bims-cagime 2023-03-19 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2023–03–19
forty-two papers selected by
Kıvanç Görgülü, Technical University of Munich

Hypoxia potentiates the inflammatory fibroblast phenotype promoted by pancreatic cancer cell-derived cytokines.
Immune determinants of the pre-metastatic niche.
In situ snapshots along a mammalian selective autophagy pathway.
Neoadjuvant therapy for pancreatic cancer.
Chronic jetlag accelerates pancreatic neoplasia in conditional Kras-mutant mice.
Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Recent advances in targeting autophagy in cancer.
Multi-range ERK responses shape the proliferative trajectory of single cells following oncogene induction.
Omics-based approaches for the systematic profiling of mitochondrial biology.
Kras oncogene ablation prevents resistance in advanced lung adenocarcinoma.
Metabolic sensing and control in mitochondria.
A TEAD2-driven endothelial-like program shapes basal-like differentiation and metastasis of pancreatic cancer.
HMGA1 induces FGF19 to drive pancreatic carcinogenesis and stroma formation.
Activated fibroblasts in cancer: Perspectives and challenges.
Organelle-selective click labeling coupled with flow cytometry allows pooled CRISPR screening of genes involved in phosphatidylcholine metabolism.
Lymphatic invasion of plakoglobin-dependent tumor cell clusters drives formation of polyclonal lung metastases in colon cancer.
Phase-specific signatures of wound fibroblasts and matrix patterns define cancer-associated fibroblast subtypes.
Spatial epigenome-transcriptome co-profiling of mammalian tissues.
Digital spatial profiling of intraductal papillary mucinous neoplasms: Toward a molecular framework for risk stratification.
Decrypting drug actions and protein modifications by dose- and time-resolved proteomics.
De novo lipogenesis fuels adipocyte autophagosome and lysosome membrane dynamics.
Longitudinal phenotypic aging metrics in the Baltimore Longitudinal Study of Aging.
BRD9-SMAD2/3 orchestrates stemness and tumorigenesis in pancreatic ductal adenocarcinoma.
Screening in serum-derived medium reveals differential response to compounds targeting metabolism.
Mitochondrial-derived vesicles retain membrane potential and contain a functional ATP synthase.
First passage time analysis of spatial mutation patterns reveals sub-clonal evolutionary dynamics in colorectal cancer.
Macropinocytosis: mechanisms and regulation.
Mitochondrial morphology controls fatty acid utilization by changing CPT1 sensitivity to malonyl-CoA.
Systemic inflammatory prognostic scores in advanced pancreatic adenocarcinoma.
Age-associated microenvironmental changes highlight the role of PDGF-C in ER+ breast cancer metastatic relapse.
SULT1A1-dependent sulfonation of alkylators is a lineage-dependent vulnerability of liver cancers.
Lactate regulates cell cycle by remodeling the anaphase promoting complex.
Generation of liver metastases in a mouse model using ultrasound-guided intravenous injection.
Precision oncology for KRASG12C-mutant colorectal cancer.
Mechanosensitive pore opening of a prokaryotic voltage-gated sodium channel.
The dietary sweetener sucralose is a negative modulator of T cell-mediated responses.
ANO1 reprograms cholesterol metabolism and the tumor microenvironment to promote cancer metastasis.
The evolving tumor microenvironment: From cancer initiation to metastatic outgrowth.
Cause for concern: the rising incidence of early-onset pancreatic cancer.
A common cancer at an uncommon age.
Top Pancreatic Tumor Articles from 2021 to Inform Your Cancer Patients.
Whole-genome doubling drives oncogenic loss of chromatin segregation.

Cancer Res. 2023 Mar 13. pii: CAN-22-2316. [Epub ahead of print]

Hypoxia potentiates the inflammatory fibroblast phenotype promoted by pancreatic cancer cell-derived cytokines.

Simon Schwoerer, Francesco V Cimino, Manon Ros, Kaloyan M Tsanov, Charles Ng, Scott W Lowe, Carlos Carmona-Fontaine, Craig B Thompson.

Cancer-associated fibroblasts (CAFs) are a major cell type in the stroma of solid tumors and can exert both tumor-promoting and tumor-restraining functions. CAF heterogeneity is frequently observed in pancreatic ductal adenocarcinoma (PDAC), a tumor characterized by a dense and hypoxic stroma that features myofibroblastic CAFs (myCAFs) and inflammatory CAFs (iCAFs) that are thought to have opposing roles in tumor progression. While CAF heterogeneity can be driven in part by tumor cell-produced cytokines, other determinants shaping CAF identity and function are largely unknown. In vivo, we found that iCAFs displayed a hypoxic gene expression and biochemical profile and were enriched in hypoxic regions of PDAC tumors, while myCAFs were excluded from these regions. Hypoxia led fibroblasts to acquire an inflammatory gene expression signature and synergized with cancer cell-derived cytokines to promote an iCAF phenotype in a HIF-1α dependent fashion. Furthermore, HIF-1α stabilization was sufficient to induce an iCAF phenotype in stromal cells introduced into PDAC organoid co-cultures and to promote PDAC tumor growth. These findings indicate hypoxia-induced HIF-1α as a regulator of CAF heterogeneity and promoter of tumor progression in PDAC.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-2316
Cancer Cell. 2023 Mar 13. pii: S1535-6108(23)00046-6. [Epub ahead of print]41(3): 546-572

Immune determinants of the pre-metastatic niche.

Laura Patras, Lee Shaashua, Irina Matei, David Lyden.

Primary tumors actively and specifically prime pre-metastatic niches (PMNs), the future sites of organotropic metastasis, preparing these distant microenvironments for disseminated tumor cell arrival. While initial studies of the PMN focused on extracellular matrix alterations and stromal reprogramming, it is increasingly clear that the far-reaching effects of tumors are in great part achieved through systemic and local PMN immunosuppression. Here, we discuss recent advances in our understanding of the tumor immune microenvironment and provide a comprehensive overview of the immune determinants of the PMN's spatiotemporal evolution. Moreover, we depict the PMN immune landscape, based on functional pre-clinical studies as well as mounting clinical evidence, and the dynamic, reciprocal crosstalk with systemic changes imposed by cancer progression. Finally, we outline emerging therapeutic approaches that alter the dynamics of the interactions driving PMN formation and reverse immunosuppression programs in the PMN ensuring early anti-tumor immune responses.

DOI: https://doi.org/10.1016/j.ccell.2023.02.018
Proc Natl Acad Sci U S A. 2023 Mar 21. 120(12): e2221712120

In situ snapshots along a mammalian selective autophagy pathway.

Meijing Li, Ishita Tripathi-Giesgen, Brenda A Schulman, Wolfgang Baumeister, Florian Wilfling.

  Selective macroautophagy (hereafter referred to as autophagy) describes a process in which cytosolic material is engulfed in a double membrane organelle called an autophagosome. Autophagosomes are carriers responsible for delivering their content to a lytic compartment for destruction. The cargo can be of diverse origin, ranging from macromolecular complexes to protein aggregates, organelles, and even invading pathogens. Each cargo is unique in composition and size, presenting different challenges to autophagosome biogenesis. Among the largest cargoes targeted by the autophagy machinery are intracellular bacteria, which can, in the case of Salmonella, range from 2 to 5 μm in length and 0.5 to 1.5 μm in width. How phagophores form and expand on such a large cargo remains mechanistically unclear. Here, we used HeLa cells infected with an auxotrophic Salmonella to study the process of phagophore biogenesis using in situ correlative cryo-ET. We show that host cells generate multiple phagophores at the site of damaged Salmonella-containing vacuoles (SCVs). The observed double membrane structures range from disk-shaped to expanded cup-shaped phagophores, which have a thin intermembrane lumen with a dilating rim region and expand using the SCV, the outer membrane of Salmonella, or existing phagophores as templates. Phagophore rims establish different forms of contact with the endoplasmic reticulum (ER) via structurally distinct molecular entities for membrane formation and expansion. Early omegasomes correlated with the marker Double-FYVE domain-Containing Protein 1 (DFCP1) are observed in close association with the ER without apparent membrane continuity. Our study provides insights into the formation of phagophores around one of the largest selective cargoes.

Keywords:  Salmonella; autophagosome; cryo-electron tomography; omegasome; xenophagy

DOI:  https://doi.org/10.1073/pnas.2221712120
Nat Rev Clin Oncol. 2023 Mar 17.

Neoadjuvant therapy for pancreatic cancer.

Christoph Springfeld, Cristina R Ferrone, Matthew H G Katz, Philip A Philip, Theodore S Hong, Thilo Hackert, Markus W Büchler, John Neoptolemos.

Patients with localized pancreatic ductal adenocarcinoma (PDAC) are best treated with surgical resection of the primary tumour and systemic chemotherapy, which provides considerably longer overall survival (OS) durations than either modality alone. Regardless, most patients will have disease relapse owing to micrometastatic disease. Although currently a matter of some debate, considerable research interest has been focused on the role of neoadjuvant therapy for all forms of resectable PDAC. Whilst adjuvant combination chemotherapy remains the standard of care for patients with resectable PDAC, neoadjuvant chemotherapy seems to improve OS without necessarily increasing the resection rate in those with borderline-resectable disease. Furthermore, around 20% of patients with unresectable non-metastatic PDAC might undergo resection following 4-6 months of induction combination chemotherapy with or without radiotherapy, even in the absence of a clear radiological response, leading to improved OS outcomes in this group. Distinct molecular and biological responses to different types of therapies need to be better understood in order to enable the optimal sequencing of specific treatment modalities to further improve OS. In this Review, we describe current treatment strategies for the various clinical stages of PDAC and discuss developments that are likely to determine the optimal sequence of multimodality therapies by integrating the fundamental clinical and molecular features of the cancer.

DOI: https://doi.org/10.1038/s41571-023-00746-1
Chronobiol Int. 2023 Mar 13. 1-21

Chronic jetlag accelerates pancreatic neoplasia in conditional Kras-mutant mice.

Patrick B Schwartz, Morgan T Walcheck, Manabu Nukaya, Derek M Pavelec, Kristina A Matkowskyj, Sean M Ronnekleiv-Kelly.

  Misalignment of the circadian clock compared to environmental cues causes circadian desynchrony, which is pervasive in humans. Clock misalignment can lead to various pathologies including obesity and diabetes, both of which are associated with pancreatic ductal adenocarcinoma - a devastating cancer with an 80% five-year mortality rate. Although circadian desynchrony is associated with an increased risk of several solid-organ cancers, the correlation between clock misalignment and pancreas cancer is unclear. Using a chronic jetlag model, we investigated the impact of clock misalignment on pancreas cancer initiation in mice harboring a pancreas-specific activated Kras mutation. We found that chronic jetlag accelerated the development of pancreatic cancer precursor lesions, with a concomitant increase in precursor lesion grade. Cell-autonomous knock-out of the clock in pancreatic epithelial cells of Kras-mutant mice demonstrated no acceleration of precursor lesion formation, indicating non-cell-autonomous clock dysfunction was responsible for the expedited tumor development. Therefore, we applied single-cell RNA sequencing over time and identified fibroblasts as the cell population manifesting the greatest clock-dependent changes, with enrichment of specific cancer-associated fibroblast pathways due to circadian misalignment.

Keywords:  Circadian; jetlag; misalignment; pancreas; pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.1080/07420528.2023.2186122
Cell. 2023 Mar 16. pii: S0092-8674(23)00164-2. [Epub ahead of print]186(6): 1127-1143.e18

Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.

Maha K Rahim, Trine Line H Okholm, Kyle B Jones, Elizabeth E McCarthy, Candace C Liu, Jacqueline L Yee, Stanley J Tamaki, Diana M Marquez, Iliana Tenvooren, Katherine Wai, Alexander Cheung, Brittany R Davidson, Vrinda Johri, Bushra Samad, William E O'Gorman, Matthew F Krummel, Annemieke van Zante, Alexis J Combes, Michael Angelo, Lawrence Fong, Alain P Algazi, Patrick Ha, Matthew H Spitzer.

  CD8+ T cell responses are critical for anti-tumor immunity. While extensively profiled in the tumor microenvironment, recent studies in mice identified responses in lymph nodes (LNs) as essential; however, the role of LNs in human cancer patients remains unknown. We examined CD8+ T cells in human head and neck squamous cell carcinomas, regional LNs, and blood using mass cytometry, single-cell genomics, and multiplexed ion beam imaging. We identified progenitor exhausted CD8+ T cells (Tpex) that were abundant in uninvolved LN and clonally related to terminally exhausted cells in the tumor. After anti-PD-L1 immunotherapy, Tpex in uninvolved LNs reduced in frequency but localized near dendritic cells and proliferating intermediate-exhausted CD8+ T cells (Tex-int), consistent with activation and differentiation. LN responses coincided with increased circulating Tex-int. In metastatic LNs, these response hallmarks were impaired, with immunosuppressive cellular niches. Our results identify important roles for LNs in anti-tumor immune responses in humans.

Keywords:  CD8(+) T cells; T cell exhaustion; cancer immunotherapy; immune checkpoint blockade; lymph nodes

DOI:  https://doi.org/10.1016/j.cell.2023.02.021
Trends Pharmacol Sci. 2023 Mar 15. pii: S0165-6147(23)00037-8. [Epub ahead of print]

Recent advances in targeting autophagy in cancer.

Vaibhav Jain, Mahendra Pal Singh, Ravi K Amaravadi.

  Autophagy is a cellular homeostasis mechanism that fuels the proliferation and survival of advanced cancers by degrading and recycling organelles and proteins. Preclinical studies have identified that within an established tumor, tumor cell autophagy and host cell autophagy conspire to support tumor growth. A growing body of evidence suggests that autophagy inhibition can augment the efficacy of chemotherapy, targeted therapy, or immunotherapy to enhance tumor shrinkage. First-generation autophagy inhibition trials in cancer using the lysosomal inhibitor hydroxychloroquine (HCQ) have produced mixed results but have guided the way for the development of more potent and specific autophagy inhibitors in clinical trials. In this review, we will discuss the role of autophagy in cancer, newly discovered molecular mechanisms of the autophagy pathway, the effects of autophagy modulation in cancer and host cells, and novel autophagy inhibitors that are entering clinical trials.

Keywords:  autophagy; cancer; hydroxychloroquine; immunotherapy, chemotherapy; lysosome

DOI:  https://doi.org/10.1016/j.tips.2023.02.003
Cell Rep. 2023 Mar 14. pii: S2211-1247(23)00263-2. [Epub ahead of print]42(3): 112252

Multi-range ERK responses shape the proliferative trajectory of single cells following oncogene induction.

Jia-Yun Chen, Clemens Hug, José Reyes, Chengzhe Tian, Luca Gerosa, Fabian Fröhlich, Bas Ponsioen, Hugo J G Snippert, Sabrina L Spencer, Ashwini Jambhekar, Peter K Sorger, Galit Lahav.

  Oncogene-induced senescence is a phenomenon in which aberrant oncogene expression causes non-transformed cells to enter a non-proliferative state. Cells undergoing oncogenic induction display phenotypic heterogeneity, with some cells senescing and others remaining proliferative. The causes of heterogeneity remain unclear. We studied the sources of heterogeneity in the responses of human epithelial cells to oncogenic BRAFV600E expression. We found that a narrow expression range of BRAFV600E generated a wide range of activities of its downstream effector ERK. In population-level and single-cell assays, ERK activity displayed a non-monotonic relationship to proliferation, with intermediate ERK activities leading to maximal proliferation. We profiled gene expression across a range of ERK activities over time and characterized four distinct ERK response classes, which we propose act in concert to generate the ERK-proliferation response. Altogether, our studies map the input-output relationships between ERK activity and proliferation, elucidating how heterogeneity can be generated during oncogene induction.

Keywords:  BRAF(V600E); CP: Cancer; ERK; cell cycle; heterogeneity; non-monotonic; oncogene-induced senescence; proliferation

DOI:  https://doi.org/10.1016/j.celrep.2023.112252
Mol Cell. 2023 Mar 16. pii: S1097-2765(23)00118-1. [Epub ahead of print]83(6): 911-926

Omics-based approaches for the systematic profiling of mitochondrial biology.

Jasmin Adriana Schäfer, F X Reymond Sutandy, Christian Münch.

Mitochondria are essential for cellular functions such as metabolism and apoptosis. They dynamically adapt to the changing environmental demands by adjusting their protein, nucleic acid, metabolite, and lipid contents. In addition, the mitochondrial components are modulated on different levels in response to changes, including abundance, activity, and interaction. A wide range of omics-based approaches has been developed to be able to explore mitochondrial adaptation and how mitochondrial function is compromised in disease contexts. Here, we provide an overview of the omics methods that allow us to systematically investigate the different aspects of mitochondrial biology. In addition, we show examples of how these methods have provided new biological insights. The emerging use of these toolboxes provides a more comprehensive understanding of the processes underlying mitochondrial function.

DOI: https://doi.org/10.1016/j.molcel.2023.02.015
J Clin Invest. 2023 Mar 16. pii: e164413. [Epub ahead of print]

Kras oncogene ablation prevents resistance in advanced lung adenocarcinoma.

Marina Salmón, Ruth Álvarez-Díaz, Coral Fustero-Torre, Oksana Brehey, Carmen G Lechuga, Manuel Sanclemente, Fernando Fernández-García, Alejandra López-García, María Carmen Martín-Guijarro, Sandra Rodríguez-Perales, Emily Bousquet-Mur, Lucía Morales-Cacho, Francisca Mulero, Fátima Al-Shahrour, Lola Martínez, Orlando Domínguez, Eduardo Caleiras, Sagrario Ortega, Carmen Guerra, Monica Musteanu, Matthias Drosten, Mariano Barbacid.

  KRASG12C inhibitors have revolutionized the clinical management of patients with KRASG12C-mutant lung adenocarcinoma. However, patient exposure to these inhibitors leads to the rapid onset of resistance. In this study, we have used genetically engineered mice to compare the therapeutic efficacy and the emergence of tumor resistance between genetic ablation of mutant Kras expression and pharmacological inhibition of oncogenic KRAS activity. Whereas Kras ablation induces massive tumor regression and prevents the appearance of resistant cells in vivo, treatment of KrasG12C/Trp53-driven lung adenocarcinomas with sotorasib, a selective KRASG12C inhibitor, caused a limited anti-tumor response similar to that observed in the clinic, including the rapid onset of resistance. Unlike in human tumors, we did not observe mutations in components of the RAS signaling pathways. Instead, sotorasib resistant tumors displayed amplification of the mutant Kras allele and activation of xenobiotic metabolism pathways, suggesting that reduction of the on-target activity of KRASG12C inhibitors is the main mechanism responsible for the onset of resistance. In sum, our results suggest that resistance to KRAS inhibitors could be prevented by achieving a more robust inhibition of KRAS signaling mimicking the results obtained upon Kras ablation.

Keywords:  Drug therapy; Lung cancer; Oncogenes; Oncology

DOI:  https://doi.org/10.1172/JCI164413
Mol Cell. 2023 Mar 16. pii: S1097-2765(23)00119-3. [Epub ahead of print]83(6): 877-889

Metabolic sensing and control in mitochondria.

Yuyang Liu, Kıvanç Birsoy.

Mitochondria are membrane-enclosed organelles with endosymbiotic origins, harboring independent genomes and a unique biochemical reaction network. To perform their critical functions, mitochondria must maintain a distinct biochemical environment and coordinate with the cytosolic metabolic networks of the host cell. This coordination requires them to sense and control metabolites and respond to metabolic stresses. Indeed, mitochondria adopt feedback or feedforward control strategies to restrain metabolic toxicity, enable metabolic conservation, ensure stable levels of key metabolites, allow metabolic plasticity, and prevent futile cycles. A diverse panel of metabolic sensors mediates these regulatory circuits whose malfunctioning leads to inborn errors of metabolism with mild to severe clinical manifestations. In this review, we discuss the logic and molecular basis of metabolic sensing and control in mitochondria. The past research outlined recurring patterns in mitochondrial metabolic sensing and control and highlighted key knowledge gaps in this organelle that are potentially addressable with emerging technological breakthroughs.

DOI: https://doi.org/10.1016/j.molcel.2023.02.016
Gastroenterology. 2023 Mar 10. pii: S0016-5085(23)00260-3. [Epub ahead of print]

A TEAD2-driven endothelial-like program shapes basal-like differentiation and metastasis of pancreatic cancer.

Hye-Been Yoo, Jin Woo Moon, Hwa-Ryeon Kim, Hee Seung Lee, Koji Miyabayashi, Chan Hee Park, Sabrina Ge, Amy Zhang, Yoo Keung Tae, Yujin Sub, Hyun-Woo Park, Heon Yung Gee, Faiyaz Notta, David A Tuveson, Seungmin Bang, Mi-Young Kim, Jae-Seok Roe.

   BACKGROUND AND AIMS: Pancreatic ductal adenocarcinoma (PDA), with its highly metastatic propensity, is one of the most lethal subtypes of pancreatic cancer. Although recent large-scale transcriptomic studies have demonstrated that heterogeneous gene expressions play an essential role in determining molecular phenotypes of PDA, biological cues for and consequences of distinct transcriptional programs remain unclear.
METHODS: We developed an experimental model that enforces the transition of PDA cells toward a basal-like subtype. We combined epigenome and transcriptome analyses with extensive in vitro and in vivo evaluations of tumorigenicity to demonstrate the validity of basal-like subtype differentiation in association with endothelial-like enhancer landscapes via TEAD2. Finally, we used loss-of-function experiments to investigate the importance of TEAD2 in regulating reprogrammed enhancer landscape and metastasis in basal-like PDA cells.
RESULTS: Aggressive characteristics of the basal-like subtype are faithfully recapitulated in vitro and in vivo, demonstrating the physiological relevance of our model. Further, we showed that basal-like subtype PDA cells acquire a TEAD2-dependent pro-angiogenic enhancer landscape. Genetic and pharmacological inhibitions of TEAD2 in basal-like subtype PDA cells impair their pro-angiogenic phenotypes in vitro and cancer progression in vivo. Lastly, we identify CD109 as a critical TEAD2 downstream mediator that maintains constitutively activated JAK-STAT signaling in basal-like PDA cells and tumors.
CONCLUSIONS: Our findings implicate a TEAD2-CD109-JAK/STAT axis in the basal-like differentiated pancreatic cancer cells and as a potential therapeutic vulnerability.

Keywords:  Enhancer reprogramming; Molecular subtype; Pancreatic cancer

DOI:  https://doi.org/10.1053/j.gastro.2023.02.049
J Clin Invest. 2023 Mar 15. pii: e151601. [Epub ahead of print]133(6):

HMGA1 induces FGF19 to drive pancreatic carcinogenesis and stroma formation.

Lionel Chia, Bowen Wang, Jung-Hyun Kim, Li Z Luo, Shuai Shuai, Iliana Herrera, Sophia Y Chen, Liping Li, Lingling Xian, Tait Huso, Mohammad Heydarian, Karen Reddy, Woo Jung Sung, Shun Ishiyama, Gongbo Guo, Elizabeth Jaffee, Lei Zheng, Leslie M Cope, Kathy Gabrielson, Laura Wood, Linda Resar.

  High mobility group A1 (HMGA1) chromatin regulators are upregulated in diverse tumors where they portend adverse outcomes, although how they function in cancer remains unclear. Pancreatic ductal adenocarcinomas (PDACs) are highly lethal tumors characterized by dense desmoplastic stroma composed predominantly of cancer-associated fibroblasts and fibrotic tissue. Here, we uncover an epigenetic program whereby HMGA1 upregulates FGF19 during tumor progression and stroma formation. HMGA1 deficiency disrupts oncogenic properties in vitro while impairing tumor inception and progression in KPC mice and subcutaneous or orthotopic models of PDAC. RNA sequencing revealed HMGA1 transcriptional networks governing proliferation and tumor-stroma interactions, including the FGF19 gene. HMGA1 directly induces FGF19 expression and increases its protein secretion by recruiting active histone marks (H3K4me3, H3K27Ac). Surprisingly, disrupting FGF19 via gene silencing or the FGFR4 inhibitor BLU9931 recapitulates most phenotypes observed with HMGA1 deficiency, decreasing tumor growth and formation of a desmoplastic stroma in mouse models of PDAC. In human PDAC, overexpression of HMGA1 and FGF19 defines a subset of tumors with extremely poor outcomes. Our results reveal what we believe is a new paradigm whereby HMGA1 and FGF19 drive tumor progression and stroma formation, thus illuminating FGF19 as a rational therapeutic target for a molecularly defined PDAC subtype.

Keywords:  Cancer; Growth factors; Oncogenes; Oncology

DOI:  https://doi.org/10.1172/JCI151601
Cancer Cell. 2023 Mar 13. pii: S1535-6108(23)00043-0. [Epub ahead of print]41(3): 434-449

Activated fibroblasts in cancer: Perspectives and challenges.

Giuseppina Caligiuri, David A Tuveson.

  Activated fibroblasts in tumors, or cancer-associated fibroblasts (CAFs), have become a popular research area over the past decade. As important players in many aspects of tumor biology, with functions ranging from collagen deposition to immunosuppression, CAFs have been the target of clinical and pre-clinical studies that have revealed their potential pro- and anti-tumorigenic dichotomy. In this review, we describe the important role of CAFs in the tumor microenvironment and the technological advances that made these discoveries possible, and we detail the models that are currently available for CAF investigation. Additionally, we present evidence to support the value of encompassing CAF investigation as a future therapeutic avenue alongside immune and cancer cells while highlighting the challenges that must be addressed for successful clinical translation of new findings.

Keywords:  activated fibroblasts; cancer-associated fibroblasts; stroma; tumor microenvironment

DOI:  https://doi.org/10.1016/j.ccell.2023.02.015
Cell Metab. 2023 Mar 07. pii: S1550-4131(23)00050-5. [Epub ahead of print]

Organelle-selective click labeling coupled with flow cytometry allows pooled CRISPR screening of genes involved in phosphatidylcholine metabolism.

Masaki Tsuchiya, Nobuhiko Tachibana, Kohjiro Nagao, Tomonori Tamura, Itaru Hamachi.

  Cellular lipid synthesis and transport are governed by intricate protein networks. Although genetic screening should contribute to deciphering the regulatory networks of lipid metabolism, technical challenges remain-especially for high-throughput readouts of lipid phenotypes. Here, we coupled organelle-selective click labeling of phosphatidylcholine (PC) with flow cytometry-based CRISPR screening technologies to convert organellar PC phenotypes into a simple fluorescence readout for genome-wide screening. This technique, named O-ClickFC, was successfully applied in genome-scale CRISPR-knockout screens to identify previously reported genes associated with PC synthesis (PCYT1A, ACACA), vesicular membrane trafficking (SEC23B, RAB5C), and non-vesicular transport (PITPNB, STARD7). Moreover, we revealed previously uncharacterized roles of FLVCR1 as a choline uptake facilitator, CHEK1 as a post-translational regulator of the PC-synthetic pathway, and CDC50A as responsible for the translocation of PC to the outside of the plasma membrane bilayer. These findings demonstrate the versatility of O-ClickFC as an unprecedented platform for genetic dissection of cellular lipid metabolism.

Keywords:  CRISPR screens; flow cytometry; lipid metabolism; organelle-selective labeling: click chemistry; phosphatidylcholine

DOI:  https://doi.org/10.1016/j.cmet.2023.02.014
Gastroenterology. 2023 Mar 09. pii: S0016-5085(23)00256-1. [Epub ahead of print]

Lymphatic invasion of plakoglobin-dependent tumor cell clusters drives formation of polyclonal lung metastases in colon cancer.

Emre Küçükköse, Jamila Laoukili, Alexander N Gorelick, Sebastian Degner, Miangela Lacle, Lotte van den Bent, Niek A Peters, André Verheem, Wei-Ting Hung, Nicola C Frenkel, Emma Wassenaar, Nico Lansu, Kristiaan J Lenos, Louis Vermeulen, Miriam Koopman, Jeanine M L Roodhart, Geert J P L Kops, Inne H M Borel Rinkes, Jeroen Hagendoorn, Kamila Naxerova, Onno Kranenburg.

   BACKGROUND AND AIMS: Colon cancer patients with liver metastases may be cured by surgery, but the presence of additional lung metastases often precludes curative treatment. Little is known about the processes driving lung metastasis. This study aimed to elucidate the mechanisms governing lung versus liver metastasis formation.
METHODS: Patient-derived organoid (PDO) cultures were established from colon tumors with distinct patterns of metastasis. Mouse models recapitulating metastatic organotropism were created by implanting PDOs into the caecum wall. Optical barcoding was applied to trace the origin and clonal composition of liver- and lung-metastases. RNA-sequencing and immunohistochemistry were used to identify candidate-determinants of metastatic organotropism. Genetic, pharmacological, and in-vitro and in-vivo modeling strategies identified essential steps in lung metastasis formation. Validation was performed by analyzing patient-derived tissues.
RESULTS: Caecum transplantation of three distinct PDOs yielded models with distinct metastatic organotropism: liver-only, lung-only, and liver-and-lung. Liver-metastases were seeded by single cells derived from select clones. Lung-metastases were seeded by polyclonal clusters of tumor cells entering the lymphatic vasculature with very limited clonal selection. Lung-specific metastasis was associated with high expression of desmosome markers, including plakoglobin. Plakoglobin deletion abrogated tumor cell-cluster formation, lymphatic invasion, and lung metastasis formation. Pharmacological inhibition of lymphangiogenesis attenuated lung metastasis formation. Primary human colon, rectum, esophagus, and stomach tumors with lung-metastases had a higher N-stage and more plakoglobin-expressing intra-lymphatic tumor cell-clusters than those without lung-metastases.
CONCLUSION: Lung and liver metastasis formation are fundamentally distinct processes, with different evolutionary bottlenecks, seeding entities, and anatomical routing. Polyclonal lung-metastases originate from plakoglobin-dependent tumor cell-clusters entering the lymphatic vasculature at the primary tumor site.

Keywords:  lymphatics; metastasis mechanism; organ tropism; patient-derived organoids

DOI:  https://doi.org/10.1053/j.gastro.2023.02.047
Matrix Biol. 2023 Mar 11. pii: S0945-053X(23)00025-2. [Epub ahead of print]

Phase-specific signatures of wound fibroblasts and matrix patterns define cancer-associated fibroblast subtypes.

Mateusz S Wietecha, David Lauenstein, Michael Cangkrama, Sybille Seiler, Juyoung Jin, Andreas Goppelt, Manfred Claassen, Mitchell P Levesque, Reinhard Dummer, Sabine Werner.

  Healing wounds and cancers present remarkable cellular and molecular parallels, but the specific roles of the healing phases are largely unknown. We developed a bioinformatics pipeline to identify genes and pathways that define distinct phases across the time-course of healing. Their comparison to cancer transcriptomes revealed that a resolution phase wound signature is associated with increased severity in skin cancer and enriches for extracellular matrix-related pathways. Comparisons of transcriptomes of early- and late-phase wound fibroblasts vs skin cancer-associated fibroblasts (CAFs) identified an "early wound" CAF subtype, which localizes to the inner tumor stroma and expresses collagen-related genes that are controlled by the RUNX2 transcription factor. A "late wound" CAF subtype localizes to the outer tumor stroma and expresses elastin-related genes. Matrix imaging of primary melanoma tissue microarrays validated these matrix signatures and identified collagen- vs elastin-rich niches within the tumor microenvironment, whose spatial organization predicts survival and recurrence. These results identify wound-regulated genes and matrix patterns with prognostic potential in skin cancer.

Keywords:  Cancer; cancer-associated fibroblast; collagen; elastin; wound healing

DOI:  https://doi.org/10.1016/j.matbio.2023.03.003
Nature. 2023 Mar 15.

Spatial epigenome-transcriptome co-profiling of mammalian tissues.

Di Zhang, Yanxiang Deng, Petra Kukanja, Eneritz Agirre, Marek Bartosovic, Mingze Dong, Cong Ma, Sai Ma, Graham Su, Shuozhen Bao, Yang Liu, Yang Xiao, Gorazd B Rosoklija, Andrew J Dwork, J John Mann, Kam W Leong, Maura Boldrini, Liya Wang, Maximilian Haeussler, Benjamin J Raphael, Yuval Kluger, Gonçalo Castelo-Branco, Rong Fan.

Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics, are becoming powerful tools for profiling of cellular states in the tissue context1-5. However, current methods capture only one layer of omics information at a time, precluding the possibility of examining the mechanistic relationship across the central dogma of molecular biology. Here, we present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications (H3K27me3, H3K27ac or H3K4me3) and gene expression on the same tissue section at near-single-cell resolution. These were applied to embryonic and juvenile mouse brain, as well as adult human brain, to map how epigenetic mechanisms control transcriptional phenotype and cell dynamics in tissue. Although highly concordant tissue features were identified by either spatial epigenome or spatial transcriptome we also observed distinct patterns, suggesting their differential roles in defining cell states. Linking epigenome to transcriptome pixel by pixel allows the uncovering of new insights in spatial epigenetic priming, differentiation and gene regulation within the tissue architecture. These technologies are of great interest in life science and biomedical research.

DOI: https://doi.org/10.1038/s41586-023-05795-1
Sci Adv. 2023 Mar 15. 9(11): eade4582

Digital spatial profiling of intraductal papillary mucinous neoplasms: Toward a molecular framework for risk stratification.

Matthew K Iyer, Chanjuan Shi, Austin M Eckhoff, Ashley Fletcher, Daniel P Nussbaum, Peter J Allen.

The histopathologic heterogeneity of intraductal papillary mucinous neoplasms (IPMN) complicates the prediction of pancreatic ductal adenocarcinoma (PDAC) risk. Intratumoral regions of pancreaticobiliary (PB), intestinal (INT), and gastric foveolar (GF) epithelium may occur with either low-grade dysplasia (LGD) or high-grade dysplasia (HGD). We used digital spatial RNA profiling of dysplastic epithelium (83 regions) from surgically resected IPMN tissues (12 patients) to differentiate subtypes and predict genes associated with malignancy. The expression patterns of PB and GF lesions diverged from INT, suggesting that PB and GF arise from a common lineage. Transcriptional dysregulation within PB lesions mirrored that of PDAC, whereas INT and GF foci did not. Tumor necrosis factor/nuclear factor κB (TNF-NFκB) and cell cycle (cycling S and cycling G2-M) programs occurred with relative prominence in PB and INT subtypes, respectively. Together, this study delineates markers of high-risk IPMN and insights into malignant progression.

DOI: https://doi.org/10.1126/sciadv.ade4582
Science. 2023 Mar 16. eade3925

Decrypting drug actions and protein modifications by dose- and time-resolved proteomics.

Jana Zecha, Florian P Bayer, Svenja Wiechmann, Julia Woortman, Nicola Berner, Julian Müller, Annika Schneider, Karl Kramer, Mar Abril-Gil, Thomas Hopf, Leonie Reichart, Lin Chen, Fynn M Hansen, Severin Lechner, Patroklos Samaras, Stephan Eckert, Ludwig Lautenbacher, Maria Reinecke, Firas Hamood, Polina Prokofeva, Larsen Vornholz, Chiara Falcomatà, Madeleine Dorsch, Ayla Schröder, Anton Venhuizen, Stephanie Wilhelm, Guillaume Médard, Gabriele Stoehr, Jürgen Ruland, Barbara M Grüner, Dieter Saur, Maike Buchner, Benjamin Ruprecht, Hannes Hahne, Matthew The, Mathias Wilhelm, Bernhard Kuster.

Although most cancer drugs modulate the activities of cellular pathways by changing post-translational modifications (PTMs), surprisingly little is known regarding the extent and the time- and dose-response characteristics of drug-regulated PTMs. Here, we introduce a proteomic assay termed decryptM that quantifies drug-PTM modulation for thousands of PTMs in cells to shed light on target engagement and drug mechanism of action (MoA). Examples range from detecting DNA damage by chemotherapeutics, to identifying drug-specific PTM signatures of kinase inhibitors, to demonstrating that rituximab kills CD20-positive B-cells by over-activating B cell receptor signaling. DecryptM profiling of 31 cancer drugs in 13 cell lines demonstrates the broad applicability of the approach. The resulting 1.8 million dose-response curves are provided as an interactive molecular resource in ProteomicsDB.

DOI: https://doi.org/10.1126/science.ade3925
Nat Commun. 2023 Mar 13. 14(1): 1362

De novo lipogenesis fuels adipocyte autophagosome and lysosome membrane dynamics.

Leslie A Rowland, Adilson Guilherme, Felipe Henriques, Chloe DiMarzio, Sean Munroe, Nicole Wetoska, Mark Kelly, Keith Reddig, Gregory Hendricks, Meixia Pan, Xianlin Han, Olga R Ilkayeva, Christopher B Newgard, Michael P Czech.

Adipocytes robustly synthesize fatty acids (FA) from carbohydrate through the de novo lipogenesis (DNL) pathway, yet surprisingly DNL contributes little to their abundant triglyceride stored in lipid droplets. This conundrum raises the hypothesis that adipocyte DNL instead enables membrane expansions to occur in processes like autophagy, which requires an abundant supply of phospholipids. We report here that adipocyte Fasn deficiency in vitro and in vivo markedly impairs autophagy, evident by autophagosome accumulation and severely compromised degradation of the autophagic substrate p62. Our data indicate the impairment occurs at the level of autophagosome-lysosome fusion, and indeed, loss of Fasn decreases certain membrane phosphoinositides necessary for autophagosome and lysosome maturation and fusion. Autophagy dependence on FA produced by Fasn is not fully alleviated by exogenous FA in cultured adipocytes, and interestingly, imaging studies reveal that Fasn colocalizes with nascent autophagosomes. Together, our studies identify DNL as a critical source of FAs to fuel autophagosome and lysosome maturation and fusion in adipocytes.

DOI: https://doi.org/10.1038/s41467-023-37016-8
Nat Aging. 2022 Jul;2(7): 635-643

Longitudinal phenotypic aging metrics in the Baltimore Longitudinal Study of Aging.

Pei-Lun Kuo, Jennifer A Schrack, Morgan E Levine, Michelle D Shardell, Eleanor M Simonsick, Chee W Chia, Ann Zenobia Moore, Toshiko Tanaka, Yang An, Ajoy Karikkineth, Majd AlGhatrif, Palchamy Elango, Linda M Zukley, Josephine M Egan, Rafael de Cabo, Susan M Resnick, Luigi Ferrucci.

To define metrics of phenotypic aging, it is essential to identify biological and environmental factors that influence the pace of aging. Previous attempts to develop aging metrics were hampered by cross-sectional designs and/or focused on younger populations. In the Baltimore Longitudinal Study of Aging (BLSA), we collected longitudinally across the adult age range a comprehensive list of phenotypes within four domains (body composition, energetics, homeostatic mechanisms and neurodegeneration/neuroplasticity) and functional outcomes. We integrated individual deviations from population trajectories into a global longitudinal phenotypic metric of aging and demonstrate that accelerated longitudinal phenotypic aging is associated with faster physical and cognitive decline, faster accumulation of multimorbidity and shorter survival. These associations are more robust compared with the use of phenotypic and epigenetic measurements at a single time point. Estimation of these metrics required repeated measures of multiple phenotypes over time but may uniquely facilitate the identification of mechanisms driving phenotypic aging and subsequent age-related functional decline.

DOI: https://doi.org/10.1038/s43587-022-00243-7
bioRxiv. 2023 Mar 02. pii: 2023.03.02.530770. [Epub ahead of print]

BRD9-SMAD2/3 orchestrates stemness and tumorigenesis in pancreatic ductal adenocarcinoma.

Yuliang Feng, Liuyang Cai, Martin Pook, Feng Liu, Chao-Hui Chang, Mai Abdel Mouti, Reshma Nibhani, Shihong Wu, Siwei Deng, Stefania Militi, James Dunford, Martin Philpott, Yanbo Fan, Guo-Chang Fan, Qi Liu, Jun Qi, Sakthivel Sadayappan, Anil G Jegga, Udo Oppermann, Yigang Wang, Wei Huang, Lei Jiang, Siim Pauklin.

The dismal prognosis of pancreatic ductal adenocarcinoma (PDAC) is linked to the presence of pancreatic cancer stem-like cells (CSCs) that respond poorly to current chemotherapy regimens. By small molecule compound screening targeting 142 epigenetic enzymes, we identified that bromodomain-containing protein BRD9, a component of the BAF histone remodelling complex, is a key chromatin regulator to orchestrate the stemness of pancreatic CSCs via cooperating with the TGFβ/Activin-SMAD2/3 signalling pathway. Inhibition and genetic ablation of BDR9 block the self-renewal, cell cycle entry into G0 phase and invasiveness of CSCs, and improve the sensitivity of CSCs to gemcitabine treatment. In addition, pharmacological inhibition of BRD9 significantly reduced the tumorigenesis in patient-derived xenografts mouse models and eliminated CSCs in tumours from pancreatic cancer patients. Mechanistically, inhibition of BRD9 disrupts enhancer-promoter looping and transcription of stemness genes in CSCs. Collectively, the data suggest BRD9 as a novel therapeutic target for PDAC treatment via modulation of CSC stemness.

DOI: https://doi.org/10.1101/2023.03.02.530770
bioRxiv. 2023 Feb 27. pii: 2023.02.25.529972. [Epub ahead of print]

Screening in serum-derived medium reveals differential response to compounds targeting metabolism.

Keene L Abbott, Ahmed Ali, Dominick Casalena, Brian T Do, Raphael Ferreira, Jaime H Cheah, Christian K Soule, Amy Deik, Tenzin Kunchok, Daniel R Schmidt, Steffen Renner, Sophie E Honeder, Michelle Wu, Sze Ham Chan, Tenzin Tseyang, Daniel Greaves, Peggy P Hsu, Christopher W Ng, Chelsea J Zhang, Ali Farsidjani, Iva Monique T Gramatikov, Nicholas J Matheson, Caroline A Lewis, Clary B Clish, Matthew G Rees, Jennifer A Roth, Lesley Mathews Griner, Alexander Muir, Douglas S Auld, Matthew G Vander Heiden.

A challenge for screening new candidate drugs to treat cancer is that efficacy in cell culture models is not always predictive of efficacy in patients. One limitation of standard cell culture is a reliance on non-physiological nutrient levels to propagate cells. Which nutrients are available can influence how cancer cells use metabolism to proliferate and impact sensitivity to some drugs, but a general assessment of how physiological nutrients affect cancer cell response to small molecule therapies is lacking. To enable screening of compounds to determine how the nutrient environment impacts drug efficacy, we developed a serum-derived culture medium that supports the proliferation of diverse cancer cell lines and is amenable to high-throughput screening. We used this system to screen several small molecule libraries and found that compounds targeting metabolic enzymes were enriched as having differential efficacy in standard compared to serum-derived medium. We exploited the differences in nutrient levels between each medium to understand why medium conditions affected the response of cells to some compounds, illustrating how this approach can be used to screen potential therapeutics and understand how their efficacy is modified by available nutrients.

DOI: https://doi.org/10.1101/2023.02.25.529972
EMBO Rep. 2023 Mar 17. e56114

Mitochondrial-derived vesicles retain membrane potential and contain a functional ATP synthase.

Reut Hazan Ben-Menachem, Dvora Lintzer, Tamar Ziv, Koyeli Das, Irit Rosenhek-Goldian, Ziv Porat, Hila Ben Ami Pilo, Sharon Karniely, Ann Saada, Neta Regev-Rudzki, Ophry Pines.

  Vesicular transport is a means of communication. While cells can communicate with each other via secretion of extracellular vesicles, less is known regarding organelle-to organelle communication, particularly in the case of mitochondria. Mitochondria are responsible for the production of energy and for essential metabolic pathways in the cell, as well as fundamental processes such as apoptosis and aging. Here, we show that functional mitochondria isolated from Saccharomyces cerevisiae release vesicles, independent of the fission machinery. We isolate these mitochondrial-derived vesicles (MDVs) and find that they are relatively uniform in size, of about 100 nm, and carry selective protein cargo enriched for ATP synthase subunits. Remarkably, we further find that these MDVs harbor a functional ATP synthase complex. We demonstrate that these vesicles have a membrane potential, produce ATP, and seem to fuse with naive mitochondria. Our findings reveal a possible delivery mechanism of ATP-producing vesicles, which can potentially regenerate ATP-deficient mitochondria and may participate in organelle-to-organelle communication.

Keywords:  ATP synthase; membrane potential; mitochondria; mitochondrial-derived vesicles; protein distribution

DOI:  https://doi.org/10.15252/embr.202256114
PLoS Comput Biol. 2023 Mar 13. 19(3): e1010952

First passage time analysis of spatial mutation patterns reveals sub-clonal evolutionary dynamics in colorectal cancer.

Magnus J Haughey, Aleix Bassolas, Sandro Sousa, Ann-Marie Baker, Trevor A Graham, Vincenzo Nicosia, Weini Huang.

The signature of early cancer dynamics on the spatial arrangement of tumour cells is poorly understood, and yet could encode information about how sub-clones grew within the expanding tumour. Novel methods of quantifying spatial tumour data at the cellular scale are required to link evolutionary dynamics to the resulting spatial architecture of the tumour. Here, we propose a framework using first passage times of random walks to quantify the complex spatial patterns of tumour cell population mixing. First, using a simple model of cell mixing we demonstrate how first passage time statistics can distinguish between different pattern structures. We then apply our method to simulated patterns of mutated and non-mutated tumour cell population mixing, generated using an agent-based model of expanding tumours, to explore how first passage times reflect mutant cell replicative advantage, time of emergence and strength of cell pushing. Finally, we explore applications to experimentally measured human colorectal cancer, and estimate parameters of early sub-clonal dynamics using our spatial computational model. We infer a wide range of sub-clonal dynamics, with mutant cell division rates varying between 1 and 4 times the rate of non-mutated cells across our sample set. Some mutated sub-clones emerged after as few as 100 non-mutant cell divisions, and others only after 50,000 divisions. The majority were consistent with boundary driven growth or short-range cell pushing. By analysing multiple sub-sampled regions in a small number of samples, we explore how the distribution of inferred dynamics could inform about the initial mutational event. Our results demonstrate the efficacy of first passage time analysis as a new methodology in spatial analysis of solid tumour tissue, and suggest that patterns of sub-clonal mixing can provide insights into early cancer dynamics.

DOI: https://doi.org/10.1371/journal.pcbi.1010952
Biochem J. 2023 Mar 15. 480(5): 335-362

Macropinocytosis: mechanisms and regulation.

Gilbert Salloum, Anne R Bresnick, Jonathan M Backer.

  Macropinocytosis is defined as an actin-dependent but coat- and dynamin-independent endocytic uptake process, which generates large intracellular vesicles (macropinosomes) containing a non-selective sampling of extracellular fluid. Macropinocytosis provides an important mechanism of immune surveillance by dendritic cells and macrophages, but also serves as an essential nutrient uptake pathway for unicellular organisms and tumor cells. This review examines the cell biological mechanisms that drive macropinocytosis, as well as the complex signaling pathways - GTPases, lipid and protein kinases and phosphatases, and actin regulatory proteins - that regulate macropinosome formation, internalization, and disposition.

Keywords:  GTPases; Rac; macropinocytosis; phosphoinositide 3-kinase

DOI:  https://doi.org/10.1042/BCJ20210584
EMBO J. 2023 Mar 14. e111901

Mitochondrial morphology controls fatty acid utilization by changing CPT1 sensitivity to malonyl-CoA.

Jennifer Ngo, Dong Wook Choi, Illana A Stanley, Linsey Stiles, Anthony J A Molina, Pei-Hsuan Chen, Ana Lako, Isabelle Chiao Han Sung, Rishov Goswami, Min-Young Kim, Nathanael Miller, Siyouneh Baghdasarian, Doyeon Kim-Vasquez, Anthony E Jones, Brett Roach, Vincent Gutierrez, Karel Erion, Ajit S Divakaruni, Marc Liesa, Nika N Danial, Orian S Shirihai.

  Changes in mitochondrial morphology are associated with nutrient utilization, but the precise causalities and the underlying mechanisms remain unknown. Here, using cellular models representing a wide variety of mitochondrial shapes, we show a strong linear correlation between mitochondrial fragmentation and increased fatty acid oxidation (FAO) rates. Forced mitochondrial elongation following MFN2 over-expression or DRP1 depletion diminishes FAO, while forced fragmentation upon knockdown or knockout of MFN2 augments FAO as evident from respirometry and metabolic tracing. Remarkably, the genetic induction of fragmentation phenocopies distinct cell type-specific biological functions of enhanced FAO. These include stimulation of gluconeogenesis in hepatocytes, induction of insulin secretion in islet β-cells exposed to fatty acids, and survival of FAO-dependent lymphoma subtypes. We find that fragmentation increases long-chain but not short-chain FAO, identifying carnitine O-palmitoyltransferase 1 (CPT1) as the downstream effector of mitochondrial morphology in regulation of FAO. Mechanistically, we determined that fragmentation reduces malonyl-CoA inhibition of CPT1, while elongation increases CPT1 sensitivity to malonyl-CoA inhibition. Overall, these findings underscore a physiologic role for fragmentation as a mechanism whereby cellular fuel preference and FAO capacity are determined.

Keywords:  CPT1; fatty acid oxidation; fission; fusion; mitochondrial dynamics

DOI:  https://doi.org/10.15252/embj.2022111901
Br J Cancer. 2023 Mar 16.

Systemic inflammatory prognostic scores in advanced pancreatic adenocarcinoma.

Lucy X Ma, Yifan Wang, Osvaldo Espin-Garcia, Michael J Allen, Gun Ho Jang, Amy Zhang, Anna Dodd, Stephanie Ramotar, Shawn Hutchinson, Mustapha Tehfe, Ravi Ramjeesingh, James Biagi, Julie M Wilson, Faiyaz Notta, Sandra E Fischer, George Zogopoulos, Steven Gallinger, Robert C Grant, Rama Khokha, Nathan Chan, Barbara T Grünwald, Jennifer J Knox, Grainne M O'Kane.

BACKGROUND: Systemic inflammatory scores may aid prognostication and patient selection for trials. We compared five scores in advanced pancreatic adenocarcinoma (PDAC).
METHODS: Unresectable/metastatic PDAC patients enrolled in the Comprehensive Molecular Characterisation of Advanced Pancreatic Ductal Adenocarcinoma for Better Treatment Selection trial (NCT02750657) were included. Patients had pre-treatment biopsies for whole genome and RNA sequencing. CD8 immunohistochemistry was available in a subset. The neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio, Prognostic Nutritional Index, Gustave Roussy Immune Score (GRIm-S), and Memorial Sloan Kettering Prognostic Score (MPS) were calculated. Overall survival (OS) was estimated using Kaplan-Meier methods. Associations between inflammatory scores, clinical/genomic characteristics, and OS were analysed.
RESULTS: We analysed 263 patients. High-risk NLR, GRIm-S and MPS were poorly prognostic. The GRIm-S had the highest predictive ability: median OS 6.4 vs. 10 months for high risk vs. low-risk (P < 0.001); HR 2.26 (P < 0.001). ECOG ≥ 1, the basal-like subtype, and low-HRDetect were additional poor prognostic factors (P < 0.01). Inflammatory scores did not associate with RNA-based classifiers or homologous recombination repair deficiency genotypes. High-risk MPS (P = 0.04) and GRIm-S (P = 0.02) patients had lower median CD8 + tumour-infiltrating lymphocytes.
CONCLUSIONS: Inflammatory scores incorporating NLR have prognostic value in advanced PDAC. Understanding immunophenotypes of poor-risk patients and using these scores in trials will advance the field.

DOI: https://doi.org/10.1038/s41416-023-02214-0
Nat Cancer. 2023 Mar 13.

Age-associated microenvironmental changes highlight the role of PDGF-C in ER+ breast cancer metastatic relapse.

Frances K Turrell, Rebecca Orha, Naomi J Guppy, Andrea Gillespie, Matthew Guelbert, Chris Starling, Syed Haider, Clare M Isacke.

Patients with estrogen receptor (ER)-positive breast cancer are at risk of metastatic relapse for decades after primary tumor resection and treatment, a consequence of dormant disseminated tumor cells (DTCs) reawakening at secondary sites. Here we use syngeneic ER+ mouse models in which DTCs display a dormant phenotype in young mice but accelerated metastatic outgrowth in an aged or fibrotic microenvironment. In young mice, low-level Pdgfc expression by ER+ DTCs is required for their maintenance in secondary sites but is insufficient to support development of macrometastases. By contrast, the platelet-derived growth factor (PDGF)-Chi environment of aging or fibrotic lungs promotes DTC proliferation and upregulates tumor cell Pdgfc expression stimulating further stromal activation, events that can be blocked by pharmacological inhibition of PDGFRα or with a PDGF-C-blocking antibody. These results highlight the role of the changing microenvironment in regulating DTC outgrowth and the opportunity to target PDGF-C signaling to limit metastatic relapse in ER+ breast cancer.

DOI: https://doi.org/10.1038/s43018-023-00525-y
Nat Cancer. 2023 Mar 13.

SULT1A1-dependent sulfonation of alkylators is a lineage-dependent vulnerability of liver cancers.

Lei Shi, William Shen, Mindy I Davis, Ke Kong, Phuong Vu, Supriya K Saha, Ramzi Adil, Johannes Kreuzer, Regina Egan, Tobie D Lee, Patricia Greninger, Jonathan H Shrimp, Wei Zhao, Ting-Yu Wei, Mi Zhou, Jason Eccleston, Jonathan Sussman, Ujjawal Manocha, Vajira Weerasekara, Hiroshi Kondo, Vindhya Vijay, Meng-Ju Wu, Sara E Kearney, Jeffrey Ho, Joseph McClanaghan, Ellen Murchie, Giovanna S Crowther, Samarjit Patnaik, Matthew B Boxer, Min Shen, David T Ting, William Y Kim, Ben Z Stanger, Vikram Deshpande, Cristina R Ferrone, Cyril H Benes, Wilhelm Haas, Matthew D Hall, Nabeel Bardeesy.

Adult liver malignancies, including intrahepatic cholangiocarcinoma and hepatocellular carcinoma, are the second leading cause of cancer-related deaths worldwide. Most individuals are treated with either combination chemotherapy or immunotherapy, respectively, without specific biomarkers for selection. Here using high-throughput screens, proteomics and in vitro resistance models, we identify the small molecule YC-1 as selectively active against a defined subset of cell lines derived from both liver cancer types. We demonstrate that selectivity is determined by expression of the liver-resident cytosolic sulfotransferase enzyme SULT1A1, which sulfonates YC-1. Sulfonation stimulates covalent binding of YC-1 to lysine residues in protein targets, enriching for RNA-binding factors. Computational analysis defined a wider group of structurally related SULT1A1-activated small molecules with distinct target profiles, which together constitute an untapped small-molecule class. These studies provide a foundation for preclinical development of these agents and point to the broader potential of exploiting SULT1A1 activity for selective targeting strategies.

DOI: https://doi.org/10.1038/s43018-023-00523-0
Nature. 2023 Mar 15.

Lactate regulates cell cycle by remodeling the anaphase promoting complex.

Weihai Liu, Yun Wang, Luiz H M Bozi, Patrick Fischer, Mark P Jedrychowski, Haopeng Xiao, Tao Wu, Narek Darabedian, Xiadi He, Evanna L Mills, Nils Burger, Sanghee Shin, Anita Reddy, Hans-Georg Sprenger, Nhien Tran, Sally Winther, Stephen M Hinshaw, Jingnan Shen, Hyuk-Soo Seo, Kijun Song, Andrew Z Xu, Luke Sebastian, Jean Zhao, Sirano Dhe-Paganon, Jianwei Che, Steven P Gygi, Haribabu Arthanari, Edward T Chouchani.

Lactate is abundant in rapidly dividing cells due to the requirement for elevated glucose catabolism to support proliferation1-6. However, it is not known whether accumulated lactate affects the proliferative state. Here, we deploy a systematic approach to determine lactate-dependent regulation of proteins across the human proteome. From these data, we elucidate a mechanism of cell cycle regulation whereby accumulated lactate remodels the anaphase promoting complex (APC/C). Remodeling of APC/C in this way is caused by direct inhibition of the SUMO protease SENP1 by lactate. We discover that accumulated lactate binds and inhibits SENP1 by forming a complex with zinc in the SENP1 active site. SENP1 inhibition by lactate stabilizes SUMOylation of two residues on APC4, which drives UBE2C binding to APC/C. This direct regulation of APC/C by lactate stimulates timed degradation of cell cycle proteins, and efficient mitotic exit in proliferative human cells. The above mechanism is initiated upon mitotic entry when lactate abundance reaches its apex. In this way, accumulation of lactate communicates the consequences of a nutrient replete growth phase to stimulate timed opening of APC/C, cell division, and proliferation. Conversely, persistent accumulation of lactate drives aberrant APC/C remodeling and can overcome anti-mitotic pharmacology via mitotic slippage. Taken together, we define a biochemical mechanism through which lactate directly regulates protein function to control cell cycle and proliferation.

DOI: https://doi.org/10.1038/s41586-023-05939-3
STAR Protoc. 2023 Mar 15. pii: S2666-1667(23)00121-1. [Epub ahead of print]4(2): 102163

Generation of liver metastases in a mouse model using ultrasound-guided intravenous injection.

Amanda Labora, Hailey Lee, Charlotte Chan, Erin Tabornal, Thuc Le, Khalid Rashid, Evan Abt, Takanobu Yamao, Hanna Mandl, Amanda Creech, Alykhan Premji, Luyi Li, Jason Link, Nanping Wu, Caius Radu, Timothy Donahue.

  Here, we present a protocol to generate a murine model of liver metastasis by directly injecting tumor cells into the portal vein under ultrasound guidance. We describe steps for animal and cell preparation and two techniques for injecting tumor cells. One technique is freehand, while the other technique is device-assisted using a 3D-printed prototype device. Finally, we describe tumor surveillance with bioluminescent imaging.

Keywords:  Cancer; Cell Biology; Health Sciences; Model Organisms

DOI:  https://doi.org/10.1016/j.xpro.2023.102163
Nat Rev Clin Oncol. 2023 Mar 13.

Precision oncology for KRASG12C-mutant colorectal cancer.

Federica Di Nicolantonio, Alberto Bardelli.

DOI: https://doi.org/10.1038/s41571-023-00748-z
Elife. 2023 Mar 13. pii: e79271. [Epub ahead of print]12

Mechanosensitive pore opening of a prokaryotic voltage-gated sodium channel.

Peter R Strege, Luke M Cowan, Constanza Alcaino, Amelia Mazzone, Christopher A Ahern, Lorin S Milescu, Gianrico Farrugia, Arthur Beyder.

  Voltage-gated ion channels orchestrate electrical activities that drive mechanical functions in contractile tissues such as the heart and gut. In turn, contractions change membrane tension and impact ion channels. Voltage-gated ion channels are mechanosensitive, but the mechanisms of mechanosensitivity remain poorly understood. Here, we leverage the relative simplicity of NaChBac, a prokaryotic voltage-gated sodium channel from Bacillus halodurans, to investigate mechanosensitivity. In whole-cell experiments on heterologously transfected HEK293 cells, shear stress reversibly altered the kinetic properties of NaChBac and increased its maximum current, comparably to the mechanosensitive eukaryotic sodium channel NaV1.5. In single-channel experiments, patch suction reversibly increased the open probability of a NaChBac mutant with inactivation removed. A simple kinetic mechanism featuring a mechanosensitive pore opening transition explained the overall response to force, whereas an alternative model with mechanosensitive voltage sensor activation diverged from the data. Structural analysis of NaChBac identified a large displacement of the hinged intracellular gate, and mutagenesis near the hinge diminished NaChBac mechanosensitivity, further supporting the proposed mechanism. Our results suggest that NaChBac is overall mechanosensitive due to the mechanosensitivity of a voltage-insensitive gating step associated with the pore opening. This mechanism may apply to eukaryotic voltage-gated ion channels, including NaV1.5.

Keywords:  cell biology; molecular biophysics; structural biology

DOI:  https://doi.org/10.7554/eLife.79271
Nature. 2023 Mar 15.

The dietary sweetener sucralose is a negative modulator of T cell-mediated responses.

Fabio Zani, Julianna Blagih, Tim Gruber, Michael D Buck, Nicholas Jones, Marc Hennequart, Clare L Newell, Steven E Pilley, Pablo Soro-Barrio, Gavin Kelly, Nathalie M Legrave, Eric C Cheung, Ian S Gilmore, Alex P Gould, Cristina Garcia-Caceres, Karen H Vousden.

Artificial sweeteners are used as calorie-free sugar substitutes in many food products and their consumption has increased substantially over the past years1. Although generally regarded as safe, some concerns have been raised about the long-term safety of the consumption of certain sweeteners2-5. In this study, we show that the intake of high doses of sucralose in mice results in immunomodulatory effects by limiting T cell proliferation and T cell differentiation. Mechanistically, sucralose affects the membrane order of T cells, accompanied by a reduced efficiency of T cell receptor signalling and intracellular calcium mobilization. Mice given sucralose show decreased CD8+ T cell antigen-specific responses in subcutaneous cancer models and bacterial infection models, and reduced T cell function in models of T cell-mediated autoimmunity. Overall, these findings suggest that a high intake of sucralose can dampen T cell-mediated responses, an effect that could be used in therapy to mitigate T cell-dependent autoimmune disorders.

DOI: https://doi.org/10.1038/s41586-023-05801-6
Cancer Res. 2023 Mar 13. pii: CAN-22-3490. [Epub ahead of print]

ANO1 reprograms cholesterol metabolism and the tumor microenvironment to promote cancer metastasis.

Chun-Miao Deng, Guo-Geng Zhang, Qin-Wen Liu, Jiao-Jiao Xu, Zhi-Chao Liu, Jing Yang, Tao-Yang Xu, Zhi-Gang Li, Fan Zhang, Bin Li.

Tumor metastasis is a complex process. A better understanding of the mechanistic underpinnings of the metastatic cascade could uncover approaches to better prevent and target metastases. Here, we integrated transcriptomic profiling in primary esophageal squamous cell carcinoma (ESCC) and matched lymph node metastatic tissues and genome-wide CRISPR/Cas9 functional screening to identify the key drivers of cancer metastasis. Anoctamin 1 (ANO1) expression was found to be elevated in primary tumors and further increased in metastatic tissues. High expression of ANO1 was associated with poor patient survival, and ANO1 overexpression promoted cancer invasion and metastasis. Mechanistically, ANO1 inactivated the LXR pathway and increased intracellular cholesterol accumulation by interacting with JUN to repress the transcription of cholesterol hydroxylase, CYP27A1. In a paracrine manner, interleukin 1β (IL-1β) secreted from ANO1-expressing ESCC cancer cells activated NFκB signaling in fibroblasts to stimulate production of the chemokine CCL1, which in turn enhanced invasion of ESCC cancer cells. Furthermore, molecular docking and in silico screening of 1,500,000 small molecules identified K786-4469 as a lead compound that targeted ANO1 and suppressed cancer metastasis in vitro and in vivo. Overall, these findings uncover a non-canonical function of ANO1 in regulating cholesterol metabolism and fibroblast function, revealing ANO1 as a potential prognostic biomarker and therapeutic target for metastatic ESCC.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-3490
Cancer Cell. 2023 Mar 13. pii: S1535-6108(23)00044-2. [Epub ahead of print]41(3): 374-403

The evolving tumor microenvironment: From cancer initiation to metastatic outgrowth.

Karin E de Visser, Johanna A Joyce.

Cancers represent complex ecosystems comprising tumor cells and a multitude of non-cancerous cells, embedded in an altered extracellular matrix. The tumor microenvironment (TME) includes diverse immune cell types, cancer-associated fibroblasts, endothelial cells, pericytes, and various additional tissue-resident cell types. These host cells were once considered bystanders of tumorigenesis but are now known to play critical roles in the pathogenesis of cancer. The cellular composition and functional state of the TME can differ extensively depending on the organ in which the tumor arises, the intrinsic features of cancer cells, the tumor stage, and patient characteristics. Here, we review the importance of the TME in each stage of cancer progression, from tumor initiation, progression, invasion, and intravasation to metastatic dissemination and outgrowth. Understanding the complex interplay between tumor cell-intrinsic, cell-extrinsic, and systemic mediators of disease progression is critical for the rational development of effective anti-cancer treatments.

DOI: https://doi.org/10.1016/j.ccell.2023.02.016
Lancet Gastroenterol Hepatol. 2023 Apr;pii: S2468-1253(23)00039-0. [Epub ahead of print]8(4): 287

Cause for concern: the rising incidence of early-onset pancreatic cancer.

The Lancet Gastroenterology Hepatology.

DOI: https://doi.org/10.1016/S2468-1253(23)00039-0
Science. 2023 Mar 17. 379(6637): 1088-1090

A common cancer at an uncommon age.

Marios Giannakis, Kimmie Ng.

The etiology of early-onset colorectal cancer needs to be understood to tackle rising incidence.

DOI: https://doi.org/10.1126/science.ade7114
Ann Surg Oncol. 2023 Mar 14.

Top Pancreatic Tumor Articles from 2021 to Inform Your Cancer Patients.

Melissa E Hogg, Laleh G Melstrom.

BACKGROUND: More than 10,000 publications about pancreatic cancer were found on PubMed during the past year.
METHODS: To best inform patients with pancreatic cancer, the obvious, frequent questions asked during patient counseling when dealing with resectable pancreatic cancer, borderline resectable pancreatic cancer, and unresectable pancreatic cancer were considered.
RESULTS: The publications highlighted are comprehensive on the current management of neoadjuvant therapy for resectable pancreatic cancer, the addition of radiation to neoadjuvant therapy for borderline resectable pancreatic cancer, the utility of arterial resections in unresectable pancreatic cancer, and the role of minimally invasive approach to pancreatic cancer surgical therapy.
CONCLUSION: These articles are high yield and comprehensive review on key issues facing surgical oncologists who operate on pancreatic cancer.

DOI: https://doi.org/10.1245/s10434-023-13277-x
Nature. 2023 Mar 15.

Whole-genome doubling drives oncogenic loss of chromatin segregation.

Ruxandra A Lambuta, Luca Nanni, Yuanlong Liu, Juan Diaz-Miyar, Arvind Iyer, Daniele Tavernari, Natalya Katanayeva, Giovanni Ciriello, Elisa Oricchio.

Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies1-8. However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic phenotypes are currently unknown. Here we show that in p53-deficient cells, WGD induces loss of chromatin segregation (LCS). This event is characterized by reduced segregation between short and long chromosomes, A and B subcompartments and adjacent chromatin domains. LCS is driven by the downregulation of CTCF and H3K9me3 in cells that bypassed activation of the tetraploid checkpoint. Longitudinal analyses revealed that LCS primes genomic regions for subcompartment repositioning in WGD cells. This results in chromatin and epigenetic changes associated with oncogene activation in tumours ensuing from WGD cells. Notably, subcompartment repositioning events were largely independent of chromosomal alterations, which indicates that these were complementary mechanisms contributing to tumour development and progression. Overall, LCS initiates chromatin conformation changes that ultimately result in oncogenic epigenetic and transcriptional modifications, which suggests that chromatin evolution is a hallmark of WGD-driven cancer.

DOI: https://doi.org/10.1038/s41586-023-05794-2