bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2022–02–06
57 papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Identification of treatment-induced vulnerabilities in pancreatic cancer patients using functional model systems.
  2. APOBEC3A drives deaminase domain-independent chromosomal instability to promote pancreatic cancer metastasis.
  3. Inhibition of SHP2 as an approach to block RAS-driven cancers.
  4. Leucine retention in lysosomes is regulated by starvation.
  5. Mutant Kras co-opts a proto-oncogenic enhancer network in inflammation-induced metaplastic progenitor cells to initiate pancreatic cancer.
  6. Unraveling and targeting RAS-driven metabolic signaling for therapeutic gain.
  7. Selective multi-kinase inhibition sensitizes mesenchymal pancreatic cancer to immune checkpoint blockade by remodeling the tumor microenvironment.
  8. Targeting the ERK mitogen-activated protein kinase cascade for the treatment of KRAS-mutant pancreatic cancer.
  9. Fungal mycobiome drives IL-33 secretion and type 2 immunity in pancreatic cancer.
  10. Therapeutic avenues for cancer neuroscience: translational frontiers and clinical opportunities.
  11. Discovery through clinical sequencing in oncology.
  12. A Novel Translational Activation of HIF1α Promotes Pancreatic Cancer Growth through Glycolytic Reprogramming.
  13. Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients.
  14. Autophagy takes it all - autophagy inducers target immune aging.
  15. Loss of glucose 6-phosphate dehydrogenase function increases oxidative stress and glutaminolysis in metastasizing melanoma cells.
  16. A tumor-derived type III collagen-rich ECM niche regulates tumor cell dormancy.
  17. Sustained weight loss, weight cycling, and weight gain during adulthood and pancreatic cancer incidence in the Women's Health Initiative (US).
  18. Mapping transcriptomic vector fields of single cells.
  19. Visceral adipose tissue remodeling in pancreatic ductal adenocarcinoma cachexia: the role of activin A signaling.
  20. A macrophage-hepatocyte glucocorticoid receptor axis coordinates fasting ketogenesis.
  21. Sex and genetic background define the metabolic, physiologic, and molecular response to protein restriction.
  22. Protocols for analyzing metabolic derangements caused by increased NADH/NAD+ ratio in cell lines and in mice.
  23. Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock.
  24. Prognosis and tumor biology of pancreatic cancer patients with isolated lung metastases: translational results from the German multicenter AIO-YMO-PAK-0515 study.
  25. Interplay between K-RAS and miRNAs.
  26. Challenges and opportunities in 2021.
  27. Delineating the evolutionary dynamics of cancer from theory to reality.
  28. Cancer research that matters.
  29. Tumour microenvironment and heterotypic interactions in pancreatic cancer.
  30. Reflecting on the golden age of cancer research.
  31. Compensatory CSF2-driven macrophage activation promotes adaptive resistance to CSF1R inhibition in breast-to-brain metastasis.
  32. Pegylated arginine deiminase drives arginine turnover and systemic autophagy to dictate energy metabolism.
  33. Radiation therapy enhances immunotherapy response in microsatellite stable colorectal and pancreatic adenocarcinoma in a phase II trial.
  34. A quick guide for clinical oncology.
  35. Inter-tissue convergence of gene expression during ageing suggests age-related loss of tissue and cellular identity.
  36. Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology.
  37. Sequence-Activated Fluorescent Nanotheranostics for Real-Time Profiling Pancreatic Cancer.
  38. Squidpy: a scalable framework for spatial omics analysis.
  39. The interplay between BAX and BAK tunes apoptotic pore growth to control mitochondrial-DNA-mediated inflammation.
  40. Architecture of the endoplasmic reticulum plays a role in proteostasis.
  41. In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density.
  42. Genomics-guided pre-clinical development of cancer therapies.
  43. Isaiah Joshua ('Josh') Fidler 1936-2020.
  44. Mitochondrial protein import determines lifespan through metabolic reprogramming and de novo serine biosynthesis.
  45. Novel systemic treatment approaches for metastatic pancreatic cancer.
  46. Enhancing anti-tumor immunity by autophagy inhibition.
  47. Zena Werb 1945-2020.
  48. Functional visualization of NK Cell-mediated killing of metastatic single tumor cells.
  49. Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers.
  50. Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation.
  51. Cost-effectiveness of neoadjuvant FOLFIRINOX versus gemcitabine plus nab-paclitaxel in borderline resectable/locally advanced pancreatic cancer patients.
  52. Hyperglycemia-induced oxidative stress promotes tumor metastasis by upregulating vWF expression in endothelial cells through the transcription factor GATA1.
  53. TERT activates endogenous retroviruses to promote an immunosuppressive tumour microenvironment.
  54. Targeting RAS oncogenesis with SOS1 inhibitors.
  55. High Incidence of Lymph-node Metastasis in a Pancreatic-cancer Patient-derived Orthotopic Xenograft (PDOX) NOG-Mouse Model.
  56. Bayesian Approach to Understand the Association Between Treatment Down-staging and Survival for Patients With Pancreatic Adenocarcinoma.
  57. The molecular subtyping resource (MouSR): a user-friendly tool for rapid biological discovery from transcriptional data.
  1. EMBO Mol Med. 2022 Feb 04. e14876
    Identification of treatment-induced vulnerabilities in pancreatic cancer patients using functional model systems.
    Katja Peschke, Hannah Jakubowsky, Arlett Schäfer, Carlo Maurer, Sebastian Lange, Felix Orben, Raquel Bernad, Felix N Harder, Matthias Eiber, Rupert Öllinger, Katja Steiger, Melissa Schlitter, Wilko Weichert, Ulrich Mayr, Veit Phillip, Christoph Schlag, Roland M Schmid, Rickmer F Braren, Bo Kong, Ihsan Ekin Demir, Helmut Friess, Roland Rad, Dieter Saur, Günter Schneider, Maximilian Reichert.
      Despite the advance and success of precision oncology in gastrointestinal cancers, the frequency of molecular-informed therapy decisions in pancreatic ductal adenocarcinoma (PDAC) is currently neglectable. We present a longitudinal precision oncology platform based on functional model systems, including patient-derived organoids, to identify chemotherapy-induced vulnerabilities. We demonstrate that treatment-induced tumor cell plasticity in vivo distinctly changes responsiveness to targeted therapies, without the presence of a selectable genetic marker, indicating that tumor cell plasticity can be functionalized. By adding a mechanistic layer to precision oncology, adaptive processes of tumors under therapy can be exploited, particularly in highly plastic tumors, such as pancreatic cancer.
    Keywords:  functional screening; pancreatic cancer; precision oncology; therapy-induced vulnerabilities; tumor cell plasticity
    DOI:  https://doi.org/10.15252/emmm.202114876
  2. Nat Cancer. 2021 Dec;2(12): 1338-1356
    APOBEC3A drives deaminase domain-independent chromosomal instability to promote pancreatic cancer metastasis.
    Sonja M Wörmann, Amy Zhang, Fredrik I Thege, Robert W Cowan, Dhwani N Rupani, Runsheng Wang, Sara L Manning, Chris Gates, Weisheng Wu, Rena Levin-Klein, Kimal I Rajapakshe, Meifang Yu, Asha S Multani, Ya'an Kang, Cullen M Taniguchi, Katharina Schlacher, Melena D Bellin, Matthew H G Katz, Michael P Kim, Jason B Fleming, Steven Gallinger, Ravikanth Maddipati, Reuben S Harris, Faiyaz Notta, Susan R Ross, Anirban Maitra, Andrew D Rhim.
      Despite efforts in understanding its underlying mechanisms, the etiology of chromosomal instability (CIN) remains unclear for many tumor types. Here, we identify CIN initiation as a previously undescribed function for APOBEC3A (A3A), a cytidine deaminase upregulated across cancer types. Using genetic mouse models of pancreatic ductal adenocarcinoma (PDA) and genomics analyses in human tumor cells we show that A3A-induced CIN leads to aggressive tumors characterized by enhanced early dissemination and metastasis in a STING-dependent manner and independently of the canonical deaminase functions of A3A. We show that A3A upregulation recapitulates numerous copy number alterations commonly observed in patients with PDA, including co-deletions in DNA repair pathway genes, which in turn render these tumors susceptible to poly (ADP-ribose) polymerase inhibition. Overall, our results demonstrate that A3A plays an unexpected role in PDA as a specific driver of CIN, with significant effects on disease progression and treatment.
    DOI:  https://doi.org/10.1038/s43018-021-00268-8
  3. Adv Cancer Res. 2022 ;pii: S0065-230X(21)00064-6. [Epub ahead of print]153 205-236
    Inhibition of SHP2 as an approach to block RAS-driven cancers.
    Yu-Ting Chou, Trever G Bivona.
      The non-receptor protein tyrosine phosphatase SHP2 (encoded by PTPN11) is a critical component of RAS/MAPK signaling by acting upstream of RAS to promote oncogenic signaling and tumor growth. Over three decades, SHP2 was considered "undruggable" because enzymatic active-site inhibitors generally showed off-target inhibition of other proteins and low membrane permeability. More recently, allosteric SHP2 inhibitors with striking inhibitory potency have been developed. These small molecules effectively block the signal transduction between receptor tyrosine kinases (RTKs) and RAS/MAPK signaling and show efficacy in preclinical cancer models. Moreover, clinical evaluation of these allosteric SHP2 inhibitors is ongoing. RAS proteins which harbor transforming properties by gain-of-function mutations are present in various cancer types. While inhibitors of KRASG12C show early clinical promise, resistance remains a challenge and other forms of oncogenic RAS remain to be selectively inhibited. Here, we summarize the role of SHP2 in RAS-driven cancers and the therapeutic potential of allosteric SHP2 inhibitors as a strategy to block RAS-driven cancers.
    Keywords:  Allosteric SHP2 inhibitor; Combination therapy; PTP; PTPN11; RAS; SHP2
    DOI:  https://doi.org/10.1016/bs.acr.2021.07.002
  4. Proc Natl Acad Sci U S A. 2022 Feb 08. pii: e2114912119. [Epub ahead of print]119(6):
    Leucine retention in lysosomes is regulated by starvation.
    Urmi Bandyopadhyay, Pavlina Todorova, Natalya N Pavlova, Yuma Tada, Craig B Thompson, Lydia W S Finley, Michael Overholtzer.
      Cells acquire essential nutrients from the environment and utilize adaptive mechanisms to survive when nutrients are scarce. How nutrients are trafficked and compartmentalized within cells and whether they are stored in response to stress remain poorly understood. Here, we investigate amino acid trafficking and uncover evidence for the lysosomal transit of numerous essential amino acids. We find that starvation induces the lysosomal retention of leucine in a manner requiring RAG-GTPases and the lysosomal protein complex Ragulator, but that this process occurs independently of mechanistic target of rapamycin complex 1 activity. We further find that stored leucine is utilized in protein synthesis and that inhibition of protein synthesis releases lysosomal stores. These findings identify a regulated starvation response that involves the lysosomal storage of leucine.
    Keywords:  leucine; lysosome; mTOR
    DOI:  https://doi.org/10.1073/pnas.2114912119
  5. Nat Cancer. 2021 Jan;2(1): 49-65
    Mutant Kras co-opts a proto-oncogenic enhancer network in inflammation-induced metaplastic progenitor cells to initiate pancreatic cancer.
    Yong Li, Yi He, Junya Peng, Zhendong Su, Zeyao Li, Bingjie Zhang, Jing Ma, Meilian Zhuo, Di Zou, Xinde Liu, Xinhong Liu, Wenze Wang, Dan Huang, Mengyue Xu, Jianbin Wang, Haiteng Deng, Jing Xue, Wei Xie, Xun Lan, Mo Chen, Yupei Zhao, Wenming Wu, Charles J David.
      Kras-activating mutations display the highest incidence in pancreatic ductal adenocarcinoma. Pancreatic inflammation accelerates mutant Kras-driven tumorigenesis in mice, suggesting high selectivity in the cells that oncogenic Kras transforms, although the mechanisms dictating this specificity are poorly understood. Here we show that pancreatic inflammation is coupled to the emergence of a transient progenitor cell population that is readily transformed in the presence of mutant KrasG12D. These progenitors harbor a proto-oncogenic transcriptional program driven by a transient enhancer network. KrasG12D mutations lock this enhancer network in place, providing a sustained Kras-dependent oncogenic program that drives tumors throughout progression. Enhancer co-option occurs through functional interactions between the Kras-activated transcription factors Junb and Fosl1 and pancreatic lineage transcription factors, potentially accounting for inter-tissue specificity of oncogene transformation. The pancreatic ductal adenocarcinoma cell of origin thus provides an oncogenic transcriptional program that fuels tumor progression beyond initiation, accounting for the intra-tissue selectivity of Kras transformation.
    DOI:  https://doi.org/10.1038/s43018-020-00134-z
  6. Adv Cancer Res. 2022 ;pii: S0065-230X(21)00081-6. [Epub ahead of print]153 267-304
    Unraveling and targeting RAS-driven metabolic signaling for therapeutic gain.
    Jonathan M DeLiberty, Ryan Robb, Claire E Gates, Kirsten L Bryant.
      RAS mutations are among the most frequent oncogenic drivers observed in human cancers. With a lack of available treatment options, RAS-mutant cancers account for many of the deadliest cancers in the United States. Recent studies established that altered metabolic requirements are a hallmark of cancer, and many of these alterations are driven by aberrant RAS signaling. Specifically, RAS-driven cancers are characterized by upregulated glycolysis, the differential channeling of glycolytic intermediates, upregulated nutrient scavenging pathways such as autophagy and macropinocytosis, and altered glutamine utilization and mitochondrial function. This unique metabolic landscape promotes tumorigenesis, proliferation, survival in nutrient deficient environments and confers resistance to conventional cytotoxic and targeted therapies. Emerging work demonstrates how these dependencies can be therapeutically exploited in vitro and in vivo with many metabolic inhibitors currently in clinical trials. This review aims to outline the unique metabolic requirements induced by aberrant RAS signaling and how these altered dependencies present opportunities for therapeutic intervention.
    Keywords:  Autophagy; Glycolysis; Macropinocytosis; Metabolism; Mitochondria; RAS; Scavenging
    DOI:  https://doi.org/10.1016/bs.acr.2021.07.010
  7. Nat Cancer. 2022 Jan 31.
    Selective multi-kinase inhibition sensitizes mesenchymal pancreatic cancer to immune checkpoint blockade by remodeling the tumor microenvironment.
    Chiara Falcomatà, Stefanie Bärthel, Sebastian A Widholz, Christian Schneeweis, Juan José Montero, Albulena Toska, Jonas Mir, Thorsten Kaltenbacher, Jeannine Heetmeyer, Jonathan J Swietlik, Jing-Yuan Cheng, Bianca Teodorescu, Oliver Reichert, Constantin Schmitt, Kathrin Grabichler, Andrea Coluccio, Fabio Boniolo, Christian Veltkamp, Magdalena Zukowska, Angelica Arenas Vargas, Woo Hyun Paik, Moritz Jesinghaus, Katja Steiger, Roman Maresch, Rupert Öllinger, Tim Ammon, Olga Baranov, Maria S Robles, Julia Rechenberger, Bernhard Kuster, Felix Meissner, Maximilian Reichert, Michael Flossdorf, Roland Rad, Marc Schmidt-Supprian, Günter Schneider, Dieter Saur.
      KRAS-mutant pancreatic ductal adenocarcinoma (PDAC) is highly immunosuppressive and resistant to targeted and immunotherapies. Among the different PDAC subtypes, basal-like mesenchymal PDAC, which is driven by allelic imbalance, increased gene dosage and subsequent high expression levels of oncogenic KRAS, shows the most aggressive phenotype and strongest therapy resistance. In the present study, we performed a systematic high-throughput combination drug screen and identified a synergistic interaction between the MEK inhibitor trametinib and the multi-kinase inhibitor nintedanib, which targets KRAS-directed oncogenic signaling in mesenchymal PDAC. This combination treatment induces cell-cycle arrest and cell death, and initiates a context-dependent remodeling of the immunosuppressive cancer cell secretome. Using a combination of single-cell RNA-sequencing, CRISPR screens and immunophenotyping, we show that this combination therapy promotes intratumor infiltration of cytotoxic and effector T cells, which sensitizes mesenchymal PDAC to PD-L1 immune checkpoint inhibition. Overall, our results open new avenues to target this aggressive and therapy-refractory mesenchymal PDAC subtype.
    DOI:  https://doi.org/10.1038/s43018-021-00326-1
  8. Adv Cancer Res. 2022 ;pii: S0065-230X(21)00079-8. [Epub ahead of print]153 101-130
    Targeting the ERK mitogen-activated protein kinase cascade for the treatment of KRAS-mutant pancreatic cancer.
    J Nathaniel Diehl, Priya S Hibshman, Irem Ozkan-Dagliyan, Craig M Goodwin, Sarah V Howard, Adrienne D Cox, Channing J Der.
      Mutational activation of the KRAS oncogene is found in ~95% of pancreatic ductal adenocarcinoma (PDAC), the major form of pancreatic cancer. With substantial experimental evidence that continued aberrant KRAS function is essential for the maintenance of PDAC tumorigenic growth, the National Cancer Institute has identified the development of effective anti-KRAS therapies as one of four major initiatives for pancreatic cancer research. The recent clinical success in the development of an anti-KRAS therapy targeting one specific KRAS mutant (G12C) supports the significant potential impact of anti-KRAS therapies. However, KRASG12C mutations comprise only 2% of KRAS mutations in PDAC. Thus, there remains a dire need for additional therapeutic approaches for targeting the majority of KRAS-mutant PDAC. Among the different directions currently being pursued for anti-KRAS drug development, one of the most promising involves inhibitors of the key KRAS effector pathway, the three-tiered RAF-MEK-ERK mitogen-activated protein kinase (MAPK) cascade. We address the promises and challenges of targeting ERK MAPK signaling as an anti-KRAS therapy for PDAC. In particular, we also summarize the key role of the MYC transcription factor and oncoprotein in supporting ERK-dependent growth of KRAS-mutant PDAC.
    Keywords:  ERK; KRAS; MYC; Mitogen-activated protein kinase; Pancreatic cancer
    DOI:  https://doi.org/10.1016/bs.acr.2021.07.008
  9. Cancer Cell. 2022 Jan 31. pii: S1535-6108(22)00005-8. [Epub ahead of print]
    Fungal mycobiome drives IL-33 secretion and type 2 immunity in pancreatic cancer.
    Aftab Alam, Eric Levanduski, Parker Denz, Helena Solleiro Villavicencio, Maulasri Bhatta, Lamees Alhorebi, Yali Zhang, Eduardo Cortes Gomez, Brian Morreale, Sharon Senchanthisai, Jun Li, Steven G Turowski, Sandra Sexton, Sheila Jani Sait, Prashant K Singh, Jianmin Wang, Anirban Maitra, Pawel Kalinski, Ronald A DePinho, Huamin Wang, Wenting Liao, Scott I Abrams, Brahm H Segal, Prasenjit Dey.
      TH2 cells and innate lymphoid cells 2 (ILC2) can stimulate tumor growth by secreting pro-tumorigenic cytokines such as interleukin-4 (IL-4), IL-5, and IL-13. However, the mechanisms by which type 2 immune cells traffic to the tumor microenvironment are unknown. Here, we show that oncogenic KrasG12D increases IL-33 expression in pancreatic ductal adenocarcinoma (PDAC) cells, which recruits and activates TH2 and ILC2 cells. Correspondingly, cancer-cell-specific deletion of IL-33 reduces TH2 and ILC2 recruitment and promotes tumor regression. Unexpectedly, IL-33 secretion is dependent on the intratumoral fungal mycobiome. Genetic deletion of IL-33 or anti-fungal treatment decreases TH2 and ILC2 infiltration and increases survival. Consistently, high IL-33 expression is observed in approximately 20% of human PDAC, and expression is mainly restricted to cancer cells. These data expand our knowledge of the mechanisms driving PDAC tumor progression and identify therapeutically targetable pathways involving intratumoral mycobiome-driven secretion of IL-33.
    Keywords:  IL-33; ILC2; Kras; PDAC; TH2; anti-fungal therapy; fungal mycobiome; innate lymphoid cells; intratumor-microbiome; type 2 immune response
    DOI:  https://doi.org/10.1016/j.ccell.2022.01.003
  10. Lancet Oncol. 2022 Feb;pii: S1470-2045(21)00596-9. [Epub ahead of print]23(2): e62-e74
    Therapeutic avenues for cancer neuroscience: translational frontiers and clinical opportunities.
    Diana D Shi, Jimmy A Guo, Hannah I Hoffman, Jennifer Su, Mari Mino-Kenudson, Jaimie L Barth, Jason M Schenkel, Jay S Loeffler, Helen A Shih, Theodore S Hong, Jennifer Y Wo, Andrew J Aguirre, Tyler Jacks, Lei Zheng, Patrick Y Wen, Timothy C Wang, William L Hwang.
      With increasing attention on the essential roles of the tumour microenvironment in recent years, the nervous system has emerged as a novel and crucial facilitator of cancer growth. In this Review, we describe the foundational, translational, and clinical advances illustrating how nerves contribute to tumour proliferation, stress adaptation, immunomodulation, metastasis, electrical hyperactivity and seizures, and neuropathic pain. Collectively, this expanding knowledge base reveals multiple therapeutic avenues for cancer neuroscience that warrant further exploration in clinical studies. We discuss the available clinical data, including ongoing trials investigating novel agents targeting the tumour-nerve axis, and the therapeutic potential for repurposing existing neuroactive drugs as an anti-cancer approach, particularly in combination with established treatment regimens. Lastly, we discuss the clinical challenges of these treatment strategies and highlight unanswered questions and future directions in the burgeoning field of cancer neuroscience.
    DOI:  https://doi.org/10.1016/S1470-2045(21)00596-9
  11. Nat Cancer. 2020 Aug;1(8): 774-783
    Discovery through clinical sequencing in oncology.
    Mark T A Donoghue, Alison M Schram, David M Hyman, Barry S Taylor.
      The molecular characterization of tumors now informs clinical cancer care for many patients. This advent of molecular oncology has been driven by the expanding number of therapeutic biomarkers that can predict sensitivity to both approved agents and investigational agents. Beyond its role in driving clinical-trial enrollments and guiding therapy in individual patients, large-scale clinical genomics in oncology also represents a rapidly expanding research resource for translational scientific discovery. Here we review the progress, opportunities, and challenges of scientific and translational discovery from prospective clinical genomic screening programs now routinely conducted for patients with cancer.
    DOI:  https://doi.org/10.1038/s43018-020-0100-0
  12. Gastroenterology. 2022 Feb 01. pii: S0016-5085(22)00095-6. [Epub ahead of print]
    A Novel Translational Activation of HIF1α Promotes Pancreatic Cancer Growth through Glycolytic Reprogramming.
    Yuqing Zhang, Courtney W Houchen, Min Li.
      
    DOI:  https://doi.org/10.1053/j.gastro.2022.01.040
  13. Cell. 2022 Feb 03. pii: S0092-8674(22)00003-4. [Epub ahead of print]185(3): 563-575.e11
    Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients.
    Bastien Nguyen, Christopher Fong, Anisha Luthra, Shaleigh A Smith, Renzo G DiNatale, Subhiksha Nandakumar, Henry Walch, Walid K Chatila, Ramyasree Madupuri, Ritika Kundra, Craig M Bielski, Brooke Mastrogiacomo, Mark T A Donoghue, Adrienne Boire, Sarat Chandarlapaty, Karuna Ganesh, James J Harding, Christine A Iacobuzio-Donahue, Pedram Razavi, Ed Reznik, Charles M Rudin, Dmitriy Zamarin, Wassim Abida, Ghassan K Abou-Alfa, Carol Aghajanian, Andrea Cercek, Ping Chi, Darren Feldman, Alan L Ho, Gopakumar Iyer, Yelena Y Janjigian, Michael Morris, Robert J Motzer, Eileen M O'Reilly, Michael A Postow, Nitya P Raj, Gregory J Riely, Mark E Robson, Jonathan E Rosenberg, Anton Safonov, Alexander N Shoushtari, William Tap, Min Yuen Teo, Anna M Varghese, Martin Voss, Rona Yaeger, Marjorie G Zauderer, Nadeem Abu-Rustum, Julio Garcia-Aguilar, Bernard Bochner, Abraham Hakimi, William R Jarnagin, David R Jones, Daniela Molena, Luc Morris, Eric Rios-Doria, Paul Russo, Samuel Singer, Vivian E Strong, Debyani Chakravarty, Lora H Ellenson, Anuradha Gopalan, Jorge S Reis-Filho, Britta Weigelt, Marc Ladanyi, Mithat Gonen, Sohrab P Shah, Joan Massague, Jianjiong Gao, Ahmet Zehir, Michael F Berger, David B Solit, Samuel F Bakhoum, Francisco Sanchez-Vega, Nikolaus Schultz.
      Metastatic progression is the main cause of death in cancer patients, whereas the underlying genomic mechanisms driving metastasis remain largely unknown. Here, we assembled MSK-MET, a pan-cancer cohort of over 25,000 patients with metastatic diseases. By analyzing genomic and clinical data from this cohort, we identified associations between genomic alterations and patterns of metastatic dissemination across 50 tumor types. We found that chromosomal instability is strongly correlated with metastatic burden in some tumor types, including prostate adenocarcinoma, lung adenocarcinoma, and HR+/HER2+ breast ductal carcinoma, but not in others, including colorectal cancer and high-grade serous ovarian cancer, where copy-number alteration patterns may be established early in tumor development. We also identified somatic alterations associated with metastatic burden and specific target organs. Our data offer a valuable resource for the investigation of the biological basis for metastatic spread and highlight the complex role of chromosomal instability in cancer progression.
    Keywords:  DNA sequencing; cancer; clinical sequencing; genomics; metastasis; molecular profiling; mutations; next-generation sequencing; organotropism; pan-cancer
    DOI:  https://doi.org/10.1016/j.cell.2022.01.003
  14. Dis Model Mech. 2022 01 01. pii: dmm049345. [Epub ahead of print]15(1):
    Autophagy takes it all - autophagy inducers target immune aging.
    Heidi Zinecker, Anna Katharina Simon.
      Autophagy, as the key nutrient recycling pathway, enables eukaryotic cells to adapt to surging cellular stress during aging and, thereby, delays age-associated deterioration. Autophagic flux declines with age and, in turn, decreases in autophagy contribute to the aging process itself and promote senescence. Here, we outline how autophagy regulates immune aging and discuss autophagy-inducing interventions that target senescent immune cells, which are major drivers of systemic aging. We examine how cutting-edge technologies, such as single-cell omics methods hold the promise to capture the complexity of molecular and cellular phenotypes associated with aging, driving the development of suitable putative biomarkers and clinical bioassays. Finally, we debate the urgency to initiate large-scale human clinical trials. We give special preference to small molecule probes and to dietary interventions that can extend healthy lifespan and are affordable for most of the world's population.
    Keywords:  Aging; Autophagy; Autophagy inducer; Immune system
    DOI:  https://doi.org/10.1242/dmm.049345
  15. Proc Natl Acad Sci U S A. 2022 Feb 08. pii: e2120617119. [Epub ahead of print]119(6):
    Loss of glucose 6-phosphate dehydrogenase function increases oxidative stress and glutaminolysis in metastasizing melanoma cells.
    Arin B Aurora, Vishal Khivansara, Ashley Leach, Jennifer G Gill, Misty Martin-Sandoval, Chendong Yang, Stacy Y Kasitinon, Divya Bezwada, Alpaslan Tasdogan, Wen Gu, Thomas P Mathews, Zhiyu Zhao, Ralph J DeBerardinis, Sean J Morrison.
      The pentose phosphate pathway is a major source of NADPH for oxidative stress resistance in cancer cells but there is limited insight into its role in metastasis, when some cancer cells experience high levels of oxidative stress. To address this, we mutated the substrate binding site of glucose 6-phosphate dehydrogenase (G6PD), which catalyzes the first step of the pentose phosphate pathway, in patient-derived melanomas. G6PD mutant melanomas had significantly decreased G6PD enzymatic activity and depletion of intermediates in the oxidative pentose phosphate pathway. Reduced G6PD function had little effect on the formation of primary subcutaneous tumors, but when these tumors spontaneously metastasized, the frequency of circulating melanoma cells in the blood and metastatic disease burden were significantly reduced. G6PD mutant melanomas exhibited increased levels of reactive oxygen species, decreased NADPH levels, and depleted glutathione as compared to control melanomas. G6PD mutant melanomas compensated for this increase in oxidative stress by increasing malic enzyme activity and glutamine consumption. This generated a new metabolic vulnerability as G6PD mutant melanomas were more dependent upon glutaminase than control melanomas, both for oxidative stress management and anaplerosis. The oxidative pentose phosphate pathway, malic enzyme, and glutaminolysis thus confer layered protection against oxidative stress during metastasis.
    Keywords:  glutaminolysis; melanoma; metastasis; oxidative stress; pentose phosphate pathway
    DOI:  https://doi.org/10.1073/pnas.2120617119
  16. Nat Cancer. 2022 Jan;3(1): 90-107
    A tumor-derived type III collagen-rich ECM niche regulates tumor cell dormancy.
    Julie S Di Martino, Ana Rita Nobre, Chandrani Mondal, Isra Taha, Eduardo F Farias, Elana J Fertig, Alexandra Naba, Julio A Aguirre-Ghiso, Jose Javier Bravo-Cordero.
      Cancer cells disseminate and seed in distant organs, where they can remain dormant for many years before forming clinically detectable metastases. Here we studied how disseminated tumor cells sense and remodel the extracellular matrix (ECM) to sustain dormancy. ECM proteomics revealed that dormant cancer cells assemble a type III collagen-enriched ECM niche. Tumor-derived type III collagen is required to sustain tumor dormancy, as its disruption restores tumor cell proliferation through DDR1-mediated STAT1 signaling. Second-harmonic generation two-photon microscopy further revealed that the dormancy-to-reactivation transition is accompanied by changes in type III collagen architecture and abundance. Analysis of clinical samples revealed that type III collagen levels were increased in tumors from patients with lymph node-negative head and neck squamous cell carcinoma compared to patients who were positive for lymph node colonization. Our data support the idea that the manipulation of these mechanisms could serve as a barrier to metastasis through disseminated tumor cell dormancy induction.
    DOI:  https://doi.org/10.1038/s43018-021-00291-9
  17. Am J Epidemiol. 2022 Feb 01. pii: kwac016. [Epub ahead of print]
    Sustained weight loss, weight cycling, and weight gain during adulthood and pancreatic cancer incidence in the Women's Health Initiative (US).
    Molly E Schwalb, Stephanie A Smith-Warner, Jianrui Hou, Thomas E Rohan, Linda Snetselaar, Juhua Luo, Jeanine M Genkinger.
      Pancreatic cancer is the fourth leading cause of cancer mortality in the US. Obesity is positively associated with pancreatic cancer risk. Current health recommendations focus on weight maintenance for healthy weight individuals and weight loss for overweight/obese individuals; however, little research has assessed associations between pancreatic cancer risk and changes in weight throughout the life-course. Using prospective cohort data, we examined the relationship between baseline adulthood weight patterns self-reported between 1993 and 1998 and pancreatic cancer risk in 136,834 post-menopausal women with 873 incident pancreatic cancer cases through September 2015 in the Women's Health Initiative. Hazard ratios (HR) and 95% confidence intervals (CI) were estimated using Cox proportional hazards models, adjusted for age, smoking habits, heavy alcohol consumption, and body mass index. Compared to women with stable weight, no significant associations were found between steady weight gain (HR=1.01 (95% CI: 0.83-1.22)), sustained weight loss (HR=1.26 (95% CI: 0.85-1.87)), or weight cycling patterns (HR=1.08 (95% CI: 0.89-1.30)) and pancreatic cancer. Results were similar when the outcome definition was restricted to pancreatic adenocarcinoma cases. Overall, we did not find evidence to suggest that weight changes in adulthood significantly impact pancreatic cancer risk among postmenopausal women.
    Keywords:  Pancreatic cancer; Women’s Health Initiative; weight cycling; weight loss; weight patterns
    DOI:  https://doi.org/10.1093/aje/kwac016
  18. Cell. 2022 Feb 01. pii: S0092-8674(21)01577-4. [Epub ahead of print]
    Mapping transcriptomic vector fields of single cells.
    Xiaojie Qiu, Yan Zhang, Jorge D Martin-Rufino, Chen Weng, Shayan Hosseinzadeh, Dian Yang, Angela N Pogson, Marco Y Hein, Kyung Hoi Joseph Min, Li Wang, Emanuelle I Grody, Matthew J Shurtleff, Ruoshi Yuan, Song Xu, Yian Ma, Joseph M Replogle, Eric S Lander, Spyros Darmanis, Ivet Bahar, Vijay G Sankaran, Jianhua Xing, Jonathan S Weissman.
      Single-cell (sc)RNA-seq, together with RNA velocity and metabolic labeling, reveals cellular states and transitions at unprecedented resolution. Fully exploiting these data, however, requires kinetic models capable of unveiling governing regulatory functions. Here, we introduce an analytical framework dynamo (https://github.com/aristoteleo/dynamo-release), which infers absolute RNA velocity, reconstructs continuous vector fields that predict cell fates, employs differential geometry to extract underlying regulations, and ultimately predicts optimal reprogramming paths and perturbation outcomes. We highlight dynamo's power to overcome fundamental limitations of conventional splicing-based RNA velocity analyses to enable accurate velocity estimations on a metabolically labeled human hematopoiesis scRNA-seq dataset. Furthermore, differential geometry analyses reveal mechanisms driving early megakaryocyte appearance and elucidate asymmetrical regulation within the PU.1-GATA1 circuit. Leveraging the least-action-path method, dynamo accurately predicts drivers of numerous hematopoietic transitions. Finally, in silico perturbations predict cell-fate diversions induced by gene perturbations. Dynamo, thus, represents an important step in advancing quantitative and predictive theories of cell-state transitions.
    Keywords:  RNA Jacobian; RNA metabolic labeling; cell-fate transitions; differential geometry analysis; dynamical systems theory; dynamo; hematopoiesis; in silico perturbation; least action path; vector field reconstruction
    DOI:  https://doi.org/10.1016/j.cell.2021.12.045
  19. Sci Rep. 2022 Jan 31. 12(1): 1659
    Visceral adipose tissue remodeling in pancreatic ductal adenocarcinoma cachexia: the role of activin A signaling.
    Pauline C Xu, Mikyoung You, Seok-Yeong Yu, Yi Luan, Maya Eldani, Thomas C Caffrey, Paul M Grandgenett, Kelly A O'Connell, Surendra K Shukla, Chandramohan Kattamuri, Michael A Hollingsworth, Pankaj K Singh, Thomas B Thompson, Soonkyu Chung, So-Youn Kim.
      Pancreatic ductal adenocarcinoma (PDAC) patients display distinct phenotypes of cachexia development, with either adipose tissue loss preceding skeletal muscle wasting or loss of only adipose tissue. Activin A levels were measured in serum and analyzed in tumor specimens of both a cohort of Stage IV PDAC patients and the genetically engineered KPC mouse model. Our data revealed that serum activin A levels were significantly elevated in Stage IV PDAC patients in comparison to age-matched non-cancer patients. Little is known about the role of activin A in adipose tissue wasting in the setting of PDAC cancer cachexia. We established a correlation between elevated activin A and remodeling of visceral adipose tissue. Atrophy and fibrosis of visceral adipose tissue was examined in omental adipose tissue of Stage IV PDAC patients and gonadal adipose tissue of an orthotopic mouse model of PDAC. Remarkably, white visceral adipose tissue from both PDAC patients and mice exhibited decreased adipocyte diameter and increased fibrotic deposition. Strikingly, expression of thermogenic marker UCP1 in visceral adipose tissues of PDAC patients and mice remained unchanged. Thus, we propose that activin A signaling could be relevant to the acceleration of visceral adipose tissue wasting in PDAC-associated cachexia.
    DOI:  https://doi.org/10.1038/s41598-022-05660-7
  20. Cell Metab. 2022 Jan 31. pii: S1550-4131(22)00004-3. [Epub ahead of print]
    A macrophage-hepatocyte glucocorticoid receptor axis coordinates fasting ketogenesis.
    Anne Loft, Søren Fisker Schmidt, Giorgio Caratti, Ulrich Stifel, Jesper Havelund, Revathi Sekar, Yun Kwon, Alba Sulaj, Kan Kau Chow, Ana Jimena Alfaro, Thomas Schwarzmayr, Nikolaj Rittig, Mads Svart, Foivos-Filippos Tsokanos, Adriano Maida, Andreas Blutke, Annette Feuchtinger, Niels Møller, Matthias Blüher, Peter Nawroth, Julia Szendrödi, Nils J Færgeman, Anja Zeigerer, Jan Tuckermann, Stephan Herzig.
      Fasting metabolism and immunity are tightly linked; however, it is largely unknown how immune cells contribute to metabolic homeostasis during fasting in healthy subjects. Here, we combined cell-type-resolved genomics and computational approaches to map crosstalk between hepatocytes and liver macrophages during fasting. We identified the glucocorticoid receptor (GR) as a key driver of fasting-induced reprogramming of the macrophage secretome including fasting-suppressed cytokines and showed that lack of macrophage GR impaired induction of ketogenesis during fasting as well as endotoxemia. Mechanistically, macrophage GR suppressed the expression of tumor necrosis factor (TNF) and promoted nuclear translocation of hepatocyte GR to activate a fat oxidation/ketogenesis-related gene program, cooperatively induced by GR and peroxisome proliferator-activated receptor alpha (PPARα) in hepatocytes. Together, our results demonstrate how resident liver macrophages directly influence ketogenesis in hepatocytes, thereby also outlining a strategy by which the immune system can set the metabolic tone during inflammatory disease and infection.
    Keywords:  fasting; genomics; glucocorticoid receptor; hepatocyte; ketogenesis; liver; macrophage; nuclear receptor; transcripional regulation; tumor necrosis factor
    DOI:  https://doi.org/10.1016/j.cmet.2022.01.004
  21. Cell Metab. 2022 Feb 01. pii: S1550-4131(21)00637-9. [Epub ahead of print]34(2): 209-226.e5
    Sex and genetic background define the metabolic, physiologic, and molecular response to protein restriction.
    Cara L Green, Heidi H Pak, Nicole E Richardson, Victoria Flores, Deyang Yu, Jay L Tomasiewicz, Sabrina N Dumas, Katherine Kredell, Jesse W Fan, Charlie Kirsh, Krittisak Chaiyakul, Michaela E Murphy, Reji Babygirija, Gregory A Barrett-Wilt, Joshua Rabinowitz, Irene M Ong, Cholsoon Jang, Judith Simcox, Dudley W Lamming.
      Low-protein diets promote metabolic health in humans and rodents. Despite evidence that sex and genetic background are key factors in the response to diet, most protein intake studies examine only a single strain and sex of mice. Using multiple strains and both sexes of mice, we find that improvements in metabolic health in response to reduced dietary protein strongly depend on sex and strain. While some phenotypes were conserved across strains and sexes, including increased glucose tolerance and energy expenditure, we observed high variability in adiposity, insulin sensitivity, and circulating hormones. Using a multi-omics approach, we identified mega-clusters of differentially expressed hepatic genes, metabolites, and lipids associated with each phenotype, providing molecular insight into the differential response to protein restriction. Our results highlight the importance of sex and genetic background in the response to dietary protein level, and the potential importance of a personalized medicine approach to dietary interventions.
    Keywords:  FGF21; UM-HET3; genetic variation; liver; metabolic health; multi-omics; precision dietetics; protein restriction; sexual dimorphism
    DOI:  https://doi.org/10.1016/j.cmet.2021.12.018
  22. STAR Protoc. 2022 Mar 18. 3(1): 101120
    Protocols for analyzing metabolic derangements caused by increased NADH/NAD+ ratio in cell lines and in mice.
    Shanshan Liu, Yan Ma, Hui Jiang.
      Mitochondrial electron transport chain (ETC) dysfunction elevates the NADH/NAD+ ratio to cause metabolic derangements. Here we describe a protocol to measure the NADH/NAD+ ratio and analyze the rewiring of glucose metabolism using [4-2H]-glucose, [3-2H]-glucose, and [U-13C]-glucose in ETC-inhibited human cancer cells. We also describe a protocol to analyze the NADH/NAD+ ratio-sensitive metabolites in mouse plasma and mouse liver following phenformin treatment. These protocols comprehensively analyze the metabolic derangements resulting from increased NADH/NAD+ ratio in in vitro and in vivo models. For complete details on the use and execution of this profile, please refer to Liu et al. (2021).
    Keywords:  Cell Biology; Cell culture; Cell-based Assays; Mass Spectrometry; Metabolism; Model Organisms
    DOI:  https://doi.org/10.1016/j.xpro.2021.101120
  23. Aging Cell. 2022 Feb 01. e13553
    Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock.
    Christopher Minteer, Marco Morselli, Margarita Meer, Jian Cao, Albert Higgins-Chen, Sabine M Lang, Matteo Pellegrini, Qin Yan, Morgan E Levine.
      Aging is associated with dramatic changes to DNA methylation (DNAm), although the causes and consequences of such alterations are unknown. Our ability to experimentally uncover mechanisms of epigenetic aging will be greatly enhanced by our ability to study and manipulate these changes using in vitro models. However, it remains unclear whether the changes elicited by cells in culture can serve as a model of what is observed in aging tissues in vivo. To test this, we serially passaged mouse embryonic fibroblasts (MEFs) and assessed changes in DNAm at each time point via reduced representation bisulfite sequencing. By developing a measure that tracked cellular aging in vitro, we tested whether it tracked physiological aging in various mouse tissues and whether anti-aging interventions modulate this measure. Our measure, termed CultureAGE, was shown to strongly increase with age when examined in multiple tissues (liver, lung, kidney, blood, and adipose). As a control, we confirmed that the measure was not a marker of cellular senescence, suggesting that it reflects a distinct yet progressive cellular aging phenomena that can be induced in vitro. Furthermore, we demonstrated slower epigenetic aging in animals undergoing caloric restriction and a resetting of our measure in lung and kidney fibroblasts when re-programmed to iPSCs. Enrichment and clustering analysis implicated EED and Polycomb group (PcG) factors as potentially important chromatin regulators in translational culture aging phenotypes. Overall, this study supports the concept that physiologically relevant aging changes can be induced in vitro and used to uncover mechanistic insights into epigenetic aging.
    Keywords:  DNA methylation; aging; calorie restriction; epigenome; in vitro techniques; longevity; oxidative stress; replicative senescence
    DOI:  https://doi.org/10.1111/acel.13553
  24. ESMO Open. 2022 Feb 01. pii: S2059-7029(22)00008-4. [Epub ahead of print]7(1): 100388
    Prognosis and tumor biology of pancreatic cancer patients with isolated lung metastases: translational results from the German multicenter AIO-YMO-PAK-0515 study.
    S F Kruger, A Lohneis, A Abendroth, A W Berger, T J Ettrich, O Waidmann, M Kapp, B Steiner, J Kumbrink, A Reischer, M Haas, C B Westphalen, D Zhang, L Miller-Phillips, P J Burger, S Kobold, J Werner, M Subklewe, M von Bergwelt-Baildon, V Kunzmann, T Seufferlein, J T Siveke, M Sinn, V Heinemann, S Ormanns, S Boeck.
       BACKGROUND: Pulmonary metastasis (M1-PUL) as first site of dissemination in pancreatic ductal adenocarcinoma (PDAC) is a rare event and may define a distinct biological subgroup.
    PATIENTS AND METHODS: Arbeitsgemeinschaft Internistische Onkologie-Young Medical Oncologists-Pankreas-0515 study (AIO-YMO-PAK-0515) was a retrospective German multicenter study investigating clinical and molecular characteristics of M1-PUL PDAC patients; 115 M1-PUL PDAC patients from 7 participating centers were included. Clinical characteristics and potential prognostic factors were defined within the M1-PUL cohort. Archival tumor samples were analyzed for Her2/neu, HNF1A and KRT81 expression. Additionally, messenger RNA (mRNA) expression analysis (using a 770-gene immune profiling panel) was carried out in the M1-PUL and in a control cohort (M1-ANY).
    RESULTS: Median overall survival in the entire M1-PUL cohort was 20 months; the most favorable prognosis (median survival: 28 months) was observed in the subgroup of 66 PDAC patients with metachronous lung metastases after previous curative-intent surgery. The number of metastatic lesions, uni- or bilateral lung involvement as well as metastasectomy were identified as potential prognostic factors. Her2/neu expression and PDAC subtyping (by HNF1A and KRT81) did not differ between the M1-PUL and the M1-ANY cohort. mRNA expression analysis revealed significant differentially expressed genes between both cohorts: CD63 and LAMP1 were among the top 20 differentially expressed genes and were identified as potential mediators of organotropism and favorable survival outcome of M1-PUL patients.
    CONCLUSION: M1-PUL represents a clinically favorable cohort in PDAC patients. Site of relapse might already be predetermined at the time of surgery and could potentially be predicted by gene expression profiling.
    Keywords:  chemotherapy; gene expression; lung metastasis; pancreatic cancer; prognosis
    DOI:  https://doi.org/10.1016/j.esmoop.2022.100388
  25. Trends Cancer. 2022 Jan 26. pii: S2405-8033(22)00002-4. [Epub ahead of print]
    Interplay between K-RAS and miRNAs.
    Bing Shui, Gaspare La Rocca, Andrea Ventura, Kevin M Haigis.
      K-RAS is frequently mutated in cancers, and its overactivation can lead to oncogene-induced senescence (OIS), a barrier to cellular transformation. Feedback onto K-RAS limits its signaling to avoid senescence while achieving the appropriate level of activation that promotes proliferation and survival. Such regulation could be mediated by miRNAs, as aberrant RAS signaling and miRNA activity coexist in several cancers, with miRNAs acting both up- and downstream of K-RAS. Several miRNAs both regulate and are regulated by K-RAS, suggesting a noncoding RNA-based feedback mechanism. Functional interactions between K-RAS and the miRNA machinery have also begun to unfold. This review comprehensively surveys the state of knowledge connecting K-RAS to miRNA function and proposes a model for the regulation of K-RAS signaling by noncoding RNAs.
    Keywords:  K-RAS; cancer; feedback regulation; miRNA
    DOI:  https://doi.org/10.1016/j.trecan.2022.01.002
  26. Nat Cancer. 2021 Dec;2(12): 1278-1283
    Challenges and opportunities in 2021.
    Leila Akkari, Stacey D Finley, Ping-Chih Ho, Misty Jenkins, Barbara B Maier, Nicholas McGranahan, Miriam Mutebi, Rushika M Perera, Carla Daniela Robles-Espinoza, Santosha Vardhana, Liling Wan, Meng Michelle Xu.
      
    DOI:  https://doi.org/10.1038/s43018-021-00294-6
  27. Nat Cancer. 2020 Jun;1(6): 580-588
    Delineating the evolutionary dynamics of cancer from theory to reality.
    Ivana Bozic, Catherine J Wu.
      Uncovering and quantifying the laws of the evolutionary dynamics of cancer, in particular in the context of specific genetic lesions and in individual patients, has the potential to revolutionize precision oncology. Recent technological advances in the study of human cancer have increased access to in vivo human data and have thereby facilitated the confirmation or refutation of existing theoretical models. In this Perspective, we discuss recent work at the intersection of quantitative mathematical models of cancer evolution and patient data that provides insights into different stages of tumor evolution, including premalignant and malignant progression and response to therapy.
    DOI:  https://doi.org/10.1038/s43018-020-0079-6
  28. Nat Cancer. 2021 Dec;2(12): 1268-1270
    Cancer research that matters.
    Alexia-Ileana Zaromytidou.
      
    DOI:  https://doi.org/10.1038/s43018-021-00302-9
  29. J Physiol Biochem. 2022 Feb 01.
    Tumour microenvironment and heterotypic interactions in pancreatic cancer.
    Raúl Muñoz Velasco, Ana García García, Paula Jiménez Sánchez, Inmaculada Montanuy Sellart, Víctor Javier Sánchez-Arévalo Lobo.
      Pancreatic ductal adenocarcinoma (PDA) is a disease with a survival rate of 9%; this is due to its chemoresistance and the large tumour stroma that occupies most of the tumour mass. It is composed of a large number of cells of the immune system, such as Treg cells, tumour-associated macrophages (TAMs), myeloid suppressor cells (MDCs) and tumour-associated neutrophiles (TANs) that generate an immunosuppressive environment by the release of inflammatory cytokines. Moreover, cancer-associated fibroblast (CAFs) provide a protective coverage that would difficult the access of chemotherapy to the tumour. According to this, new therapies that could remodel this heterogeneous tumour microenvironment, such as adoptive T cell therapies (ACT), immune checkpoint inhibitors (ICI), and CD40 agonists, should be developed for targeting PDA. This review organizes the different cell populations found in the tumour stroma involved in tumour progression in addition to the different therapies that are being studied to counteract the tumour.
    Keywords:  Immune system; Pancreatic cancer; Stroma; Therapy; Tumour microenvironment
    DOI:  https://doi.org/10.1007/s13105-022-00875-8
  30. Nat Cancer. 2021 Dec;2(12): 1271-1275
    Reflecting on the golden age of cancer research.
    Alexia-Ileana Zaromytidou.
      
    DOI:  https://doi.org/10.1038/s43018-021-00313-6
  31. Nat Cancer. 2021 Oct;2(10): 1086-1101
    Compensatory CSF2-driven macrophage activation promotes adaptive resistance to CSF1R inhibition in breast-to-brain metastasis.
    Florian Klemm, Aylin Möckl, Anna Salamero-Boix, Tijna Alekseeva, Alexander Schäffer, Michael Schulz, Katja Niesel, Roeltje R Maas, Marie Groth, Benelita T Elie, Robert L Bowman, Monika E Hegi, Roy T Daniel, Pia S Zeiner, Jenny Zinke, Patrick N Harter, Karl H Plate, Johanna A Joyce, Lisa Sevenich.
      Tumor microenvironment-targeted therapies are emerging as promising treatment options for different cancer types. Tumor-associated macrophages and microglia (TAMs) represent an abundant nonmalignant cell type in brain metastases and have been proposed to modulate metastatic colonization and outgrowth. Here we demonstrate that targeting TAMs at distinct stages of the metastatic cascade using an inhibitor of colony-stimulating factor 1 receptor (CSF1R), BLZ945, in murine breast-to-brain metastasis models leads to antitumor responses in prevention and intervention preclinical trials. However, in established brain metastases, compensatory CSF2Rb-STAT5-mediated pro-inflammatory TAM activation blunted the ultimate efficacy of CSF1R inhibition by inducing neuroinflammation gene signatures in association with wound repair responses that fostered tumor recurrence. Consequently, blockade of CSF1R combined with inhibition of STAT5 signaling via AC4-130 led to sustained tumor control, a normalization of microglial activation states and amelioration of neuronal damage.
    DOI:  https://doi.org/10.1038/s43018-021-00254-0
  32. Cell Rep Med. 2022 Jan 18. 3(1): 100498
    Pegylated arginine deiminase drives arginine turnover and systemic autophagy to dictate energy metabolism.
    Yiming Zhang, Cassandra B Higgins, Brian A Van Tine, John S Bomalaski, Brian J DeBosch.
      Obesity is a multi-systemic disorder of energy balance. Despite intense investigation, the determinants of energy homeostasis remain incompletely understood, and efficacious treatments against obesity and its complications are lacking. Here, we demonstrate that conferred arginine iminohydrolysis by the bacterial virulence factor and arginine deiminase, arcA, promotes mammalian energy expenditure and insulin sensitivity and reverses dyslipidemia, hepatic steatosis, and inflammation in obese mice. Extending this, pharmacological arginine catabolism via pegylated arginine deiminase (ADI-PEG 20) recapitulates these metabolic effects in dietary and genetically obese models. These effects require hepatic and whole-body expression of the autophagy complex protein BECN1 and hepatocyte-specific FGF21 secretion. Single-cell ATAC sequencing further reveals BECN1-dependent hepatocyte chromatin accessibility changes in response to ADI-PEG 20. The data thus reveal an unexpected therapeutic utility for arginine catabolism in modulating energy metabolism by activating systemic autophagy, which is now exploitable through readily available pharmacotherapy.
    Keywords:  ADI-PEG 20; Beclin-1; FGF21; GLUT; arcA; arginase; arginine; arginine deiminase; autophagy; caloric restriction; diabetes; energy metabolism; fasting; glucose transport; insulin resistance; liver; non-alcoholic fatty liver disease; obesity; thermogenesis
    DOI:  https://doi.org/10.1016/j.xcrm.2021.100498
  33. Nat Cancer. 2021 Nov;2(11): 1124-1135
    Radiation therapy enhances immunotherapy response in microsatellite stable colorectal and pancreatic adenocarcinoma in a phase II trial.
    Aparna R Parikh, Annamaria Szabolcs, Jill N Allen, Jeffrey W Clark, Jennifer Y Wo, Michael Raabe, Hannah Thel, David Hoyos, Arnav Mehta, Sanya Arshad, David J Lieb, Lorraine C Drapek, Lawrence S Blaszkowsky, Bruce J Giantonio, Colin D Weekes, Andrew X Zhu, Lipika Goyal, Ryan D Nipp, Jon S Dubois, Emily E Van Seventer, Bronwen E Foreman, Lauren E Matlack, Leilana Ly, Jessica A Meurer, Nir Hacohen, David P Ryan, Beow Y Yeap, Ryan B Corcoran, Benjamin D Greenbaum, David T Ting, Theodore S Hong.
      Overcoming intrinsic resistance to immune checkpoint blockade for microsatellite stable (MSS) colorectal cancer (CRC) and pancreatic ductal adenocarcinoma (PDAC) remains challenging. We conducted a single-arm, non-randomized, phase II trial (NCT03104439) combining radiation, ipilimumab and nivolumab to treat patients with metastatic MSS CRC (n = 40) and PDAC (n = 25) with an Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1. The primary endpoint was disease control rate (DCR) by intention to treat. DCRs were 25% for CRC (ten of 40; 95% confidence interval (CI), 13-41%) and 20% for PDAC (five of 25; 95% CI, 7-41%). In the per-protocol analysis, defined as receipt of radiation, DCR was 37% (ten of 27; 95% CI, 19-58%) in CRC and 29% (five of 17; 95% CI, 10-56%) in PDAC. Pretreatment biopsies revealed low tumor mutational burden for all samples but higher numbers of natural killer (NK) cells and expression of the HERVK repeat RNA in patients with disease control. This study provides proof of concept of combining radiation with immune checkpoint blockade in immunotherapy-resistant cancers.
    DOI:  https://doi.org/10.1038/s43018-021-00269-7
  34. Nat Cancer. 2021 Oct;2(10): 998-999
    A quick guide for clinical oncology.
    Ahmet Zehir, Michael F Berger.
      
    DOI:  https://doi.org/10.1038/s43018-021-00273-x
  35. Elife. 2022 Jan 31. pii: e68048. [Epub ahead of print]11
    Inter-tissue convergence of gene expression during ageing suggests age-related loss of tissue and cellular identity.
    Hamit Izgi, DingDing Han, Ulas Isildak, Shuyun Huang, Ece Kocabiyik, Philipp Khaitovich, Mehmet Somel, Handan Melike Dönertaş.
      Developmental trajectories of gene expression may reverse in their direction during ageing, a phenomenon previously linked to cellular identity loss. Our analysis of cerebral cortex, lung, liver and muscle transcriptomes of 16 mice, covering development and ageing intervals, revealed widespread but tissue-specific ageing-associated expression reversals. Cumulatively, these reversals create a unique phenomenon: mammalian tissue transcriptomes diverge from each other during postnatal development, but during ageing, they tend to converge towards similar expression levels, a process we term Divergence followed by Convergence, or DiCo. We found that DiCo was most prevalent among tissue-specific genes and associated with loss of tissue identity, which is confirmed using data from independent mouse and human datasets. Further, using publicly available single-cell transcriptome data, we showed that DiCo could be driven both by alterations in tissue cell type composition and also by cell-autonomous expression changes within particular cell types.
    Keywords:  genetics; genomics; human; mouse
    DOI:  https://doi.org/10.7554/eLife.68048
  36. Nat Cancer. 2021 Oct;2(10): 1102-1112
    Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology.
    Brendan Reardon, Nathanael D Moore, Nicholas S Moore, Eric Kofman, Saud H AlDubayan, Alexander T M Cheung, Jake Conway, Haitham Elmarakeby, Alma Imamovic, Sophia C Kamran, Tanya Keenan, Daniel Keliher, David J Konieczkowski, David Liu, Kent W Mouw, Jihye Park, Natalie I Vokes, Felix Dietlein, Eliezer M Van Allen.
      Tumor molecular profiling of single gene-variant ('first-order') genomic alterations informs potential therapeutic approaches. Interactions between such first-order events and global molecular features (for example, mutational signatures) are increasingly associated with clinical outcomes, but these 'second-order' alterations are not yet accounted for in clinical interpretation algorithms and knowledge bases. We introduce the Molecular Oncology Almanac (MOAlmanac), a paired clinical interpretation algorithm and knowledge base to enable integrative interpretation of multimodal genomic data for point-of-care decision making and translational-hypothesis generation. We benchmarked MOAlmanac to a first-order interpretation method across multiple retrospective cohorts and observed an increased number of clinical hypotheses from evaluation of molecular features and profile-to-cell line matchmaking. When applied to a prospective precision oncology trial cohort, MOAlmanac nominated a median of two therapies per patient and identified therapeutic strategies administered in 47% of patients. Overall, we present an open-source computational method for integrative clinical interpretation of individualized molecular profiles.
    DOI:  https://doi.org/10.1038/s43018-021-00243-3
  37. JACS Au. 2022 Jan 24. 2(1): 246-257
    Sequence-Activated Fluorescent Nanotheranostics for Real-Time Profiling Pancreatic Cancer.
    Yining Tao, Chenxu Yan, Dan Li, Jianfeng Dai, Yingsheng Cheng, Hui Li, Wei-Hong Zhu, Zhiqian Guo.
      Pancreatic ductal adenocarcinoma (PDAC), as one of the most malignant tumors with dense desmoplastic stroma, forms a specific matrix barrier to hinder effective diagnosis and therapy. To date, a paramount challenge is in the search for intelligent nanotheranostics for such hypopermeable tumors, especially in breaking the PDAC-specific physical barrier. The unpredictable in vivo behaviors of nanotheranostics, that is, real-time tracking where, when, and how they cross the physical barriers and are taken up by tumor cells, are the major bottleneck. Herein, we elaborately design sequence-activated nanotheranostic TCM-U11&Cy@P with dual-channel near-infrared fluorescence outputs for monitoring in vivo behaviors in a sequential fashion. This nanotheranostic with a programmable targeting capability effectively breaks through the PDAC barriers. Ultimately, the released aggregation-induced emission (AIE) particle TCM-U11 directly interacts with PDAC cells and penetrates into the deep tissue. Impressively, this fluorescent nanotheranostic intraoperatively can map human clinical PDAC specimens with high resolution. We believe that this unique sequence-activated fluorescent strategy expands the repertoire of nanotheranostics in the treatment of hypopermeable tumors.
    DOI:  https://doi.org/10.1021/jacsau.1c00553
  38. Nat Methods. 2022 Jan 31.
    Squidpy: a scalable framework for spatial omics analysis.
    Giovanni Palla, Hannah Spitzer, Michal Klein, David Fischer, Anna Christina Schaar, Louis Benedikt Kuemmerle, Sergei Rybakov, Ignacio L Ibarra, Olle Holmberg, Isaac Virshup, Mohammad Lotfollahi, Sabrina Richter, Fabian J Theis.
      Spatial omics data are advancing the study of tissue organization and cellular communication at an unprecedented scale. Flexible tools are required to store, integrate and visualize the large diversity of spatial omics data. Here, we present Squidpy, a Python framework that brings together tools from omics and image analysis to enable scalable description of spatial molecular data, such as transcriptome or multivariate proteins. Squidpy provides efficient infrastructure and numerous analysis methods that allow to efficiently store, manipulate and interactively visualize spatial omics data. Squidpy is extensible and can be interfaced with a variety of already existing libraries for the scalable analysis of spatial omics data.
    DOI:  https://doi.org/10.1038/s41592-021-01358-2
  39. Mol Cell. 2022 Jan 28. pii: S1097-2765(22)00008-9. [Epub ahead of print]
    The interplay between BAX and BAK tunes apoptotic pore growth to control mitochondrial-DNA-mediated inflammation.
    Katia Cosentino, Vanessa Hertlein, Andreas Jenner, Timo Dellmann, Milos Gojkovic, Aida Peña-Blanco, Shashank Dadsena, Noel Wajngarten, John S H Danial, Jervis Vermal Thevathasan, Markus Mund, Jonas Ries, Ana J Garcia-Saez.
      BAX and BAK are key apoptosis regulators that mediate the decisive step of mitochondrial outer membrane permeabilization. However, the mechanism by which they assemble the apoptotic pore remains obscure. Here, we report that BAX and BAK present distinct oligomerization properties, with BAK organizing into smaller structures with faster kinetics than BAX. BAK recruits and accelerates BAX assembly into oligomers that continue to grow during apoptosis. As a result, BAX and BAK regulate each other as they co-assemble into the same apoptotic pores, which we visualize. The relative availability of BAX and BAK molecules thereby determines the growth rate of the apoptotic pore and the relative kinetics by which mitochondrial contents, most notably mtDNA, are released. This feature of BAX and BAK results in distinct activation kinetics of the cGAS/STING pathway with implications for mtDNA-mediated paracrine inflammatory signaling.
    Keywords:  AFM; BAK; BAX; BCL-2; inflammatory cell death; membrane pore; mitochondria; pore-forming protein; single-molecule imaging; super-resolution microscopy
    DOI:  https://doi.org/10.1016/j.molcel.2022.01.008
  40. Autophagy. 2022 Jan 31. 1-2
    Architecture of the endoplasmic reticulum plays a role in proteostasis.
    Smriti Parashar, Susan Ferro-Novick.
      The endoplasmic reticulum (ER) forms a contiguous network of tubules and sheets. When errors in protein folding occur, misfolded proteins accumulate in the ER. Proteostasis can be restored by ER quality control pathways. Reticulophagy is an ER quality control pathway that uses resident autophagy receptors to link an ER domain to the autophagy machinery. We recently showed that the reticulophagy receptor RTN3L recruits the COPII cargo adaptor SEC24C to target disease-causing mutant proinsulin INS2Akita puncta to the lysosome for degradation. When reticulophagy is disrupted and delivery to the lysosome is blocked, large INS2Akita puncta accumulate in the ER. Photobleach analysis revealed that these puncta behave like liquid condensates and not aggregates, as previously suggested. Other reticulophagy substrates that are segregated into tubules behave like INS2Akita, whereas a substrate of the ER sheets receptor, RETREG1/FAM134B, appears to be less fluid. Large INS2Akita puncta also accumulate when ER sheets are proliferated by the loss of LNPK, or by overproduction of the sheets-producing protein, CKAP4/CLIMP63. Restoring the tubular network by overexpressing reticulons reverses this phenotype. Our findings revealed that fluid-like deleterious cargoes are segregated into tubules to prevent them from expanding and affecting cell health while they are waiting to undergo reticulophagy.
    Keywords:  ER structure; Lunapark; SEC24C; misfolded prohormones and neuropeptides; protein quality control; reticulophagy
    DOI:  https://doi.org/10.1080/15548627.2022.2030175
  41. Proc Natl Acad Sci U S A. 2022 Feb 08. pii: e2109547119. [Epub ahead of print]119(6):
    In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density.
    Minjun Jin, Franco Tavella, Shiyuan Wang, Qiong Yang.
      Cells control the properties of the cytoplasm to ensure proper functioning of biochemical processes. Recent studies showed that cytoplasmic density varies in both physiological and pathological states of cells undergoing growth, division, differentiation, apoptosis, senescence, and metabolic starvation. Little is known about how cellular processes cope with these cytoplasmic variations. Here, we study how a cell cycle oscillator comprising cyclin-dependent kinase (Cdk1) responds to changes in cytoplasmic density by systematically diluting or concentrating cycling Xenopus egg extracts in cell-like microfluidic droplets. We found that the cell cycle maintains robust oscillations over a wide range of deviations from the endogenous density: as low as 0.2× to more than 1.22× relative cytoplasmic density (RCD). A further dilution or concentration from these values arrested the system in a low or high steady state of Cdk1 activity, respectively. Interestingly, diluting an arrested cytoplasm of 1.22× RCD recovers oscillations at lower than 1× RCD. Thus, the cell cycle switches reversibly between oscillatory and stable steady states at distinct thresholds depending on the direction of tuning, forming a hysteresis loop. We propose a mathematical model which recapitulates these observations and predicts that the Cdk1/Wee1/Cdc25 positive feedback loops do not contribute to the observed robustness, supported by experiments. Our system can be applied to study how cytoplasmic density affects other cellular processes.
    Keywords:  cell cycle oscillator; cytoplasmic density; hysteresis; macromolecular crowding; robustness
    DOI:  https://doi.org/10.1073/pnas.2109547119
  42. Nat Cancer. 2020 May;1(5): 482-492
    Genomics-guided pre-clinical development of cancer therapies.
    Hayley E Francies, Ultan McDermott, Mathew J Garnett.
      Since the approval of trastuzumab for the treatment of breast cancers more than two decades ago, many clinically effective targeted anti-cancer therapies have been developed. Here we consider the evidence that supports genomics-guided drug development and review the concept of oncogene addiction, including recent findings that inform this therapeutic approach. We consider non-oncogene addiction and how this synthetic-lethal paradigm could expand the range of new therapies, particularly for currently undruggable cancers. We discuss how CRISPR-based genetic screening is enhancing the ability to identify new targets. We conclude by considering opportunities for expanding the scope and refining the use of precision cancer medicines.
    DOI:  https://doi.org/10.1038/s43018-020-0067-x
  43. Nat Cancer. 2020 Jun;1(6): 573-574
    Isaiah Joshua ('Josh') Fidler 1936-2020.
    Raghu Kalluri.
      
    DOI:  https://doi.org/10.1038/s43018-020-0084-9
  44. Nat Commun. 2022 Feb 03. 13(1): 651
    Mitochondrial protein import determines lifespan through metabolic reprogramming and de novo serine biosynthesis.
    Eirini Lionaki, Ilias Gkikas, Ioanna Daskalaki, Maria-Konstantina Ioannidi, Maria I Klapa, Nektarios Tavernarakis.
      Sustained mitochondrial fitness relies on coordinated biogenesis and clearance. Both processes are regulated by constant targeting of proteins into the organelle. Thus, mitochondrial protein import sets the pace for mitochondrial abundance and function. However, our understanding of mitochondrial protein translocation as a regulator of longevity remains enigmatic. Here, we targeted the main protein import translocases and assessed their contribution to mitochondrial abundance and organismal physiology. We find that reduction in cellular mitochondrial load through mitochondrial protein import system suppression, referred to as MitoMISS, elicits a distinct longevity paradigm. We show that MitoMISS triggers the mitochondrial unfolded protein response, orchestrating an adaptive reprogramming of metabolism. Glycolysis and de novo serine biosynthesis are causatively linked to longevity, whilst mitochondrial chaperone induction is dispensable for lifespan extension. Our findings extent the pro-longevity role of UPRmt and provide insight, relevant to the metabolic alterations that promote or undermine survival and longevity.
    DOI:  https://doi.org/10.1038/s41467-022-28272-1
  45. Expert Opin Investig Drugs. 2022 Feb 04.
    Novel systemic treatment approaches for metastatic pancreatic cancer.
    Klara Dorman, Volker Heinemann, Sebastian Kobold, Michael von Bergwelt-Baildon, Stefan Boeck.
       INTRODUCTION: Pancreatic ductal adenocarcinoma (PDAC) has a 5-year overall survival rate of 10 %, emphasizing the need for more effective therapies, especially in metastatic disease. The immunosuppressive tumor microenvironment, poor vascularization, and dense tumor stroma typical for PDAC are hurdles that need to be overcome by novel drugs. Investigations are moving towards more targeted treatments including immunotherapy and cell-based approaches.
    AREAS COVERED: This article reviews emerging drugs in clinical development for metastatic PDAC, focusing on cellular therapies and novel treatments targeting metabolism, tumor stroma, oncogenic pathways and immunosuppression. With immunotherapy and CAR T cell therapy on the rise in hematological malignancies, the transfer to solid tumors remains intriguing. Multiple exciting clinical trials investigating innovative therapeutic strategies for PDAC are currently ongoing and reviewed herein. ClinicalTrials.gov, conference abstracts and PubMed were searched in August 2021 and assessed for information on ongoing and published clinical studies.
    EXPERT OPINION: With many challenges to overcome, the optimal therapy for patients with metastatic PDAC is likely to consist of a combination of different agents. We are slowly moving from entity-dependent approaches to ones more focused on molecular and pathological features. Increasingly personalized treatment plans tailored to each patient may be the future of PDAC therapy.
    Keywords:  Pancreatic cancer; cellular therapy; immunotherapy; metastatic; novel drugs; targeted therapy
    DOI:  https://doi.org/10.1080/13543784.2022.2037552
  46. Nat Cancer. 2021 May;2(5): 484-486
    Enhancing anti-tumor immunity by autophagy inhibition.
    Andrew Thorburn, Christina G Towers.
      
    DOI:  https://doi.org/10.1038/s43018-021-00214-8
  47. Nat Cancer. 2020 Aug;1(8): 753-754
    Zena Werb 1945-2020.
    Mikala Egeblad, Lisa M Coussens, Valerie M Weaver.
      
    DOI:  https://doi.org/10.1038/s43018-020-0101-z
  48. Elife. 2022 Feb 03. pii: e76269. [Epub ahead of print]11
    Functional visualization of NK Cell-mediated killing of metastatic single tumor cells.
    Hiroshi Ichise, Shoko Tsukamoto, Tsuyoshi Hirashima, Yoshinobu Konishi, Choji Oki, Shinya Tsukiji, Satoshi Iwano, Atsushi Miyawaki, Kenta Sumiyama, Kenta Terai, Michiyuki Matsuda.
      Natural killer (NK) cells lyse invading tumor cells to limit metastatic growth in the lung, but how some cancers evade this host protective mechanism to establish a growing lesion is unknown. Here we have combined ultra-sensitive bioluminescence imaging with intravital two-photon microscopy involving genetically-encoded biosensors to examine this question. NK cells eliminated disseminated tumor cells from the lung within 24 hrs of arrival, but not thereafter. Intravital dynamic imaging revealed that 50% of NK-tumor cell encounters lead to tumor cell death in the first 4 hrs after tumor cell arrival, but after 24 hrs of arrival, nearly 100% of the interactions result in the survival of the tumor cell. During this 24 hrs period, the probability of ERK activation in NK cells upon encountering the tumor cells was decreased from 68% to 8%, which correlated with the loss of the activating ligand CD155/PVR/Necl5 from the tumor cell surface. Thus, by quantitatively visualizing the NK-tumor cell interaction at the early stage of metastasis, we have revealed the crucial parameters of NK cell immune surveillance in the lung.
    Keywords:  cell biology; immunology; inflammation; mouse
    DOI:  https://doi.org/10.7554/eLife.76269
  49. Science. 2022 Feb 03. eabl5447
    Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers.
    Frank J Lowery, Sri Krishna, Rami Yossef, Neilesh B Parikh, Praveen D Chatani, Nikolaos Zacharakis, Maria R Parkhurst, Noam Levin, Sivasish Sindiri, Abraham Sachs, Kyle J Hitscherich, Zhiya Yu, Nolan R Vale, Yong-Chen Lu, Zhili Zheng, Li Jia, Jared J Gartner, Victoria K Hill, Amy R Copeland, Shirley K Nah, Robert V Masi, Billel Gasmi, Scott Kivitz, Biman C Paria, Maria Florentin, Sanghyun P Kim, Ken-Ichi Hanada, Yong F Li, Lien T Ngo, Satyajit Ray, Mackenzie L Shindorf, Shoshana T Levi, Ryan Shepherd, Chris Toy, Anup Y Parikh, Todd D Prickett, Michael C Kelly, Rachel Beyer, Stephanie L Goff, James C Yang, Paul F Robbins, Steven A Rosenberg.
      The accurate identification of antitumor T cell receptors (TCRs) represents a major challenge to engineering cell-based cancer immunotherapies. By mapping 55 neoantigen-specific TCR clonotypes (NeoTCRs) from 10 metastatic human tumors to their single-cell transcriptomes, we identified signatures of CD8+ and CD4+ neoantigen-reactive tumor-infiltrating lymphocytes (TIL). Neoantigen-specific TIL exhibited tumor-specific expansion with dysfunctional phenotypes, distinct from blood-emigrant bystanders and regulatory TIL. Prospective prediction and testing of 73 NeoTCR signature-derived clonotypes demonstrated that half the tested TCRs recognized tumor antigens or autologous tumors. NeoTCR signatures identified TCRs targeting driver neoantigens and non-mutated viral/tumor-associated antigens, suggesting a common metastatic TIL exhaustion program. NeoTCR signatures delineate the landscape of TIL across metastatic tumors, enabling successful TCR prediction based purely on TIL transcriptomic states for use in cancer immunotherapy.
    DOI:  https://doi.org/10.1126/science.abl5447
  50. EMBO J. 2022 Feb 03. e108443
    Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation.
    Lara A Gruijs da Silva, Francesca Simonetti, Saskia Hutten, Henrick Riemenschneider, Erin L Sternburg, Lisa M Pietrek, Jakob Gebel, Volker Dötsch, Dieter Edbauer, Gerhard Hummer, Lukas S Stelzl, Dorothee Dormann.
      Post-translational modifications (PTMs) have emerged as key modulators of protein phase separation and have been linked to protein aggregation in neurodegenerative disorders. The major aggregating protein in amyotrophic lateral sclerosis and frontotemporal dementia, the RNA-binding protein TAR DNA-binding protein (TDP-43), is hyperphosphorylated in disease on several C-terminal serine residues, a process generally believed to promote TDP-43 aggregation. Here, we however find that Casein kinase 1δ-mediated TDP-43 hyperphosphorylation or C-terminal phosphomimetic mutations reduce TDP-43 phase separation and aggregation, and instead render TDP-43 condensates more liquid-like and dynamic. Multi-scale molecular dynamics simulations reveal reduced homotypic interactions of TDP-43 low-complexity domains through enhanced solvation of phosphomimetic residues. Cellular experiments show that phosphomimetic substitutions do not affect nuclear import or RNA regulatory functions of TDP-43, but suppress accumulation of TDP-43 in membrane-less organelles and promote its solubility in neurons. We speculate that TDP-43 hyperphosphorylation may be a protective cellular response to counteract TDP-43 aggregation.
    Keywords:  RNA-binding protein; TDP-43; neurodegeneration; phase separation; phosphorylation
    DOI:  https://doi.org/10.15252/embj.2021108443
  51. Cancer Rep (Hoboken). 2022 Feb 05. e1565
    Cost-effectiveness of neoadjuvant FOLFIRINOX versus gemcitabine plus nab-paclitaxel in borderline resectable/locally advanced pancreatic cancer patients.
    Myles A Ingram, Brianna N Lauren, Yoanna Pumpalova, Jiheum Park, Francesca Lim, Susan E Bates, Fay Kastrinos, Gulam A Manji, Chung Yin Kong, Chin Hur.
       BACKGROUND: The 2020 National Comprehensive Cancer Network guidelines recommend neoadjuvant FOLFIRINOX or neoadjuvant gemcitabine plus nab-paclitaxel (G-nP) for borderline resectable/locally advanced pancreatic ductal adenocarcinoma (BR/LA PDAC).
    AIM: The purpose of our study was to compare treatment outcomes, toxicity profiles, costs, and quality-of-life measures between these two treatments to further inform clinical decision-making.
    METHODS AND RESULTS: We developed a decision-analytic mathematical model to compare the total cost and health outcomes of neoadjuvant FOLFIRINOX against G-nP over 12 years. The model inputs were estimated using clinical trial data and published literature. The primary endpoint was incremental cost-effectiveness ratios (ICERs) with a willingness-to-pay threshold of $100 000 per quality-adjusted-life-year (QALY). Secondary endpoints included overall (OS) and progression-free survival (PFS), total cost of care, QALYs, PDAC resection rate, and monthly treatment-related adverse events (TRAE) costs (USD). FOLFIRINOX was the cost-effective strategy, with an ICER of $60856.47 per QALY when compared to G-nP. G-nP had an ICER of $44639.71 per QALY when compared to natural history. For clinical outcomes, more patients underwent an "R0" resection with FOLFIRINOX compared to G-nP (84.9 vs. 81.0%), but FOLFIRINOX had higher TRAE costs than G-nP ($10905.19 vs. $4894.11). A one-way sensitivity analysis found that the ICER of FOLFIRINOX exceeded the threshold when TRAE costs were higher or PDAC recurrence rates were lower.
    CONCLUSION: Our modeling analysis suggests that FOLFIRNOX is the cost-effective treatment compared to G-nP for BR/LA PDAC despite having a higher cost of total care due to TRAE costs. Trial data with sufficient follow-up are needed to confirm our findings.
    Keywords:  chemotherapy; clinical cancer research; pancreatic cancer
    DOI:  https://doi.org/10.1002/cnr2.1565
  52. Oncogene. 2022 Jan 29.
    Hyperglycemia-induced oxidative stress promotes tumor metastasis by upregulating vWF expression in endothelial cells through the transcription factor GATA1.
    Han-Seok Jeong, Da-Hye Lee, Seung-Hoon Kim, Chang-Han Lee, Hyun Mu Shin, Hang-Rae Kim, Chung-Hyun Cho.
      Diabetes mellitus (DM) characterized by hyperglycemia is a chronic metabolic disorder that leads to many symptoms and vascular complications. Despite the close association between DM and cancer progression, the response and role of endothelial cells (ECs) under diabetic conditions in tumor metastasis remain to be elucidated. In this study, we sought to determine whether and how ECs under diabetic conditions contribute to tumor metastasis. We have taken advantage of syngeneic mouse tumor models of Lewis lung carcinoma (LLC) and melanoma (B16F10) cells and a streptozotocin (STZ)-induced hyperglycemia model. We demonstrated that hyperglycemia increased the metastasis of LLC and B16F10 cells in an experimental metastasis model with an intravenous injection of the tumor cells. We also found that hyperglycemia promoted lung metastasis of tumor cells by increasing the adhesiveness of ECs to facilitate the adhesion of tumor cells to ECs rather than affecting the metastatic behavior of tumor cells themselves. From the analysis of gene expression in primary lung ECs from STZ-treated mice, we identified that vWF promoted the adhesion of tumor cells to ECs and the transendothelial migration of tumor cells. Mechanistically, hyperglycemia-induced oxidative stress in ECs, and increased oxidative stress enhanced vWF expression in ECs through an increase in the transcription factor GATA1. These results provide evidence for the role of vWF in ECs in promoting hyperglycemia-induced tumor metastasis and potential therapeutic targets for the regulation of vWF expression in ECs and hyperglycemia-induced tumor metastasis.
    DOI:  https://doi.org/10.1038/s41388-022-02207-y
  53. EMBO Rep. 2022 Feb 02. e52984
    TERT activates endogenous retroviruses to promote an immunosuppressive tumour microenvironment.
    Jian Mao, Qian Zhang, Yaxiang Wang, Yang Zhuang, Lu Xu, Xiaohe Ma, Di Guan, Junzhi Zhou, Jiang Liu, Xiaoying Wu, Qian Liang, Miao Wang, Yu-Sheng Cong.
      Telomerase plays a pivotal role in tumorigenesis by both telomere-dependent and telomere-independent activities, although the underlying mechanisms are not completely understood. Using single-sample gene set enrichment analysis (ssGSEA) across 9,264 tumour samples, we observe that expression of telomerase reverse transcriptase (TERT) is closely associated with immunosuppressive signatures. We demonstrate that TERT can activate a subclass of endogenous retroviruses (ERVs) independent of its telomerase activity to form double-stranded RNAs (dsRNAs), which are sensed by the RIG-1/MDA5-MAVS signalling pathway and trigger interferon signalling in cancer cells. Furthermore, we show that TERT-induced ERV/interferon signalling stimulates the expression of chemokines, including CXCL10, which induces the infiltration of suppressive T-cell populations with increased percentage of CD4+ and FOXP3+ cells. These data reveal an unanticipated role for telomerase as a transcriptional activator of ERVs and provide strong evidence that TERT-mediated ERV/interferon signalling contributes to immune suppression in tumours.
    Keywords:  ERVs; TERT; dsRNA; immune suppression; interferon signalling
    DOI:  https://doi.org/10.15252/embr.202152984
  54. Adv Cancer Res. 2022 ;pii: S0065-230X(21)00063-4. [Epub ahead of print]153 169-203
    Targeting RAS oncogenesis with SOS1 inhibitors.
    Roman Christian Hillig, Benjamin Bader.
      RAS proteins play major roles in many human cancers, but programs to develop direct RAS inhibitors so far have only been successful for the oncogenic KRAS mutant G12C. As an alternative approach, inhibitors for the RAS guanine nucleotide exchange factor SOS1 have been investigated by several academic groups and companies, and major progress has been achieved in recent years in the optimization of small molecule activators and inhibitors of SOS1. Here, we review the discovery and development of small molecule modulators of SOS1 and their molecular binding modes and modes of action. As targeting the RAS pathway is expected to result in the development of resistance mechanisms, SOS1 inhibitors will most likely be best applied in vertical combination approaches where two nodes of the RAS signaling pathway are hit simultaneously. We summarize the current understanding of which combination partners may be most beneficial for patients with RAS driven tumors.
    Keywords:  Activator; Cancer; Combination therapy; GEF; Guanine nucleotide exchange factor; KRAS; RASopathies; SOS1; Small molecule inhibitor; Son of sevenless
    DOI:  https://doi.org/10.1016/bs.acr.2021.07.001
  55. Anticancer Res. 2022 Feb;42(2): 739-743
    High Incidence of Lymph-node Metastasis in a Pancreatic-cancer Patient-derived Orthotopic Xenograft (PDOX) NOG-Mouse Model.
    Norihiko Sugisawa, Kentaro Miyake, Takashi Higuchi, Hiromichi Oshiro, Jun Ho Park, Kei Kawaguchi, Michael Bouvet, Michiaki Unno, Robert M Hoffman.
       BACKGROUND/AIM: Our laboratory pioneered the patient-derived orthotopic xenograft (PDOX) model. An important goal of PDOX-model development is facile visualization of metastasis in live mice. In the present report we evaluated tumor growth and metastasis in pancreatic cancer PDOX NOG [Non-obese diabetes (NOD)/Scid/IL2Rγnull]-and nude-mouse models using red fluorescent protein (RFP)-expressing tumor stroma to visualize the primary tumor and metastasis.
    MATERIALS AND METHODS: A patient-derived pancreatic cancer was initially implanted in transgenic RFP-expressing nude mice. Then, tumor fragments, which acquired RFP expressing stroma while growing in RFP-expressing nude mice were orthotopically implanted in nude and NOG mice. The primary pancreatic tumor and metastasis were observed 8 weeks after implantation.
    RESULTS: Lymph-node metastases expressing red fluorescence were detected only in NOG mice. Significantly faster growth of primary pancreatic tumors and a higher incidence of lymph-node metastasis occurred in NOG mice compared to nude mice.
    CONCLUSION: RFP-expressing tumor stroma, which traffics together with cancer cells to lymph nodes, is useful to observe tumor behavior, such as lymph-node metastasis in a PDOX NOG-mouse model which can be used for evaluation of novel anti-metastatic agents, as well as personalized therapy to identify effective drugs.
    Keywords:  NOG mouse; drug discovery; intravital imaging; lymph-node metastasis; nude mouse red fluorescent protein (RFP); pancreatic cancer; patient-derived orthotopic xenograft (PDOX); personalized therapy
    DOI:  https://doi.org/10.21873/anticanres.15532
  56. Ann Surg. 2022 Mar 01. 275(3): 415-421
    Bayesian Approach to Understand the Association Between Treatment Down-staging and Survival for Patients With Pancreatic Adenocarcinoma.
    Wilson Luiz da Costa, Hop S Tran Cao, Xiangjun Gu, Nader N Massarweh.
       OBJECTIVE: To evaluate the association between staging concordance, treatment sequencing, and response to neoadjuvant therapy (NAT) on the survival of patients with pancreatic ductal adenocarcinoma (PDAC).
    SUMMARY OF BACKGROUND DATA: NAT is increasingly utilized in the management of patients with PDAC, but it is unclear whether its benefit is contingent on tumor down-staging.
    METHODS: This was a cohort study of stage I-III PDAC patients in the National Cancer Database (2006-2015) treated with upfront resection or NAT followed by surgery. We determined staging concordance using patients' clinical and pathological staging data. For NAT patients, we used Bayesian analysis to ascertain staging concordance accounting for down-staging.
    RESULTS: Among 16,597 patients treated at 979 hospitals, 13,982 had an upfront resection and 2,615 NAT followed by surgery. Overall survival (OS) at 5-years ranged from 26.0% (95% CI 24.9%-27.1%) among cT1-2N0 patients to 18.6% (17.9%-19.2%) among cT1-3N+ ones. Patients with cT3-4 or cN+ tumors had improved OS after NAT compared to upfront surgery (all p< 0.001), while there was no difference among patients with cT1-2N0 (P = 0.16) disease. Relative to accurately staged cT1-2-3N+ or cT4 patients treated with upfront surgery, NAT was associated with a lower risk of death [HR 0.46 (0.37-0.57) for N+; HR 0.56 (0.40-0.77) for T4 disease], even among those without tumor down-staging [HR 0.81 (0.73-0.90) for N+; HR 0.48 (0.39-0.60) for T4].
    CONCLUSIONS: NAT is associated with improved survival for PDAC, particularly for patients with more advanced disease and regardless of down-staging. Consideration should be given to recommending NAT for all PDAC patients.
    DOI:  https://doi.org/10.1097/SLA.0000000000005249
  57. Dis Model Mech. 2022 Feb 03. pii: dmm.049257. [Epub ahead of print]
    The molecular subtyping resource (MouSR): a user-friendly tool for rapid biological discovery from transcriptional data.
    Baharak Ahmaderaghi, Raheleh Amirkhah, James Jackson, Tamsin R M Lannagan, Kathryn Gilroy, Sudhir B Malla, Keara L Redmond, Gerard Quinn, Simon McDade, ACRCelerate Consortium, Tim Maughan, Simon Leedham, Andrew S Campbell, Owen J Sansom, Mark Lawler, Philip D Dunne.
      Generation of transcriptional data has dramatically increased in the last decade, driving the development of analytical algorithms that enable interrogation of the biology underpinning the profiled samples. However, these resources require users to have expertise in data wrangling and analytics, reducing opportunities for biological discovery by "wet-lab" users with a limited programming skillset. Although commercial solutions exist, costs for software access can be prohibitive for academic research groups. To address these challenges, we have developed an open source and user-friendly data analysis platform for on-the-fly bioinformatic interrogation of transcriptional data derived from human or mouse tissue, called Molecular Subtyping Resource "MousR". This internet-accessible analytical tool, https://mousr.qub.ac.uk/, enables users to easily interrogate their data using an intuitive "point and click" interface, which includes a suite of molecular characterisation options including QC, differential gene expression, gene set enrichment and microenvironmental cell population analyses from RNA-Seq. The MouSR online tool provides a unique freely-available option for users to perform rapid transcriptomic analyses and comprehensive interrogation of the signalling underpinning transcriptional datasets, which alleviates a major bottleneck for biological discovery.
    Keywords:  Bioinformatics; Data Analytics; RNA-seq
    DOI:  https://doi.org/10.1242/dmm.049257
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