors additionally invoke non-autonomous autophagy in the microenvironment to support tumor growth, in part through transfer of amino acids. Here we uncover a third critical role of autophagy in mediating systemic organ wasting and nutrient mobilization for tumor growth using a well-characterized malignant tumor model in Drosophila melanogaster. Micro-computed X-ray tomography and metabolic profiling reveal that RasV12 ; scrib-/- tumors grow 10-fold in volume, while systemic organ wasting unfolds with progressive muscle atrophy, loss of body mass, -motility, -feeding, and eventually death. Tissue wasting is found to be mediated by autophagy and results in host mobilization of amino acids and sugars into circulation. Natural abundance Carbon 13 tracing demonstrates that tumor biomass is increasingly derived from host tissues as a nutrient source as wasting progresses. We conclude that host autophagy mediates organ wasting and nutrient mobilization that is utilized for tumor growth.

Keywords:   Drosophila ; autophagy; cancer cachexia; muscle; tumor; wasting

DOI:  https://doi.org/10.15252/embj.2020107336
Proc Natl Acad Sci U S A. 2021 Aug 03. pii: e2103592118. [Epub ahead of print]118(31):

UDP-glucose pyrophosphorylase 2, a regulator of glycogen synthesis and glycosylation, is critical for pancreatic cancer growth.

Andrew L Wolfe, Qingwen Zhou, Eneda Toska, Jacqueline Galeas, Angel A Ku, Richard P Koche, Sourav Bandyopadhyay, Maurizio Scaltriti, Carlito B Lebrilla, Frank McCormick, Sung Eun Kim.

  UDP-glucose pyrophosphorylase 2 (UGP2), the enzyme that synthesizes uridine diphosphate (UDP)-glucose, rests at the convergence of multiple metabolic pathways, however, the role of UGP2 in tumor maintenance and cancer metabolism remains unclear. Here, we identify an important role for UGP2 in the maintenance of pancreatic ductal adenocarcinoma (PDAC) growth in both in vitro and in vivo tumor models. We found that transcription of UGP2 is directly regulated by the Yes-associated protein 1 (YAP)-TEA domain transcription factor (TEAD) complex, identifying UGP2 as a bona fide YAP target gene. Loss of UGP2 leads to decreased intracellular glycogen levels and defects in N-glycosylation targets that are important for the survival of PDACs, including the epidermal growth factor receptor (EGFR). These critical roles of UGP2 in cancer maintenance, metabolism, and protein glycosylation may offer insights into therapeutic options for otherwise intractable PDACs.

Keywords:  N-glycosylation; PDAC; UDP-glucose; UGP2; glycogen

DOI:  https://doi.org/10.1073/pnas.2103592118
J Cell Sci. 2021 07 01. pii: jcs252197. [Epub ahead of print]134(13):

Super-resolution microscopy reveals the arrangement of inner membrane protein complexes in mammalian mitochondria.

Catherine S Palmer, Jieqiong Lou, Betty Kouskousis, Elvis Pandzic, Alexander J Anderson, Yilin Kang, Elizabeth Hinde, Diana Stojanovski.

  The mitochondrial inner membrane is a protein-rich environment containing large multimeric complexes, including complexes of the mitochondrial electron transport chain, mitochondrial translocases and quality control machineries. Although the inner membrane is highly proteinaceous, with 40-60% of all mitochondrial proteins localised to this compartment, little is known about the spatial distribution and organisation of complexes in this environment. We set out to survey the arrangement of inner membrane complexes using stochastic optical reconstruction microscopy (STORM). We reveal that subunits of the TIM23 complex, TIM23 and TIM44 (also known as TIMM23 and TIMM44, respectively), and the complex IV subunit COXIV, form organised clusters and show properties distinct from the outer membrane protein TOM20 (also known as TOMM20). Density based cluster analysis indicated a bimodal distribution of TIM44 that is distinct from TIM23, suggesting distinct TIM23 subcomplexes. COXIV is arranged in larger clusters that are disrupted upon disruption of complex IV assembly. Thus, STORM super-resolution microscopy is a powerful tool for examining the nanoscale distribution of mitochondrial inner membrane complexes, providing a 'visual' approach for obtaining pivotal information on how mitochondrial complexes exist in a cellular context.

Keywords:  COXIV; Mitochondria; Mitochondrial complexes; Nanoscopy; Protein import; STORM; TIM23

DOI:  https://doi.org/10.1242/jcs.252197
Front Med (Lausanne). 2021 ;8 674986

MCU-Dependent mROS Generation Regulates Cell Metabolism and Cell Death Modulated by the AMPK/PGC-1α/SIRT3 Signaling Pathway.

Yuxin Wang, Xiang Li, Fengchao Zhao.

  The mitochondrial calcium uniporter is an intensively investigated calcium channel, and its molecular components, structural features, and encoded genes have long been explored. Further studies have shown that the mitochondrial calcium unidirectional transporter (MCU) is a macromolecular complex related to intracellular and extracellular calcium regulation. Based on the current understanding, the MCU is crucial for maintaining cytosolic Ca2+ (cCa2+) homeostasis by modulating mitochondrial Ca2+ (mCa2+) uptake. The elevation of MCU-induced calcium levels is confirmed to be the main cause of mitochondrial reactive oxygen species (mROS) generation, which leads to disordered cellular metabolic patterns and cell death. In particular, in an I/R injury model, cancer cells, and adipocytes, MCU expression is maintained at high levels. As is well accepted, the AMPK/PGC-1α/SIRT3 pathway is believed to have an affinity for mROS formation and energy consumption. Therefore, we identified a link between MCU-related mROS formation and the AMPK/PGC-1α/SIRT3 signaling pathway in controlling cell metabolism and cell death, which may provide a new possibility of targeting the MCU to reverse relevant diseases.

Keywords:  AMPK/PGC-1α/SIRT3; cell death; metabolism; mitochondrial calcium uniporter; mitochondrial reactive oxygen species

DOI:  https://doi.org/10.3389/fmed.2021.674986
Am J Physiol Cell Physiol. 2021 07 28.

Loss of the mitochondrial phosphate carrier SLC25A3 induces remodeling of the cardiac mitochondrial protein acylome.

Jessica N Peoples, Nasab Ghazal, Duc M Duong, Katherine R Hardin, Janet R Manning, Nicholas T Seyfried, Victor Faundez, Jennifer Q Kwong.

  Mitochondria are recognized as signaling organelles because, under stress, mitochondria can trigger various signaling pathways to coordinate the cell's response. The specific pathway(s) engaged by mitochondria in response to mitochondrial energy defects in vivo and in high-energy tissues like the heart are not fully understood. Here, we investigated cardiac pathways activated in response to mitochondrial energy dysfunction by studying mice with cardiomyocyte-specific loss of the mitochondrial phosphate carrier (SLC25A3), an established model that develops cardiomyopathy as a result of defective mitochondrial ATP synthesis. Mitochondrial energy dysfunction induced a striking pattern of acylome remodeling, with significantly increased post-translational acetylation and malonylation. Mass spectrometry-based proteomics further revealed that energy dysfunction-induced remodeling of the acetylome and malonylome preferentially impacts mitochondrial proteins. Acetylation and malonylation modified a highly interconnected interactome of mitochondrial proteins, and both modifications were present on the enzyme isocitrate dehydrogenase 2 (IDH2). Intriguingly, IDH2 activity was enhanced in SLC25A3-deleted mitochondria, and further study of IDH2 sites targeted by both acetylation and malonylation revealed that these modifications can have site-specific and distinct functional effects. Finally, we uncovered a novel crosstalk between the two modifications, whereby mitochondrial energy dysfunction-induced acetylation of sirtuin 5 (SIRT5), inhibited its function. Because SIRT5 is a mitochondrial deacylase with demalonylase activity, this finding suggests that acetylation can modulate the malonylome. Together, our results position acylations as an arm of the mitochondrial response to energy dysfunction and suggest a mechanism by which focal disruption to the energy production machinery can have an expanded impact on global mitochondrial function.

Keywords:  acetylation; acylations; energy; heart; mitochondria

DOI:  https://doi.org/10.1152/ajpcell.00156.2021
FEBS J. 2021 Jul 26.

Mitochondrial fusion and fission are required for proper mitochondrial function and cell proliferation in fission yeast.

Fenfen Dong, Mengdan Zhu, Fan Zheng, Chuanhai Fu.

  Mitochondria form a branched tubular network in many types of cells, depending on a balance between mitochondrial fusion and fission. How mitochondrial fusion and fission are involved in regulating mitochondrial function and cell proliferation is not well understood. Here, we dissected the roles of mitochondrial fusion and fission in mitochondrial function and cell proliferation in fission yeast. We examined mitochondrial membrane potential by staining cells with DiOC6 and assessed mitochondrial respiration by directly measuring oxygen consumption of cells with a dissolved oxygen respirometer. We found that defects in mitochondrial fission or fusion reduce mitochondrial membrane potential and compromise mitochondrial respiration while the absence of both mitochondrial fusion and fission restores wild-type-like respiration, normal membrane potential, and tubular networks of mitochondria. Moreover, we found that the absence of either mitochondrial fission or fusion prolongs the cell cycle and that the absence of both mitochondrial fusion and fission significantly delays cell cycle progression after nitrogen replenishment. The prolonged/delayed cell cycle is likely due to the deregulation of Cdc2 activation. Hence, our work not only establishes an intimate link between mitochondrial morphology and function but also underscores the importance of mitochondrial dynamics in regulating the cell cycle.

Keywords:  Cell cycle; Dnm1; Fzo1; Mitochondria; Mitochondrial dynamics

DOI:  https://doi.org/10.1111/febs.16138
J Biol Chem. 2021 Jul 24. pii: S0021-9258(21)00807-3. [Epub ahead of print] 101005

Diverse mitochondrial abnormalities in a new cellular model of TAFFAZZIN deficiency are remediated by Cardiolipin-interacting small molecules.

Arianna F Anzmann, Olivia L Sniezek, Alexandra Pado, Veronica Busa, Frédéric M Vaz, Simion D Kreimer, Lauren R DeVine, Robert N Cole, Anne Le, Brian J Kirsch, Steven M Claypool, Hilary J Vernon.

  Barth syndrome (BTHS) is an X-linked disorder of mitochondrial phospholipid metabolism caused by pathogenic variants in the gene TAFFAZIN (TAZ), which results in abnormal cardiolipin (CL) content in the inner mitochondrial membrane. To identify unappreciated pathways of mitochondrial dysfunction in BTHS, we utilized an unbiased proteomics strategy and identified that complex I of the mitochondrial respiratory chain and the mitochondrial quality control protease PARL are altered in a new HEK293-based TAZ-deficiency model. Follow-up studies confirmed decreased steady state levels of specific complex I subunits and an assembly factor in the absence of TAZ; this decrease is in part based on decreased transcription, and results in reduced complex I assembly and function. PARL, a rhomboid protease associated with the inner mitochondrial membrane with a role in the mitochondrial response to stress such as mitochondrial membrane depolarization, is increased in TAZ-deficient cells. The increased abundance of PARL correlates with augmented processing of a downstream target, PGAM5, both at baseline and in response to mitochondrial depolarization. To clarify the relationship between abnormal CL content, complex I levels, and increased PARL expression that occurs when TAZ is missing, we used blue-native page and gene expression analysis to determine that these defects are remediated by SS-31 and bromoenol lactone, pharmacologic agents that bind CL or inhibit CL deacylation, respectively. These findings have the potential to enhance our understanding of the cardiac pathology of BTHS, where defective mitochondrial quality control and complex I dysfunction have well-recognized roles in the pathology of diverse forms of cardiac dysfunction.

Keywords:  Barth Syndrome; Cardiolipin; Mitochondrial metabolism

DOI:  https://doi.org/10.1016/j.jbc.2021.101005
NAR Cancer. 2021 Jun;3(2): zcab023

EVI1 activates tumor-promoting transcriptional enhancers in pancreatic cancer.

Hwa-Ryeon Kim, Juhye Yim, Hye-Been Yoo, Seung Eon Lee, Sumin Oh, Sungju Jung, Chang-Il Hwang, Dong-Myung Shin, TaeSoo Kim, Kyung Hyun Yoo, You-Sun Kim, Han-Woong Lee, Jae-Seok Roe.

Cancer cells utilize epigenetic alterations to acquire autonomous capabilities for tumor maintenance. Here, we show that pancreatic ductal adenocarcinoma (PDA) cells utilize super-enhancers (SEs) to activate the transcription factor EVI1 (ecotropic viral integration site 1) gene, resulting in activation of an EVI1-dependent transcription program conferring PDA tumorigenesis. Our data indicate that SE is the vital cis-acting element to maintain aberrant EVI1 transcription in PDA cells. Consistent with disease progression and inferior survival outcomes of PDA patients, we further show that EVI1 upregulation is a major cause of aggressive tumor phenotypes. Specifically, EVI1 promotes anchorage-independent growth and motility in vitro and enhances tumor propagation in vivo. Mechanistically, EVI1-dependent activation of tumor-promoting gene expression programs through the stepwise configuration of the active enhancer chromatin attributes to these phenotypes. In sum, our findings support the premise that EVI1 is a crucial driver of oncogenic transcription programs in PDA cells. Further, we emphasize the instructive role of epigenetic aberrancy in establishing PDA tumorigenesis.

DOI: https://doi.org/10.1093/narcan/zcab023
Neoplasia. 2021 Jul 21. pii: S1476-5586(21)00046-4. [Epub ahead of print]23(9): 879-886

Two transition states of the glycogen shunt and two steady states of gene expression support metabolic flexibility and the Warburg effect in cancer.

Douglas L Rothman, Robert G Shulman.

  Previously we suggested that the early Warburg effect can be explained by the use by cancer cells the glycogen shunt during a rapid increase in glucose concentration. In analogy to the Crabtree effect in yeast, the shunt plays a critical role in maintaining homeostasis of glycolytic intermediate levels during these transitions. We extend this analysis here, and propose that the recently appreciated flexibility of cancer cell glucose and glycogen metabolism involves 4 metabolic states that we recently identified in metabolic control analysis studies of yeast. Under stable conditions of low glucose and normal O2 yeast, and by analogy cancer, cells are in the Respiration State in which through gene expression for oxidizing non glucose substrates. When their environment changes to high glucose with reduced O2 levels, such as occur in tumors, they transition to the Glycolysis State due to gene expression of new glycolytic enzyme isoforms such as PKM2. These isoforms optimize metabolism to sustain the Warburg effect. When the changes in glucose and O2 levels are rapid there may be insufficient time for gene expression to adapt. The metabolic flexibility conferred by 2 states of the glycogen shunt allow the cells to survive these transitions. The model explains experimental observations in cancer such as the function of the glycogen shunt and the frequent expression of PKM2 in cells undergoing the Warburg Effect. A surprising conclusion is that the function of PKM2 is to maintain glycolytic intermediate homeostasis rather than controlling the glycolytic flux. The glycogen shunt may also have an important role in cancer metabolic reprogramming by allowing cancer cells to survive large glucose and oxygen changes during the selection of mutations that lead to the Warburg phenotype.

Keywords:  Glycogen Shunt; Homeostasis; Metabolic Flexibility; Oncogenesis; Warburg Effect

DOI:  https://doi.org/10.1016/j.neo.2021.06.004
Cell Rep. 2021 Jul 27. pii: S2211-1247(21)00833-0. [Epub ahead of print]36(4): 109420

Dysregulated oxalate metabolism is a driver and therapeutic target in atherosclerosis.

Yuhao Liu, Ying Zhao, Yousef Shukha, Haocheng Lu, Lu Wang, Zhipeng Liu, Cai Liu, Yang Zhao, Huilun Wang, Guizhen Zhao, Wenying Liang, Yanbo Fan, Lin Chang, Arif Yurdagul, Christopher B Pattillo, A Wayne Orr, Michael Aviram, Bo Wen, Minerva T Garcia-Barrio, Jifeng Zhang, Wanqing Liu, Duxin Sun, Tony Hayek, Y Eugene Chen, Oren Rom.

  Dysregulated glycine metabolism is emerging as a common denominator in cardiometabolic diseases, but its contribution to atherosclerosis remains unclear. In this study, we demonstrate impaired glycine-oxalate metabolism through alanine-glyoxylate aminotransferase (AGXT) in atherosclerosis. As found in patients with atherosclerosis, the glycine/oxalate ratio is decreased in atherosclerotic mice concomitant with suppression of AGXT. Agxt deletion in apolipoprotein E-deficient (Apoe-/-) mice decreases the glycine/oxalate ratio and increases atherosclerosis with induction of hepatic pro-atherogenic pathways, predominantly cytokine/chemokine signaling and dysregulated redox homeostasis. Consistently, circulating and aortic C-C motif chemokine ligand 5 (CCL5) and superoxide in lesional macrophages are increased. Similar findings are observed following dietary oxalate overload in Apoe-/- mice. In macrophages, oxalate induces mitochondrial dysfunction and superoxide accumulation, leading to increased CCL5. Conversely, AGXT overexpression in Apoe-/- mice increases the glycine/oxalate ratio and decreases aortic superoxide, CCL5, and atherosclerosis. Our findings uncover dysregulated oxalate metabolism via suppressed AGXT as a driver and therapeutic target in atherosclerosis.

Keywords:  AGXT; CCL5; amino acids; atherosclerosis; glycine; mitochondrial dysfunction; oxalate

DOI:  https://doi.org/10.1016/j.celrep.2021.109420
Nat Rev Cancer. 2021 Jul 27.

Mutational signatures: emerging concepts, caveats and clinical applications.

Gene Koh, Andrea Degasperi, Xueqing Zou, Sophie Momen, Serena Nik-Zainal.

Whole-genome sequencing has brought the cancer genomics community into new territory. Thanks to the sheer power provided by the thousands of mutations present in each patient's cancer, we have been able to discern generic patterns of mutations, termed 'mutational signatures', that arise during tumorigenesis. These mutational signatures provide new insights into the causes of individual cancers, revealing both endogenous and exogenous factors that have influenced cancer development. This Review brings readers up to date in a field that is expanding in computational, experimental and clinical directions. We focus on recent conceptual advances, underscoring some of the caveats associated with using the mutational signature frameworks and highlighting the latest experimental insights. We conclude by bringing attention to areas that are likely to see advancements in clinical applications.

DOI: https://doi.org/10.1038/s41568-021-00377-7
Cancer Cell. 2021 Jul 22. pii: S1535-6108(21)00380-9. [Epub ahead of print]

TRIM8 modulates the EWS/FLI oncoprotein to promote survival in Ewing sarcoma.

Bo Kyung A Seong, Neekesh V Dharia, Shan Lin, Katherine A Donovan, Shasha Chong, Amanda Robichaud, Amy Conway, Amanda Hamze, Linda Ross, Gabriela Alexe, Biniam Adane, Behnam Nabet, Fleur M Ferguson, Björn Stolte, Emily Jue Wang, Jialin Sun, Xavier Darzacq, Federica Piccioni, Nathanael S Gray, Eric S Fischer, Kimberly Stegmaier.

  Fusion-transcription factors (fusion-TFs) represent a class of driver oncoproteins that are difficult to therapeutically target. Recently, protein degradation has emerged as a strategy to target these challenging oncoproteins. The mechanisms that regulate fusion-TF stability, however, are generally unknown. Using CRISPR-Cas9 screening, we discovered tripartite motif-containing 8 (TRIM8) as an E3 ubiquitin ligase that ubiquitinates and degrades EWS/FLI, a driver fusion-TF in Ewing sarcoma. Moreover, we identified TRIM8 as a selective dependency in Ewing sarcoma compared with >700 other cancer cell lines. Mechanistically, TRIM8 knockout led to an increase in EWS/FLI protein levels that was not tolerated. EWS/FLI acts as a neomorphic substrate for TRIM8, defining the selective nature of the dependency. Our results demonstrate that fusion-TF protein stability is tightly regulated and highlight fusion oncoprotein-specific regulators as selective therapeutic targets. This study provides a tractable strategy to therapeutically exploit oncogene overdose in Ewing sarcoma and potentially other fusion-TF-driven cancers.

Keywords:  E3 ligases; EWS/FLI; Ewing sarcoma; TRIM8; fusion oncoproteins; neomorphic substrate; oncogene overdose; protein degradation; tumor dependency; ubiquitination

DOI:  https://doi.org/10.1016/j.ccell.2021.07.003
Proc Natl Acad Sci U S A. 2021 Aug 03. pii: e2025539118. [Epub ahead of print]118(31):

The p53 transcriptional response across tumor types reveals core and senescence-specific signatures modulated by long noncoding RNAs.

Ephrath Tesfaye, Elena Martinez-Terroba, Jordan Bendor, Lauren Winkler, Christiane Olivero, Kevin Chen, David M Feldser, Jesse R Zamudio, Nadya Dimitrova.

  The p53 pathway is a universal tumor suppressor mechanism that limits tumor progression by triggering apoptosis or permanent cell cycle arrest, called senescence. In recent years, efforts to reactivate p53 function in cancer have proven to be a successful therapeutic strategy in murine models and have gained traction with the development of a range of small molecules targeting mutant p53. However, knowledge of the downstream mediators of p53 reactivation in different oncogenic contexts has been limited. Here, we utilized a panel of murine cancer cell lines from three distinct tumor types susceptible to alternative outcomes following p53 restoration to define unique and shared p53 transcriptional signatures. While we found that the majority of p53-bound sites and p53-responsive transcripts are tumor-type specific, analysis of shared targets identified a core signature of genes activated by p53 across all contexts. Furthermore, we identified repression of E2F and Myc target genes as a key feature of senescence. Characterization of p53-induced transcripts revealed core and senescence-specific long noncoding RNAs (lncRNAs) that are predominantly chromatin associated and whose production is coupled to cis-regulatory activities. Functional investigation of the contributions of p53-induced lncRNAs to p53-dependent outcomes highlighted Pvt1b, the p53-dependent isoform of Pvt1, as a mediator of p53-dependent senescence via Myc repression. Inhibition of Pvt1b led to decreased activation of senescence markers and increased levels of markers of proliferation. These findings shed light on the core and outcome-specific p53 restoration signatures across different oncogenic contexts and underscore the key role of the p53-Pvt1b-Myc regulatory axis in mediating proliferative arrest.

Keywords:  lncRNA; p53; senescence; transcription; tumor suppression

DOI:  https://doi.org/10.1073/pnas.2025539118
Nat Commun. 2021 Jul 30. 12(1): 4626

PRMT1-dependent regulation of RNA metabolism and DNA damage response sustains pancreatic ductal adenocarcinoma.

Virginia Giuliani, Meredith A Miller, Chiu-Yi Liu, Stella R Hartono, Caleb A Class, Christopher A Bristow, Erika Suzuki, Lionel A Sanz, Guang Gao, Jason P Gay, Ningping Feng, Johnathon L Rose, Hideo Tomihara, Joseph R Daniele, Michael D Peoples, Jennifer P Bardenhagen, Mary K Geck Do, Qing E Chang, Bhavatarini Vangamudi, Christopher Vellano, Haoqiang Ying, Angela K Deem, Kim-Anh Do, Giannicola Genovese, Joseph R Marszalek, Jeffrey J Kovacs, Michael Kim, Jason B Fleming, Ernesto Guccione, Andrea Viale, Anirban Maitra, M Emilia Di Francesco, Timothy A Yap, Philip Jones, Giulio Draetta, Alessandro Carugo, Frederic Chedin, Timothy P Heffernan.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer that has remained clinically challenging to manage. Here we employ an RNAi-based in vivo functional genomics platform to determine epigenetic vulnerabilities across a panel of patient-derived PDAC models. Through this, we identify protein arginine methyltransferase 1 (PRMT1) as a critical dependency required for PDAC maintenance. Genetic and pharmacological studies validate the role of PRMT1 in maintaining PDAC growth. Mechanistically, using proteomic and transcriptomic analyses, we demonstrate that global inhibition of asymmetric arginine methylation impairs RNA metabolism, which includes RNA splicing, alternative polyadenylation, and transcription termination. This triggers a robust downregulation of multiple pathways involved in the DNA damage response, thereby promoting genomic instability and inhibiting tumor growth. Taken together, our data support PRMT1 as a compelling target in PDAC and informs a mechanism-based translational strategy for future therapeutic development.Statement of significancePDAC is a highly lethal cancer with limited therapeutic options. This study identified and characterized PRMT1-dependent regulation of RNA metabolism and coordination of key cellular processes required for PDAC tumor growth, defining a mechanism-based translational hypothesis for PRMT1 inhibitors.

DOI: https://doi.org/10.1038/s41467-021-24798-y
Cell Rep. 2021 Jul 27. pii: S2211-1247(21)00882-2. [Epub ahead of print]36(4): 109459

In vivo isotope tracing reveals the versatility of glucose as a brown adipose tissue substrate.

Su Myung Jung, Will G Doxsey, Johnny Le, John A Haley, Lorena Mazuecos, Amelia K Luciano, Huawei Li, Cholsoon Jang, David A Guertin.

  Active brown adipose tissue (BAT) consumes copious amounts of glucose, yet how glucose metabolism supports thermogenesis is unclear. By combining transcriptomics, metabolomics, and stable isotope tracing in vivo, we systematically analyze BAT glucose utilization in mice during acute and chronic cold exposure. Metabolite profiling reveals extensive temperature-dependent changes in the BAT metabolome and transcriptome upon cold adaptation, discovering unexpected metabolite markers of thermogenesis, including increased N-acetyl-amino acid production. Time-course stable isotope tracing further reveals rapid incorporation of glucose carbons into glycolysis and TCA cycle, as well as several auxiliary pathways, including NADPH, nucleotide, and phospholipid synthesis pathways. Gene expression differences inconsistently predict glucose fluxes, indicating that posttranscriptional mechanisms also govern glucose utilization. Surprisingly, BAT swiftly generates fatty acids and acyl-carnitines from glucose, suggesting that lipids are rapidly synthesized and immediately oxidized. These data reveal versatility in BAT glucose utilization, highlighting the value of an integrative-omics approach to understanding organ metabolism.

Keywords:  BAT; brown adipocyte; brown adipose tissue; brown fat; glucose metabolism; lipid metabolism; metabolomics; stable isotope tracing; temperature acclimation; thermogenesis

DOI:  https://doi.org/10.1016/j.celrep.2021.109459
Elife. 2021 Jul 30. pii: e60646. [Epub ahead of print]10

CXCL10/CXCR3 signaling contributes to an inflammatory microenvironment and its blockade enhances progression of murine pancreatic precancerous lesions.

Veethika Pandey, Alicia Fleming-Martinez, Ligia Bastea, Heike R Doeppler, Jillian Eisenhauer, Tam Le, Brandy Edenfield, Peter Storz.

  The development of pancreatic cancer requires recruitment and activation of different macrophage populations. However, little is known about how macrophages are attracted to the pancreas after injury or an oncogenic event, and how they crosstalk with lesion cells or other cells of the lesion microenvironment. Here, we delineate the importance of CXCL10/CXCR3 signaling during the early phase of murine pancreatic cancer. We show that CXCL10 is produced by pancreatic precancerous lesion cells in response to IFNγ signaling, and that inflammatory macrophages are recipients for this chemokine. CXCL10/CXCR3 signaling in macrophages mediates their chemoattraction to the pancreas, enhances their proliferation and maintains their inflammatory identity. Blocking of CXCL10/CXCR3 signaling in vivo shifts macrophage populations to a tumor promoting (Ym1+, Fizz+, Arg1+) phenotype, increases fibrosis and mediates progression of lesions, highlighting the importance of this pathway in PDA development. This is reversed when CXCL10 is overexpressed in PanIN cells.

Keywords:  cancer biology; cell biology; human; mouse

DOI:  https://doi.org/10.7554/eLife.60646
JCI Insight. 2021 Jul 27. pii: 147057. [Epub ahead of print]

Fatty acid mobilization from adipose tissue is mediated by CD36 post-translational modifications and intracellular trafficking.

Alexes C Daquinag, Zhanguo Gao, Cale Fussell, Linnet Immaraj, Renata Pasqualini, Wadih Arap, Askar M Akimzhanov, Maria Febbraio, Mikhail G Kolonin.

  The mechanism controlling long-chain fatty acid (LCFA) mobilization from adipose tissue (AT) is not well understood. Here, we investigated how the LCFA transporter CD36 regulates this process. By using tissue-specific knockout mouse models, we show that CD36 in both adipocytes and endothelial cells mediates both LCFA deposition into and release from AT. We demonstrate the role of adipocytic and endothelial CD36 in promoting tumor growth and chemoresistance conferred by AT-derived LCFA. We show that dynamic cysteine S-acylation of CD36 in adipocytes, endothelial cells, and cancer cells mediates intercellular LCFA transport. We demonstrate that lipolysis induction in adipocytes triggers CD36 de-acylation and deglycosylation, as well as its dissociation from interacting proteins, prohibitin-1 (PHB), and annexin 2 (ANX2). Our data indicate that lipolysis triggers caveolar endocytosis and translocation of CD36 from the cell membrane to lipid droplets. This study suggests a mechanism for both outside-in and inside-out cellular LCFA transport regulated by CD36 S- acylation and its interactions with PHB and ANX2.

Keywords:  Adipose tissue; Cancer; Cell Biology; Metabolism; Obesity

DOI:  https://doi.org/10.1172/jci.insight.147057
JCI Insight. 2021 Jul 27. pii: 147692. [Epub ahead of print]

Anterograde regulation of mitochondrial genes and FGF21 signaling by hepatic LSD1.

Yang Cao, Lingyi Tang, Kang Du, Kitt Paraiso, Qiushi Sun, Zhengxia Liu, Xiaolong Ye, Yuan Fang, Fang Yuan, Yu-Han Chen, Yumay Chen, Xiaorong Wang, Clinton Yu, Ira L Blitz, Ping H Wang, Lan Huang, Haibo Cheng, Xiang Lu, Ken Wy Cho, Marcus Seldin, Zhuyuan Fang, Qin Yang.

  Mitochondrial biogenesis and function are controlled by anterograde regulatory pathways involving more than one thousand nuclear-encoded proteins. Transcriptional networks controlling the nuclear-encoded mitochondrial genes remain to be fully elucidated. Here we show that histone demethylase LSD1 knockout from adult mouse liver (LSD1-LKO) reduces the expression of one-third of all nuclear-encoded mitochondrial genes and decreases mitochondrial biogenesis and function. LSD1-modulated histone methylation epigenetically regulates nuclear-encoded mitochondrial genes. Furthermore, LSD1 regulates gene expression and protein methylation of nicotinamide mononucleotide adenylyltransferase 1 (NMNAT1), which controls the final step of NAD+ synthesis and limits NAD+ availability in nucleus. Lsd1 knockout reduces NAD+-dependent SIRT1 and SIRT7 deacetylase activity, leading to hyperacetylation and hypofunctioning of GABPβ and PGC-1α, the major transcriptional factor/cofactor for nuclear-encoded mitochondrial genes. Despite the reduced mitochondrial function in liver, LSD1-LKO mice are protected from diet-induced hepatic steatosis and glucose intolerance, partially due to induction of hepatokine FGF21. Thus, LSD1 orchestrates a core regulatory network involving epigenetic modifications and NAD+ synthesis to control mitochondrial function and hepatokine production.

Keywords:  Diabetes; Endocrinology; Obesity

DOI:  https://doi.org/10.1172/jci.insight.147692
Methods Cell Biol. 2021 ;pii: S0091-679X(20)30187-4. [Epub ahead of print]165 1-12

A novel tool for detecting lysosomal membrane permeabilization by high-throughput fluorescence microscopy.

Karla Alvarez-Valadez, Allan Sauvat, Hélène Fohrer-Ting, Christophe Klein, Oliver Kepp, Guido Kroemer, Mojgan Djavaheri-Mergny.

  Lysosomes are placed at the center of cellular trafficking and degradative pathways. They also function as a signaling platform for nutrient sensing and metabolic reprogramming. Lysosomes play crucial roles in cellular adaptation in response to stress and are tightly connected to a variety of cell death modalities. Several stimuli can initiate the permeabilization of the lysosome membrane, thus causing cell death when the cellular adaptive system fail to repair or replace damaged lysosomes. The induction of lysosomal membrane permeabilization (LMP) triggers the rapid translocation of Galectin 3/LGALS3 from the cytosol to the lysosomal lumen, making it a valuable marker of LMP. However, Galectin 3 can also be recruited to damaged endo/phagosomal membranes. To make sure that Galectin 3 labels damaged lysosomes, it is therefore important to verify its colocalization with lysosomal markers such as lysosome-associated membrane protein 1 (LAMP1). Here, we describe a simple, fast and robust protocol that allows the detection of LMP of individual lysosomes in U2OS cells expressing mCherry-tagged Galectin 3 and mGFP-tagged LAMP1. This method permits the high-throughput detection and quantification of damaged lysosomes by fluorescence microscopy. It also offers the advantage of studying, in the same experiment, the alterations in size, shape and subcellular localization of intact and damaged lysosomes.

Keywords:  Autophagy; Cell death; Galectin 3; High-throughput fluorescence microscopy; LAMP1; Lysosomal membrane permeabilization; Lysosomes; Stress responses

DOI:  https://doi.org/10.1016/bs.mcb.2020.10.004
Nat Rev Cancer. 2021 Jul 29.

The immunological and metabolic landscape in primary and metastatic liver cancer.

Xin Li, Pierluigi Ramadori, Dominik Pfister, Marco Seehawer, Lars Zender, Mathias Heikenwalder.

The liver is the sixth most common site of primary cancer in humans, and generally arises in a background of cirrhosis and inflammation. Moreover, the liver is frequently colonized by metastases from cancers of other organs (particularly the colon) because of its anatomical location and organization, as well as its unique metabolic and immunosuppressive environment. In this Review, we discuss how the hepatic microenvironment adapts to pathologies characterized by chronic inflammation and metabolic alterations. We illustrate how these immunological or metabolic changes alter immunosurveillance and thus hinder or promote the development of primary liver cancer. In addition, we describe how inflammatory and metabolic niches affect the spreading of cancer metastases into or within the liver. Finally, we review the current therapeutic options in this context and the resulting challenges that must be surmounted.

DOI: https://doi.org/10.1038/s41568-021-00383-9
EMBO Rep. 2021 Jul 30. e53251

Integration of transcriptional and metabolic control in macrophage activation.

Gioacchino Natoli, Francesco Pileri, Francesco Gualdrini, Serena Ghisletti.

  Macrophages react to microbial and endogenous danger signals by activating a broad panel of effector and homeostatic responses. Such responses entail rapid and stimulus-specific changes in gene expression programs accompanied by extensive rewiring of metabolism, with alterations in chromatin modifications providing one layer of integration of transcriptional and metabolic regulation. A systematic and mechanistic understanding of the mutual influences between signal-induced metabolic changes and gene expression is still lacking. Here, we discuss current evidence, controversies, knowledge gaps, and future areas of investigation on how metabolic and transcriptional changes are dynamically integrated during macrophage activation. The cross-talk between metabolism and inflammatory gene expression is in part accounted for by alterations in the production, usage, and availability of metabolic intermediates that impact the macrophage epigenome. In addition, stimulus-inducible gene expression changes alter the production of inflammatory mediators, such as nitric oxide, that in turn modulate the activity of metabolic enzymes thus determining complex regulatory loops. Critical issues remain to be understood, notably whether and how metabolic rewiring can bring about gene-specific (as opposed to global) expression changes.

Keywords:  epigenetics; inflammation; macrophages; metabolism; transcription

DOI:  https://doi.org/10.15252/embr.202153251
NAR Cancer. 2021 Sep;3(3): zcab026

The small Cajal body-specific RNA 15 (SCARNA15) directs p53 and redox homeostasis via selective splicing in cancer cells.

Giulia Beneventi, Roberto Munita, Phuong Cao Thi Ngoc, Magdalena Madej, Maciej Cieśla, Sowndarya Muthukumar, Nicolai Krogh, Henrik Nielsen, Vinay Swaminathan, Cristian Bellodi.

Small Cajal body-specific RNAs (scaRNAs) guide post-transcriptional modification of spliceosomal RNA and, while commonly altered in cancer, have poorly defined roles in tumorigenesis. Here, we uncover that SCARNA15 directs alternative splicing (AS) and stress adaptation in cancer cells. Specifically, we find that SCARNA15 guides critical pseudouridylation (Ψ) of U2 spliceosomal RNA to fine-tune AS of distinct transcripts enriched for chromatin and transcriptional regulators in malignant cells. This critically impacts the expression and function of the key tumor suppressors ATRX and p53. Significantly, SCARNA15 loss impairs p53-mediated redox homeostasis and hampers cancer cell survival, motility and anchorage-independent growth. In sum, these findings highlight an unanticipated role for SCARNA15 and Ψ in directing cancer-associated splicing programs.

DOI: https://doi.org/10.1093/narcan/zcab026
Sci Rep. 2021 Jul 30. 11(1): 15510

Sirtuin 5 depletion impairs mitochondrial function in human proximal tubular epithelial cells.

Timo N Haschler, Harry Horsley, Monika Balys, Glenn Anderson, Jan-Willem Taanman, Robert J Unwin, Jill T Norman.

Ischemia is a major cause of kidney damage. Proximal tubular epithelial cells (PTECs) are highly susceptible to ischemic insults that frequently cause acute kidney injury (AKI), a potentially life-threatening condition with high mortality. Accumulating evidence has identified altered mitochondrial function as a central pathologic feature of AKI. The mitochondrial NAD+-dependent enzyme sirtuin 5 (SIRT5) is a key regulator of mitochondrial form and function, but its role in ischemic renal injury (IRI) is unknown. SIRT5 expression was increased in murine PTECs after IRI in vivo and in human PTECs (hPTECs) exposed to an oxygen/nutrient deprivation (OND) model of IRI in vitro. SIRT5-depletion impaired ATP production, reduced mitochondrial membrane potential, and provoked mitochondrial fragmentation in hPTECs. Moreover, SIRT5 RNAi exacerbated OND-induced mitochondrial bioenergetic dysfunction and swelling, and increased degradation by mitophagy. These findings suggest SIRT5 is required for normal mitochondrial function in hPTECs and indicate a potentially important role for the enzyme in the regulation of mitochondrial biology in ischemia.

DOI: https://doi.org/10.1038/s41598-021-94185-6
Elife. 2021 Jul 27. pii: e66768. [Epub ahead of print]10

miR-1 coordinately regulates lysosomal v-ATPase and biogenesis to impact proteotoxicity and muscle function during aging.

Isabelle Schiffer, Birgit Gerisch, Kazuto Kawamura, Raymond Laboy, Jennifer Hewitt, Martin Sebastian Denzel, Marcelo A Mori, Siva Vanapalli, Yidong Shen, Orsolya Symmons, Adam Antebi.

  Muscle function relies on the precise architecture of dynamic contractile elements, which must be fine-tuned to maintain motility throughout life. Muscle is also plastic, and remodeled in response to stress, growth, neural and metabolic inputs. The conserved muscle-enriched microRNA, miR-1, regulates distinct aspects of muscle development, but whether it plays a role during aging is unknown. Here we investigated Caenorhabditis elegans miR-1 in muscle function in response to proteostatic stress. mir-1 deletion improved mid-life muscle motility, pharyngeal pumping, and organismal longevity upon polyQ35 proteotoxic challenge. We identified multiple vacuolar ATPase subunits as subject to miR-1 control, and the regulatory subunit vha-13/ATP6V1A as a direct target downregulated via its 3'UTR to mediate miR-1 physiology. miR-1 further regulates nuclear localization of lysosomal biogenesis factor HLH-30/TFEB and lysosomal acidification. Our studies reveal that miR-1 coordinately regulates lysosomal v-ATPase and biogenesis to impact muscle function and health during aging.

Keywords:  C. elegans; genetics; genomics; lysosomal v-ATPase; miR-1; polyglutamine; proteostasis; vha-13

DOI:  https://doi.org/10.7554/eLife.66768
Stem Cell Reports. 2021 Jul 15. pii: S2213-6711(21)00324-6. [Epub ahead of print]

The relevance of mitochondrial DNA variants fluctuation during reprogramming and neuronal differentiation of human iPSCs.

Flavia Palombo, Camille Peron, Leonardo Caporali, Angelo Iannielli, Alessandra Maresca, Ivano Di Meo, Claudio Fiorini, Alice Segnali, Francesca L Sciacca, Ambra Rizzo, Sonia Levi, Anu Suomalainen, Alessandro Prigione, Vania Broccoli, Valerio Carelli, Valeria Tiranti.

  The generation of inducible pluripotent stem cells (iPSCs) is a revolutionary technique allowing production of pluripotent patient-specific cell lines used for disease modeling, drug screening, and cell therapy. Integrity of nuclear DNA (nDNA) is mandatory to allow iPSCs utilization, while quality control of mitochondrial DNA (mtDNA) is rarely included in the iPSCs validation process. In this study, we performed mtDNA deep sequencing during the transition from parental fibroblasts to reprogrammed iPSC and to differentiated neuronal precursor cells (NPCs) obtained from controls and patients affected by mitochondrial disorders. At each step, mtDNA variants, including those potentially pathogenic, fluctuate between emerging and disappearing, and some having functional implications. We strongly recommend including mtDNA analysis as an unavoidable assay to obtain fully certified usable iPSCs and NPCs.

Keywords:  human iPSCs; iPSCs quality control; mtDNA deep sequencing; neuronal precursor cells

DOI:  https://doi.org/10.1016/j.stemcr.2021.06.016
Trends Cancer. 2021 Jul 23. pii: S2405-8033(21)00141-2. [Epub ahead of print]

Tumour microenvironment 3D-modelling: simplicity to complexity and back again.

Edward P Carter, Reza Roozitalab, Shayin V Gibson, Richard P Grose.

  Tumours are surrounded by a host of noncancerous cells that fulfil both supportive and suppressive roles within the tumour microenvironment (TME). The drive to understand the biology behind each of these components has led to a rapid expansion in the number and use of 3D in vitro models, as researchers find ways to incorporate multiple cell types into physiomimetic configurations. The use and increasing complexity of these models does however demand many considerations. In this review we discuss approaches adopted to recapitulate complex tumour biology in tractable 3D models. We consider how these cell types can be sourced and combined and examine methods for the deconvolution of complex multicellular models into manageable and informative outputs.

Keywords:  3D model; tumour; tumour microenvironment

DOI:  https://doi.org/10.1016/j.trecan.2021.06.009
Dev Cell. 2021 Jul 20. pii: S1534-5807(21)00558-X. [Epub ahead of print]

Interaction between Ras and Src clones causes interdependent tumor malignancy via Notch signaling in Drosophila.

Masato Enomoto, Daisaku Takemoto, Tatsushi Igaki.

  Cancer tissue often comprises multiple tumor clones with distinct oncogenic alterations such as Ras or Src activation, yet the mechanism by which tumor heterogeneity drives cancer progression remains elusive. Here, we show in Drosophila imaginal epithelium that clones of Ras- or Src-activated benign tumors interact with each other to mutually promote tumor malignancy. Mechanistically, Ras-activated cells upregulate the cell-surface ligand Delta while Src-activated cells upregulate its receptor Notch, leading to Notch activation in Src cells. Elevated Notch signaling induces the transcriptional repressor Zfh1/ZEB1, which downregulates E-cadherin and cell death gene hid, leading to Src-activated invasive tumors. Simultaneously, Notch activation in Src cells upregulates the cytokine Unpaired/IL-6, which activates JAK-STAT signaling in neighboring Ras cells. Elevated JAK-STAT signaling upregulates the BTB-zinc-finger protein Chinmo, which downregulates E-cadherin and thus generates Ras-activated invasive tumors. Our findings provide a mechanistic explanation for how tumor heterogeneity triggers tumor progression via cell-cell interactions.

Keywords:  Notch signaling; Ras; Src; cell-cell interaction; tumor heterogeneity

DOI:  https://doi.org/10.1016/j.devcel.2021.07.002
Curr Biol. 2021 Jul 16. pii: S0960-9822(21)00893-9. [Epub ahead of print]

Sequential oncogenic mutations influence cell competition.

Koki Kohashi, Yusuke Mori, Rika Narumi, Kei Kozawa, Tomoko Kamasaki, Susumu Ishikawa, Mihoko Kajita, Rei Kobayashi, Yoichiro Tamori, Yasuyuki Fujita.

  At the initial stage of carcinogenesis, newly emerging transformed cells are often eliminated from epithelial layers via cell competition with the surrounding normal cells. For instance, when surrounded by normal cells, oncoprotein RasV12-transformed cells are extruded into the apical lumen of epithelia. During cancer development, multiple oncogenic mutations accumulate within epithelial tissues. However, it remains elusive whether and how cell competition is also involved in this process. In this study, using a mammalian cell culture model system, we have investigated what happens upon the consecutive mutations of Ras and tumor suppressor protein Scribble. When Ras mutation occurs under the Scribble-knockdown background, apical extrusion of Scribble/Ras double-mutant cells is strongly diminished. In addition, at the boundary with Scribble/Ras cells, Scribble-knockdown cells frequently undergo apoptosis and are actively engulfed by the neighboring Scribble/Ras cells. The comparable apoptosis and engulfment phenotypes are also observed in Drosophila epithelial tissues between Scribble/Ras double-mutant and Scribble single-mutant cells. Furthermore, mitochondrial membrane potential is enhanced in Scribble/Ras cells, causing the increased mitochondrial reactive oxygen species (ROS). Suppression of mitochondrial membrane potential or ROS production diminishes apoptosis and engulfment of the surrounding Scribble-knockdown cells, indicating that mitochondrial metabolism plays a key role in the competitive interaction between double- and single-mutant cells. Moreover, mTOR (mechanistic target of rapamycin kinase) acts downstream of these processes. These results imply that sequential oncogenic mutations can profoundly influence cell competition, a transition from loser to winner. Further studies would open new avenues for cell competition-based cancer treatment, thereby blocking clonal expansion of more malignant populations within tumors.

Keywords:  ROS; RasV12; Scribble; apoptosis; cell competition; engulfment; entosis; mTOR; mitochondria; sequential mutations

DOI:  https://doi.org/10.1016/j.cub.2021.06.064
Biochim Biophys Acta Mol Cell Res. 2021 Jul 27. pii: S0167-4889(21)00168-3. [Epub ahead of print] 119114

Mutant IDH1 inhibitors activate pSTAT3-Y705 leading to an increase in BCAT1 and YKL-40 levels in mutant IDH1-expressing cells.

Debanjan Bhattacharjee, Kancharana Balabhaskararao, Nishant Jain.

  IDH1 mutations are frequent and early events in gliomas. Mutant IDH1 produces D-2HG that causes epigenetic changes by increasing histone and DNA methylations, thereby contributing to tumor growth. Mutant IDH1 rewires metabolism and endows a few therapeutic vulnerabilities in cells. But, mutant IDH1 inhibitor(s) treatments reverse these therapeutic vulnerabilities by increasing cell growth. Nevertheless, it is unclear how mutant IDH1 inhibitor(s) increases cell growth. As mutant IDH1 inhibitor(s) increase cell growth, therefore we asked whether mutant IDH1 inhibitor(s) activate oncogenes in mutant IDH1-expressing cells. To answer this question, we used allosteric mutant IDH1 inhibitors to treat mutant IDH1-expressing HT1080 cells, and examined for activation of oncogenes by assessing the levels of our read-outs: BCAT1 and YKL-40. We found that mutant IDH1 inhibitors' treatments increased BCAT1 and YKL-40 levels in HT1080 cells. Next, we observed that mutant IDH1 inhibitors activated STAT3 by phosphorylation at Tyr-705 position (pSTAT3-Y705) and its nuclear translocation. Upon examining the molecular mechanism of pSTAT3-Y705 activation in mutant IDH1 inhibitor-treated cells, we found that mutant IDH1 strongly bound STAT3, but mutant IDH1 inhibitor treatment decreased mutant IDH1-STAT3 binding. Furthermore, we observed that STAT3-knockdown and pharmacological inhibition of STAT3 attenuated the mutant IDH1 inhibitor-mediated increase in BCAT1 and YKL-40 levels, whereas STAT3 overexpression and Interleukin-6 (STAT3 activator) treatments increased BCAT1 and YKL-40 levels. We conclude that mutant IDH1 inhibitors activate the oncogenic transcription factor-STAT3 leading to an increase in BCAT1 and YKL-40 levels in mutant IDH1-expressing cells.

Keywords:  BCAT1; IDH1; Mutant IDH1 inhibitors; STAT3; YKL-40

DOI:  https://doi.org/10.1016/j.bbamcr.2021.119114
Cell Rep. 2021 Jul 27. pii: S2211-1247(21)00858-5. [Epub ahead of print]36(4): 109441

The Cancer SENESCopedia: A delineation of cancer cell senescence.

Fleur Jochems, Bram Thijssen, Giulia De Conti, Robin Jansen, Ziva Pogacar, Kelvin Groot, Liqin Wang, Arnout Schepers, Cun Wang, Haojie Jin, Roderick L Beijersbergen, Rodrigo Leite de Oliveira, Lodewyk F A Wessels, René Bernards.

  Cellular senescence is characterized as a stable proliferation arrest that can be triggered by multiple stresses. Most knowledge about senescent cells is obtained from studies in primary cells. However, senescence features may be different in cancer cells, since the pathways that are involved in senescence induction are often deregulated in cancer. We report here a comprehensive analysis of the transcriptome and senolytic responses in a panel of 13 cancer cell lines rendered senescent by two distinct compounds. We show that in cancer cells, the response to senolytic agents and the composition of the senescence-associated secretory phenotype are more influenced by the cell of origin than by the senescence trigger. Using machine learning, we establish the SENCAN gene expression classifier for the detection of senescence in cancer cell samples. The expression profiles and senescence classifier are available as an interactive online Cancer SENESCopedia.

Keywords:  ABT-263; SASP; SENCAN; SENESCopedia; cancer; cell cycle; gene expression classifier; senescence; senolytics; transcriptome profiling

DOI:  https://doi.org/10.1016/j.celrep.2021.109441
Nature. 2021 Jul 28.

In silico saturation mutagenesis of cancer genes.

Ferran Muiños, Francisco Martínez-Jiménez, Oriol Pich, Abel Gonzalez-Perez, Nuria Lopez-Bigas.

Despite the existence of good catalogues of cancer genes1,2, identifying the specific mutations of those genes that drive tumorigenesis across tumour types is still a largely unsolved problem. As a result, most mutations identified in cancer genes across tumours are of unknown significance to tumorigenesis3. We propose that the mutations observed in thousands of tumours-natural experiments testing their oncogenic potential replicated across individuals and tissues-can be exploited to solve this problem. From these mutations, features that describe the mechanism of tumorigenesis of each cancer gene and tissue may be computed and used to build machine learning models that encapsulate these mechanisms. Here we demonstrate the feasibility of this solution by building and validating 185 gene-tissue-specific machine learning models that outperform experimental saturation mutagenesis in the identification of driver and passenger mutations. The models and their assessment of each mutation are designed to be interpretable, thus avoiding a black-box prediction device. Using these models, we outline the blueprints of potential driver mutations in cancer genes, and demonstrate the role of mutation probability in shaping the landscape of observed driver mutations. These blueprints will support the interpretation of newly sequenced tumours in patients and the study of the mechanisms of tumorigenesis of cancer genes across tissues.

DOI: https://doi.org/10.1038/s41586-021-03771-1
Cardiovasc Res. 2021 Jul 27. 117(9): e106-e109

NAD+ metabolism and cardiometabolic health: the human evidence.

Mahmoud Abdellatif, Joseph A Baur.



Keywords:  Ageing; Cardiovascular disease; Diabetes; NMN; NR; Niacin; Nicotinamide; Obesity

DOI:  https://doi.org/10.1093/cvr/cvab212
EMBO Rep. 2021 Jul 29. e51872

Calcium signaling induces a partial EMT.

Robert J Norgard, Jason R Pitarresi, Ravikanth Maddipati, Nicole M Aiello-Couzo, David Balli, Jinyang Li, Taiji Yamazoe, Maximilian D Wengyn, Ian D Millstein, Ian W Folkert, Derick N Rosario-Berrios, Il-Kyu Kim, Jared B Bassett, Riley Payne, Corbett T Berry, Xiaodong Feng, Kathryn Sun, Michele Cioffi, Priyanka Chakraborty, Mohit Kumar Jolly, J Silvio Gutkind, David Lyden, Bruce D Freedman, J Kevin Foskett, Anil K Rustgi, Ben Z Stanger.

  Epithelial plasticity, or epithelial-to-mesenchymal transition (EMT), is a well-recognized form of cellular plasticity, which endows tumor cells with invasive properties and alters their sensitivity to various agents, thus representing a major challenge to cancer therapy. It is increasingly accepted that carcinoma cells exist along a continuum of hybrid epithelial-mesenchymal (E-M) states and that cells exhibiting such partial EMT (P-EMT) states have greater metastatic competence than those characterized by either extreme (E or M). We described recently a P-EMT program operating in vivo by which carcinoma cells lose their epithelial state through post-translational programs. Here, we investigate the underlying mechanisms and report that prolonged calcium signaling induces a P-EMT characterized by the internalization of membrane-associated E-cadherin (ECAD) and other epithelial proteins as well as an increase in cellular migration and invasion. Signaling through Gαq-associated G-protein-coupled receptors (GPCRs) recapitulates these effects, which operate through the downstream activation of calmodulin-Camk2b signaling. These results implicate calcium signaling as a trigger for the acquisition of hybrid/partial epithelial-mesenchymal states in carcinoma cells.

Keywords:  E-cadherin; calcium; cellular plasticity; partial EMT

DOI:  https://doi.org/10.15252/embr.202051872
Nat Commun. 2021 07 27. 12(1): 4542

An enzymatic activation of formaldehyde for nucleotide methylation.

Charles Bou-Nader, Frederick W Stull, Ludovic Pecqueur, Philippe Simon, Vincent Guérineau, Antoine Royant, Marc Fontecave, Murielle Lombard, Bruce A Palfey, Djemel Hamdane.

Folate enzyme cofactors and their derivatives have the unique ability to provide a single carbon unit at different oxidation levels for the de novo synthesis of amino-acids, purines, or thymidylate, an essential DNA nucleotide. How these cofactors mediate methylene transfer is not fully settled yet, particularly with regard to how the methylene is transferred to the methylene acceptor. Here, we uncovered that the bacterial thymidylate synthase ThyX, which relies on both folate and flavin for activity, can also use a formaldehyde-shunt to directly synthesize thymidylate. Combining biochemical, spectroscopic and anaerobic crystallographic analyses, we showed that formaldehyde reacts with the reduced flavin coenzyme to form a carbinolamine intermediate used by ThyX for dUMP methylation. The crystallographic structure of this intermediate reveals how ThyX activates formaldehyde and uses it, with the assistance of active site residues, to methylate dUMP. Our results reveal that carbinolamine species promote methylene transfer and suggest that the use of a CH2O-shunt may be relevant in several other important folate-dependent reactions.

DOI: https://doi.org/10.1038/s41467-021-24756-8
Aging Cell. 2021 Jul 27. e13444

Nrf2 deficiency decreases NADPH from impaired IDH shuttle and pentose phosphate pathway in retinal pigmented epithelial cells to magnify oxidative stress-induced mitochondrial dysfunction.

Marisol Cano, Sayantan Datta, Lei Wang, Tongyun Liu, Miguel Flores-Bellver, Mira Sachdeva, Debasish Sinha, James T Handa.

  The nuclear factor-erythroid 2-related factor-2 (Nrf2), a major antioxidant transcription factor, is decreased in several age-related diseases including age-related macular degeneration (AMD), the most common cause of blindness among the elderly in western society. Since Nrf2's mito-protective response is understudied, we investigated its antioxidant response on mitochondria. Control and Nrf2-deficient retinal pigmented epithelial (RPE) cells were compared after treating with cigarette smoke extract (CSE). Mitochondrial antioxidant abundance and reactive oxygen species (ROS) were quantified. Mitochondrial function was assessed by TMRM assay, NADPH, electron transport chain activity, and Seahorse. Results were corroborated in Nrf2-/- mice and relevance to AMD was provided by immunohistochemistry of human globes. CSE induced mitochondrial ROS to impair mitochondrial function. H2 O2 increase in particular, was magnified by Nrf2 deficiency, and corresponded with exaggerated mitochondrial dysfunction. While Nrf2 did not affect mitochondrial antioxidant abundance, oxidized PRX3 was magnified by Nrf2 deficiency due to decreased NADPH from decreased expression of IDH2 and pentose phosphate pathway (PPP) genes. With severe CSE stress, intrinsic apoptosis was activated to increase cell death. PPP component TALDO1 immunolabeling was decreased in dysmorphic RPE of human AMD globes. Despite limited regulation of mitochondrial antioxidant expression, Nrf2 influences PPP and IDH shuttle activity that indirectly supplies NADPH for the TRX2 system. These results provide insight into how Nrf2 deficiency impacts the mitochondrial antioxidant response, and its role in AMD pathobiology.

Keywords:  aging; mitochondria; oxidative stress; reactive oxygen species

DOI:  https://doi.org/10.1111/acel.13444