bims-cagime 2023-12-10 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2023–12–10
twenty-six papers selected by
Kıvanç Görgülü, Technical University of Munich

A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas.
Inhibiting stromal Class I HDACs curbs pancreatic cancer progression.
FK506 bypasses the effect of erythroferrone in cancer cachexia skeletal muscle atrophy.
Senotherapeutic drug treatment ameliorates chemotherapy-induced cachexia.
Discovery of KRB-456, a KRAS G12D switch-I/II allosteric pocket binder that inhibits the growth of pancreatic cancer patient-derived tumors.
NAK-associated protein 1/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis.
Cancer Evolution: A Multifaceted Affair.
Ceramide regulation of autophagy: A biophysical approach.
Harnessing atomic force microscopy-based single-cell analysis to advance physical oncology.
The impact of extracellular matrix on the precision medicine utility of pancreatic cancer patient-derived organoids.
Complete set of the Atg8-E1-E2-E3 conjugation machinery forms an interaction web that mediates membrane shaping.
Radiomics analysis with three-dimensional and two-dimensional segmentation to predict survival outcomes in pancreatic cancer.
GDF15 is a major determinant of ketogenic diet-induced weight loss.
T cell migration requires ion and water influx to regulate actin polymerization.
Hyperpolarized 13 C Metabolic MRI of Patients with Pancreatic Ductal Adenocarcinoma.
A novel antidiuretic hormone governs tumour-induced renal dysfunction.
INX-315, a selective CDK2 inhibitor, induces cell cycle arrest and senescence in solid tumors.
An mTurq2-Col4a1 mouse model allows for live visualization of mammalian basement membrane development.
Organ aging signatures in the plasma proteome track health and disease.
Dictionary of immune responses to cytokines at single-cell resolution.
Endothelial cells metabolically regulate breast cancer invasion toward a microvessel.
Secretory GFP reconstitution labeling of neighboring cells interrogates cell-cell interactions in metastatic niches.
Embryo mechanics cartography: inference of 3D force atlases from fluorescence microscopy.
Reproducible image-based profiling with Pycytominer.
Myeloid cells pave the metastatic road in breast cancer.
Multiple NTS neuron populations cumulatively suppress food intake.

Dev Cell. 2023 Nov 30. pii: S1534-5807(23)00583-X. [Epub ahead of print]

A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas.

David J Falvo, Adrien Grimont, Paul Zumbo, William B Fall, Julie L Yang, Alexa Osterhoudt, Grace Pan, Andre F Rendeiro, Yinuo Meng, John E Wilkinson, Friederike Dündar, Olivier Elemento, Rhonda K Yantiss, Erika Hissong, Richard Koche, Doron Betel, Rohit Chandwani.

  Inflammation is essential to the disruption of tissue homeostasis and can destabilize the identity of lineage-committed epithelial cells. Here, we employ lineage-traced mouse models, single-cell transcriptomic and chromatin analyses, and CUT&TAG to identify an epigenetic memory of inflammatory injury in the pancreatic acinar cell compartment. Despite resolution of pancreatitis, our data show that acinar cells fail to return to their molecular baseline, with retention of elevated chromatin accessibility and H3K4me1 at metaplasia genes, such that memory represents an incomplete cell fate decision. In vivo, we find this epigenetic memory controls lineage plasticity, with diminished metaplasia in response to a second insult but increased tumorigenesis with an oncogenic Kras mutation. The lowered threshold for oncogenic transformation, in turn, can be restored by blockade of MAPK signaling. Together, we define the chromatin dynamics, molecular encoding, and recall of a prolonged epigenetic memory of inflammatory injury that impacts future responses but remains reversible.

Keywords:  ATAC-seq; CUT&TAG; cell fate; epigenetic memory; inflammatory injury; lineage plasticity; pancreatic cancer; pancreatitis; single-cell RNA sequencing; tumorigenesis

DOI:  https://doi.org/10.1016/j.devcel.2023.11.008
Nat Commun. 2023 Dec 06. 14(1): 7791

Inhibiting stromal Class I HDACs curbs pancreatic cancer progression.

Gaoyang Liang, Tae Gyu Oh, Nasun Hah, Hervé Tiriac, Yu Shi, Morgan L Truitt, Corina E Antal, Annette R Atkins, Yuwenbin Li, Cory Fraser, Serina Ng, Antonio F M Pinto, Dylan C Nelson, Gabriela Estepa, Senada Bashi, Ester Banayo, Yang Dai, Christopher Liddle, Ruth T Yu, Tony Hunter, Dannielle D Engle, Haiyong Han, Daniel D Von Hoff, Michael Downes, Ronald M Evans.

Oncogenic lesions in pancreatic ductal adenocarcinoma (PDAC) hijack the epigenetic machinery in stromal components to establish a desmoplastic and therapeutic resistant tumor microenvironment (TME). Here we identify Class I histone deacetylases (HDACs) as key epigenetic factors facilitating the induction of pro-desmoplastic and pro-tumorigenic transcriptional programs in pancreatic stromal fibroblasts. Mechanistically, HDAC-mediated changes in chromatin architecture enable the activation of pro-desmoplastic programs directed by serum response factor (SRF) and forkhead box M1 (FOXM1). HDACs also coordinate fibroblast pro-inflammatory programs inducing leukemia inhibitory factor (LIF) expression, supporting paracrine pro-tumorigenic crosstalk. HDAC depletion in cancer-associated fibroblasts (CAFs) and treatment with the HDAC inhibitor entinostat (Ent) in PDAC mouse models reduce stromal activation and curb tumor progression. Notably, HDAC inhibition (HDACi) enriches a lipogenic fibroblast subpopulation, a potential precursor for myofibroblasts in the PDAC stroma. Overall, our study reveals the stromal targeting potential of HDACi, highlighting the utility of this epigenetic modulating approach in PDAC therapeutics.

DOI: https://doi.org/10.1038/s41467-023-42178-6
Cell Rep Med. 2023 Nov 28. pii: S2666-3791(23)00500-1. [Epub ahead of print] 101306

FK506 bypasses the effect of erythroferrone in cancer cachexia skeletal muscle atrophy.

Erica Mina, Elisabeth Wyart, Roberta Sartori, Elia Angelino, Ivan Zaggia, Valentina Rausch, Mara Maldotti, Alessia Pagani, Myriam Y Hsu, Alberto Friziero, Cosimo Sperti, Alessio Menga, Andrea Graziani, Emilio Hirsch, Salvatore Oliviero, Marco Sandri, Laura Conti, Léon Kautz, Laura Silvestri, Paolo E Porporato.

  Skeletal muscle atrophy is a hallmark of cachexia, a wasting condition typical of chronic pathologies, that still represents an unmet medical need. Bone morphogenetic protein (BMP)-Smad1/5/8 signaling alterations are emerging drivers of muscle catabolism, hence, characterizing these perturbations is pivotal to develop therapeutic approaches. We identified two promoters of "BMP resistance" in cancer cachexia, specifically the BMP scavenger erythroferrone (ERFE) and the intracellular inhibitor FKBP12. ERFE is upregulated in cachectic cancer patients' muscle biopsies and in murine cachexia models, where its expression is driven by STAT3. Moreover, the knock down of Erfe or Fkbp12 reduces muscle wasting in cachectic mice. To bypass the BMP resistance mediated by ERFE and release the brake on the signaling, we targeted FKBP12 with low-dose FK506. FK506 restores BMP-Smad1/5/8 signaling, rescuing myotube atrophy by inducing protein synthesis. In cachectic tumor-bearing mice, FK506 prevents muscle and body weight loss and protects from neuromuscular junction alteration, suggesting therapeutic potential for targeting the ERFE-FKBP12 axis.

Keywords:  ERFE; FK506; FKBP12; cachexia; cancer; cancer cachexia; erythroferrone; skeletal muscle atrophy; tacrolimus; wasting

DOI:  https://doi.org/10.1016/j.xcrm.2023.101306
JCI Insight. 2023 Dec 05. pii: e169512. [Epub ahead of print]

Senotherapeutic drug treatment ameliorates chemotherapy-induced cachexia.

Davis A Englund, Alyssa M Jolliffe, Gabriel J Hanson, Zaira Aversa, Xu Zhang, Xinyi Jiang, Thomas A White, Lei Zhang, David G Monroe, Paul D Robbins, Laura J Niedernhofer, Theodore M Kamenecka, Sundeep Khosla, Nathan K LeBrasseur.

  Cachexia is a debilitating skeletal muscle wasting condition for which we currently lack effective treatments. In the context of cancer, certain chemotherapeutics cause DNA damage and cellular senescence. Senescent cells exhibit chronic activation of the transcription factor nuclear factor (NF)-κB, a known mediator of the pro-inflammatory senescence-associated secretory phenotype (SASP) and skeletal muscle atrophy. Thus, targeting NF-κB represents a logical therapeutic strategy to alleviate unintended consequences of genotoxic drugs. Herein, we show that treatment with the IKK/NF-κB inhibitor SR12343 during a course of chemotherapy reduces markers of cellular senescence and the SASP in liver, skeletal muscle, and circulation and, correspondingly, attenuates features of skeletal muscle pathology. Lastly, we demonstrate SR12343 mitigates chemotherapy-induced reductions in body weight, lean mass, fat mass, and muscle strength. These findings support senescent cells as a promising druggable target to counteract the SASP and skeletal muscle wasting in the context of chemotherapy.

Keywords:  Cellular senescence; Inflammation; Muscle Biology; Skeletal muscle

DOI:  https://doi.org/10.1172/jci.insight.169512
Cancer Res Commun. 2023 Dec 05.

Discovery of KRB-456, a KRAS G12D switch-I/II allosteric pocket binder that inhibits the growth of pancreatic cancer patient-derived tumors.

Aslamuzzaman Kazi, Alok Ranjan, Vasantha Kumar M V, Bogos Agianian, Martin Garcia Chavez, Vignesh Vudatha, Rui Wang, Rajanikanth Vangipurapu, Liwei Chen, Perry Kennedy, Karthikeyan Subramanian, Jonathan C K Quirke, Francisca Beato, Patrick Underwood, Jason B Fleming, Jose Trevino, Paul J Hergenrother, Evripidis Gavathiotis, Said M Sebti.

Currently, there are no clinically approved drugs that directly thwart mutant KRAS G12D, a major driver of human cancer. Here, we report on the discovery of a small molecule, KRB-456, that binds KRAS G12D and inhibits the growth of pancreatic cancer patient-derived tumors. Protein NMR studies revealed that KRB-456 binds the GDP-bound and GCP-bound conformation of KRAS G12D by forming interactions with a dynamic allosteric binding pocket within the switch-I/II region. Isothermal titration calorimetry demonstrated that KRB-456 binds potently to KRAS G12D with 1.5-, 2- and 6-fold higher affinity than to KRAS G12V, KRAS wild-type and KRAS G12C, respectively. KRB-456 potently inhibits the binding of KRAS G12D to the RAS-binding domain (RBD) of RAF1 as demonstrated by GST-RBD pull-down and AlphaScreen assays. Treatment of KRAS G12D-harboring human pancreatic cancer cells with KRB-456 suppresses the cellular levels of KRAS bound to GTP and inhibits the binding of KRAS to RAF1. Importantly, KRB-456 inhibits P-MEK, P-AKT and P-S6 levels in vivo and inhibits the growth of subcutaneous and orthotopic xenografts derived from pancreatic cancer patients whose tumors harbor KRAS G12D and KRAS G12V and who relapsed after chemotherapy and radiation therapy. These results warrant further development of KRB-456 for pancreatic cancer.

DOI: https://doi.org/10.1158/2767-9764.CRC-23-0222
J Cell Biol. 2024 Feb 05. pii: e202303082. [Epub ahead of print]223(2):

NAK-associated protein 1/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis.

Swagatika Paul, Shireen A Sarraf, Ki Hong Nam, Leila Zavar, Nicole DeFoor, Sahitya Ranjan Biswas, Lauren E Fritsch, Tomer M Yaron, Jared L Johnson, Emily M Huntsman, Lewis C Cantley, Alban Ordureau, Alicia M Pickrell.

Subcellular location and activation of Tank Binding Kinase 1 (TBK1) govern precise progression through mitosis. Either loss of activated TBK1 or its sequestration from the centrosomes causes errors in mitosis and growth defects. Yet, what regulates its recruitment and activation on the centrosomes is unknown. We identified that NAK-associated protein 1 (NAP1) is essential for mitosis, binding to and activating TBK1, which both localize to centrosomes. Loss of NAP1 causes several mitotic and cytokinetic defects due to inactivation of TBK1. Our quantitative phosphoproteomics identified numerous TBK1 substrates that are not only confined to the centrosomes but are also associated with microtubules. Substrate motifs analysis indicates that TBK1 acts upstream of other essential cell cycle kinases like Aurora and PAK kinases. We also identified NAP1 as a TBK1 substrate phosphorylating NAP1 at S318 to promote its degradation by the ubiquitin proteasomal system. These data uncover an important distinct function for the NAP1-TBK1 complex during cell division.

DOI: https://doi.org/10.1083/jcb.202303082
Cancer Discov. 2023 Dec 06. OF1-OF13

Cancer Evolution: A Multifaceted Affair.

Giovanni Ciriello, Luca Magnani, Sarah J Aitken, Leila Akkari, Sam Behjati, Douglas Hanahan, Dan A Landau, Nuria Lopez-Bigas, Darío G Lupiáñez, Jean-Christophe Marine, Ana Martin-Villalba, Gioacchino Natoli, Anna C Obenauf, Elisa Oricchio, Paola Scaffidi, Andrea Sottoriva, Alexander Swarbrick, Giovanni Tonon, Sakari Vanharanta, Johannes Zuber.

Cancer cells adapt and survive through the acquisition and selection of molecular modifications. This process defines cancer evolution. Building on a theoretical framework based on heritable genetic changes has provided insights into the mechanisms supporting cancer evolution. However, cancer hallmarks also emerge via heritable nongenetic mechanisms, including epigenetic and chromatin topological changes, and interactions between tumor cells and the tumor microenvironment. Recent findings on tumor evolutionary mechanisms draw a multifaceted picture where heterogeneous forces interact and influence each other while shaping tumor progression. A comprehensive characterization of the cancer evolutionary toolkit is required to improve personalized medicine and biomarker discovery.
SIGNIFICANCE: Tumor evolution is fueled by multiple enabling mechanisms. Importantly, genetic instability, epigenetic reprogramming, and interactions with the tumor microenvironment are neither alternative nor independent evolutionary mechanisms. As demonstrated by findings highlighted in this perspective, experimental and theoretical approaches must account for multiple evolutionary mechanisms and their interactions to ultimately understand, predict, and steer tumor evolution.

DOI: https://doi.org/10.1158/2159-8290.CD-23-0530
Biochim Biophys Acta Mol Cell Biol Lipids. 2023 Dec 04. pii: S1388-1981(23)00168-3. [Epub ahead of print] 159444

Ceramide regulation of autophagy: A biophysical approach.

Yaiza R Varela, Marina N Iriondo, Félix M Goñi, Alicia Alonso, L Ruth Montes.

  Specific membrane lipids play unique roles in (macro)autophagy. Those include phosphatidylethanolamine, to which LC3/GABARAP autophagy proteins become covalently bound in the process, or cardiolipin, an important effector in mitochondrial autophagy (or mitophagy). Ceramide (Cer), or N-acyl sphingosine, is one of the simplest sphingolipids, known as a stress signal in the apoptotic pathway. Moreover, Cer is increasingly being recognized as an autophagy activator, although its mechanism of action is unclear. In the present review, the proposed Cer roles in autophagy are summarized, together with some biophysical properties of Cer in membranes. Possible pathways for Cer activation of autophagy are discussed, including specific protein binding of the lipid, and Cer-dependent perturbation of bilayer properties. Cer generation of lateral inhomogeneities (domain formation) is given special attention. Recent biophysical results, including fluorescence and atomic force microscopy data, show Cer-promoted enhanced binding of LC3/GABARAP to lipid bilayers. These observations could be interpreted in terms of the putative formation of Cer-rich nanodomains.

Keywords:  Autophagy; Ceramide; Lateral phase separation; Membrane biophysics; Mitophagy; Nanodomains

DOI:  https://doi.org/10.1016/j.bbalip.2023.159444
Microsc Res Tech. 2023 Dec 06.

Harnessing atomic force microscopy-based single-cell analysis to advance physical oncology.

Mi Li.

  Single-cell analysis is an emerging and promising frontier in the field of life sciences, which is expected to facilitate the exploration of fundamental laws of physiological and pathological processes. Single-cell analysis allows experimental access to cell-to-cell heterogeneity to reveal the distinctive behaviors of individual cells, offering novel opportunities to dissect the complexity of severe human diseases such as cancers. Among the single-cell analysis tools, atomic force microscopy (AFM) is a powerful and versatile one which is able to nondestructively image the fine topographies and quantitatively measure multiple mechanical properties of single living cancer cells in their native states under aqueous conditions with unprecedented spatiotemporal resolution. Over the past few decades, AFM has been widely utilized to detect the structural and mechanical behaviors of individual cancer cells during the process of tumor formation, invasion, and metastasis, yielding numerous unique insights into tumor pathogenesis from the biomechanical perspective and contributing much to the field of cancer mechanobiology. Here, the achievements of AFM-based analysis of single cancer cells to advance physical oncology are comprehensively summarized, and challenges and future perspectives are also discussed. RESEARCH HIGHLIGHTS: Achievements of AFM in characterizing the structural and mechanical behaviors of single cancer cells are summarized, and future directions are discussed. AFM is not only capable of visualizing cellular fine structures, but can also measure multiple cellular mechanical properties as well as cell-generated mechanical forces. There is still plenty of room for harnessing AFM-based single-cell analysis to advance physical oncology.

Keywords:  atomic force microscopy; cancer cell; physical oncology; single-cell force spectroscopy; single-cell mechanics; single-cell microrheology; tumor formation and progression

DOI:  https://doi.org/10.1002/jemt.24467
JCI Insight. 2023 Dec 05. pii: e172419. [Epub ahead of print]

The impact of extracellular matrix on the precision medicine utility of pancreatic cancer patient-derived organoids.

Jan C Lumibao, Shira R Okhovat, Kristina L Peck, Xiaoxue Lin, Kathryn Lande, Shira Yomtoubian, Isabella Ng, Herve Tiriac, Andrew M Lowy, Jingjing Zou, Dannielle D Engle.

  The use of patient-derived organoids (PDOs) to characterize therapeutic sensitivity and resistance is a promising precision medicine approach, and its potential to inform clinical decisions is now being tested in several large multi-institutional clinical trials. PDOs are cultivated in extracellular matrix from basement membrane extracts (BMEs) that are most commonly acquired commercially. Each clinical site utilizes distinct BME lots and may be restricted due to the availability of commercial BME sources. However, the impact of different sources of BMEs on organoid drug response is unknown. Here, we tested the impact of BME source on proliferation, drug response, and gene expression in mouse and human pancreatic ductal adenocarcinoma (PDA) organoids. Both human and mouse organoids displayed increased proliferation in Matrigel (Corning) compared to Cultrex (RnD) and UltiMatrix (RnD). However, we observed no substantial impact on drug response when organoids were cultured in Matrigel, Cultrex, or UltiMatrix. We also did not observe major shifts in gene expression across the different BME sources, and PDOs maintained their Classical or Basal-like designation. Overall, we find that BME source (Matrigel, Cultrex, UltiMatrix) does not shift PDO dose-response curves and drug testing results, indicating that PDO pharmacotyping is a robust approach for precision medicine.

Keywords:  Cancer; Cell Biology; Drug therapy; Extracellular matrix; Oncology

DOI:  https://doi.org/10.1172/jci.insight.172419
Nat Struct Mol Biol. 2023 Dec 06.

Complete set of the Atg8-E1-E2-E3 conjugation machinery forms an interaction web that mediates membrane shaping.

Jahangir Md Alam, Tatsuro Maruyama, Daisuke Noshiro, Chika Kakuta, Tetsuya Kotani, Hitoshi Nakatogawa, Nobuo N Noda.

Atg8, a ubiquitin-like protein, is conjugated with phosphatidylethanolamine (PE) via Atg7 (E1), Atg3 (E2) and Atg12-Atg5-Atg16 (E3) enzymatic cascade and mediates autophagy. However, its molecular roles in autophagosome formation are still unclear. Here we show that Saccharomyces cerevisiae Atg8-PE and E1-E2-E3 enzymes together construct a stable, mobile membrane scaffold. The complete scaffold formation induces an in-bud in prolate-shaped giant liposomes, transforming their morphology into one reminiscent of isolation membranes before sealing. In addition to their enzymatic roles in Atg8 lipidation, all three proteins contribute nonenzymatically to membrane scaffolding and shaping. Nuclear magnetic resonance analyses revealed that Atg8, E1, E2 and E3 together form an interaction web through multivalent weak interactions, where the intrinsically disordered regions in Atg3 play a central role. These data suggest that all six Atg proteins in the Atg8 conjugation machinery control membrane shaping during autophagosome formation.

DOI: https://doi.org/10.1038/s41594-023-01132-2
World J Radiol. 2023 Nov 28. 15(11): 304-314

Radiomics analysis with three-dimensional and two-dimensional segmentation to predict survival outcomes in pancreatic cancer.

Mohammed Saleh, Mayur Virarkar, Hagar S Mahmoud, Vincenzo K Wong, Carlos Ignacio Gonzalez Baerga, Miti Parikh, Sherif B Elsherif, Priya R Bhosale.

   BACKGROUND: Radiomics can assess prognostic factors in several types of tumors, but considering its prognostic ability in pancreatic cancer has been lacking.
AIM: To evaluate the performance of two different radiomics software in assessing survival outcomes in pancreatic cancer patients.
METHODS: We retrospectively reviewed pretreatment contrast-enhanced dual-energy computed tomography images from 48 patients with biopsy-confirmed pancreatic ductal adenocarcinoma who later underwent neoadjuvant chemoradiation and surgery. Tumors were segmented using TexRad software for 2-dimensional (2D) analysis and MIM software for 3D analysis, followed by radiomic feature extraction. Cox proportional hazard modeling correlated texture features with overall survival (OS) and progression-free survival (PFS). Cox regression was used to detect differences in OS related to pretreatment tumor size and residual tumor following treatment. The Wilcoxon test was used to show the relationship between tumor volume and the percent of residual tumor. Kaplan-Meier analysis was used to compare survival in patients with different tumor densities in Hounsfield units for both 2D and 3D analysis.
RESULTS: 3D analysis showed that higher mean tumor density [hazard ratio (HR) = 0.971, P = 0.041)] and higher median tumor density (HR = 0.970, P = 0.037) correlated with better OS. 2D analysis showed that higher mean tumor density (HR = 0.963, P = 0.014) and higher mean positive pixels (HR = 0.962, P = 0.014) correlated with better OS; higher skewness (HR = 3.067, P = 0.008) and higher kurtosis (HR = 1.176, P = 0.029) correlated with worse OS. Higher entropy correlated with better PFS (HR = 0.056, P = 0.036). Models determined that patients with increased tumor size greater than 1.35 cm were likely to have a higher percentage of residual tumors of over 10%.
CONCLUSION: Several radiomics features can be used as prognostic tools for pancreatic cancer. However, results vary between 2D and 3D analyses. Mean tumor density was the only variable that could reliably predict OS, irrespective of the analysis used.

Keywords:  Cancer; Pancreas; Radiomics; Segmentation

DOI:  https://doi.org/10.4329/wjr.v15.i11.304
Cell Metab. 2023 Dec 05. pii: S1550-4131(23)00414-X. [Epub ahead of print]35(12): 2165-2182.e7

GDF15 is a major determinant of ketogenic diet-induced weight loss.

Jun Feng Lu, Meng Qing Zhu, Bo Xia, Na Na Zhang, Xiao Peng Liu, Huan Liu, Rui Xin Zhang, Jun Ying Xiao, Hui Yang, Ying Qi Zhang, Xiao Miao Li, Jiang Wei Wu.

  A ketogenic diet (KD) has been promoted as an obesity management diet, yet its underlying mechanism remains elusive. Here we show that KD reduces energy intake and body weight in humans, pigs, and mice, accompanied by elevated circulating growth differentiation factor 15 (GDF15). In GDF15- or its receptor GFRAL-deficient mice, these effects of KD disappeared, demonstrating an essential role of GDF15-GFRAL signaling in KD-mediated weight loss. Gdf15 mRNA level increases in hepatocytes upon KD feeding, and knockdown of Gdf15 by AAV8 abrogated the obesity management effect of KD in mice, corroborating a hepatic origin of GDF15 production. We show that KD activates hepatic PPARγ, which directly binds to the regulatory region of Gdf15, increasing its transcription and production. Hepatic Pparγ-knockout mice show low levels of plasma GDF15 and significantly diminished obesity management effects of KD, which could be restored by either hepatic Gdf15 overexpression or recombinant GDF15 administration. Collectively, our study reveals a previously unexplored GDF15-dependent mechanism underlying KD-mediated obesity management.

Keywords:  GDF15; GFRAL; hepatic PPARγ; ketogenic diet; obesity

DOI:  https://doi.org/10.1016/j.cmet.2023.11.003
Nat Commun. 2023 Dec 06. 14(1): 7844

T cell migration requires ion and water influx to regulate actin polymerization.

Leonard L de Boer, Lesley Vanes, Serena Melgrati, Joshua Biggs O'May, Darryl Hayward, Paul C Driscoll, Jason Day, Alexander Griffiths, Renata Magueta, Alexander Morrell, James I MacRae, Robert Köchl, Victor L J Tybulewicz.

Migration of T cells is essential for their ability to mount immune responses. Chemokine-induced T cell migration requires WNK1, a kinase that regulates ion influx into the cell. However, it is not known why ion entry is necessary for T cell movement. Here we show that signaling from the chemokine receptor CCR7 leads to activation of WNK1 and its downstream pathway at the leading edge of migrating CD4+ T cells, resulting in ion influx and water entry by osmosis. We propose that WNK1-induced water entry is required to swell the membrane at the leading edge, generating space into which actin filaments can polymerize, thereby facilitating forward movement of the cell. Given the broad expression of WNK1 pathway proteins, our study suggests that ion and water influx are likely to be essential for migration in many cell types, including leukocytes and metastatic tumor cells.

DOI: https://doi.org/10.1038/s41467-023-43423-8
J Magn Reson Imaging. 2023 Dec 02.

Hyperpolarized 13 C Metabolic MRI of Patients with Pancreatic Ductal Adenocarcinoma.

Jeremy W Gordon, Hsin-Yu Chen, Tanner Nickles, Philip M Lee, Robert Bok, Michael A Ohliger, Kimberly Okamoto, Andrew H Ko, Peder E Z Larson, Zhen J Wang.

   BACKGROUND: Pancreatic ductal adenocarcinoma (PDA) is the third leading cause of cancer-related death in the United States. However, early response assessment using the current approach of measuring changes in tumor size on computed tomography (CT) or MRI is challenging.
PURPOSE: To investigate the feasibility of hyperpolarized (HP) [1-13 C]pyruvate MRI to quantify metabolism in the normal appearing pancreas and PDA, and to assess changes in PDA metabolism following systemic chemotherapy.
STUDY TYPE: Prospective.
SUBJECTS: Six patients (65.0 ± 7.6 years, 2 females) with locally advanced or metastatic PDA enrolled prior to starting a new line of systemic chemotherapy.
FIELD STRENGTH/SEQUENCE: 3-T, T1-weighted gradient echo, metabolite-selective 13 C echoplanar imaging.
ASSESSMENT: Time-resolved HP [1-13 C]pyruvate data were acquired before (N = 6) and 4-weeks after (N = 3) treatment initiation. Pyruvate metabolism, as quantified by pharmacokinetic modeling and metabolite area-under-the-curve ratios, was assessed in manually segmented PDA and normal appearing pancreas ROIs (N = 5). The change in tumor metabolism before and 4-weeks after treatment initiation was assessed in primary PDA (N = 2) and liver metastases (N = 1), and was compared to objective tumor response defined by response evaluation criteria in solid tumors (RECIST) on subsequent CTs.
STATISTICAL TESTS: Descriptive tests (mean ± standard deviation), model fit error for pharmacokinetic rate constants.
RESULTS: Primary PDA showed reduced alanine-to-lactate ratios when compared to normal pancreas, due to increased lactate-to-pyruvate or reduced alanine-to-pyruvate ratios. Of the three patients who received HP [1-13 C]pyruvate MRI before and 4-weeks after treatment initiation, one patient had a primary tumor with early metabolic response (increase in alanine-to-lactate) and subsequent partial response according to RECIST, one patient had a primary tumor with relatively stable metabolism and subsequent stable disease by RECIST, and one patient had metastatic PDA with increase in lactate-to-pyruvate of the liver metastases and corresponding progressive disease according to RECIST.
DATA CONCLUSION: Altered pyruvate metabolism with increased lactate or reduced alanine was observed in the primary tumor. Early metabolic response assessed at 4-weeks after treatment initiation correlated with subsequent objective tumor response assessed using RECIST.
LEVEL OF EVIDENCE: 2 TECHNICAL EFFICACY: Stage 2.

Keywords:  carbon-13; hyperpolarization; pancreas; pancreatic cancer; pancreatic ductal adenocarcinoma; pyruvate

DOI:  https://doi.org/10.1002/jmri.29162
Nature. 2023 Dec 06.

A novel antidiuretic hormone governs tumour-induced renal dysfunction.

Wenhao Xu, Gerui Li, Yuan Chen, Xujun Ye, Wei Song.

Maintenance of renal function and fluid transport are essential for vertebrates and invertebrates to adapt to physiological and pathological challenges. Human patients with malignant tumours frequently develop detrimental renal dysfunction and oliguria, and previous studies suggest the involvement of chemotherapeutic toxicity and tumour-associated inflammation1,2. However, how tumours might directly modulate renal functions remains largely unclear. Here, using conserved tumour models in Drosophila melanogaster3, we characterized isoform F of ion transport peptide (ITPF) as a fly antidiuretic hormone that is secreted by a subset of yki3SA gut tumour cells, impairs renal function and causes severe abdomen bloating and fluid accumulation. Mechanistically, tumour-derived ITPF targets the G-protein-coupled receptor TkR99D in stellate cells of Malpighian tubules-an excretory organ that is equivalent to renal tubules4-to activate nitric oxide synthase-cGMP signalling and inhibit fluid excretion. We further uncovered antidiuretic functions of mammalian neurokinin 3 receptor (NK3R), the homologue of fly TkR99D, as pharmaceutical blockade of NK3R efficiently alleviates renal tubular dysfunction in mice bearing different malignant tumours. Together, our results demonstrate a novel antidiuretic pathway mediating tumour-renal crosstalk across species and offer therapeutic opportunities for the treatment of cancer-associated renal dysfunction.

DOI: https://doi.org/10.1038/s41586-023-06833-8
Cancer Discov. 2023 Dec 04.

INX-315, a selective CDK2 inhibitor, induces cell cycle arrest and senescence in solid tumors.

Catherine Dietrich, Alec Trub, Antonio Ahn, Michael Taylor, Krutika Ambani, Keefe T Chan, Kun-Hui Lu, Christabella A Mahendra, Catherine Blyth, Rhiannon Coulson, Susanne Ramm, April C Watt, Sunil Kumar Matsa, John Bisi, Jay Strum, Patrick Roberts, Shom Goel.

Cyclin-dependent kinase 2 (CDK2) is thought to play an important role in driving proliferation of certain cancers, including those harboring CCNE1 amplification and breast cancers that have acquired resistance to CDK4/6 inhibitors (CDK4/6i). The precise impact of pharmacological inhibition of CDK2 is not known due to the lack of selective CDK2 inhibitors. Here we describe INX-315, a novel and potent CDK2 inhibitor with high selectivity over other CDK family members. Using cell-based assays, patient-derived xenografts, and transgenic mouse models, we show that INX-315 (i) promotes retinoblastoma protein hypo-phosphorylation and therapy-induced senescence (TIS) in CCNE1-amplified tumors, leading to durable control of tumor growth; (ii) overcomes breast cancer resistance to CDK4/6i, restoring cell cycle control whilst re-instating the chromatin architecture of CDK4/6i-induced TIS; and (iii) delays the onset of CDK4/6i resistance in breast cancer by driving deeper suppression of E2F targets. Our results support the clinical development of selective CDK2 inhibitors.

DOI: https://doi.org/10.1158/2159-8290.CD-23-0954
J Cell Biol. 2024 Feb 05. pii: e202309074. [Epub ahead of print]223(2):

An mTurq2-Col4a1 mouse model allows for live visualization of mammalian basement membrane development.

Rebecca A Jones, Brandon Trejo, Parijat Sil, Katherine A Little, H Amalia Pasolli, Bradley Joyce, Eszter Posfai, Danelle Devenport.

Basement membranes (BMs) are specialized sheets of extracellular matrix that underlie epithelial and endothelial tissues. BMs regulate the traffic of cells and molecules between compartments, and participate in signaling, cell migration, and organogenesis. The dynamics of mammalian BMs, however, are poorly understood, largely due to a lack of models in which core BM components are endogenously labeled. Here, we describe the mTurquoise2-Col4a1 mouse in which we fluorescently tag collagen IV, the main component of BMs. Using an innovative planar-sagittal live imaging technique to visualize the BM of developing skin, we directly observe BM deformation during hair follicle budding and basal progenitor cell divisions. The BM's inherent pliability enables dividing cells to remain attached to and deform the BM, rather than lose adhesion as generally thought. Using FRAP, we show BM collagen IV is extremely stable, even during periods of rapid epidermal growth. These findings demonstrate the utility of the mTurq2-Col4a1 mouse to shed new light on mammalian BM developmental dynamics.

DOI: https://doi.org/10.1083/jcb.202309074
Nature. 2023 Dec;624(7990): 164-172

Organ aging signatures in the plasma proteome track health and disease.

Hamilton Se-Hwee Oh, Jarod Rutledge, Daniel Nachun, Róbert Pálovics, Olamide Abiose, Patricia Moran-Losada, Divya Channappa, Deniz Yagmur Urey, Kate Kim, Yun Ju Sung, Lihua Wang, Jigyasha Timsina, Dan Western, Menghan Liu, Pat Kohlfeld, John Budde, Edward N Wilson, Yann Guen, Taylor M Maurer, Michael Haney, Andrew C Yang, Zihuai He, Michael D Greicius, Katrin I Andreasson, Sanish Sathyan, Erica F Weiss, Sofiya Milman, Nir Barzilai, Carlos Cruchaga, Anthony D Wagner, Elizabeth Mormino, Benoit Lehallier, Victor W Henderson, Frank M Longo, Stephen B Montgomery, Tony Wyss-Coray.

Animal studies show aging varies between individuals as well as between organs within an individual1-4, but whether this is true in humans and its effect on age-related diseases is unknown. We utilized levels of human blood plasma proteins originating from specific organs to measure organ-specific aging differences in living individuals. Using machine learning models, we analysed aging in 11 major organs and estimated organ age reproducibly in five independent cohorts encompassing 5,676 adults across the human lifespan. We discovered nearly 20% of the population show strongly accelerated age in one organ and 1.7% are multi-organ agers. Accelerated organ aging confers 20-50% higher mortality risk, and organ-specific diseases relate to faster aging of those organs. We find individuals with accelerated heart aging have a 250% increased heart failure risk and accelerated brain and vascular aging predict Alzheimer's disease (AD) progression independently from and as strongly as plasma pTau-181 (ref. 5), the current best blood-based biomarker for AD. Our models link vascular calcification, extracellular matrix alterations and synaptic protein shedding to early cognitive decline. We introduce a simple and interpretable method to study organ aging using plasma proteomics data, predicting diseases and aging effects.

DOI: https://doi.org/10.1038/s41586-023-06802-1
Nature. 2023 Dec 06.

Dictionary of immune responses to cytokines at single-cell resolution.

Ang Cui, Teddy Huang, Shuqiang Li, Aileen Ma, Jorge L Pérez, Chris Sander, Derin B Keskin, Catherine J Wu, Ernest Fraenkel, Nir Hacohen.

Cytokines mediate cell-cell communication in the immune system and represent important therapeutic targets1-3. A myriad of studies have highlighted their central role in immune function4-13, yet we lack a global view of the cellular responses of each immune cell type to each cytokine. To address this gap, we created the Immune Dictionary, a compendium of single-cell transcriptomic profiles of more than 17 immune cell types in response to each of 86 cytokines (>1,400 cytokine-cell type combinations) in mouse lymph nodes in vivo. A cytokine-centric view of the dictionary revealed that most cytokines induce highly cell-type-specific responses. For example, the inflammatory cytokine interleukin-1β induces distinct gene programmes in almost every cell type. A cell-type-centric view of the dictionary identified more than 66 cytokine-driven cellular polarization states across immune cell types, including previously uncharacterized states such as an interleukin-18-induced polyfunctional natural killer cell state. Based on this dictionary, we developed companion software, Immune Response Enrichment Analysis, for assessing cytokine activities and immune cell polarization from gene expression data, and applied it to reveal cytokine networks in tumours following immune checkpoint blockade therapy. Our dictionary generates new hypotheses for cytokine functions, illuminates pleiotropic effects of cytokines, expands our knowledge of activation states of each immune cell type, and provides a framework to deduce the roles of specific cytokines and cell-cell communication networks in any immune response.

DOI: https://doi.org/10.1038/s41586-023-06816-9
APL Bioeng. 2023 Dec;7(4): 046116

Endothelial cells metabolically regulate breast cancer invasion toward a microvessel.

Matthew L Tan, Niaa Jenkins-Johnston, Sarah Huang, Brittany Schutrum, Sandra Vadhin, Abhinav Adhikari, Rebecca M Williams, Warren R Zipfel, Jan Lammerding, Jeffrey D Varner, Claudia Fischbach.

Breast cancer metastasis is initiated by invasion of tumor cells into the collagen type I-rich stroma to reach adjacent blood vessels. Prior work has identified that metabolic plasticity is a key requirement of tumor cell invasion into collagen. However, it remains largely unclear how blood vessels affect this relationship. Here, we developed a microfluidic platform to analyze how tumor cells invade collagen in the presence and absence of a microvascular channel. We demonstrate that endothelial cells secrete pro-migratory factors that direct tumor cell invasion toward the microvessel. Analysis of tumor cell metabolism using metabolic imaging, metabolomics, and computational flux balance analysis revealed that these changes are accompanied by increased rates of glycolysis and oxygen consumption caused by broad alterations of glucose metabolism. Indeed, restricting glucose availability decreased endothelial cell-induced tumor cell invasion. Our results suggest that endothelial cells promote tumor invasion into the stroma due, in part, to reprogramming tumor cell metabolism.

DOI: https://doi.org/10.1063/5.0171109
Nat Commun. 2023 Dec 05. 14(1): 8031

Secretory GFP reconstitution labeling of neighboring cells interrogates cell-cell interactions in metastatic niches.

Misa Minegishi, Takahiro Kuchimaru, Kaori Nishikawa, Takayuki Isagawa, Satoshi Iwano, Kei Iida, Hiromasa Hara, Shizuka Miura, Marika Sato, Shigeaki Watanabe, Akifumi Shiomi, Yo Mabuchi, Hiroshi Hamana, Hiroyuki Kishi, Tatsuyuki Sato, Daigo Sawaki, Shigeru Sato, Yutaka Hanazono, Atsushi Suzuki, Takahide Kohro, Tetsuya Kadonosono, Tomomi Shimogori, Atsushi Miyawaki, Norihiko Takeda, Hirofumi Shintaku, Shinae Kizaka-Kondoh, Satoshi Nishimura.

Cancer cells inevitably interact with neighboring host tissue-resident cells during the process of metastatic colonization, establishing a metastatic niche to fuel their survival, growth, and invasion. However, the underlying mechanisms in the metastatic niche are yet to be fully elucidated owing to the lack of methodologies for comprehensively studying the mechanisms of cell-cell interactions in the niche. Here, we improve a split green fluorescent protein (GFP)-based genetically encoded system to develop secretory glycosylphosphatidylinositol-anchored reconstitution-activated proteins to highlight intercellular connections (sGRAPHIC) for efficient fluorescent labeling of tissue-resident cells that neighbor on and putatively interact with cancer cells in deep tissues. The sGRAPHIC system enables the isolation of metastatic niche-associated tissue-resident cells for their characterization using a single-cell RNA sequencing platform. We use this sGRAPHIC-leveraged transcriptomic platform to uncover gene expression patterns in metastatic niche-associated hepatocytes in a murine model of liver metastasis. Among the marker genes of metastatic niche-associated hepatocytes, we identify Lgals3, encoding galectin-3, as a potential pro-metastatic factor that accelerates metastatic growth and invasion.

DOI: https://doi.org/10.1038/s41467-023-43855-2
Nat Methods. 2023 Dec 06.

Embryo mechanics cartography: inference of 3D force atlases from fluorescence microscopy.

Sacha Ichbiah, Fabrice Delbary, Alex McDougall, Rémi Dumollard, Hervé Turlier.

Tissue morphogenesis results from a tight interplay between gene expression, biochemical signaling and mechanics. Although sequencing methods allow the generation of cell-resolved spatiotemporal maps of gene expression, creating similar maps of cell mechanics in three-dimensional (3D) developing tissues has remained a real challenge. Exploiting the foam-like arrangement of cells, we propose a robust end-to-end computational method called 'foambryo' to infer spatiotemporal atlases of cellular forces from fluorescence microscopy images of cell membranes. Our method generates precise 3D meshes of cells' geometry and successively predicts relative cell surface tensions and pressures. We validate it with 3D foam simulations, study its noise sensitivity and prove its biological relevance in mouse, ascidian and worm embryos. 3D force inference allows us to recover mechanical features identified previously, but also predicts new ones, unveiling potential new insights on the spatiotemporal regulation of cell mechanics in developing embryos. Our code is freely available and paves the way for unraveling the unknown mechanochemical feedbacks that control embryo and tissue morphogenesis.

DOI: https://doi.org/10.1038/s41592-023-02084-7
ArXiv. 2023 Nov 22. pii: arXiv:2311.13417v1. [Epub ahead of print]

Reproducible image-based profiling with Pycytominer.

Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen Fleming, Ruifan Pei, John Arevalo, Hillary Tsang, Vincent Rubinetti, Callum Tromans-Coia, Tim Becker, Erin Weisbart, Charlotte Bunne, Alexandr A Kalinin, Rebecca Senft, Stephen J Taylor, Nasim Jamali, Adeniyi Adeboye, Hamdah Shafqat Abbasi, Allen Goodman, Juan C Caicedo, Anne E Carpenter, Beth A Cimini, Shantanu Singh, Gregory P Way.

Technological advances in high-throughput microscopy have facilitated the acquisition of cell images at a rapid pace, and data pipelines can now extract and process thousands of image-based features from microscopy images. These features represent valuable single-cell phenotypes that contain information about cell state and biological processes. The use of these features for biological discovery is known as image-based or morphological profiling. However, these raw features need processing before use and image-based profiling lacks scalable and reproducible open-source software. Inconsistent processing across studies makes it difficult to compare datasets and processing steps, further delaying the development of optimal pipelines, methods, and analyses. To address these issues, we present Pycytominer, an open-source software package with a vibrant community that establishes an image-based profiling standard. Pycytominer has a simple, user-friendly Application Programming Interface (API) that implements image-based profiling functions for processing high-dimensional morphological features extracted from microscopy images of cells. Establishing Pycytominer as a standard image-based profiling toolkit ensures consistent data processing pipelines with data provenance, therefore minimizing potential inconsistencies and enabling researchers to confidently derive accurate conclusions and discover novel insights from their data, thus driving progress in our field.
Cancer Res. 2023 Dec 06.

Myeloid cells pave the metastatic road in breast cancer.

Daniel E Michaud, Jennifer L Guerriero.

Current immunotherapeutic approaches are tailored towards biomarkers and mechanisms presented in the primary tumor microenvironment, yet few are designed against targets that arise in the metastatic site. In a recent Cancer Discovery article, Yofe and colleagues spatially and temporally mapped the evolving breast tumor metastatic environment within the lung at single cell resolution to identify immunologic cell types and mechanisms underlying the formation of metastatic nodules. The authors identified myeloid cell, monocyte, and neutrophil phenotypes as the most significant differences between the primary tumor and metastatic site. The authors also revealed the existence of a metastases-specific population of macrophages expressing Trem2 in both human and murine models that exhibit immunosuppressive features. Interestingly, Trem2+ macrophages are enriched at the invasive border of metastatic nodules compared to the metastatic core, suggesting they play an exclusionary role within the site. Characterization of the pre-metastatic lung in conjunction with pseudo-time lineage analysis revealed that Fn1+ monocytes precede metastasis formation and are the likely source of Trem2+ macrophages in developed nodules. This study supports the characterization of metastatic immune microenvironments to identify novel immunotherapeutic targets that may not exist within the primary site but play a significant role in patient outcome.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-3803
Elife. 2023 Dec 07. pii: e85640. [Epub ahead of print]12

Multiple NTS neuron populations cumulatively suppress food intake.

Weiwei Qui, Chelsea R Hutch, Yi Wang, Jennifer Wloszek, Rachel A Rucker, Martin G Myers, Darleen Sandoval.

  Several discrete groups of feeding-regulated neurons in the nucleus of the solitary tract (nucleus tractus solitarius; NTS) suppress food intake, including avoidance-promoting neurons that express Cck (NTSCck cells) and distinct Lepr- and Calcr-expressing neurons (NTSLepr and NTSCalcr cells, respectively) that suppress food intake without promoting avoidance. To test potential synergies among these cell groups we manipulated multiple NTS cell populations simultaneously. We found that activating multiple sets of NTS neurons (e.g., NTSLepr plus NTSCalcr (NTSLC), or NTSLC plus NTSCck (NTSLCK)) suppressed feeding more robustly than activating single populations. While activating groups of cells that include NTSCck neurons promoted conditioned taste avoidance (CTA), NTSLC activation produced no CTA despite abrogating feeding. Thus, the ability to promote CTA formation represents a dominant effect but activating multiple non-aversive populations augments the suppression of food intake without provoking avoidance. Furthermore, silencing multiple NTS neuron groups augmented food intake and body weight to a greater extent than silencing single populations, consistent with the notion that each of these NTS neuron populations plays crucial and cumulative roles in the control of energy balance. We found that silencing NTSLCK neurons failed to blunt the weight-loss response to vertical sleeve gastrectomy (VSG) and that feeding activated many non-NTSLCK neurons, however, suggesting that as-yet undefined NTS cell types must make additional contributions to the restraint of feeding.

Keywords:  mouse; neuroscience

DOI:  https://doi.org/10.7554/eLife.85640