bims-cagime 2024-09-29 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2024–09–29
29 papers selected by
Kıvanç Görgülü, Technical University of Munich

Polymorphisms within autophagy-related genes as susceptibility biomarkers for pancreatic cancer: A meta-analysis of three large European cohorts and functional characterization.
Genetic variation drives cancer cell adaptation to ECM stiffness.
Membrane remodeling via ubiquitin-mediated pathways.
GRP75 triggers white adipose tissue browning to promote cancer-associated cachexia.
Vitessce: integrative visualization of multimodal and spatially resolved single-cell data.
Post-Transcriptional Regulation of Rab7a in Lysosomal Positioning and Drug Resistance in Nutrient-Limited Cancer Cells.
Metabolic landscape of the healthy pancreas and pancreatic tumor microenvironment.
Membrane potential: A new hallmark of cancer.
Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution.
Were the autophagosome-lysosome/vacuole fusion models illustrated correctly in the literature?
Time-resolved proximity proteomics uncovers a membrane tension-sensitive caveolin-1 interactome at the rear of migrating cells.
Neural control of tumor immunity.
Controlling the sound of light: photoswitching optoacoustic imaging.
A single particle analysis method for detecting membrane remodelling and curvature sensing.
Development of transcriptomic tools for predicting the response to individual drug of the mFOLFIRINOX regimen in patients with metastatic pancreatic cancer.
Protocol for a non-surgical model of perineural invasion for assessing neural drivers of cancer aggressiveness in mice.
Muscle aging and sarcopenia: The pathology, etiology, and most promising therapeutic targets.
Transferrin receptor targeting chimeras for membrane protein degradation.
EyaHOST, a modular genetic system for investigation of intercellular and tumor-host interactions in Drosophila melanogaster.
Quality control of mitochondria involves lysosomes in multiple definitive ways.
Surface tension-driven sorting of human perilipins on lipid droplets.
The exchange dynamics of biomolecular condensates.
Total loss of VHL gene function impairs neuroendocrine cancer cell fitness due to excessive HIF2α activity.
A Fluorescence Lifetime-Based Novel Method for Accurate Lipid Quantification of BODIPY Vital-Stained C. elegans.
Protocol to monitor live-cell, real-time, mitochondrial respiration in mouse muscle cells using the Resipher platform.
Paracrine FGF1 signaling directs pituitary architecture and size.
Systemic Therapy for Metastatic Pancreatic Cancer-Current Landscape and Future Directions.
Established and emerging players in phospholipid scrambling: a structural perspective.
Ligand discovery by activity-based protein profiling.

Int J Cancer. 2024 Sep 25.

Polymorphisms within autophagy-related genes as susceptibility biomarkers for pancreatic cancer: A meta-analysis of three large European cohorts and functional characterization.

Fernando Gálvez-Montosa, Giulia Peduzzi, José Manuel Sanchez-Maldonado, Rob Ter Horst, Antonio J Cabrera-Serrano, Manuel Gentiluomo, Angelica Macauda, Natalia Luque, Pelin Ünal, Francisco Javier García-Verdejo, Yang Li, José Antonio López López, Angelika Stein, H Bas Bueno-de-Mesquita, Paolo Giorgio Arcidiacono, Dalila Luciola Zanette, Christoph Kahlert, Francesco Perri, Pavel Soucek, Renata Talar-Wojnarowska, George E Theodoropoulos, Jakob R Izbicki, Hussein Tamás, Hanneke Van Laarhoven, Gennaro Nappo, Maria Chiara Petrone, Martin Lovecek, Roel C H Vermeulen, Kestutis Adamonis, Fernando Jesus Reyes-Zurita, Bernd Holleczek, Jolanta Sumskiene, Beatrice Mohelníková-Duchoňová, Rita T Lawlor, Raffaele Pezzilli, Mateus Nobrega Aoki, Claudio Pasquali, Vitalija Petrenkiene, Daniela Basso, Stefania Bunduc, Annalisa Comandatore, Hermann Brenner, Stefano Ermini, Giuseppe Vanella, Mara R Goetz, Livia Archibugi, Maurizio Lucchesi, Faik Guntac Uzunoglu, Olivier Busch, Anna Caterina Milanetto, Marta Puzzono, Juozas Kupcinskas, Luca Morelli, Cosimo Sperti, Silvia Carrara, Gabriele Capurso, Casper H J van Eijck, Martin Oliverius, Susanne Roth, Francesca Tavano, Rudolf Kaaks, Andrea Szentesi, Ludmila Vodickova, Claudio Luchini, Ben Schöttker, Stefano Landi, Orsolya Dohan, Matteo Tacelli, William Greenhalf, Maria Gazouli, John P Neoptolemos, Giulia Martina Cavestro, Ugo Boggi, Anna Latiano, Péter Hegyi, Laura Ginocchi, Mihai G Netea, Pedro Sánchez-Rovira, Federico Canzian, Daniele Campa, Juan Sainz.

  Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers with patients having unresectable or metastatic disease at diagnosis, with poor prognosis and very short survival. Given that genetic variation within autophagy-related genes influences autophagic flux and susceptibility to solid cancers, we decided to investigate whether 55,583 single nucleotide polymorphisms (SNPs) within 234 autophagy-related genes could influence the risk of developing PDAC in three large independent cohorts of European ancestry including 12,754 PDAC cases and 324,926 controls. The meta-analysis of these populations identified, for the first time, the association of the BIDrs9604789 variant with an increased risk of developing the disease (ORMeta = 1.31, p = 9.67 × 10-6). We also confirmed the association of TP63rs1515496 and TP63rs35389543 variants with PDAC risk (OR = 0.89, p = 6.27 × 10-8 and OR = 1.16, p = 2.74 × 10-5). Although it is known that BID induces autophagy and TP63 promotes cell growth, cell motility and invasion, we also found that carriers of the TP63rs1515496G allele had increased numbers of FOXP3+ Helios+ T regulatory cells and CD45RA+ T regulatory cells (p = 7.67 × 10-4 and p = 1.56 × 10-3), but also decreased levels of CD4+ T regulatory cells (p = 7.86 × 10-4). These results were in agreement with research suggesting that the TP63rs1515496 variant alters binding sites for FOXA1 and CTCF, which are transcription factors involved in modulating specific subsets of regulatory T cells. In conclusion, this study identifies BID as new susceptibility locus for PDAC and confirms previous studies suggesting that the TP63 gene is involved in the development of PDAC. This study also suggests new pathogenic mechanisms of the TP63 locus in PDAC.

Keywords:  autophagy; functional characterization; genetic variants; pancreatic cancer; polymorphisms; susceptibility

DOI:  https://doi.org/10.1002/ijc.35196
Proc Natl Acad Sci U S A. 2024 Sep 24. 121(39): e2403062121

Genetic variation drives cancer cell adaptation to ECM stiffness.

Ting-Ching Wang, Suchitaa Sawhney, Daylin Morgan, Richard L Bennett, Richa Rashmi, Marcos R Estecio, Amy Brock, Irtisha Singh, Charles F Baer, Jonathan D Licht, Tanmay P Lele.

  The progression of many solid tumors is accompanied by temporal and spatial changes in the stiffness of the extracellular matrix (ECM). Cancer cells adapt to soft and stiff ECM through mechanisms that are not fully understood. It is well known that there is significant genetic heterogeneity from cell to cell in tumors, but how ECM stiffness as a parameter might interact with that genetic variation is not known. Here, we employed experimental evolution to study the response of genetically variable and clonal populations of tumor cells to variable ECM stiffness. Proliferation rates of genetically variable populations cultured on soft ECM increased over a period of several weeks, whereas clonal populations did not evolve. Tracking of DNA barcoded cell lineages revealed that soft ECM consistently selected for the same few variants. These data provide evidence that ECM stiffness exerts natural selection on genetically variable tumor populations. Soft-selected cells were highly migratory, with enriched oncogenic signatures and unusual behaviors such as spreading and traction force generation on ECMs with stiffness as low as 1 kPa. Rho-regulated cell spreading was found to be the directly selected trait, with yes-associated protein 1 translocation to the nucleus mediating fitness on soft ECM. Overall, these data show that genetic variation can drive cancer cell adaptation to ECM stiffness.

Keywords:  ECM stiffness; cancer; mechanoadaptation; mechanobiology

DOI:  https://doi.org/10.1073/pnas.2403062121
Cell Chem Biol. 2024 Sep 19. pii: S2451-9456(24)00356-8. [Epub ahead of print]31(9): 1627-1635

Membrane remodeling via ubiquitin-mediated pathways.

Anne-Claire Jacomin, Ivan Dikic.

  The dynamic process of membrane shaping and remodeling plays a vital role in cellular functions, with proteins and cellular membranes interacting intricately to adapt to various cellular needs and environmental cues. Ubiquitination-a posttranslational modification-was shown to be essential in regulating membrane structure and shape. It influences virtually all pathways relying on cellular membranes, such as endocytosis and autophagy by directing protein degradation, sorting, and oligomerization. Ubiquitin is mostly known as a protein modifier; however, it was reported that ubiquitin and ubiquitin-like proteins can associate directly with lipids, affecting membrane curvature and dynamics. In this review, we summarize some of the current knowledge on ubiquitin-mediated membrane remodeling in the context of endocytosis, autophagy, and ER-phagy.

Keywords:  ER remodeling; ER-phagy; ESCRT; autophagy; membrane remodeling; ubiquitin

DOI:  https://doi.org/10.1016/j.chembiol.2024.08.007
Signal Transduct Target Ther. 2024 Sep 26. 9(1): 253

GRP75 triggers white adipose tissue browning to promote cancer-associated cachexia.

Xu Chen, Qingnan Wu, Wei Gong, Shaolong Ju, Jiawen Fan, Xiaohan Gao, Xingyang Liu, Xiao Lei, Siqi Liu, Xiangdong Ming, Qianyu Wang, Ming Fu, Yongmei Song, Yan Wang, Qimin Zhan.

Cachexia, which affects 50-80% of cancer patients, is a debilitating syndrome that leads to 20% of cancer-related deaths. A key feature of cachexia is adipose tissue atrophy, but how it contributes to the development of cachexia is poorly understood. Here, we demonstrate in mouse models of cancer cachexia that white adipose tissue browning, which can be a characteristic early-onset manifestation, occurs prior to the loss of body weight and skeletal muscle wasting. By analysing the proteins differentially expressed in extracellular vesicles derived from cachexia-inducing tumours, we identified a molecular chaperone, Glucose-regulated protein 75 (GRP75), as a critical mediator of adipocyte browning. Mechanistically, GRP75 binds adenine nucleotide translocase 2 (ANT2) to form a GRP75-ANT2 complex. Strikingly, stabilized ANT2 enhances its interaction with uncoupling protein 1, leading to elevated expression of the latter, which, in turn, promotes adipocyte browning. Treatment with withanone, a GRP75 inhibitor, can reverse this browning and alleviate cachectic phenotypes in vivo. Overall, our findings reveal a novel mechanism by which tumour-derived GRP75 regulates white adipose tissue browning during cachexia development and suggest a potential white adipose tissue-centred targeting approach for early cachexia intervention.

DOI: https://doi.org/10.1038/s41392-024-01950-w
Nat Methods. 2024 Sep 27.

Vitessce: integrative visualization of multimodal and spatially resolved single-cell data.

Mark S Keller, Ilan Gold, Chuck McCallum, Trevor Manz, Peter V Kharchenko, Nils Gehlenborg.

Multiomics technologies with single-cell and spatial resolution make it possible to measure thousands of features across millions of cells. However, visual analysis of high-dimensional transcriptomic, proteomic, genome-mapped and imaging data types simultaneously remains a challenge. Here we describe Vitessce, an interactive web-based visualization framework for exploration of multimodal and spatially resolved single-cell data. We demonstrate integrative visualization of millions of data points, including cell-type annotations, gene expression quantities, spatially resolved transcripts and cell segmentations, across multiple coordinated views. The open-source software is available at http://vitessce.io .

DOI: https://doi.org/10.1038/s41592-024-02436-x
Traffic. 2024 Sep;25(9): e12956

Post-Transcriptional Regulation of Rab7a in Lysosomal Positioning and Drug Resistance in Nutrient-Limited Cancer Cells.

Aliye Ezgi Güleç Taşkıran, Hepşen H Hüsnügil, Zahra E Soltani, Göksu Oral, Nazlı S Menemenli, Chuanpit Hampel, Kerstin Huebner, Katharina Erlenbach-Wuensch, Ilir Sheraj, Regine Schneider-Stock, Aytekin Akyol, Nalan Liv, Sreeparna Banerjee.

  Limited nutrient availability in the tumor microenvironment can cause the rewiring of signaling and metabolic networks to confer cancer cells with survival advantages. We show here that the limitation of glucose, glutamine and serum from the culture medium resulted in the survival of a population of cancer cells with high viability and capacity to form tumors in vivo. These cells also displayed a remarkable increase in the abundance and size of lysosomes. Moreover, lysosomes were located mainly in the perinuclear region in nutrient-limited cells; this translocation was mediated by a rapid post-transcriptional increase in the key endolysosomal trafficking protein Rab7a. The acidic lysosomes in nutrient-limited cells could trap weakly basic drugs such as doxorubicin, mediating resistance of the cells to the drug, which could be partially reversed with the lysosomal inhibitor bafilomycin A1. An in vivo chorioallantoic membrane (CAM) assay indicated a remarkable decrease in microtumor volume when nutrient-limited cells were treated with 5-Fluorouracil (5-FU) and bafilomycin A1 compared to cells treated with either agent alone. Overall, our data indicate the activation of complementary pathways with nutrient limitation that can enable cancer cells to survive, proliferate and acquire drug resistance.

Keywords:  Rab7a; chemoresponse; drug trapping; lysosome; nutrient limitation

DOI:  https://doi.org/10.1111/tra.12956
JCI Insight. 2024 Aug 13. pii: e180114. [Epub ahead of print]9(18):

Metabolic landscape of the healthy pancreas and pancreatic tumor microenvironment.

Monica E Bonilla, Megan D Radyk, Matthew D Perricone, Ahmed M Elhossiny, Alexis C Harold, Paola I Medina-Cabrera, Padma Kadiyala, Jiaqi Shi, Timothy L Frankel, Eileen S Carpenter, Michael D Green, Cristina Mitrea, Costas A Lyssiotis, Marina Pasca di Magliano.

  Pancreatic cancer, one of the deadliest human malignancies, is characterized by a fibro-inflammatory tumor microenvironment and wide array of metabolic alterations. To comprehensively map metabolism in a cell type-specific manner, we harnessed a unique single-cell RNA-sequencing dataset of normal human pancreata. This was compared with human pancreatic cancer samples using a computational pipeline optimized for this study. In the cancer cells we observed enhanced biosynthetic programs. We identified downregulation of mitochondrial programs in several immune populations, relative to their normal counterparts in healthy pancreas. Although granulocytes, B cells, and CD8+ T cells all downregulated oxidative phosphorylation, the mechanisms by which this occurred were cell type specific. In fact, the expression pattern of the electron transport chain complexes was sufficient to identify immune cell types without the use of lineage markers. We also observed changes in tumor-associated macrophage (TAM) lipid metabolism, with increased expression of enzymes mediating unsaturated fatty acid synthesis and upregulation in cholesterol export. Concurrently, cancer cells exhibited upregulation of lipid/cholesterol receptor import. We thus identified a potential crosstalk whereby TAMs provide cholesterol to cancer cells. We suggest that this may be a new mechanism boosting cancer cell growth and a therapeutic target in the future.

Keywords:  Bioinformatics; Cancer; Macrophages; Oncology

DOI:  https://doi.org/10.1172/jci.insight.180114
Adv Cancer Res. 2024 ;pii: S0065-230X(24)00010-1. [Epub ahead of print]164 93-110

Membrane potential: A new hallmark of cancer.

Davide Delisi, Najmeh Eskandari, Saverio Gentile.

  Cancer remains a complex and multifaceted disease, characterized by a myriad of molecular and cellular alterations that collectively drive tumorigenesis and progression. Hanahan and Weinberg's concept of cancer hallmarks has offered a framework for comprehending the various but related aspects of cancer biology. Initially defined as a set of six hallmarks, further investigation has added more characteristics to this list that also contribute to the malignant phenotype. Changes in cellular energetics, proliferative signaling, and resistance to cell death are three of these hallmarks that have been thoroughly investigated and described. But new discoveries in the field of cancer biology have brought attention to the importance of another aspect of the biology of cancer: the dysregulation of membrane potential.

Keywords:  Hallmarks of cancer; Ion channel; Membrane potential

DOI:  https://doi.org/10.1016/bs.acr.2024.04.010
Nat Genet. 2024 Sep 24.

Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution.

Joshua S Schiffman, Andrew R D'Avino, Tamara Prieto, Yakun Pang, Yilin Fan, Srinivas Rajagopalan, Catherine Potenski, Toshiro Hara, Mario L Suvà, Charles Gawad, Dan A Landau.

Single-cell sequencing has characterized cell state heterogeneity across diverse healthy and malignant tissues. However, the plasticity or heritability of these cell states remains largely unknown. To address this, we introduce PATH (phylogenetic analysis of trait heritability), a framework to quantify cell state heritability versus plasticity and infer cell state transition and proliferation dynamics from single-cell lineage tracing data. Applying PATH to a mouse model of pancreatic cancer, we observed heritability at the ends of the epithelial-to-mesenchymal transition spectrum, with higher plasticity at more intermediate states. In primary glioblastoma, we identified bidirectional transitions between stem- and mesenchymal-like cells, which use the astrocyte-like state as an intermediary. Finally, we reconstructed a phylogeny from single-cell whole-genome sequencing in B cell acute lymphoblastic leukemia and delineated the heritability of B cell differentiation states linked with genetic drivers. Altogether, PATH replaces qualitative conceptions of plasticity with quantitative measures, offering a framework to study somatic evolution.

DOI: https://doi.org/10.1038/s41588-024-01920-6
Autophagy. 2024 Sep 24.

Were the autophagosome-lysosome/vacuole fusion models illustrated correctly in the literature?

Yongheng Liang.

  Exploration of autophagy in different species has become a hotspot in cell biology in the past decades. Macroautophagy (hereafter, autophagy) is the most widely studied type. One of the hallmarks of autophagy is the fusion of the outer membrane (OM) of a closed double-membrane mature autophagosome (AP) with the lysosomal/vacuolar single membrane. Most researchers in the autophagy field agree upon this description. However, AP-lysosome/vacuole fusion models that do not follow this description frequently appear in the literature, even published in some prestigious journals until now. Some of the misrepresented models are from autophagy laboratories with brilliant publication records. These flaws should be addressed as a public announcement in the autophagy field to avoid spreading misinformation. The editors and reviewers are the guardians to ensure correct models.

Keywords:  Autophagosome-lysosome/vacuole fusion; double membrane; inner membrane; lysosomal/vacuolar membrane; outer membrane; single membrane

DOI:  https://doi.org/10.1080/15548627.2024.2405954
Elife. 2024 Sep 24. pii: e85601. [Epub ahead of print]13

Time-resolved proximity proteomics uncovers a membrane tension-sensitive caveolin-1 interactome at the rear of migrating cells.

Eleanor Martin, Rossana Girardello, Gunnar Dittmar, Alexander Ludwig.

  Caveolae are small membrane pits with fundamental roles in mechanotransduction. Several studies have shown that caveolae flatten out in response to an increase in membrane tension, thereby acting as a mechanosensitive membrane reservoir that buffers acute mechanical stress. The dynamic assembly and disassembly of caveolae has also been implicated in the control of RhoA/ROCK-mediated actomyosin contractility at the rear of migrating cells. However, how membrane tension controls the organisation of caveolae and caveolae-mediated mechanotransduction is poorly understood. To address this, we systematically quantified protein-protein interactions of caveolin-1 in migrating RPE1 cells at steady state and in response to an acute increase in membrane tension using biotin-based proximity labelling and quantitative mass spectrometry. Our data show that caveolae are highly enriched at the rear of migrating RPE1 cells and that membrane tension rapidly and reversibly disassembles the caveolar protein coat. Membrane tension also dislodges caveolin-1 from focal adhesion proteins and several mechanosensitive cortical actin regulators including filamins and cortactin. In addition, we present evidence that ROCK and the RhoGAP ARHGAP29 are associated with caveolin-1 in a membrane tension-dependent manner, and that ARHGAP29 regulates caveolin-1 Y14 phosphorylation, caveolae rear localisation, and RPE1 cell migration. Taken together, our work uncovers a membrane tension-sensitive coupling between caveolae and the rear-localised F-actin cytoskeleton. This provides a framework for dissecting the molecular mechanisms underlying caveolae-regulated mechanotransduction pathways.

Keywords:  cell biology; human

DOI:  https://doi.org/10.7554/eLife.85601
FEBS J. 2024 Sep 20.

Neural control of tumor immunity.

Burak Kizil, Francesco De Virgiliis, Christoph Scheiermann.

  Communication between the nervous system and the immune system has evolved to optimally respond to potentially dangerous stimuli both from within and outside the body. Tumors pose a severe threat to an organism and current therapies are insufficient for tumor regression in the majority of cases. Studies show that tumors are innervated by peripheral nerves from the sensory, parasympathetic and sympathetic nervous systems. Interactions between cancer cells, nerves and immune cells regulate overall tumor progression. Clinical studies have indicated the potential of targeting the peripheral nervous system for promoting anti-tumor immune responses. This view point provides an opinion on the current evidence and therapeutic potential of manipulating neuro-immune communications in cancer.

Keywords:  cancer; cancer neuroimmunology; immune system; nervous system; neuroimmunology; tumor immunology

DOI:  https://doi.org/10.1111/febs.17280
Nat Methods. 2024 Sep 25.

Controlling the sound of light: photoswitching optoacoustic imaging.

Andre C Stiel, Vasilis Ntziachristos.

Optoacoustic (photoacoustic) imaging advances allow high-resolution optical imaging much deeper than optical microscopy. However, while label-free optoacoustics have already entered clinical application, biological imaging is in need of ubiquitous optoacoustic labels for use in ways that are similar to how fluorescent proteins propelled optical microscopy. We review photoswitching advances that shine a new light or, in analogy, 'bring a new sound' to biological optoacoustic imaging. Based on engineered labels and novel devices, switching uses light or other energy forms and enables signal modulation and synchronous detection for maximizing contrast and detection sensitivity over other optoacoustic labels. Herein, we explain contrast enhancement in the spectral versus temporal domains and review labels and key concepts of switching and their properties to modulate optoacoustic signals. We further outline systems and applications and discuss how switching can enable optoacoustic imaging of cellular or molecular contrast at depths and resolutions beyond those of other optical methods.

DOI: https://doi.org/10.1038/s41592-024-02396-2
J Cell Sci. 2024 Sep 26. pii: jcs.263533. [Epub ahead of print]

A single particle analysis method for detecting membrane remodelling and curvature sensing.

Adeline Colussi, Leonardo Almeida-Souza, Harvey T McMahon.

  In biology, shape and function are related. Therefore, it is important to understand how membrane shape is generated, stabilised and sensed by proteins and how this relates to organelle function. Here we present an assay that can detect curvature preference and membrane remodelling using free-floating liposomes using protein concentrations in a physiologically relevant ranges. The assay reproduced known curvature preferences of BAR domains and allowed the discovery of high curvature preference for the PH domain of AKT and the FYVE domain of HRS. In addition, our method reproduced the membrane vesiculation activity of the ENTH domain of Epsin1 and showed similar activity for the ANTH domains of PiCALM and Hip1R. Finally, we found that the curvature sensitivity of the N-BAR domain of Endophilin inversely correlates to membrane charge and that deletion of its N-terminal amphipathic helix increased its curvature specificity. Thus, our method is a generally applicable qualitative method for assessing membrane curvature sensing and remodelling by proteins.

Keywords:  Endophilin; Membrane curvature preference; Membrane remodeling; Single particle analysis

DOI:  https://doi.org/10.1242/jcs.263533
Front Oncol. 2024 ;14 1437200

Development of transcriptomic tools for predicting the response to individual drug of the mFOLFIRINOX regimen in patients with metastatic pancreatic cancer.

Nicolas Fraunhoffer, Carlos Teyssedou, Patrick Pessaux, Martin Bigonnet, Nelson Dusetti, Juan Iovanna.

   Background: The utilization of modified FOLFIRINOX (mFFX) therapy has shown notable advancements in patient outcomes in both localized and metastatic PDAC. Nevertheless, the effectiveness of mFFX treatment comes at the cost of elevated toxicity, leading to its restriction to patients with adequate performance status. Consequently, the administration of mFFX is contingent upon patient performance rather than rational criteria. The ideal scenario would involve the ability to assess the sensitivity of each drug within the mFFX regimen, minimizing unnecessary toxicity without compromising clinical benefits.
Methods: We developed transcriptomic signatures for each drug of the mFFX regimen (5FU, oxaliplatin and irinotecan) by integrating transcriptomic data from PDC, PDO and PDX with their corresponding chemo-response profiles to capture the biological components responsible for the response to each drug. We further validated the signatures in a cohort of 167 patients with advanced and metastatic PDAC.
Results: All three signatures captured high responder patients for OS and PFS in the mFFX arm exclusively. We then studied the response of patients to 0, 1, 2 and 3 drugs and we identified a positive correlation between the number of drugs predicted as sensitive and the OS and PFS, and the with objective response rate.
Conclusions: We developed three novel transcriptome-based signatures which define sensitivity for each mFFX components that can be used to rationalize the administration of the mFFX regimen in patients with metastatic pancreatic cancer and could help to avoid unnecessary toxic effects.

Keywords:  FOLFIRINOX; RNA signatures; chemosensitivity prediction; metastatic cancer; pancreatic cancer; precision medicine

DOI:  https://doi.org/10.3389/fonc.2024.1437200
STAR Protoc. 2024 Sep 26. pii: S2666-1667(24)00510-0. [Epub ahead of print]5(4): 103345

Protocol for a non-surgical model of perineural invasion for assessing neural drivers of cancer aggressiveness in mice.

Tiago H Zaninelli, Telma Saraiva-Santos, Brielle H Patlin, Michael Slade Stratton, David Y Chen, Felipe A Pinho-Ribeiro.

  Perineural invasion (PNI) is a significant risk factor for cancer recurrence and metastasis; however, its mechanisms relating to cancer aggressiveness remain poorly understood. Here, we present a protocol for a non-surgical model of PNI in mice using a neurotropic melanoma cell line that migrates from the skin to the sciatic nerve. We describe the steps for cell culture and injection, tumor burden measurements, mouse euthanasia, and tissue dissection. We then detail procedures for sample cross-section and confocal imaging.

Keywords:  Cancer; Model Organisms; Neuroscience

DOI:  https://doi.org/10.1016/j.xpro.2024.103345
Mol Aspects Med. 2024 Sep 22. pii: S0098-2997(24)00078-5. [Epub ahead of print]100 101319

Muscle aging and sarcopenia: The pathology, etiology, and most promising therapeutic targets.

Mercedes Grima-Terrén, Silvia Campanario, Ignacio Ramírez-Pardo, Andrés Cisneros, Xiaotong Hong, Eusebio Perdiguero, Antonio L Serrano, Joan Isern, Pura Muñoz-Cánoves.

  Sarcopenia is a progressive muscle wasting disorder that severely impacts the quality of life of elderly individuals. Although the natural aging process primarily causes sarcopenia, it can develop in response to other conditions. Because muscle function is influenced by numerous changes that occur with age, the etiology of sarcopenia remains unclear. However, recent characterizations of the aging muscle transcriptional landscape, signaling pathway disruptions, fiber and extracellular matrix compositions, systemic metabolomic and inflammatory responses, mitochondrial function, and neurological inputs offer insights and hope for future treatments. This review will discuss age-related changes in healthy muscle and our current understanding of how this can deteriorate into sarcopenia. As our elderly population continues to grow, we must understand sarcopenia and find treatments that allow individuals to maintain independence and dignity throughout an extended lifespan.

Keywords:  Aging; Atrophy; Proteostasis; Sarcopenia; Skeletal muscle

DOI:  https://doi.org/10.1016/j.mam.2024.101319
Nature. 2024 Sep 25.

Transferrin receptor targeting chimeras for membrane protein degradation.

Dingpeng Zhang, Jhoely Duque-Jimenez, Francesco Facchinetti, Garyk Brixi, Kaitlin Rhee, William W Feng, Pasi A Jänne, Xin Zhou.

Cancer cells require high levels of iron for rapid proliferation, leading to significant upregulation of cell-surface transferrin receptor 1 (TfR1), which mediates iron uptake by binding to the iron-carrying protein transferrin1-3. Leveraging this phenomenon and the fast endocytosis rate of TfR1 (refs. 4,5), we developed transferrin receptor targeting chimeras (TransTACs), a heterobispecific antibody modality for membrane protein degradation. TransTACs are engineered to drive rapid co-internalization of a target protein of interest and TfR1 from the cell surface, and to enable target protein entry into the lysosomal degradation pathway. We show that TransTACs can efficiently degrade a diverse range of single-pass, multi-pass, native or synthetic membrane proteins, including epidermal growth factor receptor, programmed cell death 1 ligand 1, cluster of differentiation 20 and chimeric antigen receptor. In example applications, TransTACs enabled the reversible control of human primary chimeric antigen receptor T cells and the targeting of drug-resistant epidermal growth factor receptor-driven lung cancer with the exon 19 deletion/T790M/C797S mutations in a mouse xenograft model. TransTACs represent a promising new family of bifunctional antibodies for precise manipulation of membrane proteins and targeted cancer therapy.

DOI: https://doi.org/10.1038/s41586-024-07947-3
bioRxiv. 2024 Sep 11. pii: 2024.09.06.611647. [Epub ahead of print]

EyaHOST, a modular genetic system for investigation of intercellular and tumor-host interactions in Drosophila melanogaster.

José Teles-Reis, Ashish Jain, Dan Liu, Rojyar Khezri, Sofia Micheli, Alicia Alfonso Gomez, Caroline Dillard, Tor Erik Rusten.

Cell biology and genetic analysis of intracellular, intercellular and inter-organ interaction studies in animal models are key for understanding development, physiology, and disease. The MARCM technique can emulate tumor development by simultaneous clonal tumor suppressor loss-of-function generation coupled with GAL4-UAS-driven oncogene and marker expression, but the utility is limited for studying tumor-host interactions due to genetic constraints. To overcome this, we introduce EyaHOST, a novel system that replaces MARCM with the QF2-QUAS binary gene expression system under the eya promoter control, unleashing the fly community genome-wide GAL4-UAS driven tools to manipulate any host cells or tissue at scale. EyaHOST generates epithelial clones in the eye epithelium similar to MARCM. EyaHOST-driven Ras V12 oncogene overexpression coupled with scribble tumor suppressor knockdown recapitulates key cancer features, including systemic catabolic switching and organ wasting. We demonstrate effective tissue-specific manipulation of host compartments such as neighbouring epithelial cells, immune cells, fat body, and muscle using fly avatars with tissue-specific GAL4 drivers. Organ-specific inhibition of autophagy or stimulation of growth-signaling through PTEN knockdown in fat body or muscle prevents cachexia-like wasting. Additionally, we show that Ras V12 , scrib RNAi tumors induce caspase-driven apoptosis in the epithelial microenvironment. Inhibition of apoptosis by p35 expression in the microenvironment promotes tumor growth. EyaHOST offers a versatile modular platform for dissecting tumor-host interactions and other mechanisms involving intercellular and inter-organ communication in Drosophila .
Highlights: * eyes absent , eye disc-specific enhancer drives clonal KD recombinase flip-out activated QF2 expression in the larval eye epithelium for simultaneous QUAS-driven gain and loss-of-function analysis of gene function. *Clones are visualized by QUAS-tagBFP or QUAS-eGFP facilitating analysis of existing fluorescent reporters.*The GAL4-UAS system and existing genome-wide genetic tools are released to independently manipulate any cell population in the animal for cell biology, intercellular or inter-organ analysis for developmental, physiological, or disease model analysis.*Fly avatars for tumor-host interaction studies with multiple organs allow live monitoring and manipulation of tumors and organs in translucent larva.

DOI: https://doi.org/10.1101/2024.09.06.611647
Autophagy. 2024 Sep 26.

Quality control of mitochondria involves lysosomes in multiple definitive ways.

Xiaowen Ma, Wen-Xing Ding.

  Mitochondria are crucial organelles in maintaining cellular homeostasis. They are involved in processes such as energy production, metabolism of lipids and glucose, and cell death regulation. Mitochondrial dysfunction can lead to various health issues such as aging, cancer, neurodegenerative diseases, and chronic liver diseases. While mitophagy is the main process for getting rid of excess or damaged mitochondria, there are additional mechanisms for preserving mitochondrial quality. One such alternative mechanism we have discovered is a hybrid organelle called mitochondrial-lysosome-related-organelle (MLRO), which functions independently of the typical autophagy process. More recently, another type of vesicle called vesicle derived from the inner mitochondrial membrane (VDIM) has been identified to break down the inner mitochondrial membrane without involving the standard autophagy pathway. In this article, we will delve into the similarities and differences between MLRO and VDIM, including their structure, regulation, and relevance to human diseases.

Keywords:  Autophagy; DNM1L/DRP1; MLRO; VDIM; mitophagy

DOI:  https://doi.org/10.1080/15548627.2024.2408712
J Cell Biol. 2024 Dec 02. pii: e202403064. [Epub ahead of print]223(12):

Surface tension-driven sorting of human perilipins on lipid droplets.

Ana Rita Dias Araújo, Abdoul Akim Bello, Joëlle Bigay, Céline Franckhauser, Romain Gautier, Julie Cazareth, Dávid Kovács, Frédéric Brau, Nicolas Fuggetta, Alenka Čopič, Bruno Antonny.

Perilipins (PLINs), the most abundant proteins on lipid droplets (LDs), display similar domain organization including amphipathic helices (AH). However, the five human PLINs bind different LDs, suggesting different modes of interaction. We established a minimal system whereby artificial LDs covered with defined polar lipids were transiently deformed to promote surface tension. Binding of purified PLIN3 and PLIN4 AH was strongly facilitated by tension but was poorly sensitive to phospholipid composition and to the presence of diacylglycerol. Accordingly, LD coverage by PLIN3 increased as phospholipid coverage decreased. In contrast, PLIN1 bound readily to LDs fully covered by phospholipids; PLIN2 showed an intermediate behavior between PLIN1 and PLIN3. In human adipocytes, PLIN3/4 were found in a soluble pool and relocated to LDs upon stimulation of fast triglyceride synthesis, whereas PLIN1 and PLIN2 localized to pre-existing LDs, consistent with the large difference in LD avidity observed in vitro. We conclude that the PLIN repertoire is adapted to handling LDs with different surface properties.

DOI: https://doi.org/10.1083/jcb.202403064
Elife. 2024 Sep 25. pii: RP91680. [Epub ahead of print]12

The exchange dynamics of biomolecular condensates.

Yaojun Zhang, Andrew G T Pyo, Ross Kliegman, Yoyo Jiang, Clifford P Brangwynne, Howard A Stone, Ned S Wingreen.

  A hallmark of biomolecular condensates formed via liquid-liquid phase separation is that they dynamically exchange material with their surroundings, and this process can be crucial to condensate function. Intuitively, the rate of exchange can be limited by the flux from the dilute phase or by the mixing speed in the dense phase. Surprisingly, a recent experiment suggests that exchange can also be limited by the dynamics at the droplet interface, implying the existence of an 'interface resistance'. Here, we first derive an analytical expression for the timescale of condensate material exchange, which clearly conveys the physical factors controlling exchange dynamics. We then utilize sticker-spacer polymer models to show that interface resistance can arise when incident molecules transiently touch the interface without entering the dense phase, i.e., the molecules 'bounce' from the interface. Our work provides insight into condensate exchange dynamics, with implications for both natural and synthetic systems.

Keywords:  biomolecular condensates; exchange dynamics; interface resistance; none; physics of living systems

DOI:  https://doi.org/10.7554/eLife.91680
Proc Natl Acad Sci U S A. 2024 Oct;121(40): e2410356121

Total loss of VHL gene function impairs neuroendocrine cancer cell fitness due to excessive HIF2α activity.

Muhannad Abu-Remaileh, Nicole S Persky, Yenarae Lee, David E Root, William G Kaelin.

  Loss-of-function germline von Hippel-Lindau (VHL) tumor suppressor mutations cause VHL disease, which predisposes individuals to kidney cancer, hemangioblastomas, and paragangliomas. The risk that a given VHL disease family will manifest some or all these tumor types is profoundly influenced by the VHL allele it carries. For example, almost all VHL disease families that develop paraganglioma have missense VHL mutations. VHL families with null VHL alleles develop kidney cancer and hemangioblastomas without a high risk of paraganglioma. The latter is surprising because the VHL gene product, pVHL, suppresses the HIF2 transcription factor and gain-of-function HIF2 mutations are also linked to paraganglioma. Paragangliomas arise from the sympathetic or parasympathetic nervous system. Given the lack of human paraganglioma cell lines, we studied the effects of inactivating VHL in neuroblastoma cell lines, which also arise from the sympathetic nervous system. We found that total loss of pVHL function profoundly impairs the fitness of neuroblastoma cell lines in a HIF2-dependent manner both ex vivo and in vivo. This fitness defect can be rescued by pVHL variants linked to paraganglioma, but not by pVHL variants associated with a low risk of paraganglioma. These findings suggest that HIF2 activity above a critical threshold prevents the development of paraganglioma.

Keywords:  hypoxia; neuroblastoma; paraganglioma; pheochromocytoma; von Hippel–Lindau

DOI:  https://doi.org/10.1073/pnas.2410356121
J Lipid Res. 2024 Sep 18. pii: S0022-2275(24)00151-2. [Epub ahead of print] 100646

A Fluorescence Lifetime-Based Novel Method for Accurate Lipid Quantification of BODIPY Vital-Stained C. elegans.

Chen Xu, Jintao Luo, Yong Yu.

  Lipid droplets (LDs) are organelles associated with lipid storage and energy metabolism, thus their morphology and quantity are of significant research interest. While commercially available BODIPY dye effectively labels LDs in various cell types, it also labels lysosome-related organelles (LROs) in C. elegans, leading to non-specific LD quantification. Here, we report that the fluorescent signals of BODIPY exhibit distinct fluorescence lifetime patterns for LROs and LDs, which can be captured, visualized, and filtered by fluorescence lifetime imaging microscopy. Furthermore, we proposed and validated a method based on fluorescence lifetime that can improve the accuracy of fat storage quantification in BODIPY vital-staining worms, which holds broad applications, including rapid and accurate LD quantification in forward genetic screening. Additionally, our method enables observing dynamic LD-LRO interactions in living worms, a unique capability of BODIPY vital-staining. Our findings highlight distinct BODIPY fluorescence lifetime characteristics of LDs and LROs, providing a valuable tool for future research on LDs, LROs, or their interactions.

Keywords:  BODIPY; C. elegans; Fat quantification; Fatty acid/Transport; Fluorescence lifetime; Fluorescence microscopy; Lipid droplets; Lipids; Lysosome-related organelles; Triglycerides

DOI:  https://doi.org/10.1016/j.jlr.2024.100646
STAR Protoc. 2024 Sep 20. pii: S2666-1667(24)00495-7. [Epub ahead of print]5(4): 103330

Protocol to monitor live-cell, real-time, mitochondrial respiration in mouse muscle cells using the Resipher platform.

Matthew Triolo, Mireille Khacho.

  Mitochondrial function is typically assessed by measuring oxygen consumption at a given time point. However, this approach cannot monitor respiratory changes that occur over time. Here, we present a protocol to measure mitochondrial respiration in freshly isolated muscle stem cells, primary skeletal muscle, and immortalized C2C12 myoblasts in real time using the Resipher platform. We describe steps for preparing and plating cells, performing media changes, setting up the software and device, and analyzing data. This method can be adapted to other cell types. For complete details on the use and execution of this protocol, please refer to Triolo et al.1.

Keywords:  Cell Biology; Metabolism; Stem Cells

DOI:  https://doi.org/10.1016/j.xpro.2024.103330
Proc Natl Acad Sci U S A. 2024 Oct;121(40): e2410269121

Paracrine FGF1 signaling directs pituitary architecture and size.

Konstantin Khetchoumian, Kevin Sochodolsky, Chrystel Lafont, Arthur Gouhier, Amandine Bemmo, Yacine Kherdjemil, Marie Kmita, Paul Le Tissier, Patrice Mollard, Helen Christian, Jacques Drouin.

  Organ architecture is established during development through intricate cell-cell communication mechanisms, yet the specific signals mediating these communications often remain elusive. Here, we used the anterior pituitary gland that harbors different interdigitated hormone-secreting homotypic cell networks to dissect cell-cell communication mechanisms operating during late development. We show that blocking differentiation of corticotrope cells leads to pituitary hypoplasia with a major effect on somatotrope cells that directly contact corticotropes. Gene knockout of the corticotrope-restricted transcription factor Tpit results in fewer somatotropes, with less secretory granules and a loss of cell polarity, resulting in systemic growth retardation. Single-cell transcriptomic analyses identified FGF1 as a corticotrope-specific Tpit dosage-dependent target gene responsible for these phenotypes. Consistently, genetic ablation of FGF1 in mice phenocopies pituitary hypoplasia and growth impairment observed in Tpit-deficient mice. These findings reveal FGF1 produced by the corticotrope cell network as an essential paracrine signaling molecule participating in pituitary architecture and size.

Keywords:  FGF1; GH deficit; cell networks; cell–cell interactions; organogenesis

DOI:  https://doi.org/10.1073/pnas.2410269121
Curr Oncol. 2024 Sep 04. 31(9): 5206-5223

Systemic Therapy for Metastatic Pancreatic Cancer-Current Landscape and Future Directions.

Daniel Netto, Melissa Frizziero, Victoria Foy, Mairéad G McNamara, Alison Backen, Richard A Hubner.

  Pancreatic ductal adenocarcinoma (PDAC) is a significant cause of cancer-associated mortality, with a rising global incidence. A paucity of strong predictive risk factors mean screening programmes are difficult to implement. Historically, a lack of identifiable and actionable driver mutations, coupled with a relatively immunosuppressed tumour microenvironment, has led to a reliance on cytotoxic chemotherapy. The NAPOLI-3 trial has reported data supporting consideration of NALIRIFOX as a new first-line standard of care. Kirsten Rat Sarcoma Virus (KRAS) G12D mutations are present in >90% of all PDAC's; exciting breakthroughs in small molecule inhibitors targeting KRAS G12D may open new modalities of treatment, and therapies targeting multiple KRAS mutations are also in early clinical trials. Although immunotherapy strategies to date have been disappointing, combination with chemotherapy and/or small molecule inhibitors hold promise and warrant further exploration.

Keywords:  KRAS; chemotherapy; metastatic; molecular profiling; pancreas

DOI:  https://doi.org/10.3390/curroncol31090385
Biochimie. 2024 Sep 18. pii: S0300-9084(24)00218-9. [Epub ahead of print]

Established and emerging players in phospholipid scrambling: a structural perspective.

Heitor Gobbi Sebinelli, Camille Syska, Alenka Čopič, Guillaume Lenoir.

  The maintenance of a diverse and non-homogeneous lipid composition in cell membranes is crucial for a multitude of cellular processes. One important example is transbilayer lipid asymmetry, which refers to a difference in lipid composition between the two leaflets of a cellular membrane. Transbilayer asymmetry is especially pronounced at the plasma membrane, where at resting state, negatively-charged phospholipids such as phosphatidylserine (PS) are almost exclusively restricted to the cytosolic leaflet, whereas sphingolipids are mostly found in the exoplasmic leaflet. Transbilayer movement of lipids is inherently slow, and for a fast cellular response, for example during apoptosis, transmembrane proteins termed scramblases facilitate the movement of polar/charged lipid headgroups through the membrane interior. In recent years, an expanding number of proteins from diverse families have been suggested to possess a lipid scramblase activity. Members of TMEM16 and XKR proteins have been implicated in blood clotting and apoptosis, whereas the scrambling activity of ATG9 and TMEM41B/VMP1 proteins contributes to the synthesis of autophagosomal membrane during autophagy. Structural studies, in vitro reconstitution of lipid scrambling, and molecular dynamics simulations have significantly advanced our understanding of the molecular mechanisms of lipid scrambling and helped delineate potential lipid transport pathways through the membrane. A number of examples also suggest that lipid scrambling activity can be combined with another activity, as is the case for TMEM16 proteins, which also function as ion channels, rhodopsin in the photoreceptor membrane, and possibly other G-protein coupled receptors.

Keywords:  Lipid scramblases; autophagy; cryo-electron microscopy; molecular dynamics simulations; transbilayer lipid asymmetry

DOI:  https://doi.org/10.1016/j.biochi.2024.09.008
Cell Chem Biol. 2024 Sep 19. pii: S2451-9456(24)00355-6. [Epub ahead of print]31(9): 1636-1651

Ligand discovery by activity-based protein profiling.

Micah J Niphakis, Benjamin F Cravatt.

Genomic technologies have led to massive gains in our understanding of human gene function and disease relevance. Chemical biologists are a primary beneficiary of this information, which can guide the prioritization of proteins for chemical probe and drug development. The vast functional and structural diversity of disease-relevant proteins, however, presents challenges for conventional small molecule screening libraries and assay development that in turn raise questions about the broader "druggability" of the human proteome. Here, we posit that activity-based protein profiling (ABPP), by generating global maps of small molecule-protein interactions in native biological systems, is well positioned to address major obstacles in human biology-guided chemical probe and drug discovery. We will support this viewpoint with case studies highlighting a range of small molecule mechanisms illuminated by ABPP that include the disruption and stabilization of biomolecular (protein-protein/nucleic acid) interactions and underscore allostery as a rich source of chemical tools for historically "undruggable" protein classes.

DOI: https://doi.org/10.1016/j.chembiol.2024.08.006