bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2022–03–27
fifty papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Ketogenic HMG-CoA lyase and its product β-hydroxybutyrate promote pancreatic cancer progression.
  2. Cancer cachexia: lessons from Drosophila.
  3. Sulforaphane reduces obesity by reversing leptin resistance.
  4. KRAS is vulnerable to reversible switch-II pocket engagement in cells.
  5. The glucose transporter GLUT3 controls T helper 17 cell responses through glycolytic-epigenetic reprogramming.
  6. KSR induces RAS-independent MAPK pathway activation and modulates the efficacy of KRAS inhibitors.
  7. Bcl-xL enforces a slow-cycling state necessary for survival in the nutrient-deprived microenvironment of pancreatic cancer.
  8. Localized glucose import, glycolytic processing, and mitochondria generate a focused ATP burst to power basement-membrane invasion.
  9. Protein synthesis control in cancer: selectivity and therapeutic targeting.
  10. Pectoralis major muscle atrophy is associated with mitochondrial energy wasting in cachectic patients with gastrointestinal cancer.
  11. Fatty Pancreas-Centered Metabolic Basis of Pancreatic Adenocarcinoma: From Obesity, Diabetes and Pancreatitis to Oncogenesis.
  12. The Interplay between Cell-Extracellular Matrix Interaction and Mitochondria Dynamics in Cancer.
  13. Hexokinase 1 cellular localization regulates the metabolic fate of glucose.
  14. What cancer survivors can teach cancer researchers.
  15. Potent suppression of neuroendocrine tumors and gastrointestinal cancers by CDH17CAR T cells without toxicity to normal tissues.
  16. Iron-induced NCOA4 condensation regulates ferritin fate and iron homeostasis.
  17. Fidelity of organellar protein targeting.
  18. Quality control of protein complex composition.
  19. Listeria delivers tetanus toxoid protein to pancreatic tumors and induces cancer cell death in mice.
  20. Recycling of autophagosomal components from autolysosomes by the recycler complex.
  21. BRAFV600E-driven lung adenocarcinoma requires copper to sustain autophagic signaling and processing.
  22. Molecular barcodes reveal tumour lineages.
  23. Carbon starvation, senescence and specific mitochondrial stresses, but not nitrogen starvation and general stresses, are major triggers for mitophagy in Arabidopsis.
  24. Molecular Pathology of Pancreatic Cancer.
  25. Chemotherapy as a regulator of extracellular matrix-cell communication: implications in therapy resistance.
  26. Seed or soil: Tracing the immune subsets in metastatic tumors.
  27. Updates in the Diagnosis of Intraductal Neoplasms of the Pancreas.
  28. The LEGO® brick road to open science and biotechnology.
  29. Ten quick tips for deep learning in biology.
  30. Permeability-Controlled Probe for Directly Visualizing the Opening of Mitochondrial Permeability Transition Pore in Native Status.
  31. Coeliac plexus radiosurgery for pain management in patients with advanced cancer : study protocol for a phase II clinical trial.
  32. Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance.
  33. KRAS mutation allele frequency threshold alters prognosis in right-sided resected pancreatic cancer.
  34. Telomere length and vitamin B12.
  35. Live cell microscopy of mitochondria-lysosome contact site formation and tethering dynamics.
  36. Managing Nutrition Impact Symptoms in Cancer Cachexia: A Case Series and Mini Review.
  37. Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx.
  38. Mitochondria transplantation between living cells.
  39. Myc Supports Self-Renewal of Basal Cells in the Esophageal Epithelium.
  40. Targeting proteostasis maintenance and autophagy in senescence.
  41. Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate.
  42. Impact of baseline culture conditions of cancer organoids when determining therapeutic response and tumor heterogeneity.
  43. Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation.
  44. The glucocorticoid receptor associates with RAS complexes to inhibit cell proliferation and tumor growth.
  45. Global mortality burden attributable to non-optimal temperatures.
  46. Ejection of damaged mitochondria and their removal by macrophages ensure efficient thermogenesis in brown adipose tissue.
  47. Pharmacological Modulation of Apoptosis and Autophagy in the Treatment of Pancreatic Cancer.
  48. Reduced reproductive success is associated with selective constraint on human genes.
  49. Landscape of KRASG12C, Associated Genomic Alterations, and Interrelation With Immuno-Oncology Biomarkers in KRAS-Mutated Cancers.
  50. Chemotherapy-induced cachexia and model-informed dosing to preserve lean mass in cancer treatment.
  1. EMBO J. 2022 Mar 21. e110466
    Ketogenic HMG-CoA lyase and its product β-hydroxybutyrate promote pancreatic cancer progression.
    Victoire Gouirand, Tristan Gicquel, Evan C Lien, Emilie Jaune-Pons, Quentin Da Costa, Pascal Finetti, Elodie Metay, Camille Duluc, Jared R Mayers, Stephane Audebert, Luc Camoin, Laurence Borge, Marion Rubis, Julie Leca, Jeremy Nigri, François Bertucci, Nelson Dusetti, Juan Lucio Iovanna, Richard Tomasini, Ghislain Bidaut, Fabienne Guillaumond, Matthew G Vander Heiden, Sophie Vasseur.
      Pancreatic ductal adenocarcinoma (PDA) tumor cells are deprived of oxygen and nutrients and therefore must adapt their metabolism to ensure proliferation. In some physiological states, cells rely on ketone bodies to satisfy their metabolic needs, especially during nutrient stress. Here, we show that PDA cells can activate ketone body metabolism and that β-hydroxybutyrate (βOHB) is an alternative cell-intrinsic or systemic fuel that can promote PDA growth and progression. PDA cells activate enzymes required for ketogenesis, utilizing various nutrients as carbon sources for ketone body formation. By assessing metabolic gene expression from spontaneously arising PDA tumors in mice, we find HMG-CoA lyase (HMGCL), involved in ketogenesis, to be among the most deregulated metabolic enzymes in PDA compared to normal pancreas. In vitro depletion of HMGCL impedes migration, tumor cell invasiveness, and anchorage-independent tumor sphere compaction. Moreover, disrupting HMGCL drastically decreases PDA tumor growth in vivo, while βOHB stimulates metastatic dissemination to the liver. These findings suggest that βOHB increases PDA aggressiveness and identify HMGCL and ketogenesis as metabolic targets for limiting PDA progression.
    Keywords:  HMGCL; ketone bodies; metastasis; pancreatic cancer; β-hydroxybutyrate
    DOI:  https://doi.org/10.15252/embj.2021110466
  2. Dis Model Mech. 2022 Mar 01. pii: dmm049298. [Epub ahead of print]15(3):
    Cancer cachexia: lessons from Drosophila.
    Ying Liu, Pedro Saavedra, Norbert Perrimon.
      Cachexia, a wasting syndrome that is often associated with cancer, is one of the primary causes of death in cancer patients. Cancer cachexia occurs largely due to systemic metabolic alterations stimulated by tumors. Despite the prevalence of cachexia, our understanding of how tumors interact with host tissues and how they affect metabolism is limited. Among the challenges of studying tumor-host tissue crosstalk are the complexity of cancer itself and our insufficient knowledge of the factors that tumors release into the blood. Drosophila is emerging as a powerful model in which to identify tumor-derived factors that influence systemic metabolism and tissue wasting. Strikingly, studies that are characterizing factors derived from different fly tumor cachexia models are identifying both common and distinct cachectic molecules, suggesting that cachexia is more than one disease and that fly models can help identify these differences. Here, we review what has been learned from studies of tumor-induced organ wasting in Drosophila and discuss the open questions.
    Keywords:   Drosophila ; Cachectic factors; Cancer cachexia; Organ wasting
    DOI:  https://doi.org/10.1242/dmm.049298
  3. Elife. 2022 Mar 24. pii: e67368. [Epub ahead of print]11
    Sulforaphane reduces obesity by reversing leptin resistance.
    Işın Çakır, Pauline Lining Pan, Colleen K Hadley, Abdulrahman El-Gamal, Amina Fadel, Dina Elsayegh, Omnia Mohamed, Nasser M Rizk, Masoud Ghamari-Langroudi.
      The ascending prevalence of obesity in recent decades is commonly associated with soaring morbidity and mortality rates, resulting in increased health-care costs and decreased quality of life. A systemic state of stress characterized by low-grade inflammation and pathological formation of reactive oxygen species (ROS) usually manifests in obesity. The transcription factor nuclear factor erythroid-derived 2-like 2 (NRF2) is the master regulator of the redox homeostasis and plays a critical role in the resolution of inflammation. Here, we show that the natural isothiocyanate and potent NRF2 activator sulforaphane reverses diet-induced obesity through a predominantly, but not exclusively, NRF2-dependent mechanism that requires a functional leptin receptor signaling and hyperleptinemia. Sulforaphane does not reduce the body weight or food intake of lean mice but induces an anorectic response when coadministered with exogenous leptin. Leptin-deficient Lepob/ob mice and leptin receptor mutant Leprdb/db mice display resistance to the weight-reducing effect of sulforaphane, supporting the conclusion that the antiobesity effect of sulforaphane requires functional leptin receptor signaling. Furthermore, our results suggest the skeletal muscle as the most notable site of action of sulforaphane whose peripheral NRF2 action signals to alleviate leptin resistance. Transcriptional profiling of six major metabolically relevant tissues highlights that sulforaphane suppresses fatty acid synthesis while promoting ribosome biogenesis, reducing ROS accumulation, and resolving inflammation, therefore representing a unique transcriptional program that leads to protection from obesity. Our findings argue for clinical evaluation of sulforaphane for weight loss and obesity-associated metabolic disorders.
    Keywords:  NRF2 activators; body weight; isothiocyanate; leptin sensitizers; medicine; mouse; obesity; sulforaphane
    DOI:  https://doi.org/10.7554/eLife.67368
  4. Nat Chem Biol. 2022 Mar 21.
    KRAS is vulnerable to reversible switch-II pocket engagement in cells.
    James D Vasta, D Matthew Peacock, Qinheng Zheng, Joel A Walker, Ziyang Zhang, Chad A Zimprich, Morgan R Thomas, Michael T Beck, Brock F Binkowski, Cesear R Corona, Matthew B Robers, Kevan M Shokat.
      Current small-molecule inhibitors of KRAS(G12C) bind irreversibly in the switch-II pocket (SII-P), exploiting the strong nucleophilicity of the acquired cysteine as well as the preponderance of the GDP-bound form of this mutant. Nevertheless, many oncogenic KRAS mutants lack these two features, and it remains unknown whether targeting the SII-P is a practical therapeutic approach for KRAS mutants beyond G12C. Here we use NMR spectroscopy and a cellular KRAS engagement assay to address this question by examining a collection of SII-P ligands from the literature and from our own laboratory. We show that the SII-Ps of many KRAS hotspot (G12, G13, Q61) mutants are accessible using noncovalent ligands, and that this accessibility is not necessarily coupled to the GDP state of KRAS. The results we describe here emphasize the SII-P as a privileged drug-binding site on KRAS and unveil new therapeutic opportunities in RAS-driven cancer.
    DOI:  https://doi.org/10.1038/s41589-022-00985-w
  5. Cell Metab. 2022 Mar 15. pii: S1550-4131(22)00087-0. [Epub ahead of print]
    The glucose transporter GLUT3 controls T helper 17 cell responses through glycolytic-epigenetic reprogramming.
    Sophia M Hochrein, Hao Wu, Miriam Eckstein, Laura Arrigoni, Josip S Herman, Fabian Schumacher, Christian Gerecke, Mathias Rosenfeldt, Dominic Grün, Burkhard Kleuser, Georg Gasteiger, Wolfgang Kastenmüller, Bart Ghesquière, Jan Van den Bossche, E Dale Abel, Martin Vaeth.
      Metabolic reprogramming is a hallmark of activated T cells. The switch from oxidative phosphorylation to aerobic glycolysis provides energy and intermediary metabolites for the biosynthesis of macromolecules to support clonal expansion and effector function. Here, we show that glycolytic reprogramming additionally controls inflammatory gene expression via epigenetic remodeling. We found that the glucose transporter GLUT3 is essential for the effector functions of Th17 cells in models of autoimmune colitis and encephalomyelitis. At the molecular level, we show that GLUT3-dependent glucose uptake controls a metabolic-transcriptional circuit that regulates the pathogenicity of Th17 cells. Metabolomic, epigenetic, and transcriptomic analyses linked GLUT3 to mitochondrial glucose oxidation and ACLY-dependent acetyl-CoA generation as a rate-limiting step in the epigenetic regulation of inflammatory gene expression. Our findings are also important from a translational perspective because inhibiting GLUT3-dependent acetyl-CoA generation is a promising metabolic checkpoint to mitigate Th17-cell-mediated inflammatory diseases.
    Keywords:  ACLY; ATP-citrate lyase; GLUT1; GLUT3; Th17 cells; acetyl-CoA; glucose metabolism; glycolysis; histone acetylation; immunometabolism
    DOI:  https://doi.org/10.1016/j.cmet.2022.02.015
  6. Mol Oncol. 2022 Mar 21.
    KSR induces RAS-independent MAPK pathway activation and modulates the efficacy of KRAS inhibitors.
    Guillem Paniagua, Harrys K C Jacob, Oksana Brehey, Sara García-Alonso, Carmen G Lechuga, Tirso Pons, Monica Musteanu, Carmen Guerra, Matthias Drosten, Mariano Barbacid.
      The kinase suppressor of RAS proteins (KSR1 and KSR2) have long been considered as scaffolding proteins required for optimal MAPK pathway signaling. However, recent evidence suggests that they play a more complex role within this pathway. Here, we demonstrate that ectopic expression of KSR1 or KSR2 is sufficient to activate the MAPK pathway and to induce cell proliferation in the absence of RAS proteins. In contrast, ectopic expression of KSR proteins is not sufficient to induce cell proliferation in the absence of either RAF or MEK proteins, indicating that they act upstream of RAF. Indeed, KSR1 requires dimerization with at least one member of the RAF family to stimulate proliferation, an event that results in the translocation of the heterodimerized RAF protein to the cell membrane. Mutations in the conserved DFG motif of KSR1 that affect ATP binding impair induction of cell proliferation. We also show that increased expression levels of KSR1 decrease the responsiveness to the KRASG12C inhibitor sotorasib in human cancer cell lines, thus suggesting that increased levels of expression of KSR may make tumor cells less dependent on KRAS oncogenic signaling.
    Keywords:  ATP binding; KRASG12C; MAPK pathway; RAS-independent proliferation; resistance; sotorasib
    DOI:  https://doi.org/10.1002/1878-0261.13213
  7. Cancer Res. 2022 Mar 22. pii: canres.CAN-22-0431-E.2022. [Epub ahead of print]
    Bcl-xL enforces a slow-cycling state necessary for survival in the nutrient-deprived microenvironment of pancreatic cancer.
    Yogev Sela, Jinyang Li, Shivahamy Maheswaran, Robert J Norgard, Salina Yuan, Maimon E Hubbi, Miriam Doepner, Jimmy P Xu, Elaine S Ho, Clementina Mesaros, Colin Sheehan, Grace Croley, Alexander Muir, Ian A Blair, Ophir Shalem, Chi V Dang, Ben Z Stanger.
      Solid tumors possess heterogeneous metabolic microenvironments where oxygen and nutrient availability are plentiful ('fertile regions') or scarce ('arid regions'). While cancer cells residing in fertile regions proliferate rapidly, most cancer cells in vivo reside in arid regions and exhibit a slow-cycling state that renders them chemoresistant. Here, we developed an in vitro system enabling systematic comparison between these populations via transcriptome analysis, metabolomic profiling, and whole-genome CRISPR screening. Metabolic deprivation led to pronounced transcriptional and metabolic reprogramming, resulting in decreased anabolic activities and distinct vulnerabilities. Reductions in anabolic, energy-consuming activities, particularly cell proliferation, were not simply byproducts of the metabolic challenge but rather essential adaptations. Mechanistically, Bcl-xL played a central role in the adaptation to nutrient and oxygen deprivation. In this setting, Bcl-xL protected quiescent cells from the lethal effects of cell cycle entry in the absence of adequate nutrients. Moreover, inhibition of Bcl-xL combined with traditional chemotherapy had a synergistic anti-tumor effect that targeted cycling cells. Bcl-xL expression was strongly associated with poor patient survival despite being confined to the slow-cycling fraction of human pancreatic cancer cells. These findings provide a rationale for combining traditional cancer therapies that target rapidly cycling cells with those that target quiescent, chemoresistant cells associated with nutrient and oxygen deprivation.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-0431
  8. Dev Cell. 2022 Mar 14. pii: S1534-5807(22)00121-6. [Epub ahead of print]
    Localized glucose import, glycolytic processing, and mitochondria generate a focused ATP burst to power basement-membrane invasion.
    Aastha Garde, Isabel W Kenny, Laura C Kelley, Qiuyi Chi, Ayse Sena Mutlu, Meng C Wang, David R Sherwood.
      Invasive cells use transient, energy-consuming protrusions to breach basement membrane (BM) barriers. Using the ATP sensor PercevalHR during anchor cell (AC) invasion in Caenorhabditis elegans, we show that BM invasion is accompanied by an ATP burst from mitochondria at the invasive front. RNAi screening and visualization of a glucose biosensor identified two glucose transporters, FGT-1 and FGT-2, which bathe invasive front mitochondria with glucose and facilitate the ATP burst to form protrusions. FGT-1 localizes at high levels along the invasive membrane, while FGT-2 is adaptive, enriching most strongly during BM breaching and when FGT-1 is absent. Cytosolic glycolytic enzymes that process glucose for mitochondrial ATP production cluster with invasive front mitochondria and promote higher mitochondrial membrane potential and ATP levels. Finally, we show that UNC-6 (netrin), which polarizes invasive protrusions, also orients FGT-1. These studies reveal a robust and integrated energy acquisition, processing, and delivery network that powers BM breaching.
    Keywords:  ATP; basement membrane; biosensor; cell invasion; glucose transporters; glycolytic enzyme clustering; invasive protrusions; live imaging; mitochondria
    DOI:  https://doi.org/10.1016/j.devcel.2022.02.019
  9. EMBO J. 2022 Mar 22. e109823
    Protein synthesis control in cancer: selectivity and therapeutic targeting.
    Joanna R Kovalski, Duygu Kuzuoglu-Ozturk, Davide Ruggero.
      Translational control of mRNAs is a point of convergence for many oncogenic signals through which cancer cells tune protein expression in tumorigenesis. Cancer cells rely on translational control to appropriately adapt to limited resources while maintaining cell growth and survival, which creates a selective therapeutic window compared to non-transformed cells. In this review, we first discuss how cancer cells modulate the translational machinery to rapidly and selectively synthesize proteins in response to internal oncogenic demands and external factors in the tumor microenvironment. We highlight the clinical potential of compounds that target different translation factors as anti-cancer therapies. Next, we detail how RNA sequence and structural elements interface with the translational machinery and RNA-binding proteins to coordinate the translation of specific pro-survival and pro-growth programs. Finally, we provide an overview of the current and emerging technologies that can be used to illuminate the mechanisms of selective translational control in cancer cells as well as within the microenvironment.
    Keywords:  cancer; protein synthesis; translation and protein quality; translation inhibitors; translational control
    DOI:  https://doi.org/10.15252/embj.2021109823
  10. J Cachexia Sarcopenia Muscle. 2022 Mar 22.
    Pectoralis major muscle atrophy is associated with mitochondrial energy wasting in cachectic patients with gastrointestinal cancer.
    Adeline Dolly, Thierry Lecomte, Nicolas Tabchouri, Morgane Caulet, Nicolas Michot, Benjamin Anon, Romain Chautard, Yoann Desvignes, Mehdi Ouaissi, Gaëlle Fromont-Hankard, Jean-François Dumas, Stéphane Servais.
       BACKGROUND: Cancer cachexia is a multifactorial syndrome characterized by involuntary and pathological weight loss, mainly due to skeletal muscle wasting, resulting in a decrease in patients' quality of life, response to cancer treatments, and survival. Our objective was to investigate skeletal muscle alterations in cachectic cancer patients.
    METHODS: This is a prospective study of patients managed for pancreatic or colorectal cancer with an indication for systemic chemotherapy (METERMUCADIG - NCT02573974). One lumbar CT image was used to determine body composition. Patients were divided into three groups [8 noncachectic (NC), 18 with mild cachexia (MC), and 19 with severe cachexia (SC)] based on the severity of weight loss and muscle mass. For each patient, a pectoralis major muscle biopsy was collected at the time of implantable chamber placement. We used high-resolution oxygraphy to measure mitochondrial muscle oxygen consumption on permeabilized muscle fibres. We also performed optical and electron microscopy analyses, as well as gene and protein expression analyses.
    RESULTS: Forty-five patients were included. Patients were 67% male, aged 67 years (interquartile range, 59-77). Twenty-three (51%) and 22 (49%) patients were managed for pancreatic and colorectal cancer, respectively. Our results show a positive correlation between median myofibres area and skeletal muscle index (P = 0.0007). Cancer cachexia was associated with a decrease in MAFbx protein expression (P < 0.01), a marker of proteolysis through the ubiquitin-proteasome pathway. Mitochondrial oxygen consumption related to energy wasting was significantly increased (SC vs. NC, P = 0.028) and mitochondrial area tended to increase (SC vs. MC, P = 0.056) in SC patients. On the contrary, mitochondria content and networks remain unaltered in cachectic cancer patients. Finally, our results show no dysfunction in lipid storage and endoplasmic reticulum homeostasis.
    CONCLUSIONS: This clinical protocol brings unique data that provide new insight to mechanisms underlying muscle wasting in cancer cachexia. We report for the first time an increase in mitochondrial energy wasting in the skeletal muscle of severe cachectic cancer patients. Additional clinical studies are essential to further the exploring and understanding of these alterations.
    Keywords:  Cancer cachexia; Clinical study; Mitochondrial bioenergetics; Myosteatosis; Pectoralis major; Proteolysis
    DOI:  https://doi.org/10.1002/jcsm.12984
  11. Biomedicines. 2022 Mar 17. pii: 692. [Epub ahead of print]10(3):
    Fatty Pancreas-Centered Metabolic Basis of Pancreatic Adenocarcinoma: From Obesity, Diabetes and Pancreatitis to Oncogenesis.
    Ming-Ling Chang.
      Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest types of cancer, and it is currently the third most common cause of cancer death in the U.S.A. Progress in the fight against PDAC has been hampered by an inability to detect it early in the overwhelming majority of patients, and also by the reduced oxygen levels and nutrient perfusion caused by new matrix formation through the activation of stromal cells in the context of desmoplasia. One harbinger of PDAC is excess intrapancreatic fat deposition, namely, fatty pancreas, which specifically affects the tumor macro- and microenvironment in the organ. Over half of PDAC patients have diabetes mellitus (DM) at the time of diagnosis, and fatty pancreas is associated with subsequent DM development. Moreover, there is a strong association between fatty pancreas and fatty liver through obesity, and a higher intrapancreatic fat percentage has been noted in acute pancreatitis patients with DM than in those without DM. All these findings suggest that the link between fatty pancreas and PDAC might occur through metabolic alterations, either DM-related or non-DM-related. Based on clinical, in vivo and in vitro evidence, the current review highlights the etiologies of fatty pancreas (including fatty infiltration and replacement) and the fatty pancreas-associated metabolic alterations involved in oncogenesis to provide crucial targets to prevent, detect, and/or effectively treat PDAC.
    Keywords:  PDAC; fatty infiltration; fatty pancreas; fatty replacement; metabolic; obesity
    DOI:  https://doi.org/10.3390/biomedicines10030692
  12. Cancers (Basel). 2022 Mar 10. pii: 1433. [Epub ahead of print]14(6):
    The Interplay between Cell-Extracellular Matrix Interaction and Mitochondria Dynamics in Cancer.
    Bian Yanes, Elena Rainero.
      The tumor microenvironment, in particular the extracellular matrix (ECM), plays a pivotal role in controlling tumor initiation and progression. In particular, the interaction between cancer cells and the ECM promotes cancer cell growth and invasion, leading to the formation of distant metastasis. Alterations in cancer cell metabolism is a key hallmark of cancer, which is often associated with alterations in mitochondrial dynamics. Recent research highlighted that, changes in mitochondrial dynamics are associated with cancer migration and metastasis-these has been extensively reviewed elsewhere. However, less is known about the interplay between the extracellular matrix and mitochondria functions. In this review, we will highlight how ECM remodeling associated with tumorigenesis contribute to the regulation of mitochondrial function, ultimately promoting cancer cell metabolic plasticity, able to fuel cancer invasion and metastasis.
    Keywords:  extracellular matrix; mitochondria dynamics; tumor microenvironment
    DOI:  https://doi.org/10.3390/cancers14061433
  13. Mol Cell. 2022 Mar 14. pii: S1097-2765(22)00166-6. [Epub ahead of print]
    Hexokinase 1 cellular localization regulates the metabolic fate of glucose.
    Adam De Jesus, Farnaz Keyhani-Nejad, Carolina M Pusec, Lauren Goodman, Justin A Geier, Joshua S Stoolman, Paulina J Stanczyk, Tivoli Nguyen, Kai Xu, Krishna V Suresh, Yihan Chen, Arianne E Rodriguez, Jason S Shapiro, Hsiang-Chun Chang, Chunlei Chen, Kriti P Shah, Issam Ben-Sahra, Brian T Layden, Navdeep S Chandel, Samuel E Weinberg, Hossein Ardehali.
      The product of hexokinase (HK) enzymes, glucose-6-phosphate, can be metabolized through glycolysis or directed to alternative metabolic routes, such as the pentose phosphate pathway (PPP) to generate anabolic intermediates. HK1 contains an N-terminal mitochondrial binding domain (MBD), but its physiologic significance remains unclear. To elucidate the effect of HK1 mitochondrial dissociation on cellular metabolism, we generated mice lacking the HK1 MBD (ΔE1HK1). These mice produced a hyper-inflammatory response when challenged with lipopolysaccharide. Additionally, there was decreased glucose flux below the level of GAPDH and increased upstream flux through the PPP. The glycolytic block below GAPDH is mediated by the binding of cytosolic HK1 with S100A8/A9, resulting in GAPDH nitrosylation through iNOS. Additionally, human and mouse macrophages from conditions of low-grade inflammation, such as aging and diabetes, displayed increased cytosolic HK1 and reduced GAPDH activity. Our data indicate that HK1 mitochondrial binding alters glucose metabolism through regulation of GAPDH.
    Keywords:  GAPDH; S-nitrosylation; hexokinase; inflammation; innate immunity; macrophage; metabolism; mitochondria; pentose phosphate pathway; subcellular localization
    DOI:  https://doi.org/10.1016/j.molcel.2022.02.028
  14. Nat Rev Cancer. 2022 Mar 23.
    What cancer survivors can teach cancer researchers.
    Victoria J Forster.
      
    DOI:  https://doi.org/10.1038/s41568-022-00468-z
  15. Nat Cancer. 2022 Mar 21.
    Potent suppression of neuroendocrine tumors and gastrointestinal cancers by CDH17CAR T cells without toxicity to normal tissues.
    Zijie Feng, Xin He, Xuyao Zhang, Yuan Wu, Bowen Xing, Alison Knowles, Qiaonan Shan, Samuel Miller, Taylor Hojnacki, Jian Ma, Bryson W Katona, Terence P F Gade, Jörg Schrader, David C Metz, Carl H June, Xianxin Hua.
      Gastrointestinal cancers (GICs) and neuroendocrine tumors (NETs) are often refractory to therapy after metastasis. Adoptive cell therapy using chimeric antigen receptor (CAR) T cells, though remarkably efficacious for treating leukemia, is yet to be developed for solid tumors such as GICs and NETs. Here we isolated a llama-derived nanobody, VHH1, and found that it bound cell surface adhesion protein CDH17 upregulated in GICs and NETs. VHH1-CAR T cells (CDH17CARTs) killed both human and mouse tumor cells in a CDH17-dependent manner. CDH17CARTs eradicated CDH17-expressing NETs and gastric, pancreatic and colorectal cancers in either tumor xenograft or autochthonous mouse models. Notably, CDH17CARTs do not attack normal intestinal epithelial cells, which also express CDH17, to cause toxicity, likely because CDH17 is localized only at the tight junction between normal intestinal epithelial cells. Thus, CDH17 represents a class of previously unappreciated tumor-associated antigens that is 'masked' in healthy tissues from attack by CAR T cells for developing safer cancer immunotherapy.
    DOI:  https://doi.org/10.1038/s43018-022-00344-7
  16. EMBO Rep. 2022 Mar 23. e54278
    Iron-induced NCOA4 condensation regulates ferritin fate and iron homeostasis.
    Sota Kuno, Hiroaki Fujita, Yu-Ki Tanaka, Yasumitsu Ogra, Kazuhiro Iwai.
      Iron is not only essential but also a toxic trace element. Under iron repletion, ferritin maintains cellular iron homeostasis by storing iron to avoid iron toxicity. Under iron depletion, the ferritin-specific autophagy adaptor NCOA4 delivers ferritin to lysosomes via macroautophagy to enable cells to use stored iron. Here, we show that NCOA4 also plays crucial roles in the regulation of ferritin fate under iron repletion. NCOA4 forms insoluble condensates via multivalent interactions generated by the binding of iron to its intrinsically disordered region. This sequesters NCOA4 away from ferritin and allows ferritin accumulation in the early phase of iron repletion. Under prolonged iron repletion, NCOA4 condensates can deliver ferritin to lysosomes via a TAX1BP1-dependent non-canonical autophagy pathway, thereby preventing relative iron deficiency due to excessive iron storage and reduced iron uptake. Together, these observations suggest that the NCOA4-ferritin axis modulates intracellular iron homeostasis in accordance with cellular iron availability.
    Keywords:  NCOA4; autophagy; ferritin; iron metabolism; phase separation
    DOI:  https://doi.org/10.15252/embr.202154278
  17. Curr Opin Cell Biol. 2022 Mar 17. pii: S0955-0674(22)00016-3. [Epub ahead of print]75 102071
    Fidelity of organellar protein targeting.
    Jiyao Song, Thomas Becker.
      The majority of cellular proteins are targeted to organelles. Cytosolic ribosomes produce these proteins as precursors with cleavable or non-cleavable targeting sequences that direct them to receptor proteins on the organelle surface. Multiple targeting factors ensure cellular sorting of the precursor proteins. In co-translational protein import, the ribosome-nascent chain complex is transported to the organellar protein translocase to couple protein synthesis and protein import. In post-translational mode, targeting factors like molecular chaperones guide the precursor proteins from ribosomes to the cell organelle. Defects in protein targeting and import cause mistargeting of proteins to different cellular compartments and challenge the balance of cellular proteostasis. Specific dislocases and degradation machineries remove such mislocalized proteins from the membrane to allow retargeting or their proteasomal turnover. In this review, we discuss targeting and quality control factors that ensure fidelity of protein targeting to mitochondria.
    DOI:  https://doi.org/10.1016/j.ceb.2022.02.005
  18. Mol Cell. 2022 Mar 11. pii: S1097-2765(22)00167-8. [Epub ahead of print]
    Quality control of protein complex composition.
    Chris Padovani, Predrag Jevtić, Michael Rapé.
      Eukaryotic cells possess hundreds of protein complexes that contain multiple subunits and must be formed at the correct time and place during development. Despite specific assembly pathways, cells frequently encounter complexes with missing or aberrant subunits that can disrupt important signaling events. Cells, therefore, employ several ubiquitin-dependent quality control pathways that can prevent, correct, or degrade flawed complexes. In this review, we will discuss our emerging understanding of such quality control of protein complex composition.
    Keywords:  aneuploidy; dimerization quality control; orphan quality control; proteasome; quality control; ubiquitin; ubiquitylation
    DOI:  https://doi.org/10.1016/j.molcel.2022.02.029
  19. Sci Transl Med. 2022 Mar 23. 14(637): eabc1600
    Listeria delivers tetanus toxoid protein to pancreatic tumors and induces cancer cell death in mice.
    Benson Chellakkan Selvanesan, Dinesh Chandra, Wilber Quispe-Tintaya, Arthee Jahangir, Ankur Patel, Kiran Meena, Rodrigo Alberto Alves Da Silva, Madeline Friedman, Lisa Gabor, Olivia Khouri, Steven K Libutti, Ziqiang Yuan, Jenny Li, Sarah Siddiqui, Amanda Beck, Lydia Tesfa, Wade Koba, Jennifer Chuy, John C McAuliffe, Rojin Jafari, David Entenberg, Yarong Wang, John Condeelis, Vera DesMarais, Vinod Balachandran, Xusheng Zhang, Ken Lin, Claudia Gravekamp.
      Pancreatic ductal adenocarcinoma (PDAC) is a highly metastatic disease. Tumors are poorly immunogenic and immunosuppressive, preventing T cell activation in the tumor microenvironment. Here, we present a microbial-based immunotherapeutic treatment for selective delivery of an immunogenic tetanus toxoid protein (TT856-1313) into PDAC tumor cells by attenuated Listeria monocytogenes. This treatment reactivated preexisting TT-specific memory T cells to kill infected tumor cells in mice. Treatment of KrasG12D,p53R172H, Pdx1-Cre (KPC) mice with Listeria-TT resulted in TT accumulation inside tumor cells, attraction of TT-specific memory CD4 T cells to the tumor microenvironment, and production of perforin and granzyme B in tumors. Low doses of gemcitabine (GEM) increased immune effects of Listeria-TT, turning immunologically cold into hot tumors in mice. In vivo depletion of T cells from Listeria-TT + GEM-treated mice demonstrated a CD4 T cell-mediated reduction in tumor burden. CD4 T cells from TT-vaccinated mice were able to kill TT-expressing Panc-02 tumor cells in vitro. In addition, peritumoral lymph node-like structures were observed in close contact with pancreatic tumors in KPC mice treated with Listeria-TT or Listeria-TT + GEM. These structures displayed CD4 and CD8 T cells producing perforin and granzyme B. Whereas CD4 T cells efficiently infiltrated the KPC tumors, CD8 T cells did not. Listeria-TT + GEM treatment of KPC mice with advanced PDAC reduced tumor burden by 80% and metastases by 87% after treatment and increased survival by 40% compared to nontreated mice. These results suggest that Listeria-delivered recall antigens could be an alternative to neoantigen-mediated cancer immunotherapy.
    DOI:  https://doi.org/10.1126/scitranslmed.abc1600
  20. Nat Cell Biol. 2022 Mar 24.
    Recycling of autophagosomal components from autolysosomes by the recycler complex.
    Chuchu Zhou, Zhe Wu, Wanqing Du, Huilin Que, Yufen Wang, Qinqin Ouyang, Fenglei Jian, Weigang Yuan, Yuan Zhao, Rui Tian, Ying Li, Yang Chen, Shuaixin Gao, Catherine C L Wong, Yueguang Rong.
      Autolysosomes contain components from autophagosomes and lysosomes. The contents inside the autolysosomal lumen are degraded during autophagy, while the fate of autophagosomal components on the autolysosomal membrane remains unknown. Here we report that the autophagosomal membrane components are not degraded, but recycled from autolysosomes through a process coined in this study as autophagosomal components recycling (ACR). We further identified a multiprotein complex composed of SNX4, SNX5 and SNX17 essential for ACR, which we termed 'recycler'. In this, SNX4 and SNX5 form a heterodimer that recognizes autophagosomal membrane proteins and is required for generating membrane curvature on autolysosomes, both via their BAR domains, to mediate the cargo sorting process. SNX17 interacts with both the dynein-dynactin complex and the SNX4-SNX5 dimer to facilitate the retrieval of autophagosomal membrane components. Our discovery of ACR and identification of the recycler reveal an important retrieval and recycling pathway on autolysosomes.
    DOI:  https://doi.org/10.1038/s41556-022-00861-8
  21. Mol Cancer Res. 2022 Mar 23. pii: molcanres.MCR-21-0250-E.2021. [Epub ahead of print]
    BRAFV600E-driven lung adenocarcinoma requires copper to sustain autophagic signaling and processing.
    Tiffany Tsang, Xingxing Gu, Caroline I Davis, Jessica M Posimo, Zoey A Miller, Donita C Brady.
      The transition metal copper (Cu) is an essential micronutrient required for development and proliferation, but the molecular mechanisms by which Cu contributes to these processes is not fully understood. While traditionally studied as a static cofactor critical for the function of Cu-dependent enzymes, an expanding role for Cu is emerging to include its novel function as a dynamic mediator of signaling processes through the direct control of protein kinase activity. We now appreciate that Cu directly binds to and influences MEK1/2 and ULK1/2 kinase activity, and show here that reductions in MAPK and autophagic signaling are associated with dampened growth and survival of oncogenic BRAF-driven lung adenocarcinoma cells upon loss of Ctr1. Efficient autophagy, clonogenic survival, and tumorigenesis of BRAF-mutant cells required ULK1 Cu-binding. While treatment with canonical MAPK inhibitors resulted in the upregulation of protective autophagy, mechanistically, the Cu chelator tetrathiomolybdate (TTM) was sufficient to target both autophagic and MAPK signaling as a means to blunt BRAF-driven tumorigenic properties. These findings support leveraging Cu chelation with TTM as an alternative therapeutic strategy to impair autophagy and MAPK signaling. as traditional MAPK monotherapies initiate autophagy signaling and promote cancer cell survival. Implications: We establish that copper chelation therapy inhibits both autophagy and MAPK signaling in BRAFV600E-driven lung adenocarcinoma, thus overcoming the upregulation of protective autophagy elicited by canonical MAPK pathway inhibitors.
    DOI:  https://doi.org/10.1158/1541-7786.MCR-21-0250
  22. Nature. 2022 Mar;603(7902): 752-754
    Molecular barcodes reveal tumour lineages.
    Jyoti Madhusoodanan.
      
    Keywords:  Cancer; Developmental biology; Genetics; Molecular biology
    DOI:  https://doi.org/10.1038/d41586-022-00798-w
  23. Autophagy. 2022 Mar 20.
    Carbon starvation, senescence and specific mitochondrial stresses, but not nitrogen starvation and general stresses, are major triggers for mitophagy in Arabidopsis.
    Sylwia M Kacprzak, Olivier Van Aken.
      Selective degradation of mitochondria by autophagy (mitophagy) is thought to play an important role in mitochondrial quality control, but our understanding of which conditions induce mitophagy in plants is limited. Here, we developed novel reporter lines to monitor mitophagy in plants and surveyed the rate of mitophagy under a wide range of stresses and developmental conditions. Especially carbon starvation induced by dark-incubation causes a dramatic increase in mitophagy within a few hours, further increasing as dark-induced senescence progresses. Natural senescence was also a strong trigger of mitophagy, peaking when leaf yellowing became prominent. In contrast, nitrogen starvation, a trigger of general autophagy, does not induce strong increases in mitophagy. Similarly, general stresses such as hydrogen peroxide, heat, UV-B and hypoxia did not appear to trigger substantial mitophagy in plants. Additionally, we exposed plants to inhibitors of the mitochondrial electron transport chain, mitochondrial translation and protein import. Although short-term treatments did not induce high mitophagy rates, longer term exposures to uncoupling agent and inhibitors of mitochondrial protein import/translation could clearly increase mitophagic flux. These findings could further be confirmed using confocal microscopy. To validate that mitophagy is mediated by the autophagy pathway, we showed that mitophagic flux is abolished or strongly decreased in atg5/AuTophaGy 5 and atg11 mutants, respectively. Finally, we observed high rates of mitophagy in etiolated seedlings, which remarkably was completely repressed within 6 h after light exposure. In conclusion, we propose that dark-induced carbon starvation, natural senescence and specific mitochondrial stresses are key triggers of mitophagy in plants.
    Keywords:  Arabidopsis; autophagy; mitochondria; mitophagy; plants; senescence
    DOI:  https://doi.org/10.1080/15548627.2022.2054039
  24. Cancers (Basel). 2022 Mar 16. pii: 1523. [Epub ahead of print]14(6):
    Molecular Pathology of Pancreatic Cancer.
    Eva Karamitopoulou.
      Pancreatic ductal adenocarcinoma (PDAC) is a biologically aggressive malignancy showing a remarkable resistance to existing therapies and is often diagnosed at an advanced stage, leaving only about 15-20% of patients with an option for surgical resection [...].
    DOI:  https://doi.org/10.3390/cancers14061523
  25. Semin Cancer Biol. 2022 Mar 21. pii: S1044-579X(22)00068-2. [Epub ahead of print]
    Chemotherapy as a regulator of extracellular matrix-cell communication: implications in therapy resistance.
    Jordi Gonzalez-Molina, Lidia Moyano-Galceran, Andrew Single, Okan Gultekin, Shno Alsalhi, Kaisa Lehti.
      The development of most solid cancers, including pancreatic, breast, lung, liver, and ovarian cancer, involves a desmoplastic reaction: a process of major remodelling of the extracellular matrix (ECM) affecting the ECM composition, mechanics, and microarchitecture. These properties of the ECM influence key cancer cell functions, including treatment resistance. Furthermore, emerging data show that various chemotherapeutic treatments lead to alterations in ECM features and ECM-cell communication. Here, we summarise the current knowledge around the effects of chemotherapy on both the ECM remodelling and ECM-cell signalling and discuss the implications of these alterations on distinct mechanisms of chemoresistance. Additionally, we provide an overview of current therapeutic strategies and ongoing clinical trials utilising anti-cancer drugs to target the ECM-cell communication and explore the future challenges of these strategies.
    Keywords:  ECM; cancer; chemoresistance; chemotherapy; plasticity
    DOI:  https://doi.org/10.1016/j.semcancer.2022.03.012
  26. Cancer Cell. 2022 Mar 15. pii: S1535-6108(22)00116-7. [Epub ahead of print]
    Seed or soil: Tracing the immune subsets in metastatic tumors.
    Xuexin Yu, Bo Li.
      Mapping the tumor-infiltrating immune subsets to an origin of malignancy or tissue niche is important for designing effective immunotherapies, yet it remains a challenging task. In this issue of Cancer Cell, Liu et al. pieced together this puzzle through a comprehensive single-cell analysis of colorectal cancer patients with liver metastases.
    DOI:  https://doi.org/10.1016/j.ccell.2022.03.001
  27. Front Physiol. 2022 ;13 856803
    Updates in the Diagnosis of Intraductal Neoplasms of the Pancreas.
    Naziheh Assarzadegan, Sepideh Babanianmansour, Jiaqi Shi.
      Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest types of cancer worldwide. There are many reasons for this dismal prognosis, including the advanced stage at the time of diagnosis and the lack of effective therapeutic approaches. Intraductal papillary mucinous neoplasms (IPMNs) represent detectable and treatable precursor lesions of PDAC. Our understanding of the pathology of IPMNs has evolved over the past few decades, and new advances in diagnostic tools have emerged. The new World Health Organization (WHO) classification scheme now recognizes the previously considered variants of IPMNs, such as intraductal oncocytic papillary neoplasms (IOPNs) and intraductal tubulopapillary neoplasms (ITPNs), as distinct neoplasms. New imaging and molecular diagnostic tests are being developed to recognize these PDAC precursor lesions better. Here, we review the advances in diagnostic tools for IPMNs, IOPNs, and ITPNs, emphasizing the new (5th edition, 2019) WHO classification for pathological diagnosis, molecular markers, new laboratory tests, and imaging tools.
    Keywords:  classification; intraductal oncocytic papillary neoplasm; intraductal papillary mucinous neoplasm; intraductal tubulopapillary neoplasm; pancreatic ductal adenocarcinoma
    DOI:  https://doi.org/10.3389/fphys.2022.856803
  28. Trends Biotechnol. 2022 Mar 18. pii: S0167-7799(22)00034-8. [Epub ahead of print]
    The LEGO® brick road to open science and biotechnology.
    Etienne Boulter, Julien Colombelli, Ricardo Henriques, Chloé C Féral.
      LEGO® is a brand of toys that have entertained generations of children. Beyond amusement, LEGO® bricks also constitute a building ecosystem of their own that creators from the general public, as well as scientists and engineers, can use to design and assemble devices for all purposes, including scientific research and biotechnology. We describe several of these constructions to highlight the construction properties of LEGO® and their advantages, caveats, and impact in biotechnology. We also discuss how this emerging trend in LEGO® building pairs with a growing interest in open-access and frugal science which aims to provide access to technology to all scientists regardless of financial wealth and technological prowess.
    Keywords:  FAIR science; LEGO® bricks; open science
    DOI:  https://doi.org/10.1016/j.tibtech.2022.02.003
  29. PLoS Comput Biol. 2022 Mar;18(3): e1009803
    Ten quick tips for deep learning in biology.
    Benjamin D Lee, Anthony Gitter, Casey S Greene, Sebastian Raschka, Finlay Maguire, Alexander J Titus, Michael D Kessler, Alexandra J Lee, Marc G Chevrette, Paul Allen Stewart, Thiago Britto-Borges, Evan M Cofer, Kun-Hsing Yu, Juan Jose Carmona, Elana J Fertig, Alexandr A Kalinin, Brandon Signal, Benjamin J Lengerich, Timothy J Triche, Simina M Boca.
      
    DOI:  https://doi.org/10.1371/journal.pcbi.1009803
  30. Anal Chem. 2022 Mar 23.
    Permeability-Controlled Probe for Directly Visualizing the Opening of Mitochondrial Permeability Transition Pore in Native Status.
    Minggang Tian, Baoli Dong, Zheming Zhang, Junling Yin, Weiying Lin.
      The opening of mitochondrial permeability transition pore (mPTP) plays a fundamental role in cell apoptosis regulation, ischemia-reperfusion injury, and neurodegenerative disorders. However, the molecular tools for detecting mPTP open in cellular native status have not been reported yet. Herein, we de novo designed a robust fluorescent probe mPTP-F to monitor mPTP opening in cellular native status for the first time. The membrane-permeable probe could accumulate into mitochondria and convert to a product poorly permeable to biomembranes, which was trapped in mitochondria to form near-infrared (NIR)-emissive aggregates. After mPTP opening, the product was released from mitochondria through the pore to form green-emissive monomers. Significantly, with mPTP-F, we discovered that formaldehyde, a signaling molecule, could induce mPTP opening. Therefore, the new probe could serve as a desirable molecular tool for the study of ischemia-reperfusion injury, cell apoptosis, and relative areas.
    DOI:  https://doi.org/10.1021/acs.analchem.1c04751
  31. BMJ Open. 2022 Mar 24. 12(3): e050169
    Coeliac plexus radiosurgery for pain management in patients with advanced cancer : study protocol for a phase II clinical trial.
    Galia Jacobson, Ronen Fluss, Amira Dany-BenShushan, Talia Golan, Tikva Meron, Camilla Zimmermann, Laura A Dawson, Aisling Barry, Marcin Miszczyk, Michael Buckstein, Dayssy Diaz Pardo, Artur Aguiar, Liat Hammer, Adam P Dicker, Maoz Ben-Ailan, Ofir Morag, David Hausner, Zvi Symon, Yaacov R Lawrence.
       INTRODUCTION: Pancreatic cancer is characterised by severe mid-back and epigastric pain caused by tumour invasion of the coeliac nerve plexus. This pain is often poorly managed with standard treatments. This clinical trial investigates a novel approach in which high-dose radiation (radiosurgery) is targeted to the retroperitoneal coeliac plexus nerve bundle. Preliminary results from a single institution pilot trial are promising: pain relief is substantial and side effects minimal. The goals of this study are to validate these findings in an international multisetting, and investigate the impact on quality of life and functional status among patients with terminal cancer.
    METHODS AND ANALYSIS: A single-arm prospective phase II clinical trial. Eligible patients are required to have severe coeliac pain of at least five on the 11-point BPI average pain scale and Eastern Cooperative Oncology Group performance status of two or better. Non-pancreatic cancers invading the coeliac plexus are also eligible. The intervention involves irradiating the coeliac plexus using a single fraction of 25 Gy. The primary endpoint is the complete or partial pain response at 3 weeks. Secondary endpoints include pain at 6 weeks, analgesic use, hope, qualitative of life, caregiver burden and functional outcomes, all measured using validated instruments. The protocol is expected to open at a number of cancer centres across the globe, and a quality assurance programme is included. The protocol requires that 90 evaluable patients" be accrued, based upon the assumption that a third of patients are non-evaluable (e.g. due to death prior to 3-weeks post-treatment assessment, or spontaneous improvement of pain pre-treatment), it is estimated that a total of 120 patients will need to be accrued. Supported by Gateway for Cancer Research and the Israel Cancer Association.
    ETHICS AND DISSEMINATION: Ethic approval for this study has been obtained at eight academic medical centres located across the Middle East, North America and Europe. Results will be disseminated through conference presentations and peer-reviewed publications.
    TRIAL REGISTRATION NUMBER: NCT03323489.
    Keywords:  adult palliative care; cancer pain; pain management; radiation oncology
    DOI:  https://doi.org/10.1136/bmjopen-2021-050169
  32. Nat Microbiol. 2022 Mar 21.
    Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance.
    Jason S L Yu, Clara Correia-Melo, Francisco Zorrilla, Lucia Herrera-Dominguez, Mary Y Wu, Johannes Hartl, Kate Campbell, Sonja Blasche, Marco Kreidl, Anna-Sophia Egger, Christoph B Messner, Vadim Demichev, Anja Freiwald, Michael Mülleder, Michael Howell, Judith Berman, Kiran R Patil, Mohammad Tauqeer Alam, Markus Ralser.
      Microbial communities are composed of cells of varying metabolic capacity, and regularly include auxotrophs that lack essential metabolic pathways. Through analysis of auxotrophs for amino acid biosynthesis pathways in microbiome data derived from >12,000 natural microbial communities obtained as part of the Earth Microbiome Project (EMP), and study of auxotrophic-prototrophic interactions in self-establishing metabolically cooperating yeast communities (SeMeCos), we reveal a metabolically imprinted mechanism that links the presence of auxotrophs to an increase in metabolic interactions and gains in antimicrobial drug tolerance. As a consequence of the metabolic adaptations necessary to uptake specific metabolites, auxotrophs obtain altered metabolic flux distributions, export more metabolites and, in this way, enrich community environments in metabolites. Moreover, increased efflux activities reduce intracellular drug concentrations, allowing cells to grow in the presence of drug levels above minimal inhibitory concentrations. For example, we show that the antifungal action of azoles is greatly diminished in yeast cells that uptake metabolites from a metabolically enriched environment. Our results hence provide a mechanism that explains why cells are more robust to drug exposure when they interact metabolically.
    DOI:  https://doi.org/10.1038/s41564-022-01072-5
  33. J Surg Oncol. 2022 Mar 25.
    KRAS mutation allele frequency threshold alters prognosis in right-sided resected pancreatic cancer.
    David Nauheim, David Moskal, Bryan Renslo, Matthew Chadwick, Wei Jiang, Charles J Yeo, Avinoam Nevler, Wilbur Bowne, Harish Lavu.
       BACKGROUND: Next-generation sequencing (NGS) provides information on genetic mutations and mutant allele frequency in tumor specimens. We investigated the prognostic significance of KRAS mutant allele frequency in patients with right-sided pancreatic ductal adenocarcinoma (PDAC) treated with surgical resection.
    METHODS: A retrospective study reviewed patients who underwent surgical resection for PDAC and analyzed tumors with an in-house mutational panel. Microdissected samples were studied using an NGS-based assay to detect over 200 hotspot mutations in 42 genes (Pan42) commonly involved in PDAC.
    RESULTS: A total of 144 PDAC right-sided surgical patients with a Pan42 panel were evaluated between 2015 and 2020; 121 patients (84%) harbored a KRAS mutation. Detected mutant allele frequencies were categorized as less than 20% (low mKRAS, n = 92) or greater than or equal to 20% (high mKRAS, n = 29). High mKRAS (KRAS ≥ 20%) patients were noted to have shorter disease-free survival after surgery (11.5 ± 2.1 vs. 19.5 ± 3.5 months, p = 0.03), more advanced tumor stage (p = 0.02), larger tumors (3.6 vs. 2.7 cm, p = 0.001), greater tumor cellularity (26% vs. 18%, p = 0.001), and higher rate of distant recurrence (p = 0.03) than low mKRAS patients.
    CONCLUSION: This study demonstrates the importance of KRAS mutant allele frequency on pathological characteristics and prognosis in right-sided PDAC treated with surgery.
    Keywords:  KRAS; allele frequency; pancreatic cancer; pancreaticoduodenectomy
    DOI:  https://doi.org/10.1002/jso.26860
  34. Vitam Horm. 2022 ;pii: S0083-6729(22)00014-0. [Epub ahead of print]119 299-324
    Telomere length and vitamin B12.
    Guruvaiah Praveen, Mudili Sivaprasad, G Bhanuprakash Reddy.
      Telomeres are non-coding nucleoprotein structures consisting of a highly conserved tandem repeat DNA sequence that caps the ends of chromosomes in eukaryotes. Telomeres confer chromosomal stability, protect the genome from nucleolytic degradation, avoid aberrant recombination and improper repair, and prevent random fusion of chromosomes. The end-replication problem results in telomere shortening with every cell division, eventually leading to cellular senescence and aging. Telomere length (TL) is thereby an ideal candidate for "biological aging." Telomeres possess guanine-rich repeats, which are highly susceptible to oxidative stress. Epidemiological studies have indicated the association of telomere attrition with mortality and various age-related diseases. Micronutrients comprising vitamins and minerals act as potential modulators of stress and can influence TL. Research has indicated that vitamin B12 (B12) regulates oxidative stress and maintains genomic stability, thereby influencing telomere integrity and cellular aging. The deficiency of B12 leads to elevated levels of homocysteine, which reduces the methylation potential and increases oxidative stress, thereby compromising the TL. Telomere shortening and mitochondrial dysfunction are independently linked to aging. However, they are connected through telomerase reverse transcriptase activity, which regulates mitochondrial biogenesis. Further, experimental evidence indicated the positive association of B12 with relative TL and mitochondrial DNA copy number, an indirect index of mitochondrial biogenesis. The present chapter provides some insights into the role of B12 in influencing TL. Exploring their association might open new avenues to understand the pathophysiology of aging and age-related diseases.
    Keywords:  8-Oxo-G; Aging; Homocysteine; Methylation; Mitochondrial DNA copy number oxidative stress; Telomerase; Telomere length; Vitamin B12
    DOI:  https://doi.org/10.1016/bs.vh.2022.01.014
  35. STAR Protoc. 2022 Jun 17. 3(2): 101262
    Live cell microscopy of mitochondria-lysosome contact site formation and tethering dynamics.
    Tayler B Belton, Eric D Leisten, Jasmine Cisneros, Yvette C Wong.
      Mitochondria-lysosome contact sites are critical for maintaining cellular homeostasis by regulating mitochondrial and lysosomal network dynamics and mediating metabolite exchange. Here, we present a protocol to quantitatively analyze the formation and tethering duration of mitochondria-lysosome contact sites by using time-lapse live confocal microscopy of LAMP1 and TOMM20. Although this protocol focuses on mammalian HeLa cells, it can be applied to other cell types for further studies on mitochondria-lysosome contact regulation and function, and elucidation of their role in human disorders. For complete details on the use and execution of this protocol, please refer to Wong et al. (2018) and Wong et al. (2019b).
    Keywords:  Cell Biology; Cell culture; Microscopy
    DOI:  https://doi.org/10.1016/j.xpro.2022.101262
  36. Front Nutr. 2022 ;9 831934
    Managing Nutrition Impact Symptoms in Cancer Cachexia: A Case Series and Mini Review.
    Adam Khorasanchi, Srinidhi Nemani, Sudeep Pandey, Egidio Del Fabbro.
      Malnutrition is common in cancer patients and can occur throughout a patient's disease course. The contributors to the clinical syndrome of cancer cachexia are often multifactorial, and produced by the cancer and associated pro-inflammatory response. Since cancer cachexia is a multifactorial syndrome, a multimodal therapeutic approach is ideal. A key component of therapy is identifying and managing symptom barriers to adequate oral intake, known as nutritional impact symptoms (NIS). NIS are associated with reduced intake and weight loss in patients with advanced cancer, and aggregate NIS are a predictor of survival in patients with Head and Neck Cancer and in patients undergoing surgery for esophageal cancer. Currently, there are no guidelines regarding the specific management of NIS in oncology patients. Experience from specialist centers suggest relatively simple assessments and inexpensive interventions are available for the diagnosis and treatment of NIS. We present three patient cases from a cachexia clinic, where NIS management decreased symptom burden and improved clinical outcomes such as weight and physical performance.
    Keywords:  cachexia; cancer; malnutrition; nutrition impact symptoms; review
    DOI:  https://doi.org/10.3389/fnut.2022.831934
  37. Nat Commun. 2022 Mar 23. 13(1): 1560
    Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx.
    Homa MohammadiPeyhani, Jasmin Hafner, Anastasia Sveshnikova, Victor Viterbo, Vassily Hatzimanikatis.
      Metabolic "dark matter" describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark matter of metabolism remains an open challenge that can be addressed globally and systematically by existing computational solutions. In this work, we use 489 generalized enzymatic reaction rules to map both known and unknown metabolic processes around a biochemical database of 1.5 million biological compounds. We predict over 5 million reactions and integrate nearly 2 million naturally and synthetically-derived compounds into the global network of biochemical knowledge, named ATLASx. ATLASx is available to researchers as a powerful online platform that supports the prediction and analysis of biochemical pathways and evaluates the biochemical vicinity of molecule classes ( https://lcsb-databases.epfl.ch/Atlas2 ).
    DOI:  https://doi.org/10.1038/s41467-022-29238-z
  38. PLoS Biol. 2022 Mar;20(3): e3001576
    Mitochondria transplantation between living cells.
    Christoph G Gäbelein, Qian Feng, Edin Sarajlic, Tomaso Zambelli, Orane Guillaume-Gentil, Benoît Kornmann, Julia A Vorholt.
      Mitochondria and the complex endomembrane system are hallmarks of eukaryotic cells. To date, it has been difficult to manipulate organelle structures within single live cells. We developed a FluidFM-based approach to extract, inject, and transplant organelles from and into living cells with subcellular spatial resolution. The technology combines atomic force microscopy, optical microscopy, and nanofluidics to achieve force and volume control with real-time inspection. We developed dedicated probes that allow minimally invasive entry into cells and optimized fluid flow to extract specific organelles. When extracting single or a defined number of mitochondria, their morphology transforms into a pearls-on-a-string phenotype due to locally applied fluidic forces. We show that the induced transition is calcium independent and results in isolated, intact mitochondria. Upon cell-to-cell transplantation, the transferred mitochondria fuse to the host cells mitochondrial network. Transplantation of healthy and drug-impaired mitochondria into primary keratinocytes allowed monitoring of mitochondrial subpopulation rescue. Fusion with the mitochondrial network of recipient cells occurred 20 minutes after transplantation and continued for over 16 hours. After transfer of mitochondria and cell propagation over generations, donor mitochondrial DNA (mtDNA) was replicated in recipient cells without the need for selection pressure. The approach opens new prospects for the study of organelle physiology and homeostasis, but also for therapy, mechanobiology, and synthetic biology.
    DOI:  https://doi.org/10.1371/journal.pbio.3001576
  39. Front Cell Dev Biol. 2022 ;10 786031
    Myc Supports Self-Renewal of Basal Cells in the Esophageal Epithelium.
    Tomoaki Hishida, Eric Vazquez-Ferrer, Yuriko Hishida-Nozaki, Yuto Takemoto, Fumiyuki Hatanaka, Kei Yoshida, Javier Prieto, Sanjeeb Kumar Sahu, Yuta Takahashi, Pradeep Reddy, David D O'Keefe, Concepcion Rodriguez Esteban, Paul S Knoepfler, Estrella Nuñez Delicado, Antoni Castells, Josep M Campistol, Ryuji Kato, Hiroshi Nakagawa, Juan Carlos Izpisua Belmonte.
      It is widely believed that cellular senescence plays a critical role in both aging and cancer, and that senescence is a fundamental, permanent growth arrest that somatic cells cannot avoid. Here we show that Myc plays an important role in self-renewal of esophageal epithelial cells, contributing to their resistance to cellular senescence. Myc is homogeneously expressed in basal cells of the esophageal epithelium and Myc positively regulates their self-renewal by maintaining their undifferentiated state. Indeed, Myc knockout induced a loss of the undifferentiated state of esophageal epithelial cells resulting in cellular senescence while forced MYC expression promoted oncogenic cell proliferation. A superoxide scavenger counteracted Myc knockout-induced senescence, therefore suggesting that a mitochondrial superoxide takes part in inducing senescence. Taken together, these analyses reveal extremely low levels of cellular senescence and senescence-associated phenotypes in the esophageal epithelium, as well as a critical role for Myc in self-renewal of basal cells in this organ. This provides new avenues for studying and understanding the links between stemness and resistance to cellular senescence.
    Keywords:  MYC; aging; cancer; mitochondria highlights; senescence
    DOI:  https://doi.org/10.3389/fcell.2022.786031
  40. Aging (Albany NY). 2022 Mar 07. 14(5): 2016-2017
    Targeting proteostasis maintenance and autophagy in senescence.
    Valentin L'Hôte, Carl Mann, Jean-Yves Thuret.
      
    Keywords:  BRAF-V600E; cellular senescence; proteostasis; selective autophagy; senolytics
    DOI:  https://doi.org/10.18632/aging.203941
  41. Proc Natl Acad Sci U S A. 2022 Mar 29. 119(13): e2120799119
    Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate.
    Ian Seim, Ammon E Posey, Wilton T Snead, Benjamin M Stormo, Daphne Klotsa, Rohit V Pappu, Amy S Gladfelter.
      SignificanceA large subclass of biomolecular condensates are linked to RNA regulation and are known as ribonucleoprotein (RNP) bodies. While extensive work has identified driving forces for biomolecular condensate formation, relatively little is known about forces that oppose assembly. Here, using a fungal RNP protein, Whi3, we show that a portion of its intrinsically disordered, glutamine-rich region modulates phase separation by forming transient alpha helical structures that promote the assembly of dilute phase oligomers. These oligomers detour Whi3 proteins from condensates, thereby impacting the driving forces for phase separation, the protein-to-RNA ratio in condensates, and the material properties of condensates. Our findings show how nanoscale conformational and oligomerization equilibria can influence mesoscale phase equilibria.
    Keywords:  oligomerization; phase separation; ribonucleoprotein complexes
    DOI:  https://doi.org/10.1073/pnas.2120799119
  42. Sci Rep. 2022 Mar 25. 12(1): 5205
    Impact of baseline culture conditions of cancer organoids when determining therapeutic response and tumor heterogeneity.
    Rebecca A DeStefanis, Jeremy D Kratz, Autumn M Olson, Aishwarya Sunil, Alyssa K DeZeeuw, Amani A Gillette, Gioia C Sha, Katherine A Johnson, Cheri A Pasch, Linda Clipson, Melissa C Skala, Dustin A Deming.
      Representative models are needed to screen new therapies for patients with cancer. Cancer organoids are a leap forward as a culture model that faithfully represents the disease. Mouse-derived cancer organoids (MDCOs) are becoming increasingly popular, however there has yet to be a standardized method to assess therapeutic response and identify subpopulation heterogeneity. There are multiple factors unique to organoid culture that could affect how therapeutic response and MDCO heterogeneity are assessed. Here we describe an analysis of nearly 3500 individual MDCOs where individual organoid morphologic tracking was performed. Change in MDCO diameter was assessed in the presence of control media or targeted therapies. Individual organoid tracking was identified to be more sensitive to treatment response than well-level assessment. The impact of different generations of mice of the same genotype, different regions of the colon, and organoid specific characteristics including baseline size, passage number, plating density, and location within the matrix were examined. Only the starting size of the MDCO altered the subsequent growth. These results were corroborated using ~ 1700 patient-derived cancer organoids (PDCOs) isolated from 19 patients. Here we establish organoid culture parameters for individual organoid morphologic tracking to determine therapeutic response and growth/response heterogeneity for translational studies.
    DOI:  https://doi.org/10.1038/s41598-022-08937-z
  43. Nat Biomed Eng. 2022 Mar 21.
    Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation.
    Benjamin E Mead, Kazuki Hattori, Lauren Levy, Shinya Imada, Norihiro Goto, Marko Vukovic, Daphne Sze, Conner Kummerlowe, Juan D Matute, Jinzhi Duan, Robert Langer, Richard S Blumberg, Jose Ordovas-Montanes, Ömer H Yilmaz, Jeffrey M Karp, Alex K Shalek.
      The cellular composition of barrier epithelia is essential to organismal homoeostasis. In particular, within the small intestine, adult stem cells establish tissue cellularity, and may provide a means to control the abundance and quality of specialized epithelial cells. Yet, methods for the identification of biological targets regulating epithelial composition and function, and of small molecules modulating them, are lacking. Here we show that druggable biological targets and small-molecule regulators of intestinal stem cell differentiation can be identified via multiplexed phenotypic screening using thousands of miniaturized organoid models of intestinal stem cell differentiation into Paneth cells, and validated via longitudinal single-cell RNA-sequencing. We found that inhibitors of the nuclear exporter Exportin 1 modulate the fate of intestinal stem cells, independently of known differentiation cues, significantly increasing the abundance of Paneth cells in the organoids and in wild-type mice. Physiological organoid models of the differentiation of intestinal stem cells could find broader utility for the screening of biological targets and small molecules that can modulate the composition and function of other barrier epithelia.
    DOI:  https://doi.org/10.1038/s41551-022-00863-9
  44. Sci Signal. 2022 Mar 22. 15(726): eabm4452
    The glucocorticoid receptor associates with RAS complexes to inhibit cell proliferation and tumor growth.
    Bozhena Caratti, Miray Fidan, Giorgio Caratti, Kristina Breitenecker, Melanie Engler, Naser Kazemitash, Rebecca Traut, Rainer Wittig, Emilio Casanova, Mohammad Reza Ahmadian, Jan P Tuckermann, Herwig P Moll, Ion Cristian Cirstea.
      Mutations that activate members of the RAS family of GTPases are associated with various cancers and drive tumor growth. The glucocorticoid receptor (GR), a member of the nuclear receptor family, has been proposed to interact with and inhibit the activation of components of the PI3K-AKT and MAPK pathways downstream of RAS. In the absence of activating ligands, we found that GR was present in cytoplasmic KRAS-containing complexes and inhibited the activation of wild-type and oncogenic KRAS in mouse embryonic fibroblasts and human lung cancer A549 cells. The DNA binding domain of GR was involved in the interaction with KRAS, but GR-dependent inhibition of RAS activation did not depend on the nuclear translocation of GR. The addition of ligand released GR-dependent inhibition of RAS, AKT, the MAPK p38, and the MAPKK MEK. CRISPR-Cas9-mediated deletion of GR in A549 cells enhanced tumor growth in xenografts in mice. Patient samples of non-small cell lung carcinomas showed lower expression of NR3C1, the gene encoding GR, compared to adjacent normal tissues and lower NR3C1 expression correlated with a worse disease outcome. These results suggest that glucocorticoids prevent the ability of GR to limit tumor growth by inhibiting RAS activation, which has potential implications for the use of glucocorticoids in patients with cancer.
    DOI:  https://doi.org/10.1126/scisignal.abm4452
  45. Lancet. 2022 Mar 19. pii: S0140-6736(22)00179-9. [Epub ahead of print]399(10330): 1113
    Global mortality burden attributable to non-optimal temperatures.
    Ana M Vicedo-Cabrera, Aurelio Tobias, Jouni J K Jaakkola, Yasushi Honda, Masahiro Hashizume, Yuming Guo, Joel Schwartz, Antonella Zanobetti, Michelle L Bell, Ben Armstrong, Klea Katsouyanni, Andy Haines, Kristie L Ebi, Antonio Gasparrini.
      
    DOI:  https://doi.org/10.1016/S0140-6736(22)00179-9
  46. Cell Metab. 2022 Mar 15. pii: S1550-4131(22)00088-2. [Epub ahead of print]
    Ejection of damaged mitochondria and their removal by macrophages ensure efficient thermogenesis in brown adipose tissue.
    Marco Rosina, Veronica Ceci, Riccardo Turchi, Li Chuan, Nicholas Borcherding, Francesca Sciarretta, María Sánchez-Díaz, Flavia Tortolici, Keaton Karlinsey, Valerio Chiurchiù, Claudia Fuoco, Rocky Giwa, Rachael L Field, Matteo Audano, Simona Arena, Alessandro Palma, Federica Riccio, Farnaz Shamsi, Giovanni Renzone, Martina Verri, Anna Crescenzi, Salvatore Rizza, Fiorella Faienza, Giuseppe Filomeni, Sander Kooijman, Stefano Rufini, Antoine A F de Vries, Andrea Scaloni, Nico Mitro, Yu-Hua Tseng, Andrés Hidalgo, Beiyan Zhou, Jonathan R Brestoff, Katia Aquilano, Daniele Lettieri-Barbato.
      Recent findings have demonstrated that mitochondria can be transferred between cells to control metabolic homeostasis. Although the mitochondria of brown adipocytes comprise a large component of the cell volume and undergo reorganization to sustain thermogenesis, it remains unclear whether an intercellular mitochondrial transfer occurs in brown adipose tissue (BAT) and regulates adaptive thermogenesis. Herein, we demonstrated that thermogenically stressed brown adipocytes release extracellular vesicles (EVs) that contain oxidatively damaged mitochondrial parts to avoid failure of the thermogenic program. When re-uptaken by parental brown adipocytes, mitochondria-derived EVs reduced peroxisome proliferator-activated receptor-γ signaling and the levels of mitochondrial proteins, including UCP1. Their removal via the phagocytic activity of BAT-resident macrophages is instrumental in preserving BAT physiology. Depletion of macrophages in vivo causes the abnormal accumulation of extracellular mitochondrial vesicles in BAT, impairing the thermogenic response to cold exposure. These findings reveal a homeostatic role of tissue-resident macrophages in the mitochondrial quality control of BAT.
    Keywords:  adipose tissue; brown adipocytes; extracellular vesicles; homeostasis; immunometabolism; macrophages; mitochondria; mitochondrial quality control; thermogenesis
    DOI:  https://doi.org/10.1016/j.cmet.2022.02.016
  47. Mini Rev Med Chem. 2022 Mar 24.
    Pharmacological Modulation of Apoptosis and Autophagy in the Treatment of Pancreatic Cancer.
    Nityaa Selvarajoo, Johnson Stanslas, Mohammad Kaisarul Islam, Sreenivasa Rao Sagineedu, Kok Lian Ho, Jonathan Chee Woei Lim.
       BACKGROUND: Pancreatic cancer is a fatal malignant neoplasm with infrequent signs and symptoms until a progressive stage. In 2020, GLOBOCAN reported that, pancreatic cancer accounts for 4.7% of all cancer deaths. Despite the availability of standard chemotherapy regiments for treatment, the survival benefits are not guaranteed because tumour cells become chemoresistant even due to the development of chemoresistance in tumour cells even with a short treatment course, where apoptosis and autophagy play critical roles.
    OBJECTIVE: This review compiled essential information on the regulatory mechanisms and roles of apoptosis and autophagy in pancreatic cancer, as well as drug-like molecules that target different pathways in pancreatic cancer eradication, with an aim of providing ideas to the scientific communities to discover novels and specific drug to treat pancreatic cancer, specifically PDAC. highlight these mechanisms which target different pathways in eradicating pancreatic cancer.
    METHOD: Electronic databases that were searched for research articles for this review were Scopus, Science Direct, PubMed, Springer Link, and Google Scholar. The published studies were identified and retrieved using selected keywords. Discussion/ Conclusion: Many small-molecule anticancer agents have been developed to regulate autophagy and apoptosis associated with pancreatic cancer treatment, where most of them target apoptosis directly through EGFR/Ras/Raf/MAPK and PI3K/Akt/mTOR pathways. The cancer drugs that regulate autophagy in treating cancer can be categorized into three groups: i) direct autophagy inducers (e.g., rapamycin), ii) indirect autophagy inducers (e.g., resveratrol), and iii) autophagy inhibitors. Resveratrol persuades both apoptosis and autophagy with cytoprotective effect, while autophagy inhibitors (e.g., 3-methyladenine, chloroquine) can turn off the protective autophagic effect for therapeutic benefits. Several studies showed that autophagy inhibition resulted in a synergistic effect with chemotherapy (e.g., combination of metformin with gemcitabine/5FU) and such drugs possess a unique clinical value in treating pancreatic cancer as well as other autophagy-dependent carcinomas.
    Keywords:  Apoptosis; Autophagy; Autophagy modulators; Cancer drugs.; Chemoresistance; Pancreatic cancer
    DOI:  https://doi.org/10.2174/1389557522666220324123605
  48. Nature. 2022 Mar 23.
    Reduced reproductive success is associated with selective constraint on human genes.
    Eugene J Gardner, Matthew D C Neville, Kaitlin E Samocha, Kieron Barclay, Martin Kolk, Mari E K Niemi, George Kirov, Hilary C Martin, Matthew E Hurles.
      Genome-wide sequencing of human populations has revealed substantial variation among genes in the intensity of purifying selection acting on damaging genetic variants1. Although genes under the strongest selective constraint are highly enriched for associations with Mendelian disorders, most of these genes are not associated with disease and therefore the nature of the selection acting on them is not known2. Here we show that genetic variants that damage these genes are associated with markedly reduced reproductive success, primarily owing to increased childlessness, with a stronger effect in males than in females. We present evidence that increased childlessness is probably mediated by genetically associated cognitive and behavioural traits, which may mean that male carriers are less likely to find reproductive partners. This reduction in reproductive success may account for 20% of purifying selection against heterozygous variants that ablate protein-coding genes. Although this genetic association may only account for a very minor fraction of the overall likelihood of being childless (less than 1%), especially when compared to more influential sociodemographic factors, it may influence how genes evolve over time.
    DOI:  https://doi.org/10.1038/s41586-022-04549-9
  49. JCO Precis Oncol. 2022 Mar;6 e2100245
    Landscape of KRASG12C, Associated Genomic Alterations, and Interrelation With Immuno-Oncology Biomarkers in KRAS-Mutated Cancers.
    Mohamed E Salem, Sherif M El-Refai, Wei Sha, Alberto Puccini, Axel Grothey, Thomas J George, Jimmy J Hwang, Bert O'Neil, Alexander S Barrett, Kunal C Kadakia, Laura W Musselwhite, Derek Raghavan, Eric Van Cutsem, Josep Tabernero, Jeanne Tie.
       PURPOSE: Promising single-agent activity from sotorasib and adagrasib in KRASG12C-mutant tumors has provided clinical evidence of effective KRAS signaling inhibition. However, comprehensive analysis of KRAS-variant prevalence, genomic alterations, and the relationship between KRAS and immuno-oncology biomarkers is lacking.
    MATERIALS AND METHODS: Retrospective analysis of deidentified records from 79,004 patients with various cancers who underwent next-generation sequencing was performed. Fisher's exact test evaluated the association between cancer subtypes and KRAS variants. Logistic regression assessed KRASG12C comutations with other oncogenes and the association between KRAS variants and immuno-oncology biomarkers.
    RESULTS: Of the 79,004 samples assessed, 13,758 (17.4%) harbored KRAS mutations, with 1,632 (11.9%) harboring KRASG12C and 12,126 (88.1%) harboring other KRAS variants (KRASnon-G12C). Compared with KRASnon-G12C across all tumor subtypes, KRASG12C was more prevalent in females (56% v 51%, false discovery rate-adjusted P value [FDR-P] = .0006), current or prior smokers (85% v 56%, FDR-P < .0001), and patients age > 60 years (73% v 63%, FDR-P ≤ .0001). The most frequent KRAS variants across all subtypes were G12D (29.5%), G12V (23.0%), G12C (11.9%), G13D (6.5%), and G12R (6.2%). KRASG12C was most prevalent in patients with non-small-cell lung cancer (9%), appendiceal (3.9%), colorectal (3.2%), tumor of unknown origin (1.6%), small bowel (1.43%), and pancreatic (1.3%) cancers. Compared with KRASnon-G12C-mutated, KRASG12C-mutated tumors were significantly associated with tumor mutational burden-high status (17.9% v 8.4%, odds ratio [OR] = 2.38; FDR-P < .0001). KRASG12C-mutated tumors exhibited a distinct comutation profile from KRASnon-G12C-mutated tumors, including higher comutations of STK11 (20.59% v 5.95%, OR = 4.10; FDR-P < .01) and KEAP1 (15.38% v 4.61%, OR = 3.76; FDR-P < .01).
    CONCLUSION: This study presents the first large-scale, pan-cancer genomic characterization of KRASG12C. The KRASG12C mutation was more prevalent in females and older patients and appeared to be associated with smoking status. KRASG12C tumors exhibited a distinct comutation profile and were associated with tumor mutational burden-high status.
    DOI:  https://doi.org/10.1200/PO.21.00245
  50. PLoS Comput Biol. 2022 Mar 21. 18(3): e1009505
    Chemotherapy-induced cachexia and model-informed dosing to preserve lean mass in cancer treatment.
    Suzan Farhang-Sardroodi, Michael A La Croix, Kathleen P Wilkie.
      Although chemotherapy is a standard treatment for cancer, it comes with significant side effects. In particular, certain agents can induce severe muscle loss, known as cachexia, worsening patient quality of life and treatment outcomes. 5-fluorouracil, an anti-cancer agent used to treat several cancers, has been shown to cause muscle loss. Experimental data indicates a non-linear dose-dependence for muscle loss in mice treated with daily or week-day schedules. We present a mathematical model of chemotherapy-induced muscle wasting that captures this non-linear dose-dependence. Area-under-the-curve metrics are proposed to quantify the treatment's effects on lean mass and tumour control. Model simulations are used to explore alternate dosing schedules, aging effects, and morphine use in chemotherapy treatment with the aim of better protecting lean mass while actively targeting the tumour, ultimately leading to improved personalization of treatment planning and improved patient quality of life.
    DOI:  https://doi.org/10.1371/journal.pcbi.1009505
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