bims-camemi 2023-04-16 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2023–04–16
48 papers selected by
Christian Frezza, Universität zu Köln

Overlooked confounding in studies of metabolite salts.
Genome-wide CRISPR screens identify ILF3 as a mediator of mTORC1-dependent amino acid sensing.
PTEN-induced kinase PINK1 supports colorectal cancer growth by regulating the labile iron pool.
A D-2-hydroxyglutarate dehydrogenase mutant reveals a critical role for ketone body metabolism in Caenorhabditis elegans development.
A plasma membrane-associated glycolytic metabolon is functionally coupled to KATP channels in pancreatic α and β cells from humans and mice.
Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease.
Evidence supporting the MICU1 occlusion mechanism and against the potentiation model in the mitochondrial calcium uniporter complex.
IDH3γ functions as a redox switch regulating mitochondrial energy metabolism and contractility in the heart.
Mannose metabolism inhibition sensitizes acute myeloid leukaemia cells to therapy by driving ferroptotic cell death.
The anorectic and thermogenic effects of pharmacological lactate in male mice are confounded by treatment osmolarity and co-administered counterions.
USP9X mediates an acute adaptive response to MAPK suppression in pancreatic cancer but creates multiple actionable therapeutic vulnerabilities.
An intermembrane space protein facilitates completion of mitochondrial division in yeast.
Circulating succinate-modifying metabolites accurately classify and reflect the status of fumarate hydratase-deficient renal cell carcinoma.
Cancer Cell-Derived PDGFB Stimulates mTORC1 Activation in Renal Carcinoma.
Tom40 in cholesterol transport.
Metabolic regulation of misfolded protein import into mitochondria.
Impact of risk factors on early cancer evolution.
Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2.
IRG1/Itaconate induces metabolic reprogramming to suppress ER-positive breast cancer cell growth.
Deregulation of ER-mitochondria contact formation and mitochondrial calcium homeostasis mediated by VDAC in fragile X syndrome.
PASK links cellular energy metabolism with a mitotic self-renewal network to establish differentiation competence.
The circadian protein BMAL1 supports endothelial cell cycle during angiogenesis.
Oxygen modulates iron homeostasis by switching iron-sensing of NCOA4.
Extrachromosomal DNA appears before cancer forms.
High-Throughput Microscopy Analysis of Mitochondrial Membrane Potential in 2D and 3D Models.
Mechanosensitive mTORC1 signaling maintains lymphatic valves.
Asparagine starvation suppresses histone demethylation through iron depletion.
Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress.
Multiomics-guided cellular immunotherapies.
Tumor progression is independent of tumor-associated macrophages in cell lineage-based mouse models of glioblastoma.
DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins.
Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus.
Molecular portraits of lung cancer evolution.
Ageing-associated changes in transcriptional elongation influence longevity.
NOX4-TIM23 interaction regulates NOX4 mitochondrial import and metabolic reprogramming.
The intratumoral microbiota: From microniches to single cells.
Metastasis.
Insights into the metastatic cascade through research autopsies.
Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape.
Epigenetic escape of immunosurveillance by malignant cell precursors.
Pancreatic cancer: Advances and challenges.
Metastatic dormancy needs STING.
Ferroptosis: Under pressure!
The relationship between epigenetic age and the hallmarks of aging in human cells.
Accelerating the understanding of cancer biology through the lens of genomics.
Antibodies against endogenous retroviruses promote lung cancer immunotherapy.
Genomic-transcriptomic evolution in lung cancer and metastasis.
The evolution of lung cancer and impact of subclonal selection in TRACERx.

Nat Metab. 2023 Apr 13.

Overlooked confounding in studies of metabolite salts.

DOI: https://doi.org/10.1038/s42255-023-00787-x
Nat Cell Biol. 2023 Apr 10.

Genome-wide CRISPR screens identify ILF3 as a mediator of mTORC1-dependent amino acid sensing.

Guokai Yan, Jinxin Yang, Wen Li, Ao Guo, Jialiang Guan, Ying Liu.

The mechanistic target of rapamycin complex 1 (mTORC1) is an essential hub that integrates nutrient signals and coordinates metabolism to control cell growth. Amino acid signals are detected by sensor proteins and relayed to the GATOR2 and GATOR1 complexes to control mTORC1 activity. Here we perform genome-wide CRISPR/Cas9 screens, coupled with an assay for mTORC1 activity based on fluorescence-activated cell sorting analysis of pS6, to identify potential regulators of mTORC1-dependent amino acid sensing. We then focus on interleukin enhancer binding factor 3 (ILF3), one of the candidate genes from the screen. ILF3 tethers the GATOR complexes to lysosomes to control mTORC1. Adding a lysosome-targeting sequence to the GATOR2 component WDR24 bypasses the requirement for ILF3 to modulate amino-acid-dependent mTORC1 signalling. ILF3 plays an evolutionarily conserved role in human and mouse cells, and in worms to regulate the mTORC1 pathway, control autophagy activity and modulate the ageing process.

DOI: https://doi.org/10.1038/s41556-023-01123-x
J Biol Chem. 2023 Apr 08. pii: S0021-9258(23)00333-2. [Epub ahead of print] 104691

PTEN-induced kinase PINK1 supports colorectal cancer growth by regulating the labile iron pool.

Brandon Chen, Nupur K Das, Indrani Talukder, Rashi Singhal, Cristina Castillo, Anthony Andren, Joseph D Mancias, Costas A Lyssiotis, Yatrik M Shah.

  Mitophagy is a cargo-specific autophagic process that recycles damaged mitochondria to promote mitochondrial turnover. PTEN-induced putative kinase 1 (PINK1) mediates the canonical mitophagic pathway. However, the role of PINK1 in diseases where mitophagy has been purported to play a role, such as colorectal cancer, in unclear.Our results here demonstrate that higher PINK1 expression is positively correlated with decreased colon cancer survival, and mitophagy is required for colon cancer growth following nutrient stress. We show that doxycycline-inducible knockdown (KD) of PINK1 in a panel of colon cancer cell lines inhibited proliferation, whereas disruption of other mitophagy receptors did not impact cell growth. We observed that PINK KD led to a decrease in mitochondrial respiration, membrane hyperpolarization, accumulation of mitochondrial DNA, and depletion of antioxidant glutathione. In addition, mitochondria are important hubs for the utilization of iron and synthesizing iron-dependent cofactors such as heme and iron sulfur clusters. We observed an increase in the iron storage protein ferritin and a decrease labile iron pool in the PINK1 KD cells, but total cellular iron or markers of iron starvation/overload were not affected. Finally, cellular iron storage and the labile iron pool are maintained via autophagic degradation of ferritin (ferritinophagy). We found overexpressing nuclear receptor coactivator 4, a key adaptor for ferritinophagy, rescued cell growth and the labile iron pool in PINK1 KD cells. These results indicate that PINK1 integrates mitophagy and ferritinophagy to regulate intracellular iron availability and is essential for maintaining intracellular iron homeostasis to support survival and growth in colorectal cancer cells.

Keywords:  colon cancer; ferritinophagy; iron; mitochondria; mitophagy

DOI:  https://doi.org/10.1016/j.jbc.2023.104691
PLoS Biol. 2023 Apr;21(4): e3002057

A D-2-hydroxyglutarate dehydrogenase mutant reveals a critical role for ketone body metabolism in Caenorhabditis elegans development.

Olga Ponomarova, Hefei Zhang, Xuhang Li, Shivani Nanda, Thomas B Leland, Bennett W Fox, Alyxandra N Starbard, Gabrielle E Giese, Frank C Schroeder, L Safak Yilmaz, Albertha J M Walhout.

In humans, mutations in D-2-hydroxyglutarate (D-2HG) dehydrogenase (D2HGDH) result in D-2HG accumulation, delayed development, seizures, and ataxia. While the mechanisms of 2HG-associated diseases have been studied extensively, the endogenous metabolism of D-2HG remains unclear in any organism. Here, we find that, in Caenorhabditis elegans, D-2HG is produced in the propionate shunt, which is transcriptionally activated when flux through the canonical, vitamin B12-dependent propionate breakdown pathway is perturbed. Loss of the D2HGDH ortholog, dhgd-1, results in embryonic lethality, mitochondrial defects, and the up-regulation of ketone body metabolism genes. Viability can be rescued by RNAi of hphd-1, which encodes the enzyme that produces D-2HG or by supplementing either vitamin B12 or the ketone bodies 3-hydroxybutyrate (3HB) and acetoacetate (AA). Altogether, our findings support a model in which C. elegans relies on ketone bodies for energy when vitamin B12 levels are low and in which a loss of dhgd-1 causes lethality by limiting ketone body production.

DOI: https://doi.org/10.1371/journal.pbio.3002057
Cell Rep. 2023 Apr 13. pii: S2211-1247(23)00405-9. [Epub ahead of print]42(4): 112394

A plasma membrane-associated glycolytic metabolon is functionally coupled to KATP channels in pancreatic α and β cells from humans and mice.

Thuong Ho, Evgeniy Potapenko, Dawn B Davis, Matthew J Merrins.

  The ATP-sensitive K+ (KATP) channel is a key regulator of hormone secretion from pancreatic islet endocrine cells. Using direct measurements of KATP channel activity in pancreatic β cells and the lesser-studied α cells, from both humans and mice, we provide evidence that a glycolytic metabolon locally controls KATP channels on the plasma membrane. The two ATP-consuming enzymes of upper glycolysis, glucokinase and phosphofructokinase, generate ADP that activates KATP. Substrate channeling of fructose 1,6-bisphosphate through the enzymes of lower glycolysis fuels pyruvate kinase, which directly consumes the ADP made by phosphofructokinase to raise ATP/ADP and close the channel. We further show the presence of a plasma membrane-associated NAD+/NADH cycle whereby lactate dehydrogenase is functionally coupled to glyceraldehyde-3-phosphate dehydrogenase. These studies provide direct electrophysiological evidence of a KATP-controlling glycolytic signaling complex and demonstrate its relevance to islet glucose sensing and excitability.

Keywords:  CP: Metabolism; K(ATP) channel; glycolysis; glycolytic metabolon; inside-out excised patch clamp; metabolic compartmentation; pyruvate kinase

DOI:  https://doi.org/10.1016/j.celrep.2023.112394
Cell. 2023 Apr 05. pii: S0092-8674(23)00275-1. [Epub ahead of print]

Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease.

Zixi Wang, Shijia Zhu, Yuemeng Jia, Yunguan Wang, Naoto Kubota, Naoto Fujiwara, Ruth Gordillo, Cheryl Lewis, Min Zhu, Tripti Sharma, Lin Li, Qiyu Zeng, Yu-Hsuan Lin, Meng-Hsiung Hsieh, Purva Gopal, Tao Wang, Matt Hoare, Peter Campbell, Yujin Hoshida, Hao Zhu.

  Somatic mutations in nonmalignant tissues accumulate with age and injury, but whether these mutations are adaptive on the cellular or organismal levels is unclear. To interrogate genes in human metabolic disease, we performed lineage tracing in mice harboring somatic mosaicism subjected to nonalcoholic steatohepatitis (NASH). Proof-of-concept studies with mosaic loss of Mboat7, a membrane lipid acyltransferase, showed that increased steatosis accelerated clonal disappearance. Next, we induced pooled mosaicism in 63 known NASH genes, allowing us to trace mutant clones side by side. This in vivo tracing platform, which we coined MOSAICS, selected for mutations that ameliorate lipotoxicity, including mutant genes identified in human NASH. To prioritize new genes, additional screening of 472 candidates identified 23 somatic perturbations that promoted clonal expansion. In validation studies, liver-wide deletion of Tbx3, Bcl6, or Smyd2 resulted in protection against hepatic steatosis. Selection for clonal fitness in mouse and human livers identifies pathways that regulate metabolic disease.

Keywords:  Gpam; Mboat7; NAFLD; NASH; Smyd2; Tbx3; chronic liver disease; fatty liver disease; in vivo screening; somatic mosaicism

DOI:  https://doi.org/10.1016/j.cell.2023.03.014
Proc Natl Acad Sci U S A. 2023 Apr 18. 120(16): e2217665120

Evidence supporting the MICU1 occlusion mechanism and against the potentiation model in the mitochondrial calcium uniporter complex.

Chen-Wei Tsai, Tsung-Yun Liu, Fan-Yi Chao, Yung-Chi Tu, Madison X Rodriguez, Anna M Van Keuren, Zhiwei Ma, John Bankston, Ming-Feng Tsai.

  The mitochondrial calcium uniporter is a Ca2+ channel that imports cytoplasmic Ca2+ into the mitochondrial matrix to regulate cell bioenergetics, intracellular Ca2+ signaling, and apoptosis. The uniporter contains the pore-forming MCU subunit, an auxiliary EMRE protein, and the regulatory MICU1/MICU2 subunits. Structural and biochemical studies have suggested that MICU1 gates MCU by blocking/unblocking the pore. However, mitoplast patch-clamp experiments argue that MICU1 does not block, but instead potentiates MCU via allosteric mechanisms. Here, we address this direct clash of the proposed MICU1 function. Supporting the MICU1-occlusion mechanism, patch-clamp demonstrates that purified MICU1 strongly suppresses MCU Ca2+ currents, and this inhibition is abolished by mutating the MCU-interacting K126 residue. Moreover, a membrane-depolarization assay shows that MICU1 prevents MCU-mediated Na+ flux into intact mitochondria under Ca2+-free conditions. Examining the observations underlying the potentiation model, we found that MICU1 occlusion was not detected in mitoplasts not because MICU1 cannot block, but because MICU1 dissociates from the uniporter complex. Furthermore, MICU1 depletion reduces uniporter transport not because MICU1 can potentiate MCU, but because EMRE is down-regulated. These results firmly establish the molecular mechanisms underlying the physiologically crucial process of uniporter regulation by MICU1.

Keywords:  calcium channels; intracellular calcium signaling; mitochondrial physiology; organellar channels

DOI:  https://doi.org/10.1073/pnas.2217665120
Nat Commun. 2023 Apr 14. 14(1): 2123

IDH3γ functions as a redox switch regulating mitochondrial energy metabolism and contractility in the heart.

Maithily S Nanadikar, Ana M Vergel Leon, Jia Guo, Gijsbert J van Belle, Aline Jatho, Elvina S Philip, Astrid F Brandner, Rainer A Böckmann, Runzhu Shi, Anke Zieseniss, Carla M Siemssen, Katja Dettmer, Susanne Brodesser, Marlen Schmidtendorf, Jingyun Lee, Hanzhi Wu, Cristina M Furdui, Sören Brandenburg, Joseph R Burgoyne, Ivan Bogeski, Jan Riemer, Arpita Chowdhury, Peter Rehling, Tobias Bruegmann, Vsevolod V Belousov, Dörthe M Katschinski.

Redox signaling and cardiac function are tightly linked. However, it is largely unknown which protein targets are affected by hydrogen peroxide (H2O2) in cardiomyocytes that underly impaired inotropic effects during oxidative stress. Here, we combine a chemogenetic mouse model (HyPer-DAO mice) and a redox-proteomics approach to identify redox sensitive proteins. Using the HyPer-DAO mice, we demonstrate that increased endogenous production of H2O2 in cardiomyocytes leads to a reversible impairment of cardiac contractility in vivo. Notably, we identify the γ-subunit of the TCA cycle enzyme isocitrate dehydrogenase (IDH)3 as a redox switch, linking its modification to altered mitochondrial metabolism. Using microsecond molecular dynamics simulations and experiments using cysteine-gene-edited cells reveal that IDH3γ Cys148 and 284 are critically involved in the H2O2-dependent regulation of IDH3 activity. Our findings provide an unexpected mechanism by which mitochondrial metabolism can be modulated through redox signaling processes.

DOI: https://doi.org/10.1038/s41467-023-37744-x
Nat Commun. 2023 Apr 14. 14(1): 2132

Mannose metabolism inhibition sensitizes acute myeloid leukaemia cells to therapy by driving ferroptotic cell death.

Keith Woodley, Laura S Dillingh, George Giotopoulos, Pedro Madrigal, Kevin M Rattigan, Céline Philippe, Vilma Dembitz, Aoife M S Magee, Ryan Asby, Louie N van de Lagemaat, Christopher Mapperley, Sophie C James, Jochen H M Prehn, Konstantinos Tzelepis, Kevin Rouault-Pierre, George S Vassiliou, Kamil R Kranc, G Vignir Helgason, Brian J P Huntly, Paolo Gallipoli.

Resistance to standard and novel therapies remains the main obstacle to cure in acute myeloid leukaemia (AML) and is often driven by metabolic adaptations which are therapeutically actionable. Here we identify inhibition of mannose-6-phosphate isomerase (MPI), the first enzyme in the mannose metabolism pathway, as a sensitizer to both cytarabine and FLT3 inhibitors across multiple AML models. Mechanistically, we identify a connection between mannose metabolism and fatty acid metabolism, that is mediated via preferential activation of the ATF6 arm of the unfolded protein response (UPR). This in turn leads to cellular accumulation of polyunsaturated fatty acids, lipid peroxidation and ferroptotic cell death in AML cells. Our findings provide further support to the role of rewired metabolism in AML therapy resistance, unveil a connection between two apparently independent metabolic pathways and support further efforts to achieve eradication of therapy-resistant AML cells by sensitizing them to ferroptotic cell death.

DOI: https://doi.org/10.1038/s41467-023-37652-0
Nat Metab. 2023 Apr 13.

The anorectic and thermogenic effects of pharmacological lactate in male mice are confounded by treatment osmolarity and co-administered counterions.

Jens Lund, Alberte Wollesen Breum, Cláudia Gil, Sarah Falk, Frederike Sass, Marie Sophie Isidor, Oksana Dmytriyeva, Pablo Ranea-Robles, Cecilie Vad Mathiesen, Astrid Linde Basse, Olivia Sveidahl Johansen, Nicole Fadahunsi, Camilla Lund, Trine Sand Nicolaisen, Anders Bue Klein, Tao Ma, Brice Emanuelli, Maximilian Kleinert, Charlotte Mehlin Sørensen, Zachary Gerhart-Hines, Christoffer Clemmensen.

Lactate is a circulating metabolite and a signalling molecule with pleiotropic physiological effects. Studies suggest that lactate modulates energy balance by lowering food intake, inducing adipose browning and increasing whole-body thermogenesis. Yet, like many other metabolites, lactate is often commercially produced as a counterion-bound salt and typically administered in vivo through hypertonic aqueous solutions of sodium L-lactate. Most studies have not controlled for injection osmolarity and the co-injected sodium ions. Here, we show that the anorectic and thermogenic effects of exogenous sodium L-lactate in male mice are confounded by the hypertonicity of the injected solutions. Our data reveal that this is in contrast to the antiobesity effect of orally administered disodium succinate, which is uncoupled from these confounders. Further, our studies with other counterions indicate that counterions can have confounding effects beyond lactate pharmacology. Together, these findings underscore the importance of controlling for osmotic load and counterions in metabolite research.

DOI: https://doi.org/10.1038/s42255-023-00780-4
Cell Rep Med. 2023 Mar 31. pii: S2666-3791(23)00117-9. [Epub ahead of print] 101007

USP9X mediates an acute adaptive response to MAPK suppression in pancreatic cancer but creates multiple actionable therapeutic vulnerabilities.

Naiara Perurena, Rebecca Lock, Rachel A Davis, Srivatsan Raghavan, Natalie F Pilla, Raymond Ng, Patrick Loi, Caroline J Guild, Abigail L Miller, Ewa Sicinska, James M Cleary, Douglas A Rubinson, Brian M Wolpin, Nathanael S Gray, Sandro Santagata, William C Hahn, Jennifer P Morton, Owen J Sansom, Andrew J Aguirre, Karen Cichowski.

  Pancreatic ductal adenocarcinomas (PDACs) frequently harbor KRAS mutations. Although MEK inhibitors represent a plausible therapeutic option, most PDACs are innately resistant to these agents. Here, we identify a critical adaptive response that mediates resistance. Specifically, we show that MEK inhibitors upregulate the anti-apoptotic protein Mcl-1 by triggering an association with its deubiquitinase, USP9X, resulting in acute Mcl-1 stabilization and protection from apoptosis. Notably, these findings contrast the canonical positive regulation of Mcl-1 by RAS/ERK. We further show that Mcl-1 inhibitors and cyclin-dependent kinase (CDK) inhibitors, which suppress Mcl-1 transcription, prevent this protective response and induce tumor regression when combined with MEK inhibitors. Finally, we identify USP9X as an additional potential therapeutic target. Together, these studies (1) demonstrate that USP9X regulates a critical mechanism of resistance in PDAC, (2) reveal an unexpected mechanism of Mcl-1 regulation in response to RAS pathway suppression, and (3) provide multiple distinct promising therapeutic strategies for this deadly malignancy.

Keywords:  CDK inhibitors; KRAS; MEK inhibitors; Mcl-1; PDAC; USP9X; therapeutic resistance

DOI:  https://doi.org/10.1016/j.xcrm.2023.101007
bioRxiv. 2023 Mar 31. pii: 2023.03.31.535139. [Epub ahead of print]

An intermembrane space protein facilitates completion of mitochondrial division in yeast.

Olivia M Connor, Srujan K Matta, Jonathan R Friedman.

Mitochondria are highly dynamic double membrane-bound organelles that maintain their shape in part through fission and fusion. Mitochondrial fission is performed by the dynamin-related protein Dnm1 (Drp1 in humans), a large GTPase that constricts and divides the mitochondria in a GTP hydrolysis-dependent manner. However, it is unclear whether factors inside mitochondria help coordinate the process and if Dnm1/Drp1 activity alone is sufficient to complete fission of both mitochondrial membranes. Here, we identify an intermembrane space protein required for mitochondrial fission in yeast, which we propose to name Mdi1. Loss of Mdi1 leads to hyper-fused mitochondria networks due to defects in mitochondrial fission, but not lack of Dnm1 recruitment to mitochondria. Mdi1 plays a conserved role in fungal species and its homologs contain a putative amphipathic α-helix, mutations in which disrupt mitochondrial morphology. One model to explain these findings is that Mdi1 associates with and distorts the mitochondrial inner membrane to enable Dnm1 to robustly complete fission. Our work reveals that Dnm1 cannot efficiently divide mitochondria without the coordinated function of a protein that resides inside mitochondria.

DOI: https://doi.org/10.1101/2023.03.31.535139
J Clin Invest. 2023 Apr 13. pii: e165028. [Epub ahead of print]

Circulating succinate-modifying metabolites accurately classify and reflect the status of fumarate hydratase-deficient renal cell carcinoma.

Liang Zheng, Zi-Ran Zhu, Tal Sneh, Weituo Zhang, Zao-Yu Wang, Guang-Yu Wu, Wei He, Hong-Gang Qi, Hang Wang, Xiao-Yu Wu, Jonatan Fernández-García, Ifat Abramovich, Yun-Ze Xu, Jin Zhang, Eyal Gottlieb.

  Germline or somatic loss-of-function mutations of fumarate hydratase (FH) predispose patients to an aggressive form of renal cell carcinoma (RCC). Since other than tumor resection, there is no effective therapy for metastatic FH-deficient RCC, an accurate method for early diagnosis is needed. Although MRI or CT scans are offered, they cannot differentiate FH-deficient tumors from other RCCs. Therefore, finding noninvasive plasma biomarkers suitable for rapid diagnosis, screening and surveillance would improve clinical outcomes. Taking advantage of the robust metabolic rewiring that occurs in FH-deficient cells, we performed plasma metabolomics analysis and identified two tumor-derived metabolites, succinyl-adenosine and succinic-cysteine, as outstanding plasma biomarkers for early diagnosis (receiver operating characteristic area under curve (ROCAUC) = 0.98). These two molecules reliably reflected the FH mutation status and tumor mass. We further identified the enzymatic cooperativity by which these biomarkers are produced within the tumor microenvironment. Longitudinal monitoring of patients demonstrated that these circulating biomarkers can be used for reporting on treatment efficacy and identifying recurrent or metastatic tumors.

Keywords:  Cancer; Genetic diseases; Metabolism; Molecular diagnosis; Oncology

DOI:  https://doi.org/10.1172/JCI165028
Int J Mol Sci. 2023 Mar 29. pii: 6447. [Epub ahead of print]24(7):

Cancer Cell-Derived PDGFB Stimulates mTORC1 Activation in Renal Carcinoma.

Asmaa Y Abuhamad, Nurul Nadia Mohamad Zamberi, Sakari Vanharanta, Siti Nur Hasanah Mohd Yusuf, M Aiman Mohtar, Saiful Effendi Syafruddin.

  Clear cell renal cell carcinoma (ccRCC) is a hypervascular tumor that is characterized by bi-allelic inactivation of the VHL tumor suppressor gene and mTOR signalling pathway hyperactivation. The pro-angiogenic factor PDGFB, a transcriptional target of super enhancer-driven KLF6, can activate the mTORC1 signalling pathway in ccRCC. However, the detailed mechanisms of PDGFB-mediated mTORC1 activation in ccRCC have remained elusive. Here, we investigated whether ccRCC cells are able to secrete PDGFB into the extracellular milieu and stimulate mTORC1 signalling activity. We found that ccRCC cells secreted PDGFB extracellularly, and by utilizing KLF6- and PDGFB-engineered ccRCC cells, we showed that the level of PDGFB secretion was positively correlated with the expression of intracellular KLF6 and PDGFB. Moreover, the reintroduction of either KLF6 or PDGFB was able to sustain mTORC1 signalling activity in KLF6-targeted ccRCC cells. We further demonstrated that conditioned media of PDGFB-overexpressing ccRCC cells was able to re-activate mTORC1 activity in KLF6-targeted cells. In conclusion, cancer cell-derived PDGFB can mediate mTORC1 signalling pathway activation in ccRCC, further consolidating the link between the KLF6-PDGFB axis and the mTORC1 signalling pathway activity in ccRCC.

Keywords:  CRISPR/Cas9; KLF6; PDGFB; mTOR signalling pathway; renal cancer

DOI:  https://doi.org/10.3390/ijms24076447
iScience. 2023 Apr 21. 26(4): 106386

Tom40 in cholesterol transport.

Himangshu S Bose, Mahuya Bose, Randy M Whittal.

  Cholesterol initiates steroid metabolism in adrenal and gonadal mitochondria, which is essential for all mammalian survival. During stress an increased cholesterol transport rapidly increases steroidogenesis; however, the mechanism of mitochondrial cholesterol transport is unknown. Using rat testicular tissue and mouse Leydig (MA-10) cells, we report for the first time that mitochondrial translocase of outer mitochondrial membrane (OMM), Tom40, is central in cholesterol transport. Cytoplasmic cholesterol-lipids complex containing StAR protein move from the mitochondria-associated ER membrane (MAM) to the OMM, increasing cholesterol load. Tom40 interacts with StAR at the OMM increasing cholesterol transport into mitochondria. An absence of Tom40 disassembles complex formation and inhibits mitochondrial cholesterol transport and steroidogenesis. Therefore, Tom40 is essential for rapid mitochondrial cholesterol transport to initiate, maintain, and regulate activity.

Keywords:  Biomolecules; Cell biology; Protein folding

DOI:  https://doi.org/10.1016/j.isci.2023.106386
bioRxiv. 2023 Mar 29. pii: 2023.03.29.534670. [Epub ahead of print]

Metabolic regulation of misfolded protein import into mitochondria.

Yuhao Wang, Linhao Ruan, Jin Zhu, Xi Zhang, Alexander Chih-Chieh Chang, Alexis Tomaszewski, Rong Li.

Mitochondria are the cellular energy hub and central target of metabolic regulation. Mitochondria also facilitate proteostasis through pathways such as the 'mitochondria as guardian in cytosol' (MAGIC) whereby cytosolic misfolded proteins are imported into and degraded inside mitochondria. In this study, a genome-wide screen in yeast uncovered that Snf1, the yeast AMP-activated protein kinase (AMPK), inhibits the import of misfolded proteins into mitochondria while promoting mitochondrial biogenesis under glucose starvation. We show that this inhibition requires a downstream transcription factor regulating mitochondrial gene expression and is likely to be conferred through substrate competition and mitochondrial import channel selectivity. We further show that Snf1/AMPK activation protects mitochondrial fitness in yeast and human cells under stress induced by misfolded proteins such as those associated with neurodegenerative diseases.

DOI: https://doi.org/10.1101/2023.03.29.534670
Cell. 2023 Apr 13. pii: S0092-8674(23)00274-X. [Epub ahead of print]186(8): 1541-1563

Impact of risk factors on early cancer evolution.

Clare E Weeden, William Hill, Emilia L Lim, Eva Grönroos, Charles Swanton.

Recent identification of oncogenic cells within healthy tissues and the prevalence of indolent cancers found incidentally at autopsies reveal a greater complexity in tumor initiation than previously appreciated. The human body contains roughly 40 trillion cells of 200 different types that are organized within a complex three-dimensional matrix, necessitating exquisite mechanisms to restrain aberrant outgrowth of malignant cells that have the capacity to kill the host. Understanding how this defense is overcome to trigger tumorigenesis and why cancer is so extraordinarily rare at the cellular level is vital to future prevention therapies. In this review, we discuss how early initiated cells are protected from further tumorigenesis and the non-mutagenic pathways by which cancer risk factors promote tumor growth. By nature, the absence of permanent genomic alterations potentially renders these tumor-promoting mechanisms clinically targetable. Finally, we consider existing strategies for early cancer interception with perspectives on the next steps for molecular cancer prevention.

DOI: https://doi.org/10.1016/j.cell.2023.03.013
Nat Cell Biol. 2023 Apr;25(4): 592-603

Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2.

Haissi Cui, Jolene K Diedrich, Douglas C Wu, Justin J Lim, Ryan M Nottingham, James J Moresco, John R Yates, Benjamin J Blencowe, Alan M Lambowitz, Paul Schimmel.

Cells respond to perturbations such as inflammation by sensing changes in metabolite levels. Especially prominent is arginine, which has known connections to the inflammatory response. Aminoacyl-tRNA synthetases, enzymes that catalyse the first step of protein synthesis, can also mediate cell signalling. Here we show that depletion of arginine during inflammation decreased levels of nuclear-localized arginyl-tRNA synthetase (ArgRS). Surprisingly, we found that nuclear ArgRS interacts and co-localizes with serine/arginine repetitive matrix protein 2 (SRRM2), a spliceosomal and nuclear speckle protein, and that decreased levels of nuclear ArgRS correlated with changes in condensate-like nuclear trafficking of SRRM2 and splice-site usage in certain genes. These splice-site usage changes cumulated in the synthesis of different protein isoforms that altered cellular metabolism and peptide presentation to immune cells. Our findings uncover a mechanism whereby an aminoacyl-tRNA synthetase cognate to a key amino acid that is metabolically controlled during inflammation modulates the splicing machinery.

DOI: https://doi.org/10.1038/s41556-023-01118-8
Am J Cancer Res. 2023 ;13(3): 1067-1081

IRG1/Itaconate induces metabolic reprogramming to suppress ER-positive breast cancer cell growth.

Hsueh-Chun Wang, Wei-Chao Chang, Der-Yen Lee, Xing-Guo Li, Mien-Chie Hung.

Most breast cancers are estrogen receptor (ER)-positive, targeted by endocrine therapies, but chemoresistance remains a significant challenge in treating the disease. Altered intracellular metabolite has closely connected with the pathogenic process of breast cancer and drug resistance. Itaconate is an anti-inflammatory metabolite generated from converting cis-aconitate in the tricarboxylic acid (TCA) cycle by the immune response gene 1 (IRG1). However, the potential role of IRG1/Itaconate in the crosstalk of metabolic pathways and tumor development is currently unknown. We tested the hypothesis that IRG1/Itaconate controls metabolic homeostasis to modulate breast cancer cell growth. We showed that breast cancers harboring an IRG1 deletion displayed a worse prognosis than those without IRG1 deletion; approximately 70% of breast cancer with IRG1 deletion were ER-positive. There was no significant difference in the IRG1 copy number, mRNA, and protein levels between ER-positive and ER-negative breast cancer cell lines and breast tumors. Itaconate selectively inhibited ER-positive breast cancer cell growth via the blockade of DNA synthesis and the induction of apoptosis. Mechanistically, IRG1 overexpression led to decreased intermediate levels of glycolysis, the TCA cycle, and lipid metabolism to compromise the entire biomass and energy of the cell. Itaconate inhibited the enzymatic activity of succinate dehydrogenase (SDH) in the mitochondrial electron-transport chain, concomitant with reactive oxygen species (ROS) production and the decreased adenylate kinase (AK) activities, which, in turn, induced AMP-activated protein kinase (AMPK) activation to restore metabolic homeostasis. These results suggest a new regulatory pathway whereby IRG1/Itaconate controls metabolic homeostasis in ER-positive breast cancer cells, which may contribute to developing more efficacious therapeutic strategies for breast cancer.

Keywords: Breast cancer; estrogen receptor; immune response gene 1; itaconate; metabolic reprogramming; tricarboxylic acid cycle
Dev Cell. 2023 Apr 10. pii: S1534-5807(23)00098-9. [Epub ahead of print]58(7): 597-615.e10

Deregulation of ER-mitochondria contact formation and mitochondrial calcium homeostasis mediated by VDAC in fragile X syndrome.

Ji Geng, Tejinder Pal Khaket, Jie Pan, Wen Li, Yan Zhang, Yong Ping, Maria Inmaculada Cobos Sillero, Bingwei Lu.

  Loss of fragile X messenger ribonucleoprotein (FMRP) causes fragile X syndrome (FXS), the most prevalent form of inherited intellectual disability. Here, we show that FMRP interacts with the voltage-dependent anion channel (VDAC) to regulate the formation and function of endoplasmic reticulum (ER)-mitochondria contact sites (ERMCSs), structures that are critical for mitochondrial calcium (mito-Ca2+) homeostasis. FMRP-deficient cells feature excessive ERMCS formation and ER-to-mitochondria Ca2+ transfer. Genetic and pharmacological inhibition of VDAC or other ERMCS components restored synaptic structure, function, and plasticity and rescued locomotion and cognitive deficits of the Drosophila dFmr1 mutant. Expressing FMRP C-terminal domain (FMRP-C), which confers FMRP-VDAC interaction, rescued the ERMCS formation and mito-Ca2+ homeostasis defects in FXS patient iPSC-derived neurons and locomotion and cognitive deficits in Fmr1 knockout mice. These results identify altered ERMCS formation and mito-Ca2+ homeostasis as contributors to FXS and offer potential therapeutic targets.

Keywords:  ER-mitochondria contact site; ERMCS; FMRP; FXS; VDAC; fragile X messenger ribonucleoprotein; fragile X syndrome; mito-Ca(2+) homeostasis; mitochondrial calcium homeostasis; voltage-dependent anion channel

DOI:  https://doi.org/10.1016/j.devcel.2023.03.002
Elife. 2023 Apr 13. pii: e81717. [Epub ahead of print]12

PASK links cellular energy metabolism with a mitotic self-renewal network to establish differentiation competence.

Michael Xiao, Chia-Hua Wu, Graham Meek, Brian Kelly, Dara Buendia Castillo, Lyndsay E A Young, Sara Martire, Sajina Dhungel, Elizabeth McCauley, Purbita Saha, Altair L Dube, Matthew S Gentry, Laura A Banaszynski, Ramon C Sun, Chintan K Kikani.

  Quiescent stem cells are activated in response to a mechanical or chemical injury to their tissue niche. Activated cells rapidly generate a heterogeneous progenitor population that regenerates the damaged tissues. While the transcriptional cadence that generates heterogeneity is known, the metabolic pathways influencing the transcriptional machinery to establish a heterogeneous progenitor population remains unclear. Here, we describe a novel pathway downstream of mitochondrial glutamine metabolism that confers stem cell heterogeneity and establishes differentiation competence by countering post-mitotic self-renewal machinery. We discovered that mitochondrial glutamine metabolism induces CBP/EP300-dependent acetylation of stem cell-specific kinase, PASK, resulting in its release from cytoplasmic granules and subsequent nuclear migration. In the nucleus, PASK catalytically outcompetes mitotic WDR5-anaphase-promoting complex/cyclosome (APC/C) interaction resulting in the loss of post-mitotic Pax7 expression and exit from self-renewal. In concordance with these findings, genetic or pharmacological inhibition of PASK or glutamine metabolism upregulated Pax7 expression, reduced stem cell heterogeneity, and blocked myogenesis in vitro and muscle regeneration in mice. These results explain a mechanism whereby stem cells co-opt the proliferative functions of glutamine metabolism to generate transcriptional heterogeneity and establish differentiation competence by countering the mitotic self-renewal network via nuclear PASK.

Keywords:  cell biology; human; mouse

DOI:  https://doi.org/10.7554/eLife.81717
Cardiovasc Res. 2023 Apr 13. pii: cvad057. [Epub ahead of print]

The circadian protein BMAL1 supports endothelial cell cycle during angiogenesis.

Matteo Astone, Roxana E Oberkersch, Giovanni Tosi, Alberto Biscontin, Massimo M Santoro.

AIMS: The circadian clock is an internal biological timer that coordinates physiology and gene expression with the 24-hour solar day. Circadian clock perturbations have been associated to vascular dysfunctions in mammals and a function of the circadian clock in angiogenesis has been suggested. However, the functional role of the circadian clock in endothelial cells (EC) and in the regulation of angiogenesis is widely unexplored.
METHODS AND RESULTS: Here, we used both in vivo and in vitro approaches to demonstrate that EC possess an endogenous molecular clock and show robust circadian oscillations of core clock genes. By impairing the EC-specific function of the circadian clock transcriptional activator BMAL1 in vivo, we detect angiogenesis defects in mouse neonatal vascular tissues, as well as in adult tumor angiogenic settings. We then investigate the function of circadian clock machinery in cultured EC and show evidence that BMAL and CLOCK knock-down impair EC cell cycle progression. By using an RNA- and ChIP-seq genome-wide approaches we identified that BMAL1 binds the promoters of CCNA1 and CDK1 genes and controls their expression in EC.
CONCLUSIONS: Our findings show that EC display a robust circadian clock and that BMAL1 regulates EC physiology in both developmental and pathological contexts. Genetic alteration of BMAL1 can affect angiogenesis in in vivo and in vitro settings.
TRANSLATIONAL PERSPECTIVE: These findings support the need to explore the manipulation of the circadian clock in vascular diseases. Further investigation of the behavior of BMAL1 and its target genes in the tumor endothelium can aim to discover novel therapeutic interventions to interfere with the endothelial circadian clock in the tumor context.

DOI: https://doi.org/10.1093/cvr/cvad057
J Biol Chem. 2023 Apr 12. pii: S0021-9258(23)00343-5. [Epub ahead of print] 104701

Oxygen modulates iron homeostasis by switching iron-sensing of NCOA4.

Sota Kuno, Kazuhiro Iwai.

  To ensure proper utilization of iron and avoid its toxicity, cells are equipped with iron-sensing proteins to maintain cellular iron homeostasis. We showed previously that NCOA4, a ferritin-specific autophagy adapter, intricately regulates the fate of ferritin; upon binding to Fe3+, NCOA4 forms insoluble condensates and regulates ferritin autophagy in iron-replete conditions. Here, we demonstrate an additional iron-sensing mechanism of NCOA4. Our results indicate that the insertion of an Fe-S cluster enables preferential recognition of NCOA4 by the HERC2 ubiquitin ligase in iron-replete conditions, resulting in degradation by the proteasome and subsequent inhibition of ferritinophagy. We also found that both condensation and ubiquitin-mediated degradation of NCOA4 can occur in the same cell, and the cellular oxygen tension determines the selection of these pathways. Fe-S cluster-mediated degradation of NCOA4 is enhanced under hypoxia, whereas NCOA4 forms condensates and degrades ferritin at higher oxygen levels. Considering the involvement of iron in oxygen handling, our findings demonstrate that the NCOA4/ferritin axis is another layer of cellular iron regulation in response to oxygen levels.

Keywords:  autophagy; ferritin; hypoxia; iron metabolism; iron-sulfur protein

DOI:  https://doi.org/10.1016/j.jbc.2023.104701
Nature. 2023 Apr 12.

Extrachromosomal DNA appears before cancer forms.

David H Wang.



Keywords:  Cancer; Medical research

DOI:  https://doi.org/10.1038/d41586-023-00982-6
Cells. 2023 Apr 05. pii: 1089. [Epub ahead of print]12(7):

High-Throughput Microscopy Analysis of Mitochondrial Membrane Potential in 2D and 3D Models.

Caterina Vianello, Federica Dal Bello, Sang Hun Shin, Sara Schiavon, Camilla Bean, Ana Paula Magalhães Rebelo, Tomáš Knedlík, Emad Norouzi Esfahani, Veronica Costiniti, Rodrigo S Lacruz, Giuseppina Covello, Fabio Munari, Tommaso Scolaro, Antonella Viola, Elena Rampazzo, Luca Persano, Sara Zumerle, Luca Scorrano, Alessio Gianelle, Marta Giacomello.

  Recent proteomic, metabolomic, and transcriptomic studies have highlighted a connection between changes in mitochondria physiology and cellular pathophysiological mechanisms. Secondary assays to assess the function of these organelles appear fundamental to validate these -omics findings. Although mitochondrial membrane potential is widely recognized as an indicator of mitochondrial activity, high-content imaging-based approaches coupled to multiparametric to measure it have not been established yet. In this paper, we describe a methodology for the unbiased high-throughput quantification of mitochondrial membrane potential in vitro, which is suitable for 2D to 3D models. We successfully used our method to analyze mitochondrial membrane potential in monolayers of human fibroblasts, neural stem cells, spheroids, and isolated muscle fibers. Moreover, by combining automated image analysis and machine learning, we were able to discriminate melanoma cells from macrophages in co-culture and to analyze the subpopulations separately. Our data demonstrated that our method is a widely applicable strategy for large-scale profiling of mitochondrial activity.

Keywords:  NSCs; TMRM; co-culture; machine learning; mitochondrial membrane potential; single muscle fibers; spheroids

DOI:  https://doi.org/10.3390/cells12071089
J Cell Biol. 2023 Jun 05. pii: e202207049. [Epub ahead of print]222(6):

Mechanosensitive mTORC1 signaling maintains lymphatic valves.

Cansaran Saygili Demir, Amélie Sabine, Muyun Gong, Olivier Dormond, Tatiana V Petrova.

Homeostatic maintenance and repair of lymphatic vessels are essential for health. We investigated the dynamics and the molecular mechanisms of lymphatic endothelial cell (LEC) renewal in adult mesenteric quiescent lymphatic vasculature using label-retention, lineage tracing, and cell ablation strategies. Unlike during development, adult LEC turnover and proliferation was confined to the valve regions of collecting vessels, with valve cells displaying the shortest lifespan. Proliferating valve sinus LECs were the main source for maintenance and repair of lymphatic valves. We identified mechanistic target of rapamycin complex 1 (mTORC1) as a mechanoresponsive pathway activated by fluid shear stress in LECs. Depending on the shear stress level, mTORC1 activity drives division of valve cells or dictates their mechanic resilience through increased protein synthesis. Overactivation of lymphatic mTORC1 in vivo promoted supernumerary valve formation. Our work provides insights into the molecular mechanisms of maintenance of healthy lymphatic vascular system.

DOI: https://doi.org/10.1083/jcb.202207049
iScience. 2023 Apr 21. 26(4): 106425

Asparagine starvation suppresses histone demethylation through iron depletion.

Jie Jiang, Sankalp Srivastava, Sheng Liu, Gretchen Seim, Rodney Claude, Minghua Zhong, Sha Cao, Utpal Davé, Reuben Kapur, Amber L Mosley, Chi Zhang, Jun Wan, Jing Fan, Ji Zhang.

  Intracellular α-ketoglutarate is an indispensable substrate for the Jumonji family of histone demethylases (JHDMs) mediating most of the histone demethylation reactions. Since α-ketoglutarate is an intermediate of the tricarboxylic acid cycle and a product of transamination, its availability is governed by the metabolism of several amino acids. Here, we show that asparagine starvation suppresses global histone demethylation. This process is neither due to the change of expression of histone-modifying enzymes nor due to the change of intracellular levels of α-ketoglutarate. Rather, asparagine starvation reduces the intracellular pool of labile iron, a key co-factor for the JHDMs to function. Mechanistically, asparagine starvation suppresses the expression of the transferrin receptor to limit iron uptake. Furthermore, iron supplementation to the culture medium restores histone demethylation and alters gene expression to accelerate cell death upon asparagine depletion. These results suggest that suppressing iron-dependent histone demethylation is part of the cellular adaptive response to asparagine starvation.

Keywords:  Biological sciences; Epigenetics; Molecular biology; Molecular mechanism of gene regulation; Physiology

DOI:  https://doi.org/10.1016/j.isci.2023.106425
Sci Adv. 2023 Apr 14. 9(15): eadf1956

Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress.

Kazuya Nishio, Tomoyuki Kawarasaki, Yuki Sugiura, Shunsuke Matsumoto, Ayano Konoshima, Yuki Takano, Mayuko Hayashi, Fumihiko Okumura, Takumi Kamura, Tsunehiro Mizushima, Kunio Nakatsukasa.

Deficiencies in mitochondrial protein import are associated with a number of diseases. However, although nonimported mitochondrial proteins are at great risk of aggregation, it remains largely unclear how their accumulation causes cell dysfunction. Here, we show that nonimported citrate synthase is targeted for proteasomal degradation by the ubiquitin ligase SCFUcc1. Unexpectedly, our structural and genetic analyses revealed that nonimported citrate synthase appears to form an enzymatically active conformation in the cytosol. Its excess accumulation caused ectopic citrate synthesis, which, in turn, led to an imbalance in carbon flux of sugar, a reduction of the pool of amino acids and nucleotides, and a growth defect. Under these conditions, translation repression is induced and acts as a protective mechanism that mitigates the growth defect. We propose that the consequence of mitochondrial import failure is not limited to proteotoxic insults, but that the accumulation of a nonimported metabolic enzyme elicits ectopic metabolic stress.

DOI: https://doi.org/10.1126/sciadv.adf1956
Nat Rev Cancer. 2023 Apr 14.

Multiomics-guided cellular immunotherapies.

Mateusz Legut.

DOI: https://doi.org/10.1038/s41568-023-00570-w
Proc Natl Acad Sci U S A. 2023 Apr 18. 120(16): e2222084120

Tumor progression is independent of tumor-associated macrophages in cell lineage-based mouse models of glioblastoma.

Mollie E Chipman, Zilai Wang, Daochun Sun, Alicia M Pedraza, Tejus A Bale, Luis F Parada.

  Macrophage targeting therapies have had limited clinical success in glioblastoma (GBM). Further understanding the GBM immune microenvironment is critical for refining immunotherapeutic approaches. Here, we use genetically engineered mouse models and orthotopic transplantation-based GBM models with identical driver mutations and unique cells of origin to examine the role of tumor cell lineage in shaping the immune microenvironment and response to tumor-associated macrophage (TAM) depletion therapy. We show that oligodendrocyte progenitor cell lineage-associated GBMs (Type 2) recruit more immune infiltrates and specifically monocyte-derived macrophages than subventricular zone neural stem cell-associated GBMs (Type 1). We then devise a TAM depletion system that offers a uniquely robust and sustained TAM depletion. We find that extensive TAM depletion in these cell lineage-based GBM models affords no survival benefit. Despite the lack of survival benefit of TAM depletion, we show that Type 1 and Type 2 GBMs have unique molecular responses to TAM depletion. In sum, we demonstrate that GBM cell lineage influences TAM ontogeny and abundance and molecular response to TAM depletion.

Keywords:  CSF1R inhibition; cell of origin; glioblastoma; microglia; tumor-associated macrophages

DOI:  https://doi.org/10.1073/pnas.2222084120
Nat Biotechnol. 2023 Apr 10.

DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins.

Yu-Hang Xing, Rui Dong, Lukuo Lee, Shruthi Rengarajan, Nicolò Riggi, Gaylor Boulay, Miguel N Rivera.

Intrinsically disordered regions (IDRs) in DNA-associated proteins are known to influence gene regulation, but their distribution and cooperative functions in genome-wide regulatory programs remain poorly understood. Here we describe DisP-seq (disordered protein precipitation followed by DNA sequencing), an antibody-independent chemical precipitation assay that can simultaneously map endogenous DNA-associated disordered proteins genome-wide through a combination of biotinylated isoxazole precipitation and next-generation sequencing. DisP-seq profiles are composed of thousands of peaks that are associated with diverse chromatin states, are enriched for disordered transcription factors (TFs) and are often arranged in large lineage-specific clusters with high local concentrations of disordered proteins and different combinations of histone modifications linked to regulatory potential. We use DisP-seq to analyze cancer cells and reveal how disordered protein-associated islands enable IDR-dependent mechanisms that control the binding and function of disordered TFs, including oncogene-dependent sequestration of TFs through long-range interactions and the reactivation of differentiation pathways upon loss of oncogenic stimuli in Ewing sarcoma.

DOI: https://doi.org/10.1038/s41587-023-01737-4
Nature. 2023 Apr 12.

Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus.

Jens Luebeck, Alvin Wei Tian Ng, Patricia C Galipeau, Xiaohong Li, Carissa A Sanchez, Annalise C Katz-Summercorn, Hoon Kim, Sriganesh Jammula, Yudou He, Scott M Lippman, Roel G W Verhaak, Carlo C Maley, Ludmil B Alexandrov, Brian J Reid, Rebecca C Fitzgerald, Thomas G Paulson, Howard Y Chang, Sihan Wu, Vineet Bafna, Paul S Mischel.

Oncogene amplification on extrachromosomal DNA (ecDNA) drives the evolution of tumours and their resistance to treatment, and is associated with poor outcomes for patients with cancer1-6. At present, it is unclear whether ecDNA is a later manifestation of genomic instability, or whether it can be an early event in the transition from dysplasia to cancer. Here, to better understand the development of ecDNA, we analysed whole-genome sequencing (WGS) data from patients with oesophageal ademocarcinoma (EAC) or Barrett's oesophagus. These data included 206 biopsies in Barrett's oesophagus surveillance and EAC cohorts from Cambridge University. We also analysed WGS and histology data from biopsies that were collected across multiple regions at 2 time points from 80 patients in a case-control study at the Fred Hutchinson Cancer Center. In the Cambridge cohorts, the frequency of ecDNA increased between Barrett's-oesophagus-associated early-stage (24%) and late-stage (43%) EAC, suggesting that ecDNA is formed during cancer progression. In the cohort from the Fred Hutchinson Cancer Center, 33% of patients who developed EAC had at least one oesophageal biopsy with ecDNA before or at the diagnosis of EAC. In biopsies that were collected before cancer diagnosis, higher levels of ecDNA were present in samples from patients who later developed EAC than in samples from those who did not. We found that ecDNAs contained diverse collections of oncogenes and immunomodulatory genes. Furthermore, ecDNAs showed increases in copy number and structural complexity at more advanced stages of disease. Our findings show that ecDNA can develop early in the transition from high-grade dysplasia to cancer, and that ecDNAs progressively form and evolve under positive selection.

DOI: https://doi.org/10.1038/s41586-023-05937-5
Nature. 2023 Apr 12.

Molecular portraits of lung cancer evolution.

Tikvah K Hayes, Matthew Meyerson.



Keywords:  Cancer; Medical research

DOI:  https://doi.org/10.1038/d41586-023-00934-0
Nature. 2023 Apr 12.

Ageing-associated changes in transcriptional elongation influence longevity.

Cédric Debès, Antonios Papadakis, Sebastian Grönke, Özlem Karalay, Luke S Tain, Athanasia Mizi, Shuhei Nakamura, Oliver Hahn, Carina Weigelt, Natasa Josipovic, Anne Zirkel, Isabell Brusius, Konstantinos Sofiadis, Mantha Lamprousi, Yu-Xuan Lu, Wenming Huang, Reza Esmaillie, Torsten Kubacki, Martin R Späth, Bernhard Schermer, Thomas Benzing, Roman-Ulrich Müller, Adam Antebi, Linda Partridge, Argyris Papantonis, Andreas Beyer.

Physiological homeostasis becomes compromised during ageing, as a result of impairment of cellular processes, including transcription and RNA splicing1-4. However, the molecular mechanisms leading to the loss of transcriptional fidelity are so far elusive, as are ways of preventing it. Here we profiled and analysed genome-wide, ageing-related changes in transcriptional processes across different organisms: nematodes, fruitflies, mice, rats and humans. The average transcriptional elongation speed (RNA polymerase II speed) increased with age in all five species. Along with these changes in elongation speed, we observed changes in splicing, including a reduction of unspliced transcripts and the formation of more circular RNAs. Two lifespan-extending interventions, dietary restriction and lowered insulin-IGF signalling, both reversed most of these ageing-related changes. Genetic variants in RNA polymerase II that reduced its speed in worms5 and flies6 increased their lifespan. Similarly, reducing the speed of RNA polymerase II by overexpressing histone components, to counter age-associated changes in nucleosome positioning, also extended lifespan in flies and the division potential of human cells. Our findings uncover fundamental molecular mechanisms underlying animal ageing and lifespan-extending interventions, and point to possible preventive measures.

DOI: https://doi.org/10.1038/s41586-023-05922-y
J Biol Chem. 2023 Apr 10. pii: S0021-9258(23)00337-X. [Epub ahead of print] 104695

NOX4-TIM23 interaction regulates NOX4 mitochondrial import and metabolic reprogramming.

Jyotsana Pandey, Jennifer L Larson-Casey, Mallikarjun H Patil, Rutwij Joshi, Chun-Sun Jiang, Yong Zhou, Chao He, A Brent Carter.

Pulmonary fibrosis is a progressive lung disease characterized by macrophage activation. Asbestos-induced expression of NADPH oxidase 4 (NOX4) in lung macrophages mediates fibrotic progression by the generation of mitochondrial ROS, modulating mitochondrial biogenesis, and promoting apoptosis resistance; however, the mechanism(s) by which NOX4 localizes to mitochondria during fibrosis is not known. Here we show that NOX4 localized to the mitochondrial matrix following asbestos exposure in lung macrophages by a direct interaction with TIM23. TIM23 and NOX4 interaction was found in lung macrophages from human subjects with asbestosis, while it was absent in mice harboring a conditional deletion of NOX4 in lung macrophages. This interaction was localized to the proximal transmembrane region of NOX4. Mechanistically, TIM23 augmented NOX4-induced mitochondrial ROS and metabolic reprogramming to oxidative phosphorylation (OXPHOS). Silencing TIM23 decreased mitochondrial ROS and OXPHOS. These observations highlight the important role of the mitochondrial translocase TIM23 interaction with NOX4. Moreover, this interaction is required for mitochondrial redox signaling and metabolic reprogramming in lung macrophages.

DOI: https://doi.org/10.1016/j.jbc.2023.104695
Cell. 2023 Apr 13. pii: S0092-8674(23)00272-6. [Epub ahead of print]186(8): 1532-1534

The intratumoral microbiota: From microniches to single cells.

Susan Bullman.

Solid tumors are composed of a complex and dynamic collection of cell types. Here I discuss the important relationships between cancer cells and bacterial members of the intratumoral microbiota that may provide a fitness advantage within the tumor ecological niche.

DOI: https://doi.org/10.1016/j.cell.2023.03.012
Cell. 2023 Apr 13. pii: S0092-8674(23)00221-0. [Epub ahead of print]186(8): 1564-1579

Metastasis.

Stefanie Gerstberger, Qingwen Jiang, Karuna Ganesh.

Most cancer-associated deaths occur due to metastasis, yet our understanding of metastasis as an evolving, heterogeneous, systemic disease and of how to effectively treat it is still emerging. Metastasis requires the acquisition of a succession of traits to disseminate, variably enter and exit dormancy, and colonize distant organs. The success of these events is driven by clonal selection, the potential of metastatic cells to dynamically transition into distinct states, and their ability to co-opt the immune environment. Here, we review the main principles of metastasis and highlight emerging opportunities to develop more effective therapies for metastatic cancer.

DOI: https://doi.org/10.1016/j.cell.2023.03.003
Trends Cancer. 2023 Apr 12. pii: S2405-8033(23)00031-6. [Epub ahead of print]

Insights into the metastatic cascade through research autopsies.

Sonya Hessey, Petros Fessas, Simone Zaccaria, Mariam Jamal-Hanjani, Charles Swanton.

  Metastasis is a complex process and the leading cause of cancer-related death globally. Recent studies have demonstrated that genomic sequencing data from paired primary and metastatic tumours can be used to trace the evolutionary origins of cells responsible for metastasis. This approach has yielded new insights into the genomic alterations that engender metastatic potential, and the mechanisms by which cancer spreads. Given that the reliability of these approaches is contingent upon how representative the samples are of primary and metastatic tumour heterogeneity, we review insights from studies that have reconstructed the evolution of metastasis within the context of their cohorts and designs. We discuss the role of research autopsies in achieving the comprehensive sampling necessary to advance the current understanding of metastasis.

Keywords:  genomic sequencing; metastasis; research autopsy; tumour evolution

DOI:  https://doi.org/10.1016/j.trecan.2023.03.002
Nat Methods. 2023 Apr 10.

Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape.

Jingyi Ren, Haowen Zhou, Hu Zeng, Connie Kangni Wang, Jiahao Huang, Xiaojie Qiu, Xin Sui, Qiang Li, Xunwei Wu, Zuwan Lin, Jennifer A Lo, Kamal Maher, Yichun He, Xin Tang, Judson Lam, Hongyu Chen, Brian Li, David E Fisher, Jia Liu, Xiao Wang.

Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and cellular function. However, the intricate subcellular dynamics of RNA remain obscured due to the limitations of existing transcriptomics methods. Here, we report TEMPOmap-a method that uncovers subcellular RNA profiles across time and space at the single-cell level. TEMPOmap integrates pulse-chase metabolic labeling with highly multiplexed three-dimensional in situ sequencing to simultaneously profile the age and location of individual RNA molecules. Using TEMPOmap, we constructed the subcellular RNA kinetic landscape in various human cells from transcription and translocation to degradation. Clustering analysis of RNA kinetic parameters across single cells revealed 'kinetic gene clusters' whose expression patterns were shaped by multistep kinetic sculpting. Importantly, these kinetic gene clusters are functionally segregated, suggesting that subcellular RNA kinetics are differentially regulated in a cell-state- and cell-type-dependent manner. Spatiotemporally resolved transcriptomics provides a gateway to uncovering new spatiotemporal gene regulation principles.

DOI: https://doi.org/10.1038/s41592-023-01829-8
EMBO J. 2023 Apr 13. e114050

Epigenetic escape of immunosurveillance by malignant cell precursors.

Claudia Galassi, Lorenzo Galluzzi.

  Newly formed malignant cells must escape immunosurveillance to generate progressing neoplastic lesions of clinical relevance. Recent data indicate that the immunogenicity of nascent cancer cells, at least in some settings, is dictated by inherent epigenetic mechanisms rather than by immunoediting and the consequent Darwinian selection of poorly immunogenic phenotypes.

Keywords:  CSDE1; SMYD3; STAT1; cancer stem cells; immunotherapy; intratumoral heterogeneity

DOI:  https://doi.org/10.15252/embj.2023114050
Cell. 2023 Apr 13. pii: S0092-8674(23)00142-3. [Epub ahead of print]186(8): 1729-1754

Pancreatic cancer: Advances and challenges.

Christopher J Halbrook, Costas A Lyssiotis, Marina Pasca di Magliano, Anirban Maitra.

Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers. Significant efforts have largely defined major genetic factors driving PDAC pathogenesis and progression. Pancreatic tumors are characterized by a complex microenvironment that orchestrates metabolic alterations and supports a milieu of interactions among various cell types within this niche. In this review, we highlight the foundational studies that have driven our understanding of these processes. We further discuss the recent technological advances that continue to expand our understanding of PDAC complexity. We posit that the clinical translation of these research endeavors will enhance the currently dismal survival rate of this recalcitrant disease.

DOI: https://doi.org/10.1016/j.cell.2023.02.014
Sci Signal. 2023 Apr 11. 16(780): eadi1372

Metastatic dormancy needs STING.

Amy E Baek.

STING activity in cancer cells prevents the progression of dormant metastasis.

DOI: https://doi.org/10.1126/scisignal.adi1372
Curr Biol. 2023 04 10. pii: S0960-9822(23)00297-X. [Epub ahead of print]33(7): R269-R272

Ferroptosis: Under pressure!

Adam Wahida, Marcus Conrad.

Ferroptosis is a disease-relevant and pervasive form of cell death triggered by iron-dependent lipid peroxidation and resulting in membrane rupture. A new study addresses how tension-sensing channels can balance and modulate membrane tension in the context of ferroptotic cell death.

DOI: https://doi.org/10.1016/j.cub.2023.03.009
Nat Aging. 2022 Jun;2(6): 484-493

The relationship between epigenetic age and the hallmarks of aging in human cells.

Sylwia Kabacik, Donna Lowe, Leonie Fransen, Martin Leonard, Siew-Lan Ang, Christopher Whiteman, Sarah Corsi, Howard Cohen, Sarah Felton, Radhika Bali, Steve Horvath, Ken Raj.

Epigenetic clocks are mathematically derived age estimators that are based on combinations of methylation values that change with age at specific CpGs in the genome. These clocks are widely used to measure the age of tissues and cells1,2. The discrepancy between epigenetic age (EpiAge), as estimated by these clocks, and chronological age is referred to as EpiAge acceleration. Epidemiological studies have linked EpiAge acceleration to a wide variety of pathologies, health states, lifestyle, mental state and environmental factors2, indicating that epigenetic clocks tap into critical biological processes that are involved in aging. Despite the importance of this inference, the mechanisms underpinning these clocks remained largely uncharacterized and unelucidated. Here, using primary human cells, we set out to investigate whether epigenetic aging is the manifestation of one or more of the aging hallmarks previously identified3. We show that although epigenetic aging is distinct from cellular senescence, telomere attrition and genomic instability, it is associated with nutrient sensing, mitochondrial activity and stem cell composition.

DOI: https://doi.org/10.1038/s43587-022-00220-0
Cell. 2023 Apr 13. pii: S0092-8674(23)00143-5. [Epub ahead of print]186(8): 1755-1771

Accelerating the understanding of cancer biology through the lens of genomics.

Dongfang Wang, Baolin Liu, Zemin Zhang.

A core mission of cancer genomics is to comprehensively chart molecular underpinnings of cancer-driving events and to provide personalized therapeutic strategies. Primarily focused on cancer cells, cancer genomics studies have successfully uncovered many drivers for major cancer types. Since the emergence of cancer immune evasion as a critical cancer hallmark, the paradigm has been elevated to the holistic tumor ecosystem, with distinct cellular components and their functional states elucidated. We highlight the milestones of cancer genomics, depict the evolving path of the field, and discuss future directions in completing the understanding of the tumor ecosystem and in advancing therapeutic strategies.

DOI: https://doi.org/10.1016/j.cell.2023.02.015
Nature. 2023 Apr 12.

Antibodies against endogenous retroviruses promote lung cancer immunotherapy.

TRACERx Consortium

B cells are frequently found in the margins of solid tumours as organized follicles in ectopic lymphoid organs called tertiary lymphoid structures (TLS)1,2. Although TLS have been found to correlate with improved patient survival and response to immune checkpoint blockade (ICB), the underlying mechanisms of this association remain elusive1,2. Here we investigate lung-resident B cell responses in patients from the TRACERx 421 (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy) and other lung cancer cohorts, and in a recently established immunogenic mouse model for lung adenocarcinoma3. We find that both human and mouse lung adenocarcinomas elicit local germinal centre responses and tumour-binding antibodies, and further identify endogenous retrovirus (ERV) envelope glycoproteins as a dominant anti-tumour antibody target. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted inhibition of KRAS(G12C) in the mouse model. ERV-reactive antibodies exert anti-tumour activity that extends survival in the mouse model, and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Finally, we find that effective immunotherapy in the mouse model requires CXCL13-dependent TLS formation. Conversely, therapeutic CXCL13 treatment potentiates anti-tumour immunity and synergizes with ICB. Our findings provide a possible mechanistic basis for the association of TLS with immunotherapy response.

DOI: https://doi.org/10.1038/s41586-023-05771-9
Nature. 2023 Apr 12.

Genomic-transcriptomic evolution in lung cancer and metastasis.

TRACERx Consortium

Intratumour heterogeneity (ITH) fuels lung cancer evolution, which leads to immune evasion and resistance to therapy1. Here, using paired whole-exome and RNA sequencing data, we investigate intratumour transcriptomic diversity in 354 non-small cell lung cancer tumours from 347 out of the first 421 patients prospectively recruited into the TRACERx study2,3. Analyses of 947 tumour regions, representing both primary and metastatic disease, alongside 96 tumour-adjacent normal tissue samples implicate the transcriptome as a major source of phenotypic variation. Gene expression levels and ITH relate to patterns of positive and negative selection during tumour evolution. We observe frequent copy number-independent allele-specific expression that is linked to epigenomic dysfunction. Allele-specific expression can also result in genomic-transcriptomic parallel evolution, which converges on cancer gene disruption. We extract signatures of RNA single-base substitutions and link their aetiology to the activity of the RNA-editing enzymes ADAR and APOBEC3A, thereby revealing otherwise undetected ongoing APOBEC activity in tumours. Characterizing the transcriptomes of primary-metastatic tumour pairs, we combine multiple machine-learning approaches that leverage genomic and transcriptomic variables to link metastasis-seeding potential to the evolutionary context of mutations and increased proliferation within primary tumour regions. These results highlight the interplay between the genome and transcriptome in influencing ITH, lung cancer evolution and metastasis.

DOI: https://doi.org/10.1038/s41586-023-05706-4
Nature. 2023 Apr 12.

The evolution of lung cancer and impact of subclonal selection in TRACERx.

TRACERx Consortium

Lung cancer is the leading cause of cancer-associated mortality worldwide1. Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource.

DOI: https://doi.org/10.1038/s41586-023-05783-5