bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021‒12‒12
fifty-three papers selected by
Kıvanç Görgülü
Technical University of Munich
  1. Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer.
  2. On the origin of pancreatic cancer.
  3. The biology of pancreatic cancer morphology.
  4. Reciprocal regulation of chaperone-mediated autophagy and the circadian clock.
  5. Carboxypeptidase A1 (CPA1) Immunohistochemistry Is Highly Sensitive and Specific for Acinar Cell Carcinoma (ACC) of the Pancreas.
  6. NEAT1 is essential for metabolic changes that promote breast cancer growth and metastasis.
  7. Quantitative assays to measure the transport activity of the mitochondrial calcium uniporter in cell lines or Xenopus oocytes.
  8. The mTOR-lysosome axis at the centre of ageing.
  9. Glucocorticoid receptor regulates PD-L1 and MHC-I in pancreatic cancer cells to promote immune evasion and immunotherapy resistance.
  10. An unexpected tumor suppressor role of SQSTM1/p62 in liver tumorigenesis.
  11. Spatial control of avidity regulates initiation and progression of selective autophagy.
  12. RB depletion is required for the continuous growth of tumors initiated by loss of RB.
  13. The flavonoid procyanidin C1 has senotherapeutic activity and increases lifespan in mice.
  14. Predicting patient response with models trained on cell lines and patient-derived xenografts by nonlinear transfer learning.
  15. Anti-cachectic regulator analysis reveals novel Perp-dependent anti-tumorigenic properties of 3-methyladenine in pancreatic cancer.
  16. Non-genetic determinants of malignant clonal fitness at single-cell resolution.
  17. Type-I collagen produced by distinct fibroblast lineages reveals specific function during embryogenesis and Osteogenesis Imperfecta.
  18. The 2021 FASEB science research conference on NAD metabolism and signaling.
  19. Autophagy inhibition mediated by MCOLN1/TRPML1 suppresses cancer metastasis via regulating a ROS-driven TP53/p53 pathway.
  20. A genetically encoded fluorescent biosensor for extracellular L-lactate.
  21. Evolution of metastasis: new tools and insights.
  22. Pathologic Examination of Pancreatic Specimens Resected for Treated Pancreatic Ductal Adenocarcinoma: Recommendations From the Pancreatobiliary Pathology Society.
  23. Coenzyme A fuels T cell anti-tumor immunity.
  24. Tumors are evolutionary island-like ecosystems.
  25. The mitochondrial protein Opa1 promotes adipocyte browning that is dependent on urea cycle metabolites.
  26. KRas-transformed epithelia cells invade and partially dedifferentiate by basal cell extrusion.
  27. Acetoacetate protects macrophages from lactic acidosis-induced mitochondrial dysfunction by metabolic reprograming.
  28. Glycometabolic rearrangements-aerobic glycolysis in pancreatic ductal adenocarcinoma (PDAC): Roles, regulatory networks, and therapeutic potential.
  29. Mechanisms and Regulation of Cellular Senescence.
  30. Lifestyle interventions for cancer survivors.
  31. MIROs and DRP1 drive mitochondrial-derived vesicle biogenesis and promote quality control.
  32. Deregulation of Transcription Factor Networks Driving Cell Plasticity and Metastasis in Pancreatic Cancer.
  33. Transcriptional control of a collagen deposition and adhesion process that promotes lung adenocarcinoma growth and metastasis.
  34. Avelumab maintenance in advanced urothelial carcinoma: biomarker analysis of the phase 3 JAVELIN Bladder 100 trial.
  35. Anti-Cancer Activity Profiling of Chemotherapeutic Agents in 3D Co-Cultures of Pancreatic Tumor Spheroids with Cancer-Associated Fibroblasts and Macrophages.
  36. Endocytic proteins with prion-like domains form viscoelastic condensates that enable membrane remodeling.
  37. Cancer-cell stiffening via cholesterol depletion enhances adoptive T-cell immunotherapy.
  38. Evolutionary assembly of cooperating cell types in an animal chemical defense system.
  39. Molecular mechanisms and consequences of mitochondrial permeability transition.
  40. Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution.
  41. When oncogenes do not cause cancer.
  42. Calpain-2 regulates hypoxia/HIF-induced plasticity toward amoeboid cancer cell migration and metastasis.
  43. Targeted Hsp70 fluorescence molecular endoscopy detects dysplasia in Barrett's esophagus.
  44. Enabling physical activity for people living with disabilities.
  45. Serial monitoring of genomic alterations in circulating tumor cells of ER-positive/HER2-negative advanced breast cancer: feasibility of precision oncology biomarker detection.
  46. MMP12 knockout prevents weight and muscle loss in tumor-bearing mice.
  47. p62 works as a hub modulation in the ageing process.
  48. Intra-pancreatic fat deposition: bringing hidden fat to the fore.
  49. Direction of epithelial folding defines impact of mechanical forces on epithelial state.
  50. Update and nomenclature proposal for mammalian lysophospholipid acyltransferases which create membrane phospholipid diversity.
  51. The enhanced cell cycle related to the response to adjuvant therapy in pancreatic ductal adenocarcinoma.
  52. Half of top cancer studies fail high-profile reproducibility effort.
  53. Mitophagy in aging and longevity.
  1. Cell. 2021 Dec 09. pii: S0092-8674(21)01332-5. [Epub ahead of print]184(25): 6119-6137.e26
    Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer.
    Srivatsan Raghavan, Peter S Winter, Andrew W Navia, Hannah L Williams, Alan DenAdel, Kristen E Lowder, Jennyfer Galvez-Reyes, Radha L Kalekar, Nolawit Mulugeta, Kevin S Kapner, Manisha S Raghavan, Ashir A Borah, Nuo Liu, Sara A Väyrynen, Andressa Dias Costa, Raymond W S Ng, Junning Wang, Emma K Hill, Dorisanne Y Ragon, Lauren K Brais, Alex M Jaeger, Liam F Spurr, Yvonne Y Li, Andrew D Cherniack, Matthew A Booker, Elizabeth F Cohen, Michael Y Tolstorukov, Isaac Wakiro, Asaf Rotem, Bruce E Johnson, James M McFarland, Ewa T Sicinska, Tyler E Jacks, Ryan J Sullivan, Geoffrey I Shapiro, Thomas E Clancy, Kimberly Perez, Douglas A Rubinson, Kimmie Ng, James M Cleary, Lorin Crawford, Scott R Manalis, Jonathan A Nowak, Brian M Wolpin, William C Hahn, Andrew J Aguirre, Alex K Shalek.
      Prognostically relevant RNA expression states exist in pancreatic ductal adenocarcinoma (PDAC), but our understanding of their drivers, stability, and relationship to therapeutic response is limited. To examine these attributes systematically, we profiled metastatic biopsies and matched organoid models at single-cell resolution. In vivo, we identify a new intermediate PDAC transcriptional cell state and uncover distinct site- and state-specific tumor microenvironments (TMEs). Benchmarking models against this reference map, we reveal strong culture-specific biases in cancer cell transcriptional state representation driven by altered TME signals. We restore expression state heterogeneity by adding back in vivo-relevant factors and show plasticity in culture models. Further, we prove that non-genetic modulation of cell state can strongly influence drug responses, uncovering state-specific vulnerabilities. This work provides a broadly applicable framework for aligning cell states across in vivo and ex vivo settings, identifying drivers of transcriptional plasticity and manipulating cell state to target associated vulnerabilities.
    Keywords:  liver metastases; pancreatic cancer; patient-derived organoid models; plasticity; single-cell RNA-sequencing; transcriptional states; tumor heterogeneity; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.cell.2021.11.017
  2. Cell Mol Gastroenterol Hepatol. 2021 Dec 04. pii: S2352-345X(21)00248-4. [Epub ahead of print]
    On the origin of pancreatic cancer.
    Elyne Backx, Katarina Coolens, Jan-Lars Van den Bossche, Isabelle Houbracken, Elisa Espinet, Ilse Rooman.
      Pancreatic ductal adenocarcinoma (PDAC) is a devastating type of cancer. While many studies have shed light into the pathobiology of PDAC, the nature of PDAC's cell of origin remains under debate. Studies in adult pancreatic tissue have unveiled a remarkable exocrine cell plasticity including transitional states, mostly exemplified by acinar to ductal cell metaplasia, but also with recent evidence hinting at duct to basal cell transitions. Single cell RNA sequencing has further revealed intrapopulation heterogeneity among acinar and duct cells. Transcriptomic and epigenomic relationships between these exocrine cell differentiation states and PDAC molecular subtypes have started to emerge, suggesting different ontogenies for different tumor subtypes. This review sheds light on these diverse aspects with particular focus on studies with human cells. Understanding the 'masked ball' of exocrine cells at origin of PDAC and leaving behind the binary acinar versus duct cell classification may significantly advance our insights in PDAC biology.
    Keywords:  heterogeneity; metaplasia; pancreas
    DOI:  https://doi.org/10.1016/j.jcmgh.2021.11.010
  3. Pathology. 2021 Dec 03. pii: S0031-3025(21)00522-5. [Epub ahead of print]
    The biology of pancreatic cancer morphology.
    Oliver G McDonald.
      Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal of all human malignancies. PDAC precursor lesions, invasive primary PDAC, and metastatic PDAC each display distinct morphologies that reflect unique biology. This 'biomorphology' is determined by a complex neoplastic history of clonal phylogenetic relationships, geographic locations, external environmental exposures, intrinsic metabolic demands, and tissue migration patterns. Understanding the biomorphological evolution of PDAC progression is not only of academic interest but also of great practical value. Applying this knowledge to surgical pathology practice facilitates the correct diagnosis on routine H&E stains without additional ancillary studies in most cases. Here I provide a concise overview of the entire biomorphological spectrum of PDAC progression beginning with initial neoplastic transformation and ending in terminal distant metastasis. Most biopsy and resection specimens are currently obtained prior to treatment. As such, our understanding of untreated PDAC biomorphology is mature. The biomorphology of treated PDAC is less defined but will assume greater importance as the frequency of neoadjuvant therapy increases. Although this overview is slanted towards pathology, it is written so that pathologists, clinicians, and scientists alike might find it instructive for their respective disciplines.
    Keywords:  Pancreatic cancer; biology; morphology; pancreatic ductal adenocarcinoma; pathology
    DOI:  https://doi.org/10.1016/j.pathol.2021.09.012
  4. Nat Cell Biol. 2021 Dec 07.
    Reciprocal regulation of chaperone-mediated autophagy and the circadian clock.
    Yves R Juste, Susmita Kaushik, Mathieu Bourdenx, Ranee Aflakpui, Sanmay Bandyopadhyay, Fernando Garcia, Antonio Diaz, Kristen Lindenau, Vincent Tu, Gregory J Krause, Maryam Jafari, Rajat Singh, Javier Muñoz, Fernando Macian, Ana Maria Cuervo.
      Circadian rhythms align physiological functions with the light-dark cycle through oscillatory changes in the abundance of proteins in the clock transcriptional programme. Timely removal of these proteins by different proteolytic systems is essential to circadian strength and adaptability. Here we show a functional interplay between the circadian clock and chaperone-mediated autophagy (CMA), whereby CMA contributes to the rhythmic removal of clock machinery proteins (selective chronophagy) and to the circadian remodelling of a subset of the cellular proteome. Disruption of this autophagic pathway in vivo leads to temporal shifts and amplitude changes of the clock-dependent transcriptional waves and fragmented circadian patterns, resembling those in sleep disorders and ageing. Conversely, loss of the circadian clock abolishes the rhythmicity of CMA, leading to pronounced changes in the CMA-dependent cellular proteome. Disruption of this circadian clock/CMA axis may be responsible for both pathways malfunctioning in ageing and for the subsequently pronounced proteostasis defect.
    DOI:  https://doi.org/10.1038/s41556-021-00800-z
  5. Am J Surg Pathol. 2022 Jan 01. 46(1): 97-104
    Carboxypeptidase A1 (CPA1) Immunohistochemistry Is Highly Sensitive and Specific for Acinar Cell Carcinoma (ACC) of the Pancreas.
    Ria Uhlig, Hendrina Contreras, Sören Weidemann, Natalia Gorbokon, Anne Menz, Franziska Büscheck, Andreas M Luebke, Martina Kluth, Claudia Hube-Magg, Andrea Hinsch, Doris Höflmayer, Christoph Fraune, Katharina Möller, Christian Bernreuther, Patrick Lebok, Guido Sauter, Waldemar Wilczak, Jakob Izbicki, Daniel Perez, Jörg Schrader, Stefan Steurer, Eike Burandt, Rainer Krech, David Dum, Till Krech, Andreas Marx, Ronald Simon, Sarah Minner, Frank Jacobsen, Till S Clauditz.
      Carboxypeptidase A1 (CPA1) is a zinc metalloprotease that is produced in pancreatic acinar cells and plays a role in cleaving C-terminal branched-chain and aromatic amino acids from dietary proteins. This study assessed the utility of immunohistochemical CPA1 staining for diagnosing pancreatic acinar cell carcinoma (ACC). A total of 12,274 tumor samples from 132 different tumor types and subtypes as well as 8 samples each of 76 different normal tissue types were interpretable by immunohistochemistry in a tissue microarray format. CPA1 was strongly expressed in acinar cells of all normal pancreas samples but not in any other normal tissues. CPA1 immunostaining was detected in 100% of 11 pancreatic ACCs and 1 mixed acinar endocrine carcinoma, but absent in 449 pancreatic ductal adenocarcinomas, 75 adenocarcinomas of the ampulla Vateri, and 11,739 other evaluable cancers from 128 different tumor entities. A weak to moderate diffuse staining of epithelial and stromal cells of cancer tissues immediately adjacent to non-neoplastic pancreatic acinar cells often occurred and was considered to be caused by the diffusion of the highly abundant CPA1 from normal acinar cells that may have suffered some autolytic cell damage. In conclusion, our data show that CPA1 is a highly sensitive and largely specific marker for normal and neoplastic pancreatic acinar cells. CPA1 immunohistochemistry greatly facilitates the otherwise often difficult diagnosis of pancreatic ACC.
    DOI:  https://doi.org/10.1097/PAS.0000000000001817
  6. Cell Metab. 2021 Dec 07. pii: S1550-4131(21)00539-8. [Epub ahead of print]33(12): 2380-2397.e9
    NEAT1 is essential for metabolic changes that promote breast cancer growth and metastasis.
    Mi Kyung Park, Li Zhang, Kyung-Won Min, Jung-Hyun Cho, Chih-Chen Yeh, Hyesu Moon, Daniel Hormaechea-Agulla, Hyejin Mun, Seungbeom Ko, Ji Won Lee, Sonali Jathar, Aubrey S Smith, Yixin Yao, Nguyen Thu Giang, Hong Ha Vu, Victoria C Yan, Mary C Bridges, Antonis Kourtidis, Florian Muller, Jeong Ho Chang, Su Jung Song, Shinichi Nakagawa, Tetsuro Hirose, Je-Hyun Yoon, Min Sup Song.
      Accelerated glycolysis is the main metabolic change observed in cancer, but the underlying molecular mechanisms and their role in cancer progression remain poorly understood. Here, we show that the deletion of the long noncoding RNA (lncRNA) Neat1 in MMTV-PyVT mice profoundly impairs tumor initiation, growth, and metastasis, specifically switching off the penultimate step of glycolysis. Mechanistically, NEAT1 directly binds and forms a scaffold bridge for the assembly of PGK1/PGAM1/ENO1 complexes and thereby promotes substrate channeling for high and efficient glycolysis. Notably, NEAT1 is upregulated in cancer patients and correlates with high levels of these complexes, and genetic and pharmacological blockade of penultimate glycolysis ablates NEAT1-dependent tumorigenesis. Finally, we demonstrate that Pinin mediates glucose-stimulated nuclear export of NEAT1, through which it exerts isoform-specific and paraspeckle-independent functions. These findings establish a direct role for NEAT1 in regulating tumor metabolism, provide new insights into the Warburg effect, and identify potential targets for therapy.
    Keywords:  ENO1; NEAT1; PGAM1; PGK1; Pinin; Warburg effect; aerobic glycolysis; breast cancer; long noncoding RNA; tumor metabolism
    DOI:  https://doi.org/10.1016/j.cmet.2021.11.011
  7. STAR Protoc. 2021 Dec 17. 2(4): 100979
    Quantitative assays to measure the transport activity of the mitochondrial calcium uniporter in cell lines or Xenopus oocytes.
    Madison X Rodriguez, Anna M Van Keuren, Ming-Feng Tsai.
      The mitochondrial calcium uniporter, which mediates mitochondrial Ca2+ uptake, regulates key cellular functions, including intracellular Ca2+ signaling, cell-fate determination, and mitochondrial bioenergetics. Here, we describe two complementary strategies to quantify the uniporter's transport activity. First, we detail a mitochondrial Ca2+ radionuclide uptake assay in cultured cell lines. Second, we describe electrophysiological recordings of the uniporter expressed in Xenopus oocytes. These approaches enable a detailed kinetic analysis of the uniporter to link its molecular properties to physiological functions. For complete details on the use and execution of this protocol, please refer to Tsai and Tsai (2018) and Phillips et al. (2019).
    Keywords:  Biophysics; Cell Biology; Cell-based Assays; Molecular Biology
    DOI:  https://doi.org/10.1016/j.xpro.2021.100979
  8. FEBS Open Bio. 2021 Dec 08.
    The mTOR-lysosome axis at the centre of ageing.
    Julian M Carosi, Celia Fourrier, Julien Bensalem, Timothy J Sargeant.
      Age-related diseases represent some of largest unmet clinical needs of our time. While treatment of specific disease-related signs has had some success (for example the effect of statin drugs on slowing progression of atherosclerosis), slowing biological ageing itself represents a target that could significantly increase health-span and reduce the prevalence of multiple age-related diseases. Mechanistic target of rapamycin complex 1 (mTORC1) is known to control fundamental processes in ageing: inhibiting this signalling complex slows biological ageing, reduces age-related disease pathology, and increases lifespan in model organisms. How mTORC1 inhibition achieves this is still subject to ongoing research. However, one mechanism by which mTORC1 inhibition is thought to slow ageing is by activating the autophagy-lysosome pathway. In this review we examine the special bi-directional relationship between mTORC1 and the lysosome. In cells, mTORC1 is located on lysosomes. From this advantageous position, it directly controls the autophagy-lysosome pathway. However, the lysosome also controls mTORC1 activity in numerous ways, creating a special two-way relationship. We then explore specific examples of how inhibition of mTORC1 and activation of the autophagy-lysosome pathway slow the molecular hallmarks of ageing. This body of literature demonstrates that the autophagy-lysosome pathway represents an excellent target for treatments that seek to slow biological ageing and increase health-span in humans.
    Keywords:  Lysosome; age-related disease; aging; autophagy; lysophagy; mTOR
    DOI:  https://doi.org/10.1002/2211-5463.13347
  9. Nat Commun. 2021 Dec 06. 12(1): 7041
    Glucocorticoid receptor regulates PD-L1 and MHC-I in pancreatic cancer cells to promote immune evasion and immunotherapy resistance.
    Yalan Deng, Xianghou Xia, Yang Zhao, Zilong Zhao, Consuelo Martinez, Wenjuan Yin, Jun Yao, Qinglei Hang, Weiche Wu, Jie Zhang, Yang Yu, Weiya Xia, Fan Yao, Di Zhao, Yutong Sun, Haoqiang Ying, Mien-Chie Hung, Li Ma.
      Despite unprecedented responses of some cancers to immune checkpoint blockade (ICB) therapies, the application of checkpoint inhibitors in pancreatic cancer has been unsuccessful. Glucocorticoids and glucocorticoid receptor (GR) signaling are long thought to suppress immunity by acting on immune cells. Here we demonstrate a previously undescribed tumor cell-intrinsic role for GR in activating PD-L1 expression and repressing the major histocompatibility complex class I (MHC-I) expression in pancreatic ductal adenocarcinoma (PDAC) cells through transcriptional regulation. In mouse models of PDAC, either tumor cell-specific depletion or pharmacologic inhibition of GR leads to PD-L1 downregulation and MHC-I upregulation in tumor cells, which in turn promotes the infiltration and activity of cytotoxic T cells, enhances anti-tumor immunity, and overcomes resistance to ICB therapy. In patients with PDAC, GR expression correlates with high PD-L1 expression, low MHC-I expression, and poor survival. Our results reveal GR signaling in cancer cells as a tumor-intrinsic mechanism of immunosuppression and suggest that therapeutic targeting of GR is a promising way to sensitize pancreatic cancer to immunotherapy.
    DOI:  https://doi.org/10.1038/s41467-021-27349-7
  10. Autophagy. 2021 Dec 06. 1-3
    An unexpected tumor suppressor role of SQSTM1/p62 in liver tumorigenesis.
    Xiaojuan Chao, Hong-Min Ni, Wen-Xing Ding.
      SQSTM1/p62 (sequestosome 1) is a macroautophagy/autophagy receptor protein that is degraded by selective autophagy. Intracellular accumulation of SQSTM1 activates multiple cell survival signaling pathways including NFΚB/NF-κB (nuclear factor kappa B), MTOR (mechanistic target of rapamycin kinase) and NFE2L2/Nrf2 (nuclear factor, erythroid derived 2, like 2). Both SQSTM1 and NFE2L2 have been considered as oncogenic, and increased accumulation of SQSTM1 and NFE2L2 activation have been frequently observed in various cancers including hepatocellular carcinoma. In a recent study, we found that deletion of Sqstm1 improved hepatic metabolic reprogramming and cell repopulation resulting in the attenuation of liver injury in mice with liver-specific deletion of Atg5 and Tsc1 that have defective hepatic autophagy and persistent MTOR complex 1 (MTORC1) activation. To our surprise, hepatocytic deletion of Sqstm1 promotes liver tumorigenesis in liver-specific atg5 and tsc1 double-knockout mice. Overall, these findings reveal a complex interplay among autophagy, SQSTM1 and MTORC1 and their differential roles either as oncogenic or tumor suppressor in liver tumorigenesis depending on the disease stage and context.
    Keywords:  ATG5; MTOR; Nrf2; Tsc1; autophagy; hepatocellular carcinoma
    DOI:  https://doi.org/10.1080/15548627.2021.2008693
  11. Nat Commun. 2021 Dec 10. 12(1): 7194
    Spatial control of avidity regulates initiation and progression of selective autophagy.
    David M Hollenstein, Mariya Licheva, Nicole Konradi, David Schweida, Hector Mancilla, Muriel Mari, Fulvio Reggiori, Claudine Kraft.
      Autophagosomes form at the endoplasmic reticulum in mammals, and between the vacuole and the endoplasmic reticulum in yeast. However, the roles of these sites and the mechanisms regulating autophagosome formation are incompletely understood. Vac8 is required for autophagy and recruits the Atg1 kinase complex to the vacuole. Here we show that Vac8 acts as a central hub to nucleate the phagophore assembly site at the vacuolar membrane during selective autophagy. Vac8 directly recruits the cargo complex via the Atg11 scaffold. In addition, Vac8 recruits the phosphatidylinositol 3-kinase complex independently of autophagy. Cargo-dependent clustering and Vac8-dependent sequestering of these early autophagy factors, along with local Atg1 activation, promote phagophore assembly site assembly at the vacuole. Importantly, ectopic Vac8 redirects autophagosome formation to the nuclear membrane, indicating that the vacuolar membrane is not specifically required. We propose that multiple avidity-driven interactions drive the initiation and progression of selective autophagy.
    DOI:  https://doi.org/10.1038/s41467-021-27420-3
  12. PLoS Genet. 2021 Dec;17(12): e1009941
    RB depletion is required for the continuous growth of tumors initiated by loss of RB.
    Alex Doan, Julia Arand, Diana Gong, Alexandros P Drainas, Yan Ting Shue, Myung Chang Lee, Shuyuan Zhang, David M Walter, Andrea C Chaikovsky, David M Feldser, Hannes Vogel, Lukas E Dow, Jan M Skotheim, Julien Sage.
      The retinoblastoma (RB) tumor suppressor is functionally inactivated in a wide range of human tumors where this inactivation promotes tumorigenesis in part by allowing uncontrolled proliferation. RB has been extensively studied, but its mechanisms of action in normal and cancer cells remain only partly understood. Here, we describe a new mouse model to investigate the consequences of RB depletion and its re-activation in vivo. In these mice, induction of shRNA molecules targeting RB for knock-down results in the development of phenotypes similar to Rb knock-out mice, including the development of pituitary and thyroid tumors. Re-expression of RB leads to cell cycle arrest in cancer cells and repression of transcriptional programs driven by E2F activity. Thus, continuous RB loss is required for the maintenance of tumor phenotypes initiated by loss of RB, and this new mouse model will provide a new platform to investigate RB function in vivo.
    DOI:  https://doi.org/10.1371/journal.pgen.1009941
  13. Nat Metab. 2021 Dec 06.
    The flavonoid procyanidin C1 has senotherapeutic activity and increases lifespan in mice.
    Qixia Xu, Qiang Fu, Zi Li, Hanxin Liu, Ying Wang, Xu Lin, Ruikun He, Xuguang Zhang, Zhenyu Ju, Judith Campisi, James L Kirkland, Yu Sun.
      Ageing-associated functional decline of organs and increased risk for age-related chronic pathologies is driven in part by the accumulation of senescent cells, which develop the senescence-associated secretory phenotype (SASP). Here we show that procyanidin C1 (PCC1), a polyphenolic component of grape seed extract (GSE), increases the healthspan and lifespan of mice through its action on senescent cells. By screening a library of natural products, we find that GSE, and PCC1 as one of its active components, have specific effects on senescent cells. At low concentrations, PCC1 appears to inhibit SASP formation, whereas it selectively kills senescent cells at higher concentrations, possibly by promoting production of reactive oxygen species and mitochondrial dysfunction. In rodent models, PCC1 depletes senescent cells in a treatment-damaged tumour microenvironment and enhances therapeutic efficacy when co-administered with chemotherapy. Intermittent administration of PCC1 to either irradiated, senescent cell-implanted or naturally aged old mice alleviates physical dysfunction and prolongs survival. We identify PCC1 as a natural senotherapeutic agent with in vivo activity and high potential for further development as a clinical intervention to delay, alleviate or prevent age-related pathologies.
    DOI:  https://doi.org/10.1038/s42255-021-00491-8
  14. Proc Natl Acad Sci U S A. 2021 Dec 07. pii: e2106682118. [Epub ahead of print]118(49):
    Predicting patient response with models trained on cell lines and patient-derived xenografts by nonlinear transfer learning.
    Soufiane M C Mourragui, Marco Loog, Daniel J Vis, Kat Moore, Anna G Manjon, Mark A van de Wiel, Marcel J T Reinders, Lodewyk F A Wessels.
      Preclinical models have been the workhorse of cancer research, producing massive amounts of drug response data. Unfortunately, translating response biomarkers derived from these datasets to human tumors has proven to be particularly challenging. To address this challenge, we developed TRANSACT, a computational framework that builds a consensus space to capture biological processes common to preclinical models and human tumors and exploits this space to construct drug response predictors that robustly transfer from preclinical models to human tumors. TRANSACT performs favorably compared to four competing approaches, including two deep learning approaches, on a set of 23 drug prediction challenges on The Cancer Genome Atlas and 226 metastatic tumors from the Hartwig Medical Foundation. We demonstrate that response predictions deliver a robust performance for a number of therapies of high clinical importance: platinum-based chemotherapies, gemcitabine, and paclitaxel. In contrast to other approaches, we demonstrate the interpretability of the TRANSACT predictors by correctly identifying known biomarkers of targeted therapies, and we propose potential mechanisms that mediate the resistance to two chemotherapeutic agents.
    Keywords:  cancer; clinical drug response; model systems; transfer learning; translational medicine
    DOI:  https://doi.org/10.1073/pnas.2106682118
  15. JCI Insight. 2021 Dec 07. pii: e153842. [Epub ahead of print]
    Anti-cachectic regulator analysis reveals novel Perp-dependent anti-tumorigenic properties of 3-methyladenine in pancreatic cancer.
    Aneesha Dasgupta, Paige C Arneson-Wissink, Rebecca E Schmitt, Dong Seong Cho, Alexandra M Ducharme, Tara L Hogenson, Eugene W Krueger, William R Bamlet, Lizhi Zhang, Gina L Razidlo, Martin E Fernandez-Zapico, Jason D Doles.
      Approximately 80% of pancreatic cancer patients suffer from cachexia and one-third die due to cachexia-related complications such as respiratory failure and cardiac arrest. Although there has been considerable research into cachexia mechanisms and interventions, there are, to date, no FDA-approved therapies. A major contributing factor could be the failure of animal models to accurately recapitulate the human condition. In this study, we generated an aged model of pancreatic cancer cachexia to compare cachexia progression in young versus aged tumor-bearing mice. Comparative skeletal muscle transcriptome analyses identified 3-methyladenine (3-MA) as a candidate anti-wasting compound. In vitro analyses confirmed anti-wasting capacity while in vivo analysis revealed potent anti-tumor effects. Transcriptome analyses of 3-MA-treated tumor cells implicated Perp as a 3-MA target gene. We subsequently 1) observed significantly higher expression of Perp in cancer cell lines compared to control cells, 2) noted a survival disadvantage associated with elevated Perp, and 3) found that 3-MA-associated Perp reduction inhibited tumor cell growth. Finally, we provide in vivo evidence that survival benefits conferred by 3-MA administration are independent of its effect on tumor progression. Taken together, we report a novel mechanism linking 3-MA to Perp inhibition, and further implicate PERP as a novel tumor promoting factor in pancreatic cancer.
    Keywords:  Cancer; Expression profiling; Muscle Biology; Oncology; Skeletal muscle
    DOI:  https://doi.org/10.1172/jci.insight.153842
  16. Nature. 2021 Dec 08.
    Non-genetic determinants of malignant clonal fitness at single-cell resolution.
    Katie A Fennell, Dane Vassiliadis, Enid Y N Lam, Luciano G Martelotto, Jesse J Balic, Sebastian Hollizeck, Tom S Weber, Timothy Semple, Qing Wang, Denise C Miles, Laura MacPherson, Yih-Chih Chan, Andrew A Guirguis, Lev M Kats, Emily S Wong, Sarah-Jane Dawson, Shalin H Naik, Mark A Dawson.
      All cancers emerge after a period of clonal selection and subsequent clonal expansion. Although the evolutionary principles imparted by genetic intratumour heterogeneity are becoming increasingly clear1, little is known about the non-genetic mechanisms that contribute to intratumour heterogeneity and malignant clonal fitness2. Here, using single-cell profiling and lineage tracing (SPLINTR)-an expressed barcoding strategy-we trace isogenic clones in three clinically relevant mouse models of acute myeloid leukaemia. We find that malignant clonal dominance is a cell-intrinsic and heritable property that is facilitated by the repression of antigen presentation and increased expression of the secretory leukocyte peptidase inhibitor gene (Slpi), which we genetically validate as a regulator of acute myeloid leukaemia. Increased transcriptional heterogeneity is a feature that enables clonal fitness in diverse tissues and immune microenvironments and in the context of clonal competition between genetically distinct clones. Similar to haematopoietic stem cells3, leukaemia stem cells (LSCs) display heritable clone-intrinsic properties of high, and low clonal output that contribute to the overall tumour mass. We demonstrate that LSC clonal output dictates sensitivity to chemotherapy and, although high- and low-output clones adapt differently to therapeutic pressure, they coordinately emerge from minimal residual disease with increased expression of the LSC program. Together, these data provide fundamental insights into the non-genetic transcriptional processes that underpin malignant clonal fitness and may inform future therapeutic strategies.
    DOI:  https://doi.org/10.1038/s41586-021-04206-7
  17. Nat Commun. 2021 Dec 10. 12(1): 7199
    Type-I collagen produced by distinct fibroblast lineages reveals specific function during embryogenesis and Osteogenesis Imperfecta.
    Yang Chen, Sujuan Yang, Sara Lovisa, Catherine G Ambrose, Kathleen M McAndrews, Hikaru Sugimoto, Raghu Kalluri.
      Type I collagen (Col1) is the most abundant protein in mammals. Col1 contributes to 90% of the total organic component of bone matrix. However, the precise cellular origin and functional contribution of Col1 in embryogenesis and bone formation remain unknown. Single-cell RNA-sequencing analysis identifies Fap+ cells and Fsp1+ cells as the major contributors of Col1 in the bone. We generate transgenic mouse models to genetically delete Col1 in various cell lineages. Complete, whole-body Col1 deletion leads to failed gastrulation and early embryonic lethality. Specific Col1 deletion in Fap+ cells causes severe skeletal defects, with hemorrhage, edema, and prenatal lethality. Specific Col1 deletion in Fsp1+ cells results in Osteogenesis Imperfecta-like phenotypes in adult mice, with spontaneous fractures and compromised bone healing. This study demonstrates specific contributions of mesenchymal cell lineages to Col1 production in organogenesis, skeletal development, and bone formation/repair, with potential insights into cell-based therapy for patients with Osteogenesis Imperfecta.
    DOI:  https://doi.org/10.1038/s41467-021-27563-3
  18. Aging (Albany NY). 2021 Dec 09. 13(undefined):
    The 2021 FASEB science research conference on NAD metabolism and signaling.
    Vera Gorbunova, Marcus Buschbeck, Xiaolu A Cambronne, Karthikeyani Chellappa, Daniela Corda, Juan Du, Marc Freichel, Jonathan Gigas, Alexander E Green, Feng Gu, Iva Guberovic, Aravinthkumar Jayabalan, Imrankhan Khansahib, Sarmistha Mukherjee, Andrei Seluanov, Matthew A Simon, Lars J Sverkeli, Nora Kory, Daniel C Levine, Ivan Matic, Andrey Nikiforov, Johannes G M Rack, Shin-Ichiro Imai, David A Sinclair, Debra Toiber, Yongjuan Zhao, Raul Mostoslavsky, Lee Kraus, Andreas H Guse.
      
    Keywords:  NAD; PARP; Sirtuins; aging; metabolism; signaling
    DOI:  https://doi.org/10.18632/aging.203766
  19. Autophagy. 2021 Dec 08. 1-23
    Autophagy inhibition mediated by MCOLN1/TRPML1 suppresses cancer metastasis via regulating a ROS-driven TP53/p53 pathway.
    Yanhong Xing, Xiangqing Wei, Yucheng Liu, Meng-Meng Wang, Zhongheng Sui, Xinyan Wang, Wucheng Zhu, Mengmei Wu, Chen Lu, Yuan-Hui Fei, Yi Jiang, Yang Zhang, Yuqing Wang, Feng Guo, Jun-Li Cao, Jiansong Qi, Wuyang Wang.
      Compelling evidence has demonstrated that macroautophagy/autophagy plays an important role in regulating multiple steps of metastatic cascades; however, the precise role of autophagy in metastasis remains unclear. This study demonstrates that autophagy inhibition induced by MCOLN1/TRPML1 suppresses cancer metastasis by evoking the ROS-mediated TP53/p53 pathway. First, we found that MCOLN1-mediated autophagy inhibition not only profoundly inhibits both migration and invasion in malignant melanoma and glioma cell lines in vitro, but also suppresses melanoma metastasis in vivo. Second, our study reveals that autophagy inhibition induced by MCOLN1 leads to damaged mitochondria accumulation followed by large quantities of ROS release. Third, we demonstrate that the elevated ROS resulting from autophagy inhibition subsequently triggers TP53 activity, which in turn modulates expression of its downstream targets which are involved in a broad spectrum of the metastatic cascade to suppress metastasis including MMP members and TWIST. In summary, our findings have established a mechanism by which autophagy inhibition suppresses metastasis via the ROS-TP53 signaling pathway. More importantly, our study demonstrates that autophagy inhibition through stimulation of MCOLN1 could evidently be one of the therapeutic potentials for combating cancer metastasis.Abbreviations: 3-MA: 3-methyladenine; AA: amino acid; ATG5: autophagy related 5; ATG12: autophagy related 12; Baf-A1: bafilomycin A1; CCCP: carbonyl cyanide m-chlorophenylhydrazone; CQ: chloroquine; DMEM: Dulbecco's Modified Eagle Medium; EMT: epithelial-mesenchymal transition; FBS: fetal bovine serum; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; HEK: human embryonic kidney; LAMP1: lysosomal associated membrane protein 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MCOLN1/TRPML1: mucolipin TRP cation channel 1; MMP: matrix metallopeptidase; NC: negative control; NRK: normal rat kidney; PBS: phosphate-buffered saline; shRNA: short hairpin RNA; siRNA: short interfering RNA; SQSTM1/p62: sequestosome 1; ULK1: unc-51 like autophagy activating kinase 1.
    Keywords:  Autophagic arrest; MCOLN1; ROS; TP53; metastasis; mitochondria turnover
    DOI:  https://doi.org/10.1080/15548627.2021.2008752
  20. Nat Commun. 2021 Dec 06. 12(1): 7058
    A genetically encoded fluorescent biosensor for extracellular L-lactate.
    Yusuke Nasu, Ciaran Murphy-Royal, Yurong Wen, Jordan N Haidey, Rosana S Molina, Abhi Aggarwal, Shuce Zhang, Yuki Kamijo, Marie-Eve Paquet, Kaspar Podgorski, Mikhail Drobizhev, Jaideep S Bains, M Joanne Lemieux, Grant R Gordon, Robert E Campbell.
      L-Lactate, traditionally considered a metabolic waste product, is increasingly recognized as an important intercellular energy currency in mammals. To enable investigations of the emerging roles of intercellular shuttling of L-lactate, we now report an intensiometric green fluorescent genetically encoded biosensor for extracellular L-lactate. This biosensor, designated eLACCO1.1, enables cellular resolution imaging of extracellular L-lactate in cultured mammalian cells and brain tissue.
    DOI:  https://doi.org/10.1038/s41467-021-27332-2
  21. Trends Cancer. 2021 Dec 03. pii: S2405-8033(21)00228-4. [Epub ahead of print]
    Evolution of metastasis: new tools and insights.
    Philippe Gui, Trever G Bivona.
      Metastasis is an evolutionary process occurring across multiple organs and timescales. Due to its continuous and dynamic nature, this multifaceted process has been challenging to investigate and remains incompletely understood, in part due to the lack of tools capable of probing genomic evolution at high enough resolution. However, technological advances in genetic sequencing and editing have provided new and powerful methods to refine our understanding of the complex series of events that lead to metastatic dissemination. In this review, we summarize the latest genetic and lineage-tracing approaches developed to unravel the genetic evolution of metastasis. The findings that have emerged have enhanced our comprehension of the mechanistic trajectories and timescales of metastasis and could provide new strategies for therapy.
    Keywords:  evolution; lineage tracing; metastasis; sequencing; single cell
    DOI:  https://doi.org/10.1016/j.trecan.2021.11.002
  22. Am J Surg Pathol. 2021 Dec 10.
    Pathologic Examination of Pancreatic Specimens Resected for Treated Pancreatic Ductal Adenocarcinoma: Recommendations From the Pancreatobiliary Pathology Society.
    Pancreatobiliary Pathology Society
      Currently, there are no internationally accepted consensus guidelines for pathologic evaluation of posttherapy pancreatectomy specimens. The Neoadjuvant Therapy Working Group of Pancreatobiliary Pathology Society was formed in 2018 to review grossing protocols, literature, and major issues and to develop recommendations for pathologic evaluation of posttherapy pancreatectomy specimens. The working group generated the following recommendations: (1) Systematic and standardized grossing and sampling protocols should be adopted for pancreatectomy specimens for treated pancreatic ductal adenocarcinoma (PDAC). (2) Consecutive mapping sections along the largest gross tumor dimension are recommended to validate tumor size by histology as required by the College of American Pathologists (CAP) cancer protocol. (3) Tumor size of treated PDACs should be measured microscopically as the largest dimension of tumor outer limits that is bound by viable tumor cells, including intervening stroma. (4) The MD Anderson grading system for tumor response has a better correlation with prognosis and better interobserver concordance among pathologists than does the CAP system. (5) A case should not be classified as a complete response unless the entire pancreas, peripancreatic tissues, ampulla of Vater, common bile duct, and duodenum adjacent to the pancreas are submitted for microscopic examination. (6) Future studies on tumor response of lymph node metastases, molecular and/or immunohistochemical markers, as well as application of artificial intelligence in grading tumor response of treated PDAC are needed. In summary, systematic, standardized pathologic evaluation, accurate tumor size measurement, and reproducible tumor response grading to neoadjuvant therapy are needed for optimal patient care. The criteria and discussions provided here may provide guidance towards these goals.
    DOI:  https://doi.org/10.1097/PAS.0000000000001853
  23. Cell Metab. 2021 Dec 07. pii: S1550-4131(21)00538-6. [Epub ahead of print]33(12): 2415-2427.e6
    Coenzyme A fuels T cell anti-tumor immunity.
    Michael St Paul, Samuel D Saibil, SeongJun Han, Kavita Israni-Winger, Scott C Lien, Rob C Laister, Azin Sayad, Susanne Penny, Rodabe N Amaria, Lauren E Haydu, Carlos R Garcia-Batres, Meghan Kates, David T Mulder, Céline Robert-Tissot, Matthew J Gold, Charles W Tran, Alisha R Elford, Linh T Nguyen, Trevor J Pugh, Devanand M Pinto, Jennifer A Wargo, Pamela S Ohashi.
      Metabolic programming is intricately linked to the anti-tumor properties of T cells. To study the metabolic pathways associated with increased anti-tumor T cell function, we utilized a metabolomics approach to characterize three different CD8+ T cell subsets with varying degrees of anti-tumor activity in murine models, of which IL-22-producing Tc22 cells displayed the most robust anti-tumor activity. Tc22s demonstrated upregulation of the pantothenate/coenzyme A (CoA) pathway and a requirement for oxidative phosphorylation (OXPHOS) for differentiation. Exogenous administration of CoA reprogrammed T cells to increase OXPHOS and adopt the CD8+ Tc22 phenotype independent of polarizing conditions via the transcription factors HIF-1α and the aryl hydrocarbon receptor (AhR). In murine tumor models, treatment of mice with the CoA precursor pantothenate enhanced the efficacy of anti-PDL1 antibody therapy. In patients with melanoma, pre-treatment plasma pantothenic acid levels were positively correlated with the response to anti-PD1 therapy. Collectively, our data demonstrate that pantothenate and its metabolite CoA drive T cell polarization, bioenergetics, and anti-tumor immunity.
    Keywords:  CD8(+) T cells; IL-22; Tc1; Tc17; Tc22; anti-PD1; coenzyme A; immunometabolism; immunotherapy; pantothenate
    DOI:  https://doi.org/10.1016/j.cmet.2021.11.010
  24. Genome Biol Evol. 2021 Dec 11. pii: evab276. [Epub ahead of print]
    Tumors are evolutionary island-like ecosystems.
    Antonia Chroni, Sudhir Kumar.
      Integration of ecological and evolutionary features has begun to understand tumor heterogeneity, tumor microenvironment, and metastatic potential. Developing a theoretical framework is intrinsic to deciphering tumors' tremendous spatial and longitudinal genetic variation patterns in patients. Here, we propose that tumors can be considered evolutionary island-like ecosystems, i.e., isolated systems that undergo evolutionary and spatiotemporal dynamic processes that shape tumor microenvironments and drive the migration of cancer cells. We examine attributes of insular systems and causes of insularity, such as physical distance and connectivity. These properties modulate migration rates of cancer cells through processes causing spatial and temporal isolation of the organs and tissues functioning as a supply of cancer cells for new colonizations. We discuss hypotheses, predictions, and limitations of tumors as islands analogy. We present emerging evidence of tumor insularity in different cancer types and discuss their relevance to the islands model. We suggest that the engagement of tumor insularity into conceptual and mathematical models holds promise to illuminate cancer evolution, tumor heterogeneity, and metastatic potential of cells.
    Keywords:  Cancer evolution; Metastasis modeling; Tumor biogeography; Tumor island
    DOI:  https://doi.org/10.1093/gbe/evab276
  25. Nat Metab. 2021 Dec 06.
    The mitochondrial protein Opa1 promotes adipocyte browning that is dependent on urea cycle metabolites.
    Camilla Bean, Matteo Audano, Tatiana Varanita, Francesca Favaretto, Marta Medaglia, Marco Gerdol, Lena Pernas, Fabio Stasi, Marta Giacomello, Stèphanie Herkenne, Maheswany Muniandy, Sini Heinonen, Emma Cazaly, Miina Ollikainen, Gabriella Milan, Alberto Pallavicini, Kirsi H Pietiläinen, Roberto Vettor, Nico Mitro, Luca Scorrano.
      White to brown/beige adipocytes conversion is a possible therapeutic strategy to tackle the current obesity epidemics. While mitochondria are key for energy dissipation in brown fat, it is unknown if they can drive adipocyte browning. Here, we show that the mitochondrial cristae biogenesis protein optic atrophy 1 (Opa1) facilitates cell-autonomous adipocyte browning. In two cohorts of patients with obesity, including weight discordant monozygotic twin pairs, adipose tissue OPA1 levels are reduced. In the mouse, Opa1 overexpression favours white adipose tissue expandability as well as browning, ultimately improving glucose tolerance and insulin sensitivity. Transcriptomics and metabolomics analyses identify the Jumanji family chromatin remodelling protein Kdm3a and urea cycle metabolites, including fumarate, as effectors of Opa1-dependent browning. Mechanistically, the higher cyclic adenosine monophosphate (cAMP) levels in Opa1 pre-adipocytes activate cAMP-responsive element binding protein (CREB), which transcribes urea cycle enzymes. Flux analyses in pre-adipocytes indicate that Opa1-dependent fumarate accumulation depends on the urea cycle. Conversely, adipocyte-specific Opa1 deletion curtails urea cycle and beige differentiation of pre-adipocytes, and is rescued by fumarate supplementation. Thus, the urea cycle links the mitochondrial dynamics protein Opa1 to white adipocyte browning.
    DOI:  https://doi.org/10.1038/s42255-021-00497-2
  26. Nat Commun. 2021 Dec 10. 12(1): 7180
    KRas-transformed epithelia cells invade and partially dedifferentiate by basal cell extrusion.
    John Fadul, Teresa Zulueta-Coarasa, Gloria M Slattum, Nadja M Redd, Mauricio Franco Jin, Michael J Redd, Stephan Daetwyler, Danielle Hedeen, Jan Huisken, Jody Rosenblatt.
      Metastasis is the main cause of carcinoma-related death, yet we know little about how it initiates due to our inability to visualize stochastic invasion events. Classical models suggest that cells accumulate mutations that first drive formation of a primary mass, and then downregulate epithelia-specific genes to cause invasion and metastasis. Here, using transparent zebrafish epidermis to model simple epithelia, we can directly image invasion. We find that KRas-transformation, implicated in early carcinogenesis steps, directly drives cell invasion by hijacking a process epithelia normally use to promote death-cell extrusion. Cells invading by basal cell extrusion simultaneously pinch off their apical epithelial determinants, endowing new plasticity. Following invasion, cells divide, enter the bloodstream, and differentiate into stromal, neuronal-like, and other cell types. Yet, only invading KRasV12 cells deficient in p53 survive and form internal masses. Together, we demonstrate that KRas-transformation alone causes cell invasion and partial dedifferentiation, independently of mass formation.
    DOI:  https://doi.org/10.1038/s41467-021-27513-z
  27. Nat Commun. 2021 Dec 08. 12(1): 7115
    Acetoacetate protects macrophages from lactic acidosis-induced mitochondrial dysfunction by metabolic reprograming.
    Clément Adam, Léa Paolini, Naïg Gueguen, Guillaume Mabilleau, Laurence Preisser, Simon Blanchard, Pascale Pignon, Florence Manero, Morgane Le Mao, Alain Morel, Pascal Reynier, Céline Beauvillain, Yves Delneste, Vincent Procaccio, Pascale Jeannin.
      Lactic acidosis, the extracellular accumulation of lactate and protons, is a consequence of increased glycolysis triggered by insufficient oxygen supply to tissues. Macrophages are able to differentiate from monocytes under such acidotic conditions, and remain active in order to resolve the underlying injury. Here we show that, in lactic acidosis, human monocytes differentiating into macrophages are characterized by depolarized mitochondria, transient reduction of mitochondrial mass due to mitophagy, and a significant decrease in nutrient absorption. These metabolic changes, resembling pseudostarvation, result from the low extracellular pH rather than from the lactosis component, and render these cells dependent on autophagy for survival. Meanwhile, acetoacetate, a natural metabolite produced by the liver, is utilized by monocytes/macrophages as an alternative fuel to mitigate lactic acidosis-induced pseudostarvation, as evidenced by retained mitochondrial integrity and function, retained nutrient uptake, and survival without the need of autophagy. Our results thus show that acetoacetate may increase tissue tolerance to sustained lactic acidosis.
    DOI:  https://doi.org/10.1038/s41467-021-27426-x
  28. Expert Opin Ther Targets. 2021 Dec 07.
    Glycometabolic rearrangements-aerobic glycolysis in pancreatic ductal adenocarcinoma (PDAC): Roles, regulatory networks, and therapeutic potential.
    Zhong Zhang, Hai-Jun Zhang.
      INTRODUCTION: Glycometabolic rearrangements (aerobic glycolysis) is a hallmark of pancreatic ductal adenocarcinoma (PDAC) and contributes to tumorigenesis and progression through numerous mechanisms. The targeting of aerobic glycolysis is recognized as a potential therapeutic strategy which offers the possibility of improving treatment outcomes for PDAC patients.AREAS COVERED: In this review, the role of aerobic glycolysis and its regulatory networks in PDAC are discussed. The targeting of aerobic glycolysis in PDAC is examined, and its therapeutic potential is evaluated. The relevant literature published from 2001 to 2021 was searched in databases including PubMed, Scopus, and Embase.
    EXPERT OPINION: Regulatory networks of aerobic glycolysis in PDAC are based on key factors such as c-Myc, hypoxia-inducible factor 1α, the mammalian target of rapamycin pathway, and non-coding RNAs. Experimental evidence suggests that modulators or inhibitors of aerobic glycolysis promote therapeutic effects in preclinical tumor models. Nevertheless, successful clinical translation of drugs that target aerobic glycolysis in PDAC is an obstacle. Moreover, it is necessary to identify the potential targets for future interventions from regulatory networks to design efficacious and safer agents.
    Keywords:  Aerobic glycolysis; HIF-1α; Key enzymes; Non-coding RNAs; Pancreatic cancer; Signaling pathways; c-Myc
    DOI:  https://doi.org/10.1080/14728222.2021.2015321
  29. Int J Mol Sci. 2021 Dec 06. pii: 13173. [Epub ahead of print]22(23):
    Mechanisms and Regulation of Cellular Senescence.
    Lauréline Roger, Fanny Tomas, Véronique Gire.
      Cellular senescence entails a state of an essentially irreversible proliferative arrest in which cells remain metabolically active and secrete a range of pro-inflammatory and proteolytic factors as part of the senescence-associated secretory phenotype. There are different types of senescent cells, and senescence can be induced in response to many DNA damage signals. Senescent cells accumulate in different tissues and organs where they have distinct physiological and pathological functions. Despite this diversity, all senescent cells must be able to survive in a nondividing state while protecting themselves from positive feedback loops linked to the constant activation of the DNA damage response. This capacity requires changes in core cellular programs. Understanding how different cell types can undergo extensive changes in their transcriptional programs, metabolism, heterochromatin patterns, and cellular structures to induce a common cellular state is crucial to preventing cancer development/progression and to improving health during aging. In this review, we discuss how senescent cells continuously evolve after their initial proliferative arrest and highlight the unifying features that define the senescent state.
    Keywords:  DNA damage signaling; aging; cell cycle arrest; cellular senescence; epigenetic and chromatin changes; metabolism alteration; mitochondrial dysfunction; senescence-associated secretory phenotype; transcriptome signature
    DOI:  https://doi.org/10.3390/ijms222313173
  30. Nat Rev Cancer. 2021 Dec 10.
    Lifestyle interventions for cancer survivors.
    Desiree Rivers.
      
    DOI:  https://doi.org/10.1038/s41568-021-00434-1
  31. Nat Cell Biol. 2021 Dec 06.
    MIROs and DRP1 drive mitochondrial-derived vesicle biogenesis and promote quality control.
    Tim König, Hendrik Nolte, Mari J Aaltonen, Takashi Tatsuta, Michiel Krols, Thomas Stroh, Thomas Langer, Heidi M McBride.
      Mitochondrial-derived vesicles (MDVs) are implicated in diverse physiological processes-for example, mitochondrial quality control-and are linked to various neurodegenerative diseases. However, their specific cargo composition and complex molecular biogenesis are still unknown. Here we report the proteome and lipidome of steady-state TOMM20+ MDVs. We identified 107 high-confidence MDV cargoes, which include all β-barrel proteins and the TOM import complex. MDV cargoes are delivered as fully assembled complexes to lysosomes, thus representing a selective mitochondrial quality control mechanism for multi-subunit complexes, including the TOM machinery. Moreover, we define key biogenesis steps of phosphatidic acid-enriched MDVs starting with the MIRO1/2-dependent formation of thin membrane protrusions pulled along microtubule filaments, followed by MID49/MID51/MFF-dependent recruitment of the dynamin family GTPase DRP1 and finally DRP1-dependent scission. In summary, we define the function of MDVs in mitochondrial quality control and present a mechanistic model for global GTPase-driven MDV biogenesis.
    DOI:  https://doi.org/10.1038/s41556-021-00798-4
  32. Front Cell Dev Biol. 2021 ;9 753456
    Deregulation of Transcription Factor Networks Driving Cell Plasticity and Metastasis in Pancreatic Cancer.
    Ruthger van Roey, Thomas Brabletz, Marc P Stemmler, Isabell Armstark.
      Pancreatic cancer is a very aggressive disease with 5-year survival rates of less than 10%. The constantly increasing incidence and stagnant patient outcomes despite changes in treatment regimens emphasize the requirement of a better understanding of the disease mechanisms. Challenges in treating pancreatic cancer include diagnosis at already progressed disease states due to the lack of early detection methods, rapid acquisition of therapy resistance, and high metastatic competence. Pancreatic ductal adenocarcinoma, the most prevalent type of pancreatic cancer, frequently shows dominant-active mutations in KRAS and TP53 as well as inactivation of genes involved in differentiation and cell-cycle regulation (e.g. SMAD4 and CDKN2A). Besides somatic mutations, deregulated transcription factor activities strongly contribute to disease progression. Specifically, transcriptional regulatory networks essential for proper lineage specification and differentiation during pancreas development are reactivated or become deregulated in the context of cancer and exacerbate progression towards an aggressive phenotype. This review summarizes the recent literature on transcription factor networks and epigenetic gene regulation that play a crucial role during tumorigenesis.
    Keywords:  ADM—acinar to ductal metaplasia; PDAC—pancreatic ductal adenocarcinoma; PanIN—pancreatic intraepithelial neoplasia; cellular plasticity; development; epigenetics (chromatin remodelling); transcription factors (TFs)
    DOI:  https://doi.org/10.3389/fcell.2021.753456
  33. JCI Insight. 2021 Dec 07. pii: e153948. [Epub ahead of print]
    Transcriptional control of a collagen deposition and adhesion process that promotes lung adenocarcinoma growth and metastasis.
    Xiaochao Tan, Priyam Banerjee, Xin Liu, Jiang Yu, Sieun Lee, Young-Ho Ahn, Chad J Creighton, Jonathan M Kurie.
      A fibrotic stroma accumulates in advanced cancers, and invasive cancer cells migrate along collagen fibers that facilitate dissemination from the primary tumor. However, the ways in which tumor cells govern these processes remain unclear. Here, we report that the epithelial-to-mesenchymal transition-activating transcription factor ZEB1 increased type I collagen (Col1) secretion and enhanced tumor cell adherence to type 1 collagen (Col1). Mechanistically, ZEB1 increased the levels of α1β1 integrin (encoded by Itga1 and Itgb1) by inhibiting PP2A activity, which reduced nuclear accumulation of HDAC4 and thereby derepressed Itga1 gene transcription. In parallel, ZEB1 relieved Itga1 from microRNA-148a-mediated silencing. High levels of Itga1 enhanced tumor cell adherence to Col1 and were essential for Col1-induced tumor growth and metastasis. Furthermore, ZEB1 enhanced Col1 secretion by increasing the expression of a kinesin protein that facilitated transport and secretion of Col1-containing vesicles. Our findings elucidate a transcriptional mechanism by which lung adenocarcinoma cells coordinate a collagen deposition and adhesion process that facilitates tumor progression.
    Keywords:  Cell migration/adhesion; Collagens; Integrins; Oncology
    DOI:  https://doi.org/10.1172/jci.insight.153948
  34. Nat Med. 2021 Dec 10.
    Avelumab maintenance in advanced urothelial carcinoma: biomarker analysis of the phase 3 JAVELIN Bladder 100 trial.
    Thomas Powles, Srikala S Sridhar, Yohann Loriot, Joaquim Bellmunt, Xinmeng Jasmine Mu, Keith A Ching, Jie Pu, Cora N Sternberg, Daniel P Petrylak, Rosa Tambaro, Louis M Dourthe, Carlos Alvarez-Fernandez, Maureen Aarts, Alessandra di Pietro, Petros Grivas, Craig B Davis.
      In a recent phase 3 randomized trial of 700 patients with advanced urothelial cancer (JAVELIN Bladder 100; NCT02603432 ), avelumab/best supportive care (BSC) significantly prolonged overall survival relative to BSC alone as maintenance therapy after first-line chemotherapy. Exploratory biomarker analyses were performed to identify biological pathways that might affect survival benefit. Tumor molecular profiling by immunohistochemistry, whole-exome sequencing and whole-transcriptome sequencing revealed that avelumab survival benefit was positively associated with PD-L1 expression by tumor cells, tumor mutational burden, APOBEC mutation signatures, expression of genes underlying innate and adaptive immune activity and the number of alleles encoding high-affinity variants of activating Fcγ receptors. Pathways connected to tissue growth and angiogenesis might have been associated with reduced survival benefit. Individual biomarkers did not comprehensively identify patients who could benefit from therapy; however, multi-parameter models incorporating genomic alteration, immune responses and tumor growth showed promising predictive utility. These results characterize the complex biologic pathways underlying survival benefit from immune checkpoint inhibition in advanced urothelial cancer and suggest that multiple biomarkers might be needed to identify patients who would benefit from treatment.
    DOI:  https://doi.org/10.1038/s41591-021-01579-0
  35. Cancers (Basel). 2021 Nov 26. pii: 5955. [Epub ahead of print]13(23):
    Anti-Cancer Activity Profiling of Chemotherapeutic Agents in 3D Co-Cultures of Pancreatic Tumor Spheroids with Cancer-Associated Fibroblasts and Macrophages.
    So-Dam Jang, Jeeyeun Song, Hyun-Ah Kim, Chang-Nim Im, Iftikhar Ali Khawar, Jong Kook Park, Hyo-Jeong Kuh.
      Activated pancreatic stellate cells (aPSCs) and M2 macrophages modulate tumor progression and therapeutic efficacy in pancreatic ductal adenocarcinoma (PDAC) via epithelial-mesenchymal transition (EMT). Here, our aim was to analyze the anti-invasion effects of anti-cancer agents where EMT-inducing cancer-stroma interaction occurs under three-dimensional (3D) culture conditions. We used microfluidic channel chips to co-culture pancreatic tumor spheroids (TSs) with aPSCs and THP-1-derived M2 macrophages (M2 THP-1 cells) embedded in type I collagen. Under stromal cell co-culture conditions, PANC-1 TSs displayed elevated expression of EMT-related proteins and increased invasion and migration. When PANC-1 TSs were exposed to gemcitabine, 5-fluorouracil, oxaliplatin, or paclitaxel, 30-50% cells were found unaffected, with no significant changes in the dose-response profiles under stromal cell co-culture conditions. This indicated intrinsic resistance to these drugs and no further induction of drug resistance by stromal cells. Paclitaxel had a significant anti-invasion effect; in contrast, oxaliplatin did not show such effect despite its specific cytotoxicity in M2 THP-1 cells. Overall, our findings demonstrate that the TS-stroma co-culture model of PDAC is useful for activity profiling of anti-cancer agents against cancer and stromal cells, and analyzing the relationship between anti-stromal activity and anti-invasion effects.
    Keywords:  3D culture; M2 macrophage; anti-cancer drug; pancreatic cancer; pancreatic stellate cell; tumor microenvironment; tumor spheroid
    DOI:  https://doi.org/10.3390/cancers13235955
  36. Proc Natl Acad Sci U S A. 2021 Dec 14. pii: e2113789118. [Epub ahead of print]118(50):
    Endocytic proteins with prion-like domains form viscoelastic condensates that enable membrane remodeling.
    Louis-Philippe Bergeron-Sandoval, Sandeep Kumar, Hossein Khadivi Heris, Catherine L A Chang, Caitlin E Cornell, Sarah L Keller, Paul François, Adam G Hendricks, Allen J Ehrlicher, Rohit V Pappu, Stephen W Michnick.
      Membrane invagination and vesicle formation are key steps in endocytosis and cellular trafficking. Here, we show that endocytic coat proteins with prion-like domains (PLDs) form hemispherical puncta in the budding yeast, Saccharomyces cerevisiae These puncta have the hallmarks of biomolecular condensates and organize proteins at the membrane for actin-dependent endocytosis. They also enable membrane remodeling to drive actin-independent endocytosis. The puncta, which we refer to as endocytic condensates, form and dissolve reversibly in response to changes in temperature and solution conditions. We find that endocytic condensates are organized around dynamic protein-protein interaction networks, which involve interactions among PLDs with high glutamine contents. The endocytic coat protein Sla1 is at the hub of the protein-protein interaction network. Using active rheology, we inferred the material properties of endocytic condensates. These experiments show that endocytic condensates are akin to viscoelastic materials. We use these characterizations to estimate the interfacial tension between endocytic condensates and their surroundings. We then adapt the physics of contact mechanics, specifically modifications of Hertz theory, to develop a quantitative framework for describing how interfacial tensions among condensates, the membrane, and the cytosol can deform the plasma membrane to enable actin-independent endocytosis.
    Keywords:  biomolecular condensates; endocytosis; protein–protein interactions; viscoelasticity
    DOI:  https://doi.org/10.1073/pnas.2113789118
  37. Nat Biomed Eng. 2021 Dec 06.
    Cancer-cell stiffening via cholesterol depletion enhances adoptive T-cell immunotherapy.
    Kewen Lei, Armand Kurum, Murat Kaynak, Lucia Bonati, Yulong Han, Veronika Cencen, Min Gao, Yu-Qing Xie, Yugang Guo, Mélanie T M Hannebelle, Yangping Wu, Guanyu Zhou, Ming Guo, Georg E Fantner, Mahmut Selman Sakar, Li Tang.
      Malignant transformation and tumour progression are associated with cancer-cell softening. Yet how the biomechanics of cancer cells affects T-cell-mediated cytotoxicity and thus the outcomes of adoptive T-cell immunotherapies is unknown. Here we show that T-cell-mediated cancer-cell killing is hampered for cortically soft cancer cells, which have plasma membranes enriched in cholesterol, and that cancer-cell stiffening via cholesterol depletion augments T-cell cytotoxicity and enhances the efficacy of adoptive T-cell therapy against solid tumours in mice. We also show that the enhanced cytotoxicity against stiffened cancer cells is mediated by augmented T-cell forces arising from an increased accumulation of filamentous actin at the immunological synapse, and that cancer-cell stiffening has negligible influence on: T-cell-receptor signalling, production of cytolytic proteins such as granzyme B, secretion of interferon gamma and tumour necrosis factor alpha, and Fas-receptor-Fas-ligand interactions. Our findings reveal a mechanical immune checkpoint that could be targeted therapeutically to improve the effectiveness of cancer immunotherapies.
    DOI:  https://doi.org/10.1038/s41551-021-00826-6
  38. Cell. 2021 Dec 09. pii: S0092-8674(21)01329-5. [Epub ahead of print]184(25): 6138-6156.e28
    Evolutionary assembly of cooperating cell types in an animal chemical defense system.
    Adrian Brückner, Jean M Badroos, Robert W Learsch, Mina Yousefelahiyeh, Sheila A Kitchen, Joseph Parker.
      How the functions of multicellular organs emerge from the underlying evolution of cell types is poorly understood. We deconstructed evolution of an organ novelty: a rove beetle gland that secretes a defensive cocktail. We show how gland function arose via assembly of two cell types that manufacture distinct compounds. One cell type, comprising a chemical reservoir within the abdomen, produces alkane and ester compounds. We demonstrate that this cell type is a hybrid of cuticle cells and ancient pheromone and adipocyte-like cells, executing its function via a mosaic of enzymes from each parental cell type. The second cell type synthesizes benzoquinones using a chimera of conserved cellular energy and cuticle formation pathways. We show that evolution of each cell type was shaped by coevolution between the two cell types, yielding a potent secretion that confers adaptive value. Our findings illustrate how cooperation between cell types arises, generating new, organ-level behaviors.
    Keywords:  Dalotia coriaria; biosynthetic pathway evolution; cell type evolution; enzyme evolution; evolution of cooperation; organ function; rove beetles; single cell RNAseq
    DOI:  https://doi.org/10.1016/j.cell.2021.11.014
  39. Nat Rev Mol Cell Biol. 2021 Dec 08.
    Molecular mechanisms and consequences of mitochondrial permeability transition.
    Massimo Bonora, Carlotta Giorgi, Paolo Pinton.
      Mitochondrial permeability transition (mPT) is a phenomenon that abruptly causes the flux of low molecular weight solutes (molecular weight up to 1,500) across the generally impermeable inner mitochondrial membrane. The mPT is mediated by the so-called mitochondrial permeability transition pore (mPTP), a supramolecular entity assembled at the interface of the inner and outer mitochondrial membranes. In contrast to mitochondrial outer membrane permeabilization, which mostly activates apoptosis, mPT can trigger different cellular responses, from the physiological regulation of mitophagy to the activation of apoptosis or necrosis. Although there are several molecular candidates for the mPTP, its molecular nature remains contentious. This lack of molecular data was a significant setback that prevented mechanistic insight into the mPTP, pharmacological targeting and the generation of informative animal models. In recent years, experimental evidence has highlighted mitochondrial F1Fo ATP synthase as a participant in mPTP formation, although a molecular model for its transition to the mPTP is still lacking. Recently, the resolution of the F1Fo ATP synthase structure by cryogenic electron microscopy led to a model for mPTP gating. The elusive molecular nature of the mPTP is now being clarified, marking a turning point for understanding mitochondrial biology and its pathophysiological ramifications. This Review provides an up-to-date reference for the understanding of the mammalian mPTP and its cellular functions. We review current insights into the molecular mechanisms of mPT and validated observations - from studies in vivo or in artificial membranes - on mPTP activity and functions. We end with a discussion of the contribution of the mPTP to human disease. Throughout the Review, we highlight the multiple unanswered questions and, when applicable, we also provide alternative interpretations of the recent discoveries.
    DOI:  https://doi.org/10.1038/s41580-021-00433-y
  40. Nat Commun. 2021 Dec 07. 12(1): 7113
    Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution.
    Ana Martinez-Val, Dorte B Bekker-Jensen, Sophia Steigerwald, Claire Koenig, Ole Østergaard, Adi Mehta, Trung Tran, Krzysztof Sikorski, Estefanía Torres-Vega, Ewa Kwasniewicz, Sólveig Hlín Brynjólfsdóttir, Lisa B Frankel, Rasmus Kjøbsted, Nicolai Krogh, Alicia Lundby, Simon Bekker-Jensen, Fridtjof Lund-Johansen, Jesper V Olsen.
      Dynamic change in subcellular localization of signaling proteins is a general concept that eukaryotic cells evolved for eliciting a coordinated response to stimuli. Mass spectrometry-based proteomics in combination with subcellular fractionation can provide comprehensive maps of spatio-temporal regulation of protein networks in cells, but involves laborious workflows that does not cover the phospho-proteome level. Here we present a high-throughput workflow based on sequential cell fractionation to profile the global proteome and phospho-proteome dynamics across six distinct subcellular fractions. We benchmark the workflow by studying spatio-temporal EGFR phospho-signaling dynamics in vitro in HeLa cells and in vivo in mouse tissues. Finally, we investigate the spatio-temporal stress signaling, revealing cellular relocation of ribosomal proteins in response to hypertonicity and muscle contraction. Proteomics data generated in this study can be explored through https://SpatialProteoDynamics.github.io .
    DOI:  https://doi.org/10.1038/s41467-021-27398-y
  41. Elife. 2021 Dec 09. pii: e74912. [Epub ahead of print]10
    When oncogenes do not cause cancer.
    Jessica Shiu, Arthur D Lander.
      Environmental cues, not oncogene-induced senescence, may stop melanocytes with an activating mutation in the BRAF gene from turning into melanoma.
    Keywords:  cancer biology; genetics; genomics; human; melanocytes; melanoma; microRNA; mutation; nevi
    DOI:  https://doi.org/10.7554/eLife.74912
  42. Curr Biol. 2021 Dec 06. pii: S0960-9822(21)01599-2. [Epub ahead of print]
    Calpain-2 regulates hypoxia/HIF-induced plasticity toward amoeboid cancer cell migration and metastasis.
    Veronika Te Boekhorst, Liying Jiang, Marius Mählen, Maaike Meerlo, Gina Dunkel, Franziska C Durst, Yanjun Yang, Herbert Levine, Boudewijn M T Burgering, Peter Friedl.
      Hypoxia, through hypoxia inducible factor (HIF), drives cancer cell invasion and metastatic progression in various cancer types. In epithelial cancer, hypoxia induces the transition to amoeboid cancer cell dissemination, yet the molecular mechanisms, relevance for metastasis, and effective intervention to combat hypoxia-induced amoeboid reprogramming remain unclear. Here, we identify calpain-2 as a key regulator and anti-metastasis target of hypoxia-induced transition from collective to amoeboid dissemination of breast and head and neck (HN) carcinoma cells. Hypoxia-induced amoeboid dissemination occurred through low extracellular matrix (ECM)-adhesive, predominantly bleb-based amoeboid movement, which was maintained by a low-oxidative and -glycolytic energy metabolism ("eco-mode"). Hypoxia induced calpain-2-mediated amoeboid conversion by deactivating β1 integrins through enzymatic cleavage of the focal adhesion adaptor protein talin-1. Consequently, targeted downregulation or pharmacological inhibition of calpain-2 restored talin-1 integrity and β1 integrin engagement and reverted amoeboid to elongated phenotypes under hypoxia. Calpain-2 activity was required for hypoxia-induced amoeboid conversion in the orthotopic mouse dermis and upregulated in invasive HN tumor xenografts in vivo, and attenuation of calpain activity prevented hypoxia-induced metastasis to the lungs. This identifies the calpain-2/talin-1/β1 integrin axis as a druggable mechanosignaling program that conserves energy yet enables metastatic dissemination that can be reverted by interfering with calpain activity.
    Keywords:  HIF; Hypoxia; amoeboid migration; blebbing; calpain-2; cancer cell; cell metabolism; integrin; metastasis
    DOI:  https://doi.org/10.1016/j.cub.2021.11.040
  43. Eur J Nucl Med Mol Imaging. 2021 Dec 09.
    Targeted Hsp70 fluorescence molecular endoscopy detects dysplasia in Barrett's esophagus.
    Hsin-Yu Fang, Stefan Stangl, Sabrina Marcazzan, Marcos J Braz Carvalho, Theresa Baumeister, Akanksha Anand, Julia Strangmann, Julia Slotta Huspenina, Timothy C Wang, Roland M Schmid, Marcus Feith, Helmut Friess, Vasilis Ntziachristos, Gabriele Multhoff, Dimitris Gorpas, Michael Quante.
      PURPOSE: The incidence of esophageal adenocarcinoma (EAC) has been increasing for decades without significant improvements in treatment. Barrett's esophagus (BE) is best established risk factor for EAC, but current surveillance with random biopsies cannot predict progression to cancer in most BE patients due to the low sensitivity and specificity of high-definition white light endoscopy.METHODS: Here, we evaluated the membrane-bound highly specific Hsp70-specific contrast agent Tumor-Penetrating Peptide (Hsp70-TPP) in guided fluorescence molecular endoscopy biopsy.
    RESULTS: Hsp70 was significantly overexpressed as determined by IHC in dysplasia and EAC compared with non-dysplastic BE in patient samples (n = 12) and in high-grade dysplastic lesions in a transgenic (L2-IL1b) mouse model of BE. In time-lapse microscopy, Hsp70-TPP was rapidly taken up and internalized  by human BE dysplastic patient-derived organoids. Flexible fluorescence endoscopy of the BE mouse model allowed a specific detection of Hsp70-TPP-Cy5.5 that corresponded closely with the degree of dysplasia but not BE. Ex vivo application of Hsp70-TPP-Cy5.5 to freshly resected whole human EAC specimens revealed a high (> 4) tumor-to-background ratio and a specific detection of previously undetected tumor infiltrations.
    CONCLUSION: In summary, these findings suggest that Hsp70-targeted imaging using fluorescently labeled TPP peptide may improve tumor surveillance in BE patients.
    Keywords:  Barrett esophagus; Esophageal adenocarcinoma; Fluorescence molecular endoscopy; Hsp70 ; Surveillance strategies
    DOI:  https://doi.org/10.1007/s00259-021-05582-y
  44. Lancet. 2021 Dec 04. pii: S0140-6736(21)02351-5. [Epub ahead of print]398(10316): 2072-2073
    Enabling physical activity for people living with disabilities.
    Nilly Waiserberg, Paula Feder-Bubis.
      
    DOI:  https://doi.org/10.1016/S0140-6736(21)02351-5
  45. Mol Oncol. 2021 Dec 06.
    Serial monitoring of genomic alterations in circulating tumor cells of ER-positive/HER2-negative advanced breast cancer: feasibility of precision oncology biomarker detection.
    Andi K Cani, Emily M Dolce, Elizabeth P Darga, Kevin Hu, Chia-Jen Liu, Jackie Pierce, Kieran Bradbury, Elaine Kilgour, Kimberly Aung, Gaia Schiavon, Danielle Carroll, T Hedley Carr, Teresa Klinowska, Justin Lindemann, Gayle Marshall, Vicky Rowlands, Elizabeth A Harrington, J Carl Barrett, Nitharsan Sathiyayogan, Christopher Morrow, Valeria Sero, Anne C Armstrong, Richard Baird, Erika Hamilton, Seock-Ah Im, Komal Jhaveri, Manish R Patel, Caroline Dive, Scott A Tomlins, Aaron M Udager, Daniel F Hayes, Costanza Paoletti.
      Nearly all estrogen receptor (ER)-positive (POS) metastatic breast cancers become refractory to endocrine (ET) and other therapies, leading to lethal disease presumably due to evolving genomic alterations. Timely monitoring of the molecular events associated with response/progression by serial tissue biopsies is logistically difficult. Use of liquid biopsies, including circulating tumor cells (CTC) and circulating tumor DNA (ctDNA) might provide highly informative, yet easily obtainable, evidence for better precision oncology care. Although ctDNA profiling has been well investigated, the CTC precision oncology genomic landscape and the advantages it may offer over ctDNA in ER-POS breast cancer remain largely unexplored. Whole blood (WB) specimens were collected at serial time points from patients with advanced ER-POS/HER2-negative (NEG) advanced breast cancer in a phase I trial of AZD9496, an oral selective ER degrader (SERD) ET. Individual CTC were isolated from WB using tandem CellSearch® /DEPArray™ technologies and genomically profiled by targeted single-cell DNA next-generation sequencing (scNGS). High-quality CTC (n=123) from 12 patients profiled by scNGS showed 100% concordance with ctDNA detection of driver estrogen receptor α (ESR1) mutations. We developed a novel CTC-based framework for precision medicine actionability reporting (MI-CTCseq) that incorporates novel features, such as clonal predominance and zygosity of targetable alterations, both unambiguously identifiable in CTC compared to ctDNA. Thus, we nominated opportunities for targeted therapies in 73% of patients, directed at alterations in phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), fibroblast growth factor receptor 2 (FGFR2) and KIT proto-oncogene, receptor tyrosine kinase (KIT). Intra-patient, inter-CTC genomic heterogeneity was observed, at times between timepoints, in subclonal alterations. Our analysis suggests that serial monitoring of the CTC genome is feasible and should enable real-time tracking of tumor evolution during progression, permitting more combination precision medicine interventions.
    Keywords:  Liquid biopsy; circulating tumor DNA; circulating tumor cells; precision medicine; tumor evolution; tumor heterogeneity
    DOI:  https://doi.org/10.1002/1878-0261.13150
  46. BMC Cancer. 2021 Dec 04. 21(1): 1297
    MMP12 knockout prevents weight and muscle loss in tumor-bearing mice.
    Lingbi Jiang, Mingming Yang, Shihui He, Zhengyang Li, Haobin Li, Ting Niu, Dehuan Xie, Yan Mei, Xiaodong He, Lili Wei, Pinzhu Huang, Mingzhe Huang, Rongxin Zhang, Lijing Wang, Jiangchao Li.
      BACKGROUND: Colorectal cancer is a malignant gastrointestinal cancer, in which some advanced patients would develop cancer cachexia (CAC). CAC is defined as a multi-factorial syndrome characterized by weight loss and muscle loss (with or without fat mass), leading to progressive dysfunction, thereby increasing morbidity and mortality. ApcMin/+ mice develop spontaneous intestinal adenoma, which provides an established model of colorectal cancer for CAC study. Upon studying the ApcMin/+ mouse model, we observed a marked decrease in weight gain beginning around week 15. Such a reduction in weight gain was rescued when ApcMin/+ mice were crossed with MMP12-/- mice, indicating that MMP12 has a role in age-related ApcMin/+-associated weight loss. As a control, the weight of MMP12-/- mice on a weekly basis, their weight were not significantly different from those of WT mice.METHODS: ApcMin/+; MMP12-/- mice were obtained by crossing ApcMin/+ mice with MMP12 knockout (MMP12 -/-) mice. Histological scores were assessed using hematoxylin-eosin (H&E) staining. MMP12 expression was confirmed by immunohistochemistry and immunofluorescence staining. ELISA, protein microarrays and quantitative Polymerase Chain Reaction (qPCR) were used to investigate whether tumor could up-regulate IL-6. Cell-based assays and western blot were used to verify the regulatory relationship between IL-6 and MMP12. Fluorescence intensity was measured to determine whether MMP12 is associated with insulin and insulin-like growth factor 1 (IGF-1) in vitro. MMP12 inhibitors were used to explore whether MMP12 could affect the body weight of ApcMin/+ mice.
    RESULTS: MMP12 knockout led to weight gain and expansion of muscle fiber cross-sectional area (all mice had C57BL/6 background) in ApcMin/+ mice, while inhibiting MMP12 could suppress weight loss in ApcMin/+ mice. MMP12 was up-regulated in muscle tissues and peritoneal macrophages of ApcMin/+ mice. IL-6 in tumor cells and colorectal cancer patients is up-regulation. IL-6 stimulated MMP12 secretion of macrophage.
    CONCLUSIONS: MMP12 is essential for controlling body weight of Apc Min/+ mice. Our study shows that it exists the crosstalk between cancer cells and macrophages in muscle tissues that tumor cells secrete IL-6 inducing macrophages to up-regulate MMP12. This study may provide a new perspective of MMP12 in the treatment for weight loss induced by CAC.
    Keywords:  ApcMin/+; Cancer cachexia; Colorectal cancer; IL-6; MMP12; Macrophage
    DOI:  https://doi.org/10.1186/s12885-021-09004-y
  47. Ageing Res Rev. 2021 Dec 07. pii: S1568-1637(21)00285-3. [Epub ahead of print] 101538
    p62 works as a hub modulation in the ageing process.
    Xiaolan Fan, Tiantian Huang, Yingdong Tong, Ziqiang Fan, Ziyue Yang, Deying Yang, Xueping Mao, Mingyao Yang.
      p62 (also known as SQSTM1) is widely used as a predictor of autophagic flux, a process that allows the degradation of harmful and unnecessary components through lysosomes to maintain protein homeostasis in cells. p62 is also a stress-induced scaffold protein that resists oxidative stress. The multiple domains in its structure allow it to be connected with a variety of vital signalling pathways, autophagy and the ubiquitin proteasome system (UPS), allowing p62 to play important roles in cell proliferation, apoptosis and survival. Recent studies have shown that p62 is also directly or indirectly involved in the ageing process. In this review, we summarize in detail the process by which p62 regulates ageing from multiple ageing-related signs with the aim of providing new insight for the study of p62 in ageing.
    Keywords:  Ageing; Autophagy; Oxidative; SQSTM1; UPS; p62
    DOI:  https://doi.org/10.1016/j.arr.2021.101538
  48. Nat Rev Gastroenterol Hepatol. 2021 Dec 08.
    Intra-pancreatic fat deposition: bringing hidden fat to the fore.
    Maxim S Petrov, Roy Taylor.
      Development of advanced modalities for detection of fat within the pancreas has transformed understanding of the role of intra-pancreatic fat deposition (IPFD) in health and disease. There is now strong evidence for the presence of minimal (but not negligible) IPFD in healthy human pancreas. Diffuse excess IPFD, or fatty pancreas disease (FPD), is more frequent than type 2 diabetes mellitus (T2DM) (the most common disease of the endocrine pancreas) and acute pancreatitis (the most common disease of the exocrine pancreas) combined. FPD is not strictly a function of high BMI; it can result from the excess deposition of fat in the islets of Langerhans, acinar cells, inter-lobular stroma, acinar-to-adipocyte trans-differentiation or replacement of apoptotic acinar cells. This process leads to a wide array of diseases characterized by excess IPFD, including but not limited to acute pancreatitis, chronic pancreatitis, pancreatic cancer, T2DM, diabetes of the exocrine pancreas. There is ample evidence for FPD being potentially reversible. Weight loss-induced decrease of intra-pancreatic fat is tightly associated with remission of T2DM and its re-deposition with recurrence of the disease. Reversing FPD will open up opportunities for preventing or intercepting progression of major diseases of the exocrine pancreas in the future.
    DOI:  https://doi.org/10.1038/s41575-021-00551-0
  49. Dev Cell. 2021 12 06. pii: S1534-5807(21)00893-5. [Epub ahead of print]56(23): 3222-3234.e6
    Direction of epithelial folding defines impact of mechanical forces on epithelial state.
    Slawomir Blonski, Julien Aureille, Sara Badawi, Damian Zaremba, Lydia Pernet, Alexei Grichine, Sandrine Fraboulet, Piotr M Korczyk, Pierre Recho, Christophe Guilluy, Monika E Dolega.
      Cell shape dynamics during development is tightly regulated and coordinated with cell fate determination. Triggered by an interplay between biochemical and mechanical signals, epithelia form complex tissues by undergoing coordinated cell shape changes, but how such spatiotemporal coordination is controlled remains an open question. To dissect biochemical signaling from purely mechanical cues, we developed a microfluidic system that experimentally triggers epithelial folding to recapitulate stereotypic deformations observed in vivo. Using this system, we observe that the apical or basal direction of folding results in strikingly different mechanical states at the fold boundary, where the balance between tissue tension and torque (arising from the imposed curvature) controls the spread of folding-induced calcium waves at a short timescale and induces spatial patterns of gene expression at longer timescales. Our work uncovers that folding-associated gradients of cell shape and their resulting mechanical stresses direct spatially distinct biochemical responses within the monolayer.
    Keywords:  RNAseq; calcium waves; epithelial folding; epithelial morphogenesis; microfluidics; tension
    DOI:  https://doi.org/10.1016/j.devcel.2021.11.008
  50. J Biol Chem. 2021 Dec 07. pii: S0021-9258(21)01279-5. [Epub ahead of print] 101470
    Update and nomenclature proposal for mammalian lysophospholipid acyltransferases which create membrane phospholipid diversity.
    William J Valentine, Keisuke Yanagida, Hiroki Kawana, Nozomu Kono, Nobuo N Noda, Junken Aoki, Hideo Shindou.
      The diversity of glycerophospholipid species in cellular membranes is immense and affects various biological functions. Glycerol-3-phosphate acyltransferases (GPATs) and lysophospholipid acyltransferases (LPLATs), in concert with phospholipase A1/2s enzymes, contribute to this diversity via selective esterification of fatty acyl chains at the sn-1 or sn-2 positions of membrane phospholipids. These enzymes are conserved across all kingdoms, and in mammals four GPATs of the 1-acylglycerol-3-phosphate O-acyltransferase (AGPAT) family and at least fourteen LPLATs, either of the AGPAT or the membrane-bound O-acyltransferase (MBOAT) families, have been identified. Here we provide an overview of the biochemical and biological activities of these mammalian enzymes, including their predicted structures, involvements in human diseases, and essential physiological roles as revealed by gene-deficient mice. Recently, the nomenclature used to refer to these enzymes has generated some confusion due to the use of multiple names to refer to the same enzyme, and instances of the same name being used to refer to completely different enzymes. Thus, this review proposes a more uniform LPLAT enzyme nomenclature, as well as providing an update of recent advances made in the study of LPLATs, continuing from our JBC mini review in 2009.
    Keywords:  LPLAT; cellular membrane; enzyme nomenclature; glycerophospholipid
    DOI:  https://doi.org/10.1016/j.jbc.2021.101470
  51. Genomics. 2021 Dec 01. pii: S0888-7543(21)00418-3. [Epub ahead of print]114(1): 95-106
    The enhanced cell cycle related to the response to adjuvant therapy in pancreatic ductal adenocarcinoma.
    Yize Mao, Weisheng Cheng, Qiuxia Yang, Liqin Li, Wanming Hu, Zeyu Shuang, Dejun Fan, Xinlei Jiang, Feng Gao, Shengping Li, Wei Wang.
      A major clinical challenge for treating patients with pancreatic ductal adenocarcinoma (PDAC) is identifying those that may benefit from adjuvant chemotherapy versus those that will not. Thus, there is a need for a robust and convenient biomarker for predicting chemotherapy response in PDAC patients. In this study, network inference was conducted by integrating the differentially expressed cell cycle signatures and target genes between the basal-like subtype and classical subtype of PDAC. As a result from this statistical analysis, two dominant cell cycle genes, RASAL2 and ASPM, were identified. Based on the expression levels of these two genes, we constructed a "Enhanced Cell Cycle" scoring system (ECC score). Patients were given an ECC score, and respectively divided into ECC-high and ECC-low groups. Survival, pathway enrichment, immune environment characteristics, and chemotherapy response analysis' were performed between the two groups in a total of 891 patients across 5 cohorts. ECC-high patients exhibited shortened recurrence-free survival (RFS) and overall survival (OS) rates. In addition, it was found that adjuvant chemotherapy could significantly improve the outcome of the ECC-high patients while ECC-low patients did not benefit from adjuvant chemotherapy. It was also found that there was less CD8+ T cell, natural killer (NK) cell, M1 macrophage, and plasma cell infiltration in ECC-high patients when compared to ECC-low patients. Also, the expression of CD73, an immune suppressor gene, and it's related hypoxia pathway were elevated in the ECC-high group when compared to the ECC-low group. In conclusion, this study showed that patients characterized as ECC-high not only had reduced RFS and OS rates, but were also more sensitive to adjuvant chemotherapy and could potentially be less sensitive to immune checkpoint inhibitors. Being able to characterize patients by these parameters would allow doctors to make more informed decisions on patient treatment regimens.
    Keywords:  Adjuvant chemotherapy; Cell cycle; Immunotherapy; Pancreatic ductal adenocarcinoma
    DOI:  https://doi.org/10.1016/j.ygeno.2021.11.036
  52. Nature. 2021 Dec 09.
    Half of top cancer studies fail high-profile reproducibility effort.
    Asher Mullard.
      
    Keywords:  Cancer; Drug discovery
    DOI:  https://doi.org/10.1038/d41586-021-03691-0
  53. IUBMB Life. 2021 Dec 10.
    Mitophagy in aging and longevity.
    Jing Guo, Wei-Chung Chiang.
      The clearance of damaged or unwanted mitochondria by autophagy (also known as mitophagy) is a mitochondrial quality control mechanism postulated to play an essential role in cellular homeostasis, metabolism, and development and confers protection against a wide range of diseases. Proper removal of damaged or unwanted mitochondria is essential for organismal health. Defects in mitophagy are associated with Parkinson's, Alzheimer's disease, cancer, and other degenerative disorders. Mitochondria regulate organismal fitness and longevity via multiple pathways, including cellular senescence, stem cell function, inflammation, mitochondrial unfolded protein response (mtUPR), and bioenergetics. Thus, mitophagy is postulated to be pivotal for maintaining organismal healthspan and lifespan and the protection against aged-related degeneration. In this review, we will summarize recent understanding of the mechanism of mitophagy and aspects of mitochondrial functions. We will focus on mitochondria-related cellular processes that are linked to aging and examine current genetic evidence that supports the hypothesis that mitophagy is a pro-longevity mechanism.
    Keywords:  aging; longevity; mitophagy
    DOI:  https://doi.org/10.1002/iub.2585
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