bims-cagime 2023-02-05 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2023‒02‒05
thirty-six papers selected by
Kıvanç Görgülü
Technical University of Munich

Slow TCA flux and ATP production in primary solid tumours but not metastases.
Mechanisms Controlling Selective Elimination of Damaged Lysosomes.
Physical Activity Delays Obesity-Associated Pancreatic Ductal Adenocarcinoma in Mice and Decreases Inflammation.
CD73-dependent adenosine signaling through Adora2b drives immunosuppression in ductal pancreatic cancer.
Arginase 1 is a key driver of immune suppression in pancreatic cancer.
Analysis of donor pancreata defines the transcriptomic signature and microenvironment of early pre-neoplastic pancreatic lesions.
Autophagy-dependent ferroptosis in cancer.
A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation resulting in pro-metastatic NF-κB signaling.
Mechanisms driving the immunoregulatory function of cancer cells.
Autophagic structures revealed by cryo-electron tomography: New clues about autophagosome biogenesis.
Metabolic function of autophagy is essential for cell survival.
MmCMS: mouse models' consensus molecular subtypes of colorectal cancer.
Glycolysis regulates KRAS plasma membrane localization and function through defined glycosphingolipids.
Area postrema neurons mediate interleukin-6 function in cancer-associated cachexia.
Lysosomal quality control: molecular mechanisms and therapeutic implications.
A mouse model of human mitofusin 2-related lipodystrophy exhibits adipose-specific mitochondrial stress and reduced leptin secretion.
Deciphering functional roles and interplay between Beclin1 and Beclin2 in autophagosome formation and mitophagy.
Thrifty energy metabolism in solid tumours.
Biologically informed deep learning to query gene programs in single-cell atlases.
The tumor-immune ecosystem in shaping metastasis.
Could senescence phenotypes strike the balance to promote tumor dormancy?
Neuronal activity-driven O-GlcNAcylation promotes mitochondrial plasticity.
Genome-wide screens identify SEL1L as an intracellular rheostat controlling collagen turnover.
Direct visualization of emergent metastatic features within an ex vivo model of the tumor microenvironment.
Next-Generation Morphometry for pathomics-data mining in histopathology.
Spatial regulation of the glycocalyx component podocalyxin is a switch for prometastatic function.
A meta-analysis of RNA-Seq studies to identify novel genes that regulate aging.
Tolerability, Attrition Rates, and Survival Outcomes of Neoadjuvant FOLFIRINOX for Non-Metastatic Pancreatic Adenocarcinoma: Intent-to-Treat Analysis.
Semi-automated 3D fluorescence speckle analyzer (3D-Speckler) for microscope calibration and nanoscale measurement.
Glycine homeostasis requires reverse SHMT flux.
Intratumoral nanobody-IL-2 fusions that bind the tumor extracellular matrix suppress solid tumor growth in mice.
Epigenetically controlled tumor antigens derived from splice junctions between exons and transposable elements.
Clinical outcome and treatment sequences of patients with advanced pancreatic cancer treated with contemporary chemotherapy protocols.
Pressure and ultrasound activate mechanosensitive TRAAK K + channels through increased membrane tension.
Curvature sensing as an emergent property of multiscale assembly of septins.
WMDS.net: a network control framework for identifying key players in transcriptome programs.

Nature. 2023 Feb 01.

Slow TCA flux and ATP production in primary solid tumours but not metastases.

Caroline R Bartman, Daniel R Weilandt, Yihui Shen, Won Dong Lee, Yujiao Han, Tara TeSlaa, Connor S R Jankowski, Laith Samarah, Noel R Park, Victoria da Silva-Diz, Maya Aleksandrova, Yetis Gultekin, Argit Marishta, Lin Wang, Lifeng Yang, Asael Roichman, Vrushank Bhatt, Taijin Lan, Zhixian Hu, Xi Xing, Wenyun Lu, Shawn Davidson, Martin Wühr, Matthew G Vander Heiden, Daniel Herranz, Jessie Yanxiang Guo, Yibin Kang, Joshua D Rabinowitz.

Tissues derive ATP from two pathways-glycolysis and the tricarboxylic acid (TCA) cycle coupled to the electron transport chain. Most energy in mammals is produced via TCA metabolism1. In tumours, however, the absolute rates of these pathways remain unclear. Here we optimize tracer infusion approaches to measure the rates of glycolysis and the TCA cycle in healthy mouse tissues, Kras-mutant solid tumours, metastases and leukaemia. Then, given the rates of these two pathways, we calculate total ATP synthesis rates. We find that TCA cycle flux is suppressed in all five primary solid tumour models examined and is increased in lung metastases of breast cancer relative to primary orthotopic tumours. As expected, glycolysis flux is increased in tumours compared with healthy tissues (the Warburg effect2,3), but this increase is insufficient to compensate for low TCA flux in terms of ATP production. Thus, instead of being hypermetabolic, as commonly assumed, solid tumours generally produce ATP at a slower than normal rate. In mouse pancreatic cancer, this is accommodated by the downregulation of protein synthesis, one of this tissue's major energy costs. We propose that, as solid tumours develop, cancer cells shed energetically expensive tissue-specific functions, enabling uncontrolled growth despite a limited ability to produce ATP.

DOI: https://doi.org/10.1038/s41586-022-05661-6
Curr Opin Physiol. 2022 Oct;pii: 100590. [Epub ahead of print]29

Mechanisms Controlling Selective Elimination of Damaged Lysosomes.

Melissa J Hoyer, Sharan Swarup, J Wade Harper.

Lysosomes are subjected to physiological and patho-physiological insults over the course of their life cycle and are accordingly repaired or recycled. Lysophagy, the selective degradation of lysosomes via autophagy, occurs upon unrepairable lysosomal membrane rupture; galectins bind to glycosylated macromolecules in the lysosome lumen, orchestrating a series of cellular responses to promote autophagic recycling of damaged lysosomes and transcriptional upregulation of lysosomal genes. Damaged lysosomes are ubiquitylated, resulting in the recruitment of ubiquitin-binding autophagy receptors, which promote assembly of an autophagosome around damaged lysosomes for delivery to healthy lysosomes for degradation. Here, we review the current state of our understanding of mechanisms used to mark and eliminate damaged lysosomes, and discuss the complexities of galectin function and ubiquitin-chain linkage types. Finally, we discuss the limitations of available data and challenges with the goal of understanding the mechanistic basis of key steps in lysophagic flux.

DOI: https://doi.org/10.1016/j.cophys.2022.100590
bioRxiv. 2023 Jan 04. pii: 2023.01.03.521203. [Epub ahead of print]

Physical Activity Delays Obesity-Associated Pancreatic Ductal Adenocarcinoma in Mice and Decreases Inflammation.

Valentina Pita-Grisanti, Kelly Dubay, Ali Lahooti, Niharika Badi, Olivia Ueltschi, Kristyn Gumpper-Fedus, Hsiang-Yin Hsueh, Ila Lahooti, Myrriah Chavez-Tomar, Samantha Terhorst, Sue E Knoblaugh, Lei Cao, Wei Huang, Christopher C Coss, Thomas A Mace, Fouad Choueiry, Alice Hinton, Jennifer M Mitchell, Rosemarie Schmandt, Michaela Onstad Grinsfelder, Karen Basen-Engquist, Zobeida Cruz-Monserrate.

BACKGROUND & AIMS: Obesity is a risk factor for pancreatic ductal adenocarcinoma (PDAC), a deadly disease with limited preventive strategies. Lifestyle interventions to decrease obesity might prevent obesity-associated PDAC. Here, we examined whether decreasing obesity by increased physical activity (PA) and/or dietary changes would decrease inflammation in humans and prevent PDAC in mice.METHODS: Circulating inflammatory-associated cytokines of overweight and obese subjects before and after a PA intervention were compared. PDAC pre-clinical models were exposed to PA and/or dietary interventions after obesity-associated cancer initiation. Body composition, tumor progression, growth, fibrosis, inflammation, and transcriptomic changes in the adipose tissue were evaluated.
RESULTS: PA decreased the levels of systemic inflammatory cytokines in overweight and obese subjects. PDAC mice on a diet-induced obesity (DIO) and PA intervention, had delayed weight gain, decreased systemic inflammation, lower grade pancreatic intraepithelial neoplasia lesions, reduced PDAC incidence, and increased anti-inflammatory signals in the adipose tissue compared to controls. PA had additional cancer prevention benefits when combined with a non-obesogenic diet after DIO. However, weight loss through PA alone or combined with a dietary intervention did not prevent tumor growth in an orthotopic PDAC model. Adipose-specific targeting of interleukin (IL)-15, an anti-inflammatory cytokine induced by PA in the adipose tissue, slowed PDAC growth.
CONCLUSIONS: PA alone or combined with diet-induced weight loss delayed the progression of PDAC and reduced systemic and adipose inflammatory signals. Therefore, obesity management via dietary interventions and/or PA, or modulating weight loss related pathways could prevent obesity-associated PDAC in high-risk obese individuals.

DOI: https://doi.org/10.1101/2023.01.03.521203
Cancer Res. 2023 Jan 31. pii: CAN-22-2553. [Epub ahead of print]

CD73-dependent adenosine signaling through Adora2b drives immunosuppression in ductal pancreatic cancer.

Erika Y Faraoni, Kanchan Singh, Vidhi Chandra, Olivereen Le Roux, Yulin Dai, Ismet Sahin, Baylee J O'Brien, Lincoln N Strickland, Le Li, Emily Vucic, Amanda N Warner, Melissa Pruski, Trent Clark, George Van Buren, Nirav C Thosani, John S Bynon, Curtis J Wray, Dafna Bar-Sagi, Kyle L Poulsen, Lana A Vornik, Michelle I Savage, Shizuko Sei, Altaf Mohammed, Zhongming Zhao, Powel H Brown, Tingting Mills, Holger K Eltzschig, Florencia McAllister, Jennifer M Bailey-Lundberg.

The microenvironment that surrounds pancreatic ductal adenocarcinoma (PDAC) is profoundly desmoplastic and immunosuppressive. Understanding triggers of immunosuppression during the process of pancreatic tumorigenesis would aid in establishing targets for effective prevention and therapy. Here, we interrogated differential molecular mechanisms dependent on cell of origin and subtype that promote immunosuppression during PDAC initiation and in established tumors. Transcriptomic analysis of cell of origin-dependent epithelial gene signatures revealed that Nt5e/CD73, a cell surface enzyme required for extracellular adenosine generation, is one of the top 10% of genes over-expressed in murine tumors arising from ductal pancreatic epithelium as opposed to those rising from acinar cells. These findings were confirmed by immunohistochemistry and high-performance liquid chromatography. Analysis in human PDAC subtypes indicated that high Nt5e in murine ductal PDAC models overlaps with high NT5E in human PDAC squamous and basal subtypes, considered to have the highest immunosuppression and worst prognosis. Multiplex immunofluorescent analysis showed that activated CD8+ T cells in the PDAC tumor microenvironment express high levels of CD73 indicating an opportunity for immunotherapeutic targeting. Delivery of CD73 small molecule inhibitors through various delivery routes reduced tumor development and growth in genetically engineered and syngeneic mouse models. In addition, the adenosine receptor Adora2b was a determinant of adenosine-mediated immunosuppression in PDAC. These findings highlight a molecular trigger of the immunosuppressive PDAC microenvironment elevated in ductal cell of origin, linking biology with subtype classification, critical components for PDAC immunoprevention and personalized approaches for immunotherapeutic intervention.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-2553
Elife. 2023 Feb 02. pii: e80721. [Epub ahead of print]12

Arginase 1 is a key driver of immune suppression in pancreatic cancer.

Rosa Elena Menjivar, Zeribe C Nwosu, Wenting Du, Katelyn L Donahue, Hanna S Hong, Carlos Espinoza, Kristee Brown, Ashley Velez-Delgado, Wei Yan, Fatima Lima, Allison Bischoff, Padma Kadiyala, Daniel Salas-Escabillas, Howard C Crawford, Filip Bednar, Eileen Carpenter, Yaqing Zhang, Christopher J Halbrook, Costas A Lyssiotis, Marina Pasca di Magliano.

  An extensive fibroinflammatory stroma rich in macrophages is a hallmark of pancreatic cancer. In this disease, it is well appreciated that macrophages are immunosuppressive and contribute to the poor response to immunotherapy; however, the mechanisms of immune suppression are complex and not fully understood. Immunosuppressive macrophages are classically defined by expression of the enzyme Arginase 1 (Arg1), which we demonstrated is potently expressed in pancreatic tumor associated macrophages from both human patients and mouse models. While routinely used as a polarization marker, Arg1 also catabolizes arginine, an amino acid required for T cell activation and proliferation. To investigate this metabolic function, we used a genetic and a pharmacologic approach to target Arg1 in pancreatic cancer. Genetic inactivation of Arg1 in macrophages, using a dual recombinase genetically engineered mouse model of pancreatic cancer, delayed formation of invasive disease, while increasing CD8+ T cell infiltration. Additionally, Arg1 deletion induced compensatory mechanisms, including Arg1 overexpression in epithelial cells, namely Tuft cells, and Arg2 overexpression in a subset of macrophages. To overcome these compensatory mechanisms, we used a pharmacological approach to inhibit arginase. Treatment of established tumors with the arginase inhibitor CB-1158 exhibited further increased CD8+ T cell infiltration, beyond that seen with the macrophage-specific knockout, and sensitized the tumors to anti-PD1 immune checkpoint blockade. Our data demonstrate that Arg1 drives immune suppression in pancreatic cancer by depleting Arginine and inhibiting T cell activation.

Keywords:  cancer biology; human; mouse

DOI:  https://doi.org/10.7554/eLife.80721
bioRxiv. 2023 Jan 15. pii: 2023.01.13.523300. [Epub ahead of print]

Analysis of donor pancreata defines the transcriptomic signature and microenvironment of early pre-neoplastic pancreatic lesions.

Eileen S Carpenter, Ahmed M Elhossiny, Padma Kadiyala, Jay Li, Jake McGue, Brian Griffith, Yaqing Zhang, Jacob Edwards, Sarah Nelson, Fatima Lima, Katelyn L Donahue, Wenting Du, Allison C Bischoff, Danyah Alomari, Hannah Watkoske, Michael Mattea, Stephanie The, Carlos Espinoza, Meredith Barrett, Christopher J Sonnenday, Nicholas Olden, Nicole Peterson, Valerie Gunchick, Vaibhav Sahai, Arvind Rao, Filip Bednar, Jiaqi Shi, Timothy L Frankel, Marina Pasca Di Magliano.

The adult healthy human pancreas has been poorly studied given lack of indication to obtain tissue from the pancreas in the absence of disease and rapid postmortem degradation. We obtained pancreata from brain dead donors thus avoiding any warm ischemia time. The 30 donors were diverse in age and race and had no known pancreas disease. Histopathological analysis of the samples revealed PanIN lesions in most individuals irrespective of age. Using a combination of multiplex immunohistochemistry, single cell RNA sequencing, and spatial transcriptomics, we provide the first ever characterization of the unique microenvironment of the adult human pancreas and of sporadic PanIN lesions. We compared healthy pancreata to pancreatic cancer and peritumoral tissue and observed distinct transcriptomic signatures in fibroblasts, and, to a lesser extent, macrophages. PanIN epithelial cells from healthy pancreata were remarkably transcriptionally similar to cancer cells, suggesting that neoplastic pathways are initiated early in tumorigenesis.Statement of significance: The causes underlying the onset of pancreatic cancer remain largely unknown, hampering early detection and prevention strategies. Here, we show that PanIN are abundant in healthy individuals and present at a much higher rate than the incidence of pancreatic cancer, setting the stage for efforts to elucidate the microenvironmental and cell intrinsic factors that restrain, or, conversely, promote, malignant progression.

DOI: https://doi.org/10.1101/2023.01.13.523300
Antioxid Redox Signal. 2023 Feb 03.

Autophagy-dependent ferroptosis in cancer.

Fangquan Chen, Xiutao Cai, Rui Kang, Jiao Liu, Doalin Tang.

SIGNIFICANCE: Autophagy is a self-degrading process that determines cell fate in response to various environmental stresses. In contrast to autophagy-mediated cell survival, the signals, mechanisms, and effects of autophagy-dependent cell death remain obscure. The discovery of autophagy-dependent ferroptosis provides a paradigm for understanding the relationship between aberrant degradation pathways and excessive lipid peroxidation in driving regulated cell death.RECENT ADVANCES: Ferroptosis was originally described as an autophagy-independent and iron-mediated non-apoptotic cell death. Current studies reveal that the level of intracellular autophagy is positively correlated with ferroptosis sensitivity. Selective autophagic degradation of proteins (e.g., ferritin, SLC40A1, ARNTL, GPX4, and CDH2) or organelles (e.g., lipid droplets or mitochondria) promotes ferroptosis by inducing iron overload and/or lipid peroxidation. Several upstream autophagosome regulators (e.g., TMEM164), downstream autophagy receptors (e.g., HPCAL1), or danger signals (e.g., DCN) are selectively required for ferroptosis-related autophagy, but not for starvation-induced autophagy. The induction of autophagy-dependent ferroptosis is an effective approach to eliminate drug-resistant cancer cells.
CRITICAL ISSUES: How different organelles selectively activate autophagy to modulate ferroptosis sensitivity is not fully understood. Identifying direct protein effectors of ferroptotic cell death remains a challenge.
FUTURE DIRECTIONS: Further understanding of the molecular mechanics and immune consequences of autophagy-dependent ferroptosis is critical for the development of precision antitumor therapies.

DOI: https://doi.org/10.1089/ars.2022.0202
Nat Cancer. 2023 Feb 02.

A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation resulting in pro-metastatic NF-κB signaling.

Patricia Altea-Manzano, Ginevra Doglioni, Yawen Liu, Alejandro M Cuadros, Emma Nolan, Juan Fernández-García, Qi Wu, Mélanie Planque, Kathrin Julia Laue, Florencia Cidre-Aranaz, Xiao-Zheng Liu, Oskar Marin-Bejar, Joke Van Elsen, Ines Vermeire, Dorien Broekaert, Sofie Demeyer, Xander Spotbeen, Jakub Idkowiak, Aurélie Montagne, Margherita Demicco, H Furkan Alkan, Nick Rabas, Carla Riera-Domingo, François Richard, Tatjana Geukens, Maxim De Schepper, Sophia Leduc, Sigrid Hatse, Yentl Lambrechts, Emily Jane Kay, Sergio Lilla, Alisa Alekseenko, Vincent Geldhof, Bram Boeckx, Celia de la Calle Arregui, Giuseppe Floris, Johannes V Swinnen, Jean-Christophe Marine, Diether Lambrechts, Vicent Pelechano, Massimiliano Mazzone, Sara Zanivan, Jan Cools, Hans Wildiers, Véronique Baud, Thomas G P Grünewald, Uri Ben-David, Christine Desmedt, Ilaria Malanchi, Sarah-Maria Fendt.

Metabolic rewiring is often considered an adaptive pressure limiting metastasis formation; however, some nutrients available at distant organs may inherently promote metastatic growth. We find that the lung and liver are lipid-rich environments. Moreover, we observe that pre-metastatic niche formation increases palmitate availability only in the lung, whereas a high-fat diet increases it in both organs. In line with this, targeting palmitate processing inhibits breast cancer-derived lung metastasis formation. Mechanistically, breast cancer cells use palmitate to synthesize acetyl-CoA in a carnitine palmitoyltransferase 1a-dependent manner. Concomitantly, lysine acetyltransferase 2a expression is promoted by palmitate, linking the available acetyl-CoA to the acetylation of the nuclear factor-kappaB subunit p65. Deletion of lysine acetyltransferase 2a or carnitine palmitoyltransferase 1a reduces metastasis formation in lean and high-fat diet mice, and lung and liver metastases from patients with breast cancer show coexpression of both proteins. In conclusion, palmitate-rich environments foster metastases growth by increasing p65 acetylation, resulting in a pro-metastatic nuclear factor-kappaB signaling.

DOI: https://doi.org/10.1038/s43018-023-00513-2
Nat Rev Cancer. 2023 Jan 30.

Mechanisms driving the immunoregulatory function of cancer cells.

Antoinette van Weverwijk, Karin E de Visser.

Tumours display an astonishing variation in the spatial distribution, composition and activation state of immune cells, which impacts their progression and response to immunotherapy. Shedding light on the mechanisms that govern the diversity and function of immune cells in the tumour microenvironment will pave the way for the development of more tailored immunomodulatory strategies for the benefit of patients with cancer. Cancer cells, by virtue of their paracrine and juxtacrine communication mechanisms, are key contributors to intertumour heterogeneity in immune contextures. In this Review, we discuss how cancer cell-intrinsic features, including (epi)genetic aberrations, signalling pathway deregulation and altered metabolism, play a key role in orchestrating the composition and functional state of the immune landscape, and influence the therapeutic benefit of immunomodulatory strategies. Moreover, we highlight how targeting cancer cell-intrinsic parameters or their downstream immunoregulatory pathways is a viable strategy to manipulate the tumour immune milieu in favour of antitumour immunity.

DOI: https://doi.org/10.1038/s41568-022-00544-4
Autophagy. 2023 Feb 01.

Autophagic structures revealed by cryo-electron tomography: New clues about autophagosome biogenesis.

Hana Popelka, Daniel J Klionsky.

  Transitions from the early to late phagophore, which occur to engulf cytoplasmic material within an autophagosome for macroautophagic/autophagic degradation, involve dynamic ultrastructural changes that are not fully understood. A recent study combined cryo-electron tomography (cryo-ET) with extensive computational analysis to get a better insight into autophagosome biogenesis in situ within yeast cells. This approach disclosed new information on the shape of autophagic structures, their contacts with surrounding organelles, membrane sources, and mechanisms of transition. Together, these results provide new directions for autophagy research, and show the potential of cryo-ET in cell biology.

Keywords:  Endoplasmic reticulum; membrane organelle; phagophore; vacuole; vesicle

DOI:  https://doi.org/10.1080/15548627.2023.2175305
Autophagy. 2023 Feb 01. 1-3

Metabolic function of autophagy is essential for cell survival.

Lucia Sedlackova, Tetsushi Kataura, Sovan Sarkar, Viktor I Korolchuk.

  Age-related human pathologies present with a multitude of molecular and metabolic phenotypes, which individually or synergistically contribute to tissue degeneration. However, current lack of understanding of the interdependence of these molecular pathologies limits the potential range of existing therapeutic intervention strategies. In our study, we set out to understand the chain of molecular events, which underlie the loss of cellular viability in macroautophagy/autophagy deficiency associated with aging and age-related disease. We discover a novel axis linking autophagy, a cellular waste disposal pathway, and a metabolite, nicotinamide adenine dinucleotide (NAD). The axis connects multiple organelles, molecules and stress response pathways mediating cellular demise when autophagy becomes dysfunctional. By elucidating the steps on the path from efficient mitochondrial recycling to NAD maintenance and ultimately cell viability, we highlight targets potentially receptive to therapeutic interventions in a range of genetic and age-related diseases associated with autophagy dysfunction.Abbreviations: IMM: inner mitochondrial membrane; NAD: nicotinamide dinucleotide; OXPHOS: oxidative phosphorylation; PARP: poly(ADP-ribose) polymerase; ROS: reactive oxygen species.

Keywords:  Aging; DNA damage; NAD; PARP; ROS; autophagy; mitochondria; mitophagy; sirtuins

DOI:  https://doi.org/10.1080/15548627.2023.2165753
Br J Cancer. 2023 Jan 30.

MmCMS: mouse models' consensus molecular subtypes of colorectal cancer.

Raheleh Amirkhah, Kathryn Gilroy, Sudhir B Malla, Tamsin R M Lannagan, Ryan M Byrne, Natalie C Fisher, Shania M Corry, Noha-Ehssan Mohamed, Hojjat Naderi-Meshkin, Megan L Mills, Andrew D Campbell, Rachel A Ridgway, Baharak Ahmaderaghi, Richard Murray, Antoni Berenguer Llergo, Rebeca Sanz-Pamplona, Alberto Villanueva, Eduard Batlle, Ramon Salazar, Mark Lawler, Owen J Sansom, Philip D Dunne.

BACKGROUND: Colorectal cancer (CRC) primary tumours are molecularly classified into four consensus molecular subtypes (CMS1-4). Genetically engineered mouse models aim to faithfully mimic the complexity of human cancers and, when appropriately aligned, represent ideal pre-clinical systems to test new drug treatments. Despite its importance, dual-species classification has been limited by the lack of a reliable approach. Here we utilise, develop and test a set of options for human-to-mouse CMS classifications of CRC tissue.METHODS: Using transcriptional data from established collections of CRC tumours, including human (TCGA cohort; n = 577) and mouse (n = 57 across n = 8 genotypes) tumours with combinations of random forest and nearest template prediction algorithms, alongside gene ontology collections, we comprehensively assess the performance of a suite of new dual-species classifiers.
RESULTS: We developed three approaches: MmCMS-A; a gene-level classifier, MmCMS-B; an ontology-level approach and MmCMS-C; a combined pathway system encompassing multiple biological and histological signalling cascades. Although all options could identify tumours associated with stromal-rich CMS4-like biology, MmCMS-A was unable to accurately classify the biology underpinning epithelial-like subtypes (CMS2/3) in mouse tumours.
CONCLUSIONS: When applying human-based transcriptional classifiers to mouse tumour data, a pathway-level classifier, rather than an individual gene-level system, is optimal. Our R package enables researchers to select suitable mouse models of human CRC subtype for their experimental testing.

DOI: https://doi.org/10.1038/s41416-023-02157-6
Nat Commun. 2023 Jan 28. 14(1): 465

Glycolysis regulates KRAS plasma membrane localization and function through defined glycosphingolipids.

Junchen Liu, Ransome van der Hoeven, Walaa E Kattan, Jeffrey T Chang, Dina Montufar-Solis, Wei Chen, Maurice Wong, Yong Zhou, Carlito B Lebrilla, John F Hancock.

Oncogenic KRAS expression generates a metabolic dependency on aerobic glycolysis, known as the Warburg effect. We report an effect of increased glycolytic flux that feeds into glycosphingolipid biosynthesis and is directly linked to KRAS oncogenic function. High resolution imaging and genetic approaches show that a defined subset of outer leaflet glycosphingolipids, including GM3 and SM4, is required to maintain KRAS plasma membrane localization, with GM3 engaging in cross-bilayer coupling to maintain inner leaflet phosphatidylserine content. Thus, glycolysis is critical for KRAS plasma membrane localization and nanoscale spatial organization. Reciprocally oncogenic KRAS selectively upregulates cellular content of these same glycosphingolipids, whose depletion in turn abrogates KRAS oncogenesis in pancreatic cancer models. Our findings expand the role of the Warburg effect beyond ATP generation and biomass building to high-level regulation of KRAS function. The positive feedforward loop between oncogenic KRAS signaling and glycosphingolipid synthesis represents a vulnerability with therapeutic potential.

DOI: https://doi.org/10.1038/s41467-023-36128-5
bioRxiv. 2023 Jan 14. pii: 2023.01.12.523716. [Epub ahead of print]

Area postrema neurons mediate interleukin-6 function in cancer-associated cachexia.

Qingtao Sun, Daniëlle van de Lisdonk, Miriam Ferrer, Bruno Gegenhuber, Melody Wu, Jessica Tollkuhn, Tobias Janowitz, Bo Li.

Interleukin-6 (IL-6) has been long considered a key player in cancer-associated cachexia 1-15 . It is believed that sustained elevation of IL-6 production during cancer progression causes brain dysfunctions, which ultimately result in cachexia 16-20 . However, how peripheral IL-6 influences the brain remains poorly understood. Here we show that neurons in the area postrema (AP), a circumventricular structure in the hindbrain, mediate the function of IL-6 in cancer-associated cachexia in mice. We found that circulating IL-6 can rapidly enter the AP and activate AP neurons. Peripheral tumor, known to increase circulating IL-6 1-5,15,18,21-23 , leads to elevated IL-6 and neuronal hyperactivity in the AP, and causes potentiated excitatory synaptic transmission onto AP neurons. Remarkably, neutralization of IL-6 in the brain of tumor-bearing mice with an IL-6 antibody prevents cachexia, reduces the hyperactivity in an AP network, and markedly prolongs lifespan. Furthermore, suppression of Il6ra , the gene encoding IL-6 receptor, specifically in AP neurons with CRISPR/dCas9 interference achieves similar effects. Silencing of Gfral-expressing AP neurons also ameliorates the cancer-associated cachectic phenotypes and AP network hyperactivity. Our study identifies a central mechanism underlying the function of peripheral IL-6, which may serve as a target for treating cancer-associated cachexia.

DOI: https://doi.org/10.1101/2023.01.12.523716
Trends Cell Biol. 2023 Jan 28. pii: S0962-8924(23)00004-1. [Epub ahead of print]

Lysosomal quality control: molecular mechanisms and therapeutic implications.

Haoxiang Yang, Jay Xiaojun Tan.

  Lysosomes are essential catabolic organelles with an acidic lumen and dozens of hydrolytic enzymes. The detrimental consequences of lysosomal leakage have been well known since lysosomes were discovered during the 1950s. However, detailed knowledge of lysosomal quality control mechanisms has only emerged relatively recently. It is now clear that lysosomal leakage triggers multiple lysosomal quality control pathways that replace, remove, or directly repair damaged lysosomes. Here, we review how lysosomal damage is sensed and resolved in mammalian cells, with a focus on the molecular mechanisms underlying different lysosomal quality control pathways. We also discuss the clinical implications and therapeutic potential of these pathways.

Keywords:  ESCRT; PITT; TFEB/TFE3; lysophagy; lysosomal biogenesis; lysosomal repair

DOI:  https://doi.org/10.1016/j.tcb.2023.01.001
Elife. 2023 Feb 01. pii: e82283. [Epub ahead of print]12

A mouse model of human mitofusin 2-related lipodystrophy exhibits adipose-specific mitochondrial stress and reduced leptin secretion.

Jake P Mann, Xiaowen Duan, Satish Patel, Luis Carlos Tábara, Fabio Scurria, Anna Alvarez-Guaita, Afreen Haider, Ineke Luijten, Matthew Page, Margherita Protasoni, Koini Lim, Sam Virtue, Stephen O'Rahilly, Martin Armstrong, Julien Prudent, Robert K Semple, David B Savage.

  Mitochondrial dysfunction has been reported in obesity and insulin resistance, but primary genetic mitochondrial dysfunction is generally not associated with these, arguing against a straightforward causal relationship. A rare exception, recently identified in humans, is a syndrome of lower body adipose loss, leptin-deficient severe upper body adipose overgrowth, and insulin resistance caused by the p.Arg707Trp mutation in MFN2, encoding mitofusin 2. How the resulting selective form of mitochondrial dysfunction leads to tissue- and adipose depot-specific growth abnormalities and systemic biochemical perturbation is unknown. To address this, Mfn2R707W/R707W knock-in mice were generated and phenotyped on chow and high fat diets. Electron microscopy revealed adipose-specific mitochondrial morphological abnormalities. Oxidative phosphorylation measured in isolated mitochondria was unperturbed, but the cellular integrated stress response was activated in adipose tissue. Fat mass and distribution, body weight, and systemic glucose and lipid metabolism were unchanged, however serum leptin and adiponectin concentrations, and their secretion from adipose explants were reduced. Pharmacological induction of the integrated stress response in wild-type adipocytes also reduced secretion of leptin and adiponectin, suggesting an explanation for the in vivo findings. These data suggest that the p.Arg707Trp MFN2 mutation selectively perturbs mitochondrial morphology and activates the integrated stress response in adipose tissue. In mice, this does not disrupt most adipocyte functions or systemic metabolism, whereas in humans it is associated with pathological adipose remodelling and metabolic disease. In both species, disproportionate effects on leptin secretion may relate to cell autonomous induction of the integrated stress response.

Keywords:  cell biology; mouse

DOI:  https://doi.org/10.7554/eLife.82283
Sci Signal. 2023 Jan 31. 16(770): eabo4457

Deciphering functional roles and interplay between Beclin1 and Beclin2 in autophagosome formation and mitophagy.

Justin M Quiles, Rita H Najor, Eileen Gonzalez, Monica Jeung, Wenjing Liang, Sarah M Burbach, Erika A Zumaya, Rachel Y Diao, Mark A Lampert, Åsa B Gustafsson.

The degradation of macromolecules and organelles by the process of autophagy is critical for cellular homeostasis and is often compromised during aging and disease. Beclin1 and Beclin2 are implicated in autophagy induction, and these homologs share a high degree of amino acid sequence similarity but have divergent N-terminal regions. Here, we investigated the functions of the Beclin homologs in regulating autophagy and mitophagy, a specialized form of autophagy that targets mitochondria. Both Beclin homologs contributed to autophagosome formation, but a mechanism of autophagosome formation independent of either Beclin homolog occurred in response to starvation or mitochondrial damage. Mitophagy was compromised only in Beclin1-deficient HeLa cells and mouse embryonic fibroblasts because of defective autophagosomal engulfment of mitochondria, and the function of Beclin1 in mitophagy required the phosphorylation of the conserved Ser15 residue by the kinase Ulk1. Mitochondria-ER-associated membranes (MAMs) are important sites of autophagosome formation during mitophagy, and Beclin1, but not Beclin2 or a Beclin1 mutant that could not be phosphorylated at Ser15, localized to MAMs during mitophagy. Our findings establish a regulatory role for Beclin1 in selective mitophagy by initiating autophagosome formation adjacent to mitochondria, a function facilitated by Ulk1-mediated phosphorylation of Ser15 in its distinct N-terminal region.

DOI: https://doi.org/10.1126/scisignal.abo4457
Nature. 2023 Feb 01.

Thrifty energy metabolism in solid tumours.



Keywords:  Cancer; Metabolism

DOI:  https://doi.org/10.1038/d41586-023-00151-9
Nat Cell Biol. 2023 Feb 02.

Biologically informed deep learning to query gene programs in single-cell atlases.

Mohammad Lotfollahi, Sergei Rybakov, Karin Hrovatin, Soroor Hediyeh-Zadeh, Carlos Talavera-López, Alexander V Misharin, Fabian J Theis.

The increasing availability of large-scale single-cell atlases has enabled the detailed description of cell states. In parallel, advances in deep learning allow rapid analysis of newly generated query datasets by mapping them into reference atlases. However, existing data transformations learned to map query data are not easily explainable using biologically known concepts such as genes or pathways. Here we propose expiMap, a biologically informed deep-learning architecture that enables single-cell reference mapping. ExpiMap learns to map cells into biologically understandable components representing known 'gene programs'. The activity of each cell for a gene program is learned while simultaneously refining them and learning de novo programs. We show that expiMap compares favourably to existing methods while bringing an additional layer of interpretability to integrative single-cell analysis. Furthermore, we demonstrate its applicability to analyse single-cell perturbation responses in different tissues and species and resolve responses of patients who have coronavirus disease 2019 to different treatments across cell types.

DOI: https://doi.org/10.1038/s41556-022-01072-x
Am J Physiol Cell Physiol. 2023 Jan 30.

The tumor-immune ecosystem in shaping metastasis.

Yang Gao, Jeffrey M Rosen, Xiang H-F Zhang.

  A better understanding of the mechanisms regulating cancer metastasis is critical to develop new therapies and decrease mortality. Emerging evidence suggests that the interactions between tumor cells and the host immune system play important roles in establishing metastasis. Tumor cells are able to recruit immune cells, which in turn promotes tumor cell invasion, intravasation, survival in circulation, extravasation, and colonization in different organs. The tumor-host immunological interactions also generate a pre-metastatic niche in distant organs which facilitates metastasis. In this review, we summarize the recent findings on how tumor cells and immune cells regulate each other to co-evolve and promote the formation of metastases at the major organ sites of metastasis.

Keywords:  Ecosystem; Immune; Metastasis; Organotropism; Tumor

DOI:  https://doi.org/10.1152/ajpcell.00132.2022
Cancer Metastasis Rev. 2023 Feb 03.

Could senescence phenotypes strike the balance to promote tumor dormancy?

Fang-Yen Chiu, Raegan M Kvadas, Zeinab Mheidly, Ashkan Shahbandi, James G Jackson.

  After treatment and surgery, patient tumors can initially respond followed by a rapid relapse, or respond well and seemingly be cured, but then recur years or decades later. The state of surviving cancer cells during the long, undetected period is termed dormancy. By definition, the dormant tumor cells do not proliferate to create a mass that is detectable or symptomatic, but also never die. An intrinsic state and microenvironment that are inhospitable to the tumor would bias toward cell death and complete eradication, while conditions that favor the tumor would enable growth and relapse. In neither case would clinical dormancy be observed. Normal cells and tumor cells can enter a state of cellular senescence after stress such as that caused by cancer therapy. Senescence is characterized by a stable cell cycle arrest mediated by chromatin modifications that cause gene expression changes and a secretory phenotype involving many cytokines and chemokines. Senescent cell phenotypes have been shown to be both tumor promoting and tumor suppressive. The balance of these opposing forces presents an attractive model to explain tumor dormancy: phenotypes of stable arrest and immune suppression could promote survival, while reversible epigenetic programs combined with cytokines and growth factors that promote angiogenesis, survival, and proliferation could initiate the emergence from dormancy. In this review, we examine the phenotypes that have been characterized in different normal and cancer cells made senescent by various stresses and how these might explain the characteristics of tumor dormancy.

Keywords:  Angiogenesis; Breast cancer; Cellular senescence; Chromatin; Immune evasion; Tumor dormancy; p53

DOI:  https://doi.org/10.1007/s10555-023-10089-z
bioRxiv. 2023 Jan 11. pii: 2023.01.11.523512. [Epub ahead of print]

Neuronal activity-driven O-GlcNAcylation promotes mitochondrial plasticity.

Seungyoon B Yu, Richard G Sanchez, Zachary D Papich, Thomas C Whisenant, Majid Ghassemian, John N Koberstein, Melissa L Stewart, Gulcin Pekkurnaz.

Neuronal activity is an energy-intensive process that is largely sustained by instantaneous fuel utilization and ATP synthesis. However, how neurons couple ATP synthesis rate to fuel availability is largely unknown. Here, we demonstrate that the metabolic sensor enzyme O-GlcNAc transferase regulates neuronal activity-driven mitochondrial bioenergetics. We show that neuronal activity upregulates O-GlcNAcylation mainly in mitochondria. Mitochondrial O-GlcNAcylation is promoted by activity-driven fuel consumption, which allows neurons to compensate for high energy expenditure based on fuel availability. To determine the proteins that are responsible for these adjustments, we mapped the mitochondrial O-GlcNAcome of neurons. Finally, we determine that neurons fail to meet activity-driven metabolic demand when O-GlcNAcylation dynamics are prevented. Our findings suggest that O-GlcNAcylation provides a fuel-dependent feedforward control mechanism in neurons to optimize mitochondrial performance based on neuronal activity. This mechanism thereby couples neuronal metabolism to mitochondrial bioenergetics and plays a key role in sustaining energy homeostasis.

DOI: https://doi.org/10.1101/2023.01.11.523512
bioRxiv. 2023 Jan 14. pii: 2023.01.13.523943. [Epub ahead of print]

Genome-wide screens identify SEL1L as an intracellular rheostat controlling collagen turnover.

Michael J Podolsky, Benjamin Kheyfets, Afaq H Beigh, Christopher D Yang, Carlos Lizama Valenzuela, Ritwik Datta, Paul J Wolters, Michael T McManus, Ling Qi, Kamran Atabai.

Accumulating evidence has implicated impaired extracellular matrix (ECM) clearance as a key factor in fibrotic disease. Despite decades of research elucidating the effectors of ECM clearance, relatively little is understood regarding the upstream regulation of this process. Collagen is the most abundant constituent of normal and fibrotic ECM in mammalian tissues. Its catabolism occurs through extracellular proteolysis and cell-mediated uptake of collagen fragments for intracellular degradation. Given the paucity of information regarding the regulation of this latter process, we executed unbiased genome-wide screens to understand the molecular underpinnings of cell-mediated collagen clearance. Using this approach, we discovered a previously unappreciated mechanism through which collagen biosynthesis is sensed by cells internally and directly regulates clearance of extracellular collagen. The sensing mechanism is dependent on endoplasmic reticulum-resident protein SEL1L and occurs via a noncanonical function of SEL1L. This pathway functions as a homeostatic negative feedback loop that limits collagen accumulation in tissues. In human fibrotic lung disease, the induction of this collagen clearance pathway by collagen synthesis is impaired, thereby contributing to the pathological accumulation of collagen in lung tissue. Thus cell-autonomous, rheostatic collagen clearance is a previously unidentified pathway of tissue homeostasis.

DOI: https://doi.org/10.1101/2023.01.13.523943
bioRxiv. 2023 Jan 09. pii: 2023.01.09.523294. [Epub ahead of print]

Direct visualization of emergent metastatic features within an ex vivo model of the tumor microenvironment.

Libi Anandi, Jeremy Garcia, Libuše Janská, Josephine Liu, Manon Ros, Carlos Carmona-Fontaine.

Preventing tumor cells from acquiring metastatic properties would significantly reduce cancer mortality 1-5 . However, due to the complex nature of this process, it remains one of the most poorly understood and untreatable aspects of cancer 6-8 . Ischemia and hypoxia in solid tumors are requisite in metastasis formation - conditions that arise far from functional blood vessels and deep within tumor tissues 9,10 . These secluded locations impede the observation of pre-metastatic tumor cells and their interactions with stromal cells, which are also critical in the initiation of this process 11,12 . Thus, the initiation of metastasis has been incredibly difficult to model in the lab and to observe in vivo . We present an ex vivo model of the tumor microenvironment, called 3MIC, which overcomes these experimental challenges and enables the observation of ischemic tumor cells in their native 3D context with high spatial and temporal resolutions. The 3MIC recreates ischemic conditions in the tumor microenvironment and facilitates the co-culture of different cell types. Using live microscopy, we showed that ischemia, but not hypoxia alone, increases the motility and invasive properties of cells derived from primary tumors. These changes are phenotypic and can occur without clonal selection. We directly observed how interactions with stromal cells such as macrophages increased tumor invasion in conjunction with the effects of an ischemic microenvironment. Finally, we tested the effects of chemotherapy drugs under different metabolic microenvironments and found that ischemic tumor cells are more resistant to paclitaxel, possibly due to a metabolic resistance mechanism. Overall, the 3MIC is a cost-effective system that allows for the dissection of the complexity of the tumor microenvironment and direct observation of the emergence of metastasis, as well as the testing of treatments that may halt this process.

DOI: https://doi.org/10.1101/2023.01.09.523294
Nat Commun. 2023 Jan 28. 14(1): 470

Next-Generation Morphometry for pathomics-data mining in histopathology.

David L Hölscher, Nassim Bouteldja, Mehdi Joodaki, Maria L Russo, Yu-Chia Lan, Alireza Vafaei Sadr, Mingbo Cheng, Vladimir Tesar, Saskia V Stillfried, Barbara M Klinkhammer, Jonathan Barratt, Jürgen Floege, Ian S D Roberts, Rosanna Coppo, Ivan G Costa, Roman D Bülow, Peter Boor.

Pathology diagnostics relies on the assessment of morphology by trained experts, which remains subjective and qualitative. Here we developed a framework for large-scale histomorphometry (FLASH) performing deep learning-based semantic segmentation and subsequent large-scale extraction of interpretable, quantitative, morphometric features in non-tumour kidney histology. We use two internal and three external, multi-centre cohorts to analyse over 1000 kidney biopsies and nephrectomies. By associating morphometric features with clinical parameters, we confirm previous concepts and reveal unexpected relations. We show that the extracted features are independent predictors of long-term clinical outcomes in IgA-nephropathy. We introduce single-structure morphometric analysis by applying techniques from single-cell transcriptomics, identifying distinct glomerular populations and morphometric phenotypes along a trajectory of disease progression. Our study provides a concept for Next-generation Morphometry (NGM), enabling comprehensive quantitative pathology data mining, i.e., pathomics.

DOI: https://doi.org/10.1038/s41467-023-36173-0
Sci Adv. 2023 Feb 03. 9(5): eabq1858

Spatial regulation of the glycocalyx component podocalyxin is a switch for prometastatic function.

Alvaro Román-Fernández, Mohammed A Mansour, Fernanda G Kugeratski, Jayanthi Anand, Emma Sandilands, Laura Galbraith, Kai Rakovic, Eva C Freckmann, Erin M Cumming, Ji Park, Konstantina Nikolatou, Sergio Lilla, Robin Shaw, David Strachan, Susan Mason, Rachana Patel, Lynn McGarry, Archana Katoch, Kirsteen J Campbell, Colin Nixon, Crispin J Miller, Hing Y Leung, John Le Quesne, James C Norman, Sara Zanivan, Karen Blyth, David M Bryant.

The glycocalyx component and sialomucin podocalyxin (PODXL) is required for normal tissue development by promoting apical membranes to form between cells, triggering lumen formation. Elevated PODXL expression is also associated with metastasis and poor clinical outcome in multiple tumor types. How PODXL presents this duality in effect remains unknown. We identify an unexpected function of PODXL as a decoy receptor for galectin-3 (GAL3), whereby the PODXL-GAL3 interaction releases GAL3 repression of integrin-based invasion. Differential cortical targeting of PODXL, regulated by ubiquitination, is the molecular mechanism controlling alternate fates. Both PODXL high and low surface levels occur in parallel subpopulations within cancer cells. Orthotopic intraprostatic xenograft of PODXL-manipulated cells or those with different surface levels of PODXL define that this axis controls metastasis in vivo. Clinically, interplay between PODXL-GAL3 stratifies prostate cancer patients with poor outcome. Our studies define the molecular mechanisms and context in which PODXL promotes invasion and metastasis.

DOI: https://doi.org/10.1126/sciadv.abq1858
Exp Gerontol. 2023 Feb 01. pii: S0531-5565(23)00028-1. [Epub ahead of print]173 112107

A meta-analysis of RNA-Seq studies to identify novel genes that regulate aging.

Mohamad D Bairakdar, Ambuj Tewari, Matthias C Truttmann.

  Aging is a ubiquitous biological process that limits the maximal lifespan of most organisms. Significant efforts by many groups have identified mechanisms that, when triggered by natural or artificial stimuli, are sufficient to either enhance or decrease maximal lifespan. Previous aging studies using the nematode Caenorhabditis elegans (C. elegans) generated a wealth of publicly available transcriptomics datasets linking changes in gene expression to lifespan regulation. However, a comprehensive comparison of these datasets across studies in the context of aging biology is missing. Here, we carry out a systematic meta-analysis of over 1200 bulk RNA sequencing (RNASeq) samples obtained from 74 peer-reviewed publications on aging-related transcriptomic changes in C. elegans. Using both differential expression analyses and machine learning approaches, we mine the pooled data for novel pro-longevity genes. We find that both approaches identify known and propose novel pro-longevity genes. Further, we find that inter-lab experimental variance complicates the application of machine learning algorithms, a limitation that was not solved using bulk RNA-Seq batch correction and normalization techniques. Taken as a whole, our results indicate that machine learning approaches may hold promise for the identification of genes that regulate aging but will require more sophisticated batch correction strategies or standardized input data to reliably identify novel pro-longevity genes.

Keywords:  Aging; C. elegans; Longevity; Machine learning; RNAseq; Reproducibility

DOI:  https://doi.org/10.1016/j.exger.2023.112107
J Am Coll Surg. 2022 Dec 08. pii: XCS.0000000000000499. [Epub ahead of print]

Tolerability, Attrition Rates, and Survival Outcomes of Neoadjuvant FOLFIRINOX for Non-Metastatic Pancreatic Adenocarcinoma: Intent-to-Treat Analysis.

Zhi Ven Fong, Fidel Lopez Verdugo, Carlos Fernandez-Del Castillo, Cristina R Ferrone, Jill N Allen, Lawrence S Blaszkowsky, Jeffrey W Clark, Aparna R Parikh, David P Ryan, Colin D Weekes, Theodore S Hong, Jennifer Y Wo, Keith D Lillemoe, Motaz Qadan.

BACKGROUND: Neoadjuvant FOLFIRINOX is increasingly utilized in the management of pancreatic ductal adenocarcinoma (PDAC). However, neoadjuvant therapy is associated with toxicity, possible disease progression, and biopsy and biliary-related complications that may preclude operative exploration. Data on the true attrition rate outside of clinical trials or resected surgical series are lacking.STUDY DESIGN: Patients with non-metastatic PDAC who initiated FOLFIRINOX from 2015 to 2020 were identified from our institution's pharmacy records. Multivariable regression and Cox proportional hazard models were used for adjusted analyses of categorical and survival outcomes, respectively.
RESULTS: Of 254 patients who initiated first-line neoadjuvant FOLFIRINOX, 199 (78.3%) underwent exploration. Fifty-four (21.3%) patients did not complete their chemotherapy cycles due to poor tolerability (46.3%), poor response (31.5%), and disease progression (14.8%), among other causes (7.4%). A total of 109 (42.9%) patients experienced grade 3/4 FOLFIRINOX-related toxicity, of whom 73 (28.7%) and 100 (39.4%) required an ED visit or inpatient admission, respectively. Finally, not undergoing surgical exploration was associated with impaired overall survival (OS) (HR 7.0, 95% CI 3.8-12.8, p<0.001). Independent predictors of not undergoing exploration were remote history of chemotherapy receipt (OR 0.06, p=0.02), inability to complete FOLFIRINOX cycles (OR 0.2, p=0.003), increase in ECOG score (OR 0.2, p<0.001), and being single or divorced (OR 0.3, p=0.018).
CONCLUSIONS: Among 254 patients with non-metastatic PDAC initiated on FOLFIRINOX, of whom 52% were locally advanced, a total of 199 (78.3%) were explored, 142 (71.4%) underwent successful resection, and 129 (90.8%) were resected with negative margins. Despite 109 (42.9)% of patients experiencing significant toxicity, most patients could be managed through treatment-related complications to complete planned neoadjuvant chemotherapy and undergo planned surgical exploration.

DOI: https://doi.org/10.1097/XCS.0000000000000499
J Cell Biol. 2023 Apr 03. pii: e202202078. [Epub ahead of print]222(4):

Semi-automated 3D fluorescence speckle analyzer (3D-Speckler) for microscope calibration and nanoscale measurement.

Jonathan Loi, Xiaofei Qu, Aussie Suzuki.

The widespread use of fluorescence microscopy has prompted the ongoing development of tools aiming to improve resolution and quantification accuracy for study of biological questions. Current calibration and quantification tools for fluorescence images face issues with usability/user experience, lack of automation, and comprehensive multidimensional measurement/correction capabilities. Here, we developed 3D-Speckler, a versatile, and high-throughput image analysis software that can provide fluorescent puncta quantification measurements such as 2D/3D particle size, spatial location/orientation, and intensities through semi-automation in a single, user-friendly interface. Integrated analysis options such as 2D/3D local background correction, chromatic aberration correction, and particle matching/filtering are also encompassed for improved precision and accuracy. We demonstrate 3D-Speckler microscope calibration capabilities by determining the chromatic aberrations, field illumination uniformity, and response to nanometer-scale emitters above and below the diffraction limit of our imaging system using multispectral beads. Furthermore, we demonstrated 3D-Speckler quantitative capabilities for offering insight into protein architectures and composition in cells.

DOI: https://doi.org/10.1083/jcb.202202078
bioRxiv. 2023 Jan 12. pii: 2023.01.11.523668. [Epub ahead of print]

Glycine homeostasis requires reverse SHMT flux.

Matthew J McBride, Craig J Hunter, Joshua D Rabinowitz.

The folate-dependent enzyme serine hydroxymethyltransferase (SHMT) reversibly converts serine into glycine and a tetrahydrofolate-bound one-carbon unit. Such one-carbon unit production plays a critical role in development, the immune system, and cancer. Here we show that the whole-body SHMT flux acts to net consume rather than produce glycine. Pharmacological inhibition of whole-body SHMT1/2 and genetic knockout of liver SHMT2 elevated circulating glycine levels up to eight-fold. Stable isotope tracing revealed that the liver converts glycine to serine, which is then converted by serine dehydratase into pyruvate and burned in the tricarboxylic acid cycle. In response to diets deficient in serine and glycine, de novo biosynthetic flux was unaltered but SHMT2- and serine dehydratase-mediated catabolic flux was lower. Thus, glucose-derived serine synthesis does not respond to systemic demand. Instead, circulating serine and glycine homeostasis is maintained through variable consumption, with liver SHMT2 as a major glycine-consuming enzyme.

DOI: https://doi.org/10.1101/2023.01.11.523668
PNAS Nexus. 2022 Nov;1(5): pgac244

Intratumoral nanobody-IL-2 fusions that bind the tumor extracellular matrix suppress solid tumor growth in mice.

Emi A Lutz, Noor Jailkhani, Noor Momin, Ying Huang, Allison Sheen, Byong H Kang, K Dane Wittrup, Richard O Hynes.

  Confining cytokine exposure to the tumors would greatly enhance cancer immunotherapy safety and efficacy. Immunocytokines, cytokines fused to tumor-targeting antibodies, have been developed with this intention, but without significant clinical success to date. A critical limitation is uptake by receptor-expressing cells in the blood, that decreases the dose at the tumor and engenders toxicity. Small-format immunocytokines, constructed with antibody fragments, are hypothesized to improve tumor specificity due to rapid systemic clearance. However, effective design criteria for small-format immunocytokines need further examination. Here, we engineer small interleukin-2 (IL-2) immunocytokines fused to nanobodies with nanomolar to picomolar affinities for the tumor-specific EIIIB domain of fibronectin (also known as EDB). Upon intravenous delivery into immunocompetent mice, such immunocytokines led to similar tumor growth delay as size-matched untargeted IL-2. Intratumoral (i.t.) delivery imparted improved survival dependent on affinity to EIIIB. I.t. administration offers a promising avenue to deliver small-format immunocytokines, given effective affinity for the tumor microenvironment.

Keywords:  cancer; cytokine; nanobody

DOI:  https://doi.org/10.1093/pnasnexus/pgac244
Sci Immunol. 2023 Feb 03. 8(80): eabm6360

Epigenetically controlled tumor antigens derived from splice junctions between exons and transposable elements.

Marianne Burbage, Ares Rocañín-Arjó, Blandine Baudon, Yago A Arribas, Antonela Merlotti, Derek C Rookhuizen, Sandrine Heurtebise-Chrétien, Mengliang Ye, Alexandre Houy, Nina Burgdorf, Guadalupe Suarez, Marine Gros, Benjamin Sadacca, Montserrat Carrascal, Andrea Garmilla, Mylène Bohec, Sylvain Baulande, Bérangère Lombard, Damarys Loew, Joshua J Waterfall, Marc-Henri Stern, Christel Goudot, Sebastian Amigorena.

Oncogenesis often implicates epigenetic alterations, including derepression of transposable elements (TEs) and defects in alternative splicing. Here, we explore the possibility that noncanonical splice junctions between exons and TEs represent a source of tumor-specific antigens. We show that mouse normal tissues and tumor cell lines express wide but distinct ranges of mRNA junctions between exons and TEs, some of which are tumor specific. Immunopeptidome analyses in tumor cell lines identified peptides derived from exon-TE splicing junctions associated to MHC-I molecules. Exon-TE junction-derived peptides were immunogenic in tumor-bearing mice. Both prophylactic and therapeutic vaccinations with junction-derived peptides delayed tumor growth in vivo. Inactivation of the TE-silencing histone 3-lysine 9 methyltransferase Setdb1 caused overexpression of new immunogenic junctions in tumor cells. Our results identify exon-TE splicing junctions as epigenetically controlled, immunogenic, and protective tumor antigens in mice, opening possibilities for tumor targeting and vaccination in patients with cancer.

DOI: https://doi.org/10.1126/sciimmunol.abm6360
Oncol Res Treat. 2023 Jan 31.

Clinical outcome and treatment sequences of patients with advanced pancreatic cancer treated with contemporary chemotherapy protocols.

Julius Roehrle, Stefan Kasper, Jürgen-Walter Treckmann, Peter Markus, Brigitte Schumacher, David Albers, Johanna Wendling, Saskia Ting, Bastian Mende, Marlene Maßmann, Maximilian Markus, Isabel Virchow, Vivian Rosery, Katharina Laue, Gregor Zaun, Karina Kostbade, Michael Pogorzelski, Timm M Reissig, Sven-Thorsten Liffers, Kurt Schmid, Hans-Ulrich Schildhaus, Martin Schuler, Jens T Siveke, Marcel Wiesweg.

Introduction Systemic therapy is firmly established in patients with advanced or metastatic pancreatic ductal adenocarcinoma (PDAC). Clinical efficacy is still modest and options are limited. Combination therapy protocols such as FOLFIRINOX and gemcitabine/nab-paclitaxel (Gem/NP) define standard-of-care. Patients may receive a sequence of both regimens as first- and second-line palliative treatment. However, there is no guidance regarding a preferred order. Methods Retrospective analysis of clinical characteristics, treatment trajectories and outcomes of patients with advanced PDAC treated at the West German Cancer Center Essen from 2014 to 2020 to inform treatment decisions with respect to predictive factors, impact of chemotherapy regimen sequence and maintenance treatment. Results We identified 170 patients with available follow-up. Of those, 160 (94.1%) pts received palliative CTX for primary metastatic, locally advanced or recurrent PDAC. Median PFS upon first palliative chemotherapy was 4.1 (3.1 - 5.9) months. First-line FOLFIRINOX associated with superior PFS (median 6.3 months) and OS (9.7 months, HR 0.7, p=0.03) as compared to gemcitabine/nab-paclitaxel or other regimens (PFS 3.0, OS 6.9 months). However, OS benefit of first-line FOLFIRINOX was lost in patients who received at least two treatment lines (median OS 12.1 vs. 13.1 months, p=0.43). A landmark analysis of patients with clinical benefit (defined at CR/PR/SD for at least 20 weeks) upon first-line therapy revealed improved OS (HR 0.53, p=0.02) for patients receiving continued deescalated maintenance therapy. Second-line regimens resulted in similar PFS (overall log-rank p=0.92, median PFS2 2.3 (1.8-2.9), per-regimen median between 1.8 and 3.9 months). A previously established systemic inflammation score proved to be strongly prognostic and allowed identification of a patient subgroup with dismal prognosis (OS 2.9 vs. 11.4 months, HR 5.23, p<0.001), independent of other prognostic factors and with no relevant interaction with the choice of first-line regimen. Conclusion In this real world population of PDAC patients treated with contemporary combination chemotherapies, a positive impact of first line FOLFIRINOX was only observed when no second or further line treatment was administered. Intensity-reduced maintenance therapy may lead to superior survival.

DOI: https://doi.org/10.1159/000529452
bioRxiv. 2023 Jan 12. pii: 2023.01.11.523644. [Epub ahead of print]

Pressure and ultrasound activate mechanosensitive TRAAK K + channels through increased membrane tension.

Ben Sorum, Trevor Docter, Vincent Panico, Robert A Rietmeijer, Stephen G Brohawn.

TRAAK is a mechanosensitive two-pore domain K + (K2P) channel found in nodes of Ranvier within myelinated axons. It displays low leak activity at rest and is activated up to one hundred-fold by increased membrane tension. Structural and functional studies have led to physical models for channel gating and mechanosensitivity, but no quantitative analysis of channel activation by tension has been reported. Here, we use simultaneous patch-clamp recording and fluorescent imaging to determine the tension response characteristics of TRAAK. TRAAK shows high sensitivity and a broad response to tension spanning nearly the entire physiologically relevant tension range. This graded response profile distinguishes TRAAK from similarly low-threshold mechanosensitive channels Piezo1 and MscS, which activate in a step-like fashion over a narrow tension range. We further use patch imaging to show that ultrasonic activation of TRAAK and MscS is due to increased membrane tension. Together, these results provide mechanistic insight into TRAAK tension gating, a framework for exploring the role of mechanosensitive K + channels at nodes of Ranvier, and biophysical context for developing ultrasound as a mechanical stimulation technique for neuromodulation.

DOI: https://doi.org/10.1101/2023.01.11.523644
Proc Natl Acad Sci U S A. 2023 Feb 07. 120(6): e2208253120

Curvature sensing as an emergent property of multiscale assembly of septins.

Wenzheng Shi, Kevin S Cannon, Brandy N Curtis, Christopher Edelmaier, Amy S Gladfelter, Ehssan Nazockdast.

  The ability of cells to sense and communicate their shape is central to many of their functions. Much is known about how cells generate complex shapes, yet how they sense and respond to geometric cues remains poorly understood. Septins are GTP-binding proteins that localize to sites of micrometer-scale membrane curvature. Assembly of septins is a multistep and multiscale process, but it is unknown how these discrete steps lead to curvature sensing. Here, we experimentally examine the time-dependent binding of septins at different curvatures and septin bulk concentrations. These experiments unexpectedly indicated that septins' curvature preference is not absolute but rather is sensitive to the combinations of membrane curvatures present in a reaction, suggesting that there is competition between different curvatures for septin binding. To understand the physical underpinning of this result, we developed a kinetic model that connects septins' self-assembly and curvature-sensing properties. Our experimental and modeling results are consistent with curvature-sensitive assembly being driven by cooperative associations of septin oligomers in solution with the bound septins. When combined, the work indicates that septin curvature sensing is an emergent property of the multistep, multiscale assembly of membrane-bound septins. As a result, curvature preference is not absolute and can be modulated by changing the physicochemical and geometric parameters involved in septin assembly, including bulk concentration, and the available membrane curvatures. While much geometry-sensitive assembly in biology is thought to be guided by intrinsic material properties of molecules, this is an important example of how curvature sensing can arise from multiscale assembly of polymers.

Keywords:  curvature sensing; kinetic modeling; multiscale assembly; septin

DOI:  https://doi.org/10.1073/pnas.2208253120
Bioinformatics. 2023 Feb 02. pii: btad071. [Epub ahead of print]

WMDS.net: a network control framework for identifying key players in transcriptome programs.

Xiang Cheng, Amanullah Md, Weigang Liu, Yi Liu, Xiaoqing Pan, Honghe Zhang, Haiming Xu, Pengyuan Liu, Yan Lu.

MOTIVATION: Mammalian cells can be transcriptionally reprogrammed to other cellular phenotypes. Controllability of such complex transitions in transcriptional networks underlying cellular phenotypes is an inherent biological characteristic. This network controllability can be interpreted by operating a few key regulators to guide the transcriptional program from one state to another. Finding the key regulators in the transcriptional program can provide key insights into the network state transition underlying cellular phenotypes.RESULTS: To address this challenge, here we proposed to identify the key regulators in the transcriptional co-expression network as a minimum dominating set (MDS) of driver nodes that can fully control the network state transition. Based on the theory of structural controllability, we developed a weighted MDS network model (WMDS.net) to find the drive nodes of differential gene co-expression networks. The weight of WMDS.net integrates the degree of nodes in the network and the significance of gene co-expression difference between two physiological states into the measurement of node controllability of the transcriptional network. To confirm its validity, we applied WMDS.net to the discovery of cancer driver genes in RNA-seq datasets from The Cancer Genome Atlas. WMDS.net is powerful among various cancer datasets and outperformed the other top-tier tools with a better balance between precision and recall.
AVAILABILITY: https://github.com/chaofen123/WMDS.net.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btad071