bims-cagime 2023-08-13 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2023–08–13
33 papers selected by
Kıvanç Görgülü, Technical University of Munich

RBPJ deficiency sensitizes pancreatic acinar cells to KRAS-mediated pancreatic intraepithelial neoplasia initiation.
Live-Cell High-Throughput Screen for Monitoring Autophagy Flux.
Generation of precision preclinical cancer models using regulated in vivo base editing.
The role of epithelial-mesenchymal transition and autophagy in pancreatic ductal adenocarcinoma invasion.
Propionyl-CoA carboxylase subunit B modulates PIK3CA-regulated immune-surveillance in a pancreatic cancer mouse model.
Post-transcriptional dynamics and RNA homeostasis in autophagy and cancer.
A Review of Nutraceuticals in Cancer Cachexia.
Fasting-sensitive SUMO-switch on Prox1 controls hepatic cholesterol metabolism.
Transformed cells maintain survival by downregulating autophagy at a high cell confluency.
The clinical terrain of immunotherapies in heterogeneous pancreatic cancer: unravelling challenges and opportunities.
Autophagy modulates the stability of Wee1 and cell cycle G2/M transition.
Relevance of Dietary Supplement Use in Gastrointestinal-Cancer-Associated Cachexia.
The pharmacoepigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity.
Breast cancer-secreted factors promote lung metastasis by signaling systemically to induce a fibrotic pre-metastatic niche.
Fibronectin fragments generated by pancreatic trypsin act as endogenous inhibitors of pancreatic tumor growth.
Mechano-dependent sorbitol accumulation supports biomolecular condensate.
Emerging therapies in cancer metabolism.
Cancer Metabolism Historical Perspectives: A Chronicle of Controversies and Consensus.
The Membrane Phase Transition Gives Rise to Responsive Plasma Membrane Structure and Function.
Humanized mouse liver reveals endothelial control of essential hepatic metabolic functions.
Distinct molecular profiles of skull bone marrow in health and neurological disorders.
Force propagation between epithelial cells depends on active coupling and mechano-structural polarization.
Allosteric regulation of switch-II domain controls KRAS oncogenicity.
DNA methylation-associated allelic inactivation regulates Keratin 19 gene expression during pancreatic development and carcinogenesis.
A membrane-associated MHC-I inhibitory axis for cancer immune evasion.
In vivo fluorescent labeling and tracking of extracellular matrix.
A review on deep learning applications in highly multiplexed tissue imaging data analysis.
The Causal Effects of Cholelithiasis on Acute Pancreatitis and Pancreatic Cancer: A Large Sample Size Mendelian Randomization Analysis.
Fibrosis induced by resident macrophages has divergent roles in pancreas inflammatory injury and PDAC.
The secretome atlas of two mouse models of progeria.
Experimental and spontaneous metastasis assays can result in divergence in clonal architecture.
Decoding of translation-regulating entities reveals heterogeneous translation deficiency patterns in cellular senescence.
Changes in Tissue Fluidity Predict Tumor Aggressiveness In Vivo.

Cell Mol Gastroenterol Hepatol. 2023 Aug 03. pii: S2352-345X(23)00145-5. [Epub ahead of print]

RBPJ deficiency sensitizes pancreatic acinar cells to KRAS-mediated pancreatic intraepithelial neoplasia initiation.

Leiling Pan, Medhanie A Mulaw, Johann Gout, Min Guo, Hina Zarrin, Peggy Schwarz, Bernd Baumann, Thomas Seufferlein, Martin Wagner, Franz Oswald.

   BACKGROUND & AIMS: Development of pancreatic ductal adenocarcinoma (PDAC) is a multi-step process intensively studied, however precocious diagnosis and effective therapy still remain unsatisfactory. The role for Notch signaling in PDAC has been discussed controversially as both, cancer-promoting and -antagonizing functions have been described. Thus, an improved understanding of the underlying molecular mechanisms is necessary. Here, we focused on RBPJ, the receiving transcription factor in the Notch pathway, examined its expression pattern in PDAC and characterized its function in mouse models of pancreatic cancer development and in the regeneration process after acute pancreatitis.
METHODS: Conditional transgenic mouse models were used for functional analysis of RBPJ in the adult pancreas, initiation of PDAC precursor lesions, and pancreatic regeneration. Pancreata and primary acinar cells were tested for ADM together with immunohistology and comprehensive transcriptional profiling by RNA-sequencing.
RESULTS: We identified reduced RBPJ expression in a subset of human PDAC specimens. Ptf1α-CreERT driven depletion of RBPJ in transgenic mice revealed that its function is dispensable for the homeostasis and maintenance of adult acinar cells. However, primary RBPJ-deficient acinar cells underwent acinar-to-ductal differentiation in ex vivo. Importantly, oncogenic KRAS expression in the context of RBPJ deficiency facilitated the development of PanIN lesions with massive fibrotic stroma formation. Interestingly, RNA-seq data revealed transcriptional profile associated with the cytokine/chemokine and extracellular matrix changes. In addition, lack of RBPJ delays the course of acute pancreatitis and critically impairs it in the context of KRASG12D expression.
CONCLUSION: Our findings imply that downregulation of RBPJ in PDAC patients derepresses Notch targets and promotes KRAS-mediated pancreatic acinar cells transformation and desmoplasia development.

Keywords:  ADM; Acinar cells; PDAC

DOI:  https://doi.org/10.1016/j.jcmgh.2023.07.013
Methods Mol Biol. 2023 ;2706 215-224

Live-Cell High-Throughput Screen for Monitoring Autophagy Flux.

Sara Cano-Franco, Hung Ho-Xuan, Lorene Brunello, Alexandra Stolz.

  Autophagy is a cellular process implicated in the renewal of cellular components and the maintenance of cellular hemostasis and therefore associated with various types of diseases. In addition, autophagy belongs to the stress response pathways and is frequently activated by chemical compounds harboring characteristics of cell toxicity. High-throughput screens analyzing autophagy flux are therefore applied in both, the field of compound identification for targeting autophagy and compound characterization for analyzing compound toxicity. In this chapter, we describe a live-cell, fluorescent-based, high-throughput screening method in 384-well format for the fast and accurate measurement of autophagy flux over time suitable for academic research, pharmacological applications, and drug discovery.

Keywords:  Autophagy; Fluorescence; GFP-LC3-RFP-LC3ΔG; Incucyte

DOI:  https://doi.org/10.1007/978-1-0716-3397-7_16
Nat Biotechnol. 2023 Aug 10.

Generation of precision preclinical cancer models using regulated in vivo base editing.

Alyna Katti, Adrián Vega-Pérez, Miguel Foronda, Jill Zimmerman, Maria Paz Zafra, Elizabeth Granowsky, Sukanya Goswami, Eric E Gardner, Bianca J Diaz, Janelle M Simon, Alexandra Wuest, Wei Luan, Maria Teresa Calvo Fernandez, Anastasia P Kadina, John A Walker, Kevin Holden, Scott W Lowe, Francisco J Sánchez Rivera, Lukas E Dow.

Although single-nucleotide variants (SNVs) make up the majority of cancer-associated genetic changes and have been comprehensively catalogued, little is known about their impact on tumor initiation and progression. To enable the functional interrogation of cancer-associated SNVs, we developed a mouse system for temporal and regulatable in vivo base editing. The inducible base editing (iBE) mouse carries a single expression-optimized cytosine base editor transgene under the control of a tetracycline response element and enables robust, doxycycline-dependent expression across a broad range of tissues in vivo. Combined with plasmid-based or synthetic guide RNAs, iBE drives efficient engineering of individual or multiple SNVs in intestinal, lung and pancreatic organoids. Temporal regulation of base editor activity allows controlled sequential genome editing ex vivo and in vivo, and delivery of sgRNAs directly to target tissues facilitates generation of in situ preclinical cancer models.

DOI: https://doi.org/10.1038/s41587-023-01900-x
Cell Death Dis. 2023 Aug 07. 14(8): 506

The role of epithelial-mesenchymal transition and autophagy in pancreatic ductal adenocarcinoma invasion.

Jian Yang, Ying Liu, Shi Liu.

Of all pancreatic cancer (PC) cases, approximately 90% are pancreatic ductal adenocarcinoma (PDAC), which progress rapidly due to its high degree of invasiveness and high metastatic potential. Epithelial-mesenchymal transition (EMT) is a prerequisite for cancer cell invasion and spread, and it is mediated by the specific cellular behaviors and the tumor microenvironment. Autophagy has long been a target of cancer therapy, and it has been considered to play a dual and contradictory role, particularly regarding EMT-mediated PDAC invasion. This review discusses the characteristics and the biological role of EMT and autophagy from a cellular perspective, explaining invasion as a survival behavior of PDAC, with the aim of providing novel insights into targeting EMT and autophagy to overcome PDAC invasion.

DOI: https://doi.org/10.1038/s41419-023-06032-3
bioRxiv. 2023 Jul 26. pii: 2023.07.24.550301. [Epub ahead of print]

Propionyl-CoA carboxylase subunit B modulates PIK3CA-regulated immune-surveillance in a pancreatic cancer mouse model.

Han V Han, Richard Efem, Barbara Rosati, Sara Maimouni, Kevin Lu, Ya-Ping Jiang, Wei-Xing Zong, Richard Z Lin.

Pancreatic ductal adenocarcinomas (PDACs) are resistant to systemic treatments including immunotherapy. Over 90% of PDACs have oncogenic KRAS mutations, and phosphoinositide 3-kinases (PI3Ks) are direct effectors of KRAS. Previously, we demonstrated that genetic ablation of PI3K isoform, Pik3ca in the KPC ( Kras G12D ; Trp53 R172H ; Pdx1-Cre ) pancreatic cancer cell line induced complete tumor elimination by infiltrating T cells in a mouse model. However, clinical trials using PI3K inhibitors for PDAC patients exhibited limited efficacy due to drug resistance. To identify potential contributors to PI3K inhibitor resistance, we conducted an in vivo genome-wide gene-deletion screen using the Pik3ca -/- KPC (named αKO) cells implanted in the mouse pancreas and discovered propionyl-CoA carboxylase subunit B (PCCB) modulates PIK3CA - mediated immune evasion. Deletion of Pccb gene in αKO cells (named p-αKO) allowed tumor progression causing death of host mice even though p-αKO tumors are infiltrated with T cells. Single-cell RNA sequencing revealed that infiltrating clonally expanded T cells in p-αKO tumors were more exhausted as compared to T cells founds in αKO tumors. Blockade of PD-L1/PD1 interaction reversed T cell exhaustion, slowed tumor growth and improved the survival of mice implanted with p-αKO cells. These results indicate that propionyl-CoA carboxylase activity modulates PIK3CA-regulated immune surveillance of PDAC.

DOI: https://doi.org/10.1101/2023.07.24.550301
Cell Death Differ. 2023 Aug 09.

Post-transcriptional dynamics and RNA homeostasis in autophagy and cancer.

Srinivasa Prasad Kolapalli, Thorbjørn M Nielsen, Lisa B Frankel.

Autophagy is an essential recycling and quality control pathway which preserves cellular and organismal homeostasis. As a catabolic process, autophagy degrades damaged and aged intracellular components in response to conditions of stress, including nutrient deprivation, oxidative and genotoxic stress. Autophagy is a highly adaptive and dynamic process which requires an intricately coordinated molecular control. Here we provide an overview of how autophagy is regulated post-transcriptionally, through RNA processing events, epitranscriptomic modifications and non-coding RNAs. We further discuss newly revealed RNA-binding properties of core autophagy machinery proteins and review recent indications of autophagy's ability to impact cellular RNA homeostasis. From a physiological perspective, we examine the biological implications of these emerging regulatory layers of autophagy, particularly in the context of nutrient deprivation and tumorigenesis.

DOI: https://doi.org/10.1038/s41418-023-01201-5
Cancers (Basel). 2023 Jul 30. pii: 3884. [Epub ahead of print]15(15):

A Review of Nutraceuticals in Cancer Cachexia.

Lucas Caeiro, Devika Gandhay, Lindsey J Anderson, Jose M Garcia.

  Cancer cachexia is largely characterized by muscle wasting and inflammation, leading to weight loss, functional impairment, poor quality of life (QOL), and reduced survival. The main barrier to therapeutic development is a lack of efficacy for improving clinically relevant outcomes, such as physical function or QOL, yet most nutraceutical studies focus on body weight. This review describes clinical and pre-clinical nutraceutical studies outside the context of complex nutritional and/or multimodal interventions, in the setting of cancer cachexia, in view of considerations for future clinical trial design. Clinical studies mostly utilized polyunsaturated fatty acids or amino acids/derivatives, and they primarily focused on body weight and, secondarily, on muscle mass and/or QOL. The few studies that measured physical function almost exclusively utilized handgrip strength with, predominantly, no time and/or group effect. Preclinical studies focused mainly on amino acids/derivatives and polyphenols, assessing body weight, muscle mass, and occasionally physical function. While this review does not provide sufficient evidence of the efficacy of nutraceuticals for cancer cachexia, more preclinical and adequately powered clinical studies are needed, and they should focus on clinically meaningful outcomes, including physical function and QOL.

Keywords:  cancer cachexia; handgrip strength; muscle mass; nutraceuticals; patient-reported outcomes; physical function; quality of life

DOI:  https://doi.org/10.3390/cancers15153884
EMBO Rep. 2023 Aug 10. e55981

Fasting-sensitive SUMO-switch on Prox1 controls hepatic cholesterol metabolism.

Ana Jimena Alfaro, Claudia Dittner, Janina Becker, Anne Loft, Amit Mhamane, Adriano Maida, Anastasia Georgiadi, Foivos-Filippos Tsokanos, Katarina Klepac, Claudia-Eveline Molocea, Rabih El-Merahbi, Karsten Motzler, Julia Geppert, Rhoda Anane Karikari, Julia Szendrödi, Annette Feuchtinger, Susanna Hofmann, Samir Karaca, Henning Urlaub, Mauricio Berriel Diaz, Frauke Melchior, Stephan Herzig.

  Accumulation of excess nutrients hampers proper liver function and is linked to nonalcoholic fatty liver disease (NAFLD) in obesity. However, the signals responsible for an impaired adaptation of hepatocytes to obesogenic dietary cues remain still largely unknown. Post-translational modification by the small ubiquitin-like modifier (SUMO) allows for a dynamic regulation of numerous processes including transcriptional reprogramming. We demonstrate that specific SUMOylation of transcription factor Prox1 represents a nutrient-sensitive determinant of hepatic fasting metabolism. Prox1 is highly SUMOylated on lysine 556 in the liver of ad libitum and refed mice, while this modification is abolished upon fasting. In the context of diet-induced obesity, Prox1 SUMOylation becomes less sensitive to fasting cues. The hepatocyte-selective knock-in of a SUMOylation-deficient Prox1 mutant into mice fed a high-fat/high-fructose diet leads to a reduction of systemic cholesterol levels, associated with the induction of liver bile acid detoxifying pathways during fasting. The generation of tools to maintain the nutrient-sensitive SUMO-switch on Prox1 may thus contribute to the development of "fasting-based" approaches for the preservation of metabolic health.

Keywords:  Bile acids; Cholesterol; Liver; Prox1; SUMOylation

DOI:  https://doi.org/10.15252/embr.202255981
J Cell Physiol. 2023 Aug 11.

Transformed cells maintain survival by downregulating autophagy at a high cell confluency.

Hye-Gyo Kim, Myeong-Han Ro, Sung-Hee Hwang, Michael Lee.

  Autophagy plays a dual role in tumorigenesis by functioning as both a tumor suppressor and promoter, depending on the stage of tumorigenesis. However, it is still unclear at what stage the role of autophagy changes during tumorigenesis. Herein, we investigated the differences in the basal levels and roles of autophagy in five cell lines at different stages of cell transformation. We found that cell lines at higher transformation stages were more sensitive to the autophagy inhibitors, suggesting that autophagy plays a more important role as the transformation progresses. Our ptfLC3 imaging analysis to measure Atg5/LC3-dependent autophagy showed increased autophagic flux in transformed cells compared to untransformed cells. However, the Cyto-ID analysis, which measures Atg5-dependent and -independent autophagic flux, showed high levels of autophagosome formation not only in the transformed cells but also in the initiated cell and Atg5 KO cell line. These results indicate that Atg5-independent autophagy may be more critical in initiated and transformed cell lines than in untransformed cells. Specially, we observed that transformed cells maintained relatively high basal autophagy levels under rapidly proliferating conditions but exhibited much lower basal autophagy levels at high confluency; however, autophagic flux was not significantly reduced in untransformed cells, even at high confluency. In addition, when continuously cultured for 3 weeks without passage, senescent cells were significantly less sensitive to autophagy inhibition than their actively proliferating counterparts. These results imply that once a cell has switched from a proliferative state to a senescent state, the inhibition of autophagy has only a minimal effect. Taken together, our results suggest that autophagy can be differentially regulated in cells at different stages of tumorigenesis under stressful conditions.

Keywords:  Atg5; LC3; autophagy; cell transformation; downregulation; senescence

DOI:  https://doi.org/10.1002/jcp.31098
J Pathol. 2023 Aug 07.

The clinical terrain of immunotherapies in heterogeneous pancreatic cancer: unravelling challenges and opportunities.

Melanie Herpels, Jun Ishihara, Anguraj Sadanandam.

  Pancreatic ductal adenocarcinoma (PDAC) is the most common and aggressive type of pancreatic cancer and has abysmal survival rates. In the past two decades, immunotherapeutic agents with success in other cancer types have gradually been trialled against PDACs at different stages of cancer progression, either as a monotherapy or in combination with chemotherapy. Unfortunately, to this day, chemotherapy still prolongs the survival rates the most and is prescribed in clinics despite the severe side effects in other cancer types. The low success rates of immunotherapy against PDAC have been attributed most frequently to its complex and multi-faceted tumour microenvironment (TME) and low mutational burden. In this review, we give a comprehensive overview of the immunotherapies tested in PDAC clinical trials thus far, their limitations, and potential explanations for their failure. We also discuss the existing classification of heterogenous PDACs into cancer, cancer-associated fibroblast, and immune subtypes and their potential opportunity in patient selection as a form of personalisation of PDAC immunotherapy. © 2023 The Pathological Society of Great Britain and Ireland.

Keywords:  cancer-associated fibroblasts; clinical trials; immune checkpoint inhibitors; immunotherapy; immunotherapy failure; pancreatic cancer; subtypes; tumour microenvironment

DOI:  https://doi.org/10.1002/path.6171
Biochem Biophys Res Commun. 2023 Aug 04. pii: S0006-291X(23)00942-7. [Epub ahead of print]677 63-69

Autophagy modulates the stability of Wee1 and cell cycle G2/M transition.

Biwei Han, Yajing Chen, Chen Song, Yali Chen, Yong Chen, Daniel Ferguson, Yunzhi Yang, Anyuan He.

The mammalian cell cycle is divided into four sequential phases, namely G1 (Gap 1), S (synthesis), G2 (Gap 2), and M (mitosis). Wee1, whose turnover is tightly and finely regulated, is a well-known kinase serving as a gatekeeper for the G2/M transition. However, the mechanism underlying the turnover of Wee1 is not fully understood. Autophagy, a highly conserved cellular process, maintains cellular homeostasis by eliminating intracellular aggregations, damaged organelles, and individual proteins. In the present study, we found autophagy deficiency in mouse liver caused G2/M arrest in two mouse models, namely Fip200 and Atg7 liver-specific knockout mice. To uncover the link between autophagy deficiency and G2/M transition, we combined transcriptomic and proteomic analysis for liver samples from control and Atg7 liver-specific knockout mice. The data suggest that the inhibition of autophagy increases the protein level of Wee1 without any alteration of its mRNA abundance. Serum starvation, an autophagy stimulus, downregulates the protein level of Wee1 in vitro. In addition, the half-life of Wee1 is extended by the addition of chloroquine, an autophagy inhibitor. LC3, a central autophagic protein functioning in autophagy substrate selection and autophagosome biogenesis, interacts with Wee1 as assessed by co-immunoprecipitation assay. Furthermore, overexpression of Wee1 leads to G2/M arrest both in vitro and in vivo. Collectively, our data indicate that autophagy could degrade Wee1-a gatekeeper of the G2/M transition, whereas the inhibition of autophagy leads to the accumulation of Wee1 and causes G2/M arrest in mouse liver.

DOI: https://doi.org/10.1016/j.bbrc.2023.08.010
Nutrients. 2023 Jul 30. pii: 3391. [Epub ahead of print]15(15):

Relevance of Dietary Supplement Use in Gastrointestinal-Cancer-Associated Cachexia.

Saunjoo L Yoon, Oliver Grundmann.

  Cancer cachexia is a multi-organ syndrome with unintentional weight loss, sarcopenia, and systemic inflammation. Gastrointestinal (GI) cancer patients are more susceptible to cachexia development due to impaired nutrient absorption and digestion. Given the widespread availability and relatively low cost of dietary supplements, we examined the evidence and effects of fish oil (omega-3 fatty acids), melatonin, probiotics, and green tea for managing symptoms of GI cancer cachexia. A literature review of four specific supplements was conducted using PubMed, Google Scholar, and CINAHL without a date restriction. Of 4621 available literature references, 26 articles were eligible for review. Fish oil decreased C-reactive protein and maintained CD4+ cell count, while melatonin indicated inconsistent findings on managing cachexia, but was well-tolerated. Probiotics decreased serum pro-inflammatory biomarkers and increased the tolerability of chemotherapy by reducing side effects. Green tea preparations and extracts showed a decreased risk of developing various cancers and did not impact tumor growth, survival, or adverse effects. Among these four supplements, probiotics are most promising for further research in preventing systemic inflammation and maintaining adequate absorption of nutrients to prevent the progression of cancer cachexia. Supplements may benefit treatment outcomes in cancer cachexia without side effects while supporting nutritional and therapeutic needs.

Keywords:  cancer cachexia; dietary supplements; gastrointestinal cancer; nutritional supplements

DOI:  https://doi.org/10.3390/nu15153391
Commun Biol. 2023 08 09. 6(1): 825

The pharmacoepigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity.

Alexander Joschua Ohnmacht, Anantharamanan Rajamani, Göksu Avar, Ginte Kutkaite, Emanuel Gonçalves, Dieter Saur, Michael Patrick Menden.

Aberrant DNA methylation accompanies genetic alterations during oncogenesis and tumour homeostasis and contributes to the transcriptional deregulation of key signalling pathways in cancer. Despite increasing efforts in DNA methylation profiling of cancer patients, there is still a lack of epigenetic biomarkers to predict treatment efficacy. To address this, we analyse 721 cancer cell lines across 22 cancer types treated with 453 anti-cancer compounds. We systematically detect the predictive component of DNA methylation in the context of transcriptional and mutational patterns, i.e., in total 19 DNA methylation biomarkers across 17 drugs and five cancer types. DNA methylation constitutes drug sensitivity biomarkers by mediating the expression of proximal genes, thereby enhancing biological signals across multi-omics data modalities. Our method reproduces anticipated associations, and in addition, we find that the NEK9 promoter hypermethylation may confer sensitivity to the NEDD8-activating enzyme (NAE) inhibitor pevonedistat in melanoma through downregulation of NEK9. In summary, we envision that epigenomics will refine existing patient stratification, thus empowering the next generation of precision oncology.

DOI: https://doi.org/10.1038/s42003-023-05198-y
Cancer Res. 2023 Aug 07. pii: CAN-22-3707. [Epub ahead of print]

Breast cancer-secreted factors promote lung metastasis by signaling systemically to induce a fibrotic pre-metastatic niche.

Noam Cohen, Dhanashree Mundhe, Sarah K Deasy, Omer Adler, Nour Ershaid, Tamar Shami, Oshrat Levi-Galibov, Rina Wassermann, Ruth Scherz-Shouval, Neta Erez.

Metastatic cancer is largely incurable and is the main cause of cancer-related deaths. The metastatic microenvironment facilitates formation of metastases. Cancer-associated fibroblasts (CAFs) are crucial players in generating a hospitable metastatic niche by mediating an inflammatory microenvironment. Fibroblasts also play a central role in modifying the architecture and stiffness of the extracellular matrix (ECM). Resolving the early changes in the metastatic niche could help identify approaches to inhibit metastatic progression. Here, we demonstrate in mouse models of spontaneous breast cancer pulmonary metastasis that fibrotic changes and rewiring of lung fibroblasts occurred at pre-metastatic stages, suggesting systemic influence by the primary tumor. Activin A (ActA), a TGFβ superfamily member, was secreted from breast tumors and its levels in the blood were highly elevated in tumor-bearing mice. ActA upregulated the expression of pro-fibrotic factors in lung fibroblasts, leading to enhanced collagen deposition in the lung pre-metastatic niche. ActA signaling was functionally important for lung metastasis, as genetic targeting of ActA in breast cancer cells significantly attenuated lung metastasis and improved survival. Moreover, high levels of ActA in human breast cancer patients were associated with lung metastatic relapse and poor survival. This study uncovers a novel mechanism by which breast cancer cells systemically rewire the stromal microenvironment in the metastatic niche to facilitate pulmonary metastasis.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-3707
J Exp Clin Cancer Res. 2023 Aug 09. 42(1): 201

Fibronectin fragments generated by pancreatic trypsin act as endogenous inhibitors of pancreatic tumor growth.

Andrea Resovi, Perla Persichitti, Laura Brunelli, Lucia Minoli, Patrizia Borsotti, Giulia Garattini, Matteo Tironi, Erica Dugnani, Miriam Redegalli, Giulia De Simone, Roberta Pastorelli, Maria Rosa Bani, Lorenzo Piemonti, Deane F Mosher, Raffaella Giavazzi, Giulia Taraboletti, Dorina Belotti.

   BACKGROUND: The pancreatic microenvironment has a defensive role against cancer but it can acquire tumor-promoting properties triggered by multiple mechanisms including alterations in the equilibrium between proteases and their inhibitors. The identification of proteolytic events, targets and pathways would set the basis for the design of new therapeutic approaches.
METHODS AND RESULTS: Here we demonstrate that spheroids isolated from human and murine healthy pancreas and co-transplanted orthotopically with pancreatic ductal adenocarcinoma (PDAC) in mouse pancreas inhibited tumor growth. The effect was mediated by trypsin-generated fibronectin (FN) fragments released by pancreatic spheroids. Tumor inhibition was observed also in a model of acute pancreatitis associated with trypsin activation. Mass spectrometry proteomic analysis of fragments and mAb against different FN epitopes identified the FN type III domain as responsible for the activity. By inhibiting integrin α5β1, FAK and FGFR1 signaling, the fragments induced tumor cell detachment and reduced cell proliferation. Consistent with the mutual relationship between the two pathways, FGF2 restored both FGFR1 and FAK signaling and promoted PDAC cell adhesion and proliferation. FAK and FGFR inhibitors additively inhibited PDAC growth in vitro and in orthotopic in vivo models.
CONCLUSIONS: This study identifies a novel role for pancreatic trypsin and fibronectin cleavage as a mechanism of protection against cancer by the pancreatic microenvironment. The finding of a FAK-FGFR cross-talk in PDAC support the combination of FAK and FGFR inhibitors for PDAC treatment to emulate the protective effect of the normal pancreas against cancer.

Keywords:  FAK; FGFR; Fibronectin; PDAC; Trypsin

DOI:  https://doi.org/10.1186/s13046-023-02778-y
bioRxiv. 2023 Jul 25. pii: 2023.07.24.550444. [Epub ahead of print]

Mechano-dependent sorbitol accumulation supports biomolecular condensate.

Stephanie Torrino, William M Oldham, Andrés R Tejedor, Ignacio S Burgos, Nesrine Rachedi, Kéren Fraissard, Caroline Chauvet, Chaima Sbai, Brendan P O'Hara, Sophie Abélanet, Frederic Brau, Stephan Clavel, Rosana Collepardo-Guevara, Jorge R Espinosa, Issam Ben-Sahra, Thomas Bertero.

Biomolecular condensates regulate a wide range of cellular functions from signaling to RNA metabolism 1, 2 , yet, the physiologic conditions regulating their formation remain largely unexplored. Biomolecular condensate assembly is tightly regulated by the intracellular environment. Changes in the chemical or physical conditions inside cells can stimulate or inhibit condensate formation 3-5 . However, whether and how the external environment of cells can also regulate biomolecular condensation remain poorly understood. Increasing our understanding of these mechanisms is paramount as failure to control condensate formation and dynamics can lead to many diseases 6, 7 . Here, we provide evidence that matrix stiffening promotes biomolecular condensation in vivo . We demonstrate that the extracellular matrix links mechanical cues with the control of glucose metabolism to sorbitol. In turn, sorbitol acts as a natural crowding agent to promote biomolecular condensation. Using in silico simulations and in vitro assays, we establish that variations in the physiological range of sorbitol, but not glucose, concentrations, are sufficient to regulate biomolecular condensates. Accordingly, pharmacologic and genetic manipulation of intracellular sorbitol concentration modulates biomolecular condensates in breast cancer - a mechano-dependent disease. We propose that sorbitol is a mechanosensitive metabolite enabling protein condensation to control mechano-regulated cellular functions. Altogether, we uncover molecular driving forces underlying protein phase transition and provide critical insights to understand the biological function and dysfunction of protein phase separation.

DOI: https://doi.org/10.1101/2023.07.24.550444
Cell Metab. 2023 Aug 08. pii: S1550-4131(23)00265-6. [Epub ahead of print]35(8): 1283-1303

Emerging therapies in cancer metabolism.

Yi Xiao, Tian-Jian Yu, Ying Xu, Rui Ding, Yi-Ping Wang, Yi-Zhou Jiang, Zhi-Ming Shao.

Metabolic reprogramming in cancer is not only a biological hallmark but also reveals treatment vulnerabilities. Numerous metabolic molecules have shown promise as treatment targets to impede tumor progression in preclinical studies, with some advancing to clinical trials. However, the intricacy and adaptability of metabolic networks hinder the effectiveness of metabolic therapies. This review summarizes the metabolic targets for cancer treatment and provides an overview of the current status of clinical trials targeting cancer metabolism. Additionally, we decipher crucial factors that limit the efficacy of metabolism-based therapies and propose future directions. With advances in integrating multi-omics, single-cell, and spatial technologies, as well as the ability to track metabolic adaptation more precisely and dynamically, clinicians can personalize metabolic therapies for improved cancer treatment.

DOI: https://doi.org/10.1016/j.cmet.2023.07.006
Cold Spring Harb Perspect Med. 2023 Aug 08. pii: a041530. [Epub ahead of print]

Cancer Metabolism Historical Perspectives: A Chronicle of Controversies and Consensus.

Chi V Dang.

A century ago, Otto Warburg's work sparked the field of cancer metabolism, which has since taken a tortuous path. As evidence accumulated over the decades, consensus views of causes of cancer emerged, whereby genetic and epigenetic oncogenic drivers promoted immune evasion and induced new blood vessels and neoplastic metabolism to support tumor growth. Neoplastic cells abandon social cues of intercellular cooperation, escape tissue confinement, metastasize, and ultimately kill the host. Herein, key milestones in the study of cancer metabolism are chronicled with an emphasis on carbohydrate metabolism. The field began with a cancer cell-autonomous view that has been refined by a richer understanding of solid cancers as growing, immune-suppressive, complex organs comprising different cell types that are nourished by a variety of nutrients and variable amounts of oxygen through abnormal neovasculatures. Based on foundational historical studies, our current understanding of cancer metabolism offers a hopeful outlook for targeting metabolism to enhance cancer therapy.

DOI: https://doi.org/10.1101/cshperspect.a041530
Cold Spring Harb Perspect Biol. 2023 Aug 08. pii: a041395. [Epub ahead of print]

The Membrane Phase Transition Gives Rise to Responsive Plasma Membrane Structure and Function.

Sarah A Shelby, Sarah L Veatch.

Several groups have recently reported evidence for the emergence of domains in cell plasma membranes when membrane proteins are organized by ligand binding or assembly of membrane proximal scaffolds. These domains recruit and retain components that favor the liquid-ordered phase, adding to a decades-old literature interrogating the contribution of membrane phase separation in plasma membrane organization and function. Here we propose that both past and present observations are consistent with a model in which membranes have a high compositional susceptibility, arising from their thermodynamic state in a single phase that is close to a miscibility phase transition. This rigorous framework naturally allows for both transient structure in the form of composition fluctuations and long-lived structure in the form of induced domains. In this way, the biological tuning of plasma membrane composition enables a responsive compositional landscape that facilitates and augments cellular biochemistry vital to plasma membrane functions.

DOI: https://doi.org/10.1101/cshperspect.a041395
Cell. 2023 Aug 01. pii: S0092-8674(23)00795-X. [Epub ahead of print]

Humanized mouse liver reveals endothelial control of essential hepatic metabolic functions.

AlcHepNet

  Hepatocytes, the major metabolic hub of the body, execute functions that are human-specific, altered in human disease, and currently thought to be regulated through endocrine and cell-autonomous mechanisms. Here, we show that key metabolic functions of human hepatocytes are controlled by non-parenchymal cells (NPCs) in their microenvironment. We developed mice bearing human hepatic tissue composed of human hepatocytes and NPCs, including human immune, endothelial, and stellate cells. Humanized livers reproduce human liver architecture, perform vital human-specific metabolic/homeostatic processes, and model human pathologies, including fibrosis and non-alcoholic fatty liver disease (NAFLD). Leveraging species mismatch and lipidomics, we demonstrate that human NPCs control metabolic functions of human hepatocytes in a paracrine manner. Mechanistically, we uncover a species-specific interaction whereby WNT2 secreted by sinusoidal endothelial cells controls cholesterol uptake and bile acid conjugation in hepatocytes through receptor FZD5. These results reveal the essential microenvironmental regulation of hepatic metabolism and its human-specific aspects.

Keywords:  FZD5; WNT2; bile acid conjugation; cholesterol; fibrosis; humanized liver; lipidomics; liver sinusoidal endothelial cells; non-alcoholic fatty liver disease; stellate cells

DOI:  https://doi.org/10.1016/j.cell.2023.07.017
Cell. 2023 Aug 03. pii: S0092-8674(23)00742-0. [Epub ahead of print]

Distinct molecular profiles of skull bone marrow in health and neurological disorders.

Zeynep Ilgin Kolabas, Louis B Kuemmerle, Robert Perneczky, Benjamin Förstera, Selin Ulukaya, Mayar Ali, Saketh Kapoor, Laura M Bartos, Maren Büttner, Ozum Sehnaz Caliskan, Zhouyi Rong, Hongcheng Mai, Luciano Höher, Denise Jeridi, Muge Molbay, Igor Khalin, Ioannis K Deligiannis, Moritz Negwer, Kenny Roberts, Alba Simats, Olga Carofiglio, Mihail I Todorov, Izabela Horvath, Furkan Ozturk, Selina Hummel, Gloria Biechele, Artem Zatcepin, Marcus Unterrainer, Johannes Gnörich, Jay Roodselaar, Joshua Shrouder, Pardis Khosravani, Benjamin Tast, Lisa Richter, Laura Díaz-Marugán, Doris Kaltenecker, Laurin Lux, Ying Chen, Shan Zhao, Boris-Stephan Rauchmann, Michael Sterr, Ines Kunze, Karen Stanic, Vanessa W Y Kan, Simon Besson-Girard, Sabrina Katzdobler, Carla Palleis, Julia Schädler, Johannes C Paetzold, Sabine Liebscher, Anja E Hauser, Ozgun Gokce, Heiko Lickert, Hanno Steinke, Corinne Benakis, Christian Braun, Celia P Martinez-Jimenez, Katharina Buerger, Nathalie L Albert, Günter Höglinger, Johannes Levin, Christian Haass, Anna Kopczak, Martin Dichgans, Joachim Havla, Tania Kümpfel, Martin Kerschensteiner, Martina Schifferer, Mikael Simons, Arthur Liesz, Natalie Krahmer, Omer A Bayraktar, Nicolai Franzmeier, Nikolaus Plesnila, Suheda Erener, Victor G Puelles, Claire Delbridge, Harsharan Singh Bhatia, Farida Hellal, Markus Elsner, Ingo Bechmann, Benjamin Ondruschka, Matthias Brendel, Fabian J Theis, Ali Erturk.

  The bone marrow in the skull is important for shaping immune responses in the brain and meninges, but its molecular makeup among bones and relevance in human diseases remain unclear. Here, we show that the mouse skull has the most distinct transcriptomic profile compared with other bones in states of health and injury, characterized by a late-stage neutrophil phenotype. In humans, proteome analysis reveals that the skull marrow is the most distinct, with differentially expressed neutrophil-related pathways and a unique synaptic protein signature. 3D imaging demonstrates the structural and cellular details of human skull-meninges connections (SMCs) compared with veins. Last, using translocator protein positron emission tomography (TSPO-PET) imaging, we show that the skull bone marrow reflects inflammatory brain responses with a disease-specific spatial distribution in patients with various neurological disorders. The unique molecular profile and anatomical and functional connections of the skull show its potential as a site for diagnosing, monitoring, and treating brain diseases.

Keywords:  3D-imaging; DISCO clearing; PET imaging; immune cell trafficking; neuroinflammation; neurological disorders; non-invasive monitoring; proteomics; scRNA-seq; skull-brain connection

DOI:  https://doi.org/10.1016/j.cell.2023.07.009
Elife. 2023 Aug 07. pii: e83588. [Epub ahead of print]12

Force propagation between epithelial cells depends on active coupling and mechano-structural polarization.

Artur Ruppel, Dennis Wörthmüller, Vladimir Misiak, Manasi Kelkar, Irène Wang, Philippe Moreau, Adrien Méry, Jean Révilloud, Guillaume Charras, Giovanni Cappello, Thomas Boudou, Ulrich Sebastian Schwarz, Martial Balland.

  Cell-generated forces play a major role in coordinating the large-scale behavior of cell assemblies, in particular during development, wound healing and cancer. Mechanical signals propagate faster than biochemical signals, but can have similar effects, especially in epithelial tissues with strong cell-cell adhesion. However, a quantitative description of the transmission chain from force generation in a sender cell, force propagation across cell-cell boundaries, and the concomitant response of receiver cells is missing. For a quantitative analysis of this important situation, here we propose a minimal model system of two epithelial cells on an H-pattern ('cell doublet'). After optogenetically activating RhoA, a major regulator of cell contractility, in the sender cell, we measure the mechanical response of the receiver cell by traction force and monolayer stress microscopies. In general, we find that the receiver cells shows an active response so that the cell doublet forms a coherent unit. However, force propagation and response of the receiver cell also strongly depends on the mechano-structural polarization in the cell assembly, which is controlled by cell-matrix adhesion to the adhesive micropattern. We find that the response of the receiver cell is stronger when the mechano-structural polarization axis is oriented perpendicular to the direction of force propagation, reminiscent of the Poisson effect in passive materials. We finally show that the same effects are at work in small tissues. Our work demonstrates that cellular organization and active mechanical response of a tissue is key to maintain signal strength and leads to the emergence of elasticity, which means that signals are not dissipated like in a viscous system, but can propagate over large distances.

Keywords:  cell biology; physics of living systems

DOI:  https://doi.org/10.7554/eLife.83588
Cancer Res. 2023 Aug 09. pii: CAN-22-3210. [Epub ahead of print]

Allosteric regulation of switch-II domain controls KRAS oncogenicity.

Moon Hee Yang, Timothy H Tran, Bethany Hunt, Rebecca Agnor, Christian W Johnson, Bing Shui, Timothy J Waybright, Jonathan A Nowak, Andrew G Stephen, Dhirendra K Simanshu, Kevin M Haigis.

RAS proteins are GTPases that regulate a wide range of cellular processes. RAS activity is dependent on its nucleotide-binding status, which is modulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). KRAS can be acetylated at lysine 104 (K104), and an acetylation-mimetic mutation of K104 to glutamine (K104Q) attenuates the in vitro transforming capacity of oncogenic KRAS by interrupting GEF induced nucleotide exchange. To assess the effect of this mutation in vivo, we used CRISPR-Cas9 to generate mouse models carrying the K104Q point mutation in wild-type and conditional KrasLSL-G12D alleles. Homozygous animals for K104Q were viable, fertile, and arose at the expected Mendelian frequency, indicating that K104Q is not a complete loss of function mutation. Consistent with our previous findings from in vitro studies, however, the oncogenic activity of KRASG12D was significantly attenuated by mutation at K104. Biochemical and structural analysis indicated that the G12D and K104Q mutations cooperate to suppress GEF-mediated nucleotide exchange, explaining the preferential effect of K104Q on oncogenic KRAS. Furthermore, K104 functioned in an allosteric network with M72, R73 and G75 on the α2 helix of the switch-II region. Intriguingly, point mutation of glutamine 75 to alanine (G75A) showed a strong negative regulatory effect on KRASG12D. These data demonstrate that lysine at position 104 is critical for the full oncogenic activity of mutant KRAS and suggest that modulating the sites in its allosteric network may provide a unique therapeutic approach in cancers expressing mutant KRAS.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-3210
J Pathol. 2023 Aug 09.

DNA methylation-associated allelic inactivation regulates Keratin 19 gene expression during pancreatic development and carcinogenesis.

Jana Krüger, Anja Fischer, Markus Breunig, Chantal Allgöwer, Lucas Schulte, Jessica Merkle, Medhanie A Mulaw, Nnamdi Okeke, Michael K Melzer, Clara Morgenstern, Ninel Azoitei, Thomas Seufferlein, Thomas Fe Barth, Reiner Siebert, Meike Hohwieler, Alexander Kleger.

  Within the pancreas, Keratin 19 (KRT19) labels the ductal lineage and is a determinant of pancreatic ductal adenocarcinoma (PDAC). To investigate KRT19 expression dynamics, we developed a human pluripotent stem cell (PSC)-based KRT19-mCherry reporter system in different genetic backgrounds to monitor KRT19 expression from its endogenous gene locus. A differentiation protocol to generate mature pancreatic duct-like organoids was applied. While KRT19/mCherry expression became evident at the early endoderm stage, mCherry signal was present in nearly all cells at the pancreatic endoderm (PE) and pancreatic progenitor (PP) stages. Interestingly, despite homogenous KRT19 expression, mCherry positivity dropped to 50% after ductal maturation, indicating a permanent switch from biallelic to monoallelic expression. DNA methylation profiling separated the distinct differentiation intermediates, with site-specific DNA methylation patterns occurring at the KRT19 locus during ductal maturation. Accordingly, the monoallelic switch was partially reverted upon treatment with a DNA-methyltransferase inhibitor. In human PDAC cohorts, high KRT19 levels correlate with low locus methylation and decreased survival. At the same time, activation of oncogenic KRASG12D signalling in our reporter system reversed monoallelic back to biallelic KRT19 expression in pancreatic duct-like organoids. Allelic reactivation was also detected in single-cell transcriptomes of human PDACs, which further revealed a positive correlation between KRT19 and KRAS expression. Accordingly, KRAS mutant PDACs had higher KRT19 mRNA but lower KRT19 gene locus DNA methylation than wildtype counterparts. KRT19 protein was additionally detected in plasma of PDAC patients, with higher concentrations correlating with shorter progression-free survival in gemcitabine/nabPaclitaxel-treated and opposing trends in FOLFIRINOX-treated patients. Apart from being an important pancreatic ductal lineage marker, KRT19 appears tightly controlled via a switch from biallelic to monoallelic expression during ductal lineage entry and is aberrantly expressed after oncogenic KRASG12D expression, indicating a role in PDAC development and malignancy. Soluble KRT19 might serve as a relevant biomarker to stratify treatment. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Keywords:  DNA-methylation; KRT19; biallelic; gene expression; in vitro differentiation; monoallelic; pancreatic cancer; pancreatic development; pancreatic organoids; pluripotent stem cells

DOI:  https://doi.org/10.1002/path.6156
Cell. 2023 Aug 02. pii: S0092-8674(23)00783-3. [Epub ahead of print]

A membrane-associated MHC-I inhibitory axis for cancer immune evasion.

Xufeng Chen, Qiao Lu, Hua Zhou, Jia Liu, Bettina Nadorp, Audrey Lasry, Zhengxi Sun, Baoling Lai, Gergely Rona, Jiangyan Zhang, Michael Cammer, Kun Wang, Wafa Al-Santli, Zoe Ciantra, Qianjin Guo, Jia You, Debrup Sengupta, Ahmad Boukhris, Hongbing Zhang, Cheng Liu, Peter Cresswell, Patricia L M Dahia, Michele Pagano, Iannis Aifantis, Jun Wang.

  Immune-checkpoint blockade has revolutionized cancer treatment, but some cancers, such as acute myeloid leukemia (AML), do not respond or develop resistance. A potential mode of resistance is immune evasion of T cell immunity involving aberrant major histocompatibility complex class I (MHC-I) antigen presentation (AP). To map such mechanisms of resistance, we identified key MHC-I regulators using specific peptide-MHC-I-guided CRISPR-Cas9 screens in AML. The top-ranked negative regulators were surface protein sushi domain containing 6 (SUSD6), transmembrane protein 127 (TMEM127), and the E3 ubiquitin ligase WWP2. SUSD6 is abundantly expressed in AML and multiple solid cancers, and its ablation enhanced MHC-I AP and reduced tumor growth in a CD8+ T cell-dependent manner. Mechanistically, SUSD6 forms a trimolecular complex with TMEM127 and MHC-I, which recruits WWP2 for MHC-I ubiquitination and lysosomal degradation. Together with the SUSD6/TMEM127/WWP2 gene signature, which negatively correlates with cancer survival, our findings define a membrane-associated MHC-I inhibitory axis as a potential therapeutic target for both leukemia and solid cancers.

Keywords:  MHC-I; SUSD6; T cell; TMEM127; WWP2; antigen presentation; cancer; immune evasion; lysosomal degradation; ubiquitination

DOI:  https://doi.org/10.1016/j.cell.2023.07.016
Nat Protoc. 2023 Aug 09.

In vivo fluorescent labeling and tracking of extracellular matrix.

Adrian Fischer, Donovan Correa-Gallegos, Juliane Wannemacher, Simon Christ, Hans-Günther Machens, Yuval Rinkevich.

Connective tissues are essential building blocks for organ development, repair and regeneration. However, we are at the early stages of understanding connective tissue dynamics. Here, we detail a method that enables in vivo fate mapping of organ extracellular matrix (ECM) by taking advantage of a crosslinking chemical reaction between amine groups and N-hydroxysuccinimide esters. This methodology enables robust labeling of ECM proteins, which complement previous affinity-based single-protein methods. This protocol is intended for entry-level scientists and the labeling step takes between 5 and 10 min. ECM 'tagging' with fluorophores using N-hydroxysuccinimide esters enables visualization of ECM spatial modifications and is particularly useful to study connective tissue dynamics in organ fibrosis, tumor stroma formation, wound healing and regeneration. This in vivo chemical fate mapping methodology is highly versatile, regardless of the tissue/organ system, and complements cellular fate-mapping techniques. Furthermore, as the basic chemistry of proteins is highly conserved between species, this method is also suitable for cross-species comparative studies of ECM dynamics.

DOI: https://doi.org/10.1038/s41596-023-00867-y
Front Bioinform. 2023 ;3 1159381

A review on deep learning applications in highly multiplexed tissue imaging data analysis.

Mohammed Zidane, Ahmad Makky, Matthias Bruhns, Alexander Rochwarger, Sepideh Babaei, Manfred Claassen, Christian M Schürch.

  Since its introduction into the field of oncology, deep learning (DL) has impacted clinical discoveries and biomarker predictions. DL-driven discoveries and predictions in oncology are based on a variety of biological data such as genomics, proteomics, and imaging data. DL-based computational frameworks can predict genetic variant effects on gene expression, as well as protein structures based on amino acid sequences. Furthermore, DL algorithms can capture valuable mechanistic biological information from several spatial "omics" technologies, such as spatial transcriptomics and spatial proteomics. Here, we review the impact that the combination of artificial intelligence (AI) with spatial omics technologies has had on oncology, focusing on DL and its applications in biomedical image analysis, encompassing cell segmentation, cell phenotype identification, cancer prognostication, and therapy prediction. We highlight the advantages of using highly multiplexed images (spatial proteomics data) compared to single-stained, conventional histopathological ("simple") images, as the former can provide deep mechanistic insights that cannot be obtained by the latter, even with the aid of explainable AI. Furthermore, we provide the reader with the advantages/disadvantages of DL-based pipelines used in preprocessing highly multiplexed images (cell segmentation, cell type annotation). Therefore, this review also guides the reader to choose the DL-based pipeline that best fits their data. In conclusion, DL continues to be established as an essential tool in discovering novel biological mechanisms when combined with technologies such as highly multiplexed tissue imaging data. In balance with conventional medical data, its role in clinical routine will become more important, supporting diagnosis and prognosis in oncology, enhancing clinical decision-making, and improving the quality of care for patients. Since its introduction into the field of oncology, deep learning (DL) has impacted clinical discoveries and biomarker predictions. DL-driven discoveries and predictions in oncology are based on a variety of biological data such as genomics, proteomics, and imaging data. DL-based computational frameworks can predict genetic variant effects on gene expression, as well as protein structures based on amino acid sequences. Furthermore, DL algorithms can capture valuable mechanistic biological information from several spatial "omics" technologies, such as spatial transcriptomics and spatial proteomics. Here, we review the impact that the combination of artificial intelligence (AI) with spatial omics technologies has had on oncology, focusing on DL and its applications in biomedical image analysis, encompassing cell segmentation, cell phenotype identification, cancer prognostication, and therapy prediction. We highlight the advantages of using highly multiplexed images (spatial proteomics data) compared to single-stained, conventional histopathological ("simple") images, as the former can provide deep mechanistic insights that cannot be obtained by the latter, even with the aid of explainable AI. Furthermore, we provide the reader with the advantages/disadvantages of the DL-based pipelines used in preprocessing the highly multiplexed images (cell segmentation, cell type annotation). Therefore, this review also guides the reader to choose the DL-based pipeline that best fits their data. In conclusion, DL continues to be established as an essential tool in discovering novel biological mechanisms when combined with technologies such as highly multiplexed tissue imaging data. In balance with conventional medical data, its role in clinical routine will become more important, supporting diagnosis and prognosis in oncology, enhancing clinical decision-making, and improving the quality of care for patients.

Keywords:  artificial intelligence; biomarker; cancer; deep learning; highly multiplexed tissue imaging; prediction; review; spatial transcriptomics

DOI:  https://doi.org/10.3389/fbinf.2023.1159381
Recent Pat Anticancer Drug Discov. 2023 Jun 26.

The Causal Effects of Cholelithiasis on Acute Pancreatitis and Pancreatic Cancer: A Large Sample Size Mendelian Randomization Analysis.

Moshi Rao, Xiaoshun Ai, Zijian Huang.

   BACKGROUND: The aim of two-sample Mendelian randomization (MR) with a large sample size was to explore the causal cholelithiasis impact on acute pancreatitis and pancreatic cancer.
METHODS: We performed the two-sample MR analysis with two models. Publicly available summary- level information for cholelithiasis was acquired from the Genome-Wide Summary Association Studies (GWAS) of FinnGen Biobank. The inverse variance weighted (IVW) method was the main method to obtain the MR estimates. Other methods were also used as supplementary methods, including MR-Egger, maximum likelihood, MR-Robust Adjusted Profile Score (MR-RAPS), weighted median, penalised weighted median method, and Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO) method.
RESULTS: After the selection of genetic instrumental variables (IVs), 11 single nucleotide polymorphisms (SNPs) (Model 1) and 22 SNPs (Model 2) were used to explore the effect of cholelithiasis on acute pancreatitis, and 10 SNPs (Model 1) and 24 SNPs (Model 2) on pancreatic cancer. The findings obtained by the fixed-effect IVW method with both Model 1 and Model 2 showed that genetically predicted cholelithiasis was significantly related to the elevated acute pancreatitis risk (Model 1: OR: 1.001, 95% CI: 1.000-1.002, p <0.001; Model 2: OR: 1.001, 95% CI: 1.000-1.002, p <0.001). Moreover, cholelithiasis would also raise the pancreatic cancer risk (Model 1: OR: 1.676, 95% CI: 1.228-2.288, p = 0.001; Model 2: OR: 1.432, 95% CI: 1.116-1.839, p = 0.005).
CONCLUSION: Genetically predicted cholelithiasis was significantly related to the elevated risk of acute pancreatitis and pancreatic cancer. More attention should be paid to patients with cholelithiasis for the primary prevention of pancreatic-related diseases.

Keywords:  Cholelithiasis; IVW method.; acute pancreatitis; large sample size; mendelian randomization; pancreatic cancer

DOI:  https://doi.org/10.2174/1574892818666230609121409
Nat Immunol. 2023 Aug 10.

Fibrosis induced by resident macrophages has divergent roles in pancreas inflammatory injury and PDAC.

John M Baer, Chong Zuo, Liang-I Kang, Angela Alarcon de la Lastra, Nicholas C Borcherding, Brett L Knolhoff, Savannah J Bogner, Yu Zhu, Liping Yang, Jennifer Laurent, Mark A Lewis, Nan Zhang, Ki-Wook Kim, Ryan C Fields, Wayne M Yokoyama, Jason C Mills, Li Ding, Gwendalyn J Randolph, David G DeNardo.

Tissue-resident macrophages (TRMs) are long-lived cells that maintain locally and can be phenotypically distinct from monocyte-derived macrophages. Whether TRMs and monocyte-derived macrophages have district roles under differing pathologies is not understood. Here, we showed that a substantial portion of the macrophages that accumulated during pancreatitis and pancreatic cancer in mice had expanded from TRMs. Pancreas TRMs had an extracellular matrix remodeling phenotype that was important for maintaining tissue homeostasis during inflammation. Loss of TRMs led to exacerbation of severe pancreatitis and death, due to impaired acinar cell survival and recovery. During pancreatitis, TRMs elicited protective effects by triggering the accumulation and activation of fibroblasts, which was necessary for initiating fibrosis as a wound healing response. The same TRM-driven fibrosis, however, drove pancreas cancer pathogenesis and progression. Together, these findings indicate that TRMs play divergent roles in the pathogenesis of pancreatitis and cancer through regulation of stromagenesis.

DOI: https://doi.org/10.1038/s41590-023-01579-x
Aging Cell. 2023 Aug 10. e13952

The secretome atlas of two mouse models of progeria.

Diego Quintana-Torres, Alejandra Valle-Cao, Pablo Bousquets-Muñoz, Sandra Freitas-Rodríguez, Francisco Rodríguez, Alejandro Lucia, Carlos López-Otín, Alejandro López-Soto, Alicia R Folgueras.

  Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disease caused by nuclear envelope alterations that lead to accelerated aging and premature death. Several studies have linked health and longevity to cell-extrinsic mechanisms, highlighting the relevance of circulating factors in the aging process as well as in age-related diseases. We performed a global plasma proteomic analysis in two preclinical progeroid models (LmnaG609G/G609G and Zmpste24-/- mice) using aptamer-based proteomic technology. Pathways related to the extracellular matrix, growth factor response and calcium ion binding were among the most enriched in the proteomic signature of progeroid samples compared to controls. Despite the global downregulation trend found in the plasma proteome of progeroid mice, several proteins associated with cardiovascular disease, the main cause of death in HGPS, were upregulated. We also developed a chronological age predictor using plasma proteome data from a cohort of healthy mice (aged 1-30 months), that reported an age acceleration when applied to progeroid mice, indicating that these mice exhibit an "old" plasma proteomic signature. Furthermore, when compared to naturally-aged mice, a great proportion of differentially expressed circulating proteins in progeroid mice were specific to premature aging, highlighting secretome-associated differences between physiological and accelerated aging. This is the first large-scale profiling of the plasma proteome in progeroid mice, which provides an extensive list of candidate circulating plasma proteins as potential biomarkers and/or therapeutic targets for further exploration and hypothesis generation in the context of both physiological and premature aging.

Keywords:  HGPS; aging; aging clock; progeria; proteomics; secretome

DOI:  https://doi.org/10.1111/acel.13952
Commun Biol. 2023 08 07. 6(1): 821

Experimental and spontaneous metastasis assays can result in divergence in clonal architecture.

Antonin Serrano, Tom Weber, Jean Berthelet, Farrah El-Saafin, Sreeja Gadipally, Emmanuelle Charafe-Jauffret, Christophe Ginestier, John M Mariadason, Samantha R Oakes, Kara Britt, Shalin H Naik, Delphine Merino.

Intratumoural heterogeneity is associated with poor outcomes in breast cancer. To understand how malignant clones survive and grow in metastatic niches, in vivo models using cell lines and patient-derived xenografts (PDX) have become the gold standard. Injections of cancer cells in orthotopic sites (spontaneous metastasis assays) or into the vasculature (experimental metastasis assays) have been used interchangeably to study the metastatic cascade from early events or post-intravasation, respectively. However, less is known about how these different routes of injection impact heterogeneity. Herein we directly compared the clonality of spontaneous and experimental metastatic assays using the human cell line MDA-MB-231 and a PDX model. Genetic barcoding was used to study the fitness of the subclones in primary and metastatic sites. Using spontaneous assays, we found that intraductal injections resulted in less diverse tumours compared to other routes of injections. Using experimental metastasis assays via tail vein injection of barcoded MDA-MB-231 cells, we also observed an asymmetry in metastatic heterogeneity between lung and liver that was not observed using spontaneous metastasis assays. These results demonstrate that these assays can result in divergent clonal outputs in terms of metastatic heterogeneity and provide a better understanding of the biases inherent to each technique.

DOI: https://doi.org/10.1038/s42003-023-05167-5
Aging Cell. 2023 Aug 07. e13893

Decoding of translation-regulating entities reveals heterogeneous translation deficiency patterns in cellular senescence.

Angelos Papaspyropoulos, Orsalia Hazapis, Abdullah Altulea, Aikaterini Polyzou, Panayotis Verginis, Konstantinos Evangelou, Maria Fousteri, Argyris Papantonis, Marco Demaria, Vassilis Gorgoulis.

  Cellular senescence constitutes a generally irreversible proliferation barrier, accompanied by macromolecular damage and metabolic rewiring. Several senescence types have been identified based on the initiating stimulus, such as replicative (RS), stress-induced (SIS) and oncogene-induced senescence (OIS). These senescence subtypes are heterogeneous and often develop subset-specific phenotypes. Reduced protein synthesis is considered a senescence hallmark, but whether this trait pertains to various senescence subtypes and if distinct molecular mechanisms are involved remain largely unknown. Here, we analyze large published or experimentally produced RNA-seq and Ribo-seq datasets to determine whether major translation-regulating entities such as ribosome stalling, the presence of uORFs/dORFs and IRES elements may differentially contribute to translation deficiency in senescence subsets. We show that translation-regulating mechanisms may not be directly relevant to RS, however uORFs are significantly enriched in SIS. Interestingly, ribosome stalling, uORF/dORF patterns and IRES elements comprise predominant mechanisms upon OIS, strongly correlating with Notch pathway activation. Our study provides for the first time evidence that major translation dysregulation mechanisms/patterns occur during cellular senescence, but at different rates depending on the stimulus type. The degree at which those mechanisms accumulate directly correlates with translation deficiency levels. Our thorough analysis contributes to elucidating crucial and so far unknown differences in the translation machinery between senescence subsets.

Keywords:  IRES elements; oncogene-induced senescence; replicative senescence; ribosome stalling; stress-induced senescence; translation deficiency; uORF/dORF

DOI:  https://doi.org/10.1111/acel.13893
Adv Sci (Weinh). 2023 Aug 08. e2303523

Changes in Tissue Fluidity Predict Tumor Aggressiveness In Vivo.

Frank Sauer, Steffen Grosser, Mehrgan Shahryari, Alexander Hayn, Jing Guo, Jürgen Braun, Susanne Briest, Benjamin Wolf, Bahriye Aktas, Lars-Christian Horn, Ingolf Sack, Josef A Käs.

  Cancer progression is caused by genetic changes and associated with various alterations in cell properties, which also affect a tumor's mechanical state. While an increased stiffness has been well known for long for solid tumors, it has limited prognostic power. It is hypothesized that cancer progression is accompanied by tissue fluidization, where portions of the tissue can change position across different length scales. Supported by tabletop magnetic resonance elastography (MRE) on stroma mimicking collagen gels and microscopic analysis of live cells inside patient derived tumor explants, an overview is provided of how cancer associated mechanisms, including cellular unjamming, proliferation, microenvironment composition, and remodeling can alter a tissue's fluidity and stiffness. In vivo, state-of-the-art multifrequency MRE can distinguish tumors from their surrounding host tissue by their rheological fingerprints. Most importantly, a meta-analysis on the currently available clinical studies is conducted and universal trends are identified. The results and conclusions are condensed into a gedankenexperiment about how a tumor can grow and eventually metastasize into its environment from a physics perspective to deduce corresponding mechanical properties. Based on stiffness, fluidity, spatial heterogeneity, and texture of the tumor front a roadmap for a prognosis of a tumor's aggressiveness and metastatic potential is presented.

Keywords:  cancer; in vivo magnetic resonance elastography; medical imaging; tissue fluidity; tumor mechanics

DOI:  https://doi.org/10.1002/advs.202303523