bims-cagime 2024-04-28 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2024‒04‒28
38 papers selected by
Kıvanç Görgülü, Technical University of Munich

IL-6 promotes tumor growth through immune evasion but is dispensable for cachexia.
Activation of lysosomal iron triggers ferroptosis in cancer.
Virtual reality-empowered deep-learning analysis of brain cells.
Cancer cell metabolism and antitumour immunity.
Axon guidance cue SEMA3A promotes the aggressive phenotype of basal-like PDAC.
DrugMap: A quantitative pan-cancer analysis of cysteine ligandability.
Organelle-targeted Laurdans measure heterogeneity in subcellular membranes and their responses to saturated lipid stress.
Molecular determinants of lipid droplet subpopulations and their fates.
Spatiotemporally resolved colorectal oncogenesis in mini-colons ex vivo.
LPCAT1-mediated membrane phospholipid remodelling promotes ferroptosis evasion and tumour growth.
Human metabolic chambers reveal a coordinated metabolic-physiologic response to nutrition.
Punctuational evolution is pervasive in distal site metastatic colonization.
The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1.
PGE2 limits effector expansion of tumour-infiltrating stem-like CD8+ T cells.
Advances in body composition: a 100-year journey.
Cancer radioresistance is characterized by a differential lipid droplet content along the cell cycle.
Single-cell analysis reveals context-dependent, cell-level selection of mtDNA.
Alanyl-tRNA synthetase, AARS1, is a lactate sensor and lactyltransferase that lactylates p53 and contributes to tumorigenesis.
Defining and benchmarking open problems in single-cell analysis.
Lysosomal Peptide Self-Assembly To Control Cell Behavior.
Profiling microRNA expression during senescence and aging: mining for a diagnostic tool of senescent-cell burden.
Whole-cortex in situ sequencing reveals input-dependent area identity.
Functional sensory circuits built from neurons of two species.
Membrane-bound O-acyltransferase 7 (MBOAT7) shapes lysosomal lipid homeostasis and function to control alcohol-associated liver injury.
Detection and quantification of Na,K-ATPase dimers in the plasma membrane of living cells by FRET-FCS.
Fast histological assessment of adipose tissue inflammation by label-free mid-infrared optoacoustic microscopy.
Metabolomics-driven discovery of therapeutic targets for cancer cachexia.
Presenting metabolomics analyses: what is in a number?
Synthetic protein circuits for programmable control of mammalian cell death.
Detecting material state changes in the nucleolus by label-free digital holographic microscopy.
Maximum entropy determination of mammalian proteome dynamics.
STING promotes homeostatic maintenance of tissues and confers longevity with aging.
Selected Ion Monitoring for Orbitrap-Based Metabolomics.
Cancer spreading patterns based on epithelial-mesenchymal plasticity.
A glycolytic metabolite that drives BRCA2 haploinsufficiency.
Circulating tumor cells shed large extracellular vesicles in capillary-sized bifurcations.
OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies.
Mapping the pancancer metastasis tumor microbiome.

EMBO Rep. 2024 Apr 26.

IL-6 promotes tumor growth through immune evasion but is dispensable for cachexia.

Young-Yon Kwon, Sheng Hui.

  Various cytokines have been implicated in cancer cachexia. One such cytokine is IL-6, deemed as a key cachectic factor in mice inoculated with colon carcinoma 26 (C26) cells, a widely used cancer cachexia model. Here we tested the causal role of IL-6 in cancer cachexia by knocking out the IL-6 gene in C26 cells. We found that the growth of IL-6 KO tumors was dramatically delayed. More strikingly, while IL-6 KO tumors eventually reached the similar size as wild-type tumors, cachexia still took place, despite no elevation in circulating IL-6. In addition, the knockout of leukemia inhibitory factor (LIF), another IL-6 family cytokine proposed as a cachectic factor in the model, also affected tumor growth but not cachexia. We further showed an increase in the infiltration of immune cell population in the IL-6 KO tumors compared with wild-type controls and the defective IL-6 KO tumor growth was rescued in immunodeficient mice while cachexia was not. Thus, IL-6 promotes tumor growth by facilitating immune evasion but is dispensable for cachexia.

Keywords:  Cancer Cachexia; Colon Carcinoma 26; IL-6; LIF; Tumor Immune Evasion

DOI:  https://doi.org/10.1038/s44319-024-00144-3
Res Sq. 2024 Apr 08. pii: rs.3.rs-4165774. [Epub ahead of print]

Activation of lysosomal iron triggers ferroptosis in cancer.

Raphaël Rodriguez, Tatiana Cañeque, Leeroy Baron, Sebastian Müller, Alanis Carmona, Ludovic Colombeau, Antoine Versini, Marie Sabatier, Julio Sampaio, Eikan Mishima, Armel Picard-Bernes, Stéphanie Solier, Jiashuo Zheng, Bettina Proneth, Leishemba Thoidingjam, Christine Gaillet, Laurence Grimaud, Cameron Fraser, Krystina Szylo, Caroline Bonnet, Emmanuelle Charafe, Christophe Ginestier, Patricia Santofimia, Nelson Dusetti, Juan Iovanna, Antonio Sa Cunha, Gabriella Pittau, Pascal Hammel, Dimitri Tzanis, Sylvie Bonvalot, Sarah Watson, Brent Stockwell, Marcus Conrad, Jessalyn Ubellacker.

Iron catalyses the oxidation of lipids in biological membranes and promotes a form of cell death referred to as ferroptosis 1-3 . Identifying where this chemistry takes place in the cell can inform the design of drugs capable of inducing or inhibiting ferroptosis in various disease-relevant settings. Whereas genetic approaches have revealed underlying mechanisms of lipid peroxide detoxification 1,4,5 , small molecules can provide unparalleled spatiotemporal control of the chemistry at work 6 . Here, we show that the ferroptosis inhibitor liproxstatin-1 (Lip-1) exerts a protective activity by inactivating iron in lysosomes. Based on this, we designed the bifunctional compound fentomycin that targets phospholipids at the plasma membrane and activates iron in lysosomes upon endocytosis, promoting oxidative degradation of phospholipids and ferroptosis. Fentomycin effectively kills primary sarcoma and pancreatic ductal adenocarcinoma cells. It acts as a lipolysis-targeting chimera (LIPTAC), preferentially targeting iron-rich CD44 high cell-subpopulations 7,8 associated with the metastatic disease and drug resistance 9,10 . Furthermore, we demonstrate that fentomycin also depletes CD44 high cells in vivo and reduces intranodal tumour growth in an immunocompetent murine model of breast cancer metastasis. These data demonstrate that lysosomal iron triggers ferroptosis and that lysosomal iron redox chemistry can be exploited for therapeutic benefits.

DOI: https://doi.org/10.21203/rs.3.rs-4165774/v1
Nat Methods. 2024 Apr 22.

Virtual reality-empowered deep-learning analysis of brain cells.

Doris Kaltenecker, Rami Al-Maskari, Moritz Negwer, Luciano Hoeher, Florian Kofler, Shan Zhao, Mihail Todorov, Zhouyi Rong, Johannes Christian Paetzold, Benedikt Wiestler, Marie Piraud, Daniel Rueckert, Julia Geppert, Pauline Morigny, Maria Rohm, Bjoern H Menze, Stephan Herzig, Mauricio Berriel Diaz, Ali Ertürk.

Automated detection of specific cells in three-dimensional datasets such as whole-brain light-sheet image stacks is challenging. Here, we present DELiVR, a virtual reality-trained deep-learning pipeline for detecting c-Fos+ cells as markers for neuronal activity in cleared mouse brains. Virtual reality annotation substantially accelerated training data generation, enabling DELiVR to outperform state-of-the-art cell-segmenting approaches. Our pipeline is available in a user-friendly Docker container that runs with a standalone Fiji plugin. DELiVR features a comprehensive toolkit for data visualization and can be customized to other cell types of interest, as we did here for microglia somata, using Fiji for dataset-specific training. We applied DELiVR to investigate cancer-related brain activity, unveiling an activation pattern that distinguishes weight-stable cancer from cancers associated with weight loss. Overall, DELiVR is a robust deep-learning tool that does not require advanced coding skills to analyze whole-brain imaging data in health and disease.

DOI: https://doi.org/10.1038/s41592-024-02245-2
Nat Rev Immunol. 2024 Apr 22.

Cancer cell metabolism and antitumour immunity.

Mara De Martino, Jeffrey C Rathmell, Lorenzo Galluzzi, Claire Vanpouille-Box.

Accumulating evidence suggests that metabolic rewiring in malignant cells supports tumour progression not only by providing cancer cells with increased proliferative potential and an improved ability to adapt to adverse microenvironmental conditions but also by favouring the evasion of natural and therapy-driven antitumour immune responses. Here, we review cancer cell-intrinsic and cancer cell-extrinsic mechanisms through which alterations of metabolism in malignant cells interfere with innate and adaptive immune functions in support of accelerated disease progression. Further, we discuss the potential of targeting such alterations to enhance anticancer immunity for therapeutic purposes.

DOI: https://doi.org/10.1038/s41577-024-01026-4
Gut. 2024 Apr 26. pii: gutjnl-2023-329807. [Epub ahead of print]

Axon guidance cue SEMA3A promotes the aggressive phenotype of basal-like PDAC.

Francesca Lupo, Francesco Pezzini, Davide Pasini, Elena Fiorini, Annalisa Adamo, Lisa Veghini, Michele Bevere, Cristina Frusteri, Pietro Delfino, Sabrina D'agosto, Silvia Andreani, Geny Piro, Antonia Malinova, Tian Wang, Francesco De Sanctis, Rita Teresa Lawlor, Chang-Il Hwang, Carmine Carbone, Ivano Amelio, Peter Bailey, Vincenzo Bronte, David Tuveson, Aldo Scarpa, Stefano Ugel, Vincenzo Corbo.

  OBJECTIVE: The dysregulation of the axon guidance pathway is common in pancreatic ductal adenocarcinoma (PDAC), yet our understanding of its biological relevance is limited. Here, we investigated the functional role of the axon guidance cue SEMA3A in supporting PDAC progression.DESIGN: We integrated bulk and single-cell transcriptomic datasets of human PDAC with in situ hybridisation analyses of patients' tissues to evaluate SEMA3A expression in molecular subtypes of PDAC. Gain and loss of function experiments in PDAC cell lines and organoids were performed to dissect how SEMA3A contributes to define a biologically aggressive phenotype.
RESULTS: In PDAC tissues, SEMA3A is expressed by stromal elements and selectively enriched in basal-like/squamous epithelial cells. Accordingly, expression of SEMA3A in PDAC cells is induced by both cell-intrinsic and cell-extrinsic determinants of the basal-like phenotype. In vitro, SEMA3A promotes cell migration as well as anoikis resistance. At the molecular level, these phenotypes are associated with increased focal adhesion kinase signalling through canonical SEMA3A-NRP1 axis. SEMA3A provides mouse PDAC cells with greater metastatic competence and favours intratumoural infiltration of tumour-associated macrophages and reduced density of T cells. Mechanistically, SEMA3A functions as chemoattractant for macrophages and skews their polarisation towards an M2-like phenotype. In SEMA3Ahigh tumours, depletion of macrophages results in greater intratumour infiltration by CD8+T cells and better control of the disease from antitumour treatment.
CONCLUSIONS: Here, we show that SEMA3A is a stress-sensitive locus that promotes the malignant phenotype of basal-like PDAC through both cell-intrinsic and cell-extrinsic mechanisms.

Keywords:  PANCREATIC CANCER

DOI:  https://doi.org/10.1136/gutjnl-2023-329807
Cell. 2024 Apr 17. pii: S0092-8674(24)00318-0. [Epub ahead of print]

DrugMap: A quantitative pan-cancer analysis of cysteine ligandability.

Mariko Takahashi, Harrison B Chong, Siwen Zhang, Tzu-Yi Yang, Matthew J Lazarov, Stefan Harry, Michelle Maynard, Brendan Hilbert, Ryan D White, Heather E Murrey, Chih-Chiang Tsou, Kira Vordermark, Jonathan Assaad, Magdy Gohar, Benedikt R Dürr, Marianne Richter, Himani Patel, Gregory Kryukov, Natasja Brooijmans, Aliyu Sidi Omar Alghali, Karla Rubio, Antonio Villanueva, Junbing Zhang, Maolin Ge, Farah Makram, Hanna Griesshaber, Drew Harrison, Ann-Sophie Koglin, Samuel Ojeda, Barbara Karakyriakou, Alexander Healy, George Popoola, Inbal Rachmin, Neha Khandelwal, Jason R Neil, Pei-Chieh Tien, Nicholas Chen, Tobias Hosp, Sanne van den Ouweland, Toshiro Hara, Lillian Bussema, Rui Dong, Lei Shi, Martin Q Rasmussen, Ana Carolina Domingues, Aleigha Lawless, Jacy Fang, Satoshi Yoda, Linh Phuong Nguyen, Sarah Marie Reeves, Farrah Nicole Wakefield, Adam Acker, Sarah Elizabeth Clark, Taronish Dubash, John Kastanos, Eugene Oh, David E Fisher, Shyamala Maheswaran, Daniel A Haber, Genevieve M Boland, Moshe Sade-Feldman, Russell W Jenkins, Aaron N Hata, Nabeel M Bardeesy, Mario L Suvà, Brent R Martin, Brian B Liau, Christopher J Ott, Miguel N Rivera, Michael S Lawrence, Liron Bar-Peled.

  Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors for a wide range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed "DrugMap," an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NF-κB1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NF-κB1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription-factor activity.

Keywords:  chemical proteomics; covalent inhibitors; cysteine ligandability; transcription factors

DOI:  https://doi.org/10.1016/j.cell.2024.03.027
bioRxiv. 2024 Apr 20. pii: 2024.04.16.589828. [Epub ahead of print]

Organelle-targeted Laurdans measure heterogeneity in subcellular membranes and their responses to saturated lipid stress.

Adrian M Wong, Itay Budin.

Cell organelles feature characteristic lipid compositions that lead to differences in membrane properties. In living cells, membrane ordering and fluidity are commonly measured using the solvatochromic dye Laurdan, whose fluorescence is sensitive to membrane packing. As a general lipophilic dye, Laurdan stains all hydrophobic environments in cells, so it is challenging to characterize membrane properties in specific organelles or assess their responses to pharmacological treatments in intact cells. Here, we describe the synthesis and application of Laurdan-derived probes that read out membrane packing of individual cellular organelles. The set of Organelle-targeted Laurdans (OTL) localizes to the ER, mitochondria, lysosomes and Golgi compartments with high specificity, while retaining the spectral resolution needed to detect biological changes in membrane packing. We show that ratiometric imaging with OTL can resolve membrane heterogeneity within organelles, as well as changes in membrane packing resulting from inhibition of lipid trafficking or bioenergetic processes. We apply these probes to characterize organelle-specific responses to saturated lipid stress. While ER and lysosomal membrane fluidity is sensitive to exogenous saturated fatty acids, that of mitochondrial membranes is protected. We then use differences in ER membrane fluidity to sort populations of cells based on their fatty acid diet, highlighting the ability of organelle-localized solvatochromic probes to distinguish between cells based on their metabolic state. These results expand the repertoire of targeted membrane probes and demonstrate their application to interrogating lipid dysregulation.

DOI: https://doi.org/10.1101/2024.04.16.589828
FEBS Lett. 2024 Apr 25.

Molecular determinants of lipid droplet subpopulations and their fates.

W Mike Henne.

  Distinct pools of lipid droplets (LDs) exist in individual cells and are demarcated both by their unique proteomes and lipid compositions. Focusing on yeast-based work, we briefly review the state of understanding of LD subsets, and how specific proteins can dictate their identities and fates through lipophagy and lipolysis-mediated turnover.

Keywords:  lipid droplet; lipolysis; microdomains; micro‐lipophagy; triglyceride

DOI:  https://doi.org/10.1002/1873-3468.14891
Nature. 2024 Apr 24.

Spatiotemporally resolved colorectal oncogenesis in mini-colons ex vivo.

L Francisco Lorenzo-Martín, Tania Hübscher, Amber D Bowler, Nicolas Broguiere, Jakob Langer, Lucie Tillard, Mikhail Nikolaev, Freddy Radtke, Matthias P Lutolf.

Three-dimensional organoid culture technologies have revolutionized cancer research by allowing for more realistic and scalable reproductions of both tumour and microenvironmental structures1-3. This has enabled better modelling of low-complexity cancer cell behaviours that occur over relatively short periods of time4. However, available organoid systems do not capture the intricate evolutionary process of cancer development in terms of tissue architecture, cell diversity, homeostasis and lifespan. As a consequence, oncogenesis and tumour formation studies are not possible in vitro and instead require the extensive use of animal models, which provide limited spatiotemporal resolution of cellular dynamics and come at a considerable cost in terms of resources and animal lives. Here we developed topobiologically complex mini-colons that are able to undergo tumorigenesis ex vivo by integrating microfabrication, optogenetic and tissue engineering approaches. With this system, tumorigenic transformation can be spatiotemporally controlled by directing oncogenic activation through blue-light exposure, and emergent colon tumours can be tracked in real-time at the single-cell resolution for several weeks without breaking the culture. These induced mini-colons display rich intratumoural and intertumoural diversity and recapitulate key pathophysiological hallmarks displayed by colorectal tumours in vivo. By fine-tuning cell-intrinsic and cell-extrinsic parameters, mini-colons can be used to identify tumorigenic determinants and pharmacological opportunities. As a whole, our study paves the way for cancer initiation research outside living organisms.

DOI: https://doi.org/10.1038/s41586-024-07330-2
Nat Cell Biol. 2024 Apr 26.

LPCAT1-mediated membrane phospholipid remodelling promotes ferroptosis evasion and tumour growth.

Ziwen Li, Yameng Hu, Haiqing Zheng, Man Li, Yuanji Liu, Rongni Feng, Xincheng Li, Shuxia Zhang, Miaoling Tang, Meisongzhu Yang, Ruyuan Yu, Yingru Xu, Xinyi Liao, Suwen Chen, Wanying Qian, Qiliang Zhang, Daolin Tang, Bo Li, Libing Song, Jun Li.

The mechanisms underlying the dynamic remodelling of cellular membrane phospholipids to prevent phospholipid peroxidation-induced membrane damage and evade ferroptosis, a non-apoptotic form of cell death driven by iron-dependent lipid peroxidation, remain poorly understood. Here we show that lysophosphatidylcholine acyltransferase 1 (LPCAT1) plays a critical role in ferroptosis resistance by increasing membrane phospholipid saturation via the Lands cycle, thereby reducing membrane levels of polyunsaturated fatty acids, protecting cells from phospholipid peroxidation-induced membrane damage and inhibiting ferroptosis. Furthermore, the enhanced in vivo tumour-forming capability of tumour cells is closely associated with the upregulation of LPCAT1 and emergence of a ferroptosis-resistant state. Combining LPCAT1 inhibition with a ferroptosis inducer synergistically triggers ferroptosis and suppresses tumour growth. Therefore, our results unveil a plausible role for LPCAT1 in evading ferroptosis and suggest it as a promising target for clinical intervention in human cancer.

DOI: https://doi.org/10.1038/s41556-024-01405-y
medRxiv. 2024 Apr 10. pii: 2024.04.08.24305087. [Epub ahead of print]

Human metabolic chambers reveal a coordinated metabolic-physiologic response to nutrition.

Andrew S Perry, Paolo Piaggi, Shi Huang, Matthew Nayor, Jane Freedman, Kari North, Jennifer Below, Clary Clish, Venkatesh L Murthy, Jonathan Krakoff, Ravi V Shah.

The emerging field of precision nutrition is based on the notion that inter-individual responses across diets of different calorie-macronutrient content may contribute to inter-individual differences in metabolism, adiposity, and weight gain. Free-living diet studies have been traditionally challenged by difficulties in controlling adherence to prescribed calories and macronutrient content and rarely allow a period of metabolic stability prior to metabolic measures (to minimize influences of weight changes). In this context, key physiologic measures central to precision nutrition responses may be most precisely quantified via whole room indirect calorimetry over 24-h, in which precise control of activity and nutrition can be achieved. In addition, these studies represent unique "N of 1" human crossover metabolic-physiologic experiments during which specific molecular pathways central to nutrient metabolism may be discerned. Here, we quantified 263 circulating metabolites during a ≈40-day inpatient admission in which up to 94 participants underwent seven monitored 24-h nutritional interventions of differing macronutrient composition in a whole-room indirect calorimeter to capture precision metabolic responses. Broadly, we observed heterogenous responses in metabolites across dietary chambers, with the exception of carnitines which tracked with 24-h respiratory quotient. We identified excursions in shared metabolic species (e.g., carnitines, glycerophospholipids, amino acids) that mapped onto gold-standard calorimetric measures of substrate oxidation preference and lipid availability. These findings support a coordinated metabolic-physiologic response to nutrition, highlighting the relevance of these controlled settings to uncover biological pathways of energy utilization during precision nutrition studies.

DOI: https://doi.org/10.1101/2024.04.08.24305087
bioRxiv. 2024 Apr 11. pii: 2024.04.08.588529. [Epub ahead of print]

Punctuational evolution is pervasive in distal site metastatic colonization.

George Butler, Sarah R Amend, Robert Axelrod, Chris Venditti, Kenneth J Pienta.

The evolution of metastasis represents a lethal stage of cancer progression. Yet, the evolutionary kinetics of metastatic disease remain unresolved. Here, using single cell CRISPR-Cas9 lineage tracing data, we show that in metastatic disease, gradual molecular evolution is punctuated by episodes of rapid evolutionary change associated with lineage divergence. By measuring punctuational effects across the metastatic cascade, we show that punctuational effects contribute more to the molecular diversity at distal site metastases compared to the paired primary tumor, suggesting qualitatively different modes of evolution may drive primary and metastatic tumor progression. This is the first empirical evidence for distinct patterns of molecular evolution at early and late stages of metastasis and demonstrates the complex interplay of cell intrinsic and extrinsic factors that shape lethal cancer.

DOI: https://doi.org/10.1101/2024.04.08.588529
bioRxiv. 2024 Apr 11. pii: 2024.04.09.588557. [Epub ahead of print]

The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1.

Rodrigo Romero, Tinyi Chu, Tania J González-Robles, Perianne Smith, Yubin Xie, Harmanpreet Kaur, Sara Yoder, Huiyong Zhao, Chenyi Mao, Wenfei Kang, Maria V Pulina, Kayla E Lawrence, Anuradha Gopalan, Samir Zaidi, Kwangmin Yoo, Jungmin Choi, Ning Fan, Olivia Gerstner, Wouter R Karthaus, Elisa DeStanchina, Kelly V Ruggles, Peter M K Westcott, Ronan Chaligné, Dana Pe'er, Charles L Sawyers.

Lineage plasticity is a recognized hallmark of cancer progression that can shape therapy outcomes. The underlying cellular and molecular mechanisms mediating lineage plasticity remain poorly understood. Here, we describe a versatile in vivo platform to identify and interrogate the molecular determinants of neuroendocrine lineage transformation at different stages of prostate cancer progression. Adenocarcinomas reliably develop following orthotopic transplantation of primary mouse prostate organoids acutely engineered with human-relevant driver alterations (e.g., Rb1-/-; Trp53-/-; cMyc+ or Pten-/-; Trp53-/-; cMyc+), but only those with Rb1 deletion progress to ASCL1+ neuroendocrine prostate cancer (NEPC), a highly aggressive, androgen receptor signaling inhibitor (ARSI)-resistant tumor. Importantly, we show this lineage transition requires a native in vivo microenvironment not replicated by conventional organoid culture. By integrating multiplexed immunofluorescence, spatial transcriptomics and PrismSpot to identify cell type-specific spatial gene modules, we reveal that ASCL1+ cells arise from KRT8+ luminal epithelial cells that progressively acquire transcriptional heterogeneity, producing large ASCL1+;KRT8- NEPC clusters. Ascl1 loss in established NEPC results in transient tumor regression followed by recurrence; however, Ascl1 deletion prior to transplantation completely abrogates lineage plasticity, yielding adenocarcinomas with elevated AR expression and marked sensitivity to castration. The dynamic feature of this model reveals the importance of timing of therapies focused on lineage plasticity and offers a platform for identification of additional lineage plasticity drivers.

DOI: https://doi.org/10.1101/2024.04.09.588557
Nature. 2024 Apr 24.

PGE2 limits effector expansion of tumour-infiltrating stem-like CD8+ T cells.

Sebastian B Lacher, Janina Dörr, Gustavo P de Almeida, Julian Hönninger, Felix Bayerl, Anna Hirschberger, Anna-Marie Pedde, Philippa Meiser, Lukas Ramsauer, Thomas J Rudolph, Nadine Spranger, Matteo Morotti, Alizee J Grimm, Sebastian Jarosch, Arman Oner, Lisa Gregor, Stefanie Lesch, Stefanos Michaelides, Luisa Fertig, Daria Briukhovetska, Lina Majed, Sophia Stock, Dirk H Busch, Veit R Buchholz, Percy A Knolle, Dietmar Zehn, Denarda Dangaj Laniti, Sebastian Kobold, Jan P Böttcher.

Cancer-specific TCF1+ stem-like CD8+ T cells can drive protective anticancer immunity through expansion and effector cell differentiation1-4; however, this response is dysfunctional in tumours. Current cancer immunotherapies2,5-9 can promote anticancer responses through TCF1+ stem-like CD8+ T cells in some but not all patients. This variation points towards currently ill-defined mechanisms that limit TCF1+CD8+ T cell-mediated anticancer immunity. Here we demonstrate that tumour-derived prostaglandin E2 (PGE2) restricts the proliferative expansion and effector differentiation of TCF1+CD8+ T cells within tumours, which promotes cancer immune escape. PGE2 does not affect the priming of TCF1+CD8+ T cells in draining lymph nodes. PGE2 acts through EP2 and EP4 (EP2/EP4) receptor signalling in CD8+ T cells to limit the intratumoural generation of early and late effector T cell populations that originate from TCF1+ tumour-infiltrating CD8+ T lymphocytes (TILs). Ablation of EP2/EP4 signalling in cancer-specific CD8+ T cells rescues their expansion and effector differentiation within tumours and leads to tumour elimination in multiple mouse cancer models. Mechanistically, suppression of the interleukin-2 (IL-2) signalling pathway underlies the PGE2-mediated inhibition of TCF1+ TIL responses. Altogether, we uncover a key mechanism that restricts the IL-2 responsiveness of TCF1+ TILs and prevents anticancer T cell responses that originate from these cells. This study identifies the PGE2-EP2/EP4 axis as a molecular target to restore IL-2 responsiveness in anticancer TILs to achieve cancer immune control.

DOI: https://doi.org/10.1038/s41586-024-07254-x
Int J Obes (Lond). 2024 Apr 20.

Advances in body composition: a 100-year journey.

Steven B Heymsfield.

Knowledge of human body composition at the dawn of the twentieth century was based largely on cadaver studies and chemical analyses of isolated organs and tissues. Matters soon changed by the nineteen twenties when the Czech anthropologist Jindřich Matiegka introduced an influential new anthropometric method of fractionating body mass into subcutaneous adipose tissue and other major body components. Today, one century later, investigators can not only quantify every major body component in vivo at the atomic, molecular, cellular, tissue-organ, and whole-body organizational levels, but go far beyond to organ and tissue-specific composition and metabolite estimates. These advances are leading to an improved understanding of adiposity structure-function relations, discovery of new obesity phenotypes, and a mechanistic basis of some weight-related pathophysiological processes and adverse clinical outcomes. What factors over the past one hundred years combined to generate these profound new body composition measurement capabilities in living humans? This perspective tracks the origins of these scientific innovations with the aim of providing insights on current methodology gaps and future research needs.

DOI: https://doi.org/10.1038/s41366-024-01511-9
Cell Div. 2024 Apr 20. 19(1): 14

Cancer radioresistance is characterized by a differential lipid droplet content along the cell cycle.

Francesca Pagliari, Jeannette Jansen, Jan Knoll, Rachel Hanley, Joao Seco, Luca Tirinato.

  BACKGROUND: Cancer radiation treatments have seen substantial advancements, yet the biomolecular mechanisms underlying cancer cell radioresistance continue to elude full understanding. The effectiveness of radiation on cancer is hindered by various factors, such as oxygen concentrations within tumors, cells' ability to repair DNA damage and metabolic changes. Moreover, the initial and radiation-induced cell cycle profiles can significantly influence radiotherapy responses as radiation sensitivity fluctuates across different cell cycle stages. Given this evidence and our prior studies establishing a correlation between cancer radiation resistance and an increased number of cytoplasmic Lipid Droplets (LDs), we investigated if LD accumulation was modulated along the cell cycle and if this correlated with differential radioresistance in lung and bladder cell lines.RESULTS: Our findings identified the S phase as the most radioresistant cell cycle phase being characterized by an increase in LDs. Analysis of the expression of perilipin genes (a family of proteins involved in the LD structure and functions) throughout the cell cycle also uncovered a unique gene cell cycle pattern.
CONCLUSIONS: In summary, although these results require further molecular studies about the mechanisms of radioresistance, the findings presented here are the first evidence that LD accumulation could participate in cancer cells' ability to better survive X-Ray radiation when cells are in the S phase. LDs can represent new players in the radioresistance processes associated with cancer metabolism. This could open new therapeutic avenues in which the use of LD-interfering drugs might enhance cancer sensitivity to radiation.

Keywords:  Cancer metabolism; Cell cycle; Lipid droplets; Perilipins; Radioresistance

DOI:  https://doi.org/10.1186/s13008-024-00116-y
Nature. 2024 Apr 24.

Single-cell analysis reveals context-dependent, cell-level selection of mtDNA.

Anna V Kotrys, Timothy J Durham, Xiaoyan A Guo, Venkata R Vantaku, Sareh Parangi, Vamsi K Mootha.

Heteroplasmy occurs when wild-type and mutant mitochondrial DNA (mtDNA) molecules co-exist in single cells1. Heteroplasmy levels change dynamically in development, disease and ageing2,3, but it is unclear whether these shifts are caused by selection or drift, and whether they occur at the level of cells or intracellularly. Here we investigate heteroplasmy dynamics in dividing cells by combining precise mtDNA base editing (DdCBE)4 with a new method, SCI-LITE (single-cell combinatorial indexing leveraged to interrogate targeted expression), which tracks single-cell heteroplasmy with ultra-high throughput. We engineered cells to have synonymous or nonsynonymous complex I mtDNA mutations and found that cell populations in standard culture conditions purge nonsynonymous mtDNA variants, whereas synonymous variants are maintained. This suggests that selection dominates over simple drift in shaping population heteroplasmy. We simultaneously tracked single-cell mtDNA heteroplasmy and ancestry, and found that, although the population heteroplasmy shifts, the heteroplasmy of individual cell lineages remains stable, arguing that selection acts at the level of cell fitness in dividing cells. Using these insights, we show that we can force cells to accumulate high levels of truncating complex I mtDNA heteroplasmy by placing them in environments where loss of biochemical complex I activity has been reported to benefit cell fitness. We conclude that in dividing cells, a given nonsynonymous mtDNA heteroplasmy can be harmful, neutral or even beneficial to cell fitness, but that the 'sign' of the effect is wholly dependent on the environment.

DOI: https://doi.org/10.1038/s41586-024-07332-0
Cell. 2024 Apr 17. pii: S0092-8674(24)00397-0. [Epub ahead of print]

Alanyl-tRNA synthetase, AARS1, is a lactate sensor and lactyltransferase that lactylates p53 and contributes to tumorigenesis.

Zhi Zong, Feng Xie, Shuai Wang, Xiaojin Wu, Zhenyu Zhang, Bing Yang, Fangfang Zhou.

  Lysine lactylation is a post-translational modification that links cellular metabolism to protein function. Here, we find that AARS1 functions as a lactate sensor that mediates global lysine lacylation in tumor cells. AARS1 binds to lactate and catalyzes the formation of lactate-AMP, followed by transfer of lactate to the lysince acceptor residue. Proteomics studies reveal a large number of AARS1 targets, including p53 where lysine 120 and lysine 139 in the DNA binding domain are lactylated. Generation and utilization of p53 variants carrying constitutively lactylated lysine residues revealed that AARS1 lactylation of p53 hinders its liquid-liquid phase separation, DNA binding, and transcriptional activation. AARS1 expression and p53 lacylation correlate with poor prognosis among cancer patients carrying wild type p53. β-alanine disrupts lactate binding to AARS1, reduces p53 lacylation, and mitigates tumorigenesis in animal models. We propose that AARS1 contributes to tumorigenesis by coupling tumor cell metabolism to proteome alteration.

Keywords:  AARS1; LLPS; alanyl-tRNA synthetase 1; lactate; lactylation; lactyltransferase; liquid-liquid phase separation; p53; tumor progression; β-alanine

DOI:  https://doi.org/10.1016/j.cell.2024.04.002
Res Sq. 2024 Apr 04. pii: rs.3.rs-4181617. [Epub ahead of print]

Defining and benchmarking open problems in single-cell analysis.

Open Problems Jamboree Members

With the growing number of single-cell analysis tools, benchmarks are increasingly important to guide analysis and method development. However, a lack of standardisation and extensibility in current benchmarks limits their usability, longevity, and relevance to the community. We present Open Problems, a living, extensible, community-guided benchmarking platform including 10 current single-cell tasks that we envision will raise standards for the selection, evaluation, and development of methods in single-cell analysis.

DOI: https://doi.org/10.21203/rs.3.rs-4181617/v1
Chembiochem. 2024 Apr 25. e202400232

Lysosomal Peptide Self-Assembly To Control Cell Behavior.

Sangshuang Li, Huaimin Wang.

  Lysosomes are membrane-enclosed organelles that play key roles in degrading and recycling cellular debris, cellular signaling, and energy metabolism processes. Confinement of amphiphilic peptides in the lysosome to construct functional nanostructures through noncovalent interactions is an emerging approach to tune the homeostasis of lysosome. After briefly introducing the importance of lysosome and its functions, we discuss the advantages of lysosomal nanostructure formation for disease therapy. We next discuss the strategy for triggering the self-assembly of peptides in the lysosome, followed by a concise outlook of the future perspective about this emerging research direction.

Keywords:  Cancer therapy; Lysosome; Peptide; nanofibers; self-assembly

DOI:  https://doi.org/10.1002/cbic.202400232
bioRxiv. 2024 Apr 10. pii: 2024.04.10.588794. [Epub ahead of print]

Profiling microRNA expression during senescence and aging: mining for a diagnostic tool of senescent-cell burden.

Moritz Weigl, Teresa L Krammer, Marianne Pultar, Matthias Wieser, Selim Chaib, Masayoshi Suda, Andreas Diendorfer, Kseniya Khamina-Kotisch, Nino Giorgadze, Tamar Pirtskhalava, Kurt O Johnson, Christina L Inman, Ailing Xue, Ingo Lämmermann, Barbara Meixner, Lichao Wang, Ming Xu, Regina Grillari, Mikolaj Ogrodnik, Tamar Tchkonia, Matthias Hackl, James L Kirkland, Johannes Grillari.

In the last decade cellular senescence, a hallmark of aging, has come into focus for pharmacologically targeting aging processes. Senolytics are one of these interventive strategies that have advanced into clinical trials, creating an unmet need for minimally invasive biomarkers of senescent cell load to identify patients at need for senotherapy. We created a landscape of miRNA and mRNA expression in five human cell types induced to senescence in-vitro and provide proof-of-principle evidence that miRNA expression can track senescence burden dynamically in-vivo using transgenic p21 high senescent cell clearance in HFD fed mice. Finally, we profiled miRNA expression in seven different tissues, total plasma, and plasma derived EVs of young and 25 months old mice. In a systematic analysis, we identified 22 candidate senomiRs with potential to serve as circulating biomarkers of senescence not only in rodents, but also in upcoming human clinical senolytic trials.

DOI: https://doi.org/10.1101/2024.04.10.588794
Nature. 2024 Apr 24.

Whole-cortex in situ sequencing reveals input-dependent area identity.

Xiaoyin Chen, Stephan Fischer, Mara C P Rue, Aixin Zhang, Didhiti Mukherjee, Patrick O Kanold, Jesse Gillis, Anthony M Zador.

The cerebral cortex is composed of neuronal types with diverse gene expression that are organized into specialized cortical areas. These areas, each with characteristic cytoarchitecture1,2, connectivity3,4 and neuronal activity5,6, are wired into modular networks3,4,7. However, it remains unclear whether these spatial organizations are reflected in neuronal transcriptomic signatures and how such signatures are established in development. Here we used BARseq, a high-throughput in situ sequencing technique, to interrogate the expression of 104 cell-type marker genes in 10.3 million cells, including 4,194,658 cortical neurons over nine mouse forebrain hemispheres, at cellular resolution. De novo clustering of gene expression in single neurons revealed transcriptomic types consistent with previous single-cell RNA sequencing studies8,9. The composition of transcriptomic types is highly predictive of cortical area identity. Moreover, areas with similar compositions of transcriptomic types, which we defined as cortical modules, overlap with areas that are highly connected, suggesting that the same modular organization is reflected in both transcriptomic signatures and connectivity. To explore how the transcriptomic profiles of cortical neurons depend on development, we assessed cell-type distributions after neonatal binocular enucleation. Notably, binocular enucleation caused the shifting of the cell-type compositional profiles of visual areas towards neighbouring cortical areas within the same module, suggesting that peripheral inputs sharpen the distinct transcriptomic identities of areas within cortical modules. Enabled by the high throughput, low cost and reproducibility of BARseq, our study provides a proof of principle for the use of large-scale in situ sequencing to both reveal brain-wide molecular architecture and understand its development.

DOI: https://doi.org/10.1038/s41586-024-07221-6
Cell. 2024 Apr 25. pii: S0092-8674(24)00358-1. [Epub ahead of print]187(9): 2143-2157.e15

Functional sensory circuits built from neurons of two species.

Benjamin T Throesch, Muhammad Khadeesh Bin Imtiaz, Rodrigo Muñoz-Castañeda, Masahiro Sakurai, Andrea L Hartzell, Kiely N James, Alberto R Rodriguez, Greg Martin, Giordano Lippi, Sergey Kupriyanov, Zhuhao Wu, Pavel Osten, Juan Carlos Izpisua Belmonte, Jun Wu, Kristin K Baldwin.

  A central question for regenerative neuroscience is whether synthetic neural circuits, such as those built from two species, can function in an intact brain. Here, we apply blastocyst complementation to selectively build and test interspecies neural circuits. Despite approximately 10-20 million years of evolution, and prominent species differences in brain size, rat pluripotent stem cells injected into mouse blastocysts develop and persist throughout the mouse brain. Unexpectedly, the mouse niche reprograms the birth dates of rat neurons in the cortex and hippocampus, supporting rat-mouse synaptic activity. When mouse olfactory neurons are genetically silenced or killed, rat neurons restore information flow to odor processing circuits. Moreover, they rescue the primal behavior of food seeking, although less well than mouse neurons. By revealing that a mouse can sense the world using neurons from another species, we establish neural blastocyst complementation as a powerful tool to identify conserved mechanisms of brain development, plasticity, and repair.

Keywords:  blastocyst complementation; brain evolution; brain regeneration; development; disease models; interspecies chimeras; neural circuits; neurons; olfaction; pluripotent stem cells

DOI:  https://doi.org/10.1016/j.cell.2024.03.042
Elife. 2024 Apr 22. pii: RP92243. [Epub ahead of print]12

Membrane-bound O-acyltransferase 7 (MBOAT7) shapes lysosomal lipid homeostasis and function to control alcohol-associated liver injury.

Venkateshwari Varadharajan, Iyappan Ramachandiran, William J Massey, Raghav Jain, Rakhee Banerjee, Anthony J Horak, Megan R McMullen, Emily Huang, Annette Bellar, Shuhui W Lorkowski, Kailash Gulshan, Robert N Helsley, Isabella James, Vai Pathak, Jaividhya Dasarathy, Nicole Welch, Srinivasan Dasarathy, David Streem, Ofer Reizes, Daniela S Allende, Jonathan D Smith, Judith Simcox, Laura E Nagy, J Mark Brown.

  Recent genome-wide association studies (GWAS) have identified a link between single-nucleotide polymorphisms (SNPs) near the MBOAT7 gene and advanced liver diseases. Specifically, the common MBOAT7 variant (rs641738) associated with reduced MBOAT7 expression is implicated in non-alcoholic fatty liver disease (NAFLD), alcohol-associated liver disease (ALD), and liver fibrosis. However, the precise mechanism underlying MBOAT7-driven liver disease progression remains elusive. Previously, we identified MBOAT7-driven acylation of lysophosphatidylinositol lipids as key mechanism suppressing the progression of NAFLD (Gwag et al., 2019). Here, we show that MBOAT7 loss of function promotes ALD via reorganization of lysosomal lipid homeostasis. Circulating levels of MBOAT7 metabolic products are significantly reduced in heavy drinkers compared to healthy controls. Hepatocyte- (Mboat7-HSKO), but not myeloid-specific (Mboat7-MSKO), deletion of Mboat7 exacerbates ethanol-induced liver injury. Lipidomic profiling reveals a reorganization of the hepatic lipidome in Mboat7-HSKO mice, characterized by increased endosomal/lysosomal lipids. Ethanol-exposed Mboat7-HSKO mice exhibit dysregulated autophagic flux and lysosomal biogenesis, associated with impaired transcription factor EB-mediated lysosomal biogenesis and autophagosome accumulation. This study provides mechanistic insights into how MBOAT7 influences ALD progression through dysregulation of lysosomal biogenesis and autophagic flux, highlighting hepatocyte-specific MBOAT7 loss as a key driver of ethanol-induced liver injury.

Keywords:  MBOAT7; alcohol-associated liver disease; autophagy; medicine; mouse

DOI:  https://doi.org/10.7554/eLife.92243
Biochim Biophys Acta Gen Subj. 2024 Apr 19. pii: S0304-4165(24)00062-X. [Epub ahead of print] 130619

Detection and quantification of Na,K-ATPase dimers in the plasma membrane of living cells by FRET-FCS.

Linnea Nordahl, Evgeny E Akkuratov, Johannes Heimgärtner, Katja Schach, Birthe Meineke, Simon Elsässer, Stefan Wennmalm, Hjalmar Brismar.

  The sodium potassium pump, Na,K-ATPase (NKA), is an integral plasma membrane protein, expressed in all eukaryotic cells. It is responsible for maintaining the transmembrane Na+ gradient and is the major determinant of the membrane potential. Self-interaction and oligomerization of NKA in cell membranes has been proposed and discussed but is still an open question. Here, we have used a combination of FRET and Fluorescence Correlation Spectroscopy, FRET-FCS, to analyze NKA in the plasma membrane of living cells. Click chemistry was used to conjugate the fluorescent labels Alexa 488 and Alexa 647 to non-canonical amino acids introduced in the NKA α1 and β1 subunits. We demonstrate that FRET-FCS can detect an order of magnitude lower concentration of green-red labeled protein pairs in a single-labeled red and green background than what is possible with cross-correlation (FCCS). We show that a significant fraction of NKA is expressed as a dimer in the plasma membrane. We also introduce a method to estimate not only the number of single and double labeled NKA, but the number of unlabeled, endogenous NKA and estimate the density of endogenous NKA at the plasma membrane to 1400 ± 800 enzymes/μm2.

Keywords:  FRET-FCS; NaK-ATPase; Non-canonical amino acids

DOI:  https://doi.org/10.1016/j.bbagen.2024.130619
Npj Imaging. 2023 ;1(1): 3

Fast histological assessment of adipose tissue inflammation by label-free mid-infrared optoacoustic microscopy.

Vito Ko, Marie C Goess, Lukas Scheel-Platz, Tao Yuan, Andriy Chmyrov, Dominik Jüstel, Jürgen Ruland, Vasilis Ntziachristos, Selina J Keppler, Miguel A Pleitez.

  Conventional histology, as well as immunohistochemistry or immunofluorescence, enables the study of morphological and phenotypical changes during tissue inflammation with single-cell accuracy. However, although highly specific, such techniques require multiple time-consuming steps to apply exogenous labels, which might result in morphological deviations from native tissue structures. Unlike these techniques, mid-infrared (mid-IR) microspectroscopy is a label-free optical imaging method that retrieves endogenous biomolecular contrast without altering the native composition of the samples. Nevertheless, due to the strong optical absorption of water in biological tissues, conventional mid-IR microspectroscopy has been limited to dried thin (5-10 µm) tissue preparations and, thus, it also requires time-consuming steps-comparable to conventional imaging techniques. Here, as a step towards label-free analytical histology of unprocessed tissues, we applied mid-IR optoacoustic microscopy (MiROM) to retrieve intrinsic molecular contrast by vibrational excitation and, simultaneously, to overcome water-tissue opacity of conventional mid-IR imaging in thick (mm range) tissues. In this proof-of-concept study, we demonstrated application of MiROM for the fast, label-free, non-destructive assessment of the hallmarks of inflammation in excised white adipose tissue; i.e., formation of crown-like structures and changes in adipocyte morphology.

Keywords:  Analytical chemistry; Applied optics; Biochemistry; Biomedical engineering; Biotechnology; Chemistry; Engineering; Imaging and sensing; Immunology; Microscopy; Optical spectroscopy; Optical techniques; Optics and photonics

DOI:  https://doi.org/10.1038/s44303-023-00003-1
J Cachexia Sarcopenia Muscle. 2024 Apr 21.

Metabolomics-driven discovery of therapeutic targets for cancer cachexia.

Pengfei Cui, Xiaoyi Li, Caihua Huang, Donghai Lin.

  Cancer cachexia (CC) is a devastating metabolic syndrome characterized by skeletal muscle wasting and body weight loss, posing a significant burden on the health and survival of cancer patients. Despite ongoing efforts, effective treatments for CC are still lacking. Metabolomics, an advanced omics technique, offers a comprehensive analysis of small-molecule metabolites involved in cellular metabolism. In CC research, metabolomics has emerged as a valuable tool for identifying diagnostic biomarkers, unravelling molecular mechanisms and discovering potential therapeutic targets. A comprehensive search strategy was implemented to retrieve relevant articles from primary databases, including Web of Science, Google Scholar, Scopus and PubMed, for CC and metabolomics. Recent advancements in metabolomics have deepened our understanding of CC by uncovering key metabolic signatures and elucidating underlying mechanisms. By targeting crucial metabolic pathways including glucose metabolism, amino acid metabolism, fatty acid metabolism, bile acid metabolism, ketone body metabolism, steroid metabolism and mitochondrial energy metabolism, it becomes possible to restore metabolic balance and alleviate CC symptoms. This review provides a comprehensive summary of metabolomics studies in CC, focusing on the discovery of potential therapeutic targets and the evaluation of modulating specific metabolic pathways for CC treatment. By harnessing the insights derived from metabolomics, novel interventions for CC can be developed, leading to improved patient outcomes and enhanced quality of life.

Keywords:  Cancer cachexia; Metabolic pathway; Metabolomics; Therapeutic target

DOI:  https://doi.org/10.1002/jcsm.13465
EMBO J. 2024 Apr 25.

Presenting metabolomics analyses: what is in a number?

Johannes Meiser, Christian Frezza.

DOI: https://doi.org/10.1038/s44318-024-00098-1
Cell. 2024 Apr 16. pii: S0092-8674(24)00347-7. [Epub ahead of print]

Synthetic protein circuits for programmable control of mammalian cell death.

Shiyu Xia, Andrew C Lu, Victoria Tobin, Kaiwen Luo, Lukas Moeller, D Judy Shon, Rongrong Du, James M Linton, Margaret Sui, Felix Horns, Michael B Elowitz.

  Natural cell death pathways such as apoptosis and pyroptosis play dual roles: they eliminate harmful cells and modulate the immune system by dampening or stimulating inflammation. Synthetic protein circuits capable of triggering specific death programs in target cells could similarly remove harmful cells while appropriately modulating immune responses. However, cells actively influence their death modes in response to natural signals, making it challenging to control death modes. Here, we introduce naturally inspired "synpoptosis" circuits that proteolytically regulate engineered executioner proteins and mammalian cell death. These circuits direct cell death modes, respond to combinations of protease inputs, and selectively eliminate target cells. Furthermore, synpoptosis circuits can be transmitted intercellularly, offering a foundation for engineering synthetic killer cells that induce desired death programs in target cells without self-destruction. Together, these results lay the groundwork for programmable control of mammalian cell death.

Keywords:  apoptosis; cell death; protein circuit; pyroptosis; synpoptosis; synthetic biology; synthetic circuit

DOI:  https://doi.org/10.1016/j.cell.2024.03.031
EMBO Rep. 2024 Apr 23.

Detecting material state changes in the nucleolus by label-free digital holographic microscopy.

Christiane Zorbas, Aynur Soenmez, Jean Léger, Christophe De Vleeschouwer, Denis Lj Lafontaine.

  Ribosome biogenesis is initiated in the nucleolus, a multiphase biomolecular condensate formed by liquid-liquid phase separation. The nucleolus is a powerful disease biomarker and stress biosensor whose morphology reflects function. Here we have used digital holographic microscopy (DHM), a label-free quantitative phase contrast microscopy technique, to detect nucleoli in adherent and suspension human cells. We trained convolutional neural networks to detect and quantify nucleoli automatically on DHM images. Holograms containing cell optical thickness information allowed us to define a novel index which we used to distinguish nucleoli whose material state had been modulated optogenetically by blue-light-induced protein aggregation. Nucleoli whose function had been impacted by drug treatment or depletion of ribosomal proteins could also be distinguished. We explored the potential of the technology to detect other natural and pathological condensates, such as those formed upon overexpression of a mutant form of huntingtin, ataxin-3, or TDP-43, and also other cell assemblies (lipid droplets). We conclude that DHM is a powerful tool for quantitatively characterizing nucleoli and other cell assemblies, including their material state, without any staining.

Keywords:  Biomolecular Condensate; Digital Holographic Microscopy; Lipid Droplet; Liquid-Liquid Phase Separation (LLPS); Nucleolus

DOI:  https://doi.org/10.1038/s44319-024-00134-5
Proc Natl Acad Sci U S A. 2024 Apr 30. 121(18): e2313107121

Maximum entropy determination of mammalian proteome dynamics.

Alexander J Dear, Gonzalo A Garcia, Georg Meisl, Galen A Collins, Tuomas P J Knowles, Alfred L Goldberg.

  Full understanding of proteostasis and energy utilization in cells will require knowledge of the fraction of cell proteins being degraded with different half-lives and their rates of synthesis. We therefore developed a method to determine such information that combines mathematical analysis of protein degradation kinetics obtained in pulse-chase experiments with Bayesian data fitting using the maximum entropy principle. This approach will enable rapid analyses of whole-cell protein dynamics in different cell types, physiological states, and neurodegenerative disease. Using it, we obtained surprising insights about protein stabilities in cultured cells normally and upon activation of proteolysis by mTOR inhibition and increasing cAMP or cGMP. It revealed that >90% of protein content in dividing mammalian cell lines is long-lived, with half-lives of 24 to 200 h, and therefore comprises much of the proteins in daughter cells. The well-studied short-lived proteins (half-lives < 10 h) together comprise <2% of cell protein mass, but surprisingly account for 10 to 20% of measurable newly synthesized protein mass. Evolution thus appears to have minimized intracellular proteolysis except to rapidly eliminate misfolded and regulatory proteins.

Keywords:  maximum entropy; protein degradation; protein half-lives; proteome; proteostasis

DOI:  https://doi.org/10.1073/pnas.2313107121
bioRxiv. 2024 Apr 08. pii: 2024.04.04.588107. [Epub ahead of print]

STING promotes homeostatic maintenance of tissues and confers longevity with aging.

Jacob W Hopkins, Katherine B Sulka, Machlan Sawden, Kimberly A Carroll, Ronald D Brown, Stephen C Bunnell, Alexander Poltorak, Albert Tai, Eric R Reed, Shruti Sharma.

Local immune processes within aging tissues are a significant driver of aging associated dysfunction, but tissue-autonomous pathways and cell types that modulate these responses remain poorly characterized. The cytosolic DNA sensing pathway, acting through cyclic GMP-AMP synthase (cGAS) and Stimulator of Interferon Genes (STING), is broadly expressed in tissues, and is poised to regulate local type I interferon (IFN-I)-dependent and independent inflammatory processes within tissues. Recent studies suggest that the cGAS/STING pathway may drive pathology in various in vitro and in vivo models of accelerated aging. To date, however, the role of the cGAS/STING pathway in physiological aging processes, in the absence of genetic drivers, has remained unexplored. This remains a relevant gap, as STING is ubiquitously expressed, implicated in multitudinous disorders, and loss of function polymorphisms of STING are highly prevalent in the human population (>50%). Here we reveal that, during physiological aging, STING-deficiency leads to a significant shortening of murine lifespan, increased pro-inflammatory serum cytokines and tissue infiltrates, as well as salient changes in histological composition and organization. We note that aging hearts, livers, and kidneys express distinct subsets of inflammatory, interferon-stimulated gene (ISG), and senescence genes, collectively comprising an immune fingerprint for each tissue. These distinctive patterns are largely imprinted by tissue-specific stromal and myeloid cells. Using cellular interaction network analyses, immunofluorescence, and histopathology data, we show that these immune fingerprints shape the tissue architecture and the landscape of cell-cell interactions in aging tissues. These age-associated immune fingerprints are grossly dysregulated with STING-deficiency, with key genes that define aging STING- sufficient tissues greatly diminished in the absence of STING. Changes in immune signatures are concomitant with a restructuring of the stromal and myeloid fractions, whereby cell:cell interactions are grossly altered and resulting in disorganization of tissue architecture in STING-deficient organs. This altered homeostasis in aging STING-deficient tissues is associated with a cross-tissue loss of homeostatic tissue-resident macrophage (TRM) populations in these tissues. Ex vivo analyses reveal that basal STING- signaling limits the susceptibility of TRMs to death-inducing stimuli and determines their in situ localization in tissue niches, thereby promoting tissue homeostasis. Collectively, these data upend the paradigm that cGAS/STING signaling is primarily pathological in aging and instead indicate that basal STING signaling sustains tissue function and supports organismal longevity. Critically, our study urges caution in the indiscriminate targeting of these pathways, which may result in unpredictable and pathological consequences for health during aging.HIGHLIGHTS: Aging tissues are associated with tissue-autonomous immune fingerprints, primarily driven by interactions of tissue stromal and myeloid populations. STING shapes these immune fingerprints of aging tissues in unexpected ways.Loss of STING alters the location, numbers, and viability of tissue resident macrophages.STING signaling is critical for longer lifespans and maintenance of tissue architecture.

DOI: https://doi.org/10.1101/2024.04.04.588107
Metabolites. 2024 Mar 25. pii: 184. [Epub ahead of print]14(4):

Selected Ion Monitoring for Orbitrap-Based Metabolomics.

Wenyun Lu, Matthew J McBride, Won Dong Lee, Xi Xing, Xincheng Xu, Xi Li, Anna M Oschmann, Yihui Shen, Caroline Bartman, Joshua D Rabinowitz.

  Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage.

Keywords:  SIM; fluxomics; full scan; isotope labeling; isotope tracing; metabolomics; orbitrap; relative standard deviation; selected ion monitoring; signal-to-noise ratio

DOI:  https://doi.org/10.3390/metabo14040184
Front Cell Dev Biol. 2024 ;12 1259953

Cancer spreading patterns based on epithelial-mesenchymal plasticity.

Rui Wang, Zhaopeng Yan.

  Introduction: Metastasis is a major cause of cancer-related deaths, underscoring the necessity to discern the rules and patterns of cancer cell spreading. Epithelial-mesenchymal plasticity contributes to cancer aggressiveness and metastasis. Despite establishing key determinants of cancer aggressiveness and metastatic ability, a comprehensive understanding of the underlying mechanism is unknown. We aimed to propose a classification system for cancer cells based on epithelial-mesenchymal plasticity, focusing on hysteresis of the epithelial-mesenchymal transition and the hybrid epithelial/mesenchymal phenotype. Methods: We extensively reviewed the concept of epithelial-mesenchymal plasticity, specifically considering the hysteresis of the epithelial-mesenchymal transition and the hybrid epithelial/mesenchymal phenotype. Results: In this review and hypothesis article, based on epithelial-mesenchymal plasticity, especially the hysteresis of epithelial-mesenchymal transition and the hybrid epithelial/mesenchymal phenotype, we proposed a classification of cancer cells, indicating that cancer cells with epithelial-mesenchymal plasticity potential could be classified into four types: irreversible hysteresis, weak hysteresis, strong hysteresis, and hybrid epithelial/mesenchymal phenotype. These four types of cancer cells had varied biology, spreading features, and prognoses. Discussion: Our results highlight that the proposed classification system offers insights into the diverse behaviors of cancer cells, providing implications for cancer aggressiveness and metastasis.

Keywords:  epithelial-mesenchymal transition; hybrid epithelial/mesenchymal phenotype; hysteresis; mesenchymal-epithelial plasticity; metastasis

DOI:  https://doi.org/10.3389/fcell.2024.1259953
Cell. 2024 Apr 25. pii: S0092-8674(24)00319-2. [Epub ahead of print]187(9): 2124-2126

A glycolytic metabolite that drives BRCA2 haploinsufficiency.

Peng Jiang.

Many types of tumor cells alter metabolic pathways to meet their energy and biosynthetic demands for proliferation or stress adaptation. In this issue of Cell, Kong et al. find that the glycolytic metabolite methylglyoxal causes cancer-associated mutant single-base substitution features by inducing BRCA2 proteolysis, leading to functional haploinsufficiency of BRCA2.

DOI: https://doi.org/10.1016/j.cell.2024.03.028
bioRxiv. 2024 Apr 20. pii: 2024.04.17.589880. [Epub ahead of print]

Circulating tumor cells shed large extracellular vesicles in capillary-sized bifurcations.

Angelos Vrynas, Sara Arfan, Karishma Satia, Salime Bazban-Shotorbani, Mymuna Ashna, Aoyu Zhang, Diana Visan, Aisher Chen, Mathew Carter, Fiona Blackhall, Kathryn L Simpson, Caroline Dive, Paul Huang, Sam H Au.

Circulating tumor cells (CTCs) and their clusters are the drivers of metastasis, but their interactions with capillary beds are poorly understood. Using microfluidic models mimicking human capillary bifurcations, we observed cell size- and bifurcation-dependent shedding of nuclei-free fragments by patient CTCs, CTC-derived explant cells and numerous cancer cell lines. Shedding reduced cell sizes up to 61%, facilitating their transit through bifurcations. We demonstrated that shed fragments were a novel class of large extracellular vesicles (LEVs), whose proteome was associated with immune-related and signaling pathways. LEVs were internalized by endothelial and immune cells, disrupted endothelial barrier integrity and polarized monocytes into M2 tumor-promoting macrophages. Cumulatively, these findings suggest that CTCs shed LEVs in capillary beds that drive key processes involved in the formation of pre-metastatic niches.

DOI: https://doi.org/10.1101/2024.04.17.589880
BMC Bioinformatics. 2024 Apr 24. 25(1): 162

OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies.

Terrence R Ernst, John D Blischak, Paul Nordlund, Joe Dalen, Justin Moore, Akshay Bhamidipati, Pankaj Dwivedi, Joe LoGrasso, Marco Rocha Curado, Brett Warren Engelmann.

  BACKGROUND: The results of high-throughput biology ('omic') experiments provide insight into biological mechanisms but can be challenging to explore, archive and share. The scale of these challenges continues to grow as omic research volume expands and multiple analytical technologies, bioinformatic pipelines, and visualization preferences have emerged. Multiple software applications exist that support omic study exploration and/or archival. However, an opportunity remains for open-source software that can archive and present the results of omic analyses with broad accommodation of study-specific analytical approaches and visualizations with useful exploration features.RESULTS: We present OmicNavigator, an R package for the archival, visualization and interactive exploration of omic studies. OmicNavigator enables bioinformaticians to create web applications that interactively display their custom visualizations and analysis results linked with app-derived analytical tools, graphics, and tables. Studies created with OmicNavigator can be viewed within an interactive R session or hosted on a server for shared access.
CONCLUSIONS: OmicNavigator can be found at https://github.com/abbvie-external/OmicNavigator.

Keywords:  Bioinformatics; Genomics; Metabolomics; Multi-omics; Omics; Open-source; Proteomics; R; Transcriptomics; Visualization

DOI:  https://doi.org/10.1186/s12859-024-05743-4
Cell. 2024 Apr 25. pii: S0092-8674(24)00356-8. [Epub ahead of print]187(9): 2126-2128

Mapping the pancancer metastasis tumor microbiome.

Chi Chun Wong, Jun Yu.

The landscape of the intratumoral microbiome in tumor metastases is largely unchartered. In this issue of Cell, Voest et al. profiled the tumor metastasis-associated microbiome in a pancancer cohort of 4,160 biopsies from 26 cancer types. This dataset offers a useful resource for understanding the role of the microbiome in metastatic cancers.

DOI: https://doi.org/10.1016/j.cell.2024.03.040