bims-cagime 2023-12-17 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2023–12–17
37 papers selected by
Kıvanç Görgülü, Technical University of Munich

The formation of ubiquitin rich condensates triggers recruitment of the ATG9A lipid transfer complex to initiate basal autophagy.
Phenotypic profiling of solute carriers characterizes serine transport in cancer.
CT Attenuation of Hepatic Pancreatic Cancer Metastases Correlates with Prognostically Detrimental Metastatic Necrosis.
Spartin-mediated lipid transfer facilitates lipid droplet turnover.
Sequestration of translation initiation factors in p62 condensates.
YAP localization mediates mechanical adaptation of human cancer cells during extravasation in vivo.
Repurposing phenothiazines for cancer therapy: compromising membrane integrity in cancer cells.
Obesity worsens mitochondrial quality control and does not protect against skeletal muscle wasting in murine cancer cachexia.
Supraphysiological glutamine as a means of depleting intracellular amino acids to enhance pancreatic cancer chemosensitivity.
Targeting cancer cell dormancy.
A fluorogenic complementation tool kit for interrogating lipid droplet-organelle interaction.
The interplay of the circadian clock and metabolic tumorigenesis.
Cells use multiple mechanisms for cell-cycle arrest upon withdrawal of individual amino acids.
It's all about the base: stromal cells are central orchestrators of metastasis.
Epinephrine inhibits PI3Kα via the Hippo kinases.
Charting the transcriptomic landscape of primary and metastatic cancers in relation to their origin and target normal tissues.
Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase.
Nanoscale structural response of biomimetic cell membranes to controlled dehydration.
Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology.
Heparanase contributes to pancreatic carcinoma progression through insulin-dependent glucose uptake.
T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.
An oncogenic phenoscape of colonic stem cell polarization.
Exploring the role of hyperinsulinemia in obesity-associated tumor development.
Research progress in the establishment of pancreatic cancer models and preclinical applications.
Inhibition of the membrane repair protein annexin-A2 prevents tumor invasion and metastasis.
The mitochondrial ATP synthase is a negative regulator of the mitochondrial permeability transition pore.
Cancer Cachexia: New Insights and Future Directions.
CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity.
Plasma membrane nanodeformations promote actin polymerization through CIP4/CDC42 recruitment and regulate type II IFN signaling.
Quantitative Analysis of Autophagy in Single Cells: Differential Response to Amino Acid and Glucose Starvation.
Label-free spatially maintained measurements of metabolic phenotypes in cells.
B3GALT6 promotes dormant breast cancer cell survival and recurrence by enabling heparan sulfate-mediated FGF signaling.
How chemokines organize the tumour microenvironment.
Mitochondrial temperature homeostasis resists external metabolic stresses.
Single-cell force spectroscopy of fluid flow-tuned cell adhesion for dissecting hemodynamics in tumor metastasis.
Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines.
Combined utility of Ki-67 index and tumor grade to stratify patients with pancreatic ductal adenocarcinoma who underwent upfront surgery.

bioRxiv. 2023 Nov 29. pii: 2023.11.28.569058. [Epub ahead of print]

The formation of ubiquitin rich condensates triggers recruitment of the ATG9A lipid transfer complex to initiate basal autophagy.

D G Broadbent, C M McEwan, T M Tsang, D M Poole, B C Naylor, J C Price, J C Schmidt, J L Andersen.

Autophagy is an essential cellular recycling process that maintains protein and organelle homeostasis. ATG9A vesicle recruitment is a critical early step in autophagy to initiate autophagosome biogenesis. The mechanisms of ATG9A vesicle recruitment are best understood in the context of starvation-induced non-selective autophagy, whereas less is known about the signals driving ATG9A vesicle recruitment to autophagy initiation sites in the absence of nutrient stress. Here we demonstrate that loss of ATG9A or the lipid transfer protein ATG2 leads to the accumulation of phosphorylated p62 aggregates in the context of basal autophagy. Furthermore, we show that p62 degradation requires the lipid scramblase activity of ATG9A. Lastly, we present evidence that poly-ubiquitin is an essential signal that recruits ATG9A and mediates autophagy foci assembly in nutrient replete cells. Together, our data support a ubiquitin-driven model of ATG9A recruitment and autophagosome formation during basal autophagy.

DOI: https://doi.org/10.1101/2023.11.28.569058
Nat Metab. 2023 Dec 08.

Phenotypic profiling of solute carriers characterizes serine transport in cancer.

Vasileios Papalazarou, Alice C Newman, Alejandro Huerta-Uribe, Nathalie M Legrave, Mattia Falcone, Tong Zhang, Lynn McGarry, Dimitris Athineos, Emma Shanks, Karen Blyth, Karen H Vousden, Oliver D K Maddocks.

Serine is a vital amino acid in tumorigenesis. While cells can perform de novo serine synthesis, most transformed cells rely on serine uptake to meet their increased biosynthetic requirements. Solute carriers (SLCs), a family of transmembrane nutrient transport proteins, are the gatekeepers of amino acid acquisition and exchange in mammalian cells and are emerging as anticancer therapeutic targets; however, the SLCs that mediate serine transport in cancer cells remain unknown. Here we perform an arrayed RNAi screen of SLC-encoding genes while monitoring amino acid consumption and cell proliferation in colorectal cancer cells using metabolomics and high-throughput imaging. We identify SLC6A14 and SLC25A15 as major cytoplasmic and mitochondrial serine transporters, respectively. We also observe that SLC12A4 facilitates serine uptake. Dual targeting of SLC6A14 and either SLC25A15 or SLC12A4 diminishes serine uptake and growth of colorectal cancer cells in vitro and in vivo, particularly in cells with compromised de novo serine biosynthesis. Our results provide insight into the mechanisms that contribute to serine uptake and intracellular handling.

DOI: https://doi.org/10.1038/s42255-023-00936-2
J Clin Med. 2023 Nov 26. pii: 7319. [Epub ahead of print]12(23):

CT Attenuation of Hepatic Pancreatic Cancer Metastases Correlates with Prognostically Detrimental Metastatic Necrosis.

Stefan Reischl, Sebastian Ziegelmayer, Markus Graf, Joshua Gawlitza, Andreas Philipp Sauter, Manuel Steinhardt, Marie-Christin Weber, Philipp-Alexander Neumann, Marcus Richard Makowski, Fabian Karl Lohöfer, Carolin Mogler, Rickmer Früdd Braren.

  Percutaneous CT-guided biopsy is a frequently performed procedure for the confirmation and molecular workup of hepatic metastases of pancreatic ductal adenocarcinoma (PDAC). Tumor necrosis of primary PDAC has shown a negative prognostic impact in recent studies. This study aims to examine predictability in CT scans and the prognostic impact of necrosis in hepatic metastases of PDAC. In this tertiary-center retrospective cohort study, we included 36 patients with hepatic metastases of PDAC who underwent CT-guided hepatic biopsies. Normalized attenuation of the biopsied metastasis was determined in venous phase contrast-enhanced planning scans obtained prior to biopsy by automatic, threshold-based 3D segmentation and manual, blinded 2D segmentation. A board-certified pathologist specialized in hepatic pathology histologically quantified the tumor necrosis and cellularity of the biopsy cylinders. We found a significant inverse-linear correlation between normalized attenuation and the fraction of necrosis (Pearson's r = 0.51, p < 0.001 for automatic 3D segmentation or Pearson's r = 0.52, p < 0.001 for manual 2D segmentation), whereas no correlation was found with tumor cellularity. Additionally, we discovered that patients with a fraction of necrosis ≥ 20% in metastases had a significantly shorter overall survival (p < 0.035). In summary, tumor necrosis of PDAC metastases can be estimated from contrast-enhanced CT scans, which could help to improve biopsy sample pattern planning. In addition, liver metastatic necrosis may serve as a prognostic biomarker in PDAC.

Keywords:  biopsy; computed tomography; imaging; intervention; necrosis; pancreatic cancer

DOI:  https://doi.org/10.3390/jcm12237319
bioRxiv. 2023 Nov 29. pii: 2023.11.29.569220. [Epub ahead of print]

Spartin-mediated lipid transfer facilitates lipid droplet turnover.

Neng Wan, Zhouping Hong, Matthew A H Parson, Justin Korfhage, John E Burke, Thomas J Melia, Karin M Reinisch.

Lipid droplets (LDs) are organelles critical for energy storage and membrane lipid homeostasis, whose number and size are carefully regulated in response to cellular conditions. The molecular mechanisms underlying lipid droplet biogenesis and degradation, however, are not well understood. The Troyer syndrome protein spartin (SPG20) supports LD delivery to autophagosomes for turnover via lipophagy. Here, we characterize spartin as a lipid transfer protein whose transfer ability is required for LD degradation. Spartin co-purifies with phospholipids and neutral lipids from cells and transfers phospholipids in vitro via its senescence domain. A senescence domain truncation that impairs lipid transfer in vitro also impairs LD turnover in cells while not affecting spartin association with either LDs or autophagosomes, supporting that spartin's lipid transfer ability is physiologically relevant. Our data indicate a role for spartin-mediated lipid transfer in LD turnover.
Significance: The Troyer syndrome protein spartin was proposed to function as a lipophagy receptor that delivers lipid droplets, organelles key for energy storage and membrane lipid homeostasis, to autophagosomes for degradation. We identify an additional function for spartin as a lipid transfer protein and show its transfer ability is required for lipid droplet degradation, including by lipophagy. Our data support that protein-mediated lipid transfer plays a role in lipid droplet turnover. Moreover, in spartin's senescence domain we have discovered a new lipid transport module that likely also features in still undiscovered aspects of lipid droplet biology and membrane homeostasis.

DOI: https://doi.org/10.1101/2023.11.29.569220
Cell Rep. 2023 Dec 12. pii: S2211-1247(23)01595-4. [Epub ahead of print]42(12): 113583

Sequestration of translation initiation factors in p62 condensates.

Alberto Danieli, Georg Vucak, Manuela Baccarini, Sascha Martens.

  Selective autophagy mediates the removal of harmful material from the cytoplasm. This cargo material is selected by cargo receptors, which orchestrate its sequestration within double-membrane autophagosomes and subsequent lysosomal degradation. The cargo receptor p62/SQSTM1 is present in cytoplasmic condensates, and a fraction of them are constantly delivered into lysosomes. However, the molecular composition of the p62 condensates is incompletely understood. To obtain insights into their composition, we develop a method to isolate these condensates and find that p62 condensates are enriched in components of the translation machinery. Furthermore, p62 interacts with translation initiation factors, and eukaryotic initiation factor 2α (eIF2α) and eIF4E are degraded by autophagy in a p62-dependent manner. Thus, p62-mediated autophagy may in part be linked to down-regulation of translation initiation. The p62 condensate isolation protocol developed here may facilitate the study of their contribution to cellular quality control and their roles in health and disease.

Keywords:  CP: Cell biology; CP: Molecular biology; SQSTM1; autophagy; cargo receptor; translation

DOI:  https://doi.org/10.1016/j.celrep.2023.113583
bioRxiv. 2023 Nov 16. pii: 2023.11.14.567015. [Epub ahead of print]

YAP localization mediates mechanical adaptation of human cancer cells during extravasation in vivo.

Woong Young So, Claudia S Wong, Udochi F Azubuike, Colin D Paul, Paniz Rezvan Sangsari, Patricia B Gordon, Hyeyeon Gong, Tapan K Maity, Perry Lim, Zhilin Yang, Christian A Haryanto, Eric Batchelor, Lisa M Jenkins, Nicole Y Morgan, Kandice Tanner.

Biophysical profiling of primary tumors has revealed that individual tumor cells fall along a highly heterogeneous continuum of mechanical phenotypes. One idea is that a subset of tumor cells is "softer" to facilitate detachment and escape from the primary site, a step required to initiate metastasis. However, it has also been postulated that cells must be able to deform and generate sufficient force to exit into distant sites. Here, we aimed to dissect the mechanical changes that occur during extravasation and organ colonization. Using multiplexed methods of intravital microscopy and optical tweezer based active microrheology, we obtained longitudinal images and mechanical profiles of cells during organ colonization in vivo . We determined that cells were softer, more liquid like upon exit of the vasculature but stiffened and became more solid like once in the new organ microenvironment. We also determined that a YAP mediated mechanogenotype influenced the global dissemination in our in vivo and in vitro models and that reducing mechanical heterogeneity could reduce extravasation. Moreover, our high throughput analysis of mechanical phenotypes of patient samples revealed that this mechanics was in part regulated by the external hydrodynamic forces that the cancer cells experienced within capillary mimetics. Our findings indicate that disseminated cancer cells can keep mutating with a continuum landscape of mechano-phenotypes, governed by the YAP-mediated mechanosensing of hydrodynamic flow.

DOI: https://doi.org/10.1101/2023.11.14.567015
Front Oncol. 2023 ;13 1320621

Repurposing phenothiazines for cancer therapy: compromising membrane integrity in cancer cells.

Syrina Fred Mehrabi, Sabina Elmi, Jesper Nylandsted.

  The limitations of current cancer therapies, including the increasing prevalence of multidrug resistance, underscore the urgency for more effective treatments. One promising avenue lies in the repurposing of existing drugs. This review explores the impact of phenothiazines, primarily used as antipsychotic agents, on key mechanisms driving tumor growth and metastasis. The cationic and amphiphilic nature of phenothiazines allows interaction with the lipid bilayer of cellular membranes, resulting in alterations in lipid composition, modulation of calcium channels, fluidity, thinning, and integrity of the plasma membrane. This is especially significant in the setting of increased metabolic activity, a higher proliferative rate, and the invasiveness of cancer cells, which often rely on plasma membrane repair. Therefore, properties of phenothiazines such as compromising plasma membrane integrity and repair, disturbing calcium regulation, inducing cytosolic K-RAS accumulation, and sphingomyelin accumulation in the plasma membrane might counteract multidrug resistance by sensitizing cancer cells to membrane damage and chemotherapy. This review outlines a comprehensive overview of the mechanisms driving the anticancer activities of phenothiazines derivates such as trifluoperazine, prochlorperazine, chlorpromazine, promethazine, thioridazine, and fluphenazine. The repurposing potential of phenothiazines paves the way for novel approaches to improve future cancer treatment.

Keywords:  annexins; cancer treatment; membrane biophysical properties; membrane integrity; membrane repair; phenothiazines; plasma membrane; repurposing

DOI:  https://doi.org/10.3389/fonc.2023.1320621
J Cachexia Sarcopenia Muscle. 2023 Dec 07.

Obesity worsens mitochondrial quality control and does not protect against skeletal muscle wasting in murine cancer cachexia.

Thomas D Cardaci, Brandon N VanderVeen, Brooke M Bullard, Sierra J McDonald, Christian A Unger, Reilly T Enos, Daping Fan, Kandy T Velázquez, Norma Frizzell, Espen E Spangenburg, E Angela Murphy.

   BACKGROUND: More than 650 million people are obese (BMI > 30) worldwide, which increases their risk for several metabolic diseases and cancer. While cachexia and obesity are at opposite ends of the weight spectrum, leading many to suggest a protective effect of obesity against cachexia, mechanistic support for obesity's benefit is lacking. Given that obesity and cachexia are both accompanied by metabolic dysregulation, we sought to investigate the impact of obesity on skeletal muscle mass loss and mitochondrial dysfunction in murine cancer cachexia.
METHODS: Male C57BL/6 mice were given a purified high fat or standard diet for 16 weeks before being implanted with 106 Lewis lung carcinoma (LLC) cells. Mice were monitored for 25 days, and hindlimb muscles were collected for cachexia indices and mitochondrial assessment via western blotting, high-resolution respirometry and transmission electron microscopy (TEM).
RESULTS: Obese LLC mice experienced significant tumour-free body weight loss similar to lean (-12.8% vs. -11.8%, P = 0.0001) but had reduced survival (33.3% vs. 6.67%, χ2 = 10.04, P = 0.0182). Obese LLC mice had reduced muscle weights (-24%, P < 0.0354) and mCSA (-16%, P = 0.0004) with similar activation of muscle p65 (P = 0.0337), and p38 (P = 0.0008). ADP-dependent coupled respiration was reduced in both Obese and Obese LLC muscle (-30%, P = 0.0072) consistent with reductions in volitional cage activity (-39%, P < 0.0001) and grip strength (-41%, P < 0.0001). TEM revealed stepwise reductions in intermyofibrillar and subsarcolemmal mitochondrial size with Obese (IMF: -37%, P = 0.0009; SS: -21%, P = 0.0101) and LLC (IMF: -40%, P = 0.0019; SS: -27%, P = 0.0383) mice. Obese LLC mice had increased pAMPK (T172; P = 0.0103) and reduced FIS1 (P = 0.0029) and DRP1 (P < 0.0001) mitochondrial fission proteins, which were each unchanged in Lean LLC. Further, mitochondrial TEM analysis revealed that Obese LLC mice had an accumulation of damaged and dysfunctional mitochondria (IMF: 357%, P = 0.0395; SS: 138%, P = 0.0174) in concert with an accumulation of p62 (P = 0.0328) suggesting impaired autophagy and clearance of damaged mitochondria. Moreover, we observed increases in electron lucent vacuoles only in Obese LLC muscle (IMF: 421%, P = 0.0260; SS: 392%, P = 0.0192), further supporting an accumulation of damaged materials that cannot be properly cleared in the obese cachectic muscle.
CONCLUSIONS: Taken together, these results demonstrate that obesity is not protective against cachexia and suggest exacerbated impairments to mitochondrial function and quality control with a particular disruption in the removal of damaged mitochondria. Our findings highlight the need for consideration of the severity of obesity and pre-existing metabolic conditions when determining the impact of weight status on cancer-induced cachexia and functional mitochondrial deficits.

Keywords:  Autophagy; High fat diet; Lewis lung carcinoma; Mitochondrial dysfunction; Mitophagy; Muscle atrophy

DOI:  https://doi.org/10.1002/jcsm.13391
Res Sq. 2023 Nov 30. pii: rs.3.rs-3647514. [Epub ahead of print]

Supraphysiological glutamine as a means of depleting intracellular amino acids to enhance pancreatic cancer chemosensitivity.

Neil Bhowmick, Hayato Muranaka, Sandrine Billet, Carlos Cruz-Hernández, Johanna Ten Hoeve, Gabrielle Gonzales, Omer Elmadbouh, Le Zhang, Bethany Smith, Mourad Tighiouart, Sungyong You, Mouad Edderkaoui, Andrew Hendifar, Stephen Pandol, Jun Gong.

Limited efficacy of systemic therapy for pancreatic ductal adenocarcinoma (PDAC) patients contributes to high mortality. Cancer cells develop strategies to secure nutrients in nutrient-deprived conditions and chemotherapy treatment. Despite the dependency of PDAC on glutamine (Gln) for growth and survival, strategies designed to suppress Gln metabolism have limited effects. Here, we demonstrated that supraphysiological concentrations of glutamine (SPG) could produce paradoxical responses leading to tumor growth inhibition alone and in combination with chemotherapy. Integrated metabolic and transcriptomic analysis revealed that the growth inhibitory effect of SPG was the result of a decrease in intracellular amino acid and nucleotide pools. Mechanistically, disruption of the sodium gradient, plasma membrane depolarization, and competitive inhibition of amino acid transport mediated amino acid deprivation. Among standard chemotherapies given to PDAC patients, gemcitabine treatment resulted in a significant enrichment of amino acid and nucleoside pools, exposing a metabolic vulnerability to SPG-induced metabolic alterations. Further analysis highlighted a superior anticancer effect of D-glutamine, a non-metabolizable enantiomer of the L-glutamine, by suppressing both amino acid uptake and glutaminolysis, in gemcitabine-treated preclinical models with no apparent toxicity. Our study suggests supraphysiological glutamine could be a means of inhibiting amino acid uptake and nucleotide biosynthesis, potentiating gemcitabine sensitivity in PDAC.

DOI: https://doi.org/10.21203/rs.3.rs-3647514/v1
Nat Rev Cancer. 2023 Dec 07.

Targeting cancer cell dormancy.

Judith Agudo, Julio A Aguirre-Ghiso, Mickie Bhatia, Lewis A Chodosh, Ana Luísa Correia, Christoph A Klein.

DOI: https://doi.org/10.1038/s41568-023-00642-x
bioRxiv. 2023 Nov 29. pii: 2023.11.29.569289. [Epub ahead of print]

A fluorogenic complementation tool kit for interrogating lipid droplet-organelle interaction.

Xiao Li, Rico Gamuyao, Ming-Lun Wu, Woo Jung Cho, Nathan B Kurtz, Sharon V King, R A Petersen, Daniel R Stabley, Caleb Lindow, Leslie Climer, Abbas Shirinifard, Francesca Ferrara, Robert E Throm, Camenzind G Robinson, Alex Carisey, Alison G Tebo, Chi-Lun Chang.

Contact sites between lipid droplets and other organelles are essential for cellular lipid and energy homeostasis. Detection of these contact sites at nanometer scale over time in living cells is challenging. Here, we developed a tool kit for detecting contact sites based on F luorogen- A ctivated B imolecular complementation at CON tact sites, FABCON, using a reversible, low affinity split fluorescent protein, splitFAST. FABCON labels contact sites with minimal perturbation to organelle interaction. Via FABCON, we quantitatively demonstrated that endoplasmic reticulum (ER)- and mitochondria (mito)-lipid droplet contact sites are dynamic foci in distinct metabolic conditions, such as during lipid droplet biogenesis and consumption. An automated analysis pipeline further classified individual contact sites into distinct subgroups based on size, likely reflecting differential regulation and function. Moreover, FABCON is generalizable to visualize a repertoire of organelle contact sites including ER-mito. Altogether, FABCON reveals insights into the dynamic regulation of lipid droplet-organelle contact sites and generates new hypotheses for further mechanistical interrogation during metabolic switch.

DOI: https://doi.org/10.1101/2023.11.29.569289
Trends Cell Biol. 2023 Dec 06. pii: S0962-8924(23)00237-4. [Epub ahead of print]

The interplay of the circadian clock and metabolic tumorigenesis.

Zheng Wang, Leina Ma, Ying Meng, Jing Fang, Daqian Xu, Zhimin Lu.

  The circadian clock and cell metabolism are both dysregulated in cancer cells through intrinsic cell-autonomous mechanisms and external influences from the tumor microenvironment. The intricate interplay between the circadian clock and cancer cell metabolism exerts control over various metabolic processes, including aerobic glycolysis, de novo nucleotide synthesis, glutamine and protein metabolism, lipid metabolism, mitochondrial metabolism, and redox homeostasis in cancer cells. Importantly, oncogenic signaling can confer a moonlighting function on core clock genes, effectively reshaping cellular metabolism to fuel cancer cell proliferation and drive tumor growth. These interwoven regulatory mechanisms constitute a distinctive feature of cancer cell metabolism.

Keywords:  cancer metabolism; dysregulated circadian clock; moonlighting function

DOI:  https://doi.org/10.1016/j.tcb.2023.11.004
Cell Rep. 2023 Dec 07. pii: S2211-1247(23)01551-6. [Epub ahead of print]42(12): 113539

Cells use multiple mechanisms for cell-cycle arrest upon withdrawal of individual amino acids.

Yao Rong, Alicia M Darnell, Kiera M Sapp, Matthew G Vander Heiden, Sabrina L Spencer.

  Amino acids are required for cell growth and proliferation, but it remains unclear when and how amino acid availability impinges on the proliferation-quiescence decision. Here, we used time-lapse microscopy and single-cell tracking of cyclin-dependent kinase 2 (CDK2) activity to assess the response of individual cells to withdrawal of single amino acids and found strikingly different cell-cycle effects depending on the amino acid. For example, upon leucine withdrawal, MCF10A cells complete two cell cycles and then enter a CDK2-low quiescence, whereas lysine withdrawal causes immediate cell-cycle stalling. Methionine withdrawal triggers a restriction point phenotype similar to serum starvation or Mek inhibition: upon methionine withdrawal, cells complete their current cell cycle and enter a CDK2-low quiescence after mitosis. Modulation of restriction point regulators p21/p27 or cyclin D1 enables short-term rescue of proliferation under methionine and leucine withdrawal, and to a lesser extent lysine withdrawal, revealing a checkpoint connecting nutrient signaling to cell-cycle entry.

Keywords:  CDK2; CP: Cell biology; amino acid withdrawal; cyclin D1; leucine; lysine; methionine; p21; p27; proliferation-quiescence decision; restriction point

DOI:  https://doi.org/10.1016/j.celrep.2023.113539
Trends Cancer. 2023 Dec 09. pii: S2405-8033(23)00235-2. [Epub ahead of print]

It's all about the base: stromal cells are central orchestrators of metastasis.

Lea Monteran, Yael Zait, Neta Erez.

  The tumor microenvironment (TME) is an integral part of tumors and plays a central role in all stages of carcinogenesis and progression. Each organ has a unique and heterogeneous microenvironment, which affects the ability of disseminated cells to grow in the new and sometimes hostile metastatic niche. Resident stromal cells, such as fibroblasts, osteoblasts, and astrocytes, are essential culprits in the modulation of metastatic progression: they transition from being sentinels of tissue integrity to being dysfunctional perpetrators that support metastatic outgrowth. Therefore, better understanding of the complexity of their reciprocal interactions with cancer cells and with other components of the TME is essential to enable the design of novel therapeutic approaches to prevent metastatic relapse.

Keywords:  astrocytes; fibroblasts; metastasis; microenvironment; osteoblasts; stromal cells

DOI:  https://doi.org/10.1016/j.trecan.2023.11.004
Cell Rep. 2023 Dec 04. pii: S2211-1247(23)01547-4. [Epub ahead of print]42(12): 113535

Epinephrine inhibits PI3Kα via the Hippo kinases.

Ting-Yu Lin, Shakti Ramsamooj, Tiffany Perrier, Katarina Liberatore, Louise Lantier, Neil Vasan, Kannan Karukurichi, Seo-Kyoung Hwang, Edward A Kesicki, Edward R Kastenhuber, Thorsten Wiederhold, Tomer M Yaron, Emily M Huntsman, Mengmeng Zhu, Yilun Ma, Marcia N Paddock, Guoan Zhang, Benjamin D Hopkins, Owen McGuinness, Robert E Schwartz, Baran A Ersoy, Lewis C Cantley, Jared L Johnson, Marcus D Goncalves.

  The phosphoinositide 3-kinase p110α is an essential mediator of insulin signaling and glucose homeostasis. We interrogated the human serine, threonine, and tyrosine kinome to search for novel regulators of p110α and found that the Hippo kinases phosphorylate p110α at T1061, which inhibits its activity. This inhibitory state corresponds to a conformational change of a membrane-binding domain on p110α, which impairs its ability to engage membranes. In human primary hepatocytes, cancer cell lines, and rodent tissues, activation of the Hippo kinases MST1/2 using forskolin or epinephrine is associated with phosphorylation of T1061 and inhibition of p110α, impairment of downstream insulin signaling, and suppression of glycolysis and glycogen synthesis. These changes are abrogated when MST1/2 are genetically deleted or inhibited with small molecules or if the T1061 is mutated to alanine. Our study defines an inhibitory pathway of PI3K signaling and a link between epinephrine and insulin signaling.

Keywords:  CP: Metabolism; CP: Molecular biology; Hippo kinases; PI3K signaling; epinephrine signaling; glucose metabolism; glycogen metabolism; insulin sensitivity; liver

DOI:  https://doi.org/10.1016/j.celrep.2023.113535
bioRxiv. 2023 Nov 02. pii: 2023.10.30.564810. [Epub ahead of print]

Charting the transcriptomic landscape of primary and metastatic cancers in relation to their origin and target normal tissues.

Neel Sanghvi, Camilo Calvo-Alcañiz, Padma S Rajagopal, Stefano Scalera, Valeria Canu, Sanju Sinha, Fiorella Schischlik, Kun Wang, Sanna Madan, Eldad Shulman, Antonios Papanicolau-Sengos, Giovanni Blandino, Eytan Ruppin, Nishanth Ulhas Nair.

Metastasis is a leading cause of cancer-related deaths, yet understanding how metastatic tumors adapt from their origin to target tissues is challenging. To address this, we assessed whether primary and metastatic tumors resemble their tissue of origin or target tissue in terms of gene expression. We analyzed gene expression profiles from various cancer types, including single-cell and bulk RNA-seq data, in both paired and unpaired primary and metastatic patient cohorts. We quantified the transcriptomic distances between tumor samples and their normal tissues, revealing that primary tumors are more similar to their tissue of origin, while metastases shift towards the target tissue. Pathway-level analysis highlighted critical transcriptomic changes during metastasis. Notably, primary cancers exhibited higher activity in cancer hallmarks, including Activating Invasion and Metastasis , compared to metastatic cancers. This comprehensive landscape analysis provides insight into how cancer tumors adapt to their metastatic environments, providing a transcriptome-wide view of the processes involved.

DOI: https://doi.org/10.1101/2023.10.30.564810
Nat Commun. 2023 Dec 08. 14(1): 8115

Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase.

Helene Jahn, Ladislav Bartoš, Grace I Dearden, Jeremy S Dittman, Joost C M Holthuis, Robert Vácha, Anant K Menon.

Mitochondria are double-membrane-bounded organelles that depend critically on phospholipids supplied by the endoplasmic reticulum. These lipids must cross the outer membrane to support mitochondrial function, but how they do this is unclear. We identify the Voltage Dependent Anion Channel (VDAC), an abundant outer membrane protein, as a scramblase-type lipid transporter that catalyzes lipid entry. On reconstitution into membrane vesicles, dimers of human VDAC1 and VDAC2 catalyze rapid transbilayer translocation of phospholipids by a mechanism that is unrelated to their channel activity. Coarse-grained molecular dynamics simulations of VDAC1 reveal that lipid scrambling occurs at a specific dimer interface where polar residues induce large water defects and bilayer thinning. The rate of phospholipid import into yeast mitochondria is an order of magnitude lower in the absence of VDAC homologs, indicating that VDACs provide the main pathway for lipid entry. Thus, VDAC isoforms, members of a superfamily of beta barrel proteins, moonlight as a class of phospholipid scramblases - distinct from alpha-helical scramblase proteins - that act to import lipids into mitochondria.

DOI: https://doi.org/10.1038/s41467-023-43570-y
Nanoscale. 2023 Dec 08.

Nanoscale structural response of biomimetic cell membranes to controlled dehydration.

Emilia Krok, Henri G Franquelim, Madhurima Chattopadhyay, Hanna Orlikowska-Rzeznik, Petra Schwille, Lukasz Piatkowski.

Although cell membranes exist in excess of water under physiological conditions, there are a number of biochemical processes, such as adsorption of biomacromolecules or membrane fusion events, that require partial or even complete transient dehydration of lipid membranes. Even though the dehydration process is crucial for understanding all fusion events, still little is known about the structural adaptation of lipid membranes when their interfacial hydration layer is perturbed. Here, we present the study of the nanoscale structural reorganization of phase-separated, supported lipid bilayers (SLBs) under a wide range of hydration conditions. Model lipid membranes were characterised using a combination of fluorescence microscopy and atomic force microscopy and, crucially, without applying any chemical or physical modifications that have previously been considered essential for maintaining the membrane integrity upon dehydration. We revealed that decreasing the hydration state of the membrane leads to an enhanced mixing of lipids characteristic of the liquid-disordered (Ld) phase with those forming the liquid-ordered (Lo) phase. This is associated with a 2-fold decrease in the hydrophobic mismatch between the Ld and Lo lipid phases and a 3-fold decrease in the line tension for the fully desiccated membrane. Importantly, the observed changes in the hydrophobic mismatch, line tension, and lipid miscibility are fully reversible upon subsequent rehydration of the membrane. These findings provide a deeper insight into the fundamental processes, such as cell-cell fusion, that require partial dehydration at the interface of two membranes.

DOI: https://doi.org/10.1039/d3nr03078d
Nat Commun. 2023 Dec 13. 14(1): 8260

Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology.

Thomas Hu, Mayar Allam, Shuangyi Cai, Walter Henderson, Brian Yueh, Aybuke Garipcan, Anton V Ievlev, Maryam Afkarian, Semir Beyaz, Ahmet F Coskun.

Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell Spatially resolved Metabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil, and endometrium tissues, respectively. The scSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet's ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.

DOI: https://doi.org/10.1038/s41467-023-43917-5
Front Cell Dev Biol. 2023 ;11 1287084

Heparanase contributes to pancreatic carcinoma progression through insulin-dependent glucose uptake.

Alexia Abecassis, Esther Hermano, Adi Yifrach, Aron Popovtzer, Amichay Meirovitz, Michael Elkin.

  Pancreatic ductal adenocarcinoma (PDAC) is an aggressive tumor, which is highly resistant to existing therapies and characterized by one of the lowest survival rates known for solid cancers. Among the reasons for this poor prognosis are unique pathophysiological features of PDAC, such as dense extracellular matrix [ECM] creating barriers to drug delivery, as well as systemically-deregulated glucose metabolism manifested by diabetic conditions (i.e., hyperinsulinemia/hyperglycemia) occurring in the majority of PDAC patients. Moreover, in addition to systemically deregulated glucose homeostasis, intracellular metabolic pathways in PDAC are rewired toward increased glucose uptake/anabolic metabolism by the tumor cells. While the role of oncogene-driven programs in governing these processes is actively studied, mechanisms linking metabolic dysregulation and ECM enzymatic remodeling to PDAC progression/therapy resistance are less appreciated. The aim of the current study was to investigate the action of heparanase (the predominant mammalian enzyme that degrades heparan sulfate glycosaminoglycan in the ECM), as a molecular link between the diabetic state and the intracellular metabolic rewiring in PDAC pathogenesis. Here we show that in PDAC elevated levels of heparanase, coupled with diabetic conditions typical for PDAC patients, promote growth and chemotherapy resistance of pancreatic carcinoma by favoring insulin receptor signaling and GLUT4-mediated glucose uptake into tumor cells. Collectively, our findings underscore previously unknown mechanism through which heparanase acts at the interface of systemic and intracellular metabolic alterations in PDAC and attest the enzyme as an important and potentially modifiable contributor to the chemo-resistance of pancreatic tumors.

Keywords:  diabetes; gemcitabine; glucose uptake; heparanase; pancreatic cancer

DOI:  https://doi.org/10.3389/fcell.2023.1287084
Cell Rep. 2023 Dec 11. pii: S2211-1247(23)01506-1. [Epub ahead of print]42(12): 113494

T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.

John W Hickey, Maximillian Haist, Nina Horowitz, Chiara Caraccio, Yuqi Tan, Andrew J Rech, Marc-Andrea Baertsch, Xavier Rovira-Clavé, Bokai Zhu, Gustavo Vazquez, Graham Barlow, Eran Agmon, Yury Goltsev, John B Sunwoo, Markus Covert, Garry P Nolan.

  Antigen-specific T cells traffic to, are influenced by, and create unique cellular microenvironments. Here we characterize these microenvironments over time with multiplexed imaging in a melanoma model of adoptive T cell therapy and human patients with melanoma treated with checkpoint inhibitor therapy. Multicellular neighborhood analysis reveals dynamic immune cell infiltration and inflamed tumor cell neighborhoods associated with CD8+ T cells. T cell-focused analysis indicates T cells are found along a continuum of neighborhoods that reflect the progressive steps coordinating the anti-tumor immune response. More effective anti-tumor immune responses are characterized by inflamed tumor-T cell neighborhoods, flanked by dense immune infiltration neighborhoods. Conversely, ineffective T cell therapies express anti-inflammatory cytokines, resulting in regulatory neighborhoods, spatially disrupting productive T cell-immune and -tumor interactions. Our study provides in situ mechanistic insights into temporal tumor microenvironment changes, cell interactions critical for response, and spatial correlates of immunotherapy outcomes, informing cellular therapy evaluation and engineering.

Keywords:  CODEX; CP: Cancer; CP: Immunology; Multiplexed tissue imaging; T cell phenotype; T cell therapy; T cells; cancer immunotherapy; checkpoint inhibitor therapy; melanoma; metabolism; spatial biology

DOI:  https://doi.org/10.1016/j.celrep.2023.113494
Cell. 2023 Dec 07. pii: S0092-8674(23)01221-7. [Epub ahead of print]186(25): 5554-5568.e18

An oncogenic phenoscape of colonic stem cell polarization.

Xiao Qin, Ferran Cardoso Rodriguez, Jahangir Sufi, Petra Vlckova, Jeroen Claus, Christopher J Tape.

  Cancer cells are regulated by oncogenic mutations and microenvironmental signals, yet these processes are often studied separately. To functionally map how cell-intrinsic and cell-extrinsic cues co-regulate cell fate, we performed a systematic single-cell analysis of 1,107 colonic organoid cultures regulated by (1) colorectal cancer (CRC) oncogenic mutations, (2) microenvironmental fibroblasts and macrophages, (3) stromal ligands, and (4) signaling inhibitors. Multiplexed single-cell analysis revealed a stepwise epithelial differentiation phenoscape dictated by combinations of oncogenes and stromal ligands, spanning from fibroblast-induced Clusterin (CLU)+ revival colonic stem cells (revCSCs) to oncogene-driven LRIG1+ hyper-proliferative CSCs (proCSCs). The transition from revCSCs to proCSCs is regulated by decreasing WNT3A and TGF-β-driven YAP signaling and increasing KRASG12D or stromal EGF/Epiregulin-activated MAPK/PI3K flux. We find that APC loss and KRASG12D collaboratively limit access to revCSCs and disrupt stromal-epithelial communication-trapping epithelia in the proCSC fate. These results reveal that oncogenic mutations dominate homeostatic differentiation by obstructing cell-extrinsic regulation of cell-fate plasticity.

Keywords:  CRC; cell plasticity; cell-cell signaling; cell-fate polarization; colonic stem cell; colorectal cancer; cue-signal-response; organoid; single-cell analysis; tumor microenvironment

DOI:  https://doi.org/10.1016/j.cell.2023.11.004
Cancer Res. 2023 Dec 14.

Exploring the role of hyperinsulinemia in obesity-associated tumor development.

Ericka Vélez-Bonet, Kristyn Gumpper-Fedus, Zobeida Cruz-Monserrate.

Although there has been a long-standing connection between hyperinsulinemia and cancer development, there is a lack of understanding of the role of the insulin receptor on cells that can become cancerous. In a recent issue of Cell Metabolism, Zhang and colleagues, using a diet-induced obesity mouse model, identified a direct function of insulin receptors on pancreatic acinar cells expressing a KRASG12D mutation in promoting obesity-associated pancreatic cancer. Furthermore, insulin receptor signaling from hyperinsulinemia promoted the secretion of digestive enzymes that contributed to acinar to ductal metaplasia. These findings highlight an important connection between obesity, diabetes, and pancreatic tumor development and suggest potential strategies for obesity-associated cancer prevention targeting the insulin receptor signaling pathways.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-3932
Cancer Innov. 2022 Oct;1(3): 207-219

Research progress in the establishment of pancreatic cancer models and preclinical applications.

Weizheng Wu, Kunming Wen, Yuxin Zhong.

  Pancreatic cancer (PC) is a highly malignant tumor in the digestive system. The transformation of tissue from normal to pancreatic intraepithelial neoplasm is driven by certain oncogenes, among which the mutation rate of the KRAS gene is as high as 90%. Currently, PC has limited treatment options, low therapeutic effects, and poor prognosis. Thus, more effective methods to combat PC are urgently needed. Some models that can more accurately reflect the biological behaviors and genomic characteristics of PC, such as its morphology, pathology, proliferation, and invasion, are being continuously developed. These include genetic engineering models, orthotopic xenograft models, and heterotopic xenograft models. Using these PC models, scientists have further verified promising drugs and potential therapeutic targets for PC treatment. This is of great significance for limiting the progression of PC with clinical intervention, improving patient outcomes, and improving survival rates.

Keywords:  genetic engineering; heterotopic; model; orthotopic; pancreatic cancer; pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.1002/cai2.31
Cell Mol Life Sci. 2023 Dec 13. 81(1): 7

Inhibition of the membrane repair protein annexin-A2 prevents tumor invasion and metastasis.

C Gounou, L Rouyer, G Siegfried, E Harté, F Bouvet, L d'Agata, E Darbo, M Lefeuvre, M A Derieppe, L Bouton, M Mélane, D Chapeau, J Martineau, V Prouzet-Mauleon, S Tan, W Souleyreau, F Saltel, F Argoul, A M Khatib, A R Brisson, R Iggo, A Bouter.

  Cancer cells are exposed to major compressive and shearing forces during invasion and metastasis, leading to extensive plasma membrane damage. To survive this mechanical stress, they need to repair membrane injury efficiently. Targeting the membrane repair machinery is thus potentially a new way to prevent invasion and metastasis. We show here that annexin-A2 (ANXA2) is required for membrane repair in invasive breast and pancreatic cancer cells. Mechanistically, we show by fluorescence and electron microscopy that cells fail to reseal shear-stress damaged membrane when ANXA2 is silenced or the protein is inhibited with neutralizing antibody. Silencing of ANXA2 has no effect on proliferation in vitro, and may even accelerate migration in wound healing assays, but reduces tumor cell dissemination in both mice and zebrafish. We expect that inhibiting membrane repair will be particularly effective in aggressive, poor prognosis tumors because they rely on the membrane repair machinery to survive membrane damage during tumor invasion and metastasis. This could be achieved either with anti-ANXA2 antibodies, which have been shown to inhibit metastasis of breast and pancreatic cancer cells, or with small molecule drugs.

Keywords:  Annexins; AsPC-1; Invasion; MDA-MB-231; Metastasis; S100 proteins; Tumor progression

DOI:  https://doi.org/10.1007/s00018-023-05049-3
Proc Natl Acad Sci U S A. 2023 Dec 19. 120(51): e2303713120

The mitochondrial ATP synthase is a negative regulator of the mitochondrial permeability transition pore.

Ryan Pekson, Felix G Liang, Joshua L Axelrod, Jaehoon Lee, Dongze Qin, Andre J H Wittig, Victor M Paulino, Min Zheng, Pablo M Peixoto, Richard N Kitsis.

  The mitochondrial permeability transition pore (mPTP) is a channel in the inner mitochondrial membrane whose sustained opening in response to elevated mitochondrial matrix Ca2+ concentrations triggers necrotic cell death. The molecular identity of mPTP is unknown. One proposed candidate is the mitochondrial ATP synthase, whose canonical function is to generate most ATP in multicellular organisms. Here, we present mitochondrial, cellular, and in vivo evidence that, rather than serving as mPTP, the mitochondrial ATP synthase inhibits this pore. Our studies confirm previous work showing persistence of mPTP in HAP1 cell lines lacking an assembled mitochondrial ATP synthase. Unexpectedly, however, we observe that Ca2+-induced pore opening is markedly sensitized by loss of the mitochondrial ATP synthase. Further, mPTP opening in cells lacking the mitochondrial ATP synthase is desensitized by pharmacological inhibition and genetic depletion of the mitochondrial cis-trans prolyl isomerase cyclophilin D as in wild-type cells, indicating that cyclophilin D can modulate mPTP through substrates other than subunits in the assembled mitochondrial ATP synthase. Mitoplast patch clamping studies showed that mPTP channel conductance was unaffected by loss of the mitochondrial ATP synthase but still blocked by cyclophilin D inhibition. Cardiac mitochondria from mice whose heart muscle cells we engineered deficient in the mitochondrial ATP synthase also demonstrate sensitization of Ca2+-induced mPTP opening and desensitization by cyclophilin D inhibition. Further, these mice exhibit strikingly larger myocardial infarctions when challenged with ischemia/reperfusion in vivo. We conclude that the mitochondrial ATP synthase does not function as mPTP and instead negatively regulates this pore.

Keywords:  mitochondrial ATP synthase; mitochondrial permeability transition pore; necrosis

DOI:  https://doi.org/10.1073/pnas.2303713120
Cancers (Basel). 2023 Nov 26. pii: 5590. [Epub ahead of print]15(23):

Cancer Cachexia: New Insights and Future Directions.

Claudia Raluca Mariean, Oana Mirela Tiucă, Alexandru Mariean, Ovidiu Simion Cotoi.

  Cancer remains a major health problem and is associated with cachexia in up to 80% of cases, leading to decreased survival and quality of life. Cachexia involves complex metabolic disturbances in both protein and energy balance, muscle wasting phenomena, weight loss, systemic inflammation, overall decreased performance status, and tolerability to treatment. The clinical impact of cancer cachexia is very complex, with early detection of cachectic patients and identification of predictive biomarkers being two key factors for improving survival. Thus, a better understanding of the complexity of cancer cachexia phenomena and its main pathophysiological mechanism is much needed. Our review highlights the most important information about cancer cachexia, aiming to disseminate updated research findings about this highly deadly condition.

Keywords:  CT-imaging; biomarkers; cachexia; cancer; clinical impact; inflammation; pathophysiology; sarcopenia

DOI:  https://doi.org/10.3390/cancers15235590
Nat Genet. 2023 Dec 08.

CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity.

Marco Varrone, Daniele Tavernari, Albert Santamaria-Martínez, Logan A Walsh, Giovanni Ciriello.

Tissues are organized in cellular niches, the composition and interactions of which can be investigated using spatial omics technologies. However, systematic analyses of tissue composition are challenged by the scale and diversity of the data. Here we present CellCharter, an algorithmic framework to identify, characterize, and compare cellular niches in spatially resolved datasets. CellCharter outperformed existing approaches and effectively identified cellular niches across datasets generated using different technologies, and comprising hundreds of samples and millions of cells. In multiple human lung cancer cohorts, CellCharter uncovered a cellular niche composed of tumor-associated neutrophil and cancer cells expressing markers of hypoxia and cell migration. This cancer cell state was spatially segregated from more proliferative tumor cell clusters and was associated with tumor-associated neutrophil infiltration and poor prognosis in independent patient cohorts. Overall, CellCharter enables systematic analyses across data types and technologies to decode the link between spatial tissue architectures and cell plasticity.

DOI: https://doi.org/10.1038/s41588-023-01588-4
Sci Adv. 2023 Dec 15. 9(50): eade1660

Plasma membrane nanodeformations promote actin polymerization through CIP4/CDC42 recruitment and regulate type II IFN signaling.

Benjamin Ledoux, Natacha Zanin, Jinsung Yang, Vincent Mercier, Charlotte Coster, Christine Dupont-Gillain, David Alsteens, Pierre Morsomme, Henri-François Renard.

In their environment, cells must cope with mechanical stresses constantly. Among these, nanoscale deformations of plasma membrane induced by substrate nanotopography are now largely accepted as a biophysical stimulus influencing cell behavior and function. However, the mechanotransduction cascades involved and their precise molecular effects on cellular physiology are still poorly understood. Here, using homemade fluorescent nanostructured cell culture surfaces, we explored the role of Bin/Amphiphysin/Rvs (BAR) domain proteins as mechanosensors of plasma membrane geometry. Our data reveal that distinct subsets of BAR proteins bind to plasma membrane deformations in a membrane curvature radius-dependent manner. Furthermore, we show that membrane curvature promotes the formation of dynamic actin structures mediated by the Rho GTPase CDC42, the F-BAR protein CIP4, and the presence of PI(4,5)P2. In addition, these actin-enriched nanodomains can serve as platforms to regulate receptor signaling as they appear to contain interferon-γ receptor (IFNγ-R) and to lead to the partial inhibition of IFNγ-induced JAK/STAT signaling.

DOI: https://doi.org/10.1126/sciadv.ade1660
bioRxiv. 2023 Dec 03. pii: 2023.12.01.569679. [Epub ahead of print]

Quantitative Analysis of Autophagy in Single Cells: Differential Response to Amino Acid and Glucose Starvation.

Katie R Martin, Stephanie L Celano, Ryan D Sheldon, Russell G Jones, Jeffrey P MacKeigan.

Autophagy is a highly conserved, intracellular recycling process by which cytoplasmic contents are degraded in the lysosome. This process occurs at a low level constitutively; however, it is induced robustly in response to stressors, in particular, starvation of critical nutrients such as amino acids and glucose. That said, the relative contribution of these inputs is ambiguous and many starvation medias are poorly defined or devoid of multiple nutrients. Here, we sought to generate a quantitative catalog of autophagy across multiple stages and in single, living cells under normal growth conditions as well as in media starved specifically of amino acids or glucose. We found that autophagy is induced by starvation of amino acids, but not glucose, in U2OS cells, and that MTORC1-mediated ULK1 regulation and autophagy are tightly linked to amino acid levels. While autophagy is engaged immediately during amino acid starvation, a heightened response occurs during a period marked by transcriptional upregulation of autophagy genes during sustained starvation. Finally, we demonstrated that cells immediately return to their initial, low-autophagy state when nutrients are restored, highlighting the dynamic relationship between autophagy and environmental conditions. In addition to sharing our findings here, we provide our data as a high-quality resource for others interested in mathematical modeling or otherwise exploring autophagy in individual cells across a population.

DOI: https://doi.org/10.1101/2023.12.01.569679
Front Bioeng Biotechnol. 2023 ;11 1293268

Label-free spatially maintained measurements of metabolic phenotypes in cells.

Linghao Hu, Nianchao Wang, Joshua D Bryant, Lin Liu, Linglin Xie, A Phillip West, Alex J Walsh.

  Metabolic reprogramming at a cellular level contributes to many diseases including cancer, yet few assays are capable of measuring metabolic pathway usage by individual cells within living samples. Here, autofluorescence lifetime imaging is combined with single-cell segmentation and machine-learning models to predict the metabolic pathway usage of cancer cells. The metabolic activities of MCF7 breast cancer cells and HepG2 liver cancer cells were controlled by growing the cells in culture media with specific substrates and metabolic inhibitors. Fluorescence lifetime images of two endogenous metabolic coenzymes, reduced nicotinamide adenine dinucleotide (NADH) and oxidized flavin adenine dinucleotide (FAD), were acquired by a multi-photon fluorescence lifetime microscope and analyzed at the cellular level. Quantitative changes of NADH and FAD lifetime components were observed for cells using glycolysis, oxidative phosphorylation, and glutaminolysis. Conventional machine learning models trained with the autofluorescence features classified cells as dependent on glycolytic or oxidative metabolism with 90%-92% accuracy. Furthermore, adapting convolutional neural networks to predict cancer cell metabolic perturbations from the autofluorescence lifetime images provided improved performance, 95% accuracy, over traditional models trained via extracted features. Additionally, the model trained with the lifetime features of cancer cells could be transferred to autofluorescence lifetime images of T cells, with a prediction that 80% of activated T cells were glycolytic, and 97% of quiescent T cells were oxidative. In summary, autofluorescence lifetime imaging combined with machine learning models can detect metabolic perturbations between glycolysis and oxidative metabolism of living samples at a cellular level, providing a label-free technology to study cellular metabolism and metabolic heterogeneity.

Keywords:  autofluorescence; cancer; fluorescence lifetime; machine learning; metabolism

DOI:  https://doi.org/10.3389/fbioe.2023.1293268
Cancer Cell. 2023 Dec 01. pii: S1535-6108(23)00399-9. [Epub ahead of print]

B3GALT6 promotes dormant breast cancer cell survival and recurrence by enabling heparan sulfate-mediated FGF signaling.

Amulya Sreekumar, Michelle Lu, Biswa Choudhury, Tien-Chi Pan, Dhruv K Pant, Matthew R Lawrence-Paul, Christopher J Sterner, George K Belka, Takashi Toriumi, Brian A Benz, Matias Escobar-Aguirre, Francesco E Marino, Jeffrey D Esko, Lewis A Chodosh.

  Breast cancer mortality results from incurable recurrences thought to be seeded by dormant, therapy-refractory residual tumor cells (RTCs). Understanding the mechanisms enabling RTC survival is therefore essential for improving patient outcomes. Here, we derive a dormancy-associated RTC signature that mirrors the transcriptional response to neoadjuvant therapy in patients and is enriched for extracellular matrix-related pathways. In vivo CRISPR-Cas9 screening of dormancy-associated candidate genes identifies the galactosyltransferase B3GALT6 as a functional regulator of RTC fitness. B3GALT6 is required for glycosaminoglycan (GAG) linkage to proteins to generate proteoglycans, and its germline loss of function in patients causes skeletal dysplasias. We find that B3GALT6-mediated biosynthesis of heparan sulfate GAGs predicts poor patient outcomes and promotes tumor recurrence by enhancing dormant RTC survival in multiple contexts, and does so via a B3GALT6-heparan sulfate/HS6ST1-heparan 6-O-sulfation/FGF1-FGFR2 signaling axis. These findings implicate B3GALT6 in cancer and nominate FGFR2 inhibition as a promising approach to eradicate dormant RTCs and prevent recurrence.

Keywords:  6-O-sulfation; B3GALT6; FGFR2; HS6ST1; breast cancer; dormancy; glycans; glycosaminoglycans; heparan sulfate; proteoglycans

DOI:  https://doi.org/10.1016/j.ccell.2023.11.008
Nat Rev Cancer. 2023 Dec 08.

How chemokines organize the tumour microenvironment.

Thorsten R Mempel, Julia K Lill, Lukas M Altenburger.

For our immune system to contain or eliminate malignant solid tumours, both myeloid and lymphoid haematopoietic cells must not only extravasate from the bloodstream into the tumour tissue but also further migrate to various specialized niches of the tumour microenvironment to functionally interact with each other, with non-haematopoietic stromal cells and, ultimately, with cancer cells. These interactions regulate local immune cell survival, proliferative expansion, differentiation and their execution of pro-tumour or antitumour effector functions, which collectively determine the outcome of spontaneous or therapeutically induced antitumour immune responses. None of these interactions occur randomly but are orchestrated and critically depend on migratory guidance cues provided by chemokines, a large family of chemotactic cytokines, and their receptors. Understanding the functional organization of the tumour immune microenvironment inevitably requires knowledge of the multifaceted roles of chemokines in the recruitment and positioning of its cellular constituents. Gaining such knowledge will not only generate new insights into the mechanisms underlying antitumour immunity or immune tolerance but also inform the development of biomarkers (or 'biopatterns') based on spatial tumour tissue analyses, as well as novel strategies to therapeutically engineer immune responses in patients with cancer. Here we will discuss recent observations on the role of chemokines in the tumour microenvironment in the context of our knowledge of their physiological functions in development, homeostasis and antimicrobial responses.

DOI: https://doi.org/10.1038/s41568-023-00635-w
Elife. 2023 Dec 11. pii: RP89232. [Epub ahead of print]12

Mitochondrial temperature homeostasis resists external metabolic stresses.

Mügen Terzioglu, Kristo Veeroja, Toni Montonen, Teemu O Ihalainen, Tiina S Salminen, Paule Bénit, Pierre Rustin, Young-Tae Chang, Takeharu Nagai, Howard T Jacobs.

  Based on studies with a fluorescent reporter dye, Mito Thermo Yellow (MTY), and the genetically encoded gTEMP ratiometric fluorescent temperature indicator targeted to mitochondria, the temperature of active mitochondria in four mammalian and one insect cell line was estimated to be up to 15°C above that of the external environment to which the cells were exposed. High mitochondrial temperature was maintained in the face of a variety of metabolic stresses, including substrate starvation or modification, decreased ATP demand due to inhibition of cytosolic protein synthesis, inhibition of the mitochondrial adenine nucleotide transporter and, if an auxiliary pathway for electron transfer was available via the alternative oxidase, even respiratory poisons acting downstream of oxidative phosphorylation (OXPHOS) complex I. We propose that the high temperature of active mitochondria is an inescapable consequence of the biochemistry of OXPHOS and is homeostatically maintained as a primary feature of mitochondrial metabolism.

Keywords:  D. melanogaster; OXPHOS; biochemistry; bioenergetics; cell biology; chemical biology; human; mitochondria; mouse; organelle; temperature; thermogenesis

DOI:  https://doi.org/10.7554/eLife.89232
Nanoscale. 2023 Dec 08.

Single-cell force spectroscopy of fluid flow-tuned cell adhesion for dissecting hemodynamics in tumor metastasis.

Jiajia Wei, Yanqi Yang, Mi Li.

Cell adhesion plays an important role in regulating the metastasis of cancer cells, and atomic force microscopy (AFM)-based single-cell force spectroscopy (SCFS) has become an important method to directly measure the adhesion forces of individual cells. Particularly, bodily fluid flow environments strongly affect the functions and behaviors of metastatic cells for successful dissemination. Nevertheless, the interactions between fluidic flow medium environment and cell adhesion remain poorly understood. In this work, AFM-based SCFS was exploited to examine the effects of fluidic flow environment on cellular adhesion. A fluidic cell culture medium device was used to simulate the fluidic flow environment experienced by cancer cells during metastasis, which was combined with AFM-based SCFS assay. A single living cancer cell was attached to the AFM tipless cantilever to prepare the single-cell probe for performing SCFS experiments on the mesothelial cells grown under the fluidic flow medium conditions, and the effects of experimental parameters (retraction speed, contact time, loading force) on the measured cellular adhesion forces were analyzed. Experimental results of SCFS assay show that cellular adhesion forces significantly decrease after growth in fluidic flow medium, whereas cellular adhesion forces increase after growth in static culture medium. Experiments performed with the use of spherical probes coated with cell adhesion-associated biomolecules also show the weakening of cell adhesion after growth in fluidic flow cell culture medium, which was subsequently confirmed by the confocal fluorescence microscopy experiments of cell adhesion molecules, vividly illustrating the remarkable effects of fluidic flow environment on cellular adhesion. The study provides a new approach to detect adhesion force dynamics involved in the interactions between cells and the fluidic flow environment at the single-cell level, which will facilitate dissecting the role of hemodynamics in tumor metastasis.

DOI: https://doi.org/10.1039/d3nr04439d
Nat Commun. 2023 Dec 09. 14(1): 8170

Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines.

Qionghua Zhu, Xin Zhao, Yuanhang Zhang, Yanping Li, Shang Liu, Jingxuan Han, Zhiyuan Sun, Chunqing Wang, Daqi Deng, Shanshan Wang, Yisen Tang, Yaling Huang, Siyuan Jiang, Chi Tian, Xi Chen, Yue Yuan, Zeyu Li, Tao Yang, Tingting Lai, Yiqun Liu, Wenzhen Yang, Xuanxuan Zou, Mingyuan Zhang, Huanhuan Cui, Chuanyu Liu, Xin Jin, Yuhui Hu, Ao Chen, Xun Xu, Guipeng Li, Yong Hou, Longqi Liu, Shiping Liu, Liang Fang, Wei Chen, Liang Wu.

Human cancer cell lines have long served as tools for cancer research and drug discovery, but the presence and the source of intra-cell-line heterogeneity remain elusive. Here, we perform single-cell RNA-sequencing and ATAC-sequencing on 42 and 39 human cell lines, respectively, to illustrate both transcriptomic and epigenetic heterogeneity within individual cell lines. Our data reveal that transcriptomic heterogeneity is frequently observed in cancer cell lines of different tissue origins, often driven by multiple common transcriptional programs. Copy number variation, as well as epigenetic variation and extrachromosomal DNA distribution all contribute to the detected intra-cell-line heterogeneity. Using hypoxia treatment as an example, we demonstrate that transcriptomic heterogeneity could be reshaped by environmental stress. Overall, our study performs single-cell multi-omics of commonly used human cancer cell lines and offers mechanistic insights into the intra-cell-line heterogeneity and its dynamics, which would serve as an important resource for future cancer cell line-based studies.

DOI: https://doi.org/10.1038/s41467-023-43991-9
BMC Surg. 2023 Dec 08. 23(1): 370

Combined utility of Ki-67 index and tumor grade to stratify patients with pancreatic ductal adenocarcinoma who underwent upfront surgery.

Bo Li, Xiaoyi Yin, Xiuwen Ding, Guoxiao Zhang, Hui Jiang, Cuimin Chen, Shiwei Guo, Gang Jin.

   OBJECTIVE: To investigate the prognostic prediction of a new indicator, combined by tumor grade and Ki-67, in patients with resected pancreatic ductal adenocarcinoma (PDAC).
METHODS: Data were retrospectively collected from consecutive patients who underwent primary resection of pancreas from December 2012 to December 2017. Tumor grade and Ki-67 were reviewed from routine pathological reports. G-Ki67 was classified as three categories as I (G1/2 and Ki-67 < 40%), II (G1/2 and Ki-67 ≥ 40%), and III(G3/4 and all Ki-67).
RESULTS: Cox regression analyses revealed that tumor stage (II vs. I: hazard ratio (HR), 3.781; 95% confidence index (CI), 2.844-5.025; P < 0.001; III vs. I: HR, 7.476; 95% CI, 5.481-10.20; P < 0.001) and G-Ki67 (II vs. I: HR, 1.299; 95% CI, 1.038-1.624; P = 0.022; III vs. I: HR, 1.942; 95% CI, 1.477-2.554; P < 0.001) were independent prognostic factors in the developing cohort. The result was rectified in the validation cohort. In subgroups analysis, G-Ki67 (II vs. I: HR, 1.866 ; 95% CI, 1.045-3.334; P = 0.035; III vs. I: HR, 2.333 ; 95% CI, 1.156-4.705; P = 0.018) also had a high differentiation for survival prediction.
CONCLUSION: Our findings indicate that three-categories of G-Ki67 in resectable PDAC according to the routine pathological descriptions provided additional prognostic information complementary to the TNM staging system.

Keywords:  Ki-67; Pancreatic ductal adenocarcinoma; Patient stratification; Tumor grade

DOI:  https://doi.org/10.1186/s12893-023-02256-4