bims-cagime 2023-07-09 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2023–07–09
27 papers selected by
Kıvanç Görgülü, Technical University of Munich

Development of a peptide drug restoring AMPK and adipose tissue functionality in cancer cachexia.
Emerging trends and research foci in autophagy of pancreatic cancer: a bibliometric and visualized study.
Human senescent fibroblasts trigger progressive lung fibrosis in mice.
Emerging roles of the MiT/TFE factors in cancer.
Spatial mapping of cellular senescence: emerging challenges and opportunities.
PTEN is both an activator and a substrate of chaperone-mediated autophagy.
Exploring switch II pocket conformation of KRAS(G12D) with mutant-selective monobody inhibitors.
Effective membrane tension: A long-range integrator of cellular dynamics.
Detection of membrane-anchoring lipid modifications of proteins in cells by radioactive metabolic labeling.
Oncogenic K-Ras suppresses global miRNA function.
Volume electron microscopy.
When a calorie is not just a calorie: Diet quality and timing as mediators of metabolism and healthy aging.
SLC38A2 and glutamine signalling in cDC1s dictate anti-tumour immunity.
Features of metabolism associated molecular patterns in pancreatic ductal adenocarcinoma.
A cellular and molecular spatial atlas of dystrophic muscle.
Diet, nutrient supply, and tumor immune responses.
Oncogene-like addiction to aneuploidy in human cancers.
Autophagy dictates sensitivity to PRMT5 inhibitor in breast cancer.
Shaping mitochondria through fed-fast and circadian cycles.
Improved imaging and preservation of lysosome dynamics using silver nanoparticle-enhanced fluorescence.
The membrane surface as a platform that organizes cellular and biochemical processes.
Spatial metabolomics principles and application to cancer research.
Updating the definition of cancer.
Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology.
Lactate Shuttling Drives the Browning of White Adipose Tissue after Burn Trauma.
Maternal hyperglycemia induces alterations in hepatic amino acid, glucose and lipid metabolism of neonatal offspring: Multi-omics insights from a diabetic pig model.
Activation of invasion by oncogenic reprogramming of cholesterol metabolism via increased NPC1 expression and macropinocytosis.

Mol Ther. 2023 Jul 04. pii: S1525-0016(23)00380-5. [Epub ahead of print]

Development of a peptide drug restoring AMPK and adipose tissue functionality in cancer cachexia.

Honglei Ji, Felix Englmaier, Pauline Morigny, Maude Giroud, Pamina Gräsle, Sebastian Brings, Julia Szendrödi, Mauricio Berriel Diaz, Oliver Plettenburg, Stephan Herzig, Maria Rohm.

Cancer cachexia is a severe systemic wasting disease that negatively affects quality of life and survival in patients with cancer. To date, treating cancer cachexia is still a major unmet clinical need. We recently discovered the destabilization of the AMPK complex in adipose tissue as a key event in cachexia-related adipose tissue dysfunction and developed an AAV-based approach to prevent AMPK degradation and prolong cachexia-free survival. Here, we show the development and optimization of a prototypic peptide, Pen-X-ACIP, where the AMPK stabilizing peptide ACIP is fused to the cell-penetrating peptide moiety penetratin via a propargylic glycine linker to enable late-stage functionalization using click chemistry. Pen-X-ACIP was efficiently taken up by adipocytes, inhibited lipolysis and restored AMPK signaling. Tissue uptake assays showed a favorable uptake profile into adipose tissue upon intraperitoneal injection. Systemic delivery of Pen-X-ACIP into tumor-bearing animals prevented the progression of cancer cachexia without affecting tumor growth, and preserved body weight and adipose tissue mass with no discernable side effects in other peripheral organs, thereby achieving proof-of-concept. As Pen-X-ACIP also exerted its anti-lipolytic activity in human adipocytes, it now provides a promising platform for further (pre)clinical development towards a novel, first-in-class approach against cancer cachexia.

DOI: https://doi.org/10.1016/j.ymthe.2023.06.020
Front Oncol. 2023 ;13 1220435

Emerging trends and research foci in autophagy of pancreatic cancer: a bibliometric and visualized study.

Linlin Fan, Zhiyong Wei, Lili Liu, Xiaojie Qi, Hong Yu.

   Objective: The purpose of this study was to analyze the trends by year, country, institution, journal, reference and keyword in publications on the autophagy of pancreatic cancer (PC) and to predict future research hotspots.
Methods: The Web of Science Core Collection was used to search for publications. The contributions of various countries/regions, institutes, authors, identified research hotspots, and promising future trends were analyzed using the VOSviewer1.6.16 and CiteSpace6.6.R2 programs. We also summarized autophagy relevant clinical trials of PC.
Results: A total of 1293 papers on the autophagy of PC published between 2013 and 2023 were included in the study. The average number of citations per article was 33.76. The China had the most publications, followed by USA, and a total of 50 influential articles were identified through co-citation analysis. Clustering analysis revealed clusters of keywords: metabolic reprogramming and ER stress, mTOR-mediated apoptosis, extracellular trap as the most concerned clusters. The co-occurrence cluster analysis showed pancreatic stellate cell, autophagy-dependent ferroptosis, autophagy-related pathway, metabolic rewiring, on-coding RNA as the highly concerned research topics in recently.
Conclusion: The number of publications and research interest have generally increased over the past few years. The China and USA have made prominent contributions to the study of the autophagy of PC. The current research hotspots mainly focus not only on the related modulation, metabolic reprogramming, ferroptosis of tumor cells themselves, but also on tumor microenvironments such as autophagy associated pancreatic stellate cells and new treatments targeting autophagy.

Keywords:  autophagy; bibliometric study; ferroptosis; pancreatic cancer; pancreatic stellate cells; tumor microenvironment

DOI:  https://doi.org/10.3389/fonc.2023.1220435
Aging (Albany NY). 2023 Jul 01. 15

Human senescent fibroblasts trigger progressive lung fibrosis in mice.

Fernanda Hernandez-Gonzalez, Neus Prats, Valentina Ramponi, José Alberto López-Domínguez, Kathleen Meyer, Mònica Aguilera, María Isabel Muñoz Martín, Daniel Martínez, Alvar Agusti, Rosa Faner, Jacobo Sellarés, Federico Pietrocola, Manuel Serrano.

  Cell senescence has recently emerged as a potentially relevant pathogenic mechanism in fibrosing interstitial lung diseases (f-ILDs), particularly in idiopathic pulmonary fibrosis. We hypothesized that senescent human fibroblasts may suffice to trigger a progressive fibrogenic reaction in the lung. To address this, senescent human lung fibroblasts, or their secretome (SASP), were instilled into the lungs of immunodeficient mice. We found that: (1) human senescent fibroblasts engraft in the lungs of immunodeficient mice and trigger progressive lung fibrosis associated to increasing levels of mouse senescent cells, whereas non-senescent fibroblasts do not trigger fibrosis; (2) the SASP of human senescent fibroblasts is pro-senescence and pro-fibrotic both in vitro when added to mouse recipient cells and in vivo when delivered into the lungs of mice, whereas the conditioned medium (CM) from non-senescent fibroblasts lacks these activities; and, (3) navitoclax, nintedanib and pirfenidone ameliorate lung fibrosis induced by senescent human fibroblasts in mice, albeit only navitoclax displayed senolytic activity. We conclude that human senescent fibroblasts, through their bioactive secretome, trigger a progressive fibrogenic reaction in the lungs of immunodeficient mice that includes the induction of paracrine senescence in the cells of the host, supporting the concept that senescent cells actively contribute to disease progression in patients with f-ILDs.

Keywords:  antifibrotics; cellular senescence; mouse model; pulmonary fibrosis; senolytic

DOI:  https://doi.org/10.18632/aging.204825
Trends Cancer. 2023 Jul 01. pii: S2405-8033(23)00106-1. [Epub ahead of print]

Emerging roles of the MiT/TFE factors in cancer.

Roberto Zoncu, Rushika M Perera.

  The microphthalmia/transcription factor E (MiT/TFE) transcription factors (TFs; TFEB, TFE3, MITF, and TFEC) play a central role in cellular catabolism and quality control and are subject to extensive layers of regulation that influence their localization, stability, and activity. Recent studies have highlighted a broader role for these TFs in driving diverse stress-adaptation pathways, which manifest in a context- and tissue-dependent manner. Several human cancers upregulate the MiT/TFE factors to survive extreme fluctuations in nutrients, energy, and pharmacological challenges. Emerging data suggest that reduced activity of the MiT/TFE factors can also promote tumorigenesis. Here, we outline recent findings relating to novel mechanisms of regulation and activity of MiT/TFE proteins across some of the most aggressive human cancers.

Keywords:  TFE3; TFEB; autophagy; cancer; lysosome; mTORC1; metabolism

DOI:  https://doi.org/10.1016/j.trecan.2023.06.005
Nat Aging. 2023 Jul 03.

Spatial mapping of cellular senescence: emerging challenges and opportunities.

Aditi U Gurkar, Akos A Gerencser, Ana L Mora, Andrew C Nelson, Anru R Zhang, Anthony B Lagnado, Archibald Enninful, Christopher Benz, David Furman, Delphine Beaulieu, Diana Jurk, Elizabeth L Thompson, Fei Wu, Fernanda Rodriguez, Grant Barthel, Hao Chen, Hemali Phatnani, Indra Heckenbach, Jeffrey H Chuang, Jeremy Horrell, Joana Petrescu, Jonathan K Alder, Jun Hee Lee, Laura J Niedernhofer, Manoj Kumar, Melanie Königshoff, Marta Bueno, Miiko Sokka, Morten Scheibye-Knudsen, Nicola Neretti, Oliver Eickelberg, Peter D Adams, Qianjiang Hu, Quan Zhu, Rebecca A Porritt, Runze Dong, Samuel Peters, Stella Victorelli, Thomas Pengo, Timur Khaliullin, Vidyani Suryadevara, Xiaonan Fu, Ziv Bar-Joseph, Zhicheng Ji, João F Passos.

Cellular senescence is a well-established driver of aging and age-related diseases. There are many challenges to mapping senescent cells in tissues such as the absence of specific markers and their relatively low abundance and vast heterogeneity. Single-cell technologies have allowed unprecedented characterization of senescence; however, many methodologies fail to provide spatial insights. The spatial component is essential, as senescent cells communicate with neighboring cells, impacting their function and the composition of extracellular space. The Cellular Senescence Network (SenNet), a National Institutes of Health (NIH) Common Fund initiative, aims to map senescent cells across the lifespan of humans and mice. Here, we provide a comprehensive review of the existing and emerging methodologies for spatial imaging and their application toward mapping senescent cells. Moreover, we discuss the limitations and challenges inherent to each technology. We argue that the development of spatially resolved methods is essential toward the goal of attaining an atlas of senescent cells.

DOI: https://doi.org/10.1038/s43587-023-00446-6
J Cell Biol. 2023 Sep 04. pii: e202208150. [Epub ahead of print]222(9):

PTEN is both an activator and a substrate of chaperone-mediated autophagy.

Katherine K Zhang, Calvin M Burns, Mary E Skinner, David B Lombard, Richard A Miller, S Joseph Endicott.

PTEN is a crucial negative regulator of the INS/PI3K/AKT pathway and is one of the most commonly mutated tumor suppressors in cancer. Global overexpression (OE) of PTEN in mice shifts metabolism to favor oxidative phosphorylation over glycolysis, reduces fat mass, and extends the lifespan of both sexes. We demonstrate that PTEN regulates chaperone-mediated autophagy (CMA). Using cultured cells and mouse models, we show that PTEN OE enhances CMA, dependent upon PTEN's lipid phosphatase activity and AKT inactivation. Reciprocally, PTEN knockdown reduces CMA, which can be rescued by inhibiting class I PI3K or AKT. Both PTEN and CMA are negative regulators of glycolysis and lipid droplet formation. We show that suppression of glycolysis and lipid droplet formation downstream of PTEN OE depends on CMA activity. Finally, we show that PTEN protein levels are sensitive to CMA and that PTEN accumulates in lysosomes with elevated CMA. Collectively, these data suggest that CMA is both an effector and a regulator of PTEN.

DOI: https://doi.org/10.1083/jcb.202208150
Proc Natl Acad Sci U S A. 2023 07 11. 120(28): e2302485120

Exploring switch II pocket conformation of KRAS(G12D) with mutant-selective monobody inhibitors.

Padma Akkapeddi, Takamitsu Hattori, Imran Khan, Eliezra Glasser, Akiko Koide, Gayatri Ketavarapu, Michael Whaby, Mariyam Zuberi, Kai Wen Teng, Julia Lefler, Lorenzo Maso, Injin Bang, Michael C Ostrowski, John P O'Bryan, Shohei Koide.

  The G12D mutation is among the most common KRAS mutations associated with cancer, in particular, pancreatic cancer. Here, we have developed monobodies, small synthetic binding proteins, that are selective to KRAS(G12D) over KRAS(wild type) and other oncogenic KRAS mutations, as well as over the G12D mutation in HRAS and NRAS. Crystallographic studies revealed that, similar to other KRAS mutant-selective inhibitors, the initial monobody bound to the S-II pocket, the groove between switch II and α3 helix, and captured this pocket in the most widely open form reported to date. Unlike other G12D-selective polypeptides reported to date, the monobody used its backbone NH group to directly recognize the side chain of KRAS Asp12, a feature that closely resembles that of a small-molecule inhibitor, MTRX1133. The monobody also directly interacted with H95, a residue not conserved in RAS isoforms. These features rationalize the high selectivity toward the G12D mutant and the KRAS isoform. Structure-guided affinity maturation resulted in monobodies with low nM KD values. Deep mutational scanning of a monobody generated hundreds of functional and nonfunctional single-point mutants, which identified crucial residues for binding and those that contributed to the selectivity toward the GTP- and GDP-bound states. When expressed in cells as genetically encoded reagents, these monobodies engaged selectively with KRAS(G12D) and inhibited KRAS(G12D)-mediated signaling and tumorigenesis. These results further illustrate the plasticity of the S-II pocket, which may be exploited for the design of next-generation KRAS(G12D)-selective inhibitors.

Keywords:  conformational plasticity; drug discovery; intracellular biologics; protein engineering; protein-protein interaction

DOI:  https://doi.org/10.1073/pnas.2302485120
Cell. 2023 Jul 06. pii: S0092-8674(23)00585-8. [Epub ahead of print]186(14): 2956-2958

Effective membrane tension: A long-range integrator of cellular dynamics.

Kinneret Keren.

Membrane tension has been proposed to mechanically couple processes along the cell's boundary. In this issue of Cell, De Belly et al. show that local protrusion or contraction elicit a global membrane tension increase within seconds, whereas tension perturbations that engage only the membrane remain localized.

DOI: https://doi.org/10.1016/j.cell.2023.05.033
STAR Protoc. 2023 Jul 04. pii: S2666-1667(23)00383-0. [Epub ahead of print]4(3): 102416

Detection of membrane-anchoring lipid modifications of proteins in cells by radioactive metabolic labeling.

Sameer Ahmed Bhat, Rachel Ferguson, Ritika Adhikari, Shafi Kuchay.

  Prenylation and palmitoylation are two major lipid modifications of cellular proteins that anchor proteins to cell membranes. Here, we present a protocol for detecting these modifications in cellular proteins by radioactive metabolic labeling. We describe steps for metabolic labeling of cells, cell harvesting for carrying out immunoprecipitations, subjecting immunocomplexes to SDS-PAGE, and transferring them to polyvinylidine flouride (PVDF) membranes. We then detail detection of labeled target proteins by exposing PVDF membranes to phosphor screens and using a phosphor imager machine. For complete details of this protocol, please refer to Liang et al.1.

Keywords:  Cell Membrane; Cell-based Assays; Protein Expression and Purification

DOI:  https://doi.org/10.1016/j.xpro.2023.102416
Mol Cell. 2023 Jun 26. pii: S1097-2765(23)00429-X. [Epub ahead of print]

Oncogenic K-Ras suppresses global miRNA function.

Bing Shui, Tyler S Beyett, Zhengyi Chen, Xiaoyi Li, Gaspare La Rocca, William M Gazlay, Michael J Eck, Ken S Lau, Andrea Ventura, Kevin M Haigis.

  K-Ras frequently acquires gain-of-function mutations (K-RasG12D being the most common) that trigger significant transcriptomic and proteomic changes to drive tumorigenesis. Nevertheless, oncogenic K-Ras-induced dysregulation of post-transcriptional regulators such as microRNAs (miRNAs) during oncogenesis is poorly understood. Here, we report that K-RasG12D promotes global suppression of miRNA activity, resulting in the upregulation of hundreds of targets. We constructed a comprehensive profile of physiological miRNA targets in mouse colonic epithelium and tumors expressing K-RasG12D using Halo-enhanced Argonaute pull-down. Combining this with parallel datasets of chromatin accessibility, transcriptome, and proteome, we uncovered that K-RasG12D suppressed the expression of Csnk1a1 and Csnk2a1, subsequently decreasing Ago2 phosphorylation at Ser825/829/832/835. Hypo-phosphorylated Ago2 increased binding to mRNAs while reducing its activity to repress miRNA targets. Our findings connect a potent regulatory mechanism of global miRNA activity to K-Ras in a pathophysiological context and provide a mechanistic link between oncogenic K-Ras and the post-transcriptional upregulation of miRNA targets.

Keywords:  Ago2; CLIP-seq; K-Ras; casein kinase; colon; colorectal cancer; miRNA

DOI:  https://doi.org/10.1016/j.molcel.2023.06.008
Nat Rev Methods Primers. 2022 Jul 07. 2 51

Volume electron microscopy.

Christopher J Peddie, Christel Genoud, Anna Kreshuk, Kimberly Meechan, Kristina D Micheva, Kedar Narayan, Constantin Pape, Robert G Parton, Nicole L Schieber, Yannick Schwab, Benjamin Titze, Paul Verkade, Aubrey Aubrey, Lucy M Collinson.

Life exists in three dimensions, but until the turn of the century most electron microscopy methods provided only 2D image data. Recently, electron microscopy techniques capable of delving deep into the structure of cells and tissues have emerged, collectively called volume electron microscopy (vEM). Developments in vEM have been dubbed a quiet revolution as the field evolved from established transmission and scanning electron microscopy techniques, so early publications largely focused on the bioscience applications rather than the underlying technological breakthroughs. However, with an explosion in the uptake of vEM across the biosciences and fast-paced advances in volume, resolution, throughput and ease of use, it is timely to introduce the field to new audiences. In this Primer, we introduce the different vEM imaging modalities, the specialized sample processing and image analysis pipelines that accompany each modality and the types of information revealed in the data. We showcase key applications in the biosciences where vEM has helped make breakthrough discoveries and consider limitations and future directions. We aim to show new users how vEM can support discovery science in their own research fields and inspire broader uptake of the technology, finally allowing its full adoption into mainstream biological imaging.

DOI: https://doi.org/10.1038/s43586-022-00131-9
Cell Metab. 2023 Jun 25. pii: S1550-4131(23)00218-8. [Epub ahead of print]

When a calorie is not just a calorie: Diet quality and timing as mediators of metabolism and healthy aging.

Maria M Mihaylova, Amandine Chaix, Mirela Delibegovic, Jon J Ramsey, Joseph Bass, Girish Melkani, Rajat Singh, Zheng Chen, William W Ja, Michele Shirasu-Hiza, Mary N Latimer, Julie A Mattison, Anna E Thalacker-Mercer, Vishwa Deep Dixit, Satchidananda Panda, Dudley W Lamming.

  An epidemic of obesity has affected large portions of the world, increasing the risk of developing many different age-associated diseases, including cancer, cardiovascular disease, and diabetes. In contrast with the prevailing notion that "a calorie is just a calorie," there are clear differences, within and between individuals, in the metabolic response to different macronutrient sources. Recent findings challenge this oversimplification; calories from different macronutrient sources or consumed at different times of day have metabolic effects beyond their value as fuel. Here, we summarize discussions conducted at a recent NIH workshop that brought together experts in calorie restriction, macronutrient composition, and time-restricted feeding to discuss how dietary composition and feeding schedule impact whole-body metabolism, longevity, and healthspan. These discussions may provide insights into the long-sought molecular mechanisms engaged by calorie restriction to extend lifespan, lead to novel therapies, and potentially inform the development of a personalized food-as-medicine approach to healthy aging.

Keywords:  calorie restriction; fasting; isoleucine; ketogenesis; methionine; protein restriction; time-restricted feeding

DOI:  https://doi.org/10.1016/j.cmet.2023.06.008
Nature. 2023 Jul 05.

SLC38A2 and glutamine signalling in cDC1s dictate anti-tumour immunity.

Chuansheng Guo, Zhiyuan You, Hao Shi, Yu Sun, Xingrong Du, Gustavo Palacios, Cliff Guy, Sujing Yuan, Nicole M Chapman, Seon Ah Lim, Xiang Sun, Jordy Saravia, Sherri Rankin, Yogesh Dhungana, Hongbo Chi.

Cancer cells evade T cell-mediated killing through tumour-immune interactions whose mechanisms are not well understood1,2. Dendritic cells (DCs), especially type-1 conventional DCs (cDC1s), mediate T cell priming and therapeutic efficacy against tumours3. DC functions are orchestrated by pattern recognition receptors3-5, although other signals involved remain incompletely defined. Nutrients are emerging mediators of adaptive immunity6-8, but whether nutrients affect DC function or communication between innate and adaptive immune cells is largely unresolved. Here we establish glutamine as an intercellular metabolic checkpoint that dictates tumour-cDC1 crosstalk and licenses cDC1 function in activating cytotoxic T cells. Intratumoral glutamine supplementation inhibits tumour growth by augmenting cDC1-mediated CD8+ T cell immunity, and overcomes therapeutic resistance to checkpoint blockade and T cell-mediated immunotherapies. Mechanistically, tumour cells and cDC1s compete for glutamine uptake via the transporter SLC38A2 to tune anti-tumour immunity. Nutrient screening and integrative analyses show that glutamine is the dominant amino acid in promoting cDC1 function. Further, glutamine signalling via FLCN impinges on TFEB function. Loss of FLCN in DCs selectively impairs cDC1 function in vivo in a TFEB-dependent manner and phenocopies SLC38A2 deficiency by eliminating the anti-tumour therapeutic effect of glutamine supplementation. Our findings establish glutamine-mediated intercellular metabolic crosstalk between tumour cells and cDC1s that underpins tumour immune evasion, and reveal glutamine acquisition and signalling in cDC1s as limiting events for DC activation and putative targets for cancer treatment.

DOI: https://doi.org/10.1038/s41586-023-06299-8
Cancer Gene Ther. 2023 Jul 06.

Features of metabolism associated molecular patterns in pancreatic ductal adenocarcinoma.

Junfei Chen, Yongjie Wang, Hua Jiang.

Exploring pancreatic ductal adenocarcinoma (PDAC) metabolic landscape would contribute to further understand PDAC from the metabolic perspective and provide more details for precise treatment design. This study aims to describe metabolic landscape of PDAC. Bioinformatics analysis was used to investigate the differences of genome, transcriptome, and proteome levels of metabolic patterns. Three subtypes (MC1, MC2, and MC3) were identified and characterized as distinct metabolic patterns. MC1, enriched in lipid metabolism and amino acid metabolism signatures, was associated with lower abundance of immune cells and stromal cells, and non-response to immunotherapy. MC2 displayed immune-activated characteristics, minor genome alterations and good response to immunotherapy. MC3 was characterized by high glucose metabolism, high pathological grade, immune-suppressed features, poor prognosis, and epithelial-mesenchymal transition phenotype. A ninety-three gene classifier preformed robust prediction and high accuracy (training set: 93.7%; validation set 1: 85.0%; validation set 2: 83.9%). Using random forest classifier, probabilities of three patterns could be predicted on pancreatic cancer cell lines, which could be used to find vulnerable targets in response to both genetic and drug perturbation. Our study revealed features of PDAC metabolic landscape, which could be expected to provide a reference for prognosis prediction and precise treatment design.

DOI: https://doi.org/10.1038/s41417-023-00639-6
Proc Natl Acad Sci U S A. 2023 Jul 18. 120(29): e2221249120

A cellular and molecular spatial atlas of dystrophic muscle.

Michael J Stec, Qi Su, Christina Adler, Lance Zhang, David R Golann, Naveen P Khan, Lampros Panagis, S Armando Villalta, Min Ni, Yi Wei, Johnathon R Walls, Andrew J Murphy, George D Yancopoulos, Gurinder S Atwal, Sandra Kleiner, Gabor Halasz, Mark W Sleeman.

  Asynchronous skeletal muscle degeneration/regeneration is a hallmark feature of Duchenne muscular dystrophy (DMD); however, traditional -omics technologies that lack spatial context make it difficult to study the biological mechanisms of how asynchronous regeneration contributes to disease progression. Here, using the severely dystrophic D2-mdx mouse model, we generated a high-resolution cellular and molecular spatial atlas of dystrophic muscle by integrating spatial transcriptomics and single-cell RNAseq datasets. Unbiased clustering revealed nonuniform distribution of unique cell populations throughout D2-mdx muscle that were associated with multiple regenerative timepoints, demonstrating that this model faithfully recapitulates the asynchronous regeneration observed in human DMD muscle. By probing spatiotemporal gene expression signatures, we found that propagation of inflammatory and fibrotic signals from locally damaged areas contributes to widespread pathology and that querying expression signatures within discrete microenvironments can identify targetable pathways for DMD therapy. Overall, this spatial atlas of dystrophic muscle provides a valuable resource for studying DMD disease biology and therapeutic target discovery.

Keywords:  Duchenne muscular dystrophy; asynchronous regeneration; skeletal muscle; spatial transcriptomics

DOI:  https://doi.org/10.1073/pnas.2221249120
Trends Cancer. 2023 Jul 01. pii: S2405-8033(23)00104-8. [Epub ahead of print]

Diet, nutrient supply, and tumor immune responses.

Claire L McIntyre, Ayantu Temesgen, Lydia Lynch.

  Nutrients are essential for cell function. Immune cells operating in the complex tumor microenvironment (TME), which has a unique nutrient composition, face challenges of adapting their metabolism to support effector functions. We discuss the impact of nutrient availability on immune function in the tumor, competition between immune cells and tumor cells for nutrients, and how this is altered by diet. Understanding which diets can promote antitumor immune responses could open a new era of treatment, where dietary modifications can be used as an adjunct to boost the success of existing cancer therapies.

Keywords:  T cells; cancer; diet; immune cells; metabolism; obesity

DOI:  https://doi.org/10.1016/j.trecan.2023.06.003
Science. 2023 Jul 06. eadg4521

Oncogene-like addiction to aneuploidy in human cancers.

Vishruth Girish, Asad A Lakhani, Sarah L Thompson, Christine M Scaduto, Leanne M Brown, Ryan A Hagenson, Erin L Sausville, Brianna E Mendelson, Pranav K Kandikuppa, Devon A Lukow, Monet Lou Yuan, Eric C Stevens, Sophia N Lee, Klaske M Schukken, Saron M Akalu, Anand Vasudevan, Charles Zou, Barbora Salovska, Wenxue Li, Joan C Smith, Alison M Taylor, Robert A Martienssen, Yansheng Liu, Ruping Sun, Jason M Sheltzer.

Most cancers exhibit aneuploidy, but its functional significance in tumor development is controversial. Here, we describe ReDACT (Restoring Disomy in Aneuploid cells using CRISPR Targeting), a set of chromosome engineering tools that allow us to eliminate specific aneuploidies from cancer genomes. Using ReDACT, we created a panel of isogenic cells that have or lack common aneuploidies, and we demonstrate that trisomy of chromosome 1q is required for malignant growth in cancers harboring this alteration. Mechanistically, gaining chromosome 1q increases the expression of MDM4 and suppresses p53 signaling, and we show that TP53 mutations are mutually-exclusive with 1q aneuploidy in human cancers. Thus, tumor cells can be dependent on specific aneuploidies, raising the possibility that these "aneuploidy addictions" could be targeted as a therapeutic strategy.

DOI: https://doi.org/10.1126/science.adg4521
Sci Rep. 2023 07 03. 13(1): 10752

Autophagy dictates sensitivity to PRMT5 inhibitor in breast cancer.

Charles Brobbey, Shasha Yin, Liu Liu, Lauren E Ball, Philip H Howe, Joe R Delaney, Wenjian Gan.

Protein arginine methyltransferase 5 (PRMT5) catalyzes mono-methylation and symmetric di-methylation on arginine residues and has emerged as a potential antitumor target with inhibitors being tested in clinical trials. However, it remains unknown how the efficacy of PRMT5 inhibitors is regulated. Here we report that autophagy blockage enhances cellular sensitivity to PRMT5 inhibitor in triple negative breast cancer cells. Genetic ablation or pharmacological inhibition of PRMT5 triggers cytoprotective autophagy. Mechanistically, PRMT5 catalyzes monomethylation of ULK1 at R532 to suppress ULK1 activation, leading to attenuation of autophagy. As a result, ULK1 inhibition blocks PRMT5 deficiency-induced autophagy and sensitizes cells to PRMT5 inhibitor. Our study not only identifies autophagy as an inducible factor that dictates cellular sensitivity to PRMT5 inhibitor, but also unearths a critical molecular mechanism by which PRMT5 regulates autophagy through methylating ULK1, providing a rationale for the combination of PRMT5 and autophagy inhibitors in cancer therapy.

DOI: https://doi.org/10.1038/s41598-023-37706-9
Biochem J. 2023 Jul 12. 480(13): 909-919

Shaping mitochondria through fed-fast and circadian cycles.

Subhash Khatri, Rubina Kazi, Ullas Kolthur-Seetharam.

  Energy and metabolic homeostasis at the level of the whole body are dictated by the balance between nutrient intake/utilization, bioenergetic potential, and energy expenditure, which are tightly coupled with fed/fast cycles and circadian oscillation. Emerging literature has highlighted the importance of each of these mechanisms that are essential to maintain physiological homeostasis. Lifestyle changes predominantly associated with altered fed-fast and circadian cycles are well established to affect systemic metabolism and energetics, and hence contribute to pathophysiological states. Therefore, it is not surprising that mitochondria have emerged as being pivotal in maintaining physiological homeostasis through daily oscillations/fluctuations in nutrient inputs and light-dark/sleep-wake cycles. Moreover, given the inherent association between mitochondrial dynamics/morphology and functions, it is important to understand the phenomenological and mechanistic underpinnings of fed-fast and circadian cycles dependent remodeling of mitochondria. In this regard, we have summarized the current status of the field in addition to providing a perspective vis-a-vis the complexity of cell-autonomous and non-cell-autonomous signals that dictate mitochondrial dynamics. We also highlight the lacunae besides speculating on prospective efforts that will possibly redefine our insights into the diurnal orchestration of fission/fusion events, which are ultimately coupled to the mitochondrial output.

Keywords:  circadian clock; fed–fast cycles; fission/fusion; metabolic sensing; mitochondrial biogenesis; mitochondrial functions

DOI:  https://doi.org/10.1042/BCJ20220378
Mol Biol Cell. 2023 Jul 05. mbcE22060200

Improved imaging and preservation of lysosome dynamics using silver nanoparticle-enhanced fluorescence.

Sumaiya A Soha, Araniy Santhireswaran, Saaimatul Huq, Jayde Casimir-Powell, Nicala Jenkins, Gregory K Hodgson, Michael Sugiyama, Costin N Antonescu, Stefania Impellizzeri, Roberto J Botelho.

The dynamics of living cells can be studied by live-cell fluorescence microscopy. However, this requires the use of excessive light energy to obtain good signal-to-noise ratio, which can then photobleach fluorochromes, and more worrisomely, lead to photo-toxicity. Upon light excitation, noble metal nanoparticles such as silver nanoparticles (AgNP) generate plasmons, which can then amplify excitation in direct proximity of the nanoparticle's surface and couple to the oscillating dipole of nearby radiating fluorophores, modifying their rate of emission and thus, enhancing their fluorescence. Here, we show that AgNP fed to cells to accumulate within lysosomes enhanced the fluorescence of lysosome-targeted Alexa488-conjugated dextran, BODIPY-cholesterol, and DQ-BSA. Moreover, AgNP increased the fluorescence of GFP fused to the cytosolic tail of LAMP1, showing that metal enhanced fluorescence can occur across the lysosomal membrane. The inclusion of AgNPs in lysosomes did not disturb lysosomal properties such as lysosomal pH, degradative capacity, autophagy and autophagic flux, and membrane integrity, though AgNP seemed to increase basal lysosome tubulation. Importantly, by using AgNP, we could track lysosome motility with reduced laser power without damaging and altering lysosome dynamics. Overall, AgNP-enhanced fluorescence may be a useful tool to study the dynamics of the endo-lysosomal pathway while minimizing photo-toxicity. [Media: see text] [Media: see text] [Media: see text] [Media: see text].

DOI: https://doi.org/10.1091/mbc.E22-06-0200
Dev Cell. 2023 Jun 28. pii: S1534-5807(23)00274-5. [Epub ahead of print]

The membrane surface as a platform that organizes cellular and biochemical processes.

Thomas A Leonard, Martin Loose, Sascha Martens.

  Membranes are essential for life. They act as semi-permeable boundaries that define cells and organelles. In addition, their surfaces actively participate in biochemical reaction networks, where they confine proteins, align reaction partners, and directly control enzymatic activities. Membrane-localized reactions shape cellular membranes, define the identity of organelles, compartmentalize biochemical processes, and can even be the source of signaling gradients that originate at the plasma membrane and reach into the cytoplasm and nucleus. The membrane surface is, therefore, an essential platform upon which myriad cellular processes are scaffolded. In this review, we summarize our current understanding of the biophysics and biochemistry of membrane-localized reactions with particular focus on insights derived from reconstituted and cellular systems. We discuss how the interplay of cellular factors results in their self-organization, condensation, assembly, and activity, and the emergent properties derived from them.

Keywords:  GTPases; kinases; membrane-localized signaling; phosphoinositides; signal transduction; vesicle traffic

DOI:  https://doi.org/10.1016/j.devcel.2023.06.001
Curr Opin Chem Biol. 2023 Jul 04. pii: S1367-5931(23)00100-X. [Epub ahead of print]76 102362

Spatial metabolomics principles and application to cancer research.

Mélanie Planque, Sebastian Igelmann, Ana Margarida Ferreira Campos, Sarah-Maria Fendt.

  Mass spectrometry imaging (MSI) is an emerging technology in cancer metabolomics. Desorption electrospray ionization (DESI) and matrix-assisted laser desorption ionization (MALDI) MSI are complementary techniques to identify hundreds of metabolites in space with close to single-cell resolution. This technology leap enables research focusing on tumor heterogeneity, cancer cell plasticity, and the communication signals between cancer and stromal cells in the tumor microenvironment (TME). Currently, unprecedented knowledge is generated using spatial metabolomics in fundamental cancer research. Yet, also translational applications are emerging, including the assessment of spatial drug distribution in organs and tumors. Moreover, clinical research investigates the use of spatial metabolomics as a rapid pathology tool during cancer surgeries. Here, we summarize MSI applications, the knowledge gained by this technology in space, future directions, and developments needed.

Keywords:  Cancer cell plasticity; Cancer research; Labelled isotope tracing; Mass spectrometry imaging; Metabolite identification; Metabolomics; Tumor heterogeneity; Tumor microenvironment (TME)

DOI:  https://doi.org/10.1016/j.cbpa.2023.102362
Mol Cancer Res. 2023 Jul 06. pii: MCR-23-0411. [Epub ahead of print]

Updating the definition of cancer.

Joel S Brown, Sarah R Amend, Robert H Austin, Robert A Gatenby, Emma U Hammarlund, Kenneth J Pienta.

Most definitions of cancer broadly conform to the current National Cancer Institute definition: "Cancer is a disease in which some of the body's cells grow uncontrollably and spread to other parts of the body". These definitions tend to describe what cancer "looks like" or "does" but do not describe what cancer "is" or "has become." While reflecting past insights, current definitions have not kept pace with the understanding that the cancer cell is itself transformed and evolving. We propose a revised definition of cancer: Cancer is a disease of uncontrolled proliferation by transformed cells subject to evolution by natural selection. We believe this definition captures the essence of the majority of previous and current definitions. To the simplest definition of cancer as a disease of uncontrolled proliferation of cells, our definition adds in the adjective "transformed" to capture the many tumorigenic processes that cancer cells adopt to metastasize. To the concept of uncontrolled proliferation of transformed cells, our proposed definition then adds "subject to evolution by natural selection." The subject to evolution by natural selection modernizes the definition to include the genetic and epigenetic changes that accumulate within a population of cancer cells that lead to the lethal phenotype.

DOI: https://doi.org/10.1158/1541-7786.MCR-23-0411
Nat Commun. 2023 Jul 07. 14(1): 4013

Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology.

Yunhao Bai, Bokai Zhu, John-Paul Oliveria, Bryan J Cannon, Dorien Feyaerts, Marc Bosse, Kausalia Vijayaragavan, Noah F Greenwald, Darci Phillips, Christian M Schürch, Samuel M Naik, Edward A Ganio, Brice Gaudilliere, Scott J Rodig, Michael B Miller, Michael Angelo, Sean C Bendall, Xavier Rovira-Clavé, Garry P Nolan, Sizun Jiang.

Cellular organization and functions encompass multiple scales in vivo. Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Expansion Microscopy (ExM) and related techniques physically expand samples for enhanced spatial resolution, but are challenging to be combined with high-plex imaging technologies to enable integrative multiscaled tissue biology insights. Here, we introduce Expand and comPRESS hydrOgels (ExPRESSO), an ExM framework that allows high-plex protein staining, physical expansion, and removal of water, while retaining the lateral tissue expansion. We demonstrate ExPRESSO imaging of archival clinical tissue samples on Multiplexed Ion Beam Imaging and Imaging Mass Cytometry platforms, with detection capabilities of > 40 markers. Application of ExPRESSO on archival human lymphoid and brain tissues resolved tissue architecture at the subcellular level, particularly that of the blood-brain barrier. ExPRESSO hence provides a platform for extending the analysis compatibility of hydrogel-expanded biospecimens to mass spectrometry, with minimal modifications to protocols and instrumentation.

DOI: https://doi.org/10.1038/s41467-023-39616-w
Am J Physiol Endocrinol Metab. 2023 Jul 05.

Lactate Shuttling Drives the Browning of White Adipose Tissue after Burn Trauma.

Dalia Barayan, Abdikarim Abdullahi, Carly M Knuth, Fadi Khalaf, Sarah Rehou, Robert A Screaton, Marc G Jeschke.

  High levels of plasma lactate are associated with increased mortality in critically injured patients, including those with severe burns. While lactate has long been considered a waste product of glycolysis, it was recently revealed that it acts as a potent inducer of white adipose tissue (WAT) browning, a response implicated in mediating post-burn cachexia, hepatic steatosis and sustained hypermetabolism. Despite the clinical presentation of hyperlactatemia and browning in burns, whether these two pathological responses are linked is currently unknown. Here, we report that elevated lactate plays a causal signaling role in mediating adverse outcomes after burn trauma by directly promoting WAT browning. Using WAT obtained from human burn patients and mouse models of thermal injury, we show that the induction of post-burn browning is positively correlated with a shift towards lactate import and metabolism. Furthermore, daily administration of L-lactate is sufficient to augment burn-induced mortality and weight loss in vivo. At the organ level, increased lactate transport amplified the thermogenic activation of WAT and its associated wasting, thereby driving post-burn hepatic lipotoxicity and dysfunction. Mechanistically, the thermogenic effects of lactate appeared to result from increased import through MCT transporters, which in turn increased intracellular redox pressure, [NADH/ NAD+], and expression of the batokine, FGF21. In fact, pharmacological inhibition of MCT-mediated lactate uptake attenuated browning and improved hepatic function in mice after injury. Collectively, our findings identify a signaling role for lactate that impacts multiple aspects of post-burn hypermetabolism, necessitating further investigation of this multifaceted metabolite in trauma and critical illness.

Keywords:  Adipose; browning; burns; hypermetabolism; lactate

DOI:  https://doi.org/10.1152/ajpendo.00084.2023
Mol Metab. 2023 Jul 04. pii: S2212-8778(23)00102-3. [Epub ahead of print] 101768

Maternal hyperglycemia induces alterations in hepatic amino acid, glucose and lipid metabolism of neonatal offspring: Multi-omics insights from a diabetic pig model.

Bachuki Shashikadze, Libera Valla, Salvo Danilo Lombardo, Cornelia Prehn, Mark Haid, Fabien Riols, Jan Bernd Stöckl, Radwa Elkhateib, Simone Renner, Birgit Rathkolb, Jörg Menche, Martin Hrabĕ de Angelis, Eckhard Wolf, Elisabeth Kemter, Thomas Fröhlich.

   OBJECTIVE: To gain mechanistic insights into adverse effects of maternal hyperglycemia on the liver of neonates, we performed a multi-omics analysis of liver tissue from piglets developed in genetically diabetic (mutant INS gene induced diabetes of youth; MIDY) or wild-type (WT) pigs.
METHODS: Proteome, metabolome and lipidome profiles of liver and clinical parameters of serum samples from 3-day-old WT piglets (n=9) born to MIDY mothers (PHG) were compared with those of WT piglets (n=10) born to normoglycemic mothers (PNG). Furthermore, protein-protein interaction network analysis was used to reveal highly interacting proteins that participate in the same molecular mechanisms and to relate these mechanisms with human pathology.
RESULTS: Hepatocytes of PHG displayed pronounced lipid droplet accumulation, although the abundances of central lipogenic enzymes such as fatty acid-synthase (FASN) were decreased. Additionally, circulating triglyceride (TG) levels were reduced as a trend. Serum levels of non-esterified free fatty acids (NEFA) were elevated in PHG, potentially stimulating hepatic gluconeogenesis. This is supported by elevated hepatic phosphoenolpyruvate carboxykinase (PCK1) and circulating alanine transaminase (ALT) levels. Even though targeted metabolomics showed strongly elevated phosphatidylcholine (PC) levels, the abundances of multiple key enzymes involved in major PC synthesis pathways - most prominently those from the Kennedy pathway - were paradoxically reduced in PHG liver. Conversely, enzymes involved in PC excretion and breakdown such as PC-specific translocase ATP-binding cassette 4 (ABCB4) and phospholipase A2 were increased in abundance.
CONCLUSIONS: Our study indicates that maternal hyperglycemia without confounding obesity induces profound molecular changes in the liver of neonatal offspring. In particular, we found evidence for stimulated gluconeogenesis and hepatic lipid accumulation independent of de novo lipogenesis. Reduced levels of PC biosynthesis enzymes and increased levels of proteins involved in PC translocation or breakdown may represent counter-regulatory mechanisms to maternally elevated PC levels. Our comprehensive multi-omics dataset provides a valuable resource for future meta-analysis studies focusing on liver metabolism in newborns from diabetic mothers.

Keywords:  Maternal diabetes; clinical parameters; liver; metabolomics; neonates; pig model; protein-protein interaction; proteomics

DOI:  https://doi.org/10.1016/j.molmet.2023.101768
Oncogene. 2023 Jul 07.

Activation of invasion by oncogenic reprogramming of cholesterol metabolism via increased NPC1 expression and macropinocytosis.

Aikaterini Skorda, Anna Røssberg Lauridsen, Chengnan Wu, Jinrong Huang, Monika Mrackova, Nuggi Ingholt Winther, Vanessa Jank, Zsofia Sztupinszki, Robert Strauss, Mesut Bilgin, Kenji Maeda, Bin Liu, Yonglun Luo, Marja Jäättelä, Tuula Kallunki.

Cancer cells are dependent on cholesterol, and they possess strictly controlled cholesterol homeostasis mechanisms. These allow them to smoothly switch between cholesterol synthesis and uptake to fulfill their needs and to adapt environmental changes. Here we describe a mechanism of how cancer cells employ oncogenic growth factor signaling to promote uptake and utilization of extracellular cholesterol via Myeloid Zinc Finger 1 (MZF1)-mediated Niemann Pick C1 (NPC1) expression and upregulated macropinocytosis. Expression of p95ErbB2, highly oncogenic, standard-treatment resistant form of ErbB2 mobilizes lysosomes and activates EGFR, invasion and macropinocytosis. This is connected to a metabolic shift from cholesterol synthesis to uptake due to macropinocytosis-enabled flow of extracellular cholesterol. NPC1 increase facilitates extracellular cholesterol uptake and is necessary for the invasion of ErbB2 expressing breast cancer spheroids and ovarian cancer organoids, indicating a regulatory role for NPC1 in the process. The ability to obtain cholesterol as a byproduct of increased macropinocytosis allows cancer cells to direct the resources needed for the energy-consuming cholesterol synthesis towards other activities such as invasion. These results demonstrate that macropinocytosis is not only an alternative energy source for cancer cells but also an efficient way to provide building material, such as cholesterol, for its macromolecules and membranes.

DOI: https://doi.org/10.1038/s41388-023-02771-x