bims-camemi 2023-06-11 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2023–06–11
34 papers selected by
Christian Frezza, Universität zu Köln

Metabolomics identifies the intestinal geography of microbial metabolite production.
De novo pyrimidine biosynthetic complexes support cancer cell proliferation and ferroptosis defence.
The Roles of Molecular Chaperones in Regulating Cell Metabolism.
Calcium and bicarbonate signaling pathways have pivotal, resonating roles in matching ATP production to demand.
Oxidative phosphorylation in bone cells.
Redundant electrostatic interactions between GATOR1 and the Rag GTPase heterodimer drives efficient amino acid sensing in human cells.
Acid-adapted cancer cells alkalinize their cytoplasm by degrading the acid-loading membrane transporter anion exchanger 2, SLC4A2.
Roles of malate and aspartate in gluconeogenesis in various physiological and pathological states.
A cytosolic surveillance mechanism activates the mitochondrial UPR.
An evolutionary mechanism to assimilate new nutrient sensors into the mTORC1 pathway.
A molecular rotor FLIM probe reveals dynamic coupling between mitochondrial inner membrane fluidity and cellular respiration.
Are Bacteria Leaky? Mechanisms of Metabolite Externalization in Bacterial Cross-Feeding.
Deciphering the cancer genome and epigenome.
Serine synthesis pathway upregulated by E-cadherin is essential for the proliferation and metastasis of breast cancers.
Epigenetic dysregulation from chromosomal transit in micronuclei.
Mitochondrial networks through the lens of mathematics.
Fumarate disarms CD8+ T cells against cancer.
Defective mitochondrial import as a challenge for cellular protein homeostasis.
Loss of the mitochondrial protein Abcb10 results in altered arginine metabolism in MEL and K562 cells and nutrient stress signaling through ATF4.
Arginine depletion attenuates renal cystogenesis in tuberous sclerosis complex model.
Reduced mitochondrial calcium uptake in macrophages is a major driver of inflammaging.
Human mitochondrial ADP/ATP carrier SLC25A4 operates with a ping-pong kinetic mechanism.
Intrinsic TGF-β signaling attenuates proximal tubule mitochondrial injury and inflammation in chronic kidney disease.
Pancreatic islet protection at the expense of secretory function involves serine-linked mitochondrial one-carbon metabolism.
NERNST: a genetically-encoded ratiometric non-destructive sensing tool to estimate NADP(H) redox status in bacterial, plant and animal systems.
Epigenetic suppression of PGC1α (PPARGC1A) causes collateral sensitivity to HMGCR-inhibitors within BRAF-treatment resistant melanomas.
MICU1 deficiency alters mitochondrial morphology and cytochrome C release.
von-Hippel Lindau and Hypoxia-Inducible Factor at the Center of Renal Cell Carcinoma Biology.
Metabolism: How a eukaryote adapted to life without respiration.
mTORC1 inhibition impairs activation of the unfolded protein response and induces cell death during ER stress in cardiomyocytes.
Distinguishing Renal Cell Carcinoma From Normal Kidney Tissue Using Mass Spectrometry Imaging Combined With Machine Learning.
SLC12A9 is a lysosome-detoxifying ammonium - chloride co-transporter.
The incretin co-agonist tirzepatide requires GIPR for hormone secretion from human islets.
Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment.

Nat Metab. 2023 Jun 05.

Metabolomics identifies the intestinal geography of microbial metabolite production.

DOI: https://doi.org/10.1038/s42255-023-00805-y
Nat Cell Biol. 2023 Jun 08.

De novo pyrimidine biosynthetic complexes support cancer cell proliferation and ferroptosis defence.

Chuanzhen Yang, Yiliang Zhao, Liao Wang, Zihao Guo, Lingdi Ma, Ronghui Yang, Ying Wu, Xuexue Li, Jing Niu, Qiaoyun Chu, Yanxia Fu, Binghui Li.

De novo pyrimidine biosynthesis is achieved by cytosolic carbamoyl-phosphate synthetase II, aspartate transcarbamylase and dihydroorotase (CAD) and uridine 5'-monophosphate synthase (UMPS), and mitochondrial dihydroorotate dehydrogenase (DHODH). However, how these enzymes are orchestrated remains enigmatical. Here we show that cytosolic glutamate oxaloacetate transaminase 1 clusters with CAD and UMPS, and this complex then connects with DHODH, which is mediated by the mitochondrial outer membrane protein voltage-dependent anion-selective channel protein 3. Therefore, these proteins form a multi-enzyme complex, named 'pyrimidinosome', involving AMP-activated protein kinase (AMPK) as a regulator. Activated AMPK dissociates from the complex to enhance pyrimidinosome assembly but inactivated UMPS, which promotes DHODH-mediated ferroptosis defence. Meanwhile, cancer cells with lower expression of AMPK are more reliant on pyrimidinosome-mediated UMP biosynthesis and more vulnerable to its inhibition. Our findings reveal the role of pyrimidinosome in regulating pyrimidine flux and ferroptosis, and suggest a pharmaceutical strategy of targeting pyrimidinosome in cancer treatment.

DOI: https://doi.org/10.1038/s41556-023-01146-4
FEBS Lett. 2023 Jun 07.

The Roles of Molecular Chaperones in Regulating Cell Metabolism.

Matthew J Binder, Anthony M Pedley.

  Fluctuations in nutrient and biomass availability, often as a result of disease, impart metabolic challenges that must be overcome in order to sustain cell survival and promote proliferation. Cells adapt to these environmental changes and stresses by adjusting their metabolic networks through a series of regulatory mechanisms. Our understanding of these rewiring events has largely been focused on those genetic transformations that alter protein expression and the biochemical mechanisms that change protein behavior, such as post-translational modifications and metabolite-based allosteric modulators. Mounting evidence suggests that a class of proteome surveillance proteins called molecular chaperones also can influence metabolic processes. Here, we summarize several ways the Hsp90 and Hsp70 chaperone families act on human metabolic enzymes and their supramolecular assemblies to change enzymatic activities and metabolite flux. We further highlight how these chaperones can assist in the translocation and degradation of metabolic enzymes. Collectively, these studies provide a new view for how metabolic processes are regulated to meet cellular demand and inspire new avenues for therapeutic intervention.

Keywords:  cellular metabolism; metabolons; molecular chaperones; protein degradation; protein folding; supramolecular complexes

DOI:  https://doi.org/10.1002/1873-3468.14682
Elife. 2023 Jun 05. pii: e84204. [Epub ahead of print]12

Calcium and bicarbonate signaling pathways have pivotal, resonating roles in matching ATP production to demand.

Maura Greiser, Mariusz Karbowski, Aaron David Kaplan, Andrew Kyle Coleman, Nicolas Verhoeven, Carmen A Mannella, W Jonathan Lederer, Liron Boyman.

  Mitochondrial ATP production in cardiac ventricular myocytes must be continually adjusted to rapidly replenish the ATP consumed by the working heart. Two systems are known to be critical in this regulation: mitochondrial matrix Ca2+ ([Ca2+]m) and blood flow that is tuned by local ventricular myocyte metabolic signaling. However, these two regulatory systems do not fully account for the physiological range of ATP consumption observed. We report here on the identity, location, and signaling cascade of a third regulatory system -- CO2/bicarbonate. CO2 is generated in the mitochondrial matrix as a metabolic waste product of the oxidation of nutrients that powers ATP production. It is a lipid soluble gas that rapidly permeates the inner mitochondrial membrane (IMM) and produces bicarbonate (HCO3-) in a reaction accelerated by carbonic anhydrase (CA). The bicarbonate level is tracked physiologically by a bicarbonate-activated adenylyl cyclase, soluble adenylyl cyclase (sAC). Using structural Airyscan super-resolution imaging and functional measurements we find that sAC is primarily inside the mitochondria of ventricular myocytes where it generates cAMP when activated by HCO3-. Our data strongly suggest that ATP production in these mitochondria is regulated by this cAMP signaling cascade operating within the inter-membrane space (IMS) by activating local EPAC1 (Exchange Protein directly Activated by cAMP) which turns on Rap1 (Ras-related protein 1). Thus, mitochondrial ATP production is shown to be increased by bicarbonate-triggered sAC signaling through Rap1. Additional evidence is presented indicating that the cAMP signaling itself does not occur directly in the matrix. We also show that this third signaling process involving bicarbonate and sAC activates the cardiac mitochondrial ATP production machinery by working independently of, yet in conjunction with, [Ca2+]m-dependent ATP production to meet the energy needs of cellular activity in both health and disease. We propose that the bicarbonate and calcium signaling arms function in a resonant or complementary manner to match mitochondrial ATP production to the full range of energy consumption in cardiac ventricular myocytes in health and disease.

Keywords:  biochemistry; chemical biology; molecular biophysics; rat; structural biology

DOI:  https://doi.org/10.7554/eLife.84204
Bone Rep. 2023 Jun;18 101688

Oxidative phosphorylation in bone cells.

Elena Sabini, Lorenzo Arboit, Mohd Parvez Khan, Giulia Lanzolla, Ernestina Schipani.

  The role of energy metabolism in bone cells is an active field of investigation. Bone cells are metabolically very active and require high levels of energy in the form of adenosine triphosphate (ATP) to support their function. ATP is generated in the cytosol via glycolysis coupled with lactic acid fermentation and in the mitochondria via oxidative phosphorylation (OXPHOS). OXPHOS is the final convergent metabolic pathway for all oxidative steps of dietary nutrients catabolism. The formation of ATP is driven by an electrochemical gradient that forms across the mitochondrial inner membrane through to the activity of the electron transport chain (ETC) complexes and requires the presence of oxygen as the final electron acceptor. The current literature supports a model in which glycolysis is the main source of energy in undifferentiated mesenchymal progenitors and terminally differentiated osteoblasts, whereas OXPHOS appears relevant in an intermediate stage of differentiation of those cells. Conversely, osteoclasts progressively increase OXPHOS during differentiation until they become multinucleated and mitochondrial-rich terminal differentiated cells. Despite the abundance of mitochondria, mature osteoclasts are considered ATP-depleted, and the availability of ATP is a critical factor that regulates the low survival capacity of these cells, which rapidly undergo death by apoptosis. In addition to ATP, bioenergetic metabolism generates reactive oxygen species (ROS) and intermediate metabolites that regulate a variety of cellular functions, including epigenetics changes of genomic DNA and histones. This review will briefly discuss the role of OXPHOS and the cross-talks OXPHOS-glycolysis in the differentiation process of bone cells.

Keywords:  Mitochondria; OXPHOS; Osteoblasts; Osteoclasts; Osteocytes

DOI:  https://doi.org/10.1016/j.bonr.2023.101688
J Biol Chem. 2023 Jun 01. pii: S0021-9258(23)01908-7. [Epub ahead of print] 104880

Redundant electrostatic interactions between GATOR1 and the Rag GTPase heterodimer drives efficient amino acid sensing in human cells.

Dylan D Doxsey, Steven D Tettoni, Shawn B Egri, Kuang Shen.

  Cells need to coordinate nutrient availability with their growth and proliferation. In eukaryotic cells, this coordination is mediated by the mechanistic target of rapamycin complex 1 (mTORC1) pathway. mTORC1 activation is regulated by two GTPase units, the Rag GTPase heterodimer and the Rheb GTPase. The RagA-RagC heterodimer controls the subcellular localization of mTORC1, and its nucleotide loading states are strictly controlled by upstream regulators including amino acid sensors. A critical negative regulator of the Rag GTPase heterodimer is GATOR1. In the absence of amino acids, GATOR1 stimulates GTP hydrolysis by the RagA subunit to turn off mTORC1 signaling. Despite the enzymatic specificity of GATOR1 to RagA, a recent cryo-EM structural model of the human GATOR1-Rag-Ragulator complex reveals an unexpected interface between Depdc5, a subunit of GATOR1, and RagC. Currently, there is no functional characterization of this interface, nor do we know its biological relevance. Here, combining structure-function analysis, enzymatic kinetic measurements, and cell-based signaling assays, we identified a critical electrostatic interaction between Depdc5 and RagC. This interaction is mediated by the positively charged Arg-1407 residue on Depdc5, and a patch of negatively charged residues on the lateral side of RagC. Abrogating this interaction impairs the GAP activity of GATOR1 and cellular response to amino acid withdrawal. Our results reveal how GATOR1 coordinates the nucleotide loading states of the Rag GTPase heterodimer, and thus precisely controls cellular behavior in the absence of amino acids.

Keywords:  GATOR1; GTPase Activating Protein; Metabolism; Rag GTPase; mTOR complex 1 (mTORC1)

DOI:  https://doi.org/10.1016/j.jbc.2023.104880
Cell Rep. 2023 Jun 03. pii: S2211-1247(23)00612-5. [Epub ahead of print]42(6): 112601

Acid-adapted cancer cells alkalinize their cytoplasm by degrading the acid-loading membrane transporter anion exchanger 2, SLC4A2.

Johanna Michl, Stefania Monterisi, Bobby White, Wiktoria Blaszczak, Alzbeta Hulikova, Gulnar Abdullayeva, Esther Bridges, Zinan Yin, Walter F Bodmer, Pawel Swietach.

  Acidic environments reduce the intracellular pH (pHi) of most cells to levels that are sub-optimal for growth and cellular functions. Yet, cancers maintain an alkaline cytoplasm despite low extracellular pH (pHe). Raised pHi is thought to be beneficial for tumor progression and invasiveness. However, the transport mechanisms underpinning this adaptation have not been studied systematically. Here, we characterize the pHe-pHi relationship in 66 colorectal cancer cell lines and identify the acid-loading anion exchanger 2 (AE2, SLC4A2) as a regulator of resting pHi. Cells adapt to chronic extracellular acidosis by degrading AE2 protein, which raises pHi and reduces acid sensitivity of growth. Acidity inhibits mTOR signaling, which stimulates lysosomal function and AE2 degradation, a process reversed by bafilomycin A1. We identify AE2 degradation as a mechanism for maintaining a conducive pHi in tumors. As an adaptive mechanism, inhibiting lysosomal degradation of AE2 is a potential therapeutic target.

Keywords:  CP: Cancer; CP: Metabolism; acid adaptation; acid-base; acidosis; chloride/bicarbonate exchanger; colorectal cancer; intracellular pH; lysosomes; tumor acidity; tumor microenvironment

DOI:  https://doi.org/10.1016/j.celrep.2023.112601
Metabolism. 2023 Jun 05. pii: S0026-0495(23)00218-4. [Epub ahead of print] 155614

Roles of malate and aspartate in gluconeogenesis in various physiological and pathological states.

Milan Holeček.

  Gluconeogenesis, a pathway for glucose synthesis from non-carbohydrate substances, begins with the synthesis of oxaloacetate (OA) from pyruvate and intermediates of citric acid cycle in hepatocyte mitochondria. The traditional view is that OA does not cross the mitochondrial membrane and must be shuttled to the cytosol, where most enzymes involved in gluconeogenesis are compartmentalized, in the form of malate. Thus, the possibility of transporting OA in the form of aspartate has been ignored. In the article is shown that malate supply to the cytosol increases only when fatty acid oxidation in the liver is activated, such as during starvation or untreated diabetes. Alternatively, aspartate synthesized from OA by mitochondrial aspartate aminotransferase (AST) is transported to the cytosol in exchange for glutamate via the aspartate-glutamate carrier 2 (AGC2). If the main substrate for gluconeogenesis is an amino acid, aspartate is converted to OA via urea cycle, therefore, ammonia detoxification and gluconeogenesis are simultaneously activated. If the main substrate is lactate, OA is synthesized by cytosolic AST, glutamate is transported to the mitochondria through AGC2, and nitrogen is not lost. It is concluded that, compared to malate, aspartate is a more suitable form of OA transport from the mitochondria for gluconeogenesis.

Keywords:  AGC2; Citrin; Mitochondrial carriers; Oxaloacetate; Urea cycle

DOI:  https://doi.org/10.1016/j.metabol.2023.155614
Nature. 2023 Jun 07.

A cytosolic surveillance mechanism activates the mitochondrial UPR.

F X Reymond Sutandy, Ines Gößner, Georg Tascher, Christian Münch.

The mitochondrial unfolded protein response (UPRmt) is essential to safeguard mitochondria from proteotoxic damage by activating a dedicated transcriptional response in the nucleus to restore proteostasis1,2. Yet, it remains unclear how the information on mitochondria misfolding stress (MMS) is signalled to the nucleus as part of the human UPRmt (refs. 3,4). Here, we show that UPRmt signalling is driven by the release of two individual signals in the cytosol-mitochondrial reactive oxygen species (mtROS) and accumulation of mitochondrial protein precursors in the cytosol (c-mtProt). Combining proteomics and genetic approaches, we identified that MMS causes the release of mtROS into the cytosol. In parallel, MMS leads to mitochondrial protein import defects causing c-mtProt accumulation. Both signals integrate to activate the UPRmt; released mtROS oxidize the cytosolic HSP40 protein DNAJA1, which leads to enhanced recruitment of cytosolic HSP70 to c-mtProt. Consequently, HSP70 releases HSF1, which translocates to the nucleus and activates transcription of UPRmt genes. Together, we identify a highly controlled cytosolic surveillance mechanism that integrates independent mitochondrial stress signals to initiate the UPRmt. These observations reveal a link between mitochondrial and cytosolic proteostasis and provide molecular insight into UPRmt signalling in human cells.

DOI: https://doi.org/10.1038/s41586-023-06142-0
bioRxiv. 2023 May 26. pii: 2023.05.25.541239. [Epub ahead of print]

An evolutionary mechanism to assimilate new nutrient sensors into the mTORC1 pathway.

Grace Y Liu, Patrick Jouandin, Raymond E Bahng, Norbert Perrimon, David M Sabatini.

Animals must sense and respond to nutrient availability in their local niche. This task is coordinated in part by the mTOR complex 1 (mTORC1) pathway, which regulates growth and metabolism in response to nutrients 1-5 . In mammals, mTORC1 senses specific amino acids through specialized sensors that act through the upstream GATOR1/2 signaling hub 6-8 . To reconcile the conserved architecture of the mTORC1 pathway with the diversity of environments that animals can occupy, we hypothesized that the pathway might maintain plasticity by evolving distinct nutrient sensors in different metazoan phyla 1,9,10 . Whether such customization occurs- and how the mTORC1 pathway might capture new nutrient inputs-is not known. Here, we identify the Drosophila melanogaster protein Unmet expectations (Unmet, formerly CG11596) as a species-restricted nutrient sensor and trace its incorporation into the mTORC1 pathway. Upon methionine starvation, Unmet binds to the fly GATOR2 complex to inhibit dTORC1. S -adenosylmethionine (SAM), a proxy for methionine availability, directly relieves this inhibition. Unmet expression is elevated in the ovary, a methionine-sensitive niche 11 , and flies lacking Unmet fail to maintain the integrity of the female germline under methionine restriction. By monitoring the evolutionary history of the Unmet-GATOR2 interaction, we show that the GATOR2 complex evolved rapidly in Dipterans to recruit and repurpose an independent methyltransferase as a SAM sensor. Thus, the modular architecture of the mTORC1 pathway allows it to co-opt preexisting enzymes and expand its nutrient sensing capabilities, revealing a mechanism for conferring evolvability on an otherwise highly conserved system.

DOI: https://doi.org/10.1101/2023.05.25.541239
Proc Natl Acad Sci U S A. 2023 Jun 13. 120(24): e2213241120

A molecular rotor FLIM probe reveals dynamic coupling between mitochondrial inner membrane fluidity and cellular respiration.

Gaurav Singh, Geen George, Sufi O Raja, Ponnuvel Kandaswamy, Manoj Kumar, Shashi Thutupalli, Sunil Laxman, Akash Gulyani.

  The inner mitochondrial membrane (IMM), housing components of the electron transport chain (ETC), is the site for respiration. The ETC relies on mobile carriers; therefore, it has long been argued that the fluidity of the densely packed IMM can potentially influence ETC flux and cell physiology. However, it is unclear if cells temporally modulate IMM fluidity upon metabolic or other stimulation. Using a photostable, red-shifted, cell-permeable molecular-rotor, Mitorotor-1, we present a multiplexed approach for quantitatively mapping IMM fluidity in living cells. This reveals IMM fluidity to be linked to cellular-respiration and responsive to stimuli. Multiple approaches combining in vitro experiments and live-cell fluorescence (FLIM) lifetime imaging microscopy (FLIM) show Mitorotor-1 to robustly report IMM 'microviscosity'/fluidity through changes in molecular free volume. Interestingly, external osmotic stimuli cause controlled swelling/compaction of mitochondria, thereby revealing a graded Mitorotor-1 response to IMM microviscosity. Lateral diffusion measurements of IMM correlate with microviscosity reported via Mitorotor-1 FLIM-lifetime, showing convergence of independent approaches for measuring IMM local-order. Mitorotor-1 FLIM reveals mitochondrial heterogeneity in IMM fluidity; between-and-within cells and across single mitochondrion. Multiplexed FLIM lifetime imaging of Mitorotor-1 and NADH autofluorescence reveals that IMM fluidity positively correlates with respiration, across individual cells. Remarkably, we find that stimulating respiration, through nutrient deprivation or chemically, also leads to increase in IMM fluidity. These data suggest that modulating IMM fluidity supports enhanced respiratory flux. Our study presents a robust method for measuring IMM fluidity and suggests a dynamic regulatory paradigm of modulating IMM local order on changing metabolic demand.

Keywords:  fluidity; fluorescence lifetime; fluorescent probe; metabolism; mitochondria

DOI:  https://doi.org/10.1073/pnas.2213241120
Annu Rev Microbiol. 2023 Jun 07.

Are Bacteria Leaky? Mechanisms of Metabolite Externalization in Bacterial Cross-Feeding.

James B McKinlay.

The metabolism of a bacterial cell stretches beyond its boundaries, often connecting with the metabolism of other cells to form extended metabolic networks that stretch across communities, and even the globe. Among the least intuitive metabolic connections are those involving cross-feeding of canonically intracellular metabolites. How and why are these intracellular metabolites externalized? Are bacteria simply leaky? Here I consider what it means for a bacterium to be leaky, and I review mechanisms of metabolite externalization from the context of cross-feeding. Despite common claims, diffusion of most intracellular metabolites across a membrane is unlikely. Instead, passive and active transporters are likely involved, possibly purging excess metabolites as part of homeostasis. Re-acquisition of metabolites by a producer limits the opportunities for cross-feeding. However, a competitive recipient can stimulate metabolite externalization and initiate a positive-feedback loop of reciprocal cross-feeding. Expected final online publication date for the Annual Review of Microbiology, Volume 77 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-micro-032521-023815
Nat Rev Cancer. 2023 Jun 07.

Deciphering the cancer genome and epigenome.

Isabel Esain-Garcia.

DOI: https://doi.org/10.1038/s41568-023-00590-6
bioRxiv. 2023 May 24. pii: 2023.05.24.541452. [Epub ahead of print]

Serine synthesis pathway upregulated by E-cadherin is essential for the proliferation and metastasis of breast cancers.

Geonhui Lee, Claudia Wong, Anna Cho, Junior J West, Ashleigh J Crawford, Gabriella C Russo, Bishwa Ranjan Si, Jungwoo Kim, Lauren Hoffner, Cholsoon Jang, Moonjung Jung, Robert D Leone, Konstantinos Konstantopoulos, Andrew J Ewald, Denis Wirtz, Sangmoo Jeong.

The loss of E-cadherin (E-cad), an epithelial cell adhesion molecule, has been implicated in the epithelial-mesenchymal transition (EMT), promoting invasion and migration of cancer cells and, consequently, metastasis. However, recent studies have demonstrated that E-cad supports the survival and proliferation of metastatic cancer cells, suggesting that our understanding of E-cad in metastasis is far from comprehensive. Here, we report that E-cad upregulates the de novo serine synthesis pathway (SSP) in breast cancer cells. The SSP provides metabolic precursors for biosynthesis and resistance to oxidative stress, critically beneficial for E-cad-positive breast cancer cells to achieve faster tumor growth and more metastases. Inhibition of PHGDH, a rate- limiting enzyme in the SSP, significantly and specifically hampered the proliferation of E-cad- positive breast cancer cells and rendered them vulnerable to oxidative stress, inhibiting their metastatic potential. Our findings reveal that E-cad adhesion molecule significantly reprograms cellular metabolism, promoting tumor growth and metastasis of breast cancers.

DOI: https://doi.org/10.1101/2023.05.24.541452
Nature. 2023 Jun 07.

Epigenetic dysregulation from chromosomal transit in micronuclei.

Albert S Agustinus, Duaa Al-Rawi, Bhargavi Dameracharla, Ramya Raviram, Bailey S C L Jones, Stephanie Stransky, Lorenzo Scipioni, Jens Luebeck, Melody Di Bona, Danguole Norkunaite, Robert M Myers, Mercedes Duran, Seongmin Choi, Britta Weigelt, Shira Yomtoubian, Andrew McPherson, Eléonore Toufektchan, Kristina Keuper, Paul S Mischel, Vivek Mittal, Sohrab P Shah, John Maciejowski, Zuzana Storchova, Enrico Gratton, Peter Ly, Dan Landau, Mathieu F Bakhoum, Richard P Koche, Simone Sidoli, Vineet Bafna, Yael David, Samuel F Bakhoum.

Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers1-4, but whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei5,6 and subsequent rupture of the micronuclear envelope7 profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice, as well as in cancer and non-transformed cells. Some of the changes in histone PTMs occur because of the rupture of the micronuclear envelope, whereas others are inherited from mitotic abnormalities before the micronucleus is formed. Using orthogonal approaches, we demonstrate that micronuclei exhibit extensive differences in chromatin accessibility, with a strong positional bias between promoters and distal or intergenic regions, in line with observed redistributions of histone PTMs. Inducing CIN causes widespread epigenetic dysregulation, and chromosomes that transit in micronuclei experience heritable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, as well as altering genomic copy number, CIN promotes epigenetic reprogramming and heterogeneity in cancer.

DOI: https://doi.org/10.1038/s41586-023-06084-7
Phys Biol. 2023 Jun 08.

Mitochondrial networks through the lens of mathematics.

Greyson Lewis, Wallace F Marshall.

  Mitochondria serve a wide range of functions within cells, most notably via their production of ATP. Although their morphology is commonly described as bean-like, mitochondria often form interconnected networks within cells that exhibit dynamic restructuring through a variety of physical changes. Further, though relationships between form and function in biology are well established, the extant toolkit for understanding mitochondrial morphology is limited. Here, we emphasize new and established methods for quantitatively describing mitochondrial networks, ranging from unweighted graph-theoretic representations to multi-scale approaches from applied topology, in particular persistent homology. We also show fundamental relationships between mitochondrial networks, mathematics, and physics, using ideas of graph planarity and statistical mechanics to better understand the full possible morphologicalspace of mitochondrial network structures. Lastly, we provide suggestions for how examination of mitochondrial network form through the language of mathematics can inform biological understanding, and vice versa.

Keywords:  graph theory; mitochondrial networks; persistent homology; planar graphs; scaling

DOI:  https://doi.org/10.1088/1478-3975/acdcdb
Cell Metab. 2023 Jun 06. pii: S1550-4131(23)00182-1. [Epub ahead of print]35(6): 907-909

Fumarate disarms CD8+ T cells against cancer.

Luigi Nezi, Teresa Manzo.

The composition of nutrients in the tumor microenvironment is a key determinant of anti-tumor CD8+ T cell response. In this issue of Cell Metabolism, Jiang and colleagues unveil that tumor-derived fumarate dampens TCR signaling in CD8+ T cells, resulting in defective activation, loss of effector functions, and associated failure of tumor control.

DOI: https://doi.org/10.1016/j.cmet.2023.05.005
FEBS Lett. 2023 Jun 05.

Defective mitochondrial import as a challenge for cellular protein homeostasis.

Klaudia K Maruszczak, Selvaraj Ayyamperumal, Agnieszka Chacinska.

  Mitochondria are organelles indispensable for the correct functioning of eukaryotic cells. Their significance for cellular homeostasis is manifested by the existence of complex quality control pathways that monitor organellar fitness. Mitochondrial biogenesis relies on the efficient import of mitochondrial precursor proteins, a large majority of which are encoded by nuclear DNA and synthesized in the cytosol. This creates a demand for highly specialized import routes that comprise cytosolic factors and organellar translocases. The passage of newly encoded mitochondrial precursor proteins through the cytosol to the translocase of the outer mitochondrial membrane (TOM) is under tight surveillance. As a result of mitochondrial import defects, mitochondrial precursor proteins accumulate in the cytosol or clog the TOM complex, which in turn stimulates cellular stress responses to minimize the consequences of these challenges. These responses are critical for maintaining protein homeostasis under conditions of mitochondrial stress. The present review summarizes recent advances in the field of mitochondrial protein import quality control and discusses the role of this quality control within the network of cellular mechanisms that maintain the cellular homeostasis of proteins.

Keywords:  cellular stress responses; mitochondria; mitochondrial dysfunction; mitochondrial quality control; protein aggregates; protein homeostasis

DOI:  https://doi.org/10.1002/1873-3468.14677
J Biol Chem. 2023 Jun 01. pii: S0021-9258(23)01905-1. [Epub ahead of print] 104877

Loss of the mitochondrial protein Abcb10 results in altered arginine metabolism in MEL and K562 cells and nutrient stress signaling through ATF4.

Marisa Miljkovic, Alexandra Seguin, Xuan Jia, James E Cox, Jonathan Leon Catrow, Hector Bergonia, John D Phillips, W Zac Stephens, Diane M Ward.

  Abcb10 is a mitochondrial membrane protein involved in hemoglobinization of red cells. Abcb10 topology and ATPase domain localization suggest it exports a substrate, likely biliverdin, out of mitochondria that is necessary for hemoglobinization. In this study we generated Abcb10 deletion cell lines in both mouse murine erythroleukemia (MEL) and human erythroid precursor human myelogenous leukemia (K562) cells to better understand the consequences of Abcb10 loss. Loss of Abcb10 resulted in an inability to hemoglobinize upon differentiation in both K562 and MEL cells with reduced heme and intermediate porphyrins and decreased levels of aminolevulinic acid synthase 2 activity. Metabolomic and transcriptional analyses revealed that Abcb10 loss gave rise to decreased cellular arginine levels, increased transcripts for cationic and neutral amino acid transporters with reduced levels of the citrulline to arginine converting enzymes argininosuccinate synthetase and argininosuccinate lyase. The reduced arginine levels in Abcb10 null cells gave rise to decreased proliferative capacity. Arginine supplementation improved both Abcb10 null proliferation and hemoglobinization upon differentiation. Abcb10 null cells showed increased phosphorylation of Eukaryotic Translation Initiation Factor 2 Subunit Alpha (eIF2A), increased expression of nutrient sensing transcription factor ATF4 and downstream targets DNA damage inducible transcript 3 (Chop), ChaC glutathione specific gamma-glutamylcyclotransferase 1 (Chac1) and arginyl-tRNA synthetase 1 (Rars). These results suggest that when the Abcb10 substrate is trapped in the mitochondria, the nutrient sensing machinery is turned on remodeling transcription to block protein synthesis necessary for proliferation and hemoglobin biosynthesis in erythroid models.

Keywords:  Arginine; differentiation; erythroid; metabolism; nutrient; transporter

DOI:  https://doi.org/10.1016/j.jbc.2023.104877
Cell Rep Med. 2023 Jun 02. pii: S2666-3791(23)00192-1. [Epub ahead of print] 101073

Arginine depletion attenuates renal cystogenesis in tuberous sclerosis complex model.

Athar Amleh, Hadass Pri Chen, Lana Watad, Ifat Abramovich, Bella Agranovich, Eyal Gottlieb, Iddo Z Ben-Dov, Morris Nechama, Oded Volovelsky.

  Cystic kidney disease is a leading cause of morbidity in patients with tuberous sclerosis complex (TSC). We characterize the misregulated metabolic pathways using cell lines, a TSC mouse model, and human kidney sections. Our study reveals a substantial perturbation in the arginine biosynthesis pathway in TSC models with overexpression of argininosuccinate synthetase 1 (ASS1). The rise in ASS1 expression is dependent on the mechanistic target of rapamycin complex 1 (mTORC1) activity. Arginine depletion prevents mTORC1 hyperactivation and cell cycle progression and averts cystogenic signaling overexpression of c-Myc and P65. Accordingly, an arginine-depleted diet substantially reduces the TSC cystic load in mice, indicating the potential therapeutic effects of arginine deprivation for the treatment of TSC-associated kidney disease.

Keywords:  ASS1; PTCs; TSC; arginine metabolism; argininosuccinate synthetase 1; cystogenesis; mTORC1; mechanistic target of rapamycin complex 1; proximal tubule cells; tuberous sclerosis complex

DOI:  https://doi.org/10.1016/j.xcrm.2023.101073
Nat Aging. 2023 Jun 05.

Reduced mitochondrial calcium uptake in macrophages is a major driver of inflammaging.

Philip V Seegren, Logan R Harper, Taylor K Downs, Xiao-Yu Zhao, Shivapriya B Viswanathan, Marta E Stremska, Rachel J Olson, Joel Kennedy, Sarah E Ewald, Pankaj Kumar, Bimal N Desai.

Mitochondrial dysfunction is linked to age-associated inflammation or inflammaging, but underlying mechanisms are not understood. Analyses of 700 human blood transcriptomes revealed clear signs of age-associated low-grade inflammation. Among changes in mitochondrial components, we found that the expression of mitochondrial calcium uniporter (MCU) and its regulatory subunit MICU1, genes central to mitochondrial Ca2+ (mCa2+) signaling, correlated inversely with age. Indeed, mCa2+ uptake capacity of mouse macrophages decreased significantly with age. We show that in both human and mouse macrophages, reduced mCa2+ uptake amplifies cytosolic Ca2+ oscillations and potentiates downstream nuclear factor kappa B activation, which is central to inflammation. Our findings pinpoint the mitochondrial calcium uniporter complex as a keystone molecular apparatus that links age-related changes in mitochondrial physiology to systemic macrophage-mediated age-associated inflammation. The findings raise the exciting possibility that restoring mCa2+ uptake capacity in tissue-resident macrophages may decrease inflammaging of specific organs and alleviate age-associated conditions such as neurodegenerative and cardiometabolic diseases.

DOI: https://doi.org/10.1038/s43587-023-00436-8
EMBO Rep. 2023 Jun 06. e57127

Human mitochondrial ADP/ATP carrier SLC25A4 operates with a ping-pong kinetic mechanism.

Camila Cimadamore-Werthein, Stephany Jaiquel Baron, Martin S King, Roger Springett, Edmund Rs Kunji.

  The mitochondrial ADP/ATP carrier (SLC25A4), also called the adenine nucleotide translocase, imports ADP into the mitochondrial matrix and exports ATP, which are key steps in oxidative phosphorylation. Historically, the carrier was thought to form a homodimer and to operate by a sequential kinetic mechanism, which involves the formation of a ternary complex with the two exchanged substrates bound simultaneously. However, recent structural and functional data have demonstrated that the mitochondrial ADP/ATP carrier works as a monomer and has a single substrate binding site, which cannot be reconciled with a sequential kinetic mechanism. Here, we study the kinetic properties of the human mitochondrial ADP/ATP carrier by using proteoliposomes and transport robotics. We show that the Km/Vmax ratio is constant for all of the measured internal concentrations. Thus, in contrast to earlier claims, we conclude that the carrier operates with a ping-pong kinetic mechanism in which substrate exchange across the membrane occurs consecutively rather than simultaneously. These data unite the kinetic and structural models, showing that the carrier operates with an alternating access mechanism.

Keywords:  ADP/ATP translocase; SLC25; adenine nucleotide translocator; bioenergetics; mitochondrial carrier family

DOI:  https://doi.org/10.15252/embr.202357127
Nat Commun. 2023 Jun 03. 14(1): 3236

Intrinsic TGF-β signaling attenuates proximal tubule mitochondrial injury and inflammation in chronic kidney disease.

Merve Kayhan, Judith Vouillamoz, Daymé Gonzalez Rodriguez, Milica Bugarski, Yasutaka Mitamura, Julia Gschwend, Christoph Schneider, Andrew Hall, David Legouis, Cezmi A Akdis, Leary Peter, Hubert Rehrauer, Leslie Gewin, Roland H Wenger, Stellor Nlandu Khodo.

Excessive TGF-β signaling and mitochondrial dysfunction fuel chronic kidney disease (CKD) progression. However, inhibiting TGF-β failed to impede CKD in humans. The proximal tubule (PT), the most vulnerable renal segment, is packed with giant mitochondria and injured PT is pivotal in CKD progression. How TGF-β signaling affects PT mitochondria in CKD remained unknown. Here, we combine spatial transcriptomics and bulk RNAseq with biochemical analyses to depict the role of TGF-β signaling on PT mitochondrial homeostasis and tubulo-interstitial interactions in CKD. Male mice carrying specific deletion of Tgfbr2 in the PT have increased mitochondrial injury and exacerbated Th1 immune response in the aristolochic acid model of CKD, partly, through impaired complex I expression and mitochondrial quality control associated with a metabolic rewiring toward aerobic glycolysis in the PT cells. Injured S3T2 PT cells are identified as the main mediators of the maladaptive macrophage/dendritic cell activation in the absence of Tgfbr2. snRNAseq database analyses confirm decreased TGF-β receptors and a metabolic deregulation in the PT of CKD patients. This study describes the role of TGF-β signaling in PT mitochondrial homeostasis and inflammation in CKD, suggesting potential therapeutic targets that might be used to mitigate CKD progression.

DOI: https://doi.org/10.1038/s41467-023-39050-y
Cell Rep. 2023 Jun 07. pii: S2211-1247(23)00626-5. [Epub ahead of print]42(6): 112615

Pancreatic islet protection at the expense of secretory function involves serine-linked mitochondrial one-carbon metabolism.

Angela Pelligra, Jessica Mrugala, Kerstin Griess, Philip Kirschner, Oliver Nortmann, Barbara Bartosinska, Andrea Köster, Natalia I Krupenko, Dominik Gebel, Philipp Westhoff, Bodo Steckel, Daniel Eberhard, Diran Herebian, Bengt-Frederik Belgardt, Jürgen Schrader, Andreas P M Weber, Sergey A Krupenko, Eckhard Lammert.

  Type 2 diabetes is characterized by insulin hypersecretion followed by reduced glucose-stimulated insulin secretion (GSIS). Here we show that acute stimulation of pancreatic islets with the insulin secretagogue dextrorphan (DXO) or glibenclamide enhances GSIS, whereas chronic treatment with high concentrations of these drugs reduces GSIS but protect islets from cell death. Bulk RNA sequencing of islets shows increased expression of genes for serine-linked mitochondrial one-carbon metabolism (OCM) after chronic, but not acute, stimulation. In chronically stimulated islets, more glucose is metabolized to serine than to citrate, and the mitochondrial ATP/ADP ratio decreases, whereas the NAPDH/NADP+ ratio increases. Activating transcription factor-4 (Atf4) is required and sufficient to activate serine-linked mitochondrial OCM genes in islets, with gain- and loss-of-function experiments showing that Atf4 reduces GSIS and is required, but not sufficient, for full DXO-mediated islet protection. In sum, we identify a reversible metabolic pathway that provides islet protection at the expense of secretory function.

Keywords:  Activating transcription factor-4 (Atf4); CP: Metabolism; K(ATP) channel; beta cell exhaustion; beta cell survival; de novo serine synthesis; diabetes; mitochondria; one-carbon metabolism; pancreatic beta cell; pancreatic islets

DOI:  https://doi.org/10.1016/j.celrep.2023.112615
Nat Commun. 2023 Jun 06. 14(1): 3277

NERNST: a genetically-encoded ratiometric non-destructive sensing tool to estimate NADP(H) redox status in bacterial, plant and animal systems.

Pamela E Molinari, Adriana R Krapp, Andrea Weiner, Hannes M Beyer, Arun Kumar Kondadi, Tim Blomeier, Melina López, Pilar Bustos-Sanmamed, Evelyn Tevere, Wilfried Weber, Andreas S Reichert, Nora B Calcaterra, Mathias Beller, Nestor Carrillo, Matias D Zurbriggen.

NADP(H) is a central metabolic hub providing reducing equivalents to multiple biosynthetic, regulatory and antioxidative pathways in all living organisms. While biosensors are available to determine NADP+ or NADPH levels in vivo, no probe exists to estimate the NADP(H) redox status, a determinant of the cell energy availability. We describe herein the design and characterization of a genetically-encoded ratiometric biosensor, termed NERNST, able to interact with NADP(H) and estimate ENADP(H). NERNST consists of a redox-sensitive green fluorescent protein (roGFP2) fused to an NADPH-thioredoxin reductase C module which selectively monitors NADP(H) redox states via oxido-reduction of the roGFP2 moiety. NERNST is functional in bacterial, plant and animal cells, and organelles such as chloroplasts and mitochondria. Using NERNST, we monitor NADP(H) dynamics during bacterial growth, environmental stresses in plants, metabolic challenges to mammalian cells, and wounding in zebrafish. NERNST estimates the NADP(H) redox poise in living organisms, with various potential applications in biochemical, biotechnological and biomedical research.

DOI: https://doi.org/10.1038/s41467-023-38739-4
Nat Commun. 2023 Jun 05. 14(1): 3251

Epigenetic suppression of PGC1α (PPARGC1A) causes collateral sensitivity to HMGCR-inhibitors within BRAF-treatment resistant melanomas.

Jiaxin Liang, Deyang Yu, Chi Luo, Christopher Bennett, Mark Jedrychowski, Steve P Gygi, Hans R Widlund, Pere Puigserver.

While targeted treatment against BRAF(V600E) improve survival for melanoma patients, many will see their cancer recur. Here we provide data indicating that epigenetic suppression of PGC1α defines an aggressive subset of chronic BRAF-inhibitor treated melanomas. A metabolism-centered pharmacological screen further identifies statins (HMGCR inhibitors) as a collateral vulnerability within PGC1α-suppressed BRAF-inhibitor resistant melanomas. Lower PGC1α levels mechanistically causes reduced RAB6B and RAB27A expression, whereby their combined re-expression reverses statin vulnerability. BRAF-inhibitor resistant cells with reduced PGC1α have increased integrin-FAK signaling and improved extracellular matrix detached survival cues that helps explain their increased metastatic ability. Statin treatment blocks cell growth by lowering RAB6B and RAB27A prenylation that reduces their membrane association and affects integrin localization and downstream signaling required for growth. These results suggest that chronic adaptation to BRAF-targeted treatments drive novel collateral metabolic vulnerabilities, and that HMGCR inhibitors may offer a strategy to treat melanomas recurring with suppressed PGC1α expression.

DOI: https://doi.org/10.1038/s41467-023-38968-7
Cell Calcium. 2023 Jun 02. pii: S0143-4160(23)00077-5. [Epub ahead of print]113 102765

MICU1 deficiency alters mitochondrial morphology and cytochrome C release.

Benjamin Gottschalk, Roland Malli, Wolfgang F Graier.

  The mitochondrial inner boundary membrane harbors a protein called MICU1, which is sensitive to Ca2+ and binds to the MICOS components Mic60 and CHCHD2. Changes in the mitochondrial cristae junction structure and organization in MICU1-/- cells lead to increased cytochrome c release, membrane potential rearrangement, and changes in mitochondrial Ca2+ uptake dynamics. These findings shed new light on the multifaceted role of MICU1, highlighting its involvement not only as an interaction partner and regulator of the MCU complex but also as a crucial determinant of mitochondrial ultrastructure and, thus, an essential player in processes initiating apoptosis.

Keywords:  Apoptosis; Ca(2+) signaling; Cristae junction; MICOS-complex; MICU1; Mitochondria

DOI:  https://doi.org/10.1016/j.ceca.2023.102765
Hematol Oncol Clin North Am. 2023 Jun 01. pii: S0889-8588(23)00045-X. [Epub ahead of print]

von-Hippel Lindau and Hypoxia-Inducible Factor at the Center of Renal Cell Carcinoma Biology.

Nitin H Shirole, William G Kaelin.

  The most common form of kidney cancer is clear cell renal cell carcinoma (ccRCC). Biallelic VHL tumor suppressor gene inactivation is the usual initiating event in both hereditary (VHL Disease) and sporadic ccRCCs. The VHL protein, pVHL, earmarks the alpha subunits of the HIF transcription factor for destruction in an oxygen-dependent manner. Deregulation of HIF2 drives ccRCC pathogenesis. Drugs inhibiting the HIF2-responsive growth factor VEGF are now mainstays of ccRCC treatment. A first-in-class allosteric HIF2 inhibitor was recently approved for treating VHL Disease-associated neoplasms and appears active against sporadic ccRCC in early clinical trials.

Keywords:  Belzutifan; Hypoxia-inducible factor; Kidney cancer; Renal cell carcinoma; von Hippel-Lindau disease

DOI:  https://doi.org/10.1016/j.hoc.2023.04.011
Curr Biol. 2023 Jun 05. pii: S0960-9822(23)00596-1. [Epub ahead of print]33(11): R444-R447

Metabolism: How a eukaryote adapted to life without respiration.

Lloyd Cool, Samuel Hanon, Kevin J Verstrepen.

A new study finds that Schizosaccharomyces japonicus, a eukaryote that lost the ability to respire, modified its central carbon metabolism to maintain efficient ATP production, cofactor regeneration, and amino-acid production. This remarkable metabolic flexibility opens new avenues towards applications.

DOI: https://doi.org/10.1016/j.cub.2023.05.002
Am J Physiol Heart Circ Physiol. 2023 Jun 09.

mTORC1 inhibition impairs activation of the unfolded protein response and induces cell death during ER stress in cardiomyocytes.

Christoph Hofmann, Zoe Löwenthal, Marjan Aghajani, Randal J Kaufman, Hugo A Katus, Norbert Frey, Christopher C Glembotski, Mirko Völkers, Shirin Doroudgar.

  The mechanistic target of rapamycin complex 1 (mTORC1) is a central regulator of protein synthesis that senses and responds to a variety of stimuli to coordinate cellular metabolism with environmental conditions. To ensure that protein synthesis is inhibited during unfavorable conditions, translation is directly coupled to the sensing of cellular protein homeostasis. Thus, translation is attenuated during endoplasmic reticulum (ER) stress by direct inhibition of the mTORC1 pathway. However, residual mTORC1 activity is maintained during prolonged ER stress which is thought to be involved in translational reprogramming and adaption to ER stress. By analyzing the dynamics of mTORC1 regulation during ER stress, we unexpectedly found that mTORC1 is transiently activated in cardiomyocytes within minutes at the onset of ER stress before being inhibited during chronic ER stress. This dynamic regulation of mTORC1 appears to be mediated, at least in part, by ATF6, as its activation was sufficient to induce the biphasic control of mTORC1. We further showed that protein synthesis remains dependent on mTORC1 throughout the ER stress response and that mTORC1 activity is essential for posttranscriptional induction of several unfolded protein response elements. Pharmacological inhibition of mTORC1 increased cell death during ER stress, indicating that the mTORC1 pathway serves adaptive functions during ER stress in cardiomyocytes potentially by controlling the expression of the protective unfolded protein response.

Keywords:  ATF6; ER stress; cardiomyocytes; cell death; mTORC1

DOI:  https://doi.org/10.1152/ajpheart.00682.2022
JCO Precis Oncol. 2023 06;7 e2200668

Distinguishing Renal Cell Carcinoma From Normal Kidney Tissue Using Mass Spectrometry Imaging Combined With Machine Learning.

Vishnu Shankar, Kanchustambham Vijayalakshmi, Rosalie Nolley, Geoffrey A Sonn, Chia-Sui Kao, Hongjuan Zhao, Ru Wen, Livia S Eberlin, Robert Tibshirani, Richard N Zare, James D Brooks.

PURPOSE: Accurately distinguishing renal cell carcinoma (RCC) from normal kidney tissue is critical for identifying positive surgical margins (PSMs) during partial and radical nephrectomy, which remains the primary intervention for localized RCC. Techniques that detect PSM with higher accuracy and faster turnaround time than intraoperative frozen section (IFS) analysis can help decrease reoperation rates, relieve patient anxiety and costs, and potentially improve patient outcomes.
MATERIALS AND METHODS: Here, we extended our combined desorption electrospray ionization mass spectrometry imaging (DESI-MSI) and machine learning methodology to identify metabolite and lipid species from tissue surfaces that can distinguish normal tissues from clear cell RCC (ccRCC), papillary RCC (pRCC), and chromophobe RCC (chRCC) tissues.
RESULTS: From 24 normal and 40 renal cancer (23 ccRCC, 13 pRCC, and 4 chRCC) tissues, we developed a multinomial lasso classifier that selects 281 total analytes from over 27,000 detected molecular species that distinguishes all histological subtypes of RCC from normal kidney tissues with 84.5% accuracy. On the basis of independent test data reflecting distinct patient populations, the classifier achieves 85.4% and 91.2% accuracy on a Stanford test set (20 normal and 28 RCC) and a Baylor-UT Austin test set (16 normal and 41 RCC), respectively. The majority of the model's selected features show consistent trends across data sets affirming its stable performance, where the suppression of arachidonic acid metabolism is identified as a shared molecular feature of ccRCC and pRCC.
CONCLUSION: Together, these results indicate that signatures derived from DESI-MSI combined with machine learning may be used to rapidly determine surgical margin status with accuracies that meet or exceed those reported for IFS.

DOI: https://doi.org/10.1200/PO.22.00668
bioRxiv. 2023 May 22. pii: 2023.05.22.541801. [Epub ahead of print]

SLC12A9 is a lysosome-detoxifying ammonium - chloride co-transporter.

Roni Levin-Konigsberg, Koushambi Mitra, AkshatKumar Nigam, Kaitlyn Spees, Pravin Hivare, Katherine Liu, Anshul Kundaje, Yamuna Krishnan, Michael C Bassik.

Ammonia is a ubiquitous, toxic by-product of cell metabolism. Its high membrane permeability and proton affinity causes ammonia to accumulate inside acidic lysosomes in its poorly membrane-permeant form: ammonium (NH 4 + ). Ammonium buildup compromises lysosomal function, suggesting the existence of mechanisms that protect cells from ammonium toxicity. Here, we identified SLC12A9 as a lysosomal ammonium exporter that preserves lysosomal homeostasis. SLC12A9 knockout cells showed grossly enlarged lysosomes and elevated ammonium content. These phenotypes were reversed upon removal of the metabolic source of ammonium or dissipation of the lysosomal pH gradient. Lysosomal chloride increased in SLC12A9 knockout cells and chloride binding by SLC12A9 was required for ammonium transport. Our data indicate that SLC12A9 is a chloride-driven ammonium co-transporter that is central in an unappreciated, fundamental mechanism of lysosomal physiology that may have special relevance in tissues with elevated ammonia, such as tumors.

DOI: https://doi.org/10.1101/2023.05.22.541801
Nat Metab. 2023 Jun 05.

The incretin co-agonist tirzepatide requires GIPR for hormone secretion from human islets.

Kimberley El, Jonathan D Douros, Francis S Willard, Aaron Novikoff, Ashot Sargsyan, Diego Perez-Tilve, David B Wainscott, Bin Yang, Alex Chen, Donald Wothe, Callum Coupland, Mattias H Tschöp, Brian Finan, David A D'Alessio, Kyle W Sloop, Timo D Müller, Jonathan E Campbell.

The incretins glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide 1 (GLP-1) mediate insulin responses that are proportionate to nutrient intake to facilitate glucose tolerance1. The GLP-1 receptor (GLP-1R) is an established drug target for the treatment of diabetes and obesity2, whereas the therapeutic potential of the GIP receptor (GIPR) is a subject of debate. Tirzepatide is an agonist at both the GIPR and GLP-1R and is a highly effective treatment for type 2 diabetes and obesity3,4. However, although tirzepatide activates GIPR in cell lines and mouse models, it is not clear whether or how dual agonism contributes to its therapeutic benefit. Islet beta cells express both the GLP-1R and the GIPR, and insulin secretion is an established mechanism by which incretin agonists improve glycemic control5. Here, we show that in mouse islets, tirzepatide stimulates insulin secretion predominantly through the GLP-1R, owing to reduced potency at the mouse GIPR. However, in human islets, antagonizing GIPR activity consistently decreases the insulin response to tirzepatide. Moreover, tirzepatide enhances glucagon secretion and somatostatin secretion in human islets. These data demonstrate that tirzepatide stimulates islet hormone secretion from human islets through both incretin receptors.

DOI: https://doi.org/10.1038/s42255-023-00811-0
Genome Med. 2023 Jun 05. 15(1): 40

Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment.

Hrvoje Misetic, Mohamed Reda Keddar, Jean-Pierre Jeannon, Francesca D Ciccarelli.

   BACKGROUND: The crosstalk between cancer and the tumour immune microenvironment (TIME) has attracted significant interest in the latest years because of its impact on cancer evolution and response to treatment. Despite this, cancer-specific tumour-TIME interactions and their mechanistic insights are still poorly understood.
METHODS: Here, we compute the significant interactions occurring between cancer-specific genetic drivers and five anti- and pro-tumour TIME features in 32 cancer types using Lasso regularised ordinal regression. Focusing on head and neck squamous cancer (HNSC), we rebuild the functional networks linking specific TIME driver alterations to the TIME state they associate with.
RESULTS: The 477 TIME drivers that we identify are multifunctional genes whose alterations are selected early in cancer evolution and recur across and within cancer types. Tumour suppressors and oncogenes have an opposite effect on the TIME and the overall anti-tumour TIME driver burden is predictive of response to immunotherapy. TIME driver alterations predict the immune profiles of HNSC molecular subtypes, and perturbations in keratinization, apoptosis and interferon signalling underpin specific driver-TIME interactions.
CONCLUSIONS: Overall, our study delivers a comprehensive resource of TIME drivers, gives mechanistic insights into their immune-regulatory role, and provides an additional framework for patient prioritisation to immunotherapy. The full list of TIME drivers and associated properties are available at http://www.network-cancer-genes.org .

Keywords:  Cancer driver genes; Cancer immunology; Computational biology; Functional networks; Head and neck cancer

DOI:  https://doi.org/10.1186/s13073-023-01197-0