bims-cagime 2024-02-11 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2024–02–11
forty papers selected by
Kıvanç Görgülü, Technical University of Munich

Detection of senescence using machine learning algorithms based on nuclear features.
A Novel Approach for Pancreas Transcriptomics Reveals the Cellular Landscape in Homeostasis and Acute Pancreatitis.
Rethinking the roles of cancer associated fibroblasts in pancreatic cancer.
Impact of KRAS mutations and co-mutations on clinical outcomes in pancreatic ductal adenocarcinoma.
RAS G-domains allosterically contribute to the recognition of lipid headgroups and acyl chains.
Multiplex protein imaging in tumour biology.
Multiplexed Imaging Mass Cytometry Analysis in Preclinical Models of Pancreatic Cancer.
Improved Clinical Staging System for Localized Pancreatic Cancer Using the ABC Factors: A TAPS Consortium Study.
Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore.
Lipid droplets provide metabolic flexibility for cancer progression.
The nuclear factor ID3 endows macrophages with a potent anti-tumour activity.
An alternative splicing signature defines the basal-like phenotype and predicts worse clinical outcome in pancreatic cancer.
PMIpred: a physics-informed web server for quantitative Protein-Membrane interaction prediction.
Inferring cancer metabolism from gene-expression data.
Lineage-specific intolerance to oncogenic drivers restricts histological transformation.
Fibroblasts in the aged pancreas drive pancreatic cancer progression.
Prognostic value of initial and longitudinal changes in body composition in metastatic pancreatic cancer.
Anatomical and Biological Considerations to Determine Resectability in Pancreatic Cancer.
The dual role of autophagy in the regulation of cancer treatment.
Contact-FP: A Dimerization-Dependent Fluorescent Protein Toolkit for Visualizing Membrane Contact Site Dynamics.
Using a CA19-9 Tumor Marker Gene Test to Assess Outcome After Pancreatic Cancer Surgery.
The cycling and aging mouse female reproductive tract at single-cell resolution.
Sarcoma cells secrete hypoxia-modified collagen VI to weaken the lung endothelial barrier and promote metastasis.
Metabolomic Investigations into Hypoxia-Mediated Metabolic Reprogramming of Pancreatic Cancer Cells.
GDF15 is a major determinant of ketogenic diet-induced weight loss.
Rearrangement of GUV-confined actin networks in response to micropipette aspiration.
Alternative Polyadenylation Characterizes Epithelial and Fibroblast Phenotypic Heterogeneity in Pancreatic Ductal Adenocarcinoma.
Discovering new drivers of cancer aneuploidy.
Sweet dreams: glycosylation controls tumor cell dormancy.
Methods to study xenografted human cancer in genetically diverse mice.
Automated Quantitative Analysis of CT Perfusion to Classify Vascular Phenotypes of Pancreatic Ductal Adenocarcinoma.
PD-L2 expression in senescent cancer cells limits tumor clearance after chemotherapy.
Selective Suppression of Integrin-Ligand Binding by Single Molecular Tension Probes Mediates Directional Cell Migration.
Mass spectrometry imaging methods for visualizing tumor heterogeneity.
A liquid biomarker signature of inflammatory proteins accurately predicts early pancreatic cancer progression during FOLFIRINOX chemotherapy.
Nab-Paclitaxel plus Gemcitabine and FOLFOX in Metastatic Pancreatic Cancer.
Brain energy metabolism is optimized to minimize the cost of enzyme synthesis and transport.
Short-term hypercaloric carbohydrate loading increases surgical stress resilience by inducing FGF21.
A Thermoplasmonic Approach for Investigating Plasma Membrane Repair in Living Cells and Model Membranes.
Precursor lesions in familial and hereditary pancreatic cancer.

Nat Commun. 2024 Feb 03. 15(1): 1041

Detection of senescence using machine learning algorithms based on nuclear features.

Imanol Duran, Joaquim Pombo, Bin Sun, Suchira Gallage, Hiromi Kudo, Domhnall McHugh, Laura Bousset, Jose Efren Barragan Avila, Roberta Forlano, Pinelopi Manousou, Mathias Heikenwalder, Dominic J Withers, Santiago Vernia, Robert D Goldin, Jesús Gil.

Cellular senescence is a stress response with broad pathophysiological implications. Senotherapies can induce senescence to treat cancer or eliminate senescent cells to ameliorate ageing and age-related pathologies. However, the success of senotherapies is limited by the lack of reliable ways to identify senescence. Here, we use nuclear morphology features of senescent cells to devise machine-learning classifiers that accurately predict senescence induced by diverse stressors in different cell types and tissues. As a proof-of-principle, we use these senescence classifiers to characterise senolytics and to screen for drugs that selectively induce senescence in cancer cells but not normal cells. Moreover, a tissue senescence score served to assess the efficacy of senolytic drugs and identified senescence in mouse models of liver cancer initiation, ageing, and fibrosis, and in patients with fatty liver disease. Thus, senescence classifiers can help to detect pathophysiological senescence and to discover and validate potential senotherapies.

DOI: https://doi.org/10.1038/s41467-024-45421-w
Gastroenterology. 2024 Feb 05. pii: S0016-5085(24)00130-6. [Epub ahead of print]

A Novel Approach for Pancreas Transcriptomics Reveals the Cellular Landscape in Homeostasis and Acute Pancreatitis.

Katherine J Aney, Woo-Jeong Jeong, Andres F Vallejo, Cassandra Burdziak, Ethan Chen, Austin Wang, Pal Koak, Kellie Wise, Kirk Jensen, Dana Pe'er, Stephanie K Dougan, Luciano Martelotto, Sahar Nissim.

   BACKGROUND & AIMS: Acinar cells produce digestive enzymes that impede transcriptomic characterization of the exocrine pancreas. Thus, single-cell RNA-sequencing (scRNA-seq) studies of the pancreas underrepresent acinar cells relative to histological expectations, and a robust approach to capture pancreatic cell responses in disease states is needed. We sought to innovate a method that overcomes these challenges to accelerate study of the pancreas in health and disease.
METHODS: We introduce FixNCut, a scRNA-seq approach where tissue is reversibly fixed with dithiobis(succinimidyl propionate) prior to dissociation and single-cell preparation. We apply FixNCut to an established mouse model of acute pancreatitis, validate findings using GeoMx whole transcriptome atlas (WTA) profiling, and integrate our data with prior studies to benchmark our method in both mouse and human pancreas datasets.
RESULTS: FixNCut achieves unprecedented definition of challenging pancreatic cells including acinar and immune populations in homeostasis and acute pancreatitis, and identifies changes in all major cell types during injury and recovery. We define the acinar transcriptome during homeostasis and acinar-to-ductal metaplasia and establish a unique gene set to measure deviation from normal acinar identity. We characterize pancreatic immune cells, and analysis of T-cell subsets reveals a polarization of the homeostatic pancreas towards type-2 immunity. We report immune responses during acute pancreatitis and recovery, including early neutrophil infiltration, expansion of dendritic cell subsets, and a substantial shift in the transcriptome of macrophages due to both resident macrophage activation and monocyte infiltration.
CONCLUSIONS: FixNCut preserves pancreatic transcriptomes to uncover novel cell states during homeostasis and following pancreatitis, establishing a broadly applicable approach and reference atlas for study of pancreas biology and disease.

Keywords:  “Acinar-to-ductal metaplasia”; “Dithiobis(succinimidyl propionate)”; “FixNCut”; “Pancreas Single-Cell RNA-Sequencing”

DOI:  https://doi.org/10.1053/j.gastro.2024.01.043
Cell Mol Gastroenterol Hepatol. 2024 Feb 03. pii: S2352-345X(24)00025-0. [Epub ahead of print]

Rethinking the roles of cancer associated fibroblasts in pancreatic cancer.

Ralph Francescone, Howard C Crawford, Debora Barbosa Vendramini-Costa.

Bearing a dismal 5-year survival rate, pancreatic ductal adenocarcinoma (PDAC) is a challenging disease that features a unique fibroinflammatory tumor microenvironment (TME). As major components of the PDAC TME, cancer associated fibroblasts (CAFs) are still poorly understood and their contribution to the several hallmarks of PDAC, such as resistance to therapies, immunosuppression, and high incidence of metastasis, is likely underestimated. There have been encouraging advances in our understanding of these fascinating cells, but many controversies remain, leaving the field still actively exploring the full scope of their contributions in PDAC progression. Here we aim to pose several important considerations regarding PDAC CAF functions. We posit that transcriptomic analyses be interpreted with caution, when aiming to uncover the functional contributions of these cells. Moreover, we propose that normalizing these functions, rather than eliminating them, will provide the opportunity to enhance therapeutic response. Finally, we propose that CAFs should not be studied in isolation, but in conjunction with its extracellular matrix, as their respective functions are coordinated and concordant.

DOI: https://doi.org/10.1016/j.jcmgh.2024.01.022
NPJ Precis Oncol. 2024 Feb 03. 8(1): 27

Impact of KRAS mutations and co-mutations on clinical outcomes in pancreatic ductal adenocarcinoma.

Abdelrahman Yousef, Mahmoud Yousef, Saikat Chowdhury, Kawther Abdilleh, Mark Knafl, Paul Edelkamp, Kristin Alfaro-Munoz, Ray Chacko, Jennifer Peterson, Brandon G Smaglo, Robert A Wolff, Shubham Pant, Michael S Lee, Jason Willis, Michael Overman, Sudheer Doss, Lynn Matrisian, Mark W Hurd, Rebecca Snyder, Matthew H G Katz, Huamin Wang, Anirban Maitra, John Paul Shen, Dan Zhao.

The relevance of KRAS mutation alleles to clinical outcome remains inconclusive in pancreatic adenocarcinoma (PDAC). We conducted a retrospective study of 803 patients with PDAC (42% with metastatic disease) at MD Anderson Cancer Center. Overall survival (OS) analysis demonstrated that KRAS mutation status and subtypes were prognostic (p < 0.001). Relative to patients with KRAS wildtype tumors (median OS 38 months), patients with KRASG12R had a similar OS (median 34 months), while patients with KRASQ61 and KRASG12D mutated tumors had shorter OS (median 20 months [HR: 1.9, 95% CI 1.2-3.0, p = 0.006] and 22 months [HR: 1.7, 95% CI 1.3-2.3, p < 0.001], respectively). There was enrichment of KRASG12D mutation in metastatic tumors (34% vs 24%, OR: 1.7, 95% CI 1.2-2.4, p = 0.001) and enrichment of KRASG12R in well and moderately differentiated tumors (14% vs 9%, OR: 1.7, 95% CI 1.05-2.99, p = 0.04). Similar findings were observed in the external validation cohort (PanCAN's Know Your Tumor® dataset, n = 408).

DOI: https://doi.org/10.1038/s41698-024-00505-0
J Cell Biol. 2024 May 06. pii: e202307121. [Epub ahead of print]223(5):

RAS G-domains allosterically contribute to the recognition of lipid headgroups and acyl chains.

Neha Arora, Huanwen Mu, Hong Liang, Wenting Zhao, Yong Zhou.

Mutant RAS are major contributors to cancer and signal primarily from nanoclusters on the plasma membrane (PM). Their C-terminal membrane anchors are main features of membrane association. However, the same RAS isoform bound to different guanine nucleotides spatially segregate. Different RAS nanoclusters all enrich a phospholipid, phosphatidylserine (PS). These findings suggest more complex membrane interactions. Our electron microscopy-spatial analysis shows that wild-types, G12V mutants, and membrane anchors of isoforms HRAS, KRAS4A, and KRAS4B prefer distinct PS species. Mechanistically, reorientation of KRAS4B G-domain exposes distinct residues, such as Arg 135 in orientation state 1 (OS1) and Arg 73/Arg 102 in OS2, to the PM and differentially facilitates the recognition of PS acyl chains. Allele-specific oncogenic mutations of KRAS4B also shift G-domain reorientation equilibrium. Indeed, KRAS4BG12V, KRAS4BG12D, KRAS4BG12C, KRAS4BG13D, and KRAS4BQ61H associate with PM lipids with headgroup and acyl chain specificities. Distribution of these KRAS4B oncogenic mutants favors different nanoscale membrane topography. Thus, RAS G-domains allosterically facilitate membrane lateral distribution.

DOI: https://doi.org/10.1083/jcb.202307121
Nat Rev Cancer. 2024 Feb 05.

Multiplex protein imaging in tumour biology.

Natalie de Souza, Shan Zhao, Bernd Bodenmiller.

Tissue imaging has become much more colourful in the past decade. Advances in both experimental and analytical methods now make it possible to image protein markers in tissue samples in high multiplex. The ability to routinely image 40-50 markers simultaneously, at single-cell or subcellular resolution, has opened up new vistas in the study of tumour biology. Cellular phenotypes, interaction, communication and spatial organization have become amenable to molecular-level analysis, and application to patient cohorts has identified clinically relevant cellular and tissue features in several cancer types. Here, we review the use of multiplex protein imaging methods to study tumour biology, discuss ongoing attempts to combine these approaches with other forms of spatial omics, and highlight challenges in the field.

DOI: https://doi.org/10.1038/s41568-023-00657-4
Int J Mol Sci. 2024 Jan 23. pii: 1389. [Epub ahead of print]25(3):

Multiplexed Imaging Mass Cytometry Analysis in Preclinical Models of Pancreatic Cancer.

Marco Erreni, Maria Rita Fumagalli, Damiano Zanini, Ermes Candiello, Giorgia Tiberi, Raffaella Parente, Raffaella D'Anna, Elena Magrini, Federica Marchesi, Paola Cappello, Andrea Doni.

  Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers. PDAC is characterized by a complex tumor microenvironment (TME), that plays a pivotal role in disease progression and resistance to therapy. Investigating the spatial distribution and interaction of TME cells with the tumor is the basis for understanding the mechanisms underlying disease progression and represents a current challenge in PDAC research. Imaging mass cytometry (IMC) is the major multiplex imaging technology for the spatial analysis of tumor heterogeneity. However, there is a dearth of reports of multiplexed IMC panels for different preclinical mouse models, including pancreatic cancer. We addressed this gap by utilizing two preclinical models of PDAC: the genetically engineered, bearing KRAS-TP53 mutations in pancreatic cells, and the orthotopic, and developed a 28-marker panel for single-cell IMC analysis to assess the abundance, distribution and phenotypes of cells involved in PDAC progression and their reciprocal functional interactions. Herein, we provide an unprecedented definition of the distribution of TME cells in PDAC and compare the diversity between transplanted and genetic disease models. The results obtained represent an important and customizable tool for unraveling the complexities of PDAC and deciphering the mechanisms behind therapy resistance.

Keywords:  PDAC; imaging mass cytometry; multiplexed imaging; pancreatic cancer; preclinical models

DOI:  https://doi.org/10.3390/ijms25031389
J Clin Oncol. 2024 Feb 05. JCO2301311

Improved Clinical Staging System for Localized Pancreatic Cancer Using the ABC Factors: A TAPS Consortium Study.

Trans-Atlantic Pancreatic Surgery (TAPS) Consortium

PURPOSE: Previous studies suggest that besides anatomy (A: resectable, borderline resectable [BR], or locally advanced [LA]) also biologic (B: carbohydrate antigen 19-9 [CA 19-9]) and conditional (C: performance status) factors should be considered when staging patients with localized pancreatic ductal adenocarcinoma (PDAC). The prognostic value of the combined ABC factors has not been quantitatively validated.
METHODS: In this retrospective cohort study, we evaluated patients with localized PDAC treated with initial (modified) fluorouracil with leucovorin, irinotecan, and oxaliplatin ([m]FOLFIRINOX) at five high-volume pancreatic cancer centers in the United States and the Netherlands (2012-2019). Multivariable Cox proportional hazards analysis was used to investigate the impact of the ABC factors for overall survival (OS).
RESULTS: Overall, 1,835 patients with localized PDAC were included. Tumor stage at diagnosis was potentially resectable in 346 (18.9%), BR in 531 (28.9%), and LA in 958 (52.2%) patients. The baseline CA 19-9 was >500 U/mL in 559 patients (32.5%). Performance status was ≥1 in 1,110 patients (60.7%). Independent poor prognostic factors for OS were BR disease (hazard ratio [HR], 1.26 [95% CI, 1.06 to 1.50]), LA disease (HR, 1.71 [95% CI, 1.45 to 2.02]), CA 19-9 >500 U/mL (HR, 1.36 [95% CI, 1.21 to 1.52]), and WHO performance status ≥1 (HR, 1.31 [95% CI, 1.16 to 1.47]). Patients were assigned 1 point for each poor ABC factor and 2 points for LA disease. The median OS for patients with score 0-4 was 49.7, 29.9, 22.0, 19.1, and 14.9 months with corresponding 5-year OS rates of 47.0%, 28.9%, 19.2%, 9.3%, and 4.8%, respectively.
CONCLUSION: The ABC factors of tumor anatomy, CA 19-9, and performance status at diagnosis were independent prognostic factors for OS in patients with localized PDAC treated with initial (m)FOLFIRINOX. Staging of patients with localized PDAC at diagnosis should be based on anatomy, CA 19-9, and performance status.

DOI: https://doi.org/10.1200/JCO.23.01311
Sci Adv. 2024 Feb 09. 10(6): eadj8027

Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore.

Shanlin Rao, Marvin Skulsuppaisarn, Lisa M Strong, Xuefeng Ren, Michael Lazarou, James H Hurley, Gerhard Hummer.

The covalent attachment of ubiquitin-like LC3 proteins (microtubule-associated proteins 1A/1B light chain 3) prepares the autophagic membrane for cargo recruitment. We resolve key steps in LC3 lipidation by combining molecular dynamics simulations and experiments in vitro and in cellulo. We show how the E3-like ligaseautophagy-related 12 (ATG12)-ATG5-ATG16L1 in complex with the E2-like conjugase ATG3 docks LC3 onto the membrane in three steps by (i) the phosphatidylinositol 3-phosphate effector protein WD repeat domain phosphoinositide-interacting protein 2 (WIPI2), (ii) helix α2 of ATG16L1, and (iii) a membrane-interacting surface of ATG3. Phosphatidylethanolamine (PE) lipids concentrate in a region around the thioester bond between ATG3 and LC3, highlighting residues with a possible role in the catalytic transfer of LC3 to PE, including two conserved histidines. In a near-complete pathway from the initial membrane recruitment to the LC3 lipidation reaction, the three-step targeting of the ATG12-ATG5-ATG16L1 machinery establishes a high level of regulatory control.

DOI: https://doi.org/10.1126/sciadv.adj8027
FEBS Lett. 2024 Feb 07.

Lipid droplets provide metabolic flexibility for cancer progression.

Rémi Safi, Pablo Menéndez, Albert Pol.

  A hallmark of cancer cells is their remarkable ability to efficiently adapt to favorable and hostile environments. Due to a unique metabolic flexibility, tumor cells can grow even in the absence of extracellular nutrients or in stressful scenarios. To achieve this, cancer cells need large amounts of lipids to build membranes, synthesize lipid-derived molecules, and generate metabolic energy in the absence of other nutrients. Tumor cells potentiate strategies to obtain lipids from other cells, metabolic pathways to synthesize new lipids, and mechanisms for efficient storage, mobilization, and utilization of these lipids. Lipid droplets (LDs) are the organelles that collect and supply lipids in eukaryotes and it is increasingly recognized that the accumulation of LDs is a new hallmark of cancer cells. Furthermore, an active role of LD proteins in processes underlying tumorigenesis has been proposed. Here, by focusing on three major classes of LD-resident proteins (perilipins, lipases, and acyl-CoA synthetases), we provide an overview of the contribution of LDs to cancer progression and discuss the role of LD proteins during the proliferation, invasion, metastasis, apoptosis, and stemness of cancer cells.

Keywords:  cancer; invasion; lipid droplets; lipids; metastasis; tumorigenesis

DOI:  https://doi.org/10.1002/1873-3468.14820
Nature. 2024 Feb 07.

The nuclear factor ID3 endows macrophages with a potent anti-tumour activity.

Zihou Deng, Pierre-Louis Loyher, Tomi Lazarov, Li Li, Zeyang Shen, Bhavneet Bhinder, Hairu Yang, Yi Zhong, Araitz Alberdi, Joan Massague, Joseph C Sun, Robert Benezra, Christopher K Glass, Olivier Elemento, Christine A Iacobuzio-Donahue, Frederic Geissmann.

Macrophage activation is controlled by a balance between activating and inhibitory receptors1-7, which protect normal tissues from excessive damage during infection8,9 but promote tumour growth and metastasis in cancer7,10. Here we report that the Kupffer cell lineage-determining factor ID3 controls this balance and selectively endows Kupffer cells with the ability to phagocytose live tumour cells and orchestrate the recruitment, proliferation and activation of natural killer and CD8 T lymphoid effector cells in the liver to restrict the growth of a variety of tumours. ID3 shifts the macrophage inhibitory/activating receptor balance to promote the phagocytic and lymphoid response, at least in part by buffering the binding of the transcription factors ELK1 and E2A at the SIRPA locus. Furthermore, loss- and gain-of-function experiments demonstrate that ID3 is sufficient to confer this potent anti-tumour activity to mouse bone-marrow-derived macrophages and human induced pluripotent stem-cell-derived macrophages. Expression of ID3 is therefore necessary and sufficient to endow macrophages with the ability to form an efficient anti-tumour niche, which could be harnessed for cell therapy in cancer.

DOI: https://doi.org/10.1038/s41586-023-06950-4
Cell Rep Med. 2024 Jan 31. pii: S2666-3791(24)00034-X. [Epub ahead of print] 101411

An alternative splicing signature defines the basal-like phenotype and predicts worse clinical outcome in pancreatic cancer.

Veronica Ruta, Chiara Naro, Marco Pieraccioli, Adriana Leccese, Livia Archibugi, Eleonora Cesari, Valentina Panzeri, Chantal Allgöwer, Paolo Giorgio Arcidiacono, Massimo Falconi, Carmine Carbone, Giampaolo Tortora, Federica Borrelli, Fabia Attili, Cristiano Spada, Giuseppe Quero, Sergio Alfieri, Claudio Doglioni, Alexander Kleger, Gabriele Capurso, Claudio Sette.

  Pancreatic ductal adenocarcinoma (PDAC) is characterized by extremely poor prognosis. PDAC presents with molecularly distinct subtypes, with the basal-like one being associated with enhanced chemoresistance. Splicing dysregulation contributes to PDAC; however, its involvement in subtype specification remains elusive. Herein, we uncover a subtype-specific splicing signature associated with prognosis in PDAC and the splicing factor Quaking (QKI) as a determinant of the basal-like signature. Single-cell sequencing analyses highlight QKI as a marker of the basal-like phenotype. QKI represses splicing events associated with the classical subtype while promoting basal-like events associated with shorter survival. QKI favors a plastic, quasi-mesenchymal phenotype that supports migration and chemoresistance in PDAC organoids and cell lines, and its expression is elevated in high-grade primary tumors and metastatic lesions. These studies identify a splicing signature that defines PDAC subtypes and indicate that QKI promotes an undifferentiated, plastic phenotype, which renders PDAC cells chemoresistant and adaptable to environmental changes.

Keywords:  RNA processing; alternative splicing; chemoresistance

DOI:  https://doi.org/10.1016/j.xcrm.2024.101411
Bioinformatics. 2024 Feb 05. pii: btae069. [Epub ahead of print]

PMIpred: a physics-informed web server for quantitative Protein-Membrane interaction prediction.

Niek van Hilten, Nino Verwei, Jeroen Methorst, Carsten Nase, Andrius Bernatavicius, Herre Jelger Risselada.

MOTIVATION: Many membrane peripheral proteins have evolved to transiently interact with the surface of (curved) lipid bilayers. Currently, methods to quantitatively predict sensing and binding free energies for protein sequences or structures are lacking, and such tools could greatly benefit the discovery of membrane-interacting motifs, as well as their de novo design.
RESULTS: Here, we trained a transformer neural network model on molecular dynamics data for >50,000 peptides that is able to accurately predict the (relative) membrane-binding free energy for any given amino acid sequence. Using this information, our physics-informed model is able to classify a peptide's membrane-associative activity as either non-binding, curvature sensing, or membrane binding. Moreover, this method can be applied to detect membrane-interaction regions in a wide variety of proteins, with comparable predictive performance as state-of-the-art data-driven tools like DREAMM, PPM3, and MODA, but with a wider applicability regarding protein diversity, and the added feature to distinguish curvature sensing from general membrane binding.
AVAILABILITY: We made these tools available as a web server, coined Protein-Membrane Interaction predictor (PMIpred), which can be accessed at https://pmipred.fkt.physik.tu-dortmund.de.

DOI: https://doi.org/10.1093/bioinformatics/btae069
Nat Rev Cancer. 2024 Feb 05.

Inferring cancer metabolism from gene-expression data.

Vakul Mohanty.

DOI: https://doi.org/10.1038/s41568-024-00670-1
Science. 2024 Feb 09. 383(6683): eadj1415

Lineage-specific intolerance to oncogenic drivers restricts histological transformation.

Eric E Gardner, Ethan M Earlie, Kate Li, Jerin Thomas, Melissa J Hubisz, Benjamin D Stein, Chen Zhang, Lewis C Cantley, Ashley M Laughney, Harold Varmus.

Lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC) are thought to originate from different epithelial cell types in the lung. Intriguingly, LUAD can histologically transform into SCLC after treatment with targeted therapies. In this study, we designed models to follow the conversion of LUAD to SCLC and found that the barrier to histological transformation converges on tolerance to Myc, which we implicate as a lineage-specific driver of the pulmonary neuroendocrine cell. Histological transformations are frequently accompanied by activation of the Akt pathway. Manipulating this pathway permitted tolerance to Myc as an oncogenic driver, producing rare, stem-like cells that transcriptionally resemble the pulmonary basal lineage. These findings suggest that histological transformation may require the plasticity inherent to the basal stem cell, enabling tolerance to previously incompatible oncogenic driver programs.

DOI: https://doi.org/10.1126/science.adj1415
Cancer Res. 2024 Feb 08.

Fibroblasts in the aged pancreas drive pancreatic cancer progression.

Daniel J Zabransky, Yash Chhabra, Mitchell E Fane, Emma Kartalia, James M Leatherman, Laura Hüser, Jacquelyn W Zimmerman, Daniel Delitto, Song Han, Todd D Armstrong, Samantha Guinn, Sneha Pramod, Elizabeth D Thompson, Steven J Hughes, Jennifer O'Connell, Josephine M Egan, Elizabeth M Jaffee, Ashani T Weeraratna.

Pancreatic cancer is more prevalent in older individuals and often carries a poorer prognosis for them. The relationship between the microenvironment and pancreatic cancer is multifactorial, and age-related changes in non-malignant cells in the tumor microenvironment may play a key role in promoting cancer aggressiveness. Since fibroblasts have profound impacts on pancreatic cancer progression, we investigated whether age-related changes in pancreatic fibroblasts influence cancer growth and metastasis. Proteomics analysis revealed that aged fibroblasts secrete different factors than young fibroblasts, including increased growth/differentiation factor 15 (GDF-15). Treating young mice with GDF-15 enhanced tumor growth, while aged GDF-15 knockout mice showed reduced tumor growth. GDF-15 activated AKT, rendering tumors sensitive to AKT inhibition in an aged but not young microenvironment. These data provide evidence for how aging alters pancreatic fibroblasts and promotes tumor progression, providing potential therapeutic targets and avenues for studying pancreatic cancer while accounting for the effects of aging.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-0086
J Cachexia Sarcopenia Muscle. 2024 Feb 08.

Prognostic value of initial and longitudinal changes in body composition in metastatic pancreatic cancer.

Min Woo Lee, Sun Kyung Jeon, Woo Hyun Paik, Jeong Hee Yoon, Ijin Joo, Jeong Min Lee, Sang Hyub Lee.

   BACKGROUND: Sarcopenia or visceral adipose tissue has been reported to be related to pancreatic cancer prognosis. However, clinical relevance of the comprehensive analysis of body compositions and their longitudinal changes is lacking. This study analysed the association between body composition changes after chemotherapy and survival in patients with metastatic pancreatic cancer.
METHODS: We retrospectively included 456 patients (mean age ± standard deviation, 61.2 ± 10.0 years; 272 males and 184 females) with metastatic pancreatic cancer who received palliative chemotherapy from May 2011 to December 2019. Using deep learning-based, fully automated segmentation of contrast-enhanced computed tomography (CT) at the time of diagnosis, cross-sectional areas of muscle, subcutaneous adipose tissue and visceral adipose tissue were extracted from a single axial image of the portal venous phase at L3 level. Skeletal muscle index (SMI), visceral adipose tissue index (VATI), subcutaneous adipose tissue index (SATI) and mean skeletal muscle attenuation (MA) were calculated, and their effect on overall survival (OS) was analysed. Longitudinal changes in body composition and prognostic values were also analysed in a subgroup of patients with 2- and 6-month follow-up CT (n = 349).
RESULTS: A total of 452 deaths occurred during follow-up in the entire cohort. The survival rate was 49.3% (95% confidence interval [CI], 44.9-54.2) at 1 year and 3.7% (95% CI, 2.0-6.8) at 5 years. In multivariable analysis, higher MA (≥44.4 HU in males and ≥34.8 HU in females) at initial CT was significantly associated with better OS in both males and females (adjusted hazard ratio [HR], 0.706; 95% CI, 0.538-0.925; P = 0.012 for males, and HR, 0.656; 95% CI, 0.475-0.906; P = 0.010 for females), whereas higher SATI (≥42.8 cm2 /m2 in males and ≥65.8 cm2 /m2 in females) was significantly associated with better OS in female patients only (adjusted HR, 0.568; 95% CI, 0.388-0.830; P = 0.003). In longitudinal analysis, SMI, VATI and SATI significantly decreased between initial and 2-month follow-up CT, whereas mean MA significantly decreased between 2- and 6-month follow-up CT. In multivariable Cox regression analysis of longitudinal changes, which was stratified by disease control state, SATI change was significantly associated with OS in male patients (adjusted HR, 0.513; 95% CI, 0.354-0.745; P < 0.001), while other body composition parameters were not.
CONCLUSIONS: In patients with metastatic pancreatic cancer, body composition mostly changed during the first 2 months after starting chemotherapy, and the prognostic factors associated with OS differed between males and females. Initial and longitudinal changes of body composition are associated with OS of metastatic pancreatic cancer.

Keywords:  body composition analysis; deep learning; pancreatic cancer; survival

DOI:  https://doi.org/10.1002/jcsm.13437
Cancers (Basel). 2024 Jan 23. pii: 489. [Epub ahead of print]16(3):

Anatomical and Biological Considerations to Determine Resectability in Pancreatic Cancer.

Ingmar F Rompen, Joseph R Habib, Christopher L Wolfgang, Ammar A Javed.

  Pancreatic ductal adenocarcinoma (PDAC) remains associated with poor outcomes with a 5-year survival of 12% across all stages of the disease. These poor outcomes are driven by a delay in diagnosis and an early propensity for systemic dissemination of the disease. Recently, aggressive surgical approaches involving complex vascular resections and reconstructions have become more common, thus allowing more locally advanced tumors to be resected. Unfortunately, however, even after the completion of surgery and systemic therapy, approximately 40% of patients experience early recurrence of disease. To determine resectability, many institutions utilize anatomical staging systems based on the presence and extent of vascular involvement of major abdominal vessels around the pancreas. However, these classification systems are based on anatomical considerations only and do not factor in the burden of systemic disease. By integrating the biological criteria, we possibly could avoid futile resections often associated with significant morbidity. Especially patients with anatomically resectable disease who have a heavy burden of radiologically undetected systemic disease most likely do not derive a survival benefit from resection. On the contrary, we could offer complex resections to those who have locally advanced or oligometastatic disease but have favorable systemic biology and are most likely to benefit from resection. This review summarizes the current literature on defining anatomical and biological resectability in patients with pancreatic cancer.

Keywords:  CA19-9; biological staging; biomarkers; pancreatic ductal adenocarcinoma; pancreatic neoplasms; resectability; tumor biology

DOI:  https://doi.org/10.3390/cancers16030489
Amino Acids. 2024 Feb 04. 56(1): 7

The dual role of autophagy in the regulation of cancer treatment.

Louis Boafo Kwantwi.

  As a catabolic process, autophagy through lysosomes degrades defective and damaged cellular materials to support homeostasis in stressful conditions. Therefore, autophagy dysregulation is associated with the induction of several human pathologies, including cancer. Although the role of autophagy in cancer progression has been extensively studied, many issues need to be addressed. The available evidence suggest that autophagy shows both cytoprotective and cytotoxic mechanisms. This dual role of autophagy in cancer has supplied a renewed interest in the development of novel and effective cancer therapies. Considering this, a deeper understanding of the molecular mechanisms of autophagy in cancer treatment is crucial. This article provides a summary of the recent advances regarding the dual and different mechanisms of autophagy-mediated therapeutic efficacy in cancer.

Keywords:  Autophagy; Drug resistance; The dual role; Therapeutic efficacy

DOI:  https://doi.org/10.1007/s00726-023-03364-4
Contact (Thousand Oaks). 2024 Jan-Dec;7:7 25152564241228911

Contact-FP: A Dimerization-Dependent Fluorescent Protein Toolkit for Visualizing Membrane Contact Site Dynamics.

Gregory E Miner, Sidney Y Smith, Wendy K Showalter, Christina M So, Joey V Ragusa, Alex E Powers, Maria Clara Zanellati, Chih-Hsuan Hsu, Michelle F Marchan, Sarah Cohen.

  Membrane contact sites (MCSs) are sites of close apposition between two organelles used to exchange ions, lipids, and information. Cells respond to changing environmental or developmental conditions by modulating the number, extent, or duration of MCSs. Because of their small size and dynamic nature, tools to study the dynamics of MCSs in live cells have been limited. Dimerization-dependent fluorescent proteins (ddFPs) targeted to organelle membranes are an ideal tool for studying MCS dynamics because they reversibly interact to fluoresce specifically at the interface between two organelles. Here, we build on previous work using ddFPs as sensors to visualize the morphology and dynamics of MCSs. We engineered a suite of ddFPs called Contact-FP that targets ddFP monomers to lipid droplets (LDs), the endoplasmic reticulum (ER), mitochondria, peroxisomes, lysosomes, plasma membrane, caveolae, and the cytoplasm. We show that these probes correctly localize to their target organelles. Using LDs as a test case, we demonstrate that Contact-FP pairs specifically localize to the interface between two target organelles. Titration of LD-mitochondria ddFPs revealed that these sensors can be used at high concentrations to drive MCSs or can be titrated down to minimally perturb and visualize endogenous MCSs. We show that Contact-FP probes can be used to: (1) visualize LD-mitochondria MCS dynamics, (2) observe changes in LD-mitochondria MCS dynamics upon overexpression of PLIN5, a known LD-mitochondrial tether, and (3) visualize two MCSs that share one organelle simultaneously (e.g., LD-mitochondria and LD-ER MCSs). Contact-FP probes can be optimized to visualize MCSs between any pair of organelles represented in the toolkit.

Keywords:  biosensors; caveolae; endoplasmic reticulum; fluorescent proteins; lipid droplets; lysosomes; membrane contact sites; mitochondria; organelles; peroxisomes; plasma membrane

DOI:  https://doi.org/10.1177/25152564241228911
Ann Surg Oncol. 2024 Feb 06.

Using a CA19-9 Tumor Marker Gene Test to Assess Outcome After Pancreatic Cancer Surgery.

Yohei Ando, Mohamad Dbouk, Amanda L Blackford, Takeichi Yoshida, Helena Saba, Elizabeth Abou Diwan, Kanako Yoshida, Lori Sokoll, James R Eshleman, Richard Burkhart, Jin He, Michael Goggins.

   BACKGROUND: Cancer antigen 19-9 (CA19-9) is widely used as a marker of pancreatic cancer tumor burden and response to therapy. Synthesis of CA19-9 and its circulating levels are determined by variants encoding the fucosyltransferases, FUT2 and FUT3. Individuals can be grouped into one of four functional FUT groups (FUT3-null, FUT-low, FUT-intermediate, FUT-high), each with its own CA19-9 reference range based on its predicted capacity to produce CA19-9. The authors hypothesized that a FUT variant-based CA19-9 tumor marker gene test could improve the prognostic performance of CA19-9.
METHODS: Preoperative and pre-treatment CA19-9 levels were measured, and FUT variants were determined in 449 patients who underwent surgery for pancreatic ductal adenocarcinoma (PDAC) at Johns Hopkins Hospital between 2010 and 2020, including 270 patients who underwent neoadjuvant therapy. Factors associated with recurrence-free and overall survival were determined in Cox proportional hazards models.
RESULTS: Higher preoperative CA19-9 levels were associated with recurrence and mortality for patients in the higher-FUT groups (FUT-intermediate, FUT-high for mortality, with adjustment for other prognostic factors; hazard ratio [HR], 1.34 and 1.58, respectively; P < 0.001), but not for those in the lower-FUT groups (FUT3-null, FUT-low). As a tumor marker, CA19-9 levels of 100 U/ml or lower after neoadjuvant therapy and normalization of CA19-9 based on FUT group were more sensitive but less specific predictors of evidence for a major pathologic response to therapy (little/no residual tumor) and of early recurrence (within 6 months).
CONCLUSION: Among patients undergoing pancreatic cancer resection, a CA19-9 tumor marker gene test modestly improved the prognostic performance of CA19-9.

Keywords:  CA19-9; Pancreatic cancer; Prognosis; Tumor marker gene test

DOI:  https://doi.org/10.1245/s10434-024-14942-5
Cell. 2024 Jan 31. pii: S0092-8674(24)00058-8. [Epub ahead of print]

The cycling and aging mouse female reproductive tract at single-cell resolution.

Ivana Winkler, Alexander Tolkachov, Fritjof Lammers, Perrine Lacour, Klaudija Daugelaite, Nina Schneider, Marie-Luise Koch, Jasper Panten, Florian Grünschläger, Tanja Poth, Bianca Machado de Ávila, Augusto Schneider, Simon Haas, Duncan T Odom, Ângela Gonçalves.

  The female reproductive tract (FRT) undergoes extensive remodeling during reproductive cycling. This recurrent remodeling and how it shapes organ-specific aging remains poorly explored. Using single-cell and spatial transcriptomics, we systematically characterized morphological and gene expression changes occurring in ovary, oviduct, uterus, cervix, and vagina at each phase of the mouse estrous cycle, during decidualization, and into aging. These analyses reveal that fibroblasts play central-and highly organ-specific-roles in FRT remodeling by orchestrating extracellular matrix (ECM) reorganization and inflammation. Our results suggest a model wherein recurrent FRT remodeling over reproductive lifespan drives the gradual, age-related development of fibrosis and chronic inflammation. This hypothesis was directly tested using chemical ablation of cycling, which reduced fibrotic accumulation during aging. Our atlas provides extensive detail into how estrus, pregnancy, and aging shape the organs of the female reproductive tract and reveals the unexpected cost of the recurrent remodeling required for reproduction.

Keywords:  aging; cervix; fibrosis; inflammation; ovary; oviduct; single cell; spatial; uterus; vagina

DOI:  https://doi.org/10.1016/j.cell.2024.01.021
Cancer Res. 2024 Feb 09.

Sarcoma cells secrete hypoxia-modified collagen VI to weaken the lung endothelial barrier and promote metastasis.

Ying Liu, Ileana Murazzi, Ashley M Fuller, Hehai Pan, Valerie M Irizarry-Negron, Ann DeVine, Rohan Katti, Nicolas Skuli, Gabrielle E Ciotti, Koreana Pak, Michael A Pack, M Celeste Simon, Kristy Weber, Kumarasen Cooper, T S Karin Eisinger-Mathason.

Intratumoral hypoxia correlates with metastasis and poor survival in sarcoma patients. Using an impedance sensing assay and a zebrafish intravital microinjection model, we demonstrated here that the hypoxia-inducible collagen-modifying enzyme lysyl hydroxylase PLOD2 and its substrate collagen type VI (COLVI) weaken the lung endothelial barrier and promote transendothelial migration. Mechanistically, hypoxia-induced PLOD2 in sarcoma cells modified COLVI, which was then secreted into the vasculature. Upon reaching the apical surface of lung endothelial cells, modified COLVI from tumor cells activated integrin β1 (ITGβ1). Furthermore, activated ITGβ1 co-localized with Kindlin2, initiating their interaction with F-actin and prompting its polymerization. Polymerized F-actin disrupted endothelial adherens junctions (AJ) and induced barrier dysfunction. Consistently, modified and secreted COLVI was required for the late stages of lung metastasis in vivo. Analysis of patient gene expression and survival data from The Cancer Genome Atlas (TCGA) revealed an association between the expression of both PLOD2 and COLVI and patient survival. Furthermore, high levels of COLVI were detected in surgically resected sarcoma metastases from patient lungs and in the blood of tumor-bearing mice. Together, this data identifies a mechanism of sarcoma lung metastasis, revealing opportunities for therapeutic intervention.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-0910
Methods Mol Biol. 2024 ;2755 191-200

Metabolomic Investigations into Hypoxia-Mediated Metabolic Reprogramming of Pancreatic Cancer Cells.

Vira Chumak, Girish H Rajacharya, Pankaj K Singh.

  Hypoxia is a crucial microenvironmental factor that defines tumor cell growth and aggressiveness. Cancer cells adapt to hypoxia by altering their metabolism. These alterations impact various cellular and physiological functions, including energy metabolism, vascularization, invasion and metastasis, genetic instability, cell immortalization, stem cell maintenance, and resistance to chemotherapy (Li et al. Technol Cancer Res Treat 20:15330338211036304, 2021). Hypoxia-inducible factor-1α (HIF-1α) is known to be a critical regulator of glycolysis that directly regulates the transcription of multiple key enzymes of the glycolysis pathway. Moreover, HIF-1α stabilization can be directly modulated by TCA-derived metabolites, including 2-ketoglutarate and succinate (Infantino et al, Int J Mol Sci 22(22), https://doi.org/10.3390/ijms22115703 , 2021). Overall, the molecular mechanisms underlying the adaptation of cellular metabolism to hypoxia impact the metabolic phenotype of cancer cells. Such adaptations include increased glucose uptake, increased lactate production, and increased levels of other metabolites that stabilize HIF-1α, leading to a vicious circle of hypoxia-induced tumor growth.

Keywords:  HIF; Hypoxia; Metabolomics; Pancreatic cancer; Tandem mass spectrometry

DOI:  https://doi.org/10.1007/978-1-0716-3633-6_14
Cell Metab. 2024 Feb 06. pii: S1550-4131(24)00004-4. [Epub ahead of print]36(2): 454-456

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

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

DOI: https://doi.org/10.1016/j.cmet.2024.01.004
Cytoskeleton (Hoboken). 2024 Feb 07.

Rearrangement of GUV-confined actin networks in response to micropipette aspiration.

Nadab H Wubshet, Cole J Young, Allen P Liu.

  Although diverse actin network architectures found inside the cell have been individually reconstituted outside of the cell, how different types of actin architectures reorganize under applied forces is not entirely understood. Recently, bottom-up reconstitution has enabled studies where dynamic and phenotypic characteristics of various actin networks can be recreated in an isolated cell-like environment. Here, by creating a giant unilamellar vesicle (GUV)-based cell model encapsulating actin networks, we investigate how actin networks rearrange in response to localized stresses applied by micropipette aspiration. We reconstitute actin bundles and branched bundles in GUVs separately and mechanically perturb them. Interestingly, we find that, when aspirated, protrusive actin bundles that are otherwise randomly oriented in the GUV lumen collapse and align along the axis of the micropipette. However, when branched bundles are aspirated, the network remains intact and outside of the pipette while the GUV membrane is aspirated into the micropipette. These results reveal distinct responses in the rearrangement of actin networks in a network architecture-dependent manner when subjected to physical forces.

Keywords:  actin network reconstitution; cell mechanics; giant unilamellar vesicle encapsulation

DOI:  https://doi.org/10.1002/cm.21836
Cancers (Basel). 2024 Feb 02. pii: 640. [Epub ahead of print]16(3):

Alternative Polyadenylation Characterizes Epithelial and Fibroblast Phenotypic Heterogeneity in Pancreatic Ductal Adenocarcinoma.

Swati Venkat, Michael E Feigin.

  Human tumors are characterized by extensive intratumoral transcriptional variability within the cancer cell and stromal compartments. This variation drives phenotypic heterogeneity, producing cell states with differential pro- and anti-tumorigenic properties. While bulk RNA sequencing cannot achieve cell-type-specific transcriptional granularity, single-cell sequencing has permitted an unprecedented view of these cell states. Despite this knowledge, we lack an understanding of the mechanistic drivers of this transcriptional and phenotypic heterogeneity. 3' untranslated region alternative polyadenylation (3' UTR-APA) drives gene expression alterations through regulation of 3' UTR length. These 3' UTR alterations modulate mRNA stability, protein expression and protein localization, resulting in cellular phenotypes including differentiation, cell proliferation, and migration. Therefore, we sought to determine whether 3' UTR-APA events could characterize phenotypic heterogeneity of tumor cell states. Here, we analyze the largest single-cell human pancreatic ductal adenocarcinoma (PDAC) dataset and resolve 3' UTR-APA patterns across PDAC cell states. We find that increased proximal 3' UTR-APA is associated with PDAC progression and characterizes a metastatic ductal epithelial subpopulation and an inflammatory fibroblast population. Furthermore, we find significant 3' UTR shortening events in cell-state-specific marker genes associated with increased expression. Therefore, we propose that 3' UTR-APA drives phenotypic heterogeneity in cancer.

Keywords:  alternative polyadenyation; gene regulation; pancreatic cancer

DOI:  https://doi.org/10.3390/cancers16030640
Nat Rev Cancer. 2024 Feb 09.

Discovering new drivers of cancer aneuploidy.

Juliann Shih.

DOI: https://doi.org/10.1038/s41568-024-00671-0
Trends Cancer. 2024 Feb 03. pii: S2405-8033(24)00011-6. [Epub ahead of print]

Sweet dreams: glycosylation controls tumor cell dormancy.

Erin Bresnahan, Jose Javier Bravo-Cordero.

  In a recent study in Cancer Cell, Sreekumar et al. used therapy-associated breast cancer mouse models as well as in vitro dormancy models to identify extracellular matrix (ECM)-related tumor cell-autonomous mechanisms of dormancy in residual tumor cells (RTCs). The study reveals an important role of the glycosylation of proteoglycans in sustaining dormancy and opens the door to leverage this biology to eliminate RTCs and prevent recurrence.

Keywords:  dormancy; extracellular matrix; glycosylation; metastasis

DOI:  https://doi.org/10.1016/j.trecan.2024.01.011
bioRxiv. 2024 Jan 25. pii: 2024.01.23.576906. [Epub ahead of print]

Methods to study xenografted human cancer in genetically diverse mice.

Muneer G Hasham, Jennifer K Sargent, Mark A Warner, Shawnna R Farley, Brian R Hoffmann, Timothy J Stodola, Catherine J Brunton, Steven C Munger.

Xenografting human cancer tissues into mice to test new cures against cancers is critical for understanding and treating the disease. However, only a few inbred strains of mice are used to study cancers, and derivatives of mainly one strain, mostly NOD/ShiLtJ, are used for therapy efficacy studies. As it has been demonstrated when human cancer cell lines or patient-derived tissues (PDX) are xenografted into mice, the neoplastic cells are human but the supporting cells that comprise the tumor (the stroma) are from the mouse. Therefore, results of studies of xenografted tissues are influenced by the host strain. We previously published that when the same neoplastic cells are xenografted into different mouse strains, the pattern of tumor growth, histology of the tumor, number of immune cells infiltrating the tumor, and types of circulating cytokines differ depending on the strain. Therefore, to better comprehend the behavior of cancer in vivo , one must xenograft multiple mouse strains. Here we describe and report a series of methods that we used to reveal the genes and proteins expressed when the same cancer cell line, MDA-MB-231, is xenografted in different hosts. First, using proteomic analysis, we show how to use the same cell line in vivo to reveal the protein changes in the neoplastic cell that help it adapt to its host. Then, we show how different hosts respond molecularly to the same cell line. We also find that using multiple strains can reveal a more suitable host than those traditionally used for a "difficult to xenograft" PDX. In addition, using complex trait genetics, we illustrate a feasible method for uncovering the alleles of the host that support tumor growth. Finally, we demonstrate that Diversity Outbred mice, the epitome of a model of mouse-strain genetic diversity, can be xenografted with human cell lines or PDX using 2-deoxy-D-glucose treatment.

DOI: https://doi.org/10.1101/2024.01.23.576906
Cancers (Basel). 2024 Jan 30. pii: 577. [Epub ahead of print]16(3):

Automated Quantitative Analysis of CT Perfusion to Classify Vascular Phenotypes of Pancreatic Ductal Adenocarcinoma.

Tom Perik, Natália Alves, John J Hermans, Henkjan Huisman.

  CT perfusion (CTP) analysis is difficult to implement in clinical practice. Therefore, we investigated a novel semi-automated CTP AI biomarker and applied it to identify vascular phenotypes of pancreatic ductal adenocarcinoma (PDAC) and evaluate their association with overall survival (OS).
METHODS: From January 2018 to November 2022, 107 PDAC patients were prospectively included, who needed to undergo CTP and a diagnostic contrast-enhanced CT (CECT). We developed a semi-automated CTP AI biomarker, through a process that involved deformable image registration, a deep learning segmentation model of tumor and pancreas parenchyma volume, and a trilinear non-parametric CTP curve model to extract the enhancement slope and peak enhancement in segmented tumors and pancreas. The biomarker was validated in terms of its use to predict vascular phenotypes and their association with OS. A receiver operating characteristic (ROC) analysis with five-fold cross-validation was performed. OS was assessed with Kaplan-Meier curves. Differences between phenotypes were tested using the Mann-Whitney U test.
RESULTS: The final analysis included 92 patients, in whom 20 tumors (21%) were visually isovascular. The AI biomarker effectively discriminated tumor types, and isovascular tumors showed higher enhancement slopes (2.9 Hounsfield unit HU/s vs. 2.0 HU/s, p < 0.001) and peak enhancement (70 HU vs. 47 HU, p < 0.001); the AUC was 0.86. The AI biomarker's vascular phenotype significantly differed in OS (p < 0.01).
CONCLUSIONS: The AI biomarker offers a promising tool for robust CTP analysis. In PDAC, it can distinguish vascular phenotypes with significant OS prognostication.

Keywords:  biomarker; pancreatic neoplasms; perfusion imaging

DOI:  https://doi.org/10.3390/cancers16030577
Nat Cancer. 2024 Feb 08.

PD-L2 expression in senescent cancer cells limits tumor clearance after chemotherapy.

DOI: https://doi.org/10.1038/s43018-023-00713-w
Adv Sci (Weinh). 2024 Feb 04. e2306497

Selective Suppression of Integrin-Ligand Binding by Single Molecular Tension Probes Mediates Directional Cell Migration.

Seong-Beom Han, Geonhui Lee, Daesan Kim, Jeong-Ki Kim, In-San Kim, Hae-Won Kim, Dong-Hwee Kim.

  Cell migration interacting with continuously changing microenvironment, is one of the most essential cellular functions, participating in embryonic development, wound repair, immune response, and cancer metastasis. The migration process is finely tuned by integrin-mediated binding to ligand molecules. Although numerous biochemical pathways orchestrating cell adhesion and motility are identified, how subcellular forces between the cell and extracellular matrix regulate intracellular signaling for cell migration remains unclear. Here, it is showed that a molecular binding force across integrin subunits determines directional migration by regulating tension-dependent focal contact formation and focal adhesion kinase phosphorylation. Molecular binding strength between integrin αv β3 and fibronectin is precisely manipulated by developing molecular tension probes that control the mechanical tolerance applied to cell-substrate interfaces. This data reveals that integrin-mediated molecular binding force reduction suppresses cell spreading and focal adhesion formation, attenuating the focal adhesion kinase (FAK) phosphorylation that regulates the persistence of cell migration. These results further demonstrate that manipulating subcellular binding forces at the molecular level can recapitulate differential cell migration in response to changes of substrate rigidity that determines the physical condition of extracellular microenvironment. Novel insights is provided into the subcellular mechanics behind global mechanical adaptation of the cell to surrounding tissue environments featuring distinct biophysical signatures.

Keywords:  FAK phosphorylation; cell adhesion; integrin αvβ3; molecular tension probes; persistent migration

DOI:  https://doi.org/10.1002/advs.202306497
Curr Opin Biotechnol. 2024 Feb 03. pii: S0958-1669(24)00004-1. [Epub ahead of print]86 103068

Mass spectrometry imaging methods for visualizing tumor heterogeneity.

Kyle D Duncan, Helena Pětrošová, Julian J Lum, David R Goodlett.

Profiling spatial distributions of lipids, metabolites, and proteins in tumors can reveal unique cellular microenvironments and provide molecular evidence for cancer cell dysfunction and proliferation. Mass spectrometry imaging (MSI) is a label-free technique that can be used to map biomolecules in tumors in situ. Here, we discuss current progress in applying MSI to uncover molecular heterogeneity in tumors. First, the analytical strategies to profile small molecules and proteins are outlined, and current methods for multimodal imaging to maximize biological information are highlighted. Second, we present and summarize biological insights obtained by MSI of tumor tissue. Finally, we discuss important considerations for designing MSI experiments and several current analytical challenges.

DOI: https://doi.org/10.1016/j.copbio.2024.103068
Neoplasia. 2024 Feb 08. pii: S1476-5586(24)00012-5. [Epub ahead of print]49 100975

A liquid biomarker signature of inflammatory proteins accurately predicts early pancreatic cancer progression during FOLFIRINOX chemotherapy.

Casper W F van Eijck, Sergio Sabroso-Lasa, Gaby J Strijk, Dana A M Mustafa, Amine Fellah, Bas Groot Koerkamp, Núria Malats, Casper H J van Eijck.

   BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is often treated with FOLFIRINOX, a chemotherapy associated with high toxicity rates and variable efficacy. Therefore, it is crucial to identify patients at risk of early progression during treatment. This study aims to explore the potential of a multi-omics biomarker for predicting early PDAC progression by employing an in-depth mathematical modeling approach.
METHODS: Blood samples were collected from 58 PDAC patients undergoing FOLFIRINOX before and after the first cycle. These samples underwent gene (GEP) and inflammatory protein expression profiling (IPEP). We explored the predictive potential of exclusively IPEP through Stepwise (Backward) Multivariate Logistic Regression modeling. Additionally, we integrated GEP and IPEP using Bayesian Kernel Regression modeling, aiming to enhance predictive performance. Ultimately, the FOLFIRINOX IPEP (FFX-IPEP) signature was developed.
RESULTS: Our findings revealed that proteins exhibited superior predictive accuracy than genes. Consequently, the FFX-IPEP signature consisted of six proteins: AMN, BANK1, IL1RL2, ITGB6, MYO9B, and PRSS8. The signature effectively identified patients transitioning from disease control to progression early during FOLFIRINOX, achieving remarkable predictive accuracy with an AUC of 0.89 in an independent test set. Importantly, the FFX-IPEP signature outperformed the conventional CA19-9 tumor marker.
CONCLUSIONS: Our six-protein FFX-IPEP signature holds solid potential as a liquid biomarker for the early prediction of PDAC progression during toxic FOLFIRINOX chemotherapy. Further validation in an external cohort is crucial to confirm the utility of the FFX-IPEP signature. Future studies should expand to predict progression under different chemotherapies to enhance the guidance of personalized treatment selection in PDAC.

Keywords:  Biomarkers; Gene Expression Profiling; Pancreatic Neoplasms; Precision Medicine; Protein Array Analysis; folfirinox

DOI:  https://doi.org/10.1016/j.neo.2024.100975
NEJM Evid. 2024 Feb;3(2): EVIDoa2300144

Nab-Paclitaxel plus Gemcitabine and FOLFOX in Metastatic Pancreatic Cancer.

Alfredo Carrato, Roberto Pazo-Cid, Teresa Macarulla, Javier Gallego, Paula Jiménez-Fonseca, Fernando Rivera, Maria Teresa Cano, Mercedes Rodriguez-Garrote, Carles Pericay, Inmaculada Alés, Laura Layos, Begoña Graña, Vega Iranzo, Inmaculada Gallego, Rocio Garcia-Carbonero, Inmaculada Ruiz de Mena, Carmen Guillén-Ponce, Enrique Aranda.

Nab-Paclitaxel plus Gemcitabine and FOLFOXThis randomized, open-label, phase II trial compared nab-paclitaxel/gemcitabine followed by modified FOLFOX versus nab-paclitaxel/gemcitabine alone for the first-line treatment of metastatic pancreatic ductal adenocarcinoma. Patients receiving nab-paclitaxel plus gemcitabine followed by modified FOLFOX-6 (oxaliplatin, leucovorin, and 5-fluorouracil) had a 12-month and 24-month overall survival of 55.3% and 22.4%, respectively, compared with 35.4% and 7.6% in the control group; there was a higher incidence of grade 3 or higher neutropenia and thrombocytopenia. No significant differences in febrile neutropenia, epistaxis or hemorrhage of grade 3 or higher in either group were reported. Two toxic deaths (2.6%) occurred in the experimental group.

DOI: https://doi.org/10.1056/EVIDoa2300144
Proc Natl Acad Sci U S A. 2024 Feb 13. 121(7): e2305035121

Brain energy metabolism is optimized to minimize the cost of enzyme synthesis and transport.

Johan Gustafsson, Jonathan L Robinson, Henrik Zetterberg, Jens Nielsen.

  The energy metabolism of the brain is poorly understood partly due to the complex morphology of neurons and fluctuations in ATP demand over time. To investigate this, we used metabolic models that estimate enzyme usage per pathway, enzyme utilization over time, and enzyme transportation to evaluate how these parameters and processes affect ATP costs for enzyme synthesis and transportation. Our models show that the total enzyme maintenance energy expenditure of the human body depends on how glycolysis and mitochondrial respiration are distributed both across and within cell types in the brain. We suggest that brain metabolism is optimized to minimize the ATP maintenance cost by distributing the different ATP generation pathways in an advantageous way across cell types and potentially also across synapses within the same cell. Our models support this hypothesis by predicting export of lactate from both neurons and astrocytes during peak ATP demand, reproducing results from experimental measurements reported in the literature. Furthermore, our models provide potential explanation for parts of the astrocyte-neuron lactate shuttle theory, which is recapitulated under some conditions in the brain, while contradicting other aspects of the theory. We conclude that enzyme usage per pathway, enzyme utilization over time, and enzyme transportation are important factors for defining the optimal distribution of ATP production pathways, opening a broad avenue to explore in brain metabolism.

Keywords:  ANLS; brain metabolism; genome-scale models; mathematical modeling; metabolism

DOI:  https://doi.org/10.1073/pnas.2305035121
Nat Commun. 2024 Feb 05. 15(1): 1073

Short-term hypercaloric carbohydrate loading increases surgical stress resilience by inducing FGF21.

Thomas Agius, Raffaella Emsley, Arnaud Lyon, Michael R MacArthur, Kevin Kiesworo, Anna Faivre, Louis Stavart, Martine Lambelet, David Legouis, Sophie de Seigneux, Déla Golshayan, Francois Lazeyras, Heidi Yeh, James F Markmann, Korkut Uygun, Alejandro Ocampo, Sarah J Mitchell, Florent Allagnat, Sébastien Déglise, Alban Longchamp.

Dietary restriction promotes resistance to surgical stress in multiple organisms. Counterintuitively, current medical protocols recommend short-term carbohydrate-rich drinks (carbohydrate loading) prior to surgery, part of a multimodal perioperative care pathway designed to enhance surgical recovery. Despite widespread clinical use, preclinical and mechanistic studies on carbohydrate loading in surgical contexts are lacking. Here we demonstrate in ad libitum-fed mice that liquid carbohydrate loading for one week drives reductions in solid food intake, while nearly doubling total caloric intake. Similarly, in humans, simple carbohydrate intake is inversely correlated with dietary protein intake. Carbohydrate loading-induced protein dilution increases expression of hepatic fibroblast growth factor 21 (FGF21) independent of caloric intake, resulting in protection in two models of surgical stress: renal and hepatic ischemia-reperfusion injury. The protection is consistent across male, female, and aged mice. In vivo, amino acid add-back or genetic FGF21 deletion blocks carbohydrate loading-mediated protection from ischemia-reperfusion injury. Finally, carbohydrate loading induction of FGF21 is associated with the induction of the canonical integrated stress response (ATF3/4, NF-kB), and oxidative metabolism (PPARγ). Together, these data support carbohydrate loading drinks prior to surgery and reveal an essential role of protein dilution via FGF21.

DOI: https://doi.org/10.1038/s41467-024-44866-3
J Vis Exp. 2024 Jan 19.

A Thermoplasmonic Approach for Investigating Plasma Membrane Repair in Living Cells and Model Membranes.

Helena Maria D Danielsen, Mohammad Reza Arastoo, Guillermo Moreno-Pescador, Poul Martin Bendix.

The cell membrane is crucial for cell survival, and ensuring its integrity is essential as the cell experiences injuries throughout its entire life cycle. To prevent damage to the membrane, cells have developed efficient plasma membrane repair mechanisms. These repair mechanisms can be studied by combining confocal microscopy and nanoscale thermoplasmonics to identify and investigate the role of key proteins, such as annexins, involved in surface repair in living cells and membrane model systems. The puncturing method employs a laser to induce highly localized heating upon nanoparticle irradiation. The use of near-infrared light minimizes phototoxicity in the biological sample, while the majority of the absorption takes place in the near-infrared resonant plasmonic nanoparticle. This thermoplasmonic method has been exploited for potential photothermal and biophysical research to enhance the understanding of intracellular mechanisms and cellular responses through vesicle and cell fusion studies. The approach has shown to be complementary to existing methods for membrane disruption, such as mechanically, chemically, or optically induced injuries, and provides a high level of control by inflicting extremely localized injuries. The extent of the injury is limited to the vicinity of the spherical nanoparticle, and no detrimental damage occurs along the beam path as opposed to pulsed lasers using different wavelengths. Despite certain limitations, such as the formation of nanobubbles, the thermoplasmonic method offers a unique tool for investigating cellular responses in plasma membrane repair in an almost native environment without compromising cell viability. When integrated with confocal microscopy, the puncturing method can provide a mechanistic understanding of membrane dynamics in model membrane systems as well as quantitative information on protein responses to membrane damage, including protein recruitment and their biophysical function. Overall, the application of this method to reduced model systems can enhance our understanding of the intricate plasma membrane repair machinery in living cells.

DOI: https://doi.org/10.3791/65776
Fam Cancer. 2024 Feb 06.

Precursor lesions in familial and hereditary pancreatic cancer.

Michael J Pflüger, Lodewijk A A Brosens, Ralph H Hruban.

  Infiltrating ductal adenocarcinoma of the pancreas, referred to here as "pancreatic cancer," is one of the deadliest of all of the solid malignancies. The five-year survival rate in the United States for individuals diagnosed today with pancreatic cancer is a dismal 12%. Many invasive cancers, including pancreatic cancer, however, arise from histologically and genetically well-characterized precursor lesions, and these precancers are curable. Precursor lesions therefore are an attractive target for early detection and treatment. This is particularly true for individuals with an increased risk of developing invasive cancer, such as individuals with a strong family history of pancreatic cancer, and individuals with a germline variant known to increase the risk of developing pancreatic cancer. There is therefore a need to understand the precursor lesions that can give rise to invasive pancreatic cancer in these individuals.

Keywords:  BRCA; CDKN2A; Familial; Germline; Intraductal papillary mucinous neoplasm; Pancreatic cancer; Precancer; Precursor

DOI:  https://doi.org/10.1007/s10689-024-00359-2