bims-cagime 2024-02-04 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2024‒02‒04
27 papers selected by
Kıvanç Görgülü, Technical University of Munich

The extracellular niche and tumor microenvironment enhance KRAS inhibitor efficacy in pancreatic cancer.
Polymorphisms in transcription factor binding sites and enhancer regions and pancreatic ductal adenocarcinoma risk.
Tumor cell-intrinsic p38 MAPK signaling promotes IL1⍺-mediated stromal inflammation and therapeutic resistance in pancreatic cancer.
Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation.
Exploring the ATG9A interactome uncovers interaction with VPS13A.
Malignant tumor cells engender second membrane-lined organelles for self-protection and tumor progression.
Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset.
R-ketorolac ameliorates cancer-associated cachexia and prolongs survival of tumour-bearing mice.
Cell polarity proteins promote macropinocytosis in response to metabolic stress.
Lung endothelium exploits susceptible tumor cell states to instruct metastatic latency.
Lipid droplets and fatty acid-induced lipotoxicity: in a nutshell.
The original colorimetric method to detect cellular senescence.
Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma.
High-throughput assessment of cellular senescence.
Exosome-derived tRNA fragments tRF-GluCTC-0005 promotes pancreatic cancer liver metastasis by activating hepatic stellate cells.
Cell competition and the regulation of protein homeostasis.
Metabolic underpinnings of cancer-related fatigue.
Folate depletion induces erythroid differentiation through perturbation of de novo purine synthesis.
Evidence for a causal link between intra-pancreatic fat deposition and pancreatic cancer: A prospective cohort and Mendelian randomization study.
A serendipitous discovery of a family of membrane remodelling proteins.
A new mass analyzer shakes up the proteomics field.
The hallmarks of aging as a conceptual framework for health and longevity research.
Caveolae disassemble upon membrane lesioning and foster cell survival.
Low-input lipidomics reveals lipid metabolism remodelling during early mammalian embryo development.
Early Cancerous Lesions of the Pancreas and Ampulla: Current Concepts and Challenges.
7-Dehydrocholesterol is an endogenous suppressor of ferroptosis.
Mitochondrial protein C15ORF48 is a stress-independent inducer of autophagy that regulates oxidative stress and autoimmunity.

Cancer Res. 2024 Jan 31.

The extracellular niche and tumor microenvironment enhance KRAS inhibitor efficacy in pancreatic cancer.

Vishnu Kumarasamy, Jianxin Wang, Costakis Frangou, Yin Wan, Andrew Dynka, Hanna Rosenheck, Prasenjit Dey, Ethan V Abel, Erik S Knudsen, Agnieszka K Witkiewicz.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease that lacks effective treatment options, highlighting the need for developing new therapeutic interventions. Here, we assessed the response to pharmacological inhibition of KRAS, the central oncogenic driver of PDAC. In a panel of PDAC cell lines, inhibition of KRASG12D with MRTX1133 yielded variable efficacy in suppressing cell growth and downstream gene expression programs in 2D cultures. Based on CRISPR-Cas9 loss-of-function screens, ITGB1 was identified as a target to enhance the therapeutic response to MRTX1133 by regulating mechanotransduction signaling and YAP/TAZ expression, which was confirmed by gene specific knockdown and combinatorial drug synergy. Interestingly, MRTX1133 was considerably more efficacious in 3D cell cultures. Moreover, MRTX1133 elicited a pronounced cytostatic effect in vivo and controlled tumor growth in PDAC patient-derived xenografts. In syngeneic models, KRASG12D inhibition led to tumor regression that did not occur in immune-deficient hosts. Digital spatial profiling on tumor tissues indicated that MRTX1133-mediated KRAS inhibition enhanced interferon-γ signaling and induced antigen presentation that modulated the tumor microenvironment. Further investigation of the immunological response using single-cell sequencing and multispectral imaging revealed that tumor regression was associated with suppression of neutrophils and influx of effector CD8+ T cells. Together, these findings demonstrate that both tumor cell-intrinsic and extrinsic events contribute to response to MRTX1133 and credential KRASG12D inhibition as a promising therapeutic strategy for a large percentage of PDAC patients.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-2504
Hum Genomics. 2024 Feb 02. 18(1): 12

Polymorphisms in transcription factor binding sites and enhancer regions and pancreatic ductal adenocarcinoma risk.

Pelin Ünal, Ye Lu, Bas Bueno-de-Mesquita, Casper H J van Eijck, Renata Talar-Wojnarowska, Andrea Szentesi, Maria Gazouli, Edita Kreivenaite, Francesca Tavano, Ewa Małecka-Wojciesko, Bálint Erőss, Martin Oliverius, Stefania Bunduc, Mateus Nóbrega Aoki, Ludmila Vodickova, Ugo Boggi, Matteo Giaccherini, Jurate Kondrackiene, Roger Chammas, Orazio Palmieri, George E Theodoropoulos, Maarten F Bijlsma, Daniela Basso, Beatrice Mohelnikova-Duchonova, Pavel Soucek, Jakob R Izbicki, Vytautas Kiudelis, Giuseppe Vanella, Paolo Giorgio Arcidiacono, Barbara Włodarczyk, Thilo Hackert, Ben Schöttker, Faik G Uzunoglu, Franco Bambi, Mara Goetz, Viktor Hlavac, Hermann Brenner, Francesco Perri, Silvia Carrara, Stefano Landi, Péter Hegyi, Frederike Dijk, Evaristo Maiello, Giovanni Capretti, Sabrina Gloria Giulia Testoni, Maria Chiara Petrone, Hannah Stocker, Stefano Ermini, Livia Archibugi, Manuel Gentiluomo, Giulia Martina Cavestro, Raffaele Pezzilli, Gregorio Di Franco, Anna Caterina Milanetto, Cosimo Sperti, John P Neoptolemos, Luca Morelli, Klara Vokacova, Claudio Pasquali, Rita T Lawlor, Francesca Bazzocchi, Juozas Kupcinskas, Gabriele Capurso, Daniele Campa, Federico Canzian.

  Genome-wide association studies (GWAS) are a powerful tool for detecting variants associated with complex traits and can help risk stratification and prevention strategies against pancreatic ductal adenocarcinoma (PDAC). However, the strict significance threshold commonly used makes it likely that many true risk loci are missed. Functional annotation of GWAS polymorphisms is a proven strategy to identify additional risk loci. We aimed to investigate single-nucleotide polymorphisms (SNP) in regulatory regions [transcription factor binding sites (TFBSs) and enhancers] that could change the expression profile of multiple genes they act upon and thereby modify PDAC risk. We analyzed a total of 12,636 PDAC cases and 43,443 controls from PanScan/PanC4 and the East Asian GWAS (discovery populations), and the PANDoRA consortium (replication population). We identified four associations that reached study-wide statistical significance in the overall meta-analysis: rs2472632(A) (enhancer variant, OR 1.10, 95%CI 1.06,1.13, p = 5.5 × 10-8), rs17358295(G) (enhancer variant, OR 1.16, 95%CI 1.10,1.22, p = 6.1 × 10-7), rs2232079(T) (TFBS variant, OR 0.88, 95%CI 0.83,0.93, p = 6.4 × 10-6) and rs10025845(A) (TFBS variant, OR 1.88, 95%CI 1.50,1.12, p = 1.32 × 10-5). The SNP with the most significant association, rs2472632, is located in an enhancer predicted to target the coiled-coil domain containing 34 oncogene. Our results provide new insights into genetic risk factors for PDAC by a focused analysis of polymorphisms in regulatory regions and demonstrating the usefulness of functional prioritization to identify loci associated with PDAC risk.

Keywords:  Association study; Enhancer; Pancreatic cancer; Single nucleotide polymorphism; Transcription factor binding site

DOI:  https://doi.org/10.1186/s40246-024-00576-x
Cancer Res. 2024 Jan 29.

Tumor cell-intrinsic p38 MAPK signaling promotes IL1⍺-mediated stromal inflammation and therapeutic resistance in pancreatic cancer.

Samara P Singh, Austin R Dosch, Siddharth Mehra, Iago De Castro Silva, Anna Bianchi, Vanessa T Garrido, Zhiqun Zhou, Andrew Adams, Haleh Amirian, Edmond W Box, Xiaodian Sun, Yuguang Ban, Jashodeep Datta, Nagaraj S Nagathihalli, Nipun B Merchant.

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a KRAS-driven inflammatory program and a desmoplastic stroma, which contribute to the profoundly chemoresistant phenotype. The tumor stroma contains an abundance of cancer-associated fibroblasts (CAFs), which engage in extensive paracrine crosstalk with tumor cells to perpetuate pro-tumorigenic inflammation. Interleukin-1α (IL1α), a pleiotropic, tumor cell-derived cytokine, plays a critical role in shaping the stromal landscape. To provide insights into the molecular mechanisms regulating IL1A expression in PDAC, we performed transcriptional profiling of TCGA datasets and pharmacologic screening in PDAC cells and identified p38α MAPK as a key positive regulator of IL1A expression. Both genetic and pharmacologic inhibition of p38 MAPK significantly diminished IL1α production in vitro. Chromatin- and co-immunoprecipitation analyses revealed that p38 MAPK coordinates the transcription factors Sp1 and the p65 subunit of NFκB to drive IL1A overexpression. Single-cell RNA-sequencing of a highly desmoplastic murine PDAC model, Ptf1aCre/+; LSL-KrasG12D/+; Tgfbr2flox/flox (PKT), confirmed that p38 MAPK inhibition significantly decreases tumor cell-derived Il1a and attenuates the inflammatory CAF phenotype in a paracrine IL1α-dependent manner. Furthermore, p38 MAPK inhibition favorably modulated intratumoral immunosuppressive myeloid populations and augmented chemotherapeutic efficacy to substantially reduce tumor burden and improve overall survival in PKT mice. These findings illustrate a cellular mechanism of tumor cell-intrinsic p38-p65/Sp1-IL1α signaling that is responsible for sustaining stromal inflammation and CAF activation, offering an attractive therapeutic approach to enhance chemosensitivity in PDAC.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-1200
Nat Cancer. 2024 Jan 29.

Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation.

Meri Rogava, Tyler J Aprati, Wei-Yu Chi, Johannes C Melms, Clemens Hug, Stephanie H Davis, Ethan M Earlie, Charlie Chung, Sachin K Deshmukh, Sharon Wu, George Sledge, Stephen Tang, Patricia Ho, Amit Dipak Amin, Lindsay Caprio, Carino Gurjao, Somnath Tagore, Bryan Ngo, Michael J Lee, Giorgia Zanetti, Yiping Wang, Sean Chen, William Ge, Luiza Martins Nascentes Melo, Gabriele Allies, Jonas Rösler, Goeffrey T Gibney, Oliver J Schmitz, Megan Sykes, Rémi J Creusot, Thomas Tüting, Dirk Schadendorf, Martin Röcken, Thomas K Eigentler, Andrei Molotkov, Akiva Mintz, Samuel F Bakhoum, Semir Beyaz, Lewis C Cantley, Peter K Sorger, Sven W Meckelmann, Alpaslan Tasdogan, David Liu, Ashley M Laughney, Benjamin Izar.

Liver metastasis (LM) confers poor survival and therapy resistance across cancer types, but the mechanisms of liver-metastatic organotropism remain unknown. Here, through in vivo CRISPR-Cas9 screens, we found that Pip4k2c loss conferred LM but had no impact on lung metastasis or primary tumor growth. Pip4k2c-deficient cells were hypersensitized to insulin-mediated PI3K/AKT signaling and exploited the insulin-rich liver milieu for organ-specific metastasis. We observed concordant changes in PIP4K2C expression and distinct metabolic changes in 3,511 patient melanomas, including primary tumors, LMs and lung metastases. We found that systemic PI3K inhibition exacerbated LM burden in mice injected with Pip4k2c-deficient cancer cells through host-mediated increase in hepatic insulin levels; however, this circuit could be broken by concurrent administration of an SGLT2 inhibitor or feeding of a ketogenic diet. Thus, this work demonstrates a rare example of metastatic organotropism through co-optation of physiological metabolic cues and proposes therapeutic avenues to counteract these mechanisms.

DOI: https://doi.org/10.1038/s43018-023-00704-x
J Cell Sci. 2024 Jan 31. pii: jcs.261081. [Epub ahead of print]

Exploring the ATG9A interactome uncovers interaction with VPS13A.

Alexander R van Vliet, Harold B J Jefferies, Peter A Faull, Jessica Chadwick, Fairouz Ibrahim, Mark J Skehel, Sharon A Tooze.

  ATG9A, the only transmembrane protein of the core autophagy pathway, cycles between the Golgi, endosomes and a vesicular compartment. ATG9A was recently shown to act as a lipid scramblase and this function is thought to require its interaction with another core autophagy protein ATG2A, which acts as a lipid transfer protein. Together ATG9A and ATG2A are proposed to function to expand the growing autophagosome. However, ATG9A is implicated in other pathways including membrane repair and lipid droplet homeostasis. To elucidate other ATG9A interactors within the autophagy pathway, or interactors beyond autophagy we performed an interactome analysis through mass spectrometry. This analysis revealed a host of proteins involved in lipid synthesis and trafficking, including ACSL3 and VPS13A and C. Furthermore, we show that ATG9A directly interacts with VPS13A and forms a complex distinct from the ATG9A:ATG2A complex.

Keywords:  ATG9A interactome; Autophagy; VPS13; Lipid Trafficking; Mass Spectrometry

DOI:  https://doi.org/10.1242/jcs.261081
Proc Natl Acad Sci U S A. 2024 Feb 06. 121(6): e2317141121

Malignant tumor cells engender second membrane-lined organelles for self-protection and tumor progression.

Tingfang Yi, Gerhard Wagner.

  Cancer is a leading cause of mortality in humans, but the efficacy of current treatments for many cancers is limited, as they lack unique mechanistically defined targets. Here, we show that, upon malignant transformation, aggressive oncocells generate a second membrane exterior to their plasma membrane to form cytocapsulas (CCs) and cytocapsular tubes (CCTs), which all together constitute cytocapsular oncocells with pleotropic biological functions in cancer patient tissues in vivo. Proteomic and biochemical analyses revealed that the PMCA2 calcium pump is highly up-regulated in CCs and CCTs in malignant tumors but not in normal tissues, thus identifying a unique cancer biomarker and target for cancer therapy. Cytocapsular oncocells are universally present in solid cancers and appear in hematologic cancers in immune organs. Multi-cell malignant tumors are also enveloped by protective CC membranes. These cytocapsular tumors (CTs) generate numerous CCTs that form freeways for cancer cell metastasis to both neighboring and distant destinations. Entire cytocapsular tumor networks (CTNs) dominate physical cancer metastasis pathways in cancer patients in vivo. Later, CCTs invade micro blood vessels and release cytocapsular oncocells into the blood, providing a source of circulating tumor cells. CTNs interconnect cytocapsular tumors in primary and secondary cancer niches, creating larger cytocapsular tumor network systems (CTNSs). Primary and secondary CTNSs are in turn interconnected, forming dynamic and integrated CTNSs. Thus, interconnected cytocapsular oncocells, CTNs, and CTNSs coordinate cancer progression via the integrated cytocapsular membrane systems.

Keywords:  PMCA2; cancer; cytocapsular oncocell; cytocapsular tube; cytocapsular tumor

DOI:  https://doi.org/10.1073/pnas.2317141121
Nat Commun. 2024 Jan 27. 15(1): 818

Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset.

Yi Xu, Michael H Nipper, Angel A Dominguez, Zhenqing Ye, Naoki Akanuma, Kevin Lopez, Janice J Deng, Destiny Arenas, Ava Sanchez, Francis E Sharkey, Colin M Court, Aatur D Singhi, Huamin Wang, Martin E Fernandez-Zapico, Lu-Zhe Sun, Siyuan Zheng, Yidong Chen, Jun Liu, Pei Wang.

Animal studies have demonstrated the ability of pancreatic acinar cells to transform into pancreatic ductal adenocarcinoma (PDAC). However, the tumorigenic potential of human pancreatic acinar cells remains under debate. To address this gap in knowledge, we expand sorted human acinar cells as 3D organoids and genetically modify them through introduction of common PDAC mutations. The acinar organoids undergo dramatic transcriptional alterations but maintain a recognizable DNA methylation signature. The transcriptomes of acinar organoids are similar to those of disease-specific cell populations. Oncogenic KRAS alone do not transform acinar organoids. However, acinar organoids can form PDAC in vivo after acquiring the four most common driver mutations of this disease. Similarly, sorted ductal cells carrying these genetic mutations can also form PDAC, thus experimentally proving that PDACs can originate from both human acinar and ductal cells. RNA-seq analysis reveal the transcriptional shift from normal acinar cells towards PDACs with enhanced proliferation, metabolic rewiring, down-regulation of MHC molecules, and alterations in the coagulation and complement cascade. By comparing PDAC-like cells with normal pancreas and PDAC samples, we identify a group of genes with elevated expression during early transformation which represent potential early diagnostic biomarkers.

DOI: https://doi.org/10.1038/s41467-024-45097-2
J Cachexia Sarcopenia Muscle. 2024 Feb 01.

R-ketorolac ameliorates cancer-associated cachexia and prolongs survival of tumour-bearing mice.

Sophia E Chrysostomou, Sandra Eder, Isabella Pototschnig, Anna-Lena Mayer, Martina Derler, Marion Mussbacher, Silvia Schauer, Dongxu Zhang, Dongmei Yan, Gennie Liu, Gerald Hoefler, Thomas Weichhart, Paul W Vesely, Lingbing Zhang, Martina Schweiger.

  BACKGROUND: Cancer-associated cachexia (CAC) is a debilitating syndrome associated with poor quality of life and reduced life expectancy of cancer patients. CAC is characterized by unintended body weight reduction due to muscle and adipose tissue loss. A major hallmark of CAC is systemic inflammation. Several non-steroidal anti-inflammatory drugs (NSAIDs) have been suggested for CAC treatment, yet no single medication has proven reliable. R-ketorolac (RK) is the R-enantiomer of a commonly used NSAID. The effect of RK on CAC has not yet been evaluated.METHODS: Ten- to 11-week-old mice were inoculated with C26 or CHX207 cancer cells or vehicle control (phosphate-buffered saline [PBS]). After cachexia onset, 2 mg/kg RK or PBS was administered daily by oral gavage. Body weight, food intake and tumour size were continuously measured. At study endpoints, blood was drawn, mice were sacrificed and tissues were excised. Immune cell abundance was analysed using a Cytek® Aurora spectral flow cytometer. Cyclooxygenase (COX) activity was determined in lung homogenates using a fluorometric kit. Muscle tissues were analysed for mRNA and protein expression by quantitative real-time PCR and western blotting analysis, respectively. Muscle fibre size was determined on histological slides after haematoxylin/eosin staining.
RESULTS: Ten-day survival rate of C26-bearing animals was 10% while RK treatment resulted in a 100% survival rate (P = 0.0009). Chemotherapy resulted in a 10% survival rate 14 days after treatment initiation, but all mice survived upon co-medication with RK and cyclophosphamide (P = 0.0001). Increased survival was associated with a protection from body weight loss in C26 (-0.61 ± 1.82 vs. -4.48 ± 2.0 g, P = 0.0004) and CHX207 (-0.49 ± 0.33 vs. -2.49 ± 0.93 g, P = 0.0003) tumour-bearing mice treated with RK, compared with untreated mice. RK ameliorated musculus quadriceps (-1.7 ± 7.1% vs. -27.8 ± 8.3%, P = 0.0007) and gonadal white adipose tissue (-18.8 ± 49% vs. -69 ± 15.6%, P = 0.094) loss in tumour-bearing mice, compared with untreated mice. Mechanistically, RK reduced circulating interleukin-6 (IL-6) concentrations from 334 ± 151 to 164 ± 123 pg/mL (P = 0.047) in C26 and from 93 ± 39 to 35 ± 6 pg/mL (P = 0.0053) in CHX207 tumour-bearing mice. Moreover, RK protected mice from cancer-induced T-lymphopenia (+1.8 ± 42% vs. -49.2 ± 12.1% in treated vs. untreated mice, respectively). RK was ineffective in ameliorating CAC in thymus-deficient nude mice, indicating that the beneficial effect of RK depends on T-cells.
CONCLUSIONS: RK improved T-lymphopenia and decreased systemic IL-6 concentrations, resulting in alleviation of cachexia and increased survival of cachexigenic tumour-bearing mice, even under chemotherapy and independent of COX inhibition. Considering its potential, we propose that the use of RK should be investigated in patients suffering from CAC.

Keywords:  cachexia; cancer; inflammation; ketorolac

DOI:  https://doi.org/10.1002/jcsm.13422
bioRxiv. 2024 Jan 30. pii: 2024.01.16.575943. [Epub ahead of print]

Cell polarity proteins promote macropinocytosis in response to metabolic stress.

Guillem Lambies, Szu-Wei Lee, Karen Duong-Polk, Pedro Aza-Blanc, Swetha Maganti, David W Dawson, Cosimo Commisso.

Macropinocytosis has emerged as a nutrient-scavenging pathway that cancer cells exploit to survive the nutrient-deprived conditions of the tumor microenvironment. Cancer cells are especially reliant on glutamine for their survival, and in pancreatic ductal adenocarcinoma (PDAC) cells, glutamine deficiency can enhance the stimulation of macropinocytosis, allowing the cells to escape metabolic stress through the production of extracellular-protein-derived amino acids. Here, we identify the atypical protein kinase C (aPKC) enzymes, PKCζ and PKCι as novel regulators of macropinocytosis. In normal epithelial cells, aPKCs are known to regulate cell polarity in association with the scaffold proteins Par3 and Par6, controlling the function of several targets, including the Par1 kinases. In PDAC cells, we identify that each of these cell polarity proteins are required for glutamine stress-induced macropinocytosis. Mechanistically, we find that the aPKCs are regulated by EGFR signaling or by the transcription factor CREM to promote the relocation of Par3 to microtubules, facilitating macropinocytosis in a dynein-dependent manner. Importantly, we determine that cell fitness impairment caused by aPKC depletion is rescued by the restoration of macropinocytosis and that aPKCs support PDAC growth in vivo. These results identify a previously unappreciated role for cell polarity proteins in the regulation of macropinocytosis and provide a better understanding of the mechanistic underpinnings that control macropinocytic uptake in the context of metabolic stress.

DOI: https://doi.org/10.1101/2024.01.16.575943
Nat Cancer. 2024 Feb 02.

Lung endothelium exploits susceptible tumor cell states to instruct metastatic latency.

Moritz Jakab, Ki Hong Lee, Alexey Uvarovskii, Svetlana Ovchinnikova, Shubhada R Kulkarni, Sevinç Jakab, Till Rostalski, Carleen Spegg, Simon Anders, Hellmut G Augustin.

In metastasis, cancer cells travel around the circulation to colonize distant sites. Due to the rarity of these events, the immediate fates of metastasizing tumor cells (mTCs) are poorly understood while the role of the endothelium as a dissemination interface remains elusive. Using a newly developed combinatorial mTC enrichment approach, we provide a transcriptional blueprint of the early colonization process. Following their arrest at the metastatic site, mTCs were found to either proliferate intravascularly or extravasate, thereby establishing metastatic latency. Endothelial-derived angiocrine Wnt factors drive this bifurcation, instructing mTCs to follow the extravasation-latency route. Surprisingly, mTC responsiveness towards niche-derived Wnt was established at the epigenetic level, which predetermined tumor cell behavior. Whereas hypomethylation enabled high Wnt activity leading to metastatic latency, methylated mTCs exhibited low activity and proliferated intravascularly. Collectively the data identify the predetermined methylation status of disseminated tumor cells as a key regulator of mTC behavior in the metastatic niche.

DOI: https://doi.org/10.1038/s43018-023-00716-7
FEBS Lett. 2024 Jan 28.

Lipid droplets and fatty acid-induced lipotoxicity: in a nutshell.

Eseiwi Obaseki, Daniel Adebayo, Sumit Bandyopadhyay, Hanaa Hariri.

  Lipid droplets (LDs) are fat storage organelles that are conserved from bacteria to humans. LDs are broken down to supply cells with fatty acids (FAs) that can be used as an energy source or membrane synthesis. An overload of FAs disrupts cellular functions and causes lipotoxicity. Thus, by acting as hubs for storing excess fat, LDs prevent lipotoxicity and preserve cellular homeostasis. LD synthesis and turnover have to be precisely regulated to maintain a balanced lipid distribution and allow for cellular adaptation during stress. Here, we discuss how prolonged exposure to excess lipids affects cellular functions, and the roles of LDs in buffering cellular stress focusing on lipotoxicity.

Keywords:  autophagy; fatty acid; lipid droplet; lipolysis; lipophagy; lipotoxicity

DOI:  https://doi.org/10.1002/1873-3468.14808
Methods Cell Biol. 2024 ;pii: S0091-679X(22)00146-7. [Epub ahead of print]181 59-72

The original colorimetric method to detect cellular senescence.

Manjari Dimri, Goberdhan P Dimri.

  Cellular senescence, whereby cells cease to proliferate, is known to contribute to the aging process and age-related pathologies. It is elicited either by cell-intrinsic mechanisms such as progressive telomere shortening or due to the extrinsic stress-related factors, which via p53-p21 and p16-pRB tumor suppressor pathways signal cells to cease proliferation. A proper identification and characterization of senescent cells is necessary to understand the process of aging, age-related pathologies, and the development of therapeutics to treat age-related dysfunctions. The landmark discovery of Senescence-Associated-Beta-Galactosidase (SA-β-Gal) marker, and a simple colorimetric method to detect SA-β-Gal greatly facilitated identification of the senescent cells in human and rodent cells pertaining to age-related diseases (Dimri et al., 1995). Despite the availability of additional senescence biomarkers, the SA-β-Gal marker and histochemical detection method remain the most widely used tool to identify senescent cells in vitro and in vivo. Here, we revisit the original colorimetric method to detect senescent cells that was first published in 1995 (Dimri et al., 1995).

Keywords:  Aging; Premature senescence; Replicative senescence; Senescence; Senescence-associated beta-galactosidase; Senescence-associated secretory phenotype (SASP)

DOI:  https://doi.org/10.1016/bs.mcb.2022.09.005
Clin Proteomics. 2024 Jan 30. 21(1): 7

Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma.

Sara R Savage, Yuefan Wang, Lijun Chen, Scott Jewell, Chelsea Newton, Yongchao Dou, Qing Kay Li, Oliver F Bathe, Ana I Robles, Gilbert S Omenn, Mathangi Thiagarajan, Hui Zhang, Galen Hostetter, Bing Zhang.

  BACKGROUND: Omics characterization of pancreatic adenocarcinoma tissue is complicated by the highly heterogeneous and mixed populations of cells. We evaluate the feasibility and potential benefit of using a coring method to enrich specific regions from bulk tissue and then perform proteogenomic analyses.METHODS: We used the Biopsy Trifecta Extraction (BioTExt) technique to isolate cores of epithelial-enriched and stroma-enriched tissue from pancreatic tumor and adjacent tissue blocks. Histology was assessed at multiple depths throughout each core. DNA sequencing, RNA sequencing, and proteomics were performed on the cored and bulk tissue samples. Supervised and unsupervised analyses were performed based on integrated molecular and histology data.
RESULTS: Tissue cores had mixed cell composition at varying depths throughout. Average cell type percentages assessed by histology throughout the core were better associated with KRAS variant allele frequencies than standard histology assessment of the cut surface. Clustering based on serial histology data separated the cores into three groups with enrichment of neoplastic epithelium, stroma, and acinar cells, respectively. Using this classification, tumor overexpressed proteins identified in bulk tissue analysis were assigned into epithelial- or stroma-specific categories, which revealed novel epithelial-specific tumor overexpressed proteins.
CONCLUSIONS: Our study demonstrates the feasibility of multi-omics data generation from tissue cores, the necessity of interval H&E stains in serial histology sections, and the utility of coring to improve analysis over bulk tissue data.

Keywords:  CPTAC; Microenvironment; Proteogenomic; Tissue coring

DOI:  https://doi.org/10.1186/s12014-024-09450-3
Methods Cell Biol. 2024 ;pii: S0091-679X(23)00061-4. [Epub ahead of print]181 151-160

High-throughput assessment of cellular senescence.

Giulia Cerrato, Allan Sauvat, Félix Peyre, Oliver Kepp, Guido Kroemer.

  Cellular senescence is a molecular process that is activated in response to a large variety of distinct stress signals. Mechanistically, cellular senescence is characterized by an arrest in cell cycle accompanied by phenotypic adaptations and physiological alterations including changes in the secretory profile of senescent cells termed the senescence-associated secretory phenotype (SASP). Here we describe a detailed, automation- compatible method for the detection of senescence-associated beta galactosidase (SA-β-gal) activity as a hallmark of cellular senescence using a conventional fluorescent microscope equipped with a transmitted light module. Moreover, we outline a protocol for the automated analysis of cellular senescence using convolutional neural networks (CNNs) and mathematical morphology. In sum, we provide a toolset for the high throughput assessment of cellular senescence based on light microscopy and automated image analysis.

Keywords:  Aging; Cancer; Deep neural networks; Immunity; SA-βgal; Senolytics

DOI:  https://doi.org/10.1016/bs.mcb.2023.02.017
Cell Death Dis. 2024 Jan 30. 15(1): 102

Exosome-derived tRNA fragments tRF-GluCTC-0005 promotes pancreatic cancer liver metastasis by activating hepatic stellate cells.

Wei Chen, Wang Peng, Ronghua Wang, Shuya Bai, Mengdie Cao, Si Xiong, Yanling Li, Yilei Yang, Jingwen Liang, Luyao Liu, Hamza O Yazdani, Yuchong Zhao, Bin Cheng.

Early metastasis is the primary factor in the very poor prognosis of pancreatic ductal adenocarcinoma (PDAC), with liver metastasis being the most common form of distant metastasis in PDAC. To investigate the mechanism of PDAC liver metastasis, we found that PDAC cells can promote the formation of pre-metastatic niches (PMNs) through exosomes to facilitate liver metastasis in the early stage. In our study, hepatic stellate cells (HSCs) were treated with PDAC-derived exosomes (PDAC-exo), and the activation of HSCs was detected. A novel transfer RNA-derived fragment, the tRF-GluCTC-0005 was obtained by small RNA sequencing from serum exosomes of PDAC patients. Bioinformatics analysis and RNA pull-down assays revealed the interaction between WDR1 and tRF-GluCTC-0005. A KPC transgenic mouse model and an AAV-mediated sh-WDR1 mouse model were used to detect the mechanism of liver metastasis in vivo. Finally, the dual luciferase reporter assay, protein mutation truncation assay, Co-IP assay, and flow cytometry assay were used to explore the molecular mechanism in HSCs activation and PMNs formation. We found that the tRF-GluCTC-0005 in exosomes binds to the 3' untranslated region of the mRNA of the WDRl in HSCs and increases mRNA stability. The N-terminals of WDR1 bind to the YAP protein directly, inhibit YAP phosphorylation, and promote the expression of YAP transcription factors. The tRF-GluCTC-0005 in PDAC-exo significantly recruits myeloid-derived suppressor cells (MDSCs) in the liver, creating a PMNs immunosuppressive microenvironment and further advancing liver metastasis from PDAC. Our results suggest that the key of PDAC liver metastasis is the activation of HSCs through upregulation of WDR1 by tRF-GluCTC-0005 in exosomes, which mediates the infiltration of MDSCs to form PMNs.

DOI: https://doi.org/10.1038/s41419-024-06482-3
Curr Opin Cell Biol. 2024 Jan 31. pii: S0955-0674(24)00002-4. [Epub ahead of print]87 102323

Cell competition and the regulation of protein homeostasis.

Shruthi Krishnan, Pranab K Paul, Tristan A Rodriguez.

  The process of embryonic development involves remarkable cellular plasticity, which governs the coordination between cells necessary to build an organism. One role of this plasticity is to ensure that when aberrant cells are eliminated, growth adjustment occurs so that the size of the tissue is maintained. An important regulator of cellular plasticity that ensures cellular cooperation is a fitness-sensing mechanism termed cell competition. During cell competition, cells with defects that lower fitness but do not affect viability, such as those that cause impaired signal transduction, slower cellular growth, mitochondrial dysregulation or impaired protein homeostasis, are killed when surrounded by fitter cells. This is accompanied by the compensatory proliferation of the surviving cells. The underlying factors and mechanisms that demarcate certain cells as less fit than their neighbouring cells and losers of cell competition are still relatively unknown. Recent evidence has pointed to mitochondrial defects and proteotoxic stress as important hallmarks of these loser cells. Here, we review recent advances in this area, focussing on the role of mitochondrial activity and protein homeostasis as major mechanisms determining competitive cell fitness during development and the importance of cell proteostasis in determining cell fitness.

Keywords:  Cell competition; Cell fitness; Losers; Mitochondrial dysregulation; Proteostasis; Winners

DOI:  https://doi.org/10.1016/j.ceb.2024.102323
Am J Physiol Endocrinol Metab. 2024 Jan 31.

Metabolic underpinnings of cancer-related fatigue.

Xinyi Zhang, Rachel J Perry.

  Cancer-related fatigue (CRF) is one of the most prevalent and detrimental complications of cancer. Emerging evidence suggests that obesity and insulin resistance are associated with CRF occurrence and severity in cancer patients and survivors. In this narrative review, we analyzed recent studies including both preclinical and clinical research on the relationship between obesity and/or insulin resistance and CRF. We also describe potential mechanisms for these relationships, though with the caveat that because the mechanisms underlying CRF are incompletely understood, the mechanisms mediating the association between obesity/insulin resistance and CRF are similarly incompletely delineated. The data suggest that, in addition to their effects to worsen CRF by directly promoting tumor growth and metastasis, obesity and insulin resistance may also contribute to CRF by inducing chronic inflammation, neuroendocrinological disturbance, and metabolic alterations. Furthermore, studies suggest that patients with obesity and insulin resistance experience more cancer-induced pain and are at more risk of emotional and behavioral disruptions correlated with CRF. However, other studies implied a potentially paradoxical impact of obesity and insulin resistance to reduce CRF symptoms. Despite the need for further investigation utilizing interventions to directly elucidate the mechanisms of cancer-related fatigue, current evidence demonstrates a correlation between obesity and/or insulin resistance and CRF, and suggests potential therapeutics for CRF by targeting obesity and/or obesity-related mediators.

Keywords:  Cancer metabolism; Cancer-related fatigue

DOI:  https://doi.org/10.1152/ajpendo.00378.2023
Sci Adv. 2024 Feb 02. 10(5): eadj9479

Folate depletion induces erythroid differentiation through perturbation of de novo purine synthesis.

Adam G Maynard, Nancy K Pohl, Annabel P Mueller, Boryana Petrova, Alan Y L Wong, Peng Wang, Andrew J Culhane, Jeannette R Brook, Leah M Hirsch, Ngoc Hoang, Orville Kirkland, Tatum Braun, Sarah Ducamp, Mark D Fleming, Hojun Li, Naama Kanarek.

Folate, an essential vitamin, is a one-carbon acceptor and donor in key metabolic reactions. Erythroid cells harbor a unique sensitivity to folate deprivation, as revealed by the primary pathological manifestation of nutritional folate deprivation: megaloblastic anemia. To study this metabolic sensitivity, we applied mild folate depletion to human and mouse erythroid cell lines and primary murine erythroid progenitors. We show that folate depletion induces early blockade of purine synthesis and accumulation of the purine synthesis intermediate and signaling molecule, 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR), followed by enhanced heme metabolism, hemoglobin synthesis, and erythroid differentiation. This is phenocopied by inhibition of folate metabolism using the inhibitor SHIN1, and by AICAR supplementation. Mechanistically, the metabolically driven differentiation is independent of mechanistic target of rapamycin complex 1 (mTORC1) and adenosine 5'-monophosphate-activated protein kinase (AMPK) and is instead mediated by protein kinase C. Our findings suggest that folate deprivation-induced premature differentiation of erythroid progenitor cells is a molecular etiology to folate deficiency-induced anemia.

DOI: https://doi.org/10.1126/sciadv.adj9479
Cell Rep Med. 2024 Jan 18. pii: S2666-3791(23)00620-1. [Epub ahead of print] 101391

Evidence for a causal link between intra-pancreatic fat deposition and pancreatic cancer: A prospective cohort and Mendelian randomization study.

Hajime Yamazaki, Samantha A Streicher, Lang Wu, Shunichi Fukuhara, Róbert Wagner, Martin Heni, Steven R Grossman, Heinz-Josef Lenz, Veronica Wendy Setiawan, Loïc Le Marchand, Brian Z Huang.

  Prior observational studies suggest an association between intra-pancreatic fat deposition (IPFD) and pancreatic ductal adenocarcinoma (PDAC); however, the causal relationship is unclear. To elucidate causality, we conduct a prospective observational study using magnetic resonance imaging (MRI)-measured IPFD data and also perform a Mendelian randomization study using genetic instruments for IPFD. In the observational study, we use UK Biobank data (N = 29,463, median follow-up: 4.5 years) and find that high IPFD (>10%) is associated with PDAC risk (adjusted hazard ratio [HR]: 3.35, 95% confidence interval [95% CI]: 1.60-7.00). In the Mendelian randomization study, we leverage eight out of nine IPFD-associated genetic variants (p < 5 × 10-8) from a genome-wide association study in the UK Biobank (N = 25,617) and find that genetically determined IPFD is associated with PDAC (odds ratio [OR] per 1-standard deviation [SD] increase in IPFD: 2.46, 95% CI: 1.38-4.40) in the Pancreatic Cancer Cohort Consortium I, II, III (PanScan I-III)/Pancreatic Cancer Case-Control Consortium (PanC4) dataset (8,275 PDAC cases and 6,723 non-cases). This study provides evidence for a potential causal role of IPFD in the pathogenesis of PDAC. Thus, reducing IPFD may lower PDAC risk.

Keywords:  fatty pancreas; pancreas cancer; pancreas fat; pancreatic adenocarcinoma; pancreatic fat; pancreatic steatosis

DOI:  https://doi.org/10.1016/j.xcrm.2023.101391
Nat Cell Biol. 2024 Feb 02.

A serendipitous discovery of a family of membrane remodelling proteins.

Pietro De Camilli.

DOI: https://doi.org/10.1038/s41556-023-01307-5
Nat Biotechnol. 2024 Feb 01.

A new mass analyzer shakes up the proteomics field.

Bernhard Kuster, Johanna Tüshaus, Florian P Bayer.

DOI: https://doi.org/10.1038/s41587-024-02129-y
Front Aging. 2024 ;5 1334261

The hallmarks of aging as a conceptual framework for health and longevity research.

Antonio G Tartiere, José M P Freije, Carlos López-Otín.

  The inexorability of the aging process has sparked the curiosity of human beings since ancient times. However, despite this interest and the extraordinary scientific advances in the field, the complexity of the process has hampered its comprehension. In this context, The Hallmarks of Aging were defined in 2013 with the aim of establishing an organized, systematic and integrative view of this topic, which would serve as a conceptual framework for aging research. Ten years later and promoted by the progress in the area, an updated version included three new hallmarks while maintaining the original scope. The aim of this review is to determine to what extent The Hallmarks of Aging achieved the purpose that gave rise to them. For this aim, we have reviewed the literature citing any of the two versions of The Hallmarks of Aging and conclude that they have served as a conceptual framework not only for aging research but also for related areas of knowledge. Finally, this review discusses the new candidates to become part of the Hallmarks list, analyzing the evidence that supports whether they should or should not be incorporated.

Keywords:  biomarkers; healthspan; lifespan; progeria; rejuvenation; senescence

DOI:  https://doi.org/10.3389/fragi.2024.1334261
iScience. 2024 Feb 16. 27(2): 108849

Caveolae disassemble upon membrane lesioning and foster cell survival.

Martin Štefl, Masanari Takamiya, Volker Middel, Miyase Tekpınar, Karin Nienhaus, Tanja Beil, Sepand Rastegar, Uwe Strähle, Gerd Ulrich Nienhaus.

  Repair of lesions in the plasma membrane is key to sustaining cellular homeostasis. Cells maintain cytoplasmic as well as membrane-bound stores of repair proteins that can rapidly precipitate at the site of membrane lesions. However, little is known about the origins of lipids and proteins for resealing and repair of the plasma membrane. Here we study the dynamics of caveolar proteins after laser-induced lesioning of plasma membranes of mammalian C2C12 tissue culture cells and muscle cells of intact zebrafish embryos. Single-molecule diffusivity measurements indicate that caveolar clusters break up into smaller entities after wounding. Unlike Annexins and Dysferlin, caveolar proteins do not accumulate at the lesion patch. In caveolae-depleted cavin1a knockout zebrafish embryos, lesion patch formation is impaired, and injured cells show reduced survival. Our data suggest that caveolae disassembly releases surplus plasma membrane near the lesion to facilitate membrane repair after initial patch formation for emergency sealing.

Keywords:  Cell biology; Membrane architecture

DOI:  https://doi.org/10.1016/j.isci.2024.108849
Nat Cell Biol. 2024 Feb 01.

Low-input lipidomics reveals lipid metabolism remodelling during early mammalian embryo development.

Ling Zhang, Jing Zhao, Sin Man Lam, Lang Chen, Yingzhuo Gao, Wenjie Wang, Yuyan Xu, Tianyu Tan, Hua Yu, Min Zhang, Xufeng Liao, Mengchen Wu, Tianyun Zhang, Jie Huang, Bowen Li, Quan D Zhou, Ning Shen, Hyeon Jeong Lee, Cunqi Ye, Da Li, Guanghou Shui, Jin Zhang.

Lipids are indispensable for energy storage, membrane structure and cell signalling. However, dynamic changes in various categories of endogenous lipids in mammalian early embryonic development have not been systematically characterized. Here we comprehensively investigated the dynamic lipid landscape during mouse and human early embryo development. Lipid signatures of different developmental stages are distinct, particularly for the phospholipid classes. We highlight that the high degree of phospholipid unsaturation is a conserved feature as embryos develop to the blastocyst stage. Moreover, we show that lipid desaturases such as SCD1 are required for in vitro blastocyst development and blastocyst implantation. One of the mechanisms is through the regulation of unsaturated fatty-acid-mediated fluidity of the plasma membrane and apical proteins and the establishment of apical-basal polarity during development of the eight-cell embryo to the blastocyst. Overall, our study provides an invaluable resource about the remodelling of the endogenous lipidome in mammalian preimplantation embryo development and mechanistic insights into the regulation of embryogenesis and implantation by lipid unsaturation.

DOI: https://doi.org/10.1038/s41556-023-01341-3
Gastroenterol Clin North Am. 2024 Mar;pii: S0889-8553(23)00111-5. [Epub ahead of print]53(1): 57-84

Early Cancerous Lesions of the Pancreas and Ampulla: Current Concepts and Challenges.

Olca Basturk, N Volkan Adsay.

  Owing to the increased use of advanced imaging techniques, mass-forming (cystic/intraductal) preinvasive neoplasms are being detected much more frequently and they have rapidly become one of the main focuses of interests in medical field. These neoplasms have very distinctive clinical and radiographic findings, exhibit a spectrum of dysplastic transformation, from low-grade dysplasia to high-grade dysplasia, and may be associated with an invasive carcinoma. Accounting for about 5% to 10% of pancreatic ductal adenocarcinomas, they provide a curable target subset in an otherwise biologically dismal pancreas cancer category.

Keywords:  Ampulla; IAPN; IOPN; IPMN; ITPN; MCN; PanIN; Pancreas

DOI:  https://doi.org/10.1016/j.gtc.2023.11.004
Nature. 2024 Jan 31.

7-Dehydrocholesterol is an endogenous suppressor of ferroptosis.

Florencio Porto Freitas, Hamed Alborzinia, Ancély Ferreira Dos Santos, Palina Nepachalovich, Lohans Pedrera, Omkar Zilka, Alex Inague, Corinna Klein, Nesrine Aroua, Kamini Kaushal, Bettina Kast, Svenja M Lorenz, Viktoria Kunz, Helene Nehring, Thamara N Xavier da Silva, Zhiyi Chen, Sena Atici, Sebastian G Doll, Emily L Schaefer, Ifedapo Ekpo, Werner Schmitz, Aline Horling, Peter Imming, Sayuri Miyamoto, Ann M Wehman, Thiago C Genaro-Mattos, Karoly Mirnics, Lokender Kumar, Judith Klein-Seetharaman, Svenja Meierjohann, Isabel Weigand, Matthias Kroiss, Georg W Bornkamm, Fernando Gomes, Luis Eduardo Soares Netto, Manjima B Sathian, David B Konrad, Douglas F Covey, Bernhard Michalke, Kurt Bommert, Ralf C Bargou, Ana Garcia-Saez, Derek A Pratt, Maria Fedorova, Andreas Trumpp, Marcus Conrad, José Pedro Friedmann Angeli.

Ferroptosis is a form of cell death that has received considerable attention not only as a means to eradicate defined tumour entities but also because it provides unforeseen insights into the metabolic adaptation that tumours exploit to counteract phospholipid oxidation1,2. Here, we identify proferroptotic activity of 7-dehydrocholesterol reductase (DHCR7) and an unexpected prosurvival function of its substrate, 7-dehydrocholesterol (7-DHC). Although previous studies suggested that high concentrations of 7-DHC are cytotoxic to developing neurons by favouring lipid peroxidation3, we now show that 7-DHC accumulation confers a robust prosurvival function in cancer cells. Because of its far superior reactivity towards peroxyl radicals, 7-DHC effectively shields (phospho)lipids from autoxidation and subsequent fragmentation. We provide validation in neuroblastoma and Burkitt's lymphoma xenografts where we demonstrate that the accumulation of 7-DHC is capable of inducing a shift towards a ferroptosis-resistant state in these tumours ultimately resulting in a more aggressive phenotype. Conclusively, our findings provide compelling evidence of a yet-unrecognized antiferroptotic activity of 7-DHC as a cell-intrinsic mechanism that could be exploited by cancer cells to escape ferroptosis.

DOI: https://doi.org/10.1038/s41586-023-06878-9
Nat Commun. 2024 Feb 01. 15(1): 953

Mitochondrial protein C15ORF48 is a stress-independent inducer of autophagy that regulates oxidative stress and autoimmunity.

Yuki Takakura, Moeka Machida, Natsumi Terada, Yuka Katsumi, Seika Kawamura, Kenta Horie, Maki Miyauchi, Tatsuya Ishikawa, Nobuko Akiyama, Takao Seki, Takahisa Miyao, Mio Hayama, Rin Endo, Hiroto Ishii, Yuya Maruyama, Naho Hagiwara, Tetsuya J Kobayashi, Naoto Yamaguchi, Hiroyuki Takano, Taishin Akiyama, Noritaka Yamaguchi.

Autophagy is primarily activated by cellular stress, such as starvation or mitochondrial damage. However, stress-independent autophagy is activated by unclear mechanisms in several cell types, such as thymic epithelial cells (TECs). Here we report that the mitochondrial protein, C15ORF48, is a critical inducer of stress-independent autophagy. Mechanistically, C15ORF48 reduces the mitochondrial membrane potential and lowers intracellular ATP levels, thereby activating AMP-activated protein kinase and its downstream Unc-51-like kinase 1. Interestingly, C15ORF48-dependent induction of autophagy upregulates intracellular glutathione levels, promoting cell survival by reducing oxidative stress. Mice deficient in C15orf48 show a reduction in stress-independent autophagy in TECs, but not in typical starvation-induced autophagy in skeletal muscles. Moreover, C15orf48-/- mice develop autoimmunity, which is consistent with the fact that the stress-independent autophagy in TECs is crucial for the thymic self-tolerance. These results suggest that C15ORF48 induces stress-independent autophagy, thereby regulating oxidative stress and self-tolerance.

DOI: https://doi.org/10.1038/s41467-024-45206-1