How tension modulates cellular transport has become a topic of interest in the recent past. However, the effect of tension on clathrin assembly and vesicle growth remains less understood. Here, we ...use the classical Helfrich theory to predict the energetic cost that clathrin is required to pay to remodel the membrane at different stages of vesicle formation. Our study reveals that this energetic cost is highly sensitive to not only the tension in the membrane but also to the instantaneous geometry of the membrane during shape evolution. Our study predicts a sharp reduction in clathrin coat size in the intermediate tension regime (0.01-0.1 mN m
−1
). Remarkably, the natural propensity of the membrane to undergo bending beyond the Ω shape causes a significant decrease in the energy needed from clathrin to drive vesicle growth. Our studies in mammalian cells confirm a reduction in clathrin coat size in an increased tension environment. In addition, our findings suggest that the two apparently distinct clathrin assembly modes, namely coated pits and coated plaques, observed in experimental investigations might be a consequence of varied tensions in the plasma membrane. Overall, the mechano-geometric sensitivity revealed in this study might also be at play during the polymerization of other membrane remodeling proteins.
How tension modulates cellular transport has become a topic of interest in the recent past. Here, we elucidate how tension, along with membrane geometry, regulates clathrin assembly and vesicle growth during endocytosis.
Lipid membranes are selective barriers that encapsulate cellular components and define the identity of organelles. A fundamental feature of membranes is an asymmetric distribution of lipids and ...proteins across them. While a basic level of asymmetry is maintained at all times, local and transient increase in asymmetry is achieved to execute drastic morphological changes in the structure of the organelles and the plasma membrane. In this study, we computationally investigate a few such biological processes. First, we model the squeezing of mitochondria and show that asymmetrically distributed proteins and conical lipids can work synergistically to trigger buckling instabilities in order to generate extreme constrictions. Our work provides the physical explanation of the role of lipids in mitochondrial fission for the first time. Second, we model the formation of vesicles induced by asymmetrically distributed proteins during cellular transport. Our study reveals that the energetic cost of remodeling the membrane is highly sensitive to not only the tension in the membrane but also to the instantaneous geometry of the membrane during the shape evolution. Third, we model the adhesion of vesicles to planar substrates induced by asymmetric distribution of proteins across the membrane. Our work furnishes a novel universal relationship for the estimation of adhesion energy of the proteins from the shape of the adhered vesicle. Lastly, we experimentally investigate the role of charge asymmetry on membrane protein interaction. Our results suggest that the charge asymmetry is critical in regulating the level of protein insertion in the membrane which could potentially play a significant role in executing programmed cell death. Overall, our work provides new quantitative insights that could be valuable in understanding the remodeling of asymmetric membranes during other vital cellular processes.
Abstract
Background: The metabolic syndrome characterized in part by obesity, hyperinsulinemia, and insulin resistance is associated with increased risk of breast cancer. However there remains a need ...to establish a circulating biomarker metabolic profile indicative of increased risk of breast cancer. In the current study, we performed a comprehensive metabolomics screen to identify biomarkers indicative of increased risk of breast cancer. Methods: Unbiased metabolomics profiling was conducted on an initial Development Set of plasmas collected from 353 newly-diagnosed breast cancer cases and 141 controls. A deep learning neural network with 3 layers each containing 32 nodes based on 11 individual lipids corresponding to discrete lipid subclasses was built for risk prediction of breast cancer. The model was validated in an independent Test Set consisting of 79 breast cancer cases and 163 controls. Using a nested case:control matched design, we evaluated the performance of the model among body mass index (BMI) strata (≥ 30 or < 30kg/m2). Results: An 11-marker lipid biomarker panel encompassing lipid subclasses with known pro-inflammatory and tumor promoting roles yielded an AUC of 0.75 (95% CI: 0.70-0.79) for distinguishing breast cancer cases from controls in the Development Set. Predictive performance of the lipid panel was comparable when stratifying cases into hormone-receptor (HR) positive, HER2-positive/HR negative, and triple-negative breast cancer subtypes. The biomarker panel had an AUC of 0.74 (95% CI: 0.68-0.81) in the independent Test Set. The predictive performance of the panel was most pronounced among obese subjects (BMI ≥ 30) with an AUC of 0.81 (95% CI: 0.71-0.91) in the Test Set. Conclusions: The lipid-based biomarker panel has utility for identifying women with ‘metabolic obesity’ who are at increased risk of breast cancer and would benefit from tailored screening.
Citation Format: Johannes Fahrmann, Ehsan Irajizad, Jody Vykoukal, Angelica Gutierrez Barrera, Jennifer Dennison, Ranran Wu, Banu K. Arun, Abenaa Brewster, Samir Hanash. A blood-based lipid panel for personalized risk assessment of breast cancer abstract. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-05-26.
Abstract
Purpose: Emerging evidence implicates the microbiome in the development of pancreatic cancer. We investigated whether increased levels of microbial-related metabolites in circulation are ...associated with pancreatic cancer risk. Methods: We applied metabolomics profiling to sera from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cohort to quantify and build a model based on 14 microbial-related metabolites. The study involved samples collected from 172 subjects within five years prior to diagnosis and 863 matched controls. Data from five PLCO centers were used for training and from two centers for validation and model selection. The model was subsequently tested using samples from three independent centers. The contributions of non-microbial-associated metabolites as well as CA19-9 was also assessed. Results: A 3-marker microbial-related metabolite panel yielded in the PLCO testing set an AUC of 0.64 (95% CI: 0.53-0.76) for 5-year probability of pancreatic cancer. Five additional non-microbial metabolites were identified that when combined with the microbiome panel yielded an AUC of 0.79 (95% CI: 0.71-0.88) for 5-year probability of pancreatic cancer in the PLCO testing set. The combined metabolite panel and CA19-9 yielded an AUC of 0.86 (95% CI: 0.77-0.95) for 2-year probability of pancreatic cancer in the PLCO testing set, which was improved compared to CA19-9 alone (AUC: 0.70 (95% CI: 0.57-0.82), p< 0.001). Conclusion: We developed a metabolite panel derived in part from the microbiome for risk assessment of pancreatic cancer, which has relevance to prevention and early detection.
Citation Format: Johannes F. Fahrmann, Ehsan Irajizad, Ana Kenney, Tiffany Tang, Jody Vykoukal, Ranran Wu, Jennifer B. Dennison, Marta Sans Escofet, James P. Long, Maureen Loftus, John A. Chabot, Michael D. Kluger, Fay Kastrinos, Lauren Brais, Ana Babic, Kunal Jajoo, Linda S. Lee, Thomas E. Clancy, Kimmie Ng, Andrea Bullock, Jeanine M. Genkinger, Anirban Maitra, Kim-Anh Do, Bin Yu, Brian M. Wolpin, Samir Hanash. Contribution of the microbiome to a metabolomic signature predictive of risk for pancreatic cancer. abstract. In: Proceedings of the AACR Special Conference: Precision Prevention, Early Detection, and Interception of Cancer; 2022 Nov 17-19; Austin, TX. Philadelphia (PA): AACR; Can Prev Res 2023;16(1 Suppl): Abstract nr P076.
Abstract
Multiple Endocine Neoplasia Type 1 (MEN1) is associated with duodenopancreatic neuroendocrine tumors (dpNETs) and metastatic dpNET is the primary cause of disease-related mortality for this ...condition. Currently, there is a paucity of prognostic factors that can reliably identify patients with MEN1-related dpNETS who are at high risk of distant metastasis. Previously, we uncovered a blood-based polyamine metabolite signature that was associated with MEN1-dpNET disease progression. In the current study, we aimed to build upon our prior findings, by exploring the contributions of proteomics for identifying circulating protein markers associated with tumor progression. We performed in-depth proteomic analysis of serially collected plasmas from a genetically engineered mouse model of Men1-pNET, Men1fl/flPdx1-CreTg, and Men1fl/fl control mice to assess dynamic changes in the plasma proteome that associated with disease progression. Findings were compared to plasma proteomic profiles from a cohort of 56 patients with MEN1 (14 with distant metastasis dpNETs (cases) and 42 with either indolent dpNETs or no dpNETs (controls)). Analyses revealed 196 proteins related to oncogenic N-MYC, YAP1, POU5F1, and SMAD that were positively associated with pNET disease progression in Men1fl/flPdx1-CreTg mice. Similarly, 187 proteins were elevated in MEN1 patients with distant metastasis compared controls. Proteins with increased levels in metastatic cases included AMY2B, CELA3B, RNASE1, IGFBP2, CHI3L1, LYZ, TIMP1, LRG1, and COL18A1 previously associated with pancreatic cancer and other neuronal proteins. Cross-species intersection revealed 19 proteins including NDC80, DEF8, SPAG17, ATM, IMMT, DNAH6, DSP, CIT, HRG, CD79A, BDP1, SERPINA11, TARBP1, and SERPIND1 that were positively associated with disease progression in Men1fl/flPdx1-CreTg mice and human subjects. Our integrated analyses identified novel circulating protein features associated with disease progression in MEN1-related dpNET.
Citation Format: Johannes F. Fahrmann, Amanda R. Wasylishen, Carolina R.C. Pieterman, Ehsan Irajizad, Jody Vykoukal, Ranran Wu, Jennifer D. Dennison, Christine B. Peterson, Guillermina Lozano, Hua Zhao, Kim-Ahn Do, Daniel M. Halperin, Sunita K. Agarwal, Jenny E. Blau, Jaydira D. Rivero, Naris Nilubol, Mary F. Walter, James M. Welch, Lee S. Weinstein, Menno R. Vriens, Rachel S. van Leeuwaarde, Mark J.C. van Treijen, Gerlof D. Valk, Nancy D. Perrier, Sam M Hanash, Hiroyuki Katayama. Blood-based proteomic signatures associated with MEN1-related duodenopancreatic neuroendocrine tumor progression. abstract. In: Proceedings of the AACR Special Conference: Precision Prevention, Early Detection, and Interception of Cancer; 2022 Nov 17-19; Austin, TX. Philadelphia (PA): AACR; Can Prev Res 2023;16(1 Suppl): Abstract nr P066.
Emerging evidence implicates microbiome involvement in the development of pancreatic cancer (PaCa). Here, we investigate whether increases in circulating microbial-related metabolites associate with ...PaCa risk by applying metabolomics profiling to 172 sera collected within 5 years prior to PaCa diagnosis and 863 matched non-subject sera from participants in the Prostate, Lung, Colorectal, and Ovarian (PLCO) cohort. We develop a three-marker microbial-related metabolite panel to assess 5-year risk of PaCa. The addition of five non-microbial metabolites further improves 5-year risk prediction of PaCa. The combined metabolite panel complements CA19-9, and individuals with a combined metabolite panel + CA19-9 score in the top 2.5th percentile have absolute 5-year risk estimates of >13%. The risk prediction model based on circulating microbial and non-microbial metabolites provides a potential tool to identify individuals at high risk of PaCa that would benefit from surveillance and/or from potential cancer interception strategies.
Abstract
Activation of the nuclear factor erythroid 2-related factor 2 (NRF2) pathway, either through gain-of-function mutations in the NRF2 encoding gene NFE2L2 or through loss-of-function of its ...suppressor, Kelch-like ECH-associated protein 1 (KEAP1), is a frequent manifestation in various malignancies. NRF2 activation exerts pro-tumoral effects in part by altering cancer cell metabolism. We previously reported a novel mechanism of NRF2 tumoral immune suppression through selective upregulation of the tryptophan metabolizing enzyme kynureninase (KYNU) in lung adenocarcinoma. In the current study, we explored the Pan-Cancer relevance of NRF2-mediated KYNU upregulation. We analyzed the gene expression dataset for 9,801 tumors representing 32 cancer types in The Cancer Genome Atlas (TCGA). Elevated KYNU expression levels paralleled increased gene-based signatures of NRF2-activation and was strongly associated with an immunosuppressive tumor microenvironment, marked by high expression of gene-based signatures of Tregs as well as immune checkpoint blockade-related genes CD274 (PDL-1), PDCD1 (PD-1), and CTLA4, regardless of cancer type. Cox proportional hazard models further revealed that increased tumoral KYNU gene expression was prognostic for poor overall survival in several cancer types, including thymoma, acute myeloid leukemia, low grade glioma, kidney renal papillary cell carcinoma, gastric adenocarcinoma, and pancreatic ductal adenocarcinoma (PDAC). Using PDAC as a model system, we confirmed that siRNA-mediated knockdown of NRF2 reduces KYNU mRNA expression, whereas activation of NFE2L2 (the encoding gene for NRF2) through either small molecule agonists or siRNA-mediated knockdown of KEAP1 upregulated KYNU. Metabolomic analyses of conditioned media from PDAC cell lines revealed elevated levels of KYNU-derived anthranilate, confirming KYNU as enzymatically functional. Collectively, our findings highlight the multi-cancer relevance of the NRF2-KYNU axis and of tumoral KYNU as a prognostic marker of poor overall survival associated with immunosuppression.
Citation Format: Ricardo A. Leon Letelier, Ali H. Abdel Sater, Yihui Chen, Ranran Wu, Jennifer B. Dennison, Soyoung Park, Ehsan Irajizad, Hiroyuki Katayama, Jody Vykoukal, Samir Hanash, Edwin J. Ostrin, Johannes F. Fahrmann. KYNU upregulation is a prominent feature of NRF2-activated cancers and is associated with tumor immunosuppression and poor prognosis abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6031.
Abstract
Background: Gastric cancer is frequently diagnosed at an advanced stage and is associated with poor outcomes. Harnessing the immune response to tumor antigens which occurs early during tumor ...development has potential for the early detection of gastric cancer.
Methods: Plasma samples from gastric cancer patients were collected before and after treatment and from healthy controls for identification of immunoglobin (Ig)-bound antigens using mass spectrometry. Ingenuity pathway analysis(IPA) was utilized to investigate networks and pathways associated with Ig bound proteins identified in plasmas from cases. A combined biomarker panel was established based on a logistic-regression model and ROC analysis was used to assess panel performance.
Results: A total of 65 Ig bound proteins were identified that were upregulated in gastric cancer patients’ plasma compared with healthy control. Canonical pathways involving these immunogenic proteins included HIF-1α, VEGF, actin cytoskeleton, and immunogenic cell death signaling which play important roles in both gastric cancer development and progression. Four of the top ten performing proteins exhibited high mRNA levels in gastric cancer tissue. The association of these four Ig bound proteins in gastric cancer plasmas was further validated using as controls a cohort of MEN1 patients plasmas. A blood-biomarker panel based on these four biomarkers was established using a logistic-regression model which yielded an area under the curve (AUC) of 0.963 (95% confidential interval CI =0.89-1.00) for gastric cancer discrimination with a sensitivity of 0.889 at 95% specificity.
Conclusion: Our data reveal a panel of plasma Ig-bound antigens associated with the development of gastric cancer with potential application for early detection and monitoring.
Citation Format: Rongzhang Dou, Ehsan Irajizad, Yining Cai, Johannes F. Fahrmann, Jody V. Vykoukal, Yihui Chen, Hiroyuki Katayama, Ali H. Abdel Sater, Melissa Pizzi, Kohei Yamashita, Matheus Sewastjanow Da Silva, Edwin J. Ostrin, Jaffer Ajani, Samir M. Hanash. Development of a plasma biomarker panel for gastric cancer detection based on an autoimmune response signature. abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5304.
Abstract Purpose: To define the metabolic alterations associated with malignant progression of intraductal papillary mucinous neoplasm (IPMN). Experimental Procedures: Matrix-assisted laser ...desorption/ionization (MALDI)-mass spectrometry (MS) was conducted for spatial characterization of lipid profiles on frozen tissue sections from resected human IPMN patients. The specimen set consisted of either low-grade dysplasia (LG) (n=15), high-grade (HG) dysplasia (n=4), or with an associated pancreatic ductal adenocarcinoma (PDAC) (n=4) as well as 15 PDAC tissues. Utilizing serial sections to the same human IPMN cases analyzed with MALDI-MS imaging, we used the Visium Spatial Gene Expression technology platform to characterize the spatiomolecular underpinnings of LG and HG IPMN. H&E images of the same tissue section used for the Visium workflow, were used to annotate the spots in the dataset covering the epithelial lining of the IPMN lesions (“epilesional” areas) and the spots covering the adjacent microenvironment surrounding the lesion (“perilesiopecific” area). Findings were compared with lipidomic analyses of cystic fluid from 89 IPMN patients. The anti-cancer efficacy of UGT8-IN-1, a selective small molecule inhibitor of ceramide galactosyltransferase (CGT, also known as UGT8), was assessed in vitro and in mutant Kras;Gnas allografts. Results: MALDI/MS-based spatial imaging of human resected IPMN tissues and pancreata from a mutant Kras;Gnas mouse model of IPMN revealed long-chain hydroxylated sulfatides, particularly the C24:0(OH) and C24:1(OH) species, to be selectively enriched in the IPMN and PDAC neoplastic epithelium. Visium spatial transcriptomics data confirmed that the cognate transcripts engaged in sulfatide biosynthesis, including UGT8, Gal3St1, and FA2H, were co-localized with areas of sulfatide enrichment. Lipidomic analyses of cystic fluid from 89 patients with IPMN identified several sulfatide species to be significantly elevated in patients with IPMN/PDAC compared to those with low-grade IPMN. Inhibition of sulfatide metabolism via UGT8-IN-1 reduced viability of Kras;Gnas murine cell lines in vitro and attenuated tumor growth in an allograft IPMN model. UGT8-IN-1 treatment resulted in reduced levels of several sulfatide species, accompanied by a concomitant increase in a subset of quantified sulfatides precursor ceramides, accumulation of mitochondrial mass and reactive oxygen species and time-dependent increases in autophagy/mitophagy markers p62/SQSTM1 and LC-3B, suggesting impaired mitophagy. Conclusion: Enhanced sulfatide metabolism is an early alteration in cystic pre-cancerous lesions of the pancreas that persists through invasive neoplasia. Targeting sulfatide biosynthesis might represent an actionable vulnerability for cancer interception. Citation Format: Yihui Chen, Marta Sans, Fredrik Thege, Rongzhang Dou, Jimin Min, Michele Yip-Schneider, Jianjun Zhang, Ranran Wu, Ehsan Irajizad, Yuki Makino, Kimal Rajapakshe, Mark Hurd, Ricardo León-Letelier, Jody Vykoukal, Jennifer Dennison, Kim-Anh Do, Robert Wolff, Paola Guerrero, Michael Kim, Max Schmidt, Anirban Maitra, Samir Hanash, Johannes Fahrmann. Integrated spatial transcriptomics and lipidomics analyses of intraductal papillary mucinous neoplasm identifies enrichment of long chain sulfatide as an early metabolic alteration abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 446.
Accessible prebiotic foods hold strong potential to jointly target gut health and metabolic health in high-risk patients. The BE GONE trial targeted the gut microbiota of obese surveillance patients ...with a history of colorectal neoplasia through a straightforward bean intervention.
This low-risk, non-invasive dietary intervention trial was conducted at MD Anderson Cancer Center (Houston, TX, USA). Following a 4-week equilibration, patients were randomized to continue their usual diet without beans (control) or to add a daily cup of study beans to their usual diet (intervention) with immediate crossover at 8-weeks. Stool and fasting blood were collected every 4 weeks to assess the primary outcome of intra and inter-individual changes in the gut microbiome and in circulating markers and metabolites within 8 weeks. This study was registered on ClinicalTrials.gov as NCT02843425, recruitment is complete and long-term follow-up continues.
Of the 55 patients randomized by intervention sequence, 87% completed the 16-week trial, demonstrating an increase on-intervention in diversity n = 48; linear mixed effect and 95% CI for inverse Simpson index: 0.16 (0.02, 0.30); p = 0.02 and shifts in multiple bacteria indicative of prebiotic efficacy, including increased Faecalibacterium, Eubacterium and Bifidobacterium (all p < 0.05). The circulating metabolome showed parallel shifts in nutrient and microbiome-derived metabolites, including increased pipecolic acid and decreased indole (all p < 0.002) that regressed upon returning to the usual diet. No significant changes were observed in circulating lipoproteins within 8 weeks; however, proteomic biomarkers of intestinal and systemic inflammatory response, fibroblast-growth factor-19 increased, and interleukin-10 receptor-α decreased (p = 0.01).
These findings underscore the prebiotic and potential therapeutic role of beans to enhance the gut microbiome and to regulate host markers associated with metabolic obesity and colorectal cancer, while further emphasizing the need for consistent and sustainable dietary adjustments in high-risk patients.
This study was funded by the American Cancer Society.
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