bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2023–03–05
thirty papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. What is cancer metabolism?
  2. Multifaceted role for p53 in pancreatic cancer suppression.
  3. Cancer cachexia: involvement of an expanding macroenvironment.
  4. Autophagy and autophagy-related pathways in cancer.
  5. Molecular mechanisms of cancer cachexia-related loss of skeletal muscle mass: data analysis from preclinical and clinical studies.
  6. CRISPR-based large-scale modeling of loss-of-function mutations to investigate mechanisms of stress resistance in cancer.
  7. Precision Oncology in Pancreatic Cancer: Experiences and Challenges of the CCCMunichLMU Molecular Tumor Board.
  8. Cancer immune evasion through KRAS and PD-L1 and potential therapeutic interventions.
  9. Systematic diet composition swap in a mouse genome-scale metabolic model reveals determinants of obesogenic diet metabolism in liver cancer.
  10. Ras protein abundance correlates with Ras isoform mutation patterns in cancer.
  11. Blebs promote cell survival by assembling oncogenic signalling hubs.
  12. A Case of an Incidental Pancreatic Cyst.
  13. Metastasis prevention: How to catch metastatic seeds.
  14. In silico tissue generation and power analysis for spatial omics.
  15. Editorial: Single cell meets metabolism and cancer biology.
  16. High-volume centers are associated with higher receipt of combined therapy in stage III pancreatic cancer.
  17. Pilot clinical trial of macimorelin to assess safety and efficacy in patients with cancer cachexia.
  18. Comprehensive Metabolic Tracing Reveals the Origin and Catabolism of Cysteine in Mammalian Tissues and Tumors.
  19. Quantification of autophagy flux in isolated mouse skeletal muscle fibers with overexpression of fluorescent protein mCherry-EGFP-LC3.
  20. ImmCellFie: A user-friendly web-based platform to infer metabolic function from omics data.
  21. Protocol for quantitative evaluation of the impact of paracrine senescence on cellular reprogramming in cultured cells and mouse models.
  22. AlphaFold-multimer predicts ATG8 protein binding motifs crucial for autophagy research.
  23. Lysosomal control of senescence and inflammation through cholesterol partitioning.
  24. MYTHO is a novel regulator of skeletal muscle autophagy and integrity.
  25. Protocol to package and concentrate adeno-associated virus serotype 8 for use in autochthonous mouse models of pancreatic cancer.
  26. Protocol to transfer epithelial acini between different extracellular matrices and orient fibril organization.
  27. Methods and applications for single-cell and spatial multi-omics.
  28. Glycation-mediated tissue-level remodeling of brain meningeal membrane by aging.
  29. Human APOBEC3B promotes tumor heterogeneity in vivo including signature mutations and metastases.
  30. H3K4me3 regulates RNA polymerase II promoter-proximal pause-release.
  1. Cell. 2023 Feb 22. pii: S0092-8674(23)00097-1. [Epub ahead of print]
    What is cancer metabolism?
    Lydia W S Finley.
      The uptake and metabolism of nutrients support fundamental cellular process from bioenergetics to biomass production and cell fate regulation. While many studies of cell metabolism focus on cancer cells, the principles of metabolism elucidated in cancer cells apply to a wide range of mammalian cells. The goal of this review is to discuss how the field of cancer metabolism provides a framework for revealing principles of cell metabolism and for dissecting the metabolic networks that allow cells to meet their specific demands. Understanding context-specific metabolic preferences and liabilities will unlock new approaches to target cancer cells to improve patient care.
    DOI:  https://doi.org/10.1016/j.cell.2023.01.038
  2. Proc Natl Acad Sci U S A. 2023 Mar 07. 120(10): e2211937120
    Multifaceted role for p53 in pancreatic cancer suppression.
    Stephano S Mello, Brittany M Flowers, Pawel K Mazur, James J Lee, Fabian Müller, Sarah K Denny, Sofia Ferreira, Kathryn Hanson, Seung K Kim, William J Greenleaf, Laura D Wood, Laura D Attardi.
      The vast majority of human pancreatic ductal adenocarcinomas (PDACs) harbor TP53 mutations, underscoring p53's critical role in PDAC suppression. PDAC can arise when pancreatic acinar cells undergo acinar-to-ductal metaplasia (ADM), giving rise to premalignant pancreatic intraepithelial neoplasias (PanINs), which finally progress to PDAC. The occurrence of TP53 mutations in late-stage PanINs has led to the idea that p53 acts to suppress malignant transformation of PanINs to PDAC. However, the cellular basis for p53 action during PDAC development has not been explored in detail. Here, we leverage a hyperactive p53 variant-p5353,54-which we previously showed is a more robust PDAC suppressor than wild-type p53, to elucidate how p53 acts at the cellular level to dampen PDAC development. Using both inflammation-induced and KRASG12D-driven PDAC models, we find that p5353,54 both limits ADM accumulation and suppresses PanIN cell proliferation and does so more effectively than wild-type p53. Moreover, p5353,54 suppresses KRAS signaling in PanINs and limits effects on the extracellular matrix (ECM) remodeling. While p5353,54 has highlighted these functions, we find that pancreata in wild-type p53 mice similarly show less ADM, as well as reduced PanIN cell proliferation, KRAS signaling, and ECM remodeling relative to Trp53-null mice. We find further that p53 enhances chromatin accessibility at sites controlled by acinar cell identity transcription factors. These findings reveal that p53 acts at multiple stages to suppress PDAC, both by limiting metaplastic transformation of acini and by dampening KRAS signaling in PanINs, thus providing key new understanding of p53 function in PDAC.
    Keywords:  ADM; PanIN; p53; pancreatic cancer; pancreatitis
    DOI:  https://doi.org/10.1073/pnas.2211937120
  3. Cancer Cell. 2023 Feb 25. pii: S1535-6108(23)00035-1. [Epub ahead of print]
    Cancer cachexia: involvement of an expanding macroenvironment.
    Benjamin R Pryce, David J Wang, Teresa A Zimmers, Michael C Ostrowski, Denis C Guttridge.
      Advanced cancers often present with the cachexia syndrome that impacts peripheral tissues, leading to involuntary weight loss and reduced prognosis. The central tissues undergoing depletion are skeletal muscle and adipose, but recent findings reveal an expanding tumor macroenvironment involving organ crosstalks that underlie the cachectic state.
    DOI:  https://doi.org/10.1016/j.ccell.2023.02.007
  4. Nat Rev Mol Cell Biol. 2023 Mar 02.
    Autophagy and autophagy-related pathways in cancer.
    Jayanta Debnath, Noor Gammoh, Kevin M Ryan.
      Maintenance of protein homeostasis and organelle integrity and function is critical for cellular homeostasis and cell viability. Autophagy is the principal mechanism that mediates the delivery of various cellular cargoes to lysosomes for degradation and recycling. A myriad of studies demonstrate important protective roles for autophagy against disease. However, in cancer, seemingly opposing roles of autophagy are observed in the prevention of early tumour development versus the maintenance and metabolic adaptation of established and metastasizing tumours. Recent studies have addressed not only the tumour cell intrinsic functions of autophagy, but also the roles of autophagy in the tumour microenvironment and associated immune cells. In addition, various autophagy-related pathways have been described, which are distinct from classical autophagy, that utilize parts of the autophagic machinery and can potentially contribute to malignant disease. Growing evidence on how autophagy and related processes affect cancer development and progression has helped guide efforts to design anticancer treatments based on inhibition or promotion of autophagy. In this Review, we discuss and dissect these different functions of autophagy and autophagy-related processes during tumour development, maintenance and progression. We outline recent findings regarding the role of these processes in both the tumour cells and the tumour microenvironment and describe advances in therapy aimed at autophagy processes in cancer.
    DOI:  https://doi.org/10.1038/s41580-023-00585-z
  5. J Cachexia Sarcopenia Muscle. 2023 Mar 02.
    Molecular mechanisms of cancer cachexia-related loss of skeletal muscle mass: data analysis from preclinical and clinical studies.
    Agnès Martin, Yann S Gallot, Damien Freyssenet.
      Cancer cachexia is a systemic hypoanabolic and catabolic syndrome that diminishes the quality of life of cancer patients, decreases the efficiency of therapeutic strategies and ultimately contributes to decrease their lifespan. The depletion of skeletal muscle compartment, which represents the primary site of protein loss during cancer cachexia, is of very poor prognostic in cancer patients. In this review, we provide an extensive and comparative analysis of the molecular mechanisms involved in the regulation of skeletal muscle mass in human cachectic cancer patients and in animal models of cancer cachexia. We summarize data from preclinical and clinical studies investigating how the protein turnover is regulated in cachectic skeletal muscle and question to what extent the transcriptional and translational capacities, as well as the proteolytic capacity (ubiquitin-proteasome system, autophagy-lysosome system and calpains) of skeletal muscle are involved in the cachectic syndrome in human and animals. We also wonder how regulatory mechanisms such as insulin/IGF1-AKT-mTOR pathway, endoplasmic reticulum stress and unfolded protein response, oxidative stress, inflammation (cytokines and downstream IL1ß/TNFα-NF-κB and IL6-JAK-STAT3 pathways), TGF-ß signalling pathways (myostatin/activin A-SMAD2/3 and BMP-SMAD1/5/8 pathways), as well as glucocorticoid signalling, modulate skeletal muscle proteostasis in cachectic cancer patients and animals. Finally, a brief description of the effects of various therapeutic strategies in preclinical models is also provided. Differences in the molecular and biochemical responses of skeletal muscle to cancer cachexia between human and animals (protein turnover rates, regulation of ubiquitin-proteasome system and myostatin/activin A-SMAD2/3 signalling pathways) are highlighted and discussed. Identifying the various and intertwined mechanisms that are deregulated during cancer cachexia and understanding why they are decontrolled will provide therapeutic targets for the treatment of skeletal muscle wasting in cancer patients.
    Keywords:  Autophagy-lysosome; Cancer cachexia; Glucocorticoids; Inflammation; Myostatin; Oxidative stress; Proteostasis; Skeletal muscle; Ubiquitin-proteasome
    DOI:  https://doi.org/10.1002/jcsm.13073
  6. STAR Protoc. 2023 Feb 11. pii: S2666-1667(23)00055-2. [Epub ahead of print]4(1): 102097
    CRISPR-based large-scale modeling of loss-of-function mutations to investigate mechanisms of stress resistance in cancer.
    Fabrizio Simeoni, Ioannis Loukas, Thomas Stuart Wilson, Paola Scaffidi.
      Dissecting mechanisms driving subclone expansion in primary cancers has been challenging. Here, we present a protocol to systematically disrupt entire gene networks and assess the functional impact of this perturbation on cancer cell fitness. By combining arrayed CRISPR libraries and high-content microscopy, we describe steps to identify classes of genes whose inactivation promotes resistance to environmental challenges faced by cancer cells during tumor growth or upon therapy. A proof-of-principle interrogation of the epigenetic regulatory network is described. For complete details on the use and execution of this protocol, please refer to Loukas et al. (2022).1.
    Keywords:  CRISPR; Cancer; Cell Biology; Cell-based Assays; Genetics; High-throughput Screening; Molecular Biology
    DOI:  https://doi.org/10.1016/j.xpro.2023.102097
  7. Target Oncol. 2023 Feb 28.
    Precision Oncology in Pancreatic Cancer: Experiences and Challenges of the CCCMunichLMU Molecular Tumor Board.
    Klara Dorman, Danmei Zhang, Kathrin Heinrich, Laurens Reeh, Lena Weiss, Michael Haas, Georg Beyer, Daniel Rössler, Elisabetta Goni, Bernhard W Renz, Jan G D'Haese, Wolfgang G Kunz, Max Seidensticker, Stefanie Corradini, Maximilian Niyazi, Steffen Ormanns, Jörg Kumbrink, Andreas Jung, Frederick Klauschen, Jens Werner, Julia Mayerle, Michael von Bergwelt-Baildon, Stefan Boeck, Volker Heinemann, C Benedikt Westphalen.
       BACKGROUND: In pancreatic cancer, systemic treatment options in addition to chemotherapy remain scarce, and so far only a small proportion of patients benefit from targeted therapies.
    OBJECTIVE: The patients with pancreatic cancer discussed in the CCCMunichLMU Molecular Tumor Board were reviewed to gain a better real-world understanding of the challenges and chances of precision oncology in this hard-to-treat cancer.
    METHODS: Patients with pancreatic cancer who received comprehensive genomic profiling and were discussed in the interdisciplinary Molecular Tumor Board between May 2017 and July 2022 were included. These patients' medical charts, comprehensive genomic profiling results, and Molecular Tumor Board recommendations were analyzed in this retrospective cohort study.
    RESULTS: Molecular profiles of 165 patients with pancreatic cancer were discussed in the Molecular Tumor Board. In the 149 cases where comprehensive genomic profiling was successful, KRAS mutations were detected in 87.9%, TP53 in 53.0%, and CDKN2A in 14.1%. 33.3% of KRAS wild-type patients harbored targetable mutations, while these were only found in 19.1% of patients with the KRAS mutation; however, this difference was not statistically significant. 63.8% of patients with successful testing received a targeted treatment recommendation by the Molecular Tumor Board; however, only 3.2% of these were put into practice. Compared to a historic cohort of patients with pancreatic cancer with synchronous metastatic disease diagnosed between 2010 and 2017, the patients from the pancreatic cancer cohort with synchronous metastatic disease had a longer survival.
    CONCLUSIONS: This single-center experience emphasizes the challenges of targeted treatment in pancreatic cancer. Very few patients ultimately received the recommended therapies, highlighting the need for more and better targeted treatment options in pancreatic cancer, early comprehensive genomic profiling to allow sufficient time to put Molecular Tumor Board recommendations into practice, and close cooperation with clinical trial units to give patients access to otherwise not available targeted treatments.
    DOI:  https://doi.org/10.1007/s11523-023-00950-0
  8. Cell Commun Signal. 2023 Mar 02. 21(1): 45
    Cancer immune evasion through KRAS and PD-L1 and potential therapeutic interventions.
    Alex Watterson, Matthew A Coelho.
      Oncogenic driver mutations have implications that extend beyond cancer cells themselves. Aberrant tumour cell signalling has various effects on the tumour microenvironment and anti-tumour immunity, with important consequences for therapy response and resistance. We provide an overview of how mutant RAS, one of the most prevalent oncogenic drivers in cancer, can instigate immune evasion programs at the tumour cell level and through remodelling interactions with the innate and adaptive immune cell compartments. Finally, we describe how immune evasion networks focused on RAS, and the immune checkpoint molecule PD-L1 can be disrupted through therapeutic intervention, and discuss potential strategies for combinatorial treatment. Video abstract.
    DOI:  https://doi.org/10.1186/s12964-023-01063-x
  9. iScience. 2023 Feb 17. 26(2): 106040
    Systematic diet composition swap in a mouse genome-scale metabolic model reveals determinants of obesogenic diet metabolism in liver cancer.
    Frederick Clasen, Patrícia M Nunes, Gholamreza Bidkhori, Nourdine Bah, Stefan Boeing, Saeed Shoaie, Dimitrios Anastasiou.
      Dietary nutrient availability and gene expression, together, influence tissue metabolic activity. Here, we explore whether altering dietary nutrient composition in the context of mouse liver cancer suffices to overcome chronic gene expression changes that arise from tumorigenesis and western-style diet (WD). We construct a mouse genome-scale metabolic model and estimate metabolic fluxes in liver tumors and non-tumoral tissue after computationally varying the composition of input diet. This approach, called Systematic Diet Composition Swap (SyDiCoS), revealed that, compared to a control diet, WD increases production of glycerol and succinate irrespective of specific tissue gene expression patterns. Conversely, differences in fatty acid utilization pathways between tumor and non-tumor liver are amplified with WD by both dietary carbohydrates and lipids together. Our data suggest that combined dietary component modifications may be required to normalize the distinctive metabolic patterns that underlie selective targeting of tumor metabolism.
    Keywords:  Biological sciences; Cancer; Cellular physiology; Physiology
    DOI:  https://doi.org/10.1016/j.isci.2023.106040
  10. Oncogene. 2023 Mar 02.
    Ras protein abundance correlates with Ras isoform mutation patterns in cancer.
    Fiona E Hood, Yasmina M Sahraoui, Rosalind E Jenkins, Ian A Prior.
      Activating mutations of Ras genes are often observed in cancer. The protein products of the three Ras genes are almost identical. However, for reasons that remain unclear, KRAS is far more frequently mutated than the other Ras isoforms in cancer and RASopathies. We have quantified HRAS, NRAS, KRAS4A and KRAS4B protein abundance across a large panel of cell lines and healthy tissues. We observe consistent patterns of KRAS > NRAS»HRAS protein expression in cells that correlate with the rank order of Ras mutation frequencies in cancer. Our data provide support for the model of a sweet-spot of Ras dosage mediating isoform-specific contributions to cancer and development. We suggest that in most cases, being the most abundant Ras isoform correlates with occupying the sweet-spot and that HRAS and NRAS expression is usually insufficient to promote oncogenesis when mutated. However, our results challenge the notion that rare codons mechanistically underpin the predominance of KRAS mutant cancers. Finally, direct measurement of mutant versus wildtype KRAS protein abundance revealed a frequent imbalance that may suggest additional non-gene duplication mechanisms for optimizing oncogenic Ras dosage.
    DOI:  https://doi.org/10.1038/s41388-023-02638-1
  11. Nature. 2023 Mar 01.
    Blebs promote cell survival by assembling oncogenic signalling hubs.
    Andrew D Weems, Erik S Welf, Meghan K Driscoll, Felix Y Zhou, Hanieh Mazloom-Farsibaf, Bo-Jui Chang, Vasanth S Murali, Gabriel M Gihana, Byron G Weiss, Joseph Chi, Divya Rajendran, Kevin M Dean, Reto Fiolka, Gaudenz Danuser.
      Most human cells require anchorage for survival. Cell-substrate adhesion activates diverse signalling pathways, without which cells undergo anoikis-a form of programmed cell death1. Acquisition of anoikis resistance is a pivotal step in cancer disease progression, as metastasizing cells often lose firm attachment to surrounding tissue2,3. In these poorly attached states, cells adopt rounded morphologies and form small hemispherical plasma membrane protrusions called blebs4-11. Bleb function has been thoroughly investigated in the context of amoeboid migration, but it has been examined far less in other scenarios12. Here we show by three-dimensional imaging and manipulation of cell morphological states that blebbing triggers the formation of plasma membrane-proximal signalling hubs that confer anoikis resistance. Specifically, in melanoma cells, blebbing generates plasma membrane contours that recruit curvature-sensing septin proteins as scaffolds for constitutively active mutant NRAS and effectors. These signalling hubs activate ERK and PI3K-well-established promoters of pro-survival pathways. Inhibition of blebs or septins has little effect on the survival of well-adhered cells, but in detached cells it causes NRAS mislocalization, reduced MAPK and PI3K activity, and ultimately, death. This unveils a morphological requirement for mutant NRAS to operate as an effective oncoprotein. Furthermore, whereas some BRAF-mutated melanoma cells do not rely on this survival pathway in a basal state, inhibition of BRAF and MEK strongly sensitizes them to both bleb and septin inhibition. Moreover, fibroblasts engineered to sustain blebbing acquire the same anoikis resistance as cancer cells even without harbouring oncogenic mutations. Thus, blebs are potent signalling organelles capable of integrating myriad cellular information flows into concerted cellular responses, in this case granting robust anoikis resistance.
    DOI:  https://doi.org/10.1038/s41586-023-05758-6
  12. Gastroenterology. 2023 Mar 01. pii: S0016-5085(23)00211-1. [Epub ahead of print]
    A Case of an Incidental Pancreatic Cyst.
    Elham Afghani, Aatur D Singhi, Anne Marie Lennon, Marco Del Chiaro.
      
    Keywords:  IPMN; Molecular marker; Pancreatic cancer; Pancreatic cyst
    DOI:  https://doi.org/10.1053/j.gastro.2023.02.026
  13. Biochim Biophys Acta Rev Cancer. 2023 Feb 24. pii: S0304-419X(23)00016-1. [Epub ahead of print] 188867
    Metastasis prevention: How to catch metastatic seeds.
    Tatiana S Gerashchenko, Anastasia A Schegoleva, Anna A Khozyainova, Evgeny L Choinzonov, Evgeny V Denisov.
      Despite considerable advances in the evolution of anticancer therapies, metastasis still remains the main cause of cancer mortality. Therefore, current strategies for cancer cure should be redirected towards prevention of metastasis. Targeting metastatic pathways represents a promising therapeutic opportunity aimed at obstructing tumor cell dissemination and metastatic colonization. In this review, we focus on preclinical studies and clinical trials over the last five years that showed high efficacy in suppressing metastasis through targeting lymph node dissemination, tumor cell extravasation, reactive oxygen species, pre-metastatic niche, exosome machinery, and dormancy.
    Keywords:  Anticancer therapy; Cancer; Dormancy; Exosome; Extravasation; Metastasis prevention; Pre-metastatic niche; Reactive oxygen species
    DOI:  https://doi.org/10.1016/j.bbcan.2023.188867
  14. Nat Methods. 2023 Mar 02.
    In silico tissue generation and power analysis for spatial omics.
    Ethan A G Baker, Denis Schapiro, Bianca Dumitrascu, Sanja Vickovic, Aviv Regev.
      As spatially resolved multiplex profiling of RNA and proteins becomes more prominent, it is increasingly important to understand the statistical power available to test specific hypotheses when designing and interpreting such experiments. Ideally, it would be possible to create an oracle that predicts sampling requirements for generalized spatial experiments. However, the unknown number of relevant spatial features and the complexity of spatial data analysis make this challenging. Here, we enumerate multiple parameters of interest that should be considered in the design of a properly powered spatial omics study. We introduce a method for tunable in silico tissue (IST) generation and use it with spatial profiling data sets to construct an exploratory computational framework for spatial power analysis. Finally, we demonstrate that our framework can be applied across diverse spatial data modalities and tissues of interest. While we demonstrate ISTs in the context of spatial power analysis, these simulated tissues have other potential use cases, including spatial method benchmarking and optimization.
    DOI:  https://doi.org/10.1038/s41592-023-01766-6
  15. Front Oncol. 2023 ;13 1125186
    Editorial: Single cell meets metabolism and cancer biology.
    Jieqiong Wang, Shibiao Wan.
      
    Keywords:  bioinformatics; cancer biology; computational biology; machine learning; metabolism; single cell analysis
    DOI:  https://doi.org/10.3389/fonc.2023.1125186
  16. Am J Surg. 2023 Feb 21. pii: S0002-9610(23)00063-6. [Epub ahead of print]
    High-volume centers are associated with higher receipt of combined therapy in stage III pancreatic cancer.
    Shay Behrens, Kristin Potter, Ranish K Patel, Issac R Schwantes, Thomas L Sutton, Alicia J Johnson, Rodney F Pommier, Brett C Sheppard.
       BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at a locally advanced stage with vascular involvement which was previously viewed as a contraindication to resection. However, high-volume centers are increasingly capable of resecting complex tumors. We aimed to explore patterns of treatment that are uncharacterized on a population level.
    METHODS: A statewide registry was queried from 2003 to 2018 for stage III PDAC. Stepwise logistic regression and Kaplan-Meier were used for statistical analysis.
    RESULTS: We identified 424 eligible patients. 348 (82%) received chemotherapy, 17 (4.0%) received resection, and 59 (13.9%) received both; median survival was 10.7, 8.7, and 22.7 months, respectively (P < 0.001). High-volume centers (≥20 cases per year; OR 5.40 [95% CI: 2.76, 10.58], P < 0.001) and later year of diagnosis (OR 1.12/year [95% CI: 1.04, 1.20], P = 0.004) were associated with higher odds of receiving combined therapy.
    CONCLUSION: PDAC patients with vascular involvement who receive both systemic chemotherapy and surgical resection have improved overall survival. High-volume centers are independently associated with higher odds of receiving combined systemic therapy and surgical resection.
    DOI:  https://doi.org/10.1016/j.amjsurg.2023.02.012
  17. J Cachexia Sarcopenia Muscle. 2023 Mar 01.
    Pilot clinical trial of macimorelin to assess safety and efficacy in patients with cancer cachexia.
    Megan Herodes, Lindsey J Anderson, Samuel Shober, Ellen A Schur, Solomon A Graf, Nicola Ammer, Ramiro Salas, Marco Marcelli, Jose M Garcia.
       BACKGROUND: Cancer cachexia is associated with reduced body weight, appetite and quality of life (QOL) with no approved treatments. Growth hormone secretagogues like macimorelin have potential to mitigate these effects.
    METHODS: This pilot study assessed the safety and efficacy of macimorelin for 1 week. Efficacy was defined a priori as 1-week change in body weight (≥0.8 kg), plasma insulin-like growth factor (IGF)-1 (≥50 ng/mL) or QOL (≥15%). Secondary outcomes included food intake, appetite, functional performance, energy expenditure and safety laboratory parameters. Patients with cancer cachexia were randomized to 0.5 or 1.0 mg/kg macimorelin or placebo; outcomes were assessed non-parametrically.
    RESULTS: Participants receiving at least one of either macimorelin dose were combined (N = 10; 100% male; median age = 65.50 ± 2.12) and compared with placebo (N = 5; 80% male; median age = 68.00 ± 6.19). Efficacy criteria achieved: body weight (macimorelin N = 2; placebo N = 0; P = 0.92); IGF-1 (macimorelin N = 0; placebo N = 0); QOL by Anderson Symptom Assessment Scale (macimorelin N = 4; placebo N = 1; P = 1.00) or Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-F; macimorelin N = 3; placebo N = 0; P = 0.50). No related serious or non-serious adverse events were reported. In macimorelin recipients, change in FACIT-F was directly associated with change in body weight (r = 0.92, P = 0.001), IGF-1 (r = 0.80, P = 0.01), and caloric intake (r = 0.83, P = 0.005), and inversely associated with change in energy expenditure (r = -0.67, P = 0.05).
    CONCLUSIONS: Daily oral macimorelin for 1 week was safe and numerically improved body weight and QOL in patients with cancer cachexia compared with placebo. Longer term administration should be evaluated for mitigation of cancer-induced reductions in body weight, appetite and QOL in larger studies.
    Keywords:  appetite; cancer cachexia; ghrelin receptor agonist; growth hormone secretagogue; macimorelin
    DOI:  https://doi.org/10.1002/jcsm.13191
  18. Cancer Res. 2023 Mar 02. pii: CAN-22-3000. [Epub ahead of print]
    Comprehensive Metabolic Tracing Reveals the Origin and Catabolism of Cysteine in Mammalian Tissues and Tumors.
    Sang Jun Yoon, Joseph A Combs, Aimee Falzone, Nicolas Prieto-Farigua, Samantha Caldwell, Hayley D Ackerman, Elsa R Flores, Gina M DeNicola.
      Cysteine plays critical roles in cellular biosynthesis, enzyme catalysis, and redox metabolism. The intracellular cysteine pool can be sustained by cystine uptake or de novo synthesis from serine and homocysteine. Demand for cysteine is increased during tumorigenesis for generating glutathione to deal with oxidative stress. While cultured cells have been shown to be highly dependent on exogenous cystine for proliferation and survival, how diverse tissues obtain and use cysteine in vivo has not been characterized. We comprehensively interrogated cysteine metabolism in normal murine tissues and cancers that arise from them using stable isotope 13C1-serine and 13C6-cystine tracing. De novo cysteine synthesis was highest in normal liver and pancreas and absent in lung tissue, while cysteine synthesis was either inactive or downregulated during tumorigenesis. By contrast, cystine uptake and metabolism to downstream metabolites was a universal feature of normal tissues and tumors. However, differences in glutathione labeling from cysteine were evident across tumor types. Thus, cystine is a major contributor to the cysteine pool in tumors, and glutathione metabolism is differentially active across tumor types.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-3000
  19. STAR Protoc. 2023 Jan 23. pii: S2666-1667(22)00751-1. [Epub ahead of print]4(1): 101871
    Quantification of autophagy flux in isolated mouse skeletal muscle fibers with overexpression of fluorescent protein mCherry-EGFP-LC3.
    Xinyu Zhou, Ju Hwan Cho, Jianxun Yi, Kyounghan Choi, Ki Ho Park, Hua Zhu, Chuanxi Cai, Erin Haggard, Jingsong Zhou, Jae-Kyun Ko, Jianjie Ma.
      Evaluation of autophagy flux could be challenging for muscle fibers due to the baseline expression of mCherry-EGFP-LC3 along the Z-line. We established a protocol to overcome this difficulty. We overexpress mChery-EGFP-LC3 in the FDB muscle of an adult mouse via electroporation. Then, we enzymatically digest FDB muscle to yield individual fibers for live cell imaging. Finally, we develop an ImageJ-based program to eliminate the baseline striation pattern and semi-automatically quantify autophagosomes (APs) and autolysosomes (ALs) for autophagy flux analysis.
    Keywords:  Cell Biology; Microscopy; Model Organisms
    DOI:  https://doi.org/10.1016/j.xpro.2022.101871
  20. STAR Protoc. 2023 Jan 25. pii: S2666-1667(23)00027-8. [Epub ahead of print]4(1): 102069
    ImmCellFie: A user-friendly web-based platform to infer metabolic function from omics data.
    Helen O Masson, David Borland, Jason Reilly, Adrian Telleria, Shalki Shrivastava, Matt Watson, Luthfi Bustillos, Zerong Li, Laura Capps, Benjamin P Kellman, Zachary A King, Anne Richelle, Nathan E Lewis, Kimberly Robasky.
      Understanding cellular metabolism is important across biotechnology and biomedical research and has critical implications in a broad range of normal and pathological conditions. Here, we introduce the user-friendly web-based platform ImmCellFie, which allows the comprehensive analysis of metabolic functions inferred from transcriptomic or proteomic data. We explain how to set up a run using publicly available omics data and how to visualize the results. The ImmCellFie algorithm pushes beyond conventional statistical enrichment and incorporates complex biological mechanisms to quantify cell activity. For complete details on the use and execution of this protocol, please refer to Richelle et al. (2021).1.
    Keywords:  Bioinformatics; Genomics; Metabolism; Systems Biology
    DOI:  https://doi.org/10.1016/j.xpro.2023.102069
  21. STAR Protoc. 2023 Feb 07. pii: S2666-1667(23)00064-3. [Epub ahead of print]4(1): 102106
    Protocol for quantitative evaluation of the impact of paracrine senescence on cellular reprogramming in cultured cells and mouse models.
    Jérémy Chantrel, Cheng Chen, Jun Zhang, Han Li.
      We present a protocol to evaluate the impact of senescence secretome on reprogramming to pluripotency using both cellular and mouse models. First, we describe the in vitro reprogramming procedure using conditioned medium derived from senescent cells. Next, to explore the impact of senescence on in vivo reprogramming, we detail the steps to identify senescent and reprogrammed cells in mouse skeletal muscle, followed by semi-automatic quantification. This protocol can be used to study the effect of paracrine senescence on cellular plasticity. For complete details on the use and execution of this protocol, please refer to von Joest et al. (2022).1.
    Keywords:  Cell Biology; Cell culture; Microscopy; Model Organisms; Stem Cells
    DOI:  https://doi.org/10.1016/j.xpro.2023.102106
  22. PLoS Biol. 2023 Feb;21(2): e3002002
    AlphaFold-multimer predicts ATG8 protein binding motifs crucial for autophagy research.
    Hallvard Lauritz Olsvik, Terje Johansen.
      In this issue of PLOS Biology, Ibrahim and colleagues demonstrate how AlphaFold-multimer, an artificial intelligence-based structure prediction tool, can be used to identify sequence motifs binding to the ATG8 family of proteins central to autophagy.
    DOI:  https://doi.org/10.1371/journal.pbio.3002002
  23. Nat Metab. 2023 Mar 02.
    Lysosomal control of senescence and inflammation through cholesterol partitioning.
    Kyeonghwan Roh, Jeonghwan Noh, Yeonju Kim, Yeji Jang, Jaejin Kim, Haebeen Choi, Yeonghyeon Lee, Moongi Ji, Donghyun Kang, Mi-Sung Kim, Man-Jeong Paik, Jongkyeong Chung, Jin-Hong Kim, Chanhee Kang.
      Whereas cholesterol is vital for cell growth, proliferation, and remodeling, dysregulation of cholesterol metabolism is associated with multiple age-related pathologies. Here we show that senescent cells accumulate cholesterol in lysosomes to maintain the senescence-associated secretory phenotype (SASP). We find that induction of cellular senescence by diverse triggers enhances cellular cholesterol metabolism. Senescence is associated with the upregulation of the cholesterol exporter ABCA1, which is rerouted to the lysosome, where it moonlights as a cholesterol importer. Lysosomal cholesterol accumulation results in the formation of cholesterol-rich microdomains on the lysosomal limiting membrane enriched with the mammalian target of rapamycin complex 1 (mTORC1) scaffolding complex, thereby sustaining mTORC1 activity to support the SASP. We further show that pharmacological modulation of lysosomal cholesterol partitioning alters senescence-associated inflammation and in vivo senescence during osteoarthritis progression in male mice. Our study reveals a potential unifying theme for the role of cholesterol in the aging process through the regulation of senescence-associated inflammation.
    DOI:  https://doi.org/10.1038/s42255-023-00747-5
  24. Nat Commun. 2023 Mar 02. 14(1): 1199
    MYTHO is a novel regulator of skeletal muscle autophagy and integrity.
    Jean-Philippe Leduc-Gaudet, Anais Franco-Romero, Marina Cefis, Alaa Moamer, Felipe E Broering, Giulia Milan, Roberta Sartori, Tomer Jordi Chaffer, Maude Dulac, Vincent Marcangeli, Dominique Mayaki, Laurent Huck, Anwar Shams, José A Morais, Elise Duchesne, Hanns Lochmuller, Marco Sandri, Sabah N A Hussain, Gilles Gouspillou.
      Autophagy is a critical process in the regulation of muscle mass, function and integrity. The molecular mechanisms regulating autophagy are complex and still partly understood. Here, we identify and characterize a novel FoxO-dependent gene, d230025d16rik which we named Mytho (Macroautophagy and YouTH Optimizer), as a regulator of autophagy and skeletal muscle integrity in vivo. Mytho is significantly up-regulated in various mouse models of skeletal muscle atrophy. Short term depletion of MYTHO in mice attenuates muscle atrophy caused by fasting, denervation, cancer cachexia and sepsis. While MYTHO overexpression is sufficient to trigger muscle atrophy, MYTHO knockdown results in a progressive increase in muscle mass associated with a sustained activation of the mTORC1 signaling pathway. Prolonged MYTHO knockdown is associated with severe myopathic features, including impaired autophagy, muscle weakness, myofiber degeneration, and extensive ultrastructural defects, such as accumulation of autophagic vacuoles and tubular aggregates. Inhibition of the mTORC1 signaling pathway in mice using rapamycin treatment attenuates the myopathic phenotype triggered by MYTHO knockdown. Skeletal muscles from human patients diagnosed with myotonic dystrophy type 1 (DM1) display reduced Mytho expression, activation of the mTORC1 signaling pathway and impaired autophagy, raising the possibility that low Mytho expression might contribute to the progression of the disease. We conclude that MYTHO is a key regulator of muscle autophagy and integrity.
    DOI:  https://doi.org/10.1038/s41467-023-36817-1
  25. STAR Protoc. 2023 Feb 09. pii: S2666-1667(23)00066-7. [Epub ahead of print]4(1): 102108
    Protocol to package and concentrate adeno-associated virus serotype 8 for use in autochthonous mouse models of pancreatic cancer.
    Meilian Zhuo, Jiangjiao Mao, Charles J David.
      We have developed an economical and rapid protocol to package and concentrate adeno-associated virus serotype 8, allowing production of high-titer virus for use in vivo within 1 week. When combined with the CRISPR-Cas9 system, this provides a straightforward method for knockout of genes of interest in the pancreas. The method can also be used to express cDNAs in the pancreas. This method shows great potential to accelerate pancreatic cancer research in autochthonous models. For complete details on the use and execution of this protocol, please refer to Li et al. (2021).1.
    Keywords:  CRISPR; Cancer; Cell Biology; Cell culture; Cell-based Assays; Flow Cytometry/Mass Cytometry; Gene Expression; Genetics; Molecular Biology
    DOI:  https://doi.org/10.1016/j.xpro.2023.102108
  26. STAR Protoc. 2023 Jan 29. pii: S2666-1667(23)00035-7. [Epub ahead of print]4(1): 102077
    Protocol to transfer epithelial acini between different extracellular matrices and orient fibril organization.
    Hiroko Katsuno-Kambe, James E Hudson, Holly K Voges, Alpha S Yap.
      Extracellular matrix (ECM) provides fundamental support for epithelial tissues and controls cell function. The chemistry and mechanical properties of ECM components, including stiffness, elasticity, and fibrillar organization, influence epithelial tissue responses. Here we present a protocol describing the culture and transfer of epithelial acini from Matrigel to collagen gel and an approach to axially align the collagen fibrils by the external gel stretching. This protocol uses the acini of MCF10A cells and needs to be modified for different cell lines. For complete details on the use and execution of this protocol, please refer to Katsuno-Kambe et al. (2021).1.
    Keywords:  Cancer; Cell Biology; Cell Culture
    DOI:  https://doi.org/10.1016/j.xpro.2023.102077
  27. Nat Rev Genet. 2023 Mar 02.
    Methods and applications for single-cell and spatial multi-omics.
    Katy Vandereyken, Alejandro Sifrim, Bernard Thienpont, Thierry Voet.
      The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome from single cells is transforming our understanding of cell biology in health and disease. In less than a decade, the field has seen tremendous technological revolutions that enable crucial new insights into the interplay between intracellular and intercellular molecular mechanisms that govern development, physiology and pathogenesis. In this Review, we highlight advances in the fast-developing field of single-cell and spatial multi-omics technologies (also known as multimodal omics approaches), and the computational strategies needed to integrate information across these molecular layers. We demonstrate their impact on fundamental cell biology and translational research, discuss current challenges and provide an outlook to the future.
    DOI:  https://doi.org/10.1038/s41576-023-00580-2
  28. Aging Cell. 2023 Feb 28. e13805
    Glycation-mediated tissue-level remodeling of brain meningeal membrane by aging.
    Hyo Min Kim, Shinheun Kim, Jueun Sim, Boo Soo Ma, Insung Yong, Youngmin Jo, Taek-Soo Kim, Jae-Byum Chang, Sung-Hye Park, Yong Jeong, Pilnam Kim.
      Collagen is a prominent target of nonenzymatic glycation, which is a hallmark of aging and causes functional alteration of the matrix. Here, we uncover glycation-mediated structural and functional changes in the collagen-enriched meningeal membrane of the human and mouse brain. Using an in vitro culture platform mimicking the meningeal membrane composed of fibrillar collagen, we showed that the accumulation of advanced glycation end products (AGEs) in the collagen membrane is responsible for glycation-mediated matrix remodeling. These changes influence fibroblast-matrix interactions, inducing cell-mediated ECM remodeling. The adherence of meningeal fibroblasts to the glycated collagen membrane was mediated by the discoidin domain-containing receptor 2 (DDR2), whereas integrin-mediated adhesion was inhibited. A-kinase anchoring protein 12 (AKAP12)-positive meningeal fibroblasts in the meningeal membrane of aged mice exhibited substantially increased expression of DDR2 and depletion of integrin beta-1 (ITGB1). In the glycated collagen membrane, meningeal fibroblasts increased the expression of matrix metalloproteinase 14 (MMP14) and less tissue inhibitor of metalloproteinase-1 (TIMP1). In contrast, the cells exhibited decreased expression of type I collagen (COL1A1). These results suggest that glycation modification by meningeal fibroblasts is intimately linked to aging-related structural and functional alterations in the meningeal membrane.
    Keywords:  brain meningeal membrane; discoidin domain-containing receptor 2; extracellular matrix remodeling; glycation; type-I collagen
    DOI:  https://doi.org/10.1111/acel.13805
  29. bioRxiv. 2023 Feb 25. pii: 2023.02.24.529970. [Epub ahead of print]
    Human APOBEC3B promotes tumor heterogeneity in vivo including signature mutations and metastases.
    Cameron Durfee, Nuri Alpay Temiz, Rena Levin-Klein, Prokopios P Argyris, Lene Als E, Sergio Carracedo, Alicia Alonso de la Vega, Joshua Proehl, Anna M Holzhauer, Zachary J Seeman, Yu-Hsiu T Lin, Rachel I Vogel, Rocio Sotillo, Hilde Nilsen, Reuben S Harris.
      The antiviral DNA cytosine deaminase APOBEC3B has been implicated as a source of mutation in many different cancers. Despite over 10 years of work, a causal relationship has yet to be established between APOBEC3B and any stage of carcinogenesis. Here we report a murine model that expresses tumor-like levels of human APOBEC3B after Cre-mediated recombination. Animals appear to develop normally with full-body expression of APOBEC3B. However, adult males manifest infertility and older animals of both sexes show accelerated rates of tumorigenesis (mostly lymphomas or hepatocellular carcinomas). Interestingly, primary tumors also show overt heterogeneity, and a subset spreads to secondary sites. Both primary and metastatic tumors exhibit increased frequencies of C-to-T mutations in TC dinucleotide motifs consistent with the established biochemical activity of APOBEC3B. Elevated levels of structural variation and insertion-deletion mutations also accumulate in these tumors. Together, these studies provide the first cause-and-effect demonstration that human APOBEC3B is an oncoprotein capable of causing a wide range of genetic changes and driving tumor formation in vivo .
    DOI:  https://doi.org/10.1101/2023.02.24.529970
  30. Nature. 2023 Mar 01.
    H3K4me3 regulates RNA polymerase II promoter-proximal pause-release.
    Hua Wang, Zheng Fan, Pavel V Shliaha, Matthew Miele, Ronald C Hendrickson, Xuejun Jiang, Kristian Helin.
      Trimethylation of histone H3 lysine 4 (H3K4me3) is associated with transcriptional start sites and has been proposed to regulate transcription initiation1,2. However, redundant functions of the H3K4 SET1/COMPASS methyltransferase complexes complicate the elucidation of the specific role of H3K4me3 in transcriptional regulation3,4. Here, using mouse embryonic stem cells as a model system, we show that acute ablation of shared subunits of the SET1/COMPASS complexes leads to a complete loss of all H3K4 methylation. Turnover of H3K4me3 occurs more rapidly than that of H3K4me1 and H3K4me2 and is dependent on KDM5 demethylases. Notably, acute loss of H3K4me3 does not have detectable effects on transcriptional initiation but leads to a widespread decrease in transcriptional output, an increase in RNA polymerase II (RNAPII) pausing and slower elongation. We show that H3K4me3 is required for the recruitment of the integrator complex subunit 11 (INTS11), which is essential for the eviction of paused RNAPII and transcriptional elongation. Thus, our study demonstrates a distinct role for H3K4me3 in transcriptional pause-release and elongation rather than transcriptional initiation.
    DOI:  https://doi.org/10.1038/s41586-023-05780-8
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