bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2022‒08‒21
thirty-two papers selected by
Kıvanç Görgülü
Technical University of Munich
  1. Multi-omics data integration and modeling unravels new mechanisms for pancreatic cancer and improves prognostic prediction.
  2. Ordered and deterministic cancer genome evolution after p53 loss.
  3. A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues.
  4. Cancer-associated fibroblasts employ NUFIP1-dependent autophagy to secrete nucleosides and support pancreatic tumor growth.
  5. PINK1-dependent and Parkin-independent mitophagy is involved in reprogramming of glycometabolism in pancreatic cancer cells.
  6. Glucose feeds the tricarboxylic acid cycle via excreted ethanol in fermenting yeast.
  7. Mouse modeling provides insights into Daxx and Atrx tumor suppressive mechanisms in the endocrine pancreas.
  8. Unified multiscale theory of cellular mechanical adaptions to substrate stiffness.
  9. Genomic and transcriptomic determinants of response to neoadjuvant therapy in rectal cancer.
  10. Endosome maturation links PI3Kα signaling to lysosome repopulation during basal autophagy.
  11. Proteasome granule formation is regulated through mitochondrial respiration and kinase signaling.
  12. Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci and is redistributed by cell-cycle progression.
  13. Prognostic and predictive value of CA 19-9 in locally advanced pancreatic cancer treated with multiagent induction chemotherapy: results from a prospective, multicenter phase II trial (NEOLAP-AIO-PAK-0113).
  14. Safety and efficacy of S-IROX (S-1, irinotecan and oxaliplatin combination therapy) in patients with advanced pancreatic cancer: A multicenter phase 1b dose-escalation and dose-expansion clinical trial.
  15. Carbon source availability drives nutrient utilization in CD8+ T cells.
  16. Metabolic changes in aging humans: current evidence and therapeutic strategies.
  17. Digital quantitative tissue image analysis of hypoxia in resected pancreatic ductal adenocarcinomas.
  18. Spatial profiling of chromatin accessibility in mouse and human tissues.
  19. p53 Activation Paradoxically Causes Liver Cancer.
  20. MUC1 is responsible for the pro-metastatic potential of calycosin in pancreatic ductal adenocarcinoma.
  21. Emerging Insights into the Molecular Architecture of Caveolin-1.
  22. How to follow lipid droplets dynamics during adipocyte metabolism.
  23. Saturation of the mitochondrial NADH shuttles drives aerobic glycolysis in proliferating cells.
  24. Impact of classical and basal-like molecular subtypes on overall survival in resected pancreatic cancer in the SPACIOUS-2 multicentre study.
  25. DetecDiv, a generalist deep-learning platform for automated cell division tracking and survival analysis.
  26. Oncohistones: Exposing the nuances and vulnerabilities of epigenetic regulation.
  27. Mitochondrial hyperfusion via metabolic sensing of regulatory amino acids.
  28. Segmentation and Quantitative Analysis of Epithelial Tissues.
  29. A protocol for rapid construction of senescent cells.
  30. Mastering the use of cellular barcoding to explore cancer heterogeneity.
  31. Transcriptional Heterogeneity of Cellular Senescence in Cancer.
  32. A practical guide for the analysis, standardization and interpretation of oxygen consumption measurements.
  1. NPJ Precis Oncol. 2022 Aug 17. 6(1): 57
    Multi-omics data integration and modeling unravels new mechanisms for pancreatic cancer and improves prognostic prediction.
    Nicolas A Fraunhoffer, Analía Meilerman Abuelafia, Martin Bigonnet, Odile Gayet, Julie Roques, Remy Nicolle, Gwen Lomberk, Raul Urrutia, Nelson Dusetti, Juan Iovanna.
      Pancreatic ductal adenocarcinoma (PDAC), has recently been found to be a heterogeneous disease, although the extension of its diversity remains to be fully understood. Here, we harmonize transcriptomic profiles derived from both PDAC epithelial and microenvironment cells to develop a Master Regulators (MR)-Gradient model that allows important inferences on transcriptional networks, epigenomic states, and metabolomics pathways that underlies this disease heterogeneity. This gradient model was generated by applying a blind source separation based on independent components analysis and robust principal component analyses (RPCA), following regulatory network inference. The result of these analyses reveals that PDAC prognosis strongly associates with the tumor epithelial cell phenotype and the immunological component. These studies were complemented by integration of methylome and metabolome datasets generated from patient-derived xenograft (PDX), together experimental measurements of metabolites, immunofluorescence microscopy, and western blot. At the metabolic level, PDAC favorable phenotype showed a positive correlation with enzymes implicated in complex lipid biosynthesis. In contrast, the unfavorable phenotype displayed an augmented OXPHOS independent metabolism centered on the Warburg effect and glutaminolysis. Epigenetically, we find that a global hypermethylation profile associates with the worst prognosis. Lastly, we report that, two antagonistic histone code writers, SUV39H1/SUV39H2 (H3K9Me3) and KAT2B (H3K9Ac) were identified key deregulated pathways in PDAC. Our analysis suggests that the PDAC phenotype, as it relates to prognosis, is determined by a complex interaction of transcriptomic, epigenomic, and metabolic features. Furthermore, we demonstrated that PDAC prognosis could be modulated through epigenetics.
    DOI:  https://doi.org/10.1038/s41698-022-00299-z
  2. Nature. 2022 Aug 17.
    Ordered and deterministic cancer genome evolution after p53 loss.
    Timour Baslan, John P Morris, Zhen Zhao, Jose Reyes, Yu-Jui Ho, Kaloyan M Tsanov, Jonathan Bermeo, Sha Tian, Sean Zhang, Gokce Askan, Aslihan Yavas, Nicolas Lecomte, Amanda Erakky, Anna M Varghese, Amy Zhang, Jude Kendall, Elena Ghiban, Lubomir Chorbadjiev, Jie Wu, Nevenka Dimitrova, Kalyani Chadalavada, Gouri J Nanjangud, Chaitanya Bandlamudi, Yixiao Gong, Mark T A Donoghue, Nicholas D Socci, Alex Krasnitz, Faiyaz Notta, Steve D Leach, Christine A Iacobuzio-Donahue, Scott W Lowe.
      Although p53 inactivation promotes genomic instability1 and presents a route to malignancy for more than half of all human cancers2,3, the patterns through which heterogenous TP53 (encoding human p53) mutant genomes emerge and influence tumorigenesis remain poorly understood. Here, in a mouse model of pancreatic ductal adenocarcinoma that reports sporadic p53 loss of heterozygosity before cancer onset, we find that malignant properties enabled by p53 inactivation are acquired through a predictable pattern of genome evolution. Single-cell sequencing and in situ genotyping of cells from the point of p53 inactivation through progression to frank cancer reveal that this deterministic behaviour involves four sequential phases-Trp53 (encoding mouse p53) loss of heterozygosity, accumulation of deletions, genome doubling, and the emergence of gains and amplifications-each associated with specific histological stages across the premalignant and malignant spectrum. Despite rampant heterogeneity, the deletion events that follow p53 inactivation target functionally relevant pathways that can shape genomic evolution and remain fixed as homogenous events in diverse malignant populations. Thus, loss of p53-the 'guardian of the genome'-is not merely a gateway to genetic chaos but, rather, can enable deterministic patterns of genome evolution that may point to new strategies for the treatment of TP53-mutant tumours.
    DOI:  https://doi.org/10.1038/s41586-022-05082-5
  3. Nat Commun. 2022 Aug 16. 13(1): 4827
    A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues.
    Dominik Saul, Robyn Laura Kosinsky, Elizabeth J Atkinson, Madison L Doolittle, Xu Zhang, Nathan K LeBrasseur, Robert J Pignolo, Paul D Robbins, Laura J Niedernhofer, Yuji Ikeno, Diana Jurk, João F Passos, LaTonya J Hickson, Ailing Xue, David G Monroe, Tamara Tchkonia, James L Kirkland, Joshua N Farr, Sundeep Khosla.
      Although cellular senescence drives multiple age-related co-morbidities through the senescence-associated secretory phenotype, in vivo senescent cell identification remains challenging. Here, we generate a gene set (SenMayo) and validate its enrichment in bone biopsies from two aged human cohorts. We further demonstrate reductions in SenMayo in bone following genetic clearance of senescent cells in mice and in adipose tissue from humans following pharmacological senescent cell clearance. We next use SenMayo to identify senescent hematopoietic or mesenchymal cells at the single cell level from human and murine bone marrow/bone scRNA-seq data. Thus, SenMayo identifies senescent cells across tissues and species with high fidelity. Using this senescence panel, we are able to characterize senescent cells at the single cell level and identify key intercellular signaling pathways. SenMayo also represents a potentially clinically applicable panel for monitoring senescent cell burden with aging and other conditions as well as in studies of senolytic drugs.
    DOI:  https://doi.org/10.1038/s41467-022-32552-1
  4. Nat Cancer. 2022 Aug 18.
    Cancer-associated fibroblasts employ NUFIP1-dependent autophagy to secrete nucleosides and support pancreatic tumor growth.
    Meng Yuan, Bo Tu, Hengchao Li, Huanhuan Pang, Nan Zhang, Minghe Fan, Jingru Bai, Wei Wang, Zhaoqi Shu, Christopher C DuFort, Sihan Huo, Jie Zhai, Ke Yao, Lina Wang, Haoqiang Ying, Wei-Guo Zhu, Deliang Fu, Zeping Hu, Ying Zhao.
      Cancer-associated fibroblasts (CAFs) are one of the most prominent and active components in the pancreatic tumor microenvironment. Our data show that CAFs are critical for survival from pancreatic ductal adenocarcinoma (PDAC) on glutamine deprivation. Specifically, we uncovered a role for nucleosides, which are secreted by CAFs through autophagy in a nuclear fragile X mental retardation-interacting protein 1 (NUFIP1)-dependent manner, increased glucose utilization and promoted growth of PDAC. Moreover, we demonstrate that CAF-derived nucleosides induced glucose consumption under glutamine-deprived conditions and displayed a dependence on MYC. Using an orthotopic mouse model of PDAC, we found that inhibiting nucleoside secretion by targeting NUFIP1 in the stroma reduced tumor weight. This finding highlights a previously unappreciated metabolic network within pancreatic tumors in which diverse nutrients are used to promote growth in an austere tumor microenvironment.
    DOI:  https://doi.org/10.1038/s43018-022-00426-6
  5. Biochem Biophys Res Commun. 2022 Aug 05. pii: S0006-291X(22)01109-3. [Epub ahead of print]625 167-173
    PINK1-dependent and Parkin-independent mitophagy is involved in reprogramming of glycometabolism in pancreatic cancer cells.
    Natsumi Miyazaki, Reika Shiratori, Taichi Oshima, Zhiheng Zhang, Robert Valencia, Joshua Kranrod, Liye Fang, John M Seubert, Kousei Ito, Shigeki Aoki.
      Cancer cells rely on glycolysis to generate ATP for survival. However, inhibiting glycolysis is insufficient for the eradication of cancer cells because glycolysis-suppressed cells undergo metabolic reprogramming toward mitochondrial oxidative phosphorylation. We previously described that upon glycolytic suppression in pancreatic cancer cells, intracellular glycometabolism is shifted toward mitochondrial oxidative phosphorylation in an autophagy-dependent manner for cellular survival. Here, we hypothesized that mitophagy, which selectively degrades mitochondria via autophagy, is involved in mitochondrial activation under metabolic reprogramming. We revealed that glycolytic suppression notably increased mitochondrial membrane potential and mitophagy in a pancreatic cancer cell model (PANC-1). PTEN-induced kinase 1 (PINK1), a ubiquitin kinase that regulates mitophagy in healthy cells, regulated mitochondrial activation through mitophagy by glycolytic suppression. However, Parkin, a ubiquitin ligase regulated by PINK1 in healthy cells to induce mitophagy, was not involved in the PINK1-dependent mitophagy of the cancer glycometabolism. These results imply that cancer cells and healthy cells have different regulatory pieces of machinery for mitophagy, and inhibition of cancer-specific mechanisms may be a potential strategy for cancer therapy targeting metabolic reprogramming.
    Keywords:  Glycometabolism; Mitophagy; PINK1; Pancreatic cancer; Parkin
    DOI:  https://doi.org/10.1016/j.bbrc.2022.08.004
  6. Nat Chem Biol. 2022 Aug 15.
    Glucose feeds the tricarboxylic acid cycle via excreted ethanol in fermenting yeast.
    Tianxia Xiao, Artem Khan, Yihui Shen, Li Chen, Joshua D Rabinowitz.
      Ethanol and lactate are typical waste products of glucose fermentation. In mammals, glucose is catabolized by glycolysis into circulating lactate, which is broadly used throughout the body as a carbohydrate fuel. Individual cells can both uptake and excrete lactate, uncoupling glycolysis from glucose oxidation. Here we show that similar uncoupling occurs in budding yeast batch cultures of Saccharomyces cerevisiae and Issatchenkia orientalis. Even in fermenting S. cerevisiae that is net releasing ethanol, media 13C-ethanol rapidly enters and is oxidized to acetaldehyde and acetyl-CoA. This is evident in exogenous ethanol being a major source of both cytosolic and mitochondrial acetyl units. 2H-tracing reveals that ethanol is also a major source of both NADH and NADPH high-energy electrons, and this role is augmented under oxidative stress conditions. Thus, uncoupling of glycolysis from the oxidation of glucose-derived carbon via rapidly reversible reactions is a conserved feature of eukaryotic metabolism.
    DOI:  https://doi.org/10.1038/s41589-022-01091-7
  7. Dis Model Mech. 2022 Aug 17. pii: dmm.049552. [Epub ahead of print]
    Mouse modeling provides insights into Daxx and Atrx tumor suppressive mechanisms in the endocrine pancreas.
    Chang Sun, Jeannelyn S Estrella, Elizabeth M Whitley, Gilda P Chau, Guillermina Lozano, Amanda R Wasylishen.
      Genome sequencing has revealed the importance of epigenetic regulators in tumorigenesis. The genes encoding the chromatin remodeling complex DAXX:ATRX are frequently mutated in pancreatic neuroendocrine tumors (PanNETs); however, the underlying mechanisms of how mutations contribute to tumorigenesis are only partially understood, in part because of the lack of relevant pre-clinical models. Here we used genetically engineered mouse models combined with environmental stress to evaluate the tumor suppressor functions of Daxx and Atrx in the mouse pancreas. Daxx or Atrx loss, alone or in combination with Men1 loss, do not drive nor accelerate pancreatic neuroendocrine tumorigenesis. Moreover, Daxx loss does not cooperate with environmental stresses (ionizing radiation or pancreatitis) or with the loss of other tumor suppressors (Pten or p53) to promote pancreatic neuroendocrine tumorigenesis. However, due to promiscuity of the Cre promoter used, hepatocellular carcinomas (HCC) and osteosarcomas were observed in some instances. Overall, our findings suggest that Daxx and Atrx are not robust tumor suppressors in the endocrine pancreas of mice and indicate the context of a human genome is essential for tumorigenesis.
    Keywords:  Atrx; Daxx; Men1; Mouse models; Pancreatic Neuroendocrine tumor
    DOI:  https://doi.org/10.1242/dmm.049552
  8. Biophys J. 2022 Aug 16. pii: S0006-3495(22)00669-5. [Epub ahead of print]
    Unified multiscale theory of cellular mechanical adaptions to substrate stiffness.
    Peng-Cheng Chen, Xi-Qiao Feng, Bo Li.
      Rigidity of extracellular matrix markedly regulates many cellular processes. However, how cells detect and respond to matrix rigidity remains incompletely understood. Here, we propose a unified two-dimensional multiscale framework accounting for the chemomechanical feedback to explore the interrelated cellular mechanosensing, polarization, and migration, which constitute the dynamic cascade in cellular response to matrix stiffness but are often modeled separately in previous theories. By combining integrin dynamics and intracellular force transduction, we show that substrate stiffness can act as a switch to activate or deactivate cell polarization. Our theory quantitatively reproduces rich stiffness-dependent cellular dynamics, including spreading, polarity selection, migration pattern, durotaxis, and even negative durotaxis, reported in a wide spectrum of cell types and reconciles some inconsistent experimental observations. We find that a specific bipolarized mode can determine the optimal substrate stiffness, which enables the fastest cell migration rather than the largest traction forces that cells applied on the substrate. We identify that such a mechanical adaption stems from the force balance across the whole cell. These findings could yield universal insights into various stiffness-mediated cellular processes within the context of tissue morphogenesis, wound healing, and cancer invasion.
    Keywords:  Cell migration; Cell polarity; Chemomechanical feedback; Durotaxis.; Substrate stiffness
    DOI:  https://doi.org/10.1016/j.bpj.2022.08.009
  9. Nat Med. 2022 Aug;28(8): 1646-1655
    Genomic and transcriptomic determinants of response to neoadjuvant therapy in rectal cancer.
    Walid K Chatila, Jin K Kim, Henry Walch, Michael R Marco, Chin-Tung Chen, Fan Wu, Dana M Omer, Danny N Khalil, Karuna Ganesh, Xuan Qu, Anisha Luthra, Seo-Hyun Choi, Yu-Jui Ho, Ritika Kundra, Katharine I Groves, Oliver S Chow, Andrea Cercek, Martin R Weiser, Maria Widmar, Iris H Wei, Emmanouil P Pappou, Garrett M Nash, Philip B Paty, Qian Shi, Efsevia Vakiani, S Duygu Selcuklu, Mark T A Donoghue, David B Solit, Michael F Berger, Jinru Shia, Raphael Pelossof, Paul B Romesser, Rona Yaeger, J Joshua Smith, Nikolaus Schultz, Francisco Sanchez-Vega, Julio Garcia-Aguilar.
      The incidence of rectal cancer is increasing in patients younger than 50 years. Locally advanced rectal cancer is still treated with neoadjuvant radiation, chemotherapy and surgery, but recent evidence suggests that patients with a complete response can avoid surgery permanently. To define correlates of response to neoadjuvant therapy, we analyzed genomic and transcriptomic profiles of 738 untreated rectal cancers. APC mutations were less frequent in the lower than in the middle and upper rectum, which could explain the more aggressive behavior of distal tumors. No somatic alterations had significant associations with response to neoadjuvant therapy in a treatment-agnostic manner, but KRAS mutations were associated with faster relapse in patients treated with neoadjuvant chemoradiation followed by consolidative chemotherapy. Overexpression of IGF2 and L1CAM was associated with decreased response to neoadjuvant therapy. RNA-sequencing estimates of immune infiltration identified a subset of microsatellite-stable immune hot tumors with increased response and prolonged disease-free survival.
    DOI:  https://doi.org/10.1038/s41591-022-01930-z
  10. EMBO J. 2022 Aug 15. e110398
    Endosome maturation links PI3Kα signaling to lysosome repopulation during basal autophagy.
    Samuel J Rodgers, Emily I Jones, Senthil Arumugam, Sabryn A Hamila, Jill Danne, Rajendra Gurung, Matthew J Eramo, Randini Nanayakkara, Georg Ramm, Meagan J McGrath, Christina A Mitchell.
      Autophagy depends on the repopulation of lysosomes to degrade intracellular components and recycle nutrients. How cells co-ordinate lysosome repopulation during basal autophagy, which occurs constitutively under nutrient-rich conditions, is unknown. Here, we identify an endosome-dependent phosphoinositide pathway that links PI3Kα signaling to lysosome repopulation during basal autophagy. We show that PI3Kα-derived PI(3)P generated by INPP4B on late endosomes was required for basal but not starvation-induced autophagic degradation. PI(3)P signals were maintained as late endosomes matured into endolysosomes, and served as the substrate for the 5-kinase, PIKfyve, to generate PI(3,5)P2 . The SNX-BAR protein, SNX2, was recruited to endolysosomes by PI(3,5)P2 and promoted lysosome reformation. Inhibition of INPP4B/PIKfyve-dependent lysosome reformation reduced autophagic clearance of protein aggregates during proteotoxic stress leading to increased cytotoxicity. Therefore under nutrient-rich conditions, PI3Kα, INPP4B, and PIKfyve sequentially contribute to basal autophagic degradation and protection from proteotoxic stress via PI(3,5)P2 -dependent lysosome reformation from endolysosomes. These findings reveal that endosome maturation couples PI3Kα signaling to lysosome reformation during basal autophagy.
    Keywords:  INPP4B; PI3Kα; PIKfyve; autophagy; lysosome
    DOI:  https://doi.org/10.15252/embj.2021110398
  11. J Cell Sci. 2022 Aug 17. pii: jcs.259778. [Epub ahead of print]
    Proteasome granule formation is regulated through mitochondrial respiration and kinase signaling.
    Kenrick A Waite, Jeroen Roelofs.
      In yeast, proteasomes are enriched in cell nuclei where they execute important cellular functions. Nutrient-stress can change this localization indicating proteasomes respond to the cell's metabolic state. However, the signals that connect these processes remain poorly understood. Carbon starvation triggers a reversible translocation of proteasomes to cytosolic condensates known as proteasome storage granules (PSGs). Surprisingly, we observed strongly reduced levels of proteasome granules when cells had active cellular respiration prior to starvation. This suggests the mitochondrial activity of cells is a determining factor in the response of proteasomes to carbon starvation. Consistent with this, upon inhibition of mitochondrial function we observed proteasomes relocalize to granules. These links between proteasomes and metabolism involve specific signaling pathways, as we identified a MAP kinase cascade that is critical to the formation of proteasome granules after respiratory growth but not following glycolytic growth. Furthermore, the yeast homolog of AMP kinase, Snf1, is important for proteasome granule formation induced by mitochondrial inhibitors, while dispensable for granule formation following carbon starvation. We propose a model where mitochondrial activity promotes proteasome nuclear localization.
    Keywords:  MAP kinases; Mitochondrial inhibition; Mitochondrial respiration; Proteaphagy; Proteasome; Proteasome storage granules (PSG)
    DOI:  https://doi.org/10.1242/jcs.259778
  12. Mol Cell. 2022 Aug 12. pii: S1097-2765(22)00710-9. [Epub ahead of print]
    Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci and is redistributed by cell-cycle progression.
    Ioannis Sanidas, Hanjun Lee, Purva H Rumde, Gaylor Boulay, Robert Morris, Gabriel Golczer, Marcelo Stanzione, Soroush Hajizadeh, Jun Zhong, Meagan B Ryan, Ryan B Corcoran, Benjamin J Drapkin, Miguel N Rivera, Nicholas J Dyson, Michael S Lawrence.
      The interaction of RB with chromatin is key to understanding its molecular functions. Here, for first time, we identify the full spectrum of chromatin-bound RB. Rather than exclusively binding promoters, as is often described, RB targets three fundamentally different types of loci (promoters, enhancers, and insulators), which are largely distinguishable by the mutually exclusive presence of E2F1, c-Jun, and CTCF. While E2F/DP facilitates RB association with promoters, AP-1 recruits RB to enhancers. Although phosphorylation in CDK sites is often portrayed as releasing RB from chromatin, we show that the cell cycle redistributes RB so that it enriches at promoters in G1 and at non-promoter sites in cycling cells. RB-bound promoters include the classic E2F-targets and are similar between lineages, but RB-bound enhancers associate with different categories of genes and vary between cell types. Thus, RB has a well-preserved role controlling E2F in G1, and it targets cell-type-specific enhancers and CTCF sites when cells enter S-phase.
    Keywords:  AP-1; CTCF; E2F; PanChIP; RB phosphorylation; RB-bound enhancers; RB-bound promoters; cell-cycle regulation; regulation of RB activity; retinoblastoma protein
    DOI:  https://doi.org/10.1016/j.molcel.2022.07.014
  13. ESMO Open. 2022 Aug 12. pii: S2059-7029(22)00180-6. [Epub ahead of print]7(4): 100552
    Prognostic and predictive value of CA 19-9 in locally advanced pancreatic cancer treated with multiagent induction chemotherapy: results from a prospective, multicenter phase II trial (NEOLAP-AIO-PAK-0113).
    German Pancreatic Cancer Group (AIO-PAK) and NEOLAP investigators
      BACKGROUND: The prognostic and predictive value of carbohydrate antigen 19-9 (CA 19-9) in locally advanced pancreatic cancer (LAPC) has not yet been defined from prospective randomized controlled trials (RCTs).PATIENTS AND METHODS: A total of 165 LAPC patients were treated within the NEOLAP RCT for 16 weeks with multiagent induction chemotherapy [ICT; either nab-paclitaxel/gemcitabine alone or nab-paclitaxel/gemcitabine followed by FOLFIRINOX (combination of fluorouracil, leucovorin, irinotecan, and oxaliplatin)] followed by surgical exploration of all patients without evidence of disease progression. CA 19-9 was determined at baseline and after ICT and correlated with overall survival (OS) and secondary R0 resection rate.
    RESULTS: From the NEOLAP study population (N = 165) 133 patients (81%) were evaluable for CA 19-9 at baseline and 81/88 patients (92%) for post-ICT CA 19-9 response. Median OS (mOS) in the CA 19-9 cohort (n = 133) was 16.2 months [95% confidence interval (CI) 13.0-19.4] and R0 resection (n = 31; 23%) was associated with a significant survival benefit [40.8 months (95% CI 21.7-59.8)], while R1 resected patients (n = 14; 11%) had no survival benefit [14.0 (95% CI 11.7-16.3) months, hazard ratio (HR) 0.27; P = 0.001]. After ICT most patients showed a CA 19-9 response (median change from baseline: -82%; relative decrease ≥55%: 83%; absolute decrease to ≤50 U/ml: 43%). Robust CA 19-9 response (decrease to ≤50U/ml) was significantly associated with mOS [27.8 (95% CI 18.4-37.2) versus 16.5 (95% CI 11.7-21.2) months, HR 0.49; P = 0.013], whereas CA 19-9 baseline levels were not prognostic for OS. Multivariate analysis demonstrated that a robust CA 19-9 response was an independent predictive factor for R0 resection. Using a CA 19-9 decrease to ≤61 U/ml as optimal cut-off (by receiver operating characteristic analysis) yielded 72% sensitivity and 62% specificity for successful R0 resection, whereas CA 19-9 nonresponders (<20% decrease or increase) had no chance for successful R0 resection.
    CONCLUSIONS: CA 19-9 response after multiagent ICT provides relevant prognostic and predictive information and is useful in selecting LAPC patients for explorative surgery.
    CLINICAL TRIAL NUMBER: ClinicalTrials.govNCT02125136; https://clinicaltrials.gov/ct2/show/NCT02125136; EudraCT 2013-004796-12; https://www.clinicaltrialsregister.eu/ctr-search/trial/2013-004796-12/results.
    Keywords:  CA 19-9; NEOLAP; R0 resection rate; locally advanced pancreatic cancer; multiagent induction chemotherapy
    DOI:  https://doi.org/10.1016/j.esmoop.2022.100552
  14. Eur J Cancer. 2022 Aug 12. pii: S0959-8049(22)00361-6. [Epub ahead of print]174 40-47
    Safety and efficacy of S-IROX (S-1, irinotecan and oxaliplatin combination therapy) in patients with advanced pancreatic cancer: A multicenter phase 1b dose-escalation and dose-expansion clinical trial.
    Akihiro Ohba, Hideki Ueno, Satoshi Shiba, Naohiro Okano, Takaaki Kobayashi, Fumio Nagashima, Naoki Sasahira, Mitsuhito Sasaki, Hiroshi Imaoka, Yasunari Sakamoto, Shunsuke Kondo, Chigusa Morizane, Masato Ozaka, Masafumi Ikeda, Junji Furuse, Takuji Okusaka.
      BACKGROUND: This phase 1b trial evaluated the toxicity and efficacy of S-1, irinotecan, and oxaliplatin combination therapy (S-IROX) as first-line chemotherapy in patients with advanced pancreatic cancer (APC).METHODS: Patients aged 20-75 years with APC and an Eastern Cooperative Oncology Group performance status of 0 or 1 were eligible to receive escalating doses of S-1 (60 or 80 mg m2·day) on days 1-7, fixed doses of oxaliplatin (85 mg/m2) biweekly, and escalating doses of irinotecan (150, 165, or 180 mg/m2) once every 2 weeks. In the dose-escalation cohort, a 3 + 3 design was used to determine the maximum-tolerated dose (MTD) and explore the recommended dose (RD). A dose-expansion cohort was added to further evaluate the safety and efficacy of the combination. This trial was registered at UMIN-CTR (UMIN000012054).
    RESULTS: Approximately 47 patients were enrolled, of whom 45 were eligible for the analysis. The MTD was not determined, but the RD was determined to be dose level 1 based on a review of data from each level. Among the 45 patients, the ORR was 51.1% [95% confidence interval (CI), 35.8-66.3%]. The median progression-free survival and median overall survival was 6.9 months (95% CI, 5.1-8.8 months) and 15.8 months (95% CI, 9.8-20.8 months), respectively. Common adverse events included neutropenia, elevated liver enzyme levels, diarrhoea, and nausea.
    CONCLUSIONS: The S-IROX regimen showed promising efficacy with manageable toxicities in Japanese patients with APC. A randomised phase 2/3 trial comparing S-IROX, mFOLFIRINOX, and gemcitabine plus nab-paclitaxel is currently ongoing (jRCTs031190009).
    Keywords:  Irinotecan; Oxaliplatin; Pancreatic cancer; S-1
    DOI:  https://doi.org/10.1016/j.ejca.2022.06.010
  15. Cell Metab. 2022 Aug 11. pii: S1550-4131(22)00311-4. [Epub ahead of print]
    Carbon source availability drives nutrient utilization in CD8+ T cells.
    Irem Kaymak, Katarzyna M Luda, Lauren R Duimstra, Eric H Ma, Joseph Longo, Michael S Dahabieh, Brandon Faubert, Brandon M Oswald, McLane J Watson, Susan M Kitchen-Goosen, Lisa M DeCamp, Shelby E Compton, Zhen Fu, Ralph J DeBerardinis, Kelsey S Williams, Ryan D Sheldon, Russell G Jones.
      How environmental nutrient availability impacts T cell metabolism and function remains poorly understood. Here, we report that the presence of physiologic carbon sources (PCSs) in cell culture medium broadly impacts glucose utilization by CD8+ T cells, independent of transcriptional changes in metabolic reprogramming. The presence of PCSs reduced glucose contribution to the TCA cycle and increased effector function of CD8+ T cells, with lactate directly fueling the TCA cycle. In fact, CD8+ T cells responding to Listeria infection preferentially consumed lactate over glucose as a TCA cycle substrate in vitro, with lactate enhancing T cell bioenergetic and biosynthetic capacity. Inhibiting lactate-dependent metabolism in CD8+ T cells by silencing lactate dehydrogenase A (Ldha) impaired both T cell metabolic homeostasis and proliferative expansion in vivo. Together, our data indicate that carbon source availability shapes T cell glucose metabolism and identifies lactate as a bioenergetic and biosynthetic fuel for CD8+ effector T cells.
    Keywords:  (13)C tracing; T cells; TCA cycle; immunometabolism; lactate; metabolic programming; metabolomics
    DOI:  https://doi.org/10.1016/j.cmet.2022.07.012
  16. J Clin Invest. 2022 Aug 15. pii: e158451. [Epub ahead of print]132(16):
    Metabolic changes in aging humans: current evidence and therapeutic strategies.
    Allyson K Palmer, Michael D Jensen.
      Aging and metabolism are inextricably linked, and many age-related changes in body composition, including increased central adiposity and sarcopenia, have underpinnings in fundamental aging processes. These age-related changes are further exacerbated by a sedentary lifestyle and can be in part prevented by maintenance of activity with aging. Here we explore the age-related changes seen in individual metabolic tissues - adipose, muscle, and liver - as well as globally in older adults. We also discuss the available evidence for therapeutic interventions such as caloric restriction, resistance training, and senolytic and senomorphic drugs to maintain healthy metabolism with aging, focusing on data from human studies.
    DOI:  https://doi.org/10.1172/JCI158451
  17. Front Oncol. 2022 ;12 926497
    Digital quantitative tissue image analysis of hypoxia in resected pancreatic ductal adenocarcinomas.
    Iram Siddiqui, Jade Bilkey, Trevor D McKee, Stefano Serra, Melania Pintilie, Trevor Do, Jing Xu, Ming-Sound Tsao, Steve Gallinger, Richard P Hill, David W Hedley, Neesha C Dhani.
      Background: Tumor hypoxia is theorized to contribute to the aggressive biology of pancreatic ductal adenocarcinoma (PDAC). We previously reported that hypoxia correlated with rapid tumor growth and metastasis in patient-derived xenografts. Anticipating a prognostic relevance of hypoxia in patient tumors, we developed protocols for automated semi-quantitative image analysis to provide an objective, observer-independent measure of hypoxia. We further validated this method which can reproducibly estimate pimonidazole-detectable hypoxia in a high-through put manner.Methods: We studied the performance of three automated image analysis platforms in scoring pimonidazole-detectable hypoxia in resected PDAC (n = 10) in a cohort of patients enrolled in PIMO-PANC. Multiple stained tumor sections were analyzed on three independent image-analysis platforms, Aperio Genie (AG), Definiens Tissue Studio (TS), and Definiens Developer (DD), which comprised of a customized rule set.
    Results: The output from Aperio Genie (AG) had good concordance with manual scoring, but the workflow was resource-intensive and not suited for high-throughput analysis. TS analysis had high levels of variability related to misclassification of cells class, while the customized rule set of DD had a high level of reliability with an intraclass coefficient of more than 85%.
    Discussion: This work demonstrates the feasibility of developing a robust, high-performance pipeline for an automated, quantitative scoring of pimonidazole-detectable hypoxia in patient tumors.
    Keywords:  ductal adenocarcinoma (PDAC); hypoxia; image analysis; tumor heterogeneity; tumor microenvironment
    DOI:  https://doi.org/10.3389/fonc.2022.926497
  18. Nature. 2022 Aug 17.
    Spatial profiling of chromatin accessibility in mouse and human tissues.
    Yanxiang Deng, Marek Bartosovic, Sai Ma, Di Zhang, Petra Kukanja, Yang Xiao, Graham Su, Yang Liu, Xiaoyu Qin, Gorazd B Rosoklija, Andrew J Dwork, J John Mann, Mina L Xu, Stephanie Halene, Joseph E Craft, Kam W Leong, Maura Boldrini, Gonçalo Castelo-Branco, Rong Fan.
      Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context1. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping2-5, but the ability to capture spatial epigenetic information of tissue at the cellular level and genome scale is lacking. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry6 and microfluidic deterministic barcoding5. Profiling mouse embryos using spatial-ATAC-seq delineated tissue-region-specific epigenetic landscapes and identified gene regulators involved in the development of the central nervous system. Mapping the accessible genome in the mouse and human brain revealed the intricate arealization of brain regions. Applying spatial-ATAC-seq to tonsil tissue resolved the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology progresses spatial biology by enabling spatially resolved chromatin accessibility profiling to improve our understanding of cell identity, cell state and cell fate decision in relation to epigenetic underpinnings in development and disease.
    DOI:  https://doi.org/10.1038/s41586-022-05094-1
  19. Cancer Res. 2022 Aug 16. 82(16): 2824-2825
    p53 Activation Paradoxically Causes Liver Cancer.
    Michelle C Barton, Guillermina Lozano.
      Activation of p53 regulates a transcriptional program that can cause cell cycle arrest, senescence, apoptosis, and ferroptosis, which are potent tumor suppressive mechanisms. Unexpectedly, Makino and colleagues show in this issue of Cancer Research that the constitutive activation of p53 in murine hepatocytes leads to tumor development. Detailed analyses indicate that p53 activation leads to loss of hepatocytes, increased expression of chemokines and humoral factors, and expansion of the hepatic progenitor cell population. These progenitor cells are highly proliferative, show chromosomal instability, and eventually transform. In chronic liver disease in humans, activation of p53 is associated with increased liver cancer development. This study highlights the complexity and non-cell autonomous nature of the physiologic p53 response. See related article by Makino et al., p. 2860.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-2065
  20. Am J Cancer Res. 2022 ;12(7): 3242-3258
    MUC1 is responsible for the pro-metastatic potential of calycosin in pancreatic ductal adenocarcinoma.
    Wenqing Chen, Zhu Zhang, Ken Kin-Lam Yung, Joshua Ka-Shun Ko.
      Pancreatic ductal adenocarcinoma (PDAC) is a prominent type of pancreatic cancer. We have recently unveiled that the anti-tumor adjuvant calycosin concurrently possesses growth-inhibitory and pro-metastatic potential in PDAC development by regulating transforming growth factor β (TGF-β), which plays dual roles as both tumor suppressor and tumor promoter. Hence, we are interested to explore if the pro-metastatic property of the drug could be attenuated for effective treatment of PDAC. Through network pharmacology, MUC1 had been identified as the most common drug target of herbal Astragalus constituents (including calycosin) in treating PDAC. Following MUC1 gene silencing, the drug effects of calycosin on migratory activity, growth and metabolic regulation of PDAC cells were assessed by using immunofluorescence microscopy, quantitative real-time polymerase chain reaction (qRT-PCR), Western immunoblotting, co-immunoprecipitation (Co-IP), wound healing assay and flow cytometry, respectively. Through in vivo experiments, we further validated the working relationship between MUC1 and TGF-β. Results have elucidated that MUC1 gene suppression could switch off the migratory and pro-metastatic drive of calycosin while retaining its growth-inhibitory power by inducing apoptosis and cell cycle arrest, as well as facilitating autophagy and metabolic regulation. The underlying mechanism involves downregulation of TGF-β that acts via modulation of AMP-activated protein kinase (AMPK), Sirtuin 1 (Sirt1) and fibroblast growth factor 21 (FGF21) signaling. These findings have provided new insights in the safe and target-specific treatment of PDAC.
    Keywords:  Calycosin; MUC1; TGF-β; metastasis; pancreatic ductal adenocarcinoma
  21. J Membr Biol. 2022 Aug 16.
    Emerging Insights into the Molecular Architecture of Caveolin-1.
    Melanie D Ohi, Anne K Kenworthy.
      Caveolins are an unusual family of membrane proteins whose primary biological function is to build small invaginated membrane structures at the surface of cells known as caveolae. Caveolins and caveolae regulate numerous signaling pathways, lipid homeostasis, intracellular transport, cell adhesion, and cell migration. They also serve as sensors and protect the plasma membrane from mechanical stress. Despite their many important functions, the molecular basis for how these 50-100 nm "little caves" are assembled and regulate cell physiology has perplexed researchers for 70 years. One major impediment to progress has been the lack of information about the structure of caveolin complexes that serve as building blocks for the assembly of caveolae. Excitingly, recent advances have finally begun to shed light on this long-standing question. In this review, we highlight new developments in our understanding of the structure of caveolin oligomers, including the landmark discovery of the molecular architecture of caveolin-1 complexes using cryo-electron microscopy.
    Keywords:  Caveolae; Caveolin; Cryo-electron microscopy; Membrane nanodomains; Membrane protein structure
    DOI:  https://doi.org/10.1007/s00232-022-00259-5
  22. J Cell Physiol. 2022 Aug 20.
    How to follow lipid droplets dynamics during adipocyte metabolism.
    Nadav Kislev, Shira Eidelheit, Shaked Perlmutter, Dafna Benayahu.
      Lipid droplets (LDs) are important cellular organelles due to their ability to accumulate and store lipids. LD dynamics are associated with various cellular and metabolic processes. Accurate monitoring of LD's size and shape is of prime importance as it indicates the metabolic status of the cells. Unintrusive continuous quantification techniques have a clear advantage in analyzing LDs as they measure and monitor the cells' metabolic function and droplets over time. Here, we present a novel machine-learning-based method for LDs analysis by segmentation of phase-contrast images of differentiated adipocytes (in vitro) and adipose tissue (in vivo). We developed a new workflow based on the ImageJ waikato environment for knowledge analysis segmentation plugin, which provides an accurate, label-free, live single-cell, and organelle quantification of LD-related parameters. By applying the new method on differentiating 3T3-L1 cells, the size of LDs was analyzed over time in differentiated adipocytes and their correlation with other morphological parameters. Moreover, we analyzed the LDs dynamics during catabolic changes such as lipolysis and lipophagy and demonstrated its ability to identify different cellular subpopulations based on their structural, numerical, and spatial variability. This analysis was also implemented on unstained ex vivo adipose tissues to measure adipocyte size, an important readout of the tissue's metabolism. The presented approach can be applied in different LD-related metabolic conditions to provide a better understanding of LD biogenesis and function in vivo and in vitro while serving as a new platform that enables rapid and accurate screening of data sets.
    Keywords:  adipocyte metabolism; adipose tissue; lipid droplets; lipolysis
    DOI:  https://doi.org/10.1002/jcp.30857
  23. Mol Cell. 2022 Aug 12. pii: S1097-2765(22)00703-1. [Epub ahead of print]
    Saturation of the mitochondrial NADH shuttles drives aerobic glycolysis in proliferating cells.
    Yahui Wang, Ethan Stancliffe, Ronald Fowle-Grider, Rencheng Wang, Cheng Wang, Michaela Schwaiger-Haber, Leah P Shriver, Gary J Patti.
      Proliferating cells exhibit a metabolic phenotype known as "aerobic glycolysis," which is characterized by an elevated rate of glucose fermentation to lactate irrespective of oxygen availability. Although several theories have been proposed, a rationalization for why proliferating cells seemingly waste glucose carbon by excreting it as lactate remains elusive. Using the NCI-60 cell lines, we determined that lactate excretion is strongly correlated with the activity of mitochondrial NADH shuttles, but not proliferation. Quantifying the fluxes of the malate-aspartate shuttle (MAS), the glycerol 3-phosphate shuttle (G3PS), and lactate dehydrogenase under various conditions demonstrated that proliferating cells primarily transform glucose to lactate when glycolysis outpaces the mitochondrial NADH shuttles. Increasing mitochondrial NADH shuttle fluxes decreased glucose fermentation but did not reduce the proliferation rate. Our results reveal that glucose fermentation, a hallmark of cancer, is a secondary consequence of MAS and G3PS saturation rather than a unique metabolic driver of cellular proliferation.
    Keywords:  NADH shuttles; aerobic glycolysis; cancer metabolism; glycerol 3-phosphate shuttle; isotope-tracer analysis; malate-aspartate shuttle; metabolic flux; metabolomics; the Warburg effect
    DOI:  https://doi.org/10.1016/j.molcel.2022.07.007
  24. Br J Surg. 2022 Aug 18. pii: znac272. [Epub ahead of print]
    Impact of classical and basal-like molecular subtypes on overall survival in resected pancreatic cancer in the SPACIOUS-2 multicentre study.
    Dutch Pancreatic Cancer Group
      BACKGROUND: The recently identified classical and basal-like molecular subtypes of pancreatic cancer impact on overall survival (OS). However, the added value of routine subtyping in both clinical practice and randomized trials is still unclear, as most studies do not consider clinicopathological parameters. This study examined the clinical prognostic value of molecular subtyping in patients with resected pancreatic cancer.METHODS: Subtypes were determined on fresh-frozen resected pancreatic cancer samples from three Dutch centres using the Purity Independent Subtyping of Tumours classification. Patient, treatment, and histopathological variables were compared between subtypes. The prognostic value of subtyping in (simulated) pre- and postoperative settings was assessed using Kaplan-Meier and Cox regression analyses.
    RESULTS: Of 199 patients with resected pancreatic cancer, 164 (82.4 per cent) were classified as the classical and 35 (17.6 per cent) as the basal-like subtype. Patients with a basal-like subtype had worse OS (11 versus 16 months (HR 1.49, 95 per cent c.i. 1.03 to 2.15; P = 0.035)) than patients with a classical subtype. In multivariable Cox regression analysis, including only clinical variables, the basal-like subtype was a statistically significant predictor for poor OS (HR 1.61, 95 per cent c.i. 1.11 to 2.34; P = 0.013). When histopathological variables were added to this model, the prognostic value of subtyping decreased (HR 1.49, 95 per cent c.i. 1.01 to 2.19; P = 0.045).
    CONCLUSION: The basal-like subtype was associated with worse OS in patients with resected pancreatic cancer. Adding molecular classification to inform on tumor biology may be used in patient stratification.
    DOI:  https://doi.org/10.1093/bjs/znac272
  25. Elife. 2022 Aug 17. pii: e79519. [Epub ahead of print]11
    DetecDiv, a generalist deep-learning platform for automated cell division tracking and survival analysis.
    Théo Aspert, Didier Hentsch, Gilles Charvin.
      Automating the extraction of meaningful temporal information from sequences of microscopy images represents a major challenge to characterize dynamical biological processes. So far, strong limitations in the ability to quantitatively analyze single-cell trajectories have prevented large-scale investigations to assess the dynamics of entry into replicative senescence in yeast. Here, we have developed DetecDiv, a microfluidic-based image acquisition platform combined with deep learning-based software for high-throughput single-cell division tracking. We show that DetecDiv can automatically reconstruct cellular replicative lifespans with high accuracy and performs similarly with various imaging platforms and geometries of microfluidic traps. In addition, this methodology provides comprehensive temporal cellular metrics using time-series classification and image semantic segmentation. Last, we show that this method can be further applied to automatically quantify the dynamics of cellular adaptation and real-time cell survival upon exposure to environmental stress. Hence, this methodology provides an all-in-one toolbox for high-throughput phenotyping for cell cycle, stress response, and replicative lifespan assays.
    Keywords:  S. cerevisiae; cell biology; computational biology; systems biology
    DOI:  https://doi.org/10.7554/eLife.79519
  26. Mol Cell. 2022 Aug 18. pii: S1097-2765(22)00704-3. [Epub ahead of print]82(16): 2925-2938
    Oncohistones: Exposing the nuances and vulnerabilities of epigenetic regulation.
    Michelle M Mitchener, Tom W Muir.
      Work over the last decade has uncovered a new layer of epigenetic dysregulation. It is now appreciated that somatic missense mutations in histones, the packaging agents of genomic DNA, are often associated with human pathologies, especially cancer. Although some of these "oncohistone" mutations are thought to be key drivers of cancer, the impacts of the majority of them on disease onset and progression remain to be elucidated. Here, we survey this rapidly expanding research field with particular emphasis on how histone mutants, even at low dosage, can corrupt chromatin states. This work is unveiling the remarkable intricacies of epigenetic control mechanisms. Throughout, we highlight how studies of oncohistones have leveraged, and in some cases fueled, the advances in our ability to manipulate and interrogate chromatin at the molecular level.
    DOI:  https://doi.org/10.1016/j.molcel.2022.07.008
  27. Cell Rep. 2022 Aug 16. pii: S2211-1247(22)01015-4. [Epub ahead of print]40(7): 111198
    Mitochondrial hyperfusion via metabolic sensing of regulatory amino acids.
    Mahmud O Abdullah, Run X Zeng, Chelsea L Margerum, David Papadopoli, Cian Monnin, Kaylee B Punter, Charles Chu, Mohammad Al-Rofaidi, Naser F Al-Tannak, Domenica Berardi, Zahra Rattray, Nicholas J W Rattray, Sheela A Abraham, Eeva-Liisa Eskelinen, David G Watson, Daina Avizonis, Ivan Topisirovic, Edmond Y W Chan.
      The relationship between nutrient starvation and mitochondrial dynamics is poorly understood. We find that cells facing amino acid starvation display clear mitochondrial fusion as a means to evade mitophagy. Surprisingly, further supplementation of glutamine (Q), leucine (L), and arginine (R) did not reverse, but produced stronger mitochondrial hyperfusion. Interestingly, the hyperfusion response to Q + L + R was dependent upon mitochondrial fusion proteins Mfn1 and Opa1 but was independent of MTORC1. Metabolite profiling indicates that Q + L + R addback replenishes amino acid and nucleotide pools. Inhibition of fumarate hydratase, glutaminolysis, or inosine monophosphate dehydrogenase all block Q + L + R-dependent mitochondrial hyperfusion, which suggests critical roles for the tricarboxylic acid (TCA) cycle and purine biosynthesis in this response. Metabolic tracer analyses further support the idea that supplemented Q promotes purine biosynthesis by serving as a donor of amine groups. We thus describe a metabolic mechanism for direct sensing of cellular amino acids to control mitochondrial fusion and cell fate.
    Keywords:  CP: Cell biology; CP: Metabolism; Drp1; Mfn1; Mfn2; Opa1; amino acid sensing; arginine; dynamics; fusion; glutamine; hyperfusion; leucine; mitochondria; stable isotope tracer
    DOI:  https://doi.org/10.1016/j.celrep.2022.111198
  28. Methods Mol Biol. 2022 ;2540 387-399
    Segmentation and Quantitative Analysis of Epithelial Tissues.
    Benoit Aigouy, Benjamin Prud'homme.
      Epithelial tissues regulate exchanges with the environment. They are highly dynamic and can acquire virtually any shape. At the cellular level, they are composed of cells tightly connected by junctions. Most often epithelia are amenable to live imaging; however, the vast number of cells composing an epithelium makes large-scale studies tedious. Here, we present Tissue Analyzer (TA), an open-source tool that can be used to segment epithelia and monitor cell and tissue dynamics.
    Keywords:  2D; 3D; Cells; Deep learning; Epithelia; Open source; Quantitative biology; Segmentation; Tissue Analyzer; Tracking
    DOI:  https://doi.org/10.1007/978-1-0716-2541-5_20
  29. Front Integr Neurosci. 2022 ;16 929788
    A protocol for rapid construction of senescent cells.
    Xing Yu, Jing Quan, Shuai Chen, Xinyue Yang, Shuai Huang, Gang Yang, Yujing Zhang.
      Aging may be the largest factor for a variety of chronic diseases that influence survival, independence, and wellbeing. Evidence suggests that aging could be thought of as the modifiable risk factor to delay or alleviate age-related conditions as a group by regulating essential aging mechanisms. One such mechanism is cellular senescence, which is a special form of most cells that are present as permanent cell cycle arrest, apoptosis resistance, expression of anti-proliferative molecules, acquisition of pro-inflammatory, senescence-associated secretory phenotype (SASP), and others. Most cells cultured in vitro or in vivo may undergo cellular senescence after accruing a set number of cell divisions or provoked by excessive endogenous and exogenous stress or damage. Senescent cells occur throughout life and play a vital role in various physiological and pathological processes such as embryogenesis, wound healing, host immunity, and tumor suppression. In contrast to the beneficial senescent processes, the accumulation of senescent also has deleterious effects. These non-proliferating cells lead to the decrease of regenerative potential or functions of tissues, inflammation, and other aging-associated diseases because of the change of tissue microenvironment with the acquisition of SASP. While it is understood that age-related diseases occur at the cellular level from the cellular senescence, the mechanisms of cellular senescence in age-related disease progression remain largely unknown. Simplified and rapid models such as in vitro models of the cellular senescence are critically needed to deconvolute mechanisms of age-related diseases. Here, we obtained replicative senescent L02 hepatocytes by culturing the cells for 20 weeks. Then, the conditioned medium containing supernatant from replicative senescent L02 hepatocytes was used to induce cellular senescence, which could rapidly induce hepatocytes into senescence. In addition, different methods were used to validate senescence, including senescence-associated β-galactosidase (SA-β-gal), the rate of DNA synthesis using 5-ethynyl-2'-deoxyuridine (EdU) incorporation assay, and senescence-related proteins. At last, we provide example results and discuss further applications of the protocol.
    Keywords:  SASP; aging; biomarker; cellular senescence; senescent cell models
    DOI:  https://doi.org/10.3389/fnint.2022.929788
  30. Nat Rev Cancer. 2022 Aug 18.
    Mastering the use of cellular barcoding to explore cancer heterogeneity.
    Antonin Serrano, Jean Berthelet, Shalin H Naik, Delphine Merino.
      Tumours are often composed of a multitude of malignant clones that are genomically unique, and only a few of them may have the ability to escape cancer therapy and grow as symptomatic lesions. As a result, tumours with a large degree of genomic diversity have a higher chance of leading to patient death. However, clonal fate can be driven by non-genomic features. In this context, new technologies are emerging not only to track the spatiotemporal fate of individual cells and their progeny but also to study their molecular features using various omics analysis. In particular, the recent development of cellular barcoding facilitates the labelling of tens to millions of cancer clones and enables the identification of the complex mechanisms associated with clonal fate in different microenvironments and in response to therapy. In this Review, we highlight the recent discoveries made using lentiviral-based cellular barcoding techniques, namely genetic and optical barcoding. We also emphasize the strengths and limitations of each of these technologies and discuss some of the key concepts that must be taken into consideration when one is designing barcoding experiments. Finally, we suggest new directions to further improve the use of these technologies in cancer research.
    DOI:  https://doi.org/10.1038/s41568-022-00500-2
  31. Mol Cells. 2022 Aug 19.
    Transcriptional Heterogeneity of Cellular Senescence in Cancer.
    Muhammad Junaid, Aejin Lee, Jaehyung Kim, Tae Jun Park, Su Bin Lim.
      Cellular senescence plays a paradoxical role in tumorigenesis through the expression of diverse senescence-associated (SA) secretory phenotypes (SASPs). The heterogeneity of SA gene expression in cancer cells not only promotes cancer stemness but also protects these cells from chemotherapy. Despite the potential correlation between cancer and SA biomarkers, many transcriptional changes across distinct cell populations remain largely unknown. During the past decade, single-cell RNA sequencing (scRNA-seq) technologies have emerged as powerful experimental and analytical tools to dissect such diverse senescence-derived transcriptional changes. Here, we review the recent sequencing efforts that successfully characterized scRNA-seq data obtained from diverse cancer cells and elucidated the role of senescent cells in tumor malignancy. We further highlight the functional implications of SA genes expressed specifically in cancer and stromal cell populations in the tumor microenvironment. Translational research leveraging scRNA-seq profiling of SA genes will facilitate the identification of novel expression patterns underlying cancer susceptibility, providing new therapeutic opportunities in the era of precision medicine.
    Keywords:  cancer; cellular heterogeneity; senescence; single-cell RNA sequencing
    DOI:  https://doi.org/10.14348/molcells.2022.0036
  32. Nat Metab. 2022 Aug 15.
    A practical guide for the analysis, standardization and interpretation of oxygen consumption measurements.
    Ajit S Divakaruni, Martin Jastroch.
      Measurement of oxygen consumption is a powerful and uniquely informative experimental technique. It can help identify mitochondrial mechanisms of action following pharmacologic and genetic interventions, and characterize energy metabolism in physiology and disease. The conceptual and practical benefits of respirometry have made it a frontline technique to understand how mitochondrial function can interface with-and in some cases control-cell physiology. Nonetheless, an appreciation of the complexity and challenges involved with such measurements is required to avoid common experimental and analytical pitfalls. Here we provide a practical guide to oxygen consumption measurements covering the selection of experimental models and instrumentation, as well as recommendations for the collection, interpretation and normalization of data. These guidelines are provided with the intention of aiding experimental design and enhancing the overall reputability, transparency and reliability of oxygen consumption measurements.
    DOI:  https://doi.org/10.1038/s42255-022-00619-4
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