bims-cagime 2023-04-30 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2023–04–30
37 papers selected by
Kıvanç Görgülü, Technical University of Munich

Cachexia: A systemic consequence of progressive, unresolved disease.
Apoptotic cell death in disease-Current understanding of the NCCD 2023.
Metabolically fitter with fibronectin.
Sexual identity of enterocytes regulates autophagy to determine intestinal health, lifespan and responses to rapamycin.
Diabetes increases mortality in patients with pancreatic and colorectal cancer by promoting cachexia and its associated inflammatory status.
Identification of potential selective autophagy receptors from protein-content profiling of autophagosomes.
HAPLN1 potentiates peritoneal metastasis in pancreatic cancer.
Mouse models for immuno-oncology.
The Warburg effect: a signature of mitochondrial overload.
Splicing Factor SRSF1 Promotes Pancreatitis and KRASG12D-Mediated Pancreatic Cancer.
Integrative genetic analysis identifies FLVCR1 as a plasma-membrane choline transporter in mammals.
Parallel phospholipid transfer by Vps13 and Atg2 determines autophagosome biogenesis dynamics.
3D spheroid culture to examine adaptive therapy response in invading tumor cells.
A druggable copper-signalling pathway that drives inflammation.
DPP4 inhibition impairs senohemostasis to improve plaque stability in atherosclerotic mice.
Simultaneous targeting of PD-1 and IL-2Rβγ with radiation therapy inhibits pancreatic cancer growth and metastasis.
ATG9 vesicles comprise the seed membrane of mammalian autophagosomes.
Fibroblasts in pancreatic cancer: molecular and clinical perspectives.
3D bioprinted functional skeletal muscle models have potential applications for studies of muscle wasting in cancer cachexia.
Preoperative Rapid Weight Loss as a Prognostic Predictor After Surgical Resection for Pancreatic Cancer.
Nucleophagy delays aging and preserves germline immortality.
The critical immune basis for differential responses to immunotherapy in primary versus metastatic pancreatic cancer.
Pancreatic cancer is associated with medication changes prior to clinical diagnosis.
An unexpected timer for cell division.
Biological age is increased by stress and restored upon recovery.
The effects of caloric restriction on adipose tissue and metabolic health are sex- and age-dependent.
Optimal cancer evasion in a dynamic immune microenvironment generates diverse post-escape tumor antigenicity profiles.
The p-rpS6-zone delineates wounding responses and the healing process.
The importance of aging in cancer research.
Tumor loss-of-function mutations in STK11/LKB1 induce cachexia.
Secreted HLA Fc-Fusion Profiles Immunopeptidome in Hypoxic PDAC and Cellular Senescence.
Regulation of phospholipid distribution in the lipid bilayer by flippases and scramblases.
Proteomic profiling of extracellular matrix components from patient metastases identifies consistently elevated proteins for developing nanobodies that target primary tumors and metastases.
Nuclear morphology is a deep learning biomarker of cellular senescence.
Quantitative analysis of autophagy reveals the role of ATG9 and ATG2 in autophagosome formation.
Phosphatidic acid: from biophysical properties to diverse functions.
Trends in Subcutaneous Tumour Height and Impact on Measurement Accuracy.

Cell. 2023 Apr 27. pii: S0092-8674(23)00325-2. [Epub ahead of print]186(9): 1824-1845

Cachexia: A systemic consequence of progressive, unresolved disease.

Miriam Ferrer, Tracy G Anthony, Janelle S Ayres, Giulia Biffi, Justin C Brown, Bette J Caan, Elizabeth M Cespedes Feliciano, Anthony P Coll, Richard F Dunne, Marcus D Goncalves, Jonas Grethlein, Steven B Heymsfield, Sheng Hui, Mariam Jamal-Hanjani, Jie Min Lam, David Y Lewis, David McCandlish, Karen M Mustian, Stephen O'Rahilly, Norbert Perrimon, Eileen P White, Tobias Janowitz.

Cachexia, a systemic wasting condition, is considered a late consequence of diseases, including cancer, organ failure, or infections, and contributes to significant morbidity and mortality. The induction process and mechanistic progression of cachexia are incompletely understood. Refocusing academic efforts away from advanced cachexia to the etiology of cachexia may enable discoveries of new therapeutic approaches. Here, we review drivers, mechanisms, organismal predispositions, evidence for multi-organ interaction, model systems, clinical research, trials, and care provision from early onset to late cachexia. Evidence is emerging that distinct inflammatory, metabolic, and neuro-modulatory drivers can initiate processes that ultimately converge on advanced cachexia.

DOI: https://doi.org/10.1016/j.cell.2023.03.028
Cell Death Differ. 2023 Apr 26.

Apoptotic cell death in disease-Current understanding of the NCCD 2023.

Ilio Vitale, Federico Pietrocola, Emma Guilbaud, Stuart A Aaronson, John M Abrams, Dieter Adam, Massimiliano Agostini, Patrizia Agostinis, Emad S Alnemri, Lucia Altucci, Ivano Amelio, David W Andrews, Rami I Aqeilan, Eli Arama, Eric H Baehrecke, Siddharth Balachandran, Daniele Bano, Nickolai A Barlev, Jiri Bartek, Nicolas G Bazan, Christoph Becker, Francesca Bernassola, Mathieu J M Bertrand, Marco E Bianchi, Mikhail V Blagosklonny, J Magarian Blander, Giovanni Blandino, Klas Blomgren, Christoph Borner, Carl D Bortner, Pierluigi Bove, Patricia Boya, Catherine Brenner, Petr Broz, Thomas Brunner, Rune Busk Damgaard, George A Calin, Michelangelo Campanella, Eleonora Candi, Michele Carbone, Didac Carmona-Gutierrez, Francesco Cecconi, Francis K-M Chan, Guo-Qiang Chen, Quan Chen, Youhai H Chen, Emily H Cheng, Jerry E Chipuk, John A Cidlowski, Aaron Ciechanover, Gennaro Ciliberto, Marcus Conrad, Juan R Cubillos-Ruiz, Peter E Czabotar, Vincenzo D'Angiolella, Mads Daugaard, Ted M Dawson, Valina L Dawson, Ruggero De Maria, Bart De Strooper, Klaus-Michael Debatin, Ralph J Deberardinis, Alexei Degterev, Giannino Del Sal, Mohanish Deshmukh, Francesco Di Virgilio, Marc Diederich, Scott J Dixon, Brian D Dynlacht, Wafik S El-Deiry, John W Elrod, Kurt Engeland, Gian Maria Fimia, Claudia Galassi, Carlo Ganini, Ana J Garcia-Saez, Abhishek D Garg, Carmen Garrido, Evripidis Gavathiotis, Motti Gerlic, Sourav Ghosh, Douglas R Green, Lloyd A Greene, Hinrich Gronemeyer, Georg Häcker, György Hajnóczky, J Marie Hardwick, Ygal Haupt, Sudan He, David M Heery, Michael O Hengartner, Claudio Hetz, David A Hildeman, Hidenori Ichijo, Satoshi Inoue, Marja Jäättelä, Ana Janic, Bertrand Joseph, Philipp J Jost, Thirumala-Devi Kanneganti, Michael Karin, Hamid Kashkar, Thomas Kaufmann, Gemma L Kelly, Oliver Kepp, Adi Kimchi, Richard N Kitsis, Daniel J Klionsky, Ruth Kluck, Dmitri V Krysko, Dagmar Kulms, Sharad Kumar, Sergio Lavandero, Inna N Lavrik, John J Lemasters, Gianmaria Liccardi, Andreas Linkermann, Stuart A Lipton, Richard A Lockshin, Carlos López-Otín, Tom Luedde, Marion MacFarlane, Frank Madeo, Walter Malorni, Gwenola Manic, Roberto Mantovani, Saverio Marchi, Jean-Christophe Marine, Seamus J Martin, Jean-Claude Martinou, Pier G Mastroberardino, Jan Paul Medema, Patrick Mehlen, Pascal Meier, Gerry Melino, Sonia Melino, Edward A Miao, Ute M Moll, Cristina Muñoz-Pinedo, Daniel J Murphy, Maria Victoria Niklison-Chirou, Flavia Novelli, Gabriel Núñez, Andrew Oberst, Dimitry Ofengeim, Joseph T Opferman, Moshe Oren, Michele Pagano, Theocharis Panaretakis, Manolis Pasparakis, Josef M Penninger, Francesca Pentimalli, David M Pereira, Shazib Pervaiz, Marcus E Peter, Paolo Pinton, Giovanni Porta, Jochen H M Prehn, Hamsa Puthalakath, Gabriel A Rabinovich, Krishnaraj Rajalingam, Kodi S Ravichandran, Markus Rehm, Jean-Ehrland Ricci, Rosario Rizzuto, Nirmal Robinson, Cecilia M P Rodrigues, Barak Rotblat, Carla V Rothlin, David C Rubinsztein, Thomas Rudel, Alessandro Rufini, Kevin M Ryan, Kristopher A Sarosiek, Akira Sawa, Emre Sayan, Kate Schroder, Luca Scorrano, Federico Sesti, Feng Shao, Yufang Shi, Giuseppe S Sica, John Silke, Hans-Uwe Simon, Antonella Sistigu, Anastasis Stephanou, Brent R Stockwell, Flavie Strapazzon, Andreas Strasser, Liming Sun, Erwei Sun, Qiang Sun, Gyorgy Szabadkai, Stephen W G Tait, Daolin Tang, Nektarios Tavernarakis, Carol M Troy, Boris Turk, Nicoletta Urbano, Peter Vandenabeele, Tom Vanden Berghe, Matthew G Vander Heiden, Jacqueline L Vanderluit, Alexei Verkhratsky, Andreas Villunger, Silvia von Karstedt, Anne K Voss, Karen H Vousden, Domagoj Vucic, Daniela Vuri, Erwin F Wagner, Henning Walczak, David Wallach, Ruoning Wang, Ying Wang, Achim Weber, Will Wood, Takahiro Yamazaki, Huang-Tian Yang, Zahra Zakeri, Joanna E Zawacka-Pankau, Lin Zhang, Haibing Zhang, Boris Zhivotovsky, Wenzhao Zhou, Mauro Piacentini, Guido Kroemer, Lorenzo Galluzzi.

Apoptosis is a form of regulated cell death (RCD) that involves proteases of the caspase family. Pharmacological and genetic strategies that experimentally inhibit or delay apoptosis in mammalian systems have elucidated the key contribution of this process not only to (post-)embryonic development and adult tissue homeostasis, but also to the etiology of multiple human disorders. Consistent with this notion, while defects in the molecular machinery for apoptotic cell death impair organismal development and promote oncogenesis, the unwarranted activation of apoptosis promotes cell loss and tissue damage in the context of various neurological, cardiovascular, renal, hepatic, infectious, neoplastic and inflammatory conditions. Here, the Nomenclature Committee on Cell Death (NCCD) gathered to critically summarize an abundant pre-clinical literature mechanistically linking the core apoptotic apparatus to organismal homeostasis in the context of disease.

DOI: https://doi.org/10.1038/s41418-023-01153-w
Sci Signal. 2023 04 25. 16(782): eadi3398

Metabolically fitter with fibronectin.

Wei Wong.

Activation of hepatic autophagy by skeletal muscle-secreted fibronectin underlies the metabolic benefits of exercise.

DOI: https://doi.org/10.1126/scisignal.adi3398
Nat Aging. 2022 Dec;2(12): 1145-1158

Sexual identity of enterocytes regulates autophagy to determine intestinal health, lifespan and responses to rapamycin.

Jennifer C Regan, Yu-Xuan Lu, Enric Ureña, Ralf L Meilenbrock, James H Catterson, Disna Kißler, Jenny Fröhlich, Emilie Funk, Linda Partridge.

Pharmacological attenuation of mTOR presents a promising route for delay of age-related disease. Here we show that treatment of Drosophila with the mTOR inhibitor rapamycin extends lifespan in females, but not in males. Female-specific, age-related gut pathology is markedly slowed by rapamycin treatment, mediated by increased autophagy. Treatment increases enterocyte autophagy in females, via the H3/H4 histone-Bchs axis, whereas males show high basal levels of enterocyte autophagy that are not increased by rapamycin feeding. Enterocyte sexual identity, determined by transformerFemale expression, dictates sexually dimorphic cell size, H3/H4-Bchs expression, basal rates of autophagy, fecundity, intestinal homeostasis and lifespan extension in response to rapamycin. Dimorphism in autophagy is conserved in mice, where intestine, brown adipose tissue and muscle exhibit sex differences in autophagy and response to rapamycin. This study highlights tissue sex as a determining factor in the regulation of metabolic processes by mTOR and the efficacy of mTOR-targeted, anti-aging drug treatments.

DOI: https://doi.org/10.1038/s43587-022-00308-7
Mol Metab. 2023 Apr 22. pii: S2212-8778(23)00063-7. [Epub ahead of print] 101729

Diabetes increases mortality in patients with pancreatic and colorectal cancer by promoting cachexia and its associated inflammatory status.

Alexandra Chovsepian, Olga Prokopchuk, Gabriela Petrova, Tefta Gjini, Hanna Kuzi, Simone Heisz, Klaus-Peter Janssen, Marc E Martignoni, Helmut Friess, Hans Hauner, Maria Rohm.

   OBJECTIVES: Cancer is considered an emerging diabetes complication, with higher incidence and worse prognosis in patients with diabetes. Cancer is frequently associated with cachexia, a systemic metabolic disease causing wasting. It is currently unclear how diabetes affects the development and progression of cachexia.
METHODS: We investigated the interplay between diabetes and cancer cachexia retrospectively in a cohort of 345 patients with colorectal and pancreatic cancer. We recorded body weight, fat mass, muscle mass, clinical serum values, and survival of these patients. Patients were grouped either into diabetic/non-diabetic groups based on previous diagnosis, or into obese/non-obese groups based on body mass index (BMI≥30kg/m2 was considered obese).
RESULTS: The pre-existence of type 2 diabetes, but not obesity, in patients with cancer led to increased cachexia incidence (80%, compared to 61% without diabetes, p≤0.05), higher weight loss (8.9 % vs. 6.0 %, p≤0.001), and reduced survival probability (median survival days: 689 vs. 538, Chi square=4.96, p≤0.05) irrespective of the initial body weight or tumor progression. Patients with diabetes and cancer showed higher serum levels of C-reactive protein (0.919 μg/mL vs. 0.551 μg/mL, p≤0.01) and interleukin 6 (5.98 pg/mL vs. 3.75 pg/mL, p≤0.05) as well as lower serum albumin levels (3.98 g/dL vs. 4.18 g/dL, p≤0.05) than patients with cancer without diabetes. In a sub-analysis of patients with pancreatic cancer, pre-existing diabetes worsened weight loss (9.95% vs. 6.93%, p≤0.01), and increased the duration of hospitalization (24.41 days vs. 15.85 days, p≤0.001). Further, diabetes aggravated clinical manifestations of cachexia, as changes in the aforementioned biomarkers were more pronounced in patients with diabetes and cachexia co-existence, compared to cachectic patients without diabetes (C-reactive protein: 2.300 μg/mL vs. 0.571 μg/mL, p≤0.0001; hemoglobin: 11.24 g/dL vs. 12.52 g/dL, p≤0.05).
CONCLUSIONS: We show for the first time that pre-existing diabetes aggravates cachexia development in patients with colorectal and pancreatic cancer. This is important when considering cachexia biomarkers and weight management in patients with co-existing diabetes and cancer.

Keywords:  body weight; cancer cachexia; colorectal cancer; inflammation; pancreatic cancer; type 2 diabetes

DOI:  https://doi.org/10.1016/j.molmet.2023.101729
J Cell Biochem. 2023 Apr 23.

Identification of potential selective autophagy receptors from protein-content profiling of autophagosomes.

Alberto Cristiani, Arghya Dutta, Sergio Alejandro Poveda-Cuevas, Andreas Kern, Ramachandra M Bhaskara.

  Selective autophagy receptors (SARs) are central to cellular homeostatic and organellar recycling pathways. Over the last two decades, more than 30 SARs have been discovered and validated using a variety of experimental approaches ranging from cell biology to biochemistry, including high-throughput imaging and screening methods. Yet, the extent of selective autophagy pathways operating under various cellular contexts, for example, under basal and starvation conditions, remains unresolved. Currently, our knowledge of all known SARs and their associated cargo components is fragmentary and limited by experimental data with varying degrees of resolution. Here, we use classical predictive and modeling approaches to integrate high-quality autophagosome content profiling data with disparate datasets. We identify a global set of potential SARs and their associated cargo components active under basal autophagy, starvation-induced, and proteasome-inhibition conditions. We provide a detailed account of cellular components, biochemical pathways, and molecular processes that are degraded via autophagy. Our analysis yields a catalog of new potential SARs that satisfy the characteristics of bonafide, well-characterized SARs. We categorize them by the subcellular compartments they emerge from and classify them based on their likely mode of action. Our structural modeling validates a large subset of predicted interactions with the human ATG8 family of proteins and shows characteristic, conserved LC3-interacting region (LIR)-LIR docking site (LDS) and ubiquitin-interacting motif (UIM)-UIM docking site (UDS) binding modes. Our analysis also revealed the most abundant cargo molecules targeted by these new SARs. Our findings expand the repertoire of SARs and provide unprecedented details into the global autophagic state of HeLa cells. Taken together, our findings provide motivation for the design of new experiments, testing the role of these novel factors in selective autophagy.

Keywords:  autophagosomes; cell biology; computational biology; data analysis; molecular models; proteomics; receptors

DOI:  https://doi.org/10.1002/jcb.30405
Nat Commun. 2023 Apr 24. 14(1): 2353

HAPLN1 potentiates peritoneal metastasis in pancreatic cancer.

Lena Wiedmann, Francesca De Angelis Rigotti, Nuria Vaquero-Siguero, Elisa Donato, Elisa Espinet, Iris Moll, Elisenda Alsina-Sanchis, Hanibal Bohnenberger, Elena Fernandez-Florido, Ronja Mülfarth, Margherita Vacca, Jennifer Gerwing, Lena-Christin Conradi, Philipp Ströbel, Andreas Trumpp, Carolin Mogler, Andreas Fischer, Juan Rodriguez-Vita.

Pancreatic ductal adenocarcinoma (PDAC) frequently metastasizes into the peritoneum, which contributes to poor prognosis. Metastatic spreading is promoted by cancer cell plasticity, yet its regulation by the microenvironment is incompletely understood. Here, we show that the presence of hyaluronan and proteoglycan link protein-1 (HAPLN1) in the extracellular matrix enhances tumor cell plasticity and PDAC metastasis. Bioinformatic analysis showed that HAPLN1 expression is enriched in the basal PDAC subtype and associated with worse overall patient survival. In a mouse model for peritoneal carcinomatosis, HAPLN1-induced immunomodulation favors a more permissive microenvironment, which accelerates the peritoneal spread of tumor cells. Mechanistically, HAPLN1, via upregulation of tumor necrosis factor receptor 2 (TNFR2), promotes TNF-mediated upregulation of Hyaluronan (HA) production, facilitating EMT, stemness, invasion and immunomodulation. Extracellular HAPLN1 modifies cancer cells and fibroblasts, rendering them more immunomodulatory. As such, we identify HAPLN1 as a prognostic marker and as a driver for peritoneal metastasis in PDAC.

DOI: https://doi.org/10.1038/s41467-023-38064-w
Trends Cancer. 2023 Apr 20. pii: S2405-8033(23)00041-9. [Epub ahead of print]

Mouse models for immuno-oncology.

Marcus Bosenberg, Edison T Liu, Chun I Yu, Karolina Palucka.

  Realizing the clinical promise of cancer immunotherapy is hindered by gaps in our knowledge of in vivo mechanisms underlying treatment response as well as treatment limiting toxicity. Preclinical in vivo model systems and technologies are required to address these knowledge gaps and to surmount the challenges faced in the clinical application of immunotherapy. Mice are commonly used for basic and translational research to support development and testing of immune interventions, including for cancer. Here, we discuss the advantages and the limitations of current models as well as future developments.

Keywords:  cancer immunotherapy; collaborative cross mice; diversity outbred mice; genetically engineered mice; humanized mice; mouse model

DOI:  https://doi.org/10.1016/j.trecan.2023.03.009
Trends Cell Biol. 2023 Apr 26. pii: S0962-8924(23)00070-3. [Epub ahead of print]

The Warburg effect: a signature of mitochondrial overload.

Yahui Wang, Gary J Patti.

  A long-standing question in cancer biology has been why oxygenated tumors ferment the majority of glucose they consume to lactate rather than oxidizing it in their mitochondria, a phenomenon known as the 'Warburg effect.' An abundance of evidence shows not only that most cancer cells have fully functional mitochondria but also that mitochondrial activity is important to proliferation. It is therefore difficult to rationalize the metabolic benefit of cancer cells switching from respiration to fermentation. An emerging perspective is that rather than mitochondrial metabolism being suppressed in tumors, as is often suggested, mitochondrial activity increases to the level of saturation. As such, the Warburg effect becomes a signature of excess glucose being released as lactate due to mitochondrial overload.

Keywords:  Warburg effect; aerobic fermentation; aerobic glycolysis; cancer metabolism; mitochondrial metabolism

DOI:  https://doi.org/10.1016/j.tcb.2023.03.013
Cancer Discov. 2023 Apr 26. pii: CD-22-1013. [Epub ahead of print]

Splicing Factor SRSF1 Promotes Pancreatitis and KRASG12D-Mediated Pancreatic Cancer.

Ledong Wan, Kuang-Ting Lin, Mohammad Alinoor Rahman, Yuma Ishigami, Zhikai Wang, Mads A Jensen, John E Wilkinson, Youngkyu Park, David A Tuveson, Adrian R Krainer.

Inflammation is strongly associated with pancreatic ductal adenocarcinoma (PDAC), a highly lethal malignancy. Dysregulated RNA splicing factors have been widely reported in tumorigenesis, but their involvement in pancreatitis and PDAC is not well understood. Here, we report that the splicing factor SRSF1 is highly expressed in pancreatitis, PDAC precursor lesions, and tumors. Increased SRSF1 is sufficient to induce pancreatitis and accelerate KRASG12D-mediated PDAC. Mechanistically, SRSF1 activates MAPK signaling-partly by upregulating interleukin 1 receptor type 1 (IL1R1) through alternative-splicing-regulated mRNA stability. Additionally, SRSF1 protein is destabilized through a negative feedback mechanism in phenotypically normal epithelial cells expressing KRASG12D in mouse pancreas, and in pancreas organoids acutely expressing KRASG12D, buffering MAPK signaling and maintaining pancreas-cell homeostasis. This negative-feedback regulation of SRSF1 is overcome by hyperactive MYC, facilitating PDAC tumorigenesis. Our findings implicate SRSF1 in the etiology of pancreatitis and PDAC, and point to SRSF1-misregulated alternative splicing as a potential therapeutic target.

DOI: https://doi.org/10.1158/2159-8290.CD-22-1013
Cell Metab. 2023 Apr 20. pii: S1550-4131(23)00130-4. [Epub ahead of print]

Integrative genetic analysis identifies FLVCR1 as a plasma-membrane choline transporter in mammals.

Timothy C Kenny, Artem Khan, Yeeun Son, Lishu Yue, Søren Heissel, Anurag Sharma, H Amalia Pasolli, Yuyang Liu, Eric R Gamazon, Hanan Alwaseem, Richard K Hite, Kıvanç Birsoy.

  Genome-wide association studies (GWASs) of serum metabolites have the potential to uncover genes that influence human metabolism. Here, we combined an integrative genetic analysis that associates serum metabolites to membrane transporters with a coessentiality map of metabolic genes. This analysis revealed a connection between feline leukemia virus subgroup C cellular receptor 1 (FLVCR1) and phosphocholine, a downstream metabolite of choline metabolism. Loss of FLVCR1 in human cells strongly impairs choline metabolism due to the inhibition of choline import. Consistently, CRISPR-based genetic screens identified phospholipid synthesis and salvage machinery as synthetic lethal with FLVCR1 loss. Cells and mice lacking FLVCR1 exhibit structural defects in mitochondria and upregulate integrated stress response (ISR) through heme-regulated inhibitor (HRI) kinase. Finally, Flvcr1 knockout mice are embryonic lethal, which is partially rescued by choline supplementation. Altogether, our findings propose FLVCR1 as a major choline transporter in mammals and provide a platform to discover substrates for unknown metabolite transporters.

Keywords:  FLVCR1; PCARP; choline; metabolism; mitochondria; phosphatidylcholine

DOI:  https://doi.org/10.1016/j.cmet.2023.04.003
J Cell Biol. 2023 Jul 03. pii: e202211039. [Epub ahead of print]222(7):

Parallel phospholipid transfer by Vps13 and Atg2 determines autophagosome biogenesis dynamics.

Rahel Dabrowski, Susanna Tulli, Martin Graef.

During autophagy, rapid membrane assembly expands small phagophores into large double-membrane autophagosomes. Theoretical modeling predicts that the majority of autophagosomal phospholipids are derived from highly efficient non-vesicular phospholipid transfer (PLT) across phagophore-ER contacts (PERCS). Currently, the phagophore-ER tether Atg2 is the only PLT protein known to drive phagophore expansion in vivo. Here, our quantitative live-cell imaging analysis reveals a poor correlation between the duration and size of forming autophagosomes and the number of Atg2 molecules at PERCS of starving yeast cells. Strikingly, we find that Atg2-mediated PLT is non-rate limiting for autophagosome biogenesis because membrane tether and the PLT protein Vps13 localizes to the rim and promotes the expansion of phagophores in parallel with Atg2. In the absence of Vps13, the number of Atg2 molecules at PERCS determines the duration and size of forming autophagosomes with an apparent in vivo transfer rate of ∼200 phospholipids per Atg2 molecule and second. We propose that conserved PLT proteins cooperate in channeling phospholipids across organelle contact sites for non-rate-limiting membrane assembly during autophagosome biogenesis.

DOI: https://doi.org/10.1083/jcb.202211039
In Vitro Model. 2022 ;1(6): 463-471

3D spheroid culture to examine adaptive therapy response in invading tumor cells.

Felix Weiss, Nader Atlasy, Vince van Reijmersdal, Henk Stunnenberg, Cornelia Hulsbergen-Veelken, Peter Friedl.

  3D in vitro culture models of cancer cells in extracellular matrix (ECM) have been developed to investigate drug targeting and resistance or, alternatively, mechanisms of invasion; however, models allowing analysis of shared pathways mediating invasion and therapy resistance are lacking. To evaluate therapy response associated with cancer cell invasion, we here used 3D invasion culture of tumor spheroids in 3D fibrillar collagen and applied Ethanol-Ethyl cinnamate (EtOH-ECi) based optical clearing to detect both spheroid core and invasion zone by subcellular-resolved 3D microscopy. When subjected to a single dose of irradiation (4 Gy), we detected significant cell survival in the invasion zone. By physical separation of the core and invasion zone, we identified differentially regulated genes preferentially engaged in invading cells controlling cell division, repair, and survival. This imaging-based 3D invasion culture may be useful for the analysis of complex therapy-response patterns in cancer cells in drug discovery and invasion-associated resistance development.
Supplementary Information: The online version contains supplementary material available at 10.1007/s44164-022-00040-x.

Keywords:  3D matrix culture; Cancer invasion; Irradiation; Molecular profiling; RNAseq; Resistance; Spheroid; Therapy response

DOI:  https://doi.org/10.1007/s44164-022-00040-x
Nature. 2023 Apr 26.

A druggable copper-signalling pathway that drives inflammation.

Stéphanie Solier, Sebastian Müller, Tatiana Cañeque, Antoine Versini, Arnaud Mansart, Fabien Sindikubwabo, Leeroy Baron, Laila Emam, Pierre Gestraud, G Dan Pantoș, Vincent Gandon, Christine Gaillet, Ting-Di Wu, Florent Dingli, Damarys Loew, Sylvain Baulande, Sylvère Durand, Valentin Sencio, Cyril Robil, François Trottein, David Péricat, Emmanuelle Näser, Céline Cougoule, Etienne Meunier, Anne-Laure Bègue, Hélène Salmon, Nicolas Manel, Alain Puisieux, Sarah Watson, Mark A Dawson, Nicolas Servant, Guido Kroemer, Djillali Annane, Raphaël Rodriguez.

Inflammation is a complex physiological process triggered in response to harmful stimuli1. It involves cells of the immune system capable of clearing sources of injury and damaged tissues. Excessive inflammation can occur as a result of infection and is a hallmark of several diseases2-4. The molecular bases underlying inflammatory responses are not fully understood. Here we show that the cell surface glycoprotein CD44, which marks the acquisition of distinct cell phenotypes in the context of development, immunity and cancer progression, mediates the uptake of metals including copper. We identify a pool of chemically reactive copper(II) in mitochondria of inflammatory macrophages that catalyses NAD(H) redox cycling by activating hydrogen peroxide. Maintenance of NAD+ enables metabolic and epigenetic programming towards the inflammatory state. Targeting mitochondrial copper(II) with supformin (LCC-12), a rationally designed dimer of metformin, induces a reduction of the NAD(H) pool, leading to metabolic and epigenetic states that oppose macrophage activation. LCC-12 interferes with cell plasticity in other settings and reduces inflammation in mouse models of bacterial and viral infections. Our work highlights the central role of copper as a regulator of cell plasticity and unveils a therapeutic strategy based on metabolic reprogramming and the control of epigenetic cell states.

DOI: https://doi.org/10.1038/s41586-023-06017-4
J Clin Invest. 2023 Apr 25. pii: e165933. [Epub ahead of print]

DPP4 inhibition impairs senohemostasis to improve plaque stability in atherosclerotic mice.

Allison B Herman, Dimitrios Tsitsipatis, Carlos Anerillas, Krystyna Mazan-Mamczarz, Angelica E Carr, Jordan M Gregg, Mingyi Wang, Jing Zhang, Marc Michel, Charnae' Henry-Smith, Sophia C Harris, Rachel Munk, Jennifer L Martindale, Yulan Piao, Jinshui Fan, Julie A Mattison, Supriyo De, Kotb Abdelmohsen, Robert W Maul, Toshiko Tanaka, Ann Z Moore, Megan E DeMouth, Simone Sidoli, Luigi Ferrucci, Yie Liu, Rafael de Cabo, Edward G Lakatta, Myriam Gorospe.

  Senescent vascular smooth muscle cells (VSMCs) accumulate in the vasculature with age and tissue damage, and secrete factors that promote atherosclerotic plaque vulnerability and disease. Here, we report increased levels and activity of dipeptidyl peptidase 4 (DPP4), a serine protease, in senescent VSMCs. Analysis of the conditioned media from senescent VSMCs revealed a unique senescence-associated secretory phenotype (SASP) signature comprising many complement and coagulation factors; silencing or inhibiting DPP4 reduced these factors and increased cell death. Serum samples from persons with high risk for cardiovascular disease contained high levels of DPP4-regulated complement and coagulation factors. Importantly, DPP4 inhibition reduced senescent cell burden and coagulation and improved plaque stability, while single-cell resolution of senescent VSMCs reflected the senomorphic and senolytic effects of DPP4 inhibition in murine atherosclerosis. We propose that DPP4-regulated factors could be exploited therapeutically to reduce senescent cell function, reverse senohemostasis, and improve vascular disease.

Keywords:  Aging; Atherosclerosis; Cellular senescence; Vascular Biology

DOI:  https://doi.org/10.1172/JCI165933
Cancer Cell. 2023 Apr 24. pii: S1535-6108(23)00117-4. [Epub ahead of print]

Simultaneous targeting of PD-1 and IL-2Rβγ with radiation therapy inhibits pancreatic cancer growth and metastasis.

Miles Piper, Maureen Hoen, Laurel B Darragh, Michael W Knitz, Diemmy Nguyen, Jacob Gadwa, Greta Durini, Idil Karakoc, Abby Grier, Brooke Neupert, Benjamin Van Court, Khalid N M Abdelazeem, Justin Yu, Nicholas A Olimpo, Sophia Corbo, Richard Blake Ross, Tiffany T Pham, Molishree Joshi, Ross M Kedl, Anthony J Saviola, Maria Amann, Pablo Umaña, Laura Codarri Deak, Christian Klein, Angelo D'Alessandro, Sana D Karam.

  In pancreatic ductal adenocarcinoma (PDAC) patients, we show that response to radiation therapy (RT) is characterized by increased IL-2Rβ and IL-2Rγ along with decreased IL-2Rα expression. The bispecific PD1-IL2v is a PD-1-targeted IL-2 variant (IL-2v) immunocytokine with engineered IL-2 cis targeted to PD-1 and abolished IL-2Rα binding, which enhances tumor-antigen-specific T cell activation while reducing regulatory T cell (Treg) suppression. Using PD1-IL2v in orthotopic PDAC KPC-driven tumor models, we show marked improvement in local and metastatic survival, along with a profound increase in tumor-infiltrating CD8+ T cell subsets with a transcriptionally and metabolically active phenotype and preferential activation of antigen-specific CD8+ T cells. In combination with single-dose RT, PD1-IL2v treatment results in a robust, durable expansion of polyfunctional CD8+ T cells, T cell stemness, tumor-specific memory immune response, natural killer (NK) cell activation, and decreased Tregs. These data show that PD1-IL2v leads to profound local and distant response in PDAC.

Keywords:  NK cells; T cell stemness; Tregs; antigen specificity; cancer immunotherapy; cytotoxic T lymphocyte; immune memory; metabolomics; metastasis; tumor immunology

DOI:  https://doi.org/10.1016/j.ccell.2023.04.001
J Cell Biol. 2023 Jul 03. pii: e202208088. [Epub ahead of print]222(7):

ATG9 vesicles comprise the seed membrane of mammalian autophagosomes.

Taryn J Olivas, Yumei Wu, Shenliang Yu, Lin Luan, Peter Choi, Emily D Guinn, Shanta Nag, Pietro V De Camilli, Kallol Gupta, Thomas J Melia.

As the autophagosome forms, its membrane surface area expands rapidly, while its volume is kept low. Protein-mediated transfer of lipids from another organelle to the autophagosome likely drives this expansion, but as these lipids are only introduced into the cytoplasmic-facing leaflet of the organelle, full membrane growth also requires lipid scramblase activity. ATG9 harbors scramblase activity and is essential to autophagosome formation; however, whether ATG9 is integrated into mammalian autophagosomes remains unclear. Here we show that in the absence of lipid transport, ATG9 vesicles are already competent to collect proteins found on mature autophagosomes, including LC3-II. Further, we use styrene-maleic acid lipid particles to reveal the nanoscale organization of protein on LC3-II membranes; ATG9 and LC3-II are each fully integrated into expanding autophagosomes. The ratios of these two proteins at different stages of maturation demonstrate that ATG9 proteins are not continuously integrated, but rather are present on the seed vesicles only and become diluted in the expanding autophagosome membrane.

DOI: https://doi.org/10.1083/jcb.202208088
Trends Mol Med. 2023 Apr 24. pii: S1471-4914(23)00052-7. [Epub ahead of print]

Fibroblasts in pancreatic cancer: molecular and clinical perspectives.

Rita Rebelo, Cristina P R Xavier, Elisa Giovannetti, M Helena Vasconcelos.

  Pancreatic stellate cells (PSCs) and cancer-associated fibroblasts (CAFs) are highly abundant cells in the pancreatic tumor microenvironment (TME) that modulate desmoplasia. The formation of a dense stroma leads to immunosuppression and therapy resistance that are major causes of treatment failure in pancreatic ductal adenocarcinoma (PDAC). Recent evidence suggests that several subpopulations of CAFs in the TME can interconvert, explaining the dual roles (antitumorigenic and protumorigenic) of CAFs in PDAC and the contradictory results of CAF-targeted therapies in clinical trials. This highlights the need to clarify CAF heterogeneity and their interactions with PDAC cells. This review focuses on the communication between activated PSCs/CAFs and PDAC cells, as well as on the mechanisms underlying this crosstalk. CAF-focused therapies and emerging biomarkers are also outlined.

Keywords:  biomarkers; cancer-associated fibroblasts (CAFs); extracellular vesicles (EVs); intercellular communication; pancreatic stellate cells (PSCs); therapeutic approaches

DOI:  https://doi.org/10.1016/j.molmed.2023.03.002
Biomater Adv. 2023 Apr 19. pii: S2772-9508(23)00149-8. [Epub ahead of print]150 213426

3D bioprinted functional skeletal muscle models have potential applications for studies of muscle wasting in cancer cachexia.

Andrea García-Lizarribar, Aranzazu Villasante, Jose Antonio Lopez-Martin, Marta Flandez, M Carmen Soler-Vázquez, Dolors Serra, Laura Herrero, Ana Sagrera, Alejo Efeyan, Josep Samitier.

  Acquired muscle diseases such as cancer cachexia are responsible for the poor prognosis of many patients suffering from cancer. In vitro models are needed to study the underlying mechanisms of those pathologies. Extrusion bioprinting is an emerging tool to emulate the aligned architecture of fibers while implementing additive manufacturing techniques in tissue engineering. However, designing bioinks that reconcile the rheological needs of bioprinting and the biological requirements of muscle tissue is a challenging matter. Here we formulate a biomaterial with dual crosslinking to modulate the physical properties of bioprinted models. We design 3D bioprinted muscle models that resemble the mechanical properties of native tissue and show improved proliferation and high maturation of differentiated myotubes suggesting that the GelMA-AlgMA-Fibrin biomaterial possesses myogenic properties. The electrical stimulation of the 3D model confirmed the contractile capability of the tissue and enhanced the formation of sarcomeres. Regarding the functionality of the models, they served as platforms to recapitulate skeletal muscle diseases such as muscle wasting produced by cancer cachexia. The genetic expression of 3D models demonstrated a better resemblance to the muscular biopsies of cachectic mouse models. Altogether, this biomaterial is aimed to fabricate manipulable skeletal muscle in vitro models in a non-costly, fast and feasible manner.

Keywords:  Bioprinting; Cachexia; Skeletal muscle; Tissue-engineering

DOI:  https://doi.org/10.1016/j.bioadv.2023.213426
Pancreas. 2022 Nov-Dec 01;51(10):51(10): 1388-1397

Preoperative Rapid Weight Loss as a Prognostic Predictor After Surgical Resection for Pancreatic Cancer.

Makoto Nishikawa, Junji Yamamoto, Takahiro Einama, Mayumi Hoshikawa, Toshimitsu Iwasaki, Akiko Nakazawa, Yasuhiro Takihara, Takazumi Tsunenari, Yoji Kishi.

OBJECTIVE: The aim of the study is to evaluate the influence of cachexia at the time of diagnosis of pancreatic ductal adenocarcinoma (PDAC) on prognosis in patients undergoing surgical resection.
METHODS: Patients with data on preoperative body weight (BW) change followed by surgical resection during 2008-2017 were selected. Large BW loss was defined as weight loss >5% or >2% in individuals with body mass index less than 20 kg/m2 within 1 year preoperatively. Influence of large BW loss, ΔBW defined as preoperative BW change (%) per month, prognostic nutrition index, and indices of sarcopenia.
RESULTS: We evaluated 165 patients with PDAC. Preoperatively, 78 patients were categorized as having large BW loss. ΔBW was ≤ -1.34% per month (rapid) and > -1.34% per month (slow) in 95 and 70 patients, respectively. The median postoperative overall survival of rapid and slow ΔBW groups was 1.4 and 4.4 years, respectively (P < 0.001). In multivariate analyses rapid ΔBW (hazard ratio [HR], 3.88); intraoperative blood loss ≥430 mL (HR, 1.89); tumor size ≥2.9 cm (HR, 1.74); and R1/2 resection (HR, 1.77) were independent predictors of worse survival.
CONCLUSIONS: Preoperative rapid BW loss ≥1.34% per month was an independent predictor of worse survival of patients with PDAC.

DOI: https://doi.org/10.1097/MPA.0000000000002186
Nat Aging. 2023 Jan;3(1): 34-46

Nucleophagy delays aging and preserves germline immortality.

Margarita-Elena Papandreou, Georgios Konstantinidis, Nektarios Tavernarakis.

Marked alterations in nuclear ultrastructure are a universal hallmark of aging, progeroid syndromes and other age-related pathologies. Here we show that autophagy of nuclear proteins is an important determinant of fertility and aging. Impairment of nucleophagy diminishes stress resistance, germline immortality and longevity. We found that the nematode Caenorhabditis elegans nuclear envelope anchor protein, nuclear anchorage protein 1 (ANC-1) and its mammalian ortholog nesprin-2 are cleared out by autophagy and restrict nucleolar size, a biomarker of aging. We further uncovered a germline immortality assurance mechanism, which involves nucleolar degradation at the most proximal oocyte by ANC-1 and key autophagic components. Perturbation of this clearance pathway causes tumor-like structures in C. elegans, and genetic ablation of nesprin-2 causes ovarian carcinomas in mice. Thus, autophagic recycling of nuclear components is a conserved soma longevity and germline immortality mechanism that promotes youthfulness and delays aging under conditions of stress.

DOI: https://doi.org/10.1038/s43587-022-00327-4
Oncotarget. 2023 Apr 24. 14 364-365

The critical immune basis for differential responses to immunotherapy in primary versus metastatic pancreatic cancer.

Brian Diskin, Sarah Schwartz, George Miller.



Keywords:  immunnotherapy; liver metastasis; pancreatic cancer

DOI:  https://doi.org/10.18632/oncotarget.28373
Nat Commun. 2023 Apr 28. 14(1): 2437

Pancreatic cancer is associated with medication changes prior to clinical diagnosis.

Yin Zhang, Qiao-Li Wang, Chen Yuan, Alice A Lee, Ana Babic, Kimmie Ng, Kimberly Perez, Jonathan A Nowak, Jesper Lagergren, Meir J Stampfer, Edward L Giovannucci, Chris Sander, Michael H Rosenthal, Peter Kraft, Brian M Wolpin.

Patients with pancreatic ductal adenocarcinoma (PDAC) commonly develop symptoms and signs in the 1-2 years before diagnosis that can result in changes to medications. We investigate recent medication changes and PDAC diagnosis in Nurses' Health Study (NHS; females) and Health Professionals Follow-up Study (HPFS; males), including up to 148,973 U.S. participants followed for 2,994,057 person-years and 991 incident PDAC cases. Here we show recent initiation of antidiabetic (NHS) or anticoagulant (NHS, HFS) medications and cessation of antihypertensive medications (NHS, HPFS) are associated with pancreatic cancer diagnosis in the next 2 years. Two-year PDAC risk increases as number of relevant medication changes increases (P-trend <1 × 10-5), with participants who recently start antidiabetic and stop antihypertensive medications having multivariable-adjusted hazard ratio of 4.86 (95%CI, 1.74-13.6). These changes are not associated with diagnosis of other digestive system cancers. Recent medication changes should be considered as candidate features in multi-factor risk models for PDAC, though they are not causally implicated in development of PDAC.

DOI: https://doi.org/10.1038/s41467-023-38088-2
Nature. 2023 Apr 26.

An unexpected timer for cell division.

Silke Hauf.



Keywords:  Cancer; Cell biology

DOI:  https://doi.org/10.1038/d41586-023-01355-9
Cell Metab. 2023 Apr 04. pii: S1550-4131(23)00093-1. [Epub ahead of print]

Biological age is increased by stress and restored upon recovery.

Jesse R Poganik, Bohan Zhang, Gurpreet S Baht, Alexander Tyshkovskiy, Amy Deik, Csaba Kerepesi, Sun Hee Yim, Ake T Lu, Amin Haghani, Tong Gong, Anna M Hedman, Ellika Andolf, Göran Pershagen, Catarina Almqvist, Clary B Clish, Steve Horvath, James P White, Vadim N Gladyshev.

  Aging is classically conceptualized as an ever-increasing trajectory of damage accumulation and loss of function, leading to increases in morbidity and mortality. However, recent in vitro studies have raised the possibility of age reversal. Here, we report that biological age is fluid and exhibits rapid changes in both directions. At epigenetic, transcriptomic, and metabolomic levels, we find that the biological age of young mice is increased by heterochronic parabiosis and restored following surgical detachment. We also identify transient changes in biological age during major surgery, pregnancy, and severe COVID-19 in humans and/or mice. Together, these data show that biological age undergoes a rapid increase in response to diverse forms of stress, which is reversed following recovery from stress. Our study uncovers a new layer of aging dynamics that should be considered in future studies. The elevation of biological age by stress may be a quantifiable and actionable target for future interventions.

Keywords:  aging; biological age; dynamics; epigenetic aging clocks; recovery; stress

DOI:  https://doi.org/10.1016/j.cmet.2023.03.015
Elife. 2023 Apr 25. pii: e88080. [Epub ahead of print]12

The effects of caloric restriction on adipose tissue and metabolic health are sex- and age-dependent.

Karla J Suchacki, Benjamin J Thomas, Yoshiko Matsumoto Ikushima, Kuan-Chan Chen, Claire Fyfe, Adriana A S Tavares, Richard J Sulston, Andrea Lovdel, Holly J Woodward, Xuan Han, Domenico Mattiucci, Eleanor J Brain, Carlos Jose Alcaide-Corral, Hiroshi Kobayashi, Gillian Gray, Phillip D Whitfield, Roland H Stimson, Nicholas M Morton, Alexandra M Johnstone, William P Cawthorn.

  Caloric restriction (CR) is a nutritional intervention that reduces the risk of age-related diseases in numerous species, including humans. CR's metabolic effects, including decreased fat mass and improved insulin sensitivity, play an important role in its broader health benefits. However, the extent and basis of sex differences in CR's health benefits are unknown. We found that 30% CR in young (3-month-old) male mice decreased fat mass and improved glucose tolerance and insulin sensitivity, whereas these effects were blunted or absent in young female mice. Females' resistance to fat and weight loss was associated with decreased lipolysis, lower systemic energy expenditure and fatty acid oxidation, and increased postprandial lipogenesis compared to males. Positron emission tomography-computed tomography (PET/CT) with 18F-fluorodeoxyglucose (18F-FDG) showed that peripheral glucose uptake was comparable between sexes. Instead, the sex differences in glucose homeostasis were associated with altered hepatic ceramide content and substrate metabolism: compared to CR males, CR females had lower TCA cycle activity but higher blood ketone concentrations, a marker of hepatic acetyl-CoA content. This suggests that males use hepatic acetyl-CoA for the TCA cycle whereas in females it accumulates, thereby stimulating gluconeogenesis and limiting hypoglycaemia during CR. In aged mice (18-months old), when females are anoestrus, CR decreased fat mass and improved glucose homeostasis to a similar extent in both sexes. Finally, in a cohort of overweight and obese humans CR-induced fat loss was also sex- and age-dependent: younger females (<45 years) resisted fat loss compared to younger males while in older subjects (>45 years) this sex difference was absent. Collectively, these studies identify age-dependent sex differences in the metabolic effects of CR and highlight adipose tissue, the liver and oestrogen as key determinants of CR's metabolic benefits. These findings have important implications for understanding the interplay between diet and health and for maximising the benefits of CR in humans.

Keywords:  human; medicine

DOI:  https://doi.org/10.7554/eLife.88080
Elife. 2023 Apr 25. pii: e82786. [Epub ahead of print]12

Optimal cancer evasion in a dynamic immune microenvironment generates diverse post-escape tumor antigenicity profiles.

Jason T George, Herbert Levine.

  The failure of cancer treatments, including immunotherapy, continues to be a major obstacle in preventing durable remission. This failure often results from tumor evolution, both genotypic and phenotypic, away from sensitive cell states. Here, we propose a mathematical framework for studying the dynamics of adaptive immune evasion that tracks the number of tumor-associated antigens available for immune targeting. We solve for the unique optimal cancer evasion strategy using stochastic dynamic programming and demonstrate that this policy results in increased cancer evasion rates compared to a passive, fixed strategy. Our foundational model relates the likelihood and temporal dynamics of cancer evasion to features of the immune microenvironment, where tumor immunogenicity reflects a balance between cancer adaptation and host recognition. In contrast with a passive strategy, optimally adaptive evaders navigating varying selective environments result in substantially heterogeneous post-escape tumor antigenicity, giving rise to immunogenically hot and cold tumors.

Keywords:  adaptive resistance; cancer biology; cancer immunotherapy; evolutionary biology; immunology; inflammation; none; stochastic dynamic programming

DOI:  https://doi.org/10.7554/eLife.82786
Dev Cell. 2023 Apr 18. pii: S1534-5807(23)00154-5. [Epub ahead of print]

The p-rpS6-zone delineates wounding responses and the healing process.

Nadja Anneliese Ruth Ring, Helene Dworak, Barbara Bachmann, Barbara Schädl, Karla Valdivieso, Tomaz Rozmaric, Patrick Heimel, Ines Fischer, Eirini Klinaki, Aniko Gutasi, Kornelia Schuetzenberger, Gabriele Leinfellner, James Ferguson, Susanne Drechsler, Michael Mildner, Markus Schosserer, Paul Slezak, Oded Meyuhas, Florian Gruber, Johannes Grillari, Heinz Redl, Mikolaj Ogrodnik.

  The spatial boundaries of tissue response to wounding are unknown. Here, we show that in mammals, the ribosomal protein S6 (rpS6) is phosphorylated in response to skin injury, forming a zone of activation surrounding the region of the initial insult. This p-rpS6-zone forms within minutes after wounding and is present until healing is complete. The zone is a robust marker of healing as it encapsulates features of the healing process, including proliferation, growth, cellular senescence, and angiogenesis. A mouse model that is unable to phosphorylate rpS6 shows an initial acceleration of wound closure, but results in impaired healing, identifying p-rpS6 as a modulator but not a driver of healing. Finally, the p-rpS6-zone accurately reports on the status of dermal vasculature and the effectiveness of healing, visually dividing an otherwise homogeneous tissue into regions with distinct properties.

Keywords:  S6; cellular senescence; immediate response; mTOR; p-rpS6; p-rpS6-zone; regeneration; tissue damage; wound healing; wound marker

DOI:  https://doi.org/10.1016/j.devcel.2023.04.001
Nat Aging. 2022 May;2(5): 365-366

The importance of aging in cancer research.

DOI: https://doi.org/10.1038/s43587-022-00231-x
JCI Insight. 2023 Apr 24. pii: e165419. [Epub ahead of print]8(8):

Tumor loss-of-function mutations in STK11/LKB1 induce cachexia.

Puneeth Iyengar, Aakash Y Gandhi, Jorge Granados, Tong Guo, Arun Gupta, Jinhai Yu, Ernesto M Llano, Faya Zhang, Ang Gao, Asha Kandathil, Dorothy Williams, Boning Gao, Luc Girard, Venkat S Malladi, John M Shelton, Bret M Evers, Raquibul Hannan, Chul Ahn, John D Minna, Rodney E Infante.

  Cancer cachexia (CC), a wasting syndrome of muscle and adipose tissue resulting in weight loss, is observed in 50% of patients with solid tumors. Management of CC is limited by the absence of biomarkers and knowledge of molecules that drive its phenotype. To identify such molecules, we injected 54 human non-small cell lung cancer (NSCLC) lines into immunodeficient mice, 17 of which produced an unambiguous phenotype of cachexia or non-cachexia. Whole-exome sequencing revealed that 8 of 10 cachexia lines, but none of the non-cachexia lines, possessed mutations in serine/threonine kinase 11 (STK11/LKB1), a regulator of nutrient sensor AMPK. Silencing of STK11/LKB1 in human NSCLC and murine colorectal carcinoma lines conferred a cachexia phenotype after cell transplantation into immunodeficient (human NSCLC) and immunocompetent (murine colorectal carcinoma) models. This host wasting was associated with an alteration in the immune cell repertoire of the tumor microenvironments that led to increases in local mRNA expression and serum levels of CC-associated cytokines. Mutational analysis of circulating tumor DNA from patients with NSCLC identified 89% concordance between STK11/LKB1 mutations and weight loss at cancer diagnosis. The current data provide evidence that tumor STK11/LKB1 loss of function is a driver of CC, simultaneously serving as a genetic biomarker for this wasting syndrome.

Keywords:  Genetic variation; Lung cancer; Metabolism; Molecular genetics; Oncology

DOI:  https://doi.org/10.1172/jci.insight.165419
bioRxiv. 2023 Apr 12. pii: 2023.04.10.536290. [Epub ahead of print]

Secreted HLA Fc-Fusion Profiles Immunopeptidome in Hypoxic PDAC and Cellular Senescence.

Nicholas J Rettko, Lisa L Kirkemo, James A Wells.

Human leukocyte antigens (HLA) display peptides largely from intracellular proteins on the surface of cells in major histocompatibility complex (MHC)-peptide complexes. These complexes provide a biological window into the cell, and peptides derived from disease-associated antigens can serve as biomarkers and therapeutic targets. Thus, proper identification of peptides and the corresponding presenting HLA allele in disease phenotypes is important for the design and execution of therapeutic strategies using engineered T-cell receptors or antibodies. Yet, current mass spectrometry methods for profiling the immunopeptidome typically require large and complex sample inputs, complicating the study of several disease phenotypes and lowering the confidence of both peptide and allele identification. Here, we describe a novel secreted HLA (sHLA) Fc-fusion construct that allows for simple peptide identification from single HLA alleles in two important disease models: hypoxic pancreatic ductal adenocarcinoma (PDAC) and cellular senescence. We identify hypoxia and senescence-associated peptides that could act as future targets for immunotherapy. More generally, the method streamlines the time between sample preparation and injection from days to hours, yielding allele-restricted target identification in a temporally controlled manner. Overall, this method identified >30,000 unique HLA-associated peptides across two different HLA alleles and seven cell lines. Notably, âˆ¼9,300 of these unique HLA-associated peptides had previously not been identified in the Immune Epitope Database. We believe the sHLA Fc-fusion capture technology will accelerate the study of the immunopeptidome as therapeutic interest in HLA-peptide complexes increases in cancer and beyond.

DOI: https://doi.org/10.1101/2023.04.10.536290
Nat Rev Mol Cell Biol. 2023 Apr 27.

Regulation of phospholipid distribution in the lipid bilayer by flippases and scramblases.

Takaharu Sakuragi, Shigekazu Nagata.

Cellular membranes function as permeability barriers that separate cells from the external environment or partition cells into distinct compartments. These membranes are lipid bilayers composed of glycerophospholipids, sphingolipids and cholesterol, in which proteins are embedded. Glycerophospholipids and sphingolipids freely move laterally, whereas transverse movement between lipid bilayers is limited. Phospholipids are asymmetrically distributed between membrane leaflets but change their location in biological processes, serving as signalling molecules or enzyme activators. Designated proteins - flippases and scramblases - mediate this lipid movement between the bilayers. Flippases mediate the confined localization of specific phospholipids (phosphatidylserine (PtdSer) and phosphatidylethanolamine) to the cytoplasmic leaflet. Scramblases randomly scramble phospholipids between leaflets and facilitate the exposure of PtdSer on the cell surface, which serves as an important signalling molecule and as an 'eat me' signal for phagocytes. Defects in flippases and scramblases cause various human diseases. We herein review the recent research on the structure of flippases and scramblases and their physiological roles. Although still poorly understood, we address the mechanisms by which they translocate phospholipids between lipid bilayers and how defects cause human diseases.

DOI: https://doi.org/10.1038/s41580-023-00604-z
Cancer Res. 2023 Apr 26. pii: CAN-22-1532. [Epub ahead of print]

Proteomic profiling of extracellular matrix components from patient metastases identifies consistently elevated proteins for developing nanobodies that target primary tumors and metastases.

Noor Jailkhani, Karl R Clauser, Howard H Mak, Steffen Rickelt, Chenxi Tian, Charles A Whittaker, Kenneth K Tanabe, Stephen R Purdy, Steven A Carr, Richard O Hynes.

Metastases are hard to detect and treat, and they cause most cancer-related deaths. The relative lack of therapies targeting metastases represents a major unmet clinical need. The extracellular matrix (ECM) forms a major component of the tumor microenvironment in both primary and metastatic tumors, and certain ECM proteins can be selectively and abundantly expressed in tumors. Nanobodies against ECM proteins that show selective abundance in metastases have the potential to be used as vehicles for delivery of imaging and therapeutic cargoes. Here, we describe a strategy to develop phage-display libraries of nanobodies against ECM proteins expressed in human metastases, using as immunogens entire ECM-enriched preparations from triple-negative breast cancer (TNBC) and colorectal carcinoma (CRC) metastases to different organs as immunogens. In parallel, LC-MS/MS-based proteomics were used to define a metastasis-associated ECM signature shared by metastases from TNBC and CRC, and this conserved set of ECM proteins was selectively elevated in other tumors. As proof of concept, selective and high-affinity nanobodies were isolated against an example protein from this signature, Tenascin-C (TNC), known to be abundant in many tumor types and to play a role in metastasis. TNC was abundantly expressed in patient metastases and widely expressed across diverse metastatic sites originating from several primary tumor types. Immuno-PET/CT showed that anti-TNC nanobodies bind TNBC tumors and metastases with excellent specificity. We propose that such generic nanobodies against tumors and metastases are promising cancer-agnostic tools for delivery of therapeutics to tumor and metastatic ECM.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-1532
Nat Aging. 2022 Aug;2(8): 742-755

Nuclear morphology is a deep learning biomarker of cellular senescence.

Indra Heckenbach, Garik V Mkrtchyan, Michael Ben Ezra, Daniela Bakula, Jakob Sture Madsen, Malte Hasle Nielsen, Denise Oró, Brenna Osborne, Anthony J Covarrubias, M Laura Idda, Myriam Gorospe, Laust Mortensen, Eric Verdin, Rudi Westendorp, Morten Scheibye-Knudsen.

Cellular senescence is an important factor in aging and many age-related diseases, but understanding its role in health is challenging due to the lack of exclusive or universal markers. Using neural networks, we predict senescence from the nuclear morphology of human fibroblasts with up to 95% accuracy, and investigate murine astrocytes, murine neurons, and fibroblasts with premature aging in culture. After generalizing our approach, the predictor recognizes higher rates of senescence in p21-positive and ethynyl-2'-deoxyuridine (EdU)-negative nuclei in tissues and shows an increasing rate of senescent cells with age in H&E-stained murine liver tissue and human dermal biopsies. Evaluating medical records reveals that higher rates of senescent cells correspond to decreased rates of malignant neoplasms and increased rates of osteoporosis, osteoarthritis, hypertension and cerebral infarction. In sum, we show that morphological alterations of the nucleus can serve as a deep learning predictor of senescence that is applicable across tissues and species and is associated with health outcomes in humans.

DOI: https://doi.org/10.1038/s43587-022-00263-3
J Cell Biol. 2023 Jul 03. pii: e202210078. [Epub ahead of print]222(7):

Quantitative analysis of autophagy reveals the role of ATG9 and ATG2 in autophagosome formation.

David G Broadbent, Carlo Barnaba, Gloria I Perez, Jens C Schmidt.

Autophagy is a catabolic pathway required for the recycling of cytoplasmic materials. To define the mechanisms underlying autophagy it is critical to quantitatively characterize the dynamic behavior of autophagy factors in living cells. Using a panel of cell lines expressing HaloTagged autophagy factors from their endogenous loci, we analyzed the abundance, single-molecule dynamics, and autophagosome association kinetics of autophagy proteins involved in autophagosome biogenesis. We demonstrate that autophagosome formation is inefficient and ATG2-mediated tethering to donor membranes is a key commitment step in autophagosome formation. Furthermore, our observations support the model that phagophores are initiated by the accumulation of autophagy factors on mobile ATG9 vesicles, and that the ULK1 complex and PI3-kinase form a positive feedback loop required for autophagosome formation. Finally, we demonstrate that the duration of autophagosome biogenesis is ∼110 s. In total, our work provides quantitative insight into autophagosome biogenesis and establishes an experimental framework to analyze autophagy in human cells.

DOI: https://doi.org/10.1083/jcb.202210078
FEBS J. 2023 Apr 27.

Phosphatidic acid: from biophysical properties to diverse functions.

Hejiang Zhou, Yanwu Huo, Na Yang, Taotao Wei.

  Phosphatidic acid (PA), the simplest phospholipid, acts as a key metabolic intermediate and second messenger that impacts diverse cellular and physiological processes across species ranging from microbes to plants and mammals. The cellular levels of PA dynamically change in response to stimuli, and multiple enzymatic reactions can mediate its production and degradation. PA acts as a signaling molecule and regulates various cellular processes via its effects on membrane tethering, enzymatic activities of target proteins, and vesicular trafficking. Due to its unique physicochemical properties compared with other phospholipids, PA has emerged as a class of new lipid mediators influencing membrane structure, dynamics, protein interactions. This review will summarize the biosynthesis, dynamics, and cellular functions and properties of PA.

Keywords:  biosynthesis; dynamics; lipid property; phosphatidic acid; signal transduction

DOI:  https://doi.org/10.1111/febs.16809
Cancer Inform. 2023 ;22 11769351231165181

Trends in Subcutaneous Tumour Height and Impact on Measurement Accuracy.

Daniel Brough, Hope Amos, Karl Turley, Jake Murkin.

  Tumour volume is typically calculated using only length and width measurements, using width as a proxy for height in a 1:1 ratio. When tracking tumour growth over time, important morphological information and measurement accuracy is lost by ignoring height, which we show is a unique variable. Lengths, widths, and heights of 9522 subcutaneous tumours in mice were measured using 3D and thermal imaging. The average height:width ratio was found to be 1:3 proving that using width as a proxy for height overestimates tumour volume. Comparing volumes calculated with and without tumour height to the true volumes of excised tumours indeed showed that using the volume formula including height produced volumes 36X more accurate (based off of percentage difference). Monitoring the height:width relationship (prominence) across tumour growth curves indicated that prominence varied, and that height could change independent of width. Twelve cell lines were investigated individually; the scale of tumour prominence was cell line-dependent with relatively less prominent tumours (MC38, BL2, LL/2) and more prominent tumours (RENCA, HCT116) detected. Prominence trends across the growth cycle were also dependent on cell line; prominence was correlated with tumour growth in some cell lines (4T1, CT26, LNCaP), but not others (MC38, TC-1, LL/2). When pooled, invasive cell lines produced tumours that were significantly less prominent at volumes >1200 mm3 compared to non-invasive cell lines (P < .001). Modelling was used to show the impact of the increased accuracy gained by including height in volume calculations on several efficacy study outcomes. Variations in measurement accuracy contribute to experimental variation and irreproducibility of data, therefore we strongly advise researchers to measure height to improve accuracy in tumour studies.

Keywords:  Tumour biology; accuracy; imaging; in silico; in vivo; metastasis; preclinical oncology; volume calculation

DOI:  https://doi.org/10.1177/11769351231165181