bims-cagime 2022-12-11 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2022‒12‒11
37 papers selected by
Kıvanç Görgülü
Technical University of Munich

Functional noninvasive detection of glycolytic pancreatic ductal adenocarcinoma.
Regulation of autophagosome biogenesis and mitochondrial bioenergetics by the cholesterol transport protein GRAMD1C.
Review of the endocrine organ-like tumor hypothesis of cancer cachexia in pancreatic ductal adenocarcinoma.
Autophagy Inhibition Signals through Senescence to Promote Tumor Suppression.
Gp130 is expressed in pancreatic cancer and can be targeted by the small inhibitor molecule SC144.
Age-associated remodeling of T cell immunity and metabolism.
Spatial biology of cancer evolution.
Crosstalk between pro-survival sphingolipid metabolism and complement signaling induces inflammasome-mediated tumor metastasis.
Extracellular galectin 4 drives immune evasion and promotes T-cell apoptosis in pancreatic cancer.
Biophysical determinants of cancer organotropism.
Biology, vulnerabilities and clinical applications of circulating tumour cells.
Negative prognostic impact of sarcopenia before and after neoadjuvant chemotherapy for pancreatic cancer.
Closing the autophagosome is easy-PC.
Cxcr3 constrains pancreatic cancer dissemination through instructing T cell fate.
Efficacy of a small molecule inhibitor of KrasG12D in immunocompetent models of pancreatic cancer.
Association of Adjuvant Chemotherapy in Patients With Resected Pancreatic Adenocarcinoma After Multiagent Neoadjuvant Chemotherapy.
A systematic review of basket and umbrella trials in oncology: the importance of tissue of origin and molecular target.
PHGDH and cancer: new job for an old enzyme!
Current methods for studying metastatic potential of tumor cells.
Survival impact of occult liver metastasis and peritoneal dissemination compared with radiologically defined distant organ metastasis in pancreatic ductal adenocarcinoma.
Selective Inhibitors of Autophagy Reveal New Link between the Cell Cycle and Autophagy and Lead to Discovery of Novel Synergistic Drug Combinations.
Mitochondrial cristae architecture protects against mtDNA release and inflammation.
Weakly migratory metastatic breast cancer cells activate fibroblasts via microvesicle-Tg2 to facilitate dissemination and metastasis.
Efficacy of Global Leadership Initiative on Malnutrition as potential cachexia screening tool for patients with solid cancer.
Neoadjuvant chemotherapy and radiotherapy outcomes in borderline-resectable and locally-advanced pancreatic cancer patients.
Dendritic cells direct circadian anti-tumor immune responses.
amica: an interactive and user-friendly web-platform for the analysis of proteomics data.
Elevated methionine flux drives pyroptosis evasion in persister cancer cells.
PD-1 and TIM-3 differentially regulate subsets of mouse IL-17A-producing γδ T cells.
STRAINS: A big data method for classifying cellular response to stimuli at the tissue scale.
Tissue RNA Integrity in Visium Spatial Protocol (Fresh Frozen Samples).
Catalase-deficient mice induce aging faster through lysosomal dysfunction.
Resected Early-Onset Pancreatic Cancer: Practices and Outcomes in an International Dual-Center Study.
SHP2 inhibition mitigates adaptive resistance to MEK inhibitors in KRAS-mutant gastric cancer through the suppression of KSR1 activity.
Tumor-on-a-chip: Perfusable vascular incorporation brings new approach to tumor metastasis research and drug development.
Fibroblast inflammatory priming determines regenerative versus fibrotic skin repair in reindeer.
Impact of the Human Cell Atlas on medicine.

Cancer Metab. 2022 Dec 09. 10(1): 24

Functional noninvasive detection of glycolytic pancreatic ductal adenocarcinoma.

Irina Heid, Corinna Münch, Sinan Karakaya, Smiths S Lueong, Alina M Winkelkotte, Sven T Liffers, Laura Godfrey, Phyllis F Y Cheung, Konstantinos Savvatakis, Geoffrey J Topping, Florian Englert, Lukas Kritzner, Martin Grashei, Andrea Tannapfel, Richard Viebahn, Heiner Wolters, Waldemar Uhl, Deepak Vangala, Esther M M Smeets, Erik H J G Aarntzen, Daniel Rauh, Wilko Weichert, Jörg D Hoheisel, Stephan A Hahn, Franz Schilling, Rickmer Braren, Marija Trajkovic-Arsic, Jens T Siveke.

  BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) lacks effective treatment options beyond chemotherapy. Although molecular subtypes such as classical and QM (quasi-mesenchymal)/basal-like with transcriptome-based distinct signatures have been identified, deduced therapeutic strategies and targets remain elusive. Gene expression data show enrichment of glycolytic genes in the more aggressive and therapy-resistant QM subtype. However, whether the glycolytic transcripts are translated into functional glycolysis that could further be explored for metabolic targeting in QM subtype is still not known.METHODS: We used different patient-derived PDAC model systems (conventional and primary patient-derived cells, patient-derived xenografts (PDX), and patient samples) and performed transcriptional and functional metabolic analysis. These included RNAseq and Illumina HT12 bead array, in vitro Seahorse metabolic flux assays and metabolic drug targeting, and in vivo hyperpolarized [1-13C]pyruvate and [1-13C]lactate magnetic resonance spectroscopy (HP-MRS) in PDAC xenografts.
RESULTS: We found that glycolytic metabolic dependencies are not unambiguously functionally exposed in all QM PDACs. Metabolic analysis demonstrated functional metabolic heterogeneity in patient-derived primary cells and less so in conventional cell lines independent of molecular subtype. Importantly, we observed that the glycolytic product lactate is actively imported into the PDAC cells and used in mitochondrial oxidation in both classical and QM PDAC cells, although more actively in the QM cell lines. By using HP-MRS, we were able to noninvasively identify highly glycolytic PDAC xenografts by detecting the last glycolytic enzymatic step and prominent intra-tumoral [1-13C]pyruvate and [1-13C]lactate interconversion in vivo.
CONCLUSION: Our study adds functional metabolic phenotyping to transcriptome-based analysis and proposes a functional approach to identify highly glycolytic PDACs as candidates for antimetabolic therapeutic avenues.

Keywords:  Glycolysis; Hyperpolarized magnetic resonance spectroscopy; Lactate; Molecular subtype; PDAC

DOI:  https://doi.org/10.1186/s40170-022-00298-5
Autophagy. 2022 Dec 05.

Regulation of autophagosome biogenesis and mitochondrial bioenergetics by the cholesterol transport protein GRAMD1C.

Chara Charsou, Matthew Yoke Wui Ng, Anne Simonsen.

  Autophagosomes are crucial components of the cellular recycling machinery that form at endoplasmic reticulum (ER)-associated sites. As the autophagosome membrane is largely devoid of transmembrane proteins, autophagosome biogenesis is thought to be largely regulated by lipid transfer and lipid modifications, as well as membrane-associated proteins. While the membrane origin of autophagosomes and their lipid composition are still incompletely understood, previous studies have found the autophagosome membrane to be enriched in unsaturated fatty acids and have little cholesterol, suggesting that cholesterol removal is an integral step during autophagosome biogenesis. In our study, we demonstrate that short term cholesterol depletion leads to a rapid induction of autophagy and identify the ER-localized cholesterol transport protein GRAMD1C as a negative regulator of starvation-induced macroautophagy/autophagy.

Keywords:  Aster; GRAMD1C; VASt; autophagy; ccRCC; cholesterol

DOI:  https://doi.org/10.1080/15548627.2022.2155020
Front Oncol. 2022 ;12 1057930

Review of the endocrine organ-like tumor hypothesis of cancer cachexia in pancreatic ductal adenocarcinoma.

Ying-Chun Yu, Azaj Ahmed, Hsueh-Chou Lai, Wei-Chung Cheng, Juan-Chern Yang, Wei-Chun Chang, Lu-Min Chen, Yan-Shen Shan, Wen-Lung Ma.

  Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal types of solid tumors, associated with a high prevalence of cachexia (~80%). PDAC-derived cachexia (PDAC-CC) is a systemic disease involving the complex interplay between the tumor and multiple organs. The endocrine organ-like tumor (EOLT) hypothesis may explain the systemic crosstalk underlying the deleterious homeostatic shifts that occur in PDAC-CC. Several studies have reported a markedly heterogeneous collection of cachectic mediators, signaling mechanisms, and metabolic pathways, including exocrine pancreatic insufficiency, hormonal disturbance, pro-inflammatory cytokine storm, digestive and tumor-derived factors, and PDAC progression. The complexities of PDAC-CC necessitate a careful review of recent literature summarizing cachectic mediators, corresponding metabolic functions, and the collateral impacts on wasting organs. The EOLT hypothesis suggests that metabolites, genetic instability, and epigenetic changes (microRNAs) are involved in cachexia development. Both tumors and host tissues can secrete multiple cachectic factors (beyond only inflammatory mediators). Some regulatory molecules, metabolites, and microRNAs are tissue-specific, resulting in insufficient energy production to support tumor/cachexia development. Due to these complexities, changes in a single factor can trigger bi-directional feedback circuits that exacerbate PDAC and result in the development of irreversible cachexia. We provide an integrated review based on 267 papers and 20 clinical trials from PubMed and ClinicalTrials.gov database proposed under the EOLT hypothesis that may provide a fundamental understanding of cachexia development and response to current treatments.

Keywords:  cachexia; endocrine organ-like tumour (EOLT); muscle wasting; pancreatic ductal adenocarcinoma (PDAC); tissue wasting

DOI:  https://doi.org/10.3389/fonc.2022.1057930
Autophagy. 2022 Dec 06.

Autophagy Inhibition Signals through Senescence to Promote Tumor Suppression.

Nanfang Peng, Helen H Kang, Yan Feng, Alexander M Minikes, Xuejun Jiang.

  Macroautophagy/autophagy, a stress-responsive cellular survival mechanism, plays important and context-dependent roles in cancer, and its inhibition has been implicated as a promising cancer therapeutic approach. The detailed mechanisms underlying the function of autophagy in cancer have not been fully understood. In this study, we show that autophagy inhibition promotes both the efficacy of chemotherapy for the treatment of glioblastoma (GBM) and therapy-induced senescence of GBM cells. As a specific cell fate characterized by permanent cell cycle arrest, senescence is also associated with the expression of a panel of specific secreted protein factors known as senescence-associated secretory phenotype (SASP). Intriguingly, we found that autophagy inhibition not only quantitatively enhanced GBM cell senescence but also qualitatively altered the spectrum of SASP. The altered SASP had increased potent activity to induce paracrine senescence of neighboring GBM cells, to skew macrophage polarization toward the anti-tumor M1 state, and to block the recruitment of pro-tumor neutrophils to GBM tumor tissues. Taken together, this study reveals novel functional communication between autophagy and senescence and suggests cancer therapeutic approaches harnessing autophagy blockage in inducing senescence-mediated antitumor immunity.

Keywords:  SASP; antitumor immunity; autophagy; glioblastoma multiform; senescence

DOI:  https://doi.org/10.1080/15548627.2022.2155794
J Cancer Res Clin Oncol. 2022 Dec 10.

Gp130 is expressed in pancreatic cancer and can be targeted by the small inhibitor molecule SC144.

Ioannis Pozios, Nina A Hering, Emily Guenzler, Marco Arndt, Sefer Elezkurtaj, Thomas Knösel, Christiane J Bruns, Georgios A Margonis, Katharina Beyer, Hendrik Seeliger.

  PURPOSE: Interleukin 6 (IL-6), Oncostatin M (OSM), and downstream effector STAT3 are pro-tumorigenic agents in pancreatic ductal adenocarcinoma (PDAC). Glycoprotein 130 (gp130) is a compound of the IL-6 and OSM receptor complex that triggers STAT3 signaling. SC144 is a small molecule gp130 inhibitor with anticancer activity. This study examines the gp130 expression in human PDAC specimens and the in vitro effects of SC144 in PDAC cell lines.METHODS: Tissue micro-arrays were constructed from 175 resected human PDAC. The gp130 expression in tumor epithelium and stroma was determined by immunohistochemistry, and survival analysis was performed. Growth inhibition by SC144 was assessed in vitro using BrdU and MTT assays. Western blotting was performed to evaluate the SC144 effect on IL-6 and OSM signaling.
RESULTS: Gp130 was expressed in the epithelium of 78.8% and the stroma of 9.4% of the tumor samples. The median overall survival for patients with or without epithelial gp130 expression was 16.7 months and 15.9 months, respectively (p = 0.830). Patients with no stromal gp130 expression showed poorer survival than patients with stromal gp130 expression (median 16.2 and 22.9 months, respectively), but this difference did not reach significance (p = 0.144). SC144 inhibited cell proliferation and viability and suppressed IL-6- and OSM-stimulated STAT3Y705 phosphorylation in PDAC cells.
CONCLUSION: Gp130 is expressed in the epithelium of most human PDAC, but stromal expression is rare. The small molecule gp130 inhibitor SC144 potently inhibits PDAC progression in vitro and may abrogate IL-6 or OSM/gp130/STAT3 signaling. These results suggest gp130 as a novel drug target for pancreatic cancer therapy.

Keywords:  Interleukin 6; Oncostatin M; Pancreatic cancer; SC144; STAT3; gp130

DOI:  https://doi.org/10.1007/s00432-022-04518-9
Cell Metab. 2022 Nov 29. pii: S1550-4131(22)00496-X. [Epub ahead of print]

Age-associated remodeling of T cell immunity and metabolism.

SeongJun Han, Peter Georgiev, Alison E Ringel, Arlene H Sharpe, Marcia C Haigis.

  Aging results in remodeling of T cell immunity and is associated with poor clinical outcomes in age-related diseases such as cancer. Among the hallmarks of aging, changes in host and cellular metabolism critically affect the development, maintenance, and function of T cells. Although metabolic perturbations impact anti-tumor T cell responses, the link between age-associated metabolic dysfunction and anti-tumor immunity remains unclear. In this review, we summarize recent advances in our understanding of aged T cell metabolism, with a focus on the bioenergetic and immunologic features of T cell subsets unique to the aging process. We also survey insights into mechanisms of metabolic T cell dysfunction in aging and discuss the impacts of aging on the efficacy of cancer immunotherapy. As the average life expectancy continues to increase, understanding the interplay between age-related metabolic reprogramming and maladaptive T cell immunity will be instrumental for the development of therapeutic strategies for older patients.

Keywords:  T cells; aging; cancer; immunity; immunotherapy; metabolism; mitochondria

DOI:  https://doi.org/10.1016/j.cmet.2022.11.005
Nat Rev Genet. 2022 Dec 09.

Spatial biology of cancer evolution.

Zaira Seferbekova, Artem Lomakin, Lucy R Yates, Moritz Gerstung.

The natural history of cancers can be understood through the lens of evolution given that the driving forces of cancer development are mutation and selection of fitter clones. Cancer growth and progression are spatial processes that involve the breakdown of normal tissue organization, invasion and metastasis. For these reasons, spatial patterns are an integral part of histological tumour grading and staging as they measure the progression from normal to malignant disease. Furthermore, tumour cells are part of an ecosystem of tumour cells and their surrounding tumour microenvironment. A range of new spatial genomic, transcriptomic and proteomic technologies offers new avenues for the study of cancer evolution with great molecular and spatial detail. These methods enable precise characterizations of the tumour microenvironment, cellular interactions therein and micro-anatomical structures. In conjunction with spatial genomics, it emerges that tumours and microenvironments co-evolve, which helps explain observable patterns of heterogeneity and offers new routes for therapeutic interventions.

DOI: https://doi.org/10.1038/s41576-022-00553-x
Cell Rep. 2022 Dec 06. pii: S2211-1247(22)01620-5. [Epub ahead of print]41(10): 111742

Crosstalk between pro-survival sphingolipid metabolism and complement signaling induces inflammasome-mediated tumor metastasis.

Alhaji H Janneh, Mohamed Faisal Kassir, F Cansu Atilgan, Han Gyul Lee, Megan Sheridan, Natalia Oleinik, Zdzislaw Szulc, Christina Voelkel-Johnson, Hung Nguyen, Hong Li, Yuri K Peterson, Elisabetta Marangoni, Ozge Saatci, Ozgur Sahin, Michael Lilly, Carl Atkinson, Stephen Tomlinson, Shikhar Mehrotra, Besim Ogretmen.

  Crosstalk between metabolic and signaling events that induce tumor metastasis remains elusive. Here, we determine how oncogenic sphingosine 1-phosphate (S1P) metabolism induces intracellular C3 complement activation to enhance migration/metastasis. We demonstrate that increased S1P metabolism activates C3 complement processing through S1P receptor 1 (S1PR1). S1P/S1PR1-activated intracellular C3b-α'2 is associated with PPIL1 through glutamic acid 156 (E156) and aspartic acid 111 (D111) residues, resulting in NLRP3/inflammasome induction. Inactivation mutations of S1PR1 to prevent S1P signaling or mutations of C3b-α'2 to prevent its association with PPIL1 attenuate inflammasome activation and reduce lung colonization/metastasis in mice. Also, activation of the S1PR1/C3/PPIL1/NLRP3 axis is highly associated with human metastatic melanoma tissues and patient-derived xenografts. Moreover, targeting S1PR1/C3/PPIL1/NLRP3 signaling using molecular, genetic, and pharmacologic tools prevents lung colonization/metastasis of various murine cancer cell lines using WT and C3a-receptor1 knockout (C3aR1-/-) mice. These data provide strategies for treating high-grade/metastatic tumors by targeting the S1PR1/C3/inflammasome axis.

Keywords:  CP: Cancer; CP: Metabolism; S1P; S1P receptor 1; S1PR1; complement signaling; inflammasome; metastasis; sphingolipids; sphingosine 1-phosphate

DOI:  https://doi.org/10.1016/j.celrep.2022.111742
Cancer Immunol Res. 2022 Dec 07. pii: CIR-21-1088. [Epub ahead of print]

Extracellular galectin 4 drives immune evasion and promotes T-cell apoptosis in pancreatic cancer.

Tommy Lidström, Joshua Cumming, Rahul Gaur, Lars Frängsmyr, Ioannis S Pateras, Matthias J Mickert, Oskar Franklin, Mattias N E Forsell, Niklas Arnberg, Mitesh Dongre, Cedric Patthey, Daniel Öhlund.

Pancreatic ductal adenocarcinoma (PDAC) is characterized by rich deposits of extracellular matrix (ECM), affecting the pathophysiology of the disease. Here, we identified galectin 4 (gal 4) as a cancer cell-produced protein that was deposited into the ECM of PDAC tumors and detected high circulating levels of gal 4 in PDAC patients. In orthotopic transplantation experiments, we observed increased infiltration of T cells and prolonged survival in immunocompetent mice transplanted with cancer cells with reduced expression of gal 4. Increased survival was not observed in immunodeficient RAG1-/- mice, demonstrating that the effect was mediated by the adaptive immune system. By performing single-cell RNA-sequencing, we found that the myeloid compartment and cancer-associated fibroblast (CAF) subtypes were altered in the transplanted tumors. Reduced gal 4 expression associated with a higher proportion of myofibroblastic CAFs and reduced numbers of inflammatory CAFs. We also found higher proportions of M1 macrophages, T cells, and antigen-presenting dendritic cells in tumors with reduced gal 4 expression. Using a co-culture system, we observed that extracellular gal 4 induced apoptosis in T cells by binding N-glycosylation residues on CD3ε/δ. Hence, we show that gal 4 is involved in immune evasion and identify gal 4 as a promising drug target for overcoming immunosuppression in PDAC.

DOI: https://doi.org/10.1158/2326-6066.CIR-21-1088
Trends Cancer. 2022 Dec 06. pii: S2405-8033(22)00251-5. [Epub ahead of print]

Biophysical determinants of cancer organotropism.

Udochi F Azubuike, Kandice Tanner.

  Metastasis remains the leading cause of cancer lethality. The 'seed/soil' hypothesis provides the framework to explain this cancer phenomenon where the concept of organotropism has been in part mechanistically explained by the properties of the tumor cells and their compatibility with the stromal environment of the distal site. The 'mechanical' hypothesis counters that non-random seeding is driven solely by the circulation patterns and vascular networks of organ systems. We incorporate concepts of mechanobiology and revisit the two hypotheses to provide additional insights into the mechanisms that regulate organ selection during metastatic outgrowth. We focus on the latter stages of the metastatic cascade and examine the role of the endothelium in regulating organ selectivity.

Keywords:  biophysics; circulation; endothelium; mechanobiology; metastasis; microrheology; seed/soil

DOI:  https://doi.org/10.1016/j.trecan.2022.11.002
Nat Rev Cancer. 2022 Dec 09.

Biology, vulnerabilities and clinical applications of circulating tumour cells.

Alexander Ring, Bich Doan Nguyen-Sträuli, Andreas Wicki, Nicola Aceto.

In recent years, exceptional technological advances have enabled the identification and interrogation of rare circulating tumour cells (CTCs) from blood samples of patients, leading to new fields of research and fostering the promise for paradigm-changing, liquid biopsy-based clinical applications. Analysis of CTCs has revealed distinct biological phenotypes, including the presence of CTC clusters and the interaction between CTCs and immune or stromal cells, impacting metastasis formation and providing new insights into cancer vulnerabilities. Here we review the progress made in understanding biological features of CTCs and provide insight into exploiting these developments to design future clinical tools for improving the diagnosis and treatment of cancer.

DOI: https://doi.org/10.1038/s41568-022-00536-4
Pancreatology. 2022 Nov 28. pii: S1424-3903(22)00818-3. [Epub ahead of print]

Negative prognostic impact of sarcopenia before and after neoadjuvant chemotherapy for pancreatic cancer.

Mitsuhiro Shimura, Masamichi Mizuma, Fuyuhiko Motoi, Akiko Kusaka, Shuichi Aoki, Masahiro Iseki, Koetsu Inoue, Daisuke Douchi, Shun Nakayama, Takayuki Miura, Masaharu Ishida, Hideo Ohtsuka, Kei Nakagawa, Takanori Morikawa, Takashi Kamei, Michiaki Unno.

  OBJECTIVES: To elucidate the prognostic impact of sarcopenia before and after neoadjuvant chemotherapy (NAC) for pancreatic cancer (PC).METHODS: We retrospectively studied 75 consecutive PC patients who underwent neoadjuvant gemcitabine plus S-1 combination therapy followed by pancreatectomy between 2008 and 2016. According to the skeletal muscle volume index (SMI), the patients were divided into the muscle attenuation group (MAG) and normal group (NG) before or after NAC. Prognostic factors for overall survival (OS) were analyzed by Cox proportional hazards models.
RESULTS: The MAG showed significantly poorer OS than the NG before and after NAC. Pre-NAC, median OS was 20.0 months in the MAG versus 49.0 months in the NG (p = 0.006). Post-NAC, median OS was 21.3 months in the MAG versus 48.8 months in the NG (p = 0.014). Multivariate analysis, excluding muscle attenuation after NAC because of confounding factors and lower hazard ratio (2.08, 95% confidence interval: 1.14-3.78, p = 0.016) than that before NAC (2.14, 1.23-3.70, p = 0.007) by univariate analysis, revealed the following independent prognostic factors: muscle attenuation pre-NAC (2.25, 1.26-4.05, p = 0.007); borderline resectability (1.96, 1.04-3.69, p = 0.038); operative blood loss (2.60, 1.38-4.88, p = 0.003); and distant metastasis (3.31, 1.40-7.82, p = 0.006).
CONCLUSIONS: Sarcopenia before and after NAC for PC is suggested to be a poor prognostic factor, with a stronger impact before than after NAC.

Keywords:  Muscle attenuation; Neoadjuvant chemotherapy; Pancreatic cancer; Prognosis; Sarcopenia

DOI:  https://doi.org/10.1016/j.pan.2022.11.010
EMBO J. 2022 Dec 07. e113046

Closing the autophagosome is easy-PC.

Devin M Fuller, Thomas J Melia.

In their recent article, Polyansky et al identify phosphatidylcholine (PC) as the most abundant lipid in the autophagosome membrane and demonstrate that eliminating de novo PC synthesis sharply impairs autophagic processing. In the absence of PC synthesis, open cup-like structures accumulate, implicating PC as a key component in the closure of autophagosomes.

DOI: https://doi.org/10.15252/embj.2022113046
Cancer Immunol Immunother. 2022 Dec 06.

Cxcr3 constrains pancreatic cancer dissemination through instructing T cell fate.

Adam L Burrack, Ellen J Spartz, Meagan R Rollins, Ebony A Miller, Maria Firulyova, Eduardo Cruz, Michael F Goldberg, Iris X Wang, Hezkiel Nanda, Steven Shen, Konstantin Zaitsev, Ingunn M Stromnes.

  Pancreatic ductal adenocarcinoma (PDA) is a lethal and metastatic malignancy resistant to therapy. Elucidating how pancreatic tumor-specific T cells differentiate and are maintained in vivo could inform novel therapeutic avenues to promote T cell antitumor activity. Here, we show that the spleen is a critical site harboring tumor-specific CD8 T cells that functionally segregate based on differential Cxcr3 and Klrg1 expression. Cxcr3+ Klrg1- T cells express the memory stem cell marker Tcf1, whereas Cxcr3-Klrg1 + T cells express GzmB consistent with terminal differentiation. We identify a Cxcr3+ Klrg1+ intermediate T cell subpopulation in the spleen that is highly enriched for tumor specificity. However, tumor-specific T cells infiltrating primary tumors progressively downregulate both Cxcr3 and Klrg1 while upregulating exhaustion markers PD-1 and Lag-3. We show that antigen-specific T cell infiltration into PDA is Cxcr3 independent. Further, Cxcr3-deficiency results in enhanced antigen-specific T cell IFNγ production in primary tumors, suggesting that Cxcr3 promotes loss of effector function. Ultimately, however, Cxcr3 was critical for mitigating cancer cell dissemination following immunotherapy with CD40 agonist + anti-PD-L1 or T cell receptor engineered T cell therapy targeting mesothelin. In the absence of Cxcr3, splenic Klrg1 + GzmB + antitumor T cells wain while pancreatic cancer disseminates suggesting a role for these cells in eliminating circulating metastatic tumor cells. Intratumoral myeloid cells are poised to produce Cxcl10, whereas splenic DC subsets produce Cxcl9 following immunotherapy supporting differential roles for these chemokines on T cell differentiation. Together, our study supports that Cxcr3 mitigates tumor cell dissemination by impacting peripheral T cell fate rather than intratumoral T cell trafficking.

Keywords:  Cxcr3; Metastasis; PD-L1; PDA; Pancreatic cancer; T cells

DOI:  https://doi.org/10.1007/s00262-022-03338-7
Cancer Discov. 2022 Dec 06. pii: CD-22-1066. [Epub ahead of print]

Efficacy of a small molecule inhibitor of KrasG12D in immunocompetent models of pancreatic cancer.

Samantha B Kemp, Noah Cheng, Nune Markosyan, Rina Sor, Il-Kyu Kim, Jill Hallin, Jason Shoush, Liz Quinones, Natalie V Brown, Jared B Bassett, Nikhil Joshi, Salina Yuan, Molly Smith, William P Vostrejs, Kia Z Perez-Vale, Benjamin Kahn, Feiyan Mo, Timothy R Donahue, Caius G Radu, Cynthia Clendenin, James G Christensen, Robert H Vonderheide, Ben Z Stanger.

Mutations in the KRAS oncogene are found in more than 90% of patients with pancreatic ductal adenocarcinoma (PDAC), with Gly-to-Asp mutations (KRASG12D) being most common. Here, we tested the efficacy of a small molecule KRASG12D inhibitor, MRTX1133, in implantable and autochthonous PDAC models with an intact immune system. In vitro studies validated the specificity and potency of MRTX1133. In vivo, MRTX1133 prompted deep tumor regressions in all models tested, including complete or near-complete remissions after 14d. Concomitant with tumor cell apoptosis and proliferative arrest, drug treatment led to marked shifts in the tumor microenvironment (TME), including changes in fibroblasts, matrix, and macrophages. T cells were necessary for MRTX1133's full anti-tumor effect, and T cell depletion accelerated tumor regrowth after therapy. These results validate the specificity, potency, and efficacy of MRTX1133 in immunocompetent KRASG12D-mutant PDAC models, providing a rationale for clinical testing and a platform for further investigation of combination therapies.

DOI: https://doi.org/10.1158/2159-8290.CD-22-1066
JAMA Oncol. 2022 Dec 08.

Association of Adjuvant Chemotherapy in Patients With Resected Pancreatic Adenocarcinoma After Multiagent Neoadjuvant Chemotherapy.

Toshitaka Sugawara, Salvador Rodriguez Franco, Samantha Sherman, Michael J Kirsch, Kathryn Colborn, Jun Ishida, Samuele Grandi, Mohammed H Al-Musawi, Ana Gleisner, Richard D Schulick, Marco Del Chiaro.

Importance: The total number of patients with pancreatic ductal adenocarcinoma (PDAC) who receive neoadjuvant chemotherapy (NAC) is increasing. However, the added role of adjuvant chemotherapy (AC) in these patients remains unknown.Objective: To evaluate the association of AC with overall survival (OS) in patients with PDAC who received multiagent NAC followed by curative-intent surgery.
Design, Setting, and Participants: This retrospective, matched-cohort study used data from the National Cancer Database and included patients with PDAC diagnosed between 2010 and 2018. The study included patients at least 18 years of age who received multiagent NAC followed by surgical resection and had available records of the pathological findings. Patients were excluded if they had clinical or pathological stage IV disease or died within 90 days of their operation.
Exposures: All included patients received NAC and underwent resection for primary PDAC. Some patients received adjuvant chemotherapy.
Main Outcomes and Measures: The main outcome was the OS of patients who received AC (AC group) vs those who did not (non-AC group). Interactions between pathological findings and AC were investigated in separate multivariable Cox regression models.
Results: In total, 1132 patients (mean [SD] age, 63.5 [9.4] years; 577 [50.1%] male; 970 [85.7%] White) were included, 640 patients in the non-AC group and 492 patients in the AC group. After being matched by propensity score according to demographic and pathological characteristics, 444 patients remained in each group. The multivariable Cox regression model adjusted for all covariates revealed an association between AC and improved survival (hazard ratio, 0.71; 95% CI, 0.59-0.85; P < .001). Subgroup interaction analysis revealed that AC was significantly associated with better OS (26.6 vs 21.2 months; P = .002), but the benefit varied by age, pathological T category, and tumor differentiation. Of note, AC was associated with better survival in patients with any pathological N category and positive margin status.
Conclusions and Relevance: In this cohort study, AC following multiagent NAC and resection in patients with PDAC was associated with significant survival benefit compared with that in patients who did not receive AC. These findings suggest that patients with aggressive tumors may benefit from AC to achieve prolonged survival, even after multiagent NAC and curative-intent resection.

DOI: https://doi.org/10.1001/jamaoncol.2022.5808
Eur J Cancer. 2022 Nov 02. pii: S0959-8049(22)01330-2. [Epub ahead of print]178 227-233

A systematic review of basket and umbrella trials in oncology: the importance of tissue of origin and molecular target.

Alyson Haslam, Timothée Olivier, Jordan Tuia, Vinay Prasad.

  INTRODUCTION: We sought to characterise oncology basket and umbrella trials that have been implemented, determine how many have been completed, and calculate the response rate, by tumour type and drug target.METHODS: We conducted a retrospective, cross-sectional review of PubMed, Embase, and clinicaltrials.gov for all oncology basket and umbrella trials. We included all trials and publications reporting on the results of these trials, and we calculated overall response rates, stratified by tumour type and drug target.
RESULTS: Most basket and umbrella trials are phase II and non-randomised in design. Of the 180 basket trials, 99 (55.0%) had published results and 81 (45.0%) did not. Of the 73 umbrella trials, 28 (38.4%) had published results and 45 (61.6%) did not. The median response rate was 14.0 (IQR: 4.2, 31.2) for basket trials and 17.8 (IQR: 3.8, 40.4) for umbrella trials. These responses varied, depending on tumour type and drug target.
CONCLUSIONS: Understanding what is known about these trials, especially given the limited but heterogenous response reported in these trials, provides context about the strengths and limitations of drugs, especially since several drugs have been approved in recent years for tumour-agnostic indications, based on the results of these types of trials.

Keywords:  Basket trial; Response rate; Tumour agnostic; Umbrella trial

DOI:  https://doi.org/10.1016/j.ejca.2022.10.027
EMBO J. 2022 Dec 07. e113068

PHGDH and cancer: new job for an old enzyme!

Duygu Kuzuoglu-Ozturk.

How do cancer cells bolster their energy metabolism under conditions of stress? Recent work by Shu et al (2022) unveils a novel, non-canonical function of the de novo serine synthesis pathway enzyme phosphoglycerate dehydrogenase (PHGDH) as a regulator of mitochondrial translation and tumor progression in liver cancer.

DOI: https://doi.org/10.15252/embj.2022113068
Cancer Cell Int. 2022 Dec 09. 22(1): 394

Current methods for studying metastatic potential of tumor cells.

Pavla Bouchalova, Pavel Bouchal.

  Cell migration and invasiveness significantly contribute to desirable physiological processes, such as wound healing or embryogenesis, as well as to serious pathological processes such as the spread of cancer cells to form tumor metastasis. The availability of appropriate methods for studying these processes is essential for understanding the molecular basis of cancer metastasis and for identifying suitable therapeutic targets for anti-metastatic treatment. This review summarizes the current status of these methods: In vitro methods for studying cell migration involve two-dimensional (2D) assays (wound-healing/scratch assay), and methods based on chemotaxis (the Dunn chamber). The analysis of both cell migration and invasiveness in vitro require more complex systems based on the Boyden chamber principle (Transwell migration/invasive test, xCELLigence system), or microfluidic devices with three-dimensional (3D) microscopy visualization. 3D culture techniques are rapidly becoming routine and involve multicellular spheroid invasion assays or array chip-based, spherical approaches, multi-layer/multi-zone culture, or organoid non-spherical models, including multi-organ microfluidic chips. The in vivo methods are mostly based on mice, allowing genetically engineered mice models and transplant models (syngeneic mice, cell line-derived xenografts and patient-derived xenografts including humanized mice models). These methods currently represent a solid basis for the state-of-the art research that is focused on understanding metastatic fundamentals as well as the development of targeted anti-metastatic therapies, and stratified treatment in oncology.

Keywords:  2D and 3D in vitro assays; In vivo models; Invasiveness; Metastasis; Migration

DOI:  https://doi.org/10.1186/s12935-022-02801-w
Pancreatology. 2022 Dec 01. pii: S1424-3903(22)00821-3. [Epub ahead of print]

Survival impact of occult liver metastasis and peritoneal dissemination compared with radiologically defined distant organ metastasis in pancreatic ductal adenocarcinoma.

Daisuke Hashimoto, Tatsuma Sakaguchi, Sohei Satoi, Tomohisa Yamamoto, So Yamaki, Mitsuaki Ishida, Yuki Matsui, Nobuhiro Shibata, Shogen Boku, Utae Katsushima, Tsukasa Ikeura, Mitsugu Sekimoto.

  BACKGROUND: Characteristics and prognoses of patients with occult metastases (OM) of pancreatic ductal adenocarcinoma (PDAC) compared with radiologically defined metastases (RM) have been rarely reported.OBJECTIVE: We aimed to clarify the prognosis of OM compared with RM and to establish a treatment strategy for PDAC patients with OM.
METHODS: This single-institution, retrospective study evaluated patients with unresectable PDAC between 2008 and 2018. OM was defined as abdominal metastasis that was detected by staging laparoscopy or open laparotomy but not in the initial assessment of radiological images.
RESULTS: OM and RM were identified in 135 and 112 patients, respectively. Eastern Cooperative Oncology Group Performance Status (ECOG PS), neutrophil to lymphocyte ratio (NLR), tumor diameter, and rate of local unresectability were significantly lower in the OM group. Median overall survival (OS) of OM was significantly better than that of RM (13.0 vs 8.9 months, p < 0.001). In multivariate analysis of OS, ECOG PS ≥ 1 (HR 1.64, p = 0.009), NLR ≥5 (HR 1.97, p = 0.004), carbohydrate antigen (CA) 19-9 ≥1000 (HR 1.68, p = 0.001), tumor diameter ≥40 mm (HR 1.40, p = 0.027), conversion surgery (HR 0.12, p < 0.001), and multiple lines of chemotherapy (HR 0.38, p < 0.001) were independent predictors. However, type of metastasis (OM vs RM) not an independent predictor (HR 1.10, p = 0.590).
CONCLUSION: The prognosis of PDAC with OM was relatively better than that with RM, but general and nutritional statuses, primary tumor size and CA19-9, conversion surgery and multiple lines of chemotherapy were independent predictors but not tumor burden.

Keywords:  Conversion surgery; Liver metastasis; Pancreatic ductal adenocarcinoma; Peritoneal dissemination; Staging laparoscopy

DOI:  https://doi.org/10.1016/j.pan.2022.11.012
ACS Chem Biol. 2022 Dec 05.

Selective Inhibitors of Autophagy Reveal New Link between the Cell Cycle and Autophagy and Lead to Discovery of Novel Synergistic Drug Combinations.

Kisa Sung, Agata Kurowski, Carisse Lansiquot, Kanny K Wan, Samarjit Patnaik, Martin J Walsh, Michael B Lazarus.

Autophagy is a conserved metabolic pathway that is central to many diseases. Recently, there has been a lot of interest in targeting autophagy with small molecule inhibitors as a possible therapeutic strategy. However, many of the compounds used for autophagy are nonselective. Here, we explored the inhibition of autophagy in pancreatic cancer cells using established selective small molecule inhibitors and discovered an unexpected link between the autophagy pathway and progression through the cell cycle. Our findings revealed that treatments with inhibitors that have different autophagy pathway targets block cell replication and activate other metabolic pathways to compensate for the blockade in autophagy. An unbiased screen looking for known drugs that might synergize with autophagy inhibition revealed new combination treatments that might provide a blueprint for therapeutic approaches to pancreatic cancer. The drugs quizartinib and THZ1 showed a strong synergistic effect in pancreatic cells with autophagy inhibition.

DOI: https://doi.org/10.1021/acschembio.2c00710
Cell Rep. 2022 Dec 06. pii: S2211-1247(22)01657-6. [Epub ahead of print]41(10): 111774

Mitochondrial cristae architecture protects against mtDNA release and inflammation.

Baiyu He, Huatong Yu, Shanshan Liu, Huayun Wan, Song Fu, Siqi Liu, Jun Yang, Zihan Zhang, Huanwei Huang, Qi Li, Fengchao Wang, Zhaodi Jiang, Qinghua Liu, Hui Jiang.

  Mitochondrial damage causes mitochondrial DNA (mtDNA) release to activate the type I interferon (IFN-I) response via the cGAS-STING pathway. mtDNA-induced inflammation promotes autoimmune- and aging-related degenerative disorders. However, the global picture of inflammation-inducing mitochondrial damages remains obscure. Here, we have performed a mitochondria-targeted CRISPR knockout screen for regulators of the IFN-I response. Strikingly, our screen reveals dozens of hits enriched with key regulators of cristae architecture, including phospholipid cardiolipin and protein complexes such as OPA1, mitochondrial contact site and cristae organization (MICOS), sorting and assembly machinery (SAM), mitochondrial intermembrane space bridging (MIB), prohibitin (PHB), and the F1Fo-ATP synthase. Disrupting these cristae organizers consistently induces mtDNA release and the STING-dependent IFN-I response. Furthermore, knocking out MTX2, a subunit of the SAM complex whose null mutations cause progeria in humans, induces a robust STING-dependent IFN-I response in mouse liver. Taken together, beyond revealing the central role of cristae architecture to prevent mtDNA release and inflammation, our results mechanistically link mitochondrial cristae disorganization and inflammation, two emerging hallmarks of aging and aging-related degenerative diseases.

Keywords:  CP: Cell biology; CP: Molecular biology; MICOS; Metaxin2; OPA1; SAM; cGAS-STING; cristae architecture; inflammation; mtDNA release; type I interferon response

DOI:  https://doi.org/10.1016/j.celrep.2022.111774
Elife. 2022 Dec 07. pii: e74433. [Epub ahead of print]11

Weakly migratory metastatic breast cancer cells activate fibroblasts via microvesicle-Tg2 to facilitate dissemination and metastasis.

Samantha C Schwager, Katherine Young, Lauren A Hapach, Caroline M Carlson, Jenna A Mosier, Tanner J McArdle, Wenjun Wang, Curtis Schunk, Anissa L Jayathilake, Madison E Bates, Francois Bordeleau, Marc A Antonyak, Richard A Cerione, Cynthia A Reinhart-King.

  Cancer cell migration is highly heterogeneous, and the migratory capability of cancer cells is thought to be an indicator of metastatic potential. It is becoming clear that a cancer cell does not have to be inherently migratory to metastasize, with weakly migratory cancer cells often found to be highly metastatic. However, the mechanism through which weakly migratory cells escape from the primary tumor remains unclear. Here, utilizing phenotypically sorted highly and weakly migratory human breast cancer cells, we demonstrate that weakly migratory metastatic cells disseminate from the primary tumor via communication with stromal cells. While highly migratory cells are capable of single cell migration, weakly migratory cells rely on cell-cell signaling with fibroblasts to escape the primary tumor. Weakly migratory cells release microvesicles rich in tissue transglutaminase 2 (Tg2) which activate murine fibroblasts and lead weakly migratory cancer cell migration in vitro. These microvesicles also induce tumor stiffening and fibroblast activation in vivo and enhance the metastasis of weakly migratory cells. Our results identify microvesicles and Tg2 as potential therapeutic targets for metastasis and reveal a novel aspect of the metastatic cascade in which weakly migratory cells release microvesicles which activate fibroblasts to enhance cancer cell dissemination.

Keywords:  cancer biology; human; mouse

DOI:  https://doi.org/10.7554/eLife.74433
Nutr J. 2022 Dec 07. 21(1): 73

Efficacy of Global Leadership Initiative on Malnutrition as potential cachexia screening tool for patients with solid cancer.

Mengmeng Song, Qi Zhang, Tong Liu, Meng Tang, Xi Zhang, Guotian Ruan, Xiaowei Zhang, Kangping Zhang, Yizhong Ge, Ming Yang, Wei Li, Minghua Cong, Kunhua Wang, Chunhua Song, Hanping Shi.

  PURPOSE: Cachexia has a very high prevalence in patients with cancer, and lacks effective screening tools yet. Global Leadership Initiative on Malnutrition (GLIM) is a novel malnutrition assessment tool, with increased important roles in malnutrition diagnosis for patients with cancer. However, whether GLIM can be used as an effective screening tool remains unknown.METHODS: We performed a multicenter cohort study including 8,478 solid tumor patients from 40 clinical centers throughout China. Cachexia was diagnosed based on the 2011 international cancer cachexia consensus. The receiver operating characteristic curves (ROC) and decision curve analysis (DCA) were developed to determine the efficacy and clinical net benefit of GLIM and Patient-Generated Subjective Global Assessment (PG-SGA) in the detection of cancer cachexia, respectively.
RESULTS: According to the consensus guidelines, 1,441 (17.0%) cancer patients were diagnosed with cachexia among 8,478 patients in the present study. The sensitivity of one-step GLIM and two-step GLIM for detecting cachexia were 100 and 88.8%, respectively, while that of PG-SGA was 86.2%. The accuracies of one-step GLIM and two-step GLIM reached 67.4 and 91.3%, which were higher than that of PG-SGA (63.1%). The area under the curves (AUCs) of one-step GLIM (0.835) and two-step GLIM (0.910) were higher than PG-SGA (0.778) in patients with cancer. The DCA also revealed that two-step GLIM had better clinical effect than PG-SGA between 20-50% threshold probabilities.
CONCLUSION: GLIM could be used as an effective tool in screening cancer cachexia, two-step GLIM criteria show more accurate while one-step GLIM criteria is more sensitive.
TRIAL REGISTRATION: ChiCTR1800020329.

Keywords:  Cachexia; Cancer; GLIM; PG-SGA; Screening tools

DOI:  https://doi.org/10.1186/s12937-022-00829-2
Cancer Med. 2022 Dec 07.

Neoadjuvant chemotherapy and radiotherapy outcomes in borderline-resectable and locally-advanced pancreatic cancer patients.

Gregory P Botta, Tridu R Huynh, Samantha R Spierling-Bagsic, Alexander Agelidis, Randolph Schaffer, Ray Lin, Darren Sigal.

  BACKGROUND: There is no agreed upon standard of care for borderline-resectable pancreatic cancer (BRPC) or locally-advanced pancreatic cancer (LAPC) patients regarding the benefit of chemotherapy or radiation alone or in combination.PATIENTS AND METHODS: We completed a retrospective cohort analysis of BRPC and LAPC patients at a cancer center with expertise in multi-disciplinary pancreatic ductal adenocarcinoma (PDAC) treatment over a 5-year period from 03/01/2014 to 03/01/2019 (cut-off date). The total evaluable newly diagnosed, treatment naïve, BRPC, and LAPC patients with adequate organ function and ability to obtain treatment after multidisciplinary review was 52 patients. After analysis, patients were evaluated for rates of resection, extent of resection (R0 or R1), median progression-free survival (mPFS), and median overall survival (mOS).
RESULTS: Patients were treated with chemotherapy alone (gemcitabine and nab-paclitaxel = 77% (20/26); FOLFIRINOX = 19% (5/26); single agent gemcitabine 3.8% (1/26)), or chemotherapy followed by chemoradiation (gemcitabine +5 Gy × 5 weeks), or chemoradiation alone prior to re-staging and potential resection. Of the 29% (15/52) of patients who went on to surgical resection, 73% (11/15) achieved R0 resection. An R0 resection was achieved in 35% (9/26) of patients treated with chemotherapy alone, 7.6% (1/13) in a patient treated with chemotherapy followed by radiation, and 7.6% (1/13) with concurrent chemoradiotherapy alone. Chemotherapy alone achieved a mPFS of 16.4 months (p < 0.0025) and mOS of 26.2 months (p < 0.0001), chemotherapy followed by chemoradiation was 13.0 months and 14.9 months respectively, while concurrent chemoradiotherapy was 6.9 months and 7.3 months.
CONCLUSIONS AND RELEVANCE: BRPC and LAPC patients capable of surgery after only receiving neoadjuvant treatment with chemotherapy had higher rates of R0 resection with prolonged median PFS and OS compared with any patient needing combination chemotherapy with radiotherapy.

Keywords:  chemotherapy; pancreatic cancer; radiation; resection

DOI:  https://doi.org/10.1002/cam4.5523
Nature. 2022 Dec 05.

Dendritic cells direct circadian anti-tumor immune responses.

Chen Wang, Coline Barnoud, Mara Cenerenti, Mengzhu Sun, Irene Caffa, Burak Kizil, Ruben Bill, Yuanlong Liu, Robert Pick, Laure Garnier, Olga A Gkountidi, Louise M Ince, Stephan Holtkamp, Nadine Fournier, Olivier Michielin, Daniel E Speiser, Stéphanie Hugues, Alessio Nencioni, Mikaël J Pittet, Camilla Jandus, Christoph Scheiermann.

The process of cancer immunosurveillance is a mechanism of tumor suppression that can protect the host from cancer development throughout its lifetime1,2. Yet, it is unknown whether its effectiveness fluctuates over a single day. Here, we demonstrate that the initial time-of-day of tumor engraftment dictates ensuing tumor size across murine cancer models. Using immunodeficient mice and animals lacking lineage-specific circadian functions, we show that dendritic cells (DCs) and CD8+ T cells exert circadian anti-tumor functions that control melanoma volume. Specifically, we find that rhythmic trafficking of DCs to the tumor draining lymph node (dLN) governs a circadian response of tumor antigen-specific CD8+ T cells, which is dependent on circadian expression of the co-stimulatory molecule CD80. Consequently, cancer immunotherapy is more effective when synchronized with DC functions, shows circadian outcomes in mice and suggests similar effects in humans. These data demonstrate that circadian rhythms of anti-tumor immune components are not only critical for the control of tumor size but can also be exploited therapeutically.

DOI: https://doi.org/10.1038/s41586-022-05605-0
BMC Genomics. 2022 Dec 09. 23(1): 817

amica: an interactive and user-friendly web-platform for the analysis of proteomics data.

Sebastian Didusch, Moritz Madern, Markus Hartl, Manuela Baccarini.

  BACKGROUND: Quantitative proteomics has become an increasingly prominent tool in the study of life sciences. A substantial hurdle for many biologists are, however, the intricacies involved in the associated high throughput data analysis.RESULTS: In order to facilitate this task for users with limited background knowledge, we have developed amica, a freely available open-source web-based software that accepts proteomic input files from different sources. amica provides quality control, differential expression, biological network and over-representation analysis on the basis of minimal user input. Scientists can use amica's query interface interactively to compare multiple conditions and rapidly identify enriched or depleted proteins. They can visualize their results using customized output graphics, and ultimately export the results in a tab-separated format that can be shared with collaborators. The code for the application, input data and documentation can be accessed online at https://github.com/tbaccata/amica and is also incorporated in the web application.
CONCLUSIONS: The strong emphasis on dynamic user interactions, the integration of various databases and the option to download processed data, facilitate the analysis of complex proteomic data for both first-time users and experienced bioinformaticians. A freely available version of amica is available at https://bioapps.maxperutzlabs.ac.at/app/amica .

Keywords:  Data analysis; Data visualization; LC-MS/MS; Proteomics; Web application

DOI:  https://doi.org/10.1186/s12864-022-09058-7
Cancer Res. 2022 Dec 08. pii: CAN-22-1002. [Epub ahead of print]

Elevated methionine flux drives pyroptosis evasion in persister cancer cells.

Asmaa El-Kenawi, Anders Berglund, Veronica Estrella, Yonghong Zhang, Min Liu, Ryan M Putney, Sean Yoder, Joseph Johnson, Joel Brown, Robert Gatenby.

Induction of cell death represents a primary goal of most anti-cancer treatments. Despite the efficacy of such approaches, a small population of "persisters" develop evasion strategies to therapy-induced cell death. While previous studies have identified mechanisms of resistance to apoptosis, the mechanisms by which persisters dampen other forms of cell death, such as pyroptosis, remain to be elucidated. Pyroptosis is a form of inflammatory cell death that involves formation of membrane pores, ion gradient imbalance, water inflow and membrane rupture. Herein, we investigate mechanisms by which cancer persisters resist pyroptosis, survive, then proliferate in the presence of tyrosine kinase inhibitors (TKI). Lung, prostate and esophageal cancer persister cells remaining after treatments exhibited several hallmarks indicative of pyroptosis resistance. The inflammatory attributes of persisters included chronic activation of inflammasome, STING, and type I interferons. Comprehensive metabolomic characterization uncovered that TKI-induced pyroptotic persisters display high methionine consumption and excessive taurine production. Elevated methionine flux or exogenous taurine preserved plasma membrane integrity via osmolyte-mediated effects. Increased dependency on methionine flux decreased the level of one carbon metabolism intermediate S-(5'-adenosyl)-L-homocysteine, a determinant of cell methylation capacity. The consequent increase in methylation potential induced DNA hypermethylation of genes regulating metal ion balance and intrinsic immune response. This enabled thwarting TKI resistance by using the hypomethylating agent decitabine. In summary, the evolution of resistance to pyroptosis can occur via a stepwise process of physical acclimation and epigenetic changes without existing or recurrent mutations. .

DOI: https://doi.org/10.1158/0008-5472.CAN-22-1002
J Exp Med. 2023 Feb 06. pii: e20211431. [Epub ahead of print]220(2):

PD-1 and TIM-3 differentially regulate subsets of mouse IL-17A-producing γδ T cells.

Sarah C Edwards, Ann Hedley, Wilma H M Hoevenaar, Robert Wiesheu, Teresa Glauner, Anna Kilbey, Robin Shaw, Katerina Boufea, Nizar Batada, Shinya Hatano, Yasunobu Yoshikai, Karen Blyth, Crispin Miller, Kristina Kirschner, Seth B Coffelt.

IL-17A-producing γδ T cells in mice consist primarily of Vγ6+ tissue-resident cells and Vγ4+ circulating cells. How these γδ T cell subsets are regulated during homeostasis and cancer remains poorly understood. Using single-cell RNA sequencing and flow cytommetry, we show that lung Vγ4+ and Vγ6+ cells from tumor-free and tumor-bearing mice express contrasting cell surface molecules as well as distinct co-inhibitory molecules, which function to suppress their expansion. Vγ6+ cells express constitutively high levels of PD-1, whereas Vγ4+ cells upregulate TIM-3 in response to tumor-derived IL-1β and IL-23. Inhibition of either PD-1 or TIM-3 in mammary tumor-bearing mice increased Vγ6+ and Vγ4+ cell numbers, respectively. We found that genetic deletion of γδ T cells elicits responsiveness to anti-PD-1 and anti-TIM-3 immunotherapy in a mammary tumor model that is refractory to T cell checkpoint inhibitors, indicating that IL-17A-producing γδ T cells instigate resistance to immunotherapy. Together, these data demonstrate how lung IL-17A-producing γδ T cell subsets are differentially controlled by PD-1 and TIM-3 in steady-state and cancer.

DOI: https://doi.org/10.1084/jem.20211431
PLoS One. 2022 ;17(12): e0278626

STRAINS: A big data method for classifying cellular response to stimuli at the tissue scale.

Jingyang Zheng, Thomas Wyse Jackson, Lisa A Fortier, Lawrence J Bonassar, Michelle L Delco, Itai Cohen.

Cellular response to stimulation governs tissue scale processes ranging from growth and development to maintaining tissue health and initiating disease. To determine how cells coordinate their response to such stimuli, it is necessary to simultaneously track and measure the spatiotemporal distribution of their behaviors throughout the tissue. Here, we report on a novel SpatioTemporal Response Analysis IN Situ (STRAINS) tool that uses fluorescent micrographs, cell tracking, and machine learning to measure such behavioral distributions. STRAINS is broadly applicable to any tissue where fluorescence can be used to indicate changes in cell behavior. For illustration, we use STRAINS to simultaneously analyze the mechanotransduction response of 5000 chondrocytes-over 20 million data points-in cartilage during the 50 ms to 4 hours after the tissue was subjected to local mechanical injury, known to initiate osteoarthritis. We find that chondrocytes exhibit a range of mechanobiological responses indicating activation of distinct biochemical pathways with clear spatial patterns related to the induced local strains during impact. These results illustrate the power of this approach.

DOI: https://doi.org/10.1371/journal.pone.0278626
Methods Mol Biol. 2023 ;2584 191-203

Tissue RNA Integrity in Visium Spatial Protocol (Fresh Frozen Samples).

Federica Antico, Marta Gai, Maddalena Arigoni.

  The transcriptome of a tissue can be acquired both by single-cell RNAseq (scRNA-seq) and by spatial transcriptomics (ST). The dissociation step, which is mandatory in scRNA-seq methods, might lead to the loss of fragile cells and of spatial information, thus limiting the acquisition of the tissue cellular organization. Spatial transcriptomics methods moderate the above-mentioned issues and provide single-cell transcripts detection over an intact fresh frozen tissue section. Visium platform, commercialized from 10× Genomics, provides a whole transcriptome spatial transcriptomics platform, which does not require dedicated instruments, other than those available in any pathology laboratory. In spatial transcriptomics, proper tissue handling is mandatory to preserve the morphological quality of the tissue sections and the integrity of mRNA transcripts. Proper tissue handling is critical for downstream library preparation and sequencing performance. In this chapter, we describe the most critical steps of Visium protocol on fresh frozen tissues and we provide indications on how to interpret the data obtained from the quality control analysis recommended during the workflow.

Keywords:  RNA quality control; Spatial Transcriptomics; Tissue preparation; Visium

DOI:  https://doi.org/10.1007/978-1-0716-2756-3_8
Cell Commun Signal. 2022 Dec 06. 20(1): 192

Catalase-deficient mice induce aging faster through lysosomal dysfunction.

Raghbendra Kumar Dutta, Joon No Lee, Yunash Maharjan, Channy Park, Seong-Kyu Choe, Ye-Shih Ho, Hyug Moo Kwon, Raekil Park.

  BACKGROUND: Lysosomes are a central hub for cellular metabolism and are involved in the regulation of cell homeostasis through the degradation or recycling of unwanted or dysfunctional organelles through the autophagy pathway. Catalase, a peroxisomal enzyme, plays an important role in cellular antioxidant defense by decomposing hydrogen peroxide into water and oxygen. In accordance with pleiotropic significance, both impaired lysosomes and catalase have been linked to many age-related pathologies with a decline in lifespan. Aging is characterized by progressive accumulation of macromolecular damage and the production of high levels of reactive oxygen species. Although lysosomes degrade the most long-lived proteins and organelles via the autophagic pathway, the role of lysosomes and their effect on catalase during aging is not known. The present study investigated the role of catalase and lysosomal function in catalase-knockout (KO) mice.METHODS: We performed experiments on WT and catalase KO younger (9 weeks) and mature adult (53 weeks) male mice and Mouse embryonic fibroblasts isolated from WT and KO mice from E13.5 embryos as in vivo and in ex-vivo respectively. Mouse phenotyping studies were performed with controls, and a minimum of two independent experiments were performed with more than five mice in each group.
RESULTS: We found that at the age of 53 weeks (mature adult), catalase-KO mice exhibited an aging phenotype faster than wild-type (WT) mice. We also found that mature adult catalase-KO mice induced leaky lysosome by progressive accumulation of lysosomal content, such as cathespin D, into the cytosol. Leaky lysosomes inhibited autophagosome formation and triggered impaired autophagy. The dysregulation of autophagy triggered mTORC1 (mechanistic target of rapamycin complex 1) activation. However, the antioxidant N-acetyl-L-cysteine and mTORC1 inhibitor rapamycin rescued leaky lysosomes and aging phenotypes in catalase-deficient mature adult mice.
CONCLUSIONS: This study unveils the new role of catalase and its role in lysosomal function during aging. Video abstract.

Keywords:  Aging; Catalase; Lysosome; ROS; mTORC1

DOI:  https://doi.org/10.1186/s12964-022-00969-2
Ann Surg Oncol. 2022 Dec 07.

Resected Early-Onset Pancreatic Cancer: Practices and Outcomes in an International Dual-Center Study.

Carl-Stephan Leonhardt, Benedict Kinny-Köster, Thomas Hank, Joseph R Habib, Sami Shoucair, Ulla Klaiber, John L Cameron, Thilo Hackert, Christopher L Wolfgang, Markus W Büchler, Jin He, Oliver Strobel.

BACKGROUND: Early-onset pancreatic cancer (EOPC), defined as age ≤ 45 years at diagnosis, accounts for 3% of all pancreatic cancer cases. Although differences in tumor biology have been suggested, available data are sparse and specific treatment recommendations are lacking. This study explores the clinicopathological features and oncologic outcomes of resected EOPC.PATIENTS AND METHODS: Patients with EOPC undergoing resection between 2002 and 2018 were identified from the Heidelberg University Hospital and Johns Hopkins University registries. Median overall survival (OS) and recurrence-free survival (RFS) were analyzed, and prognostic factors were identified.
RESULTS: The final cohort included 164 patients, most of whom had pancreatic ductal adenocarcinoma (PDAC, n = 136; 82.9%) or IPMN-associated pancreatic cancer (n = 17; 10.4%). Twenty (12.1%) patients presented with stage 1 disease, 42 (25.6%) with stage 2, 75 (45.7%) with stage 3, and 22 (13.4%) with oligometastatic stage 4 disease. Most patients underwent upfront resection (n = 113, 68.9%), whereas 51 (31.1%) individuals received preoperative treatment. Median OS and RFS were 26.0 and 12.4 months, respectively. Stage-specific median survival was 70.6, 41.8, 23.8, and 16.9 months for stage 1, 2, 3, and 4 tumors, respectively. Factors independently associated with shorter OS and RFS were R1 resections and AJCC stages 3 and 4. Notably, AJCC 3-N2 and AJCC 3-T4 tumors had a median OS of 20 months versus 29.5 months, respectively.
CONCLUSION: Despite frequently presenting with advanced disease, oncologic outcomes in EOPC patients are satisfactory even in locally advanced cancers, justifying aggressive surgical approaches. Further research is needed to tailor current guidelines to this rare population.

DOI: https://doi.org/10.1245/s10434-022-12901-6
Cancer Lett. 2022 Dec 06. pii: S0304-3835(22)00516-X. [Epub ahead of print] 216029

SHP2 inhibition mitigates adaptive resistance to MEK inhibitors in KRAS-mutant gastric cancer through the suppression of KSR1 activity.

Wenfang Zheng, Zhiyi Yang, Ping Song, Yingchao Sun, Pan Liu, Lei Yue, Kaiqi Lv, Xinjie Wang, Yuqin Shen, Jianmin Si, Xue Zhang, Yuehai Ke, Hongqiang Cheng, Weiling Hu.

  Despite the promising antitumor activity of RAF/MEK inhibitors for RAS-driven cancers, not all patients respond to these therapies. Adaptive resistance has been reported as a major culprit in non-responders, which can be reversed by SHP2 inhibitors (SHP2is) in multiple cancer cells, however the underlying mechanisms remain unknown. In this study, we found that KRAS-mutant gastric cancer cells respond e to MEK inhibitors (MEKis) with adaptive resistance. Markedly, SHP2 activation accompanied by ERK signaling restoration in MEKi-treated cells, and an MEKi and SHP2i combination had a synergistic effect on downstream signaling blockade. In vivo, SHP099 combined with AZD6244 (selumetinib) was highly efficacious for the treatment of xenografts. Mechanistically, SHP2 was found to interact with the scaffold protein KSR1 through its protein tyrosine phosphatase domain. KSR1 knockdown sensitized cells to AZD6244, whereas a KSR1 activating mutation (S269A) diminished the synergistic anti-proliferative effect of SHP2is and MEKi. Interestingly, activated SHP2, during adaptive resistance to MEKis, impaired the interaction with KSR1, activating KSR1 to promote MAPK signaling. In conclusion, SHP2 promotes adaptive resistance to MEKis by activating KSR1; selumetinib combined with SHP099 might be an available therapeutic strategy for KRAS-mutant gastric cancers.

Keywords:  KRAS-Mutant gastric cancer; KSR1; MAPK signaling; MEK inhibitor; SHP2

DOI:  https://doi.org/10.1016/j.canlet.2022.216029
Front Bioeng Biotechnol. 2022 ;10 1057913

Tumor-on-a-chip: Perfusable vascular incorporation brings new approach to tumor metastasis research and drug development.

Ruixin Wang, Chenghao Zhang, Danxue Li, Yang Yao.

  The extracellular matrix interacts with cancer cells and is a key factor in the development of cancer. Traditional two-dimensional models cannot mimic the natural in situ environment of cancer tissues, whereas three-dimensional (3D) models such as spherical culture, bioprinting, and microfluidic approaches can achieve in vitro reproduction of certain structures and components of the tumor microenvironment, including simulation of the hypoxic environment of tumor tissue. However, the lack of a perfusable vascular network is a limitation of most 3D models. Solid tumor growth and metastasis require angiogenesis, and tumor models with microvascular networks have been developed to better understand underlying mechanisms. Tumor-on-a-chip technology combines the advantages of microfluidics and 3D cell culture technology for the simulation of tumor tissue complexity and characteristics. In this review, we summarize progress in constructing tumor-on-a-chip models with efficiently perfused vascular networks. We also discuss the applications of tumor-on-a-chip technology to studying the tumor microenvironment and drug development. Finally, we describe the creation of several common tumor models based on this technology to provide a deeper understanding and new insights into the design of vascularized cancer models. We believe that the tumor-on-a-chip approach is an important development that will provide further contributions to the field.

Keywords:  microfluidic; tumor micro environment; tumor model; tumor-on-a-chip; vascularization

DOI:  https://doi.org/10.3389/fbioe.2022.1057913
Cell. 2022 Dec 08. pii: S0092-8674(22)01414-3. [Epub ahead of print]185(25): 4717-4736.e25

Fibroblast inflammatory priming determines regenerative versus fibrotic skin repair in reindeer.

Sarthak Sinha, Holly D Sparks, Elodie Labit, Hayley N Robbins, Kevin Gowing, Arzina Jaffer, Eren Kutluberk, Rohit Arora, Micha Sam Brickman Raredon, Leslie Cao, Scott Swanson, Peng Jiang, Olivia Hee, Hannah Pope, Matt Workentine, Kiran Todkar, Nilesh Sharma, Shyla Bharadia, Keerthana Chockalingam, Luiz G N de Almeida, Mike Adam, Laura Niklason, S Steven Potter, Ashley W Seifert, Antoine Dufour, Vincent Gabriel, Nicole L Rosin, Ron Stewart, Greg Muench, Robert McCorkell, John Matyas, Jeff Biernaskie.

  Adult mammalian skin wounds heal by forming fibrotic scars. We report that full-thickness injuries of reindeer antler skin (velvet) regenerate, whereas back skin forms fibrotic scar. Single-cell multi-omics reveal that uninjured velvet fibroblasts resemble human fetal fibroblasts, whereas back skin fibroblasts express inflammatory mediators mimicking pro-fibrotic adult human and rodent fibroblasts. Consequently, injury elicits site-specific immune responses: back skin fibroblasts amplify myeloid infiltration and maturation during repair, whereas velvet fibroblasts adopt an immunosuppressive phenotype that restricts leukocyte recruitment and hastens immune resolution. Ectopic transplantation of velvet to scar-forming back skin is initially regenerative, but progressively transitions to a fibrotic phenotype akin to the scarless fetal-to-scar-forming transition reported in humans. Skin regeneration is diminished by intensifying, or enhanced by neutralizing, these pathologic fibroblast-immune interactions. Reindeer represent a powerful comparative model for interrogating divergent wound healing outcomes, and our results nominate decoupling of fibroblast-immune interactions as a promising approach to mitigate scar.

Keywords:  fetal human fibroblast; fibroblast; immune modulation; inflammation; inflammatory priming; myeloid cell maturation; reindeer; scar; skin regeneration; stromal-immune crosstalk; wound healing

DOI:  https://doi.org/10.1016/j.cell.2022.11.004
Nat Med. 2022 Dec 08.

Impact of the Human Cell Atlas on medicine.

Jennifer E Rood, Aidan Maartens, Anna Hupalowska, Sarah A Teichmann, Aviv Regev.

Single-cell atlases promise to provide a 'missing link' between genes, diseases and therapies. By identifying the specific cell types, states, programs and contexts where disease-implicated genes act, we will understand the mechanisms of disease at the cellular and tissue levels and can use this understanding to develop powerful disease diagnostics; identify promising new drug targets; predict their efficacy, toxicity and resistance mechanisms; and empower new kinds of therapies, from cancer therapies to regenerative medicine. Here, we lay out a vision for the potential of cell atlases to impact the future of medicine, and describe how advances over the past decade have begun to realize this potential in common complex diseases, infectious diseases (including COVID-19), rare diseases and cancer.

DOI: https://doi.org/10.1038/s41591-022-02104-7