bims-cagime 2023-11-05 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2023–11–05
25 papers selected by
Kıvanç Görgülü, Technical University of Munich

Metabolic pathway analysis using stable isotopes in patients with cancer.
A mechanosensitive caveolae-invadosome interplay drives matrix remodelling for cancer cell invasion.
Alone you go faster, together you go farther.
The Lin28b/Wnt5a axis drives pancreas cancer through crosstalk between cancer associated fibroblasts and tumor epithelium.
Septins modulate the autophagy response after nutrient starvation.
IL-1β+ macrophages fuel pathogenic inflammation in pancreatic cancer.
Differential modulation of cellular phenotype and drug sensitivity by extracellular matrix proteins in primary and metastatic pancreatic cancer cells.
Emerging markers of cancer cachexia and their relationship to sarcopenia.
Hyperinsulinemia acts via acinar insulin receptors to initiate pancreatic cancer by increasing digestive enzyme production and inflammation.
Mitochondrial complexome and import network.
PDK4-dependent hypercatabolism and lactate production of senescent cells promotes cancer malignancy.
Tumor-specific GPX4 degradation enhances ferroptosis-initiated antitumor immune response in mouse models of pancreatic cancer.
Targeting MTHFD2 to exploit cancer-specific metabolism and the DNA damage response.
Protocol of the IntenSify-Trial: An open-label phase I trial of the CYP3A inhibitor cobicistat and the cytostatics gemcitabine and nab-paclitaxel in patients with advanced stage or metastatic pancreatic ductal adenocarcinoma to evaluate the combination's pharmacokinetics, safety, and efficacy.
Autoregulatory control of mitochondrial glutathione homeostasis.
Allosteric PI3K-alpha inhibition overcomes on-target resistance to orthosteric inhibitors mediated by secondary PIK3CA mutations.
Inducible tricolor reporter mouse for parallel imaging of lysosomes, mitochondria, and microtubules.
Cancer-on-chip models for metastasis: importance of the tumor microenvironment.
Differential lipid analysis of oxaliplatin-sensitive and resistant HCT116 cells reveals different levels of drug-induced lipid droplet formation.
Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors.
The mechanism of Atg15-mediated membrane disruption in autophagy.
Clonal tracking in cancer and metastasis.
mSphere of Influence: Hooray for HaloTag! A novel tool to study autophagy in mammalian cells.
Acute pancreatitis and metabolic syndrome: genetic correlations and causal associations.
Protocol for isolating single cells from human pancreatic cancer tissues and analyzing major immune cell populations using flow cytometry.

Nat Rev Cancer. 2023 Oct 31.

Metabolic pathway analysis using stable isotopes in patients with cancer.

Caroline R Bartman, Brandon Faubert, Joshua D Rabinowitz, Ralph J DeBerardinis.

Metabolic reprogramming is central to malignant transformation and cancer cell growth. How tumours use nutrients and the relative rates of reprogrammed pathways are areas of intense investigation. Tumour metabolism is determined by a complex and incompletely defined combination of factors intrinsic and extrinsic to cancer cells. This complexity increases the value of assessing cancer metabolism in disease-relevant microenvironments, including in patients with cancer. Stable-isotope tracing is an informative, versatile method for probing tumour metabolism in vivo. It has been used extensively in preclinical models of cancer and, with increasing frequency, in patients with cancer. In this Review, we describe approaches for using in vivo isotope tracing to define fuel preferences and pathway engagement in tumours, along with some of the principles that have emerged from this work. Stable-isotope infusions reported so far have revealed that in humans, tumours use a diverse set of nutrients to supply central metabolic pathways, including the tricarboxylic acid cycle and amino acid synthesis. Emerging data suggest that some activities detected by stable-isotope tracing correlate with poor clinical outcomes and may drive cancer progression. We also discuss current challenges in isotope tracing, including comparisons of in vivo and in vitro models, and opportunities for future discovery in tumour metabolism.

DOI: https://doi.org/10.1038/s41568-023-00632-z
Nat Cell Biol. 2023 Oct 30.

A mechanosensitive caveolae-invadosome interplay drives matrix remodelling for cancer cell invasion.

Pedro Monteiro, David Remy, Eline Lemerle, Fiona Routet, Anne-Sophie Macé, Chloé Guedj, Benoit Ladoux, Stéphane Vassilopoulos, Christophe Lamaze, Philippe Chavrier.

Invadosomes and caveolae are mechanosensitive structures that are implicated in metastasis. Here, we describe a unique juxtaposition of caveola clusters and matrix degradative invadosomes at contact sites between the plasma membrane of cancer cells and constricting fibrils both in 2D and 3D type I collagen matrix environments. Preferential association between caveolae and straight segments of the fibrils, and between invadosomes and bent segments of the fibrils, was observed along with matrix remodelling. Caveola recruitment precedes and is required for invadosome formation and activity. Reciprocally, invadosome disruption results in the accumulation of fibril-associated caveolae. Moreover, caveolae and the collagen receptor β1 integrin co-localize at contact sites with the fibrils, and integrins control caveola recruitment to fibrils. In turn, caveolae mediate the clearance of β1 integrin and collagen uptake in an invadosome-dependent and collagen-cleavage-dependent mechanism. Our data reveal a reciprocal interplay between caveolae and invadosomes that coordinates adhesion to and proteolytic remodelling of confining fibrils to support tumour cell dissemination.

DOI: https://doi.org/10.1038/s41556-023-01272-z
Mol Oncol. 2023 Oct 30.

Alone you go faster, together you go farther.

Nicola Aceto.

  The metastatic process is an extraordinarily complex step-by-step procedure, characterized by many analogies with migratory patterns of humans or animals across our planet. The ongoing interrogation of circulating tumor cells (CTCs), caught in the act of spreading from one location to another, is revealing distinct behaviors including biological, physical, and mechanical features that impact on their likelihood to form metastasis. In this viewpoint, I will discuss some of these findings and provide a perspective on the metastatic journey, open questions, as well as opportunities to exploit some of the most recent discoveries for the development of anti-metastasis medicines.

Keywords:  Circulating tumor cells; circulating tumor cell clusters; colonization; intravasation; metastasis

DOI:  https://doi.org/10.1002/1878-0261.13549
Nat Commun. 2023 Oct 28. 14(1): 6885

The Lin28b/Wnt5a axis drives pancreas cancer through crosstalk between cancer associated fibroblasts and tumor epithelium.

Zhaoqi Shu, Minghe Fan, Bo Tu, Zhiheng Tang, Haojie Wang, Haimeng Li, Hengchao Li, Meng Yuan, Jingru Bai, Sihan Huo, Lina Wang, Wei-Guo Zhu, Wei Wang, Xiaoyun Liu, Shaokun Shu, Ying Zhao.

Bidirectional signal transduction between tumor epithelial cells and tumor microenvironment (TME) is important for tumor development. Here we show that Lin28b/let-7 pathway is indispensable for modulating the expression of Wnt5a in tumor epithelium, which could be secreted and then up-regulates Lin28b in cancer-associated fibroblasts (CAFs). Moreover, we demonstrate that Lin28b in CAFs promoted growth of PDAC by inducing cytokine PCSK9's production. Using an orthotopic mouse model of PDAC, we find that depletion of Lin28b in CAFs reduced tumor weight, highlighting the importance of Lin28b in PDAC stroma. Thus, our study shows that the Lin28b-Wnt5a axis plays a critical role in bidirectional crosstalk between pancreatic tumor epithelium and TME and results in a pro-‍tumorigenic contexture.

DOI: https://doi.org/10.1038/s41467-023-42508-8
Mol Biol Cell. 2023 Nov 01. mbcE22110520

Septins modulate the autophagy response after nutrient starvation.

Luis Perucho-Jaimes, Jonathan Do, Alexandria Van Elgort, Kenneth B Kaplan.

The pathways that induce macroautophagy (referred to as autophagy hereafter) in response to the stress of starvation are well conserved and essential under nutrient limiting conditions. However, less is understood about the mechanisms that modulate the autophagy response. Here we present evidence that after induction of autophagy in budding yeast septin filaments rapidly assemble into discrete patches distributed along the cell cortex. These patches gradually mature over 12h of nutrient deprivation to form extended structures around Atg9-membranes tethered at the cortical endoplasmic reticulum, a class of membranes that are limiting for autophagosome biogenesis. Loss of cortical septin structures alters the kinetics of autophagy activation and most dramatically extends the duration of the autophagy response. In wild type cells, diffusion of Atg9-membranes at the cell cortex undergoes transient pauses that are dependent on septins, and septins at the bud neck block the diffusion of Atg9-membranes between mother and daughter cells. We conclude that septins reorganize at the cell cortex during autophagy to locally limit access of Atg9-membranes to autophagosome assembly sites, and thus modulate the autophagy response during nutrient-deprivation. [Media: see text] [Media: see text] [Media: see text] [Media: see text].

DOI: https://doi.org/10.1091/mbc.E22-11-0520
Nature. 2023 Nov 01.

IL-1β+ macrophages fuel pathogenic inflammation in pancreatic cancer.

Nicoletta Caronni, Federica La Terza, Francesco M Vittoria, Giulia Barbiera, Luca Mezzanzanica, Vincenzo Cuzzola, Simona Barresi, Marta Pellegatta, Paolo Canevazzi, Garett Dunsmore, Carlo Leonardi, Elisa Montaldo, Eleonora Lusito, Erica Dugnani, Antonio Citro, Melissa S F Ng, Marco Schiavo Lena, Denise Drago, Annapaola Andolfo, Silvia Brugiapaglia, Alessandro Scagliotti, Alessandra Mortellaro, Vincenzo Corbo, Zhaoyuan Liu, Anna Mondino, Paolo Dellabona, Lorenzo Piemonti, Carla Taveggia, Claudio Doglioni, Paola Cappello, Francesco Novelli, Matteo Iannacone, Lai Guan Ng, Florent Ginhoux, Stefano Crippa, Massimo Falconi, Chiara Bonini, Luigi Naldini, Marco Genua, Renato Ostuni.

Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with high resistance to therapies1. Inflammatory and immunomodulatory signals co-exist in the pancreatic tumour microenvironment, leading to dysregulated repair and cytotoxic responses. Tumour-associated macrophages (TAMs) have key roles in PDAC2, but their diversity has prevented therapeutic exploitation. Here we combined single-cell and spatial genomics with functional experiments to unravel macrophage functions in pancreatic cancer. We uncovered an inflammatory loop between tumour cells and interleukin-1β (IL-1β)-expressing TAMs, a subset of macrophages elicited by a local synergy between prostaglandin E2 (PGE2) and tumour necrosis factor (TNF). Physical proximity with IL-1β+ TAMs was associated with inflammatory reprogramming and acquisition of pathogenic properties by a subset of PDAC cells. This occurrence was an early event in pancreatic tumorigenesis and led to persistent transcriptional changes associated with disease progression and poor outcomes for patients. Blocking PGE2 or IL-1β activity elicited TAM reprogramming and antagonized tumour cell-intrinsic and -extrinsic inflammation, leading to PDAC control in vivo. Targeting the PGE2-IL-1β axis may enable preventive or therapeutic strategies for reprogramming of immune dynamics in pancreatic cancer.

DOI: https://doi.org/10.1038/s41586-023-06685-2
Mol Biol Cell. 2023 Oct 30. mbcE23020075

Differential modulation of cellular phenotype and drug sensitivity by extracellular matrix proteins in primary and metastatic pancreatic cancer cells.

Olalekan H Usman, Sampath Kumar, Reddick R Walker, Gengqiang Xie, Hyeje Sumajit, AbdelAziz R Jalil, Subramanian Ramakrishnan, Lawrence J Dooling, Yue Julia Wang, Jerome Irianto.

Pancreatic cancer adenocarcinoma (PDAC) is reported to be the third highest cause of cancer-related deaths in the United States. PDAC is known for its high proportion of stroma, which accounts for 90% of the tumor mass. The stroma is made up of extracellular matrix (ECM) and non-malignant cells such as inflammatory cells, cancer-associated fibroblasts, and lymphatic and blood vessels. Here, we decoupled the effects of the ECM on PDAC cell lines by culturing cells on surfaces coated with different ECM proteins. Our data show that the primary tumor-derived cell lines have different morphology depending on the ECM proteins on which they are cultured, while metastatic lesion-derived PDAC lines' morphology does not change with respect to the different ECM proteins. Similarly, ECM proteins modulate the proliferation rate and the gemcitabine sensitivity of the primary tumor PDAC cell lines, but not the metastatic PDAC lines. Lastly, transcriptomics analysis of the primary tumor PDAC cells cultured on different ECM proteins reveals the regulation of various pathways, such as cell cycle, cell adhesion molecules, and focal adhesion, including the regulation of several integrin genes that are essential for ECM recognition.

DOI: https://doi.org/10.1091/mbc.E23-02-0075
J Cancer Res Clin Oncol. 2023 Oct 31.

Emerging markers of cancer cachexia and their relationship to sarcopenia.

Melanie Lipshitz, J Visser, R Anderson, D G Nel, T Smit, H C Steel, B Rapoport.

   PURPOSE: Emerging biomarkers of cancer cachexia and their roles in sarcopenia and prognosis are poorly understood. Baseline assessments of anthropometrics, sarcopenia, cachexia status and biomarkers of cachexia were measured in patients with advanced cancer and healthy controls. Thereafter, relationships of the biomarkers with cachexia and sarcopenia were explored.
METHODS: A prospective case-control design was used, including 40 patients with advanced cancer and 40 gender, age-matched controls. Bioelectrical impedance [skeletal muscle index (SMI)] and hand dynamometry [hand grip strength (HGS)] assessed sarcopenia and a validated tool classified cancer cachexia. Albumin, lymphocyte and platelet counts, haemoglobin, C-reactive protein (CRP), pro-inflammatory cytokines/chemokines and citrullinated histone H3 (H3Cit) were measured.
RESULTS: Patients had significantly lower SMI (6.67 kg/m2 versus 7.67 kg/m2, p = < 0.01) and HGS (24.42 kg versus 29.62 kg) compared to controls, with 43% being sarcopenic. Significant differences were found for albumin, lymphocyte and platelet counts, haemoglobin, CRP, and tumour necrosis factor α (TNFα), (p < 0.01). Interleukin (IL)-6 (p < 0.04), IL-8 (p = 0.02), neutrophil/lymphocyte ratio (NLR), p = 0.02, platelet/lymphocyte (PLR) ratio, p < 0.01 and systemic immune inflammatory index (SII), p < 0.01 differed significantly. No difference was observed for CXC motif chemokine ligand 5 [CXCL5 or epithelial neutrophil-activating peptide 78 (ENA78)] or H3Cit. Albumin and haemoglobin correlated negatively with total protein, skeletal muscle mass and SMI (all p < 0.01). The presence of sarcopenia associated significantly with albumin, haemoglobin and CRP.
CONCLUSION: Significant relationships and differences of haemoglobin, CRP and albumin supports future use of these biomarkers in cancer cachexia. CXCL5 and H3Cit as valuable biomarkers in cancer cachexia remains to be defined.

Keywords:  Biomarkers; Cachexia; Hand grip strength; Sarcopenia; Skeletal muscle index

DOI:  https://doi.org/10.1007/s00432-023-05465-9
Cell Metab. 2023 Oct 26. pii: S1550-4131(23)00372-8. [Epub ahead of print]

Hyperinsulinemia acts via acinar insulin receptors to initiate pancreatic cancer by increasing digestive enzyme production and inflammation.

Anni M Y Zhang, Yi Han Xia, Jeffrey S H Lin, Ken H Chu, Wei Chuan K Wang, Titine J J Ruiter, Jenny C C Yang, Nan Chen, Justin Chhuor, Shilpa Patil, Haoning Howard Cen, Elizabeth J Rideout, Vincent R Richard, David F Schaeffer, Rene P Zahedi, Christoph H Borchers, James D Johnson, Janel L Kopp.

  The rising pancreatic cancer incidence due to obesity and type 2 diabetes is closely tied to hyperinsulinemia, an independent cancer risk factor. Previous studies demonstrated reducing insulin production suppressed pancreatic intraepithelial neoplasia (PanIN) pre-cancerous lesions in Kras-mutant mice. However, the pathophysiological and molecular mechanisms remained unknown, and in particular it was unclear whether hyperinsulinemia affected PanIN precursor cells directly or indirectly. Here, we demonstrate that insulin receptors (Insr) in KrasG12D-expressing pancreatic acinar cells are dispensable for glucose homeostasis but necessary for hyperinsulinemia-driven PanIN formation in the context of diet-induced hyperinsulinemia and obesity. Mechanistically, this was attributed to amplified digestive enzyme protein translation, triggering of local inflammation, and PanIN metaplasia in vivo. In vitro, insulin dose-dependently increased acinar-to-ductal metaplasia formation in a trypsin- and Insr-dependent manner. Collectively, our data shed light on the mechanisms connecting obesity-driven hyperinsulinemia and pancreatic cancer development.

Keywords:  Kras; PanIN; acinar cells; hyperinsulinemia; inflammation; insulin receptor; insulin resistance; obesity; pancreatic cancer; pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.1016/j.cmet.2023.10.003
Trends Cell Biol. 2023 Oct 30. pii: S0962-8924(23)00208-8. [Epub ahead of print]

Mitochondrial complexome and import network.

Fabian den Brave, Uwe Schulte, Bernd Fakler, Nikolaus Pfanner, Thomas Becker.

  Mitochondria perform crucial functions in cellular metabolism, protein and lipid biogenesis, quality control, and signaling. The systematic analysis of protein complexes and interaction networks provided exciting insights into the structural and functional organization of mitochondria. Most mitochondrial proteins do not act as independent units, but are interconnected by stable or dynamic protein-protein interactions. Protein translocases are responsible for importing precursor proteins into mitochondria and form central elements of several protein interaction networks. These networks include molecular chaperones and quality control factors, metabolite channels and respiratory chain complexes, and membrane and organellar contact sites. Protein translocases link the distinct networks into an overarching network, the mitochondrial import network (MitimNet), to coordinate biogenesis, membrane organization and function of mitochondria.

Keywords:  cell organelles; energetics; metabolism; mitochondria; morphology; protein assembly; protein networks; protein sorting

DOI:  https://doi.org/10.1016/j.tcb.2023.10.004
Nat Metab. 2023 Oct 30.

PDK4-dependent hypercatabolism and lactate production of senescent cells promotes cancer malignancy.

Xuefeng Dou, Qiang Fu, Qilai Long, Shuning Liu, Yejun Zou, Da Fu, Qixia Xu, Zhirui Jiang, Xiaohui Ren, Guilong Zhang, Xiaoling Wei, Qingfeng Li, Judith Campisi, Yuzheng Zhao, Yu Sun.

Senescent cells remain metabolically active, but their metabolic landscape and resulting implications remain underexplored. Here, we report upregulation of pyruvate dehydrogenase kinase 4 (PDK4) upon senescence, particularly in some stromal cell lines. Senescent cells display a PDK4-dependent increase in aerobic glycolysis and enhanced lactate production but maintain mitochondrial respiration and redox activity, thus adopting a special form of metabolic reprogramming. Medium from PDK4+ stromal cells promotes the malignancy of recipient cancer cells in vitro, whereas inhibition of PDK4 causes tumor regression in vivo. We find that lactate promotes reactive oxygen species production via NOX1 to drive the senescence-associated secretory phenotype, whereas PDK4 suppression reduces DNA damage severity and restrains the senescence-associated secretory phenotype. In preclinical trials, PDK4 inhibition alleviates physical dysfunction and prevents age-associated frailty. Together, our study confirms the hypercatabolic nature of senescent cells and reveals a metabolic link between cellular senescence, lactate production, and possibly, age-related pathologies, including but not limited to cancer.

DOI: https://doi.org/10.1038/s42255-023-00912-w
Sci Transl Med. 2023 Nov;15(720): eadg3049

Tumor-specific GPX4 degradation enhances ferroptosis-initiated antitumor immune response in mouse models of pancreatic cancer.

Jingbo Li, Jiao Liu, Zhuan Zhou, Runliu Wu, Xin Chen, Chunhua Yu, Brent Stockwell, Guido Kroemer, Rui Kang, Daolin Tang.

Lipid peroxidation-dependent ferroptosis has become an emerging strategy for tumor therapy. However, current strategies not only selectively induce ferroptosis in malignant cells but also trigger ferroptosis in immune cells simultaneously, which can compromise anti-tumor immunity. Here, we used In-Cell Western assays combined with an unbiased drug screening to identify the compound N6F11 as a ferroptosis inducer that triggered the degradation of glutathione peroxidase 4 (GPX4), a key ferroptosis repressor, specifically in cancer cells. N6F11 did not cause the degradation of GPX4 in immune cells, including dendritic, T, natural killer, and neutrophil cells. Mechanistically, N6F11 bound to the RING domain of E3 ubiquitin ligase tripartite motif containing 25 (TRIM25) in cancer cells to trigger TRIM25-mediated K48-linked ubiquitination of GPX4, resulting in its proteasomal degradation. Functionally, N6F11 treatment caused ferroptotic cancer cell death that initiated HMGB1-dependent antitumor immunity mediated by CD8+ T cells. N6F11 also sensitized immune checkpoint blockade that targeted CD274/PD-L1 in advanced cancer models, including genetically engineered mouse models of pancreatic cancer driven by KRAS and TP53 mutations. These findings may establish a safe and efficient strategy to boost ferroptosis-driven antitumor immunity.

DOI: https://doi.org/10.1126/scitranslmed.adg3049
Cancer Res. 2023 Nov 03.

Targeting MTHFD2 to exploit cancer-specific metabolism and the DNA damage response.

Louise Ramos, Martin Henriksson, Thomas Helleday, Alanna C Green.

The one-carbon metabolism enzyme methylenetetrahydrofolate dehydrogenase/cyclohydrolase 2 (MTHFD2) is a promising therapeutic target in cancer. MTHFD2 is upregulated across numerous cancer types, promotes growth and metastasis of cancer, and correlates with poorer survival. Recent studies have developed small molecule inhibitors of the isozymes MTHFD2 and MTHFD1 that show promise as anti-cancer agents through different mechanisms. This review discusses the current understanding of the function of MTHFD2 in cancer and the status of inhibitors for treating MTHFD2-overexpressing cancers.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-1290
Clin Transl Sci. 2023 Nov 03.

Protocol of the IntenSify-Trial: An open-label phase I trial of the CYP3A inhibitor cobicistat and the cytostatics gemcitabine and nab-paclitaxel in patients with advanced stage or metastatic pancreatic ductal adenocarcinoma to evaluate the combination's pharmacokinetics, safety, and efficacy.

Nicolas Hohmann, Martin Ronald Sprick, Azaz Ahmed, Jürgen Burhenne, Marietta Kirchner, Lucian Le Cornet, Markus Kratzmann, Jacek Hajda, Albrecht Stenzinger, Karen Steindorf, Stefan Delorme, Heinz-Peter Schlemmer, Sabine Riethdorf, Ron van Schaik, Klaus Pantel, Jens Siveke, Thomas Seufferlein, Dirk Jäger, Walter E Haefeli, Andreas Trumpp, Christoph Springfeld.

Expression of CYP3A5 protein is a basal and acquired resistance mechanism of pancreatic ductal adenocarcinoma cells conferring protection against the CYP3A and CYP2C8 substrate paclitaxel through metabolic degradation. Inhibition of CYP3A isozymes restores the cells sensitivity to paclitaxel. The combination of gemcitabine and nab-paclitaxel is an established regimen for the treatment of metastasized or locally advanced inoperable pancreatic cancer. Cobicistat is a CYP3A inhibitor developed for the pharmacoenhancement of protease inhibitors. The addition of cobicistat to gemcitabine and nab-paclitaxel may increase the antitumor effect. We will conduct a phase I dose escalation trial with a classical 3 + 3 design to investigate the safety, tolerability, and pharmacokinetics (PKs) of gemcitabine, nab-paclitaxel, and cobicistat. Although the doses of gemcitabine (1000 mg/m2 ) and cobicistat (150 mg) are fixed, three dose levels of nab-paclitaxel (75, 100, and 125 mg/m2 ) will be explored to account for a potential PK drug interaction. After the dose escalation phase, we will set the recommended dose for expansion (RDE) and treat up to nine patients in an expansion part of the trial. The trial is registered under the following identifiers EudraCT-Nr. 2019-001439-29, drks.de: DRKS00029409, and ct.gov: NCT05494866. Overcoming resistance to paclitaxel by CYP3A5 inhibition may lead to an increased efficacy of the gemcitabine and nab-paclitaxel regimen. Safety, efficacy, PK, and RDE data need to be acquired before investigating this combination in a large-scale clinical study.

DOI: https://doi.org/10.1111/cts.13661
Science. 2023 Nov 02. eadf4154

Autoregulatory control of mitochondrial glutathione homeostasis.

Yuyang Liu, Shanshan Liu, Anju Tomar, Frederick S Yen, Gokhan Unlu, Nathalie Ropek, Ross A Weber, Ying Wang, Artem Khan, Mark Gad, Junhui Peng, Erdem Terzi, Hanan Alwaseem, Alexandra E Pagano, Søren Heissel, Henrik Molina, Benjamin Allwein, Timothy C Kenny, Richard L Possemato, Li Zhao, Richard K Hite, Ekaterina V Vinogradova, Sheref S Mansy, Kıvanç Birsoy.

Mitochondria must maintain adequate amounts of metabolites for protective and biosynthetic functions. However, how mitochondria sense the abundance of metabolites and regulate metabolic homeostasis is not well understood. We focused on glutathione (GSH), a critical redox metabolite in mitochondria and identified a feedback mechanism that controls its abundance through the mitochondrial GSH transporter, SLC25A39. Under physiological conditions, SLC25A39 is rapidly degraded by a mitochondrial protease, AFG3L2. Depletion of GSH dissociates AFG3L2 from SLC25A39, causing a compensatory increase in mitochondrial GSH uptake. Genetic and proteomic analysis identified a putative iron-sulfur cluster in the matrix-facing loop of SLC25A39 to be essential for this regulation, coupling mitochondrial iron homeostasis to GSH import. Altogether, our work revealed a paradigm for the autoregulatory control of metabolic homeostasis in organelles.

DOI: https://doi.org/10.1126/science.adf4154
Cancer Discov. 2023 Nov 02.

Allosteric PI3K-alpha inhibition overcomes on-target resistance to orthosteric inhibitors mediated by secondary PIK3CA mutations.

Andreas Varkaris, Ferran Fece de la Cruz, Elizabeth E Martin, Bryanna L Norden, Nicholas Chevalier, Allison M Kehlmann, Ignaty Leshchiner, Haley Barnes, Sara Ehnstrom, Anastasia-Maria Stavridi, Xin Yuan, Janice S Kim, Haley Ellis, Alkistis Papatheodoridi, Hakan Gunaydin, Brian P Danysh, Laxmi Parida, Ioannis Sanidas, Yongli Ji, Kayao Lau, Gerburg M Wulf, Aditya Bardia, Laura M Spring, Steven J Isakoff, Jochen K Lennerz, Levi Pierce, Ermira Pazolli, Gad Getz, Ryan B Corcoran, Dejan Juric.

PIK3CA mutations occur in ~8% of cancers, including ~40% of HR-positive breast cancers, where the PI3K-alpha (PI3Ka)-selective inhibitor alpelisib is FDA-approved in combination with fulvestrant. Although prior studies have identified resistance mechanisms, such as PTEN loss, clinical acquired resistance to PI3Ka inhibitors remains poorly understood. Through serial liquid biopsies and rapid autopsies in 39 patients with advanced breast cancer developing acquired resistance to PI3Ka-inhibitors, we observe that 50% of patients acquire genomic alterations within the PI3K-pathway, including PTEN loss and activating AKT1 mutations. Notably, while secondary PIK3CA mutations were previously reported to increase sensitivity to PI3Ka-inhibitors, we identified emergent secondary resistance mutations in PIK3CA that alter the inhibitor binding pocket. Some mutations had differential effects on PI3Ka-selective vs. pan-PI3K inhibitors, but resistance induced by all mutations could be overcome by the novel allosteric pan-mutant-selective PI3Ka-inhibitor RLY-2608. Together, these findings provide insights to guide strategies to overcome resistance in PIK3CA-mutated cancers.

DOI: https://doi.org/10.1158/2159-8290.CD-23-0704
J Cell Biol. 2024 Jan 01. pii: e202305086. [Epub ahead of print]223(1):

Inducible tricolor reporter mouse for parallel imaging of lysosomes, mitochondria, and microtubules.

Vera Hutchison, Anne Lynch, Andrés Mauricio Gutierrez-Gamez, Jichao Chen.

Cell type-specific use of the same DNA blueprint generates diverse cell types. Such diversity must also be executed via differential deployment of the same subcellular machinery. However, our understanding of the size, distribution, and dynamics of subcellular machinery in native tissues and their connection to cellular diversity remains limited. We generate and characterize an inducible tricolor reporter mouse, dubbed "Kaleidoscope," for simultaneous imaging of lysosomes, mitochondria, and microtubules in any cell type and at a single-cell resolution. The expected subcellular compartments are labeled in culture and in tissues with no impact on cellular and organismal viability. Quantitative and live imaging of the tricolor reporter captures cell type-specific organelle features and kinetics in the lung, as well as their changes after Sendai virus infection. Yap/Taz mutant lung epithelial cells undergo accelerated lamellar body maturation, a subcellular manifestation of their molecular defects. A comprehensive toolbox of reporters for all subcellular structures is expected to transform our understanding of cell biology in tissues.

DOI: https://doi.org/10.1083/jcb.202305086
Trends Biotechnol. 2023 Oct 30. pii: S0167-7799(23)00292-5. [Epub ahead of print]

Cancer-on-chip models for metastasis: importance of the tumor microenvironment.

Mohammad Jouybar, Charlotte M de Winde, Katarina Wolf, Peter Friedl, Reina E Mebius, Jaap M J den Toonder.

  Cancer-on-chip (CoC) models, based on microfluidic chips harboring chambers for 3D tumor-cell culture, enable us to create a controlled tumor microenvironment (TME). CoC models are therefore increasingly used to systematically study effects of the TME on the various steps in cancer metastasis. Moreover, CoC models have great potential for developing novel cancer therapies and for predicting patient-specific response to cancer treatments. We review recent developments in CoC models, focusing on three main TME components: (i) the anisotropic extracellular matrix (ECM) architectures, (ii) the vasculature, and (iii) the immune system. We aim to provide guidance to biologists to choose the best CoC approach for addressing questions about the role of the TME in metastasis, and to inspire engineers to develop novel CoC technologies.

Keywords:  Cancer-on-chip; extracellular matrix; immune system; tumor microenvironment; vasculature

DOI:  https://doi.org/10.1016/j.tibtech.2023.10.001
Anal Bioanal Chem. 2023 Nov 02.

Differential lipid analysis of oxaliplatin-sensitive and resistant HCT116 cells reveals different levels of drug-induced lipid droplet formation.

Tyler S Larson, Thomas J DiProspero, Gary L Glish, Matthew R Lockett.

  Lipid droplets (LDs) are intracellular storage vesicles composed of a neutral lipid core surrounded by a glycerophospholipid membrane. LD accumulation is associated with different stages of cancer progression and stress responses resulting from chemotherapy. In previous work, a novel dual nano-electrospray ionization source and data-dependent acquisition method for measuring the relative abundances of lipid species between two extracts were described and validated. Here, this same source and method were used to determine if oxaliplatin-sensitive and resistant cells undergo similar lipid profile changes, with the goal of identifying potential signatures that could predict the effectiveness of an oxaliplatin-containing treatment. Oxaliplatin is commonly used in the treatment of colorectal cancer. When compared to a no-drug control, oxaliplatin dosing caused significant increases in triglyceride (TG) and cholesterol ester (CE) species. These increases were more pronounced in the oxaliplatin-sensitive cells than in oxaliplatin-resistant cells. The increased neutral lipid abundance correlated with LD formation, as confirmed by confocal micrographs of Nile Red-stained cells. Untargeted proteomic analyses also support LD formation after oxaliplatin treatment, with an increased abundance of LD-associated proteins in both the sensitive and resistant cells.

Keywords:  Colorectal cancer; Differential ion mobility spectrometry; Mass spectrometry; Shotgun lipidomics

DOI:  https://doi.org/10.1007/s00216-023-05010-0
Nat Chem Biol. 2023 Oct 30.

Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors.

Maria Reinecke, Paul Brear, Larsen Vornholz, Benedict-Tilmann Berger, Florian Seefried, Stephanie Wilhelm, Patroklos Samaras, Laszlo Gyenis, David William Litchfield, Guillaume Médard, Susanne Müller, Jürgen Ruland, Marko Hyvönen, Mathias Wilhelm, Bernhard Kuster.

Medicinal chemistry has discovered thousands of potent protein and lipid kinase inhibitors. These may be developed into therapeutic drugs or chemical probes to study kinase biology. Because of polypharmacology, a large part of the human kinome currently lacks selective chemical probes. To discover such probes, we profiled 1,183 compounds from drug discovery projects in lysates of cancer cell lines using Kinobeads. The resulting 500,000 compound-target interactions are available in ProteomicsDB and we exemplify how this molecular resource may be used. For instance, the data revealed several hundred reasonably selective compounds for 72 kinases. Cellular assays validated GSK986310C as a candidate SYK (spleen tyrosine kinase) probe and X-ray crystallography uncovered the structural basis for the observed selectivity of the CK2 inhibitor GW869516X. Compounds targeting PKN3 were discovered and phosphoproteomics identified substrates that indicate target engagement in cells. We anticipate that this molecular resource will aid research in drug discovery and chemical biology.

DOI: https://doi.org/10.1038/s41589-023-01459-3
J Cell Biol. 2023 Dec 04. pii: e202306120. [Epub ahead of print]222(12):

The mechanism of Atg15-mediated membrane disruption in autophagy.

Yoko Kagohashi, Michiko Sasaki, Alexander I May, Tomoko Kawamata, Yoshinori Ohsumi.

Autophagy is a lysosomal/vacuolar delivery system that degrades cytoplasmic material. During autophagy, autophagosomes deliver cellular components to the vacuole, resulting in the release of a cargo-containing autophagic body (AB) into the vacuole. AB membranes must be disrupted for degradation of cargo to occur. The lipase Atg15 and vacuolar proteases Pep4 and Prb1 are known to be necessary for this disruption and cargo degradation, but the mechanistic underpinnings remain unclear. In this study, we establish a system to detect lipase activity in the vacuole and show that Atg15 is the sole vacuolar phospholipase. Pep4 and Prb1 are required for the activation of Atg15 lipase function, which occurs following delivery of Atg15 to the vacuole by the MVB pathway. In vitro experiments reveal that Atg15 is a phospholipase B of broad substrate specificity that is likely implicated in the disruption of a range of membranes. Further, we use isolated ABs to demonstrate that Atg15 alone is able to disrupt AB membranes.

DOI: https://doi.org/10.1083/jcb.202306120
Cancer Metastasis Rev. 2023 Nov 01.

Clonal tracking in cancer and metastasis.

Syed Mohammed Musheer Aalam, Long Viet Nguyen, Megan L Ritting, Nagarajan Kannan.

  The eradication of many cancers has proven challenging due to the presence of functionally and genetically heterogeneous clones maintained by rare cancer stem cells (CSCs), which contribute to disease progression, treatment refractoriness, and late relapse. The characterization of functional CSC activity has necessitated the development of modern clonal tracking strategies. This review describes viral-based and CRISPR-Cas9-based cellular barcoding, lineage tracing, and imaging-based approaches. DNA-based cellular barcoding technology is emerging as a powerful and robust strategy that has been widely applied to in vitro and in vivo model systems, including patient-derived xenograft models. This review also highlights the potential of these methods for use in the clinical and drug discovery contexts and discusses the important insights gained from such approaches.

Keywords:  Cancer stem cells; Cellular barcoding; Clonal dynamics; Clonal tracking

DOI:  https://doi.org/10.1007/s10555-023-10149-4
mSphere. 2023 Oct 31. e0048223

mSphere of Influence: Hooray for HaloTag! A novel tool to study autophagy in mammalian cells.

Laura Cheney.

  Laura Cheney works at the crossroads of HIV and autophagy, a critical biological process for cellular homeostasis, to understand more completely the pathogenesis of HIV-associated neurocognitive impairment. In this mSphere of Influence article, she reflects on how "A pulse-chasable reporter processing assay for mammalian autophagic flux with HaloTag" by Willa Wen-You Yim, Hayashi Yamamoto, and Noboru Mizushima (eLife 11:e78923, 2022, https://doi.org/10.7554/eLife.78923) expands the tools for studying autophagy and inspired her to use this technology to develop a reporter to study autophagy of mitochondria, termed mitophagy, to further her own research goals.

Keywords:  Atg8/LC3 processing assay; HIV associated neurocognitive impairment; HaloTag; antiretroviral therapy; autophagy; mitophagy

DOI:  https://doi.org/10.1128/msphere.00482-23
Endocrine. 2023 Nov 03.

Acute pancreatitis and metabolic syndrome: genetic correlations and causal associations.

ShuangJing Zhu, Zhen Ding.

   BACKGROUND: Although there is a definite correlation between the Metabolic Syndrome (MetS) and Acute Pancreatitis (AP), cause is yet unknown. The current work combined linkage disequilibrium score (LDSC) regression and Mendelian randomization (MR) approaches to fill this important information gap.
METHODS: In this study, we harnessed the power of publicly available gene-wide association databases (GWAS) to explore the intricate relationship between MetS and its components with AP. The cornerstone of our analysis was the Inverse-Variance Weighted (IVW) method, serving as our primary analytical tool. In addition to IVW, we complemented our investigation with several other robust MR methods, including MR-Egger, Weighted Median, Maximum Likelihood, and MR-PRESSO. By employing this diverse set of analytical approaches, we sought to ensure the comprehensiveness and robustness of our findings.
RESULT: LDSC regression indicated a genetic correlation between MetS and AP. Univariate MR results indicated a genetic association between MetS (OR = 1.084; 95% CI, 1.005-1.170; P = 0.037), BMI (OR = 1.459; 95% CI, 1.325-1.606; P = 1.46E-14), WHR (OR = 1.189; 95% CI, 1.068-1.323; P = 1.56 E-03), TG (OR = 1.110; 95% CI, 1.001-1.231; P = 0.047), and FI (OR = 1.798; 95% CI, 1.245-2.595; P = 1.74E-03) were able to significantly increase the risk of AP. The results of multivariate MR analysis revealed that these causality associations still existed.
CONCLUSION: Our investigation has yielded compelling evidence that substantiates the presence of both a genetic correlation and a causal relationship between MetS and AP.

Keywords:  Acute pancreatitis; Body Mass Index; Linkage disequilibrium score regression; Mendelian randomization; Metabolic syndrome

DOI:  https://doi.org/10.1007/s12020-023-03584-4
STAR Protoc. 2023 Oct 31. pii: S2666-1667(23)00646-9. [Epub ahead of print]4(4): 102679

Protocol for isolating single cells from human pancreatic cancer tissues and analyzing major immune cell populations using flow cytometry.

Jinyuan Song, Junlei Zhang, Yongtao Ji, Jianghui Tang, Jianpeng Sheng, Tingbo Liang, Xueli Bai.

  Here, we present a protocol for collecting, dissociating, isolating, staining, and analyzing immune cells from pancreatic cancer tissues for flow cytometry. The isolated cells can also be used for single-cell RNA sequencing and other related procedures. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2023).1.

Keywords:  Cancer; Cell Biology; Cell Isolation; Clinical Protocol; Flow Cytometry; Health Sciences; Single Cell

DOI:  https://doi.org/10.1016/j.xpro.2023.102679