bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2024–06–23
43 papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Interaction between MED12 and ΔNp63 activates basal identity in pancreatic ductal adenocarcinoma.
  2. A Novel AMPK Inhibitor Sensitizes Pancreatic Cancer Cells to Ferroptosis Induction.
  3. CREB activation drives acinar to ductal reprogramming and promote pancreatic cancer progression in animal models of alcoholic chronic pancreatitis.
  4. KRAS promotes GLI2-dependent transcription during pancreatic carcinogenesis.
  5. Diet predisposes to pancreatic cancer through cellular nutrient sensing pathways.
  6. Development and validation of AI-assisted transcriptomic signatures to personalize adjuvant chemotherapy in patients with pancreatic ductal adenocarcinoma.
  7. Perspectives in collective cell migration - moving forward.
  8. High resolution long-read telomere sequencing reveals dynamic mechanisms in aging and cancer.
  9. Differences in intratumor innate lymphoid cell composition between orthotopic and spontaneous pancreatic mouse models.
  10. Protocol to study the immune profile of syngeneic mouse tumor models.
  11. In vivo CRISPR screens reveal SCAF1 and USP15 as drivers of pancreatic cancer.
  12. Senescence and tissue fibrosis: opportunities for therapeutic targeting.
  13. Sequestosome-1 (SQSTM1/p62) as a target in dopamine catabolite-mediated cellular dyshomeostasis.
  14. Calorie restriction and calorie-restriction mimetics activate chaperone-mediated autophagy.
  15. Eukaryotic cell size regulation and its implications for cellular function and dysfunction.
  16. Endoplasmic reticulum-plasma membrane contact gradients direct cell migration.
  17. Interactions between diet and gut microbiota in cancer.
  18. Intratumoral immune triads are required for immunotherapy-mediated elimination of solid tumors.
  19. Bidirectional activation of stem-like programs between metastatic cancer and alveolar type 2 cells within the niche.
  20. Therapy-induced senescence is finally escapable, what is next?
  21. Genetic Evidence for a Causal Link between Intra-Pancreatic Fat Deposition and Pancreatitis: a Mendelian Randomization Study.
  22. Deep cell phenotyping and spatial analysis of multiplexed imaging with TRACERx-PHLEX.
  23. Bimodality in Ras signaling originates from processivity of the Ras activator SOS without deterministic bistability.
  24. Why do patients with cancer die?
  25. Asymmetric crowders and membrane morphology at the nexus of intracellular trafficking and oncology.
  26. A phosphorylation-controlled switch confers cell cycle-dependent protein relocalization.
  27. Robust and consistent biomarker candidates identification by a machine learning approach applied to pancreatic ductal adenocarcinoma metastasis.
  28. Principal component-based clinical aging clocks identify signatures of healthy aging and targets for clinical intervention.
  29. Cellular senescence in normal physiology.
  30. A Nine-Year-Old Child With Metastatic Pancreatic Adenocarcinoma.
  31. Bellybutton: accessible and customizable deep-learning image segmentation.
  32. Fine-tuning spatial-temporal dynamics and surface receptor expression support plasma cell-intrinsic longevity.
  33. Suppressed basal mitophagy drives cellular aging phenotypes that can be reversed by a p62-targeting small molecule.
  34. The road less travelled.
  35. Leveraging Senescent Cancer Cell Membrane to Potentiate Cancer Immunotherapy Through Biomimetic Nanovaccine.
  36. Digital telomere measurement by long-read sequencing distinguishes healthy aging from disease.
  37. The AID2 system offers a potent tool for rapid, reversible, or sustained degradation of essential proteins in live mice.
  38. Blocking the utilization of carbon sources via two pathways to induce tumor starvation for cancer treatment.
  39. Strand-resolved mutagenicity of DNA damage and repair.
  40. Coinfecting phages impede each other's entry into the cell.
  41. Membrane nanotubes transform into double-membrane sheets at condensate droplets.
  42. Freestanding bilayer microscope for single-molecule imaging of membrane proteins.
  43. Model of Active Solids: Rigid Body Motion and Shape-Changing Mechanisms.
  1. Nat Genet. 2024 Jun 17.
    Interaction between MED12 and ΔNp63 activates basal identity in pancreatic ductal adenocarcinoma.
    Diogo Maia-Silva, Patrick J Cunniff, Allison C Schier, Damianos Skopelitis, Marygrace C Trousdell, Philip Moresco, Yuan Gao, Vahag Kechejian, Xue-Yan He, Yunus Sahin, Ledong Wan, Aktan Alpsoy, Jynelle Liverpool, Adrian R Krainer, Mikala Egeblad, David L Spector, Douglas T Fearon, Camila O Dos Santos, Dylan J Taatjes, Christopher R Vakoc.
      The presence of basal lineage characteristics signifies hyperaggressive human adenocarcinomas of the breast, bladder and pancreas. However, the biochemical mechanisms that maintain this aberrant cell state are poorly understood. Here we performed marker-based genetic screens in search of factors needed to maintain basal identity in pancreatic ductal adenocarcinoma (PDAC). This approach revealed MED12 as a powerful regulator of the basal cell state in this disease. Using biochemical reconstitution and epigenomics, we show that MED12 carries out this function by bridging the transcription factor ΔNp63, a known master regulator of the basal lineage, with the Mediator complex to activate lineage-specific enhancer elements. Consistent with this finding, the growth of basal-like PDAC is hypersensitive to MED12 loss when compared to PDAC cells lacking basal characteristics. Taken together, our genetic screens have revealed a biochemical interaction that sustains basal identity in human cancer, which could serve as a target for tumor lineage-directed therapeutics.
    DOI:  https://doi.org/10.1038/s41588-024-01790-y
  2. Adv Sci (Weinh). 2024 Jun 17. e2307695
    A Novel AMPK Inhibitor Sensitizes Pancreatic Cancer Cells to Ferroptosis Induction.
    Carolin Schneider, Jorina Hilbert, Franziska Genevaux, Stefanie Höfer, Lukas Krauß, Felix Schicktanz, Constanza Tapia Contreras, Shaishavi Jansari, Aristeidis Papargyriou, Thorsten Richter, Abdallah M Alfayomy, Chiara Falcomatà, Christian Schneeweis, Felix Orben, Ruppert Öllinger, Florian Wegwitz, Angela Boshnakovska, Peter Rehling, Denise Müller, Philipp Ströbel, Volker Ellenrieder, Lena Conradi, Elisabeth Hessmann, Michael Ghadimi, Marian Grade, Matthias Wirth, Katja Steiger, Roland Rad, Bernhard Kuster, Wolfgang Sippl, Maximilian Reichert, Dieter Saur, Günter Schneider.
      Cancer cells must develop strategies to adapt to the dynamically changing stresses caused by intrinsic or extrinsic processes, or therapeutic agents. Metabolic adaptability is crucial to mitigate such challenges. Considering metabolism as a central node of adaptability, it is focused on an energy sensor, the AMP-activated protein kinase (AMPK). In a subtype of pancreatic ductal adenocarcinoma (PDAC) elevated AMPK expression and phosphorylation is identified. Using drug repurposing that combined screening experiments and chemoproteomic affinity profiling, it is identified and characterized PF-3758309, initially developed as an inhibitor of PAK4, as an AMPK inhibitor. PF-3758309 shows activity in pre-clinical PDAC models, including primary patient-derived organoids. Genetic loss-of-function experiments showed that AMPK limits the induction of ferroptosis, and consequently, PF-3758309 treatment restores the sensitivity toward ferroptosis inducers. The work established a chemical scaffold for the development of specific AMPK-targeting compounds and deciphered the framework for the development of AMPK inhibitor-based combination therapies tailored for PDAC.
    Keywords:  AMPK; ferroptosis; pancreatic cancer
    DOI:  https://doi.org/10.1002/advs.202307695
  3. bioRxiv. 2024 Jan 05. pii: 2024.01.05.574376. [Epub ahead of print]
    CREB activation drives acinar to ductal reprogramming and promote pancreatic cancer progression in animal models of alcoholic chronic pancreatitis.
    Supriya Srinivasan, Siddharth Mehra, Anna Bianchi, Samara Singh, Austin R Dosch, Haleh Amirian, Sudhakar Jinka, Varunkumar Krishnamoorthy, Iago De Castro Silva, Edmond Worley Box, Vanessa Garrido, Tulasigeri M Totiger, Zhiqun Zhou, Yuguang Ban, Jashodeep Datta, Michael VanSaun, Nipun Merchant, Nagaraj S Nagathihalli.
       BACKGROUND AND AIMS: In vivo induction of alcoholic chronic pancreatitis (ACP) causes significant acinar damage, increased fibroinflammatory response, and heightened activation of cyclic response element binding protein 1 (CREB) when compared with alcohol (A) or chronic pancreatitis (CP) mediated pancreatic damage. However, the study elucidating the cooperative interaction between CREB and the oncogenic Kras G12D/+ ( Kras* ) in promoting pancreatic cancer progression with ACP remains unexplored.
    METHODS: Experimental ACP induction was established in multiple mouse models, followed by euthanization of the animals at various time intervals during the recovery periods. Tumor latency was determined in these mice cohorts. Here, we established CREB deletion ( Creb fl/fl ) in Ptf1a CreERTM/+ ;LSL-Kras G12D+/- (KC) genetic mouse models (KCC -/- ). Western blot, phosphokinase array, and qPCR were used to analyze the pancreata of Ptf1a CreERTM+/- , KC and KCC -/- mice. The pancreata of ACP-induced KC mice were subjected to single-cell RNA sequencing (scRNAseq). Further studies involved conducting lineage tracing and acinar cell explant cultures.
    RESULTS: ACP induction in KC mice had detrimental effects on the pancreatic damage repair mechanism. The persistent existence of acinar cell-derived ductal lesions demonstrated a prolonged state of hyperactivated CREB. Persistent CREB activation leads to acinar cell reprogramming and increased pro-fibrotic inflammation in KC mice. Acinar-specific Creb ablation reduced advanced PanINs lesions, hindered tumor progression, and restored acinar cell function in ACP-induced mouse models.
    CONCLUSIONS: Our findings demonstrate that CREB cooperates with Kras* to perpetuate an irreversible ADM and PanIN formation. Moreover, CREB sustains oncogenic activity to promote the progression of premalignant lesions toward cancer in the presence of ACP.
    DOI:  https://doi.org/10.1101/2024.01.05.574376
  4. Cancer Res Commun. 2024 Jun 20.
    KRAS promotes GLI2-dependent transcription during pancreatic carcinogenesis.
    Ashley N Sigafoos, Ezequiel J Tolosa, Ryan M Carr, Maite G Fernández-Barrena, Luciana L Almada, David R Pease, Tara L Hogenson, Glancis Luzeena Raja Arul, Fatemeh Mousavi, Sandhya Sen, Renzo E Vera, David L Marks, Luis F Flores, Kayla C LaRue-Nolan, Chen Wu, William R Bamlet, Anne M Vrabel, Hugues Sicotte, Erin L Schenk, Thomas C Smyrk, Lizhi Zhang, Kari G Rabe, Ann L Oberg, Peter G Zaphiropoulos, Eric Chevet, Rondell P Graham, Catherine E Hagen, Marina Pasca di Magliano, Sherine F Elsawa, Christopher L Pin, Junhao Mao, Robert R McWilliams, Martin E Fernandez-Zapico.
      Aberrant activation of GLI transcription factors has been implicated in the pathogenesis of different tumor types including pancreatic ductal adenocarcinoma (PDAC). However, the mechanistic link with established drivers of this disease remains in part elusive. Here, using a new genetically-engineered mouse model overexpressing constitutively active mouse form of GLI2 and a combination of genome wide assays, we provide evidence of a novel mechanism underlying the interplay between KRAS, a major driver of PDAC development, and GLI2 to control oncogenic gene expression. These mice, also expressing KrasG12D, show significantly reduced median survival rate and accelerated tumorigenesis compared to the KrasG12D only expressing mice. Analysis of the mechanism using RNA-seq demonstrate higher levels of GLI2 targets, particularly tumor growth promoting genes including Ccnd1, N-Myc and Bcl2, in KrasG12D mutant cells. Further, ChIP-seq studies showed that in these cells KrasG12D increases the levels of H3K4me3 at the promoter of GLI2 targets without affecting significantly the levels of other major active chromatin marks. Importantly, Gli2 knockdown reduces H3K4me3 enrichment and gene expression induced by mutant Kras. In summary, we demonstrate that Gli2 plays a significant role in pancreatic carcinogenesis by acting as a downstream effector of KrasG12D to control gene expression.
    DOI:  https://doi.org/10.1158/2767-9764.CRC-23-0464
  5. FEBS Lett. 2024 Jun 17.
    Diet predisposes to pancreatic cancer through cellular nutrient sensing pathways.
    Roberta Noè, Alessandro Carrer.
      Pancreatic cancer is a lethal disease with limited effective treatments. A deeper understanding of its molecular mechanisms is crucial to reduce incidence and mortality. Epidemiological evidence suggests a link between diet and disease risk, though dietary recommendations for at-risk individuals remain debated. Here, we propose that cell-intrinsic nutrient sensing pathways respond to specific diet-derived cues to facilitate oncogenic transformation of pancreatic epithelial cells. This review explores how diet influences pancreatic cancer predisposition through nutrient sensing and downstream consequences for (pre-)cancer cell biology. We also examine experimental evidence connecting specific food intake to pancreatic cancer progression, highlighting nutrient sensing as a promising target for therapeutic development to mitigate disease risk.
    Keywords:  carbohydrates; diet; lipids; nutrient sensing; pancreatic cancer
    DOI:  https://doi.org/10.1002/1873-3468.14959
  6. Ann Oncol. 2024 Jun 19. pii: S0923-7534(24)00741-5. [Epub ahead of print]
    Development and validation of AI-assisted transcriptomic signatures to personalize adjuvant chemotherapy in patients with pancreatic ductal adenocarcinoma.
    N Fraunhoffer, P Hammel, T Conroy, R Nicolle, J-B Bachet, A Harlé, V Rebours, A Turpin, M B Abdelghani, E Mitry, J Biagi, B Chanez, M Bigonnet, A Lopez, L Evesque, T Lecomte, E Assenat, O Bouché, D Renouf, A Lambert, L Monard, M Mauduit, J Cros, J Iovanna, N Dusetti.
       BACKGROUND: After surgical resection of pancreatic ductal adenocarcinoma (PDAC), patients are predominantly treated with adjuvant chemotherapy, commonly consisting of gemcitabine-based regimens or the modified FOLFIRINOX regimen (mFFX). While mFFX has been shown to be more effective than gemcitabine-based regimens, it is also associated with higher toxicity. Current treatment decisions are based on patient performance status rather than on the molecular characteristics of the tumor. To address this gap, the goal of this study was to develop drug-specific transcriptomic signatures for personalized chemotherapy treatment.
    PATIENTS AND METHODS: We used PDAC datasets from preclinical models, encompassing chemotherapy response profiles for the mFFX-regimen components. From them we identified specific gene transcripts associated with chemotherapy response. Three transcriptomic AI-signatures were obtained by combining Independent Component Analysis, Least Absolute Shrinkage and the Selection Operator-Random Forest approach. We integrated a previously developed gemcitabine signature with three newly developed ones. The machine learning strategy employed to enhance these signatures incorporates transcriptomic features from the tumor microenvironment, leading to the development of the Pancreas-View tool ultimately clinically validated in a cohort of 343 patients from the PRODIGE-24/CCTG PA6 trial.
    RESULTS: Patients who were predicted to be sensitive to the administered drugs (n=164; 47.8%) had longer disease-free survival (DFS) than the other patients. The median DFS in the mFFX sensitive group treated with mFFX was 50.0 months (stratified HR: 0.31; 95% CI, 0.21-0.44; p<0.001) and 33.7 months (stratified HR: 0.40; 95% CI, 0.17-0.59; p<0.001) in the gemcitabine sensitive group when treated with gemcitabine. Comparatively patients with signature predictions unmatched with the treatments (n=86; 25.1%) or those resistant to all drugs (n=93; 27.1%) had shorter DFS (10.6 and 10.8 months, respectively).
    CONCLUSIONS: This study presents a transcriptome-based tool that was developed using preclinical models and machine learning to accurately predict sensitivity to mFFX and gemcitabine.
    Keywords:  FOLFIRINOX; PRODIGE-24/CCTG PA6 trial; artificial intelligence; gemcitabine; pancreatic cancer; transcriptomic signatures
    DOI:  https://doi.org/10.1016/j.annonc.2024.06.010
  7. J Cell Sci. 2024 Jun 15. pii: jcs261549. [Epub ahead of print]137(12):
    Perspectives in collective cell migration - moving forward.
    Samantha J Stehbens, Elena Scarpa, Melanie D White.
      Collective cell migration, where cells move as a cohesive unit, is a vital process underlying morphogenesis and cancer metastasis. Thanks to recent advances in imaging and modelling, we are beginning to understand the intricate relationship between a cell and its microenvironment and how this shapes cell polarity, metabolism and modes of migration. The use of biophysical and mathematical models offers a fresh perspective on how cells migrate collectively, either flowing in a fluid-like state or transitioning to more static states. Continuing to unite researchers in biology, physics and mathematics will enable us to decode more complex biological behaviours that underly collective cell migration; only then can we understand how this coordinated movement of cells influences the formation and organisation of tissues and directs the spread of metastatic cancer. In this Perspective, we highlight exciting discoveries, emerging themes and common challenges that have arisen in recent years, and possible ways forward to bridge the gaps in our current understanding of collective cell migration.
    Keywords:  Cell biology; Collective cell migration; Metastasis; Modelling; Morphogenesis
    DOI:  https://doi.org/10.1242/jcs.261549
  8. Nat Commun. 2024 Jun 18. 15(1): 5149
    High resolution long-read telomere sequencing reveals dynamic mechanisms in aging and cancer.
    Tobias T Schmidt, Carly Tyer, Preeyesh Rughani, Candy Haggblom, Jeffrey R Jones, Xiaoguang Dai, Kelly A Frazer, Fred H Gage, Sissel Juul, Scott Hickey, Jan Karlseder.
      Telomeres are the protective nucleoprotein structures at the end of linear eukaryotic chromosomes. Telomeres' repetitive nature and length have traditionally challenged the precise assessment of the composition and length of individual human telomeres. Here, we present Telo-seq to resolve bulk, chromosome arm-specific and allele-specific human telomere lengths using Oxford Nanopore Technologies' native long-read sequencing. Telo-seq resolves telomere shortening in five population doubling increments and reveals intrasample, chromosome arm-specific, allele-specific telomere length heterogeneity. Telo-seq can reliably discriminate between telomerase- and ALT-positive cancer cell lines. Thus, Telo-seq is a tool to study telomere biology during development, aging, and cancer at unprecedented resolution.
    DOI:  https://doi.org/10.1038/s41467-024-48917-7
  9. Methods Cell Biol. 2024 ;pii: S0091-679X(24)00115-8. [Epub ahead of print]188 153-169
    Differences in intratumor innate lymphoid cell composition between orthotopic and spontaneous pancreatic mouse models.
    Sara Lamorte, Alisha R Elford, Douglas C Chung, Kiichi Murakami, Tracy L McGaha, Nicolas Jacquelot.
      Pancreatic cancer remains an unmet medical need. Late diagnosis and the lack of efficient treatment significantly impact the prognosis of patients suffering from pancreatic cancer. Improving patient outcomes requires a deeper comprehension of the tumor ecosystem. To achieve this, a thorough exploration of the tumor microenvironment using pre-clinical models that accurately replicate human disease is imperative, particularly in understanding the dynamics of immune cell subsets. Surprisingly, the impact of model variations on the composition of the tumor microenvironment has been largely neglected. In this study, we introduce an orthotopic model of pancreatic ductal adenocarcinoma and a spontaneous model of insulinoma. Our findings reveal striking differences in the innate lymphoid cell infiltrate, highlighting the importance of considering model-specific influences when investigating the tumor microenvironment.
    Keywords:  Flow cytometry; ILC2; Innate lymphoid cells; Insulinoma; Mouse model; PDAC; Pancreatic cancer; Tumor microenvironment
    DOI:  https://doi.org/10.1016/bs.mcb.2024.04.001
  10. STAR Protoc. 2024 Jun 14. pii: S2666-1667(24)00304-6. [Epub ahead of print]5(3): 103139
    Protocol to study the immune profile of syngeneic mouse tumor models.
    Sayuri Miyauchi, Kei-Ichiro Arimoto, Mengdan Liu, Yue Zhang, Dong-Er Zhang.
      Flow cytometry, single-cell RNA sequencing, and other analyses enable us to capture immune profiles of the tumor microenvironment. Here, we present a protocol to characterize the immune profile of tumor-bearing mice. We describe steps for establishing mouse models and preparing single-cell suspensions from tumor tissue and other immune-related organs, which can be further analyzed by flow cytometry and other omics assays. We then detail procedures for staining, flow cytometry analysis, and phenotyping of the immune cell populations. For complete details on the use and execution of this protocol, please refer to Miyauchi et al.1.
    Keywords:  cancer; flow cytometry; immunology; single cell
    DOI:  https://doi.org/10.1016/j.xpro.2024.103139
  11. Nat Commun. 2024 Jun 20. 15(1): 5266
    In vivo CRISPR screens reveal SCAF1 and USP15 as drivers of pancreatic cancer.
    Sebastien Martinez, Shifei Wu, Michael Geuenich, Ahmad Malik, Ramona Weber, Tristan Woo, Amy Zhang, Gun Ho Jang, Dzana Dervovic, Khalid N Al-Zahrani, Ricky Tsai, Nassima Fodil, Philippe Gros, Steven Gallinger, G Gregory Neely, Faiyaz Notta, Ataman Sendoel, Kieran Campbell, Ulrich Elling, Daniel Schramek.
      Functionally characterizing the genetic alterations that drive pancreatic cancer is a prerequisite for precision medicine. Here, we perform somatic CRISPR/Cas9 mutagenesis screens to assess the transforming potential of 125 recurrently mutated pancreatic cancer genes, which revealed USP15 and SCAF1 as pancreatic tumor suppressors. Mechanistically, we find that USP15 functions in a haploinsufficient manner and that loss of USP15 or SCAF1 leads to reduced inflammatory TNFα, TGF-β and IL6 responses and increased sensitivity to PARP inhibition and Gemcitabine. Furthermore, we find that loss of SCAF1 leads to the formation of a truncated, inactive USP15 isoform at the expense of full-length USP15, functionally coupling SCAF1 and USP15. Notably, USP15 and SCAF1 alterations are observed in 31% of pancreatic cancer patients. Our results highlight the utility of in vivo CRISPR screens to integrate human cancer genomics and mouse modeling for the discovery of cancer driver genes with potential prognostic and therapeutic implications.
    DOI:  https://doi.org/10.1038/s41467-024-49450-3
  12. Trends Mol Med. 2024 Jun 17. pii: S1471-4914(24)00134-5. [Epub ahead of print]
    Senescence and tissue fibrosis: opportunities for therapeutic targeting.
    Steven O'Reilly, Pei-Suen Tsou, John Varga.
      Cellular senescence is a key hallmark of aging. It has now emerged as a key mediator in normal tissue turnover and is associated with a variety of age-related diseases, including organ-specific fibrosis and systemic sclerosis (SSc). This review discusses the recent evidence of the role of senescence in tissue fibrosis, with an emphasis on SSc, a systemic autoimmune rheumatic disease. We discuss the physiological role of these cells, their role in fibrosis, and that targeting these cells specifically could be a new therapeutic avenue in fibrotic disease. We argue that targeting senescent cells, with senolytics or senomorphs, is a viable therapeutic target in fibrotic diseases which remain largely intractable.
    Keywords:  SASP; fibrosis; myofibroblasts; senescence; systemic sclerosis
    DOI:  https://doi.org/10.1016/j.molmed.2024.05.012
  13. Cell Death Dis. 2024 Jun 18. 15(6): 424
    Sequestosome-1 (SQSTM1/p62) as a target in dopamine catabolite-mediated cellular dyshomeostasis.
    Anna Masato, Annapaola Andolfo, Giulia Favetta, Edoardo Niccolò Bellini, Susanna Cogo, Luisa Dalla Valle, Daniela Boassa, Elisa Greggio, Nicoletta Plotegher, Luigi Bubacco.
      Alterations in the dopamine catabolic pathway are known to contribute to the degeneration of nigrostriatal neurons in Parkinson's disease (PD). The progressive cellular buildup of the highly reactive intermediate 3,4-dihydroxyphenylacetaldehye (DOPAL) generates protein cross-linking, oligomerization of the PD-linked αSynuclein (αSyn) and imbalance in protein quality control. In this scenario, the autophagic cargo sequestome-1 (SQSTM1/p62) emerges as a target of DOPAL-dependent oligomerization and accumulation in cytosolic clusters. Although DOPAL-induced oxidative stress and activation of the Nrf2 pathway promote p62 expression, p62 oligomerization rather seems to be a consequence of direct DOPAL modification. DOPAL-induced p62 clusters are positive for ubiquitin and accumulate within lysosomal-related structures, likely affecting the autophagy-lysosomal functionality. Finally, p62 oligomerization and clustering is synergistically augmented by DOPAL-induced αSyn buildup. Hence, the substantial impact on p62 proteostasis caused by DOPAL appears of relevance for dopaminergic neurodegeneration, in which the progressive failure of degradative pathways and the deposition of proteins like αSyn, ubiquitin and p62 in inclusion bodies represent a major trait of PD pathology.
    DOI:  https://doi.org/10.1038/s41419-024-06763-x
  14. Proc Natl Acad Sci U S A. 2024 Jun 25. 121(26): e2317945121
    Calorie restriction and calorie-restriction mimetics activate chaperone-mediated autophagy.
    Maryam Jafari, Adrián Macho-González, Antonio Diaz, Kristen Lindenau, Olaya Santiago-Fernández, Mei Zeng, Ashish C Massey, Rafael de Cabo, Susmita Kaushik, Ana Maria Cuervo.
      Chaperone-mediated autophagy (CMA) is part of the mammalian cellular proteostasis network that ensures protein quality control, maintenance of proteome homeostasis, and proteome changes required for the adaptation to stress. Loss of proteostasis is one of the hallmarks of aging. CMA decreases with age in multiple rodent tissues and human cell types. A decrease in lysosomal levels of the lysosome-associated membrane protein type 2A (LAMP2A), the CMA receptor, has been identified as a main reason for declined CMA in aging. Here, we report constitutive activation of CMA with calorie restriction (CR), an intervention that extends healthspan, in old rodent livers and in an in vitro model of CR with cultured fibroblasts. We found that CR-mediated upregulation of CMA is due to improved stability of LAMP2A at the lysosome membrane. We also explore the translational value of our observations using calorie-restriction mimetics (CRMs), pharmacologically active substances that reproduce the biochemical and functional effects of CR. We show that acute treatment of old mice with CRMs also robustly activates CMA in several tissues and that this activation is required for the higher resistance to lipid dietary challenges conferred by treatment with CRMs. We conclude that part of the beneficial effects associated with CR/CRMs could be a consequence of the constitutive activation of CMA mediated by these interventions.
    Keywords:  aging; autophagy; dietary restriction; gerotherapeutics; lysosomes
    DOI:  https://doi.org/10.1073/pnas.2317945121
  15. Physiol Rev. 2024 Jun 20.
    Eukaryotic cell size regulation and its implications for cellular function and dysfunction.
    Yagya Chadha, Arohi Khurana, Kurt M Schmoller.
      Depending on cell type, environmental inputs, and disease, the cells in the human body can have widely different sizes. In recent years, it became clear that cell size is a major regulator of cell function. However, we are only beginning to understand how optimization of cell function determines a given cell's optimal size. Here, we review currently known size control strategies of eukaryotic cells, and the intricate link of cell size to intracellular biomolecular scaling, organelle homeostasis and cell cycle progression. We detail the cell size dependent regulation of early development and the impact of cell size on cell differentiation. Given the importance of cell size for normal cellular physiology, cell size control must account for changing environmental conditions. We describe how cells sense environmental stimuli, such as nutrient availability, and accordingly adapt their size by regulating cell growth and cell cycle progression. Moreover, we discuss the correlation of pathological states with misregulation of cell size, and how for a long time, this was considered a downstream consequence of cellular dysfunction. We review newer studies that reveal a reversed causality, with misregulated cell size leading to pathophysiological phenotypes such as senescence and aging. In summary, we highlight important roles of cell size in cellular function and dysfunction, which could have major implications for both diagnostics and treatment in the clinic.
    Keywords:  Cell cycle; Cell growth; Cell size; Organelle homeostasis; Protein homeostasis
    DOI:  https://doi.org/10.1152/physrev.00046.2023
  16. Nature. 2024 Jun 12.
    Endoplasmic reticulum-plasma membrane contact gradients direct cell migration.
    Bo Gong, Jake D Johnston, Alexander Thiemicke, Alex de Marco, Tobias Meyer.
      Directed cell migration is driven by the front-back polarization of intracellular signalling1-3. Receptor tyrosine kinases and other inputs activate local signals that trigger membrane protrusions at the front2,4-6. Equally important is a long-range inhibitory mechanism that suppresses signalling at the back to prevent the formation of multiple fronts7-9. However, the identity of this mechanism is unknown. Here we report that endoplasmic reticulum-plasma membrane (ER-PM) contact sites are polarized in single and collectively migrating cells. The increased density of these ER-PM contacts at the back provides the ER-resident PTP1B phosphatase more access to PM substrates, which confines receptor signalling to the front and directs cell migration. Polarization of the ER-PM contacts is due to microtubule-regulated polarization of the ER, with more RTN4-rich curved ER at the front and more CLIMP63-rich flattened ER at the back. The resulting ER curvature gradient leads to small and unstable ER-PM contacts only at the front. These contacts flow backwards and grow to large and stable contacts at the back to form the front-back ER-PM contact gradient. Together, our study suggests that the structural polarity mediated by ER-PM contact gradients polarizes cell signalling, directs cell migration and prolongs cell migration.
    DOI:  https://doi.org/10.1038/s41586-024-07527-5
  17. Nat Microbiol. 2024 Jun 21.
    Interactions between diet and gut microbiota in cancer.
    Geicho Nakatsu, Natalia Andreeva, Meghan H MacDonald, Wendy S Garrett.
      Dietary patterns and specific dietary components, in concert with the gut microbiota, can jointly shape susceptibility, resistance and therapeutic response to cancer. Which diet-microbial interactions contribute to or mitigate carcinogenesis and how they work are important questions in this growing field. Here we interpret studies of diet-microbial interactions to assess dietary determinants of intestinal colonization by opportunistic and oncogenic bacteria. We explore how diet-induced expansion of specific gut bacteria might drive colonic epithelial tumorigenesis or create immuno-permissive tumour milieus and introduce recent findings that provide insight into these processes. Additionally, we describe available preclinical models that are widely used to study diet, microbiome and cancer interactions. Given the rising clinical interest in dietary modulations in cancer treatment, we highlight promising clinical trials that describe the effects of different dietary alterations on the microbiome and cancer outcomes.
    DOI:  https://doi.org/10.1038/s41564-024-01736-4
  18. Cancer Cell. 2024 Jun 19. pii: S1535-6108(24)00193-4. [Epub ahead of print]
    Intratumoral immune triads are required for immunotherapy-mediated elimination of solid tumors.
    Gabriel Espinosa-Carrasco, Edison Chiu, Aurora Scrivo, Paul Zumbo, Asim Dave, Doron Betel, Sung Wook Kang, Hee-Jin Jang, Matthew D Hellmann, Bryan M Burt, Hyun-Sung Lee, Andrea Schietinger.
      Tumor-specific CD8+ T cells are frequently dysfunctional and unable to halt tumor growth. We investigated whether tumor-specific CD4+ T cells can be enlisted to overcome CD8+ T cell dysfunction within tumors. We find that the spatial positioning and interactions of CD8+ and CD4+ T cells, but not their numbers, dictate anti-tumor responses in the context of adoptive T cell therapy as well as immune checkpoint blockade (ICB): CD4+ T cells must engage with CD8+ T cells on the same dendritic cell during the effector phase, forming a three-cell-type cluster (triad) to license CD8+ T cell cytotoxicity and cancer cell elimination. When intratumoral triad formation is disrupted, tumors progress despite equal numbers of tumor-specific CD8+ and CD4+ T cells. In patients with pleural mesothelioma treated with ICB, triads are associated with clinical responses. Thus, CD4+ T cells and triads are required for CD8+ T cell cytotoxicity during the effector phase and tumor elimination.
    Keywords:  CD4 T cell; CD8 T cell; Cancer; adoptive T cell transfer; cancer immunotherapy; dendritic cell; immune checkpoint blockade; triad; tumor; tumor antigen
    DOI:  https://doi.org/10.1016/j.ccell.2024.05.025
  19. Dev Cell. 2024 May 31. pii: S1534-5807(24)00338-1. [Epub ahead of print]
    Bidirectional activation of stem-like programs between metastatic cancer and alveolar type 2 cells within the niche.
    Felipe S Rodrigues, Adam Karoutas, Stefanie Ruhland, Nicolas Rabas, Tatiana Rizou, Stefania Di Blasio, Rute M M Ferreira, Victoria L Bridgeman, Robert Goldstone, Miriam L Sopena, Joo-Hyeon Lee, Luigi Ombrato, Ilaria Malanchi.
      A key step for metastatic outgrowth involves the generation of a deeply altered microenvironment (niche) that supports the malignant behavior of cancer cells. The complexity of the metastatic niche has posed a significant challenge in elucidating the underlying programs driving its origin. Here, by focusing on early stages of breast cancer metastasis to the lung in mice, we describe a cancer-dependent chromatin remodeling and activation of developmental programs in alveolar type 2 (AT2) cells within the niche. We show that metastatic cells can prime AT2 cells into a reprogrammed multilineage state. In turn, this cancer-induced reprogramming of AT2 cells promoted stem-like features in cancer cells and enhanced their initiation capacity. In conclusion, we propose the concept of "reflected stemness" as an early phenomenon during metastatic niche initiation, wherein metastatic cells reprogram the local tissue into a stem-like state that enhances intrinsic cancer-initiating potential, creating a positive feedback loop where tumorigenic programs are amplified.
    Keywords:  Metastasis; Sox9; alveolar type 2 cells; breast cancer; lung stem cells; metastasis-initiating cells; metastatic niche; multilineage state; tissue reprogramming
    DOI:  https://doi.org/10.1016/j.devcel.2024.05.020
  20. Cell Cycle. 2024 Jun 16. 1-9
    Therapy-induced senescence is finally escapable, what is next?
    Tareq Saleh.
      Several breakthrough articles have recently confirmed the ability of tumor cells to escape the stable cell cycle arrest imposed by Therapy-Induced Senescence (TIS). Subsequently, accepting the hypothesis that TIS is escapable should encourage serious reassessments of the fundamental roles of senescence in cancer treatment. The potential for escape from TIS undermines the well-established tumor suppressor function of senescence, proposes it as a mechanism of tumor dormancy leading to disease recurrence and invites for further investigation of its unfavorable contribution to cancer therapy outcomes. Moreover, escaping TIS strongly indicates that the elimination of senescent tumor cells, primarily through pharmacological means, is a suitable approach for increasing the efficacy of cancer treatment, one that still requires further exploration. This commentary provides an overview of the recent evidence that unequivocally demonstrated the ability of therapy-induced senescent tumor cells in overcoming the terminal growth arrest fate and provides future perspectives on the roles of TIS in tumor biology.
    Keywords:  Senescence; cancer; dormancy; escape; reversible; senolytic
    DOI:  https://doi.org/10.1080/15384101.2024.2364579
  21. medRxiv. 2024 Jun 04. pii: 2024.06.03.24308330. [Epub ahead of print]
    Genetic Evidence for a Causal Link between Intra-Pancreatic Fat Deposition and Pancreatitis: a Mendelian Randomization Study.
    Hajime Yamazaki, Martin Heni, Róbert Wagner, Shunichi Fukuhara, Steven R Grossman, Sihao Han, Lang Wu, Samantha A Streicher, Brian Z Huang.
       Introduction: Recent associative studies have linked intra-pancreatic fat deposition (IPFD) with risk of pancreatitis, but the causal relationship remains unclear.
    Methods: Utilizing Mendelian randomization, we evaluated the causal association between genetically predicted IPFD and pancreatitis. This approach utilized genetic variants from genome-wide association studies of IPFD (n=25,617), acute pancreatitis (n=6,787 cases/361,641 controls), and chronic pancreatitis (n=3,875 cases/361,641 controls).
    Results: Genetically predicted IPFD was significantly associated with acute pancreatitis (OR per 1-SD increase: 1.40[95%CI:1.12-1.76], p=0.0032) and chronic pancreatitis (OR:1.64[95%CI:1.13-2.39], p=0.0097).
    Discussion: Our findings support a causal role of IPFD in pancreatitis, suggesting that reducing IPFD could lower the risk of pancreatitis.
    Keywords:  exocrine pancreas; fatty pancreas; pancreas fat; pancreatic fat; pancreatic steatosis
    DOI:  https://doi.org/10.1101/2024.06.03.24308330
  22. Nat Commun. 2024 Jun 15. 15(1): 5135
    Deep cell phenotyping and spatial analysis of multiplexed imaging with TRACERx-PHLEX.
    Alastair Magness, Emma Colliver, Katey S S Enfield, Claudia Lee, Masako Shimato, Emer Daly, David A Moore, Monica Sivakumar, Karishma Valand, Dina Levi, Crispin T Hiley, Philip S Hobson, Febe van Maldegem, James L Reading, Sergio A Quezada, Julian Downward, Erik Sahai, Charles Swanton, Mihaela Angelova.
      The growing scale and dimensionality of multiplexed imaging require reproducible and comprehensive yet user-friendly computational pipelines. TRACERx-PHLEX performs deep learning-based cell segmentation (deep-imcyto), automated cell-type annotation (TYPEx) and interpretable spatial analysis (Spatial-PHLEX) as three independent but interoperable modules. PHLEX generates single-cell identities, cell densities within tissue compartments, marker positivity calls and spatial metrics such as cellular barrier scores, along with summary graphs and spatial visualisations. PHLEX was developed using imaging mass cytometry (IMC) in the TRACERx study, validated using published Co-detection by indexing (CODEX), IMC and orthogonal data and benchmarked against state-of-the-art approaches. We evaluated its use on different tissue types, tissue fixation conditions, image sizes and antibody panels. As PHLEX is an automated and containerised Nextflow pipeline, manual assessment, programming skills or pathology expertise are not essential. PHLEX offers an end-to-end solution in a growing field of highly multiplexed data and provides clinically relevant insights.
    DOI:  https://doi.org/10.1038/s41467-024-48870-5
  23. Sci Adv. 2024 Jun 21. 10(25): eadi0707
    Bimodality in Ras signaling originates from processivity of the Ras activator SOS without deterministic bistability.
    Albert A Lee, Neil H Kim, Steven Alvarez, He Ren, Joseph B DeGrandchamp, L J Nugent Lew, Jay T Groves.
      Ras is a small GTPase that is central to important functional decisions in diverse cell types. An important aspect of Ras signaling is its ability to exhibit bimodal or switch-like activity. We describe the total reconstitution of a receptor-mediated Ras activation-deactivation reaction catalyzed by SOS and p120-RasGAP on supported lipid membrane microarrays. The results reveal a bimodal Ras activation response, which is not a result of deterministic bistability but is rather driven by the distinct processivity of the Ras activator, SOS. Furthermore, the bimodal response is controlled by the condensation state of the scaffold protein, LAT, to which SOS is recruited. Processivity-driven bimodality leads to stochastic bursts of Ras activation even under strongly deactivating conditions. This behavior contrasts deterministic bistability and may be more resistant to pharmacological inhibition.
    DOI:  https://doi.org/10.1126/sciadv.adi0707
  24. Nat Rev Cancer. 2024 Jun 19.
    Why do patients with cancer die?
    Adrienne Boire, Katy Burke, Thomas R Cox, Theresa Guise, Mariam Jamal-Hanjani, Tobias Janowitz, Rosandra Kaplan, Rebecca Lee, Charles Swanton, Matthew G Vander Heiden, Erik Sahai.
      Cancer is a major cause of global mortality, both in affluent countries and increasingly in developing nations. Many patients with cancer experience reduced life expectancy and have metastatic disease at the time of death. However, the more precise causes of mortality and patient deterioration before death remain poorly understood. This scarcity of information, particularly the lack of mechanistic insights, presents a challenge for the development of novel treatment strategies to improve the quality of, and potentially extend, life for patients with late-stage cancer. In addition, earlier deployment of existing strategies to prolong quality of life is highly desirable. In this Roadmap, we review the proximal causes of mortality in patients with cancer and discuss current knowledge about the interconnections between mechanisms that contribute to mortality, before finally proposing new and improved avenues for data collection, research and the development of treatment strategies that may improve quality of life for patients.
    DOI:  https://doi.org/10.1038/s41568-024-00708-4
  25. Mechanobiol Med. 2024 Sep;pii: 100071. [Epub ahead of print]2(3):
    Asymmetric crowders and membrane morphology at the nexus of intracellular trafficking and oncology.
    Kshitiz Parihar, Seung-Hyun B Ko, Ryan P Bradley, Phillip Taylor, N Ramakrishnan, Tobias Baumgart, Wei Guo, Valerie M Weaver, Paul A Janmey, Ravi Radhakrishnan.
      A definitive understanding of the interplay between protein binding/migration and membrane curvature evolution is emerging but needs further study. The mechanisms defining such phenomena are critical to intracellular transport and trafficking of proteins. Among trafficking modalities, exosomes have drawn attention in cancer research as these nano-sized naturally occurring vehicles are implicated in intercellular communication in the tumor microenvironment, suppressing anti-tumor immunity and preparing the metastatic niche for progression. A significant question in the field is how the release and composition of tumor exosomes are regulated. In this perspective article, we explore how physical factors such as geometry and tissue mechanics regulate cell cortical tension to influence exosome production by co-opting the biophysics as well as the signaling dynamics of intracellular trafficking pathways and how these exosomes contribute to the suppression of anti-tumor immunity and promote metastasis. We describe a multiscale modeling approach whose impact goes beyond the fundamental investigation of specific cellular processes toward actual clinical translation. Exosomal mechanisms are critical to developing and approving liquid biopsy technologies, poised to transform future non-invasive, longitudinal profiling of evolving tumors and resistance to cancer therapies to bring us one step closer to the promise of personalized medicine.
    Keywords:  Curvature sensing; Morphological transitions; Multiscale modeling; Oncology; Trafficking
    DOI:  https://doi.org/10.1016/j.mbm.2024.100071
  26. bioRxiv. 2024 Jun 06. pii: 2024.06.05.597552. [Epub ahead of print]
    A phosphorylation-controlled switch confers cell cycle-dependent protein relocalization.
    Xiaofu Cao, Shiying Huang, Mateusz M Wagner, Yuan-Ting Cho, Din-Chi Chiu, Krista M Wartchow, Artur Lazarian, Laura Beth McIntire, Marcus B Smolka, Jeremy M Baskin.
      Tools for acute manipulation of protein localization enable elucidation of spatiotemporally defined functions, but their reliance on exogenous triggers can interfere with cell physiology. This limitation is particularly apparent for studying mitosis, whose highly choreographed events are sensitive to perturbations. Here we exploit the serendipitous discovery of a phosphorylation-controlled, cell cycle-dependent localization change of the adaptor protein PLEKHA5 to develop a system for mitosis-specific protein recruitment to the plasma membrane that requires no exogenous stimulus. Mitosis-enabled Anchor-away/Recruiter System (MARS) comprises an engineered, 15-kDa module derived from PLEKHA5 capable of recruiting functional protein cargoes to the plasma membrane during mitosis, either through direct fusion or via GFP-GFP nanobody interaction. Applications of MARS include both knock sideways to rapidly extract proteins from their native localizations during mitosis and conditional recruitment of lipid-metabolizing enzymes for mitosis-selective editing of plasma membrane lipid content, without the need for exogenous triggers or perturbative synchronization methods.
    DOI:  https://doi.org/10.1101/2024.06.05.597552
  27. BMC Med Inform Decis Mak. 2024 Jun 20. 24(Suppl 4): 175
    Robust and consistent biomarker candidates identification by a machine learning approach applied to pancreatic ductal adenocarcinoma metastasis.
    Tanakamol Mahawan, Teifion Luckett, Ainhoa Mielgo Iza, Natapol Pornputtapong, Eva Caamaño Gutiérrez.
       BACKGROUND: Machine Learning (ML) plays a crucial role in biomedical research. Nevertheless, it still has limitations in data integration and irreproducibility. To address these challenges, robust methods are needed. Pancreatic ductal adenocarcinoma (PDAC), a highly aggressive cancer with low early detection rates and survival rates, is used as a case study. PDAC lacks reliable diagnostic biomarkers, especially metastatic biomarkers, which remains an unmet need. In this study, we propose an ML-based approach for discovering disease biomarkers, apply it to the identification of a PDAC metastatic composite biomarker candidate, and demonstrate the advantages of harnessing data resources.
    METHODS: We utilised primary tumour RNAseq data from five public repositories, pooling samples to maximise statistical power and integrating data by correcting for technical variance. Data were split into train and validation sets. The train dataset underwent variable selection via a 10-fold cross-validation process that combined three algorithms in 100 models per fold. Genes found in at least 80% of models and five folds were considered robust to build a consensus multivariate model. A random forest model was constructed using selected genes from the train dataset and tested in the validation set. We also assessed the goodness of prediction by recalibrating a model using only the validation data. The biological context and relevance of signals was explored through enrichment and pathway analyses using QIAGEN Ingenuity Pathway Analysis and GeneMANIA.
    RESULTS: We developed a pipeline that can detect robust signatures to build composite biomarkers. We tested the pipeline in PDAC, exploiting transcriptomics data from different sources, proposing a composite biomarker candidate comprised of fifteen genes consistently selected that showed very promising predictive capability. Biological contextualisation revealed links with cancer progression and metastasis, underscoring their potential relevance. All code is available in GitHub.
    CONCLUSION: This study establishes a robust framework for identifying composite biomarkers across various disease contexts. We demonstrate its potential by proposing a plausible composite biomarker candidate for PDAC metastasis. By reusing data from public repositories, we highlight the sustainability of our research and the wider applications of our pipeline. The preliminary findings shed light on a promising validation and application path.
    Keywords:  Biomarker identification; Machine Learning; Metastasis; PDAC; Pancreatic cancer
    DOI:  https://doi.org/10.1186/s12911-024-02578-0
  28. Nat Aging. 2024 Jun 19.
    Principal component-based clinical aging clocks identify signatures of healthy aging and targets for clinical intervention.
    Sheng Fong, Kamil Pabis, Djakim Latumalea, Nomuundari Dugersuren, Maximilian Unfried, Nicholas Tolwinski, Brian Kennedy, Jan Gruber.
      Clocks that measure biological age should predict all-cause mortality and give rise to actionable insights to promote healthy aging. Here we applied dimensionality reduction by principal component analysis to clinical data to generate a clinical aging clock (PCAge) identifying signatures (principal components) separating healthy and unhealthy aging trajectories. We found signatures of metabolic dysregulation, cardiac and renal dysfunction and inflammation that predict unsuccessful aging, and we demonstrate that these processes can be impacted using well-established drug interventions. Furthermore, we generated a streamlined aging clock (LinAge), based directly on PCAge, which maintains equivalent predictive power but relies on substantially fewer features. Finally, we demonstrate that our approach can be tailored to individual datasets, by re-training a custom clinical clock (CALinAge), for use in the Comprehensive Assessment of Long-term Effects of Reducing Intake of Energy (CALERIE) study of caloric restriction. Our analysis of CALERIE participants suggests that 2 years of mild caloric restriction significantly reduces biological age. Altogether, we demonstrate that this dimensionality reduction approach, through integrating different biological markers, can provide targets for preventative medicine and the promotion of healthy aging.
    DOI:  https://doi.org/10.1038/s43587-024-00646-8
  29. Science. 2024 Jun 21. 384(6702): 1300-1301
    Cellular senescence in normal physiology.
    João Pedro de Magalhães.
      Long associated with aging, senescent cells can promote health and have physiological roles.
    DOI:  https://doi.org/10.1126/science.adj7050
  30. Cureus. 2024 May;16(5): e60670
    A Nine-Year-Old Child With Metastatic Pancreatic Adenocarcinoma.
    Katelin Magnan, Linford Williams, Qian Wang, Julia Meade.
      Pancreatic ductal adenocarcinoma is exceedingly rare in children. Here, we report the case of a nine-year-old boy diagnosed with pancreatic ductal adenocarcinoma. The patient was treated per the National Comprehensive Cancer Network® (NCCN®) guidelines for adults with pancreatic cancer. Though the patient had multiple episodes of progression, the patient has remained alive with the disease 18 months after the initial diagnosis.
    Keywords:  cancer-genetics; chemotherapy for pdac and biliary tract carcinoma; pancreatic adenocarcinoma treatment; rare case report; survival of pediatric cancer
    DOI:  https://doi.org/10.7759/cureus.60670
  31. Sci Rep. 2024 Jun 20. 14(1): 14281
    Bellybutton: accessible and customizable deep-learning image segmentation.
    Sam Dillavou, Jesse M Hanlan, Anthony T Chieco, Hongyi Xiao, Sage Fulco, Kevin T Turner, Douglas J Durian.
      The conversion of raw images into quantifiable data can be a major hurdle and time-sink in experimental research, and typically involves identifying region(s) of interest, a process known as segmentation. Machine learning tools for image segmentation are often specific to a set of tasks, such as tracking cells, or require substantial compute or coding knowledge to train and use. Here we introduce an easy-to-use (no coding required), image segmentation method, using a 15-layer convolutional neural network that can be trained on a laptop: Bellybutton. The algorithm trains on user-provided segmentation of example images, but, as we show, just one or even a sub-selection of one training image can be sufficient in some cases. We detail the machine learning method and give three use cases where Bellybutton correctly segments images despite substantial lighting, shape, size, focus, and/or structure variation across the regions(s) of interest. Instructions for easy download and use, with further details and the datasets used in this paper are available at pypi.org/project/Bellybuttonseg .
    DOI:  https://doi.org/10.1038/s41598-024-63906-y
  32. Elife. 2024 Jun 18. pii: RP89712. [Epub ahead of print]12
    Fine-tuning spatial-temporal dynamics and surface receptor expression support plasma cell-intrinsic longevity.
    Zhixin Jing, Phillip Galbo, Luis Ovando, Megan Demouth, Skylar Welte, Rosa Park, Kartik Chandran, Yinghao Wu, Thomas MacCarthy, Deyou Zheng, David Fooksman.
      Durable serological memory following vaccination is critically dependent on the production and survival of long-lived plasma cells (LLPCs). Yet, the factors that control LLPC specification and survival remain poorly resolved. Using intravital two-photon imaging, we find that in contrast to most plasma cells (PCs) in the bone marrow (BM), LLPCs are uniquely sessile and organized into clusters that are dependent on APRIL, an important survival factor. Using deep, bulk RNA sequencing, and surface protein flow-based phenotyping, we find that LLPCs express a unique transcriptome and phenotype compared to bulk PCs, fine-tuning expression of key cell surface molecules, CD93, CD81, CXCR4, CD326, CD44, and CD48, important for adhesion and homing. Conditional deletion of Cxcr4 in PCs following immunization leads to rapid mobilization from the BM, reduced survival of antigen-specific PCs, and ultimately accelerated decay of antibody titer. In naïve mice, the endogenous LLPCs BCR repertoire exhibits reduced diversity, reduced somatic mutations, and increased public clones and IgM isotypes, particularly in young mice, suggesting LLPC specification is non-random. As mice age, the BM PC compartment becomes enriched in LLPCs, which may outcompete and limit entry of new PCs into the LLPC niche and pool.
    Keywords:  CXCR4; antibody; bone marrow; immunology; inflammation; long-lived plasma cells; mouse; multiphoton; vaccination
    DOI:  https://doi.org/10.7554/eLife.89712
  33. Dev Cell. 2024 May 20. pii: S1534-5807(24)00295-8. [Epub ahead of print]
    Suppressed basal mitophagy drives cellular aging phenotypes that can be reversed by a p62-targeting small molecule.
    George Kelly, Tetsushi Kataura, Johan Panek, Gailing Ma, Hanna Salmonowicz, Ashley Davis, Hannah Kendall, Charlotte Brookes, Daniel Moscoh Ayine-Tora, Peter Banks, Glyn Nelson, Laura Dobby, Patricia R Pitrez, Laura Booth, Lydia Costello, Gavin D Richardson, Penny Lovat, Stefan Przyborski, Lino Ferreira, Laura Greaves, Karolina Szczepanowska, Thomas von Zglinicki, Satomi Miwa, Max Brown, Michael Flagler, John E Oblong, Charles C Bascom, Bernadette Carroll, Jóhannes Reynisson, Viktor I Korolchuk.
      Selective degradation of damaged mitochondria by autophagy (mitophagy) is proposed to play an important role in cellular homeostasis. However, the molecular mechanisms and the requirement of mitochondrial quality control by mitophagy for cellular physiology are poorly understood. Here, we demonstrated that primary human cells maintain highly active basal mitophagy initiated by mitochondrial superoxide signaling. Mitophagy was found to be mediated by PINK1/Parkin-dependent pathway involving p62 as a selective autophagy receptor (SAR). Importantly, this pathway was suppressed upon the induction of cellular senescence and in naturally aged cells, leading to a robust shutdown of mitophagy. Inhibition of mitophagy in proliferating cells was sufficient to trigger the senescence program, while reactivation of mitophagy was necessary for the anti-senescence effects of NAD precursors or rapamycin. Furthermore, reactivation of mitophagy by a p62-targeting small molecule rescued markers of cellular aging, which establishes mitochondrial quality control as a promising target for anti-aging interventions.
    Keywords:  PINK1; Parkin; aging; autophagy; mitophagy; nicotinamide; nicotinamide riboside; p62; rapamycin; redox; senescence
    DOI:  https://doi.org/10.1016/j.devcel.2024.04.020
  34. Nat Rev Cancer. 2024 Jun 21.
    The road less travelled.
      
    DOI:  https://doi.org/10.1038/s41568-024-00720-8
  35. Adv Sci (Weinh). 2024 Jun 12. e2400630
    Leveraging Senescent Cancer Cell Membrane to Potentiate Cancer Immunotherapy Through Biomimetic Nanovaccine.
    Chao Yang, Yinglu Chen, Jie Liu, Wensheng Zhang, Yan He, Fangman Chen, Xiaochun Xie, Jie Tang, Shan Guan, Dan Shao, Zheng Wang, Liang Wang.
      Senescent cancer cells are endowed with high immunogenic potential that has been leveraged to elicit antitumor immunity and potentially complement anticancer therapies. However, the efficacy of live senescent cancer cell-based vaccination is limited by interference from immunosuppressive senescence-associated secretory phenotype and pro-tumorigenic capacity of senescent cells. Here, a senescent cancer cell-based nanovaccine with strong immunogenicity and favorable potential for immunotherapy is reported. The biomimetic nanovaccine integrating a senescent cancer cell membrane-coated nanoadjuvant outperforms living senescent cancer cells in enhancing dendritic cells (DCs) internalization, improving lymph node targeting, and enhancing immune responses. In contrast to nanovaccines generated from immunogenic cell death-induced tumor cells, senescent nanovaccines facilitate DC maturation, eliciting superior antitumor protection and improving therapeutic outcomes in melanoma-challenged mice with fewer side effects when combined with αPD-1. The study suggests a versatile biomanufacturing approach to maximize immunogenic potential and minimize adverse effects of senescent cancer cell-based vaccination and advances the design of biomimetic nanovaccines for cancer immunotherapy.
    Keywords:  biomimetic; engineered membrane; immunotherapy; nanovaccine; senescent cancer cell
    DOI:  https://doi.org/10.1002/advs.202400630
  36. Nat Commun. 2024 Jun 18. 15(1): 5148
    Digital telomere measurement by long-read sequencing distinguishes healthy aging from disease.
    Santiago E Sanchez, Yuchao Gu, Yan Wang, Anudeep Golla, Annika Martin, William Shomali, Dirk Hockemeyer, Sharon A Savage, Steven E Artandi.
      Telomere length is an important biomarker of organismal aging and cellular replicative potential, but existing measurement methods are limited in resolution and accuracy. Here, we deploy digital telomere measurement (DTM) by nanopore sequencing to understand how distributions of human telomere length change with age and disease. We measure telomere attrition and de novo elongation with up to 30 bp resolution in genetically defined populations of human cells, in blood cells from healthy donors and in blood cells from patients with genetic defects in telomere maintenance. We find that human aging is accompanied by a progressive loss of long telomeres and an accumulation of shorter telomeres. In patients with defects in telomere maintenance, the accumulation of short telomeres is more pronounced and correlates with phenotypic severity. We apply machine learning to train a binary classification model that distinguishes healthy individuals from those with telomere biology disorders. This sequencing and bioinformatic pipeline will advance our understanding of telomere maintenance mechanisms and the use of telomere length as a clinical biomarker of aging and disease.
    DOI:  https://doi.org/10.1038/s41467-024-49007-4
  37. bioRxiv. 2024 Jun 04. pii: 2024.06.04.597287. [Epub ahead of print]
    The AID2 system offers a potent tool for rapid, reversible, or sustained degradation of essential proteins in live mice.
    Valentina C Sladky, Margaret A Strong, Daniel Tapias-Gomez, Cayla E Jewett, Chelsea G Drown, Phillip M Scott, Andrew J Holland.
      Studying essential genes required for dynamic processes in live mice is challenging as genetic perturbations are irreversible and limited by slow protein depletion kinetics. The first-generation auxin-inducible-degron (AID) system is a powerful tool for analyzing inducible protein loss in cultured cells. However, auxin administration is toxic to mice, preventing its long-term use in animals. Here, we use an optimized second-generation AID system to achieve the conditional and reversible loss of the essential centrosomal protein CEP192 in live mice. We show that the auxin derivative 5-Ph-IAA is well tolerated over two weeks and drives near-complete CEP192-mAID degradation in less than one hour in vivo . Prolonged CEP192 loss led to cell division failure and cell death in proliferative tissues. Thus, the second-generation AID system is well suited for rapid and/or sustained protein depletion in live mice, offering a valuable new tool for interrogating protein function in vivo .
    DOI:  https://doi.org/10.1101/2024.06.04.597287
  38. Nanomedicine. 2024 Jun 15. pii: S1549-9634(24)00033-9. [Epub ahead of print] 102764
    Blocking the utilization of carbon sources via two pathways to induce tumor starvation for cancer treatment.
    Zhihui Zhu, Pan Qiao, Mengyu Liu, Fangfang Sun, Meilin Geng, Hanchun Yao.
      Glucose oxidase (GOx) is often used to starvation therapy. However, only consuming glucose cannot completely block the energy metabolism of tumor cells. Lactate can support tumor cell survival in the absence of glucose. Here, we constructed a nanoplatform (Met@HMnO2-GOx/HA) that can deplete glucose while inhibiting the compensatory use of lactate by cells to enhance the effect of tumor starvation therapy. GOx can catalyze glucose into gluconic acid and H2O2, and then HMnO2 catalyzes H2O2 into O2 to compensate for the oxygen consumed by GOx, allowing the reaction to proceed sustainably. Furthermore, metformin (Met) can inhibit the conversion of lactate to pyruvate in a redox-dependent manner and reduce the utilization of lactate by tumor cells. Met@HMnO2-GOx/HA nanoparticles maximize the efficacy of tumor starvation therapy by simultaneously inhibiting cellular utilization of two carbon sources. Therefore, this platform is expected to provide new strategies for tumor treatment.
    Keywords:  Carbon sources; Glucose oxidase; Lactate; Metformin; Starvation therapy
    DOI:  https://doi.org/10.1016/j.nano.2024.102764
  39. Nature. 2024 Jun;630(8017): 744-751
    Strand-resolved mutagenicity of DNA damage and repair.
    Liver Cancer Evolution Consortium
      DNA base damage is a major source of oncogenic mutations1. Such damage can produce strand-phased mutation patterns and multiallelic variation through the process of lesion segregation2. Here we exploited these properties to reveal how strand-asymmetric processes, such as replication and transcription, shape DNA damage and repair. Despite distinct mechanisms of leading and lagging strand replication3,4, we observe identical fidelity and damage tolerance for both strands. For small alkylation adducts of DNA, our results support a model in which the same translesion polymerase is recruited on-the-fly to both replication strands, starkly contrasting the strand asymmetric tolerance of bulky UV-induced adducts5. The accumulation of multiple distinct mutations at the site of persistent lesions provides the means to quantify the relative efficiency of repair processes genome wide and at single-base resolution. At multiple scales, we show DNA damage-induced mutations are largely shaped by the influence of DNA accessibility on repair efficiency, rather than gradients of DNA damage. Finally, we reveal specific genomic conditions that can actively drive oncogenic mutagenesis by corrupting the fidelity of nucleotide excision repair. These results provide insight into how strand-asymmetric mechanisms underlie the formation, tolerance and repair of DNA damage, thereby shaping cancer genome evolution.
    DOI:  https://doi.org/10.1038/s41586-024-07490-1
  40. Curr Biol. 2024 Jun 11. pii: S0960-9822(24)00675-4. [Epub ahead of print]
    Coinfecting phages impede each other's entry into the cell.
    Thu Vu Phuc Nguyen, Yuchen Wu, Tianyou Yao, Jimmy T Trinh, Lanying Zeng, Yann R Chemla, Ido Golding.
      The developmental choice made by temperate phages, between cell death (lysis) and viral dormancy (lysogeny), is influenced by the relative abundance of viruses and hosts in the environment. The paradigm for this abundance-driven decision is phage lambda of E. coli, whose propensity to lysogenize increases with the number of viruses coinfecting the same bacterium. It is believed that lambda uses this number to infer whether phages or bacteria outnumber each other. However, this interpretation is premised on an accurate mapping between the extracellular phage-to-bacteria ratio and the intracellular multiplicity of infection (MOI). Here, we show this premise to be faulty. By simultaneously labeling phage capsids and genomes, we find that, while the number of phages landing on each cell reliably samples the population ratio, the number of phages entering the cell does not. Single-cell infections, performed in a microfluidic device and interpreted using a stochastic model, reveal that the probability and rate of phage entry decrease with the number of adsorbed phages. This decrease reflects an MOI-dependent perturbation to host physiology caused by phage attachment, as evidenced by compromised membrane integrity and loss of membrane potential. The dependence of entry dynamics on the surrounding medium results in a strong impact on the infection outcome, while the protracted entry of coinfecting phages increases the heterogeneity in infection outcome at a given MOI. Our findings in lambda, and similar results we obtained for phages T5 and P1, demonstrate the previously unappreciated role played by entry dynamics in determining the outcome of bacteriophage infection.
    Keywords:  Escherichia coli; bacteriophage; biophysics; genome ejection; lambda; lysogeny; mathematical modeling; membrane potential; microbiology; microscopy
    DOI:  https://doi.org/10.1016/j.cub.2024.05.032
  41. Proc Natl Acad Sci U S A. 2024 Jun 25. 121(26): e2321579121
    Membrane nanotubes transform into double-membrane sheets at condensate droplets.
    Ziliang Zhao, Vahid Satarifard, Reinhard Lipowsky, Rumiana Dimova.
      Cellular membranes exhibit a multitude of highly curved morphologies such as buds, nanotubes, cisterna-like sheets defining the outlines of organelles. Here, we mimic cell compartmentation using an aqueous two-phase system of dextran and poly(ethylene glycol) encapsulated in giant vesicles. Upon osmotic deflation, the vesicle membrane forms nanotubes, which undergo surprising morphological transformations at the liquid-liquid interfaces inside the vesicles. At these interfaces, the nanotubes transform into cisterna-like double-membrane sheets (DMS) connected to the mother vesicle via short membrane necks. Using super-resolution (stimulated emission depletion) microscopy and theoretical considerations, we construct a morphology diagram predicting the tube-to-sheet transformation, which is driven by a decrease in the free energy. Nanotube knots can prohibit the tube-to-sheet transformation by blocking water influx into the tubes. Because both nanotubes and DMSs are frequently formed by cellular membranes, understanding the formation and transformation between these membrane morphologies provides insight into the origin and evolution of cellular organelles.
    Keywords:  condensate interface; double-membrane sheet; giant unilamellar vesicles (GUV); stimulated emission depletion (STED); tube-to-sheet transformation
    DOI:  https://doi.org/10.1073/pnas.2321579121
  42. Sci Adv. 2024 Jun 21. 10(25): eado4722
    Freestanding bilayer microscope for single-molecule imaging of membrane proteins.
    Gonzalo Pérez-Mitta, Yeliz Sezgin, Weiwei Wang, Roderick MacKinnon.
      Integral membrane proteins (IMPs) constitute a large fraction of organismal proteomes, playing fundamental roles in physiology and disease. Despite their importance, the mechanisms underlying dynamic features of IMPs, such as anomalous diffusion, protein-protein interactions, and protein clustering, remain largely unknown due to the high complexity of cell membrane environments. Available methods for in vitro studies are insufficient to study IMP dynamics systematically. This publication introduces the freestanding bilayer microscope (FBM), which combines the advantages of freestanding bilayers with single-particle tracking. The FBM, based on planar lipid bilayers, enables the study of IMP dynamics with single-molecule resolution and unconstrained diffusion. This paper benchmarks the FBM against total internal reflection fluorescence imaging on supported bilayers and is used here to estimate ion channel open probability and to examine the diffusion behavior of an ion channel in phase-separated bilayers. The FBM emerges as a powerful tool to examine membrane protein/lipid organization and dynamics to understand cell membrane processes.
    DOI:  https://doi.org/10.1126/sciadv.ado4722
  43. Phys Rev Lett. 2024 Jun 07. 132(23): 238303
    Model of Active Solids: Rigid Body Motion and Shape-Changing Mechanisms.
    Claudio Hernández-López, Paul Baconnier, Corentin Coulais, Olivier Dauchot, Gustavo Düring.
      Active solids such as cell collectives, colloidal clusters, and active metamaterials exhibit diverse collective phenomena, ranging from rigid body motion to shape-changing mechanisms. The nonlinear dynamics of such active materials remains, however, poorly understood when they host zero-energy deformation modes and when noise is present. Here, we show that stress propagation in a model of active solids induces the spontaneous actuation of multiple soft floppy modes, even without exciting vibrational modes. By introducing an adiabatic approximation, we map the dynamics onto an effective Landau free energy, predicting mode selection and the onset of collective dynamics. These results open new ways to study and design living and robotic materials with multiple modes of locomotion and shape change.
    DOI:  https://doi.org/10.1103/PhysRevLett.132.238303
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