bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021–10–03
47 papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Ketogenic Diets in Pancreatic Cancer and Associated Cachexia: Cellular Mechanisms and Clinical Perspectives.
  2. Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy.
  3. Matrix stiffness drives stromal autophagy and promotes formation of a protumorigenic niche.
  4. Selective Autophagy as a Potential Therapeutic Target in Age-Associated Pathologies.
  5. Autophagy and the Hallmarks of Aging.
  6. Localization of KRAS downstream target ARL4C to invasive pseudopods accelerates pancreatic cancer cell invasion.
  7. Molecular characterisation of pancreatic ductal adenocarcinoma with NTRK fusions and review of the literature.
  8. Comparative Untargeted Metabolomic Profiling of Induced Mitochondrial Fusion in Pancreatic Cancer.
  9. Glucose and Amino Acid Metabolic Dependencies Linked to Stemness and Metastasis in Different Aggressive Cancer Types.
  10. Trypsin-mediated sensitization to ferroptosis increases the severity of pancreatitis in mice.
  11. KDM6A Regulates Cell Plasticity and Pancreatic Cancer Progression by Non-Canonical Activin Pathway.
  12. NUPR1 inhibitor ZZW-115 induces ferroptosis in a mitochondria-dependent manner.
  13. Renalase is a novel tissue and serological biomarker in pancreatic ductal adenocarcinoma.
  14. Deletion of NEMO Inhibits EMT and Reduces Metastasis in KPC Mice.
  15. The multifaceted regulation of mitophagy by endogenous metabolites.
  16. Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice.
  17. Mitochondrial DNA and MitomiR Variations in Pancreatic Cancer: Potential Diagnostic and Prognostic Biomarkers.
  18. Cancer Signaling Drives Cancer Metabolism: AKT and the Warburg Effect.
  19. TERT-expressing acinar cells implicated in early pancreatic tumour formation.
  20. A genetic model of methionine restriction extends Drosophila health- and lifespan.
  21. Sequestsome-1/p62-targeted small molecules for pancreatic cancer therapy.
  22. Unveiling the K+-sensitivity of cell metabolism using genetically encoded, FRET-based K+, glucose, and ATP biosensors.
  23. Interpretation of cancer mutations using a multiscale map of protein systems.
  24. Predictors of Biological Age: The Implications for Wellness and Aging Research.
  25. Geriatric Nutrition Risk Index: Prognostic factor related to inflammation in elderly patients with cancer cachexia.
  26. An anti-tumor coup: TIM3 ablation activates the immune arsenal.
  27. Intravital imaging technology guides FAK-mediated priming in pancreatic cancer precision medicine according to Merlin status.
  28. Atlas of clinically distinct cell states and ecosystems across human solid tumors.
  29. The tumor microenvironment in pancreatic ductal adenocarcinoma: current perspectives and future directions.
  30. A Universal Approach to Analyzing Transmission Electron Microscopy with ImageJ.
  31. Structural basis and regulation of the reductive stress response.
  32. Cellular Plasticity: A Route to Senescence Exit and Tumorigenesis.
  33. Oncogene-dependent sloppiness in mRNA translation.
  34. Distinct CDK6 complexes determine tumor cell response to CDK4/6 inhibitors and degraders.
  35. Codon optimality in cancer.
  36. Live-Cell Probe for In Situ Single-Cell Monitoring of Mitochondrial DNA Methylation.
  37. Bile acid metabolism dysregulation associates with cancer cachexia: roles of liver and gut microbiome.
  38. Systematic investigation of cytokine signaling activity at the tissue and single-cell levels.
  39. The Protexin complex counters resection on stalled forks to promote homologous recombination and crosslink repair.
  40. Organoids derived from neoadjuvant FOLFIRINOX patients recapitulate therapy resistance in pancreatic ductal adenocarcinoma.
  41. The role of lysosomal membrane proteins in glucose and lipid metabolism.
  42. The surprise element: A hallmark of creativity in scientists, artists, and comedians.
  43. In vivo autophagy quantification: Measuring LC3 and P62 puncta in 3D image system from zebrafish larvae.
  44. A Four Autophagy-Related Gene-Based Prognostic Signature for Pancreatic Cancer.
  45. RosettaSX: Reliable gene expression signature scoring of cancer models and patients.
  46. Perineural Invasion and Associated Pain Transmission in Pancreatic Cancer.
  47. SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling.
  1. Nutrients. 2021 Sep 15. pii: 3202. [Epub ahead of print]13(9):
    Ketogenic Diets in Pancreatic Cancer and Associated Cachexia: Cellular Mechanisms and Clinical Perspectives.
    Natalia E Cortez, Gerardo G Mackenzie.
      Pancreatic ductal adenocarcinoma (PDAC) is an aggressive and extremely therapy-resistant cancer. It is estimated that up to 80% of PDAC patients present with cachexia, a multifactorial disorder characterized by the involuntary and ongoing wasting of skeletal muscle that affects therapeutic response and survival. During the last decade, there has been an increased interest in exploring dietary interventions to complement the treatment of PDAC and associated cachexia. Ketogenic diets (KDs) have gained attention for their anti-tumor potential. Characterized by a very low carbohydrate, moderate protein, and high fat composition, this diet mimics the metabolic changes that occur in fasting. Numerous studies report that a KD reduces tumor growth and can act as an adjuvant therapy in various cancers, including pancreatic cancer. However, research on the effect and mechanisms of action of KDs on PDAC-associated cachexia is limited. In this narrative review, we summarize the evidence of the impact of KDs in PDAC treatment and cachexia mitigation. Furthermore, we discuss key cellular mechanisms that explain KDs' potential anti-tumor and anti-cachexia effects, focusing primarily on reprogramming of cell metabolism, epigenome, and the gut microbiome. Finally, we provide a perspective on future research needed to advance KDs into clinical use.
    Keywords:  cancer cachexia; cell metabolism; ketogenic diet; ketone bodies; microbiome; pancreatic cancer; pancreatic ductal adenocarcinoma
    DOI:  https://doi.org/10.3390/nu13093202
  2. Elife. 2021 Sep 29. pii: e72328. [Epub ahead of print]10
    Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy.
    Vinay V Eapen, Sharan Swarup, Melissa J Hoyer, Joao A Paulo, Wade Harper.
      Removal of damaged organelles via the process of selective autophagy constitutes a major form of cellular quality control. Damaged organelles are recognized by a dedicated surveillance machinery, leading to the assembly of an autophagosome around the damaged organelle, prior to fusion with the degradative lysosomal compartment. Lysosomes themselves are also prone to damage and are degraded through the process of lysophagy. While early steps involve recognition of ruptured lysosomal membranes by glycan-binding Galectins and ubiquitylation of transmembrane lysosomal proteins, many steps in the process, and their inter-relationships, remain poorly understood, including the role and identity of cargo receptors required for completion of lysophagy. Here, we employ quantitative organelle capture and proximity biotinylation proteomics of autophagy adaptors, cargo receptors, and Galectins in response to acute lysosomal damage, thereby revealing the landscape of lysosome-associated proteome remodeling during lysophagy. Among proteins dynamically recruited to damaged lysosomes were ubiquitin-binding autophagic cargo receptors. Using newly developed lysophagic flux reporters including Lyso-Keima, we demonstrate that TAX1BP1, together with its associated kinase TBK1, are both necessary and sufficient to promote lysophagic flux in both HeLa cells and induced neurons (iNeurons). While the related receptor OPTN can drive damage-dependent lysophagy when overexpressed, cells lacking either OPTN or CALCOCO2 still maintain significant lysophagic flux in HeLa cells. Mechanistically, TAX1BP1-driven lysophagy requires its N-terminal SKICH domain, which binds both TBK1 and the autophagy regulatory factor RB1CC1, and requires upstream ubiquitylation events for efficient recruitment and lysophagic flux. These results identify TAX1BP1 as a central component in the lysophagy pathway and provide a proteomic resource for future studies of the lysophagy process.
    Keywords:  biochemistry; cell biology; chemical biology; human
    DOI:  https://doi.org/10.7554/eLife.72328
  3. Proc Natl Acad Sci U S A. 2021 Oct 05. pii: e2105367118. [Epub ahead of print]118(40):
    Matrix stiffness drives stromal autophagy and promotes formation of a protumorigenic niche.
    Anna Hupfer, Anna Brichkina, Anke Koeniger, Corinna Keber, Carsten Denkert, Petra Pfefferle, Frederik Helmprobst, Axel Pagenstecher, Alexander Visekruna, Matthias Lauth.
      Increased stiffness of solid tissues has long been recognized as a diagnostic feature of several pathologies, most notably malignant diseases. In fact, it is now well established that elevated tissue rigidity enhances disease progression and aggressiveness and is associated with a poor prognosis in patients as documented, for instance, for lung fibrosis or the highly desmoplastic cancer of the pancreas. The underlying mechanisms of the interplay between physical properties and cellular behavior are, however, not very well understood. Here, we have found that switching culture conditions from soft to stiff substrates is sufficient to evoke (macro) autophagy in various fibroblast types. Mechanistically, this is brought about by stiffness-sensing through an Integrin αV-focal adhesion kinase module resulting in sequestration and posttranslational stabilization of the metabolic master regulator AMPKα at focal adhesions, leading to the subsequent induction of autophagy. Importantly, stiffness-induced autophagy in stromal cells such as fibroblasts and stellate cells critically supports growth of adjacent cancer cells in vitro and in vivo. This process is Integrin αV dependent, opening possibilities for targeting tumor-stroma crosstalk. Our data thus reveal that the mere change in mechanical tissue properties is sufficient to metabolically reprogram stromal cell populations, generating a tumor-supportive metabolic niche.
    Keywords:  AMPK; ITGAV; autophagy; pancreatic stellate cells; tumor stroma
    DOI:  https://doi.org/10.1073/pnas.2105367118
  4. Metabolites. 2021 Aug 31. pii: 588. [Epub ahead of print]11(9):
    Selective Autophagy as a Potential Therapeutic Target in Age-Associated Pathologies.
    Margarita-Elena Papandreou, Nektarios Tavernarakis.
      Progressive accumulation of damaged cellular constituents contributes to age-related diseases. Autophagy is the main catabolic process, which recycles cellular material in a multitude of tissues and organs. Autophagy is activated upon nutrient deprivation, and oncogenic, heat or oxidative stress-induced stimuli to selectively degrade cell constituents and compartments. Specificity and accuracy of the autophagic process is maintained via the precision of interaction of autophagy receptors or adaptors and substrates by the intricate, stepwise orchestration of specialized integrating stimuli. Polymorphisms in genes regulating selective autophagy have been linked to aging and age-associated disorders. The involvement of autophagy perturbations in aging and disease indicates that pharmacological agents balancing autophagic flux may be beneficial, in these contexts. Here, we introduce the modes and mechanisms of selective autophagy, and survey recent experimental evidence of dysfunctional autophagy triggering severe pathology. We further highlight identified pharmacological targets that hold potential for developing therapeutic interventions to alleviate cellular autophagic cargo burden and associated pathologies.
    Keywords:  age-related disease; aggrephagy; aging; mitophagy; neurodegeneration; nucleophagy; pexophagy; rapamycin; selective autophagy
    DOI:  https://doi.org/10.3390/metabo11090588
  5. Ageing Res Rev. 2021 Sep 23. pii: S1568-1637(21)00215-4. [Epub ahead of print] 101468
    Autophagy and the Hallmarks of Aging.
    Susmita Kaushik, Inmaculada Tasset, Esperanza Arias, Olatz Pampliega, Esther Wong, Marta Martinez-Vicente, Ana Maria Cuervo.
      Autophagy, an essential cellular process that mediates degradation of proteins and organelles in lysosomes, has been tightly linked to cellular quality control for its role as part of the proteostasis network. The current interest in identifying the cellular and molecular determinants of aging, has highlighted the important contribution of malfunctioning of autophagy with age to the loss of proteostasis that characterizes all old organisms. However, the diversity of cellular functions of the different types of autophagy and the often reciprocal interactions of autophagy with other determinants of aging, is placing autophagy at the center of the aging process. In this work, we summarize evidence for the contribution of autophagy to health- and lifespan and provide examples of the bidirectional interplay between autophagic pathways and several of the so-called hallmarks of aging. This central role of autophagy in aging, and the dependence on autophagy of many geroprotective interventions, has motivated a search for direct modulators of autophagy that could be used to slow aging and extend healthspan. Here, we review some of those ongoing therapeutic efforts and comment on the potential of targeting autophagy in aging.
    Keywords:  aging; chaperones; lysosomes; organelle turnover; proteolysis; proteostasis
    DOI:  https://doi.org/10.1016/j.arr.2021.101468
  6. Elife. 2021 Sep 30. pii: e66721. [Epub ahead of print]10
    Localization of KRAS downstream target ARL4C to invasive pseudopods accelerates pancreatic cancer cell invasion.
    Akikazu Harada, Shinji Matsumoto, Yoshiaki Yasumizu, Toshiyuki Akama, Hidetoshi Eguchi, Akira Kikuchi.
      Pancreatic cancer has a high mortality rate due to metastasis. Whereas KRAS is mutated in most pancreatic cancer patients, controlling KRAS or its downstream effectors has not been succeeded clinically. ARL4C is a small G protein whose expression is induced by the Wnt and EGF-RAS pathways. In the present study, we found that ARL4C is frequently overexpressed in pancreatic cancer patients and showed that its localization to invasive pseudopods is required for cancer cell invasion. IQGAP1 was identified as a novel interacting protein for ARL4C. ARL4C recruited IQGAP1 and its downstream effector, MMP14, to invasive pseudopods. Specific localization of ARL4C, IQGAP1, and MMP14 was the active site of invasion, which induced degradation of the extracellular matrix. Moreover, subcutaneously injected antisense oligonucleotide against ARL4C into tumor-bearing mice suppressed metastasis of pancreatic cancer. These results suggest that ARL4C-IQGAP1-MMP14 signaling is activated at invasive pseudopods of pancreatic cancer cells.
    Keywords:  cancer biology; cell biology; human
    DOI:  https://doi.org/10.7554/eLife.66721
  7. J Clin Pathol. 2021 Sep 28. pii: jclinpath-2021-207781. [Epub ahead of print]
    Molecular characterisation of pancreatic ductal adenocarcinoma with NTRK fusions and review of the literature.
    Michael J Allen, Amy Zhang, Prashant Bavi, Jaesung C Kim, Gun Ho Jang, Deirdre Kelly, Sheron Perera, Rob E Denroche, Faiyaz Notta, Julie M Wilson, Anna Dodd, Stephanie Ramotar, Shawn Hutchinson, Sandra E Fischer, Robert C Grant, Steven Gallinger, Jennifer J Knox, Grainne M O'Kane.
       AIMS: The majority of pancreatic ductal adenocarcinomas (PDACs) harbour oncogenic mutations in KRAS with variants in TP53, CDKN2A and SMAD4 also prevalent. The presence of oncogenic fusions including NTRK fusions are rare but important to identify. Here we ascertain the prevalence of NTRK fusions and document their genomic characteristics in a large series of PDAC.
    METHODS: Whole genome sequencing and RNAseq were performed on a series of patients with resected or locally advanced/metastatic PDAC collected between 2008 and 2020 at a single institution. A subset of specimens underwent immunohistochemistry (IHC) analysis. Clinical and molecular characterisation and IHC sensitivity and specificity were evaluated.
    RESULTS: 400 patients were included (resected n=167; locally advanced/metastatic n=233). Three patients were identified as harbouring an NTRK fusion, two EML4-NTRK3 (KRAS-WT) and a single novel KANK1-NTRK3 fusion. The latter occurring in the presence of a subclonal KRAS mutation. Typical PDAC drivers were present including mutations in TP53 and CDKN2A. Substitution base signatures and tumour mutational burden were similar to typical PDAC. The prevalence of NTRK fusions was 0.8% (3/400), while in KRAS wild-type tumours, it was 6.25% (2/32). DNA prediction alone documented six false-positive cases. RNA analysis correctly identified the in-frame fusion transcripts. IHC analysis was negative in the KANK1-NTRK3 fusion but positive in a EML4-NTRK3 case, highlighting lower sensitivity of IHC.
    CONCLUSION: NTRK fusions are rare; however, with emerging therapeutic options targeting these fusions, detection is vital. Reflex testing for KRAS mutations and subsequent RNA-based screening could help identify these cases in PDAC.
    Keywords:  genes; molecular; neoplasm; pancreatic neoplasms; pathology
    DOI:  https://doi.org/10.1136/jclinpath-2021-207781
  8. Metabolites. 2021 Sep 15. pii: 627. [Epub ahead of print]11(9):
    Comparative Untargeted Metabolomic Profiling of Induced Mitochondrial Fusion in Pancreatic Cancer.
    Nicholas D Nguyen, Meifang Yu, Vinit Y Reddy, Ariana C Acevedo-Diaz, Enzo C Mesarick, Joseph Abi Jaoude, Min Yuan, John M Asara, Cullen M Taniguchi.
      Mitochondria are dynamic organelles that constantly alter their shape through the recruitment of specialized proteins, like mitofusin-2 (Mfn2) and dynamin-related protein 1 (Drp1). Mfn2 induces the fusion of nearby mitochondria, while Drp1 mediates mitochondrial fission. We previously found that the genetic or pharmacological activation of mitochondrial fusion was tumor suppressive against pancreatic ductal adenocarcinoma (PDAC) in several model systems. The mechanisms of how these different inducers of mitochondrial fusion reduce pancreatic cancer growth are still unknown. Here, we characterized and compared the metabolic reprogramming of these three independent methods of inducing mitochondrial fusion in KPC cells: overexpression of Mfn2, genetic editing of Drp1, or treatment with leflunomide. We identified significantly altered metabolites via robust, orthogonal statistical analyses and found that mitochondrial fusion consistently produces alterations in the metabolism of amino acids. Our unbiased methodology revealed that metabolic perturbations were similar across all these methods of inducing mitochondrial fusion, proposing a common pathway for metabolic targeting with other drugs.
    Keywords:  fission; fusion; leflunomide; metabolomic reprogramming; metabolomics; mitochondrial morphology; mitofusin-2; pancreatic cancer
    DOI:  https://doi.org/10.3390/metabo11090627
  9. Front Pharmacol. 2021 ;12 723798
    Glucose and Amino Acid Metabolic Dependencies Linked to Stemness and Metastasis in Different Aggressive Cancer Types.
    Andrea Chisari, Irene Golán, Sabrina Campisano, Caroline Gélabert, Aristidis Moustakas, Patricia Sancho, Laia Caja.
      Malignant cells are commonly characterised by being capable of invading tissue, growing self-sufficiently and uncontrollably, being insensitive to apoptosis induction and controlling their environment, for example inducing angiogenesis. Amongst them, a subpopulation of cancer cells, called cancer stem cells (CSCs) shows sustained replicative potential, tumor-initiating properties and chemoresistance. These characteristics make CSCs responsible for therapy resistance, tumor relapse and growth in distant organs, causing metastatic dissemination. For these reasons, eliminating CSCs is necessary in order to achieve long-term survival of cancer patients. New insights in cancer metabolism have revealed that cellular metabolism in tumors is highly heterogeneous and that CSCs show specific metabolic traits supporting their unique functionality. Indeed, CSCs adapt differently to the deprivation of specific nutrients that represent potentially targetable vulnerabilities. This review focuses on three of the most aggressive tumor types: pancreatic ductal adenocarcinoma (PDAC), hepatocellular carcinoma (HCC) and glioblastoma (GBM). The aim is to prove whether CSCs from different tumour types share common metabolic requirements and responses to nutrient starvation, by outlining the diverse roles of glucose and amino acids within tumour cells and in the tumour microenvironment, as well as the consequences of their deprivation. Beyond their role in biosynthesis, they serve as energy sources and help maintain redox balance. In addition, glucose and amino acid derivatives contribute to immune responses linked to tumourigenesis and metastasis. Furthermore, potential metabolic liabilities are identified and discussed as targets for therapeutic intervention.
    Keywords:  GBM-glioblastoma multiforme; HCC-hepatocellular carcinoma; PDAC-pancreatic ductal adenocarcinoma; amino acid; cancer stem cell (CSC); glucose; therapy
    DOI:  https://doi.org/10.3389/fphar.2021.723798
  10. Cell Mol Gastroenterol Hepatol. 2021 Sep 22. pii: S2352-345X(21)00196-X. [Epub ahead of print]
    Trypsin-mediated sensitization to ferroptosis increases the severity of pancreatitis in mice.
    Ke Liu, Jiao Liu, Borong Zou, Changfeng Li, Herbert J Zeh, Rui Kang, Guido Kroemer, Jun Huang, Daolin Tang.
       BACKGROUND & AIMS: Pancreatitis is characterized by acinar cell death and persistent inflammation. Ferroptosis is a type of lipid peroxidation-dependent necrosis, which is negatively regulated by GPX4. We studied how trypsin, a serine protease secreted by pancreatic acinar cells, affects the contribution of ferroptosis to triggering pancreatitis.
    METHODS: In vitro, the mouse pancreatic acinar cell line 266-6 and mouse primary pancreatic acinar cells (mPACs) were used to investigate the effect of exogenous trypsin on ferroptosis sensitivity. Short hairpin RNAs were designed to silence gene expression, whereas a library of 1080 approved drugs was used to identify new ferroptosis inhibitors in 266-6 cells. In vivo, a Cre/LoxP system was utilized to generate mice with a pancreas-specific knockout of Gpx4 (Pdx1-Cre;Gpx4flox/flox mice). Acute or chronic pancreatitis was induced in these mice (Gpx4flox/flox mice served as controls) by cerulein injections or a Lieber-DeCarli alcoholic liquid diet. Pancreatic tissues, acinar cells, and serum were collected and analyzed by histology, immunoblot, qPCR, ELISA, or immunohistochemical analyses.
    RESULTS: Supraphysiological doses of trypsin (500 or 1000 ng/ml) alone did not trigger significant cell death in 266-6 cells and mPACs, but did increase the sensitivity of these cells to ferroptosis upon treatment with cerulein, L-arginine, alcohol, erastin, or RSL3. PSMD4-dependent lipid peroxidation caused ferroptosis in pancreatic acinar cells by promoting the proteasomal degradation of GPX4. The drug screening campaign identified the antipsychotic drug olanzapine as an antioxidant inhibiting ferroptosis in pancreatic acinar cells. Mice lacking pancreatic Gpx4 developed more severe pancreatitis after cerulein infection or ethanol feeding than control mice. Conversely, olanzapine administration protected against pancreatic ferroptotic damage and experimental pancreatitis in Gpx4-deficient mice.
    CONCLUSIONS: Trypsin-mediated sensititization to ferroptotic damage increases the severity of pancreatitis in mice, and this process can be reversed by olanzapine.
    Keywords:  Acinar cells; animal model; cell death; digestive enzyme; sterile inflammation
    DOI:  https://doi.org/10.1016/j.jcmgh.2021.09.008
  11. Cell Mol Gastroenterol Hepatol. 2021 Sep 25. pii: S2352-345X(21)00204-6. [Epub ahead of print]
    KDM6A Regulates Cell Plasticity and Pancreatic Cancer Progression by Non-Canonical Activin Pathway.
    Zhujun Yi, Shanqiao Wei, Lin Jin, Sivakumar Jeyarajan, Jing Yang, Yumei Gu, Hong Sun Kim, Shula Schechter, Shuang Lu, Michelle T Paulsen, Karan Bedi, Ishwarya Venkata Narayanan, Mats Ljungman, Howard C Crawford, Marina Pasca di Magliano, Kai Ge, Yali Dou, Jiaqi Shi.
       BACKGROUND & AIMS: Inactivating mutations of KDM6A, a histone demethylase, were frequently found in pancreatic ductal adenocarcinoma (PDAC). We investigated the role of KDM6A in PDAC development.
    METHODS: We performed a pancreatic tissue microarray analysis of KDM6A protein levels. We used human PDAC cell lines for KDM6A knockout and knockdown experiments. We performed Bru-seq analysis to elucidate the effects of KDM6A loss on global transcription. We performed studies with Ptf1aCre; LSL-KrasG12D; Trp53R172H/+; Kdm6afl/fl or fl/Y, Ptf1aCre; Kdm6afl/fl or fl/Y, and orthotopic xenograft mice to investigate the impacts of Kdm6a deficiency on pancreatic tumorigenesis and pancreatitis.
    RESULTS: Loss of KDM6A was associated with metastasis in PDAC patients. Bru-seq analysis revealed upregulation of the epithelial-mesenchymal transition pathway in PDAC cells deficient of KDM6A. Loss of KDM6A promoted mesenchymal morphology, migration, and invasion in PDAC cells in vitro. Mechanistically, activin A and subsequent p38 activation likely mediated the role of KDM6A loss. Inhibiting either activin A or p38 reversed the effect. Pancreas-specific Kdm6a-knockout mice pancreata demonstrated accelerated PDAC progression, developed a more aggressive undifferentiated type PDAC, and increased metastases in the background of Kras and p53 mutations. Kdm6a-deficient pancreata in a pancreatitis model had a delayed recovery with increased PDAC precursor lesions compared to wild-type pancreata.
    CONCLUSIONS: Loss of KDM6A accelerates PDAC progression and metastasis, most likely by a non-canonical p38-dependant activin A pathway. KDM6A also promotes pancreatic tissue recovery from pancreatitis. Activin A might be utilized as a therapeutic target for KDM6A-deficient PDACs.
    Keywords:  activin A; cancer cell plasticity; epigenetics; metastasis
    DOI:  https://doi.org/10.1016/j.jcmgh.2021.09.014
  12. Cell Death Discov. 2021 Oct 01. 7(1): 269
    NUPR1 inhibitor ZZW-115 induces ferroptosis in a mitochondria-dependent manner.
    Can Huang, Patricia Santofimia-Castaño, Xi Liu, Yi Xia, Ling Peng, Célia Gotorbe, Jose Luis Neira, Daolin Tang, Jacques Pouyssegur, Juan Iovanna.
      Ferroptosis is an iron-dependent cell death characterized by the accumulation of hydroperoxided phospholipids. Here, we report that the NUPR1 inhibitor ZZW-115 induces ROS accumulation followed by a ferroptotic cell death, which could be prevented by ferrostatin-1 (Fer-1) and ROS-scavenging agents. The ferroptotic activity can be improved by inhibiting antioxidant factors in pancreatic ductal adenocarcinoma (PDAC)- and hepatocellular carcinoma (HCC)-derived cells. In addition, ZZW-115-treatment increases the accumulation of hydroperoxided lipids in these cells. We also found that a loss of activity and strong deregulation of key enzymes involved in the GSH- and GPX-dependent antioxidant systems upon ZZW-115 treatment. These results have been validated in xenografts induced with PDAC- and HCC-derived cells in nude mice during the treatment with ZZW-115. More importantly, we demonstrate that ZZW-115-induced mitochondrial morphological changes, compatible with the ferroptotic process, as well as mitochondrial network disorganization and strong mitochondrial metabolic dysfunction, which are rescued by both Fer-1 and N-acetylcysteine (NAC). Of note, the expression of TFAM, a key regulator of mitochondrial biogenesis, is downregulated by ZZW-115. Forced expression of TFAM is able to rescue morphological and functional mitochondrial alterations, ROS production, and cell death induced by ZZW-115 or genetic inhibition of NUPR1. Altogether, these results demonstrate that the mitochondrial cell death mediated by NUPR1 inhibitor ZZW-115 is fully rescued by Fer-1 but also via TFAM complementation. In conclusion, TFAM could be considered as an antagonist of the ferroptotic cell death.
    DOI:  https://doi.org/10.1038/s41420-021-00662-2
  13. PLoS One. 2021 ;16(9): e0250539
    Renalase is a novel tissue and serological biomarker in pancreatic ductal adenocarcinoma.
    Yasheen Gao, Melinda Wang, Xiaojia Guo, Joanna Hu, Tian-Min Chen, Sade M B Finn, Jill Lacy, John W Kunstman, Charles H Cha, Melena D Bellin, Marie E Robert, Gary V Desir, Fred S Gorelick.
      Dysregulated expression of the secretory protein renalase can promote pancreatic ductal adenocarcinoma (PDAC) growth in animal models. We characterized renalase expression in premalignant and malignant PDAC tissue and investigated whether plasma renalase levels corresponded to clinical PDAC characteristics. Renalase immunohistochemistry was used to determine the presence and distribution of renalase in normal pancreas, chronic pancreatitis, PDAC precursor lesions, and PDAC tissues. Associations between pretreatment plasma renalase and PDAC clinical status were assessed in patients with varied clinical stages of PDAC and included tumor characteristics, surgical resection in locally advanced/borderline resectable PDAC, and overall survival. Data were retrospectively obtained and correlated using non-parametric analysis. Little to no renalase was detected by histochemistry in the normal pancreatic head in the absence of abdominal trauma. In chronic pancreatitis, renalase immunoreactivity localized to peri-acinar spindle-shaped cells in some samples. It was also widely present in PDAC precursor lesions and PDAC tissue. Among 240 patients with PDAC, elevated plasma renalase levels were associated with worse tumor characteristics, including greater angiolymphatic invasion (80.0% vs. 58.1%, p = 0.012) and greater node positive disease (76.5% vs. 56.5%, p = 0.024). Overall survival was worse in patients with high plasma renalase levels with median follow-up of 27.70 months vs. 65.03 months (p < 0.001). Renalase levels also predicted whether patients with locally advanced/borderline resectable PDAC underwent resection (AUC 0.674; 95%CI 0.42-0.82, p = 0.04). Overall tissue renalase was increased in both premalignant and malignant PDAC tissues compared to normal pancreas. Elevated plasma renalase levels were associated with advanced tumor characteristics, decreased overall survival, and reduced resectability in patients with locally advanced/borderline resectable PDAC. These studies show that renalase levels are increased in premalignant pancreatic tissues and that its levels in plasma correspond to the clinical behavior of PDAC.
    DOI:  https://doi.org/10.1371/journal.pone.0250539
  14. Cancers (Basel). 2021 Sep 10. pii: 4541. [Epub ahead of print]13(18):
    Deletion of NEMO Inhibits EMT and Reduces Metastasis in KPC Mice.
    Miltiadis Tsesmelis, Kanishka Tiwary, Katja Steiger, Nadine Sperb, Melanie Gerstenlauer, Uta Manfras, Harald J Maier, Patrick C Hermann, Lap Kwan Chan, Thomas Wirth.
      Pancreatic ductal adenocarcinoma (PDAC) remains a largely incurable cancer type. Its high mortality is attributed to the lack of efficient biomarkers for early detection combined with its high metastatic properties. The aim of our study was to investigate the role of NF-κB signaling in the development and metastasis of PDAC. We used the well-established KPC mouse model, and, through genetic manipulation, we deleted NF-κB essential modulator (NEMO) in the pancreata of KPC mice. Interestingly, NEMO deletion altered the differentiation status of the primary tumor but did not significantly affect its development. However, in the absence of NEMO, the median survival of the mice was prolonged by 13.5 days (16%). In addition, examination of the liver demonstrated that, whereas KPC mice occasionally developed liver macro-metastasis, NEMO deletion completely abrogated this outcome. Further analysis of the tumor revealed that the expression of epithelial-mesenchymal transition (EMT) transcription factors was diminished in the absence of NEMO. Conclusively, our study provides evidence that NF-κB is dispensable for the progression of high-grade PanINs towards PDAC. In contrast, NF-κB signaling is essential for the development of metastasis by regulating the gene expression program of EMT.
    Keywords:  EMT; KPC; NEMO; NF-κB; PDAC; metastasis; pancreatic cancer
    DOI:  https://doi.org/10.3390/cancers13184541
  15. Autophagy. 2021 Sep 29. 1-24
    The multifaceted regulation of mitophagy by endogenous metabolites.
    Ting Zhang, Qian Liu, Weihua Gao, Sheikh Arslan Sehgal, Hao Wu.
      Owing to the dominant functions of mitochondria in multiple cellular metabolisms and distinct types of regulated cell death, maintaining a functional mitochondrial network is fundamental for the cellular homeostasis and body fitness in response to physiological adaptations and stressed conditions. The process of mitophagy, in which the dysfunctional or superfluous mitochondria are selectively engulfed by autophagosome and subsequently degraded in lysosome, has been well formulated as one of the major mechanisms for mitochondrial quality control. To date, the PINK1-PRKN-dependent and receptors (including proteins and lipids)-dependent pathways have been characterized to determine the mitophagy in mammalian cells. The mitophagy is highly responsive to the dynamics of endogenous metabolites, including iron-, calcium-, glycolysis-TCA-, NAD+-, amino acids-, fatty acids-, and cAMP-associated metabolites. Herein, we summarize the recent advances toward the molecular details of mitophagy regulation in mammalian cells. We also highlight the key regulations of mammalian mitophagy by endogenous metabolites, shed new light on the bidirectional interplay between mitophagy and cellular metabolisms, with attempting to provide a perspective insight into the nutritional intervention of metabolic disorders with mitophagy deficit.Abbreviations: acetyl-CoA: acetyl-coenzyme A; ACO1: aconitase 1; ADCYs: adenylate cyclases; AMPK: AMP-activated protein kinase; ATM: ATM serine/threonine kinase; BCL2L1: BCL2 like 1; BCL2L13: BCL2 like 13; BNIP3: BCL2 interacting protein 3; BNIP3L: BCL2 interacting protein 3 like; Ca2+: calcium ion; CALCOCO2: calcium binding and coiled-coil domain 2; CANX: calnexin; CO: carbon monoxide; CYCS: cytochrome c, somatic; DFP: deferiprone; DNM1L: dynamin 1 like; ER: endoplasmic reticulum; FKBP8: FKBP prolyl isomerase 8; FOXO3: forkhead box O3; FTMT: ferritin mitochondrial; FUNDC1: FUN14 domain containing 1; GABA: γ-aminobutyric acid; GSH: glutathione; HIF1A: hypoxia inducible factor 1 subunit alpha; IMMT: inner membrane mitochondrial protein; IRP1: iron regulatory protein 1; ISC: iron-sulfur cluster; ITPR2: inositol 1,4,5-trisphosphate type 2 receptor; KMO: kynurenine 3-monooxygenase; LIR: LC3 interacting region; MAM: mitochondria-associated membrane; MAP1LC3: microtubule associated protein 1 light chain 3; MFNs: mitofusins; mitophagy: mitochondrial autophagy; mPTP: mitochondrial permeability transition pore; MTOR: mechanistic target of rapamycin kinase; NAD+: nicotinamide adenine dinucleotide; NAM: nicotinamide; NMN: nicotinamide mononucleotide; NO: nitric oxide; NPA: Niemann-Pick type A; NR: nicotinamide riboside; NR4A1: nuclear receptor subfamily 4 group A member 1; NRF1: nuclear respiratory factor 1; OPA1: OPA1 mitochondrial dynamin like GTPase; OPTN: optineurin; PARL: presenilin associated rhomboid like; PARPs: poly(ADP-ribose) polymerases; PC: phosphatidylcholine; PHB2: prohibitin 2; PINK1: PTEN induced kinase 1; PPARG: peroxisome proliferator activated receptor gamma; PPARGC1A: PPARG coactivator 1 alpha; PRKA: protein kinase AMP-activated; PRKDC: protein kinase, DNA-activated, catalytic subunit; PRKN: parkin RBR E3 ubiquitin protein ligase; RHOT: ras homolog family member T; ROS: reactive oxygen species; SIRTs: sirtuins; STK11: serine/threonine kinase 11; TCA: tricarboxylic acid; TP53: tumor protein p53; ULK1: unc-51 like autophagy activating kinase 1; VDAC1: voltage dependent anion channel 1.
    Keywords:  Cell metabolism; metabolite; mitochondria; mitophagy; mitophagy receptor
    DOI:  https://doi.org/10.1080/15548627.2021.1975914
  16. Nat Commun. 2021 Sep 28. 12(1): 5680
    Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice.
    Bashar Hamza, Alex B Miller, Lara Meier, Max Stockslager, Sheng Rong Ng, Emily M King, Lin Lin, Kelsey L DeGouveia, Nolawit Mulugeta, Nicholas L Calistri, Haley Strouf, Christina Bray, Felicia Rodriguez, William A Freed-Pastor, Christopher R Chin, Grissel C Jaramillo, Megan L Burger, Robert A Weinberg, Alex K Shalek, Tyler Jacks, Scott R Manalis.
      Existing preclinical methods for acquiring dissemination kinetics of rare circulating tumor cells (CTCs) en route to forming metastases have not been capable of providing a direct measure of CTC intravasation rate and subsequent half-life in the circulation. Here, we demonstrate an approach for measuring endogenous CTC kinetics by continuously exchanging CTC-containing blood over several hours between un-anesthetized, tumor-bearing mice and healthy, tumor-free counterparts. By tracking CTC transfer rates, we extrapolated half-life times in the circulation of between 40 and 260 s and intravasation rates between 60 and 107,000 CTCs/hour in mouse models of small-cell lung cancer (SCLC), pancreatic ductal adenocarcinoma (PDAC), and non-small cell lung cancer (NSCLC). Additionally, direct transfer of only 1-2% of daily-shed CTCs using our blood-exchange technique from late-stage, SCLC-bearing mice generated macrometastases in healthy recipient mice. We envision that our technique will help further elucidate the role of CTCs and the rate-limiting steps in metastasis.
    DOI:  https://doi.org/10.1038/s41467-021-25917-5
  17. Int J Mol Sci. 2021 Sep 07. pii: 9692. [Epub ahead of print]22(18):
    Mitochondrial DNA and MitomiR Variations in Pancreatic Cancer: Potential Diagnostic and Prognostic Biomarkers.
    Loredana Moro.
      Pancreatic cancer is an aggressive disease with poor prognosis. Only about 15-20% of patients diagnosed with pancreatic cancer can undergo surgical resection, while the remaining 80% are diagnosed with locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC). In these cases, chemotherapy and radiotherapy only confer marginal survival benefit. Recent progress has been made in understanding the pathobiology of pancreatic cancer, with a particular effort in discovering new diagnostic and prognostic biomarkers, novel therapeutic targets, and biomarkers that can predict response to chemo- and/or radiotherapy. Mitochondria have become a focus in pancreatic cancer research due to their roles as powerhouses of the cell, important subcellular biosynthetic factories, and crucial determinants of cell survival and response to chemotherapy. Changes in the mitochondrial genome (mtDNA) have been implicated in chemoresistance and metastatic progression in some cancer types. There is also growing evidence that changes in microRNAs that regulate the expression of mtDNA-encoded mitochondrial proteins (mitomiRs) or nuclear-encoded mitochondrial proteins (mitochondria-related miRs) could serve as diagnostic and prognostic cancer biomarkers. This review discusses the current knowledge on the clinical significance of changes of mtDNA, mitomiRs, and mitochondria-related miRs in pancreatic cancer and their potential role as predictors of cancer risk, as diagnostic and prognostic biomarkers, and as molecular targets for personalized cancer therapy.
    Keywords:  mitochondrial genome; mitochondrial microRNAs; pancreatic cancer
    DOI:  https://doi.org/10.3390/ijms22189692
  18. Cancer Res. 2021 Oct 01. 81(19): 4896-4898
    Cancer Signaling Drives Cancer Metabolism: AKT and the Warburg Effect.
    Aaron M Hosios, Brendan D Manning.
      The Warburg effect, the propensity of some cells to metabolize glucose to lactate in the presence of oxygen (also known as aerobic glycolysis), has long been observed in cancer and other contexts of cell proliferation, but only in the past two decades have significant gains been made in understanding how and why this metabolic transformation occurs. In 2004, Cancer Research published a study by Elstrom and colleagues that provided one of the first connections between a specific oncogene and aerobic glycolysis. Studying hematopoietic and glioblastoma cell lines, they demonstrated that constitutive activation of AKT promotes an increased glycolytic rate without altering proliferation or oxygen consumption in culture. They proposed that it is this effect that allows constitutive AKT activation to transform cells and found that it sensitizes cells to glucose deprivation. In the years since, mechanistic understanding of oncogenic control of metabolism, and glycolysis specifically, has deepened substantially. Current work seeks to understand the benefits and liabilities associated with glycolytic metabolism and to identify inhibitors that might be of clinical benefit to target glycolytic cancer cells.See related article by Elstrom and colleagues, Cancer Res 2004;64:3892-9.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-2647
  19. Nat Rev Gastroenterol Hepatol. 2021 Sep 29.
    TERT-expressing acinar cells implicated in early pancreatic tumour formation.
    Katrina Ray.
      
    DOI:  https://doi.org/10.1038/s41575-021-00533-2
  20. Proc Natl Acad Sci U S A. 2021 Oct 05. pii: e2110387118. [Epub ahead of print]118(40):
    A genetic model of methionine restriction extends Drosophila health- and lifespan.
    Andrey A Parkhitko, Lin Wang, Elizabeth Filine, Patrick Jouandin, Dmitry Leshchiner, Richard Binari, John M Asara, Joshua D Rabinowitz, Norbert Perrimon.
      Loss of metabolic homeostasis is a hallmark of aging and is characterized by dramatic metabolic reprogramming. To analyze how the fate of labeled methionine is altered during aging, we applied 13C5-Methionine labeling to Drosophila and demonstrated significant changes in the activity of different branches of the methionine metabolism as flies age. We further tested whether targeted degradation of methionine metabolism components would "reset" methionine metabolism flux and extend the fly lifespan. Specifically, we created transgenic flies with inducible expression of Methioninase, a bacterial enzyme capable of degrading methionine and revealed methionine requirements for normal maintenance of lifespan. We also demonstrated that microbiota-derived methionine is an alternative and important source in addition to food-derived methionine. In this genetic model of methionine restriction (MetR), we also demonstrate that either whole-body or tissue-specific Methioninase expression can dramatically extend Drosophila health- and lifespan and exerts physiological effects associated with MetR. Interestingly, while previous dietary MetR extended lifespan in flies only in low amino acid conditions, MetR from Methioninase expression extends lifespan independently of amino acid levels in the food. Finally, because impairment of the methionine metabolism has been previously associated with the development of Alzheimer's disease, we compared methionine metabolism reprogramming between aging flies and a Drosophila model relevant to Alzheimer's disease, and found that overexpression of human Tau caused methionine metabolism flux reprogramming similar to the changes found in aged flies. Altogether, our study highlights Methioninase as a potential agent for health- and lifespan extension.
    Keywords:  13C-Methionine labeling; Alzheimer’s disease; Methioninase; aging; methionine restriction
    DOI:  https://doi.org/10.1073/pnas.2110387118
  21. Drug Discov Today. 2021 Sep 27. pii: S1359-6446(21)00405-0. [Epub ahead of print]
    Sequestsome-1/p62-targeted small molecules for pancreatic cancer therapy.
    Jacob Cuyler, Pranav Murthy, Neal G Spada, Terry McGuire, Michael T Lotze, Xiang-Qun Xie.
      Pancreatic ductal adenocarcinoma (PDAC) is characterized by heightened autophagy and systemic immune dysfunction. Modest improvements in clinical outcomes have been demonstrated in completed clinical trials targeting autophagy with combination hydroxychloroquine (HCQ) and chemotherapy. Recent mechanistic insights into the role of autophagy-dependent immune evasion have prompted the need for more precise and druggable targets of autophagy inhibition. Sequestosome-1 (SQSTM-1) is a multidomain scaffold protein with well-established roles in autophagy, tumor necrosis factor alpha (TNFα)- and NF-κB-related signaling pathways. SQSTM1 overexpression is frequently observed in PDAC, correlating with clinical stage and outcome. Given the unique molecular structure of SQSTM-1 and its diverse activity, identifying means of limiting SQSTM-1-dependent autophagy to promote an effective immune response in PDAC could be a promising treatment strategy.
    Keywords:  Sequestome-1; autophagy; drug discovery; hydroxychloroquine; p62; pancreatic cancer
    DOI:  https://doi.org/10.1016/j.drudis.2021.09.011
  22. STAR Protoc. 2021 Dec 17. 2(4): 100843
    Unveiling the K+-sensitivity of cell metabolism using genetically encoded, FRET-based K+, glucose, and ATP biosensors.
    Helmut Bischof, Sandra Burgstaller, Wolfgang F Graier, Robert Lukowski, Roland Malli.
      Investigating dynamic changes of mitochondrial ATP and cytosolic glucose levels of single living cells over time by genetically encoded biosensors provides an informative readout of their metabolic activities. Here, we describe how to monitor the metabolic K+-sensitivity of HEK293 cells exploiting ATP-, glucose-, and K+ probes. Fluorescence live-cell imaging of these Förster resonance energy transfer-based biosensors over time in response to gramicidin, an ionophoric peptide, indicated an absolute dependency of cellular ATP homeostasis on high intracellular K+ levels. For complete information on the generation and use of this protocol please refer to Bischof et al. (2021).
    Keywords:  Cancer; Cell Biology; Cell culture; Chemistry; Metabolism; Microscopy; Molecular Biology; Molecular/Chemical Probes
    DOI:  https://doi.org/10.1016/j.xpro.2021.100843
  23. Science. 2021 Oct;374(6563): eabf3067
    Interpretation of cancer mutations using a multiscale map of protein systems.
    Fan Zheng, Marcus R Kelly, Dana J Ramms, Marissa L Heintschel, Kai Tao, Beril Tutuncuoglu, John J Lee, Keiichiro Ono, Helene Foussard, Michael Chen, Kari A Herrington, Erica Silva, Sophie N Liu, Jing Chen, Christopher Churas, Nicholas Wilson, Anton Kratz, Rudolf T Pillich, Devin N Patel, Jisoo Park, Brent Kuenzi, Michael K Yu, Katherine Licon, Dexter Pratt, Jason F Kreisberg, Minkyu Kim, Danielle L Swaney, Xiaolin Nan, Stephanie I Fraley, J Silvio Gutkind, Nevan J Krogan, Trey Ideker.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/science.abf3067
  24. Gerontol Geriatr Med. 2021 Jan-Dec;7:7 23337214211046419
    Predictors of Biological Age: The Implications for Wellness and Aging Research.
    Trevor Lohman, Gurinder Bains, Lee Berk, Everett Lohman.
      As healthspan and lifespan research breakthroughs have become more commonplace, the need for valid, practical markers of biological age is becoming increasingly paramount. The accessibility and affordability of biological age predictors that can reveal information about mortality and morbidity risk, as well as remaining years of life, has profound clinical and research implications. In this review, we examine 5 groups of aging biomarkers capable of providing accurate biological age estimations. The unique capabilities of these biomarkers have far reaching implications for the testing of both pharmaceutical and non-pharmaceutical interventions designed to slow or reverse biological aging. Additionally, the enhanced validity and availability of these tools may have increasingly relevant clinical value. The authors of this review explore those implications, with an emphasis on lifestyle modification research, and provide an overview of the current evidence regarding 5 biological age predictor categories: Telomere length, composite biomarkers, DNA methylation "epigenetic clocks," transcriptional predictors of biological age, and functional age predictors.
    Keywords:  aging; biogerontology; cardiovascular diseases and risk; cellular processes; chronic diseases; frailty; genetics
    DOI:  https://doi.org/10.1177/23337214211046419
  25. J Cachexia Sarcopenia Muscle. 2021 Sep 29.
    Geriatric Nutrition Risk Index: Prognostic factor related to inflammation in elderly patients with cancer cachexia.
    Guo-Tian Ruan, Qi Zhang, Xi Zhang, Meng Tang, Meng-Meng Song, Xiao-Wei Zhang, Xiang-Rui Li, Kang-Ping Zhang, Yi-Zhong Ge, Ming Yang, Qin-Qin Li, Yong-Bing Chen, Kai-Ying Yu, Ming-Hua Cong, Wei Li, Kun-Hua Wang, Han-Ping Shi.
       BACKGROUND: Systemic inflammation and cachexia are associated with adverse clinical outcomes in elderly patients with cancer. The Geriatric Nutritional Risk Index (GNRI) is a simple and useful tool to assess these conditions, but its predictive ability for elderly patients with cancer cachexia (EPCC) is unknown.
    METHODS: This multicentre cohort study included 746 EPCC with an average age of 72.00 ± 5.24 years, of whom 489 (65.5%) were male. The patients were divided into two groups (high GNRI group ≥91.959 vs. low GNRI group <91.959) according to the optimal cut-off value of the ROC curve. The calibration curves were performed to analyse the prognostic, predictive ability of GNRI. Comprehensive survival analyses were utilized to explore the relationship between GNRI and the overall survival (OS) of EPCC. Interaction analysis was used to investigate the comprehensive effects of low GNRI and subgroup parameters on the OS of EPCC.
    RESULTS: In this study, a total of 2560 patients were diagnosed with cancer cachexia, including 746 cases of EPCC. During the 3.6 year median follow-up, we observed 403 deaths. The overall mortality rate for EPCC at 12 months was 34.3% (95% CI: 62.3% to 69.2%), and resulting in rate of 278 events per 1000 patient-years. The GNRI score of EPCC was significantly lower than those of young patients with cancer cachexia (P < 0.001). The 1, 3, and 5 year calibration curves showed that the GNRI score had good survival prediction in the OS of EPCC. The GNRI could predict the OS of EPCC, whether as a continuous variable or a categorical variable. Particularly, we also found that low GNRI score (<91.959) of EPCC had a worse prognosis than those with a high GNRI score (≥91.959, P = 0.001, HR = 1.728, 95% CI: 1.244-2.401). Consistent results were observed in the tumour subgroups of gastric cancer and colorectal cancer. Notably, similar results were observed in the sensitivity analysis. In the subgroup analysis, the low GNRI has a combined effect with age (<70 years) on poor OS of EPCC. The results of the prognostic risk model found that the lower the GNRI score, the greater the prognostic risk score, and the greater the risk of death in EPCC.
    CONCLUSIONS: For the first time, this study found that the GNRI score can serve as an independent prognostic factor for the OS of EPCC.
    Keywords:  Cancer cachexia; Elderly; GNRI; Overall survival; Systemic inflammation
    DOI:  https://doi.org/10.1002/jcsm.12800
  26. Signal Transduct Target Ther. 2021 Sep 27. 6(1): 348
    An anti-tumor coup: TIM3 ablation activates the immune arsenal.
    Kıvanç Görgülü, Derya Kabacaoğlu, Hana Algül.
      
    DOI:  https://doi.org/10.1038/s41392-021-00757-3
  27. Sci Adv. 2021 Oct;7(40): eabh0363
    Intravital imaging technology guides FAK-mediated priming in pancreatic cancer precision medicine according to Merlin status.
    Australian Pancreatic Genome Initiative (APGI)
      [Figure: see text].
    DOI:  https://doi.org/10.1126/sciadv.abh0363
  28. Cell. 2021 Sep 28. pii: S0092-8674(21)01061-8. [Epub ahead of print]
    Atlas of clinically distinct cell states and ecosystems across human solid tumors.
    Bogdan A Luca, Chloé B Steen, Magdalena Matusiak, Armon Azizi, Sushama Varma, Chunfang Zhu, Joanna Przybyl, Almudena Espín-Pérez, Maximilian Diehn, Ash A Alizadeh, Matt van de Rijn, Andrew J Gentles, Aaron M Newman.
      Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understanding processes as diverse as development, aging, and cancer. Here we introduce EcoTyper, a machine learning framework for large-scale identification and validation of cell states and multicellular communities from bulk, single-cell, and spatially resolved gene expression data. When applied to 12 major cell lineages across 16 types of human carcinoma, EcoTyper identified 69 transcriptionally defined cell states. Most states were specific to neoplastic tissue, ubiquitous across tumor types, and significantly prognostic. By analyzing cell-state co-occurrence patterns, we discovered ten clinically distinct multicellular communities with unexpectedly strong conservation, including three with myeloid and stromal elements linked to adverse survival, one enriched in normal tissue, and two associated with early cancer development. This study elucidates fundamental units of cellular organization in human carcinoma and provides a framework for large-scale profiling of cellular ecosystems in any tissue.
    Keywords:  CIBERSORTx; EcoTyper; cancer genomics; cell states; cellular communities; ecosystems; ecotypes; expression deconvolution; tumor immunology; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.cell.2021.09.014
  29. Cancer Metastasis Rev. 2021 Sep 30.
    The tumor microenvironment in pancreatic ductal adenocarcinoma: current perspectives and future directions.
    Cameron J Herting, Isaac Karpovsky, Gregory B Lesinski.
      Pancreatic ductal adenocarcinoma (PDAC) is among the most lethal malignancies and is characterized by a unique tumor microenvironment (TME) consisting of an abundant stromal component. Many features contained with the PDAC stroma contribute to resistance to cytotoxic and immunotherapeutic regimens, as well as the propensity for this tumor to metastasize. At the cellular level, PDAC cells crosstalk with a complex mixture of non-neoplastic cell types including fibroblasts, endothelial cells, and immune cells. These intricate interactions fuel the progression and therapeutic resistance of this aggressive cancer. Moreover, data suggest the polarization of these cell types, in particular immune and fibroblast populations, dictate how PDAC tumors grow, metastasize, and respond to therapy. As a result, current research is focused on how to best target these populations to render tumors responsive to treatment. Herein, we summarize the cell populations implicated in providing a supporting role for the development and progression of PDAC. We focus on stromal fibroblasts and immune subsets that have been widely researched. We discuss factors which govern the phenotype of these populations and provide insight on how they have been targeted therapeutically. This review provides an overview of the tumor microenvironment and postulates that cellular and soluble factors within the microenvironment can be specifically targeted to improve patient outcomes.
    Keywords:  Cancer-associated fibroblasts; Pancreatic cancer; Tumor microenvironment immunotherapy
    DOI:  https://doi.org/10.1007/s10555-021-09988-w
  30. Cells. 2021 Aug 24. pii: 2177. [Epub ahead of print]10(9):
    A Universal Approach to Analyzing Transmission Electron Microscopy with ImageJ.
    Jacob Lam, Prasanna Katti, Michelle Biete, Margaret Mungai, Salma AshShareef, Kit Neikirk, Edgar Garza Lopez, Zer Vue, Trace A Christensen, Heather K Beasley, Taylor A Rodman, Sandra A Murray, Jeffrey L Salisbury, Brian Glancy, Jianqiang Shao, Renata O Pereira, E Dale Abel, Antentor Hinton.
      Transmission electron microscopy (TEM) is widely used as an imaging modality to provide high-resolution details of subcellular components within cells and tissues. Mitochondria and endoplasmic reticulum (ER) are organelles of particular interest to those investigating metabolic disorders. A straightforward method for quantifying and characterizing particular aspects of these organelles would be a useful tool. In this protocol, we outline how to accurately assess the morphology of these important subcellular structures using open source software ImageJ, originally developed by the National Institutes of Health (NIH). Specifically, we detail how to obtain mitochondrial length, width, area, and circularity, in addition to assessing cristae morphology and measuring mito/endoplasmic reticulum (ER) interactions. These procedures provide useful tools for quantifying and characterizing key features of sub-cellular morphology, leading to accurate and reproducible measurements and visualizations of mitochondria and ER.
    Keywords:  ImageJ; Mitochondria Endoplasmic Reticulum Contacts (MERCs); TEM analysis; TEM quantification; cristae; image analysis; image processing; mitochondria
    DOI:  https://doi.org/10.3390/cells10092177
  31. Cell. 2021 Sep 21. pii: S0092-8674(21)01049-7. [Epub ahead of print]
    Structural basis and regulation of the reductive stress response.
    Andrew G Manford, Elijah L Mena, Karen Y Shih, Christine L Gee, Rachael McMinimy, Brenda Martínez-González, Rumi Sherriff, Brandon Lew, Madeline Zoltek, Fernando Rodríguez-Pérez, Makda Woldesenbet, John Kuriyan, Michael Rape.
      Although oxidative phosphorylation is best known for producing ATP, it also yields reactive oxygen species (ROS) as invariant byproducts. Depletion of ROS below their physiological levels, a phenomenon known as reductive stress, impedes cellular signaling and has been linked to cancer, diabetes, and cardiomyopathy. Cells alleviate reductive stress by ubiquitylating and degrading the mitochondrial gatekeeper FNIP1, yet it is unknown how the responsible E3 ligase CUL2FEM1B can bind its target based on redox state and how this is adjusted to changing cellular environments. Here, we show that CUL2FEM1B relies on zinc as a molecular glue to selectively recruit reduced FNIP1 during reductive stress. FNIP1 ubiquitylation is gated by pseudosubstrate inhibitors of the BEX family, which prevent premature FNIP1 degradation to protect cells from unwarranted ROS accumulation. FEM1B gain-of-function mutation and BEX deletion elicit similar developmental syndromes, showing that the zinc-dependent reductive stress response must be tightly regulated to maintain cellular and organismal homeostasis.
    Keywords:  BEX2; BEX3; CUL2; FEM1B; mitochondria; oxidative phosphorylation; reactive oxygen species; reductive stress; ubiquitin
    DOI:  https://doi.org/10.1016/j.cell.2021.09.002
  32. Cancers (Basel). 2021 Sep 11. pii: 4561. [Epub ahead of print]13(18):
    Cellular Plasticity: A Route to Senescence Exit and Tumorigenesis.
    Hadrien De Blander, Anne-Pierre Morel, Aruni P Senaratne, Maria Ouzounova, Alain Puisieux.
      Senescence is a dynamic, multistep program that results in permanent cell cycle arrest and is triggered by developmental or environmental, oncogenic or therapy-induced stress signals. Senescence is considered as a tumor suppressor mechanism that prevents the risk of neoplastic transformation by restricting the proliferation of damaged cells. Cells undergoing senescence sustain important morphological changes, chromatin remodeling and metabolic reprogramming, and secrete pro-inflammatory factors termed senescence-associated secretory phenotype (SASP). SASP activation is required for the clearance of senescent cells by innate immunity. Therefore, escape from senescence and the associated immune editing would be a prerequisite for tumor initiation and progression as well as therapeutic resistance. One of the possible mechanisms for overcoming senescence could be the acquisition of cellular plasticity resulting from the accumulation of genomic alterations and genetic and epigenetic reprogramming. The modified composition of the SASP produced by these reprogrammed cancer cells would create a permissive environment, allowing their immune evasion. Additionally, the SASP produced by cancer cells could enhance the cellular plasticity of neighboring cells, thus hindering their recognition by the immune system. Here, we propose a comprehensive review of the literature, highlighting the role of cellular plasticity in the pro-tumoral activity of senescence in normal cells and in the cancer context.
    Keywords:  cellular plasticity; epithelial-mesenchymal transition; immune evasion; reprogramming; senescence
    DOI:  https://doi.org/10.3390/cancers13184561
  33. Mol Cell. 2021 Sep 21. pii: S1097-2765(21)00736-X. [Epub ahead of print]
    Oncogene-dependent sloppiness in mRNA translation.
    Julien Champagne, Abhijeet Pataskar, Naomi Blommaert, Remco Nagel, Demi Wernaart, Sofia Ramalho, Juliana Kenski, Onno B Bleijerveld, Esther A Zaal, Celia R Berkers, Maarten Altelaar, Daniel S Peeper, William J Faller, Reuven Agami.
      mRNA translation is a highly conserved and tightly controlled mechanism for protein synthesis. Despite protein quality control mechanisms, amino acid shortage in melanoma induces aberrant proteins by ribosomal frameshifting. The extent and the underlying mechanisms related to this phenomenon are yet unknown. Here, we show that tryptophan depletion-induced ribosomal frameshifting is a widespread phenomenon in cancer. We termed this event sloppiness and strikingly observed its association with MAPK pathway hyperactivation. Sloppiness is stimulated by RAS activation in primary cells, suppressed by pharmacological inhibition of the oncogenic MAPK pathway in sloppy cells, and restored in cells with acquired resistance to MAPK pathway inhibition. Interestingly, sloppiness causes aberrant peptide presentation at the cell surface, allowing recognition and specific killing of drug-resistant cancer cells by T lymphocytes. Thus, while oncogenes empower cancer progression and aggressiveness, they also expose a vulnerability by provoking the production of aberrant peptides through sloppiness.
    Keywords:  MAPK pathway; T cell killing; T cell recognition; aberrant peptides; acquired drug resistance; antigen presentation; cancer; protein synthesis; ribosomal frameshifting
    DOI:  https://doi.org/10.1016/j.molcel.2021.09.002
  34. Nat Cancer. 2021 Apr;2(4): 429-443
    Distinct CDK6 complexes determine tumor cell response to CDK4/6 inhibitors and degraders.
    Xuewei Wu, Xiaobao Yang, Yan Xiong, Ruitong Li, Takahiro Ito, Tamer A Ahmed, Zoi Karoulia, Christos Adamopoulos, Hong Wang, Li Wang, Ling Xie, Jing Liu, Beatrix Ueberheide, Stuart A Aaronson, Xian Chen, Sean G Buchanan, William R Sellers, Jian Jin, Poulikos I Poulikakos.
      CDK4/6 inhibitors (CDK4/6i) are effective in metastatic breast cancer, but they have been only modestly effective in most other tumor types. Here we show that tumors expressing low CDK6 rely on CDK4 function, and are exquisitely sensitive to CDK4/6i. In contrast, tumor cells expressing both CDK4 and CDK6 have increased reliance on CDK6 to ensure cell cycle progression. We discovered that CDK4/6i and CDK4/6 degraders potently bind and inhibit CDK6 selectively in tumors in which CDK6 is highly thermo-unstable and strongly associated with the HSP90/CDC37 complex. In contrast, CDK4/6i and CDK4/6 degraders are ineffective in antagonizing tumor cells expressing thermostable CDK6, due to their weaker binding to CDK6 in these cells. Thus, we uncover a general mechanism of intrinsic resistance to CDK4/6i and CDK4/6i-derived degraders and the need for novel inhibitors targeting the CDK4/6i-resistant, thermostable form of CDK6 for application as cancer therapeutics.
    DOI:  https://doi.org/10.1038/s43018-021-00174-z
  35. Oncogene. 2021 Sep 28.
    Codon optimality in cancer.
    Sarah L Gillen, Joseph A Waldron, Martin Bushell.
      A key characteristic of cancer cells is their increased proliferative capacity, which requires elevated levels of protein synthesis. The process of protein synthesis involves the translation of codons within the mRNA coding sequence into a string of amino acids to form a polypeptide chain. As most amino acids are encoded by multiple codons, the nucleotide sequence of a coding region can vary dramatically without altering the polypeptide sequence of the encoded protein. Although mutations that do not alter the final amino acid sequence are often thought of as silent/synonymous, these can still have dramatic effects on protein output. Because each codon has a distinct translation elongation rate and can differentially impact mRNA stability, each codon has a different degree of 'optimality' for protein synthesis. Recent data demonstrates that the codon preference of a transcriptome matches the abundance of tRNAs within the cell and that this supply and demand between tRNAs and mRNAs varies between different cell types. The largest observed distinction is between mRNAs encoding proteins associated with proliferation or differentiation. Nevertheless, precisely how codon optimality and tRNA expression levels regulate cell fate decisions and their role in malignancy is not fully understood. This review describes the current mechanistic understanding on codon optimality, its role in malignancy and discusses the potential to target codon optimality therapeutically in the context of cancer.
    DOI:  https://doi.org/10.1038/s41388-021-02022-x
  36. ACS Sens. 2021 Sep 29.
    Live-Cell Probe for In Situ Single-Cell Monitoring of Mitochondrial DNA Methylation.
    Han Zhao, Donghan Ma, Junkai Xie, Oscar Sanchez, Fang Huang, Chongli Yuan.
      Mitochondria, as the center of energy production, play an important role in cell homeostasis by regulating the cellular metabolism and mediating the cellular response to stress. Epigenetic changes such as DNA and histone methylation have been increasingly recognized to play a significant role in homeostasis and stress response. The cross-talking between the metabolome and the epigenome has attracted significant attention in recent years but with a major focus on how metabolism contributes to epigenomic changes. Few studies have focused on how epigenetic modifications may alter the mitochondrial composition and activity. In this work, we designed a novel probe targeting methylated CpGs of mitochondrial DNA (mtDNA). We demonstrated the capability of our probe to reveal the spatial distribution of methylated mtDNA and capture the mtDNA methylation changes at a single-cell level. We were also able to track single-cell mtDNA and nDNA methylation simultaneously and discovered the unsynchronized dynamics of the nucleus and mitochondria. Our tool offers a unique opportunity to understand the epigenetic regulation of mtDNA and its dynamic response to the microenvironment and cellular changes.
    Keywords:  DNA CpG methylation; epigenetics; live-cell probe; mitochondria; super-resolution microscopy
    DOI:  https://doi.org/10.1021/acssensors.1c00731
  37. J Cachexia Sarcopenia Muscle. 2021 Sep 28.
    Bile acid metabolism dysregulation associates with cancer cachexia: roles of liver and gut microbiome.
    Lixing Feng, Wanli Zhang, Qiang Shen, Chunxiao Miao, Lijuan Chen, Yiwei Li, Xiaofan Gu, Meng Fan, Yushui Ma, Hui Wang, Xuan Liu, Xiongwen Zhang.
       BACKGROUND: Cancer cachexia is a multifactorial metabolic syndrome in which bile acid (BA) metabolism might be involved. The aim of the present study was to clarify the contribution of liver and gut microbiota to BA metabolism disturbance in cancer cachexia and to check the possibility of targeting BA metabolism using agents such as tauroursodeoxycholic acid (TUDCA) for cancer cachexia therapy.
    METHODS: The BA profiles in liver, intestine, and serum of mice with cancer cachexia induced by inoculation of colon C26 tumour cells were analysed using metabolomics methods and compared with that of control mice. Proteomic analysis of liver protein expression profile and 16S rRNA gene sequencing analysis of gut microbiota composition in cancer cachexia mice were conducted. Expression levels of genes related to farnesoid X receptor (FXR) signalling pathway in the intestine and liver tissues were analysed using RT-PCR analysis. The BA profiles in serum of clinical colon cancer patients with or without cachexia were also analysed and compared with that of healthy volunteers. The effects of TUDCA in treating cancer cachexia mice were observed.
    RESULTS: In the liver of cancer cachexia mice, expression of BA synthesis enzymes was inhibited while the amount of total BAs increased (P < 0.05). The ratios of conjugated BAs/un-conjugated BAs significantly increased in cancer cachexia mice liver (P < 0.01). Gut microbiota dysbiosis such as decrease in Lachnospiraceae and increase in Enterobacteriaceae was observed in the intestine of cancer cachexia mice, and microbial metabolism of BAs was reduced. Increase in expression of FGF15 in intestine (P < 0.01) suggested the activation of FXR signalling pathway which might contribute to the regulation of BA synthesis enzymes, transporters, and metabolic enzymes. Increase in the BA conjugation was observed in the serum of cancer cachexia mice. Results of clinical patients showed changes in BA metabolism, especially the increase in BA conjugation, and also suggested compensatory mechanism in BA metabolism regulation. Oral administration of 50 mg/kg TUDCA could significantly ameliorate the decrease in body weight (P < 0.001), muscle loss (P < 0.001), and atrophy of heart and liver (P < 0.05) in cancer cachexia mice without influence on tumour growth.
    CONCLUSIONS: Bile acid metabolism dysregulation such as decrease in BA synthesis, increase in BA conjugation, and decrease in BA microbial metabolism was involved in development of cancer cachexia in mice. Targeting BA metabolism using agents such as TUDCA might be helpful for cancer cachexia therapy.
    Keywords:  Bile acids; Cancer cachexia; Gut microbiota; Liver; TUDCA
    DOI:  https://doi.org/10.1002/jcsm.12798
  38. Nat Methods. 2021 Sep 30.
    Systematic investigation of cytokine signaling activity at the tissue and single-cell levels.
    Peng Jiang, Yu Zhang, Beibei Ru, Yuan Yang, Trang Vu, Rohit Paul, Amer Mirza, Grégoire Altan-Bonnet, Lingrui Liu, Eytan Ruppin, Lalage Wakefield, Kai W Wucherpfennig.
      Cytokines are critical for intercellular communication in human health and disease, but the investigation of cytokine signaling activity has remained challenging due to the short half-lives of cytokines and the complexity/redundancy of cytokine functions. To address these challenges, we developed the Cytokine Signaling Analyzer (CytoSig; https://cytosig.ccr.cancer.gov/ ), providing both a database of target genes modulated by cytokines and a predictive model of cytokine signaling cascades from transcriptomic profiles. We collected 20,591 transcriptome profiles for human cytokine, chemokine and growth factor responses. This atlas of transcriptional patterns induced by cytokines enabled the reliable prediction of signaling activities in distinct cell populations in infectious diseases, chronic inflammation and cancer using bulk and single-cell transcriptomic data. CytoSig revealed previously unidentified roles of many cytokines, such as BMP6 as an anti-inflammatory factor, and identified candidate therapeutic targets in human inflammatory diseases, such as CXCL8 for severe coronavirus disease 2019.
    DOI:  https://doi.org/10.1038/s41592-021-01274-5
  39. Mol Cell. 2021 Sep 28. pii: S1097-2765(21)00742-5. [Epub ahead of print]
    The Protexin complex counters resection on stalled forks to promote homologous recombination and crosslink repair.
    Richard O Adeyemi, Nicholas A Willis, Andrew E H Elia, Connor Clairmont, Shibo Li, Xiaohua Wu, Alan D D'Andrea, Ralph Scully, Stephen J Elledge.
      Protection of stalled replication forks is critical to genomic stability. Using genetic and proteomic analyses, we discovered the Protexin complex containing the ssDNA binding protein SCAI and the DNA polymerase REV3. Protexin is required specifically for protecting forks stalled by nucleotide depletion, fork barriers, fragile sites, and DNA inter-strand crosslinks (ICLs), where it promotes homologous recombination and repair. Protexin loss leads to ssDNA accumulation and profound genomic instability in response to ICLs. Protexin interacts with RNA POL2, and both oppose EXO1's resection of DNA on forks remodeled by the FANCM translocase activity. This pathway acts independently of BRCA/RAD51-mediated fork stabilization, and cells with BRCA2 mutations were dependent on SCAI for survival. These data suggest that Protexin and its associated factors establish a new fork protection pathway that counteracts fork resection in part through a REV3 polymerase-dependent resynthesis mechanism of excised DNA, particularly at ICL stalled forks.
    Keywords:  CRISPR; EXO1; FANCM; Protexin; REV3L; SCAI; homologous recombination; inter-strand crosslinks; replication stress; resection
    DOI:  https://doi.org/10.1016/j.molcel.2021.09.008
  40. Clin Cancer Res. 2021 Sep 27. pii: clincanres.1681.2021. [Epub ahead of print]
    Organoids derived from neoadjuvant FOLFIRINOX patients recapitulate therapy resistance in pancreatic ductal adenocarcinoma.
    Elham Aida Farshadi, Jiang Chang, Bharath Sampadi, Michail Doukas, Freek Van 't Land, Fleur van der Sijde, Eveline E Vietsch, Joris Pothof, Bas Groot Koerkamp, Casper H J van Eijck.
       PURPOSE: We investigated whether organoids can be generated from resected tumors of patients who received eight cycles of neoadjuvant FOLFIRINOX chemotherapy before surgery, and evaluated the sensitivity/resistance of these surviving cancer cells to cancer therapy.
    EXPERIMENTAL DESIGN: We generated a library of 10 PDAC organoid lines: five each from treatment-naive and FOLFIRINOX-treated patients. We, first, assessed the histological, genetic, and transcriptional characteristics of the organoids and their matched primary PDAC tissue. Next, the organoids' response to treatment with single agents - 5-FU, irinotecan, and oxaliplatin - of the FOLFIRINOX regimen as well as combined regimen was evaluated. Finally, global mRNA-seq analyses were performed to identify FOLFIRINOX resistance pathways.
    RESULTS: All 10 patient-derived PDAC organoids recapitulate histological, genetic, and transcriptional characteristics of their primary tumor tissue. Neoadjuvant FOLFIRINOXtreated organoids display resistance to FOLFIRINOX (5/5), irinotecan (5/5) and oxaliplatin (4/5) when compared to treatment-naive organoids (FOLFIRINOX: 1/5, irinotecan: 2/5, oxaliplatin: 0/5). 5-FU treatment responses between naive and treated organoids were similar. Comparative global transcriptome analysis of treatment-naive and FOLFIRINOX samples - in both organoids and corresponding matched tumor tissues - uncovered modulated pathways mainly involved in genomic instability, energy metabolism, and innate immune system.
    CONCLUSION: Resistance development in neoadjuvant FOLFIRINOX organoids, recapitulating their primary tumor resistance, suggests continuation of FOLFIRINOX therapy as an adjuvant treatment may not be advantageous for these patients. Gene expression profiles of PDAC organoids identify targetable pathways involved in chemoresistance development upon neoadjuvant FOLFIRINOX treatment, thus opening up combination therapy possibilities.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-21-1681
  41. FASEB J. 2021 Oct;35(10): e21848
    The role of lysosomal membrane proteins in glucose and lipid metabolism.
    Jing Gu, Mengya Geng, Mengxiang Qi, Lizhuo Wang, Yao Zhang, Jialin Gao.
      Lysosomes have long been regarded as the "garbage dump" of the cell. More recently, however, researchers have revealed novel roles for lysosomal membranes in autophagy, ion transport, nutrition sensing, and membrane fusion and repair. With active research into lysosomal membrane proteins (LMP), increasing evidence has become available showing that LMPs are inextricably linked to glucose and lipid metabolism, and this relationship represents mutual influence and regulation. In this review, we summarize the roles of LMPs in relation to glucose and lipid metabolism, and describe their roles in glucose transport, glycolysis, cholesterol transport, and lipophagy. The role of transport proteins can be traced back to the original discoveries of GLUT8, NPC1, and NPC2, which were all found to have significant roles in the pathways involved in glucose and lipid metabolism. CLC-5 and SIDT2-knockout animals show serious phenotypic disorders of metabolism, and V-ATPase and LAMP-2 have been found to interact with proteins related to glucose and lipid metabolism. These findings all emphasize the critical role of LMPs in glycolipid metabolism and help to strengthen our understanding of the independent and close relationship between LMPs and glycolipid metabolism.
    Keywords:  glucose metabolism; lipid metabolism; lysosomal membrane protein
    DOI:  https://doi.org/10.1096/fj.202002602R
  42. Cell. 2021 Aug 27. pii: S0092-8674(21)00949-1. [Epub ahead of print]
    The surprise element: A hallmark of creativity in scientists, artists, and comedians.
    Joseph L Goldstein.
      Truly creative works of science and art produce unexpected and surprising results-just like the punch line of a good joke that generates an unfamiliar twist on a familiar idea. Surprise stimulates curiosity, which triggers a search to reveal the mystery of things unknown.
    DOI:  https://doi.org/10.1016/j.cell.2021.08.007
  43. J Cell Biochem. 2021 Oct;122(10): 1435-1444
    In vivo autophagy quantification: Measuring LC3 and P62 puncta in 3D image system from zebrafish larvae.
    Abdalla Elbialy.
      Autophagy is a central pathway in maintaining cellular homeostasis through the recycling of damaged proteins and organelles. Detection of LC3 protein levels by immunofluorescence or western blot analysis is one of the most common ways to measure autophagy. For quantitative autophagy analysis, LC3 western blot analysis is commonly used, whereas immunostaining is used for qualitative autophagy analysis. However, zebrafish larvae have a lot of proteases that rapidly degrade LC3 protein in samples. P62 is another autophagy marker that bind to damaged proteins and can reflects autophagic status. This study demonstrates a fast and accurate way to quantify autophagy from LC3 and/or P62 immunostaining images. We used a three-dimensional analysis of whole-mount LC3 immunostaining images of zebrafish larvae. Counting LC3 and P62 punctate by two dimensions can be used as a qualitative method for the analysis of autophagy. However, here we demonstrate that 3D image analysis can be used as a quantitative, rapid tool for monitoring autophagy in zebrafish larvae and avoiding drawbacks of LC3 western blot analysis.
    Keywords:  3D image; LC3; P62; autophagy; quantification
    DOI:  https://doi.org/10.1002/jcb.30021
  44. Crit Rev Eukaryot Gene Expr. 2021 ;31(4): 89-100
    A Four Autophagy-Related Gene-Based Prognostic Signature for Pancreatic Cancer.
    Qing Zhou, Xi Chen, Qiuyan Chen, Haosheng Liu, Lu Hao.
      This study aimed to screen autophagy-related genes (ARGs) that affect the prognosis of pancreatic cancer patients based on The Cancer Genome Atlas (TCGA) gene expression data and genotype-tissue expression (GTEx) databases. The expression data of pancreatic cancer and normal pancreas were downloaded from TCGA and GTEx databases. Human ARGs list was obtained through the Human Autophagy Database (HADB) and GeneCards database. The Wilcox test was performed to screen differentially expressed ARGs. Differentially expressed ARGs were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses. The CIBER-SORT algorithm was utilized to analyze immune cell infiltration in samples. A total of 21 up-regulated ARGs and 11 down-regulated ARGs were screened in the TCGA-GTEx integrated data set. The enrichment analysis of GO and KEGG showed that 32 differentially expressed ARGs were significantly enriched in autophagy-related pathways. Univariate Cox regression analysis showed that 12 candidate ARGs were significantly related to the prognosis of pancreatic cancer patients. Multivariate Cox regression analysis found that ATG16L2, GNAI3, APOL1, and PTK6 genes may be the key ARGs affecting the prognosis of pancreatic cancer patients. Based on these four key ARGs, a prognostic risk assessment model was constructed, and pancreatic cancer patients were classified into the high-risk and low-risk group according to the risk value. Survival analysis and ROC analysis confirmed that the prognostic risk assessment model can accurately predict the prognosis of patients with pancreatic cancer. Immune infiltration analysis found that B cells naive, B cells memory, plasma cells, T cells CD8, T cells CD4 memory resting, monocytes and macrophages M0 were significantly different in tissue samples of pancreatic cancer patients in the high and low risk groups. Pearson's correlation coefficient showed that the four key ARGs may affect the development of pancreatic cancer by affecting immune cell components in the tumor micro-environment. In conclusion, ATG16L2, GNAI3, APOL1, and PTK6 may be related to the prognosis of pancreatic cancer patients. The prognostic risk assessment model constructed based on these four key ARGs could accurately predict the prognosis of pancreatic cancer patients.
    DOI:  https://doi.org/10.1615/CritRevEukaryotGeneExpr.2021038733
  45. Neoplasia. 2021 Sep 25. pii: S1476-5586(21)00075-0. [Epub ahead of print]23(11): 1069-1077
    RosettaSX: Reliable gene expression signature scoring of cancer models and patients.
    Julian Kreis, Boro Nedić, Johanna Mazur, Miriam Urban, Sven-Eric Schelhorn, Thomas Grombacher, Felix Geist, Benedikt Brors, Michael Zühlsdorf, Eike Staub.
      Gene expression signatures have proven their potential to characterize important cancer phenomena like oncogenic signaling pathway activities, cellular origins of tumors, or immune cell infiltration into tumor tissues. Large collections of expression signatures provide the basis for their application to data sets, but the applicability of each signature in a new experimental context must be reassessed. We apply a methodology that utilizes the previously developed concept of coherent expression of genes in signatures to identify translatable signatures before scoring their activity in single tumors. We present a web interface (www.rosettasx.com) that applies our methodology to expression data from the Cancer Cell Line Encyclopaedia and The Cancer Genome Atlas. Configurable heat maps visualize per-cancer signature scores for 293 hand-curated literature-derived gene sets representing a wide range of cancer-relevant transcriptional modules and phenomena. The platform allows users to complement heatmaps of signature scores with molecular information on SNVs, CNVs, gene expression, gene dependency, and protein abundance or to analyze own signatures. Clustered heatmaps and further plots to drill-down results support users in studying oncological processes in cancer subtypes, thereby providing a rich resource to explore how mechanisms of cancer interact with each other as demonstrated by exemplary analyses of 2 cancer types.
    Keywords:  Analyses; Cancer expression profiling; Cancer subtypes; Gene expression signature; Multiomics Analyses; Web service
    DOI:  https://doi.org/10.1016/j.neo.2021.08.005
  46. Cancers (Basel). 2021 Sep 13. pii: 4594. [Epub ahead of print]13(18):
    Perineural Invasion and Associated Pain Transmission in Pancreatic Cancer.
    Jialun Wang, Yu Chen, Xihan Li, Xiaoping Zou.
      Pancreatic ductal adenocarcinoma (PDAC) is one of the cancers with the highest incidence of perineural invasion (PNI), which often indicates a poor prognosis. Aggressive tumor cells invade nerves, causing neurogenic inflammation; the tumor microenvironment also induces nerves to undergo a series of structural and functional reprogramming. In turn, neurons and the surrounding glial cells promote the development of pancreatic cancer through autocrine and/or paracrine signaling. In addition, hyperalgesia in PDAC patients implies alterations of pain transmission in the peripheral and central nervous systems. Currently, the studies on this topic are relatively limited. This review will elaborate on the mechanisms of tumor-neural interactions and its possible relationship with pain from several aspects that have been focused on in recent years.
    Keywords:  nerve remodeling; pain; pancreatic cancer; perineural invasion
    DOI:  https://doi.org/10.3390/cancers13184594
  47. Cell Stem Cell. 2021 Sep 22. pii: S1934-5909(21)00380-5. [Epub ahead of print]
    SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling.
    Wei Gu, Hua Wang, Xiaofeng Huang, Judith Kraiczy, Pratik N P Singh, Charles Ng, Sezin Dagdeviren, Sean Houghton, Oscar Pellon-Cardenas, Ying Lan, Yaohui Nie, Jiaoyue Zhang, Kushal K Banerjee, Emily J Onufer, Brad W Warner, Jason Spence, Ellen Scherl, Shahin Rafii, Richard T Lee, Michael P Verzi, David Redmond, Randy Longman, Kristian Helin, Ramesh A Shivdasani, Qiao Zhou.
      Adult stem cells maintain regenerative tissue structure and function by producing tissue-specific progeny, but the factors that preserve their tissue identities are not well understood. The small and large intestines differ markedly in cell composition and function, reflecting their distinct stem cell populations. Here we show that SATB2, a colon-restricted chromatin factor, singularly preserves LGR5+ adult colonic stem cell and epithelial identity in mice and humans. Satb2 loss in adult mice leads to stable conversion of colonic stem cells into small intestine ileal-like stem cells and replacement of the colonic mucosa with one that resembles the ileum. Conversely, SATB2 confers colonic properties on the mouse ileum. Human colonic organoids also adopt ileal characteristics upon SATB2 loss. SATB2 regulates colonic identity in part by modulating enhancer binding of the intestinal transcription factors CDX2 and HNF4A. Our study uncovers a conserved core regulator of colonic stem cells able to mediate cross-tissue plasticity in mature intestines.
    Keywords:  SATB2, intestine regeneration, colonic mucosa, stem cell conversion, enhancer remodelingintestine
    DOI:  https://doi.org/10.1016/j.stem.2021.09.004
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