bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021–08–22
37 papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Selective Autophagy.
  2. Capturing cancer evolution using genetically engineered mouse models (GEMMs).
  3. Nrf2 expression in pancreatic stellate cells promotes progression of cancer.
  4. LDL receptor-peptide conjugate as in vivo tool for specific targeting of pancreatic ductal adenocarcinoma.
  5. Dietary fructose improves intestinal cell survival and nutrient absorption.
  6. TLR2 activation promotes tumour growth and associates with patient survival and chemotherapy response in pancreatic ductal adenocarcinoma.
  7. Perioperative blood transfusions and survival in resected pancreatic adenocarcinoma patients given multimodality therapy.
  8. Mechanobiology: forcing the second act.
  9. Keap1 mutation renders lung adenocarcinomas dependent on Slc33a1.
  10. ZNF768 links oncogenic RAS to cellular senescence.
  11. AMPK: a key regulator of energy stress and calcium-induced autophagy.
  12. DOG1 is commonly expressed in pancreatic adenocarcinoma but unrelated to cancer aggressiveness.
  13. Entosis is induced by ultraviolet radiation.
  14. Emerging principles of cancer biophysics.
  15. Acquired resistance to PRMT5 inhibition induces concomitant collateral sensitivity to paclitaxel.
  16. Epigenetic age prediction.
  17. Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer.
  18. DAXX represents a new type of protein-folding enabler.
  19. Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes.
  20. Targeted Degradation of the Oncogenic Phosphatase SHP2.
  21. Targeted transcriptome and KRAS mutation analysis improve the diagnostic performance of EUS-FNA biopsies in pancreatic cancer.
  22. Lipid Carriers in Cancer: Context Matters.
  23. AGITG MASTERPLAN: a randomised phase II study of modified FOLFIRINOX alone or in combination with stereotactic body radiotherapy for patients with high-risk and locally advanced pancreatic cancer.
  24. Matrix stiffness primes cells for future oxidative stress.
  25. Skeletal muscle mitochondrial network dynamics in metabolic disorders and aging.
  26. Combined heterogeneity in cell size and deformability promotes cancer invasiveness.
  27. Network analyses reveal negative link between changes in adipose tissue GDF15 and BMI during dietary induced weight loss.
  28. JAK/STAT of all trades: Linking inflammation with cancer development, tumor progression, and therapy resistance.
  29. Molecular mechanism of prestin electromotive signal amplification.
  30. Data science in cell imaging.
  31. Autophagy is a major metabolic regulator involved in cancer therapy resistance.
  32. Tumour fatty acid metabolism in the context of therapy resistance and obesity.
  33. The senescence-associated secretory phenotype: Fueling a wound that never heals.
  34. Tumor organoids: Opportunities and challenges to guide precision medicine.
  35. Anti-PD-1/L1 lead-in before MAPK inhibitor combination maximizes antitumor immunity and efficacy.
  36. The MEMIC is an ex vivo system to model the complexity of the tumor microenvironment.
  37. Going your own way: Self-guidance mechanisms in cell migration.
  1. Cancer Sci. 2021 Aug 18.
    Selective Autophagy.
    Mohammad Omar Faruk, Yoshinobu Ichimura, Masaaki Komatsu.
      While starvation-induced autophagy is thought to randomly degrade cellular components, under certain circumstances autophagy selectively recognizes, sequesters, and degrades specific targets via autophagosomes. This process is called selective autophagy, and it contributes to cellular homeostasis by degrading specific soluble proteins, supramolecular complexes, liquid-liquid phase-separated droplets, abnormal or excess organelles, and pathogenic invasive bacteria. This means that autophagy, like the ubiquitin-proteasome system, strictly regulates diverse cellular functions through its selectivity. In this short review, we focus on the mechanism of "selective" autophagy, which is rapidly being elucidated.
    Keywords:  ; autophagy; ATG8-family proteins; liquid-liquid phase separation; selective autophagy; selective autophagy receptors
    DOI:  https://doi.org/10.1111/cas.15112
  2. Trends Cell Biol. 2021 Aug 13. pii: S0962-8924(21)00143-4. [Epub ahead of print]
    Capturing cancer evolution using genetically engineered mouse models (GEMMs).
    William Hill, Deborah R Caswell, Charles Swanton.
      Initiating from a single cell, cancer undergoes clonal evolution, leading to a high degree of intratumor heterogeneity (ITH). The arising genetic heterogeneity between cancer cells is influenced by exogenous and endogenous forces that shape the composition of clones within tumors. Preclinical mouse models have provided a valuable tool for understanding cancer, helping to build a fundamental understanding of tumor initiation, progression, and metastasis. Until recently, genetically engineered mouse models (GEMMS) of cancer had lacked the genetic diversity found in human tumors, in which evolution may be driven by long-term carcinogen exposure and DNA damage. However, advances in sequencing technology and in our understanding of the drivers of genetic instability have given us the knowledge to generate new mouse models, offering an approach to functionally explore mechanisms of tumor evolution.
    Keywords:  cancer evolution; mouse models; tumor heterogeneity
    DOI:  https://doi.org/10.1016/j.tcb.2021.07.003
  3. Am J Physiol Gastrointest Liver Physiol. 2021 08 18.
    Nrf2 expression in pancreatic stellate cells promotes progression of cancer.
    Yu Tanaka, Shin Hamada, Ryotaro Matsumoto, Keiko Taguchi, Masayuki Yamamoto, Atsushi Masamune.
      It was previously identified that systemic Nrf2-deletion attenuates pancreatic cancer progression in a mutant K-ras/p53-expressing mouse model (KPC mouse). In this study, the type of cell that is responsible for the retarded cancer progression was elucidated. Human pancreatic cancers were first examined, and elevated expression of NRF2-target gene products in a-smooth muscle actin-positive cells was found, suggesting that pancreatic stellate cells (PSCs) are involved in this process. Closer examination of primary cultured PSCs from Nrf2-deleted mice revealed that the cells were less proliferative and retained a lower migration capacity. The conditioned medium of Nrf2-deleted PSCs exhibited reduced growth-stimulating effects in pancreatic cancer cells. KPC mouse-derived pancreatic cancer cells co-injected with wild-type PSCs developed significantly larger subcutaneous tumors in immunodeficient mice than those co-injected with Nrf2-deleted PSCs. These results demonstrate that Nrf2 actively contributes to the function of PSCs to sustain KPC cancer progression, thus, suggesting that Nrf2 inhibition in PSCs may be therapeutically important in pancreatic cancer.
    Keywords:  Nrf2; oxidative stress; pancreatic fibrosis; pancreatic stellate cell; stroma
    DOI:  https://doi.org/10.1152/ajpgi.00120.2021
  4. Commun Biol. 2021 Aug 19. 4(1): 987
    LDL receptor-peptide conjugate as in vivo tool for specific targeting of pancreatic ductal adenocarcinoma.
    Angélina Acier, Magali Godard, Fanny Gassiot, Pascal Finetti, Marion Rubis, Jonathan Nowak, François Bertucci, Juan L Iovanna, Richard Tomasini, Pascaline Lécorché, Guillaume Jacquot, Michel Khrestchatisky, Jamal Temsamani, Cédric Malicet, Sophie Vasseur, Fabienne Guillaumond.
      Despite clinical advances in diagnosis and treatment, pancreatic ductal adenocarcinoma (PDAC) remains the third leading cause of cancer death, and is still associated with poor prognosis and dismal survival rates. Identifying novel PDAC-targeted tools to tackle these unmet clinical needs is thus an urgent requirement. Here we use a peptide conjugate that specifically targets PDAC through low-density lipoprotein receptor (LDLR). We demonstrate by using near-infrared fluorescence imaging the potential of this conjugate to specifically detect and discriminate primary PDAC from healthy organs including pancreas and from benign mass-forming chronic pancreatitis, as well as detect metastatic pancreatic cancer cells in healthy liver. This work paves the way towards clinical applications in which safe LDLR-targeting peptide conjugate promotes tumor-specific delivery of imaging and/or therapeutic agents, thereby leading to substantial improvements of the PDAC patient's outcome.
    DOI:  https://doi.org/10.1038/s42003-021-02508-0
  5. Nature. 2021 Aug 18.
    Dietary fructose improves intestinal cell survival and nutrient absorption.
    Samuel R Taylor, Shakti Ramsamooj, Roger J Liang, Alyna Katti, Rita Pozovskiy, Neil Vasan, Seo-Kyoung Hwang, Navid Nahiyaan, Nancy J Francoeur, Emma M Schatoff, Jared L Johnson, Manish A Shah, Andrew J Dannenberg, Robert P Sebra, Lukas E Dow, Lewis C Cantley, Kyu Y Rhee, Marcus D Goncalves.
      Fructose consumption is linked to the rising incidence of obesity and cancer, which are two of the leading causes of morbidity and mortality globally1,2. Dietary fructose metabolism begins at the epithelium of the small intestine, where fructose is transported by glucose transporter type 5 (GLUT5; encoded by SLC2A5) and phosphorylated by ketohexokinase to form fructose 1-phosphate, which accumulates to high levels in the cell3,4. Although this pathway has been implicated in obesity and tumour promotion, the exact mechanism that drives these pathologies in the intestine remains unclear. Here we show that dietary fructose improves the survival of intestinal cells and increases intestinal villus length in several mouse models. The increase in villus length expands the surface area of the gut and increases nutrient absorption and adiposity in mice that are fed a high-fat diet. In hypoxic intestinal cells, fructose 1-phosphate inhibits the M2 isoform of pyruvate kinase to promote cell survival5-7. Genetic ablation of ketohexokinase or stimulation of pyruvate kinase prevents villus elongation and abolishes the nutrient absorption and tumour growth that are induced by feeding mice with high-fructose corn syrup. The ability of fructose to promote cell survival through an allosteric metabolite thus provides additional insights into the excess adiposity generated by a Western diet, and a compelling explanation for the promotion of tumour growth by high-fructose corn syrup.
    DOI:  https://doi.org/10.1038/s41586-021-03827-2
  6. Oncogene. 2021 Aug 16.
    TLR2 activation promotes tumour growth and associates with patient survival and chemotherapy response in pancreatic ductal adenocarcinoma.
    Joanne Lundy, Linden J Gearing, Hugh Gao, Alison C West, Louise McLeod, Virginie Deswaerte, Liang Yu, Sean Porazinski, Marina Pajic, Paul J Hertzog, Daniel Croagh, Brendan J Jenkins.
      Pancreatic ductal adenocarcinoma (PDAC) has an extremely poor prognosis, and is plagued by a paucity of targeted treatment options and tumour resistance to chemotherapeutics. The causal link between chronic inflammation and PDAC suggests that molecular regulators of the immune system promote disease pathogenesis and/or therapeutic resistance, yet their identity is unclear. Here, we couple endoscopic ultrasound-guided fine-needle aspiration, which captures tumour biopsies from all stages, with whole transcriptome profiling of PDAC patient primary tumours to reveal enrichment of the innate immune Toll-like receptor 2 (TLR2) molecular pathway. Augmented TLR2 expression associated with a 4-gene "TLR2 activation" signature, and was prognostic for survival and predictive for gemcitabine-based chemoresistance. Furthermore, antibody-mediated anti-TLR2 therapy suppressed the growth of human PDAC tumour xenografts, independent of a functional immune system. Our results support TLR2-based therapeutic targeting for precision medicine in PDAC, with further clinical utility that TLR2 activation is prognostic and predictive for chemoresponsiveness.
    DOI:  https://doi.org/10.1038/s41388-021-01992-2
  7. J Surg Oncol. 2021 Aug 16.
    Perioperative blood transfusions and survival in resected pancreatic adenocarcinoma patients given multimodality therapy.
    Timothy E Newhook, Laura R Prakash, Jose Soliz, Shannon Hancher-Hodges, B Bryce Speer, Jonathan A Wilks, Morgan L Bruno, Whitney L Dewhurst, Elsa M Arvide, Jessica E Maxwell, Naruhiko Ikoma, Michael P Kim, Jeffrey E Lee, Matthew H G Katz, Ching-Wei D Tzeng.
       BACKGROUND AND OBJECTIVES: The impact of perioperative blood transfusion (PBT) on outcomes for pancreatic ductal adenocarcinoma (PDAC) patients given multimodality therapy (MMT) remains undefined. We sought to evaluate the association of PBT with survival after PDAC resection.
    METHODS: Pancreatectomy patients (July 2011-December 2017) who received MMT were abstracted from a prospective database. Overall survival (OS) was compared by PBT within 30 days, 24 h (24HR-BT), or 24 h until 30 days (Postop-BT).
    RESULTS: Most (76.6%) of 312 MMT patients underwent neoadjuvant therapy (NT). Eighty-nine patients (28.5%) received PBT; 58 (18.6%) 24HR-BT, and 31 (9.9%) Postop-BT. Compared with surgery-first, NT patients received more 24HR-BTs (22.2% vs. 6.8%, p = 0.003) and PBTs overall (32.6% vs. 15.1%, p = 0.004). Overall median OS was 45 months. The association of PBT with shorter median OS appeared limited to first 24-h transfusions (34 months 24HR-BT vs. 48 months Postop-BT vs. 53 months no-PBT, p = 0.009) and was dose-dependent, with a median OS of 52 months for 0 units 24HR-BT, 35 months for 1 unit, and 25 months for ≥2 units (p = 0.004). Independent predictors of OS included node-positivity (hazard ratio [HR]: 1.93, p < 0.001), perineural invasion (HR: 1.64, p = 0.050), postoperative pancreatic fistula (HR: 1.94, p = 0.018), and 24HR-BT (HR: 1.75, p = 0.001).
    CONCLUSIONS: Transfusions given within 24 h are associated with dose-dependent decreases in survival after pancreatectomy for PDAC.
    Keywords:  blood transfusion; multimodality therapy; neoadjuvant therapy; pancreatic cancer; perioperative transfusion
    DOI:  https://doi.org/10.1002/jso.26650
  8. Mol Biol Cell. 2021 Aug 19. 32(18): 1611-1613
    Mechanobiology: forcing the second act.
    Valerie M Weaver.
      
    DOI:  https://doi.org/10.1091/mbc.E21-07-0343
  9. Nat Cancer. 2020 Jun;1(6): 589-602
    Keap1 mutation renders lung adenocarcinomas dependent on Slc33a1.
    Rodrigo Romero, Francisco J Sánchez-Rivera, Peter M K Westcott, Kim L Mercer, Arjun Bhutkar, Alexander Muir, Tania J González-Robles, Swanny A Lamboy-Rodríguez, Laura Z Liao, Sheng Rong Ng, Leanne Li, Caterina I Colón, Santiago Naranjo, Mary Clare Beytagh, Caroline A Lewis, Peggy P Hsu, Roderick T Bronson, Matthew G Vander Heiden, Tyler Jacks.
      Approximately 20-30% of human lung adenocarcinomas (LUAD) harbor loss-of-function (LOF) mutations in Kelch-like ECH Associated-Protein 1 (KEAP1), which lead to hyperactivation of the nuclear factor, erythroid 2-like 2 (NRF2) antioxidant pathway and correlate with poor prognosis1-3. We previously showed that Keap1 mutation accelerates KRAS-driven LUAD and produces a marked dependency on glutaminolysis4. To extend the investigation of genetic dependencies in the context of Keap1 mutation, we performed a druggable genome CRISPR-Cas9 screen in Keap1-mutant cells. This analysis uncovered a profound Keap1 mutant-specific dependency on solute carrier family 33 member 1 (Slc33a1), an endomembrane-associated protein with roles in autophagy regulation5, as well as a series of functionally-related genes implicated in the unfolded protein response. Targeted genetic and biochemical experiments using mouse and human Keap1-mutant tumor lines, as well as preclinical genetically-engineered mouse models (GEMMs) of LUAD, validate Slc33a1 as a robust Keap1-mutant-specific dependency. Furthermore, unbiased genome-wide CRISPR screening identified additional genes related to Slc33a1 dependency. Overall, our study provides a strong rationale for stratification of patients harboring KEAP1-mutant or NRF2-hyperactivated tumors as likely responders to targeted SLC33A1 inhibition and underscores the value of integrating functional genetic approaches with GEMMs to identify and validate genotype-specific therapeutic targets.
    DOI:  https://doi.org/10.1038/s43018-020-0071-1
  10. Nat Commun. 2021 08 17. 12(1): 4841
    ZNF768 links oncogenic RAS to cellular senescence.
    Romain Villot, Audrey Poirier, Inan Bakan, Karine Boulay, Erlinda Fernández, Romain Devillers, Luciano Gama-Braga, Laura Tribouillard, Andréanne Gagné, Éma Duchesne, Danielle Caron, Jean-Sébastien Bérubé, Jean-Christophe Bérubé, Yan Coulombe, Michèle Orain, Yves Gélinas, Stéphane Gobeil, Yohan Bossé, Jean-Yves Masson, Sabine Elowe, Steve Bilodeau, Venkata Manem, Philippe Joubert, Frédérick A Mallette, Mathieu Laplante.
      RAS proteins are GTPases that lie upstream of a signaling network impacting cell fate determination. How cells integrate RAS activity to balance proliferation and cellular senescence is still incompletely characterized. Here, we identify ZNF768 as a phosphoprotein destabilized upon RAS activation. We report that ZNF768 depletion impairs proliferation and induces senescence by modulating the expression of key cell cycle effectors and established p53 targets. ZNF768 levels decrease in response to replicative-, stress- and oncogene-induced senescence. Interestingly, ZNF768 overexpression contributes to bypass RAS-induced senescence by repressing the p53 pathway. Furthermore, we show that ZNF768 interacts with and represses p53 phosphorylation and activity. Cancer genomics and immunohistochemical analyses reveal that ZNF768 is often amplified and/or overexpressed in tumors, suggesting that cells could use ZNF768 to bypass senescence, sustain proliferation and promote malignant transformation. Thus, we identify ZNF768 as a protein linking oncogenic signaling to the control of cell fate decision and proliferation.
    DOI:  https://doi.org/10.1038/s41467-021-24932-w
  11. J Mol Med (Berl). 2021 Aug 16.
    AMPK: a key regulator of energy stress and calcium-induced autophagy.
    Rimpi Saikia, Jomon Joseph.
      Autophagy is a well-known cell-survival strategy orchestrated by a conserved set of proteins. It equips the cells with mechanisms to attain homeostasis during unfavorable conditions such as stress by breaking down the cellular components and reusing them for energy as well as for building new components required for survival. A basal level of autophagy is required for achieving homeostasis under normal conditions through regular turnover of macromolecules and organelles. Initiation of autophagy is regulated by two key components of the nutrient/energy sensor pathways; mammalian target of rapamycin 1 (mTORC1) and AMP-activated kinase (AMPK). Under energy-deprived conditions, AMPK is activated triggering autophagy, whereas, in nutrient-rich conditions, the growth-promoting kinase mTORC1 is activated inhibiting autophagy. Thus, the reciprocal regulation of autophagy by AMPK and mTORC1 defines a fundamental mechanism by which cells respond to nutrient availability. Interestingly, cytoplasmic calcium is also found to be an activator of AMPK and autophagy through a calmodulin/CaMKKβ pathway. However, the physiological significance of the regulation of autophagy by cytoplasmic calcium is currently unclear. This review focuses on the current understanding of the mechanism of autophagy and its regulation by AMPK.
    Keywords:  AMPK; Autophagy; CaMKKβ; Calcium; Energy homeostasis; LKB1; mTORC1
    DOI:  https://doi.org/10.1007/s00109-021-02125-8
  12. PeerJ. 2021 ;9 e11905
    DOG1 is commonly expressed in pancreatic adenocarcinoma but unrelated to cancer aggressiveness.
    Kristina Jansen, Franziska Büscheck, Katharina Moeller, Martina Kluth, Claudia Hube-Magg, Niclas Christian Blessin, Daniel Perez, Jakob Izbicki, Michael Neipp, Hamid Mofid, Thies Daniels, Ulf Nahrstedt, Christoph Fraune, Frank Jacobsen, Christian Bernreuther, Patrick Lebok, Guido Sauter, Ria Uhlig, Waldemar Wilczak, Ronald Simon, Stefan Steurer, Eike Burandt, Andreas Marx, Till Krech, Till Clauditz.
       Background: DOG1 (ANO1; TMEM16A) is a voltage-gated calcium-activated chloride and bicarbonate channel. DOG1 is physiologically expressed in Cajal cells, where it plays an important role in regulating intestinal motility and its expression is a diagnostic hallmark of gastrointestinal stromal tumors (GIST). Data on a possible role of DOG1 in pancreatic cancer are rare and controversial. The aim of our study was to clarify the prevalence of DOG1 expression in pancreatic cancer and to study its association with parameters of cancer aggressiveness.
    Methods: DOG1 expression was analyzed by immunohistochemistry in 599 pancreatic cancers in a tissue microarray format and in 12 cases of pancreatitis on large tissue sections.
    Results: DOG1 expression was always absent in normal pancreas but a focal weak expression was seen in four of 12 cases of pancreatitis. DOG1 expression was, however, common in pancreatic cancer. Membranous and cytoplasmic DOG1 expression in tumor cells was highest in pancreatic ductal adenocarcinomas (61% of 444 interpretable cases), followed by cancers of the ampulla Vateri (43% of 51 interpretable cases), and absent in 6 acinus cell carcinomas. DOG1 expression in tumor associated stroma cells was seen in 76 of 444 (17%) pancreatic ductal adenocarcinomas and in seven of 51 (14%) cancers of the ampulla Vateri. Both tumoral and stromal DOG1 expression were unrelated to tumor stage, grade, lymph node and distant metastasis, mismatch repair protein deficiency and the density of CD8 positive cytotoxic T-lymphocytes in the subgroups of ductal adenocarcinomas and cancers of ampulla Vateri. Overall, the results of our study indicate that DOG1 may represent a potential biomarker for pancreatic cancer diagnosis and a putative therapeutic target in pancreatic cancer. However, DOG1 expression is unrelated to pancreatic cancer aggressiveness.
    Keywords:  DOG1; Immunohistochemistry; Pancreatic adenocarcinoma; Tissue micro array
    DOI:  https://doi.org/10.7717/peerj.11905
  13. iScience. 2021 Aug 20. 24(8): 102902
    Entosis is induced by ultraviolet radiation.
    Ruoyao Chen, Abhineet Ram, John G Albeck, Michael Overholtzer.
      Entosis is a cell death mechanism that is executed through neighbor cell ingestion and killing that occurs in cancer tissues and during development. Here, we identify JNK and p38 stress-activated kinase signaling as an inducer of entosis in cells exposed to ultraviolet (UV) radiation. Cells with high levels of stress signaling are ingested and killed by those with low levels, a result of heterogeneity arising within cell populations over time. In stressed cells, entosis occurs as part of mixed-cell death response with parallel induction of apoptosis and necrosis, and we find that inhibition of one form of cell death leads to increased rates of another. Together, these findings identify stress-activated kinase signaling as a new inducer of entosis and demonstrate cross talk between different forms of cell death that can occur in parallel in response to UV radiation.
    Keywords:  Cell biology; Cellular physiology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2021.102902
  14. Fac Rev. 2021 ;10 61
    Emerging principles of cancer biophysics.
    Woong Young So, Kandice Tanner.
      Cancer is a multi-step process where normal cells become transformed, grow, and may disseminate to establish new lesions within the body. In recent years, the physical properties of individual cells and the tissue microenvironment have been shown to be potent determinants of cancer progression. Biophysical tools have long been used to examine cell and tissue mechanics, morphology, and migration. However, exciting developments have linked these physical traits to gene expression changes that drive metastatic seeding, organ selectivity, and tumor growth. Here, we present some vignettes to address recent studies to show progress in harnessing biophysical tools and concepts to gain insights into metastasis.
    Keywords:  microenvironment; rheology; tissue biophysics
    DOI:  https://doi.org/10.12703/r/10-61
  15. Proc Natl Acad Sci U S A. 2021 Aug 24. pii: e2024055118. [Epub ahead of print]118(34):
    Acquired resistance to PRMT5 inhibition induces concomitant collateral sensitivity to paclitaxel.
    Helen S Mueller, Colin E Fowler, Simona Dalin, Enrico Moiso, Tee Udomlumleart, Salil Garg, Michael T Hemann, Jacqueline A Lees.
      Epigenetic regulators play key roles in cancer and are increasingly being targeted for treatment. However, for many, little is known about mechanisms of resistance to the inhibition of these regulators. We have generated a model of resistance to inhibitors of protein arginine methyltransferase 5 (PRMT5). This study was conducted in Kras G12D;Tp53-null lung adenocarcinoma (LUAD) cell lines. Resistance to PRMT5 inhibitors (PRMT5i) arose rapidly, and barcoding experiments showed that this resulted from a drug-induced transcriptional state switch, not selection of a preexisting population. This resistant state is both stable and conserved across variants arising from distinct LUAD lines. Moreover, it brought with it vulnerabilities to other chemotherapeutics, especially the taxane paclitaxel. This paclitaxel sensitivity depended on the presence of stathmin 2 (STMN2), a microtubule regulator that is specifically expressed in the resistant state. Remarkably, STMN2 was also essential for resistance to PRMT5 inhibition. Thus, a single gene is required for both acquisition of resistance to PRMT5i and collateral sensitivity to paclitaxel in our LUAD cells. Accordingly, the combination of PRMT5i and paclitaxel yielded potent and synergistic killing of the murine LUAD cells. Importantly, the synergy between PRMT5i and paclitaxel also extended to human cancer cell lines. Finally, analysis of The Cancer Genome Atlas patient data showed that high STMN2 levels correlate with complete regression of tumors in response to taxane treatment. Collectively, this study reveals a recurring mechanism of PRMT5i resistance in LUAD and identifies collateral sensitivities that have potential clinical relevance.
    Keywords:  PRMT5i resistance; STMN2; collateral sensitivity
    DOI:  https://doi.org/10.1073/pnas.2024055118
  16. Aging Cell. 2021 Aug 20. e13452
    Epigenetic age prediction.
    Daniel J Simpson, Tamir Chandra.
      Advanced age is the main common risk factor for cancer, cardiovascular disease and neurodegeneration. Yet, more is known about the molecular basis of any of these groups of diseases than the changes that accompany ageing itself. Progress in molecular ageing research was slow because the tools predicting whether someone aged slowly or fast (biological age) were unreliable. To understand ageing as a risk factor for disease and to develop interventions, the molecular ageing field needed a quantitative measure; a clock for biological age. Over the past decade, a number of age predictors utilising DNA methylation have been developed, referred to as epigenetic clocks. While they appear to estimate biological age, it remains unclear whether the methylation changes used to train the clocks are a reflection of other underlying cellular or molecular processes, or whether methylation itself is involved in the ageing process. The precise aspects of ageing that the epigenetic clocks capture remain hidden and seem to vary between predictors. Nonetheless, the use of epigenetic clocks has opened the door towards studying biological ageing quantitatively, and new clocks and applications, such as forensics, appear frequently. In this review, we will discuss the range of epigenetic clocks available, their strengths and weaknesses, and their applicability to various scientific queries.
    Keywords:  ageing; composite predictors; epigenetic clocks; minimised clocks; mortality
    DOI:  https://doi.org/10.1111/acel.13452
  17. EMBO Mol Med. 2021 Aug 19. e14123
    Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer.
    Florian Uhlitz, Philip Bischoff, Stefan Peidli, Anja Sieber, Alexandra Trinks, Mareen Lüthen, Benedikt Obermayer, Eric Blanc, Yana Ruchiy, Thomas Sell, Soulafa Mamlouk, Roberto Arsie, Tzu-Ting Wei, Kathleen Klotz-Noack, Roland F Schwarz, Birgit Sawitzki, Carsten Kamphues, Dieter Beule, Markus Landthaler, Christine Sers, David Horst, Nils Blüthgen, Markus Morkel.
      In colorectal cancer, oncogenic mutations transform a hierarchically organized and homeostatic epithelium into invasive cancer tissue lacking visible organization. We sought to define transcriptional states of colorectal cancer cells and signals controlling their development by performing single-cell transcriptome analysis of tumors and matched non-cancerous tissues of twelve colorectal cancer patients. We defined patient-overarching colorectal cancer cell clusters characterized by differential activities of oncogenic signaling pathways such as mitogen-activated protein kinase and oncogenic traits such as replication stress. RNA metabolic labeling and assessment of RNA velocity in patient-derived organoids revealed developmental trajectories of colorectal cancer cells organized along a mitogen-activated protein kinase activity gradient. This was in contrast to normal colon organoid cells developing along graded Wnt activity. Experimental targeting of EGFR-BRAF-MEK in cancer organoids affected signaling and gene expression contingent on predictive KRAS/BRAF mutations and induced cell plasticity overriding default developmental trajectories. Our results highlight directional cancer cell development as a driver of non-genetic cancer cell heterogeneity and re-routing of trajectories as a response to targeted therapy.
    Keywords:  ERK; RNA velocity; SLAM-Seq; cancer profiling; single-cell RNA sequencing
    DOI:  https://doi.org/10.15252/emmm.202114123
  18. Nature. 2021 Aug 18.
    DAXX represents a new type of protein-folding enabler.
    Liangqian Huang, Trisha Agrawal, Guixin Zhu, Sixiang Yu, Liming Tao, JiaBei Lin, Ronen Marmorstein, James Shorter, Xiaolu Yang.
      Protein quality control systems are crucial for cellular function and organismal health. At present, most known protein quality control systems are multicomponent machineries that operate via ATP-regulated interactions with non-native proteins to prevent aggregation and promote folding1, and few systems that can broadly enable protein folding by a different mechanism have been identified. Moreover, proteins that contain the extensively charged poly-Asp/Glu (polyD/E) region are common in eukaryotic proteomes2, but their biochemical activities remain undefined. Here we show that DAXX, a polyD/E protein that has been implicated in diverse cellular processes3-10, possesses several protein-folding activities. DAXX prevents aggregation, solubilizes pre-existing aggregates and unfolds misfolded species of model substrates and neurodegeneration-associated proteins. Notably, DAXX effectively prevents and reverses aggregation of its in vivo-validated client proteins, the tumour suppressor p53 and its principal antagonist MDM2. DAXX can also restore native conformation and function to tumour-associated, aggregation-prone p53 mutants, reducing their oncogenic properties. These DAXX activities are ATP-independent and instead rely on the polyD/E region. Other polyD/E proteins, including ANP32A and SET, can also function as stand-alone, ATP-independent molecular chaperones, disaggregases and unfoldases. Thus, polyD/E proteins probably constitute a multifunctional protein quality control system that operates via a distinctive mechanism.
    DOI:  https://doi.org/10.1038/s41586-021-03824-5
  19. Nat Commun. 2021 08 17. 12(1): 4995
    Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes.
    Alex S Genshaft, Carly G K Ziegler, Constantine N Tzouanas, Benjamin E Mead, Alex M Jaeger, Andrew W Navia, Ryan P King, Miyeko D Mana, Siyi Huang, Vanessa Mitsialis, Scott B Snapper, Ömer H Yilmaz, Tyler Jacks, Jeffrey F Van Humbeck, Alex K Shalek.
      A cell's phenotype and function are influenced by dynamic interactions with its microenvironment. To examine cellular spatiotemporal activity, we developed SPACECAT-Spatially PhotoActivatable Color Encoded Cell Address Tags-to annotate, track, and isolate cells while preserving viability. In SPACECAT, samples are stained with photocaged fluorescent molecules, and cells are labeled by uncaging those molecules with user-patterned near-UV light. SPACECAT offers single-cell precision and temporal stability across diverse cell and tissue types. Illustratively, we target crypt-like regions in patient-derived intestinal organoids to enrich for stem-like and actively mitotic cells, matching literature expectations. Moreover, we apply SPACECAT to ex vivo tissue sections from four healthy organs and an autochthonous lung tumor model. Lastly, we provide a computational framework to identify spatially-biased transcriptome patterns and enriched phenotypes. This minimally perturbative and broadly applicable method links cellular spatiotemporal and/or behavioral phenotypes with diverse downstream assays, enabling insights into the connections between tissue microenvironments and (dys)function.
    DOI:  https://doi.org/10.1038/s41467-021-25279-y
  20. Biochemistry. 2021 Aug 19.
    Targeted Degradation of the Oncogenic Phosphatase SHP2.
    Vidyasiri Vemulapalli, Katherine A Donovan, Tom C M Seegar, Julia M Rogers, Munhyung Bae, Ryan J Lumpkin, Ruili Cao, Matthew T Henke, Soumya S Ray, Eric S Fischer, Gregory D Cuny, Stephen C Blacklow.
      SHP2 is a protein tyrosine phosphatase that plays a critical role in the full activation of the Ras-MAPK pathway upon stimulation of receptor tyrosine kinases, which are frequently amplified or mutationally activated in human cancer. In addition, activating mutations in SHP2 result in developmental disorders and hematologic malignancies. Several allosteric inhibitors have been developed for SHP2 and are currently in clinical trials. Here, we report the development and evaluation of a SHP2 PROTAC created by conjugating RMC-4550 with pomalidomide using a PEG linker. This molecule is highly selective for SHP2, induces degradation of SHP2 in leukemic cells at submicromolar concentrations, inhibits MAPK signaling, and suppresses cancer cell growth. SHP2 PROTACs serve as an alternative strategy for targeting ERK-dependent cancers and are useful tools alongside allosteric inhibitors for dissecting the mechanisms by which SHP2 exerts its oncogenic activity.
    DOI:  https://doi.org/10.1021/acs.biochem.1c00377
  21. Clin Cancer Res. 2021 Aug 16. pii: clincanres.1107.2021. [Epub ahead of print]
    Targeted transcriptome and KRAS mutation analysis improve the diagnostic performance of EUS-FNA biopsies in pancreatic cancer.
    Joanne Lundy, Hugh Gao, William Berry, Samar Masoumi-Moghaddam, Brendan J Jenkins, Daniel Croagh.
       BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) carries a poor prognosis, and current diagnostic tests have suboptimal sensitivity. Incorporating standard cytology with targeted transcriptomic and mutation analysis may improve the accuracy of diagnostic biopsies, thus reducing the burden of repeat procedures and delays to treatment initiation.
    METHODS: We reviewed the accuracy of 308 EUS-FNA PDAC biopsies using a large multicenter clinical and biospecimen database, then performed RNA sequencing on 134 EUS-FNA biopsies spanning all stages of disease. We identified a transcriptomic diagnostic gene signature which was validated using external datasets and 60 further diagnostic EUS-FNAs. KRAS ddPCR analysis was performed and correlated with signature gene expression.
    RESULTS: The sensitivity of EUS-FNA cytology in diagnosing solid pancreatic masses in our retrospective cohort (n=308) was 78.6% (95% CI 73.2 to 83.2%). KRAS mutation analysis and our custom transcriptomic signature significantly improved upon the diagnostic accuracy of standard cytology to 91.3% in external validation sets and 91.6% in our validation cohort (n=60). Exploratory ddPCR analysis of KRAS mutant allele fraction (MAF%) correlated with signature performance and may represent a novel surrogate marker of tumour cellularity in EUS-FNA biopsies.
    CONCLUSIONS: Our findings support EUS-FNA biopsies as a feasible tissue source for integrated genomic and transcriptomic analysis of PDAC across all tumour stages, including cases with non-diagnostic cytology. Our transcriptome-derived genetic signature in combination with tissue KRAS mutation analysis significantly improves upon the diagnostic accuracy of current standard procedures, and has potential clinical utility in improving the speed and accuracy of diagnosis for patients presenting with PDAC.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-21-1107
  22. Cancer Res. 2021 Aug 15. 81(16): 4186-4187
    Lipid Carriers in Cancer: Context Matters.
    Mara H Sherman.
      Investigating immune suppression mechanisms in cancer may inform on strategies to overcome resistance to current immunotherapies, common across solid tumor types but near ubiquitous in pancreatic ductal adenocarcinoma (PDAC). A recent study by Kemp and colleagues in Cancer Research identified an immuno-modulatory axis originating in tumor-associated macrophages whereby macrophage-derived apolipoprotein E (APOE) activates NF-κB in tumor cells in a paracrine manner, inducing expression of immunosuppressive chemokines. In contrast, APOE promotes antitumor immunity in other cancer types including melanoma, highlighting the context dependency of APOE signaling and its impact on the tumor microenvironment. As new immunotherapy approaches increasingly aim to modulate both the myeloid and lymphoid compartments of the PDAC immune milieu, identification of specific mechanisms that foster macrophage-mediated immune suppression may facilitate the development of effective strategies that enable the immune system to tackle these tumors.See related article by Kemp et al., p. 4305.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-1930
  23. BMC Cancer. 2021 Aug 19. 21(1): 936
    AGITG MASTERPLAN: a randomised phase II study of modified FOLFIRINOX alone or in combination with stereotactic body radiotherapy for patients with high-risk and locally advanced pancreatic cancer.
    Andrew Oar, Mark Lee, Hien Le, Kate Wilson, Chris Aiken, Lorraine Chantrill, John Simes, Nam Nguyen, Andrew Barbour, Jaswinder Samra, Katrin M Sjoquist, Alisha Moore, David Espinoza, Val Gebski, Sonia Yip, Julie Chu, Andrew Kneebone, David Goldstein.
       BACKGROUND: Among patients with non-metastatic pancreatic cancer, 80% have high-risk, borderline resectable or locally advanced cancer, with a 5-year overall survival of 12%. MASTERPLAN evaluates the safety and activity of stereotactic body radiotherapy (SBRT) in addition to chemotherapy in these patients.
    METHODS AND DESIGN: MASTERPLAN is a multi-centre randomised phase II trial of 120 patients with histologically confirmed potentially operable pancreatic cancer (POPC) or inoperable pancreatic cancer (IPC). POPC includes patients with borderline resectable or high-risk tumours; IPC is defined as locally advanced or medically inoperable pancreatic cancer. Randomisation is 2:1 to chemotherapy + SBRT (investigational arm) or chemotherapy alone (control arm) by minimisation and stratified by patient cohort (POPC v IPC), planned induction chemotherapy and institution. Chemotherapy can have been commenced ≤28 days prior to randomisation. Both arms receive 6 × 2 weekly cycles of modified FOLFIRINOX (oxaliplatin (85 mg/m2 IV), irinotecan (150 mg/m2), 5-fluorouracil (2400 mg/m2 CIV), leucovorin (50 mg IV bolus)) plus SBRT in the investigational arm. Gemcitabine+nab-paclitaxel is permitted for patients unsuitable for mFOLFIRINOX. SBRT is 40Gy in five fractions with planning quality assurance to occur in real time. Following initial chemotherapy ± SBRT, resectability will be evaluated. For resected patients, adjuvant chemotherapy is six cycles of mFOLFIRINOX. Where gemcitabine+nab-paclitaxel was used initially, the adjuvant treatment is 12 weeks of gemcitabine and capecitabine or mFOLFIRINOX. Unresectable or medically inoperable patients with stable/responding disease will continue with a further six cycles of mFOLFIRINOX or three cycles of gemcitabine+nab-paclitaxel, whatever was used initially. The primary endpoint is 12-month locoregional control. Secondary endpoints are safety, surgical morbidity and mortality, radiological response rates, progression-free survival, pathological response rates, surgical resection rates, R0 resection rate, quality of life, deterioration-free survival and overall survival. Tertiary/correlative objectives are radiological measures of nutrition and sarcopenia, and serial tissue, blood and microbiome samples to be assessed for associations between clinical endpoints and potential predictive/prognostic biomarkers. Interim analysis will review rates of locoregional recurrence, distant failure and death after 40 patients complete 12 months follow-up. Fifteen Australian and New Zealand sites will recruit over a 4-year period, with minimum follow-up period of 12 months.
    DISCUSSION: MASTERPLAN evaluates SBRT in both resectable and unresectable patients with pancreatic ductal adenocarcinoma.
    TRIAL REGISTRATION: Australia New Zealand Clinical Trials Registry ACTRN12619000409178 , 13/03/2019. Protocol version: 2.0, 19 May 2019.
    Keywords:  Borderline resectable; Gemcitabine; Modified FOLFIRINOX; Nab-paclitaxel; Pancreas; Pancreatic cancer; SBRT; Stereotactic radiotherapy; mFOLFIRINOX
    DOI:  https://doi.org/10.1186/s12885-021-08666-y
  24. Trends Cancer. 2021 Aug 17. pii: S2405-8033(21)00162-X. [Epub ahead of print]
    Matrix stiffness primes cells for future oxidative stress.
    Paul V Taufalele, Cynthia A Reinhart-King.
      Focus on metabolic reprogramming has re-emerged in recent years due to the far-reaching consequences of metabolism on nearly all cellular behaviors. In a recent study in Cell Metabolism, Tharp et al. show that adhesion-dependent mechanical signaling induces mitochondrial and metabolic reprogramming to help cells adapt to future oxidative stress.
    Keywords:  ROS; matrix stiffness; mechanosignaling; mitohormesis
    DOI:  https://doi.org/10.1016/j.trecan.2021.08.003
  25. Trends Mol Med. 2021 Aug 17. pii: S1471-4914(21)00198-2. [Epub ahead of print]
    Skeletal muscle mitochondrial network dynamics in metabolic disorders and aging.
    Ciarán E Fealy, Lotte Grevendonk, Joris Hoeks, Matthijs K C Hesselink.
      With global demographics trending towards an aging population, the numbers of individuals with an age-associated loss of independence is increasing. A key contributing factor is loss of skeletal muscle mitochondrial, metabolic, and contractile function. Recent advances in imaging technologies have demonstrated the importance of mitochondrial morphology and dynamics in the pathogenesis of disease. In this review, we examine the evidence for altered mitochondrial dynamics as a mechanism in age and obesity-associated loss of skeletal muscle function, with a particular focus on the available human data. We highlight some of the areas where more data are needed to identify the specific mechanisms connecting mitochondrial morphology and skeletal muscle dysfunction.
    Keywords:  aging; metabolic disease; mitochondria; mitochondrial dynamics; sarcopenia
    DOI:  https://doi.org/10.1016/j.molmed.2021.07.013
  26. J Cell Sci. 2021 Apr 01. pii: jcs250225. [Epub ahead of print]134(7):
    Combined heterogeneity in cell size and deformability promotes cancer invasiveness.
    Asadullah, Sandeep Kumar, Neha Saxena, Madhurima Sarkar, Amlan Barai, Shamik Sen.
      Phenotypic heterogeneity is increasingly acknowledged to confer several advantages to cancer progression and drug resistance. Here, we probe the collective importance of heterogeneity in cell size and deformability in breast cancer invasion. A computational model of invasion of a heterogeneous cell aggregate predicts that combined heterogeneity in cell size and deformability enhances invasiveness of the whole population, with maximum invasiveness at intermediate cell-cell adhesion. We then show that small cells of varying deformability, a subpopulation predicted to be enriched at the invasive front, exhibit considerable overlap with the biophysical properties of cancer stem cells (CSCs). In MDA-MB-231 cells, these include CD44hi CD24- mesenchymal CSCs, which are small and soft, and CD44hi CD24+ hybrid CSCs, which exhibit a wide range of size and deformability. We validate our predictions by tracking the pattern of cell invasion from spheroids implanted in three-dimensional collagen gels, wherein we show temporal enrichment of CD44hi cells at the invasive front. Collectively, our results illustrate the advantages imparted by biophysical heterogeneity in enhancing cancer invasiveness. This article has an associated First Person interview with the first author of the paper.
    Keywords:  Biophysical heterogeneity; Breast cancer invasion; Cancer stem cells
    DOI:  https://doi.org/10.1242/jcs.250225
  27. J Clin Endocrinol Metab. 2021 Aug 20. pii: dgab621. [Epub ahead of print]
    Network analyses reveal negative link between changes in adipose tissue GDF15 and BMI during dietary induced weight loss.
    Alyssa Imbert, Nathalie Vialaneix, Julien Marquis, Julie Vion, Aline Charpagne, Sylviane Metairon, Claire Laurens, Cedric Moro, Nathalie Boulet, Ondine Walter, Grégory Lefebvre, Jörg Hager, Dominique Langin, Wim H M Saris, Arne Astrup, Nathalie Viguerie, Armand Valsesia.
       CONTEXT: Adipose tissue (AT) transcriptome studies provide holistic pictures of adaptation to weight and related bioclinical settings changes.
    OBJECTIVE: To implement AT gene expression profiling and investigate the link between changes in bioclinical parameters and AT gene expression during three steps of a two-phase dietary intervention (DI).
    DESIGN: AT transcriptome profiling was obtained from sequencing 1051 samples, corresponding to 556 distinct individuals enrolled in a weight loss intervention (8-week low calorie diet (LCD) at 800 kcal/d) followed with a 6-month ad libitum randomized DI.
    METHODS: Transcriptome profiles obtained with QuantSeq sequencing were benchmarked against Illumina RNAseq. RT-qPCR was used to further confirm associations. Cell specificity was assessed using freshly isolated cells and THP-1 cell line.
    RESULTS: During LCD, five modules were found, of which three included at least one bio-clinical variable. Change in BMI connected with changes in mRNA level of genes with inflammatory response signature. In this module, change in BMI was negatively associated to changes in expression of genes encoding secreted protein (GDF15, CCL3 and SPP1). Through all phases of the DI, change in GDF15 was connected to changes in SPP1, CCL3, LIPA and CD68. Further characterization showed that these genes were specific to macrophages (with LIPA, CD68 and GDF15 expressed in anti-inflammatory macrophages) and GDF15 also expressed in preadipocytes.
    CONCLUSION: Network analyses identified a novel AT feature with GDF15 upregulated with calorie restriction induced weight loss, concomitantly to macrophage markers. In AT, GDF15 was expressed in preadipocytes and macrophages where it was a hallmark of anti-inflammatory cells.
    Keywords:  Adipocyte; inflammation; low calorie diet; macrophage; network analyses; weight loss
    DOI:  https://doi.org/10.1210/clinem/dgab621
  28. Carcinogenesis. 2021 Aug 20. pii: bgab075. [Epub ahead of print]
    JAK/STAT of all trades: Linking inflammation with cancer development, tumor progression, and therapy resistance.
    Hatem E Sabaawy, Bríd M Ryan, Hossein Khiabanian, Sharon R Pine.
      Inflammation is at the forefront of carcinogenesis, tumor progression, and resistance to therapy. The JAK/STAT signaling axis is a central pathway that mediates the cellular response to inflammation and contributes to carcinogenesis. The JAK/STAT pathway coordinates intercellular communication between tumor cells and their immune microenvironment, and JAK/STAT activation leads to the expression of a variety of proteins involved in cell proliferation, cell survival, stemness, self-renewal, evasion of immunosurveillance mechanisms, and overall tumor progression. Activation of JAK/STAT signaling also mediates resistance to radiation therapy or cytotoxic agents, and modulates tumor cell responses to molecularly targeted and immune modulating drugs. Despite extensive research focused on understanding its signaling mechanisms and downstream phenotypic and functional consequences in hematological disorders, the importance of JAK/STAT signaling in solid tumor initiation and progression has been underappreciated. We highlight the role of chronic inflammation in cancer, the epidemiological evidence for contribution of JAK/STAT to carcinogenesis, the current cancer prevention measures involving JAK/STAT inhibition, and the impact of JAK/STAT signaling activity on cancer development, progression, and treatment resistance. We also discuss recent therapeutic advances in targeting key factors within the JAK/STAT pathway with single agents, and the use of these agents in combination with other targeted therapies and immune checkpoint inhibitors.
    DOI:  https://doi.org/10.1093/carcin/bgab075
  29. Cell. 2021 Aug 10. pii: S0092-8674(21)00893-X. [Epub ahead of print]
    Molecular mechanism of prestin electromotive signal amplification.
    Jingpeng Ge, Johannes Elferich, Sepehr Dehghani-Ghahnaviyeh, Zhiyu Zhao, Marc Meadows, Henrique von Gersdorff, Emad Tajkhorshid, Eric Gouaux.
      Hearing involves two fundamental processes: mechano-electrical transduction and signal amplification. Despite decades of studies, the molecular bases for both remain elusive. Here, we show how prestin, the electromotive molecule of outer hair cells (OHCs) that senses both voltage and membrane tension, mediates signal amplification by coupling conformational changes to alterations in membrane surface area. Cryoelectron microscopy (cryo-EM) structures of human prestin bound with chloride or salicylate at a common "anion site" adopt contracted or expanded states, respectively. Prestin is ensconced within a perimeter of well-ordered lipids, through which it induces dramatic deformation in the membrane and couples protein conformational changes to the bulk membrane. Together with computational studies, we illustrate how the anion site is allosterically coupled to changes in the transmembrane domain cross-sectional area and the surrounding membrane. These studies provide insight into OHC electromotility by providing a structure-based mechanism of the membrane motor prestin.
    Keywords:  cochlear amplification; cryo-EM; electromotility; hearing; intrinsic voltage sensor; mechanotransduction; membrane protein; outer hair cells; prestin; protein lipid interaction
    DOI:  https://doi.org/10.1016/j.cell.2021.07.034
  30. J Cell Sci. 2021 Apr 01. pii: jcs254292. [Epub ahead of print]134(7):
    Data science in cell imaging.
    Meghan K Driscoll, Assaf Zaritsky.
      Cell imaging has entered the 'Big Data' era. New technologies in light microscopy and molecular biology have led to an explosion in high-content, dynamic and multidimensional imaging data. Similar to the 'omics' fields two decades ago, our current ability to process, visualize, integrate and mine this new generation of cell imaging data is becoming a critical bottleneck in advancing cell biology. Computation, traditionally used to quantitatively test specific hypotheses, must now also enable iterative hypothesis generation and testing by deciphering hidden biologically meaningful patterns in complex, dynamic or high-dimensional cell image data. Data science is uniquely positioned to aid in this process. In this Perspective, we survey the rapidly expanding new field of data science in cell imaging. Specifically, we highlight how data science tools are used within current image analysis pipelines, propose a computation-first approach to derive new hypotheses from cell image data, identify challenges and describe the next frontiers where we believe data science will make an impact. We also outline steps to ensure broad access to these powerful tools - democratizing infrastructure availability, developing sensitive, robust and usable tools, and promoting interdisciplinary training to both familiarize biologists with data science and expose data scientists to cell imaging.
    Keywords:  Data science; Deep learning; Imaging; Machine learning; Microscopy
    DOI:  https://doi.org/10.1242/jcs.254292
  31. Cell Rep. 2021 Aug 17. pii: S2211-1247(21)00959-1. [Epub ahead of print]36(7): 109528
    Autophagy is a major metabolic regulator involved in cancer therapy resistance.
    Laura Poillet-Perez, Jean-Emmanuel Sarry, Carine Joffre.
      Autophagy sustains cellular homeostasis and metabolism in numerous diseases. By regulating cancer metabolism, both tumor and microenvironmental autophagy promote tumor growth. However, autophagy can support cancer progression through other biological functions such as immune response regulation or cytokine/growth factor secretion. Moreover, autophagy is induced in numerous tumor types as a resistance mechanism following therapy, highlighting autophagy inhibition as a promising target for anti-cancer therapy. Thus, better understanding the mechanisms involved in tumor growth and resistance regulation through autophagy, which are not fully understood, will provide insights into patient treatment.
    Keywords:  Poillet-Perez et al. review how both tumor and microenvironmental autophagy promote tumor growth by regulating cancer metabolism and the immune response. Moreover; autophagy is induced as a cell death or resistance mechanism following therapy. Better understanding the role of autophagy and the mechanisms involved will provide insights into patient treatment
    DOI:  https://doi.org/10.1016/j.celrep.2021.109528
  32. Nat Rev Cancer. 2021 Aug 20.
    Tumour fatty acid metabolism in the context of therapy resistance and obesity.
    Andrew J Hoy, Shilpa R Nagarajan, Lisa M Butler.
      Fatty acid metabolism is known to support tumorigenesis and disease progression as well as treatment resistance through enhanced lipid synthesis, storage and catabolism. More recently, the role of membrane fatty acid composition, for example, ratios of saturated, monounsaturated and polyunsaturated fatty acids, in promoting cell survival while limiting lipotoxicity and ferroptosis has been increasingly appreciated. Alongside these insights, it has become clear that tumour cells exhibit plasticity with respect to fatty acid metabolism, responding to extratumoural and systemic metabolic signals, such as obesity and cancer therapeutics, to promote the development of aggressive, treatment-resistant disease. Here, we describe cellular fatty acid metabolic changes that are connected to therapy resistance and contextualize obesity-associated changes in host fatty acid metabolism that likely influence the local tumour microenvironment to further modify cancer cell behaviour while simultaneously creating potential new vulnerabilities.
    DOI:  https://doi.org/10.1038/s41568-021-00388-4
  33. Mech Ageing Dev. 2021 Aug 16. pii: S0047-6374(21)00133-0. [Epub ahead of print] 111561
    The senescence-associated secretory phenotype: Fueling a wound that never heals.
    Tanya Pulido, Michael C Velarde, Fatouma Alimirah.
      Wound healing is impaired with advanced age and certain chronic conditions, such as diabetes and obesity. Moreover, common cancer treatments, including chemotherapy and radiation, can cause unintended tissue damage and impair wound healing. Available wound care treatments are not always effective, as some wounds fail to heal or recur after treatment. Hence, a more thorough understanding of the pathophysiology of chronic, nonhealing wounds may offer new ideas for the development of effective wound care treatments. Cancers are sometimes referred to as wounds that never heal, sharing mechanisms similar to wound healing. We describe in this review how cellular senescence and the senescence-associated secretory phenotype (SASP) contribute to chronic wounds versus cancer.
    Keywords:  Cancer; Cellular senescence; Chronic wounds; Inflammation; Senescence-associated secretory phenotype; Wound healing
    DOI:  https://doi.org/10.1016/j.mad.2021.111561
  34. Cancer Cell. 2021 Aug 07. pii: S1535-6108(21)00399-8. [Epub ahead of print]
    Tumor organoids: Opportunities and challenges to guide precision medicine.
    Vivien Veninga, Emile E Voest.
      Tumor organoids have been proposed as a model system for precision medicine. The ability of tumor organoids to retain characteristics of the original tumor makes them unique for cancer research on an individual patient level. Hence, the idea to use tumor organoids for clinical decision making and optimize patient outcome is tempting. In vitro responses of tumor organoids to a wide array of drugs have been positively correlated to patient responses. However, substantial challenges remain and prospective studies with large cohorts are highly needed before implementation in clinical cancer care can be considered. Because of their personalized characteristics and the immediate link with patient data, tumor organoids also have great potential in preclinical research. Here, we provide a critical overview of both clinical and preclinical advances using tumor organoids.
    Keywords:  cancer; clinical implementation; precision medicine; preclinical research; tumor organoids
    DOI:  https://doi.org/10.1016/j.ccell.2021.07.020
  35. Cancer Cell. 2021 Aug 18. pii: S1535-6108(21)00402-5. [Epub ahead of print]
    Anti-PD-1/L1 lead-in before MAPK inhibitor combination maximizes antitumor immunity and efficacy.
    Yujue Wang, Sixue Liu, Zhentao Yang, Alain P Algazi, Shirley H Lomeli, Yan Wang, Megan Othus, Aayoung Hong, Xiaoyan Wang, Chris E Randolph, Alexis M Jones, Marcus W Bosenberg, Stephanie D Byrum, Alan J Tackett, Henry Lopez, Clayton Yates, David B Solit, Antoni Ribas, Marco Piva, Gatien Moriceau, Roger S Lo.
      Rationally sequencing and combining PD-1/L1-and MAPK-targeted therapies may overcome innate and acquired resistance. Since increased clinical benefit of MAPK inhibitors (MAPKi) is associated with previous immune checkpoint therapy, we compare the efficacies of sequential and/or combinatorial regimens in subcutaneous murine models of melanoma driven by BrafV600, Nras, or Nf1 mutations as well as colorectal and pancreatic carcinoma driven by KrasG12C. Anti-PD-1/L1 lead-in preceding MAPKi combination optimizes response durability by promoting pro-inflammatory polarization of macrophages and clonal expansion of interferon-γhi, and CD8+ cytotoxic and proliferative (versus CD4+ regulatory) T cells that highly express activation genes. Since therapeutic resistance of melanoma brain metastasis (MBM) limits patient survival, we demonstrate that sequencing anti-PD-1/L1 therapy before MAPKi combination suppresses MBM and improves mouse survival with robust T cell clonal expansion in both intracranial and extracranial metastatic sites. We propose clinically testing brief anti-PD-1/L1 (± anti-CTLA-4) dosing before MAPKi co-treatment to suppress therapeutic resistance.
    Keywords:  BRAF/NRAS/KRAS/NF1; MAPK/BRAF/MEK inhibitor resistance; anti-CTLA-4; anti-PD-1/L1; brain metastasis; colorectal carcinoma; melanoma; pancreatic ductal adenocarcinoma; sequential-combination therapy; tumor immune microenvironment
    DOI:  https://doi.org/10.1016/j.ccell.2021.07.023
  36. Dis Model Mech. 2021 Aug 01. pii: dmm048942. [Epub ahead of print]14(8):
    The MEMIC is an ex vivo system to model the complexity of the tumor microenvironment.
    Libuše Janská, Libi Anandi, Nell C Kirchberger, Zoran S Marinkovic, Logan T Schachtner, Gizem Guzelsoy, Carlos Carmona-Fontaine.
      There is an urgent need for accurate, scalable and cost-efficient models of the tumor microenvironment. Here, we detail how to fabricate and use the metabolic microenvironment chamber (MEMIC) - a 3D-printed ex vivo model of intratumoral heterogeneity. A major driver of the cellular and molecular diversity in tumors is accessibility to the blood stream. Whereas perivascular tumor cells have direct access to oxygen and nutrients, cells further from the vasculature must survive under progressively more ischemic environments. The MEMIC simulates this differential access to nutrients, allow co-culturing any number of cell types, and it is optimized for live imaging and other microscopy-based analyses. Owing to a modular design and full experimental control, the MEMIC provides insights into the tumor microenvironment that would be difficult to obtain via other methods. As proof of principle, we show that cells sense gradual changes in metabolite concentration leading to predictable molecular and cellular spatial patterns. We propose the MEMIC as a complement to standard in vitro and in vivo experiments, diversifying the tools available to accurately model, perturb and monitor the tumor microenvironment.
    Keywords:  Tissue mimetics; Tumor metabolism; Tumor microenvironment
    DOI:  https://doi.org/10.1242/dmm.048942
  37. Curr Opin Cell Biol. 2021 Aug 14. pii: S0955-0674(21)00081-8. [Epub ahead of print]72 116-123
    Going your own way: Self-guidance mechanisms in cell migration.
    Mie Wong, Darren Gilmour.
      How cells and tissues migrate from one location to another is a question of significant biological and medical relevance. Migration is generally thought to be controlled by external hardwired guidance cues, which cells follow by polarizing their internal locomotory machinery in the imposed direction. However, a number of recently discovered 'self-guidance' mechanisms have revealed that migrating cells have more control over the path they follow than previously thought. Here, directional information is generated by the migrating cells themselves via a dynamic interplay of cell-intrinsic and -extrinsic regulators. In this review, we discuss how self-guidance can emerge from mechanisms acting at different levels of scale and how these enable cells to rapidly adapt to environmental challenges.
    DOI:  https://doi.org/10.1016/j.ceb.2021.07.004
This page is being maintained by Thomas Krichel. It was last updated on 2024‒11‒22 at 4:12.