bims-cagime 2022-06-26 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2022–06–26
27 papers selected by
Kıvanç Görgülü, Technical University of Munich

Adaptive stimulation of macropinocytosis overcomes aspartate limitation in cancer cells under hypoxia.
Targeting autophagy as a therapeutic strategy against pancreatic cancer.
Balancing nutrient and energy demand and supply via autophagy.
A special subtype: Revealing the potential intervention and great value of KRAS wildtype pancreatic cancer.
Therapeutic Aspects and Molecular Targets of Autophagy to Control Pancreatic Cancer Management.
Serum biomarker panel diagnostics in pancreatic ductal adenocarcinoma: the clinical utility of soluble interleukins, IFN-γ, TNF-α and PD-1/PD-L1 in comparison to established serum tumor markers.
Glycan degradation promotes macroautophagy.
The metastatic spread of breast cancer accelerates during sleep.
The Liver Pre-Metastatic Niche in Pancreatic Cancer: A Potential Opportunity for Intervention.
Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited.
Mapping Phenotypic Plasticity upon the Cancer Cell State Landscape Using Manifold Learning.
Metabolic cycles and signals for insulin secretion.
Can we predict the progression of premalignant pancreatic cystic tumors to ductal adenocarcinoma?
A ferroptosis defense mechanism mediated by glycerol-3-phosphate dehydrogenase 2 in mitochondria.
Targeted protein degradation via the autophagy-lysosome system: AUTOTAC (AUTOphagy-TArgeting Chimera).
CAM-Delam Assay to Score Metastatic Properties by Quantifying Delamination and Invasion Capacity of Cancer Cells.
Mitochondrial Dysfunction and the Glycolytic Switch Induced by Caveolin-1 Phosphorylation Promote Cancer Cell Migration, Invasion, and Metastasis.
Using CRISPR-Cas9 to Dissect Cancer Mutations in Cell Lines.
Challenges and opportunities for physician-scientists in advancing cancer research.
Liver cancer heterogeneity modeled by in situ genome editing of hepatocytes.
Adaptive Dynamic Therapy and Survivorship for Operable Pancreatic Cancer.
Dual stromal targeting sensitizes pancreatic adenocarcinoma for anti-PD-1 therapy.
Depleting Ly6G Positive Myeloid Cells Reduces Pancreatic Cancer-Induced Skeletal Muscle Atrophy.
The Use of Seahorse XF Assays to Interrogate Real-Time Energy Metabolism in Cancer Cell Lines.
Targeting mitochondrial metabolism for metastatic cancer therapy.
Shaping fuel utilization by mitochondria.
Decoding the transcriptome of denervated muscle at single-nucleus resolution.

Nat Metab. 2022 Jun 20.

Adaptive stimulation of macropinocytosis overcomes aspartate limitation in cancer cells under hypoxia.

Javier Garcia-Bermudez, Michael A Badgley, Sheela Prasad, Lou Baudrier, Yuyang Liu, Konnor La, Mariluz Soula, Robert T Williams, Norihiro Yamaguchi, Rosa F Hwang, Laura J Taylor, Elisa de Stanchina, Bety Rostandy, Hanan Alwaseem, Henrik Molina, Dafna Bar-Sagi, Kıvanç Birsoy.

Stress-adaptive mechanisms enable tumour cells to overcome metabolic constraints under nutrient and oxygen shortage. Aspartate is an endogenous metabolic limitation under hypoxic conditions, but the nature of the adaptive mechanisms that contribute to aspartate availability and hypoxic tumour growth are poorly understood. Here we identify GOT2-catalysed mitochondrial aspartate synthesis as an essential metabolic dependency for the proliferation of pancreatic tumour cells under hypoxic culture conditions. In contrast, GOT2-catalysed aspartate synthesis is dispensable for pancreatic tumour formation in vivo. The dependence of pancreatic tumour cells on aspartate synthesis is bypassed in part by a hypoxia-induced potentiation of extracellular protein scavenging via macropinocytosis. This effect is mutant KRAS dependent, and is mediated by hypoxia-inducible factor 1 (HIF1A) and its canonical target carbonic anhydrase-9 (CA9). Our findings reveal high plasticity of aspartate metabolism and define an adaptive regulatory role for macropinocytosis by which mutant KRAS tumours can overcome nutrient deprivation under hypoxic conditions.

DOI: https://doi.org/10.1038/s42255-022-00583-z
J Gastroenterol. 2022 Jun 21.

Targeting autophagy as a therapeutic strategy against pancreatic cancer.

Keisuke Yamamoto, Dosuke Iwadate, Hiroyuki Kato, Yousuke Nakai, Keisuke Tateishi, Mitsuhiro Fujishiro.

  Macroautophagy (hereafter autophagy) is a catabolic process through which cytosolic components are captured in the autophagosome and degraded in the lysosome. Autophagy plays two major roles: nutrient recycling under starvation or stress conditions and maintenance of cellular homeostasis by removing the damaged organelles or protein aggregates. In established cancer cells, autophagy-mediated nutrient recycling promotes tumor progression, whereas in normal/premalignant cells, autophagy suppresses tumor initiation by eliminating the oncogenic/harmful molecules. Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease that is refractory to most currently available treatment modalities, including immune checkpoint blockade and molecular-targeted therapy. One prominent feature of PDAC is its constitutively active and elevated autophagy-lysosome function, which enables PDAC to thrive in its nutrient-scarce tumor microenvironment. In addition to metabolic support, autophagy promotes PDAC progression in a metabolism-independent manner by conferring resistance to therapeutic treatment or facilitating immune evasion. Besides to cell-autonomous autophagy in cancer cells, host autophagy (autophagy in non-cancer cells) supports PDAC progression, further highlighting autophagy as a promising therapeutic target in PDAC. Based on a growing list of compelling preclinical evidence, there are numerous ongoing clinical trials targeting the autophagy-lysosome pathway in PDAC. Given the multifaceted and context-dependent roles of autophagy in both cancer cells and normal host cells, a deeper understanding of the mechanisms underlying the tumor-promoting roles of autophagy as well as of the consequences of autophagy inhibition is necessary for the development of autophagy inhibition-based therapies against PDAC.

Keywords:  Anti-tumor immunity; Autophagy; Host autophagy; Lysosome; PDAC

DOI:  https://doi.org/10.1007/s00535-022-01889-1
Curr Biol. 2022 Jun 20. pii: S0960-9822(22)00707-2. [Epub ahead of print]32(12): R684-R696

Balancing nutrient and energy demand and supply via autophagy.

Congcong He.

Maintaining nutrient and energy homeostasis is crucial for the survival and function of cells and organisms in response to environmental stress. Cells have evolved a stress-induced catabolic pathway, termed autophagy, to adapt to stress conditions such as starvation. During autophagy, damaged or non-essential cellular structures are broken down in lysosomes, and the resulting metabolites are reused for core biosynthetic processes or energy production. Recent studies have revealed that autophagy can target and degrade different types of nutrient stores and produce a variety of metabolites and fuels, including amino acids, nucleotides, lipids and carbohydrates. Here, we will focus on how autophagy functions to balance cellular nutrient and energy demand and supply - specifically, how energy deprivation switches on autophagic catabolism, how autophagy halts anabolism by degrading the protein synthesis machinery, and how bulk and selective autophagy-derived metabolites recycle and feed into a variety of bioenergetic and anabolic pathways during stress conditions. Recent new insights and progress in these areas provide a better understanding of how resource mobilization and reallocation sustain essential metabolic and anabolic activities under unfavorable conditions.

DOI: https://doi.org/10.1016/j.cub.2022.04.071
Biochim Biophys Acta Rev Cancer. 2022 Jun 19. pii: S0304-419X(22)00076-2. [Epub ahead of print] 188751

A special subtype: Revealing the potential intervention and great value of KRAS wildtype pancreatic cancer.

Zhi-Hang Xu, Wen-Quan Wang, Liang Liu, Wen-Hui Lou.

  Pancreatic ductal adenocarcinoma (PDAC) is the predominant form of pancreatic cancer and has devastating consequences on affected families and society. Its dismal prognosis is attributed to poor specificity of symptoms during early stages. It is widely believed that PDAC patients with the wildtype (WT) KRAS gene benefit more from currently available treatments than those with KRAS mutations. The oncogenic genetic changes alternations generally found in KRAS wildtype PDAC are related to either the KRAS pathway or microsatellite instability/mismatch repair deficiency (MSI/dMMR), which enable the application of tailored treatments based on each patient's genetic characteristics. This review focuses on targeted therapies against alternative tumour mechanisms in KRAS WT PDAC.

Keywords:  KRAS; MSI; dMMR; kinase fusion; pancreatic cancer; precision medicine

DOI:  https://doi.org/10.1016/j.bbcan.2022.188751
Biomedicines. 2022 Jun 20. pii: 1459. [Epub ahead of print]10(6):

Therapeutic Aspects and Molecular Targets of Autophagy to Control Pancreatic Cancer Management.

Md Ataur Rahman, Kazi Rejvee Ahmed, M D Hasanur Rahman, Md Anowar Khasru Parvez, In-Seon Lee, Bonglee Kim.

  Pancreatic cancer (PC) begins within the organ of the pancreas, which produces digestive enzymes, and is one of the formidable cancers for which appropriate treatment strategies are urgently needed. Autophagy occurs in the many chambers of PC tissue, including cancer cells, cancer-related fibroblasts, and immune cells, and can be fine-tuned by various promotive and suppressive signals. Consequently, the impacts of autophagy on pancreatic carcinogenesis and progression depend greatly on its stage and conditions. Autophagy inhibits the progress of preneoplastic damage during the initial phase. However, autophagy encourages tumor formation during the development phase. Several studies have reported that both a tumor-promoting and a tumor-suppressing function of autophagy in cancer that is likely cell-type dependent. However, autophagy is dispensable for pancreatic ductal adenocarcinoma (PDAC) growth, and clinical trials with autophagy inhibitors, either alone or in combination with other therapies, have had limited success. Autophagy's dual mode of action makes it therapeutically challenging despite autophagy inhibitors providing increased longevity in medical studies, highlighting the need for a more rigorous review of current findings and more precise targeting strategies. Indeed, the role of autophagy in PC is complicated, and numerous factors must be considered when transitioning from bench to bedside. In this review, we summarize the evidence for the tumorigenic and protective role of autophagy in PC tumorigenesis and describe recent advances in the understanding of how autophagy may be regulated and controlled in PDAC.

Keywords:  PC; PDAC; autophagy; pancreatic cancer; pancreatic ductal adenocarcinoma; tumor-promoting; tumor-suppressive

DOI:  https://doi.org/10.3390/biomedicines10061459
J Cancer Res Clin Oncol. 2022 Jun 23.

Serum biomarker panel diagnostics in pancreatic ductal adenocarcinoma: the clinical utility of soluble interleukins, IFN-γ, TNF-α and PD-1/PD-L1 in comparison to established serum tumor markers.

Klara Dorman, Miriam Gerckens, Stephan Kruger, Kimberly Krueger, Zsuzsanna Mayer, Alexander Rupp, Danmei Zhang, Lena Weiss, C Benedikt Westphalen, Michael Haas, Michael Guenther, Steffen Ormanns, Frank Klawonn, Jens Werner, Michael von Bergwelt-Baildon, Volker Heinemann, Stefan Boeck, Stefan Holdenrieder.

   PURPOSE: Novel biomarkers to better predict outcome and select the best therapeutic strategy for the individual patient are necessary for pancreatic ductal adenocarcinoma (PDAC).
METHODS: Using a panel assay, multiple biomarkers (IFN-γ, IL-10, IL-6, IL-8, TNF-α, CEA, CA 19-9, CYFRA 21-1, HE4, PD-1 and PD-L1 levels) were measured in serum samples of 162 patients with resected, locally advanced and metastatic PDAC in this retrospective single-center study. Optimal cut-off values to differentiate prognostic subgroups with significantly different overall survival (OS) were determined by receiver operator characteristics and Youden Index analysis. Marker levels were assessed before the start of chemotherapy and correlated with OS by univariate and multivariate Cox analysis.
RESULTS: Median OS for resected patients was 28.2 months, for locally advanced patients 17.9 months and for patients with metastatic disease 8.6 months. CYFRA 21-1 and IL-8 discriminated metastatic from locally advanced patients best (AUC 0.85 and AUC 0.81, respectively). In univariate analyses, multiple markers showed prognostic relevance in the various subgroups. However, multivariate Cox models comprised only CYFRA 21-1 in the resected group (HR 1.37, p = 0.015), IL-10 in locally advanced PDAC (HR 10.01, p = 0.014), as well as CYFRA 21-1 and CA 19-9 in metastatic PDAC (p = 0.008 and p = 0.010) as an independent prognostic marker for overall survival.
CONCLUSION: IL-10 levels may have independent prognostic value in locally advanced PDAC, whereas CYFRA 21-1 levels are prognostic after PDAC surgery. CYFRA 21-1 and IL-8 have been identified to best discriminate metastatic from locally advanced patients.

Keywords:  Biomarker; Cytokine; Interleukin; PD-1/PD-L1; Pancreatic cancer

DOI:  https://doi.org/10.1007/s00432-022-04112-z
Proc Natl Acad Sci U S A. 2022 Jun 28. 119(26): e2111506119

Glycan degradation promotes macroautophagy.

Alice D Baudot, Victoria M-Y Wang, Josh D Leach, Jim O'Prey, Jaclyn S Long, Viola Paulus-Hock, Sergio Lilla, David M Thomson, John Greenhorn, Farah Ghaffar, Colin Nixon, Miep H Helfrich, Douglas Strathdee, Judith Pratt, Francesco Marchesi, Sara Zanivan, Kevin M Ryan.

  Macroautophagy promotes cellular homeostasis by delivering cytoplasmic constituents to lysosomes for degradation [Mizushima, Nat. Cell Biol. 20, 521-527 (2018)]. However, while most studies have focused on the mechanisms of protein degradation during this process, we report here that macroautophagy also depends on glycan degradation via the glycosidase, α-l-fucosidase 1 (FUCA1), which removes fucose from glycans. We show that cells lacking FUCA1 accumulate lysosomal glycans, which is associated with impaired autophagic flux. Moreover, in a mouse model of fucosidosis-a disease characterized by inactivating mutations in FUCA1 [Stepien et al., Genes (Basel) 11, E1383 (2020)]-glycan and autophagosome/autolysosome accumulation accompanies tissue destruction. Mechanistically, using lectin capture and mass spectrometry, we identified several lysosomal enzymes with altered fucosylation in FUCA1-null cells. Moreover, we show that the activity of some of these enzymes in the absence of FUCA1 can no longer be induced upon autophagy stimulation, causing retardation of autophagic flux, which involves impaired autophagosome-lysosome fusion. These findings therefore show that dysregulated glycan degradation leads to defective autophagy, which is likely a contributing factor in the etiology of fucosidosis.

Keywords:  fucosidosis; lysosomes; macroautophagy; α-l-fucosidase 1

DOI:  https://doi.org/10.1073/pnas.2111506119
Nature. 2022 Jun 22.

The metastatic spread of breast cancer accelerates during sleep.

Zoi Diamantopoulou, Francesc Castro-Giner, Fabienne Dominique Schwab, Christiane Foerster, Massimo Saini, Selina Budinjas, Karin Strittmatter, Ilona Krol, Bettina Seifert, Viola Heinzelmann-Schwarz, Christian Kurzeder, Christoph Rochlitz, Marcus Vetter, Walter Paul Weber, Nicola Aceto.

The metastatic spread of cancer is achieved by the haematogenous dissemination of circulating tumour cells (CTCs). Generally, however, the temporal dynamics that dictate the generation of metastasis-competent CTCs are largely uncharacterized, and it is often assumed that CTCs are constantly shed from growing tumours or are shed as a consequence of mechanical insults1. Here we observe a striking and unexpected pattern of CTC generation dynamics in both patients with breast cancer and mouse models, highlighting that most spontaneous CTC intravasation events occur during sleep. Further, we demonstrate that rest-phase CTCs are highly prone to metastasize, whereas CTCs generated during the active phase are devoid of metastatic ability. Mechanistically, single-cell RNA sequencing analysis of CTCs reveals a marked upregulation of mitotic genes exclusively during the rest phase in both patients and mouse models, enabling metastasis proficiency. Systemically, we find that key circadian rhythm hormones such as melatonin, testosterone and glucocorticoids dictate CTC generation dynamics, and as a consequence, that insulin directly promotes tumour cell proliferation in vivo, yet in a time-dependent manner. Thus, the spontaneous generation of CTCs with a high proclivity to metastasize does not occur continuously, but it is concentrated within the rest phase of the affected individual, providing a new rationale for time-controlled interrogation and treatment of metastasis-prone cancers.

DOI: https://doi.org/10.1038/s41586-022-04875-y
Cancers (Basel). 2022 Jun 20. pii: 3028. [Epub ahead of print]14(12):

The Liver Pre-Metastatic Niche in Pancreatic Cancer: A Potential Opportunity for Intervention.

Peter Gumberger, Bergthor Bjornsson, Per Sandström, Linda Bojmar, Constantinos P Zambirinis.

  Cancer-related mortality is primarily a consequence of metastatic dissemination and associated complications. Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies and tends to metastasize early, especially in the liver. Emerging evidence suggests that organs that develop metastases exhibit microscopic changes that favor metastatic growth, collectively known as "pre-metastatic niches". By definition, a pre-metastatic niche is chronologically established before overt metastatic outgrowth, and its generation involves the release of tumor-derived secreted factors that modulate cells intrinsic to the recipient organ, as well as recruitment of additional cells from tertiary sites, such as bone marrow-all orchestrated by the primary tumor. The pre-metastatic niche is characterized by tumor-promoting inflammation with tumor-supportive and immune-suppressive features, remodeling of the extracellular matrix, angiogenic modulation and metabolic alterations that support growth of disseminated tumor cells. In this paper, we review the current state of knowledge of the hepatic pre-metastatic niche in PDAC and attempt to create a framework to guide future diagnostic and therapeutic studies.

Keywords:  PDAC; immunotherapy; liver metastasis; pancreatic cancer; pre-metastatic niche

DOI:  https://doi.org/10.3390/cancers14123028
Nat Metab. 2022 Jun 23.

Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited.

Zhaoqi Li, Brian W Ji, Purushottam D Dixit, Konstantine Tchourine, Evan C Lien, Aaron M Hosios, Keene L Abbott, Justine C Rutter, Anna M Westermark, Elizabeth F Gorodetsky, Lucas B Sullivan, Matthew G Vander Heiden, Dennis Vitkup.

Production of oxidized biomass, which requires regeneration of the cofactor NAD+, can be a proliferation bottleneck that is influenced by environmental conditions. However, a comprehensive quantitative understanding of metabolic processes that may be affected by NAD+ deficiency is currently missing. Here, we show that de novo lipid biosynthesis can impose a substantial NAD+ consumption cost in proliferating cancer cells. When electron acceptors are limited, environmental lipids become crucial for proliferation because NAD+ is required to generate precursors for fatty acid biosynthesis. We find that both oxidative and even net reductive pathways for lipogenic citrate synthesis are gated by reactions that depend on NAD+ availability. We also show that access to acetate can relieve lipid auxotrophy by bypassing the NAD+ consuming reactions. Gene expression analysis demonstrates that lipid biosynthesis strongly anti-correlates with expression of hypoxia markers across tumor types. Overall, our results define a requirement for oxidative metabolism to support biosynthetic reactions and provide a mechanistic explanation for cancer cell dependence on lipid uptake in electron acceptor-limited conditions, such as hypoxia.

DOI: https://doi.org/10.1038/s42255-022-00588-8
Cancer Discov. 2022 Jun 23. OF1-OF13

Mapping Phenotypic Plasticity upon the Cancer Cell State Landscape Using Manifold Learning.

Daniel B Burkhardt, Beatriz P San Juan, John G Lock, Smita Krishnaswamy, Christine L Chaffer.

Phenotypic plasticity describes the ability of cancer cells to undergo dynamic, nongenetic cell state changes that amplify cancer heterogeneity to promote metastasis and therapy evasion. Thus, cancer cells occupy a continuous spectrum of phenotypic states connected by trajectories defining dynamic transitions upon a cancer cell state landscape. With technologies proliferating to systematically record molecular mechanisms at single-cell resolution, we illuminate manifold learning techniques as emerging computational tools to effectively model cell state dynamics in a way that mimics our understanding of the cell state landscape. We anticipate that "state-gating" therapies targeting phenotypic plasticity will limit cancer heterogeneity, metastasis, and therapy resistance.
SIGNIFICANCE: Nongenetic mechanisms underlying phenotypic plasticity have emerged as significant drivers of tumor heterogeneity, metastasis, and therapy resistance. Herein, we discuss new experimental and computational techniques to define phenotypic plasticity as a scaffold to guide accelerated progress in uncovering new vulnerabilities for therapeutic exploitation.

DOI: https://doi.org/10.1158/2159-8290.CD-21-0282
Cell Metab. 2022 Jun 14. pii: S1550-4131(22)00223-6. [Epub ahead of print]

Metabolic cycles and signals for insulin secretion.

Matthew J Merrins, Barbara E Corkey, Richard G Kibbey, Marc Prentki.

In this review, we focus on recent developments in our understanding of nutrient-induced insulin secretion that challenge a key aspect of the "canonical" model, in which an oxidative phosphorylation-driven rise in ATP production closes KATP channels. We discuss the importance of intrinsic β cell metabolic oscillations; the phasic alignment of relevant metabolic cycles, shuttles, and shunts; and how their temporal and compartmental relationships align with the triggering phase or the secretory phase of pulsatile insulin secretion. Metabolic signaling components are assigned regulatory, effectory, and/or homeostatic roles vis-à-vis their contribution to glucose sensing, signal transmission, and resetting the system. Taken together, these functions provide a framework for understanding how allostery, anaplerosis, and oxidative metabolism are integrated into the oscillatory behavior of the secretory pathway. By incorporating these temporal as well as newly discovered spatial aspects of β cell metabolism, we propose a much-refined MitoCat-MitoOx model of the signaling process for the field to evaluate.

DOI: https://doi.org/10.1016/j.cmet.2022.06.003
Future Oncol. 2022 Jun 22.

Can we predict the progression of premalignant pancreatic cystic tumors to ductal adenocarcinoma?

Swathikan Chidambaram, Michal Kawka, Tamara Mh Gall, David Cunningham, Long R Jiao.

  Pancreatic ductal adenocarcinoma (PDAC) is the most prevalent malignant pancreatic tumor. Few studies have shown how often PDACs arise from cystic precursor lesions. This special report aims to summarize the evidence on the progression of precancerous lesions to PDAC. A review of the literature found four studies that discussed pancreatic intraepithelial lesions (PanINs), three that discussed mucinous cystic neoplasms (MCN) and five that discussed intraductal papillary neoplasms (IPMN). PanINs were the most common precursors lesion, with approximately 80% of PDACs originating from this lesion. The lack of evidence characterizing the features of PDAC precursor cystic lesions potentially leads to a subset of patients undergoing surgery unnecessarily. Advancements in molecular techniques could allow the study of cystic lesions at a genetic level, leading to more personalized management.

Keywords:  IPMN; MCN; PDAC; PanIN; pancreatic cancer; pancreatic cysts; personalized medicine

DOI:  https://doi.org/10.2217/fon-2021-1545
Proc Natl Acad Sci U S A. 2022 Jun 28. 119(26): e2121987119

A ferroptosis defense mechanism mediated by glycerol-3-phosphate dehydrogenase 2 in mitochondria.

Shiqi Wu, Chao Mao, Lavanya Kondiparthi, Masha V Poyurovsky, Kellen Olszewski, Boyi Gan.

  Mechanisms of defense against ferroptosis (an iron-dependent form of cell death induced by lipid peroxidation) in cellular organelles remain poorly understood, hindering our ability to target ferroptosis in disease treatment. In this study, metabolomic analyses revealed that treatment of cancer cells with glutathione peroxidase 4 (GPX4) inhibitors results in intracellular glycerol-3-phosphate (G3P) depletion. We further showed that supplementation of cancer cells with G3P attenuates ferroptosis induced by GPX4 inhibitors in a G3P dehydrogenase 2 (GPD2)-dependent manner; GPD2 deletion sensitizes cancer cells to GPX4 inhibition-induced mitochondrial lipid peroxidation and ferroptosis, and combined deletion of GPX4 and GPD2 synergistically suppresses tumor growth by inducing ferroptosis in vivo. Mechanistically, inner mitochondrial membrane-localized GPD2 couples G3P oxidation with ubiquinone reduction to ubiquinol, which acts as a radical-trapping antioxidant to suppress ferroptosis in mitochondria. Taken together, these results reveal that GPD2 participates in ferroptosis defense in mitochondria by generating ubiquinol.

Keywords:  GPD2; cell death; ferroptosis; lipid peroxidation; mitochondria

DOI:  https://doi.org/10.1073/pnas.2121987119
Autophagy. 2022 Jun 19.

Targeted protein degradation via the autophagy-lysosome system: AUTOTAC (AUTOphagy-TArgeting Chimera).

Chang Hoon Ji, Min Ju Lee, Hee Yeon Kim, Ah Jung Heo, Daniel Youngjae Park, Yun Kyung Kim, Bo Yeon Kim, Yong Tae Kwon.

  Targeted protein degradation allows targeting undruggable proteins for therapeutic applications as well as eliminating proteins of interest for research purposes. While several types of degraders that harness the proteasome or the lysosome have been developed, a technology that simultaneously degrades targets and accelerates cellular autophagic flux remains unavailable. In this study, we developed a general chemical tool by which given intracellular proteins are targeted to macroautophagy for lysosomal degradation. This platform technology, termed AUTOTAC (AUTOphagy-TArgeting Chimera), employs bifunctional molecules composed of target-binding ligands (TBLs) linked to autophagy-targeting ligands (ATLs). Upon binding to targets via the TBL, the ATL binds the ZZ domain of the otherwise dormant autophagy receptor SQSTM1/p62 (sequestosome 1), which activates SQSTM1 associated with targets and sequesters them into oligomeric species for autophagic targeting and lysosomal degradation. AUTOTACs were used to degrade various oncoproteins or aggregation-prone proteins in neurodegeneration both in vitro and/or in vivo. We suggest that AUTOTAC provides a platform for selective proteolysis as a research tool and in drug development.

Keywords:  N-degron pathway; N-terminal arginylation; SQSTM1/p62; chemical tools; neurodegeneration; protein quality control; proteinopathy; proteolysis; selective autophagy; targeted protein degradation (TPD)

DOI:  https://doi.org/10.1080/15548627.2022.2091338
J Vis Exp. 2022 Jun 02.

CAM-Delam Assay to Score Metastatic Properties by Quantifying Delamination and Invasion Capacity of Cancer Cells.

Tami Green, Lina Šlekienė, Lena Gunhaga.

The major cause of cancer-related deaths is metastasis formation (i.e., when cancer cells spread from the primary tumor to distant organs and form secondary tumors). Delamination, defined as the degradation of the basal lamina and basement membrane, is the initial process that facilitates the transmigration and spread of cancer cells to other tissues and organs. Scoring the delamination capacity of cancer cells would indicate the metastatic potential of these cells. We have developed a standardized method, the ex ovo CAM-Delam assay, to visualize and quantify the ability of cancer cells to delaminate and invade, thereby being able to assess metastatic aggressiveness. Briefly, the CAM-Delam method includes seeding cancer cells in silicone rings on the chick chorioallantoic membrane (CAM) at embryonic day 10, followed by incubation from hours to a few days. The CAM-Delam assay includes the use of an internal humidified chamber during chick embryo incubation. This novel approach increased embryo survival from 10%-50% to 80%-90%, which resolved previous technical problems with low embryo survival rates in different CAM assays. Next, the CAM samples with associated cancer cell clusters were isolated, fixed, and frozen. Finally, cryostat-sectioned samples were visualized and analyzed for basement membrane damage and cancer cell invasion using immunohistochemistry. By evaluating various known metastatic and non-metastatic cancer cell lines designed to express green fluorescent protein (GFP), the CAM-Delam quantitative results showed that the delamination capacity patterns reflect metastatic aggressiveness and can be scored into four categories. Future use of this assay, apart from quantifying delamination capacity as an indication of metastatic aggressiveness, is to unravel the molecular mechanisms that control delamination, invasion, the formation of micrometastases, and changes in the tumor microenvironment.

DOI: https://doi.org/10.3791/64025
Cancers (Basel). 2022 Jun 10. pii: 2862. [Epub ahead of print]14(12):

Mitochondrial Dysfunction and the Glycolytic Switch Induced by Caveolin-1 Phosphorylation Promote Cancer Cell Migration, Invasion, and Metastasis.

Natalia Díaz-Valdivia, Layla Simón, Jorge Díaz, Samuel Martinez-Meza, Pamela Contreras, Renato Burgos-Ravanal, Viviana I Pérez, Balz Frei, Lisette Leyton, Andrew F G Quest.

  Cancer cells often display impaired mitochondrial function, reduced oxidative phosphorylation, and augmented aerobic glycolysis (Warburg effect) to fulfill their bioenergetic and biosynthetic needs. Caveolin-1 (CAV1) is a scaffolding protein that promotes cancer cell migration, invasion, and metastasis in a manner dependent on CAV1 phosphorylation on tyrosine-14 (pY14). Here, we show that CAV1 expression increased glycolysis rates, while mitochondrial respiration was reduced by inhibition of the mitochondrial complex IV. These effects correlated with increased reactive oxygen species (ROS) levels that favored CAV1-induced migration and invasion. Interestingly, pY14-CAV1 promoted the metabolic switch associated with increased migration/invasion and augmented ROS-inhibited PTP1B, a phosphatase that controls pY14 levels. Finally, the glycolysis inhibitor 2-deoxy-D-glucose reduced CAV1-enhanced migration in vitro and metastasis in vivo of murine melanoma cells. In conclusion, CAV1 promotes the Warburg effect and ROS production, which inhibits PTP1B to augment CAV1 phosphorylation on tyrosine-14, thereby increasing the metastatic potential of cancer cells.

Keywords:  PTP1B; caveolin-1; metabolic switch; metastasis; mitochondrial complex IV; tyrosine-14 phosphorylation

DOI:  https://doi.org/10.3390/cancers14122862
Methods Mol Biol. 2022 ;2508 235-260

Using CRISPR-Cas9 to Dissect Cancer Mutations in Cell Lines.

Shady Sayed, Duran Sürün, Jovan Mircetic, Olga Alexandra Sidorova, Frank Buchholz.

  The CRISPR-Cas9 technology has revolutionized the scope and pace of biomedical research, enabling the targeting of specific genomic sequences for a wide spectrum of applications. Here we describe assays to functionally interrogate mutations identified in cancer cells utilizing both CRISPR-Cas9 nuclease and base editors. We provide guidelines to interrogate known cancer driver mutations or functionally screen for novel vulnerability mutations with these systems in characterized human cancer cell lines. The proposed platform should be transferable to primary cancer cells, opening up a path for precision oncology on a functional level.

Keywords:  CRISPR-Cas9; Cancer cell lines; Mutations

DOI:  https://doi.org/10.1007/978-1-0716-2376-3_18
Trends Cancer. 2022 Jun 15. pii: S2405-8033(22)00115-7. [Epub ahead of print]

Challenges and opportunities for physician-scientists in advancing cancer research.

Nancy E Davidson, Richard J Gilbertson, Anthony Letai, Ross L Levine, Florencia McAllister, Lillian L Siu.

DOI: https://doi.org/10.1016/j.trecan.2022.05.004
Sci Adv. 2022 Jun 24. 8(25): eabn5683

Liver cancer heterogeneity modeled by in situ genome editing of hepatocytes.

Mei Tang, Yang Zhao, Jianhui Zhao, Shumei Wei, Mingwei Liu, Nairen Zheng, Didi Geng, Shixun Han, Yuchao Zhang, Guoxuan Zhong, Shuaifeng Li, Xiuming Zhang, Chenliang Wang, Huan Yan, Xiaolei Cao, Li Li, Xueli Bai, Junfang Ji, Xin-Hua Feng, Jun Qin, Tingbo Liang, Bin Zhao.

Mechanistic study and precision treatment of primary liver cancer (PLC) are hindered by marked heterogeneity, which is challenging to recapitulate in any given liver cancer mouse model. Here, we report the generation of 25 mouse models of PLC by in situ genome editing of hepatocytes recapitulating 25 single or combinations of human cancer driver genes. These mouse tumors represent major histopathological types of human PLCs and could be divided into three human-matched molecular subtypes based on transcriptomic and proteomic profiles. Phenotypical characterization identified subtype- or genotype-specific alterations in immune microenvironment, metabolic reprogramming, cell proliferation, and expression of drug targets. Furthermore, single-cell analysis and expression tracing revealed spatial and temporal dynamics in expression of pyruvate kinase M2 (Pkm2). Tumor-specific knockdown of Pkm2 by multiplexed genome editing reversed the Warburg effect and suppressed tumorigenesis in a genotype-specific manner. Our study provides mouse PLC models with defined genetic drivers and characterized phenotypical heterogeneity suitable for mechanistic investigation and preclinical testing.

DOI: https://doi.org/10.1126/sciadv.abn5683
JAMA Netw Open. 2022 Jun 01. 5(6): e2218355

Adaptive Dynamic Therapy and Survivorship for Operable Pancreatic Cancer.

Samer AlMasri, Mazen Zenati, Abdulrahman Hammad, Ibrahim Nassour, Hao Liu, Melissa E Hogg, Herbert J Zeh, Brian Boone, Nathan Bahary, Aatur D Singhi, Kenneth K Lee, Alessandro Paniccia, Amer H Zureikat.

Importance: Neoadjuvant therapy is increasingly used in localized pancreatic carcinoma, and survival is correlated with carbohydrate antigen 19-9 (CA19-9) levels and histopathologic response following neoadjuvant therapy. With several regimens now available, the choice of chemotherapy could be best dictated by response to neoadjuvant therapy (as measured by CA19-9 levels and/or pathologic response), a strategy defined herein as adaptive dynamic therapy.
Objective: To evaluate the association of adaptive dynamic therapy with oncologic outcomes in patients with surgically resected pancreatic cancer.
Design, Setting, and Participants: This retrospective cohort study included patients with localized pancreatic cancer who were treated with either gemcitabine/nab-paclitaxel or fluorouracil, leucovorin, irinotecan, and oxaliplatin (FOLFIRINOX) preoperatively between 2010 and 2019 at a high-volume tertiary care academic center. Participants were identified from a prospectively maintained database and had a median follow-up of 49 months. Data were analyzed from October 17 to November 24, 2020.
Exposures: The adaptive dynamic therapy group included 219 patients who remained on or switched to an alternative regimen as dictated by CA19-9 response and for whom the adjuvant regimen was selected based on CA19-9 and/or pathologic response. The nonadaptive dynamic therapy group included 103 patients who had their chemotherapeutic regimen selected independent of CA19-9 and/or tumoral response.
Main Outcomes and Measures: Prognostic implications of dynamic perioperative therapy assessed through Kaplan-Meier analysis, Cox regression, and inverse probability weighted estimators.
Results: A total of 322 consecutive patients (mean [SD] age, 65.1 [9] years; 162 [50%] women) were identified. The adaptive dynamic therapy group, compared with the nonadaptive dynamic therapy group, had a more pronounced median (IQR) decrease in CA19-9 levels (-80% [-92% to -56%] vs -45% [-81% to -13%]; P < .001), higher incidence of complete or near-complete tumoral response (25 [12%] vs 2 [2%]; P = .007), and lower median (IQR) number of lymph node metastasis (1 [0 to 4] vs 2 [0 to 4]; P = .046). Overall survival was significantly improved in the dynamic group compared with the nondynamic group (38.7 months [95% CI, 34.0 to 46.7 months] vs 26.5 months [95% CI, 23.5 to 32.9 months]; P = .03), and on adjusted analysis, dynamic therapy was independently associated with improved survival (hazard ratio, 0.73; 95% CI, 0.53 to 0.99; P = .04). On inverse probability weighted analysis of 320 matched patients, the average treatment effect of dynamic therapy was to increase overall survival by 11.1 months (95% CI, 1.5 to 20.7 months; P = .02).
Conclusions and Relevance: In this cohort study that sought to evaluate the role of adaptive dynamic therapy in localized pancreatic cancer, selecting a chemotherapeutic regimen based on response to preoperative therapy was associated with improved survival. These findings support an individualized and in vivo assessment of response to perioperative therapy in pancreatic cancer.

DOI: https://doi.org/10.1001/jamanetworkopen.2022.18355
Gastroenterology. 2022 Jun 16. pii: S0016-5085(22)00645-X. [Epub ahead of print]

Dual stromal targeting sensitizes pancreatic adenocarcinoma for anti-PD-1 therapy.

Alex B Blair, Jianxin Wang, John Davelaar, Andrew Baker, Keyu Li, Nan Niu, Junke Wang, Yingkuan Shao, Vanessa Funes, Pan Li, Jonathan A Pachter, Dan Maneval, Felipe Dezem, Jasmine Plummer, Keith Syson Chan, Jun Gong, Andrew E Hendifar, Stephen J Pandol, Richard Burkhart, Yuqing Zhang, Lei Zheng, Arsen Osipov.

   BACKGROUND AND AIMS: The stroma in pancreatic ductal adenocarcinoma (PDAC) contributes to its immunosuppressive nature and therapeutic resistance. Herein we sought to modify signaling and enhance immunotherapy efficacy by targeting multiple stromal components through both intracellular and extracellular mechanisms.
METHODS: A murine liver metastasis syngeneic model of PDAC was treated with focal adhesion kinase inhibitor (FAKi), anti-PD-1 antibody and stromal hyaluronan (HA) degradation by PEGPH20 to assess immune and stromal modulating effects of these agents and their combinations.
RESULTS: The results showed that HA degradation by PEGPH20 and reduction in phosphorylated FAK expression by FAKi leads to improved survival in PDAC-bearing mice treated with anti-PD-1 antibody. HA degradation in combination with FAKi and anti-PD-1 antibody increases T-cell infiltration and alters T-cell phenotype towards effector memory T-cells. FAKi alters the expression of T-cell modulating cytokines and leads to changes in T-cell metabolism and increases in effector T-cell signatures. HA degradation in combination with anti-PD-1 antibody and FAKi treatments reduces granulocytes including granulocytic-MDSCs and decreases CXCR4 expressing myeloid cells, particularly the CXCR4 expressing granulocytes. Anti-CXCR4 antibody combined with FAKi and anti-PD-1 antibody significantly decreases metastatic rates in the PDAC liver metastasis model.
CONCLUSION: This represents the first preclinical study to identify synergistic effects of targeting both intracellular and extracellular components within the PDAC stroma and supports testing anti-CXCR4 antibody in combination with FAKi as a PDAC treatment strategy.

Keywords:  CXCR4; FAK; Pancreatic ductal adenocarcinoma; anti-PD-1 antibody; hyaluronan

DOI:  https://doi.org/10.1053/j.gastro.2022.06.027
Cells. 2022 Jun 10. pii: 1893. [Epub ahead of print]11(12):

Depleting Ly6G Positive Myeloid Cells Reduces Pancreatic Cancer-Induced Skeletal Muscle Atrophy.

Michael R Deyhle, Chandler S Callaway, Daria Neyroud, Andrew C D'Lugos, Sarah M Judge, Andrew R Judge.

  Immune cells can mount desirable anti-cancer immunity. However, some immune cells can support cancer disease progression. The presence of cancer can lead to production of immature myeloid cells from the bone marrow known as myeloid-derived suppressor cells (MDSCs). The immunosuppressive and pro-tumorigenic effects of MDSCs are well understood. Whether MDSCs are involved in promoting cancer cachexia is not well understood. We orthotopically injected the pancreas of mice with KPC cells or PBS. One group of tumor-bearing mice was treated with an anti-Ly6G antibody that depletes granulocytic MDSCs and neutrophils; the other received a control antibody. Anti-Ly6G treatment delayed body mass loss, reduced tibialis anterior (TA) muscle wasting, abolished TA muscle fiber atrophy, reduced diaphragm muscle fiber atrophy of type IIb and IIx fibers, and reduced atrophic gene expression in the TA muscles. Anti-ly6G treatment resulted in greater than 50% Ly6G+ cell depletion efficiency in the tumors and TA muscles. These data show that, in the orthotopic KPC model, anti-Ly6G treatment reduces the number of Ly6G+ cells in the tumor and skeletal muscle and reduces skeletal muscle atrophy. These data implicate Ly6G+ cells, including granulocytic MDSCs and neutrophils, as possible contributors to the development of pancreatic cancer-induced skeletal muscle wasting.

Keywords:  MDSC; atrophy; cachexia; immunosuppression; skeletal muscle

DOI:  https://doi.org/10.3390/cells11121893
Methods Mol Biol. 2022 ;2508 225-234

The Use of Seahorse XF Assays to Interrogate Real-Time Energy Metabolism in Cancer Cell Lines.

Jenna K Caines, David A Barnes, Mark D Berry.

  The propensity of cancer cells to preferentially undergo anaerobic metabolism despite oxygen being abundant is referred to as the Warburg effect. Measuring cellular metabolism is therefore central to understanding the cellular physiology of cancer cells. The Seahorse XFe Analyzer series allows real-time measurement of cellular metabolism. In the basic assay, two parameters, the oxygen consumption rate (OCR) and the extracellular acidification rate (ECAR), are used to determine real-time changes in the energy needs of live cells: OCR provides a measure of aerobic mitochondrial respiration; ECAR gives a measure of anaerobic glycolysis. Through the use of various respiration inhibitors, the Seahorse assay allows baseline respiration rate and total aerobic and anaerobic ATP production to be determined under a variety of experimental conditions. Here we describe the protocol for completing the Seahorse Real-Time ATP Rate Assay for adherent and suspension cancer cell lines. Depending on individual experimental results, more refined subsequent assays can then be performed to specifically determine, for example, the ability to utilize different substrates by the cell lines in the presence and absence of pharmacological and/or genetic interventions.

Keywords:  ATP; Cancer cell metabolism; Energy metabolism; Glycolysis; Mitochondria; Seahorse

DOI:  https://doi.org/10.1007/978-1-0716-2376-3_17
Mol Carcinog. 2022 Jun 20.

Targeting mitochondrial metabolism for metastatic cancer therapy.

Antonino Passaniti, Myoung Sook Kim, Brian M Polster, Paul Shapiro.

  Primary tumors evolve metabolic mechanisms favoring glycolysis for adenosine triphosphate (ATP) generation and antioxidant defenses. In contrast, metastatic cells frequently depend on mitochondrial respiration and oxidative phosphorylation (OxPhos). This reliance of metastatic cells on OxPhos can be exploited using drugs that target mitochondrial metabolism. Therefore, therapeutic agents that act via diverse mechanisms, including the activation of signaling pathways that promote the production of reactive oxygen species (ROS) and/or a reduction in antioxidant defenses may elevate oxidative stress and inhibit tumor cell survival. In this review, we will provide (1) a mechanistic analysis of function-selective extracellular signal-regulated kinase-1/2 (ERK1/2) inhibitors that inhibit cancer cells through enhanced ROS, (2) a review of the role of mitochondrial ATP synthase in redox regulation and drug resistance, (3) a rationale for inhibiting ERK signaling and mitochondrial OxPhos toward the therapeutic goal of reducing tumor metastasis and treatment resistance. Recent reports from our laboratories using metastatic melanoma and breast cancer models have shown the preclinical efficacy of novel and rationally designed therapeutic agents that target ERK1/2 signaling and mitochondrial ATP synthase, which modulate ROS events that may prevent or treat metastatic cancer. These findings and those of others suggest that targeting a tumor's metabolic requirements and vulnerabilities may inhibit metastatic pathways and tumor growth. Approaches that exploit the ability of therapeutic agents to alter oxidative balance in tumor cells may be selective for cancer cells and may ultimately have an impact on clinical efficacy and safety. Elucidating the translational potential of metabolic targeting could lead to the discovery of new approaches for treatment of metastatic cancer.

Keywords:  cancer metastasis; drug mechanisms; kinase signaling; mitochondria; reactive oxygen species; targeting OxPhos

DOI:  https://doi.org/10.1002/mc.23436
Curr Biol. 2022 Jun 20. pii: S0960-9822(22)00765-5. [Epub ahead of print]32(12): R618-R623

Shaping fuel utilization by mitochondria.

Lukas Alan, Luca Scorrano.

Mitochondria are central to cellular metabolism. They provide intermediate metabolites that are used in biosynthetic pathways and they process diet-derived nutrients into the energy-rich compound ATP. Mitochondrial ATP biosynthesis is a marvel of thermodynamic efficiency. Via the tricarboxylic acid cycle (TCA) and fatty acid β-oxidation, mitochondria extract electrons from dietary carbon compounds and pass them to nucleotides that ultimately deliver them to the respiratory chain complexes located in invaginations in the inner mitochondrial membrane (IMM) known as cristae. The respiratory chain complexes donate electrons in stepwise redox reactions to molecular oxygen and, with the exception of complex II, use the liberated energy to pump protons across the proton-impermeable IMM, generating a proton electrochemical gradient. This gradient is then utilized by the ATP synthase, which, in a rotary mechanism, catalyzes the formation of the high-energy γ-phosphate chemical bond between ADP and inorganic phosphate. The conversion of the chemical energy of carbon compounds into a physical, vectorial form of energy (the electrochemical gradient) maximizes the yield of the ATP biosynthetic process and is perhaps one of the foundations of life as we know it.

DOI: https://doi.org/10.1016/j.cub.2022.05.006
J Cachexia Sarcopenia Muscle. 2022 Jun 20.

Decoding the transcriptome of denervated muscle at single-nucleus resolution.

Hongchun Lin, Xinxin Ma, Yuxiang Sun, Hui Peng, Yanlin Wang, Sandhya Sara Thomas, Zhaoyong Hu.

   BACKGROUND: Skeletal muscle exhibits remarkable plasticity under both physiological and pathological conditions. One major manifestation of this plasticity is muscle atrophy that is an adaptive response to catabolic stimuli. Because the heterogeneous transcriptome responses to catabolism in different types of muscle cells are not fully characterized, we applied single-nucleus RNA sequencing (snRNA-seq) to unveil muscle atrophy related transcriptional changes at single nucleus resolution.
METHODS: Using a sciatic denervation mouse model of muscle atrophy, snRNA-seq was performed to generate single-nucleus transcriptional profiles of the gastrocnemius muscle from normal and denervated mice. Various bioinformatics analyses, including unsupervised clustering, functional enrichment analysis, trajectory analysis, regulon inference, metabolic signature characterization and cell-cell communication prediction, were applied to illustrate the transcriptome changes of the individual cell types.
RESULTS: A total of 29 539 muscle nuclei (normal vs. denervation: 15 739 vs. 13 800) were classified into 13 nuclear types according to the known cell markers. Among these, the type IIb myonuclei were further divided into two subgroups, which we designated as type IIb1 and type IIb2 myonuclei. In response to denervation, the proportion of type IIb2 myonuclei increased sharply (78.12% vs. 38.45%, P < 0.05). Concomitantly, trajectory analysis revealed that denervated type IIb2 myonuclei clearly deviated away from the normal type IIb2 myonuclei, indicating that this subgroup underwent robust transcriptional reprogramming upon denervation. Signature genes in denervated type IIb2 myonuclei included Runx1, Gadd45a, Igfn1, Robo2, Dlg2, and Sh3d19 (P < 0.001). The gene regulatory network analysis captured a group of atrophy-related regulons (Foxo3, Runx1, Elk4, and Bhlhe40) whose activities were enhanced (P < 0.01), especially in the type IIb2 myonuclei. The metabolic landscape in the myonuclei showed that most of the metabolic pathways were down-regulated by denervation (P < 0.001), while some of the metabolic signalling, such as glutathione metabolism, was specifically activated in the denervated type IIb2 myonulei. We also investigated the transcriptomic alterations in the type I myofibres, muscle stem cells, fibro-adipogenic progenitors, macrophages, endothelial cells and pericytes and characterized their signature responses to denervation. By predicting the cell-cell interactions, we observed that the communications between myofibres and muscle resident cells were diminished by denervation.
CONCLUSIONS: Our results define the myonuclear transition, metabolic remodelling, and gene regulation networks reprogramming associated with denervation-induced muscle atrophy and illustrate the molecular basis of the heterogeneity and plasticity of muscle cells in response to catabolism. These results provide a useful resource for exploring the molecular mechanism of muscle atrophy.

Keywords:  Denervation; Muscle atrophy; Muscle metabolism; Skeletal muscle; snRNA-seq

DOI:  https://doi.org/10.1002/jcsm.13023