bims-camemi 2023-07-23 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2023–07–23
forty-one papers selected by
Christian Frezza, Universität zu Köln

Liver mitochondrial cristae organizing protein MIC19 promotes energy expenditure and pedestrian locomotion by altering nucleotide metabolism.
How nearby nutrients shape tumor growth.
NDUFS4 Regulates Cristae Remodeling in Diabetic Kidney Disease.
Identity, structure, and function of the mitochondrial permeability transition pore: controversies, consensus, recent advances, and future directions.
FDX1 regulates cellular protein lipoylation through direct binding to LIAS.
Microbial metabolism and the power of the small.
ATFS-1 counteracts mitochondrial DNA damage by promoting repair over transcription.
p53 restoration in small cell lung cancer identifies a latent cyclophilin-dependent necrosis mechanism.
QUAS-R: An SLC1A5-mediated glutamine uptake assay with single-cell resolution reveals metabolic heterogeneity with immune populations.
Perivascular niches: critical hubs in cancer evolution.
Inhibition of RNA Degradation Integrates the Metabolic Signals Induced by Osmotic Stress into the Arabidopsis Circadian System.
Experimental evolution of metabolism under nutrient restriction: enhanced amino acid catabolism and a key role of branched-chain amino acids.
Targeting an allosteric site in dynamin-related protein 1 to inhibit Fis1-mediated mitochondrial dysfunction.
Fatty acid oxidation organizes mitochondrial supercomplexes to sustain astrocytic ROS and cognition.
S-Nitrosylation-mediated dysfunction of TCA cycle enzymes in synucleinopathy studied in postmortem human brains and hiPSC-derived neurons.
H3K36 methylation maintains cell identity by regulating opposing lineage programmes.
Regulation of VKORC1L1 is critical for p53-mediated tumor suppression through vitamin K metabolism.
Histone methyltransferase NSD2 activates PKCα to drive metabolic reprogramming and lenalidomide resistance in multiple myeloma.
Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma.
Mitochondria during T cell aging.
Parkin regulates amino acid homeostasis at mitochondria-lysosome (M/L) contact sites in Parkinson's disease.
Hydroxyproline metabolism enhances IFN-γ-induced PD-L1 expression and inhibits autophagic flux.
Therapeutic Targeting of Mitochondrial Plasticity and Redox Control to Overcome Cancer Chemoresistance.
F-ATP synthase inhibitory factor 1 regulates metabolic reprogramming involving its interaction with c-Myc and PGC1α.
The role of hydrogen sulfide in the retina.
Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma.
Activation of transsulfuration pathway to maintain cysteine is a thermogenic checkpoint for the conservation of energy.
Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells.
An atlas of healthy and injured cell states and niches in the human kidney.
ATR protects ongoing and newly assembled DNA replication forks through distinct mechanisms.
Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics.
Metabolic clogging of mannose triggers dNTP loss and genomic instability in human cancer cells.
The human placenta exhibits a unique transcriptomic void.
Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B12 delivery and repair.
Adipose tissue and skeletal muscle wasting precede clinical diagnosis of pancreatic cancer.
Mitofissin: a novel mitochondrial fission protein that facilitates mitophagy.
Tumors produce glucocorticoids by metabolite recycling, not synthesis, and activate Tregs to promote growth.
Proteogenomics of clear cell renal cell carcinoma response to tyrosine kinase inhibitor.
Lysosomal enzyme trafficking: from molecular mechanisms to human diseases.
Nuclear translocation of mitochondrial dehydrogenases as an adaptive cardioprotective mechanism.
Fatty acid desaturase 2 determines the lipidomic landscape and steroidogenic function of the adrenal gland.

Cell Metab. 2023 Jul 14. pii: S1550-4131(23)00225-5. [Epub ahead of print]

Liver mitochondrial cristae organizing protein MIC19 promotes energy expenditure and pedestrian locomotion by altering nucleotide metabolism.

Jee Hyung Sohn, Beste Mutlu, Pedro Latorre-Muro, Jiaxin Liang, Christopher F Bennett, Kfir Sharabi, Noa Kantorovich, Mark Jedrychowski, Steven P Gygi, Alexander S Banks, Pere Puigserver.

  Liver mitochondria undergo architectural remodeling that maintains energy homeostasis in response to feeding and fasting. However, the specific components and molecular mechanisms driving these changes and their impact on energy metabolism remain unclear. Through comparative mouse proteomics, we found that fasting induces strain-specific mitochondrial cristae formation in the liver by upregulating MIC19, a subunit of the MICOS complex. Enforced MIC19 expression in the liver promotes cristae formation, mitochondrial respiration, and fatty acid oxidation while suppressing gluconeogenesis. Mice overexpressing hepatic MIC19 show resistance to diet-induced obesity and improved glucose homeostasis. Interestingly, MIC19 overexpressing mice exhibit elevated energy expenditure and increased pedestrian locomotion. Metabolite profiling revealed that uracil accumulates in the livers of these mice due to increased uridine phosphorylase UPP2 activity. Furthermore, uracil-supplemented diet increases locomotion in wild-type mice. Thus, MIC19-induced mitochondrial cristae formation in the liver increases uracil as a signal to promote locomotion, with protective effects against diet-induced obesity.

Keywords:  brisk walking; diabetes; fatty liver; mitochondrial cristae; obesity; uracil

DOI:  https://doi.org/10.1016/j.cmet.2023.06.015
Elife. 2023 07 17. pii: e89825. [Epub ahead of print]12

How nearby nutrients shape tumor growth.

Nada Kalaany.

  Studying the nutrient composition immediately surrounding pancreatic cancer cells provides new insights into their metabolic properties and how they can evade the immune system to promote disease progression.

Keywords:  amino acid homeostasis; biochemistry; cancer; cancer biology; chemical biology; human; immunotherapy; metabolism; mouse; nutrient stress; tumor microenvironment

DOI:  https://doi.org/10.7554/eLife.89825
Res Sq. 2023 Jun 30. pii: rs.3.rs-3070079. [Epub ahead of print]

NDUFS4 Regulates Cristae Remodeling in Diabetic Kidney Disease.

Farhad Danesh, Koki Mise, Jianyin Long, Daniel Galvan, Zengchun Ye, Guizhen Fan, Irina Serysheva, Travis Moore, Jun Wada, Paul Schumacker, Benny Chang.

The mitochondrial electron transport chain (ETC) is a highly adaptive process to meet metabolic demands of the cell, and its dysregulation has been associated with diverse clinical pathologies. However, the role and nature of impaired ETC in kidney diseases remains poorly understood. Here, we generated diabetic mice with podocyte-specific overexpression of Ndufs4, an accessory subunit of mitochondrial complex I, as a model to investigate the role of ETC integrity in diabetic kidney disease (DKD). We find that these conditional mice exhibit significant improvements in cristae morphology, mitochondrial dynamics, and albuminuria. By coupling proximity labeling with super-resolution imaging, we also identify the role of cristae shaping proteins in linking NDUFS4 with improved cristae morphology. Taken together, we discover the central role of NDUFS4 as a powerful regulator of cristae remodeling, respiratory supercomplexes assembly, and mitochondrial ultrastructure in vitro and in vivo . We propose that targeting NDUFS4 represents a promising approach to slow the progression of DKD.

DOI: https://doi.org/10.21203/rs.3.rs-3070079/v1
Cell Death Differ. 2023 Jul 17.

Identity, structure, and function of the mitochondrial permeability transition pore: controversies, consensus, recent advances, and future directions.

Paolo Bernardi, Christoph Gerle, Andrew P Halestrap, Elizabeth A Jonas, Jason Karch, Nelli Mnatsakanyan, Evgeny Pavlov, Shey-Shing Sheu, Alexander A Soukas.

The mitochondrial permeability transition (mPT) describes a Ca2+-dependent and cyclophilin D (CypD)-facilitated increase of inner mitochondrial membrane permeability that allows diffusion of molecules up to 1.5 kDa in size. It is mediated by a non-selective channel, the mitochondrial permeability transition pore (mPTP). Sustained mPTP opening causes mitochondrial swelling, which ruptures the outer mitochondrial membrane leading to subsequent apoptotic and necrotic cell death, and is implicated in a range of pathologies. However, transient mPTP opening at various sub-conductance states may contribute several physiological roles such as alterations in mitochondrial bioenergetics and rapid Ca2+ efflux. Since its discovery decades ago, intensive efforts have been made to identify the exact pore-forming structure of the mPT. Both the adenine nucleotide translocase (ANT) and, more recently, the mitochondrial F1FO (F)-ATP synthase dimers, monomers or c-subunit ring alone have been implicated. Here we share the insights of several key investigators with different perspectives who have pioneered mPT research. We critically assess proposed models for the molecular identity of the mPTP and the mechanisms underlying its opposing roles in the life and death of cells. We provide in-depth insights into current controversies, seeking to achieve a degree of consensus that will stimulate future innovative research into the nature and role of the mPTP.

DOI: https://doi.org/10.1038/s41418-023-01187-0
J Biol Chem. 2023 Jul 13. pii: S0021-9258(23)02074-4. [Epub ahead of print] 105046

FDX1 regulates cellular protein lipoylation through direct binding to LIAS.

Margaret B Dreishpoon, Nolan R Bick, Boryana Petrova, Douglas M Warui, Alison Cameron, Squire J Booker, Naama Kanarek, Todd R Golub, Peter Tsvetkov.

Ferredoxins are a family of iron-sulfur (Fe-S) cluster proteins that serve as essential electron donors in numerous cellular processes that are conserved through evolution. The promiscuous nature of ferredoxins as electron donors enables them to participate in many metabolic processes including steroid, heme, vitamin D and Fe-S cluster biosynthesis in different organisms. However, the unique natural function(s) of each of the two human ferredoxins (FDX1 and FDX2) are still poorly characterized. We recently reported that FDX1 is both a crucial regulator of copper ionophore induced cell death and serves as an upstream regulator of cellular protein lipoylation, a mitochondrial lipid-based post translational modification naturally occurring on four mitochondrial enzymes that are crucial for TCA cycle function. Here we show that FDX1 directly regulates protein lipoylation by binding the lipoyl synthase (LIAS) enzyme promoting its functional binding to the lipoyl carrier protein GCSH and not through indirect regulation of cellular Fe-S cluster biosynthesis. Metabolite profiling revealed that the predominant cellular metabolic outcome of FDX1 loss-of-function is manifested through the regulation of the four lipoylation-dependent enzymes ultimately resulting in loss of cellular respiration and sensitivity to mild glucose starvation. Transcriptional profiling established that FDX1 loss-of-function results in the induction of both compensatory metabolism related genes and the integrated stress response, consistent with our findings that FDX1 loss-of-function is conditionally lethal. Together, our findings establish that FDX1 directly engages with LIAS, promoting its role in cellular protein lipoylation, a process essential in maintaining cell viability under low glucose conditions.

DOI: https://doi.org/10.1016/j.jbc.2023.105046
Nat Metab. 2023 Jul 19.

Microbial metabolism and the power of the small.

DOI: https://doi.org/10.1038/s42255-023-00860-5
Nat Cell Biol. 2023 Jul 17.

ATFS-1 counteracts mitochondrial DNA damage by promoting repair over transcription.

Chuan-Yang Dai, Chai Chee Ng, Grace Ching Ching Hung, Ina Kirmes, Laetitia A Hughes, Yunguang Du, Christopher A Brosnan, Arnaud Ahier, Anne Hahn, Cole M Haynes, Oliver Rackham, Aleksandra Filipovska, Steven Zuryn.

The ability to balance conflicting functional demands is critical for ensuring organismal survival. The transcription and repair of the mitochondrial genome (mtDNA) requires separate enzymatic activities that can sterically compete1, suggesting a life-long trade-off between these two processes. Here in Caenorhabditis elegans, we find that the bZIP transcription factor ATFS-1/Atf5 (refs. 2,3) regulates this balance in favour of mtDNA repair by localizing to mitochondria and interfering with the assembly of the mitochondrial pre-initiation transcription complex between HMG-5/TFAM and RPOM-1/mtRNAP. ATFS-1-mediated transcriptional inhibition decreases age-dependent mtDNA molecular damage through the DNA glycosylase NTH-1/NTH1, as well as the helicase TWNK-1/TWNK, resulting in an enhancement in the functional longevity of cells and protection against decline in animal behaviour caused by targeted and severe mtDNA damage. Together, our findings reveal that ATFS-1 acts as a molecular focal point for the control of balance between genome expression and maintenance in the mitochondria.

DOI: https://doi.org/10.1038/s41556-023-01192-y
Nat Commun. 2023 Jul 21. 14(1): 4403

p53 restoration in small cell lung cancer identifies a latent cyclophilin-dependent necrosis mechanism.

Jonuelle Acosta, Qinglan Li, Nelson F Freeburg, Nivitha Murali, Alexandra Indeglia, Grant P Grothusen, Michelle Cicchini, Hung Mai, Amy C Gladstein, Keren M Adler, Katherine R Doerig, Jinyang Li, Miguel Ruiz-Torres, Kimberly L Manning, Ben Z Stanger, Luca Busino, Maureen Murphy, Liling Wan, David M Feldser.

The p53 tumor suppressor regulates multiple context-dependent tumor suppressive programs. Although p53 is mutated in ~90% of small cell lung cancer (SCLC) tumors, how p53 mediates tumor suppression in this context is unknown. Here, using a mouse model of SCLC in which endogenous p53 expression can be conditionally and temporally regulated, we show that SCLC tumors maintain a requirement for p53 inactivation. However, we identify tumor subtype heterogeneity between SCLC tumors such that p53 reactivation induces senescence in a subset of tumors, while in others, p53 induces necrosis. We pinpoint cyclophilins as critical determinants of a p53-induced transcriptional program that is specific to SCLC tumors and cell lines poised to undergo p53-mediated necrosis. Importantly, inhibition of cyclophilin isomerase activity, or genetic ablation of specific cyclophilin genes, suppresses p53-mediated necrosis by limiting p53 transcriptional output without impacting p53 chromatin binding. Our study demonstrates that intertumoral heterogeneity in SCLC influences the biological response to p53 restoration, describes a cyclophilin-dependent mechanism of p53-regulated cell death, and uncovers putative mechanisms for the treatment of this most-recalcitrant tumor type.

DOI: https://doi.org/10.1038/s41467-023-40161-9
Cell Rep. 2023 Jul 19. pii: S2211-1247(23)00839-2. [Epub ahead of print]42(8): 112828

QUAS-R: An SLC1A5-mediated glutamine uptake assay with single-cell resolution reveals metabolic heterogeneity with immune populations.

Leonard R Pelgrom, Gavin M Davis, Simon O'Shaughnessy, Emilie J M Wezenberg, Sander I Van Kasteren, David K Finlay, Linda V Sinclair.

  System-level analysis of single-cell data is rapidly transforming the field of immunometabolism. Given the competitive demand for nutrients in immune microenvironments, there is a need to understand how and when immune cells access these nutrients. Here, we describe a new approach for single-cell analysis of nutrient uptake where we use in-cell biorthogonal labeling of a functionalized amino acid after transport into the cell. In this manner, the bona fide active uptake of glutamine via SLC1A5/ASCT2 could be quantified. We used this assay to interrogate the transport capacity of complex immune subpopulations, both in vitro and in vivo. Taken together, our findings provide an easy sensitive single-cell assay to assess which cells support their function via SLC1A5-mediated uptake. This is a significant addition to the single-cell metabolic toolbox required to decode the metabolic landscape of complex immune microenvironments.

Keywords:  CP: Immunology; CP: Metabolism; SLC1A5; amino acid transport; glutamine uptake; lymphocytes

DOI:  https://doi.org/10.1016/j.celrep.2023.112828
Trends Cancer. 2023 Jul 13. pii: S2405-8033(23)00112-7. [Epub ahead of print]

Perivascular niches: critical hubs in cancer evolution.

Ada Nowosad, Jean-Christophe Marine, Panagiotis Karras.

  Tumors are heterogeneous ecosystems in which cancer cells coexist within a complex tumor immune microenvironment (TIME). The malignant, stromal, and immune cell compartments establish a plethora of bidirectional cell-cell communication crosstalks that influence tumor growth and metastatic dissemination, which we are only beginning to understand. Cancer cells either co-opt or promote the formation of new blood and lymphatic vessels to cope with their need for nutrients and oxygen. Recent studies have highlighted additional key roles for the tumor vasculature and have identified the perivascular niche as a cellular hub, where intricate and dynamic cellular interactions promote cancer stemness, immune evasion, dormancy, and metastatic spreading. Here, we review these findings, and discuss how they may be exploited therapeutically.

Keywords:  cancer stemness; cell plasticity; cell–cell communication; immune evasion; metastasis; perivascular niche

DOI:  https://doi.org/10.1016/j.trecan.2023.06.010
J Exp Bot. 2023 Jul 15. pii: erad274. [Epub ahead of print]

Inhibition of RNA Degradation Integrates the Metabolic Signals Induced by Osmotic Stress into the Arabidopsis Circadian System.

Putri Prasetyaningrum, Suzanne Litthauer, Franco Vegliani, Martin William Battle, Matthew William Wood, Xinmeng Liu, Cathryn Dickson, Matthew Alan Jones.

  The circadian clock system acts as an endogenous timing reference that coordinates many metabolic and physiological processes in plants. Previous studies have shown that the application of osmotic stress delays circadian rhythms via 3'-Phospho-Adenosine 5'-Phosphate (PAP), a retrograde signalling metabolite that is produced in response to redox stress within organelles. PAP accumulation leads to the inhibition of EXORIBONUCLEASEs (XRNs), which are responsible for RNA degradation. Interestingly, we are now able to demonstrate that post-transcriptional processing is crucial for the circadian response to osmotic stress. Our data show that osmotic stress increases the stability of specific circadian RNAs, suggesting that RNA metabolism plays a vital role in circadian clock coordination during drought. Inactivation of XRN4 is sufficient to extend circadian rhythms as part of this response, with PRR7 and LWD1 identified as transcripts that are post-transcriptionally regulated to delay circadian progression.

Keywords:  Arabidopsis; Circadian; Drought; Osmotic stress; Post-transcriptional; RNA degradation

DOI:  https://doi.org/10.1093/jxb/erad274
Evol Lett. 2023 Aug;7(4): 273-284

Experimental evolution of metabolism under nutrient restriction: enhanced amino acid catabolism and a key role of branched-chain amino acids.

Fanny Cavigliasso, Loriane Savary, Jorge E Spangenberg, Hector Gallart-Ayala, Julijana Ivanisevic, Tadeusz J Kawecki.

  Periodic food shortage is a common ecological stressor for animals, likely to drive physiological and metabolic adaptations to alleviate its consequences, particularly for juveniles that have no option but to continue to grow and develop despite undernutrition. Here we study changes in metabolism associated with adaptation to nutrient shortage, evolved by replicate Drosophila melanogaster populations maintained on a nutrient-poor larval diet for over 240 generations. In a factorial metabolomics experiment we showed that both phenotypic plasticity and genetically-based adaptation to the poor diet involved wide-ranging changes in metabolite abundance; however, the plastic response did not predict the evolutionary change. Compared to nonadapted larvae exposed to the poor diet for the first time, the adapted larvae showed lower levels of multiple free amino acids in their tissues-and yet they grew faster. By quantifying accumulation of the nitrogen stable isotope 15N we show that adaptation to the poor diet led to an increased use of amino acids for energy generation. This apparent "waste" of scarce amino acids likely results from the trade-off between acquisition of dietary amino acids and carbohydrates observed in these populations. The three branched-chain amino acids (leucine, isoleucine, and valine) showed a unique pattern of depletion in adapted larvae raised on the poor diet. A diet supplementation experiment demonstrated that these amino acids are limiting for growth on the poor diet, suggesting that their low levels resulted from their expeditious use for protein synthesis. These results demonstrate that selection driven by nutrient shortage not only promotes improved acquisition of limiting nutrients, but also has wide-ranging effects on how the nutrients are used. They also show that the abundance of free amino acids in the tissues does not, in general, reflect the nutritional condition and growth potential of an animal.

Keywords:  Drosophila melanogaster; deamination; dietary restriction; experimental evolution; malnutrition; metabolomics

DOI:  https://doi.org/10.1093/evlett/qrad018
Nat Commun. 2023 07 19. 14(1): 4356

Targeting an allosteric site in dynamin-related protein 1 to inhibit Fis1-mediated mitochondrial dysfunction.

Luis Rios, Suman Pokhrel, Sin-Jin Li, Gwangbeom Heo, Bereketeab Haileselassie, Daria Mochly-Rosen.

The large cytosolic GTPase, dynamin-related protein 1 (Drp1), mediates both physiological and pathological mitochondrial fission. Cell stress triggers Drp1 binding to mitochondrial Fis1 and subsequently, mitochondrial fragmentation, ROS production, metabolic collapse, and cell death. Because Drp1 also mediates physiological fission by binding to mitochondrial Mff, therapeutics that inhibit pathological fission should spare physiological mitochondrial fission. P110, a peptide inhibitor of Drp1-Fis1 interaction, reduces pathology in numerous models of neurodegeneration, ischemia, and sepsis without blocking the physiological functions of Drp1. Since peptides have pharmacokinetic limitations, we set out to identify small molecules that mimic P110's benefit. We map the P110-binding site to a switch I-adjacent grove (SWAG) on Drp1. Screening for SWAG-binding small molecules identifies SC9, which mimics P110's benefits in cells and a mouse model of endotoxemia. We suggest that the SWAG-binding small molecules discovered in this study may reduce the burden of Drp1-mediated pathologies and potentially pathologies associated with other members of the GTPase family.

DOI: https://doi.org/10.1038/s41467-023-40043-0
Nat Metab. 2023 Jul 17.

Fatty acid oxidation organizes mitochondrial supercomplexes to sustain astrocytic ROS and cognition.

Brenda Morant-Ferrando, Daniel Jimenez-Blasco, Paula Alonso-Batan, Jesús Agulla, Rebeca Lapresa, Dario Garcia-Rodriguez, Sara Yunta-Sanchez, Irene Lopez-Fabuel, Emilio Fernandez, Peter Carmeliet, Angeles Almeida, Marina Garcia-Macia, Juan P Bolaños.

Having direct access to brain vasculature, astrocytes can take up available blood nutrients and metabolize them to fulfil their own energy needs and deliver metabolic intermediates to local synapses1,2. These glial cells should be, therefore, metabolically adaptable to swap different substrates. However, in vitro and in vivo studies consistently show that astrocytes are primarily glycolytic3-7, suggesting glucose is their main metabolic precursor. Notably, transcriptomic data8,9 and in vitro10 studies reveal that mouse astrocytes are capable of mitochondrially oxidizing fatty acids and that they can detoxify excess neuronal-derived fatty acids in disease models11,12. Still, the factual metabolic advantage of fatty acid use by astrocytes and its physiological impact on higher-order cerebral functions remain unknown. Here, we show that knockout of carnitine-palmitoyl transferase-1A (CPT1A)-a key enzyme of mitochondrial fatty acid oxidation-in adult mouse astrocytes causes cognitive impairment. Mechanistically, decreased fatty acid oxidation rewired astrocytic pyruvate metabolism to facilitate electron flux through a super-assembled mitochondrial respiratory chain, resulting in attenuation of reactive oxygen species formation. Thus, astrocytes naturally metabolize fatty acids to preserve the mitochondrial respiratory chain in an energetically inefficient disassembled conformation that secures signalling reactive oxygen species and sustains cognitive performance.

DOI: https://doi.org/10.1038/s42255-023-00835-6
Cell Chem Biol. 2023 Jul 04. pii: S2451-9456(23)00196-4. [Epub ahead of print]

S-Nitrosylation-mediated dysfunction of TCA cycle enzymes in synucleinopathy studied in postmortem human brains and hiPSC-derived neurons.

Paschalis-Thomas Doulias, Hongmei Yang, Alexander Y Andreyev, Nima Dolatabadi, Henry Scott, Charlene K Raspur, Parth R Patel, Tomohiro Nakamura, Steven R Tannenbaum, Harry Ischiropoulos, Stuart A Lipton.

A causal relationship between mitochondrial metabolic dysfunction and neurodegeneration has been implicated in synucleinopathies, including Parkinson disease (PD) and Lewy body dementia (LBD), but underlying mechanisms are not fully understood. Here, using human induced pluripotent stem cell (hiPSC)-derived neurons with mutation in the gene encoding α-synuclein (αSyn), we report the presence of aberrantly S-nitrosylated proteins, including tricarboxylic acid (TCA) cycle enzymes, resulting in activity inhibition assessed by carbon-labeled metabolic flux experiments. This inhibition principally affects α-ketoglutarate dehydrogenase/succinyl coenzyme-A synthetase, metabolizing α-ketoglutarate to succinate. Notably, human LBD brain manifests a similar pattern of aberrantly S-nitrosylated TCA enzymes, indicating the pathophysiological relevance of these results. Inhibition of mitochondrial energy metabolism in neurons is known to compromise dendritic length and synaptic integrity, eventually leading to neuronal cell death. Our evidence indicates that aberrant S-nitrosylation of TCA cycle enzymes contributes to this bioenergetic failure.

DOI: https://doi.org/10.1016/j.chembiol.2023.06.018
Nat Cell Biol. 2023 Jul 17.

H3K36 methylation maintains cell identity by regulating opposing lineage programmes.

Michael S Hoetker, Masaki Yagi, Bruno Di Stefano, Justin Langerman, Simona Cristea, Lai Ping Wong, Aaron J Huebner, Jocelyn Charlton, Weixian Deng, Chuck Haggerty, Ruslan I Sadreyev, Alexander Meissner, Franziska Michor, Kathrin Plath, Konrad Hochedlinger.

The epigenetic mechanisms that maintain differentiated cell states remain incompletely understood. Here we employed histone mutants to uncover a crucial role for H3K36 methylation in the maintenance of cell identities across diverse developmental contexts. Focusing on the experimental induction of pluripotency, we show that H3K36M-mediated depletion of H3K36 methylation endows fibroblasts with a plastic state poised to acquire pluripotency in nearly all cells. At a cellular level, H3K36M facilitates epithelial plasticity by rendering fibroblasts insensitive to TGFβ signals. At a molecular level, H3K36M enables the decommissioning of mesenchymal enhancers and the parallel activation of epithelial/stem cell enhancers. This enhancer rewiring is Tet dependent and redirects Sox2 from promiscuous somatic to pluripotency targets. Our findings reveal a previously unappreciated dual role for H3K36 methylation in the maintenance of cell identity by integrating a crucial developmental pathway into sustained expression of cell-type-specific programmes, and by opposing the expression of alternative lineage programmes through enhancer methylation.

DOI: https://doi.org/10.1038/s41556-023-01191-z
Cell Metab. 2023 Jul 12. pii: S1550-4131(23)00224-3. [Epub ahead of print]

Regulation of VKORC1L1 is critical for p53-mediated tumor suppression through vitamin K metabolism.

Xin Yang, Zhe Wang, Fereshteh Zandkarimi, Yanqing Liu, Shoufu Duan, Zhiming Li, Ning Kon, Zhiguo Zhang, Xuejun Jiang, Brent R Stockwell, Wei Gu.

  Here, we identified vitamin K epoxide reductase complex subunit 1 like 1 (VKORC1L1) as a potent ferroptosis repressor. VKORC1L1 protects cells from ferroptosis by generating the reduced form of vitamin K, a potent radical-trapping antioxidant, to counteract phospholipid peroxides independent of the canonical GSH/GPX4 mechanism. Notably, we found that VKORC1L1 is also a direct transcriptional target of p53. Activation of p53 induces downregulation of VKORC1L1 expression, thus sensitizing cells to ferroptosis for tumor suppression. Interestingly, a small molecular inhibitor of VKORC1L1, warfarin, is widely prescribed as an FDA-approved anticoagulant drug. Moreover, warfarin represses tumor growth by promoting ferroptosis in both immunodeficient and immunocompetent mouse models. Thus, by downregulating VKORC1L1, p53 executes the tumor suppression function by activating an important ferroptosis pathway involved in vitamin K metabolism. Our study also reveals that warfarin is a potential repurposing drug in cancer therapy, particularly for tumors with high levels of VKORC1L1 expression.

Keywords:  VKORC1L1; ferroptosis; lipid peroxidation; p53; radical-trapping antioxidants; transcription; tumor suppression; vitamin K; warfarin

DOI:  https://doi.org/10.1016/j.cmet.2023.06.014
Cancer Res. 2023 Jul 18. pii: CAN-22-3481. [Epub ahead of print]

Histone methyltransferase NSD2 activates PKCα to drive metabolic reprogramming and lenalidomide resistance in multiple myeloma.

Phyllis S Y Chong, Jing-Yuan Chooi, Julia S L Lim, Aaron C Y Leow, Sabrina Hui Min Toh, Irfan Azaman, Mun Yee Koh, Phaik Ju Teoh, Tuan Zea Tan, Tae-Hoon Chung, Wee Joo Chng.

Multiple myeloma (MM) cells undergo metabolic reprogramming in response to the hypoxic and nutrient-deprived bone marrow microenvironment. Primary oncogenes in recurrent translocations might be able to drive metabolic heterogeneity to survive the microenvironment that can present new vulnerabilities for therapeutic targeting. t(4;14) translocation leads to the universal overexpression of histone methyltransferase NSD2 that promotes plasma cell transformation through a global increase in H3K36me2. Here, we identified PKCα as an epigenetic target that contributes to the oncogenic potential of NSD2. RNA-sequencing of t(4;14) MM cell lines revealed a significant enrichment in the regulation of metabolic processes by PKCα, and the glycolytic gene, hexokinase 2 (HK2), was transcriptionally regulated by PKCα in a PI3K/Akt-dependent manner. Loss of PKCα displaced mitochondria-bound HK2 and reversed sensitivity to the glycolytic inhibitor 3-bromopyruvate. Additionally, the perturbation of glycolytic flux led to a metabolic shift to a less energetic state and decreased ATP production. Metabolomics analysis indicated lactate as a differential metabolite associated with PKCα. As a result, PKCα conferred resistance to the immunomodulatory drugs (IMiD) lenalidomide in a cereblon-independent manner and could be phenocopied by either overexpression of HK2 or direct supplementation of lactate. Clinically, t(4;14) MM patients had elevated plasma lactate levels and did not benefit from lenalidomide-based regimens. Altogether, this study provides insights into the epigenetic-metabolism crosstalk in MM and highlights the opportunity for therapeutic intervention that leverages the distinct metabolic program in t(4;14) myeloma.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-3481
Nat Commun. 2023 Jul 15. 14(1): 4239

Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma.

OCCAMS Consortium

A variety of mutational processes drive cancer development, but their dynamics across the entire disease spectrum from pre-cancerous to advanced neoplasia are poorly understood. We explore the mutagenic processes shaping oesophageal adenocarcinoma tumorigenesis in 997 instances comprising distinct stages of this malignancy, from Barrett Oesophagus to primary tumours and advanced metastatic disease. The mutational landscape is dominated by the C[T > C/G]T substitution enriched signatures SBS17a/b, which are linked with TP53 mutations, increased proliferation, genomic instability and disease progression. The APOBEC mutagenesis signature is a weak but persistent signal amplified in primary tumours. We also identify prevalent alterations in DNA damage repair pathways, with homologous recombination, base and nucleotide excision repair and translesion synthesis mutated in up to 50% of the cohort, and surprisingly uncoupled from transcriptional activity. Among these, the presence of base excision repair deficiencies show remarkably poor prognosis in the cohort. In this work, we provide insights on the mutational aetiology and changes enabling the transition from pre-neoplastic to advanced oesophageal adenocarcinoma.

DOI: https://doi.org/10.1038/s41467-023-39957-6
Semin Immunol. 2023 Jul 18. pii: S1044-5323(23)00099-4. [Epub ahead of print]69 101808

Mitochondria during T cell aging.

Jose Ignacio Escrig-Larena, Sandra Delgado-Pulido, María Mittelbrunn.

  Mitochondrial dysfunction is a hallmark of aging that contributes to inflammaging. It is characterized by alterations of the mitochondrial DNA, reduced respiratory capacity, decreased mitochondrial membrane potential and increased reactive oxygen species production. These primary alterations disrupt other interconnected and important mitochondrial-related processes such as metabolism, mitochondrial dynamics and biogenesis, mitophagy, calcium homeostasis or apoptosis. In this review, we gather the current knowledge about the different mitochondrial processes which are altered during aging, with special focus on their contribution to age-associated T cell dysfunction and inflammaging.

Keywords:  Aging; Apoptosis; Calcium homeostasis; Inflammaging; Lymphocyte; Mitochondria; Mitochondrial dynamics; Mitokines; Mitophagy; MtDNA; ROS; T cells

DOI:  https://doi.org/10.1016/j.smim.2023.101808
Sci Adv. 2023 Jul 21. 9(29): eadh3347

Parkin regulates amino acid homeostasis at mitochondria-lysosome (M/L) contact sites in Parkinson's disease.

Wesley Peng, Leonie F Schröder, Pingping Song, Yvette C Wong, Dimitri Krainc.

Mutations in the E3 ubiquitin ligase parkin are the most common cause of early-onset Parkinson's disease (PD). Although parkin modulates mitochondrial and endolysosomal homeostasis during cellular stress, whether parkin regulates mitochondrial and lysosomal cross-talk under physiologic conditions remains unresolved. Using transcriptomics, metabolomics and super-resolution microscopy, we identify amino acid metabolism as a disrupted pathway in iPSC-derived dopaminergic neurons from patients with parkin PD. Compared to isogenic controls, parkin mutant neurons exhibit decreased mitochondria-lysosome contacts via destabilization of active Rab7. Subcellular metabolomics in parkin mutant neurons reveals amino acid accumulation in lysosomes and their deficiency in mitochondria. Knockdown of the Rab7 GTPase-activating protein TBC1D15 restores mitochondria-lysosome tethering and ameliorates cellular and subcellular amino acid profiles in parkin mutant neurons. Our data thus uncover a function of parkin in promoting mitochondrial and lysosomal amino acid homeostasis through stabilization of mitochondria-lysosome contacts and suggest that modulation of interorganelle contacts may serve as a potential target for ameliorating amino acid dyshomeostasis in disease.

DOI: https://doi.org/10.1126/sciadv.adh3347
Cell Chem Biol. 2023 Jul 03. pii: S2451-9456(23)00194-0. [Epub ahead of print]

Hydroxyproline metabolism enhances IFN-γ-induced PD-L1 expression and inhibits autophagic flux.

Stephan H Spangenberg, Amelia Palermo, Nathalia R Gazaniga, Francisco Martínez-Peña, Carlos Guijas, Emily N Chin, Markus M Rinschen, Philipp N Sander, Bill Webb, Laura E Pereira, Ying Jia, Lance Meitz, Gary Siuzdak, Luke L Lairson.

  The immune checkpoint protein PD-L1 plays critical roles in both immune system homeostasis and tumor progression. Impaired PD-1/PD-L1 function promotes autoimmunity and PD-L1 expression within tumors promotes immune evasion. If and how changes in metabolism or defined metabolites regulate PD-L1 expression is not fully understood. Here, using a metabolomics activity screening-based approach, we have determined that hydroxyproline (Hyp) significantly and directly enhances adaptive (i.e., IFN-γ-induced) PD-L1 expression in multiple relevant myeloid and cancer cell types. Mechanistic studies reveal that Hyp acts as an inhibitor of autophagic flux, which allows it to regulate this negative feedback mechanism, thereby contributing to its overall effect on PD-L1 expression. Due to its prevalence in fibrotic tumors, these findings suggest that hydroxyproline could contribute to the establishment of an immunosuppressive tumor microenvironment and that Hyp metabolism could be targeted to pharmacologically control PD-L1 expression for the treatment of cancer or autoimmune diseases.

Keywords:  PD-L1; autophagy; collagen; hydroxyproline; immune checkpoint protein; metabolomics activity screening; phenotypic screening

DOI:  https://doi.org/10.1016/j.chembiol.2023.06.016
Antioxid Redox Signal. 2023 Jul 20.

Therapeutic Targeting of Mitochondrial Plasticity and Redox Control to Overcome Cancer Chemoresistance.

Stephen Ralph, Shalini Mani, Geeta Swargiary, Madhu Rani, Samiksha Wasnik, Shashi Prakash Singh, Annu Devi.

Mitochondria are subcellular organelles performing essential metabolic functions contributing to cellular bioenergetics and regulation of cell growth or death. The basic mitochondrial function in fulfilling the need for cell growth and vitality is evidenced by the conditional state whereby cancer cells with depleted mitochondrial DNA (rho zero cells) are no longer capable of forming tumors until newly recruited mitochondria are internalized into the rho zero cells. Herein lies the absolute dependency on mitochondria for tumor growth. In addition, mitochondria are key regulators of cell death (by apoptosis, necroptosis, or other forms of cell death) and are therefore important targets for anticancer therapy. Mitochondrial plasticity regulating their state of fusion or fission is also key to the chemoresistance properties of cancer cells by promoting pro-survival pathways enabling the mitochondria to mitigate against the cellular stresses and extreme conditions within the tumor microenvironment caused by chemotherapy, hypoxia, or oxidative stress. This review discusses many characteristics of mitochondria, the processes and pathways controlling the dynamic changes occurring in the morphology of mitochondria, the roles of reactive oxygen species, and their relationship with mitochondrial fission or fusion. It also examines the relationship of redox to mitophagy when mitochondria become compromised and its effect on cancer cell survival, stemness and the changes accompanying malignant progression from primary tumors to metastatic disease. A challenging question that arises is whether the changes in mitochondrial dynamics and their regulation can provide opportunities for improving drug targeting during cancer treatment and enhancing survival outcomes.

DOI: https://doi.org/10.1089/ars.2023.0379
Front Oncol. 2023 ;13 1207603

F-ATP synthase inhibitory factor 1 regulates metabolic reprogramming involving its interaction with c-Myc and PGC1α.

Lishu Guo, Zhenglong Gu.

  F-ATP synthase inhibitory factor 1 (IF1) is an intrinsic inhibitor of F-ATP synthase. It is known that IF1 mediates metabolic phenotypes and cell fate, yet the molecular mechanisms through which IF1 fulfills its physiological functions are not fully understood. Ablation of IF1 favors metabolic switch to oxidative metabolism from glycolysis. c-Myc and PGC1α are critical for metabolic reprogramming. This work identified that IF1 interacted with Thr-58 phosphorylated c-Myc, which might thus mediate the activity of c-Myc and promote glycolysis. The interaction of IF1 with PGC1α inhibited oxidative respiration. c-Myc and PGC1α were localized to mitochondria under mitochondrial stress in an IF1-dependent manner. Furthermore, IF1 was found to be required for the protective effect of hypoxia on c-Myc- and PGC1α-induced cell death. This study suggested that the interactions of IF1 with transcription factors c-Myc and PGC1α might be involved in IF1-regulatory metabolic reprogramming and cell fate.

Keywords:  F-ATP synthase inhibitory factor 1; PGC1α; c-Myc; metabolic reprogramming; mitochondria; p-c-Myc

DOI:  https://doi.org/10.3389/fonc.2023.1207603
Exp Eye Res. 2023 Jul 15. pii: S0014-4835(23)00189-6. [Epub ahead of print] 109568

The role of hydrogen sulfide in the retina.

Alex Cornwell, Alireza Badiei.

  The discovery of the hydrogen sulfide (H2S) and the transsulfuration pathway (TSP) responsible for its synthesis in the mammalian retina has highlighted this molecule's wide range of physiological processes that influence cellular signaling, redox homeostasis, and cellular metabolism. The multi-level regulatory program that influences H2S levels in the retina depends on the relative expression and activity of TSP enzymes, which regulate the abundance of competitive substrates that support or abrogate H2S synthesis. In addition, and apart from TSP, intracellular H2S levels are regulated by mitochondrial sulfide oxidizing pathways. Retinal layers natively express differing levels of TSP enzymes, which highlight the differences in the metabolite and substrate requirement. Recent studies indicate that these systems are susceptible to pathophysiologies affecting the retina. Dysregulation at any level can upset the balance of redox and signaling processes and possibly upset oxidative stress, apoptotic signaling, ion channels, and immune response within this sensitive tissue. H2S donors are a potential therapeutic in such cases and have been demonstrated to bridge the gap, positively impacting the damaged retina. Here, we review the recent findings of H2S, how its multi-level regulation impacts the retina, and how its dysregulation is implicated in retinal pathologies.

Keywords:  Cellular metabolism; Hydrogen sulfide; Inflammation; Ion channels; Oxidative stress; Redox; Retina

DOI:  https://doi.org/10.1016/j.exer.2023.109568
Nat Commun. 2023 07 17. 14(1): 4259

Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma.

Xiao Chen, Yinglu Li, Fang Zhu, Xinjing Xu, Brian Estrella, Manuel A Pazos, John T McGuire, Dimitris Karagiannis, Varun Sahu, Mustafo Mustafokulov, Claudio Scuoppo, Francisco J Sánchez-Rivera, Yadira M Soto-Feliciano, Laura Pasqualucci, Alberto Ciccia, Jennifer E Amengual, Chao Lu.

Interplay between chromatin-associated complexes and modifications critically contribute to the partitioning of epigenome into stable and functionally distinct domains. Yet there is a lack of systematic identification of chromatin crosstalk mechanisms, limiting our understanding of the dynamic transition between chromatin states during development and disease. Here we perform co-dependency mapping of genes using CRISPR-Cas9-mediated fitness screens in pan-cancer cell lines to quantify gene-gene functional relationships. We identify 145 co-dependency modules and further define the molecular context underlying the essentiality of these modules by incorporating mutational, epigenome, gene expression and drug sensitivity profiles of cell lines. These analyses assign new protein complex composition and function, and predict new functional interactions, including an unexpected co-dependency between two transcriptionally counteracting chromatin complexes - polycomb repressive complex 2 (PRC2) and MLL-MEN1 complex. We show that PRC2-mediated H3K27 tri-methylation regulates the genome-wide distribution of MLL1 and MEN1. In lymphoma cells with EZH2 gain-of-function mutations, the re-localization of MLL-MEN1 complex drives oncogenic gene expression and results in a hypersensitivity to pharmacologic inhibition of MEN1. Together, our findings provide a resource for discovery of trans-regulatory interactions as mechanisms of chromatin regulation and potential targets of synthetic lethality.

DOI: https://doi.org/10.1038/s41467-023-39990-5
Res Sq. 2023 Jun 30. pii: rs.3.rs-3069713. [Epub ahead of print]

Activation of transsulfuration pathway to maintain cysteine is a thermogenic checkpoint for the conservation of energy.

Vishwa Dixit, Aileen Lee, Yuki Sugiura, Yun-Hee Youm, Tamara Dlugos, Rae Maeda, Daniel Coman, Olga Spadaro, Sviatoslav Sidorov, Irina Shcukina, Prabhakar Sairam Andhey, Steven Smith, Eric Ravussin, Fahmeed Hyder, Maxim Artyomov.

Pro-longevity dietary interventions such as caloric restriction (CR)1 and methionine restriction2 (MR) are associated with 'browning' of white adipose tissue in rodents, an adaptive response that increases heat production to maintain core-body temperature for the survival of homeotherms3,4. Here, the analysis of metabolome and transcriptome of adipose tissue of healthy humans5 identified that sustained caloric restriction (CR) decreases methionine cycle and lowers cysteine levels despite elevated expression of enzyme cystathionine γ-lyase (CTH), which catalyzes the synthesis of cysteine in the transsulfuration (TSP) pathway6,7. Cysteine starvation of global, but not adipocyte- or hepatocyte-specific Cth deficient mice, triggered lethal thermogenesis through conversion of white adipose tissue into uncoupled "brown"-like adipocytes. This manifests as depletion of energy reserves and drastic weight-loss. Mechanistically, cysteine starvation-induced thermogenesis and energy expenditure increases adipose noradrenaline bioavailability and induces a UCP1-independent response that partially requires FGF21. Therapeutically, reduction of cysteine reversed obesity by increasing thermogenesis and lowering inflammation. These findings establish that adaptation to dietary restriction requires activation of TSP to defend organismal cysteine levels that serves as a thermogenic checkpoint for regulation of core-body temperature and conservation of energy.

DOI: https://doi.org/10.21203/rs.3.rs-3069713/v1
Nature. 2023 Jul 19.

Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells.

Yogesh Goyal, Gianna T Busch, Maalavika Pillai, Jingxin Li, Ryan H Boe, Emanuelle I Grody, Manoj Chelvanambi, Ian P Dardani, Benjamin Emert, Nicholas Bodkin, Jonas Braun, Dylan Fingerman, Amanpreet Kaur, Naveen Jain, Pavithran T Ravindran, Ian A Mellis, Karun Kiani, Gretchen M Alicea, Mitchell E Fane, Syeda Subia Ahmed, Haiyin Li, Yeqing Chen, Cedric Chai, Jessica Kaster, Russell G Witt, Rossana Lazcano, Davis R Ingram, Sarah B Johnson, Khalida Wani, Margaret C Dunagin, Alexander J Lazar, Ashani T Weeraratna, Jennifer A Wargo, Meenhard Herlyn, Arjun Raj.

Even among genetically identical cancer cells, resistance to therapy frequently emerges from a small subset of those cells1-7. Molecular differences in rare individual cells in the initial population enable certain cells to become resistant to therapy7-9; however, comparatively little is known about the variability in the resistance outcomes. Here we develop and apply FateMap, a framework that combines DNA barcoding with single-cell RNA sequencing, to reveal the fates of hundreds of thousands of clones exposed to anti-cancer therapies. We show that resistant clones emerging from single-cell-derived cancer cells adopt molecularly, morphologically and functionally distinct resistant types. These resistant types are largely predetermined by molecular differences between cells before drug addition and not by extrinsic factors. Changes in the dose and type of drug can switch the resistant type of an initial cell, resulting in the generation and elimination of certain resistant types. Samples from patients show evidence for the existence of these resistant types in a clinical context. We observed diversity in resistant types across several single-cell-derived cancer cell lines and cell types treated with a variety of drugs. The diversity of resistant types as a result of the variability in intrinsic cell states may be a generic feature of responses to external cues.

DOI: https://doi.org/10.1038/s41586-023-06342-8
Nature. 2023 Jul;619(7970): 585-594

An atlas of healthy and injured cell states and niches in the human kidney.

KPMP Consortium

Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles and interactions within tissue neighbourhoods1. Here we applied multiple single-cell and single-nucleus assays (>400,000 nuclei or cells) and spatial imaging technologies to a broad spectrum of healthy reference kidneys (45 donors) and diseased kidneys (48 patients). This has provided a high-resolution cellular atlas of 51 main cell types, which include rare and previously undescribed cell populations. The multi-omic approach provides detailed transcriptomic profiles, regulatory factors and spatial localizations spanning the entire kidney. We also define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive (successful or maladaptive repair), transitioning and degenerative states. Molecular signatures permitted the localization of these states within injury neighbourhoods using spatial transcriptomics, while large-scale 3D imaging analysis (around 1.2 million neighbourhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways that are relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents a comprehensive benchmark of cellular states, neighbourhoods, outcome-associated signatures and publicly available interactive visualizations.

DOI: https://doi.org/10.1038/s41586-023-05769-3
Cell Rep. 2023 Jul 15. pii: S2211-1247(23)00803-3. [Epub ahead of print]42(7): 112792

ATR protects ongoing and newly assembled DNA replication forks through distinct mechanisms.

Wendy Leung, Antoine Simoneau, Sneha Saxena, Jessica Jackson, Parasvi S Patel, Mangsi Limbu, Alessandro Vindigni, Lee Zou.

  The ATR kinase safeguards genomic integrity during S phase, but how ATR protects DNA replication forks remains incompletely understood. Here, we combine four distinct assays to analyze ATR functions at ongoing and newly assembled replication forks upon replication inhibition by hydroxyurea. At ongoing forks, ATR inhibitor (ATRi) increases MRE11- and EXO1-mediated nascent DNA degradation from PrimPol-generated, single-stranded DNA (ssDNA) gaps. ATRi also exposes template ssDNA through fork uncoupling and nascent DNA degradation. Electron microscopy reveals that ATRi reduces reversed forks by increasing gap-dependent nascent DNA degradation. At new forks, ATRi triggers MRE11- and CtIP-initiated template DNA degradation by EXO1, exposing nascent ssDNA. Upon PARP inhibition, ATRi preferentially exacerbates gap-dependent nascent DNA degradation at ongoing forks in BRCA1/2-deficient cells and disrupts the restored gap protection in BRCA1-deficient, PARP-inhibitor-resistant cells. Thus, ATR protects ongoing and new forks through distinct mechanisms, providing an extended view of ATR's functions in stabilizing replication forks.

Keywords:  ATR; BRCA; CP: Molecular biology; PARP inhibitor; gaps; replication; replication fork; single-stranded DNA

DOI:  https://doi.org/10.1016/j.celrep.2023.112792
Nat Biomed Eng. 2023 Jul 20.

Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics.

Matthew E H White, Ludwig R Sinn, D Marc Jones, Joost de Folter, Simran Kaur Aulakh, Ziyue Wang, Helen R Flynn, Lynn Krüger, Pinkus Tober-Lau, Vadim Demichev, Florian Kurth, Michael Mülleder, Véronique Blanchard, Christoph B Messner, Markus Ralser.

Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named 'OxoScan-MS', identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive and untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from patients with COVID-19 and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples.

DOI: https://doi.org/10.1038/s41551-023-01067-5
Elife. 2023 07 18. pii: e83870. [Epub ahead of print]12

Metabolic clogging of mannose triggers dNTP loss and genomic instability in human cancer cells.

Yoichiro Harada, Yu Mizote, Takehiro Suzuki, Akiyoshi Hirayama, Satsuki Ikeda, Mikako Nishida, Toru Hiratsuka, Ayaka Ueda, Yusuke Imagawa, Kento Maeda, Yuki Ohkawa, Junko Murai, Hudson H Freeze, Eiji Miyoshi, Shigeki Higashiyama, Heiichiro Udono, Naoshi Dohmae, Hideaki Tahara, Naoyuki Taniguchi.

  Mannose has anticancer activity that inhibits cell proliferation and enhances the efficacy of chemotherapy. How mannose exerts its anticancer activity, however, remains poorly understood. Here, using genetically engineered human cancer cells that permit the precise control of mannose metabolic flux, we demonstrate that the large influx of mannose exceeding its metabolic capacity induced metabolic remodeling, leading to the generation of slow-cycling cells with limited deoxyribonucleoside triphosphates (dNTPs). This metabolic remodeling impaired dormant origin firing required to rescue stalled forks by cisplatin, thus exacerbating replication stress. Importantly, pharmacological inhibition of de novo dNTP biosynthesis was sufficient to retard cell cycle progression, sensitize cells to cisplatin, and inhibit dormant origin firing, suggesting dNTP loss-induced genomic instability as a central mechanism for the anticancer activity of mannose.

Keywords:  cancer biology; cell biology; chemotherapy; dormant origins; genomic instability; human; mannose; metabolism; mouse; replication stress

DOI:  https://doi.org/10.7554/eLife.83870
Cell Rep. 2023 Jul 13. pii: S2211-1247(23)00811-2. [Epub ahead of print]42(7): 112800

The human placenta exhibits a unique transcriptomic void.

Sungsam Gong, Francesca Gaccioli, Irving L M H Aye, Giulia Avellino, Emma Cook, Andrew R J Lawson, Luke M R Harvey, Gordon C S Smith, D Stephen Charnock-Jones.

  The human placenta exhibits a unique genomic architecture with an unexpectedly high mutation burden and many uniquely expressed genes. The aim of this study is to identify transcripts that are uniquely absent or depleted in the placenta. Here, we show that 40 of 46 of the other organs have no selectively depleted transcripts and that, of the remaining six, the liver has the largest number, with 26. In contrast, the term placenta has 762 depleted transcripts. Gene Ontology analysis of this depleted set highlighted multiple pathways reflecting known unique elements of placental physiology. For example, transcripts associated with neuronal function are in the depleted set-as expected given the lack of placental innervation. However, this demonstrated overrepresentation of genes involved in mitochondrial function (p = 5.8 × 10-10), including PGC-1α, the master regulator of mitochondrial biogenesis, and genes involved in polyamine metabolism (p = 2.1 × 10-4).

Keywords:  CP: Developmental biology; CP: Molecular biology

DOI:  https://doi.org/10.1016/j.celrep.2023.112800
Nat Commun. 2023 07 19. 14(1): 4332

Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B12 delivery and repair.

Romila Mascarenhas, Markus Ruetz, Harsha Gouda, Natalie Heitman, Madeline Yaw, Ruma Banerjee.

G-proteins function as molecular switches to power cofactor translocation and confer fidelity in metal trafficking. The G-protein, MMAA, together with MMAB, an adenosyltransferase, orchestrate cofactor delivery and repair of B12-dependent human methylmalonyl-CoA mutase (MMUT). The mechanism by which the complex assembles and moves a >1300 Da cargo, or fails in disease, are poorly understood. Herein, we report the crystal structure of the human MMUT-MMAA nano-assembly, which reveals a dramatic 180° rotation of the B12 domain, exposing it to solvent. The complex, stabilized by MMAA wedging between two MMUT domains, leads to ordering of the switch I and III loops, revealing the molecular basis of mutase-dependent GTPase activation. The structure explains the biochemical penalties incurred by methylmalonic aciduria-causing mutations that reside at the MMAA-MMUT interfaces we identify here.

DOI: https://doi.org/10.1038/s41467-023-40077-4
Nat Commun. 2023 07 18. 14(1): 4317

Adipose tissue and skeletal muscle wasting precede clinical diagnosis of pancreatic cancer.

Ana Babic, Michael H Rosenthal, Tilak K Sundaresan, Natalia Khalaf, Valerie Lee, Lauren K Brais, Maureen Loftus, Leah Caplan, Sarah Denning, Anamol Gurung, Joanna Harrod, Khoschy Schawkat, Chen Yuan, Qiao-Li Wang, Alice A Lee, Leah H Biller, Matthew B Yurgelun, Kimmie Ng, Jonathan A Nowak, Andrew J Aguirre, Sangeeta N Bhatia, Matthew G Vander Heiden, Stephen K Van Den Eeden, Bette J Caan, Brian M Wolpin.

Patients with pancreatic cancer commonly develop weight loss and muscle wasting. Whether adipose tissue and skeletal muscle losses begin before diagnosis and the potential utility of such losses for earlier cancer detection are not well understood. We quantify skeletal muscle and adipose tissue areas from computed tomography (CT) imaging obtained 2 months to 5 years before cancer diagnosis in 714 pancreatic cancer cases and 1748 matched controls. Adipose tissue loss is identified up to 6 months, and skeletal muscle wasting is identified up to 18 months before the clinical diagnosis of pancreatic cancer and is not present in the matched control population. Tissue losses are of similar magnitude in cases diagnosed with localized compared with metastatic disease and are not correlated with at-diagnosis circulating levels of CA19-9. Skeletal muscle wasting occurs in the 1-2 years before pancreatic cancer diagnosis and may signal an upcoming diagnosis of pancreatic cancer.

DOI: https://doi.org/10.1038/s41467-023-40024-3
Autophagy. 2023 Jul 16.

Mitofissin: a novel mitochondrial fission protein that facilitates mitophagy.

Tomoyuki Fukuda, Kentaro Furukawa, Tatsuro Maruyama, Nobuo N Noda, Tomotake Kanki.

  Mitophagy is a selective form of autophagy that targets dysfunctional or superfluous mitochondria for degradation. During mitophagy, specific selective autophagy receptors (SARs) mark a portion of mitochondria to recruit the autophagy-related (Atg) machinery and nucleate a phagophore. The phagophore expands and surrounds the mitochondrial cargo, forming an autophagosome. Fission plays a crucial role in separating the targeted portion of mitochondria from the main body to sequester it within the autophagosome. Our recent study, utilizing fission and budding yeasts as model systems, has identified Atg44 as a mitochondrial fission factor that generates mitochondrial fragments suitable for phagophore engulfment. Atg44 resides in the mitochondrial intermembrane space (IMS) and interacts with lipid membranes, with the capacity of mediating membrane fragility and fission. Based on our findings, we propose the term mitofissin to refer to Atg44 and its homologous proteins, which might participate in diverse cellular processes requiring membrane remodeling across various species.

Keywords:  Atg44; autophagy; mitochondria; mitochondrial fission; mitofissin; mitophagy; yeast

DOI:  https://doi.org/10.1080/15548627.2023.2237343
J Clin Invest. 2023 Jul 20. pii: e164599. [Epub ahead of print]

Tumors produce glucocorticoids by metabolite recycling, not synthesis, and activate Tregs to promote growth.

Matthew D Taves, Shizuka Otsuka, Michaela A Taylor, Kaitlynn M Donahue, Thomas J Meyer, Margaret C Cam, Jonathan D Ashwell.

  Glucocorticoids are steroid hormones with potent immunosuppressive properties. Their primary source is the adrenals, where they are generated via de novo synthesis from cholesterol. In addition, many tissues have a recycling pathway in which glucocorticoids are regenerated from inactive metabolites by the enzyme 11β-HSD1 (encoded by Hsd11b1). Here we find that multiple tumor types express Hsd11b1 and produce active glucocorticoids. Genetic ablation of Hsd11b1 in such cells had no effect on in vitro growth but reduced in vivo tumor progression, which corresponded with increased frequencies of tumor-infiltrating CD8+ T cells (TIL) expressing activation markers and producing effector cytokines. Tumor-derived glucocorticoids were found to promote signatures of Treg activation and suppress signatures of Tconv activation in tumor-infiltrating Treg. Indeed, CD8+ T cell activation was restored and tumor growth reduced in mice with Treg-specific glucocorticoid receptor deficiency. Importantly, pharmacologic inhibition of 11β-HSD1 reduced tumor growth to the same degree as gene knockout, and rendered immunotherapy-resistant tumors susceptible to PD-1 blockade. Given that HSD11B1 expression is upregulated in many human tumors and that inhibition of 11β-HSD1 is well-tolerated in clinical studies, these data suggest that targeting 11β-HSD1 may be a beneficial adjunct in cancer therapy.

Keywords:  Adaptive immunity; Cancer; Immunology; Oncology

DOI:  https://doi.org/10.1172/JCI164599
Nat Commun. 2023 07 17. 14(1): 4274

Proteogenomics of clear cell renal cell carcinoma response to tyrosine kinase inhibitor.

Hailiang Zhang, Lin Bai, Xin-Qiang Wu, Xi Tian, Jinwen Feng, Xiaohui Wu, Guo-Hai Shi, Xiaoru Pei, Jiacheng Lyu, Guojian Yang, Yang Liu, Wenhao Xu, Aihetaimujiang Anwaier, Yu Zhu, Da-Long Cao, Fujiang Xu, Yue Wang, Hua-Lei Gan, Meng-Hong Sun, Jian-Yuan Zhao, Yuanyuan Qu, Dingwei Ye, Chen Ding.

The tyrosine kinase inhibitor (TKI) Sunitinib is one the therapies approved for advanced renal cell carcinoma. Here, we undertake proteogenomic profiling of 115 tumors from patients with clear cell renal cell carcinoma (ccRCC) undergoing Sunitinib treatment and reveal the molecular basis of differential clinical outcomes with TKI therapy. We find that chromosome 7q gain-induced mTOR signaling activation is associated with poor therapeutic outcomes with Sunitinib treatment, whereas the aristolochic acid signature and VHL mutation synergistically caused enhanced glycolysis is correlated with better prognosis. The proteomic and phosphoproteomic analysis further highlights the responsibility of mTOR signaling for non-response to Sunitinib. Immune landscape characterization reveals diverse tumor microenvironment subsets in ccRCC. Finally, we construct a multi-omics classifier that can detect responder and non-responder patients (receiver operating characteristic-area under the curve, 0.98). Our study highlights associations between ccRCC molecular characteristics and the response to TKI, which can facilitate future improvement of therapeutic responses.

DOI: https://doi.org/10.1038/s41467-023-39981-6
Trends Cell Biol. 2023 Jul 18. pii: S0962-8924(23)00128-9. [Epub ahead of print]

Lysosomal enzyme trafficking: from molecular mechanisms to human diseases.

Thomas Braulke, Jan E Carette, Wilhelm Palm.

  Lysosomes degrade and recycle macromolecules that are delivered through the biosynthetic, endocytic, and autophagic routes. Hydrolysis of the different classes of macromolecules is catalyzed by about 70 soluble enzymes that are transported from the Golgi apparatus to lysosomes in a mannose 6-phosphate (M6P)-dependent process. The molecular machinery that generates M6P tags for receptor-mediated targeting of lysosomal enzymes was thought to be understood in detail. However, recent studies on the M6P pathway have identified a previously uncharacterized core component, yielded structural insights in known components, and uncovered functions in various human diseases. Here we review molecular mechanisms of lysosomal enzyme trafficking and discuss its relevance for rare lysosomal disorders, cancer, and viral infection.

Keywords:  LYSET; cancer metabolism; lysosomal enzymes; lysosomal storage disorders; mannose 6-phosphate pathway; viral infections

DOI:  https://doi.org/10.1016/j.tcb.2023.06.005
Nat Commun. 2023 07 19. 14(1): 4360

Nuclear translocation of mitochondrial dehydrogenases as an adaptive cardioprotective mechanism.

Shubhi Srivastava, Priyanka Gajwani, Jordan Jousma, Hiroe Miyamoto, Youjeong Kwon, Arundhati Jana, Peter T Toth, Gege Yan, Sang-Ging Ong, Jalees Rehman.

Chemotherapy-induced cardiac damage remains a leading cause of death amongst cancer survivors. Anthracycline-induced cardiotoxicity is mediated by severe mitochondrial injury, but little is known about the mechanisms by which cardiomyocytes adaptively respond to the injury. We observed the translocation of selected mitochondrial tricarboxylic acid (TCA) cycle dehydrogenases to the nucleus as an adaptive stress response to anthracycline-cardiotoxicity in human induced pluripotent stem cell-derived cardiomyocytes and in vivo. The expression of nuclear-targeted mitochondrial dehydrogenases shifts the nuclear metabolic milieu to maintain their function both in vitro and in vivo. This protective effect is mediated by two parallel pathways: metabolite-induced chromatin accessibility and AMP-kinase (AMPK) signaling. The extent of chemotherapy-induced cardiac damage thus reflects a balance between mitochondrial injury and the protective response initiated by the nuclear pool of mitochondrial dehydrogenases. Our study identifies nuclear translocation of mitochondrial dehydrogenases as an endogenous adaptive mechanism that can be leveraged to attenuate cardiomyocyte injury.

DOI: https://doi.org/10.1038/s41467-023-40084-5
Sci Adv. 2023 Jul 21. 9(29): eadf6710

Fatty acid desaturase 2 determines the lipidomic landscape and steroidogenic function of the adrenal gland.

Anke Witt, Ivona Mateska, Alessandra Palladini, Anupam Sinha, Michele Wölk, Akiko Harauma, Nicole Bechmann, Christina Pamporaki, Andreas Dahl, Michael Rothe, Irakli Kopaliani, Christian Adolf, Anna Riester, Ben Wielockx, Stefan R Bornstein, Matthias Kroiss, Mirko Peitzsch, Toru Moriguchi, Maria Fedorova, Michal Grzybek, Triantafyllos Chavakis, Peter Mirtschink, Vasileia Ismini Alexaki.

Corticosteroids regulate vital processes, including stress responses, systemic metabolism, and blood pressure. Here, we show that corticosteroid synthesis is related to the polyunsaturated fatty acid (PUFA) content of mitochondrial phospholipids in adrenocortical cells. Inhibition of the rate-limiting enzyme of PUFA synthesis, fatty acid desaturase 2 (FADS2), leads to perturbations in the mitochondrial lipidome and diminishes steroidogenesis. Consistently, the adrenocortical mitochondria of Fads2-/- mice fed a diet with low PUFA concentration are structurally impaired and corticoid levels are decreased. On the contrary, FADS2 expression is elevated in the adrenal cortex of obese mice, and plasma corticosterone is increased, which can be counteracted by dietary supplementation with the FADS2 inhibitor SC-26192 or icosapent ethyl, an eicosapentaenoic acid ethyl ester. In humans, FADS2 expression is elevated in aldosterone-producing adenomas compared to non-active adenomas or nontumorous adrenocortical tissue and correlates with expression of steroidogenic genes. Our data demonstrate that FADS2-mediated PUFA synthesis determines adrenocortical steroidogenesis in health and disease.

DOI: https://doi.org/10.1126/sciadv.adf6710