bims-cagime 2024-06-09 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2024‒06‒09
47 papers selected by
Kıvanç Görgülü, Technical University of Munich

Area postrema neurons mediate interleukin-6 function in cancer cachexia.
Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow.
In vivo CRISPR screening identifies geranylgeranyl diphosphate as a pancreatic cancer tumor growth dependency.
Determining the ERK-regulated phosphoproteome driving KRAS-mutant cancer.
Engineering focusing on cancer.
De novo and salvage purine synthesis pathways across tissues and tumors.
Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress.
Hungry for fat: Metabolic crosstalk with lipid-rich CAFs fuels pancreatic cancer.
Defining the KRAS- and ERK-dependent transcriptome in KRAS-mutant cancers.
A Hypoxia-Epigenetics Axis Drives EMT in Pancreatic Cancer.
PDAC heterogeneity resolved spatially at the single-cell level: new biological answers, new questions on optimal translation†.
The ribotoxic stress response drives UV-mediated cell death.
A developmental constraint model of cancer cell states and tumor heterogeneity.
Plasma membrane abundance dictates phagocytic capacity and functional cross-talk in myeloid cells.
Partitioning to ordered membrane domains regulates the kinetics of secretory traffic.
Apoptotic cells promote circulating tumor cell survival and metastasis.
An unexpected role for the ketogenic diet in triggering tumor metastasis by modulating BACH1-mediated transcription.
ZBTB11 Depletion Targets Metabolic Vulnerabilities in K-Ras Inhibitor Resistant PDAC.
Identification of Ppy-lineage cells as a novel origin of pancreatic ductal adenocarcinoma.
DYRK1B blockade promotes tumoricidal macrophage activity in pancreatic cancer.
Atg45 is an autophagy receptor for glycogen, a non-preferred cargo of bulk autophagy in yeast.
SenNet recommendations for detecting senescent cells in different tissues.
Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk, promoting immunosuppression and immunotherapy resistance.
Autophagy suppression in DNA damaged cells occurs through a newly identified p53-proteasome-LC3 axis.
Insights into the mechanobiology of cancer metastasis via microfluidic technologies.
IDH1 inhibition potentiates chemotherapy efficacy in pancreatic cancer.
Protocol for the detection of mechanosensitive response of proteins in cultured cells under compressive stress.
Impact of cancer cachexia on survival in patients with pancreatic cancer and the efficacy of first-line chemotherapy.
MechanoProDB: a web-based database for exploring the mechanical properties of proteins.
Protocol for separating cancer cell subpopulations by metabolic activity using flow cytometry.
A matter of timing.
Fibrotic tumors tune metabolism for immune evasion.
RNA vaccines for cancer: Principles to practice.
A mild increase in nutrient signaling to mTORC1 in mice leads to parenchymal damage, myeloid inflammation and shortened lifespan.
On mechanical phase and form.
Spatial interactions modulate tumor growth and immune infiltration.
SEOM clinical guidelines for cancer anorexia-cachexia syndrome (2023).
Associations of body composition parameters with postoperative outcome and perineural tumour invasion after oncological pancreatic resection.
PI3Kγ inhibition combined with DNA vaccination unleashes a B-cell-dependent antitumor immunity that hampers pancreatic cancer.
Unsaturation effects on lipid transmembrane asymmetry.
ATG16L1 induces the formation of phagophore-like membrane cups.
Lipid unsaturation promotes BAX and BAK pore activity during apoptosis.
Neuronal activity-driven O-GlcNAcylation promotes mitochondrial plasticity.
Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.
UnitedMet harnesses RNA-metabolite covariation to impute metabolite levels in clinical samples.
Engineering cancer's end: An interdisciplinary approach to confront the complexities of cancer.
MFSD1 with its accessory subunit GLMP functions as a general dipeptide uniporter in lysosomes.

Nat Commun. 2024 Jun 01. 15(1): 4682

Area postrema neurons mediate interleukin-6 function in cancer cachexia.

Qingtao Sun, Daniëlle van de Lisdonk, Miriam Ferrer, Bruno Gegenhuber, Melody Wu, Youngkyu Park, David A Tuveson, Jessica Tollkuhn, Tobias Janowitz, Bo Li.

Interleukin-6 (IL-6) has been long considered a key player in cancer cachexia. It is believed that sustained elevation of IL-6 production during cancer progression causes brain dysfunctions, which ultimately result in cachexia. However, how peripheral IL-6 influences the brain remains poorly understood. Here we show that neurons in the area postrema (AP), a circumventricular structure in the hindbrain, is a critical mediator of IL-6 function in cancer cachexia in male mice. We find that circulating IL-6 can rapidly enter the AP and activate neurons in the AP and its associated network. Peripheral tumor, known to increase circulating IL-6, leads to elevated IL-6 in the AP, and causes potentiated excitatory synaptic transmission onto AP neurons and AP network hyperactivity. Remarkably, neutralization of IL-6 in the brain of tumor-bearing mice with an anti-IL-6 antibody attenuates cachexia and the hyperactivity in the AP network, and markedly prolongs lifespan. Furthermore, suppression of Il6ra, the gene encoding IL-6 receptor, specifically in AP neurons with CRISPR/dCas9 interference achieves similar effects. Silencing Gfral-expressing AP neurons also attenuates cancer cachectic phenotypes and AP network hyperactivity. Our study identifies a central mechanism underlying the function of peripheral IL-6, which may serve as a target for treating cancer cachexia.

DOI: https://doi.org/10.1038/s41467-024-48971-1
Curr Opin Cell Biol. 2024 May 31. pii: S0955-0674(24)00056-5. [Epub ahead of print]88 102377

Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow.

Yongli Zhang, Chenxiang Lin.

Nonvesicular lipid transport among different membranes or membrane domains plays crucial roles in lipid homeostasis and organelle biogenesis. However, the forces that drive such lipid transport are not well understood. We propose that lipids tend to flow towards the membrane area with a higher membrane protein density in a process termed lipid osmosis. This process lowers the membrane tension in the area, resulting in a membrane tension difference called osmotic membrane tension. We examine the thermodynamic basis and experimental evidence of lipid osmosis and osmotic membrane tension. We predict that lipid osmosis can drive bulk lipid flows between different membrane regions through lipid transfer proteins, scramblases, or similar barriers that selectively pass lipids but not membrane proteins. We also speculate on the biological functions of lipid osmosis. Finally, we explore other driving forces for lipid transfer and describe potential methods and systems to further test our theory.

DOI: https://doi.org/10.1016/j.ceb.2024.102377
Mol Metab. 2024 May 31. pii: S2212-8778(24)00095-4. [Epub ahead of print] 101964

In vivo CRISPR screening identifies geranylgeranyl diphosphate as a pancreatic cancer tumor growth dependency.

Casie S Kubota, Stephanie L Myers, Toni T Seppälä, Richard A Burkhart, Peter J Espenshade.

Cancer cells must maintain lipid supplies for their proliferation and do so by upregulating lipogenic gene programs. The sterol regulatory element-binding proteins (SREBPs) act as modulators of lipid homeostasis by acting as transcriptional activators of genes required for fatty acid and cholesterol synthesis and uptake. SREBPs have been recognized as chemotherapeutic targets in multiple cancers, however it is not well understood which SREBP target genes are essential for tumorigenesis. Using parallel in vitro and in vivo CRISPR knockout screens, we identified terpenoid backbone biosynthesis genes as essential for pancreatic ductal adenocarcinoma (PDAC) tumor development. Specifically, we identified the non-sterol isoprenoid product of the mevalonate pathway, geranylgeranyl diphosphate (GGPP), as an essential lipid for tumor growth. Mechanistically, we observed that restricting mevalonate pathway activity using statins and SREBP inhibitors synergistically induced apoptosis and caused disruptions in small G protein prenylation that have pleiotropic effects on cellular signaling pathways. Finally, we demonstrated that geranylgeranyl diphosphate synthase 1 (GGPS1) knockdown significantly reduces tumor burden in an orthotopic xenograft mouse model. These findings indicate that PDAC tumors selectively require GGPP over other lipids such as cholesterol and fatty acids and that this is a targetable vulnerability of pancreatic cancer cells.

DOI: https://doi.org/10.1016/j.molmet.2024.101964
Science. 2024 Jun 07. 384(6700): eadk0850

Determining the ERK-regulated phosphoproteome driving KRAS-mutant cancer.

Jennifer E Klomp, J Nathaniel Diehl, Jeffrey A Klomp, A Cole Edwards, Runying Yang, Alexis J Morales, Khalilah E Taylor, Kristina Drizyte-Miller, Kirsten L Bryant, Antje Schaefer, Jared L Johnson, Emily M Huntsman, Tomer M Yaron, Mariaelena Pierobon, Elisa Baldelli, Alex W Prevatte, Natalie K Barker, Laura E Herring, Emanuel F Petricoin, Lee M Graves, Lewis C Cantley, Adrienne D Cox, Channing J Der, Clint A Stalnecker.

To delineate the mechanisms by which the ERK1 and ERK2 mitogen-activated protein kinases support mutant KRAS-driven cancer growth, we determined the ERK-dependent phosphoproteome in KRAS-mutant pancreatic cancer. We determined that ERK1 and ERK2 share near-identical signaling and transforming outputs and that the KRAS-regulated phosphoproteome is driven nearly completely by ERK. We identified 4666 ERK-dependent phosphosites on 2123 proteins, of which 79 and 66%, respectively, were not previously associated with ERK, substantially expanding the depth and breadth of ERK-dependent phosphorylation events and revealing a considerably more complex function for ERK in cancer. We established that ERK controls a highly dynamic and complex phosphoproteome that converges on cyclin-dependent kinase regulation and RAS homolog guanosine triphosphatase function (RHO GTPase). Our findings establish the most comprehensive molecular portrait and mechanisms by which ERK drives KRAS-dependent pancreatic cancer growth.

DOI: https://doi.org/10.1126/science.adk0850
Cancer Cell. 2024 May 24. pii: S1535-6108(24)00160-0. [Epub ahead of print]

Engineering focusing on cancer.

Kayvan R Keshari, Daniel A Heller, Rostislav Boltyanskiy, Hedvig Hricak, Thomas Magaldi, Michael Overholtzer.

While cancer research and care have benefited from revolutionary advances in the ability to manipulate and study living systems, the field is limited by a lack of synergy to leverage the power of engineering approaches. Cancer engineering is an emerging subfield of biomedical engineering that unifies engineering and cancer biology to better understand, diagnose, and treat cancer. We highlight cancer engineering's unique challenges, the importance of creating dedicated centers and departments that enable translational collaboration, and educational approaches to arm a new generation of scientists with engineering expertise and a fundamental understanding of cancer biology to transform clinical cancer care.

DOI: https://doi.org/10.1016/j.ccell.2024.04.013
Cell. 2024 May 30. pii: S0092-8674(24)00520-8. [Epub ahead of print]

De novo and salvage purine synthesis pathways across tissues and tumors.

Diem H Tran, Dohun Kim, Rushendhiran Kesavan, Harrison Brown, Trishna Dey, Mona Hoseini Soflaee, Hieu S Vu, Alpaslan Tasdogan, Jason Guo, Divya Bezwada, Houssam Al Saad, Feng Cai, Ashley Solmonson, Halie Rion, Rawand Chabatya, Salma Merchant, Nathan J Manales, Vanina T Tcheuyap, Megan Mulkey, Thomas P Mathews, James Brugarolas, Sean J Morrison, Hao Zhu, Ralph J DeBerardinis, Gerta Hoxhaj.

  Purine nucleotides are vital for RNA and DNA synthesis, signaling, metabolism, and energy homeostasis. To synthesize purines, cells use two principal routes: the de novo and salvage pathways. Traditionally, it is believed that proliferating cells predominantly rely on de novo synthesis, whereas differentiated tissues favor the salvage pathway. Unexpectedly, we find that adenine and inosine are the most effective circulating precursors for supplying purine nucleotides to tissues and tumors, while hypoxanthine is rapidly catabolized and poorly salvaged in vivo. Quantitative metabolic analysis demonstrates comparative contribution from de novo synthesis and salvage pathways in maintaining purine nucleotide pools in tumors. Notably, feeding mice nucleotides accelerates tumor growth, while inhibiting purine salvage slows down tumor progression, revealing a crucial role of the salvage pathway in tumor metabolism. These findings provide fundamental insights into how normal tissues and tumors maintain purine nucleotides and highlight the significance of purine salvage in cancer.

Keywords:  cancer metabolism; de novo purine synthesis; in vivo isotope tracing; nucleotide diet; nucleotide metabolism; purine bases; purine degradation; purine salvage; tissue; tumor growth

DOI:  https://doi.org/10.1016/j.cell.2024.05.011
Dev Cell. 2024 May 30. pii: S1534-5807(24)00327-7. [Epub ahead of print]

Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress.

Brian T Do, Peggy P Hsu, Sidney Y Vermeulen, Zhishan Wang, Taghreed Hirz, Keene L Abbott, Najihah Aziz, Joseph M Replogle, Stefan Bjelosevic, Jonathan Paolino, Samantha A Nelson, Samuel Block, Alicia M Darnell, Raphael Ferreira, Hanyu Zhang, Jelena Milosevic, Daniel R Schmidt, Christopher Chidley, Isaac S Harris, Jonathan S Weissman, Yana Pikman, Kimberly Stegmaier, Sihem Cheloufi, Xiaofeng A Su, David B Sykes, Matthew G Vander Heiden.

  Control of cellular identity requires coordination of developmental programs with environmental factors such as nutrient availability, suggesting that perturbing metabolism can alter cell state. Here, we find that nucleotide depletion and DNA replication stress drive differentiation in human and murine normal and transformed hematopoietic systems, including patient-derived acute myeloid leukemia (AML) xenografts. These cell state transitions begin during S phase and are independent of ATR/ATM checkpoint signaling, double-stranded DNA break formation, and changes in cell cycle length. In systems where differentiation is blocked by oncogenic transcription factor expression, replication stress activates primed regulatory loci and induces lineage-appropriate maturation genes despite the persistence of progenitor programs. Altering the baseline cell state by manipulating transcription factor expression causes replication stress to induce genes specific for alternative lineages. The ability of replication stress to selectively activate primed maturation programs across different contexts suggests a general mechanism by which changes in metabolism can promote lineage-appropriate cell state transitions.

Keywords:  cancer; cell fate; cell state; dependencies; differentiation; epigenetics; hematopoiesis; metabolism; nucleotides; replication; replication stress

DOI:  https://doi.org/10.1016/j.devcel.2024.05.010
Cell Metab. 2024 Jun 04. pii: S1550-4131(24)00183-9. [Epub ahead of print]36(6): 1172-1174

Hungry for fat: Metabolic crosstalk with lipid-rich CAFs fuels pancreatic cancer.

Kostas A Papavassiliou, Athanasios G Papavassiliou.

Some cancers prefer to metabolize lipids for their growth and metastasis. In a recent Cancer Cell study, Niu et al. revealed that SET domain containing 2, histone lysine methyltransferase (SETD2)-deficient pancreatic cancer cells induce the differentiation of lipid-laden cancer-associated fibroblasts (CAFs), which, in turn, transport lipids to promote tumor growth.

DOI: https://doi.org/10.1016/j.cmet.2024.05.007
Science. 2024 Jun 07. 384(6700): eadk0775

Defining the KRAS- and ERK-dependent transcriptome in KRAS-mutant cancers.

Jeffrey A Klomp, Jennifer E Klomp, Clint A Stalnecker, Kirsten L Bryant, A Cole Edwards, Kristina Drizyte-Miller, Priya S Hibshman, J Nathaniel Diehl, Ye S Lee, Alexis J Morales, Khalilah E Taylor, Sen Peng, Nhan L Tran, Laura E Herring, Alex W Prevatte, Natalie K Barker, Laura D Hover, Jill Hallin, Saikat Chowdhury, Oluwadara Coker, Hey Min Lee, Craig M Goodwin, Prson Gautam, Peter Olson, James G Christensen, John P Shen, Scott Kopetz, Lee M Graves, Kian-Huat Lim, Andrea Wang-Gillam, Krister Wennerberg, Adrienne D Cox, Channing J Der.

How the KRAS oncogene drives cancer growth remains poorly understood. Therefore, we established a systemwide portrait of KRAS- and extracellular signal-regulated kinase (ERK)-dependent gene transcription in KRAS-mutant cancer to delineate the molecular mechanisms of growth and of inhibitor resistance. Unexpectedly, our KRAS-dependent gene signature diverges substantially from the frequently cited Hallmark KRAS signaling gene signature, is driven predominantly through the ERK mitogen-activated protein kinase (MAPK) cascade, and accurately reflects KRAS- and ERK-regulated gene transcription in KRAS-mutant cancer patients. Integration with our ERK-regulated phospho- and total proteome highlights ERK deregulation of the anaphase promoting complex/cyclosome (APC/C) and other components of the cell cycle machinery as key processes that drive pancreatic ductal adenocarcinoma (PDAC) growth. Our findings elucidate mechanistically the critical role of ERK in driving KRAS-mutant tumor growth and in resistance to KRAS-ERK MAPK targeted therapies.

DOI: https://doi.org/10.1126/science.adk0775
Cancer Res. 2024 Jun 04. 84(11): 1739-1741

A Hypoxia-Epigenetics Axis Drives EMT in Pancreatic Cancer.

Matthias Wirth, Günter Schneider.

Epithelial-to-mesenchymal transition (EMT) is a classical cellular plasticity process induced by various cell-intrinsic and -extrinsic triggers. Although prominent factors, such as TGFβ, mediate EMT via well-characterized pathways, alternative avenues are less well understood. Transcriptomic subtyping of pancreatic ductal adenocarcinoma (PDAC) has demonstrated that basal-like PDACs enrich a mesenchymal-like expression program, emphasizing the relevance of EMT in the disease. In this issue of Cancer Research, Brown and colleagues demonstrate the tight connection of EMT to hypoxia. Through a detailed mechanistic analysis, the authors deciphered that hypoxia-induced signals are integrated by the histone H3 lysine 36 di-methylation (H3K36me2) mark. On the one hand, hypoxia decreased activity of the H3K36me2 eraser KDM2A, while on the other hand promoting stabilization of the H3K36me2 writer NSD2. Hypoxia diminished the expression of a set of serine-threonine phosphatases, subsequently resulting in SRC kinase family-dependent activation of canonical MEK, ERK, and JNK signaling to impinge on NSD2 expression. In addition, reduced expression of the protein phosphatase PP2Cδ was linked to increased NSD2 protein expression. These discoveries illuminate the close relationship of hypoxia signaling to the epigenetic machinery and cellular plasticity processes. See related article by Brown et al., p. 1764.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-3578
J Pathol. 2024 Jun 03.

PDAC heterogeneity resolved spatially at the single-cell level: new biological answers, new questions on optimal translation†.

Irene Felipe, Francisco X Real.

  Pancreatic cancer is a highly aggressive disease. Developing new strategies and using powerful methodologies for its early detection, coupled with in-depth comprehension of the mechanisms governing subtype evolution, will not only help to stratify PDAC patients' prognosis but also prevent unfavourable subtype plasticity upon treatment with chemotherapy. Michiels et al have developed a new approach to better capture PDAC heterogeneity at the single tumour duct spatial resolution level, leveraging detection of transcripts for mutant KRAS and multiple subtype markers. Their study sheds light on the association of mutant KRAS and PDAC phenotypic heterogeneity. The findings support functional cooperation of plastic tumour cells and opens new challenges towards PDAC patient stratification and therapeutic intervention. Pathology-based tools will be of prime importance to address these issues in a clinically meaningful manner. © 2024 The Pathological Society of Great Britain and Ireland.

Keywords:  KRAS; molecular heterogeneity; pancreatic cancer; plasticity; spatial biology; transcriptomic subtypes

DOI:  https://doi.org/10.1002/path.6293
Cell. 2024 May 31. pii: S0092-8674(24)00527-0. [Epub ahead of print]

The ribotoxic stress response drives UV-mediated cell death.

Niladri K Sinha, Connor McKenney, Zhong Y Yeow, Jeffrey J Li, Ki Hong Nam, Tomer M Yaron-Barir, Jared L Johnson, Emily M Huntsman, Lewis C Cantley, Alban Ordureau, Sergi Regot, Rachel Green.

  While ultraviolet (UV) radiation damages DNA, eliciting the DNA damage response (DDR), it also damages RNA, triggering transcriptome-wide ribosomal collisions and eliciting a ribotoxic stress response (RSR). However, the relative contributions, timing, and regulation of these pathways in determining cell fate is unclear. Here we use time-resolved phosphoproteomic, chemical-genetic, single-cell imaging, and biochemical approaches to create a chronological atlas of signaling events activated in cells responding to UV damage. We discover that UV-induced apoptosis is mediated by the RSR kinase ZAK and not through the DDR. We identify two negative-feedback modules that regulate ZAK-mediated apoptosis: (1) GCN2 activation limits ribosomal collisions and attenuates ZAK-mediated RSR and (2) ZAK activity leads to phosphodegron autophosphorylation and its subsequent degradation. These events tune ZAK's activity to collision levels to establish regimes of homeostasis, tolerance, and death, revealing its key role as the cellular sentinel for nucleic acid damage.

Keywords:  DNA damage response; GCN2; UV radiation; ZAK; apoptosis; collisions; phosphoproteomics; ribosomes; ribotoxic stress; signaling

DOI:  https://doi.org/10.1016/j.cell.2024.05.018
Cell. 2024 Jun 06. pii: S0092-8674(24)00458-6. [Epub ahead of print]187(12): 2907-2918

A developmental constraint model of cancer cell states and tumor heterogeneity.

Ayushi S Patel, Itai Yanai.

  Cancer is a disease that stems from a fundamental liability inherent to multicellular life forms in which an individual cell is capable of reneging on the interests of the collective organism. Although cancer is commonly described as an evolutionary process, a less appreciated aspect of tumorigenesis may be the constraints imposed by the organism's developmental programs. Recent work from single-cell transcriptomic analyses across a range of cancer types has revealed the recurrence, plasticity, and co-option of distinct cellular states among cancer cell populations. Here, we note that across diverse cancer types, the observed cell states are proximate within the developmental hierarchy of the cell of origin. We thus posit a model by which cancer cell states are directly constrained by the organism's "developmental map." According to this model, a population of cancer cells traverses the developmental map, thereby generating a heterogeneous set of states whose interactions underpin emergent tumor behavior.

Keywords:  cancer cell states; cellular plasticity; developmental constraints; tumor heterogeneity; tumorigenesis

DOI:  https://doi.org/10.1016/j.cell.2024.04.032
Sci Immunol. 2024 Jun 07. 9(96): eadl2388

Plasma membrane abundance dictates phagocytic capacity and functional cross-talk in myeloid cells.

Benjamin Y Winer, Alexander H Settle, Alexandrina M Yakimov, Carlos Jeronimo, Tomi Lazarov, Murray Tipping, Michelle Saoi, Anjelique Sawh, Anna-Liisa L Sepp, Michael Galiano, Justin S A Perry, Yung Yu Wong, Frederic Geissmann, Justin Cross, Ting Zhou, Lance C Kam, H Amalia Pasolli, Tobias Hohl, Jason G Cyster, Orion D Weiner, Morgan Huse.

Professional phagocytes like neutrophils and macrophages tightly control what they consume, how much they consume, and when they move after cargo uptake. We show that plasma membrane abundance is a key arbiter of these cellular behaviors. Neutrophils and macrophages lacking the G protein subunit Gβ4 exhibited profound plasma membrane expansion, accompanied by marked reduction in plasma membrane tension. These biophysical changes promoted the phagocytosis of bacteria, fungus, apoptotic corpses, and cancer cells. We also found that Gβ4-deficient neutrophils are defective in the normal inhibition of migration following cargo uptake. Sphingolipid synthesis played a central role in these phenotypes by driving plasma membrane accumulation in cells lacking Gβ4. In Gβ4 knockout mice, neutrophils not only exhibited enhanced phagocytosis of inhaled fungal conidia in the lung but also increased trafficking of engulfed pathogens to other organs. Together, these results reveal an unexpected, biophysical control mechanism central to myeloid functional decision-making.

DOI: https://doi.org/10.1126/sciimmunol.adl2388
Elife. 2024 Jun 05. pii: RP89306. [Epub ahead of print]12

Partitioning to ordered membrane domains regulates the kinetics of secretory traffic.

Ivan Castello-Serrano, Frederick A Heberle, Barbara Diaz-Rohrer, Rossana Ippolito, Carolyn R Shurer, Pablo Lujan, Felix Campelo, Kandice R Levental, Ilya Levental.

  The organelles of eukaryotic cells maintain distinct protein and lipid compositions required for their specific functions. The mechanisms by which many of these components are sorted to their specific locations remain unknown. While some motifs mediating subcellular protein localization have been identified, many membrane proteins and most membrane lipids lack known sorting determinants. A putative mechanism for sorting of membrane components is based on membrane domains known as lipid rafts, which are laterally segregated nanoscopic assemblies of specific lipids and proteins. To assess the role of such domains in the secretory pathway, we applied a robust tool for synchronized secretory protein traffic (RUSH, Retention Using Selective Hooks) to protein constructs with defined affinity for raft phases. These constructs consist solely of single-pass transmembrane domains (TMDs) and, lacking other sorting determinants, constitute probes for membrane domain-mediated trafficking. We find that while raft affinity can be sufficient for steady-state PM localization, it is not sufficient for rapid exit from the endoplasmic reticulum (ER), which is instead mediated by a short cytosolic peptide motif. In contrast, we find that Golgi exit kinetics are highly dependent on raft affinity, with raft preferring probes exiting the Golgi ~2.5-fold faster than probes with minimal raft affinity. We rationalize these observations with a kinetic model of secretory trafficking, wherein Golgi export can be facilitated by protein association with raft domains. These observations support a role for raft-like membrane domains in the secretory pathway and establish an experimental paradigm for dissecting its underlying machinery.

Keywords:  cell biology; membrane structure; membrane transport; none; physics of living systems; secretory trafficking

DOI:  https://doi.org/10.7554/eLife.89306
bioRxiv. 2024 May 22. pii: 2024.05.21.595217. [Epub ahead of print]

Apoptotic cells promote circulating tumor cell survival and metastasis.

Cassidy E Hagan, Annelise G Snyder, Mark Headley, Andrew Oberst.

During tumor progression and especially following cytotoxic therapy, cell death of both tumor and stromal cells is widespread. Despite clinical observations that high levels of apoptotic cells correlate with poorer patient outcomes, the physiological effects of dying cells on tumor progression remain incompletely understood. Here, we report that circulating apoptotic cells robustly enhance tumor cell metastasis to the lungs. Using intravenous metastasis models, we observed that the presence of apoptotic cells, but not cells dying by other mechanisms, supports circulating tumor cell (CTC) survival following arrest in the lung vasculature. Apoptotic cells promote CTC survival by recruiting platelets to the forming metastatic niche. Apoptotic cells externalize the phospholipid phosphatidylserine to the outer leaflet of the plasma membrane, which we found increased the activity of the coagulation initiator Tissue Factor, thereby triggering the formation of platelet clots that protect proximal CTCs. Inhibiting the ability of apoptotic cells to induce coagulation by knocking out Tissue Factor, blocking phosphatidylserine, or administering the anticoagulant heparin abrogated the pro-metastatic effect of apoptotic cells. This work demonstrates a previously unappreciated role for apoptotic cells in facilitating metastasis by establishing CTC-supportive emboli, and suggests points of intervention that may reduce the pro-metastatic effect of apoptotic cells.GRAPHICAL ABSTRACT:

DOI: https://doi.org/10.1101/2024.05.21.595217
Sci Adv. 2024 Jun 07. 10(23): eadm9481

An unexpected role for the ketogenic diet in triggering tumor metastasis by modulating BACH1-mediated transcription.

Zhenyi Su, Yanqing Liu, Zhangchuan Xia, Anil K Rustgi, Wei Gu.

We have found that the ketogenic (Keto) diet is able to, unexpectedly, promote the metastatic potential of cancer cells in complementary mouse models. Notably, the Keto diet-induced tumor metastasis is dependent on BTB domain and CNC homolog 1 (BACH1) and its up-regulation of pro-metastatic targets, including cell migration-inducing hyaluronidase 1, in response to the Keto diet. By contrast, upon genetic knockout or pharmacological inhibition of endogenous BACH1, the Keto diet-mediated activation of those targets is largely diminished, and the effects on tumor metastasis are completely abolished. Mechanistically, upon administration of the Keto diet, the levels of activating transcription factor 4 (ATF4) are markedly induced. Through direct interaction with BACH1, ATF4 is recruited to those pro-metastatic target promoters and enhances BACH1-mediated transcriptional activation. Together, these data implicate a distinct transcription regulatory program of BACH1 for tumor metastasis induced by the Keto diet. Our study also raises a potential health risk of the Keto diet in human patients with cancer.

DOI: https://doi.org/10.1126/sciadv.adm9481
bioRxiv. 2024 May 21. pii: 2024.05.19.594824. [Epub ahead of print]

ZBTB11 Depletion Targets Metabolic Vulnerabilities in K-Ras Inhibitor Resistant PDAC.

Nathan L Tran, Jiewei Jiang, Min Ma, Gillian E Gadbois, Kevin C M Gulay, Alyssa Verano, Haowen Zhou, Chun-Teng Huang, David A Scott, Anne G Bang, Herve Tiriac, Andrew M Lowy, Eric S Wang, Fleur M Ferguson.

Over 95% of pancreatic ductal adenocarcinomas (PDAC) harbor oncogenic mutations in K-Ras. Upon treatment with K-Ras inhibitors, PDAC cancer cells undergo metabolic reprogramming towards an oxidative phosphorylation-dependent, drug-resistant state. However, direct inhibition of complex I is poorly tolerated in patients due to on-target induction of peripheral neuropathy. In this work, we develop molecular glue degraders against ZBTB11, a C2H2 zinc finger transcription factor that regulates the nuclear transcription of components of the mitoribosome and electron transport chain. Our ZBTB11 degraders leverage the differences in demand for biogenesis of mitochondrial components between human neurons and rapidly-dividing pancreatic cancer cells, to selectively target the K-Ras inhibitor resistant state in PDAC. Combination treatment of both K-Ras inhibitor-resistant cell lines and multidrug resistant patient-derived organoids resulted in superior anti-cancer activity compared to single agent treatment, while sparing hiPSC-derived neurons. Proteomic and stable isotope tracing studies revealed mitoribosome depletion and impairment of the TCA cycle as key events that mediate this response. Together, this work validates ZBTB11 as a vulnerability in K-Ras inhibitor-resistant PDAC and provides a suite of molecular glue degrader tool compounds to investigate its function.

DOI: https://doi.org/10.1101/2024.05.19.594824
J Pathol. 2024 Jun 04.

Identification of Ppy-lineage cells as a novel origin of pancreatic ductal adenocarcinoma.

Ofejiro Blessing Pereye, Yuko Nakagawa, Takashi Sato, Ayako Fukunaka, Shuhei Aoyama, Yuya Nishida, Wakana Mizutani, Nanami Kobayashi, Yohei Morishita, Tetsunari Oyama, Reika Kawabata-Iwakawa, Hirotaka Watada, Hiroki Mizukami, Akihisa Fukuda, Yoshio Fujitani.

  The Ppy gene encodes pancreatic polypeptide (PP) secreted by PP- or γ-cells, which are a subtype of endocrine cells localised mainly in the islet periphery. For a detailed characterisation of PP cells, we aimed to establish PP cell lines. To this end, we generated a mouse model harbouring the SV40 large T antigen (TAg) in the Rosa26 locus, which is expressed upon Ppy-promoter-mediated Cre-loxP recombination. Whereas Insulin1-CreERT-mediated TAg expression in beta cells resulted in insulinoma, surprisingly, Ppy-Cre-mediated TAg expression resulted in the malignant transformation of Ppy-lineage cells. These mice showed distorted islet structural integrity at 5 days of age compared with normal islets. CK19+ duct-like lesions contiguous with the islets were observed at 2 weeks of age, and mice developed aggressive pancreatic ductal adenocarcinoma (PDAC) at 4 weeks of age, suggesting that PDAC can originate from the islet/endocrine pancreas. This was unexpected as PDAC is believed to originate from the exocrine pancreas. RNA-sequencing analysis of Ppy-lineage islet cells from 7-day-old TAg+ mice showed a downregulation and an upregulation of endocrine and exocrine genes, respectively, in addition to the upregulation of genes and pathways associated with PDAC. These results suggest that the expression of an oncogene in Ppy-lineage cells induces a switch from endocrine cell fate to PDAC. Our findings demonstrate that Ppy-lineage cells may be an origin of PDAC and may provide novel insights into the pathogenesis of pancreatic cancer, as well as possible therapeutic strategies. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Keywords:  PDAC; Ppy gene; SV40 large T; endocrine pancreas; islets; pancreatic cancer; pancreatic polypeptide

DOI:  https://doi.org/10.1002/path.6295
Gut. 2024 Jun 04. pii: gutjnl-2023-331854. [Epub ahead of print]

DYRK1B blockade promotes tumoricidal macrophage activity in pancreatic cancer.

Anna Brichkina, Miriam Ems, Roman Suezov, Rajeev Singh, Veronika Lutz, Felix S R Picard, Andrea Nist, Thorsten Stiewe, Johannes Graumann, Michael Daude, Wibke E Diederich, Florian Finkernagel, Ho-Ryun Chung, Detlef K Bartsch, Katrin Roth, Corinna Keber, Carsten Denkert, Magdalena Huber, Thomas M Gress, Matthias Lauth.

  OBJECTIVE: Highly malignant pancreatic ductal adenocarcinoma (PDAC) is characterised by an abundant immunosuppressive and fibrotic tumour microenvironment (TME). Future therapeutic attempts will therefore demand the targeting of tumours and stromal compartments in order to be effective. Here we investigate whether dual specificity and tyrosine phosphorylation-regulated kinase 1B (DYRK1B) fulfil these criteria and represent a promising anticancer target in PDAC.DESIGN: We used transplantation and autochthonous mouse models of PDAC with either genetic Dyrk1b loss or pharmacological DYRK1B inhibition, respectively. Mechanistic interactions between tumour cells and macrophages were studied in direct or indirect co-culture experiments. Histological analyses used tissue microarrays from patients with PDAC. Additional methodological approaches included bulk mRNA sequencing (transcriptomics) and proteomics (secretomics).
RESULTS: We found that DYRK1B is mainly expressed by pancreatic epithelial cancer cells and modulates the influx and activity of TME-associated macrophages through effects on the cancer cells themselves as well as through the tumour secretome. Mechanistically, genetic ablation or pharmacological inhibition of DYRK1B strongly attracts tumoricidal macrophages and, in addition, downregulates the phagocytosis checkpoint and 'don't eat me' signal CD24 on cancer cells, resulting in enhanced tumour cell phagocytosis. Consequently, tumour cells lacking DYRK1B hardly expand in transplantation experiments, despite their rapid growth in culture. Furthermore, combining a small-molecule DYRK1B-directed therapy with mammalian target of rapamycin inhibition and conventional chemotherapy stalls the growth of established tumours and results in a significant extension of life span in a highly aggressive autochthonous model of PDAC.
CONCLUSION: In light of DYRK inhibitors currently entering clinical phase testing, our data thus provide a novel and clinically translatable approach targeting both the cancer cell compartment and its microenvironment.

Keywords:  immunotherapy; macrophages; molecular carcinogenesis; pancreatic cancer; pancreatic tumours

DOI:  https://doi.org/10.1136/gutjnl-2023-331854
iScience. 2024 Jun 21. 27(6): 109810

Atg45 is an autophagy receptor for glycogen, a non-preferred cargo of bulk autophagy in yeast.

Takahiro Isoda, Eigo Takeda, Sachiko Hosokawa, Shukun Hotta-Ren, Yoshinori Ohsumi.

  The mechanisms governing autophagy of proteins and organelles have been well studied, but how other cytoplasmic components such as RNA and polysaccharides are degraded remains largely unknown. In this study, we examine autophagy of glycogen, a storage form of glucose. We find that cells accumulate glycogen in the cytoplasm during nitrogen starvation and that this carbohydrate is rarely observed within autophagosomes and autophagic bodies. However, sequestration of glycogen by autophagy is observed following prolonged nitrogen starvation. We identify a yet-uncharacterized open reading frame, Yil024c (herein Atg45), as encoding a cytosolic receptor protein that mediates autophagy of glycogen (glycophagy). Furthermore, we show that, during sporulation, Atg45 is highly expressed and is associated with an increase in glycophagy. Our results suggest that cells regulate glycophagic activity by controlling the expression level of Atg45.

Keywords:  Biomolecules; Cell biology; Glycobiology; Model organism

DOI:  https://doi.org/10.1016/j.isci.2024.109810
Nat Rev Mol Cell Biol. 2024 Jun 03.

SenNet recommendations for detecting senescent cells in different tissues.

Vidyani Suryadevara, Adam D Hudgins, Adarsh Rajesh, Alberto Pappalardo, Alla Karpova, Amit K Dey, Ann Hertzel, Anthony Agudelo, Azucena Rocha, Bikem Soygur, Birgit Schilling, Chase M Carver, Cristina Aguayo-Mazzucato, Darren J Baker, David A Bernlohr, Diana Jurk, Dilyana B Mangarova, Ellen M Quardokus, Elizabeth Ann L Enninga, Elizabeth L Schmidt, Feng Chen, Francesca E Duncan, Francesco Cambuli, Gagandeep Kaur, George A Kuchel, Gung Lee, Heike E Daldrup-Link, Helene Martini, Hemali Phatnani, Iman M Al-Naggar, Irfan Rahman, Jia Nie, João F Passos, Jonathan C Silverstein, Judith Campisi, Julia Wang, Kanako Iwasaki, Karina Barbosa, Kay Metis, Kerem Nernekli, Laura J Niedernhofer, Li Ding, Lichao Wang, Lisa C Adams, Liu Ruiyang, Madison L Doolittle, Marcos G Teneche, Marissa J Schafer, Ming Xu, Mohammadjavad Hajipour, Mozhgan Boroumand, Nathan Basisty, Nicholas Sloan, Nikolai Slavov, Olena Kuksenko, Paul Robson, Paul T Gomez, Periklis Vasilikos, Peter D Adams, Priscila Carapeto, Quan Zhu, Ramalakshmi Ramasamy, Rolando Perez-Lorenzo, Rong Fan, Runze Dong, Ruth R Montgomery, Sadiya Shaikh, Sanja Vickovic, Shanshan Yin, Shoukai Kang, Sonja Suvakov, Sundeep Khosla, Vesna D Garovic, Vilas Menon, Yanxin Xu, Yizhe Song, Yousin Suh, Zhixun Dou, Nicola Neretti.

Once considered a tissue culture-specific phenomenon, cellular senescence has now been linked to various biological processes with both beneficial and detrimental roles in humans, rodents and other species. Much of our understanding of senescent cell biology still originates from tissue culture studies, where each cell in the culture is driven to an irreversible cell cycle arrest. By contrast, in tissues, these cells are relatively rare and difficult to characterize, and it is now established that fully differentiated, postmitotic cells can also acquire a senescence phenotype. The SenNet Biomarkers Working Group was formed to provide recommendations for the use of cellular senescence markers to identify and characterize senescent cells in tissues. Here, we provide recommendations for detecting senescent cells in different tissues based on a comprehensive analysis of existing literature reporting senescence markers in 14 tissues in mice and humans. We discuss some of the recent advances in detecting and characterizing cellular senescence, including molecular senescence signatures and morphological features, and the use of circulating markers. We aim for this work to be a valuable resource for both seasoned investigators in senescence-related studies and newcomers to the field.

DOI: https://doi.org/10.1038/s41580-024-00738-8
Nat Cancer. 2024 Jun 06.

Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk, promoting immunosuppression and immunotherapy resistance.

Tommaso Scolaro, Marta Manco, Mathieu Pecqueux, Ricardo Amorim, Rosa Trotta, Heleen H Van Acker, Matthias Van Haele, Niranjan Shirgaonkar, Stefan Naulaerts, Jan Daniluk, Fran Prenen, Chiara Varamo, Donatella Ponti, Ginevra Doglioni, Ana Margarida Ferreira Campos, Juan Fernandez Garcia, Silvia Radenkovic, Pegah Rouhi, Aleksandar Beatovic, Liwei Wang, Yu Wang, Amalia Tzoumpa, Asier Antoranz, Ara Sargsian, Mario Di Matteo, Emanuele Berardi, Jermaine Goveia, Bart Ghesquière, Tania Roskams, Stefaan Soenen, Thomas Voets, Bella Manshian, Sarah-Maria Fendt, Peter Carmeliet, Abhishek D Garg, Ramanuj DasGupta, Baki Topal, Massimiliano Mazzone.

Many individuals with cancer are resistant to immunotherapies. Here, we identify the gene encoding the pyrimidine salvage pathway enzyme cytidine deaminase (CDA) among the top upregulated metabolic genes in several immunotherapy-resistant tumors. We show that CDA in cancer cells contributes to the uridine diphosphate (UDP) pool. Extracellular UDP hijacks immunosuppressive tumor-associated macrophages (TAMs) through its receptor P2Y6. Pharmacologic or genetic inhibition of CDA in cancer cells (or P2Y6 in TAMs) disrupts TAM-mediated immunosuppression, promoting cytotoxic T cell entry and susceptibility to anti-programmed cell death protein 1 (anti-PD-1) treatment in resistant pancreatic ductal adenocarcinoma (PDAC) and melanoma models. Conversely, CDA overexpression in CDA-depleted PDACs or anti-PD-1-responsive colorectal tumors or systemic UDP administration (re)establishes resistance. In individuals with PDAC, high CDA levels in cancer cells correlate with increased TAMs, lower cytotoxic T cells and possibly anti-PD-1 resistance. In a pan-cancer single-cell atlas, CDAhigh cancer cells match with T cell cytotoxicity dysfunction and P2RY6high TAMs. Overall, we suggest CDA and P2Y6 as potential targets for cancer immunotherapy.

DOI: https://doi.org/10.1038/s43018-024-00771-8
bioRxiv. 2024 May 23. pii: 2024.05.21.595139. [Epub ahead of print]

Autophagy suppression in DNA damaged cells occurs through a newly identified p53-proteasome-LC3 axis.

D'Feau J Lieu, Molly K Crowder, Jordan R Kryza, Batcha Tamilselvam, Paul J Kaminski, Ik-Jung Kim, Yingxing Li, Eunji Jeong, Michidmaa Enkhbaatar, Henry Chen, Sophia B Son, Hanlin Mok, Kenneth A Bradley, Heidi Phillips, Steven R Blanke.

Macroautophagy is thought to have a critical role in shaping and refining cellular proteostasis in eukaryotic cells recovering from DNA damage. Here, we report a mechanism by which autophagy is suppressed in cells exposed to bacterial toxin-, chemical-, or radiation-mediated sources of genotoxicity. Autophagy suppression is directly linked to cellular responses to DNA damage, and specifically the stabilization of the tumor suppressor p53, which is both required and sufficient for regulating the ubiquitination and proteasome-dependent reduction in cellular pools of microtubule-associated protein 1 light chain 3 (LC3A/B), a key precursor of autophagosome biogenesis and maturation, in both epithelial cells and an ex vivo organoid model. Our data indicate that suppression of autophagy, through a newly identified p53-proteasome-LC3 axis, is a conserved cellular response to multiple sources of genotoxicity. Such a mechanism could potentially be important for realigning proteostasis in cells undergoing DNA damage repair.

DOI: https://doi.org/10.1101/2024.05.21.595139
APL Bioeng. 2024 Jun;8(2): 021506

Insights into the mechanobiology of cancer metastasis via microfluidic technologies.

Lanfeng Liang, Xiao Song, Hao Zhao, Chwee Teck Lim.

During cancer metastasis, cancer cells will encounter various microenvironments with diverse physical characteristics. Changes in these physical characteristics such as tension, stiffness, viscosity, compression, and fluid shear can generate biomechanical cues that affect cancer cells, dynamically influencing numerous pathophysiological mechanisms. For example, a dense extracellular matrix drives cancer cells to reorganize their cytoskeleton structures, facilitating confined migration, while this dense and restricted space also acts as a physical barrier that potentially results in nuclear rupture. Identifying these pathophysiological processes and understanding their underlying mechanobiological mechanisms can aid in the development of more effective therapeutics targeted to cancer metastasis. In this review, we outline the advances of engineering microfluidic devices in vitro and their role in replicating tumor microenvironment to mimic in vivo settings. We highlight the potential cellular mechanisms that mediate their ability to adapt to different microenvironments. Meanwhile, we also discuss some important mechanical cues that still remain challenging to replicate in current microfluidic devices in future direction. While much remains to be explored about cancer mechanobiology, we believe the developments of microfluidic devices will reveal how these physical cues impact the behaviors of cancer cells. It will be crucial in the understanding of cancer metastasis, and potentially contributing to better drug development and cancer therapy.

DOI: https://doi.org/10.1063/5.0195389
Cancer Res. 2024 Jun 06.

IDH1 inhibition potentiates chemotherapy efficacy in pancreatic cancer.

Mehrdad Zarei, Omid Hajihassani, Jonathan J Hue, Alexander W Loftus, Hallie J Graor, Faith Nakazzi, Parnian Naji, Christina S Boutros, Vinayak Uppin, Ali Vaziri-Gohar, Akram Shalaby, John M Asara, Luke D Rothermel, Jonathan R Brody, Jordan M Winter.

Pancreatic ductal adenocarcinoma (PDAC) is associated with a five-year overall survival rate of just 13%, and development of chemotherapy resistance is nearly universal. PDAC cells overexpress wild-type IDH1 that can enable them to overcome metabolic stress, suggesting it could represent a therapeutic target in PDAC. Here, we found that anti-IDH1 therapy enhanced the efficacy of conventional chemotherapeutics. Chemotherapy treatment induced ROS and increased TCA cycle activity in PDAC cells, along with the induction of wild-type IDH1 expression as a key resistance factor. IDH1 facilitated PDAC survival following chemotherapy treatment by supporting mitochondrial function and antioxidant defense to neutralize reactive oxygen species through the generation of alpha-ketoglutarate and NADPH, respectively. Pharmacologic inhibition of wild-type IDH1 with ivosidenib synergized with conventional chemotherapeutics in vitro and potentiated the efficacy of sub-therapeutic doses of these drugs in vivo in murine PDAC models. This promising treatment approach is translatable through available and safe oral inhibitors and provides the basis of an open and accruing clinical trial testing this combination (NCT05209074).

DOI: https://doi.org/10.1158/0008-5472.CAN-23-1895
STAR Protoc. 2024 May 31. pii: S2666-1667(24)00263-6. [Epub ahead of print]5(2): 103098

Protocol for the detection of mechanosensitive response of proteins in cultured cells under compressive stress.

Chao Wang, Yuhan Wang, Ting Gang Chew.

  Here, we present a protocol to detect mechanosensitive responses of proteins in cells under compressive stress. We describe steps for preparing elastic gels to compress cells grown on an imaging chamber. We then detail procedures for imaging proteins at the cell cortex using high-resolution confocal microscopy. The protocol can be applied to examine the mechanosensitive response of fluorescently tagged proteins in mitotic cells or round interphase cells adhering to the imaging surface. For complete details on the use and execution of this protocol, please refer to Wang et al.1.

Keywords:  Cell Biology; Cell-based Assays; Microscopy

DOI:  https://doi.org/10.1016/j.xpro.2024.103098
Int J Clin Oncol. 2024 Jun 03.

Impact of cancer cachexia on survival in patients with pancreatic cancer and the efficacy of first-line chemotherapy.

Tsutomu Nishida, Kana Hosokawa, Aya Sugimoto.

DOI: https://doi.org/10.1007/s10147-024-02564-6
Database (Oxford). 2024 Jun 05. pii: baae047. [Epub ahead of print]2024

MechanoProDB: a web-based database for exploring the mechanical properties of proteins.

Ismahene Mesbah, Bianca Habermann, Felix Rico.

The mechanical stability of proteins is crucial for biological processes. To understand the mechanical functions of proteins, it is important to know the protein structure and mechanical properties. Protein mechanics is usually investigated through force spectroscopy experiments and simulations that probe the forces required to unfold the protein of interest. While there is a wealth of data in the literature on force spectroscopy experiments and steered molecular dynamics simulations of forced protein unfolding, this information is spread and difficult to access by non-experts. Here, we introduce MechanoProDB, a novel web-based database resource for collecting and mining data obtained from experimental and computational works. MechanoProDB provides a curated repository for a wide range of proteins, including muscle proteins, adhesion molecules and membrane proteins. The database incorporates relevant parameters that provide insights into the mechanical stability of proteins and their conformational stability such as the unfolding forces, energy landscape parameters and contour lengths of unfolding steps. Additionally, it provides intuitive annotations of the unfolding pathways of each protein, allowing users to explore the individual steps during mechanical unfolding. The user-friendly interface of MechanoProDB allows researchers to efficiently navigate, search and download data pertaining to specific protein folds or experimental conditions. Users can visualize protein structures using interactive tools integrated within the database, such as Mol*, and plot available data through integrated plotting tools. To ensure data quality and reliability, we have carefully manually verified and curated the data currently available on MechanoProDB. Furthermore, the database also features an interface that enables users to contribute new data and annotations, promoting community-driven comprehensiveness. The freely available MechanoProDB aims to streamline and accelerate research in the field of mechanobiology and biophysics by offering a unique platform for data sharing and analysis. MechanoProDB is freely available at https://mechanoprodb.ibdm.univ-amu.fr.

DOI: https://doi.org/10.1093/database/baae047
STAR Protoc. 2024 Jun 01. pii: S2666-1667(24)00270-3. [Epub ahead of print]5(2): 103105

Protocol for separating cancer cell subpopulations by metabolic activity using flow cytometry.

Wiktoria Blaszczak, Bobby White, Pawel Swietach.

  Cells, even from the same line, can maintain heterogeneity in metabolic activity. Here, we present a protocol, adapted for fluorescence-activated cell sorting (FACS), that separates resuspended cells according to their metabolic rate. We describe steps for driving lactate efflux, which produces an alkaline transient proportional to fermentative rate. This pH signature, measured using pH-sensitive dyes, identifies cells with the highest metabolic rate. We then describe a fluorimetric assay of oxygen consumption and acid production to confirm the metabolic contrast between subpopulations. For complete details on the use and execution of this protocol, please refer to Blaszczak et al.1.

Keywords:  Cancer; Flow Cytometry; Metabolism

DOI:  https://doi.org/10.1016/j.xpro.2024.103105
Elife. 2024 Jun 04. pii: e99181. [Epub ahead of print]13

A matter of timing.

Zhiqi Tian, Jiajie Diao.

  A change in the electric charge of autophagosome membranes controls the recruitment of SNARE proteins to ensure that membrane fusion occurs at the right time during autophagy.

Keywords:  SNARE; autophagosome; autophagy; cell biology; human; membrane charge; mouse; phosphatidylinositol 4-phosphate; syntaxin 17

DOI:  https://doi.org/10.7554/eLife.99181
Nat Cancer. 2024 Jun 03.

Fibrotic tumors tune metabolism for immune evasion.

Matthew D Perricone, Costas A Lyssiotis.

DOI: https://doi.org/10.1038/s43018-024-00758-5
Cancer Cell. 2024 Jun 06. pii: S1535-6108(24)00168-5. [Epub ahead of print]

RNA vaccines for cancer: Principles to practice.

Pablo Guasp, Charlotte Reiche, Zachary Sethna, Vinod P Balachandran.

  Vaccines are the most impactful medicines to improve health. Though potent against pathogens, vaccines for cancer remain an unfulfilled promise. However, recent advances in RNA technology coupled with scientific and clinical breakthroughs have spurred rapid discovery and potent delivery of tumor antigens at speed and scale, transforming cancer vaccines into a tantalizing prospect. Yet, despite being at a pivotal juncture, with several randomized clinical trials maturing in upcoming years, several critical questions remain: which antigens, tumors, platforms, and hosts can trigger potent immunity with clinical impact? Here, we address these questions with a principled framework of cancer vaccination from antigen detection to delivery. With this framework, we outline features of emergent RNA technology that enable rapid, robust, real-time vaccination with somatic mutation-derived neoantigens-an emerging "ideal" antigen class-and highlight latent features that have sparked the belief that RNA could realize the enduring vision for vaccines against cancer.

Keywords:  RNA; cancer; neoantigen; vaccine

DOI:  https://doi.org/10.1016/j.ccell.2024.05.005
Nat Aging. 2024 Jun 07.

A mild increase in nutrient signaling to mTORC1 in mice leads to parenchymal damage, myeloid inflammation and shortened lifespan.

Ana Ortega-Molina, Cristina Lebrero-Fernández, Alba Sanz, Miguel Calvo-Rubio, Nerea Deleyto-Seldas, Lucía de Prado-Rivas, Ana Belén Plata-Gómez, Elena Fernández-Florido, Patricia González-García, Yurena Vivas-García, Elena Sánchez García, Osvaldo Graña-Castro, Nathan L Price, Alejandra Aroca-Crevillén, Eduardo Caleiras, Daniel Monleón, Consuelo Borrás, María Casanova-Acebes, Rafael de Cabo, Alejo Efeyan.

The mechanistic target of rapamycin complex 1 controls cellular anabolism in response to growth factor signaling and to nutrient sufficiency signaled through the Rag GTPases. Inhibition of mTOR reproducibly extends longevity across eukaryotes. Here we report that mice that endogenously express active mutant variants of RagC exhibit multiple features of parenchymal damage that include senescence, expression of inflammatory molecules, increased myeloid inflammation with extensive features of inflammaging and a ~30% reduction in lifespan. Through bone marrow transplantation experiments, we show that myeloid cells are abnormally activated by signals emanating from dysfunctional RagC-mutant parenchyma, causing neutrophil extravasation that inflicts additional inflammatory damage. Therapeutic suppression of myeloid inflammation in aged RagC-mutant mice attenuates parenchymal damage and extends survival. Together, our findings link mildly increased nutrient signaling to limited lifespan in mammals, and support a two-component process of parenchymal damage and myeloid inflammation that together precipitate a time-dependent organ deterioration that limits longevity.

DOI: https://doi.org/10.1038/s43587-024-00635-x
Cell. 2024 Jun 06. pii: S0092-8674(24)00471-9. [Epub ahead of print]187(12): 2898-2900

On mechanical phase and form.

Windie Höfs, Sara A Wickström.

Epithelial folding is a fundamental biological process that requires epithelial interactions with the underlying mesenchyme. In this issue of Cell, Huycke et al. investigate intestinal villus formation. They discover that water-droplet-like behavior of mesenchymal cells drives their coalescence into uniformly patterned aggregates, which generate forces on the epithelium to initiate folding.

DOI: https://doi.org/10.1016/j.cell.2024.04.045
Res Sq. 2024 May 22. pii: rs.3.rs-3962451. [Epub ahead of print]

Spatial interactions modulate tumor growth and immune infiltration.

Jeffrey West, Sadegh Marzban, Sonal Srivast, Sharon Kartika, Rafael Bravo, Rachel Safriel, Aidan Zarski, Alexander Anderson, Christine Chung, Antonio Amelio.

Lenia, a cellular automata framework used in artificial life, provides a natural setting to implement mathematical models of cancer incorporating features such as morphogenesis, homeostasis, motility, reproduction, growth, stimuli response, evolvability, and adaptation. Historically, agent-based models of cancer progression have been constructed with rules that govern birth, death and migration, with attempts to map local rules to emergent global growth dynamics. In contrast, Lenia provides a flexible framework for considering a spectrum of local (cell-scale) to global (tumor-scale) dynamics by defining an interaction kernel governing density-dependent growth dynamics. Lenia can recapitulate a range of cancer model classifications including local or global, deterministic or stochastic, non-spatial or spatial, single or multi-population, and off or on-lattice. Lenia is subsequently used to develop data-informed models of 1) single-population growth dynamics, 2) multi-population cell-cell competition models, and 3) cell migration or chemotaxis. Mathematical modeling provides important mechanistic insights. First, short-range interaction kernels provide a mechanism for tumor cell survival under conditions with strong Allee effects. Next, we find that asymmetric interaction tumor-immune kernels lead to poor immune response. Finally, modeling recapitulates immune-ECM interactions where patterns of collagen formation provide immune protection, indicated by an emergent inverse relationship between disease stage and immune coverage.

DOI: https://doi.org/10.21203/rs.3.rs-3962451/v1
Clin Transl Oncol. 2024 Jun 01.

SEOM clinical guidelines for cancer anorexia-cachexia syndrome (2023).

Ainara Soria Rivas, Yolanda Escobar Álvarez, Ana Blasco Cordellat, Margarita Majem Tarruella, Kevin Molina Mata, Marta Motilla de la Cámara, Mª Del Mar Muñoz Sánchez, Marta Zafra Poves, Carmen Beato Zambrano, Luis Cabezón Gutierrez.

  Cancer-related anorexia-cachexia syndrome (CACS) is a debilitating condition afflicting up to 80% of advanced-stage cancer patients. Characterized by progressive weight loss, muscle wasting, and metabolic abnormalities, CACS significantly compromises patients' quality of life and treatment outcomes. This comprehensive review navigates through its intricate physiopathology, elucidating its stages and diagnostic methodologies. CACS manifests in three distinct stages: pre-cachexia, established cachexia, and refractory cachexia. Early detection is pivotal for effective intervention and is facilitated by screening tools, complemented by nutritional assessments and professional evaluations. The diagnostic process unravels the complex interplay of metabolic dysregulation and tumor-induced factors contributing to CACS. Management strategies, tailored to individual patient profiles, encompass a spectrum of nutritional interventions. These include dietary counseling, oral nutritional supplements, and, when necessary, enteral nutrition and a judicious use of parenteral nutrition. Specific recommendations for caloric intake, protein requirements, and essential nutrients address the unique challenges posed by CACS. While pharmacological agents like megestrol acetate may be considered, their use requires careful evaluation of potential risks. At its core, this review underscores the imperative for a holistic and personalized approach to managing CACS, integrating nutritional interventions and pharmacological strategies based on a nuanced understanding of patient's condition.

Keywords:  Anorexia; Anorexia-cachexia syndrome; Cachexia; Cancer; Malnutrition; Sarcopenia

DOI:  https://doi.org/10.1007/s12094-024-03502-8
BMC Surg. 2024 Jun 04. 24(1): 175

Associations of body composition parameters with postoperative outcome and perineural tumour invasion after oncological pancreatic resection.

Tara C Mueller, Martin Henselmann, Stefan Reischl, Carsten Jaeger, Charlotte Trefzer, Ihsan Ekin Demir, Helmut Friess, Marc E Martignoni.

  BACKGROUND: Pancreatic cancer is often accompanied by wasting conditions. While surgery is the primary curative approach, it poses a substantial risk of postoperative complications, hindering subsequent treatments. Therefore, identifying patients at high risk for complications and optimizing their perioperative general condition is crucial. Sarcopenia and other body composition abnormalities have shown to adversely affect surgical and oncological outcomes in various cancer patients. As most pancreatic tumours are located close to the neuronal control centre for the digestive tract, it is possible that neural infiltration in this area deranges bowel functions and contributes to malabsorption and malnutrition and ultimately worsen sarcopenia and weight loss.METHODS: A retrospective analysis of CT scans was performed for pancreatic cancer patients who underwent surgical tumour resection at a single high-volume centre from 2007 to 2023. Sarcopenia prevalence was assessed by skeletal muscle index (SMI), and visceral obesity was determined by the visceral adipose tissue area (VAT). Obesity and malnutrition were determined by the GLIM criteria. Sarcopenic obesity was defined as simultaneous sarcopenia and obesity. Postoperative complications, mortality and perineural tumour invasion, were compared among patients with body composition abnormalities.
RESULTS: Of 437 patients studied, 46% were female, the median age was 69 (61;74) years. CT analysis revealed 54.9% of patients with sarcopenia, 23.7% with sarcopenic obesity and 45.9% with visceral obesity. Sarcopenia and sarcopenic obesity were more prevalent in elderly and male patients. Postoperative surgical complications occurred in 67.7% of patients, most of which were mild (41.6%). Severe complications occurred in 22.7% of cases and the mortality rate was 3.4%. Severe postoperative complications were significantly more common in patients with sarcopenia or sarcopenic obesity. Visceral obesity or malnutrition based on BMI alone, did not significantly impact complications. Perineural invasion was found in 80.1% of patients and was unrelated to malnutrition or body composition parameters.
CONCLUSIONS: This is the first and largest study evaluating the associations of CT-based body mass analysis with surgical outcome and histopathological perineural tumour invasion in pancreatic cancer patients. The results suggest that elderly and male patients are at high risk for sarcopenia and should be routinely evaluated by CT before undergoing pancreatic surgery, irrespective of their BMI. Confirmation of the results in prospective studies is needed to assess if pancreatic cancer patients with radiographic sarcopenia benefit from preoperative amelioration of muscle mass and function by exercise and nutritional interventions.

Keywords:  Body composition; Malnutrition; Pancreatic cancer; Perineural tumour invasion; Postoperative complications

DOI:  https://doi.org/10.1186/s12893-024-02457-5
J Exp Clin Cancer Res. 2024 Jun 01. 43(1): 157

PI3Kγ inhibition combined with DNA vaccination unleashes a B-cell-dependent antitumor immunity that hampers pancreatic cancer.

Claudia Curcio, Gianluca Mucciolo, Cecilia Roux, Silvia Brugiapaglia, Alessandro Scagliotti, Giorgia Guadagnin, Laura Conti, Dario Longo, Demis Grosso, Mauro Giulio Papotti, Emilio Hirsch, Paola Cappello, Judith A Varner, Francesco Novelli.

Phosphoinositide-3-kinase γ (PI3Kγ) plays a critical role in pancreatic ductal adenocarcinoma (PDA) by driving the recruitment of myeloid-derived suppressor cells (MDSC) into tumor tissues, leading to tumor growth and metastasis. MDSC also impair the efficacy of immunotherapy. In this study we verify the hypothesis that MDSC targeting, via PI3Kγ inhibition, synergizes with α-enolase (ENO1) DNA vaccination in counteracting tumor growth.Mice that received ENO1 vaccination followed by PI3Kγ inhibition had significantly smaller tumors compared to those treated with ENO1 alone or the control group, and correlated with i) increased circulating anti-ENO1 specific IgG and IFNγ secretion by T cells, ii) increased tumor infiltration of CD8+ T cells and M1-like macrophages, as well as up-modulation of T cell activation and M1-like related transcripts, iii) decreased infiltration of Treg FoxP3+ T cells, endothelial cells and pericytes, and down-modulation of the stromal compartment and T cell exhaustion gene transcription, iv) reduction of mature and neo-formed vessels, v) increased follicular helper T cell activation and vi) increased "antigen spreading", as many other tumor-associated antigens were recognized by IgG2c "cytotoxic" antibodies. PDA mouse models genetically devoid of PI3Kγ showed an increased survival and a pattern of transcripts in the tumor area similar to that of pharmacologically-inhibited PI3Kγ-proficient mice. Notably, tumor reduction was abrogated in ENO1 + PI3Kγ inhibition-treated mice in which B cells were depleted.These data highlight a novel role of PI3Kγ in B cell-dependent immunity, suggesting that PI3Kγ depletion strengthens the anti-tumor response elicited by the ENO1 DNA vaccine.

DOI: https://doi.org/10.1186/s13046-024-03080-1
J Chem Phys. 2024 Jun 07. pii: 215102. [Epub ahead of print]160(21):

Unsaturation effects on lipid transmembrane asymmetry.

Yong-Hao Ma, Bolin Li, Chu Wang, Jingjing Yang, Xiaofeng Han, Xiaolin Lu.

Within cell plasma membranes, unsaturated lipids are asymmetrically distributed over the inner and outer leaflets, offering an attractive local structural feature. However, the mechanism to keep lipid transmembrane asymmetry and the closely related transmembrane movement (flip-flop) for unsaturated lipids remain poorly understood. Here, we applied sum frequency generation vibrational spectroscopy to investigate this lipid transmembrane asymmetry upon mimicking the cell membrane homeostatic processes. On the one hand, unsaturated lipids were found to hinder the flip-flop process and preserve lipid transmembrane asymmetry in model cell membranes, owing to the steric hindrance caused by their bent tails. On the other hand, local unsaturated lipids in the mixed unsaturated/saturated lipid bilayer were conducive to the formation of the local asymmetry. Therefore, lipid unsaturation can be recognized as an intrinsic key factor to form and maintain lipid transmembrane asymmetry in cell membranes.

DOI: https://doi.org/10.1063/5.0209950
Nat Struct Mol Biol. 2024 Jun 04.

ATG16L1 induces the formation of phagophore-like membrane cups.

Jagan Mohan, Satish B Moparthi, Christine Girard-Blanc, Daniele Campisi, Stéphane Blanchard, Charlotte Nugues, Sowmya Rama, Audrey Salles, Esthel Pénard, Stéphane Vassilopoulos, Thomas Wollert.

The hallmark of non-selective autophagy is the formation of cup-shaped phagophores that capture bulk cytoplasm. The process is accompanied by the conjugation of LC3B to phagophores by an E3 ligase complex comprising ATG12-ATG5 and ATG16L1. Here we combined two complementary reconstitution approaches to reveal the function of LC3B and its ligase complex during phagophore expansion. We found that LC3B forms together with ATG12-ATG5-ATG16L1 a membrane coat that remodels flat membranes into cups that closely resemble phagophores. Mechanistically, we revealed that cup formation strictly depends on a close collaboration between LC3B and ATG16L1. Moreover, only LC3B, but no other member of the ATG8 protein family, promotes cup formation. ATG16L1 truncates that lacked the C-terminal membrane binding domain catalyzed LC3B lipidation but failed to assemble coats, did not promote cup formation and inhibited the biogenesis of non-selective autophagosomes. Our results thus demonstrate that ATG16L1 and LC3B induce and stabilize the characteristic cup-like shape of phagophores.

DOI: https://doi.org/10.1038/s41594-024-01300-y
Nat Commun. 2024 Jun 03. 15(1): 4700

Lipid unsaturation promotes BAX and BAK pore activity during apoptosis.

Shashank Dadsena, Rodrigo Cuevas Arenas, Gonçalo Vieira, Susanne Brodesser, Manuel N Melo, Ana J García-Sáez.

BAX and BAK are proapoptotic members of the BCL2 family that directly mediate mitochondrial outer membrane permeabilition (MOMP), a central step in apoptosis execution. However, the molecular architecture of the mitochondrial apoptotic pore remains a key open question and especially little is known about the contribution of lipids to MOMP. By performing a comparative lipidomics analysis of the proximal membrane environment of BAK isolated in lipid nanodiscs, we find a significant enrichment of unsaturated species nearby BAK and BAX in apoptotic conditions. We then demonstrate that unsaturated lipids promote BAX pore activity in model membranes, isolated mitochondria and cellular systems, which is further supported by molecular dynamics simulations. Accordingly, the fatty acid desaturase FADS2 not only enhances apoptosis sensitivity, but also the activation of the cGAS/STING pathway downstream mtDNA release. The correlation of FADS2 levels with the sensitization to apoptosis of different lung and kidney cancer cell lines by co-treatment with unsaturated fatty acids supports the relevance of our findings. Altogether, our work provides an insight on how local lipid environment affects BAX and BAK function during apoptosis.

DOI: https://doi.org/10.1038/s41467-024-49067-6
Dev Cell. 2024 Jun 04. pii: S1534-5807(24)00325-3. [Epub ahead of print]

Neuronal activity-driven O-GlcNAcylation promotes mitochondrial plasticity.

Seungyoon B Yu, Haoming Wang, Richard G Sanchez, Natasha M Carlson, Khanh Nguyen, Andrew Zhang, Zachary D Papich, Ahmed A Abushawish, Zachary Whiddon, Weronika Matysik, Jie Zhang, Thomas C Whisenant, Majid Ghassemian, John N Koberstein, Melissa L Stewart, Samuel A Myers, Gulcin Pekkurnaz.

  Neuronal activity is an energy-intensive process that is largely sustained by instantaneous fuel utilization and ATP synthesis. However, how neurons couple ATP synthesis rate to fuel availability is largely unknown. Here, we demonstrate that the metabolic sensor enzyme O-linked N-acetyl glucosamine (O-GlcNAc) transferase regulates neuronal activity-driven mitochondrial bioenergetics in hippocampal and cortical neurons. We show that neuronal activity upregulates O-GlcNAcylation in mitochondria. Mitochondrial O-GlcNAcylation is promoted by activity-driven glucose consumption, which allows neurons to compensate for high energy expenditure based on fuel availability. To determine the proteins that are responsible for these adjustments, we mapped the mitochondrial O-GlcNAcome of neurons. Finally, we determine that neurons fail to meet activity-driven metabolic demand when O-GlcNAcylation dynamics are prevented. Our findings suggest that O-GlcNAcylation provides a fuel-dependent feedforward control mechanism in neurons to optimize mitochondrial performance based on neuronal activity. This mechanism thereby couples neuronal metabolism to mitochondrial bioenergetics and plays a key role in sustaining energy homeostasis.

Keywords:  ATP synthesis; O-GlcNAc transferase; O-GlcNAcylation; glycosylation; mitochondria; neuronal metabolism; synaptic activity

DOI:  https://doi.org/10.1016/j.devcel.2024.05.008
Nat Methods. 2024 Jun 06.

Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.

Erik Wernersson, Eleni Gelali, Gabriele Girelli, Su Wang, David Castillo, Christoffer Mattsson Langseth, Quentin Verron, Huy Q Nguyen, Shyamtanu Chattoraj, Anna Martinez Casals, Hans Blom, Emma Lundberg, Mats Nilsson, Marc A Marti-Renom, Chao-Ting Wu, Nicola Crosetto, Magda Bienko.

Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of extractable biological information. To overcome these limitations, here we develop Deconwolf, an open-source, user-friendly software for high-performance deconvolution of widefield fluorescence microscopy images, which efficiently runs on laptop computers. Deconwolf enables accurate quantification of crowded diffraction limited fluorescence dots in DNA and RNA fluorescence in situ hybridization images and allows robust detection of individual transcripts in tissue sections imaged with ×20 air objectives. Deconvolution of in situ spatial transcriptomics images with Deconwolf increased the number of transcripts identified more than threefold, while the application of Deconwolf to images obtained by fluorescence in situ sequencing of barcoded Oligopaint probes drastically improved chromosome tracing. Deconwolf greatly facilitates the use of deconvolution in many bioimaging applications.

DOI: https://doi.org/10.1038/s41592-024-02294-7
medRxiv. 2024 May 25. pii: 2024.05.24.24307903. [Epub ahead of print]

UnitedMet harnesses RNA-metabolite covariation to impute metabolite levels in clinical samples.

Amy X Xie, Wesley Tansey, Ed Reznik.

Comprehensively studying metabolism requires the measurement of metabolite levels. However, in contrast to the broad availability of gene expression data, metabolites are rarely measured in large molecularly-defined cohorts of tissue samples. To address this basic barrier to metabolic discovery, we propose a Bayesian framework ("UnitedMet") which leverages the empirical strength of RNA-metabolite covariation to impute otherwise unmeasured metabolite levels from widely available transcriptomic data. We demonstrate that UnitedMet is equally capable of imputing whole pool sizes as well as the outcomes of isotope tracing experiments. We apply UnitedMet to investigate the metabolic impact of driver mutations in kidney cancer, identifying a novel association between BAP1 and a highly oxidative tumor phenotype. We similarly apply UnitedMet to determine that advanced kidney cancers upregulate oxidative phosphorylation relative to early-stage disease, that oxidative metabolism in kidney cancer is associated with inferior outcomes to combination therapy, and that kidney cancer metastases themselves demonstrate elevated oxidative phosphorylation relative to primary tumors. UnitedMet therefore enables the assessment of metabolic phenotypes in contexts where metabolite measurements were not taken or are otherwise infeasible, opening new avenues for the generation and evaluation of metabolite-centered hypotheses. UnitedMet is open source and publicly available ( https://github.com/reznik-lab/UnitedMet ).

DOI: https://doi.org/10.1101/2024.05.24.24307903
Cancer Cell. 2024 May 30. pii: S1535-6108(24)00185-5. [Epub ahead of print]

Engineering cancer's end: An interdisciplinary approach to confront the complexities of cancer.

Elsa R Flores, W Gregory Sawyer.

Cancer engineering is an interdisciplinary approach that promises to confront the complexities of cancer and accelerate transformative discoveries by integrating innovative fields across engineering and the physical sciences with a focus on cancer. We offer a conceptual framework for the hallmarks of cancer engineering, integrating 12 fields: system dynamics; imaging, radiation, and spectroscopy; robotics and controls; solid mechanics; fluid mechanics; chemistry and nanomaterials; mathematics and simulation; cellular and protein engineering; kinetics and thermodynamics; materials science; manufacturing and biofabrication; and microsystems.

DOI: https://doi.org/10.1016/j.ccell.2024.05.017
Nat Cell Biol. 2024 Jun 05.

MFSD1 with its accessory subunit GLMP functions as a general dipeptide uniporter in lysosomes.

Katharina Esther Julia Jungnickel, Océane Guelle, Miharu Iguchi, Wentao Dong, Vadim Kotov, Florian Gabriel, Cécile Debacker, Julien Dairou, Isabelle McCort-Tranchepain, Nouf N Laqtom, Sze Ham Chan, Akika Ejima, Kenji Sato, David Massa López, Paul Saftig, Ahmad Reza Mehdipour, Monther Abu-Remaileh, Bruno Gasnier, Christian Löw, Markus Damme.

The lysosomal degradation of macromolecules produces diverse small metabolites exported by specific transporters for reuse in biosynthetic pathways. Here we deorphanized the major facilitator superfamily domain containing 1 (MFSD1) protein, which forms a tight complex with the glycosylated lysosomal membrane protein (GLMP) in the lysosomal membrane. Untargeted metabolomics analysis of MFSD1-deficient mouse lysosomes revealed an increase in cationic dipeptides. Purified MFSD1 selectively bound diverse dipeptides, while electrophysiological, isotope tracer and fluorescence-based studies in Xenopus oocytes and proteoliposomes showed that MFSD1-GLMP acts as a uniporter for cationic, neutral and anionic dipeptides. Cryoelectron microscopy structure of the dipeptide-bound MFSD1-GLMP complex in outward-open conformation characterized the heterodimer interface and, in combination with molecular dynamics simulations, provided a structural basis for its selectivity towards diverse dipeptides. Together, our data identify MFSD1 as a general lysosomal dipeptide uniporter, providing an alternative route to recycle lysosomal proteolysis products when lysosomal amino acid exporters are overloaded.

DOI: https://doi.org/10.1038/s41556-024-01436-5