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Defining the ontogeny of tumor-associated macrophages (TAM) is important to develop therapeutic targets for mesothelioma. We identified two distinct macrophage populations in mouse peritoneal and pleural cavities, the monocyte-derived, small peritoneal/pleural macrophages (SPM), and the tissue-resident large peritoneal/pleural macrophages (LPM). SPM rapidly increased in tumor microenvironment after tumor challenge and contributed to the vast majority of M2-like TAM. The selective depletion of M2-like TAM by conditional deletion of the Dicer1 gene in myeloid cells (D-/-) promoted tumor rejection. Sorted SPM M2-like TAM initiated tumorigenesis in vivo and in vitro, confirming their capacity to support tumor development. The transcriptomic and single-cell RNA sequencing analysis demonstrated that both SPM and LPM contributed to the tumor microenvironment by promoting the IL-2-STAT5 signaling pathway, inflammation, and epithelial-mesenchymal transition. However, while SPM preferentially activated the KRAS and TNF-α/NFkB signaling pathways, LPM activated the IFN-γ response. The importance of LPM in the immune response was confirmed by depleting LPM with intrapleural clodronate liposomes, which abrogated the antitumoral memory immunity. SPM gene signature could be identified in pleural effusion and tumor from patients with untreated mesothelioma. Five genes, TREM2, STAB1, LAIR1, GPNMB, and MARCO, could potentially be specific therapeutic targets. Accordingly, Trem2 gene deletion led to reduced SPM M2-like TAM with compensatory increase in LPM and slower tumor growth. Overall, these experiments demonstrate that SPM M2-like TAM play a key role in mesothelioma development, while LPM more specifically contribute to the immune response. Therefore, selective targeting of monocyte-derived TAM may enhance antitumor immunity through compensatory expansion of tissue-resident TAM.
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Mesotelioma Maligno , Mesotelioma , Animales , Ratones , Mesotelioma Maligno/metabolismo , Mesotelioma Maligno/patología , Macrófagos Asociados a Tumores/patología , Macrófagos/metabolismo , Mesotelioma/metabolismo , Monocitos/patología , Microambiente Tumoral , Glicoproteínas de Membrana/metabolismo , Receptores Inmunológicos/metabolismo , Moléculas de Adhesión Celular Neuronal/metabolismoRESUMEN
INTRODUCTION: Lung transplantation is an established treatment for patients with end-stage lung disease. However, ischaemia reperfusion injury remains a barrier to achieving better survival outcomes. Here, we aim to investigate the metabolomic and transcriptomic profiles in human lungs before and after reperfusion, to identify mechanisms relevant to clinical outcome. METHODS: We analysed 67 paired human lung tissue samples collected from 2008 to 2011, at the end of cold preservation and 2 hours after reperfusion. Gene expression analysis was performed with R. Pathway analysis was conducted with Ingenuity Pathway Analysis. MetaboAnalyst and OmicsNet were used for metabolomics analysis and omics data integration, respectively. Association of identified metabolites with transplant outcome was investigated with Kaplan-Meier estimate and Cox proportional hazard models. RESULTS: Activation of energy metabolism and reduced antioxidative biochemicals were found by metabolomics. Upregulation of genes related to cytokines and inflammatory mediators, together with major signalling pathways were revealed by transcriptomics. Purine metabolism was identified as the most significantly enriched pathway at reperfusion, based on integrative analysis of the two omics data sets. Elevated expression of purine nucleoside phosphorylase (PNP) could be attributed to activation of multiple transcriptional pathways. PNP catabolised reactions were evidenced by changes in related metabolites, especially decreased levels of inosine and increased levels of uric acid. Multivariable analyses showed significant association of inosine and uric acid levels with intensive care unit length of stay and ventilation time. CONCLUSION: Oxidative stress, especially through purine metabolism pathway, is a major metabolic event during reperfusion and may contribute to the ischaemia reperfusion injury of lung grafts.
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Trasplante de Pulmón , Daño por Reperfusión , Humanos , Ácido Úrico , Pulmón/metabolismo , Reperfusión , Daño por Reperfusión/metabolismo , Inosina/metabolismoRESUMEN
BACKGROUND AND AIMS: Kupffer cells (KCs) are the resident intravascular phagocyte population of the liver and critical to the capture and killing of bacteria. Calcineurin/nuclear factor of activated T cells (NFAT) inhibitors (CNIs) such as tacrolimus are used to prevent rejection in solid organ transplant recipients. Although their effect on lymphocytes has been studied extensively, there are limited experimental data about if and how CNIs shape innate immunity, and whether this contributes to the higher rates of infection observed in patients taking CNIs. APPROACH AND RESULTS: Here, we investigated the impact of tacrolimus treatment on innate immunity and, more specifically, on the capability of Kupffer cells (KCs) to fight infections. Retrospective analysis of data of >2,700 liver transplant recipients showed that taking calcineurin inhibitors such as tacrolimus significantly increased the likelihood of Staphylococcus aureus infection. Using a mouse model of acute methicillin-resistant S. aureus (MRSA) bacteremia, most bacteria were sequestered in the liver and we found that bacteria were more likely to disseminate and kill the host in tacrolimus-treated mice. Using imaging, we unveiled the mechanism underlying this observation: the reduced capability of KCs to capture, phagocytose, and destroy bacteria in tacrolimus-treated animals. Furthermore, in a gene expression analysis of infected KCs, the triggering receptor expressed on myeloid cells 1 (TREM1) pathway was the one with the most significant down-regulation after tacrolimus treatment. TREM1 inhibition likewise inhibited KC bacteria capture. TREM1 levels on neutrophils as well as the overall neutrophil response after infection were unaffected by tacrolimus treatment. CONCLUSIONS: Our results indicate that tacrolimus treatment has a significant impact directly on KCs and on TREM1, thereby compromising their capacity to fend off infections.
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Bacteriemia/etiología , Inmunosupresores/efectos adversos , Macrófagos del Hígado/efectos de los fármacos , Trasplante de Órganos/efectos adversos , Infecciones Estafilocócicas/etiología , Tacrolimus/efectos adversos , Animales , Femenino , Citometría de Flujo , Humanos , Inmunosupresores/uso terapéutico , Macrófagos del Hígado/fisiología , Masculino , Staphylococcus aureus Resistente a Meticilina , Ratones , Persona de Mediana Edad , Trasplante de Órganos/métodos , Fagocitosis/efectos de los fármacos , Especies Reactivas de Oxígeno/metabolismo , Estudios Retrospectivos , Tacrolimus/uso terapéuticoRESUMEN
INTRODUCTION: Transplantation of lungs from donation after circulatory death (DCD) in addition to donation after brain death (DBD) became routine worldwide to address the global organ shortage. The development of ex vivo lung perfusion (EVLP) for donor lung assessment and repair contributed to the increased use of DCD lungs. We hypothesise that a better understanding of the differences between lungs from DBD and DCD donors, and between EVLP and directly transplanted (non-EVLP) lungs, will lead to the discovery of the injury-specific targets for donor lung repair and reconditioning. METHODS: Tissue biopsies from human DBD (n=177) and DCD (n=65) donor lungs, assessed with or without EVLP, were collected at the end of cold ischaemic time. All samples were processed with microarray assays. Gene expression, network and pathway analyses were performed using R, Ingenuity Pathway Analysis and STRING. Results were validated with protein assays, multiple logistic regression and 10-fold cross-validation. RESULTS: Our analyses showed that lungs from DBD donors have upregulation of inflammatory cytokines and pathways. In contrast, DCD lungs display a transcriptome signature of pathways associated with cell death, apoptosis and necrosis. Network centrality revealed specific drug targets to rehabilitate DBD lungs. Moreover, in DBD lungs, tumour necrosis factor receptor-1/2 signalling pathways and macrophage migration inhibitory factor-associated pathways were activated in the EVLP group. A panel of genes that differentiate the EVLP from the non-EVLP group in DBD lungs was identified. CONCLUSION: The examination of gene expression profiling indicates that DBD and DCD lungs have distinguishable biological transcriptome signatures.
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Trasplante de Pulmón , Transcriptoma , Circulación Extracorporea , Humanos , Pulmón , Perfusión , Donantes de TejidosRESUMEN
BACKGROUND: Chemokines are major regulators of cell trafficking and adhesion. The chemokine CXCL12 and its receptors, CXCR4 and CXCR7, have been reported as biomarkers in various cancers, including esophageal cancer; however, there are few studies in esophageal adenocarcinoma (EAC). In this study, we investigated the relationship between expression of CXCL12, CXCR4, and CXCR7, and prognosis in patients with EAC. METHODS: This study examined 55 patients with EAC who were treated in Toronto General Hospital from 2001 to 2010. Tissue microarray immunohistochemistry was used to evaluate the expression of CXCL12, CXCR4, and CXCR7. Evaluation of immunohistochemistry was performed by a pathologist without knowledge of patients' information and results were compared with the patients' clinicopathological features and survival. RESULTS: High CXCR7 expression was significantly associated with lymphatic invasion (present vs absent, P = 0.005) and higher number of lymph node metastases (pN0-1 vs pN2-3, P = 0.0014). Patients with high CXCR7 expression (n = 23) were associated with worse overall (OS) and disease-free survival (DFS) (P = 0.0221, P = 0.0090, respectively), and patients with high CXCL12 (n = 24) tended to have worse OS and DFS (P = 0.1091, P = 0.1477, respectively). High expression of both CXCR7 and CXCL12 was an independent prognostic factor for OS and DFS on multivariate analysis (HR = 0.3, 95% CI: 0.1-0.9, P = 0.0246, HR = 0.3, 95% CI: 0.1-0.8, P = 0.0134, respectively). CONCLUSIONS: High CXCR7 expression was associated with poor prognosis in patients with EAC, and high expression of CXCR7 with its ligand CXCL12 had a stronger association with prognosis. Further study of this potential biomarker using whole tissue samples and a larger sample size is warranted.
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Adenocarcinoma , Neoplasias Esofágicas , Receptores CXCR , Quimiocina CXCL12 , Humanos , Metástasis Linfática , Pronóstico , Receptores CXCR4RESUMEN
BACKGROUND AND AIMS: Liver transplantation (LT) can be offered to patients with Hepatocellular carcinoma (HCC) beyond Milan criteria. However, there are currently limited molecular markers on HCC explant histology to predict recurrence, which arises in up to 20% of LT recipients. The goal of our study was to derive a combined proteomic/transcriptomic signature on HCC explant predictive of recurrence post-transplant using unbiased, high-throughput approaches. METHODS: Patients who received a LT for HCC beyond Milan criteria in the context of hepatitis B cirrhosis were identified. Tumor explants from patients with post-transplant HCC recurrence (N = 7) versus those without recurrence (N = 4) were analyzed by mass spectrometry and gene expression array. Univariate analysis was used to generate a combined proteomic/transcriptomic signature linked to recurrence. Significantly predictive genes and proteins were verified and internally validated by immunoblotting and immunohistochemistry. RESULTS: Seventy-nine proteins and 636 genes were significantly differentially expressed in HCC tumors with subsequent recurrence (p < 0.05). Univariate survival analysis identified Aldehyde Dehydrogenase 1 Family Member A1 (ALDH1A1) gene (HR = 0.084, 95%CI 0.01-0.68, p = 0.0152), ALDH1A1 protein (HR = 0.039, 95%CI 0.16-0.91, p = 0.03), Galectin 3 Binding Protein (LGALS3BP) gene (HR = 7.14, 95%CI 1.20-432.96, p = 0.03), LGALS3BP protein (HR = 2.6, 95%CI 1.1-6.1, p = 0.036), Galectin 3 (LGALS3) gene (HR = 2.89, 95%CI 1.01-8.3, p = 0.049) and LGALS3 protein (HR = 2.6, 95%CI 1.2-5.5, p = 0.015) as key dysregulated analytes in recurrent HCC. In concordance with our proteome findings, HCC recurrence was linked to decreased ALDH1A1 and increased LGALS3 protein expression by Western Blot. LGALS3BP protein expression was validated in 29 independent HCC samples. CONCLUSIONS: Significantly increased LGALS3 and LGALS3BP gene and protein expression on explant were associated with post-transplant recurrence, whereas increased ALDH1A1 was associated with absence of recurrence in patients transplanted for HCC beyond Milan criteria. This combined proteomic/transcriptomic signature could help in predicting HCC recurrence risk and guide post-transplant surveillance.
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INTRODUCTION: Liver regeneration is a normal response to liver injury. The aim of this study was to determine the molecular basis of liver regeneration, through an integrative analysis of high-throughput gene expression datasets. METHODS: We identified and curated datasets pertaining to liver regeneration from the Gene Expression Omnibus, where regenerating liver tissue was compared to healthy liver samples. The key dysregulated genes and pathways were identified using Ingenuity Pathway Analysis software. There were three eligible datasets in total. RESULTS: In the early phase after hepatectomy, inflammatory pathways such as Nrf2 oxidative stress-mediated response and cytokine signaling were significantly upregulated. At peak regeneration, we discovered that cell cycle genes were predominantly expressed to promote cell proliferation. Using the Betweenness centrality algorithm, we discovered that Jun is the key central gene in liver regeneration. Calcineurin inhibitors may inhibit liver regeneration, based on predictive modeling. CONCLUSION: There is a paucity of human literature in defining the molecular mechanisms of liver regeneration along a time continuum. Nonetheless, using an integrative computational analysis approach to the available high-throughput data, we determine that the oxidative stress response and cytokine signaling are key early after hepatectomy, whereas cell cycle control is important at peak regeneration. The transcription factor Jun is central to liver regeneration and a potential therapeutic target. Future studies of regeneration in humans along a time continuum are needed to better define the underlying mechanisms, and ultimately enhance care of patients with acute and chronic liver failure while awaiting transplant.
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Regulación de la Expresión Génica , Hepatectomía , Regeneración Hepática/genética , Transducción de Señal/genética , Biología de Sistemas/métodos , Animales , Recolección de Datos , Conjuntos de Datos como Asunto , Factor de Crecimiento Epidérmico/genética , Femenino , Factores de Crecimiento de Fibroblastos/genética , Humanos , Trasplante de Hígado/métodos , Masculino , Valores de Referencia , Factor de Necrosis Tumoral alfa/genéticaRESUMEN
BACKGROUND: Medulloblastoma is associated with rare hereditary cancer predisposition syndromes; however, consensus medulloblastoma predisposition genes have not been defined and screening guidelines for genetic counselling and testing for paediatric patients are not available. We aimed to assess and define these genes to provide evidence for future screening guidelines. METHODS: In this international, multicentre study, we analysed patients with medulloblastoma from retrospective cohorts (International Cancer Genome Consortium [ICGC] PedBrain, Medulloblastoma Advanced Genomics International Consortium [MAGIC], and the CEFALO series) and from prospective cohorts from four clinical studies (SJMB03, SJMB12, SJYC07, and I-HIT-MED). Whole-genome sequences and exome sequences from blood and tumour samples were analysed for rare damaging germline mutations in cancer predisposition genes. DNA methylation profiling was done to determine consensus molecular subgroups: WNT (MBWNT), SHH (MBSHH), group 3 (MBGroup3), and group 4 (MBGroup4). Medulloblastoma predisposition genes were predicted on the basis of rare variant burden tests against controls without a cancer diagnosis from the Exome Aggregation Consortium (ExAC). Previously defined somatic mutational signatures were used to further classify medulloblastoma genomes into two groups, a clock-like group (signatures 1 and 5) and a homologous recombination repair deficiency-like group (signatures 3 and 8), and chromothripsis was investigated using previously established criteria. Progression-free survival and overall survival were modelled for patients with a genetic predisposition to medulloblastoma. FINDINGS: We included a total of 1022 patients with medulloblastoma from the retrospective cohorts (n=673) and the four prospective studies (n=349), from whom blood samples (n=1022) and tumour samples (n=800) were analysed for germline mutations in 110 cancer predisposition genes. In our rare variant burden analysis, we compared these against 53â105 sequenced controls from ExAC and identified APC, BRCA2, PALB2, PTCH1, SUFU, and TP53 as consensus medulloblastoma predisposition genes according to our rare variant burden analysis and estimated that germline mutations accounted for 6% of medulloblastoma diagnoses in the retrospective cohort. The prevalence of genetic predispositions differed between molecular subgroups in the retrospective cohort and was highest for patients in the MBSHH subgroup (20% in the retrospective cohort). These estimates were replicated in the prospective clinical cohort (germline mutations accounted for 5% of medulloblastoma diagnoses, with the highest prevalence [14%] in the MBSHH subgroup). Patients with germline APC mutations developed MBWNT and accounted for most (five [71%] of seven) cases of MBWNT that had no somatic CTNNB1 exon 3 mutations. Patients with germline mutations in SUFU and PTCH1 mostly developed infant MBSHH. Germline TP53 mutations presented only in childhood patients in the MBSHH subgroup and explained more than half (eight [57%] of 14) of all chromothripsis events in this subgroup. Germline mutations in PALB2 and BRCA2 were observed across the MBSHH, MBGroup3, and MBGroup4 molecular subgroups and were associated with mutational signatures typical of homologous recombination repair deficiency. In patients with a genetic predisposition to medulloblastoma, 5-year progression-free survival was 52% (95% CI 40-69) and 5-year overall survival was 65% (95% CI 52-81); these survival estimates differed significantly across patients with germline mutations in different medulloblastoma predisposition genes. INTERPRETATION: Genetic counselling and testing should be used as a standard-of-care procedure in patients with MBWNT and MBSHH because these patients have the highest prevalence of damaging germline mutations in known cancer predisposition genes. We propose criteria for routine genetic screening for patients with medulloblastoma based on clinical and molecular tumour characteristics. FUNDING: German Cancer Aid; German Federal Ministry of Education and Research; German Childhood Cancer Foundation (Deutsche Kinderkrebsstiftung); European Research Council; National Institutes of Health; Canadian Institutes for Health Research; German Cancer Research Center; St Jude Comprehensive Cancer Center; American Lebanese Syrian Associated Charities; Swiss National Science Foundation; European Molecular Biology Organization; Cancer Research UK; Hertie Foundation; Alexander and Margaret Stewart Trust; V Foundation for Cancer Research; Sontag Foundation; Musicians Against Childhood Cancer; BC Cancer Foundation; Swedish Council for Health, Working Life and Welfare; Swedish Research Council; Swedish Cancer Society; the Swedish Radiation Protection Authority; Danish Strategic Research Council; Swiss Federal Office of Public Health; Swiss Research Foundation on Mobile Communication; Masaryk University; Ministry of Health of the Czech Republic; Research Council of Norway; Genome Canada; Genome BC; Terry Fox Research Institute; Ontario Institute for Cancer Research; Pediatric Oncology Group of Ontario; The Family of Kathleen Lorette and the Clark H Smith Brain Tumour Centre; Montreal Children's Hospital Foundation; The Hospital for Sick Children: Sonia and Arthur Labatt Brain Tumour Research Centre, Chief of Research Fund, Cancer Genetics Program, Garron Family Cancer Centre, MDT's Garron Family Endowment; BC Childhood Cancer Parents Association; Cure Search Foundation; Pediatric Brain Tumor Foundation; Brainchild; and the Government of Ontario.
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Biomarcadores de Tumor/genética , Neoplasias Cerebelosas/genética , Metilación de ADN , Pruebas Genéticas/métodos , Mutación de Línea Germinal , Meduloblastoma/genética , Modelos Genéticos , Adolescente , Adulto , Neoplasias Cerebelosas/mortalidad , Neoplasias Cerebelosas/patología , Neoplasias Cerebelosas/terapia , Niño , Preescolar , Análisis Mutacional de ADN , Femenino , Perfilación de la Expresión Génica , Predisposición Genética a la Enfermedad , Herencia , Humanos , Lactante , Masculino , Meduloblastoma/mortalidad , Meduloblastoma/patología , Meduloblastoma/terapia , Linaje , Fenotipo , Valor Predictivo de las Pruebas , Supervivencia sin Progresión , Estudios Prospectivos , Reproducibilidad de los Resultados , Estudios Retrospectivos , Factores de Riesgo , Transcriptoma , Secuenciación del Exoma , Adulto JovenRESUMEN
Graft injury affects over 50% of liver transplant (LT) recipients, but non-invasive biomarkers to diagnose and guide treatment are currently limited. We aimed to develop a biomarker of graft injury by integrating serum metabolomic profiles with clinical variables. Serum from 55 LT recipients with biopsy confirmed metabolic dysfunction-associated steatohepatitis (MASH), T-cell mediated rejection (TCMR) and biliary complications was collected and processed using a combination of LC-MS/MS assay. The metabolomic profiles were integrated with clinical information using a multi-class Machine Learning (ML) classifier. The model's efficacy was assessed through the Out-of-Bag (OOB) error estimate evaluation. Our ML model yielded an overall accuracy of 79.66% with an OOB estimate of the error rate at 19.75%. The model exhibited a maximum ability to distinguish MASH, with an OOB error estimate of 7.4% compared to 22.2% for biliary and 29.6% for TCMR. The metabolites serine and serotonin emerged as the topmost predictors. When predicting binary outcomes using three models: Biliary (biliary vs. rest), MASH (MASH vs. rest) and TCMR (TCMR vs. rest); the AUCs were 0.882, 0.972 and 0.896, respectively. Our ML tool integrating serum metabolites with clinical variables shows promise as a non-invasive, multi-class serum biomarker of graft pathology.
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OBJECTIVE: Previous reports showed enhanced graft function in both healthy and injured porcine lungs after preservation at 10 °C. The objective of the study is to elucidate the mechanism of lung protection by 10 °C and identify potential therapeutic targets to improve organ preservation. METHODS: Metabolomics data were analyzed from healthy and injured porcine lungs that underwent extended hypothermic preservation on ice and at 10 °C. Tissue sampled before and after preservation were subjected to untargeted metabolic profiling. Principal component analysis was performed to test for the separability of the paired samples. Significantly changed metabolites between the 2 time points were identified and analyzed to determine the underlying metabolic pathways. The levels of respiratory activity of lung tissue at hypothermic temperatures were confirmed using high resolution respirometry. RESULTS: In both healthy and injured lungs (n = 5 per intervention), principal component analysis suggested minimal change in metabolites after ice preservation but significant change of metabolites after 10 °C preservation, which was associated with significantly improved lung function as assessed by ex vivo lung perfusion and lung transplantation. For healthy lungs, lipid energy pathway was found primarily active at 10 °C. For injured lungs, additional carbohydrate energy pathway and anti-ferroptosis pathways aiding organ repair were identified. These metabolic features are also key features involved in mammal hibernation. CONCLUSIONS: Untargeted metabolomics revealed a dynamic metabolic gradient for lungs stored at 10 °C. Elucidating the underlying mechanisms behind this pathway regulation may lead to strategies that will allow organs "hibernate" for days, potentially making organ banking a reality.
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Cancer, one of the leading causes of death worldwide, is a disease characterized by uncontrolled cell growth within the body. While there have been many improvements in the treatment of cancer clinically, there is now an urgent need to improve cancer-related communication. This study explores the impact of online health information, specifically cancer-related information and prevention, among members of the general public. Through a randomized survey, we examined what information leads people to take action to minimize their cancer risk and communicate with their providers. Through evaluation of the various modes of communication, we were able to provide insight into which are more effective and better received by members of the general public. Through this, ways of bettering these avenues of communication and strengthening the bond between them will be highlighted and more easily elaborated on by future studies. The results of our study indicated that 60% of participants asserted that they are motivated by online preventive information to take steps to limit their cancer risk, while only roughly 44% of participants overall agreed that their doctor has communicated with them about when proper cancer screenings should be scheduled for the future. Although patients may be turning to the Internet now more than ever due to various reasons, when comparing self-reported rates of comprehension among the study participants, 35% agreed that the cancer-related information they can access online is confusing, while fewer than 22% of participants agreed that the cancer-related information they receive directly from their doctor is confusing. This is indicative of the limitations the Internet may have when undertaking the role of being a medical resource, especially when acting as a replacement for in-person medical appointments where patients can communicate directly with their physicians. Ultimately, these results provide a unique perspective into how people receive, evaluate, and implement cancer-preventive steps and general health-related information in a post-COVID-19 world, where the Internet is now strongly embedded in healthcare.
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Long-term survival of transplant recipients is significantly impacted by malignancy. We aimed to determine whether calcineurin inhibitor (CNI)-treated recipients converted to and weaned off molecular target of rapamycin inhibitor (mTOR-I) therapy have favorable changes in their molecular profiles in regard to malignancy risk. We performed gene expression profiling from liver biopsy and blood (PBMC) specimens followed by network analysis of key dysregulated genes, associated diseases and disorders, molecular and cellular functions using IPA software. Twenty non-immune, non-viremic patients were included, and 8 of them achieved tolerance. Two comparisons were performed: (1) tolerance time point vs tacrolimus monotherapy and (2) tolerance time point vs sirolimus monotherapy. Upon achieving tolerance, IPA predicted significant activation of DNA damage response (p = 5.40e-04) and inhibition of DNA replication (p = 7.56e-03). Conversion from sirolimus to tolerance showed decrease in HCC (p = 1.30e-02), hepatic steatosis (p = 5.60e-02) and liver fibrosis (p = 2.91e-02) associated genes. In conclusion, this longitudinal study of patients eventually achieving tolerance reveals an evolving molecular profile associated with decreased cancer risk and improved hepatic steatosis and liver fibrosis. This provides a biological rationale for attempting conversion to mTOR-I therapy and tolerance following liver transplantation particularly in patients at higher risk of cancer incidence and progression post-transplant.
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Carcinoma Hepatocelular , Neoplasias Hepáticas , Trasplante de Hígado , Humanos , Inmunosupresores/efectos adversos , Trasplante de Hígado/efectos adversos , Carcinoma Hepatocelular/epidemiología , Carcinoma Hepatocelular/genética , Estudios Longitudinales , Leucocitos Mononucleares , Neoplasias Hepáticas/epidemiología , Neoplasias Hepáticas/genética , Sirolimus , Cirrosis Hepática , Serina-Treonina Quinasas TOR , Rechazo de Injerto , Receptores de TrasplantesRESUMEN
Background: Non-alcoholic steatohepatitis (NASH) has become a leading indication for liver transplantation. However, it often recurs in the graft and can also arise de novo in individuals transplanted for other indications. Post-transplant NASH (PT-NASH) is more aggressive and leads to accelerated fibrosis. The mechanistic basis of PT-NASH has not yet been defined and no specific therapeutic strategies are currently available. Methods: Here, we profiled the transcriptomes of livers with PT-NASH from liver transplant recipients to identify dysregulated genes, pathways, and molecular interaction networks. Results: Transcriptomic changes in the PI3K-Akt pathway were observed in association with metabolic alterations in PT-NASH. Other significant changes in gene expression were associated with DNA replication, cell cycle, extracellular matrix organization, and wound healing. A systematic comparison with non-transplant NASH (NT-NASH) liver transcriptomes indicated an increased activation of wound healing and angiogenesis pathways in the post-transplant condition. Conclusion: Beyond altered lipid metabolism, dysregulation of wound healing and tissue repair mechanisms may contribute to the accelerated development of fibrosis associated with PT-NASH. This presents an attractive therapeutic avenue to explore for PT-NASH to optimize the benefit and survival of the graft.
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Trasplante de Hígado , Enfermedad del Hígado Graso no Alcohólico , Humanos , Transcriptoma , Enfermedad del Hígado Graso no Alcohólico/genética , Fosfatidilinositol 3-Quinasas , Perfilación de la Expresión GénicaRESUMEN
Cancer is pervasive across multicellular species, but what explains differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades (amphibians, sauropsids and mammals) we found that neoplasia and malignancy prevalence increases with adult weight (contrary to Peto's Paradox) and somatic mutation rate, but decreases with gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%) the black-footed penguin (<0.4%), ferrets (63%) and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer.
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Cancer is pervasive across multicellular species. Are there any patterns that can explain differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades (amphibians, sauropsids and mammals) we found that neoplasia and malignancy prevalence increases with adult weight and decreases with gestation time, contrary to Petoâ™s Paradox. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%) the black-footed penguin (<0.4%), ferrets (63%) and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer.
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BACKGROUND: Sporadic Amyotrophic Lateral Sclerosis (sALS) is a devastating, complex disease of unknown etiology. We studied this disease with microarray technology to capture as much biological complexity as possible. The Affymetrix-focused BaFL pipeline takes into account problems with probes that arise from physical and biological properties, so we adapted it to handle the long-oligonucleotide probes on our arrays (hence LO-BaFL). The revised method was tested against a validated array experiment and then used in a meta-analysis of peripheral white blood cells from healthy control samples in two experiments. We predicted differentially expressed (DE) genes in our sALS data, combining the results obtained using the TM4 suite of tools with those from the LO-BaFL method. Those predictions were tested using qRT-PCR assays. RESULTS: LO-BaFL filtering and DE testing accurately predicted previously validated DE genes in a published experiment on coronary artery disease (CAD). Filtering healthy control data from the sALS and CAD studies with LO-BaFL resulted in highly correlated expression levels across many genes. After bioinformatics analysis, twelve genes from the sALS DE gene list were selected for independent testing using qRT-PCR assays. High-quality RNA from six healthy Control and six sALS samples yielded the predicted differential expression for 7 genes: TARDBP, SKIV2L2, C12orf35, DYNLT1, ACTG1, B2M, and ILKAP. Four of the seven have been previously described in sALS studies, while ACTG1, B2M and ILKAP appear in the context of this disease for the first time. Supplementary material can be accessed at: http://webpages.uncc.edu/~cbaciu/LO-BaFL/supplementary_data.html. CONCLUSION: LO-BaFL predicts DE results that are broadly similar to those of other methods. The small healthy control cohort in the sALS study is a reasonable foundation for predicting DE genes. Modifying the BaFL pipeline allowed us to remove noise and systematic errors, improving the power of this study, which had a small sample size. Each bioinformatics approach revealed DE genes not predicted by the other; subsequent PCR assays confirmed seven of twelve candidates, a relatively high success rate.
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Esclerosis Amiotrófica Lateral/genética , Perfilación de la Expresión Génica/estadística & datos numéricos , Análisis de Secuencia por Matrices de Oligonucleótidos/estadística & datos numéricos , Programas Informáticos , Interpretación Estadística de Datos , Humanos , Leucocitos/metabolismo , Análisis por Micromatrices/métodosRESUMEN
Rapid development of biotechnology has led to the generation of vast amounts of multi-omics data, necessitating the advancement of bioinformatics and artificial intelligence to enable computational modeling to diagnose and predict clinical outcome. Both conventional machine learning and new deep learning algorithms screen existing data unbiasedly to uncover patterns and create models that can be valuable in informing clinical decisions. We summarized published literature on the use of AI models trained on omics datasets, with and without clinical data, to diagnose, risk-stratify, and predict survivability of patients with non-malignant liver diseases. A total of 20 different models were tested in selected studies. Generally, the addition of omics data to regular clinical parameters or individual biomarkers improved the AI model performance. For instance, using NAFLD fibrosis score to distinguish F0-F2 from F3-F4 fibrotic stages, the area under the curve (AUC) was 0.87. When integrating metabolomic data by a GMLVQ model, the AUC drastically improved to 0.99. The use of RF on multi-omics and clinical data in another study to predict progression of NAFLD to NASH resulted in an AUC of 0.84, compared to 0.82 when using clinical data only. A comparison of RF, SVM and kNN models on genomics data to classify immune tolerant phase in chronic hepatitis B resulted in AUC of 0.8793-0.8838 compared to 0.6759-0.7276 when using various serum biomarkers. Overall, the integration of omics was shown to improve prediction performance compared to models built only on clinical parameters, indicating a potential use for personalized medicine in clinical setting.
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BACKGROUND: Our recent work has challenged 4°C as an optimal lung preservation temperature by showing storage at 10°C to allow for the extension of preservation periods. Despite these findings, the impact of 10°C storage has not been evaluated in the setting of injured donor lungs. METHODS: Aspiration injury was created through bronchoscopic delivery of gastric juice (pH: 1.8). Injured donor lungs (n = 5/group) were then procured and blindly randomized to storage at 4°C (on ice) or at 10°C (in a thermoelectric cooler) for 12 hours. A third group included immediate transplantation. A left lung transplant was performed thereafter followed by 4 hours of graft evaluation. RESULTS: After transplantation, lungs stored at 10°C showed significantly better oxygenation when compared to 4°C group (343 ± 43 mm Hg vs 128 ± 76 mm Hg, p = 0.03). Active metabolism occurred during the 12 hours storage period at 10°C, producing cytoprotective metabolites within the graft. When compared to lungs undergoing immediate transplant, lungs preserved at 10°C tended to have lower peak airway pressures (p = 0.15) and higher dynamic lung compliances (p = 0.09). Circulating cell-free mitochondrial DNA within the recipient plasma was significantly lower for lungs stored at 10°C in comparison to those underwent immediate transplant (p = 0.048), alongside a tendency of lower levels of tissue apoptotic cell death (p = 0.075). CONCLUSIONS: We demonstrate 10°C as a potentially superior storage temperature for injured donor lungs in a pig model when compared to the current clinical standard (4°C) and immediate transplantation. Continuing protective metabolism at 10°C for donor lungs may result in better transplant outcomes.
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Trasplante de Pulmón , Daño por Reperfusión , Animales , Modelos Animales de Enfermedad , Pulmón/metabolismo , Preservación de Órganos , Daño por Reperfusión/metabolismo , Porcinos , TemperaturaRESUMEN
Current understanding of mechanisms of ischemia-reperfusion-induced lung injury during lung preservation and transplantation is mainly based on clinical observations and animal studies. Herein, we used cell and systems biology approaches to explore these mechanisms at transcriptomics levels, especially by focusing on the differences between human lung endothelial and epithelial cells, which are crucial for maintaining essential lung structure and function. Human pulmonary microvascular endothelial cells and human lung epithelial cells were cultured to confluent, subjected to different cold ischemic times (CIT) to mimic static cold storage with preservation solution, and then subjected to warm reperfusion with a serum containing culture medium to simulate lung transplantation. Cell morphology, viability, and transcriptomic profiles were studied. Ischemia-reperfusion injury induced a CIT time-dependent cell death, which was associated with dramatic changes in gene expression. Under normal control conditions, endothelial cells showed gene clusters enriched in the vascular process and inflammation, while epithelial cells showed gene clusters enriched in protein biosynthesis and metabolism. CIT 6 h alone or after reperfusion had little effect on these phenotypic characteristics. After CIT 18 h, protein-biosynthesis-related gene clusters disappeared in epithelial cells; after reperfusion, metabolism-related gene clusters in epithelial cells and multiple gene clusters in the endothelial cells also disappeared. Human pulmonary endothelial and epithelial cells have distinct phenotypic transcriptomic signatures. Severe cellular injury reduces these gene expression signatures in a cell-type-dependent manner. Therapeutics that preserve these transcriptomic signatures may represent new treatment to prevent acute lung injury during lung transplantation.
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Células Endoteliales/metabolismo , Células Epiteliales/metabolismo , Perfilación de la Expresión Génica , Trasplante de Pulmón , Daño por Reperfusión/genética , Daño por Reperfusión/patología , Transcriptoma/genética , Línea Celular , Criopreservación , Regulación de la Expresión Génica , Humanos , Pulmón/irrigación sanguínea , Microvasos/patología , Familia de Multigenes , FenotipoRESUMEN
BACKGROUND: Hepatocellular Carcinoma (HCC) is a sexually dimorphic cancer, with female sex being independently protective against HCC incidence and progression. The aim of our study was to understand the mechanism of estrogen receptor signaling in driving sex differences in hepatocarcinogenesis. METHODS: We integrated 1,268 HCC patient sample profiles from publicly available gene expression data to identify the most differentially expressed genes (DEGs). We mapped DEGs into a physical protein interaction network and performed network topology analysis to identify the most important proteins. Experimental validation was performed in vitro on HCC cell lines, in and in vivo, using HCC mouse model. RESULTS: We showed that the most central protein, ESR1, is HCC prognostic, as increased ESR1 expression was protective for overall survival, with HR=0.45 (95%CI 0.32-0.64, p=4.4E-06), and was more pronounced in women. Transfection of HCC cell lines with ESR1 and exposure to estradiol affected expression of genes involved in the Wnt/ß-catenin signaling pathway. ER-α (protein product of ESR1) agonist treatment in a mouse model of HCC resulted in significantly longer survival and decreased tumor burden (p<0.0001), with inhibition of Wnt/ß-Catenin signaling. In vitro experiments confirmed colocalization of ß-catenin with ER-α, leading to inhibition of ß-catenin-mediated transcription of target genes c-Myc and Cyclin D1. CONCLUSION: Combined, the centrality of ESR1 and its inhibition of the Wnt/ß-catenin signaling axis provide a biological rationale for protection against HCC incidence and progression in women.