bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2024–10–13
thirty papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1.
  2. Cancer-induced systemic pre-conditioning of distant organs: building a niche for metastatic cells.
  3. The Evolutionary Forest of Pancreatic Cancer.
  4. Disruption of cellular plasticity by repeat RNAs in human pancreatic cancer.
  5. Inhibition of Ribosome Biogenesis in vivo Causes p53-Dependent Death and p53-Independent Dysfunction.
  6. Pancreatic cancer cells overexpressing interleukin 6 induce T-cell-mediated tumor clearance and durable anti-tumor immune response.
  7. An RNA damage response network mediates the lethality of 5-FU in colorectal cancer.
  8. Biogenesis of omegasomes and autophagosomes in mammalian autophagy.
  9. Biomolecular condensates mediate bending and scission of endosome membranes.
  10. Stress granules are not present in Kras mutant cancers and do not control tumor growth.
  11. CASPER: A Phase I trial combining calaspargase pegol-mnkl and cobimetinib in pancreatic cancer.
  12. Unexpected asymmetric distribution of cholesterol and phospholipids in equilibrium model membranes.
  13. Identifying specific functional roles for senescence across cell types.
  14. In vitro and in vivo reconstitution systems reveal the membrane remodeling ability of LC3B and ATG16L1 to form phagophore-like membrane cups.
  15. Vasoactive intestinal peptide promotes secretory differentiation and mitigates radiation-induced intestinal injury.
  16. Precision preclinical modeling to advance cancer treatment.
  17. Cryo-electron tomography pipeline for plasma membranes.
  18. Galvanin is an electric-field sensor for directed cell migration.
  19. The brain-body energy conservation model of aging.
  20. Lipids in the tumor microenvironment: immune modulation and metastasis.
  21. DELE1 maintains muscle proteostasis to promote growth and survival in mitochondrial myopathy.
  22. Lung-resident alveolar macrophages regulate the timing of breast cancer metastasis.
  23. Single-shot 20-fold expansion microscopy.
  24. AutoGater: a weakly supervised neural network model to gate cells in flow cytometric analyses.
  25. High mitochondrial DNA content is a key determinant of stemness, proliferation, cell migration, and cancer metastasis in vivo.
  26. Leptin as a surrogate immune-metabolic marker to predict impact of anti-cachectic therapy: results of a prospective randomized trial in multiple solid tumors.
  27. Long-term breast cancer response to CDK4/6 inhibition defined by TP53-mediated geroconversion.
  28. T lymphocyte recruitment to melanoma brain tumors depends on distinct venous vessels.
  29. Autophagy and the pancreas: Healthy and disease states.
  30. Scalable, compressed phenotypic screening using pooled perturbations.
  1. Nat Cancer. 2024 Oct 11.
    The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1.
    Rodrigo Romero, Tinyi Chu, Tania J González Robles, Perianne Smith, Yubin Xie, Harmanpreet Kaur, Sara Yoder, Huiyong Zhao, Chenyi Mao, Wenfei Kang, Maria V Pulina, Kayla E Lawrence, Anuradha Gopalan, Samir Zaidi, Kwangmin Yoo, Jungmin Choi, Ning Fan, Olivia Gerstner, Wouter R Karthaus, Elisa DeStanchina, Kelly V Ruggles, Peter M K Westcott, Ronan Chaligné, Dana Pe'er, Charles L Sawyers.
      Lineage plasticity is a hallmark of cancer progression that impacts therapy outcomes, yet the mechanisms mediating this process remain unclear. Here, we introduce a versatile in vivo platform to interrogate neuroendocrine lineage transformation throughout prostate cancer progression. Transplanted mouse prostate organoids with human-relevant driver mutations (Rb1-/-; Trp53-/-; cMyc+ or Pten-/-; Trp53-/-; cMyc+) develop adenocarcinomas, but only those with Rb1 deletion advance to aggressive, ASCL1+ neuroendocrine prostate cancer (NEPC) resistant to androgen receptor signaling inhibitors. Notably, this transition requires an in vivo microenvironment not replicated by conventional organoid culture. Using multiplexed immunofluorescence and spatial transcriptomics, we reveal that ASCL1+ cells arise from KRT8+ luminal cells, progressing into transcriptionally heterogeneous ASCL1+;KRT8- NEPC. Ascl1 loss in established NEPC causes transient regression followed by recurrence, but its deletion before transplantation abrogates lineage plasticity, resulting in castration-sensitive adenocarcinomas. This dynamic model highlights the importance of therapy timing and offers a platform to identify additional lineage plasticity drivers.
    DOI:  https://doi.org/10.1038/s43018-024-00838-6
  2. Nat Rev Cancer. 2024 Oct 10.
    Cancer-induced systemic pre-conditioning of distant organs: building a niche for metastatic cells.
    Nicolas Rabas, Rute M M Ferreira, Stefania Di Blasio, Ilaria Malanchi.
      From their early genesis, tumour cells integrate with the surrounding normal cells to form an abnormal structure that is tightly integrated with the host organism via blood and lymphatic vessels and even neural associations. Using these connections, emerging cancers send a plethora of mediators that efficiently perturb the entire organism and induce changes in distant tissues. These perturbations serendipitously favour early metastatic establishment by promoting a more favourable tissue environment (niche) that supports the persistence of disseminated tumour cells within a foreign tissue. Because the establishment of early metastatic niches represents a key limiting step for metastasis, the creation of a more suitable pre-conditioned tissue strongly enhances metastatic success. In this Review, we provide an updated view of the mechanisms and mediators of primary tumours described so far that induce a pro-metastatic conditioning of distant organs, which favours early metastatic niche formation. We reflect on the nature of cancer-induced systemic conditioning, considering that non-cancer-dependent perturbations of tissue homeostasis are also able to trigger pro-metastatic conditioning. We argue that a more holistic view of the processes catalysing metastatic progression is needed to identify preventive or therapeutic opportunities.
    DOI:  https://doi.org/10.1038/s41568-024-00752-0
  3. Cancer Discov. 2024 Oct 08.
    The Evolutionary Forest of Pancreatic Cancer.
    Katelyn M Mullen, Jungeui Hong, Marc A Attiyeh, Akimasa Hayashi, Hitomi Sakamoto, Zachary A Kohutek, Caitlin A McIntyre, Haochen Zhang, Alvin P Makohon-Moore, Amanda Zucker, Laura D Wood, Matthew A Myers, Brian J Arnold, Simone Zaccaria, Joanne F Chou, Marinela Capanu, Nicholas D Socci, Benjamin J Raphael, Christine A Iacobuzio-Donahue.
      The genomic features of pancreatic ductal adenocarcinoma (PDAC) have been well described, yet the evolutionary contexts within which those features occur remains unexplored. We studied the genome landscapes, phylogenies and clonal compositions of 91 PDACs in relation to clinicopathologic features. There was no difference in the number of driver mutations or the evolutionary timing that each mutation occurred. High truncal density, a metric of the accumulation of somatic mutations in the lineage that gave rise to each PDAC, was significantly associated with worse overall survival. Polyclonal, monoclonal or mixed polyclonal/monoclonal metastases were identified across the cohort highlighting multiple forms of inter-tumoral heterogeneity. Advanced stage and treated PDACs had higher odds of being polyclonal, whereas oligometastatic PDACs had fewer driver alterations, a lower fractional allelic loss and increased likelihood of being monoclonal. In sum, our findings reveal novel insights into the dynamic nature of the PDAC genome beyond established genetic paradigms.
    DOI:  https://doi.org/10.1158/2159-8290.CD-23-1541
  4. Cell. 2024 Oct 01. pii: S0092-8674(24)01072-9. [Epub ahead of print]
    Disruption of cellular plasticity by repeat RNAs in human pancreatic cancer.
    Eunae You, Patrick Danaher, Chenyue Lu, Siyu Sun, Luli Zou, Ildiko E Phillips, Alexandra S Rojas, Natalie I Ho, Yuhui Song, Michael J Raabe, Katherine H Xu, Peter M Richieri, Hao Li, Natalie Aston, Rebecca L Porter, Bidish K Patel, Linda T Nieman, Nathan Schurman, Briana M Hudson, Khrystyna North, Sarah E Church, Vikram Deshpande, Andrew S Liss, Tae K Kim, Yi Cui, Youngmi Kim, Benjamin D Greenbaum, Martin J Aryee, David T Ting.
      Aberrant expression of repeat RNAs in pancreatic ductal adenocarcinoma (PDAC) mimics viral-like responses with implications on tumor cell state and the response of the surrounding microenvironment. To better understand the relationship of repeat RNAs in human PDAC, we performed spatial molecular imaging at single-cell resolution in 46 primary tumors, revealing correlations of high repeat RNA expression with alterations in epithelial state in PDAC cells and myofibroblast phenotype in cancer-associated fibroblasts (CAFs). This loss of cellular identity is observed with dosing of extracellular vesicles (EVs) and individual repeat RNAs of PDAC and CAF cell culture models pointing to cell-cell intercommunication of these viral-like elements. Differences in PDAC and CAF responses are driven by distinct innate immune signaling through interferon regulatory factor 3 (IRF3). The cell-context-specific viral-like responses to repeat RNAs provide a mechanism for modulation of cellular plasticity in diverse cell types in the PDAC microenvironment.
    Keywords:  cancer-associated fibroblast; cellular plasticity; extracellular vesicles; pancreatic cancer; repeat RNA; spatial transcriptomics; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.cell.2024.09.024
  5. bioRxiv. 2024 Sep 26. pii: 2024.09.25.614959. [Epub ahead of print]
    Inhibition of Ribosome Biogenesis in vivo Causes p53-Dependent Death and p53-Independent Dysfunction.
    Charles J Cho, Thanh Nguyen, Amala K Rougeau, Yang-Zhe Huang, Sarah To, Xiaobo Lin, Supuni Thalalla Gamage, Jordan L Meier, Jason C Mills.
      Ribosomes are critical for cell function; their synthesis (known as ribosome biogenesis; "RiBi") is complex and energy-intensive. Surprisingly little is known about RiBi in differentiated cells in vivo in adult tissue. Here, we generated mice with conditional deletion of Nat10 , an essential gene for RiBi and translation, to investigate effects of RiBi blockade in vivo. We focused on RiBi in a long-lived, ribosome-rich cell population, pancreatic acinar cells, during homeostasis and tumorigenesis. We observed a surprising latency of several weeks between Nat10 deletion and onset of structural and functional abnormalities and p53-dependent acinar cell death, which was associated with translocation of ribosomal proteins RPL5 and RPL11 into acinar cell nucleoplasm. Indeed, deletion of Trp53 could rescue acinar cells from apoptotic cell death; however, Nat10 Δ / Δ ; Trp53 Δ / Δ acinar cells remained morphologically and functionally abnormal. Moreover, the deletion of Trp53 did not rescue the lethality of inducible, globally deleted Nat10 in adult mice nor did it rescue embryonic lethality of global Nat10 deletion, emphasizing p53-independent consequences of RiBi inhibition. Deletion of Nat10 in acinar cells blocked Kras -oncogene-driven pancreatic intraepithelial neoplasia and subsequent pancreatic ductal adenocarcinoma, regardless of Trp53 mutation status. Together, our results provide initial insights into how cells respond to defects in RiBi and translation in vivo .
    DOI:  https://doi.org/10.1101/2024.09.25.614959
  6. bioRxiv. 2024 Sep 27. pii: 2024.09.26.615308. [Epub ahead of print]
    Pancreatic cancer cells overexpressing interleukin 6 induce T-cell-mediated tumor clearance and durable anti-tumor immune response.
    Paige C Arneson-Wissink, Alexandra Q Bartlett, Heike Mendez, Xinxia Zhu, Jessica Dickie, Matthew McWhorter, Peter R Levasseur, Parham Diba, Katelyn T Byrne, Gregory D Scott, Robert Eil, Aaron J Grossberg.
      Tumor immune resistance is recognized as a contributor to low survivorship in pancreatic ductal adenocarcinoma (PDAC). We developed a novel murine model of spontaneous PDAC clearance, generated by overexpressing interleukin-6 (IL-6) in orthotopically implanted PDAC cancer cells (OT-PDAC IL6 ). Circulating IL-6 was 100-fold higher in OT-PDAC IL6 than in OT-PDAC parental mice. OT-PDAC IL6 tumors were present at 5 days post-implantation, and undetectable by 10 days post implantation. Flow cytometry revealed increased T cells and NK cells, and decreased T regulatory cells in OT-PDAC IL6 as compared to OT-PDAC parental tumors. Increased lymphoid aggregates were apparent by histological assessment and may account for elevated T cell content. Antibody-based depletion of CD4 + and CD8 + T cells prevented tumor clearance and significantly reduced survival of OT-PDAC IL6 mice. The anti-tumor immune response to OT-PDAC IL6 rendered mice immune to re-challenge with OT-PDAC parental tumors. In high concentrations, IL-6 acts in opposition to previously described pro-tumorigenic effects by enhancing the T cell-mediated anti-tumor response to PDAC.
    Statement of Significance: Interleukin 6 overexpression in pancreatic ductal adenocarcinoma cells induces T cell-driven tumor clearance that is rapid and durable. Supraphysiologic levels of interleukin 6 are sufficient to drive an anti-tumor immune microenvironment hallmarked by increased lymphoid aggregate formation, increased CD4 T cell abundance, and decreased Treg abundance.
    DOI:  https://doi.org/10.1101/2024.09.26.615308
  7. Cell Rep Med. 2024 Oct 03. pii: S2666-3791(24)00523-8. [Epub ahead of print] 101778
    An RNA damage response network mediates the lethality of 5-FU in colorectal cancer.
    Jung-Kuei Chen, Karl A Merrick, Yi Wen Kong, Anita Izrael-Tomasevic, George Eng, Erika D Handly, Jesse C Patterson, Ian G Cannell, Lucia Suarez-Lopez, Aaron M Hosios, Anh Dinh, Donald S Kirkpatrick, Kebing Yu, Christopher M Rose, Jonathan M Hernandez, Haeun Hwangbo, Adam C Palmer, Matthew G Vander Heiden, Ömer H Yilmaz, Michael B Yaffe.
      5-fluorouracil (5-FU), a major anti-cancer therapeutic, is believed to function primarily by inhibiting thymidylate synthase, depleting deoxythymidine triphosphate (dTTP), and causing DNA damage. Here, we show that clinical combinations of 5-FU with oxaliplatin or irinotecan show no synergy in human colorectal cancer (CRC) trials and sub-additive killing in CRC cell lines. Using selective 5-FU metabolites, phospho- and ubiquitin proteomics, and primary human CRC organoids, we demonstrate that 5-FU-mediated CRC cell killing primarily involves an RNA damage response during ribosome biogenesis, causing lysosomal degradation of damaged rRNAs and proteasomal degradation of ubiquitinated ribosomal proteins. Tumor types clinically responsive to 5-FU treatment show upregulated rRNA biogenesis while 5-FU clinically non-responsive tumor types do not, instead showing greater sensitivity to 5-FU's DNA damage effects. Finally, we show that treatments upregulating ribosome biogenesis, including KDM2A inhibition, promote RNA-dependent cell killing by 5-FU, demonstrating the potential for combinatorial targeting of this ribosomal RNA damage response for improved cancer therapy.
    Keywords:  5-FU; 5-FU-based chemotherapy; RNA damage; ribosomal RNA; ribosomal protein
    DOI:  https://doi.org/10.1016/j.xcrm.2024.101778
  8. Biochem Soc Trans. 2024 Oct 11. pii: BST20240015. [Epub ahead of print]
    Biogenesis of omegasomes and autophagosomes in mammalian autophagy.
    Puck N Norell, Daniele Campisi, Jagan Mohan, Thomas Wollert.
      Autophagy is a highly conserved catabolic pathway that maintains cellular homeostasis by promoting the degradation of damaged or superfluous cytoplasmic material. A hallmark of autophagy is the generation of membrane cisternae that sequester autophagic cargo. Expansion of these structures allows cargo to be engulfed in a highly selective and exclusive manner. Cytotoxic stress or starvation induces the formation of autophagosomes that sequester bulk cytoplasm instead of selected cargo. This rather nonselective pathway is essential for maintaining vital cellular functions during adverse conditions and is thus a major stress response pathway. Both selective and nonselective autophagy rely on the same molecular machinery. However, due to the different nature of cargo to be sequestered, the involved molecular mechanisms are fundamentally different. Although intense research over the past decades has advanced our understanding of autophagy, fundamental questions remain to be addressed. This review will focus on molecular principles and open questions regarding the formation of omegasomes and phagophores in nonselective mammalian autophagy.
    Keywords:  autophagy; nonselective autophagy; omegasome; phagophore
    DOI:  https://doi.org/10.1042/BST20240015
  9. Nature. 2024 Oct 09.
    Biomolecular condensates mediate bending and scission of endosome membranes.
    Yanning Wang, Shulin Li, Marcel Mokbel, Alexander I May, Zizhen Liang, Yonglun Zeng, Weiqi Wang, Honghong Zhang, Feifei Yu, Katharina Sporbeck, Liwen Jiang, Sebastian Aland, Jaime Agudo-Canalejo, Roland L Knorr, Xiaofeng Fang.
      Multivesicular bodies are key endosomal compartments implicated in cellular quality control through their degradation of membrane-bound cargo proteins1-3. The ATP-consuming ESCRT protein machinery mediates the capture and engulfment of membrane-bound cargo proteins through invagination and scission of multivesicular-body membranes to form intraluminal vesicles4,5. Here we report that the plant ESCRT component FREE16 forms liquid-like condensates that associate with membranes to drive intraluminal vesicle formation. We use a minimal physical model, reconstitution experiments and in silico simulations to identify the dynamics of this process and describe intermediate morphologies of nascent intraluminal vesicles. Furthermore, we find that condensate-wetting-induced line tension forces and membrane asymmetries are sufficient to mediate scission of the membrane neck without the ESCRT protein machinery or ATP consumption. Genetic manipulation of the ESCRT pathway in several eukaryotes provides additional evidence for condensate-mediated membrane scission in vivo. We find that the interplay between condensate and machinery-mediated scission mechanisms is indispensable for osmotic stress tolerance in plants. We propose that condensate-mediated scission represents a previously undescribed scission mechanism that depends on the physicomolecular properties of the condensate and is involved in a range of trafficking processes. More generally, FREE1 condensate-mediated membrane scission in multivesicular-body biogenesis highlights the fundamental role of wetting in intracellular dynamics and organization.
    DOI:  https://doi.org/10.1038/s41586-024-07990-0
  10. EMBO Rep. 2024 Oct 10.
    Stress granules are not present in Kras mutant cancers and do not control tumor growth.
    Maxime Libert, Sophie Quiquempoix, Jean S Fain, Sébastien Pyr Dit Ruys, Malak Haidar, Margaux Wulleman, Gaëtan Herinckx, Didier Vertommen, Christelle Bouchart, Tatjana Arsenijevic, Jean-Luc Van Laethem, Patrick Jacquemin.
      Stress granules (SG) are membraneless ribonucleoprotein-based cytoplasmic organelles that assemble in response to stress. Their formation is often associated with an almost global suppression of translation, and the aberrant assembly or disassembly of these granules has pathological implications in neurodegeneration and cancer. In cancer, and particularly in the presence of oncogenic KRAS mutations, in vivo studies concluded that SG increase the resistance of cancer cells to stress. Hence, SG have recently been considered a promising target for therapy. Here, starting from our observations that genes coding for SG proteins are stimulated during development of pancreatic ductal adenocarcinoma, we analyze the formation of SG during tumorigenesis. We resort to in vitro, in vivo and in silico approaches, using mouse models, human samples and human data. Our analyses do not support that SG are formed during tumorigenesis of KRAS-driven cancers, at least that their presence is not universal, leading us to propose that caution is required before considering SG as therapeutic targets.
    Keywords:  Cancer; KRAS; PDAC; Stress Granules
    DOI:  https://doi.org/10.1038/s44319-024-00284-6
  11. Future Oncol. 2024 Oct 08. 1-11
    CASPER: A Phase I trial combining calaspargase pegol-mnkl and cobimetinib in pancreatic cancer.
    Charles D Lopez, Adel Kardosh, Emerson Y Chen, Guillaume Pegna, Alexander Guimaraes, Bryan Foster, Brian Brinkerhoff, Shaun M Goodyear, Jeong-Youn Lim, Erin Taber, Brindha Rajagopalan, Exodus Edmerson, Johnson Vo, Katherine Nelson, Anna Jackson, Tasha Gingerich, Anne Fahlman, Christopher Lessenich, Francesca Fennell, Diane Ventura, Preeyam Roy, Dove Keith, Brett Sheppard, Jonathan R Brody, Gordon B Mills, Ze'ev A Ronai, Rosalie C Sears.
      Asparagine synthetase (ASNS) catalyzes the biosynthesis of asparagine from aspartate and glutamine. Cells lacking ASNS, however, are auxotrophic for asparagine. Use of L-asparaginase to promote asparagine starvation in solid tumors with low ASNS levels, such as pancreatic ductal adenocarcinoma (PDAC), is a rationale treatment strategy. However, tumor cell resistance to L-asparaginase has limited its clinical utility. Our preclinical studies show that RAS/MAPK signaling circumvents L-asparaginase-induced tumor killing, but L-asparaginase and MEK inhibition potentiated tumor killing; suggesting that this combination may provide meaningful clinical benefit to patients with PDAC. This Phase I trial (NCT05034627) will evaluate the safety and tolerability of the MEK inhibitor, cobimetinib, in combination with pegylated L-asparaginase, L calaspargase pegol-mknl, in patients with locally-advanced or metastatic PDAC.
    Keywords:  L-asparaginase; MEK inhibition; calaspargase pegol-mknl; cobimetinib; drug resistance; metabolic reprogramming; pancreatic cancer
    DOI:  https://doi.org/10.1080/14796694.2024.2395235
  12. Biophys J. 2024 Oct 09. pii: S0006-3495(24)00663-5. [Epub ahead of print]
    Unexpected asymmetric distribution of cholesterol and phospholipids in equilibrium model membranes.
    Yuli Zhu, Lionel Porcar, Thirupathi Ravula, Krishna C Batchu, Tera Lavoie, Ying Liu, Ursula Perez-Salas.
      Lipid compositional asymmetry across the leaflets of the plasma membrane is a ubiquitous feature in eukaryotic cells. How this asymmetry is maintained is thought to be primarily controlled by active transport of lipids between leaflets. This strategy is facilitated by the fact that long tail phospholipids and sphingolipids diffuse through the lipid bilayer slowly - taking many hours or days. However, a lipid like cholesterol - which is the most abundant lipid in the plasma membrane of animal cells - has been harder to pin-point in terms of its favored side. In the present work we show that when a saturated lipid is added to a mix of the unsaturated lipid palmitoyl-oleoyl-phosphatidylcholine (POPC) and cholesterol, both cholesterol and the long tail phospholipids organize asymmetrically across the membrane's leaflets naturally. In these extruded unilamellar vesicles, most cholesterol as well as the saturated lipid - dipalmitoylphosphatidylcholine (DPPC) or sphingomyelin (SM) - segregated to the inner leaflet while POPC preferentially localized in the outer leaflet. This asymmetric arrangement generated a slight phospholipid number imbalance favoring the outer leaflet and thus opposite to where cholesterol and the saturated lipids preferentially partitioned. These results were obtained using Magic Angle Spinning (MAS) NMR in combination with Small Angle Neutron Scattering (SANS) using isotope labeling to differentiate lipid species. We suggest that sidedness in membranes can be driven by thermodynamic processes. In addition, our MAS NMR results show that the lower bound for cholesterol's flip-flop half-time at 45°C is 10ms, which is at least two orders of magnitude slower than current MD simulations predict. This result stands in stark contrast to previous work that suggested that cholesterol's flip-flop half-time at 37°C has an upper bound of 10ms.
    Keywords:  cholesterol asymmetry; cholesterol flip-flop; magic angle spinning NMR; membrane asymmetry; phospholipid asymmetry; small angle neutron scattering
    DOI:  https://doi.org/10.1016/j.bpj.2024.10.004
  13. Cell. 2024 Oct 01. pii: S0092-8674(24)01069-9. [Epub ahead of print]
    Identifying specific functional roles for senescence across cell types.
    Huan Zhao, Zixin Liu, Hui Chen, Maoying Han, Mingjun Zhang, Kuo Liu, Hengwei Jin, Xiuxiu Liu, Mengyang Shi, Wenjuan Pu, Markus Werner, Michael Meister, Stefan G Kauschke, Ruilin Sun, Jinjin Wang, Ruling Shen, Qing-Dong Wang, Xin Ma, Jan S Tchorz, Bin Zhou.
      Cellular senescence plays critical roles in aging, regeneration, and disease; yet, the ability to discern its contributions across various cell types to these biological processes remains limited. In this study, we generated an in vivo genetic toolbox consisting of three p16Ink4a-related intersectional genetic systems, enabling pulse-chase tracing (Sn-pTracer), Cre-based tracing and ablation (Sn-cTracer), and gene manipulation combined with tracing (Sn-gTracer) of defined p16Ink4a+ cell types. Using liver injury and repair as an example, we found that macrophages and endothelial cells (ECs) represent distinct senescent cell populations with different fates and functions during liver fibrosis and repair. Notably, clearance of p16Ink4a+ macrophages significantly mitigates hepatocellular damage, whereas eliminating p16Ink4a+ ECs aggravates liver injury. Additionally, targeted reprogramming of p16Ink4a+ ECs through Kdr overexpression markedly reduces liver fibrosis. This study illuminates the functional diversity of p16Ink4a+ cells and offers insights for developing cell-type-specific senolytic therapies in the future.
    Keywords:  Cdkn2a; aging; cellular senescence; dual recombinases; endothelial cell; lineage tracing; liver fibrosis; liver repair; macrophage; p16(Ink4a)
    DOI:  https://doi.org/10.1016/j.cell.2024.09.021
  14. Autophagy. 2024 Oct 10. 1-2
    In vitro and in vivo reconstitution systems reveal the membrane remodeling ability of LC3B and ATG16L1 to form phagophore-like membrane cups.
    Ge Yu, Daniel J Klionsky.
      Macroautophagy/autophagy is a conserved pathway allowing the cell to clear and recycle unwanted materials. While decades of research have revealed molecular players and their hierarchical relationships in autophagy, the detailed mechanism by which these molecules function remains largely unknown. In a recent study, Jagan et al. revealed the membrane remodeling ability of two important proteins, MAP1LC3B/LC3B and ATG16L1, in autophagy. LC3B and the ATG12-ATG5-ATG16L1 complex function synergically to induce the formation of phagophore-like membrane cups on membranes both in vitro and in vivo. In addition, the authors showed that the recently characterized C-terminal membrane-binding domain of ATG16L1 is required for the cup formation and the subsequent transition to autophagic vesicles. Together this research provides more insight into the molecular function of LC3B and ATG16L1, as well as a possible mechanism for phagophore biogenesis.
    Keywords:  ATG16L1; LC3B; autophagy; macroautophagy; membrane remodeling; phagophore biogenesis
    DOI:  https://doi.org/10.1080/15548627.2024.2406127
  15. Stem Cell Res Ther. 2024 Oct 08. 15(1): 348
    Vasoactive intestinal peptide promotes secretory differentiation and mitigates radiation-induced intestinal injury.
    Tatiana Agibalova, Anneke Hempel, H Carlo Maurer, Mohab Ragab, Anastasia Ermolova, Jessica Wieland, Caroline Waldherr Ávila de Melo, Fabian Heindl, Maximilian Giller, Julius Clemens Fischer, Markus Tschurtschenthaler, Birgit Kohnke-Ertel, Rupert Öllinger, Katja Steiger, Ihsan Ekin Demir, Dieter Saur, Michael Quante, Roland M Schmid, Moritz Middelhoff.
       BACKGROUND: Vasoactive intestinal peptide (VIP) is a neuronal peptide with prominent distribution along the enteric nervous system. While effects of VIP on intestinal motility, mucosal vasodilation, secretion, and mucosal immune cell function are well-studied, the direct impact of VIP on intestinal epithelial cell turnover and differentiation remains less understood. Intestinal stem and progenitor cells are essential for the maintenance of intestinal homeostasis and regeneration, and their functions can be modulated by factors of the stem cell niche, including neuronal mediators. Here, we investigated the role of VIP in regulating intestinal epithelial homeostasis and regeneration following irradiation-induced injury.
    METHODS: Jejunal organoids were derived from male and female C57Bl6/J, Lgr5-EGFP-IRES-CreERT2 or Lgr5-EGFP-IRES-CreERT2/R26R-LSL-TdTomato mice and treated with VIP prior to analysis. Injury conditions were induced by exposing organoids to 6 Gy of irradiation (IR). To investigate protective effects of VIP in vivo, mice received 12 Gy of abdominal IR followed by intraperitoneal injections of VIP.
    RESULTS: We observed that VIP promotes epithelial differentiation towards a secretory phenotype predominantly via the p38 MAPK pathway. Moreover, VIP prominently modulated epithelial proliferation as well as the number and proliferative activity of Lgr5-EGFP+ progenitor cells under homeostatic conditions. In the context of acute irradiation injury in vitro, we observed that IR injury renders Lgr5-EGFP+ progenitor cells more susceptible to VIP-induced modulations, which coincided with the strong promotion of epithelial regeneration by VIP. Finally, the observed effects translate into an in vivo model of abdominal irradiation, where VIP showed to prominently mitigate radiation-induced injury.
    CONCLUSIONS: VIP prominently governs intestinal homeostasis by regulating epithelial progenitor cell proliferation and differentiation and promotes intestinal regeneration following acute irradiation injury.
    Keywords:  Intestinal progenitor cells; Irradiation; Regeneration; VIP
    DOI:  https://doi.org/10.1186/s13287-024-03958-z
  16. J Natl Cancer Inst. 2024 Oct 09. pii: djae249. [Epub ahead of print]
    Precision preclinical modeling to advance cancer treatment.
    David H Gutmann, Jesse S Boehm, Elinor K Karlsson, Eric Padron, Mukund Seshadri, Deann Wallis, Joshua C Snyder.
      A new era of cancer management is underway in which treatments are being developed for the entire continuum of the disease process. The availability of genetically engineered and naturally occurring preclinical models serve as instructive platforms for evaluating therapeutic mechanisms. However, a major clinical challenge is that the entire malignancy process occurs across multiple scales including genetic mutations, malignant changes in cell behavior, dysregulated tumor microenvironments, and systemic adaptations in the host. A multi-disciplinary group of investigators coalesced at the National Cancer Institute Oncology Models Forum (NCI-OMF) with the overall goal to provide updates on the use of precision preclinical models of cancer. The benefits and limitations of preclinical models were discussed in order to identify strategies for maximizing opportunities in modeling that could inform future cancer prevention and treatment approaches. Our shared perspective is that the continuum of single cell, multi-cell, organoid, and in situ models are remarkable resources for the clinical challenges ahead. We provide a roadmap for parsing already available models and include preliminary recommendations for the application of next generation preclinical modeling in cancer intervention.
    DOI:  https://doi.org/10.1093/jnci/djae249
  17. bioRxiv. 2024 Jun 28. pii: 2024.06.27.600657. [Epub ahead of print]
    Cryo-electron tomography pipeline for plasma membranes.
    Willy W Sun, Dennis J Michalak, Kem A Sochacki, Prasanthi Kunamaneni, Marco A Alfonzo-Méndez, Andreas M Arnold, Marie-Paule Strub, Jenny E Hinshaw, Justin W Taraska.
      Cryo-electron tomography (cryoET) provides sub-nanometer protein structure within the dense cellular environment. Existing sample preparation methods are insufficient at accessing the plasma membrane and its associated proteins. Here, we present a correlative cryo-electron tomography pipeline optimally suited to image large ultra-thin areas of isolated basal and apical plasma membranes. The pipeline allows for angstrom-scale structure determination with sub-tomogram averaging and employs a genetically-encodable rapid chemically-induced electron microscopy visible tag for marking specific proteins within the complex cell environment. The pipeline provides fast, efficient, distributable, low-cost sample preparation and enables targeted structural studies of identified proteins at the plasma membrane of cells.
    DOI:  https://doi.org/10.1101/2024.06.27.600657
  18. bioRxiv. 2024 Sep 24. pii: 2024.09.23.614580. [Epub ahead of print]
    Galvanin is an electric-field sensor for directed cell migration.
    Nathan M Belliveau, Matthew J Footer, Amy Platenkamp, Heonsu Kim, Tara E Eustis, Julie A Theriot.
      Directed cell migration is critical for the rapid response of immune cells, such as neutrophils, following tissue injury or infection. Endogenous electric fields, generated by the disruption of the transepithelial potential across the skin, help to guide the movement of immune and skin cells toward the wound site. However, the mechanisms by which cells sense these physical cues remain largely unknown. Through a CRISPR-based screen, we identified Galvanin, a previously uncharacterized single-pass transmembrane protein that is required for human neutrophils to change their direction of migration in response to an applied electric field. Our results indicate that Galvanin rapidly relocalizes to the anodal side of a cell on exposure to an electric field, and that the net charge on its extracellular domain is necessary and sufficient to drive this relocalization. The spatial pattern of neutrophil protrusion and retraction changes immediately upon Galvanin relocalization, suggesting that it acts as a direct sensor of the electric field that then transduces spatial information about a cell's electrical environment to the migratory apparatus. The apparent mechanism of cell steering by sensor relocalization represents a new paradigm for directed cell migration.
    DOI:  https://doi.org/10.1101/2024.09.23.614580
  19. Nat Aging. 2024 Oct 08.
    The brain-body energy conservation model of aging.
    Evan D Shaulson, Alan A Cohen, Martin Picard.
      Aging involves seemingly paradoxical changes in energy metabolism. Molecular damage accumulation increases cellular energy expenditure, yet whole-body energy expenditure remains stable or decreases with age. We resolve this apparent contradiction by positioning the brain as the mediator and broker in the organismal energy economy. As somatic tissues accumulate damage over time, costly intracellular stress responses are activated, causing aging or senescent cells to secrete cytokines that convey increased cellular energy demand (hypermetabolism) to the brain. To conserve energy in the face of a shrinking energy budget, the brain deploys energy conservation responses, which suppress low-priority processes, producing fatigue, physical inactivity, blunted sensory capacities, immune alterations and endocrine 'deficits'. We term this cascade the brain-body energy conservation (BEC) model of aging. The BEC outlines (1) the energetic cost of cellular aging, (2) how brain perception of senescence-associated hypermetabolism may drive the phenotypic manifestations of aging and (3) energetic principles underlying the modifiability of aging trajectories by stressors and geroscience interventions.
    DOI:  https://doi.org/10.1038/s43587-024-00716-x
  20. Front Oncol. 2024 ;14 1435480
    Lipids in the tumor microenvironment: immune modulation and metastasis.
    Gloria Pascual, Salvador Aznar Benitah.
      Tumor cells can undergo metabolic adaptations that support their growth, invasion, and metastasis, such as reprogramming lipid metabolism to meet their energy demands and to promote survival in harsh microenvironmental conditions, including hypoxia and acidification. Metabolic rewiring, and especially alterations in lipid metabolism, not only fuel tumor progression but also influence immune cell behavior within the tumor microenvironment (TME), leading to immunosuppression and immune evasion. These processes, in turn, may contribute to the metastatic spread of cancer. The diverse metabolic profiles of immune cell subsets, driven by the TME and tumor-derived signals, contribute to the complex immune landscape in tumors, affecting immune cell activation, differentiation, and effector functions. Understanding and targeting metabolic heterogeneity among immune cell subsets will be crucial for developing effective cancer immunotherapies that can overcome immune evasion mechanisms and enhance antitumor immunity.
    Keywords:  cancer immunotherapy; lipid metabolism; metabolic adaptations; tumor metabolism; tumor micreoenvironment (TME)
    DOI:  https://doi.org/10.3389/fonc.2024.1435480
  21. EMBO J. 2024 Oct 08.
    DELE1 maintains muscle proteostasis to promote growth and survival in mitochondrial myopathy.
    Hsin-Pin Lin, Jennifer D Petersen, Alexandra J Gilsrud, Angelo Madruga, Theresa M D'Silva, Xiaoping Huang, Mario K Shammas, Nicholas P Randolph, Kory R Johnson, Yan Li, Drew R Jones, Michael E Pacold, Derek P Narendra.
      Mitochondrial dysfunction causes devastating disorders, including mitochondrial myopathy, but how muscle senses and adapts to mitochondrial dysfunction is not well understood. Here, we used diverse mouse models of mitochondrial myopathy to show that the signal for mitochondrial dysfunction originates within mitochondria. The mitochondrial proteins OMA1 and DELE1 sensed disruption of the inner mitochondrial membrane and, in response, activated the mitochondrial integrated stress response (mt-ISR) to increase the building blocks for protein synthesis. In the absence of the mt-ISR, protein synthesis in muscle was dysregulated causing protein misfolding, and mice with early-onset mitochondrial myopathy failed to grow and survive. The mt-ISR was similar following disruptions in mtDNA maintenance (Tfam knockout) and mitochondrial protein misfolding (CHCHD10 G58R and S59L knockin) but heterogenous among mitochondria-rich tissues, with broad gene expression changes observed in heart and skeletal muscle and limited changes observed in liver and brown adipose tissue. Taken together, our findings identify that the DELE1 mt-ISR mediates a similar response to diverse forms of mitochondrial stress and is critical for maintaining growth and survival in early-onset mitochondrial myopathy.
    Keywords:  Mitochondria Unfolded Protein Response (mt-UPR); Mitochondrial Disorders; Mitohormesis; Mitonuclear Communication; Mitophagy
    DOI:  https://doi.org/10.1038/s44318-024-00242-x
  22. Cell. 2024 Oct 04. pii: S0092-8674(24)01034-1. [Epub ahead of print]
    Lung-resident alveolar macrophages regulate the timing of breast cancer metastasis.
    Erica Dalla, Michael Papanicolaou, Matthew D Park, Nicole Barth, Rui Hou, Deisy Segura-Villalobos, Luis Valencia Salazar, Dan Sun, Alistair R R Forrest, Maria Casanova-Acebes, David Entenberg, Miriam Merad, Julio A Aguirre-Ghiso.
      Breast disseminated cancer cells (DCCs) can remain dormant in the lungs for extended periods, but the mechanisms limiting their expansion are not well understood. Research indicates that tissue-resident alveolar macrophages suppress breast cancer metastasis in lung alveoli by inducing dormancy. Through ligand-receptor mapping and intravital imaging, it was found that alveolar macrophages express transforming growth factor (TGF)-β2. This expression, along with persistent macrophage-cancer cell interactions via the TGF-βRIII receptor, maintains cancer cells in a dormant state. Depleting alveolar macrophages or losing the TGF-β2 receptor in cancer cells triggers metastatic awakening. Aggressive breast cancer cells are either suppressed by alveolar macrophages or evade this suppression by avoiding interaction and downregulating the TGF-β2 receptor. Restoring TGF-βRIII in aggressive cells reinstates TGF-β2-mediated macrophage growth suppression. Thus, alveolar macrophages act as a metastasis immune barrier, and downregulation of TGF-β2 signaling allows cancer cells to overcome macrophage-mediated growth suppression.
    Keywords:  TGFβ2; TGFβR3; alveolar macrophage; breast cancer; dormancy; homeostasis; intravital imaging; lung metastasis; reawakening
    DOI:  https://doi.org/10.1016/j.cell.2024.09.016
  23. Nat Methods. 2024 Oct 11.
    Single-shot 20-fold expansion microscopy.
    Shiwei Wang, Tay Won Shin, Harley B Yoder, Ryan B McMillan, Hanquan Su, Yixi Liu, Chi Zhang, Kylie S Leung, Peng Yin, Laura L Kiessling, Edward S Boyden.
      Expansion microscopy (ExM) is in increasingly widespread use throughout biology because its isotropic physical magnification enables nanoimaging on conventional microscopes. To date, ExM methods either expand specimens to a limited range (~4-10× linearly) or achieve larger expansion factors through iterating the expansion process a second time (~15-20× linearly). Here, we present an ExM protocol that achieves ~20× expansion (yielding <20-nm resolution on a conventional microscope) in a single expansion step, achieving the performance of iterative expansion with the simplicity of a single-shot protocol. This protocol, which we call 20ExM, supports postexpansion staining for brain tissue, which can facilitate biomolecular labeling. 20ExM may find utility in many areas of biological investigation requiring high-resolution imaging.
    DOI:  https://doi.org/10.1038/s41592-024-02454-9
  24. Sci Rep. 2024 10 09. 14(1): 23581
    AutoGater: a weakly supervised neural network model to gate cells in flow cytometric analyses.
    Mohammed Eslami, Robert C Moseley, Hamed Eramian, Daniel Bryce, Steven B Haase.
      Flow cytometry is a useful and efficient method for the rapid characterization of a cell population based on the optical and fluorescence properties of individual cells. Ideally, the cell population would consist of only healthy viable cells as dead cells can confound the analysis. Thus, separating out healthy cells from dying and dead cells, and any potential debris, is an important first step in analysis of flow cytometry data. While gating of debris can be conducted using measured optical properties, identifying dead and dying cells often requires utilizing fluorescent stains (e.g. Sytox, a nucleic acid stain that stains cells with compromised cell membranes) to identify cells that should be excluded from downstream analyses. These stains prolong the experimental preparation process and use a flow cytometer's fluorescence channels that could otherwise be used to measure additional fluorescent markers within the cells (e.g. reporter proteins). Here we outline a stain-free method for identifying viable cells for downstream processing by gating cells that are dying or dead. AutoGater is a weakly supervised deep learning model that can separate healthy populations from unhealthy and dead populations using only light-scatter channels. In addition, AutoGater harmonizes different measurements of dead cells such as Sytox and CFUs.
    DOI:  https://doi.org/10.1038/s41598-024-66936-8
  25. Cell Death Dis. 2024 Oct 11. 15(10): 745
    High mitochondrial DNA content is a key determinant of stemness, proliferation, cell migration, and cancer metastasis in vivo.
    Marta Mauro-Lizcano, Filippo Di Pisa, Luis Larrea Murillo, Conor J Sugden, Federica Sotgia, Michael P Lisanti.
      Here, we examined the potential role of mitochondrial DNA (mtDNA) levels in conveying aggressive phenotypes in cancer cells, using two widely-used breast cell lines as model systems (MCF7[ER+] and MDA-MB-231[ER-]). These human breast cancer cell lines were fractionated into mtDNA-high and mtDNA-low cell sub-populations by flow cytometry, using SYBR Gold as a vital probe to stain mitochondrial nucleoids in living cells. Enrichment of mtDNA-high and mtDNA-low cell sub-populations was independently validated, using a specific DNA-binding mAb probe (AC-30-10), and mitochondrial-based functional assays. As predicted, mtDNA-high MCF7 cells showed significant increases in mitochondrial mass, membrane potential, and superoxide production, as well as increased mitochondrial respiration and ATP production. Moreover, mtDNA-high MCF7 cells demonstrated increases in stemness features, such as anchorage-independent growth and CD44 levels, as well as drug-resistance to Gemcitabine and Tamoxifen. Proliferation rates were also significantly increased, with a dramatic shift towards the S- and G2/M-phases of the cell cycle; this was indeed confirmed by RNA-Seq analysis. Complementary results were obtained with MDA-MB-231 cells. More specifically, mtDNA-high MDA-MB-231 cells showed increases in stemness features and ATP production, as well as rapid cell cycle progression. Moreover, mtDNA-high MDA-MB-231 cells also exhibited increases in both cell migration and invasion, suggesting a role for mtDNA in distant metastasis. To test this hypothesis more directly, a preclinical in vivo model was utilized. For this purpose, MDA-MB-231 tumour cell grafts were treated with an established mtDNA synthesis inhibitor, namely Alovudine (3'-deoxy-3'-fluorothymidine). As expected, drug-induced depletion of mtDNA led to a shift from mitochondrial to glycolytic metabolism. Interestingly, Alovudine very effectively reduced the formation of spontaneous metastases by nearly 70%, but minimally inhibited tumour growth by approximately 20%. Taken together, these data suggest that high mtDNA content is a key driver of stemness, proliferation, and migration, as well as cancer cell metastasis.
    DOI:  https://doi.org/10.1038/s41419-024-07103-9
  26. ESMO Open. 2024 Oct 09. pii: S2059-7029(24)01508-4. [Epub ahead of print]9(10): 103738
    Leptin as a surrogate immune-metabolic marker to predict impact of anti-cachectic therapy: results of a prospective randomized trial in multiple solid tumors.
    C Madeddu, G Gramignano, E Lai, G Pinna, L Tanca, M C Cherchi, C Floris, D Farci, A Pretta, M Scartozzi, A Macciò.
       DESCRIPTION OF THE WORK: Leptin is a reliable predictive and surrogate marker of the efficacy of multitargeted treatment of cancer cachexia.
    PURPOSE: To the best of our knowledge, no study has assessed the predictive role of biomarkers in establishing the effectiveness of anti-cachectic treatment, which remains a complex issue. Herein, we aimed to find a marker that can detect early response to anti-cachectic treatment.
    PATIENTS AND METHODS: From January 2012 to December 2022, all consecutive eligible advanced cancer patients with cachexia were prospectively enrolled in an exploratory and validation cohort according to eligibility criteria. All patients received a combined anti-cachectic treatment consisting of megestrol acetate plus celecoxib plus l-carnitine plus antioxidants that showed efficacy in a previous phase III randomized study. Primary endpoints were an increase in lean body mass (LBM), a decrease in resting energy expenditure (REE), a decrease in fatigue, and improvement in global quality of life.
    RESULTS: A total of 553 consecutive patients were recruited. Twenty patients dropped out, equally distributed over the exploratory (11 patients) and validation (9 patients) cohorts, for early death due to disease progression. Then, 533 patients were deemed assessable. Leptin level changes inversely correlated with circulating levels of inflammatory mediators and reflected the improvement of body composition, energy metabolism, functional performance, and quality of life. At multivariate regression analysis, at week 8, leptin change was an independent predictor of LBM, skeletal muscle index (SMI), grip strength increase, and REE; at week 16, leptin change was an independent predictor of the same parameters and improvement in Eastern Cooperative Oncology Group performance status. The ability of leptin to predict changes in LBM, SMI, REE, and grip strength was superior to that of other inflammatory markers when comparing the receiver operating curves. Moreover, increasing delta leptin values were associated with significantly better outcomes in LBM, SMI, REE, grip strength, and fatigue.
    CONCLUSIONS: Leptin is a reliable predictive marker for multitargeted anti-cachectic treatment outcomes. Thus, it can be an ideal candidate for monitoring and predicting the effects of anti-cachectic treatment and a surrogate marker of the immune-metabolic actions of the selected drugs.
    Keywords:  cachexia; combined approach; inflammation; leptin; quality of life; sarcopenia
    DOI:  https://doi.org/10.1016/j.esmoop.2024.103738
  27. Cancer Cell. 2024 Oct 04. pii: S1535-6108(24)00357-X. [Epub ahead of print]
    Long-term breast cancer response to CDK4/6 inhibition defined by TP53-mediated geroconversion.
    Rei Kudo, Anton Safonov, Catherine Jones, Enrico Moiso, Jonathan R Dry, Hong Shao, Sharanya Nag, Edaise M da Silva, Selma Yeni Yildirim, Qing Li, Elizabeth O'Connell, Payal Patel, Marie Will, Atsushi Fushimi, Marimar Benitez, Martina Bradic, Li Fan, Harikrishna Nakshatri, Dhivya R Sudhan, Christopher R Denz, Jorge S Reis-Filho, Shom Goel, Andrew Koff, Britta Weigelt, Qamar J Khan, Pedram Razavi, Sarat Chandarlapaty.
      Inhibition of CDK4/6 kinases has led to improved outcomes in breast cancer. Nevertheless, only a minority of patients experience long-term disease control. Using a large, clinically annotated cohort of patients with metastatic hormone receptor-positive (HR+) breast cancer, we identify TP53 loss (27.6%) and MDM2 amplification (6.4%) to be associated with lack of long-term disease control. Human breast cancer models reveal that p53 loss does not alter CDK4/6 activity or G1 blockade but instead promotes drug-insensitive p130 phosphorylation by CDK2. The persistence of phospho-p130 prevents DREAM complex assembly, enabling cell-cycle re-entry and tumor progression. Inhibitors of CDK2 can overcome p53 loss, leading to geroconversion and manifestation of senescence phenotypes. Complete inhibition of both CDK4/6 and CDK2 kinases appears to be necessary to facilitate long-term response across genomically diverse HR+ breast cancers.
    Keywords:  CDK2; CDK4/6; breast cancer; cell cycle; cyclin dependent kinase; drug resistance; p53; quiescence; senescence
    DOI:  https://doi.org/10.1016/j.ccell.2024.09.009
  28. Immunity. 2024 Sep 28. pii: S1074-7613(24)00447-3. [Epub ahead of print]
    T lymphocyte recruitment to melanoma brain tumors depends on distinct venous vessels.
    Julia M Messmer, Calvin Thommek, Manuel Piechutta, Varun Venkataramani, Rebekka Wehner, Dana Westphal, Marc Schubert, Chanté D Mayer, Maike Effern, Anna S Berghoff, Daniel Hinze, Iris Helfrich, Dirk Schadendorf, Wolfgang Wick, Michael Hölzel, Matthia A Karreman, Frank Winkler.
      To improve immunotherapy for brain tumors, it is important to determine the principal intracranial site of T cell recruitment from the bloodstream and their intracranial route to brain tumors. Using intravital microscopy in mouse models of intracranial melanoma, we discovered that circulating T cells preferably adhered and extravasated at a distinct type of venous blood vessel in the tumor vicinity, peritumoral venous vessels (PVVs). Other vascular structures were excluded as alternative T cell routes to intracranial melanomas. Anti-PD-1/CTLA-4 immune checkpoint inhibitors increased intracranial T cell motility, facilitating migration from PVVs to the tumor and subsequently inhibiting intracranial tumor growth. The endothelial adhesion molecule ICAM-1 was particularly expressed on PVVs, and, in samples of human brain metastases, ICAM-1 positivity of PVV-like vessels correlated with intratumoral T cell infiltration. These findings uncover a distinct mechanism by which the immune system can access and control brain tumors and potentially influence other brain pathologies.
    Keywords:  brain cancer; brain metastases; brain metastasis; cancer; immunotherapy; intravital imaging; lymphocyte recruitment; melanoma; tumor immunology
    DOI:  https://doi.org/10.1016/j.immuni.2024.09.003
  29. Front Cell Dev Biol. 2024 ;12 1460616
    Autophagy and the pancreas: Healthy and disease states.
    Zixian Zhou, Pengcheng Zhang, Juan Li, Jiaqi Yao, Yuhong Jiang, Meihua Wan, Wenfu Tang, Ling Liu.
      Macroautophagy/autophagy is an intracellular degradation pathway that has an important effect on both healthy and diseased pancreases. It protects the structure and function of the pancreas by maintaining organelle homeostasis and removing damaged organelles. A variety of pancreas-related diseases, such as diabetes, pancreatitis, and pancreatic cancer, are closely associated with autophagy. Genetic studies that address autophagy confirm this view. Loss of autophagy homeostasis (lack or overactivation) can lead to a series of adverse reactions, such as oxidative accumulation, increased inflammation, and cell death. There is growing evidence that stimulating or inhibiting autophagy is a potential therapeutic strategy for various pancreatic diseases. In this review, we discuss the multiple roles of autophagy in physiological and pathological conditions of the pancreas, including its role as a protective or pathogenic factor.
    Keywords:  autophagy; genetic studies; organelle homeostasis; pancreas; zymophagy
    DOI:  https://doi.org/10.3389/fcell.2024.1460616
  30. Nat Biotechnol. 2024 Oct 07.
    Scalable, compressed phenotypic screening using pooled perturbations.
    Nuo Liu, Walaa E Kattan, Benjamin E Mead, Conner Kummerlowe, Thomas Cheng, Sarah Ingabire, Jaime H Cheah, Christian K Soule, Anita Vrcic, Jane K McIninch, Sergio Triana, Manuel Guzman, Tyler T Dao, Joshua M Peters, Kristen E Lowder, Lorin Crawford, Ava P Amini, Paul C Blainey, William C Hahn, Brian Cleary, Bryan Bryson, Peter S Winter, Srivatsan Raghavan, Alex K Shalek.
      High-throughput phenotypic screens using biochemical perturbations and high-content readouts are constrained by limitations of scale. To address this, we establish a method of pooling exogenous perturbations followed by computational deconvolution to reduce required sample size, labor and cost. We demonstrate the increased efficiency of compressed experimental designs compared to conventional approaches through benchmarking with a bioactive small-molecule library and a high-content imaging readout. We then apply compressed screening in two biological discovery campaigns. In the first, we use early-passage pancreatic cancer organoids to map transcriptional responses to a library of recombinant tumor microenvironment protein ligands, uncovering reproducible phenotypic shifts induced by specific ligands distinct from canonical reference signatures and correlated with clinical outcome. In the second, we identify the pleotropic modulatory effects of a chemical compound library with known mechanisms of action on primary human peripheral blood mononuclear cell immune responses. In sum, our approach empowers phenotypic screens with information-rich readouts to advance drug discovery efforts and basic biological inquiry.
    DOI:  https://doi.org/10.1038/s41587-024-02403-z
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