bims-cagime 2024-04-14 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2024‒04‒14
34 papers selected by
Kıvanç Görgülü, Technical University of Munich

A pleiotropy scan to discover new susceptibility loci for pancreatic ductal adenocarcinoma.
A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments.
Transformation of autophagic SQSTM1 droplets to SQSTM1-dependent P-bodies.
Exploiting pancreatic cancer metabolism: challenges and opportunities.
Tumor-selective activity of RAS-GTP inhibition in pancreatic cancer.
Nardilysin-regulated scission mechanism activates polo-like kinase 3 to suppress the development of pancreatic cancer.
Clinical Relevance of Physical Function Outcomes in Cancer Cachexia.
The crosstalk between macrophages and cancer cells potentiates pancreatic cancer cachexia.
Transfer learning reveals cancer-associated fibroblasts are associated with epithelial-mesenchymal transition and inflammation in cancer cells in pancreatic ductal adenocarcinoma.
Lymphatic vessels in the age of cancer immunotherapy.
Metabolic Signaling in Cancer Metastasis.
Concurrent inhibition of oncogenic and wild-type RAS-GTP for cancer therapy.
A Molecular Voyage: Multiomics Insights into Circulating Tumor Cells.
Efficacy and Safety of Adagrasib plus Cetuximab in Patients with KRASG12C-Mutated Metastatic Colorectal Cancer.
Single-cell senescence identification reveals senescence heterogeneity, trajectory, and modulators.
Perilipin membrane integration determines lipid droplet heterogeneity in differentiating adipocytes.
Metabolic fingerprinting by nuclear magnetic resonance of hepatocellular carcinoma cells during p53 reactivation-induced senescence.
The lipid droplet lipidome.
Revealing genomic secrets of archival FFPE samples.
COPII with ALG2 and ESCRTs control lysosome-dependent microautophagy of ER exit sites.
SPACe (Swift Phenotypic Analysis of Cells): an open-source, single cell analysis of Cell Painting data.
Collagen Lattice Model, Populated with Heterogeneous Cancer-Associated Fibroblasts, Facilitates Advanced Reconstruction of Pancreatic Cancer Microenvironment.
The Legacy of Jeff Norton: From Cachexia to the Earlier Detection of Pancreatic Cancer 36 Years of Mentoring a Surgical Scientist.
Lipidomes define immune cell identity.
Comparative molecular profiling of pancreatic ductal adenocarcinoma of the head versus body and tail.
Judith Campisi (1948-2024).
A guide to ferroptosis in cancer.
Chemical Strategies for the Detection and Elimination of Senescent Cells.
A 3D in vitro assay to study combined immune cell infiltration and cytotoxicity.
Interrogating Matrix Stiffness and Metabolomics in Pancreatic Ductal Carcinoma Using an Openable Microfluidic Tumor-on-a-Chip.
Molecular architecture of the actin cytoskeleton: From single cells to whole organisms using cryo-electron tomography.
A lipid atlas of human and mouse immune cells provides insights into ferroptosis susceptibility.
Association of an impaired GH-IGF-I axis with cardiac wasting in patients with advanced cancer.
Noninvasive virtual biopsy using micro-registered optical coherence tomography (OCT) in human subjects.

Mutagenesis. 2024 Apr 12. pii: geae012. [Epub ahead of print]

A pleiotropy scan to discover new susceptibility loci for pancreatic ductal adenocarcinoma.

M Giaccherini, M Rende, M Gentiluomo, C Corradi, L Archibugi, S Ermini, E Maiello, L Morelli, C H J van Eijck, G M Cavestro, M Schneider, A Mickevicius, K Adamonis, D Basso, V Hlavac, D Gioffreda, R Talar-Wojnarowska, B Schöttker, M Lovecek, G Vanella, M Gazouli, M Uno, E Malecka-Wojciesko, P Vodicka, M Goetz, M F Bijlsma, M C Petrone, F Bazzocchi, M Kiudelis, A Szentesi, S Carrara, G Nappo, H Brenner, A C Milanetto, P Soucek, V Katzke, G Peduzzi, C Rizzato, C Pasquali, X Chen, G Capurso, T Hackert, B Bueno-de-Mesquita, F G G Uzunoglu, P Hegyi, W Greenhalf, G E E Theodoropoulos, C Sperti, F Perri, M Oliverius, A Mambrini, F Tavano, R Farinella, P G Arcidiacono, M Lucchesi, S Bunduc, J Kupcinskas, G Di Franco, S Stocker, J P Neoptolemos, F Bambi, K Jamroziak, S G G Testoni, M N Aoki, B Mohelnikova-Duchonova, J R Izbicki, R Pezzilli, R T Lawlor, E F Kauffmann, E López de Maturana, N Malats, F Canzian, D Campa.

  Pleiotropic variants (i.e., genetic polymorphisms influencing more than one phenotype) are often associated with cancer risk. A scan of pleiotropic variants was successfully conducted ten years ago in relation to pancreatic ductal adenocarcinoma susceptibility. However, in the last decade, genetic association studies performed on several human traits have greatly increased the number of known pleiotropic variants. Based on the hypothesis that variants already associated with a least one trait have a higher probability of association with other traits, 61,052 variants reported to be associated by at least one genome wide association study (GWAS) with at least one human trait were tested in the present study consisting of two phases (discovery and validation), comprising a total of 16,055 pancreatic ductal adenocarcinoma (PDAC) cases and 212,149 controls. The meta-analysis of the two phases showed two loci (10q21.1-rs4948550 (P=6.52×10-5) and 7q36.3-rs288762 (P=3.03×10-5) potentially associated with PDAC risk. 10q21.1-rs4948550 shows a high degree of pleiotropy and it is also associated with colorectal cancer risk while 7q36.3-rs288762 is situated 28,558 base pairs upstream of the Sonic Hedgehog (SHH) gene, which is involved in the cell differentiation process and PDAC etiopathogenesis. In conclusion, none of the single nucleotide polymorphisms (SNPs) showed a formally statistically significant association after correction for multiple testing. However, given their pleiotropic nature and association with various human traits including colorectal cancer, the two SNPs showing the best associations with PDAC risk merit further investigation through fine mapping and ad hoc functional studies.

Keywords:  genetic susceptibility; pancreatic cancer; pleiotropy; single nucleotide polymorphism

DOI:  https://doi.org/10.1093/mutage/geae012
Nat Cell Biol. 2024 Apr 11.

A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments.

Christopher Chidley, Alicia M Darnell, Benjamin L Gaudio, Evan C Lien, Anna M Barbeau, Matthew G Vander Heiden, Peter K Sorger.

Blocking the import of nutrients essential for cancer cell proliferation represents a therapeutic opportunity, but it is unclear which transporters to target. Here we report a CRISPR interference/activation screening platform to systematically interrogate the contribution of nutrient transporters to support cancer cell proliferation in environments ranging from standard culture media to tumours. We applied this platform to identify the transporters of amino acids in leukaemia cells and found that amino acid transport involves high bidirectional flux dependent on the microenvironment composition. While investigating the role of transporters in cystine starved cells, we uncovered a role for serotonin uptake in preventing ferroptosis. Finally, we identified transporters essential for cell proliferation in subcutaneous tumours and found that levels of glucose and amino acids can restrain proliferation in that environment. This study establishes a framework for systematically identifying critical cellular nutrient transporters, characterizing their function and exploring how the tumour microenvironment impacts cancer metabolism.

DOI: https://doi.org/10.1038/s41556-024-01402-1
Autophagy. 2024 Apr 10. 1-2

Transformation of autophagic SQSTM1 droplets to SQSTM1-dependent P-bodies.

Evelina Valionyte, Elizabeth R Barrow, Chris R Baxter, Sharon Herath, Shouqing Luo.

  SQSTM1/p62 droplets play crucial roles in droplets-based macroautophagy/autophagy including selective autophagy and bulk autophagy. We observed that under several stress milieus, SQSTM1 droplets entirely colocalize with P-body markers, and these stress-induced SQSTM1 droplets contain mRNAs. We thus determined that under certain stress conditions, autophagic SQSTM1 droplets are converted to a type of enlarged P-bodies, designated SQSTM1/p62-dependent P-bodies (pd-PBs). Stress-enhanced SQSTM1 droplet formation drives the nucleation of pd-PBs through the interaction between SQSTM1 and the RNA-binding protein DDX6. Furthermore, pd-PBs sequester PYCARD, facilitating the assembly of NLRP3 inflammasomes, and in turn induce inflammation-related cytotoxicity. Our study suggests that under stress settings, autophagic SQSTM1 droplets are transformed to pd-PBs, underlining a critical role of SQSTM1 in P-body condensation.

Keywords:  Autophagy; NLRP3 inflammasome; P-bodies; PYCARD; SQSTM1

DOI:  https://doi.org/10.1080/15548627.2024.2340413
Trends Mol Med. 2024 Apr 10. pii: S1471-4914(24)00063-7. [Epub ahead of print]

Exploiting pancreatic cancer metabolism: challenges and opportunities.

Maria Chiara De Santis, B Bockorny, E Hirsch, P Cappello, M Martini.

  Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive form of pancreatic cancer, known for its challenging diagnosis and limited treatment options. The focus on metabolic reprogramming as a key factor in tumor initiation, progression, and therapy resistance has gained prominence. In this review we focus on the impact of metabolic changes on the interplay among stromal, immune, and tumor cells, as glutamine and branched-chain amino acids (BCAAs) emerge as pivotal players in modulating immune cell functions and tumor growth. We also discuss ongoing clinical trials that explore metabolic modulation for PDAC, targeting mitochondrial metabolism, asparagine and glutamine addiction, and autophagy inhibition. Overcoming challenges in understanding nutrient effects on immune-stromal-tumor interactions holds promise for innovative therapeutic strategies.

Keywords:  heterogeneity; immunotherapy; metabolic reprogramming; mitochondrial metabolism; pancreatic cancer; tumor microenvironment

DOI:  https://doi.org/10.1016/j.molmed.2024.03.008
Nature. 2024 Apr 08.

Tumor-selective activity of RAS-GTP inhibition in pancreatic cancer.

Urszula N Wasko, Jingjing Jiang, Tanner C Dalton, Alvaro Curiel-Garcia, A Cole Edwards, Yingyun Wang, Bianca Lee, Margo Orlen, Sha Tian, Clint A Stalnecker, Kristina Drizyte-Miller, Marie Menard, Julien Dilly, Stephen A Sastra, Carmine F Palermo, Marie C Hasselluhn, Amanda R Decker-Farrell, Stephanie Chang, Lingyan Jiang, Xing Wei, Yu C Yang, Ciara Helland, Haley Courtney, Yevgeniy Gindin, Karl Muonio, Ruiping Zhao, Samantha B Kemp, Cynthia Clendenin, Rina Sor, William P Vostrejs, Priya S Hibshman, Amber M Amparo, Connor Hennessey, Matthew G Rees, Melissa M Ronan, Jennifer A Roth, Jens Brodbeck, Lorenzo Tomassoni, Basil Bakir, Nicholas D Socci, Laura E Herring, Natalie K Barker, Junning Wang, James M Cleary, Brian M Wolpin, John A Chabot, Michael D Kluger, Gulam A Manji, Kenneth Y Tsai, Miroslav Sekulic, Stephen M Lagana, Andrea Califano, Elsa Quintana, Zhengping Wang, Jacqueline A M Smith, Matthew Holderfield, David Wildes, Scott W Lowe, Michael A Badgley, Andrew J Aguirre, Robert H Vonderheide, Ben Z Stanger, Timour Baslan, Channing J Der, Mallika Singh, Kenneth P Olive.

Broad-spectrum RAS inhibition holds the potential to benefit roughly a quarter of human cancer patients whose tumors are driven by RAS mutations1,2. RMC-7977 is a highly selective inhibitor of the active GTP-bound forms of KRAS, HRAS, and NRAS, with affinity for both mutant and wild type (WT) variants (RAS(ON) multi-selective)3. As >90% of human pancreatic ductal adenocarcinoma (PDAC) cases are driven by activating mutations in KRAS4, we assessed the therapeutic potential of the RAS(ON) multi-selective inhibitor RMC-7977 in a comprehensive range of PDAC models. We observed broad and pronounced anti-tumor activity across models following direct RAS inhibition at exposures that were well-tolerated in vivo. Pharmacological analyses revealed divergent responses to RMC-7977 in tumor versus normal tissues. Treated tumors exhibited waves of apoptosis along with sustained proliferative arrest whereas normal tissues underwent only transient decreases in proliferation, with no evidence of apoptosis. In the autochthonous KPC model, RMC-7977 treatment resulted in a profound extension of survival followed by on-treatment relapse. Analysis of relapsed tumors identified Myc copy number gain as a prevalent candidate resistance mechanism, which could be overcome by combinatorial TEAD inhibition in vitro. Together, these data establish a strong preclinical rationale for the use of broad-spectrum RAS-GTP inhibition in the setting of PDAC and identify a promising candidate combination therapeutic regimen to overcome monotherapy resistance.

DOI: https://doi.org/10.1038/s41586-024-07379-z
Nat Commun. 2024 Apr 11. 15(1): 3149

Nardilysin-regulated scission mechanism activates polo-like kinase 3 to suppress the development of pancreatic cancer.

Jie Fu, Jianhua Ling, Ching-Fei Li, Chi-Lin Tsai, Wenjuan Yin, Junwei Hou, Ping Chen, Yu Cao, Ya'an Kang, Yichen Sun, Xianghou Xia, Zhou Jiang, Kenei Furukawa, Yu Lu, Min Wu, Qian Huang, Jun Yao, David H Hawke, Bih-Fang Pan, Jun Zhao, Jiaxing Huang, Huamin Wang, E I Mustapha Bahassi, Peter J Stambrook, Peng Huang, Jason B Fleming, Anirban Maitra, John A Tainer, Mien-Chie Hung, Chunru Lin, Paul J Chiao.

Pancreatic ductal adenocarcinoma (PDAC) develops through step-wise genetic and molecular alterations including Kras mutation and inactivation of various apoptotic pathways. Here, we find that development of apoptotic resistance and metastasis of KrasG12D-driven PDAC in mice is accelerated by deleting Plk3, explaining the often-reduced Plk3 expression in human PDAC. Importantly, a 41-kDa Plk3 (p41Plk3) that contains the entire kinase domain at the N-terminus (1-353 aa) is activated by scission of the precursor p72Plk3 at Arg354 by metalloendopeptidase nardilysin (NRDC), and the resulting p32Plk3 C-terminal Polo-box domain (PBD) is removed by proteasome degradation, preventing the inhibition of p41Plk3 by PBD. We find that p41Plk3 is the activated form of Plk3 that regulates a feed-forward mechanism to promote apoptosis and suppress PDAC and metastasis. p41Plk3 phosphorylates c-Fos on Thr164, which in turn induces expression of Plk3 and pro-apoptotic genes. These findings uncover an NRDC-regulated post-translational mechanism that activates Plk3, establishing a prototypic regulation by scission mechanism.

DOI: https://doi.org/10.1038/s41467-024-47242-3
Cancers (Basel). 2024 Apr 01. pii: 1395. [Epub ahead of print]16(7):

Clinical Relevance of Physical Function Outcomes in Cancer Cachexia.

Lucas Caeiro, Sofia Jaramillo Quiroz, Jenna S Hegarty, Ellen Grewe, Jose M Garcia, Lindsey J Anderson.

  Managing clinical manifestations of cancer/treatment burden on functional status and quality of life remains paramount across the cancer trajectory, particularly for patients with cachexia who display reduced functional capacity. However, clinically relevant criteria for classifying functional impairment at a single point in time or for classifying meaningful functional changes subsequent to disease and/or treatment progression are lacking. This unmet clinical need remains a major obstacle to the development of therapies for cancer cachexia. This review aims to describe current literature-based evidence for clinically meaningful criteria for (1) functional impairment at a single timepoint between cancer patients with or without cachexia and (2) changes in physical function over time across interventional studies conducted in patients with cancer cachexia. The most common functional assessment in cross-sectional and interventional studies was hand grip strength (HGS). We observed suggestive evidence that an HGS deficit between 3 and 6 kg in cancer cachexia may display clinical relevance. In interventional studies, we observed that long-duration multimodal therapies with a focus on skeletal muscle may benefit HGS in patients with considerable weight loss. Future studies should derive cohort-specific clinically relevant criteria to confirm these observations in addition to other functional outcomes and investigate appropriate patient-reported anchors.

Keywords:  cancer cachexia; gait speed; hand grip strength; minimal clinically important difference; minimal important change; minimal important difference; physical function; quality of life; six-minute walk test; stair climb power

DOI:  https://doi.org/10.3390/cancers16071395
Cancer Cell. 2024 Mar 29. pii: S1535-6108(24)00094-1. [Epub ahead of print]

The crosstalk between macrophages and cancer cells potentiates pancreatic cancer cachexia.

Mingyang Liu, Yu Ren, Zhijun Zhou, Jingxuan Yang, Xiuhui Shi, Yang Cai, Alex X Arreola, Wenyi Luo, Kar-Ming Fung, Chao Xu, Ryan D Nipp, Michael S Bronze, Lei Zheng, Yi-Ping Li, Courtney W Houchen, Yuqing Zhang, Min Li.

  With limited treatment options, cachexia remains a major challenge for patients with cancer. Characterizing the interplay between tumor cells and the immune microenvironment may help identify potential therapeutic targets for cancer cachexia. Herein, we investigate the critical role of macrophages in potentiating pancreatic cancer induced muscle wasting via promoting TWEAK (TNF-like weak inducer of apoptosis) secretion from the tumor. Specifically, depletion of macrophages reverses muscle degradation induced by tumor cells. Macrophages induce non-autonomous secretion of TWEAK through CCL5/TRAF6/NF-κB pathway. TWEAK promotes muscle atrophy by activating MuRF1 initiated muscle remodeling. Notably, tumor cells recruit and reprogram macrophages via the CCL2/CCR2 axis and disrupting the interplay between macrophages and tumor cells attenuates muscle wasting. Collectively, this study identifies a feedforward loop between pancreatic cancer cells and macrophages, underlying the non-autonomous activation of TWEAK secretion from tumor cells thereby providing promising therapeutic targets for pancreatic cancer cachexia.

Keywords:  CCL2; CCL5; RELB; TWEAK; cancer cachexia; macrophages; metabolic reprogramming; muscle wasting; p65; tumor microenvironment

DOI:  https://doi.org/10.1016/j.ccell.2024.03.009
Cancer Res. 2024 Apr 08.

Transfer learning reveals cancer-associated fibroblasts are associated with epithelial-mesenchymal transition and inflammation in cancer cells in pancreatic ductal adenocarcinoma.

Samantha Guinn, Benedict Kinny-Köster, Joseph A Tandurella, Jacob T Mitchell, Dimitrios N Sidiropoulos, Melanie Loth, Melissa R Lyman, Alexandra B Pucsek, Daniel J Zabransky, Jae W Lee, Emma Kartalia, Mili Ramani, Toni T Seppälä, Christopher Cherry, Reecha Suri, Haley Zlomke, Jignasha Patel, Jin He, Christopher L Wolfgang, Jun Yu, Lei Zheng, David P Ryan, David T Ting, Alec C Kimmelman, Anuj Gupta, Ludmila Danilova, Jennifer H Elisseeff, Laura D Wood, Genevieve Stein-O'Brien, Luciane T Kagohara, Elizabeth M Jaffee, Richard A Burkhart, Elana J Fertig, Jacquelyn W Zimmerman.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy characterized by an immunosuppressive tumor microenvironment enriched with cancer associated fibroblasts (CAFs). This study utilized a convergence approach to identify tumor cell and CAF interactions through the integration of single-cell data from human tumors with human organoid co-culture experiments. Analysis of a comprehensive atlas of PDAC single-cell RNA sequencing (scRNA-seq) data indicated that CAF density is associated with increased inflammation and epithelial-mesenchymal transition (EMT) in epithelial cells. Transfer learning using transcriptional data from patient-derived organoid and CAF co-cultures provided in silico validation of CAF induction of inflammatory and EMT epithelial cell states. Further experimental validation in co-cultures demonstrated integrin beta 1 (ITGB1) and vascular endothelial factor A (VEGF-A) interactions with neuropilin-1 (NRP1) mediating CAF-epithelial cell crosstalk. Together, this study introduces transfer learning from human single-cell data to organoid co-culture analyses for experimental validation of discoveries of cell-cell crosstalk and identifies fibroblast-mediated regulation of EMT and inflammation.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-1660
Nat Rev Cancer. 2024 Apr 11.

Lymphatic vessels in the age of cancer immunotherapy.

Triantafyllia Karakousi, Tenny Mudianto, Amanda W Lund.

Lymphatic transport maintains homeostatic health and is necessary for immune surveillance, and yet lymphatic growth is often associated with solid tumour development and dissemination. Although tumour-associated lymphatic remodelling and growth were initially presumed to simply expand a passive route for regional metastasis, emerging research puts lymphatic vessels and their active transport at the interface of metastasis, tumour-associated inflammation and systemic immune surveillance. Here, we discuss active mechanisms through which lymphatic vessels shape their transport function to influence peripheral tissue immunity and the current understanding of how tumour-associated lymphatic vessels may both augment and disrupt antitumour immune surveillance. We end by looking forward to emerging areas of interest in the field of cancer immunotherapy in which lymphatic vessels and their transport function are likely key players: the formation of tertiary lymphoid structures, immune surveillance in the central nervous system, the microbiome, obesity and ageing. The lessons learnt support a working framework that defines the lymphatic system as a key determinant of both local and systemic inflammatory networks and thereby a crucial player in the response to cancer immunotherapy.

DOI: https://doi.org/10.1038/s41568-024-00681-y
Cancer Discov. 2024 Mar 29. OF1-OF19

Metabolic Signaling in Cancer Metastasis.

Sarah Krieg, Sara Isabel Fernandes, Constantinos Kolliopoulos, Ming Liu, Sarah-Maria Fendt.

Metastases, which are the leading cause of death in patients with cancer, have metabolic vulnerabilities. Alterations in metabolism fuel the energy and biosynthetic needs of metastases but are also needed to activate cell state switches in cells leading to invasion, migration, colonization, and outgrowth in distant organs. Specifically, metabolites can activate protein kinases as well as receptors and they are crucial substrates for posttranslational modifications on histone and nonhistone proteins. Moreover, metabolic enzymes can have moonlighting functions by acting catalytically, mainly as protein kinases, or noncatalytically through protein-protein interactions. Here, we summarize the current knowledge on metabolic signaling in cancer metastasis.SIGNIFICANCE: Effective drugs for the prevention and treatment of metastases will have an immediate impact on patient survival. To overcome the current lack of such drugs, a better understanding of the molecular processes that are an Achilles heel in metastasizing cancer cells is needed. One emerging opportunity is the metabolic changes cancer cells need to undergo to successfully metastasize and grow in distant organs. Mechanistically, these metabolic changes not only fulfill energy and biomass demands, which are often in common between cancer and normal but fast proliferating cells, but also metabolic signaling which enables the cell state changes that are particularly important for the metastasizing cancer cells.

DOI: https://doi.org/10.1158/2159-8290.CD-24-0174
Nature. 2024 Apr 08.

Concurrent inhibition of oncogenic and wild-type RAS-GTP for cancer therapy.

Matthew Holderfield, Bianca J Lee, Jingjing Jiang, Aidan Tomlinson, Kyle J Seamon, Alessia Mira, Enrico Patrucco, Grace Goodhart, Julien Dilly, Yevgeniy Gindin, Nuntana Dinglasan, Yingyun Wang, Lick Pui Lai, Shurui Cai, Lingyan Jiang, Nicole Nasholm, Nataliya Shifrin, Cristina Blaj, Harshit Shah, James W Evans, Nilufar Montazer, Oliver Lai, Jade Shi, Ethan Ahler, Elsa Quintana, Stephanie Chang, Anthony Salvador, Abby Marquez, Jim Cregg, Yang Liu, Anthony Milin, Anqi Chen, Tamar Bar Ziv, Dylan Parsons, John E Knox, Jennifer E Klomp, Jennifer Roth, Matthew Rees, Melissa Ronan, Antonio Cuevas-Navarro, Feng Hu, Piro Lito, David Santamaria, Andrew J Aguirre, Andrew M Waters, Channing J Der, Chiara Ambrogio, Zhengping Wang, Adrian L Gill, Elena S Koltun, Jacqueline A M Smith, David Wildes, Mallika Singh.

RAS oncogenes (collectively NRAS, HRAS and especially KRAS) are among the most frequently mutated genes in cancer, with common driver mutations occurring at codons 12, 13 and 611. Small molecule inhibitors of the KRAS(G12C) oncoprotein have demonstrated clinical efficacy in patients with multiple cancer types and have led to regulatory approvals for the treatment of non-small cell lung cancer2,3. Nevertheless, KRASG12C mutations account for only around 15% of KRAS-mutated cancers4,5, and there are no approved KRAS inhibitors for the majority of patients with tumours containing other common KRAS mutations. Here we describe RMC-7977, a reversible, tri-complex RAS inhibitor with broad-spectrum activity for the active state of both mutant and wild-type KRAS, NRAS and HRAS variants (a RAS(ON) multi-selective inhibitor). Preclinically, RMC-7977 demonstrated potent activity against RAS-addicted tumours carrying various RAS genotypes, particularly against cancer models with KRAS codon 12 mutations (KRASG12X). Treatment with RMC-7977 led to tumour regression and was well tolerated in diverse RAS-addicted preclinical cancer models. Additionally, RMC-7977 inhibited the growth of KRASG12C cancer models that are resistant to KRAS(G12C) inhibitors owing to restoration of RAS pathway signalling. Thus, RAS(ON) multi-selective inhibitors can target multiple oncogenic and wild-type RAS isoforms and have the potential to treat a wide range of RAS-addicted cancers with high unmet clinical need. A related RAS(ON) multi-selective inhibitor, RMC-6236, is currently under clinical evaluation in patients with KRAS-mutant solid tumours (ClinicalTrials.gov identifier: NCT05379985).

DOI: https://doi.org/10.1038/s41586-024-07205-6
Cancer Discov. 2024 Apr 05. OF1-OF14

A Molecular Voyage: Multiomics Insights into Circulating Tumor Cells.

Yu Wei Zhang, Ana Gvozdenovic, Nicola Aceto.

Circulating tumor cells (CTCs) play a pivotal role in metastasis, the leading cause of cancer-associated death. Recent improvements of CTC isolation tools, coupled with a steady development of multiomics technologies at single-cell resolution, have enabled an extensive exploration of CTC biology, unlocking insights into their molecular profiles. A detailed molecular portrait requires CTC interrogation across various levels encompassing genomic, epigenetic, transcriptomic, proteomic and metabolic features. Here, we review how state-of-the-art multiomics applied to CTCs are shedding light on how cancer spreads. Further, we highlight the potential implications of CTC profiling for clinical applications aimed at enhancing cancer diagnosis and treatment.SIGNIFICANCE: Exploring the complexity of cancer progression through cutting-edge multiomics studies holds the promise of uncovering novel aspects of cancer biology and identifying therapeutic vulnerabilities to suppress metastasis.

DOI: https://doi.org/10.1158/2159-8290.CD-24-0218
Cancer Discov. 2024 Apr 08. OF1-OF12

Efficacy and Safety of Adagrasib plus Cetuximab in Patients with KRASG12C-Mutated Metastatic Colorectal Cancer.

Rona Yaeger, Nataliya V Uboha, Meredith S Pelster, Tanios S Bekaii-Saab, Minal Barve, Joel Saltzman, Joshua K Sabari, Julio A Peguero, Andrew Scott Paulson, Pasi A Jänne, Marcia Cruz-Correa, Kenna Anderes, Karen Velastegui, Xiaohong Yan, Hirak Der-Torossian, Samuel J Klempner, Scott E Kopetz.

Adagrasib, an irreversible, selective KRASG12C inhibitor, may be an effective treatment in KRASG12C-mutated colorectal cancer, particularly when combined with an anti-EGFR antibody. In this analysis of the KRYSTAL-1 trial, patients with previously treated KRASG12C-mutated unresectable or metastatic colorectal cancer received adagrasib (600 mg twice daily) plus cetuximab. The primary endpoint was objective response rate (ORR) by blinded independent central review. Ninety-four patients received adagrasib plus cetuximab. With a median follow-up of 11.9 months, ORR was 34.0%, disease control rate was 85.1%, and median duration of response was 5.8 months (95% confidence interval [CI], 4.2-7.6). Median progression-free survival was 6.9 months (95% CI, 5.7-7.4) and median overall survival was 15.9 months (95% CI, 11.8-18.8). Treatment-related adverse events (TRAEs) occurred in all patients; grade 3-4 in 27.7% and no grade 5. No TRAEs led to adagrasib discontinuation. Exploratory analyses suggest circulating tumor DNA may identify features of response and acquired resistance.SIGNIFICANCE: Adagrasib plus cetuximab demonstrates promising clinical activity and tolerable safety in heavily pretreated patients with unresectable or metastatic KRASG12C-mutated colorectal cancer. These data support a potential new standard of care and highlight the significance of testing and identification of KRASG12C mutations in patients with colorectal cancer.

DOI: https://doi.org/10.1158/2159-8290.CD-24-0217
Cell Metab. 2024 Apr 08. pii: S1550-4131(24)00088-3. [Epub ahead of print]

Single-cell senescence identification reveals senescence heterogeneity, trajectory, and modulators.

Wanyu Tao, Zhengqing Yu, Jing-Dong J Han.

  Cellular senescence underlies many aging-related pathologies, but its heterogeneity poses challenges for studying and targeting senescent cells. We present here a machine learning program senescent cell identification (SenCID), which accurately identifies senescent cells in both bulk and single-cell transcriptome. Trained on 602 samples from 52 senescence transcriptome datasets spanning 30 cell types, SenCID identifies six major senescence identities (SIDs). Different SIDs exhibit different senescence baselines, stemness, gene functions, and responses to senolytics. SenCID enables the reconstruction of senescent trajectories under normal aging, chronic diseases, and COVID-19. Additionally, when applied to single-cell Perturb-seq data, SenCID helps reveal a hierarchy of senescence modulators. Overall, SenCID is an essential tool for precise single-cell analysis of cellular senescence, enabling targeted interventions against senescent cells.

Keywords:  computational tool; senescence; senescence identification; senescence quantification; senescence regulators; single cell; trajectory

DOI:  https://doi.org/10.1016/j.cmet.2024.03.009
Cell Rep. 2024 Apr 09. pii: S2211-1247(24)00421-2. [Epub ahead of print]43(4): 114093

Perilipin membrane integration determines lipid droplet heterogeneity in differentiating adipocytes.

Mario Majchrzak, Ozren Stojanović, Dalila Ajjaji, Kalthoum Ben M'barek, Mohyeddine Omrane, Abdou Rachid Thiam, Robin W Klemm.

  The storage of fat within lipid droplets (LDs) of adipocytes is critical for whole-body health. Acute fatty acid (FA) uptake by differentiating adipocytes leads to the formation of at least two LD classes marked by distinct perilipins (PLINs). How this LD heterogeneity arises is an important yet unresolved cell biological problem. Here, we show that an unconventional integral membrane segment (iMS) targets the adipocyte specific LD surface factor PLIN1 to the endoplasmic reticulum (ER) and facilitates high-affinity binding to the first LD class. The other PLINs remain largely excluded from these LDs until FA influx recruits them to a second LD population. Preventing ER targeting turns PLIN1 into a soluble, cytoplasmic LD protein, reduces its LD affinity, and switches its LD class specificity. Conversely, moving the iMS to PLIN2 leads to ER insertion and formation of a separate LD class. Our results shed light on how differences in organelle targeting and disparities in lipid affinity of LD surface factors contribute to formation of LD heterogeneity.

Keywords:  CP: Cell biology; CP: Metabolism; CYTOLD; ERTOLD; LD affinity; LD heterogeneity; LD targeting; PLIN1

DOI:  https://doi.org/10.1016/j.celrep.2024.114093
NMR Biomed. 2024 Apr 08. e5157

Metabolic fingerprinting by nuclear magnetic resonance of hepatocellular carcinoma cells during p53 reactivation-induced senescence.

Philipp Knopf, Jesus Pacheco-Torres, Laimdota Zizmare, Noriko Mori, Flonne Wildes, Benyuan Zhou, Balaji Krishnamachary, Yelena Mironchik, Manfred Kneilling, Christoph Trautwein, Bernd J Pichler, Zaver M Bhujwalla.

  Cellular senescence is characterized by stable cell cycle arrest. Senescent cells exhibit a senescence-associated secretory phenotype that can promote tumor progression. The aim of our study was to identify specific nuclear magnetic resonance (NMR) spectroscopy-based markers of cancer cell senescence. For metabolic studies, we employed murine liver carcinoma Harvey Rat Sarcoma Virus (H-Ras) cells, in which reactivation of p53 expression induces senescence. Senescent and nonsenescent cell extracts were subjected to high-resolution proton (1H)-NMR spectroscopy-based metabolomics, and dynamic metabolic changes during senescence were analyzed using a magnetic resonance spectroscopy (MRS)-compatible cell perfusion system. Additionally, the ability of intact senescent cells to degrade the extracellular matrix (ECM) was quantified in the cell perfusion system. Analysis of senescent H-Ras cell extracts revealed elevated sn-glycero-3-phosphocholine, myoinositol, taurine, and creatine levels, with decreases in glycine, o-phosphocholine, threonine, and valine. These metabolic findings were accompanied by a greater degradation index of the ECM in senescent H-Ras cells than in control H-Ras cells. MRS studies with the cell perfusion system revealed elevated creatine levels in senescent cells on Day 4, confirming the 1H-NMR results. These senescence-associated changes in metabolism and ECM degradation strongly impact growth and redox metabolism and reveal potential MRS signals for detecting senescent cancer cells in vivo.

Keywords:  MR spectroscopy; cellular homeostasis; metabolomics; p53; senescence

DOI:  https://doi.org/10.1002/nbm.5157
FEBS Lett. 2024 Apr 11.

The lipid droplet lipidome.

Michele Wölk, Maria Fedorova.

  Lipid droplets (LDs) are intracellular organelles with a hydrophobic core formed by neutral lipids surrounded by a phospholipid monolayer harboring a variety of regulatory and enzymatically active proteins. Over the last few decades, our understanding of LD biology has evolved significantly. Nowadays, LDs are appreciated not just as passive energy storage units, but rather as active players in the regulation of lipid metabolism and quality control machineries. To fulfill their functions in controlling cellular metabolic states, LDs need to be highly dynamic and responsive organelles. A large body of evidence supports a dynamic nature of the LD proteome and its contact sites with other organelles. However, much less is known about the lipidome of LDs. Numerous examples clearly indicate the intrinsic link between LD lipids and proteins, calling for a deeper characterization of the LD lipidome in various physiological and pathological settings. Here, we reviewed the current state of knowledge in the field of the LD lipidome, providing a brief overview of the lipid classes and their molecular species present within the neutral core and phospholipid monolayer.

Keywords:  lipid droplets; lipid molecular species; lipidome; neutral core; phospholipid monolayer

DOI:  https://doi.org/10.1002/1873-3468.14874
Nat Rev Cancer. 2024 Apr 08.

Revealing genomic secrets of archival FFPE samples.

Kaile Wang.

DOI: https://doi.org/10.1038/s41568-024-00686-7
Dev Cell. 2024 Apr 06. pii: S1534-5807(24)00195-3. [Epub ahead of print]

COPII with ALG2 and ESCRTs control lysosome-dependent microautophagy of ER exit sites.

Ya-Cheng Liao, Song Pang, Wei-Ping Li, Gleb Shtengel, Heejun Choi, Kathy Schaefer, C Shan Xu, Jennifer Lippincott-Schwartz.

  Endoplasmic reticulum exit sites (ERESs) are tubular outgrowths of endoplasmic reticulum that serve as the earliest station for protein sorting and export into the secretory pathway. How these structures respond to different cellular conditions remains unclear. Here, we report that ERESs undergo lysosome-dependent microautophagy when Ca2+ is released by lysosomes in response to nutrient stressors such as mTOR inhibition or amino acid starvation in mammalian cells. Targeting and uptake of ERESs into lysosomes were observed by super-resolution live-cell imaging and focus ion beam scanning electron microscopy (FIB-SEM). The mechanism was ESCRT dependent and required ubiquitinated SEC31, ALG2, and ALIX, with a knockout of ALG2 or function-blocking mutations of ALIX preventing engulfment of ERESs by lysosomes. In vitro, reconstitution of the pathway was possible using lysosomal lipid-mimicking giant unilamellar vesicles and purified recombinant components. Together, these findings demonstrate a pathway of lysosome-dependent ERES microautophagy mediated by COPII, ALG2, and ESCRTS induced by nutrient stress.

Keywords:  ALG2; COPII; ER exit sites; ESCRTs; FIB-SEM; autophagy; cellular stress; lysosome; mTOR

DOI:  https://doi.org/10.1016/j.devcel.2024.03.027
bioRxiv. 2024 Mar 26. pii: 2024.03.21.586132. [Epub ahead of print]

SPACe (Swift Phenotypic Analysis of Cells): an open-source, single cell analysis of Cell Painting data.

Fabio Stossi, Pankaj K Singh, Michela Marini, Kazem Safari, Adam T Szafran, Alejandra Rivera Tostado, Christopher D Candler, Maureen G Mancini, Elina A Mosa, Michael J Bolt, Demetrio Labate, Michael A Mancini.

Phenotypic profiling by high throughput microscopy has become one of the leading tools for screening large sets of perturbations in cellular models. Of the numerous methods used over the years, the flexible and economical Cell Painting (CP) assay has been central in the field, allowing for large screening campaigns leading to a vast number of data-rich images. Currently, to analyze data of this scale, available open-source software ( i.e. , CellProfiler) requires computational resources that are not available to most laboratories worldwide. In addition, the image-embedded cell-to-cell variation of responses within a population, while collected and analyzed, is usually averaged and unused. Here we introduce SPACe ( S wift P henotypic A nalysis of Ce lls), an open source, Python-based platform for the analysis of single cell image-based morphological profiles produced by CP experiments. SPACe can process a typical dataset approximately ten times faster than CellProfiler on common desktop computers without loss in mechanism of action (MOA) recognition accuracy. It also computes directional distribution-based distances (Earth Mover's Distance - EMD) of morphological features for quality control and hit calling. We highlight several advantages of SPACe analysis on CP assays, including reproducibility across multiple biological replicates, easy applicability to multiple (∼20) cell lines, sensitivity to variable cell-to-cell responses, and biological interpretability to explain image-based features. We ultimately illustrate the advantages of SPACe in a screening campaign of cell metabolism small molecule inhibitors which we performed in seven cell lines to highlight the importance of testing perturbations across models.

DOI: https://doi.org/10.1101/2024.03.21.586132
Int J Mol Sci. 2024 Mar 27. pii: 3740. [Epub ahead of print]25(7):

Collagen Lattice Model, Populated with Heterogeneous Cancer-Associated Fibroblasts, Facilitates Advanced Reconstruction of Pancreatic Cancer Microenvironment.

Xiaoyu Song, Yuma Nihashi, Yukiko Imai, Nobuhito Mori, Noritaka Kagaya, Hikaru Suenaga, Kazuo Shin-Ya, Masamichi Yamamoto, Daiki Setoyama, Yuya Kunisaki, Yasuyuki S Kida.

  Pancreatic ductal adenocarcinoma (PDAC) is a solid-tumor malignancy. To enhance the treatment landscape of PDAC, a 3D model optimized for rigorous drug screening is essential. Within the PDAC tumor microenvironment, a dense stroma comprising a large extracellular matrix and cancer-associated fibroblasts (CAFs) is well-known for its vital role in modulating tumor growth, cellular heterogeneity, bidirectional paracrine signaling, and chemoresistance. In this study, we employed a fibroblast-populated collagen lattice (FPCL) modeling approach that has the ability to replicate fibroblast contractility in the collagenous matrix to build dense stroma. This FPCL model allows CAF differentiation by facilitating multifaceted cell-cell interactions between cancer cells and CAFs, with the differentiation further influenced by mechanical forces and hypoxia carried within the 3D structure. Our FPCL models displayed hallmark features, including ductal gland structures and differentiated CAFs with spindle shapes. Through morphological explorations alongside in-depth transcriptomic and metabolomic profiling, we identified substantial molecular shifts from the nascent to mature model stages and potential metabolic biomarkers, such as proline. The initial pharmacological assays highlighted the effectiveness of our FPCL model in screening for improved therapeutic strategies. In conclusion, our PDAC modeling platform mirrors complex tumor microenvironmental dynamics and offers an unparalleled perspective for therapeutic exploration.

Keywords:  3D tumor model; cancer-associated fibroblasts; drug screening; pancreatic ductal adenocarcinoma; tumor microenvironment

DOI:  https://doi.org/10.3390/ijms25073740
Ann Surg Oncol. 2024 Apr 06.

The Legacy of Jeff Norton: From Cachexia to the Earlier Detection of Pancreatic Cancer 36 Years of Mentoring a Surgical Scientist.

Brett C Sheppard.

DOI: https://doi.org/10.1245/s10434-024-15218-8
Nat Cell Biol. 2024 Apr 08.

Lipidomes define immune cell identity.

Kandice R Levental, Whitney S Henry.

DOI: https://doi.org/10.1038/s41556-024-01398-8
NPJ Precis Oncol. 2024 Apr 06. 8(1): 85

Comparative molecular profiling of pancreatic ductal adenocarcinoma of the head versus body and tail.

Maen Abdelrahim, Abdullah Esmail, Anup Kasi, Nestor F Esnaola, Joanne Xiu, Yasmine Baca, Benjamin A Weinberg.

Pancreatic ductal adenocarcinoma (PDAC) of the head (H) and body/tail (B/T) differ in embryonic origin, cell composition, blood supply, lymphatic and venous drainage, and innervation. We aimed to compare the molecular and tumor immune microenvironment (TIME) profiles of PDAC of the H vs. B/T. A total of 3499 PDAC samples were analyzed via next-generation sequencing (NGS) of RNA (whole transcriptome, NovaSeq), DNA (NextSeq, 592 genes or NovaSeq, whole exome sequencing), and immunohistochemistry (Caris Life Sciences, Phoenix, AZ). Significance was determined as p values adjusted for multiple corrections (q) of <0.05. Anatomic subsites of PDAC tumors were grouped by primary tumor sites into H (N = 2058) or B/T (N = 1384). There were significantly more metastatic tumors profiled from B/T vs. H (57% vs. 44%, p < 0.001). KRAS mutations (93.8% vs. 90.2%), genomic loss of heterozygosity (12.7% vs. 9.1%), and several copy number alterations (FGF3, FGF4, FGF19, CCND1, ZNF703, FLT4, MUTYH, TNFRS14) trended higher in B/T when compared to H (p < 0.05 but q > 0.05). Expression analysis of immuno-oncology (IO)-related genes showed significantly higher expression of CTLA4 and PDCD1 in H (q < 0.05, fold change 1.2 and 1.3) and IDO1 and PDCD1LG2 expression trended higher in B/T (p < 0.05, fold change 0.95). To our knowledge, this is one of the largest cohorts of PDAC tumors subjected to broad molecular profiling. Differences in IO-related gene expression and TIME cell distribution suggest that response to IO therapies may differ in PDAC arising from H vs. B/T. Subtle differences in the genomic profiles of H vs. B/T tumors were observed.

DOI: https://doi.org/10.1038/s41698-024-00571-4
Nat Rev Cancer. 2024 Apr 10.

Judith Campisi (1948-2024).

Pierre-Yves Desprez, Pankaj Kapahi.

DOI: https://doi.org/10.1038/s41568-024-00687-6
Mol Oncol. 2024 Apr 08.

A guide to ferroptosis in cancer.

Fatma Isil Yapici, Christina M Bebber, Silvia von Karstedt.

  Ferroptosis is a newly identified iron-dependent type of regulated cell death that can also be regarded as death caused by the specific collapse of the lipid antioxidant defence machinery. Ferroptosis has gained increasing attention as a potential therapeutic strategy for therapy-resistant cancer types. However, many ferroptosis-inducing small molecules do not reach the pharmacokinetic requirements for their effective clinical use yet. Nevertheless, their clinical optimization is under development. In this review, we summarize the current understanding of molecular pathways regulating ferroptosis, how cells protect themselves from the induction of ferroptotic cell death, and how a better understanding of cancer cell metabolism can represent vulnerabilities for ferroptosis-based therapies. Lastly, we discuss the context-dependent effect of ferroptosis on various cell types within the tumor microenvironment and address controversies on how tissue ferroptosis might impact systemic cancer immunity in a paracrine manner.

Keywords:  cancer biology; cancer metabolism; cell death; ferroptosis; inflammation; iron

DOI:  https://doi.org/10.1002/1878-0261.13649
Acc Chem Res. 2024 Apr 11.

Chemical Strategies for the Detection and Elimination of Senescent Cells.

Jessie García-Fleitas, Alba García-Fernández, Vicente Martí-Centelles, Félix Sancenón, Andrea Bernardos, Ramón Martínez-Máñez.

ConspectusCellular senescence can be defined as an irreversible stopping of cell proliferation that arises in response to various stress signals. Cellular senescence is involved in diverse physiological and pathological processes in different tissues, exerting effects on processes as differentiated as embryogenesis, tissue repair and remodeling, cancer, aging, and tissue fibrosis. In addition, the development of some pathologies, aging, cancer, and other age-related diseases has been related to senescent cell accumulation. Due to the complexity of the senescence phenotype, targeting senescent cells is not trivial, is challenging, and is especially relevant for in vivo detection in age-related diseases and tissue samples. Despite the elimination of senescent cells (senolysis) using specific drugs (senolytics) that have been shown to be effective in numerous preclinical disease models, the clinical translation is still limited due to the off-target effects of current senolytics and associated toxicities. Therefore, the development of new chemical strategies aimed at detecting and eliminating senescent cells for the prevention and selective treatment of senescence-associated diseases is of great interest. Such strategies not only will contribute to a deeper understanding of this rapidly evolving field but also will delineate and inspire new possibilities for future research.In this Account, we report our recent research in the development of new chemical approaches for the detection and elimination of senescent cells based on new probes, nanoparticles, and prodrugs. The designed systems take advantage of the over-representation in senescent cells of certain biomarkers such as β-galactosidase and lipofuscin. One- and two-photon probes, for higher tissue penetration, have been developed. Moreover, we also present a renal clearable fluorogenic probe for the in vivo detection of the β-galactosidase activity, allowing for correlation with the senescent burden in living animals. Moreover, as an alternative to molecular-based probes, we also developed nanoparticles for senescence detection. Besides, we describe advances in new therapeutic agents to selectively eradicate senescent cells using β-galactosidase activity-sensitive gated nanoparticles loaded with cytotoxic or senolytic agents or new prodrugs aiming to increase the selectivity and reduction of off-target toxicities of current drugs. Moreover, new advances therapies have been applied in vitro and in vivo. Studies with the probes, nanoparticles, and prodrugs have been applied in several in vitro and in vivo models of cancer, fibrosis, aging, and drug-induced cardiotoxicity in which senescence plays an important role. We discuss the benefits of these chemical strategies toward the development of more specific and sophisticated probes, nanoparticles, and prodrugs targeting senescent cells.

DOI: https://doi.org/10.1021/acs.accounts.3c00794
bioRxiv. 2024 Mar 28. pii: 2024.03.27.586980. [Epub ahead of print]

A 3D in vitro assay to study combined immune cell infiltration and cytotoxicity.

Ashleigh J Crawford, Adrian Johnston, Wenxuan Du, Eban A Hanna, David Schell, Zeqi Wan, Ting-Hsi Chen, Fan Wu, Kehan Ren, Yeongseo Lim, Praful R Nair, Denis Wirtz.

Immune cell-mediated killing of cancer cells in a solid tumor is prefaced by a multi-step infiltration cascade of invasion, directed migration, and cytotoxic activities. In particular, immune cells must invade and migrate through a series of different extracellular matrix (ECM) boundaries and domains before reaching and killing their target tumor cells. These infiltration events are a central challenge to the clinical success of CAR T cells against solid tumors. The current standard in vitro cell killing assays measure cell cytotoxicity in an obstacle-free, two-dimensional (2D) microenvironment, which precludes the study of 3D immune cell-ECM interactions. Here, we present a 3D combined infiltration/cytotoxicity assay based on an oil-in-water microtechnology. This assay measures stromal invasion following extravasation, migration through the stromal matrix, and invasion of the solid tumor in addition to cell killing. We compare this 3D cytotoxicity assay to the benchmark 2D assay through tumor assembloid cocultures with immune cells and engineered immune cells. This assay is amenable to an array of imaging techniques, which allows direct observation and quantification of each stage of infiltration in different immune and oncological contexts. We establish the 3D infiltration/cytotoxicity assay as an important tool for the mechanistic study of immune cell interactions with the tumor microenvironment.

DOI: https://doi.org/10.1101/2024.03.27.586980
ACS Appl Mater Interfaces. 2024 Apr 12.

Interrogating Matrix Stiffness and Metabolomics in Pancreatic Ductal Carcinoma Using an Openable Microfluidic Tumor-on-a-Chip.

Michael D Mohan, Neda Latifi, Robert Flick, Craig A Simmons, Edmond W K Young.

  Pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense fibrotic stroma that contributes to aggressive tumor biology and therapeutic resistance. Current in vitro PDAC models lack sufficient optical and physical access for fibrous network visualization, in situ mechanical stiffness measurement, and metabolomic profiling. Here, we describe an openable multilayer microfluidic PDAC-on-a-chip platform that consists of pancreatic tumor cells (PTCs) and pancreatic stellate cells (PSCs) embedded in a 3D collagen matrix that mimics the stroma. Our system allows fibrous network visualization via reflected light confocal (RLC) microscopy, in situ mechanical stiffness testing using atomic force microscopy (AFM), and compartmentalized hydrogel extraction for PSC metabolomic profiling via mass spectrometry (MS) analysis. In comparing cocultures of gel-embedded PSCs and PTCs with PSC-only monocultures, RLC microscopy identified a significant decrease in pore size and corresponding increase in fiber density. In situ AFM indicated significant increases in stiffness, and hallmark characteristics of PSC activation were observed using fluorescence microscopy. PSCs in coculture also demonstrated localized fiber alignment and densification as well as increased collagen production. Finally, an untargeted MS study putatively identified metabolic contributions consistent with in vivo PDAC studies. Taken together, this platform can potentially advance our understanding of tumor-stromal interactions toward the discovery of novel therapies.

Keywords:  atomic force microscopy; hydrogel; mass spectroscopy; matrix stiffness; metabolomics; organ-on-a-chip; tumor microenvironment

DOI:  https://doi.org/10.1021/acsami.4c00556
Curr Opin Cell Biol. 2024 Apr 11. pii: S0955-0674(24)00035-8. [Epub ahead of print]88 102356

Molecular architecture of the actin cytoskeleton: From single cells to whole organisms using cryo-electron tomography.

Jonathan Schneider, Marion Jasnin.

  Cryo-electron tomography (cryo-ET) has begun to provide intricate views of cellular architecture at unprecedented resolutions. Considerable efforts are being made to further optimize and automate the cryo-ET workflow, from sample preparation to data acquisition and analysis, to enable visual proteomics inside of cells. Here, we will discuss the latest advances in cryo-ET that go hand in hand with their application to the actin cytoskeleton. The development of deep learning tools for automated annotation of tomographic reconstructions and the serial lift-out sample preparation procedure will soon make it possible to perform high-resolution structural biology in a whole new range of samples, from multicellular organisms to organoids and tissues.

Keywords:  Actin filaments; Automation; Cryo-electron tomography; Deep learning-based data analysis; Lift-out; Molecular sociology; Tomogram acquisition

DOI:  https://doi.org/10.1016/j.ceb.2024.102356
Nat Cell Biol. 2024 Apr 08.

A lipid atlas of human and mouse immune cells provides insights into ferroptosis susceptibility.

Pooranee K Morgan, Gerard Pernes, Kevin Huynh, Corey Giles, Sudip Paul, Adam Alexander T Smith, Natalie A Mellett, Amy Liang, Tilly van Buuren-Milne, Camilla Bertuzzo Veiga, Thomas J C Collins, Yangsong Xu, Man K S Lee, T Michael De Silva, Peter J Meikle, Graeme I Lancaster, Andrew J Murphy.

The cellular lipidome comprises thousands of unique lipid species. Here, using mass spectrometry-based targeted lipidomics, we characterize the lipid landscape of human and mouse immune cells ( www.cellularlipidatlas.com ). Using this resource, we show that immune cells have unique lipidomic signatures and that processes such as activation, maturation and development impact immune cell lipid composition. To demonstrate the potential of this resource to provide insights into immune cell biology, we determine how a cell-specific lipid trait-differences in the abundance of polyunsaturated fatty acid-containing glycerophospholipids (PUFA-PLs)-influences immune cell biology. First, we show that differences in PUFA-PL content underpin the differential susceptibility of immune cells to ferroptosis. Second, we show that low PUFA-PL content promotes resistance to ferroptosis in activated neutrophils. In summary, we show that the lipid landscape is a defining feature of immune cell identity and that cell-specific lipid phenotypes underpin aspects of immune cell physiology.

DOI: https://doi.org/10.1038/s41556-024-01377-z
Clin Res Cardiol. 2024 Apr 08.

Association of an impaired GH-IGF-I axis with cardiac wasting in patients with advanced cancer.

Ann-Kathrin Fröhlich, Jan Porthun, Khawaja M Talha, Alessia Lena, Sara Hadzibegovic, Ursula Wilkenshoff, Frederike Sonntag, Anja Nikolski, Luisa Valentina Ramer, Tanja Zeller, Ulrich Keller, Lars Bullinger, Stefan D Anker, Wilhelm Haverkamp, Stephan von Haehling, Wolfram Doehner, Ursula Rauch, Carsten Skurk, John G F Cleland, Javed Butler, Andrew J S Coats, Ulf Landmesser, Mahir Karakas, Markus S Anker.

  BACKGROUND: Growth hormone (GH) resistance is characterized by high GH levels but low levels of insulin-like growth factor-I (IGF-I) and growth hormone binding protein (GHBP) and, for patients with chronic disease, is associated with the development of cachexia.OBJECTIVES: We investigated whether GH resistance is associated with changes in left ventricular (LV) mass (cardiac wasting) in patients with cancer.
METHODS: We measured plasma IGF-I, GH, and GHBP in 159 women and 148 men with cancer (83% stage III/IV). Patients were grouped by tertile of echocardiographic LVmass/height2 (women, < 50, 50-61, > 61 g/m2; men, < 60, 60-74, > 74 g/m2) and by presence of wasting syndrome with unintentional weight loss (BMI < 24 kg/m2 and weight loss ≥ 5% in the prior 12 months). Repeat echocardiograms were obtained usually within 3-6 months for 85 patients.
RESULTS: Patients in the lowest LVmass/height2 tertile had higher plasma GH (median (IQR) for 1st, 2nd, and 3rd tertile women, 1.8 (0.9-4.2), 0.8 (0.2-2.2), 0.5 (0.3-1.6) ng/mL, p = 0.029; men, 2.1 (0.8-3.2), 0.6 (0.1-1.7), 0.7 (0.2-1.9) ng/mL, p = 0.003). Among women, lower LVmass was associated with higher plasma IGF-I (68 (48-116), 72 (48-95), 49 (35-76) ng/mL, p = 0.007), whereas such association did not exist for men. Patients with lower LVmass had lower log IGF-I/GH ratio (women, 1.60 ± 0.09, 2.02 ± 0.09, 1.88 ± 0.09, p = 0.004; men, 1.64 ± 0.09, 2.14 ± 0.11, 2.04 ± 0.11, p = 0.002). GHBP was not associated with LVmass. Patients with wasting syndrome with unintentional weight loss had higher plasma GH and GHBP, lower log IGF-I/GH ratio, and similar IGF-I. Overall, GHBP correlated inversely with log IGF-I/GH ratio (women, r = - 0.591, p < 0.001; men, r = - 0.575, p < 0.001). Additionally, higher baseline IGF-I was associated with a decline in LVmass during follow-up (r = - 0.318, p = 0.003).
CONCLUSION: In advanced cancer, reduced LVmass is associated with increased plasma GH and reduced IGF-I/GH ratio, suggesting increasing GH resistance, especially for patients with wasting syndrome with unintentional weight loss. Higher baseline IGF-I was associated with a decrease in relative LVmass during follow-up.

Keywords:  Cachexia; Cancer; Cardiology; Echocardiography; Growth hormone; Insulin-like growth factor-I; Left ventricular mass

DOI:  https://doi.org/10.1007/s00392-024-02400-x
Sci Adv. 2024 Apr 12. 10(15): eadi5794

Noninvasive virtual biopsy using micro-registered optical coherence tomography (OCT) in human subjects.

Yonatan Winetraub, Aidan Van Vleck, Edwin Yuan, Itamar Terem, Jinjing Zhao, Caroline Yu, Warren Chan, Hanh Do, Saba Shevidi, Maiya Mao, Jacqueline Yu, Megan Hong, Erick Blankenberg, Kerri E Rieger, Steven Chu, Sumaira Aasi, Kavita Y Sarin, Adam de la Zerda.

Histological hematoxylin and eosin-stained (H&E) tissue sections are used as the gold standard for pathologic detection of cancer, tumor margin detection, and disease diagnosis. Producing H&E sections, however, is invasive and time-consuming. While deep learning has shown promise in virtual staining of unstained tissue slides, true virtual biopsy requires staining of images taken from intact tissue. In this work, we developed a micron-accuracy coregistration method [micro-registered optical coherence tomography (OCT)] that can take a two-dimensional (2D) H&E slide and find the exact corresponding section in a 3D OCT image taken from the original fresh tissue. We trained a conditional generative adversarial network using the paired dataset and showed high-fidelity conversion of noninvasive OCT images to virtually stained H&E slices in both 2D and 3D. Applying these trained neural networks to in vivo OCT images should enable physicians to readily incorporate OCT imaging into their clinical practice, reducing the number of unnecessary biopsy procedures.

DOI: https://doi.org/10.1126/sciadv.adi5794