bims-cagime 2023-12-31 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2023‒12‒31
25 papers selected by
Kıvanç Görgülü, Technical University of Munich

Cancer-associated Fibroblast Induces Acinar-to-ductal Cell Transdifferentiation and Pancreatic Cancer Initiation via LAMA5/ITGA4 axis.
Molecular characteristics of early-onset pancreatic ductal adenocarcinoma.
A pancreatic cancer organoid platform identifies an inhibitor specific to mutant KRAS.
Automated tracking of cell migration in phase contrast images with CellTraxx.
Delta Radiomic Features Predict Resection Margin Status and Overall Survival in Neoadjuvant-Treated Pancreatic Cancer Patients.
Drivers of cancer metastasis - Arise early and remain present.
A mitophagy sensor PPTC7 controls BNIP3 and NIX degradation to regulate mitochondrial mass.
VIPpred: a novel model for predicting variant impact on phosphorylation events driving carcinogenesis.
Dynamic IL-6R/STAT3 signaling leads to heterogeneity of metabolic phenotype in pancreatic ductal adenocarcinoma cells.
A versatile method for the identification of senolytic compounds.
Single-cell RNA-seq analyses inform necroptosis-associated myeloid lineages influence the immune landscape of pancreas cancer.
Risk factors for early-onset pancreatic ductal adenocarcinoma: A systematic literature review.
Artificial intelligence-based analysis of body composition predicts outcome in patients receiving long-term mechanical circulatory support.
Impact of Recombinant Granulocyte Colony-Stimulating Factor During Neoadjuvant Therapy on Outcomes of Resected Pancreatic Cancer.
Proteogenomic Data Integration Reveals CXCL10 as a Potentially Downstream Causal Mediator for IL-6 Signaling on Atherosclerosis.
Long-term outcomes of neoadjuvant gemcitabine, nab-paclitaxel, and S1 (GAS) in borderline resectable pancreatic cancer with arterial contact: Results from a phase II trial.
Microfluidic devices for precise measurements of cell directionality reveal a role for glutamine during cell migration.
New Horizons in Hyperpolarized 13C MRI.
Intrapancreatic fat deposition and nutritional treatment: the role of various dietary approaches.
FGFR1 signaling facilitates obesity-driven pulmonary outgrowth in metastatic breast cancer.
Dipping contacts - a novel type of contact site at the interface between membraneless organelles and membranes.
A life off the beaten track in biomechanics: Imperfect elasticity, cytoskeletal glassiness, and epithelial unjamming.
MMP3C: an in-silico framework to depict cancer metabolic plasticity using gene expression profiles.
Inferring secretory and metabolic pathway activity from omic data with secCellFie.
Improving Cell-Free Expression of Model Membrane Proteins by Tuning Ribosome Cotranslational Membrane Association and Nascent Chain Aggregation.

Gastroenterology. 2023 Dec 26. pii: S0016-5085(23)05683-4. [Epub ahead of print]

Cancer-associated Fibroblast Induces Acinar-to-ductal Cell Transdifferentiation and Pancreatic Cancer Initiation via LAMA5/ITGA4 axis.

Seema Parte, Annant B Kaur, Rama Krishna Nimmakayala, Ayoola O Ogunleye, Ramakanth Chirravuri, Raghupathy Vengoji, Frank Leon, Palanisamy Nallasamy, Sanchita Rauth, Zahraa Wajih Alsafwani, Subodh Lele, Jesse L Cox, Ishfaq Bhat, Shailender Singh, Surinder K Batra, Moorthy P Ponnusamy.

  BACKGROUND & AIMS: Pancreatic ductal adenocarcinoma (PDAC) is characterized by desmoplastic stroma surrounding most tumors. Activated stromal fibroblasts, namely Cancer-associated fibroblasts (CAFs), play a major role in PDAC progression. Here we analyzed if CAFs influence acinar cells and impact PDAC initiation, namely "Acinar to Ductal Metaplasia" (ADM). ADM connection with PDAC pathophysiology is indicated but not yet established. Hence, we hypothesized that CAF secretome might play a significant role in ADM in PDAC initiation.METHODS: Mouse and human acinar cell organoids, acinar cells cocultured with CAFs and exposed to CAF-conditioned media (CAF-CM), acinar cell explants, and CAF cocultures, etc., were examined by qRT-PCR, RNA-seq, immunoblotting and confocal microscopy. Data from LC-MS/MS analysis of CAF CM and RNAseq data of acinar cells post-CM exposure were integrated using bioinformatics tools to identify molecular mechanism for CAF-induced ADM. Using confocal microscopy, immunoblotting, and qRT-PCR analysis, we validated the depletion of key signaling axis in cell-line, acinar explant coculture, and mCAFs.
RESULTS: Close association of acino-ductal (UEA1, Amylase, Ck19) markers and mCAFs (α-SMA) in LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx1Cre (KPC) and LSL-KrasG12D/+; Pdx1Cre (KC) autochthonous progression tumor tissue was observed. Caerulein treatment-induced mCAFs increased Ck19 and decreased Amylase in wild-type (WT) and KC pancreas. Likewise, acinar-mCAF cocultures revealed induction of ductal transdifferentiation in cell-line, acinar-organoid, and explant coculture formats in WT and KC mice pancreas. Proteomic and transcriptomic data integration revealed a novel Laminin5/Integrinα4/Stat3 axis responsible for CAF-mediated acinar to ductal cell transdifferentiation.
CONCLUSION: Results collectively suggest the first evidence for CAF-influenced acino-ductal phenotypic switchover, thus highlighting tumor micro-environment role in the pancreatic carcinogenesis inception.

Keywords:  acinar-ductal metaplasia; pre-neoplastic pancreatic lesions; stroma secretome

DOI:  https://doi.org/10.1053/j.gastro.2023.12.018
Mol Oncol. 2023 Dec 25.

Molecular characteristics of early-onset pancreatic ductal adenocarcinoma.

Silvana Debernardi, Lukasz Liszka, Chara Ntala, Katja Steiger, Irene Esposito, Emanuela Carlotti, Ann-Marie Baker, Stuart McDonald, Trevor Graham, Branko Dmitrovic, Roger M Feakins, Tatjana Crnogorac-Jurcevic.

  The median age of patients with pancreatic ductal adenocarcinoma (PDAC) at diagnosis is 71 years; however, around 10% present with early-onset pancreatic cancer (EOPC), i.e., before age 50. The molecular mechanisms underlying such an early onset are unknown. We assessed the role of common PDAC drivers (KRAS, TP53, CDKN2A and SMAD4) and determined their mutational status and protein expression in 90 formalin-fixed, paraffin-embedded tissues, including multiple primary and matched metastases, from 37 EOPC patients. KRAS was mutated in 88% of patients; p53 was altered in 94%, and p16 and SMAD4 were lost in 86% and 71% of patients, respectively. Meta-synthesis showed a higher rate of p53 alterations in EOPC than in late-onset PDAC (94% v 69%, P=0.0009) and significantly higher loss of SMAD4 (71% v 44%, P=0.0025). The majority of EOPC patients accumulated aberrations in all four drivers; in addition, high tumour heterogeneity was observed across all tissues. The cumulative effect of an exceptionally high rate of alterations in all common PDAC driver genes combined with high tumour heterogeneity suggest an important mechanism underlying the early onset of PDAC.

Keywords:  EOPC; KRAS; SMAD4; early onset; metastasis; mutations; p16; p53; pancreatic cancer; tumour heterogeneity

DOI:  https://doi.org/10.1002/1878-0261.13576
Cell Stem Cell. 2023 Dec 14. pii: S1934-5909(23)00411-3. [Epub ahead of print]

A pancreatic cancer organoid platform identifies an inhibitor specific to mutant KRAS.

Xiaohua Duan, Tuo Zhang, Lingling Feng, Neranjan de Silva, Benjamin Greenspun, Xing Wang, Jenna Moyer, M Laura Martin, Rohit Chandwani, Olivier Elemento, Steven D Leach, Todd Evans, Shuibing Chen, Fong Cheng Pan.

  KRAS mutations, mainly G12D and G12V, are found in more than 90% of pancreatic ductal adenocarcinoma (PDAC) cases. The success of drugs targeting KRASG12C suggests the potential for drugs specifically targeting these alternative PDAC-associated KRAS mutations. Here, we report a high-throughput drug-screening platform using a series of isogenic murine pancreatic organoids that are wild type (WT) or contain common PDAC driver mutations, representing both classical and basal PDAC phenotypes. We screened over 6,000 compounds and identified perhexiline maleate, which can inhibit the growth and induce cell death of pancreatic organoids carrying the KrasG12D mutation both in vitro and in vivo and primary human PDAC organoids. scRNA-seq analysis suggests that the cholesterol synthesis pathway is upregulated specifically in the KRAS mutant organoids, including the key cholesterol synthesis regulator SREBP2. Perhexiline maleate decreases SREBP2 expression levels and reverses the KRAS mutant-induced upregulation of the cholesterol synthesis pathway.

Keywords:  KRAS; SREBP2; cholesterol biosynthesis; colon cancer organoids; lung cancer organoids; orthotopic transplantation; pancreatic organoid; perhexiline maleate; targeted therapy

DOI:  https://doi.org/10.1016/j.stem.2023.11.011
Sci Rep. 2023 12 27. 13(1): 22982

Automated tracking of cell migration in phase contrast images with CellTraxx.

Børge Holme, Birgitte Bjørnerud, Nina Marie Pedersen, Laura Rodriguez de la Ballina, Jørgen Wesche, Ellen Margrethe Haugsten.

The ability of cells to move and migrate is required during development, but also in the adult in processes such as wound healing and immune responses. In addition, cancer cells exploit the cells' ability to migrate and invade to spread into nearby tissue and eventually metastasize. The majority of cancer deaths are caused by metastasis and the process of cell migration is therefore intensively studied. A common way to study cell migration is to observe cells through an optical microscope and record their movements over time. However, segmenting and tracking moving cells in phase contrast time-lapse video sequences is a challenging task. Several tools to track the velocity of migrating cells have been developed. Unfortunately, most of the automated tools are made for fluorescence images even though unlabelled cells are often preferred to avoid phototoxicity. Consequently, researchers are constrained with laborious manual tracking tools using ImageJ or similar software. We have therefore developed a freely available, user-friendly, automated tracking tool called CellTraxx. This software makes it easy to measure the velocity and directness of migrating cells in phase contrast images. Here, we demonstrate that our tool efficiently recognizes and tracks unlabelled cells of different morphologies and sizes (HeLa, RPE1, MDA-MB-231, HT1080, U2OS, PC-3) in several types of cell migration assays (random migration, wound healing and cells embedded in collagen). We also provide a detailed protocol and download instructions for CellTraxx.

DOI: https://doi.org/10.1038/s41598-023-50227-9
Ann Surg Oncol. 2023 Dec 27.

Delta Radiomic Features Predict Resection Margin Status and Overall Survival in Neoadjuvant-Treated Pancreatic Cancer Patients.

Kai Wang, John D Karalis, Ahmed Elamir, Alessandro Bifolco, Megan Wachsmann, Giovanni Capretti, Paola Spaggiari, Sebastian Enrico, Kishore Balasubramanian, Nafeesah Fatimah, Giada Pontecorvi, Martina Nebbia, Adam Yopp, Ravi Kaza, Ivan Pedrosa, Herbert Zeh, Patricio Polanco, Alessandro Zerbi, Jing Wang, Todd Aguilera, Matteo Ligorio.

BACKGROUND: Neoadjuvant therapy (NAT) emerged as the standard of care for patients with pancreatic ductal adenocarcinoma (PDAC) who undergo surgery; however, surgery is morbid, and tools to predict resection margin status (RMS) and prognosis in the preoperative setting are needed. Radiomic models, specifically delta radiomic features (DRFs), may provide insight into treatment dynamics to improve preoperative predictions.METHODS: We retrospectively collected clinical, pathological, and surgical data (patients with resectable, borderline, locally advanced, and metastatic disease), and pre/post-NAT contrast-enhanced computed tomography (CT) scans from PDAC patients at the University of Texas Southwestern Medical Center (UTSW; discovery) and Humanitas Hospital (validation cohort). Gross tumor volume was contoured from CT scans, and 257 radiomics features were extracted. DRFs were calculated by direct subtraction of pre/post-NAT radiomic features. Cox proportional models and binary prediction models, including/excluding clinical variables, were constructed to predict overall survival (OS), disease-free survival (DFS), and RMS.
RESULTS: The discovery and validation cohorts comprised 58 and 31 patients, respectively. Both cohorts had similar clinical characteristics, apart from differences in NAT (FOLFIRINOX vs. gemcitabine/nab-paclitaxel; p < 0.05) and type of surgery resections (pancreatoduodenectomy, distal or total pancreatectomy; p < 0.05). The model that combined clinical variables (pre-NAT carbohydrate antigen (CA) 19-9, the change in CA19-9 after NAT (∆CA19-9), and resectability status) and DRFs outperformed the clinical feature-based models and other radiomics feature-based models in predicting OS (UTSW: 0.73; Humanitas: 0.66), DFS (UTSW: 0.75; Humanitas: 0.64), and RMS (UTSW 0.73; Humanitas: 0.69).
CONCLUSIONS: Our externally validated, predictive/prognostic delta-radiomics models, which incorporate clinical variables, show promise in predicting the risk of predicting RMS in NAT-treated PDAC patients and their OS or DFS.

DOI: https://doi.org/10.1245/s10434-023-14805-5
Biochim Biophys Acta Rev Cancer. 2023 Dec 25. pii: S0304-419X(23)00209-3. [Epub ahead of print] 189060

Drivers of cancer metastasis - Arise early and remain present.

Dagmara Dymerska, Anna A Marusiak.

  Cancer and its metastases arise from mutations of genes, drivers that promote a tumor's growth. Analyses of driver events provide insights into cancer cell history and may lead to a better understanding of oncogenesis. We reviewed 27 metastatic research studies, including pan-cancer studies, individual cancer studies, and phylogenetic analyses, and summarized our current knowledge of metastatic drivers. All of the analyzed studies had a high level of consistency of driver mutations between primary tumors and metastasis, indicating that most drivers appear early in cancer progression and are maintained in metastatic cells. Additionally, we reviewed data from around 50,000 metastatic cancer patients and compiled a list of genes altered in metastatic lesions. We performed Gene Ontology analysis and confirmed that the most significantly enriched processes in metastatic lesions were the epigenetic regulation of gene expression, signal transduction, cell cycle, programmed cell death, DNA damage, hypoxia and EMT. In this review, we explore the most recent discoveries regarding genetic factors in the advancement of cancer, specifically those that drive metastasis.

Keywords:  Drivers; Genomic profiling; Metastasis; Molecular screening; Mutations; cancer

DOI:  https://doi.org/10.1016/j.bbcan.2023.189060
Mol Cell. 2023 Dec 21. pii: S1097-2765(23)01014-6. [Epub ahead of print]

A mitophagy sensor PPTC7 controls BNIP3 and NIX degradation to regulate mitochondrial mass.

Yuqiu Sun, Yu Cao, Huayun Wan, Adalet Memetimin, Yang Cao, Lin Li, Chongyang Wu, Meng Wang, She Chen, Qi Li, Yan Ma, Mengqiu Dong, Hui Jiang.

  Mitophagy mediated by BNIP3 and NIX critically regulates mitochondrial mass. Cellular BNIP3 and NIX levels are tightly controlled by SCFFBXL4-mediated ubiquitination to prevent excessive mitochondrial loss and lethal disease. Here, we report that knockout of PPTC7, a mitochondrial matrix protein, hyperactivates BNIP3-/NIX-mediated mitophagy and causes perinatal lethality that is rescued by NIX knockout in mice. Biochemically, the PPTC7 precursor is trapped by BNIP3 and NIX to the mitochondrial outer membrane, where PPTC7 scaffolds assembly of a substrate-PPTC7-SCFFBXL4 holocomplex to degrade BNIP3 and NIX, forming a homeostatic regulatory loop. PPTC7 possesses an unusually weak mitochondrial targeting sequence to facilitate its outer membrane retention and mitophagy control. Starvation upregulates PPPTC7 expression in mouse liver to repress mitophagy, which critically maintains hepatic mitochondrial mass, bioenergetics, and gluconeogenesis. Collectively, PPTC7 functions as a mitophagy sensor that integrates homeostatic and physiological signals to dynamically control BNIP3 and NIX degradation, thereby maintaining mitochondrial mass and cellular homeostasis.

Keywords:  Cullin; FBXL4; PPTC7; metabolism; mitochondrial mass; mitophagy receptors BNIP3 and NIX; ubiquitin

DOI:  https://doi.org/10.1016/j.molcel.2023.11.038
Brief Bioinform. 2023 Nov 22. pii: bbad480. [Epub ahead of print]25(1):

VIPpred: a novel model for predicting variant impact on phosphorylation events driving carcinogenesis.

Xiaofeng Xu, Ying Li, Taoyu Chen, Chao Hou, Liang Yang, Peiyu Zhu, Yi Zhang, Tingting Li.

  Disrupted protein phosphorylation due to genetic variation is a widespread phenomenon that triggers oncogenic transformation of healthy cells. However, few relevant phosphorylation disruption events have been verified due to limited biological experimental methods. Because of the lack of reliable benchmark datasets, current bioinformatics methods primarily use sequence-based traits to study variant impact on phosphorylation (VIP). Here, we increased the number of experimentally supported VIP events from less than 30 to 740 by manually curating and reanalyzing multi-omics data from 916 patients provided by the Clinical Proteomic Tumor Analysis Consortium. To predict VIP events in cancer cells, we developed VIPpred, a machine learning method characterized by multidimensional features that exhibits robust performance across different cancer types. Our method provided a pan-cancer landscape of VIP events, which are enriched in cancer-related pathways and cancer driver genes. We found that variant-induced increases in phosphorylation events tend to inhibit the protein degradation of oncogenes and promote tumor suppressor protein degradation. Our work provides new insights into phosphorylation-related cancer biology as well as novel avenues for precision therapy.

Keywords:  cancer driver; multi-omics data; pan-cancer landscape; protein degradation; variant impact on phosphorylation

DOI:  https://doi.org/10.1093/bib/bbad480
Cell Rep. 2023 Dec 22. pii: S2211-1247(23)01624-8. [Epub ahead of print]43(1): 113612

Dynamic IL-6R/STAT3 signaling leads to heterogeneity of metabolic phenotype in pancreatic ductal adenocarcinoma cells.

Wiktoria Blaszczak, Bobby White, Stefania Monterisi, Pawel Swietach.

  Malignancy is enabled by pro-growth mutations and adequate energy provision. However, global metabolic activation would be self-terminating if it depleted tumor resources. Cancer cells could avoid this by rationing resources, e.g., dynamically switching between "baseline" and "activated" metabolic states. Using single-cell metabolic phenotyping of pancreatic ductal adenocarcinoma cells, we identify MIA-PaCa-2 as having broad heterogeneity of fermentative metabolism. Sorting by a readout of lactic acid permeability separates cells by fermentative and respiratory rates. Contrasting phenotypes persist for 4 days and are unrelated to cell cycling or glycolytic/respiratory gene expression; however, transcriptomics links metabolically active cells with interleukin-6 receptor (IL-6R)-STAT3 signaling. We verify this by IL-6R/STAT3 knockdowns and sorting by IL-6R status. IL-6R/STAT3 activates fermentation and transcription of its inhibitor, SOCS3, resulting in delayed negative feedback that underpins transitions between metabolic states. Among cells manifesting wide metabolic heterogeneity, dynamic IL-6R/STAT3 signaling may allow cell cohorts to take turns in progressing energy-intense processes without depleting shared resources.

Keywords:  CP: Cancer; CP: Metabolism; PDAC; SOCS; feedback; fermentation; glycolysis; heterogeneity; homeostasis; interleukin-6; microenvironment; rationing; variation

DOI:  https://doi.org/10.1016/j.celrep.2023.113612
Cell Stress. 2023 Dec;7(12): 105-111

A versatile method for the identification of senolytic compounds.

Chiara Annunziata, Francesca Castoldi, Schlegel Jan, Hazel X Ang, Mina Ristovska, Stefania Melini, Robert Welch, Christian G Riedel, Federico Pietrocola.

  The increased burden of senescent cells is as a well-established hallmark of aging and age-related diseases. This finding sparked significant interest in the identification of molecules capable of selectively eliminating senescent cells, so-called senolytics. Here, we fine-tuned a method for the identification of senolytics that is compatible with high-content fluorescence microscopy. We used spectral detector imaging to measure the emission spectrum of unlabeled control or senescent cells. We observed that senescent cells exhibited higher levels of autofluorescence than their non-senescent counterparts, particularly in the cytoplasmic region. Building on this result, we devised a senolytic assay based on co-culturing quiescent and senescent cells, fluorescently tagged in the nuclear region through the overexpression of H2B-GFP and H2B-RFP, respectively. We validated this approach by showing that first generation senolytics were effective in reducing the number of RFP+ nuclei leaving the count of GFP+ nuclei unaffected. The result was confirmed by flow cytometry analysis of nuclei isolated from these quiescent-senescent cell co-cultures. We found that this system enables to capture cell type-specific effects of senolytics as in the case of fisetin, which kills senescent Mouse Embryonic Fibroblasts but not senescent human melanoma SK-MEL-103 cells. This approach is amenable to genetic and chemical screening for the discovery of senolytic compounds in that it overcomes the limitations of current methods, which rely upon costly chemical reagents or fluorescence microscopy using cells labeled with fluorescent cytoplasmic probes that overlap with the autofluorescence signal emitted by senescent cells.

Keywords:  cell death; fluorescence microscopy; navitoclax; nucleus; senescence

DOI:  https://doi.org/10.15698/cst2023.12.292
Front Immunol. 2023 ;14 1263633

Single-cell RNA-seq analyses inform necroptosis-associated myeloid lineages influence the immune landscape of pancreas cancer.

Weiwei Dong, Huixia Zhao, Shanshan Xiao, Liuqing Zheng, Tongqiang Fan, Li Wang, He Zhang, Yanyan Hu, Jingwen Yang, Tao Wang, Wenhua Xiao.

  Introduction: Tumor-infiltrating myeloid cells (TIMs) are key regulators in tumor progression, but the similarity and distinction of their fundamental properties in pancreatic ductal adenocarcinoma (PDAC) remain elusive.Method: In this study, we conducted scRNA-seq data analysis of cells from 12 primary tumor (PT) tissues, 4 metastatic (Met) tumor tissues, 3 adjacent normal pancreas tissues (Para), and PBMC samples across 16 PDAC patients, and revealed a heterogeneous TIMs environment in PDAC.
Result: Systematic comparisons between tumor and non-tumor samples of myeloid lineages identified 10 necroptosis-associated genes upregulated in PDAC tumors compared to 5 upregulated in paratumor or healthy peripheral blood. A novel RTM (resident tissue macrophages), GLUL-SQSTM1- RTM, was found to act as a positive regulator of immunity. Additionally, HSP90AA1+HSP90AB1+ mast cells exhibited pro-immune characteristics, and JAK3+TLR4+ CD16 monocytes were found to be anti-immune. The findings were validated through clinical outcomes and cytokines analyses. Lastly, intercellular network reconstruction supported the associations between the identified novel clusters, cancer cells, and immune cell populations.
Conclusion: Our analysis comprehensively characterized major myeloid cell lineages and identified three subsets of myeloid-derived cells associated with necroptosis. These findings not only provide a valuable resource for understanding the multi-dimensional characterization of the tumor microenvironment in PDAC but also offer valuable mechanistic insights that can guide the design of effective immuno-oncology treatment strategies.

Keywords:   scRNA-seq; PDAC; TIMs; TME; necroptosis

DOI:  https://doi.org/10.3389/fimmu.2023.1263633
Eur J Cancer. 2023 Dec 12. pii: S0959-8049(23)00773-6. [Epub ahead of print]198 113471

Risk factors for early-onset pancreatic ductal adenocarcinoma: A systematic literature review.

Sreenivasa R Chandana, Laura Woods, Fiona Maxwell, Ruth Gandolfo, Tanios Bekaii-Saab.

  BACKGROUND: Emerging cancer trends suggest an increase in pancreatic cancer incidence in individuals younger than its typical age of onset, potentially reflecting changes in population exposures and lifestyles.PATIENTS AND METHODS: We conducted a PRISMA-standard systematic literature review to identify non-heritable risk factors for early-onset pancreatic ductal adenocarcinoma (PDAC) (PROSPERO number: CRD42022299397). Systematic searches of MEDLINE and Embase bibliographic databases were performed (January 2022), and publications were screened against predetermined eligibility criteria; data were extracted using standardised data fields. The STROBE checklist was used to assess the completeness of reporting as a proxy for publication quality. Data were categorised by risk factor and analysed descriptively.
RESULTS: In total, 24 publications were included. All publications reported observational study data; thresholds for age group comparisons ranged between 40 and 65 years. Lifestyle factors investigated included smoking, alcohol consumption, obesity, physical inactivity, meat intake, socioeconomic status and geographical residence. Clinical factors investigated included pancreatitis, diabetes/insulin resistance, prior cancer and cancer stage at diagnosis, hepatitis B infection, metabolic syndrome and long-term proton pump inhibitor exposure. Publication STROBE scores were 6-21 (maximum, 22). Eight studies reported results adjusted for confounders. Potential non-heritable risk factors for early-onset PDAC that warrant further investigation included smoking, alcohol consumption, pancreatitis and hepatitis B infection.
CONCLUSION: Evidence for non-heritable risk factors for early-onset PDAC is heterogeneous, but four factors were identified that might aid the identification of at-risk individuals who may benefit from screening and risk reduction strategies.

Keywords:  Early-onset; Pancreatic adenocarcinoma; Risk factors; Systematic literature review; Young

DOI:  https://doi.org/10.1016/j.ejca.2023.113471
J Cachexia Sarcopenia Muscle. 2023 Dec 26.

Artificial intelligence-based analysis of body composition predicts outcome in patients receiving long-term mechanical circulatory support.

Isabell Anna Just, Felix Schoenrath, Luise Roehrich, Emanuel Heil, Julia Stein, Timo Alexander Auer, Uli Fehrenbach, Evgenij Potapov, Natalia Solowjowa, Felix Balzer, Dominik Geisel, Juergen Braun, Georg Boening.

  BACKGROUND: Obesity is a known cardiovascular risk factor and associated with higher postoperative complication rates in patients undergoing cardiac surgery. In heart failure (HF), conflicting evidence in terms of survival has been reported, whereas sarcopenia is associated with poor prognosis. An increasing number of HF patients require left ventricular assist device (LVAD) implantations. The postoperative mortality has improved in recent years but is still relatively high. The impact of body composition on outcome in this population remains unclear. The aim of this investigation was to examine the preoperative computed tomography (CT) body composition as a predictor of the postoperative outcome in advanced HF patients, who receive LVAD implantations.METHODS: Preoperative CT scans of 137 patients who received LVADs between 2015 and 2020 were retrospectively analysed using an artificial intelligence (AI)-powered automated software tool based on a convolutional neural network, U-net, developed for image segmentation (Visage Version 7.1, Visage Imaging GmbH, Berlin, Germany). Assessment of body composition included visceral and subcutaneous adipose tissue areas (VAT and SAT), psoas and total abdominal muscle areas and sarcopenia (defined by lumbar skeletal muscle indexes). The body composition parameters were correlated with postoperative major complication rates, survival and postoperative 6-min walk distance (6MWD) and quality of life (QoL).
RESULTS: The mean age of patients was 58.21 ± 11.9 years; 122 (89.1%) were male. Most patients had severe HF requiring inotropes (Interagency Registry for Mechanically Assisted Circulatory Support [INTERMACS] profile I-III, 71.9%) secondary to coronary artery diseases or dilated cardiomyopathy (96.4%). Forty-four (32.1%) patients were obese (body mass index ≥ 30 kg/m2 ), 96 (70.1%) were sarcopene and 19 (13.9%) were sarcopene obese. Adipose tissue was associated with a significantly higher risk of postoperative infections (VAT 172.23 cm2 [54.96, 288.32 cm2 ] vs. 124.04 cm2 [56.57, 186.25 cm2 ], P = 0.022) and in-hospital mortality (VAT 168.11 cm2 [134.19, 285.27 cm2 ] vs. 135.42 cm2 [49.44, 227.91 cm2 ], P = 0.033; SAT 227.28 cm2 [139.38, 304.35 cm2 ] vs. 173.81 cm2 [97.65, 254.16 cm2 ], P = 0.009). Obese patients showed no improvement of 6MWD and QoL within 6 months postoperatively (obese: +0.94 ± 161.44 months, P = 0.982; non-obese: +166.90 ± 139.00 months, P < 0.000; obese: +0.088 ± 0.421, P = 0.376; non-obese: +0.199 ± 0.324, P = 0.002, respectively). Sarcopenia did not influence the postoperative outcome and survival within 1 year after LVAD implantation.
CONCLUSIONS: Preoperative AI-based CT body composition identifies patients with poor outcome after LVAD implantation. Greater adipose tissue areas are associated with an increased risk for postoperative infections, in-hospital mortality and impaired 6MWD and QoL within 6 months postoperatively.

Keywords:  artificial intelligence; body composition; cachexia; left ventricular assist device; obesity paradox; sarcopenia

DOI:  https://doi.org/10.1002/jcsm.13402
J Natl Compr Canc Netw. 2023 Dec 27. 1-13

Impact of Recombinant Granulocyte Colony-Stimulating Factor During Neoadjuvant Therapy on Outcomes of Resected Pancreatic Cancer.

Pranav Murthy, Mazen S Zenati, Samer S AlMasri, Annissa DeSilva, Aatur D Singhi, Alessandro Paniccia, Kenneth K Lee, Richard L Simmons, Nathan Bahary, Michael T Lotze, Amer H Zureikat.

  BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease characterized by chronic inflammation and a tolerogenic immune response. The granulocyte colony-stimulating factor (G-CSF)-neutrophil axis promotes oncogenesis and progression of PDAC. Despite frequent use of recombinant G-CSF in the management and prevention of chemotherapy-induced neutropenia, its impact on oncologic outcomes of patients with resected PDAC is unclear.PATIENTS AND METHODS: This cohort study assessing the impact of G-CSF administration was conducted on 351 patients with PDAC treated with neoadjuvant therapy (NAT) and pancreatic resection at a high-volume tertiary care academic center from 2014 to 2019. Participants were identified from a prospectively maintained database and had a median follow-up of 45.8 months.
RESULTS: Patients receiving G-CSF (n=138; 39.3%) were younger (64.0 vs 66.7 years; P=.008), had lower body mass index (26.5 vs 27.9; P=.021), and were more likely to receive 5-FU-based chemotherapy (42.0% vs 28.2%; P<.0001). No differences were observed in baseline or clinical tumor staging. Patients receiving G-CSF were more likely to have an elevated (>5.53) post-NAT neutrophil-to-lymphocyte ratio (45.0% vs 29.6%; P=.004). G-CSF recipients also demonstrated higher circulating levels of neutrophil extracellular traps (+709 vs -619 pg/mL; P=.006). On multivariate analysis, G-CSF treatment was associated with perineural invasion (hazard ratio [HR], 2.65; 95% CI, 1.16-6.03; P=.021) and margin-positive resection (HR, 1.67; 95% CI, 1.01-2.77; P=.046). Patients receiving G-CSF had decreased overall survival (OS) compared with nonrecipients (median OS, 29.2 vs 38.7 months; P=.001). G-CSF administration was a negative independent predictor of OS (HR, 2.02; 95% CI, 1.45-2.79; P<.0001). In the inverse probability weighted analysis of 301 matched patients, neoadjuvant G-CSF administration was associated with reduced OS.
CONCLUSIONS: In patients with localized PDAC receiving NAT prior to surgical extirpation, G-CSF administration may be associated with worse oncologic outcomes and should be further evaluated.

Keywords:  G-CSF; NLR; Neoadjuvant therapy; Pancreatic Cancer

DOI:  https://doi.org/10.6004/jnccn.2023.7070
Circulation. 2023 Dec 28.

Proteogenomic Data Integration Reveals CXCL10 as a Potentially Downstream Causal Mediator for IL-6 Signaling on Atherosclerosis.

Savvina Prapiadou, Luka Živković, Barbara Thorand, Marc J George, Sander W van der Laan, Rainer Malik, Christian Herder, Wolfgang Koenig, Thor Ueland, Ola Kleveland, Pål Aukrust, Lars Gullestad, Jürgen Bernhagen, Gerard Pasterkamp, Annette Peters, Aroon D Hingorani, Jonathan Rosand, Martin Dichgans, Christopher D Anderson, Marios K Georgakis.

  BACKGROUND: Genetic and experimental studies support a causal involvement of IL-6 (interleukin-6) signaling in atheroprogression. Although trials targeting IL-6 signaling are underway, any benefits must be balanced against an impaired host immune response. Dissecting the mechanisms that mediate the effects of IL-6 signaling on atherosclerosis could offer insights about novel drug targets with more specific effects.METHODS: Leveraging data from 522 681 individuals, we constructed a genetic instrument of 26 variants in the gene encoding the IL-6R (IL-6 receptor) that proxied for pharmacological IL-6R inhibition. Using Mendelian randomization, we assessed its effects on 3281 plasma proteins quantified with an aptamer-based assay in the INTERVAL cohort (n=3301). Using mediation Mendelian randomization, we explored proteomic mediators of the effects of genetically proxied IL-6 signaling on coronary artery disease, large artery atherosclerotic stroke, and peripheral artery disease. For significant mediators, we tested associations of their circulating levels with incident cardiovascular events in a population-based study (n=1704) and explored the histological, transcriptomic, and cellular phenotypes correlated with their expression levels in samples from human atherosclerotic lesions.
RESULTS: We found significant effects of genetically proxied IL-6 signaling on 70 circulating proteins involved in cytokine production/regulation and immune cell recruitment/differentiation, which correlated with the proteomic effects of pharmacological IL-6R inhibition in a clinical trial. Among the 70 significant proteins, genetically proxied circulating levels of CXCL10 (C-X-C motif chemokine ligand 10) were associated with risk of coronary artery disease, large artery atherosclerotic stroke, and peripheral artery disease, with up to 67% of the effects of genetically downregulated IL-6 signaling on these end points mediated by decreases in CXCL10. Higher midlife circulating CXCL10 levels were associated with a larger number of cardiovascular events over 20 years, whereas higher CXCL10 expression in human atherosclerotic lesions correlated with a larger lipid core and a transcriptomic profile reflecting immune cell infiltration, adaptive immune system activation, and cytokine signaling.
CONCLUSIONS: Integrating multiomics data, we found a proteomic signature of IL-6 signaling activation and mediators of its effects on cardiovascular disease. Our analyses suggest the interferon-γ-inducible chemokine CXCL10 to be a potentially causal mediator for atherosclerosis in 3 vascular compartments and, as such, could serve as a promising drug target for atheroprotection.

Keywords:  Mendelian randomization analysis; atherosclerosis; interleukin-6

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.123.064974
J Hepatobiliary Pancreat Sci. 2023 Dec 29.

Long-term outcomes of neoadjuvant gemcitabine, nab-paclitaxel, and S1 (GAS) in borderline resectable pancreatic cancer with arterial contact: Results from a phase II trial.

Kenichiro Uemura, Naru Kondo, Takeshi Sudo, Tatsuaki Sumiyoshi, Ryuta Shintakuya, Kenjiro Okada, Kenta Baba, Takumi Harada, Yoshiaki Murakami, Shinya Takahashi.

  BACKGROUND/PURPOSE: This study reports the long-term results of a phase II trial evaluating the clinical efficacy of neoadjuvant gemcitabine, nab-paclitaxel, and S1 (GAS) in borderline resectable pancreatic cancer with arterial contact (BRPC-A).METHODS: A multicenter, single-arm, phase II trial was conducted. Patients received six cycles of GAS and patients without progressive disease were intended for R0 resection.
RESULTS: Of the 47 patients, 45 (96%) underwent pancreatectomy. At the time of this analysis, all patients were updated with no loss to follow-up. A total of 30 patients died, while the remaining 17 patients were followed for a median of 68.1 months. The updated median overall survival (OS) was 41.0 months, with 2- and 5-year OS rates of 68.0% and 44.6%, respectively. Multivariate analysis in the preoperative model showed that a tumor diameter reduction rate ≥10% and a CA19-9 reduction rate ≥95% after neoadjuvant chemotherapy remained independently associated with favorable survival. In the postoperative multivariate model, no lymph node metastasis, no major surgical complications, and completion of adjuvant chemotherapy were independently associated with improved OS.
CONCLUSIONS: This long-term evaluation of the neoadjuvant GAS trial demonstrated the high efficacy of the regimen, suggesting that it is a promising treatment option for patients with BRPC-A.

Keywords:  S-1; borderline resectable pancreatic cancer; gemcitabine; nab-paclitaxel; neoadjuvant chemotherapy

DOI:  https://doi.org/10.1002/jhbp.1412
Sci Rep. 2023 Dec 27. 13(1): 23032

Microfluidic devices for precise measurements of cell directionality reveal a role for glutamine during cell migration.

Nil Gural, Daniel Irimia.

Cancer cells that migrate from tumors into surrounding tissues are responsible for cancer dissemination through the body. Microfluidic devices have been instrumental in discovering unexpected features of cancer cell migration, including the migration in self-generated gradients and the contributions of cell-cell contact during collective migration. Here, we design microfluidic channels with five successive bifurcations to characterize the directionality of cancer cell migration with high precision. We uncover an unexpected role for glutamine in epithelial cancer cell orientation, which could be replaced by alfa-keto glutarate but not glucose.

DOI: https://doi.org/10.1038/s41598-023-49866-9
Mol Imaging Biol. 2023 Dec 26.

New Horizons in Hyperpolarized 13C MRI.

Myriam M Chaumeil, James A Bankson, Kevin M Brindle, Shdema Epstein, Ferdia A Gallagher, Martin Grashei, Caroline Guglielmetti, Joshua D Kaggie, Kayvan R Keshari, Stephan Knecht, Christoffer Laustsen, Andreas B Schmidt, Daniel Vigneron, Yi-Fen Yen, Franz Schilling.

  Hyperpolarization techniques significantly enhance the sensitivity of magnetic resonance (MR) and thus present fascinating new directions for research and applications with in vivo MR imaging and spectroscopy (MRI/S). Hyperpolarized 13C MRI/S, in particular, enables real-time non-invasive assessment of metabolic processes and holds great promise for a diverse range of clinical applications spanning fields like oncology, neurology, and cardiology, with a potential for improving early diagnosis of disease, patient stratification, and therapy response assessment. Despite its potential, technical challenges remain for achieving clinical translation. This paper provides an overview of the discussions that took place at the international workshop "New Horizons in Hyperpolarized 13C MRI," in March 2023 at the Bavarian Academy of Sciences and Humanities, Munich, Germany. The workshop covered new developments, as well as future directions, in topics including polarization techniques (particularly focusing on parahydrogen-based methods), novel probes, considerations related to data acquisition and analysis, and emerging clinical applications in oncology and other fields.

Keywords:  Consensus; Hyperpolarized 13C; MR spectroscopy; MRI; Metabolic imaging; Metabolism

DOI:  https://doi.org/10.1007/s11307-023-01888-5
Nutr Rev. 2023 Dec 28. pii: nuad159. [Epub ahead of print]

Intrapancreatic fat deposition and nutritional treatment: the role of various dietary approaches.

Giuseppe Della Pepa, Dominic Salamone, Roberta Testa, Lutgarda Bozzetto, Giuseppina Costabile.

  Ectopic fat accumulation in various organs and tissues, such as the liver, muscle, kidney, heart, and pancreas, is related to impaired capacity of adipose tissue to accumulate triglycerides, as a consequence of overnutrition and an unhealthy lifestyle. Ectopic fat promotes organ dysfunction and is a key factor in the development and progression of cardiometabolic diseases. Interest in intrapancreatic fat deposition (IPFD) has developed in the last few years, particularly in relation to improvement in methodological techniques for detection of fat in the pancreas, and to growing evidence for the role that IPFD might have in glucose metabolism disorders and cardiometabolic disease. Body weight reduction represents the main option for reducing fat, and the evidence consistently shows that hypocaloric diets are effective in reducing IPFD. Changes in diet composition, independently of changes in energy intake, might offer a more feasible and safe alternative treatment to energy restriction. This current narrative review focused particularly on the possible beneficial role of the diet and its nutrient content, in hypocaloric and isocaloric conditions, in reducing IPFD in individuals with high cardiometabolic risk, highlighting the possible effects of differences in calorie quantity and calorie quality. This review also describes plausible mechanisms by which the various dietary approaches could modulate IPFD.

Keywords:  dietary interventions; dietary quality; ectopic fat; intrapancreatic fat deposition

DOI:  https://doi.org/10.1093/nutrit/nuad159
Mol Cancer Res. 2023 Dec 28.

FGFR1 signaling facilitates obesity-driven pulmonary outgrowth in metastatic breast cancer.

Eylem Kulkoyluoglu Cotul, Muhammad Hassan Safdar, Sebastian Juan Paez, Aneesha Kulkarni, Mitchell G Ayers, Hang Lin, Zilin Xianyu, Dorothy Teegarden, Stephen D Hursting, Michael K Wendt.

Survival of dormant, disseminated breast cancer (BC) cells contributes to tumor relapse and metastasis. Women with a body mass index greater than 35 have an increased risk of developing metastatic recurrence. Herein, we investigated the effect of diet-induced obesity (DIO) on primary tumor growth and metastatic progression using both metastatic and systemically dormant mouse models of BC. This approach led to increased PT growth and pulmonary metastasis. We developed a novel protocol to induce obesity in Balb/c mice by combining dietary and hormonal interventions with a thermoneutral housing strategy. In contrast to standard housing conditions, ovariectomized Balb/c mice fed a high fat diet under thermoneutral conditions became obese over a period of 10 weeks, resulting in a 250% gain in fat mass. Obese mice injected with the D2.OR model developed macroscopic pulmonary nodules compared to the dormant phenotype of these cells in mice fed a control diet. Analysis of the serum from obese Balb/c mice revealed increased levels of fibroblast growth factor 2 (FGF2) as compared to lean mice. We demonstrate that serum from obese animals, exogenous FGF stimulation, or constitutive stimulation through autocrine and paracrine FGF2 is sufficient to break dormancy and drive pulmonary outgrowth. Blockade of fibroblast growth factor receptor (FGFR) signaling or specific depletion of FGFR1 prevented obesity-associated outgrowth of the D2.OR model. Implications: Overall, this study developed a novel DIO model that allowed for demonstration of FGF2:FGFR1 signaling as a key molecular mechanism connecting obesity to breakage of systemic tumor dormancy and metastatic progression.

DOI: https://doi.org/10.1158/1541-7786.MCR-23-0955
J Cell Sci. 2023 Dec 15. pii: jcs261413. [Epub ahead of print]136(24):

Dipping contacts - a novel type of contact site at the interface between membraneless organelles and membranes.

Christian Hoffmann, Dragomir Milovanovic.

  Liquid-liquid phase separation is a major mechanism for organizing macromolecules, particularly proteins with intrinsically disordered regions, in compartments not limited by a membrane or a scaffold. The cell can therefore be perceived as a complex emulsion containing many of these membraneless organelles, also referred to as biomolecular condensates, together with numerous membrane-bound organelles. It is currently unclear how such a complex concoction operates to allow for intracellular trafficking, signaling and metabolic processes to occur with high spatiotemporal precision. Based on experimental observations of synaptic vesicle condensates - a membraneless organelle that is in fact packed with membranes - we present here the framework of dipping contacts: a novel type of contact site between membraneless organelles and membranes. In this Hypothesis, we propose that our framework of dipping contacts can serve as a foundation to investigate the interface that couples the diffusion and material properties of condensates to biochemical processes occurring in membranes. The identity and regulation of this interface is especially critical in the case of neurodegenerative diseases, where aberrant inclusions of misfolded proteins and damaged organelles underlie cellular pathology.

Keywords:  Dipping contacts; Liquid–liquid phase separation; Membranes; Neurodegenerative diseases; Synapse

DOI:  https://doi.org/10.1242/jcs.261413
Biophys Rev (Melville). 2023 Dec;4(4): 041304

A life off the beaten track in biomechanics: Imperfect elasticity, cytoskeletal glassiness, and epithelial unjamming.

Lior Atia, Jeffrey J Fredberg.

Textbook descriptions of elasticity, viscosity, and viscoelasticity fail to account for certain mechanical behaviors that typify soft living matter. Here, we consider three examples. First, strong empirical evidence suggests that within lung parenchymal tissues, the frictional stresses expressed at the microscale are fundamentally not of viscous origin. Second, the cytoskeleton (CSK) of the airway smooth muscle cell, as well as that of all eukaryotic cells, is more solid-like than fluid-like, yet its elastic modulus is softer than the softest of soft rubbers by a factor of 104-105. Moreover, the eukaryotic CSK expresses power law rheology, innate malleability, and fluidization when sheared. For these reasons, taken together, the CSK of the living eukaryotic cell is reminiscent of the class of materials called soft glasses, thus likening it to inert materials such as clays, pastes slurries, emulsions, and foams. Third, the cellular collective comprising a confluent epithelial layer can become solid-like and jammed, fluid-like and unjammed, or something in between. Esoteric though each may seem, these discoveries are consequential insofar as they impact our understanding of bronchospasm and wound healing as well as cancer cell invasion and embryonic development. Moreover, there are reasons to suspect that certain of these phenomena first arose in the early protist as a result of evolutionary pressures exerted by the primordial microenvironment. We have hypothesized, further, that each then became passed down virtually unchanged to the present day as a conserved core process. These topics are addressed here not only because they are interesting but also because they track the journey of one laboratory along a path less traveled by.

DOI: https://doi.org/10.1063/5.0179719
Brief Bioinform. 2023 Nov 22. pii: bbad471. [Epub ahead of print]25(1):

MMP3C: an in-silico framework to depict cancer metabolic plasticity using gene expression profiles.

Xingyu Chen, Min Deng, Zihan Wang, Chen Huang.

  Metabolic plasticity enables cancer cells to meet divergent demands for tumorigenesis, metastasis and drug resistance. Landscape analysis of tumor metabolic plasticity spanning different cancer types, in particular, metabolic crosstalk within cell subpopulations, remains scarce. Therefore, we proposed a new in-silico framework, termed as MMP3C (Modeling Metabolic Plasticity by Pathway Pairwise Comparison), to depict tumor metabolic plasticity based on transcriptome data. Next, we performed an extensive metabo-plastic analysis of over 6000 tumors comprising 13 cancer types. The metabolic plasticity within distinct cell subpopulations, particularly interplay with tumor microenvironment, were explored at single-cell resolution. Ultimately, the metabo-plastic events were screened out for multiple clinical applications via machine learning methods. The pilot research indicated that 6 out of 13 cancer types exhibited signs of the Warburg effect, implying its high reliability and robustness. Across 13 cancer types, high metabolic organized heterogeneity was found, and four metabo-plastic subtypes were determined, which link to distinct immune and metabolism patterns impacting prognosis. Moreover, MMP3C analysis of approximately 60 000 single cells of eight breast cancer patients unveiled several metabo-plastic events correlated to tumorigenesis, metastasis and immunosuppression. Notably, the metabolic features screened out by MMP3C are potential biomarkers for diagnosis, tumor classification and prognosis. MMP3C is a practical cross-platform tool to capture tumor metabolic plasticity, and our study unveiled a core set of metabo-plastic pairs among diverse cancer types, which provides bases toward improving response and overcoming resistance in cancer therapy.

Keywords:  metabolism plasticity; pan-cancer; tumor microenvironment

DOI:  https://doi.org/10.1093/bib/bbad471
Metab Eng. 2023 Dec 23. pii: S1096-7176(23)00179-9. [Epub ahead of print]

Inferring secretory and metabolic pathway activity from omic data with secCellFie.

Helen O Masson, Mojtaba Samoudi, Caressa M Robinson, Chih-Chung Kuo, Linus Weiss, Km Shams Ud Doha, Alex Campos, Vijay Tejwani, Hussain Dahodwala, Patrice Menard, Bjorn G Voldborg, Bradley Robasky, Susan T Sharfstein, Nathan E Lewis.

  Understanding protein secretion has considerable importance in biotechnology and important implications in a broad range of normal and pathological conditions including development, immunology, and tissue function. While great progress has been made in studying individual proteins in the secretory pathway, measuring and quantifying mechanistic changes in the pathway's activity remains challenging due to the complexity of the biomolecular systems involved. Systems biology has begun to address this issue with the development of algorithmic tools for analyzing biological pathways; however most of these tools remain accessible only to experts in systems biology with extensive computational experience. Here, we expand upon the user-friendly CellFie tool which quantifies metabolic activity from omic data to include secretory pathway functions, allowing any scientist to infer properties of protein secretion from omic data. We demonstrate how the secretory expansion of CellFie (secCellFie) can help predict metabolic and secretory functions across diverse immune cells, hepatokine secretion in a cell model of NAFLD, and antibody production in Chinese Hamster Ovary cells.

Keywords:  Computational biology; Genome-scale model; Metabolism; Omic data; Secretory pathway; Systems biology

DOI:  https://doi.org/10.1016/j.ymben.2023.12.006
ACS Synth Biol. 2023 Dec 27.

Improving Cell-Free Expression of Model Membrane Proteins by Tuning Ribosome Cotranslational Membrane Association and Nascent Chain Aggregation.

Jan Steinkühler, Justin A Peruzzi, Antje Krüger, Citlayi G Villaseñor, Miranda L Jacobs, Michael C Jewett, Neha P Kamat.

  Cell-free gene expression (CFE) systems are powerful tools for transcribing and translating genes outside of a living cell. Synthesis of membrane proteins is of particular interest, but their yield in CFE is substantially lower than that for soluble proteins. In this paper, we study the CFE of membrane proteins and develop a quantitative kinetic model. We identify that ribosome stalling during the translation of membrane proteins is a strong predictor of membrane protein synthesis due to aggregation between the ribosome nascent chains. Synthesis can be improved by the addition of lipid membranes, which incorporate protein nascent chains and, therefore, kinetically compete with aggregation. We show that the balance between peptide-membrane association and peptide aggregation rates determines the yield of the synthesized membrane protein. We define a membrane protein expression score that can be used to rationalize the engineering of lipid composition and the N-terminal domain of a native and computationally designed membrane proteins produced through CFE.

Keywords:  PURE; biophysics; cell-free gene expression; cotranslational synthesis; membrane proteins; synthetic biology

DOI:  https://doi.org/10.1021/acssynbio.3c00357