bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2023–05–14
twenty-one papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation.
  2. A prime editor mouse to model a broad spectrum of somatic mutations in vivo.
  3. EDA2R-NIK signalling promotes muscle atrophy linked to cancer cachexia.
  4. Pharmacologically targeting KRAS G12D in PDAC models: tumor cell intrinsic and extrinsic impact.
  5. Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis.
  6. Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer.
  7. Priming therapy by targeting enhancer-initiated pathways in patient-derived pancreatic cancer cells.
  8. Smaller panel, similar results: genomic profiling and molecularly informed therapy in pancreatic cancer.
  9. Lymph nodes: at the intersection of cancer treatment and progression.
  10. In situ architecture of the ER-mitochondria encounter structure.
  11. Genetic Evidence Causally Linking Pancreas Fat to Pancreatic Cancer: A Mendelian Randomization Study.
  12. Antagonizing the irreversible thrombomodulin-initiated proteolytic signaling alleviates age-related liver fibrosis via senescent cell killing.
  13. Human Mitoribosome Profiling: A Re-engineered Approach Tailored to Study Mitochondrial Translation.
  14. Structure and function of lipid droplet assembly complexes.
  15. The peritumor microenvironment: physics and immunity.
  16. Visualizing Protein Localizations in Fixed Cells: Caveats and the Underlying Mechanisms.
  17. Spatial resolution of cellular senescence dynamics in human colorectal liver metastasis.
  18. Upregulation of the ERRγ-VDAC1 axis underlies the molecular pathogenesis of pancreatitis.
  19. Pancreatitis points to key role of dendritic cells in pancreatic cancer.
  20. ATG16L1 is equipped with two distinct WIPI2-binding sites to drive autophagy.
  21. Riboformer: A Deep Learning Framework for Predicting Context-Dependent Translation Dynamics.
  1. Nat Commun. 2023 May 08. 14(1): 2642
    Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation.
    Jonathan J Swietlik, Stefanie Bärthel, Chiara Falcomatà, Diana Fink, Ankit Sinha, Jingyuan Cheng, Stefan Ebner, Peter Landgraf, Daniela C Dieterich, Henrik Daub, Dieter Saur, Felix Meissner.
      Cell-selective proteomics is a powerful emerging concept to study heterocellular processes in tissues. However, its high potential to identify non-cell-autonomous disease mechanisms and biomarkers has been hindered by low proteome coverage. Here, we address this limitation and devise a comprehensive azidonorleucine labeling, click chemistry enrichment, and mass spectrometry-based proteomics and secretomics strategy to dissect aberrant signals in pancreatic ductal adenocarcinoma (PDAC). Our in-depth co-culture and in vivo analyses cover more than 10,000 cancer cell-derived proteins and reveal systematic differences between molecular PDAC subtypes. Secreted proteins, such as chemokines and EMT-promoting matrisome proteins, associated with distinct macrophage polarization and tumor stromal composition, differentiate classical and mesenchymal PDAC. Intriguingly, more than 1,600 cancer cell-derived proteins including cytokines and pre-metastatic niche formation-associated factors in mouse serum reflect tumor activity in circulation. Our findings highlight how cell-selective proteomics can accelerate the discovery of diagnostic markers and therapeutic targets in cancer.
    DOI:  https://doi.org/10.1038/s41467-023-38171-8
  2. Nat Biotechnol. 2023 May 11.
    A prime editor mouse to model a broad spectrum of somatic mutations in vivo.
    Zackery A Ely, Nicolas Mathey-Andrews, Santiago Naranjo, Samuel I Gould, Kim L Mercer, Gregory A Newby, Christina M Cabana, William M Rideout, Grissel Cervantes Jaramillo, Jennifer M Khirallah, Katie Holland, Peyton B Randolph, William A Freed-Pastor, Jessie R Davis, Zachary Kulstad, Peter M K Westcott, Lin Lin, Andrew V Anzalone, Brendan L Horton, Nimisha B Pattada, Sean-Luc Shanahan, Zhongfeng Ye, Stefani Spranger, Qiaobing Xu, Francisco J Sánchez-Rivera, David R Liu, Tyler Jacks.
      Genetically engineered mouse models only capture a small fraction of the genetic lesions that drive human cancer. Current CRISPR-Cas9 models can expand this fraction but are limited by their reliance on error-prone DNA repair. Here we develop a system for in vivo prime editing by encoding a Cre-inducible prime editor in the mouse germline. This model allows rapid, precise engineering of a wide range of mutations in cell lines and organoids derived from primary tissues, including a clinically relevant Kras mutation associated with drug resistance and Trp53 hotspot mutations commonly observed in pancreatic cancer. With this system, we demonstrate somatic prime editing in vivo using lipid nanoparticles, and we model lung and pancreatic cancer through viral delivery of prime editing guide RNAs or orthotopic transplantation of prime-edited organoids. We believe that this approach will accelerate functional studies of cancer-associated mutations and complex genetic combinations that are challenging to construct with traditional models.
    DOI:  https://doi.org/10.1038/s41587-023-01783-y
  3. Nature. 2023 May 10.
    EDA2R-NIK signalling promotes muscle atrophy linked to cancer cachexia.
    Sevval Nur Bilgic, Aylin Domaniku, Batu Toledo, Samet Agca, Bahar Z C Weber, Dilsad H Arabaci, Zeynep Ozornek, Pascale Lause, Jean-Paul Thissen, Audrey Loumaye, Serkan Kir.
      Skeletal muscle atrophy is a hallmark of the cachexia syndrome that is associated with poor survival and reduced quality of life in patients with cancer1. Muscle atrophy involves excessive protein catabolism and loss of muscle mass and strength2. An effective therapy against muscle wasting is currently lacking because mechanisms driving the atrophy process remain incompletely understood. Our gene expression analysis in muscle tissues indicated upregulation of ectodysplasin A2 receptor (EDA2R) in tumour-bearing mice and patients with cachectic cancer. Here we show that activation of EDA2R signalling promotes skeletal muscle atrophy. Stimulation of primary myotubes with the EDA2R ligand EDA-A2 triggered pronounced cellular atrophy by induction of the expression of muscle atrophy-related genes Atrogin1 and MuRF1. EDA-A2-driven myotube atrophy involved activation of the non-canonical NFĸB pathway and was dependent on NFκB-inducing kinase (NIK) activity. Whereas EDA-A2 overexpression promoted muscle wasting in mice, deletion of either EDA2R or muscle NIK protected tumour-bearing mice from loss of muscle mass and function. Tumour-induced oncostatin M (OSM) upregulated muscle EDA2R expression, and muscle-specific oncostatin M receptor (OSMR)-knockout mice were resistant to tumour-induced muscle wasting. Our results demonstrate that EDA2R-NIK signalling mediates cancer-associated muscle atrophy in an OSM-OSMR-dependent manner. Thus, therapeutic targeting of these pathways may be beneficial in prevention of muscle loss.
    DOI:  https://doi.org/10.1038/s41586-023-06047-y
  4. bioRxiv. 2023 Apr 20. pii: 2023.03.18.533261. [Epub ahead of print]
    Pharmacologically targeting KRAS G12D in PDAC models: tumor cell intrinsic and extrinsic impact.
    Vishnu Kumarasamy, Costakis Frangou, Jianxin Wang, Yin Wan, Andrew Dynka, Hanna Rosenheck, Prasenjit Dey, Ethan V Abel, Erik S Knudsen, Agnieszka K Witkiewicz.
      Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease for which new therapeutic interventions are needed. Here we assessed the cellular response to pharmacological KRAS inhibition, which target the central oncogenic factor in PDAC. In a panel of PDAC cell lines, pharmaceutical inhibition of KRAS G12D allele, with MRTX1133 yields variable efficacy in the suppression of cell growth and downstream gene expression programs in 2D culture. CRISPR screens identify new drivers for enhanced therapeutic response that regulate focal adhesion and signaling cascades, which were confirmed by gene specific knockdowns and combinatorial drug synergy. Interestingly, MRTX1133 is considerably more efficacious in the context of 3D cell cultures and in vivo PDAC patient-derived xenografts. In syngeneic models, KRAS G12D inhibition elicits potent tumor regression that did not occur in immune-deficient hosts. Digital spatial profiling on tumor tissues indicates that MRTX1133 activates interferon-γ signaling and induces antigen presentation that modulate the tumor microenvironment. Further investigation on the immunological response using single cell sequencing and multispectral imaging reveals that tumor regression is associated with suppression of neutrophils and influx of effector CD8 + T-cells. Thus, both tumor cell intrinsic and extrinsic events contribute to response and credential KRAS G12D inhibition as promising strategy for a large percentage of PDAC tumors.
    DOI:  https://doi.org/10.1101/2023.03.18.533261
  5. Science. 2023 May 12. 380(6645): eadd5327
    Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis.
    Cassandra Burdziak, Direna Alonso-Curbelo, Thomas Walle, José Reyes, Francisco M Barriga, Doron Haviv, Yubin Xie, Zhen Zhao, Chujun Julia Zhao, Hsuan-An Chen, Ojasvi Chaudhary, Ignas Masilionis, Zi-Ning Choo, Vianne Gao, Wei Luan, Alexandra Wuest, Yu-Jui Ho, Yuhong Wei, Daniela F Quail, Richard Koche, Linas Mazutis, Ronan Chaligné, Tal Nawy, Scott W Lowe, Dana Pe'er.
      The response to tumor-initiating inflammatory and genetic insults can vary among morphologically indistinguishable cells, suggesting as yet uncharacterized roles for epigenetic plasticity during early neoplasia. To investigate the origins and impact of such plasticity, we performed single-cell analyses on normal, inflamed, premalignant, and malignant tissues in autochthonous models of pancreatic cancer. We reproducibly identified heterogeneous cell states that are primed for diverse, late-emerging neoplastic fates and linked these to chromatin remodeling at cell-cell communication loci. Using an inference approach, we revealed signaling gene modules and tissue-level cross-talk, including a neoplasia-driving feedback loop between discrete epithelial and immune cell populations that was functionally validated in mice. Our results uncover a neoplasia-specific tissue-remodeling program that may be exploited for pancreatic cancer interception.
    DOI:  https://doi.org/10.1126/science.add5327
  6. Nature. 2023 May 10.
    Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer.
    Luis A Rojas, Zachary Sethna, Kevin C Soares, Cristina Olcese, Nan Pang, Erin Patterson, Jayon Lihm, Nicholas Ceglia, Pablo Guasp, Alexander Chu, Rebecca Yu, Adrienne Kaya Chandra, Theresa Waters, Jennifer Ruan, Masataka Amisaki, Abderezak Zebboudj, Zagaa Odgerel, George Payne, Evelyna Derhovanessian, Felicitas Müller, Ina Rhee, Mahesh Yadav, Anton Dobrin, Michel Sadelain, Marta Łuksza, Noah Cohen, Laura Tang, Olca Basturk, Mithat Gönen, Seth Katz, Richard Kinh Do, Andrew S Epstein, Parisa Momtaz, Wungki Park, Ryan Sugarman, Anna M Varghese, Elizabeth Won, Avni Desai, Alice C Wei, Michael I D'Angelica, T Peter Kingham, Ira Mellman, Taha Merghoub, Jedd D Wolchok, Ugur Sahin, Özlem Türeci, Benjamin D Greenbaum, William R Jarnagin, Jeffrey Drebin, Eileen M O'Reilly, Vinod P Balachandran.
      Pancreatic ductal adenocarcinoma (PDAC) is lethal in 88% of patients1, yet harbours mutation-derived T cell neoantigens that are suitable for vaccines 2,3. Here in a phase I trial of adjuvant autogene cevumeran, an individualized neoantigen vaccine based on uridine mRNA-lipoplex nanoparticles, we synthesized mRNA neoantigen vaccines in real time from surgically resected PDAC tumours. After surgery, we sequentially administered atezolizumab (an anti-PD-L1 immunotherapy), autogene cevumeran (a maximum of 20 neoantigens per patient) and a modified version of a four-drug chemotherapy regimen (mFOLFIRINOX, comprising folinic acid, fluorouracil, irinotecan and oxaliplatin). The end points included vaccine-induced neoantigen-specific T cells by high-threshold assays, 18-month recurrence-free survival and oncologic feasibility. We treated 16 patients with atezolizumab and autogene cevumeran, then 15 patients with mFOLFIRINOX. Autogene cevumeran was administered within 3 days of benchmarked times, was tolerable and induced de novo high-magnitude neoantigen-specific T cells in 8 out of 16 patients, with half targeting more than one vaccine neoantigen. Using a new mathematical strategy to track T cell clones (CloneTrack) and functional assays, we found that vaccine-expanded T cells comprised up to 10% of all blood T cells, re-expanded with a vaccine booster and included long-lived polyfunctional neoantigen-specific effector CD8+ T cells. At 18-month median follow-up, patients with vaccine-expanded T cells (responders) had a longer median recurrence-free survival (not reached) compared with patients without vaccine-expanded T cells (non-responders; 13.4 months, P = 0.003). Differences in the immune fitness of the patients did not confound this correlation, as responders and non-responders mounted equivalent immunity to a concurrent unrelated mRNA vaccine against SARS-CoV-2. Thus, adjuvant atezolizumab, autogene cevumeran and mFOLFIRINOX induces substantial T cell activity that may correlate with delayed PDAC recurrence.
    DOI:  https://doi.org/10.1038/s41586-023-06063-y
  7. EBioMedicine. 2023 May 04. pii: S2352-3964(23)00167-6. [Epub ahead of print]92 104602
    Priming therapy by targeting enhancer-initiated pathways in patient-derived pancreatic cancer cells.
    Nicolas A Fraunhoffer, Aura I Moreno Vega, Analía Meilerman Abuelafia, Marie Morvan, Emilie Lebarbier, Tristan Mary-Huard, Michael Zimmermann, Gwen Lomberk, Raul Urrutia, Nelson Dusetti, Yuna Blum, Remy Nicolle, Juan Iovanna.
       BACKGROUND: Systems biology leveraging multi-OMICs technologies, is rapidly advancing development of precision therapies and matching patients to targeted therapies, leading to improved responses. A new pillar of precision oncology lies in the power of chemogenomics to discover drugs that sensitizes malignant cells to other therapies. Here, we test a chemogenomic approach using epigenomic inhibitors (epidrugs) to reset patterns of gene expression driving the malignant behavior of pancreatic tumors.
    METHODS: We tested a targeted library of ten epidrugs targeting regulators of enhancers and super-enhancers on reprogramming gene expression networks in seventeen patient-derived primary pancreatic cancer cell cultures (PDPCCs), of both basal and classical subtypes. We subsequently evaluated the ability of these epidrugs to sensitize pancreatic cancer cells to five chemotherapeutic drugs that are clinically used for this malignancy.
    FINDINGS: To comprehend the impact of epidrug priming at the molecular level, we evaluated the effect of each epidrugs at the transcriptomic level of PDPCCs. The activating epidrugs showed a higher number of upregulated genes than the repressive epidrugs (χ2 test p-value <0.01). Furthermore, we developed a classifier using the baseline transcriptome of epidrug-primed-chemosensitized PDPCCs to predict the best epidrug-priming regime to a given chemotherapy. Six signatures with a significant association with the chemosensitization centroid (R ≤ -0.80; p-value < 0.01) were identified and validated in a subset of PDPCCs.
    INTERPRETATION: We conclude that targeting enhancer-initiated pathways in patient-derived primary cells, represents a promising approach for developing new therapies for human pancreatic cancer.
    FUNDING: This work was supported by INCa (Grants number 2018-078 to ND and 2018- 079 to JI), Canceropole PACA (ND), Amidex Foundation (ND), and INSERM (JI).
    Keywords:  Epidrugs; PDAC; Priming chemotherapies; Transcriptome
    DOI:  https://doi.org/10.1016/j.ebiom.2023.104602
  8. ESMO Open. 2023 May 04. pii: S2059-7029(23)00765-2. [Epub ahead of print]8(3): 101539
    Smaller panel, similar results: genomic profiling and molecularly informed therapy in pancreatic cancer.
    T M Reissig, I Tzianopoulos, S-T Liffers, V K Rosery, M Guyot, S Ting, M Wiesweg, S Kasper, P Meister, T Herold, H H Schmidt, B Schumacher, D Albers, P Markus, J Treckmann, M Schuler, H-U Schildhaus, J T Siveke.
       BACKGROUND: Pancreatic cancer has a dismal prognosis. One reason is resistance to cytotoxic drugs. Molecularly matched therapies might overcome this resistance but the best approach to identify those patients who may benefit is unknown. Therefore, we sought to evaluate a molecularly guided treatment approach.
    MATERIALS AND METHODS: We retrospectively analyzed the clinical outcome and mutational status of patients with pancreatic cancer who received molecular profiling at the West German Cancer Center Essen from 2016 to 2021. We carried out a 47-gene DNA next-generation sequencing (NGS) panel. Furthermore, we assessed microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR) status and, sequentially and only in case of KRAS wild-type, gene fusions via RNA-based NGS. Patient data and treatment were retrieved from the electronic medical records.
    RESULTS: Of 190 included patients, 171 had pancreatic ductal adenocarcinoma (90%). One hundred and three patients had stage IV pancreatic cancer at diagnosis (54%). MMR analysis in 94 patients (94/190, 49.5%) identified 3 patients with dMMR (3/94, 3.2%). Notably, we identified 32 patients with KRAS wild-type status (16.8%). To identify driver alterations in these patients, we conducted an RNA-based fusion assay on 13 assessable samples and identified 5 potentially actionable fusions (5/13, 38.5%). Overall, we identified 34 patients with potentially actionable alterations (34/190, 17.9%). Of these 34 patients, 10 patients (10/34, 29.4%) finally received at least one molecularly targeted treatment and 4 patients had an exceptional response (>9 months on treatment).
    CONCLUSIONS: Here, we show that a small-sized gene panel can suffice to identify relevant therapeutic options for pancreatic cancer patients. Informally comparing with previous large-scale studies, this approach yields a similar detection rate of actionable targets. We propose molecular sequencing of pancreatic cancer as standard of care to identify KRAS wild-type and rare molecular subsets for targeted treatment strategies.
    Keywords:  Archer; KRAS wild-type; NGS; targeted sequencing; targeted therapy
    DOI:  https://doi.org/10.1016/j.esmoop.2023.101539
  9. Trends Cell Biol. 2023 May 04. pii: S0962-8924(23)00075-2. [Epub ahead of print]
    Lymph nodes: at the intersection of cancer treatment and progression.
    Nathan E Reticker-Flynn, Edgar G Engleman.
      Metastasis to lymph nodes (LNs) is a common feature of disease progression in most solid organ malignancies. Consequently, LN biopsy and lymphadenectomy are common clinical practices, not only because of their diagnostic utility but also as a means of deterring further metastatic spread. LN metastases have the potential to seed additional tissues and can induce metastatic tolerance, a process by which tumor-specific immune tolerance in LNs promotes further disease progression. Nonetheless, phylogenetic studies have revealed that distant metastases are not necessarily derived from nodal metastases. Furthermore, immunotherapy efficacy is increasingly being attributed to initiation of systemic immune responses within LNs. We argue that lymphadenectomy and nodal irradiation should be approached with caution, particularly in patients receiving immunotherapy.
    Keywords:  immune checkpoint blockade; immunotherapy; lymph nodes; lymphadenectomy; metastasis; tolerance
    DOI:  https://doi.org/10.1016/j.tcb.2023.04.001
  10. Nature. 2023 May 10.
    In situ architecture of the ER-mitochondria encounter structure.
    Michael R Wozny, Andrea Di Luca, Dustin R Morado, Andrea Picco, Rasha Khaddaj, Pablo Campomanes, Lazar Ivanović, Patrick C Hoffmann, Elizabeth A Miller, Stefano Vanni, Wanda Kukulski.
      The endoplasmic reticulum and mitochondria are main hubs of eukaryotic membrane biogenesis that rely on lipid exchange via membrane contact sites1-3, but the underpinning mechanisms remain poorly understood. In yeast, tethering and lipid transfer between the two organelles is mediated by the endoplasmic reticulum-mitochondria encounter structure (ERMES), a four-subunit complex of unresolved stoichiometry and architecture4-6. Here we determined the molecular organization of ERMES within Saccharomyces cerevisiae cells using integrative structural biology by combining quantitative live imaging, cryo-correlative microscopy, subtomogram averaging and molecular modelling. We found that ERMES assembles into approximately 25 discrete bridge-like complexes distributed irregularly across a contact site. Each bridge consists of three synaptotagmin-like mitochondrial lipid binding protein domains oriented in a zig-zag arrangement. Our molecular model of ERMES reveals a pathway for lipids. These findings resolve the in situ supramolecular architecture of a major inter-organelle lipid transfer machinery and provide a basis for the mechanistic understanding of lipid fluxes in eukaryotic cells.
    DOI:  https://doi.org/10.1038/s41586-023-06050-3
  11. medRxiv. 2023 Apr 26. pii: 2023.04.20.23288770. [Epub ahead of print]
    Genetic Evidence Causally Linking Pancreas Fat to Pancreatic Cancer: A Mendelian Randomization Study.
    Hajime Yamazaki, Samantha A Streicher, Lang Wu, Shunichi Fukuhara, Róbert Wagner, Martin Heni, Steven R Grossman, Heinz-Josef Lenz, Veronica Wendy Setiawan, Loic Le Marchand, Brian Z Huang.
       Background & Aims: Pancreatic ductal adenocarcinoma (PDAC) is highly lethal, and any clues to understanding its elusive etiology could lead to breakthroughs in prevention, early detection, or treatment. Observational studies have shown a relationship between pancreas fat accumulation and PDAC, but the causality of this link is unclear. We therefore investigated whether pancreas fat is causally associated with PDAC using two-sample Mendelian randomization.
    Methods: We leveraged eight genetic variants associated with pancreas fat (P<5×10 -8 ) from a genome-wide association study (GWAS) in the UK Biobank (25,617 individuals), and assessed their association with PDAC in the Pancreatic Cancer Cohort Consortium I-III and the Pancreatic Cancer Case-Control Consortium dataset (8,275 PDAC cases and 6,723 non-cases). Causality was assessed using the inverse-variance weighted method. Although none of these genetic variants were associated with body mass index (BMI) at genome-wide significance, we further conducted a sensitivity analysis excluding genetic variants with a nominal BMI association in GWAS summary statistics from the UK Biobank and the Genetic Investigation of Anthropometric Traits consortium dataset (806,834 individuals).
    Results: Genetically determined higher levels of pancreas fat using the eight genetic variants was associated with increased risk of PDAC. For one standard deviation increase in pancreas fat levels (i.e., 7.9% increase in pancreas fat fraction), the odds ratio of PDAC was 2.46 (95%CI:1.38-4.40, P=0.002). Similar results were obtained after excluding genetic variants nominally linked to BMI (odds ratio:3.79, 95%CI:1.66-8.65, P=0.002).
    Conclusions: This study provides genetic evidence for a causal role of pancreas fat in the pathogenesis of PDAC. Thus, reducing pancreas fat could lower the risk of PDAC.
    DOI:  https://doi.org/10.1101/2023.04.20.23288770
  12. Cell Res. 2023 May 11.
    Antagonizing the irreversible thrombomodulin-initiated proteolytic signaling alleviates age-related liver fibrosis via senescent cell killing.
    Christopher C Pan, Raquel Maeso-Díaz, Tylor R Lewis, Kun Xiang, Lianmei Tan, Yaosi Liang, Liuyang Wang, Fengrui Yang, Tao Yin, Calvin Wang, Kuo Du, De Huang, Seh Hoon Oh, Ergang Wang, Bryan Jian Wei Lim, Mengyang Chong, Peter B Alexander, Xuebiao Yao, Vadim Y Arshavsky, Qi-Jing Li, Anna Mae Diehl, Xiao-Fan Wang.
      Cellular senescence is a stress-induced, stable cell cycle arrest phenotype which generates a pro-inflammatory microenvironment, leading to chronic inflammation and age-associated diseases. Determining the fundamental molecular pathways driving senescence instead of apoptosis could enable the identification of senolytic agents to restore tissue homeostasis. Here, we identify thrombomodulin (THBD) signaling as a key molecular determinant of the senescent cell fate. Although normally restricted to endothelial cells, THBD is rapidly upregulated and maintained throughout all phases of the senescence program in aged mammalian tissues and in senescent cell models. Mechanistically, THBD activates a proteolytic feed-forward signaling pathway by stabilizing a multi-protein complex in early endosomes, thus forming a molecular basis for the irreversibility of the senescence program and ensuring senescent cell viability. Therapeutically, THBD signaling depletion or inhibition using vorapaxar, an FDA-approved drug, effectively ablates senescent cells and restores tissue homeostasis in liver fibrosis models. Collectively, these results uncover proteolytic THBD signaling as a conserved pro-survival pathway essential for senescent cell viability, thus providing a pharmacologically exploitable senolytic target for senescence-associated diseases.
    DOI:  https://doi.org/10.1038/s41422-023-00820-4
  13. Methods Mol Biol. 2023 ;2661 257-280
    Human Mitoribosome Profiling: A Re-engineered Approach Tailored to Study Mitochondrial Translation.
    Iliana Soto, Mary Couvillion, L Stirling Churchman.
      To understand the human mitochondrial translation process, tools are required to dissect this system at a global scale. The mechanisms and regulation of translation in mitochondria are different from those in the cytosol, and mitochondrial ribosomes have distinct biochemical properties. In this chapter, we describe in detail the modifications we have made to the ribosome profiling approach to adapt it to the unique characteristics of the human mitochondrial ribosome. This approach maximizes the fraction of mitochondrial ribosomes recovered, providing a snapshot of the mitochondrial translation landscape with minimal bias. We also describe the use of mouse lysate as an internal spike-in control for normalization, allowing quantification of global changes in translation across samples. Finally, we outline the bioinformatic pipelines to process the raw reads and identify mitoribosome A sites in the absence of untranslated regions flanking open reading frames. This method offers a subcodon-resolution time-sensitive global approach to explore the mitochondrial translation process in human cells.
    Keywords:  Human mitochondrial translation; Mitochondrial ribosome profiling
    DOI:  https://doi.org/10.1007/978-1-0716-3171-3_15
  14. Curr Opin Struct Biol. 2023 May 05. pii: S0959-440X(23)00080-5. [Epub ahead of print]80 102606
    Structure and function of lipid droplet assembly complexes.
    Tobias C Walther, Siyoung Kim, Henning Arlt, Gregory A Voth, Robert V Farese.
      Cells store lipids as a reservoir of metabolic energy and membrane component precursors in organelles called lipid droplets (LDs). LD formation occurs in the endoplasmic reticulum (ER) at LD assembly complexes (LDAC), consisting of an oligomeric core of seipin and accessory proteins. LDACs determine the sites of LD formation and are required for this process to occur normally. Seipin oligomers form a cage-like structure in the membrane that may serve to facilitate the phase transition of neutral lipids in the membrane to form an oil droplet within the LDAC. Modeling suggests that, as the LD grows, seipin anchors it to the ER bilayer and conformational shifts of seipin transmembrane segments open the LDAC dome toward the cytoplasm, enabling the emerging LD to egress from the ER.
    Keywords:  Endoplasmic reticulum; Lipid droplet; Phase separation; Phospholipids; Seipin; Sterol esters; Surface tension; Triacylglycerol
    DOI:  https://doi.org/10.1016/j.sbi.2023.102606
  15. Trends Cancer. 2023 May 06. pii: S2405-8033(23)00060-2. [Epub ahead of print]
    The peritumor microenvironment: physics and immunity.
    Sue Zhang, Kathryn Regan, Julian Najera, Mark W Grinstaff, Meenal Datta, Hadi T Nia.
      Cancer initiation and progression drastically alter the microenvironment at the interface between healthy and malignant tissue. This site, termed the peritumor, bears unique physical and immune attributes that together further promote tumor progression through interconnected mechanical signaling and immune activity. In this review, we describe the distinct physical features of the peritumoral microenvironment and link their relationship to immune responses. The peritumor is a region rich in biomarkers and therapeutic targets and thus is a key focus for future cancer research as well as clinical outlooks, particularly to understand and overcome novel mechanisms of immunotherapy resistance.
    Keywords:  immunotherapy; peritumor; physical immunity; physical oncology; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.trecan.2023.04.004
  16. J Phys Chem B. 2023 May 10.
    Visualizing Protein Localizations in Fixed Cells: Caveats and the Underlying Mechanisms.
    Shawn R Yoshida, Barun K Maity, Shasha Chong.
      Fluorescence microscopy techniques have been widely adopted in biology for their ability to visualize the structure and dynamics of a wide range of cellular and subcellular processes. The specificity and sensitivity that these techniques afford have made them primary tools in the characterization of protein localizations within cells. Many of the fluorescence microscopy techniques require cells to be fixed via chemical or alternative methods before being imaged. However, some fixation methods have been found to induce the redistribution of particular proteins in the cell, resulting in artifacts in the characterization of protein localizations and functions under physiological conditions. Here, we review the ability of commonly used cell fixation methods to faithfully preserve the localizations of proteins that bind to chromatin, undergo liquid-liquid phase separation (LLPS), and are involved in the formation of various membrane-bound organelles. We also review the mechanisms underlying various fixation artifacts and discuss potential alternative fixation methods to minimize the artifacts while investigating different proteins and cellular structures. Overall, fixed-cell fluorescence microscopy is a very powerful tool in biomedical research; however, each experiment demands the careful selection of an appropriate fixation method to avoid potential artifacts and may benefit from live-cell imaging validation.
    DOI:  https://doi.org/10.1021/acs.jpcb.3c01658
  17. Aging Cell. 2023 May 08. e13853
    Spatial resolution of cellular senescence dynamics in human colorectal liver metastasis.
    Ombretta Garbarino, Luca Lambroia, Gianluca Basso, Veronica Marrella, Barbara Franceschini, Cristiana Soldani, Fabio Pasqualini, Desiree Giuliano, Guido Costa, Clelia Peano, Davide Barbarossa, Destro Annarita, Andreina Salvati, Luigi Terracciano, Guido Torzilli, Matteo Donadon, Francesca Faggioli.
      Hepatic metastasis is a clinical challenge for colorectal cancer (CRC). Senescent cancer cells accumulate in CRC favoring tumor dissemination. Whether this mechanism progresses also in metastasis is unexplored. Here, we integrated spatial transcriptomics, 3D-microscopy, and multicellular transcriptomics to study the role of cellular senescence in human colorectal liver metastasis (CRLM). We discovered two distinct senescent metastatic cancer cell (SMCC) subtypes, transcriptionally located at the opposite pole of epithelial (e) to mesenchymal (m) transition. SMCCs differ in chemotherapy susceptibility, biological program, and prognostic roles. Mechanistically, epithelial (e)SMCC initiation relies on nucleolar stress, whereby c-myc dependent oncogene hyperactivation induces ribosomal RPL11 accumulation and DNA damage response. In a 2D pre-clinical model, we demonstrated that RPL11 co-localized with HDM2, a p53-specific ubiquitin ligase, leading to senescence activation in (e)SMCCs. On the contrary, mesenchymal (m)SMCCs undergo TGFβ paracrine activation of NOX4-p15 effectors. SMCCs display opposing effects also in the immune regulation of neighboring cells, establishing an immunosuppressive environment or leading to an active immune workflow. Both SMCC signatures are predictive biomarkers whose unbalanced ratio determined the clinical outcome in CRLM and CRC patients. Altogether, we provide a comprehensive new understanding of the role of SMCCs in CRLM and highlight their potential as new therapeutic targets to limit CRLM progression.
    Keywords:  EMT; cellular senescence; colorectal cancer liver metastasis; prognostic role; senescence-associated secretory phenotype; spatial transcriptomics
    DOI:  https://doi.org/10.1111/acel.13853
  18. Proc Natl Acad Sci U S A. 2023 05 16. 120(20): e2219644120
    Upregulation of the ERRγ-VDAC1 axis underlies the molecular pathogenesis of pancreatitis.
    Dipanjan Chanda, Themis Thoudam, Ibotombi Singh Sinam, Chae Won Lim, Myeongjin Kim, Jiale Wang, Kyeong-Min Lee, Jing Ma, Romil Saxena, Jinhyuk Choi, Chang Joo Oh, Hoyul Lee, Yong Hyun Jeon, Sung Jin Cho, Hoe-Yune Jung, Keun-Gyu Park, Hueng-Sik Choi, Jae Myoung Suh, Johan Auwerx, Baoan Ji, Suthat Liangpunsakul, Jae-Han Jeon, In-Kyu Lee.
      Emerging evidence suggest that transcription factors play multiple roles in the development of pancreatitis, a necroinflammatory condition lacking specific therapy. Estrogen-related receptor γ (ERRγ), a pleiotropic transcription factor, has been reported to play a vital role in pancreatic acinar cell (PAC) homeostasis. However, the role of ERRγ in PAC dysfunction remains hitherto unknown. Here, we demonstrated in both mice models and human cohorts that pancreatitis is associated with an increase in ERRγ gene expression via activation of STAT3. Acinar-specific ERRγ haploinsufficiency or pharmacological inhibition of ERRγ significantly impaired the progression of pancreatitis both in vitro and in vivo. Using systematic transcriptomic analysis, we identified that voltage-dependent anion channel 1 (VDAC1) acts as a molecular mediator of ERRγ. Mechanistically, we showed that induction of ERRγ in cultured acinar cells and mouse pancreata enhanced VDAC1 expression by directly binding to specific site of the Vdac1 gene promoter and resulted in VDAC1 oligomerization. Notably, VDAC1, whose expression and oligomerization were dependent on ERRγ, modulates mitochondrial Ca2+ and ROS levels. Inhibition of the ERRγ-VDAC1 axis could alleviate mitochondrial Ca2+ accumulation, ROS formation and inhibit progression of pancreatitis. Using two different mouse models of pancreatitis, we showed that pharmacological blockade of ERRγ-VDAC1 pathway has therapeutic benefits in mitigating progression of pancreatitis. Likewise, using PRSS1R122H-Tg mice to mimic human hereditary pancreatitis, we demonstrated that ERRγ inhibitor also alleviated pancreatitis. Our findings highlight the importance of ERRγ in pancreatitis progression and suggests its therapeutic intervention for prevention and treatment of pancreatitis.
    Keywords:  ERRγ; VDAC1; mitochondrial Ca2+; nuclear receptor; pancreatitis
    DOI:  https://doi.org/10.1073/pnas.2219644120
  19. Nat Rev Immunol. 2023 May 09.
    Pancreatitis points to key role of dendritic cells in pancreatic cancer.
    Lucas Baldran-Groves, Jeroen Melief.
      
    DOI:  https://doi.org/10.1038/s41577-023-00885-7
  20. Autophagy. 2023 May 10.
    ATG16L1 is equipped with two distinct WIPI2-binding sites to drive autophagy.
    Xinyu Gong, Lifeng Pan.
      The recruitment of ATG12-ATG5-ATG16L1 complex to phagophore mediated by the specific interaction between ATG16L1 and WIPI2, is pivotal to the formation of autophagosomes during macroautophagy. Recently, we reported that ATG16L1 contains two distinct WIPI2-binding sites, the previously reported WIPI2-binding site (WBS1), and the newly identified site (WBS2). By determining the crystal structures of WIPI2 with ATG16L1 WBS1 and WBS2 respectively, we uncovered that, unlike ATG16L1 WBS1, ATG16L1 WBS2 and its binding mechanism to WIPI2 are conserved from yeast to mammals. Using cell-based functional assays, we further demonstrated that the integrity of two WIPI2-binding sites of ATG16L1 is essential for normal autophagic flux. In summary, our study provided mechanistic insights into the interaction of two key autophagic proteins, ATG16L1 and WIPI2, and revealed a dual-binding-site mode adopted by ATG16L1 to associate with WIPI2.
    Keywords:  ATG16L1; Macroautophagy; WIPI2; autophagosome
    DOI:  https://doi.org/10.1080/15548627.2023.2213038
  21. bioRxiv. 2023 Apr 28. pii: 2023.04.24.538053. [Epub ahead of print]
    Riboformer: A Deep Learning Framework for Predicting Context-Dependent Translation Dynamics.
    Bin Shao, Jiawei Yan, Jing Zhang, Allen R Buskirk.
      Translation elongation is essential for maintaining cellular proteostasis, and alterations in the translational landscape are associated with a range of diseases. Ribosome profiling allows detailed measurement of translation at genome scale. However, it remains unclear how to disentangle biological variations from technical artifacts and identify sequence determinant of translation dysregulation. Here we present Riboformer, a deep learning-based framework for modeling context-dependent changes in translation dynamics. Riboformer leverages the transformer architecture to accurately predict ribosome densities at codon resolution. It corrects experimental artifacts in previously unseen datasets, reveals subtle differences in synonymous codon translation and uncovers a bottleneck in protein synthesis. Further, we show that Riboformer can be combined with in silico mutagenesis analysis to identify sequence motifs that contribute to ribosome stalling across various biological contexts, including aging and viral infection. Our tool offers a context-aware and interpretable approach for standardizing ribosome profiling datasets and elucidating the regulatory basis of translation kinetics.
    DOI:  https://doi.org/10.1101/2023.04.24.538053
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