bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2022‒06‒19
28 papers selected by
Kıvanç Görgülü
Technical University of Munich
  1. Mass spectrometry-based draft of the mouse proteome.
  2. Distinct mechanisms of innate and adaptive immune regulation underlie poor oncologic outcomes associated with KRAS-TP53 co-alteration in pancreatic cancer.
  3. Metabolic-scale gene activation screens identify SLCO2B1 as a heme transporter that enhances cellular iron availability.
  4. Autophagy in PDGFRA+ mesenchymal cells is required for intestinal homeostasis and mammalian survival.
  5. Signatures of copy number alterations in human cancer.
  6. Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.
  7. A guide to membrane atg8ylation and autophagy with reflections on immunity.
  8. Iron-Sensitive Prodrugs That Trigger Active Ferroptosis in Drug-Tolerant Pancreatic Cancer Cells.
  9. The influence of age, sex, and exercise on autophagy, mitophagy, and lysosome biogenesis in skeletal muscle.
  10. A glitch in the matrix: Age-dependent changes in the extracellular matrix facilitate common sites of metastasis.
  11. A pan-cancer compendium of chromosomal instability.
  12. Activity of acute pancreatitis is modified by secreted protein acidic and rich in cysteine ablation.
  13. An exercise-inducible metabolite that suppresses feeding and obesity.
  14. Hallmarks of DNA replication stress.
  15. Systematically quantifying morphological features reveals constraints on organoid phenotypes.
  16. Interleukin-17 governs hypoxic adaptation of injured epithelium.
  17. Tumor-Stroma Interaction in PDAC as a New Approach for Liquid Biopsy and its Potential Clinical Implications.
  18. Multidisciplinary approaches to cancer cachexia: current service models and future perspectives.
  19. Regulation of the lysosome by sphingolipids: potential role in aging.
  20. CancerNet: a unified deep learning network for pan-cancer diagnostics.
  21. Surgical resection of pancreatic cancer with synchronous hepatic oligometastases: Real benefit or selection bias?
  22. The local microenvironment matters in preclinical basic and translational studies of cancer immunology and immunotherapy.
  23. Discovery and Optimization of Pyrrolopyrimidine Derivatives as Selective Disruptors of the Perinucleolar Compartment, a Marker of Tumor Progression toward Metastasis.
  24. Tumour invasion and dissemination.
  25. Safety and tumour-specific immunological responses of combined dendritic cell vaccination and anti-CD40 agonistic antibody treatment for patients with metastatic pancreatic cancer: protocol for a phase I, open-label, single-arm, dose-escalation study (REACtiVe-2 trial).
  26. Size regulation of multiple organelles competing for a limiting subunit pool.
  27. Measuring biological age using omics data.
  28. cGAS-STING drives the IL-6-dependent survival of chromosomally instable cancers.
  1. Nat Methods. 2022 Jun 16.
    Mass spectrometry-based draft of the mouse proteome.
    Piero Giansanti, Patroklos Samaras, Yangyang Bian, Chen Meng, Andrea Coluccio, Martin Frejno, Hannah Jakubowsky, Sophie Dobiasch, Rashmi R Hazarika, Julia Rechenberger, Julia Calzada-Wack, Johannes Krumm, Sebastian Mueller, Chien-Yun Lee, Nicole Wimberger, Ludwig Lautenbacher, Zonera Hassan, Yun-Chien Chang, Chiara Falcomatà, Florian P Bayer, Stefanie Bärthel, Tobias Schmidt, Roland Rad, Stephanie E Combs, Matthew The, Frank Johannes, Dieter Saur, Martin Hrabe de Angelis, Mathias Wilhelm, Günter Schneider, Bernhard Kuster.
      The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. Here, we present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and several lines of analyses exemplify which insights can be gleaned from the data. For instance, tissue- and cell-type resolved profiles provide protein evidence for the expression of 17,000 genes, thousands of isoforms and 50,000 phosphorylation sites in vivo. Proteogenomic comparison of mouse, human and Arabidopsis reveal common and distinct mechanisms of gene expression regulation and, despite many similarities, numerous differentially abundant orthologs that likely serve species-specific functions. We leverage the mouse proteome by integrating phenotypic drug (n > 400) and radiation response data with the proteomes of 66 pancreatic ductal adenocarcinoma (PDAC) cell lines to reveal molecular markers for sensitivity and resistance. This unique atlas complements other molecular resources for the mouse and can be explored online via ProteomicsDB and PACiFIC.
    DOI:  https://doi.org/10.1038/s41592-022-01526-y
  2. Oncogene. 2022 Jun 14.
    Distinct mechanisms of innate and adaptive immune regulation underlie poor oncologic outcomes associated with KRAS-TP53 co-alteration in pancreatic cancer.
    Jashodeep Datta, Anna Bianchi, Iago De Castro Silva, Nilesh U Deshpande, Long Long Cao, Siddharth Mehra, Samara Singh, Christine Rafie, Xiaodian Sun, Xi Chen, Xizi Dai, Antonio Colaprico, Prateek Sharma, Austin R Dosch, Asha Pillai, Peter J Hosein, Nagaraj S Nagathihalli, Krishna V Komanduri, Julie M Wilson, Yuguang Ban, Nipun B Merchant.
      Co-occurrent KRAS and TP53 mutations define a majority of patients with pancreatic ductal adenocarcinoma (PDAC) and define its pro-metastatic proclivity. Here, we demonstrate that KRAS-TP53 co-alteration is associated with worse survival compared with either KRAS-alone or TP53-alone altered PDAC in 245 patients with metastatic disease treated at a tertiary referral cancer center, and validate this observation in two independent molecularly annotated datasets. Compared with non-TP53 mutated KRAS-altered tumors, KRAS-TP53 co-alteration engenders disproportionately innate immune-enriched and CD8+ T-cell-excluded immune signatures. Leveraging in silico, in vitro, and in vivo models of human and murine PDAC, we discover a novel intersection between KRAS-TP53 co-altered transcriptomes, TP63-defined squamous trans-differentiation, and myeloid-cell migration into the tumor microenvironment. Comparison of single-cell transcriptomes between KRAS-TP53 co-altered and KRAS-altered/TP53WT tumors revealed cancer cell-autonomous transcriptional programs that orchestrate innate immune trafficking and function. Moreover, we uncover granulocyte-derived inflammasome activation and TNF signaling as putative paracrine mediators of innate immunoregulatory transcriptional programs in KRAS-TP53 co-altered PDAC. Immune subtyping of KRAS-TP53 co-altered PDAC reveals conflation of intratumor heterogeneity with progenitor-like stemness properties. Coalescing these distinct molecular characteristics into a KRAS-TP53 co-altered "immunoregulatory program" predicts chemoresistance in metastatic PDAC patients enrolled in the COMPASS trial, as well as worse overall survival.
    DOI:  https://doi.org/10.1038/s41388-022-02368-w
  3. Mol Cell. 2022 Jun 09. pii: S1097-2765(22)00491-9. [Epub ahead of print]
    Metabolic-scale gene activation screens identify SLCO2B1 as a heme transporter that enhances cellular iron availability.
    Gokhan Unlu, Benjamin Prizer, Ranya Erdal, Hsi-Wen Yeh, Erol C Bayraktar, Kıvanç Birsoy.
      Iron is the most abundant transition metal essential for numerous cellular processes. Although most mammalian cells acquire iron through transferrin receptors, molecular players of iron utilization under iron restriction are incompletely understood. To address this, we performed metabolism-focused CRISPRa gain-of-function screens, which revealed metabolic limitations under stress conditions. Iron restriction screens identified not only expected members of iron utilization pathways but also SLCO2B1, a poorly characterized membrane carrier. SLCO2B1 expression is sufficient to increase intracellular iron, bypass the essentiality of the transferrin receptor, and enable proliferation under iron restriction. Mechanistically, SLCO2B1 mediates heme analog import in cellular assays. Heme uptake by SLCO2B1 provides sufficient iron for proliferation through heme oxygenases. Notably, SLCO2B1 is predominantly expressed in microglia in the brain, and primary Slco2b1-/- mouse microglia exhibit strong defects in heme analog import. Altogether, our work identifies SLCO2B1 as a microglia-enriched plasma membrane heme importer and provides a genetic platform to identify metabolic limitations under stress conditions.
    Keywords:  CRISPRa; SLCO2B1; heme; iron; metabolic limitation
    DOI:  https://doi.org/10.1016/j.molcel.2022.05.024
  4. Autophagy. 2022 Jun 16.
    Autophagy in PDGFRA+ mesenchymal cells is required for intestinal homeostasis and mammalian survival.
    Yang Yang, Eileen White.
      Macroautophagy/autophagy defects are a risk factor for intestinal bowel disease (IBD), but the mechanism remains unclear. We previously demonstrated that conditional whole-body deletion of the essential Atg7 (autophagy related 7) gene in adult mice (atg7Δ/Δ) causes specific tissue damage and shortens lifespan to three months primarily due to neurodegeneration with surprisingly no disturbing effects on the intestine. In contrast, we recently found that conditional whole-body deletion of other essential autophagy genes, Atg5 or Rb1cc1/Fip200 (atg5Δ/Δ or rb1cc1Δ/Δ), cause death within five days due to rapid inhibition of autophagy, elimination of intestinal stem cells, and loss of barrier function in the ileum. atg5Δ/Δ mice lose PDGFRA/PDGFRα+ mesenchymal cells (PMCs) and WNT signaling essential for stem cell renewal. Depletion of aspartate and nucleotides in atg5Δ/Δ ileum was revealed by novel mass-spectrometry imaging (MALDI-MSI), consistent with metabolic insufficiency underlying PMCs loss. The difference in the autophagy gene knockout phenotypes is likely due to distinct kinetics of autophagy loss because gradual whole-body atg5 deletion extends lifespan, phenocopying deletion of Atg7 or Atg12. Therefore, we established that autophagy is required for ileum PMC metabolism, stem cell maintenance and mammalian survival. PMC loss caused by autophagy deficiency may therefore contribute to IBD.
    Keywords:  Autophagy; IBD; PDGFRα+ mesenchymal cells; WNT signaling; intestinal stem cells
    DOI:  https://doi.org/10.1080/15548627.2022.2090694
  5. Nature. 2022 Jun 15.
    Signatures of copy number alterations in human cancer.
    Christopher D Steele, Ammal Abbasi, S M Ashiqul Islam, Amy L Bowes, Azhar Khandekar, Kerstin Haase, Shadi Hames-Fathi, Dolapo Ajayi, Annelien Verfaillie, Pawan Dhami, Alex McLatchie, Matt Lechner, Nicholas Light, Adam Shlien, David Malkin, Andrew Feber, Paula Proszek, Tom Lesluyes, Fredrik Mertens, Adrienne M Flanagan, Maxime Tarabichi, Peter Van Loo, Ludmil B Alexandrov, Nischalan Pillay.
      Gains and losses of DNA are prevalent in cancer and emerge as a consequence of inter-related processes of replication stress, mitotic errors, spindle multipolarity and breakage-fusion-bridge cycles, among others, which may lead to chromosomal instability and aneuploidy1,2. These copy number alterations contribute to cancer initiation, progression and therapeutic resistance3-5. Here we present a conceptual framework to examine the patterns of copy number alterations in human cancer that is widely applicable to diverse data types, including whole-genome sequencing, whole-exome sequencing, reduced representation bisulfite sequencing, single-cell DNA sequencing and SNP6 microarray data. Deploying this framework to 9,873 cancers representing 33 human cancer types from The Cancer Genome Atlas6 revealed a set of 21 copy number signatures that explain the copy number patterns of 97% of samples. Seventeen copy number signatures were attributed to biological phenomena of whole-genome doubling, aneuploidy, loss of heterozygosity, homologous recombination deficiency, chromothripsis and haploidization. The aetiologies of four copy number signatures remain unexplained. Some cancer types harbour amplicon signatures associated with extrachromosomal DNA, disease-specific survival and proto-oncogene gains such as MDM2. In contrast to base-scale mutational signatures, no copy number signature was associated with many known exogenous cancer risk factors. Our results synthesize the global landscape of copy number alterations in human cancer by revealing a diversity of mutational processes that give rise to these alterations.
    DOI:  https://doi.org/10.1038/s41586-022-04738-6
  6. Nat Biotechnol. 2022 Jun 13.
    Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.
    Shaolong Cao, Jennifer R Wang, Shuangxi Ji, Peng Yang, Yaoyi Dai, Shuai Guo, Matthew D Montierth, John Paul Shen, Xiao Zhao, Jingxiao Chen, Jaewon James Lee, Paola A Guerrero, Nicholas Spetsieris, Nikolai Engedal, Sinja Taavitsainen, Kaixian Yu, Julie Livingstone, Vinayak Bhandari, Shawna M Hubert, Najat C Daw, P Andrew Futreal, Eleni Efstathiou, Bora Lim, Andrea Viale, Jianjun Zhang, Matti Nykter, Bogdan A Czerniak, Powel H Brown, Charles Swanton, Pavlos Msaouel, Anirban Maitra, Scott Kopetz, Peter Campbell, Terence P Speed, Paul C Boutros, Hongtu Zhu, Alfonso Urbanucci, Jonas Demeulemeester, Peter Van Loo, Wenyi Wang.
      Single-cell RNA sequencing studies have suggested that total mRNA content correlates with tumor phenotypes. Technical and analytical challenges, however, have so far impeded at-scale pan-cancer examination of total mRNA content. Here we present a method to quantify tumor-specific total mRNA expression (TmS) from bulk sequencing data, taking into account tumor transcript proportion, purity and ploidy, which are estimated through transcriptomic/genomic deconvolution. We estimate and validate TmS in 6,590 patient tumors across 15 cancer types, identifying significant inter-tumor variability. Across cancers, high TmS is associated with increased risk of disease progression and death. TmS is influenced by cancer-specific patterns of gene alteration and intra-tumor genetic heterogeneity as well as by pan-cancer trends in metabolic dysregulation. Taken together, our results indicate that measuring cell-type-specific total mRNA expression in tumor cells predicts tumor phenotypes and clinical outcomes.
    DOI:  https://doi.org/10.1038/s41587-022-01342-x
  7. J Cell Biol. 2022 Jul 04. pii: e202203083. [Epub ahead of print]221(7):
    A guide to membrane atg8ylation and autophagy with reflections on immunity.
    Vojo Deretic, Michael Lazarou.
      The process of membrane atg8ylation, defined herein as the conjugation of the ATG8 family of ubiquitin-like proteins to membrane lipids, is beginning to be appreciated in its broader manifestations, mechanisms, and functions. Classically, membrane atg8ylation with LC3B, one of six mammalian ATG8 family proteins, has been viewed as the hallmark of canonical autophagy, entailing the formation of characteristic double membranes in the cytoplasm. However, ATG8s are now well described as being conjugated to single membranes and, most recently, proteins. Here we propose that the atg8ylation is coopted by multiple downstream processes, one of which is canonical autophagy. We elaborate on these biological outputs, which impact metabolism, quality control, and immunity, emphasizing the context of inflammation and immunological effects. In conclusion, we propose that atg8ylation is a modification akin to ubiquitylation, and that it is utilized by different systems participating in membrane stress responses and membrane remodeling activities encompassing autophagy and beyond.
    DOI:  https://doi.org/10.1083/jcb.202203083
  8. J Am Chem Soc. 2022 Jun 13.
    Iron-Sensitive Prodrugs That Trigger Active Ferroptosis in Drug-Tolerant Pancreatic Cancer Cells.
    Michał Antoszczak, Sebastian Müller, Tatiana Cañeque, Ludovic Colombeau, Nelson Dusetti, Patricia Santofimia-Castaño, Christine Gaillet, Alain Puisieux, Juan Lucio Iovanna, Raphaël Rodriguez.
      Persister cancer cells represent rare populations of cells resistant to therapy. Cancer cells can exploit epithelial-mesenchymal plasticity to adopt a drug-tolerant state that does not depend on genetic alterations. Small molecules that can interfere with cell plasticity or kill cells in a cell state-dependent manner are highly sought after. Salinomycin has been shown to kill cancer cells in the mesenchymal state by sequestering iron in lysosomes, taking advantage of the iron addiction of this cell state. Here, we report the chemo- and stereoselective synthesis of a series of structurally complex small molecule chimeras of salinomycin derivatives and the iron-reactive dihydroartemisinin. We show that these chimeras accumulate in lysosomes and can react with iron to release bioactive species, thereby inducing ferroptosis in drug-tolerant pancreatic cancer cells and biopsy-derived organoids of pancreatic ductal adenocarcinoma. This work paves the way toward the development of new cancer medicines acting through active ferroptosis.
    DOI:  https://doi.org/10.1021/jacs.2c03973
  9. Skelet Muscle. 2022 Jun 11. 12(1): 13
    The influence of age, sex, and exercise on autophagy, mitophagy, and lysosome biogenesis in skeletal muscle.
    Matthew Triolo, Ashley N Oliveira, Rita Kumari, David A Hood.
      BACKGROUND: Aging decreases skeletal muscle mass and quality. Maintenance of healthy muscle is regulated by a balance between protein and organellar synthesis and their degradation. The autophagy-lysosome system is responsible for the selective degradation of protein aggregates and organelles, such as mitochondria (i.e., mitophagy). Little data exist on the independent and combined influence of age, biological sex, and exercise on the autophagy system and lysosome biogenesis. The purpose of this study was to characterize sex differences in autophagy and lysosome biogenesis in young and aged muscle and to determine if acute exercise influences these processes.METHODS: Young (4-6 months) and aged (22-24 months) male and female mice were assigned to a sedentary or an acute exercise group. Mitochondrial content, the autophagy-lysosome system, and mitophagy were measured via protein analysis. A TFEB-promoter-construct was utilized to examine Tfeb transcription, and nuclear-cytosolic fractions allowed us to examine TFEB localization in sedentary and exercised muscle with age and sex.
    RESULTS: Our results indicate that female mice, both young and old, had more mitochondrial protein than age-matched males. However, mitochondria in the muscle of females had a reduced respiratory capacity. Mitochondrial content was only reduced with age in the male cohort. Young female mice had a greater abundance of autophagy, mitophagy, and lysosome proteins than young males; however, increases were evident with age irrespective of sex. Young sedentary female mice had indices of greater autophagosomal turnover than male counterparts. Exhaustive exercise was able to stimulate autophagic clearance solely in young male mice. Similarly, nuclear TFEB protein was enhanced to a greater extent in young male, compared to young female mice following exercise, but no changes were observed in aged mice. Finally, TFEB-promoter activity was upregulated following exercise in both young and aged muscle.
    CONCLUSIONS: The present study demonstrates that biological sex influences mitochondrial homeostasis, the autophagy-lysosome system, and mitophagy in skeletal muscle with age. Furthermore, our data suggest that young male mice have a more profound ability to activate these processes with exercise than in the other groups. Ultimately, this may contribute to a greater remodeling of muscle in response to exercise training in males.
    Keywords:  Aging; Autophagy; Lysosomes; Mitophagy; Muscle; Sex differences; TFEB
    DOI:  https://doi.org/10.1186/s13395-022-00296-7
  10. Aging Cancer. 2020 Dec;1(1-4): 19-29
    A glitch in the matrix: Age-dependent changes in the extracellular matrix facilitate common sites of metastasis.
    Gloria E Marino, Ashani T Weeraratna.
      People over 55 years old represent the majority of cancer patients and suffer from increased metastatic burden compared to the younger patient population. As the aging population increases globally, it is prudent to understand how the intrinsic aging process contributes to cancer progression. As we age, we incur aberrant changes in the extracellular matrix (ECM) of our organs, which contribute to numerous pathologies, including cancer. Notably, the lung, liver, and bone represent the most common sites of distal metastasis for all cancer types. In this review, we describe how age-dependent changes in the ECM of these organs influence cancer progression. Further, we outline how these alterations prime the premetastatic niche and why these may help explain the disparity in outcome for older cancer patients.
    Keywords:  aging; cancer biology; metastasis; microenvironment
    DOI:  https://doi.org/10.1002/aac2.12013
  11. Nature. 2022 Jun 15.
    A pan-cancer compendium of chromosomal instability.
    Ruben M Drews, Barbara Hernando, Maxime Tarabichi, Kerstin Haase, Tom Lesluyes, Philip S Smith, Lena Morrill Gavarró, Dominique-Laurent Couturier, Lydia Liu, Michael Schneider, James D Brenton, Peter Van Loo, Geoff Macintyre, Florian Markowetz.
      Chromosomal instability (CIN) results in the accumulation of large-scale losses, gains and rearrangements of DNA1. The broad genomic complexity caused by CIN is a hallmark of cancer2; however, there is no systematic framework to measure different types of CIN and their effect on clinical phenotypes pan-cancer. Here we evaluate the extent, diversity and origin of CIN across 7,880 tumours representing 33 cancer types. We present a compendium of 17 copy number signatures that characterize specific types of CIN, with putative aetiologies supported by multiple independent data sources. The signatures predict drug response and identify new drug targets. Our framework refines the understanding of impaired homologous recombination, which is one of the most therapeutically targetable types of CIN. Our results illuminate a fundamental structure underlying genomic complexity in human cancers and provide a resource to guide future CIN research.
    DOI:  https://doi.org/10.1038/s41586-022-04789-9
  12. United European Gastroenterol J. 2022 Jun 14.
    Activity of acute pancreatitis is modified by secreted protein acidic and rich in cysteine ablation.
    Christoph Ammer-Herrmenau, Laurin Wolf, Syeda S Nasrin, Iswarya Ramu, Roberta Roggiolani, Robert G Goetze, Soeren M Buchholz, Mathias Sendler, Volker Ellenrieder, Albrecht Neesse.
      BACKGROUND: Acute pancreatitis (AP) is a frequent cause for hospitalization. However, molecular determinants that modulate severity of experimental pancreatitis are only partially understood.OBJECTIVE: To investigate the role of secreted protein acidic and rich in cysteine (SPARC) during cerulein-induced AP in mice.
    METHODS: AP was induced by repeated cerulein injections in SPARC knock-out mice (SPARC-/- ) and control littermates (SPARC+/+ ). Secreted protein acidic and rich in cysteine expression and severity of AP were determined by histopathological scoring, immunohistochemistry, and biochemical assays. For functional analysis, primary murine acinar cell cultures with subsequent amylase release assays were employed. Proteome profiler assay and ELISA were conducted from pancreatic tissue lysates, and co-immunofluorescence was performed.
    RESULTS: Upon cerulein induction, SPARC expression was robustly induced in pancreatic stellate cells (PSCs) but not in acinar cells. Genetic SPARC ablation resulted in attenuated severity of AP with significantly reduced levels of pancreatic necrosis, apoptosis, immune cell infiltration, and reduced fibrosis upon chronic stimulation. However, the release of amylase upon cerulein stimulation in primary acinar cell culture from SPARC+/+ and SPARC-/- was indistinguishable. Notably, immune cell derived C-C Motif Chemokine Ligand 2 (CCL2) was highly elevated in SPARC+/+ pancreatic tissue potentially linking PSC derived SPARC with CCL2 induction in AP.
    CONCLUSION: SPARC mediates the severity of AP. The potential link between SPARC and the CCL2 axis could open new avenues for tailored therapeutic interventions in AP patients and warrants further investigations.
    Keywords:  BM-40; CCL2; SPARC; acute pancreatitis; cerulein; osteonectin
    DOI:  https://doi.org/10.1002/ueg2.12262
  13. Nature. 2022 Jun 15.
    An exercise-inducible metabolite that suppresses feeding and obesity.
    Veronica L Li, Yang He, Kévin Contrepois, Hailan Liu, Joon T Kim, Amanda L Wiggenhorn, Julia T Tanzo, Alan Sheng-Hwa Tung, Xuchao Lyu, Peter-James H Zushin, Robert S Jansen, Basil Michael, Kang Yong Loh, Andrew C Yang, Christian S Carl, Christian T Voldstedlund, Wei Wei, Stephanie M Terrell, Benjamin C Moeller, Rick M Arthur, Gareth A Wallis, Koen van de Wetering, Andreas Stahl, Bente Kiens, Erik A Richter, Steven M Banik, Michael P Snyder, Yong Xu, Jonathan Z Long.
      Exercise confers protection against obesity, type 2 diabetes and other cardiometabolic diseases1-5. However, the molecular and cellular mechanisms that mediate the metabolic benefits of physical activity remain unclear6. Here we show that exercise stimulates the production of N-lactoyl-phenylalanine (Lac-Phe), a blood-borne signalling metabolite that suppresses feeding and obesity. The biosynthesis of Lac-Phe from lactate and phenylalanine occurs in CNDP2+ cells, including macrophages, monocytes and other immune and epithelial cells localized to diverse organs. In diet-induced obese mice, pharmacological-mediated increases in Lac-Phe reduces food intake without affecting movement or energy expenditure. Chronic administration of Lac-Phe decreases adiposity and body weight and improves glucose homeostasis. Conversely, genetic ablation of Lac-Phe biosynthesis in mice increases food intake and obesity following exercise training. Last, large activity-inducible increases in circulating Lac-Phe are also observed in humans and racehorses, establishing this metabolite as a molecular effector associated with physical activity across multiple activity modalities and mammalian species. These data define a conserved exercise-inducible metabolite that controls food intake and influences systemic energy balance.
    DOI:  https://doi.org/10.1038/s41586-022-04828-5
  14. Mol Cell. 2022 Jun 16. pii: S1097-2765(22)00438-5. [Epub ahead of print]82(12): 2298-2314
    Hallmarks of DNA replication stress.
    Sneha Saxena, Lee Zou.
      Faithful DNA replication is critical for the maintenance of genomic integrity. Although DNA replication machinery is highly accurate, the process of DNA replication is constantly challenged by DNA damage and other intrinsic and extrinsic stresses throughout the genome. A variety of cellular stresses interfering with DNA replication, which are collectively termed replication stress, pose a threat to genomic stability in both normal and cancer cells. To cope with replication stress and maintain genomic stability, cells have evolved a complex network of cellular responses to alleviate and tolerate replication problems. This review will focus on the major sources of replication stress, the impacts of replication stress in cells, and the assays to detect replication stress, offering an overview of the hallmarks of DNA replication stress.
    Keywords:  ATR; DNA damage; DNA repair; DNA replication; cancer; cell cycle; checkpoint; genomic integrity; genomic stability; replication stress
    DOI:  https://doi.org/10.1016/j.molcel.2022.05.004
  15. Cell Syst. 2022 Jun 08. pii: S2405-4712(22)00229-0. [Epub ahead of print]
    Systematically quantifying morphological features reveals constraints on organoid phenotypes.
    Lauren E Beck, Jasmine Lee, Christopher Coté, Margaret C Dunagin, Ilya Lukonin, Nikkita Salla, Marcello K Chang, Alex J Hughes, Joseph D Mornin, Zev J Gartner, Prisca Liberali, Arjun Raj.
      Organoids recapitulate complex 3D organ structures and represent a unique opportunity to probe the principles of self-organization. While we can alter an organoid's morphology by manipulating the culture conditions, the morphology of an organoid often resembles that of its original organ, suggesting that organoid morphologies are governed by a set of tissue-specific constraints. Here, we establish a framework to identify constraints on an organoid's morphological features by quantifying them from microscopy images of organoids exposed to a range of perturbations. We apply this framework to Madin-Darby canine kidney cysts and show that they obey a number of constraints taking the form of scaling relationships or caps on certain parameters. For example, we found that the number, but not size, of cells increases with increasing cyst size. We also find that these constraints vary with cyst age and can be altered by varying the culture conditions. We observed similar sets of constraints in intestinal organoids. This quantitative framework for identifying constraints on organoid morphologies may inform future efforts to engineer organoids.
    Keywords:  design principles; morphology; organoids
    DOI:  https://doi.org/10.1016/j.cels.2022.05.008
  16. Science. 2022 Jun 16. eabg9302
    Interleukin-17 governs hypoxic adaptation of injured epithelium.
    Piotr Konieczny, Yue Xing, Ikjot Sidhu, Ipsita Subudhi, Kody P Mansfield, Brandon Hsieh, Douglas E Biancur, Samantha B Larsen, Michael Cammer, Dongqing Li, Ning Xu Landén, Cynthia Loomis, Adriana Heguy, Anastasia N Tikhonova, Aristotelis Tsirigos, Shruti Naik.
      Mammalian cells autonomously activate hypoxia-inducible transcription factors to ensure survival in low-oxygen environments. We report that injury-induced hypoxia is insufficient to trigger hypoxia-inducible factor 1 alpha (HIF1α) in damaged epithelium. Instead, multimodal single-cell and spatial transcriptomics analyses and functional studies reveal that RORγt+ γδ T cell-derived interleukin (IL)-17A, is necessary and sufficient to activate HIF1α. Protein kinase B (AKT) and ERK1/2 signaling proximal of IL-17RC activates mammalian target of rapamycin (mTOR) and consequently HIF1α. The IL-17A-HIF1α drives glycolysis in wound front epithelia. Epithelial-specific loss of IL-17RC, HIF1α, or blockade of glycolysis derails repair. Our findings underscore the coupling of inflammatory, metabolic, and migratory programs to expedite epithelial healing and illuminate the immune cell-derived inputs in cellular adaptation to hypoxic stress during repair.
    DOI:  https://doi.org/10.1126/science.abg9302
  17. Front Cell Dev Biol. 2022 ;10 918795
    Tumor-Stroma Interaction in PDAC as a New Approach for Liquid Biopsy and its Potential Clinical Implications.
    Julian Götze, Christine Nitschke, Faik G Uzunoglu, Klaus Pantel, Marianne Sinn, Harriet Wikman.
      The extremely poor prognosis for patients with pancreatic ductal adenocarcinoma (PDAC) has remained unchanged for decades. As a hallmark of PDAC histology, the distinct desmoplastic response in the tumor microenvironment is considered a key factor exerting pro- and antitumor effects. Increasing emphasis has been placed on cancer-associated fibroblasts (CAFs), whose heterogeneity and functional diversity is reflected in the numerous subtypes. The myofibroblastic CAFs (myCAFs), inflammatory CAFs (iCAFs) and antigen presenting CAFs (apCAFs) are functionally divergent CAF subtypes with tumor promoting as well as repressing effects. Precise knowledge of the underlying interactions is the basis for a variety of treatment approaches, which are subsumed under the term antistromal therapy. Clinical implementation is still pending due to the lack of benefit-as well as paradoxical preclinical findings. While the prominent significance of CAFs in the immediate environment of the tumor is becoming clear, less is known about the circulating (c)CAFs. cCAFs are of particular interest as they seem not only to be potential new liquid biopsy biomarkers but also to support the survival of circulating tumor cells (CTC) in the bloodstream. In PDAC, CTCs correlate with an unfavorable outcome and can also be employed to monitor treatment response, but the current clinical relevance is limited. In this review, we discuss CTCs, cCAFs, secretomes that include EVs or fragments of collagen turnover as liquid biopsy biomarkers, and clinical approaches to target tumor stroma in PDAC.
    Keywords:  cancer-associated fibroblasts (CAFs); circulating tumor cells (CTCs); liquid biopsy; pancreatic cancer; tumor microenvironment
    DOI:  https://doi.org/10.3389/fcell.2022.918795
  18. Expert Rev Anticancer Ther. 2022 Jun 14.
    Multidisciplinary approaches to cancer cachexia: current service models and future perspectives.
    Vanessa C Vaughan, Peter Martin.
      INTRODUCTION: : Cancer cachexia remains a complex unmet need in oncology care, despite its high prevalence and high impact. Patients with cachexia experience numerous complications, including reduced tolerance and effectiveness of anti-cancer therapy, reduced mobility, and reduced functional status, leading to decreased quality of life and survival.AREAS COVERED: : As the cachexia field moves toward greater consensus of definitions and measurements, we highlight the tools currently available for the identification and staging of cachexia, and the barriers that people with cancer face in the timely identification and management of cachexia. Multidisciplinary cachexia service models have emerged to address practice gaps and needs identified by patients and clinicians, with person-centred approaches to cachexia care demonstrating promising improvements in patient outcome, but controlled trials of clinical service models are lacking.
    EXPERT OPINION: : While significant advances have been made in the understanding of cachexia, future trials of clinical service models require further standardisation of definitions and key outcome measures, with more robust controlled study designs to establish the efficacy of proposed best practice. We remain excited with the potential benefit of these innovative models and continue to advocate for the implementation of dedicated multidisciplinary cachexia teams to ensure patients and their families receive the right support, in the right place, at the right time.
    Keywords:  cancer cachexia; clinical service models; multidisciplinary care; palliative rehabilitation; supportive cancer care
    DOI:  https://doi.org/10.1080/14737140.2022.2088516
  19. J Biol Chem. 2022 Jun 09. pii: S0021-9258(22)00559-2. [Epub ahead of print] 102118
    Regulation of the lysosome by sphingolipids: potential role in aging.
    Haiqing Tang, Xiaokun Huang, Shanshan Pang.
      Sphingolipids are a class of bioactive complex lipids that have been closely associated with aging and aging-related diseases. However, the mechanism through which sphingolipids control aging has long been a mystery. Emerging studies reveal that sphingolipids exert tight control over lysosomal homeostasis and function, as evidenced by sphingolipid-related diseases, including but not limited to lysosomal storage disorders. These diseases are defined by primary lysosomal defects and a few secondary defects such as mitochondrial dysfunction. Intriguingly, recent research indicates that the majority of these defects are also associated with aging, implying that sphingolipid-related diseases and aging may share common mechanisms. We propose that the lysosome is a pivotal hub for sphingolipid-mediated aging regulation. This review discusses the critical roles of sphingolipid metabolism in regulating various lysosomal functions, with an emphasis on how such regulation may contribute to aging and aging-related diseases.
    Keywords:  aging; lifespan; lysosomal calcium; lysosomal cell death; lysosome; lysosome-mitochondria communication; mTOR; sphingolipid
    DOI:  https://doi.org/10.1016/j.jbc.2022.102118
  20. BMC Bioinformatics. 2022 Jun 13. 23(1): 229
    CancerNet: a unified deep learning network for pan-cancer diagnostics.
    Steven Gore, Rajeev K Azad.
      BACKGROUND: Despite remarkable advances in cancer research, cancer remains one of the leading causes of death worldwide. Early detection of cancer and localization of the tissue of its origin are key to effective treatment. Here, we leverage technological advances in machine learning or artificial intelligence to design a novel framework for cancer diagnostics. Our proposed framework detects cancers and their tissues of origin using a unified model of cancers encompassing 33 cancers represented in The Cancer Genome Atlas (TCGA). Our model exploits the learned features of different cancers reflected in the respective dysregulated epigenomes, which arise early in carcinogenesis and differ remarkably between different cancer types or subtypes, thus holding a great promise in early cancer detection.RESULTS: Our comprehensive assessment of the proposed model on the 33 different tissues of origin demonstrates its ability to detect and classify cancers to a high accuracy (> 99% overall F-measure). Furthermore, our model distinguishes cancers from pre-cancerous lesions to metastatic tumors and discriminates between hypomethylation changes due to age related epigenetic drift and true cancer.
    CONCLUSIONS: Beyond detection of primary cancers, our proposed computational model also robustly detects tissues of origin of secondary cancers, including metastatic cancers, second primary cancers, and cancers of unknown primaries. Our assessment revealed the ability of this model to characterize pre-cancer samples, a significant step forward in early cancer detection. Deployed broadly this model can deliver accurate diagnosis for a greatly expanded target patient population.
    Keywords:  Cancer; Deep learning; Metastatic cancer; Neural network
    DOI:  https://doi.org/10.1186/s12859-022-04783-y
  21. Scand J Surg. 2022 Apr-Jun;111(2):111(2): 14574969221096513
    Surgical resection of pancreatic cancer with synchronous hepatic oligometastases: Real benefit or selection bias?
    Daniel Ansari, Roland Andersson.
      In this editorial, we review the evidence for liver resection in patients with oligometastatic pancreatic cancer.
    Keywords:  Pancreatic cancer; hepatic oligometastases; surgery
    DOI:  https://doi.org/10.1177/14574969221096513
  22. Cancer Cell. 2022 Jun 13. pii: S1535-6108(22)00229-X. [Epub ahead of print]
    The local microenvironment matters in preclinical basic and translational studies of cancer immunology and immunotherapy.
    William W Ho, Mikael J Pittet, Dai Fukumura, Rakesh K Jain.
      
    DOI:  https://doi.org/10.1016/j.ccell.2022.05.016
  23. J Med Chem. 2022 Jun 13.
    Discovery and Optimization of Pyrrolopyrimidine Derivatives as Selective Disruptors of the Perinucleolar Compartment, a Marker of Tumor Progression toward Metastasis.
    Kevin J Frankowski, Samarjit Patnaik, Chen Wang, Noel Southall, Dipannita Dutta, Soumitta De, Dandan Li, Christopher Dextras, Yi-Han Lin, Marthe Bryant-Connah, Danielle Davis, Feijun Wang, Leah M Wachsmuth, Pranav Shah, Jordan Williams, Md Kabir, Edward Zhu, Bolormaa Baljinnyam, Amy Wang, Xin Xu, John Norton, Marc Ferrer, Steve Titus, Anton Simeonov, Wei Zheng, Lesley A Mathews Griner, Ajit Jadhav, Jeffrey Aubé, Mark J Henderson, Udo Rudloff, Frank J Schoenen, Sui Huang, Juan J Marugan.
      The perinucleolar compartment (PNC) is a dynamic subnuclear body found at the periphery of the nucleolus. The PNC is enriched with RNA transcripts and RNA-binding proteins, reflecting different states of genome organization. PNC prevalence positively correlates with cancer progression and metastatic capacity, making it a useful marker for metastatic cancer progression. A high-throughput, high-content assay was developed to identify novel small molecules that selectively reduce PNC prevalence in cancer cells. We identified and further optimized a pyrrolopyrimidine series able to reduce PNC prevalence in PC3M cancer cells at submicromolar concentrations without affecting cell viability. Structure-activity relationship exploration of the structural elements necessary for activity resulted in the discovery of several potent compounds. Analysis of in vitro drug-like properties led to the discovery of the bioavailable analogue, metarrestin, which has shown potent antimetastatic activity with improved survival in rodent models and is currently being evaluated in a first-in-human phase 1 clinical trial.
    DOI:  https://doi.org/10.1021/acs.jmedchem.2c00204
  24. Biochem Soc Trans. 2022 Jun 17. pii: BST20220452. [Epub ahead of print]
    Tumour invasion and dissemination.
    Ryan Lusby, Philip Dunne, Vijay K Tiwari.
      Activating invasion and metastasis are one of the primary hallmarks of cancer, the latter representing the leading cause of death in cancer patients. Whilst many advances in this area have been made in recent years, the process of cancer dissemination and the underlying mechanisms governing invasion are still poorly understood. Cancer cells exhibit multiple invasion strategies, including switching between modes of invasion and plasticity in response to therapies, surgical interventions and environmental stimuli. The ability of cancer cells to switch migratory modes and their inherent plasticity highlights the critical challenge preventing the successful design of cancer and anti-metastatic therapies. This mini-review presents current knowledge on the critical models of tumour invasion and dissemination. We also discuss the current issues surrounding current treatments and arising therapeutic opportunities. We propose that the establishment of novel approaches to study the key biological mechanisms underlying the metastatic cascade is critical in finding novel targets that could ultimately lead to complete inhibition of cancer cell invasion and dissemination.
    Keywords:  cancer; cell shape; metastasis
    DOI:  https://doi.org/10.1042/BST20220452
  25. BMJ Open. 2022 Jun 16. 12(6): e060431
    Safety and tumour-specific immunological responses of combined dendritic cell vaccination and anti-CD40 agonistic antibody treatment for patients with metastatic pancreatic cancer: protocol for a phase I, open-label, single-arm, dose-escalation study (REACtiVe-2 trial).
    Sai Ping Lau, Freek R van 't Land, Sjoerd H van der Burg, Marjolein Y V Homs, Martijn P Lolkema, Joachim G J V Aerts, Casper H J van Eijck.
      INTRODUCTION: The prognosis of patients with advanced pancreatic ductal adenocarcinoma (PDAC) is dismal and conventional chemotherapy treatment delivers limited survival improvement. Immunotherapy may complement our current treatment strategies. We previously demonstrated that the combination of an allogeneic tumour-lysate dendritic cell (DC) vaccine with an anti-CD40 agonistic antibody resulted in robust antitumour responses with survival benefit in a murine PDAC model. In the Rotterdam PancrEAtic Cancer Vaccination-2 trial, we aim to translate our findings into patients. This study will determine the safety of DC/anti-CD40 agonistic antibody combination treatment, and treatment-induced tumour-specific immunological responses.METHODS AND ANALYSIS: In this open-label, single-centre (Erasmus Univsersity Medical Center, Rotterdam, Netherlands), single-arm, phase I dose finding study, adult patients with metastatic pancreatic cancer with progressive disease after FOLFIRINOX chemotherapy will receive monocyte-derived DCs loaded with an allogeneic tumour lysate in conjunction with a CD40 agonistic antibody. This combination-immunotherapy regimen will be administered three times every 2 weeks, and booster treatments will be given after 3 and 6 months following the third injection. A minimum of 12 and a maximum of 18 patients will be included. The primary endpoint is safety and tolerability of the combination immunotherapy. To determine the maximum tolerated dose, DCs will be given at a fixed dosage and anti-CD40 agonist in a traditional 3+3 dose-escalation design. Secondary endpoints include radiographic response according to the RECIST (V.1.1) and iRECIST criteria, and the detection of antitumour specific immune responses.
    ETHICS AND DISSEMINATION: The Central Committee on Research Involving Human Subjects (CCMO; NL76592.000.21) and the Medical Ethics Committee (METC; MEC-2021-0566) of the Erasmus M.C. University Medical Center Rotterdam approved the conduct of the trial. Written informed consent will be required for all participants. The results of the trial will be submitted for publication in a peer-reviewed scientific journal.
    TRIAL REGISTRATION NUMBER: NL9723.
    Keywords:  CD40; Dendritic Cell; Immunotherapy; Pancreatic cancer; Vaccines
    DOI:  https://doi.org/10.1136/bmjopen-2021-060431
  26. PLoS Comput Biol. 2022 Jun 17. 18(6): e1010253
    Size regulation of multiple organelles competing for a limiting subunit pool.
    Deb Sankar Banerjee, Shiladitya Banerjee.
      How cells regulate the size of intracellular structures and organelles is a longstanding question. Recent experiments suggest that size control of intracellular structures is achieved through the depletion of a limiting subunit pool in the cytoplasm. While the limiting pool model ensures organelle-to-cell size scaling, it does not provide a mechanism for robust size control of multiple co-existing structures. Here we develop a generalized theory for size-dependent growth of intracellular structures to demonstrate that robust size control of multiple intracellular structures, competing for a limiting subunit pool, is achieved via a negative feedback between the growth rate and the size of the individual structure. This design principle captures size maintenance of a wide variety of subcellular structures, from cytoskeletal filaments to three-dimensional organelles. We identify the feedback motifs for structure size regulation based on known molecular processes, and compare our theory to existing models of size regulation in biological assemblies. Furthermore, we show that positive feedback between structure size and growth rate can lead to bistable size distribution and spontaneous size selection.
    DOI:  https://doi.org/10.1371/journal.pcbi.1010253
  27. Nat Rev Genet. 2022 Jun 17.
    Measuring biological age using omics data.
    Jarod Rutledge, Hamilton Oh, Tony Wyss-Coray.
      Age is the key risk factor for diseases and disabilities of the elderly. Efforts to tackle age-related diseases and increase healthspan have suggested targeting the ageing process itself to 'rejuvenate' physiological functioning. However, achieving this aim requires measures of biological age and rates of ageing at the molecular level. Spurred by recent advances in high-throughput omics technologies, a new generation of tools to measure biological ageing now enables the quantitative characterization of ageing at molecular resolution. Epigenomic, transcriptomic, proteomic and metabolomic data can be harnessed with machine learning to build 'ageing clocks' with demonstrated capacity to identify new biomarkers of biological ageing.
    DOI:  https://doi.org/10.1038/s41576-022-00511-7
  28. Nature. 2022 Jun 15.
    cGAS-STING drives the IL-6-dependent survival of chromosomally instable cancers.
    Christy Hong, Michael Schubert, Andréa E Tijhuis, Marta Requesens, Maurits Roorda, Anouk van den Brink, Lorena Andrade Ruiz, Petra L Bakker, Tineke van der Sluis, Wietske Pieters, Mengting Chen, René Wardenaar, Bert van der Vegt, Diana C J Spierings, Marco de Bruyn, Marcel A T M van Vugt, Floris Foijer.
      Chromosomal instability (CIN) drives cancer cell evolution, metastasis and therapy resistance, and is associated with poor prognosis1. CIN leads to micronuclei that release DNA into the cytoplasm after rupture, which triggers activation of inflammatory signalling mediated by cGAS and STING2,3. These two proteins are considered to be tumour suppressors as they promote apoptosis and immunosurveillance. However, cGAS and STING are rarely inactivated in cancer4, and, although they have been implicated in metastasis5, it is not known why loss-of-function mutations do not arise in primary tumours4. Here we show that inactivation of cGAS-STING signalling selectively impairs the survival of triple-negative breast cancer cells that display CIN. CIN triggers IL-6-STAT3-mediated signalling, which depends on the cGAS-STING pathway and the non-canonical NF-κB pathway. Blockade of IL-6 signalling by tocilizumab, a clinically used drug that targets the IL-6 receptor (IL-6R), selectively impairs the growth of cultured triple-negative breast cancer cells that exhibit CIN. Moreover, outgrowth of chromosomally instable tumours is significantly delayed compared with tumours that do not display CIN. Notably, this targetable vulnerability is conserved across cancer types that express high levels of IL-6 and/or IL-6R in vitro and in vivo. Together, our work demonstrates pro-tumorigenic traits of cGAS-STING signalling and explains why the cGAS-STING pathway is rarely inactivated in primary tumours. Repurposing tocilizumab could be a strategy to treat cancers with CIN that overexpress IL-6R.
    DOI:  https://doi.org/10.1038/s41586-022-04847-2
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