bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2024‒06‒16
39 papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Electron transport chain inhibition increases cellular dependence on purine transport and salvage.
  2. K128 ubiquitination constrains RAS activity by expanding its binding interface with GAP proteins.
  3. Lessons Learned from Cancer Metabolism for Physiology and Disease.
  4. Exploiting ferroptosis vulnerabilities in cancer.
  5. Lysophosphatidylcholine acyltransferase 1 suppresses nanoclustering and function of KRAS.
  6. A Fully-Automated Senescence Test (FAST) for the high-throughput quantification of senescence-associated markers.
  7. The glutathione S-transferase Gstt1 drives survival and dissemination in metastases.
  8. Membrane-induced 2D phase separation of the focal adhesion protein talin.
  9. Aging represses lung tumorigenesis and alters tumor suppression.
  10. Endogenous p53 inhibitor TIRR dissociates systemic metabolic health from oncogenic activity.
  11. KPC-luciferase-expressing cells elicit an anti-tumor immune response in a mouse model of pancreatic cancer.
  12. Protocol for whole-mount immunofluorescence staining of ECM gel-embedded innervated pancreatic organoids.
  13. SGLT2 regulates immune-mediated senolysis.
  14. Regulation of cell function and identity by cellular senescence.
  15. The Bioenergetic Landscape of Cancer.
  16. Ultrasensitive and multiplexed tracking of single cells using whole-body PET/CT.
  17. A high-fat diet induces changes in mesenteric adipose tissue accelerating early-stage pancreatic carcinogenesis in mice.
  18. Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.
  19. Metabolic Signaling in Cancer.
  20. Let it be: Preserving tumor-draining lymph nodes in the era of immuno-oncology.
  21. Tumor Promoters and Opportunities for Molecular Cancer Prevention.
  22. Charge-regulated fluorescent anchors enable high-fidelity tracking of plasma membrane dynamics during biological events.
  23. Protocol for measuring cell cycle Zn2+ dynamics using a FRET-based biosensor.
  24. Exploring the origins of pancreatic cancer.
  25. Finding the sweet spot: Targeting RAS in tumors while sparing normal tissue.
  26. Unique architectural features of mammalian mitochondrial protein synthesis.
  27. Hematoxylin and Eosin Architecture Uncovers Clinically Divergent Niches in Pancreatic Cancer.
  28. The Space Omics and Medical Atlas (SOMA) and international astronaut biobank.
  29. Unlocking the promise of RAS inhibition in pancreatic cancer.
  30. Exploring Heterogeneity: A Dive into Pre-Clinical Models of Cancer Cachexia.
  31. A Thy-1-negative immunofibroblast population emerges as a key determinant of fibrotic outcomes to biomaterials.
  32. Suppression of autophagy induces senescence in the heart.
  33. Realization of cellomics to dive into the whole-body or whole-organ cell cloud.
  34. Mapping the landscape of histomorphological cancer phenotypes using self-supervised learning on unannotated pathology slides.
  35. Metabolic inflexibility promotes mitochondrial health during liver regeneration.
  36. A firm-push-to-open and light-push-to-lock strategy for a general chemical platform to develop activatable dual-modality NIR-II probes.
  37. Progress of single-cell RNA sequencing combined with spatial transcriptomics in tumour microenvironment and treatment of pancreatic cancer.
  38. SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data.
  39. Proteolysis-free amoeboid migration of melanoma cells through crowded environments via bleb-driven worrying.
  1. Cell Metab. 2024 Jun 07. pii: S1550-4131(24)00190-6. [Epub ahead of print]
    Electron transport chain inhibition increases cellular dependence on purine transport and salvage.
    Zheng Wu, Divya Bezwada, Feng Cai, Robert C Harris, Bookyung Ko, Varun Sondhi, Chunxiao Pan, Hieu S Vu, Phong T Nguyen, Brandon Faubert, Ling Cai, Hongli Chen, Misty Martin-Sandoval, Duyen Do, Wen Gu, Yuanyuan Zhang, Yuannyu Zhang, Bailey Brooks, Sherwin Kelekar, Lauren G Zacharias, K Celeste Oaxaca, Joao S Patricio, Thomas P Mathews, Javier Garcia-Bermudez, Min Ni, Ralph J DeBerardinis.
      Mitochondria house many metabolic pathways required for homeostasis and growth. To explore how human cells respond to mitochondrial dysfunction, we performed metabolomics in fibroblasts from patients with various mitochondrial disorders and cancer cells with electron transport chain (ETC) blockade. These analyses revealed extensive perturbations in purine metabolism, and stable isotope tracing demonstrated that ETC defects suppress de novo purine synthesis while enhancing purine salvage. In human lung cancer, tumors with markers of low oxidative mitochondrial metabolism exhibit enhanced expression of the salvage enzyme hypoxanthine phosphoribosyl transferase 1 (HPRT1) and high levels of the HPRT1 product inosine monophosphate. Mechanistically, ETC blockade activates the pentose phosphate pathway, providing phosphoribosyl diphosphate to drive purine salvage supplied by uptake of extracellular bases. Blocking HPRT1 sensitizes cancer cells to ETC inhibition. These findings demonstrate how cells remodel purine metabolism upon ETC blockade and uncover a new metabolic vulnerability in tumors with low respiration.
    Keywords:  HPRT1; NAD(+):NADH ratio; electron transport chain; metabolomics; purine metabolism; stable isotopes
    DOI:  https://doi.org/10.1016/j.cmet.2024.05.014
  2. EMBO J. 2024 Jun 10.
    K128 ubiquitination constrains RAS activity by expanding its binding interface with GAP proteins.
    Wout Magits, Mikhail Steklov, Hyunbum Jang, Raj N Sewduth, Amir Florentin, Benoit Lechat, Aidana Sheryazdanova, Mingzhen Zhang, Michal Simicek, Gali Prag, Ruth Nussinov, Anna Sablina.
      The RAS pathway is among the most frequently activated signaling nodes in cancer. However, the mechanisms that alter RAS activity in human pathologies are not entirely understood. The most prevalent post-translational modification within the GTPase core domain of NRAS and KRAS is ubiquitination at lysine 128 (K128), which is significantly decreased in cancer samples compared to normal tissue. Here, we found that K128 ubiquitination creates an additional binding interface for RAS GTPase-activating proteins (GAPs), NF1 and RASA1, thus increasing RAS binding to GAP proteins and promoting GAP-mediated GTP hydrolysis. Stimulation of cultured cancer cells with growth factors or cytokines transiently induces K128 ubiquitination and restricts the extent of wild-type RAS activation in a GAP-dependent manner. In KRAS mutant cells, K128 ubiquitination limits tumor growth by restricting RAL/ TBK1 signaling and negatively regulating the autocrine circuit induced by mutant KRAS. Reduction of K128 ubiquitination activates both wild-type and mutant RAS signaling and elicits a senescence-associated secretory phenotype, promoting RAS-driven pancreatic tumorigenesis.
    Keywords:  NF1; RAS Interactome; RAS Signaling; Senescence-Associated Secretory Phenotype; Ubiquitination
    DOI:  https://doi.org/10.1038/s44318-024-00146-w
  3. Cold Spring Harb Perspect Med. 2024 Jun 10. pii: a041554. [Epub ahead of print]
    Lessons Learned from Cancer Metabolism for Physiology and Disease.
    Sydney L Campbell, Heather R Christofk.
      Tumor cells divide rapidly and dramatically alter their metabolism to meet biosynthetic and bioenergetic needs. Through studying the aberrant metabolism of cancer cells, other contexts in which metabolism drives cell state transitions become apparent. In this work, we will discuss how principles established by the field of cancer metabolism have led to discoveries in the contexts of physiology and tissue injury, mammalian embryonic development, and virus infection. We present specific examples of findings from each of these fields that have been shaped by the study of cancer metabolism. We also discuss the next important scientific questions facing these subject areas collectively. Altogether, these examples demonstrate that the study of "cancer metabolism" is indeed the study of cell metabolism in the context of a tumor, and undoubtedly discoveries from each of the fields discussed here will continue to build on each other in the future.
    DOI:  https://doi.org/10.1101/cshperspect.a041554
  4. Nat Cell Biol. 2024 Jun 10.
    Exploiting ferroptosis vulnerabilities in cancer.
    Toshitaka Nakamura, Marcus Conrad.
      Ferroptosis is a distinct lipid peroxidation-dependent form of necrotic cell death. This process has been increasingly contemplated as a new target for cancer therapy because of an intrinsic or acquired ferroptosis vulnerability in difficult-to-treat cancers and tumour microenvironments. Here we review recent advances in our understanding of the molecular mechanisms that underlie ferroptosis and highlight available tools for the modulation of ferroptosis sensitivity in cancer cells and communication with immune cells within the tumour microenvironment. We further discuss how these new insights into ferroptosis-activating pathways can become new armouries in the fight against cancer.
    DOI:  https://doi.org/10.1038/s41556-024-01425-8
  5. bioRxiv. 2024 Jun 02. pii: 2024.05.30.596653. [Epub ahead of print]
    Lysophosphatidylcholine acyltransferase 1 suppresses nanoclustering and function of KRAS.
    Neha Arora, Hong Liang, Wantong Yao, Haoqiang Ying, Junchen Liu, Yong Zhou.
      KRAS is frequently mutated in cancer, contributing to 20% of all human cancer especially pancreatic, colorectal and lung cancer. Signaling of the constitutively active KRAS oncogenic mutants is mostly compartmentalized to proteolipid nanoclusters on the plasma membrane (PM). Signaling nanoclusters of many KRAS mutants selectively enrich phosphatidylserine (PS) lipids with unsaturated sn-2 acyl chains, but not the fully saturated PS species. Thus, remodeling PS acyl chains may suppress KRAS oncogenesis. Lysophosphatidylcholine acyltransferases (LPCATs) remodel sn-2 acyl chains of phospholipids, with LPCAT1 preferentially generating the fully saturated lipids. Here, we show that stable expression of LPCAT1 depletes major PS species with unsaturated sn-2 chains while decreasing minor phosphatidylcholine (PC) species with the corresponding acyl chains. LPCAT1 expression more effectively disrupts the nanoclustering of oncogenic GFP-KRAS G12V , which is restored by acute addback of exogenous unsaturated PS. LPCAT1 expression compromises signaling and oncogenic activities of the KRAS-dependent pancreatic tumor lines. LPCAT1 expression sensitizes human pancreatic tumor MiaPaCa-2 cells to KRAS G12C specific inhibitor, Sotorasib. Statistical analyses of patient data further reveal that pancreatic cancer patients with KRAS mutations express less LPCAT1. Higher LPCAT1 expression also improves survival probability of pancreatic and lung adenocarcinoma patients with KRAS mutations. Thus, PS acyl chain remodeling selectively suppresses KRAS oncogenesis.
    DOI:  https://doi.org/10.1101/2024.05.30.596653
  6. Geroscience. 2024 Jun 13.
    A Fully-Automated Senescence Test (FAST) for the high-throughput quantification of senescence-associated markers.
    Francesco Neri, Selma N Takajjart, Chad A Lerner, Pierre-Yves Desprez, Birgit Schilling, Judith Campisi, Akos A Gerencser.
      Cellular senescence is a major driver of aging and age-related diseases. Quantification of senescent cells remains challenging due to the lack of senescence-specific markers and generalist, unbiased methodology. Here, we describe the Fully-Automated Senescence Test (FAST), an image-based method for the high-throughput, single-cell assessment of senescence in cultured cells. FAST quantifies three of the most widely adopted senescence-associated markers for each cell imaged: senescence-associated β-galactosidase activity (SA-β-Gal) using X-Gal, proliferation arrest via lack of 5-ethynyl-2'-deoxyuridine (EdU) incorporation, and enlarged morphology via increased nuclear area. The presented workflow entails microplate image acquisition, image processing, data analysis, and graphing. Standardization was achieved by (i) quantifying colorimetric SA-β-Gal via optical density; (ii) implementing staining background controls; and (iii) automating image acquisition, image processing, and data analysis. In addition to the automated threshold-based scoring, a multivariate machine learning approach is provided. We show that FAST accurately quantifies senescence burden and is agnostic to cell type and microscope setup. Moreover, it effectively mitigates false-positive senescence marker staining, a common issue arising from culturing conditions. Using FAST, we compared X-Gal with fluorescent C12FDG live-cell SA-β-Gal staining on the single-cell level. We observed only a modest correlation between the two, indicating that those stains are not trivially interchangeable. Finally, we provide proof of concept that our method is suitable for screening compounds that modify senescence burden. This method will be broadly useful to the aging field by enabling rapid, unbiased, and user-friendly quantification of senescence burden in culture, as well as facilitating large-scale experiments that were previously impractical.
    Keywords:  Aging; Cellular senescence; High-content image analysis; High-throughput screening; Machine learning; Senescence-associated-β-galactosidase
    DOI:  https://doi.org/10.1007/s11357-024-01167-3
  7. Nat Cell Biol. 2024 Jun;26(6): 975-990
    The glutathione S-transferase Gstt1 drives survival and dissemination in metastases.
    Christina M Ferrer, Hyo Min Cho, Ruben Boon, Tiziano Bernasocchi, Lai Ping Wong, Murat Cetinbas, Elizabeth R Haggerty, Irene Mitsiades, Gregory R Wojtkiewicz, Daniel E McLoughlin, Reem Aboushousha, Hend Abdelhamid, Sita Kugel, Esther Rheinbay, Ruslan Sadreyev, Dejan Juric, Yvonne M W Janssen-Heininger, Raul Mostoslavsky.
      Identifying the adaptive mechanisms of metastatic cancer cells remains an elusive question in the treatment of metastatic disease, particularly in pancreatic cancer (pancreatic adenocarcinoma, PDA). A loss-of-function shRNA targeted screen in metastatic-derived cells identified Gstt1, a member of the glutathione S-transferase superfamily, as uniquely required for dissemination and metastasis, but dispensable for primary tumour growth. Gstt1 is expressed in latent disseminated tumour cells (DTCs), is retained within a subpopulation of slow-cycling cells within existing metastases, and its inhibition leads to complete regression of macrometastatic tumours. This distinct Gstt1high population is highly metastatic and retains slow-cycling phenotypes, epithelial-mesenchymal transition features and DTC characteristics compared to the Gstt1low population. Mechanistic studies indicate that in this subset of cancer cells, Gstt1 maintains metastases by binding and glutathione-modifying intracellular fibronectin, in turn promoting its secretion and deposition into the metastatic microenvironment. We identified Gstt1 as a mediator of metastasis, highlighting the importance of heterogeneity and its influence on the metastatic tumour microenvironment.
    DOI:  https://doi.org/10.1038/s41556-024-01426-7
  8. Nat Commun. 2024 Jun 11. 15(1): 4986
    Membrane-induced 2D phase separation of the focal adhesion protein talin.
    Thomas Litschel, Charlotte F Kelley, Xiaohang Cheng, Leon Babl, Naoko Mizuno, Lindsay B Case, Petra Schwille.
      Focal adhesions form liquid-like assemblies around activated integrin receptors at the plasma membrane. How they achieve their flexible properties is not well understood. Here, we use recombinant focal adhesion proteins to reconstitute the core structural machinery in vitro. We observe liquid-liquid phase separation of the core focal adhesion proteins talin and vinculin for a spectrum of conditions and interaction partners. Intriguingly, we show that binding to PI(4,5)P2-containing membranes triggers phase separation of these proteins on the membrane surface, which in turn induces the enrichment of integrin in the clusters. We suggest a mechanism by which 2-dimensional biomolecular condensates assemble on membranes from soluble proteins in the cytoplasm: lipid-binding triggers protein activation and thus, liquid-liquid phase separation of these membrane-bound proteins. This could explain how early focal adhesions maintain a structured and force-resistant organization into the cytoplasm, while still being highly dynamic and able to quickly assemble and disassemble.
    DOI:  https://doi.org/10.1038/s41467-024-49222-z
  9. bioRxiv. 2024 May 31. pii: 2024.05.28.596319. [Epub ahead of print]
    Aging represses lung tumorigenesis and alters tumor suppression.
    Emily G Shuldiner, Saswati Karmakar, Min K Tsai, Jess D Hebert, Yuning J Tang, Laura Andrejka, Minwei Wang, Colin R Detrick, Hongchen Cai, Rui Tang, Dmitri A Petrov, Monte M Winslow.
      Most cancers are diagnosed in persons over the age of sixty, but little is known about how age impacts tumorigenesis. While aging is accompanied by mutation accumulation - widely understood to contribute to cancer risk - it is also associated with numerous other cellular and molecular changes likely to impact tumorigenesis. Moreover, cancer incidence decreases in the oldest part of the population, suggesting that very old age may reduce carcinogenesis. Here we show that aging represses tumor initiation and growth in genetically engineered mouse models of human lung cancer. Moreover, aging dampens the impact of inactivating many, but not all, tumor suppressor genes with the impact of inactivating PTEN, a negative regulator of the PI3K/AKT pathway, weakened to a disproportionate extent. Single-cell transcriptomic analysis revealed that neoplastic cells from tumors in old mice retain many age-related transcriptomic changes, showing that age has an enduring impact that persists through oncogenic transformation. Furthermore, the consequences of PTEN inactivation were strikingly age-dependent, with PTEN deficiency reducing signatures of aging in cancer cells and the tumor microenvironment. Our findings suggest that the relationship between age and lung cancer incidence may reflect an integration of the competing effects of driver mutation accumulation and tumor suppressive effects of aging.
    DOI:  https://doi.org/10.1101/2024.05.28.596319
  10. Cell Rep. 2024 Jun 09. pii: S2211-1247(24)00665-X. [Epub ahead of print]43(6): 114337
    Endogenous p53 inhibitor TIRR dissociates systemic metabolic health from oncogenic activity.
    Eva Tsaousidou, Jędrzej Chrzanowski, Pascal Drané, Grace Y Lee, Nadine Bahour, Zeqiu Branden Wang, Shijun Deng, Zhe Cao, Kaimeng Huang, Yizhou He, Mateusz Kaminski, Dominika Michalek, Ekin Güney, Kalindi Parmar, Wojciech Fendler, Dipanjan Chowdhury, Gökhan S Hotamışlıgil.
      It is unclear whether metabolic health corresponds to reduced oncogenesis or vice versa. We study Tudor-interacting repair regulator (TIRR), an inhibitor of p53 binding protein 1 (53BP1)-mediated p53 activation, and the physiological consequences of enhancing tumor suppressor activity. Deleting TIRR selectively activates p53, significantly protecting against cancer but leading to a systemic metabolic imbalance in mice. TIRR-deficient mice are overweight and insulin resistant, even under normal chow diet. Similarly, reduced TIRR expression in human adipose tissue correlates with higher BMI and insulin resistance. Despite the metabolic challenges, TIRR loss improves p53 heterozygous (p53HET) mouse survival and correlates with enhanced progression-free survival in patients with various p53HET carcinomas. Finally, TIRR's oncoprotective and metabolic effects are dependent on p53 and lost upon p53 deletion in TIRR-deficient mice, with glucose homeostasis and orexigenesis being primarily regulated by TIRR expression in the adipose tissue and the CNS, respectively, as evidenced by tissue-specific models. In summary, TIRR deletion provides a paradigm of metabolic deregulation accompanied by reduced oncogenesis.
    Keywords:  CP: Cancer; CP: Metabolism; cancer metabolism; cancer mouse model of p53 activation; cancer protection; in vivo physiology in cancer; mevalonate pathway suppression; obesity and cancer; overweight and cancer; p53 activation; p53 derepression; p53 inhibitor; type 2 diabetes and cancer
    DOI:  https://doi.org/10.1016/j.celrep.2024.114337
  11. Sci Rep. 2024 06 13. 14(1): 13602
    KPC-luciferase-expressing cells elicit an anti-tumor immune response in a mouse model of pancreatic cancer.
    Daniele Pereira Ferrari, Fernanda Ramos-Gomes, Frauke Alves, M Andrea Markus.
      Mouse models for the study of pancreatic ductal adenocarcinoma (PDAC) are well-established and representative of many key features observed in human PDAC. To monitor tumor growth, cancer cells that are implanted in mice are often transfected with reporter genes, such as firefly luciferase (Luc), enabling in vivo optical imaging over time. Since Luc can induce an immune response, we aimed to evaluate whether the expression of Luc could affect the growth of KPC tumors in mice by inducing immunogenicity. Although both cell lines, KPC and Luc transduced KPC (KPC-Luc), had the same proliferation rate, KPC-Luc tumors had significantly smaller sizes or were absent 13 days after orthotopic cell implantation, compared to KPC tumors. This coincided with the loss of bioluminescence signal over the tumor region. Immunophenotyping of blood and spleen from KPC-Luc tumor-bearing mice showed a decreased number of macrophages and CD4+ T cells, and an increased accumulation of natural killer (NK) cells in comparison to KPC tumor mice. Higher infiltration of CD8+ T cells was found in KPC-Luc tumors than in their controls. Moreover, the immune response against Luc peptide was stronger in splenocytes from mice implanted with KPC-Luc cells compared to those isolated from KPC wild-type mice, indicating increased immunogenicity elicited by the presence of Luc in the PDAC tumor cells. These results must be considered when evaluating the efficacy of anti-cancer therapies including immunotherapies in immunocompetent PDAC or other cancer mouse models that use Luc as a reporter for bioluminescence imaging.
    DOI:  https://doi.org/10.1038/s41598-024-64053-0
  12. STAR Protoc. 2024 Jun 13. pii: S2666-1667(24)00297-1. [Epub ahead of print]5(2): 103132
    Protocol for whole-mount immunofluorescence staining of ECM gel-embedded innervated pancreatic organoids.
    Hüseyin Erdinç Beşikcioğlu, Ümmügülsüm Yurteri, Linhan Ye, Fang Zhang, Alessandra Moretti, Ibrahim Halil Gürcinar, Alper Dogruöz, Didem Karakas, Helmut Friess, Guralp Onur Ceyhan, Rouzanna Istvanffy, Ihsan Ekin Demir.
      The mandatory usage of extracellular matrix (ECM) gels in 3D cultures limits antibody penetration and increases background, while the removal of ECM gel causes disruption of morphology and sample loss. These factors pose challenges to effective immune labeling-based staining. Here, we present a protocol for whole-mount immunofluorescence staining of gel-embedded pancreatic organoids. We describe steps for sample fixation, blocking, and antibody incubation. We detail procedures for washing antibodies and mounting.
    Keywords:  Microscopy; Model Organisms; Organoids
    DOI:  https://doi.org/10.1016/j.xpro.2024.103132
  13. Nat Aging. 2024 Jun 10.
    SGLT2 regulates immune-mediated senolysis.
    Guangran Guo, Corina Amor.
      
    DOI:  https://doi.org/10.1038/s43587-024-00651-x
  14. J Cell Biol. 2024 Aug 05. pii: e202401112. [Epub ahead of print]223(8):
    Regulation of cell function and identity by cellular senescence.
    Anda Huna, Amélie Massemin, Gabriela Makulyte, Jean-Michel Flaman, Nadine Martin, David Bernard.
      During aging and in some contexts, like embryonic development, wound healing, and diseases such as cancer, senescent cells accumulate and play a key role in different pathophysiological functions. A long-held belief was that cellular senescence decreased normal cell functions, given the loss of proliferation of senescent cells. This view radically changed following the discovery of the senescence-associated secretory phenotype (SASP), factors released by senescent cells into their microenvironment. There is now accumulating evidence that cellular senescence also promotes gain-of-function effects by establishing, reinforcing, or changing cell identity, which can have a beneficial or deleterious impact on pathophysiology. These effects may involve both proliferation arrest and autocrine SASP production, although they largely remain to be defined. Here, we provide a historical overview of the first studies on senescence and an insight into emerging trends regarding the effects of senescence on cell identity.
    DOI:  https://doi.org/10.1083/jcb.202401112
  15. Mol Metab. 2024 Jun 12. pii: S2212-8778(24)00097-8. [Epub ahead of print] 101966
    The Bioenergetic Landscape of Cancer.
    Elizabeth R M Zunica, Christopher L Axelrod, L Anne Gilmore, Erich Gnaiger, John P Kirwan.
      Bioenergetic remodeling of core energy metabolism is essential to the initiation, survival, and progression of cancer cells through exergonic supply of adenosine triphosphate (ATP) and metabolic intermediates, as well as control of redox homeostasis. Mitochondria are evolutionarily conserved organelles that mediate cell survival by conferring energetic plasticity and adaptive potential. Mitochondrial ATP synthesis is coupled to the oxidation of a variety of substrates generated through diverse metabolic pathways. As such, inhibition of the mitochondrial bioenergetic system by restricting metabolite availability, direct inhibition of the respiratory Complexes, altering organelle structure, or coupling efficiency may restrict carcinogenic potential and cancer progression. Here, we review the role of bioenergetics as the principal conductor of energetic functions and carcinogenesis while highlighting the therapeutic potential of targeting mitochondrial functions.
    Keywords:  Bioenergetics; Cancer; Cell Survival; Energy Transformation; Mitochondria
    DOI:  https://doi.org/10.1016/j.molmet.2024.101966
  16. Sci Adv. 2024 Jun 14. 10(24): eadk5747
    Ultrasensitive and multiplexed tracking of single cells using whole-body PET/CT.
    Hieu T M Nguyen, Neeladrisingha Das, Matthew Ricks, Xiaoxu Zhong, Eri Takematsu, Yuting Wang, Carlos Ruvalcaba, Brahim Mehadji, Emilie Roncali, Charles K F Chan, Guillem Pratx.
      In vivo molecular imaging tools are crucially important for elucidating how cells move through complex biological systems; however, achieving single-cell sensitivity over the entire body remains challenging. Here, we report a highly sensitive and multiplexed approach for tracking upward of 20 single cells simultaneously in the same subject using positron emission tomography (PET). The method relies on a statistical tracking algorithm (PEPT-EM) to achieve a sensitivity of 4 becquerel per cell and a streamlined workflow to reliably label single cells with over 50 becquerel per cell of 18F-fluorodeoxyglucose (FDG). To demonstrate the potential of the method, we tracked the fate of more than 70 melanoma cells after intracardiac injection and found they primarily arrested in the small capillaries of the pulmonary, musculoskeletal, and digestive organ systems. This study bolsters the evolving potential of PET in offering unmatched insights into the earliest phases of cell trafficking in physiological and pathological processes and in cell-based therapies.
    DOI:  https://doi.org/10.1126/sciadv.adk5747
  17. J Nutr Biochem. 2024 Jun 12. pii: S0955-2863(24)00123-2. [Epub ahead of print] 109690
    A high-fat diet induces changes in mesenteric adipose tissue accelerating early-stage pancreatic carcinogenesis in mice.
    Aya S Ead, Joanna Wirkus, Karen Matsukuma, Gerardo G Mackenzie.
      BACKGROUND: Increased adiposity is a significant risk factor for pancreatic cancer development. Multiple preclinical studies have documented that high-fat, high caloric diets, rich in omega-6 fatty acids (FA) accelerate pancreatic cancer development. However, the effect of a high-fat, low sucrose diet (HFD), on pancreatic carcinogenesis remains unclear. We evaluated the impact of a HFD on early-stage pancreatic carcinogenesis in the clinically relevant KrasLSL-G12D/+; Ptf1aCre/+ (KC) genetically engineered mouse model, and characterized the role of the mesenteric adipose tissue (MAT).METHODS: Cohorts of male and female KC mice were randomly assigned to a control diet (CD) or a HFD, matched for FA composition (9:1 of omega-6 FA: omega-3 FA), and fed their diets for eight weeks.
    RESULTS: After eight weeks on a HFD, KC mice had significantly higher body weight, fat mass, and serum leptin compared to CD-fed KC mice. Furthermore, a HFD accelerated pancreatic acinar-to-ductal metaplasia (ADM) and proliferation, associated with increased activation of ERK and STAT3, and macrophage infiltration in the pancreas, compared to CD-fed KC mice. Metabolomics analysis of the MAT revealed sex differences between diet groups. In females, a HFD altered metabolites related to FA (α-linolenic acid and linoleic acid) and amino acid metabolism (alanine, aspartate, glutamate). In males, a HFD significantly affected pathways related to alanine, aspartate, glutamate, linoleic acid, and the citric acid cycle.
    CONCLUSIONS: A HFD accelerates early pancreatic ADM through multifaceted mechanisms, including effects at the tumor and surrounding MAT. The sex-dependent changes in MAT metabolites could explain some of the sex differences in HFD-induced pancreatic ADM.
    Keywords:  Diet; fat; lipids; obesity; pancreatic cancer; pancreatic cancer risk
    DOI:  https://doi.org/10.1016/j.jnutbio.2024.109690
  18. Nat Biotechnol. 2024 Jun 11.
    Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.
    PCAWG Evolution and Heterogeneity Working Group
      Subclonal reconstruction algorithms use bulk DNA sequencing data to quantify parameters of tumor evolution, allowing an assessment of how cancers initiate, progress and respond to selective pressures. We launched the ICGC-TCGA (International Cancer Genome Consortium-The Cancer Genome Atlas) DREAM Somatic Mutation Calling Tumor Heterogeneity and Evolution Challenge to benchmark existing subclonal reconstruction algorithms. This 7-year community effort used cloud computing to benchmark 31 subclonal reconstruction algorithms on 51 simulated tumors. Algorithms were scored on seven independent tasks, leading to 12,061 total runs. Algorithm choice influenced performance substantially more than tumor features but purity-adjusted read depth, copy-number state and read mappability were associated with the performance of most algorithms on most tasks. No single algorithm was a top performer for all seven tasks and existing ensemble strategies were unable to outperform the best individual methods, highlighting a key research need. All containerized methods, evaluation code and datasets are available to support further assessment of the determinants of subclonal reconstruction accuracy and development of improved methods to understand tumor evolution.
    DOI:  https://doi.org/10.1038/s41587-024-02250-y
  19. Cold Spring Harb Perspect Med. 2024 Jun 10. pii: a041544. [Epub ahead of print]
    Metabolic Signaling in Cancer.
    Laura V Pinheiro, Pedro Costa-Pinheiro, Kathryn E Wellen.
      Metabolic reprogramming in cancer allows cells to survive in harsh environments and sustain macromolecular biosynthesis to support proliferation. In addition, metabolites play crucial roles as signaling molecules. Metabolite fluctuations are detected by various sensors in the cell to regulate gene expression, metabolism, and signal transduction. Metabolic signaling mechanisms contribute to tumorigenesis by altering the physiology of cancer cells themselves, as well as that of neighboring cells in the tumor microenvironment. In this review, we discuss principles of metabolic signaling and provide examples of how cancer cells take advantage of metabolic signals to promote cell proliferation and evade the immune system, thereby contributing to tumor growth and progression.
    DOI:  https://doi.org/10.1101/cshperspect.a041544
  20. Cancer Cell. 2024 Jun 10. pii: S1535-6108(24)00183-1. [Epub ahead of print]42(6): 930-933
    Let it be: Preserving tumor-draining lymph nodes in the era of immuno-oncology.
    Robert Saddawi-Konefka, Shiruyeh Schokrpur, J Silvio Gutkind.
      Solid cancers often progress via metastasis to lymph nodes. Consequently, lymphadenectomy is central to stage cancers and eradicates disease spread. However, mounting evidence suggests that cancer immunotherapies drive antitumor immune responses within lymph nodes. This implies that immunotherapy, delivered with standard oncologic therapies, may require specific treatment sequencing to initiate immunosurveillance and affect primary tumor responses. As supported by recent preclinical and clinical studies, lymphatic-preserving strategies may offer the best promise for driving the next generation of breakthrough immunotherapy approaches.
    DOI:  https://doi.org/10.1016/j.ccell.2024.05.015
  21. Cancer Discov. 2024 Jun 12. OF1-OF7
    Tumor Promoters and Opportunities for Molecular Cancer Prevention.
    William Hill, Clare E Weeden, Charles Swanton.
      Environmental carcinogens increase cancer incidence via both mutagenic and non-mutagenic mechanisms. There are over 500 known or suspected carcinogens classified by the International Agency for Research on Cancer. Sequencing of both cancerous and histologically non-cancerous tissue has been instrumental in improving our understanding of how environmental carcinogens cause cancer. Understanding how and defining which environmental or lifestyle exposures drive cancer will support cancer prevention. Recent research is revisiting the mechanisms of early tumorigenesis, paving the way for an era of molecular cancer prevention. Significance: Recent data have improved our understanding of how carcinogens cause cancer, which may reveal novel opportunities for molecular cancer prevention.
    DOI:  https://doi.org/10.1158/2159-8290.CD-24-0128
  22. Chem Sci. 2024 Jun 12. 15(23): 8934-8945
    Charge-regulated fluorescent anchors enable high-fidelity tracking of plasma membrane dynamics during biological events.
    Jiaqi Zuo, Aohui Peng, Penglei Wu, Junyi Chen, Chuangye Yao, Junjun Pan, Engao Zhu, Yingye Weng, Kewei Zhang, Hui Feng, Zhigang Jin, Zhaosheng Qian.
      Many biological processes generally require long-term visualization tools for time-scale dynamic changes of the plasma membrane, but there is still a lack of design rules for such imaging tools based on small-molecule fluorescent probes. Herein, we revealed the key regulatory roles of charge number and species of fluorescent dyes in the anchoring ability of the plasma membrane and found that the introduction of multi-charged units and appropriate charge species is often required for fluorescent dyes with strong plasma membrane anchoring ability by systematically investigating the structure-function relationship of cyanostyrylpyridium (CSP) dyes with different charge numbers and species and their imaging performance for the plasma membrane. The CSP-DBO dye constructed exhibits strong plasma membrane anchoring ability in staining the plasma membrane of cells, in addition to many other advantages such as excellent biocompatibility and general universality of cell types. Such a fluorescent anchor has been successfully used to monitor chemically induced plasma membrane damage and dynamically track various cellular biological events such as cell fusion and cytokinesis over a long period of time by continuously monitoring the dynamic morphological changes of the plasma membrane, providing a valuable precise visualization tool to study the physiological response to chemical stimuli and reveal the structural morphological changes and functions of the plasma membrane during these important biological events from a dynamic perspective. Furthermore, CSP-DBO exhibits excellent biocompatibility and imaging capability in vivo such as labelling the plasma membrane in vivo and monitoring the metabolic process of lipofuscin as an aging indicator.
    DOI:  https://doi.org/10.1039/d4sc01423e
  23. STAR Protoc. 2024 Jun 09. pii: S2666-1667(24)00287-9. [Epub ahead of print]5(2): 103122
    Protocol for measuring cell cycle Zn2+ dynamics using a FRET-based biosensor.
    Samuel E Holtzen, Ananya Rakshit, Amy E Palmer.
      The exchangeable Zn2+ pool in cells is not static but responds to perturbations as well as fluctuates naturally through the cell cycle. Here, we present a protocol to carry out long-term live-cell imaging of cells expressing a cytosolic Zn2+ sensor. We then describe how to track cells using the published pipeline EllipTrack and how to analyze the single-cell traces to determine changes in labile Zn2+ in response to perturbation. For complete details on the use and execution of this protocol, please refer to Rakshit and Holtzen et al.1.
    Keywords:  Cell Biology; Microscopy; Single Cell
    DOI:  https://doi.org/10.1016/j.xpro.2024.103122
  24. Nat Genet. 2024 Jun;56(6): 1038
    Exploring the origins of pancreatic cancer.
    Safia Danovi.
      
    DOI:  https://doi.org/10.1038/s41588-024-01814-7
  25. Cancer Cell. 2024 Jun 10. pii: S1535-6108(24)00188-0. [Epub ahead of print]42(6): 943-945
    Finding the sweet spot: Targeting RAS in tumors while sparing normal tissue.
    Naiara Perurena, Karen Cichowski.
      The development of mutant-selective KRAS inhibitors represents a major therapeutic advance; however, patients can develop resistance through feedback mechanisms and genetic alterations in the RAS pathway. Three publications in Nature and Cancer Discovery describe a promising RAS(ON) multi-selective inhibitor that simultaneously targets oncogenic RAS and multiple potential resistance mechanisms while sparing normal tissue.
    DOI:  https://doi.org/10.1016/j.ccell.2024.05.020
  26. Trends Cell Biol. 2024 Jun 08. pii: S0962-8924(24)00097-7. [Epub ahead of print]
    Unique architectural features of mammalian mitochondrial protein synthesis.
    Oliver Rackham, Martin Saurer, Nenad Ban, Aleksandra Filipovska.
      Mitochondria rely on coordinated expression of their own mitochondrial DNA (mtDNA) with that of the nuclear genome for their biogenesis. The bacterial ancestry of mitochondria has given rise to unique and idiosyncratic features of the mtDNA and its expression machinery that can be specific to different organisms. In animals, the mitochondrial protein synthesis machinery has acquired many new components and mechanisms over evolution. These include several new ribosomal proteins, new stop codons and ways to recognise them, and new mechanisms to deliver nascent proteins into the mitochondrial inner membrane. Here we describe the mitochondrial protein synthesis machinery in mammals and its unique mechanisms of action elucidated to date and highlight the technologies poised to reveal the next generation of discoveries in mitochondrial translation.
    Keywords:  RNA; mitochondria; mitochondrial disease; ribosomes; translation
    DOI:  https://doi.org/10.1016/j.tcb.2024.05.001
  27. Tissue Eng Part A. 2024 Jun 14.
    Hematoxylin and Eosin Architecture Uncovers Clinically Divergent Niches in Pancreatic Cancer.
    Jason L Guo, David M Lopez, Shamik Mascharak, Deshka S Foster, Anum Khan, Michael F Davitt, Alan T Nguyen, Austin R Burcham, Malini S Chinta, Nicholas J Guardino, Michelle Griffin, Elisabeth Miller, Michael Januszyk, Shyam S Raghavan, Teri A Longacre, Daniel J Delitto, Jeffrey A Norton, Michael T Longaker.
      Pancreatic ductal adenocarcinoma (PDAC) represents one of the only cancers with an increasing incidence rate and is often associated with intra- and peri-tumoral scarring, referred to as desmoplasia. This scarring is highly heterogeneous in extracellular matrix (ECM) architecture and plays complex roles in both tumor biology and clinical outcomes that are not yet fully understood. Using hematoxylin and eosin (H&E), a routine histological stain utilized in existing clinical workflows, we quantified ECM architecture in 85 patient samples to assess relationships between desmoplastic architecture and clinical outcomes such as survival time and disease recurrence. By utilizing unsupervised machine learning (ML) to summarize a latent space across 147 local (e.g. fiber length, solidity) and global (e.g. fiber branching, porosity) H&E-based features, we identified a continuum of histological architectures that were associated with differences in both survival and recurrence. Further, we mapped H&E architectures to a CO-Detection by indEXing (CODEX) reference atlas, revealing localized cell- and protein-based niches associated with outcome-positive vs. outcome-negative scarring in the tumor microenvironment. Overall, our study utilizes standard H&E staining to uncover clinically relevant associations between desmoplastic organization and PDAC outcomes, offering a translatable pipeline to support prognostic decision-making and a blueprint of spatial-biological factors for modeling by tissue engineering methods.
    DOI:  https://doi.org/10.1089/ten.TEA.2024.0039
  28. Nature. 2024 Jun 11.
    The Space Omics and Medical Atlas (SOMA) and international astronaut biobank.
    Eliah G Overbey, JangKeun Kim, Braden T Tierney, Jiwoon Park, Nadia Houerbi, Alexander G Lucaci, Sebastian Garcia Medina, Namita Damle, Deena Najjar, Kirill Grigorev, Evan E Afshin, Krista A Ryon, Karolina Sienkiewicz, Laura Patras, Remi Klotz, Veronica Ortiz, Matthew MacKay, Annalise Schweickart, Christopher R Chin, Maria A Sierra, Matias F Valenzuela, Ezequiel Dantas, Theodore M Nelson, Egle Cekanaviciute, Gabriel Deards, Jonathan Foox, S Anand Narayanan, Caleb M Schmidt, Michael A Schmidt, Julian C Schmidt, Sean Mullane, Seth Stravers Tigchelaar, Steven Levitte, Craig Westover, Chandrima Bhattacharya, Serena Lucotti, Jeremy Wain Hirschberg, Jacqueline Proszynski, Marissa Burke, Ashley Kleinman, Daniel J Butler, Conor Loy, Omary Mzava, Joan Lenz, Doru Paul, Christopher Mozsary, Lauren M Sanders, Lynn E Taylor, Chintan O Patel, Sharib A Khan, Mir Suhail, Syed G Byhaqui, Burhan Aslam, Aaron S Gajadhar, Lucy Williamson, Purvi Tandel, Qiu Yang, Jessica Chu, Ryan W Benz, Asim Siddiqui, Daniel Hornburg, Kelly Blease, Juan Moreno, Andrew Boddicker, Junhua Zhao, Bryan Lajoie, Ryan T Scott, Rachel R Gilbert, San-Huei Lai Polo, Andrew Altomare, Semyon Kruglyak, Shawn Levy, Ishara Ariyapala, Joanne Beer, Bingqing Zhang, Briana M Hudson, Aric Rininger, Sarah E Church, Afshin Beheshti, George M Church, Scott M Smith, Brian E Crucian, Sara R Zwart, Irina Matei, David C Lyden, Francine Garrett-Bakelman, Jan Krumsiek, Qiuying Chen, Dawson Miller, Joe Shuga, Stephen Williams, Corey Nemec, Guy Trudel, Martin Pelchat, Odette Laneuville, Iwijn De Vlaminck, Steven Gross, Kelly L Bolton, Susan M Bailey, Richard Granstein, David Furman, Ari M Melnick, Sylvain V Costes, Bader Shirah, Min Yu, Anil S Menon, Jaime Mateus, Cem Meydan, Christopher E Mason.
      Spaceflight induces molecular, cellular, and physiological shifts in astronauts and poses myriad biomedical challenges to the human body, which are becoming increasingly relevant as more humans venture into space1-6. Yet, current frameworks for aerospace medicine are nascent and lag far behind advancements in precision medicine on Earth, underscoring the need for rapid development of space medicine databases, tools, and protocols. Here, we present the Space Omics and Medical Atlas (SOMA), an integrated data and sample repository for clinical, cellular, and multi-omic research profiles from a diverse range of missions, including the NASA Twins Study7, JAXA CFE study8,9, SpaceX Inspiration4 crew10-12, plus Axiom and Polaris. The SOMA resource represents a >10-fold increase in publicly available human space omics data, with matched samples available from the Cornell Aerospace Medicine Biobank. The Atlas includes extensive molecular and physiological profiles encompassing genomics, epigenomics, transcriptomics, proteomics, metabolomics, and microbiome data sets, which reveal some consistent features across missions, including cytokine shifts, telomere elongation, and gene expression changes, as well as mission-specific molecular responses and links to orthologous, tissue-specific murine data sets. Leveraging the datasets, tools, and resources in SOMA can help accelerate precision aerospace medicine, bringing needed health monitoring, risk mitigation, and countermeasures data for upcoming lunar, Mars, and exploration-class missions.
    DOI:  https://doi.org/10.1038/s41586-024-07639-y
  29. Nat Rev Gastroenterol Hepatol. 2024 Jun 14.
    Unlocking the promise of RAS inhibition in pancreatic cancer.
    Saurav D Haldar, Nilofer S Azad.
      
    DOI:  https://doi.org/10.1038/s41575-024-00951-y
  30. Am J Physiol Cell Physiol. 2024 Jun 10.
    Exploring Heterogeneity: A Dive into Pre-Clinical Models of Cancer Cachexia.
    Francielly Morena da Silva, Ana Regina Cabrera, Nicholas P Greene.
      Cancer Cachexia (CC) is a multifactorial and complex syndrome experienced by up to 80% of cancer patients and implicated in ~40% of cancer-related deaths. Given its significant impact on patients' quality of life and prognosis, there has been a growing emphasis on elucidating the underlying mechanisms of CC using pre-clinical models. However, the mechanisms of cachexia appear to differ across several variables including tumor type and model and biologic variables such as sex. These differences may be exacerbated by variance in experimental approaches and data reporting. This review examines literature spanning from 2011 to March 2024, focusing on common pre-clinical models of CC, including Lewis Lung Carcinoma, pancreatic KPC, and colorectal colon-26 and Apcmin/+ models. Our analysis reveals considerable heterogeneity in phenotypic outcomes, and investigated mechanisms within each model, with particular attention to sex differences which may be exacerbated through methodological differences. While searching for unified mechanisms is critical, we posit that effective treatment approaches are likely to leverage the heterogeneity presented by the tumor and pertinent biological variables to direct specific interventions. In exploring this heterogeneity, it becomes critical to consider methodological and data reporting approaches to best inform further research.
    Keywords:  ApcMin/+; Biological Sex; Colon-26 (C26); KPC; Lewis Lung Carcinoma (LLC)
    DOI:  https://doi.org/10.1152/ajpcell.00317.2024
  31. Sci Adv. 2024 Jun 14. 10(24): eadf2675
    A Thy-1-negative immunofibroblast population emerges as a key determinant of fibrotic outcomes to biomaterials.
    Daniel Abebayehu, Blaise N Pfaff, Grace C Bingham, Andrew E Miller, Mathew Kibet, Surabhi Ghatti, Donald R Griffin, Thomas H Barker.
      Fibrosis-associated fibroblasts have been identified across various fibrotic disorders, but not in the context of biomaterials, fibrotic encapsulation, and the foreign body response. In other fibrotic disorders, a fibroblast subpopulation defined by Thy-1 loss is strongly correlated with fibrosis yet we do not know what promotes Thy-1 loss. We have previously shown that Thy-1 is an integrin regulator enabling normal fibroblast mechanosensing, and here, leveraging nonfibrotic microporous annealed particle (MAP) hydrogels versus classical fibrotic bulk hydrogels, we demonstrate that Thy1-/- mice mount a fibrotic response to MAP gels that includes inflammatory signaling. We found that a distinct and cryptic α-smooth muscle actin-positive Thy-1- fibroblast population emerges in response to interleuklin-1β (IL-1β) and tumor necrosis factor-α (TNFα). Furthermore, IL-1β/TNFα-induced Thy-1- fibroblasts consist of two distinct subpopulations that are strongly proinflammatory. These findings illustrate the emergence of a unique proinflammatory, profibrotic fibroblast subpopulation that is central to fibrotic encapsulation of biomaterials.
    DOI:  https://doi.org/10.1126/sciadv.adf2675
  32. bioRxiv. 2024 May 30. pii: 2024.05.26.595978. [Epub ahead of print]
    Suppression of autophagy induces senescence in the heart.
    Peiyong Zhai, Eun-Ah Sung, Yuka Shiheido-Watanabe, Koichiro Takayama, Yimin Tian, Junichi Sadoshima.
      Aging is a critical risk factor for heart disease, including ischemic heart disease and heart failure. Cellular senescence, characterized by DNA damage, resistance to apoptosis and the senescence-associated secretory phenotype (SASP), occurs in many cell types, including cardiomyocytes. Senescence precipitates the aging process in surrounding cells and the organ through paracrine mechanisms. Generalized autophagy, which degrades cytosolic materials in a non-selective manner, is decreased during aging in the heart. This decrease causes deterioration of cellular quality control mechanisms, facilitates aging and negatively affects lifespan in animals, including mice. Although suppression of generalized autophagy could promote senescence, it remains unclear whether the suppression of autophagy directly stimulates senescence in cardiomyocytes, which, in turn, promotes myocardial dysfunction in the heart. We addressed this question using mouse models with a loss of autophagy function. Suppression of general autophagy in cardiac-specific Atg7 knockout ( Atg7 cKO) mice caused accumulation of senescent cardiomyocytes. Induction of senescence via downregulation of Atg7 was also observed in chimeric Atg7 cardiac-specific KO mice and cultured cardiomyocytes in vitro , suggesting that the effect of autophagy suppression upon induction of senescence is cell autonomous. ABT-263, a senolytic agent, reduced the number of senescent myocytes and improved cardiac function in Atg7 cKO mice. Suppression of autophagy and induction of senescence were also observed in doxorubicin-treated hearts, where activation of autophagy alleviated senescence in cardiomyocytes and cardiac dysfunction. These results suggest that suppression of general autophagy directly induces senescence in cardiomyocytes, which in turn promotes cardiac dysfunction.
    DOI:  https://doi.org/10.1101/2024.05.26.595978
  33. Nat Methods. 2024 Jun 13.
    Realization of cellomics to dive into the whole-body or whole-organ cell cloud.
    Tomoki T Mitani, Etsuo A Susaki, Katsuhiko Matsumoto, Hiroki R Ueda.
      
    DOI:  https://doi.org/10.1038/s41592-024-02307-5
  34. Nat Commun. 2024 Jun 11. 15(1): 4596
    Mapping the landscape of histomorphological cancer phenotypes using self-supervised learning on unannotated pathology slides.
    Adalberto Claudio Quiros, Nicolas Coudray, Anna Yeaton, Xinyu Yang, Bojing Liu, Hortense Le, Luis Chiriboga, Afreen Karimkhan, Navneet Narula, David A Moore, Christopher Y Park, Harvey Pass, Andre L Moreira, John Le Quesne, Aristotelis Tsirigos, Ke Yuan.
      Cancer diagnosis and management depend upon the extraction of complex information from microscopy images by pathologists, which requires time-consuming expert interpretation prone to human bias. Supervised deep learning approaches have proven powerful, but are inherently limited by the cost and quality of annotations used for training. Therefore, we present Histomorphological Phenotype Learning, a self-supervised methodology requiring no labels and operating via the automatic discovery of discriminatory features in image tiles. Tiles are grouped into morphologically similar clusters which constitute an atlas of histomorphological phenotypes (HP-Atlas), revealing trajectories from benign to malignant tissue via inflammatory and reactive phenotypes. These clusters have distinct features which can be identified using orthogonal methods, linking histologic, molecular and clinical phenotypes. Applied to lung cancer, we show that they align closely with patient survival, with histopathologically recognised tumor types and growth patterns, and with transcriptomic measures of immunophenotype. These properties are maintained in a multi-cancer study.
    DOI:  https://doi.org/10.1038/s41467-024-48666-7
  35. Science. 2024 Jun 14. 384(6701): eadj4301
    Metabolic inflexibility promotes mitochondrial health during liver regeneration.
    Xun Wang, Cameron J Menezes, Yuemeng Jia, Yi Xiao, Siva Sai Krishna Venigalla, Feng Cai, Meng-Hsiung Hsieh, Wen Gu, Liming Du, Jessica Sudderth, Dohun Kim, Spencer D Shelton, Claire B Llamas, Yu-Hsuan Lin, Min Zhu, Salma Merchant, Divya Bezwada, Sherwin Kelekar, Lauren G Zacharias, Thomas P Mathews, Gerta Hoxhaj, R Max Wynn, Uttam K Tambar, Ralph J DeBerardinis, Hao Zhu, Prashant Mishra.
      Mitochondria are critical for proper organ function and mechanisms to promote mitochondrial health during regeneration would benefit tissue homeostasis. We report that during liver regeneration, proliferation is suppressed in electron transport chain (ETC)-dysfunctional hepatocytes due to an inability to generate acetyl-CoA from peripheral fatty acids through mitochondrial β-oxidation. Alternative modes for acetyl-CoA production from pyruvate or acetate are suppressed in the setting of ETC dysfunction. This metabolic inflexibility forces a dependence on ETC-functional mitochondria and restoring acetyl-CoA production from pyruvate is sufficient to allow ETC-dysfunctional hepatocytes to proliferate. We propose that metabolic inflexibility within hepatocytes can be advantageous by limiting the expansion of ETC-dysfunctional cells.
    DOI:  https://doi.org/10.1126/science.adj4301
  36. Sci Adv. 2024 Jun 14. 10(24): eado2037
    A firm-push-to-open and light-push-to-lock strategy for a general chemical platform to develop activatable dual-modality NIR-II probes.
    Lili Shen, Jian Li, Chenglong Wen, Hao Wang, Nian Liu, Xinhui Su, Jianzhong Chen, Xin Li.
      Activatable near-infrared (NIR) imaging in the NIR-II range is crucial for deep tissue bioanalyte tracking. However, designing such probes remains challenging due to the limited availability of general chemical strategies. Here, we introduced a foundational platform for activatable probes, using analyte-triggered smart modulation of the π-conjugation system of a NIR-II-emitting rhodamine hybrid. By tuning the nucleophilicity of the ortho-carboxy moiety, we achieved an electronic effect termed "firm-push-to-open and light-push-to-lock," which enables complete spirocyclization of the probe before sensing and allows for efficient zwitterion formation when the light-pushing aniline carbamate trigger is transformed into a firm-pushing aniline. This platform produces dual-modality NIR-II imaging probes with ~50-fold fluorogenic and activatable photoacoustic signals in live mice, surpassing reported probes with generally below 10-fold activatable signals. Demonstrating generality, we successfully designed probes for hydrogen peroxide (H2O2) and hydrogen sulfide (H2S). We envision a widespread adoption of the chemical platform for designing activatable NIR-II probes across diverse applications.
    DOI:  https://doi.org/10.1126/sciadv.ado2037
  37. J Transl Med. 2024 Jun 12. 22(1): 563
    Progress of single-cell RNA sequencing combined with spatial transcriptomics in tumour microenvironment and treatment of pancreatic cancer.
    Jie Zhu, Ke Zhang, Yuan Chen, Xinyu Ge, Junqing Wu, Peng Xu, Jie Yao.
      In recent years, single-cell analyses have revealed the heterogeneity of the tumour microenvironment (TME) at the genomic, transcriptomic, and proteomic levels, further improving our understanding of the mechanisms of tumour development. Single-cell RNA sequencing (scRNA-seq) technology allow analysis of the transcriptome at the single-cell level and have unprecedented potential for exploration of the characteristics involved in tumour development and progression. These techniques allow analysis of transcript sequences at higher resolution, thereby increasing our understanding of the diversity of cells found in the tumour microenvironment and how these cells interact in complex tumour tissue. Although scRNA-seq has emerged as an important tool for studying the tumour microenvironment in recent years, it cannot be used to analyse spatial information for cells. In this regard, spatial transcriptomics (ST) approaches allow researchers to understand the functions of individual cells in complex multicellular organisms by understanding their physical location in tissue sections. In particular, in related research on tumour heterogeneity, ST is an excellent complementary approach to scRNA-seq, constituting a new method for further exploration of tumour heterogeneity, and this approach can also provide unprecedented insight into the development of treatments for pancreatic cancer (PC). In this review, based on the methods of scRNA-seq and ST analyses, research progress on the tumour microenvironment and treatment of pancreatic cancer is further explained.
    Keywords:  Pancreatic cancer; Single-cell RNA sequencing; Spatial transcriptomics; Treatment; Tumour microenvironment
    DOI:  https://doi.org/10.1186/s12967-024-05307-3
  38. J Open Source Softw. 2024 ;pii: 6604. [Epub ahead of print]9(97):
    SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data.
    Ajit J Nirmal, Peter K Sorger.
      Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors ("Catching up with Multiplexed Tissue Imaging," 2022). A critical aspect of such "tissue profiling" is quantifying the spatial relationships among cells at different scales from the interaction of neighboring cells to recurrent communities of cells of multiple types. This often involves statistical analysis of 107 or more cells in which up to 100 biomolecules (commonly proteins) have been measured. While software tools currently cater to the analysis of spatial transcriptomics data (Liu et al., 2022), there remains a need for toolkits explicitly tailored to the complexities of multiplexed imaging data including the need to seamlessly integrate image visualization with data analysis and exploration. We introduce SCIMAP, a Python package specifically crafted to address these challenges. With SCIMAP, users can efficiently preprocess, analyze, and visualize large datasets, facilitating the exploration of spatial relationships and their statistical significance. SCIMAP's modular design enables the integration of new algorithms, enhancing its capabilities for spatial analysis.
    DOI:  https://doi.org/10.21105/joss.06604
  39. Dev Cell. 2024 Jun 05. pii: S1534-5807(24)00342-3. [Epub ahead of print]
    Proteolysis-free amoeboid migration of melanoma cells through crowded environments via bleb-driven worrying.
    Meghan K Driscoll, Erik S Welf, Andrew Weems, Etai Sapoznik, Felix Zhou, Vasanth S Murali, Juan Manuel García-Arcos, Minna Roh-Johnson, Matthieu Piel, Kevin M Dean, Reto Fiolka, Gaudenz Danuser.
      In crowded microenvironments, migrating cells must find or make a path. Amoeboid cells are thought to find a path by deforming their bodies to squeeze through tight spaces. Yet, some amoeboid cells seem to maintain a near-spherical morphology as they move. To examine how they do so, we visualized amoeboid human melanoma cells in dense environments and found that they carve tunnels via bleb-driven degradation of extracellular matrix components without the need for proteolytic degradation. Interactions between adhesions and collagen at the cell front induce a signaling cascade that promotes bleb enlargement via branched actin polymerization. Large blebs abrade collagen, creating feedback between extracellular matrix structure, cell morphology, and polarization that enables both path generation and persistent movement.
    Keywords:  amoeboid; blebbing; cell migration; computer vision; extracellular matrix remodeling; fluorescence microscopy; light-sheet microscopy; macropinocytosis; melanoma
    DOI:  https://doi.org/10.1016/j.devcel.2024.05.024
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