bims-cagime 2023-02-26 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2023‒02‒26
twenty-six papers selected by
Kıvanç Görgülü
Technical University of Munich

Exercise-activated hepatic autophagy via the FN1-α5β1 integrin pathway drives metabolic benefits of exercise.
Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia.
Oncogenic Kras G12D specific non-covalent inhibitor reprograms tumor microenvironment to prevent and reverse early pre-neoplastic pancreatic lesions and in combination with immunotherapy regresses advanced PDAC in a CD8 + T cells dependent manner.
Bicarbonate transport as regulator of anti-tumour immunity in pancreatic cancer.
Metabolic programming and immune suppression in the tumor microenvironment.
Phase Ib and Expansion Study of Gemcitabine, Nab-Paclitaxel, and Ficlatuzumab in Patients With Metastatic Pancreatic Cancer.
Cancer-associated cachexia - understanding the tumour macroenvironment and microenvironment to improve management.
The LC3B FRET biosensor monitors the modes of action of ATG4B during autophagy in living cells.
Microbiota-derived 3-IAA influences chemotherapy efficacy in pancreatic cancer.
Local senolysis in aged mice only partially replicates the benefits of systemic senolysis.
Engine shutdown: migrastatic strategies and prevention of metastases.
Spatial profiling technologies illuminate the tumor microenvironment.
Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell-secreted Cytokines.
Exploiting the intrinsic misfolding propensity of the KRAS oncoprotein.
LLPS vs. LLCPS: analogies and differences.
Local irradiation of patient-derived tumors in immunodeficient mice.
Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss.
Genome-wide CRISPR/Cas9 screens reveal shared and cell-specific mechanisms of resistance to SHP2 inhibition.
Real-World Data Validation of NAPOLI-1 Nomogram for the Prediction of Overall Survival in Metastatic Pancreatic Cancer.
An organelle-specific photoactivation and dual-isotope labeling strategy reveals phosphatidylethanolamine metabolic flux.
Biomolecular actuators for genetically selective acoustic manipulation of cells.
Lipidomic profiling of rat hepatic stellate cells during activation reveals a two-stage process accompanied by increased levels of lysosomal lipids.
No survival benefit with suboptimal CA19-9 response: defining effective neoadjuvant chemotherapy in resectable or borderline resectable pancreatic cancer.
SMITH: Spatially Constrained Stochastic Model for Simulation of Intra-Tumour Heterogeneity.
Pericyte stem cells induce Ly6G+ cell accumulation and immunotherapy resistance in pancreatic cancer.
Cell class-specific electric field entrainment of neural activity.

Cell Metab. 2023 Feb 14. pii: S1550-4131(23)00011-6. [Epub ahead of print]

Exercise-activated hepatic autophagy via the FN1-α5β1 integrin pathway drives metabolic benefits of exercise.

Kenta Kuramoto, Huijia Liang, Jung-Hwa Hong, Congcong He.

  How exercise elicits systemic metabolic benefits in both muscles and non-contractile tissues is unclear. Autophagy is a stress-induced lysosomal degradation pathway that mediates protein and organelle turnover and metabolic adaptation. Exercise activates autophagy in not only contracting muscles but also non-contractile tissues including the liver. However, the role and mechanism of exercise-activated autophagy in non-contractile tissues remain mysterious. Here, we show that hepatic autophagy activation is essential for exercise-induced metabolic benefits. Plasma or serum from exercised mice is sufficient to activate autophagy in cells. By proteomic studies, we identify fibronectin (FN1), which was previously considered as an extracellular matrix protein, as an exercise-induced, muscle-secreted, autophagy-inducing circulating factor. Muscle-secreted FN1 mediates exercise-induced hepatic autophagy and systemic insulin sensitization via the hepatic receptor α5β1 integrin and the downstream IKKα/β-JNK1-BECN1 pathway. Thus, we demonstrate that hepatic autophagy activation drives exercise-induced metabolic benefits against diabetes via muscle-secreted soluble FN1 and hepatic α5β1 integrin signaling.

Keywords:  ATG7; BECN1; autophagy; exercise; fibronectin; insulin sensitivity; integrin; liver; muscle

DOI:  https://doi.org/10.1016/j.cmet.2023.01.011
bioRxiv. 2023 Feb 18. pii: 2023.02.17.528937. [Epub ahead of print]

Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia.

Miriam Ferrer, Nicholas Mourikis, Emma E Davidson, Sam O Kleeman, Marta Zaccaria, Jill Habel, Rachel Rubino, Thomas R Flint, Claire M Connell, Michael Lukey, Eileen P White, Anthony P Coll, Ashok R Venkitaraman, Tobias Janowitz.

The dependency of cancer cells on glucose can be targeted with high-fat low-carbohydrate ketogenic diet (KD). However, hepatic ketogenesis is suppressed in IL-6 producing cancers, which prevents the utilization of this nutrient source as energy for the organism. In two IL-6 associated murine models of cancer cachexia we describe delayed tumor growth but accelerated onset of cancer cachexia and shortened survival when mice are fed KD. Mechanistically, we find this uncoupling is a consequence of the biochemical interaction of two simultaneously occurring NADPH-dependent pathways. Within the tumor, increased production of lipid peroxidation products (LPPs) and, consequently, saturation of the glutathione (GSH) system leads to ferroptotic death of cancer cells. Systemically, redox imbalance and NADPH depletion impairs the biosynthesis of corticosterone, the main regulator of metabolic stress, in the adrenal glands. Administration of dexamethasone, a potent glucocorticoid, improves food intake, normalizes glucose homeostasis and utilization of nutritional substrates, delays onset of cancer cachexia and extends survival of tumor-bearing mice fed KD, while preserving reduced tumor growth. Our study highlights that the outcome of systemic interventions cannot necessarily be extrapolated from the effect on the tumor alone, but that they have to be investigated for anti-cancer and host effects. These findings may be relevant to clinical research efforts that investigate nutritional interventions such as KD in patients with cancer.

DOI: https://doi.org/10.1101/2023.02.17.528937
bioRxiv. 2023 Feb 18. pii: 2023.02.15.528757. [Epub ahead of print]

Oncogenic Kras G12D specific non-covalent inhibitor reprograms tumor microenvironment to prevent and reverse early pre-neoplastic pancreatic lesions and in combination with immunotherapy regresses advanced PDAC in a CD8 + T cells dependent manner.

Krishnan K Mahadevan, Kathleen M McAndrews, Valerie S LeBleu, Sujuan Yang, Hengyu Lyu, Bingrui Li, Amari M Sockwell, Michelle L Kirtley, Sami J Morse, Barbara A Moreno Diaz, Michael P Kim, Ningping Feng, Anastasia M Lopez, Paola A Guerrero, Hikaru Sugimoto, Kent A Arian, Haoqiang Ying, Yasaman Barekatain, Patience J Kelly, Anirban Maitra, Timothy P Heffernan, Raghu Kalluri.

Pancreatic ductal adenocarcinoma (PDAC) is associated with mutations in Kras, a known oncogenic driver of PDAC; and the KRAS G12D mutation is present in nearly half of PDAC patients. Recently, a non-covalent small molecule inhibitor (MRTX1133) was identified with specificity to the Kras G12D mutant protein. Here we explore the impact of Kras G12D inhibition by MRTX1133 on advanced PDAC and its influence on the tumor microenvironment. Employing different orthotopic xenograft and syngeneic tumor models, eight different PDXs, and two different autochthonous genetic models, we demonstrate that MRTX1133 reverses early PDAC growth, increases intratumoral CD8 + effector T cells, decreases myeloid infiltration, and reprograms cancer associated fibroblasts. Autochthonous genetic mouse models treated with MRTX1133 leads to regression of both established PanINs and advanced PDAC. Regression of advanced PDAC requires CD8 + T cells and immune checkpoint blockade therapy (iCBT) synergizes with MRTX1133 to eradicate PDAC and prolong overall survival. Mechanistically, inhibition of mutant Kras in advanced PDAC and human patient derived organoids (PDOs) induces Fas expression in cancer cells and facilitates CD8 + T cell mediated death. These results demonstrate the efficacy of MRTX1133 in different mouse models of PDAC associated with reprogramming of stromal fibroblasts and a dependency on CD8 + T cell mediated tumor clearance. Collectively, this study provides a rationale for a synergistic combination of MRTX1133 with iCBT in clinical trials.

DOI: https://doi.org/10.1101/2023.02.15.528757
Mol Oncol. 2023 Feb 21.

Bicarbonate transport as regulator of anti-tumour immunity in pancreatic cancer.

Emily J Kay, Sara Zanivan.

  Bicarbonate transport is a pre-existing mechanism of pH regulation in pancreatic ductal cells. In a recent study, Cappellesso et al. demonstrated that pancreatic ductal adenocarcinoma metabolic rewiring creates an acidic environment, enhanced by bicarbonate import into cancer cells via SLC4A4. This acidity favours pro-tumourigenic immunosuppression. Targeting SLC4A4 neutralises environmental pH and restores anti-tumour immunity, sensitising tumours to immune checkpoint blockade.

Keywords:  Acidosis; Cancer; Immunotherapy; Metabolism; T-cells; Tumour microenvironment

DOI:  https://doi.org/10.1002/1878-0261.13400
Cancer Cell. 2023 Feb 09. pii: S1535-6108(23)00009-0. [Epub ahead of print]

Metabolic programming and immune suppression in the tumor microenvironment.

Emily N Arner, Jeffrey C Rathmell.

  Increased glucose metabolism and uptake are characteristic of many tumors and used clinically to diagnose and monitor cancer progression. In addition to cancer cells, the tumor microenvironment (TME) encompasses a wide range of stromal, innate, and adaptive immune cells. Cooperation and competition between these cell populations supports tumor proliferation, progression, metastasis, and immune evasion. Cellular heterogeneity leads to metabolic heterogeneity because metabolic programs within the tumor are dependent not only on the TME cellular composition but also on cell states, location, and nutrient availability. In addition to driving metabolic plasticity of cancer cells, altered nutrients and signals in the TME can lead to metabolic immune suppression of effector cells and promote regulatory immune cells. Here we discuss how metabolic programming of cells within the TME promotes tumor proliferation, progression, and metastasis. We also discuss how targeting metabolic heterogeneity may offer therapeutic opportunities to overcome immune suppression and augment immunotherapies.

Keywords:  immune; metabolism; metastasis; plasticity; tumor microenvironment

DOI:  https://doi.org/10.1016/j.ccell.2023.01.009
Oncologist. 2023 Feb 18. pii: oyad002. [Epub ahead of print]

Phase Ib and Expansion Study of Gemcitabine, Nab-Paclitaxel, and Ficlatuzumab in Patients With Metastatic Pancreatic Cancer.

Kimberly Perez, Anna M Chiarella, James M Cleary, Nora Horick, Colin Weekes, Thomas Abrams, Lawrence Blaszkowsky, Peter Enzinger, Marios Giannakis, Lipika Goyal, Jeffrey A Meyerhardt, Douglas Rubinson, Matthew B Yurgelun, Wolfram Goessling, Bruce J Giantonio, Lauren Brais, Victoria Germon, Danielle Stonely, Srivatsan Raghavan, Basil Bakir, Koushik Das, Jason R Pitarresi, Andrew J Aguirre, Michael Needle, Anil K Rustgi, Brian M Wolpin.

  BACKGROUND: In preclinical pancreatic ductal adenocarcinoma (PDAC) models, inhibition of hepatocyte growth factor (HGF) signaling using ficlatuzumab, a recombinant humanized anti-HGF antibody, and gemcitabine reduced tumor burden.METHODS: Patients with previously untreated metastatic PDAC enrolled in a phase Ib dose escalation study with 3 + 3 design of 2 dose cohorts of ficlatuzumab 10 and 20 mg/kg administered intravenously every other week with gemcitabine 1000 mg/m2 and albumin-bound paclitaxel 125 mg/m2 given 3 weeks on and 1 week off. This was followed by an expansion phase at the maximally tolerated dose of the combination.
RESULTS: Twenty-six patients (sex, 12 male:14 female; median age, 68 years [range, 49-83 years]) were enrolled, 22 patients were evaluable. No dose-limiting toxicities were identified (N = 7 pts) and ficlatuzumab at 20 mg/kg was chosen as the maximum tolerated dose. Among the 21 patients treated at the MTD, best response by RECISTv1.1: 6 (29%) partial response, 12 (57%) stable disease, 1 (5%) progressive disease, and 2 (9%) not evaluable. Median progression-free survival and overall survival times were 11.0 months (95% CI, 7.6-11.4 months) and 16.2 months (95% CI, 9.1 months to not reached), respectively. Toxicities attributed to ficlatuzumab included hypoalbuminemia (grade 3, 16%; any grade, 52%) and edema (grade 3, 8%; any grade, 48%). Immunohistochemistry for c-Met pathway activation demonstrated higher tumor cell p-Met levels in patients who experienced response to therapy.
CONCLUSION: In this phase Ib trial, ficlatuzumab, gemcitabine, and albumin-bound paclitaxel were associated with durable treatment responses and increased rates of hypoalbuminemia and edema.

Keywords:   nab-paclitaxel; ficlatuzumab; gemcitabine; metastatic pancreatic cancer; phase Ib clinical trial

DOI:  https://doi.org/10.1093/oncolo/oyad002
Nat Rev Clin Oncol. 2023 Feb 20.

Cancer-associated cachexia - understanding the tumour macroenvironment and microenvironment to improve management.

Josep M Argilés, Francisco J López-Soriano, Britta Stemmler, Silvia Busquets.

Cachexia is a devastating, multifactorial and often irreversible systemic syndrome characterized by substantial weight loss (mainly of skeletal muscle and adipose tissue) that occurs in around 50-80% of patients with cancer. Although this condition mainly affects skeletal muscle (which accounts for approximately 40% of total body weight), cachexia is a multi-organ syndrome that also involves white and brown adipose tissue, and organs including the bones, brain, liver, gut and heart. Notably, cachexia accounts for up to 20% of cancer-related deaths. Cancer-associated cachexia is invariably associated with systemic inflammation, anorexia and increased energy expenditure. Understanding these mechanisms is essential, and the progress achieved in this area over the past decade could help to develop new therapeutic approaches. In this Review, we examine the currently available evidence on the roles of both the tumour macroenvironment and microenvironment in cancer-associated cachexia, and provide an overview of the novel therapeutic strategies developed to manage this syndrome.

DOI: https://doi.org/10.1038/s41571-023-00734-5
Autophagy. 2023 Feb 22. 1-21

The LC3B FRET biosensor monitors the modes of action of ATG4B during autophagy in living cells.

Elif Begüm Gökerküçük, Angélique Cheron, Marc Tramier, Giulia Bertolin.

  Although several mechanisms of macroautophagy/autophagy have been dissected in the last decade, following this pathway in real time remains challenging. Among the early events leading to its activation, the ATG4B protease primes the key autophagy player MAP1LC3B/LC3B. Given the lack of reporters to follow this event in living cells, we developed a Förster's resonance energy transfer (FRET) biosensor responding to the priming of LC3B by ATG4B. The biosensor was generated by flanking LC3B within a pH-resistant donor-acceptor FRET pair, Aquamarine-tdLanYFP. We here showed that the biosensor has a dual readout. First, FRET indicates the priming of LC3B by ATG4B and the resolution of the FRET image makes it possible to characterize the spatial heterogeneity of the priming activity. Second, quantifying the number of Aquamarine-LC3B puncta determines the degree of autophagy activation. We then showed that there are pools of unprimed LC3B upon ATG4B downregulation, and the priming of the biosensor is abolished in ATG4B knockout cells. The lack of priming can be rescued with the wild-type ATG4B or with the partially active W142A mutant, but not with the catalytically dead C74S mutant. Moreover, we screened for commercially-available ATG4B inhibitors, and illustrated their differential mode of action by implementing a spatially-resolved, broad-to-sensitive analysis pipeline combining FRET and the quantification of autophagic puncta. Finally, we uncovered the CDK1-dependent regulation of the ATG4B-LC3B axis at mitosis. Therefore, the LC3B FRET biosensor paves the way for a highly-quantitative monitoring of the ATG4B activity in living cells and in real time, with unprecedented spatiotemporal resolution.Abbreviations: Aqua: aquamarine; ATG: autophagy related; AURKA: aurora kinase A; BafA1: bafilomycin A1; CDK1: cyclin dependent kinase 1; DKO: double knockout; FLIM: fluorescence lifetime imaging microscopy; FP: fluorescence protein; FRET: Förster's resonance energy transfer; GABARAP: GABA type A receptor-associated protein; HBSS: Hanks' balanced salt solution; KO: knockout; LAMP2: lysosomal associated membrane protein 2; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NSC: NSC 185058; PE: phosphatidylethanolamine; SKO: single knockout; TKO: triple knockout; ULK1: unc-51 like autophagy activating kinase 1; WT: wild-type; ZPCK: Z-L-phe chloromethyl ketone.

Keywords:  ATG4B; FRET-FLIM; LC3B; autophagy; biosensor

DOI:  https://doi.org/10.1080/15548627.2023.2179845
Nature. 2023 Feb 22.

Microbiota-derived 3-IAA influences chemotherapy efficacy in pancreatic cancer.

Joseph Tintelnot, Yang Xu, Till R Lesker, Martin Schönlein, Leonie Konczalla, Anastasios D Giannou, Penelope Pelczar, Dominik Kylies, Victor G Puelles, Agata A Bielecka, Manuela Peschka, Filippo Cortesi, Kristoffer Riecken, Maximilian Jung, Lena Amend, Tobias S Bröring, Marija Trajkovic-Arsic, Jens T Siveke, Thomas Renné, Danmei Zhang, Stefan Boeck, Till Strowig, Faik G Uzunoglu, Cenap Güngör, Alexander Stein, Jakob R Izbicki, Carsten Bokemeyer, Marianne Sinn, Alec C Kimmelman, Samuel Huber, Nicola Gagliani.

Pancreatic ductal adenocarcinoma (PDAC) is expected to be the second most deadly cancer by 2040, owing to the high incidence of metastatic disease and limited responses to treatment1,2. Less than half of all patients respond to the primary treatment for PDAC, chemotherapy3,4, and genetic alterations alone cannot explain this5. Diet is an environmental factor that can influence the response to therapies, but its role in PDAC is unclear. Here, using shotgun metagenomic sequencing and metabolomic screening, we show that the microbiota-derived tryptophan metabolite indole-3-acetic acid (3-IAA) is enriched in patients who respond to treatment. Faecal microbiota transplantation, short-term dietary manipulation of tryptophan and oral 3-IAA administration increase the efficacy of chemotherapy in humanized gnotobiotic mouse models of PDAC. Using a combination of loss- and gain-of-function experiments, we show that the efficacy of 3-IAA and chemotherapy is licensed by neutrophil-derived myeloperoxidase. Myeloperoxidase oxidizes 3-IAA, which in combination with chemotherapy induces a downregulation of the reactive oxygen species (ROS)-degrading enzymes glutathione peroxidase 3 and glutathione peroxidase 7. All of this results in the accumulation of ROS and the downregulation of autophagy in cancer cells, which compromises their metabolic fitness and, ultimately, their proliferation. In humans, we observed a significant correlation between the levels of 3-IAA and the efficacy of therapy in two independent PDAC cohorts. In summary, we identify a microbiota-derived metabolite that has clinical implications in the treatment of PDAC, and provide a motivation for considering nutritional interventions during the treatment of patients with cancer.

DOI: https://doi.org/10.1038/s41586-023-05728-y
J Clin Invest. 2023 Feb 21. pii: e162519. [Epub ahead of print]

Local senolysis in aged mice only partially replicates the benefits of systemic senolysis.

Joshua N Farr, Dominik Saul, Madison L Doolittle, Japneet Kaur, Jennifer L Rowsey, Stephanie J Vos, Mitchell N Froemming, Anthony B Lagnado, Yi Zhu, Megan M Weivoda, Yuji Ikeno, Robert J Pignolo, Laura J Niedernhofer, Paul D Robbins, Diana Jurk, João F Passos, Nathan K LeBrasseur, Tamara Tchkonia, James L Kirkland, David G Monroe, Sundeep Khosla.

  Clearance of senescent cells (SnCs) can prevent several age-related pathologies, including bone loss. However, the local versus systemic roles of SnCs in mediating tissue dysfunction remain unclear. Thus, we developed a mouse model (p16-LOX-ATTAC) that allows for inducible SnC elimination (senolysis) in a cell-specific manner and compared the effects of local versus systemic senolysis during aging using bone as a prototype tissue. Specific removal of Sn osteocytes prevented age-related bone loss at the spine, but not the femur, by improving bone formation without affecting osteoclasts or marrow adipocytes. By contrast, systemic senolysis prevented bone loss at the spine and femur and not only improved bone formation, but also reduced osteoclasts and marrow adipocytes. Transplantation of SnCs into the peritoneal cavity of young mice caused bone loss and also induced senescence in distant host osteocytes. Collectively, our findings provide the first proof-of-concept evidence that local senolysis has health benefits in the context of aging, but importantly, local senolysis only partially replicates the benefits of systemic senolysis. Further, we establish that SnCs, through their SASP, lead to senescence in distant cells. Therefore, our study indicates that optimizing senolytic drugs may require systemic instead of local SnC targeting to extend healthy aging.

Keywords:  Aging; Bone Biology; Bone disease; Cellular senescence; Osteoporosis

DOI:  https://doi.org/10.1172/JCI162519
Trends Cancer. 2023 Feb 15. pii: S2405-8033(23)00001-8. [Epub ahead of print]

Engine shutdown: migrastatic strategies and prevention of metastases.

Martina Raudenská, Kateřina Petrláková, Tamara Juriňáková, Jindřiška Leischner Fialová, Michaela Fojtů, Milan Jakubek, Daniel Rösel, Jan Brábek, Michal Masařík.

  Most cancer-related deaths among patients with solid tumors are caused by metastases. Migrastatic strategies represent a unique therapeutic approach to prevent all forms of cancer cell migration and invasion. Because the migration machinery has been shown to promote metastatic dissemination, successful migrastatic therapy may reduce the need for high-dose cytotoxic therapies that are currently used to prevent the risk of metastatic dissemination. In this review we focus on anti-invasive and antimetastatic strategies that hold promise for the treatment of solid tumors. The best targets for migrastatic therapy would be those that are required by all forms of motility, such as ATP availability, mitochondrial metabolism, and cytoskeletal dynamics and cell contractility.

Keywords:  cancer; cancer therapy; cell migration; metastasis; migrastatic therapy; mitochondria-targeting therapy; nanocarriers

DOI:  https://doi.org/10.1016/j.trecan.2023.01.001
Cancer Cell. 2023 Feb 13. pii: S1535-6108(23)00010-7. [Epub ahead of print]

Spatial profiling technologies illuminate the tumor microenvironment.

Ofer Elhanani, Raz Ben-Uri, Leeat Keren.

  The tumor microenvironment (TME) is composed of many different cellular and acellular components that together drive tumor growth, invasion, metastasis, and response to therapies. Increasing realization of the significance of the TME in cancer biology has shifted cancer research from a cancer-centric model to one that considers the TME as a whole. Recent technological advancements in spatial profiling methodologies provide a systematic view and illuminate the physical localization of the components of the TME. In this review, we provide an overview of major spatial profiling technologies. We present the types of information that can be extracted from these data and describe their applications, findings and challenges in cancer research. Finally, we provide a future perspective of how spatial profiling could be integrated into cancer research to improve patient diagnosis, prognosis, stratification to treatment and development of novel therapeutics.

Keywords:  multiplexed imaging; spatial profiling; spatial transcriptomics; tumor microenvironment

DOI:  https://doi.org/10.1016/j.ccell.2023.01.010
Cancer Discov. 2023 Feb 22. pii: CD-22-1125. [Epub ahead of print]

Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell-secreted Cytokines.

Yoshinaga Ito, Deng Pan, Wubing Zhang, Xixi Zhang, Tiffany Y Juan, Jason W Pyrdol, Oleksandr Kyrysyuk, John G Doench, X Shirley Liu, Kai W Wucherpfennig.

Tumor heterogeneity is a major barrier to cancer therapy, including immunotherapy. Activated T cells can efficiently kill tumor cells following recognition of MHC class I (MHC-I) bound peptides, but this selection pressure favors outgrowth of MHC-I deficient tumor cells. We performed a genome-scale screen to discover alternative pathways for T cell-mediated killing of MHC-I deficient tumor cells. Autophagy and TNF signaling emerged as top pathways, and inactivation of Rnf31 (TNF signaling) and Atg5 (autophagy) sensitized MHC-I deficient tumor cells to apoptosis by T cell-derived cytokines. Mechanistic studies demonstrated that inhibition of autophagy amplified pro-apoptotic effects of cytokines in tumor cells. Antigens from apoptotic MHC-I deficient tumor cells were efficiently cross-presented by dendritic cells, resulting in heightened tumor infiltration by IFNa and TNFg-producing T cells. Tumors with a substantial population of MHC-I deficient cancer cells could be controlled by T cells when both pathways were targeted using genetic or pharmacological approaches.

DOI: https://doi.org/10.1158/2159-8290.CD-22-1125
Proc Natl Acad Sci U S A. 2023 Feb 28. 120(9): e2214921120

Exploiting the intrinsic misfolding propensity of the KRAS oncoprotein.

Kobe Janssen, Filip Claes, Dido Van de Velde, Vanessa L Wehbi, Bert Houben, Yulia Lampi, Mieke Nys, Laleh Khodaparast, Ladan Khodaparast, Nikolaos Louros, Rob van der Kant, Joffre Verniers, Teresa Garcia, Meine Ramakers, Katerina Konstantoulea, Katerina Maragkou, Ramon Duran-Romaña, Mónica Musteanu, Mariano Barbacid, Bernard Scorneaux, Els Beirnaert, Joost Schymkowitz, Frederic Rousseau.

  Mutant KRAS is a major driver of oncogenesis in a multitude of cancers but remains a challenging target for classical small molecule drugs, motivating the exploration of alternative approaches. Here, we show that aggregation-prone regions (APRs) in the primary sequence of the oncoprotein constitute intrinsic vulnerabilities that can be exploited to misfold KRAS into protein aggregates. Conveniently, this propensity that is present in wild-type KRAS is increased in the common oncogenic mutations at positions 12 and 13. We show that synthetic peptides (Pept-ins™) derived from two distinct KRAS APRs could induce the misfolding and subsequent loss of function of oncogenic KRAS, both of recombinantly produced protein in solution, during cell-free translation and in cancer cells. The Pept-ins exerted antiproliferative activity against a range of mutant KRAS cell lines and abrogated tumor growth in a syngeneic lung adenocarcinoma mouse model driven by mutant KRAS G12V. These findings provide proof-of-concept that the intrinsic misfolding propensity of the KRAS oncoprotein can be exploited to cause its functional inactivation.

Keywords:  KRAS; oncogene; peptide; protein aggregation; protein folding

DOI:  https://doi.org/10.1073/pnas.2214921120
Soft Matter. 2023 Feb 20.

LLPS vs. LLCPS: analogies and differences.

Paride Azzari, Raffaele Mezzenga.

We compare the process of Liquid-Liquid Phase Separation (LLPS) of flexible macromolecular solutions, with the Liquid-Liquid Crystalline Phase Separation (LLCPS) of semiflexible polymers and rigid filamentous colloids, which involves the formation of a liquid phase that possesses a directional alignment. Although the observed phase separation follows a similar dynamic path, namely nucleation and growth or spinodal decomposition separating two phases of dilute and concentrated compositions, the underlying physics that defines the theoretical framework of LLCPS is completely different from the one of LLPS. We review the main theories that describe the phase separation processes and relying on thermodynamics and dynamical arguments, we highlight the differences and analogies between these two phase separation phenomena, attempting to clarify the inner mechanisms that regulate those two processes. A particular focus is given to metastable phases, as these intermediate states represent a key element in understanding how phase separation works.

DOI: https://doi.org/10.1039/d2sm01455f
STAR Protoc. 2023 Feb 07. pii: S2666-1667(23)00056-4. [Epub ahead of print]4(1): 102098

Local irradiation of patient-derived tumors in immunodeficient mice.

Amber P van der Zalm, Sanne Bootsma, Hans M Rodermond, Arlene L Oei, Maarten F Bijlsma.

  Severe combined immunodeficient mice are typically used for xenografting experiments and show reliable tumor engraftment; however, their Prkdscid mutation renders them highly sensitive to irradiation. Here, we describe a protocol that allows safe local irradiation of tumor xenografts in immunodeficient mice. We detail the steps for the establishment and handling of patient-derived cancer cultures, subcutaneous injection of cancer cells on the mouse hind limb, localized irradiation in mice, tumor monitoring, and tumor characterization via histological and immunohistochemical assessment. For complete details on the use and execution of this protocol, please refer to Dings et al. (2022).1.

Keywords:  Cancer; Cell Culture; Health Sciences; Microscopy; Model Organisms

DOI:  https://doi.org/10.1016/j.xpro.2023.102098
JCI Insight. 2023 Feb 23. pii: e162835. [Epub ahead of print]

Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss.

Jacqueline A Larouche, Emily C Wallace, Bonnie D Spence, Eric Buras, Carlos A Aguilar.

  Volumetric muscle loss (VML) is an acute trauma that results in persistent inflammation, supplantation of muscle tissue with fibrotic scarring, and decreased muscle function. The cell types, nature of cellular communication, and tissue locations that drive the aberrant VML response have remained elusive. Herein, we used spatial transcriptomics on a mouse model of VML and observed VML engenders a unique spatial pro-fibrotic pattern driven by crosstalk between fibrotic and inflammatory macrophages and mesenchymal derived cells. The dysregulated response impinged on muscle stem cell mediated repair, and targeting this circuit resulted in increased regeneration and reductions in inflammation and fibrosis. Collectively, these results enhance our understanding of the cellular crosstalk that drives aberrant regeneration and provides further insight into possible avenues for fibrotic therapy exploration.

Keywords:  Adult stem cells; Fibrosis; Muscle Biology; Skeletal muscle; Stem cells

DOI:  https://doi.org/10.1172/jci.insight.162835
J Exp Med. 2023 May 01. pii: e20221563. [Epub ahead of print]220(5):

Genome-wide CRISPR/Cas9 screens reveal shared and cell-specific mechanisms of resistance to SHP2 inhibition.

Wei Wei, Mitchell J Geer, Xinyi Guo, Igor Dolgalev, Neville E Sanjana, Benjamin G Neel.

SHP2 (PTPN11) acts upstream of SOS1/2 to enable RAS activation. Allosteric SHP2 inhibitors (SHP2i) in the clinic prevent SHP2 activation, block proliferation of RTK- or cycling RAS mutant-driven cancers, and overcome "adaptive resistance." To identify SHP2i resistance mechanisms, we performed genome-wide CRISPR/Cas9 knockout screens on two SHP2i-sensitive cell lines, recovering genes expected to cause resistance (NF1, PTEN, CDKN1B, LZTR1, and RASA2) and novel targets (INPPL1, MAP4K5, epigenetic modifiers). We screened 14 additional lines with a focused CRISPR library targeting common "hits" from the genome-wide screens. LZTR1 deletion conferred resistance in 12/14 lines, followed by MAP4K5 (8/14), SPRED2/STK40 (6/14), and INPPL1 (5/14). INPPL1, MAP4K5, or LZTR1 deletion reactivated ERK signaling. INPPL1-mediated sensitization to SHP2i required its NPXY motif but not lipid phosphatase activity. MAP4K5 acted upstream of MEK through a kinase-dependent target(s); LZTR1 had cell-dependent effects on RIT and RAS stability. INPPL1, MAP4K5, or LZTR1 deletion also conferred SHP2i resistance in vivo. Defining the SHP2i resistance landscape could suggest effective combination approaches.

DOI: https://doi.org/10.1084/jem.20221563
Cancers (Basel). 2023 Feb 05. pii: 1008. [Epub ahead of print]15(4):

Real-World Data Validation of NAPOLI-1 Nomogram for the Prediction of Overall Survival in Metastatic Pancreatic Cancer.

Yung-Yeh Su, Nai-Jung Chiang, Yi-Hsin Yang, Chia-Jui Yen, Li-Yuan Bai, Chang-Fang Chiu, Shih-Chang Chuang, Shih-Hung Yang, Wen-Chi Chou, Jen-Shi Chen, Tai-Jan Chiu, Yen-Yang Chen, De-Chuan Chan, Cheng-Ming Peng, Sz-Chi Chiu, Chung-Pin Li, Yan-Shen Shan, Li-Tzong Chen.

  BACKGROUND: The nomogram derived from the pivotal phase III NAPOLI-1 study demonstrated a significant ability to predict median overall survival (OS) in gemcitabine-refractory metastatic pancreatic ductal adenocarcinoma (PDAC) treated with liposomal irinotecan plus fluorouracil and leucovorin (nal-IRI+5-FU/LV). However, the NAPOLI-1 nomogram has not been validated in a real-world setting and therefore the applicability of the NAPOLI-1 nomogram in daily practice remains unknown. This study aims to evaluate the NAPOLI-1 nomogram in a multicenter real-world cohort.METHODS: The NAPOLI-1 nomogram was applied to a previously established cohort of metastatic PDAC patients treated with nal-IRI+5-FU/LV in nine participating centers in Taiwan. Patients were divided into three risk groups according to the NAPOLI-1 nomogram. The survival impact of relative dose intensity at 6 weeks (RDI at 6 weeks) in different risk groups was also investigated.
RESULTS: Of the 473 included patients, the median OSs of patients classified as low (n = 156), medium (n = 186), and high (n = 131) risk were 10.9, 6.3, and 4.3 months, respectively (p < 0.0001). The survival impact of RDI at 6 weeks remained significant after stratification by risk groups, adjustment with Cox regression, inverse probability weighting, or propensity score matching.
CONCLUSIONS: Our results support the usefulness of the NAPOLI-1 nomogram for risk stratification in gemcitabine-refractory metastatic PDAC treated with nal-IRI+5-FU/LV in daily practice. We further showed that the RDI at 6 weeks is an independent prognostic factor beyond the NAPOLI-1 nomogram.

Keywords:  nal-IRI; nomogram; pancreatic cancer; real-world

DOI:  https://doi.org/10.3390/cancers15041008
Chem Sci. 2023 Feb 15. 14(7): 1687-1695

An organelle-specific photoactivation and dual-isotope labeling strategy reveals phosphatidylethanolamine metabolic flux.

Clémence Simon, Antonino Asaro, Suihan Feng, Howard Riezman.

Phosphatidylethanolamine metabolism plays essential roles in eukaryotic cells but has not been completely investigated due to its complexity. This is because lipid species, unlike proteins or nucleic acids, cannot be easily manipulated at the single molecule level or controlled with subcellular resolution, two of the key factors toward understanding their functions. Here, we use the organelle-targeting photoactivation method to study PE metabolism in living cells with a high spatiotemporal resolution. Containing predefined PE structures, probes which can be selectively introduced into the ER or mitochondria were designed to compare their metabolic products according to their subcellular localization. We combined photo-uncaging with dual stable isotopic labeling to track PE metabolism in living cells by mass spectrometry analysis. Our results reveal that both mitochondria- and ER-released PE participate in phospholipid remodeling, and that PE methylation can be detected only under particular conditions. Thus, our method provides a framework to study phospholipid metabolism at subcellular resolution.

DOI: https://doi.org/10.1039/d2sc06069h
Sci Adv. 2023 Feb 22. 9(8): eadd9186

Biomolecular actuators for genetically selective acoustic manipulation of cells.

Di Wu, Diego Baresch, Colin Cook, Zhichao Ma, Mengtong Duan, Dina Malounda, David Maresca, Maria P Abundo, Justin Lee, Shirin Shivaei, David R Mittelstein, Tian Qiu, Peer Fischer, Mikhail G Shapiro.

The ability to physically manipulate specific cells is critical for the fields of biomedicine, synthetic biology, and living materials. Ultrasound has the ability to manipulate cells with high spatiotemporal precision via acoustic radiation force (ARF). However, because most cells have similar acoustic properties, this capability is disconnected from cellular genetic programs. Here, we show that gas vesicles (GVs)-a unique class of gas-filled protein nanostructures-can serve as genetically encodable actuators for selective acoustic manipulation. Because of their lower density and higher compressibility relative to water, GVs experience strong ARF with opposite polarity to most other materials. When expressed inside cells, GVs invert the cells' acoustic contrast and amplify the magnitude of their ARF, allowing the cells to be selectively manipulated with sound waves based on their genotype. GVs provide a direct link between gene expression and acoustomechanical actuation, opening a paradigm for selective cellular control in a broad range of contexts.

DOI: https://doi.org/10.1126/sciadv.add9186
J Biol Chem. 2023 Feb 17. pii: S0021-9258(23)00174-6. [Epub ahead of print] 103042

Lipidomic profiling of rat hepatic stellate cells during activation reveals a two-stage process accompanied by increased levels of lysosomal lipids.

Martijn R Molenaar, Maya W Haaker, A Bas Vaandrager, Martin Houweling, J Bernd Helms.

  Hepatic stellate cells (HSCs) are liver-resident cells best known for their role in vitamin A storage under physiological conditions. Upon liver injury, HSCs activate into myofibroblast-like cells, a key process in the onset of liver fibrosis. Lipids play an important role during HSC activation. Here we provide a comprehensive characterization of the lipidomes of primary rat HSCs during 17 days of activation in vitro. For lipidomic data interpretation, we expanded our previously described Lipid Ontology (LION) and associated web application (LION/Web) with the LION-PCA heatmap module, which generates heatmaps of the most typical LION-signatures in lipidomic datasets. Furthermore, we used LION to perform pathway analysis to determine the significant metabolic conversions in lipid pathways. Together, we identify two distinct stages of HSC activation. In the first stage, we observe a decrease of saturated phosphatidylcholine (PC), sphingomyelin and phosphatidic acid, and an increase in phosphatidylserine and polyunsaturated bis(monoacylglycero)phosphate (BMP), a lipid class typically localized at endo- and lysosomes. In the second activation stage, BMPs, hexosylceramides and ether-linked PCs are elevated, resembling a lysosomal lipid storage disease profile. The presence of isomeric structures of BMP in HSCs was confirmed ex vivo in MS-imaging datasets of steatosed liver sections. Finally, treatment with pharmaceuticals targeting the lysosomal integrity led to cell death in primary HSCs but not in HeLa cells. In summary, our combined data suggest that lysosomes play a critical role during a two-stage activation process of HSCs.

Keywords:  bioinformatics; hepatic stellate cell (HSC); lipidomics; lysosome; phospholipid turnover; polyunsaturated fatty acid (PUFA)

DOI:  https://doi.org/10.1016/j.jbc.2023.103042
HPB (Oxford). 2023 Feb 03. pii: S1365-182X(23)00029-1. [Epub ahead of print]

No survival benefit with suboptimal CA19-9 response: defining effective neoadjuvant chemotherapy in resectable or borderline resectable pancreatic cancer.

Hao Liu, Mark D'Alesio, Samer AlMasri, Abdulrahman Hammad, Annissa Desilva, Steven Lebowitz, Caroline Rieser, Eishan Ashwat, Erica Hampton, Hussein Khachfe, Mckenna Laffey, Aatur Singhi, Nathan Bahary, Kenneth Lee, Amer Zureikat, Alessandro Paniccia.

BACKGROUND/PURPOSE: Neoadjuvant chemotherapy (NAC) is gaining popularity over a surgery-first (SF) approach in treating resectable and borderline resectable pancreatic ductal adenocarcinoma (PDAC). However, what constitutes effective neoadjuvant chemotherapy is unknown.METHODS: We retrospectively analyzed resectable and borderline resectable PDAC patients who underwent pancreaticoduodenectomy (2010-2019) at a single institution. Optimal CA19-9 response was defined as normalization AND >50% reduction. We utilized Kaplan-Meier and multivariable-adjusted Cox models and competing risk subdistribution methods for statistical analysis.
RESULTS: 586 patients were included in this study. The multivariable-adjusted analysis demonstrated OS benefit in the NAC group only when OS was calculated from diagnosis (HR = 0.72, p = 0.02), but not from surgery (HR = 0.81, p = 0.1). However, in 59 patients who achieved optimal CA19-9 response, OS is significantly longer than the 134 patients with suboptimal CA19-9 response (39.3 m vs. 21.5 m, p = 0.005) or the 117 SF patients (39.3 m vs. 19.5 m, p < 0.001). Notably, a suboptimal CA19-9 response conferred no OS advantage compared to SF patients. The accumulative incidence of liver metastases (but not other metastases) was significantly reduced only in patients with optimal CA19-9 response to NAC (multivariable-adjusted subdistribution HR = 0.26, p = 0.03).
CONCLUSION: CA19-9 response to NAC may serve as the marker for effective NAC. These findings warrant validation in a multi-institutional study.

DOI: https://doi.org/10.1016/j.hpb.2023.01.016
Bioinformatics. 2023 Feb 24. pii: btad102. [Epub ahead of print]

SMITH: Spatially Constrained Stochastic Model for Simulation of Intra-Tumour Heterogeneity.

Adam Streck, Tom L Kaufmann, Roland F Schwarz.

MOTIVATION: Simulations of cancer evolution are highly useful to study the effects of selection and mutation rates on cellular fitness. However, most methods are either lattice-based and cannot simulate realistically-sized tumours, or they omit spatial constraints and lack the clonal dynamics of real-world tumours.RESULTS: SMITH is an efficient and explainable model of cancer evolution that combines a branching process with a new confinement mechanism limiting clonal growth based on the the size of the individual clones as well as the overall tumour population. We demonstrate how confinement is sufficient to induce the rich clonal dynamics observed in spatial models and cancer samples across tumour types, while allowing for a clear geometric interpretation and simulation of one billion cells within a few minutes on a desktop PC.
AVAILABILITY AND IMPLEMENTATION: SMITH is implemented in C# and freely available at https://bitbucket.org/schwarzlab/smith. For visualisations we provide the accompanying Python package PyFish at https://bitbucket.org/schwarzlab/pyfish.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btad102
EMBO Rep. 2023 Feb 21. e56524

Pericyte stem cells induce Ly6G+ cell accumulation and immunotherapy resistance in pancreatic cancer.

Zhichong Wu, Kevin Thierry, Sophie Bachy, Xinyi Zhang, Pia Gamradt, Hector Hernandez-Vargas, Ivan Mikaelian, Laurie Tonon, Roxanne Pommier, Yajie Zhao, Philippe Bertolino, Ana Hennino.

  We report the identification of a cell population that shares pericyte, stromal and stemness features, does not harbor the KrasG12D mutation and drives tumoral growth in vitro and in vivo. We term these cells pericyte stem cells (PeSCs) and define them as CD45- EPCAM- CD29+ CD106+ CD24+ CD44+ cells. We perform studies with p48-Cre;KrasG12D (KC), pdx1-Cre;KrasG12D ;Ink4a/Arffl/fl (KIC) and pdx1-Cre;KrasG12D ;p53R172H (KPC) and tumor tissues from PDAC and chronic pancreatitis patients. We also perform single-cell RNAseq analysis and reveal a unique signature of PeSC. Under steady-state conditions, PeSCs are barely detectable in the pancreas but present in the neoplastic microenvironment both in humans and mice. The coinjection of PeSCs and tumor epithelial cells leads to increased tumor growth, differentiation of Ly6G+ myeloid-derived suppressor cells, and a decreased amount of F4/80+ macrophages and CD11c+ dendritic cells. This population induces resistance to anti-PD-1 immunotherapy when coinjected with epithelial tumor cells. Our data reveal the existence of a cell population that instructs immunosuppressive myeloid cell responses to bypass PD-1 targeting and thus suggest potential new approaches for overcoming resistance to immunotherapy in clinical settings.

Keywords:  PD-1 therapy; myeloid-derived suppressor cells; pancreatic cancer; pericyte stem cells

DOI:  https://doi.org/10.15252/embr.202256524
bioRxiv. 2023 Feb 15. pii: 2023.02.14.528526. [Epub ahead of print]

Cell class-specific electric field entrainment of neural activity.

Soo Yeun Lee, Fahimeh Baftizadeh, Luke Campagnola, Tim Jarsky, Christof Koch, Costas A Anastassiou.

Electric fields affect the activity of neurons and brain circuits, yet how this interaction happens at the cellular level remains enigmatic. Lack of understanding on how to stimulate the human brain to promote or suppress specific activity patterns significantly limits basic research and clinical applications. Here we study how electric fields impact the subthreshold and spiking properties of major cortical neuronal classes. We find that cortical neurons in rodent neocortex and hippocampus as well as human cortex exhibit strong and cell class-dependent entrainment that depends on the stimulation frequency. Excitatory pyramidal neurons with their typically slower spike rate entrain to slow and fast electric fields, while inhibitory classes like Pvalb and SST with their fast spiking predominantly phase lock to fast fields. We show this spike-field entrainment is the result of two effects: non-specific membrane polarization occurring across classes and class-specific excitability properties. Importantly, these properties of spike-field and class-specific entrainment are present in cells across cortical areas and species (mouse and human). These findings open the door to the design of selective and class-specific neuromodulation technologies.

DOI: https://doi.org/10.1101/2023.02.14.528526