Themis: advancing precision oncology through comprehensive molecular subtyping and optimization.

Recent advances in tumor molecular subtyping have revolutionized precision oncology, offering novel avenues for patient-specific treatment strategies. However, a comprehensive and independent comparison of these subtyping methodologies remains unexplored. This study introduces 'Themis' (Tumor HEterogeneity analysis on Molecular subtypIng System), an evaluation platform that encapsulates a few representative tumor molecular subtyping methods, including Stemness, Anoikis, Metabolism, and pathway-based classifications, utilizing 38 test datasets curated from The Cancer Genome Atlas (TCGA) and significant studies. Our self-designed quantitative analysis uncovers the relative strengths, limitations, and applicability of each method in different clinical contexts. Crucially, Themis serves as a vital tool in identifying the most appropriate subtyping methods for specific clinical scenarios. It also guides fine-tuning existing subtyping methods to achieve more accurate phenotype-associated results. To demonstrate the practical utility, we apply Themis to a breast cancer dataset, showcasing its efficacy in selecting the most suitable subtyping methods for personalized medicine in various clinical scenarios. This study bridges a crucial gap in cancer research and lays a foundation for future advancements in individualized cancer therapy and patient management.

scSTAR reveals hidden heterogeneity with a real-virtual cell pair structure across conditions in single-cell RNA sequencing data.

Cell-state transition can reveal additional information from single-cell ribonucleic acid (RNA)-sequencing data in time-resolved biological phenomena. However, most of the current methods are based on the time derivative of the gene expression state, which restricts them to the short-term evolution of cell states. Here, we present single-cell State Transition Across-samples of RNA-seq data (scSTAR), which overcomes this limitation by constructing a paired-cell projection between biological conditions with an arbitrary time span by maximizing the covariance between two feature spaces using partial least square and minimum squared error methods. In mouse ageing data, the response to stress in CD4+ memory T cell subtypes was found to be associated with ageing. A novel Treg subtype characterized by mTORC activation was identified to be associated with antitumour immune suppression, which was confirmed by immunofluorescence microscopy and survival analysis in 11 cancers from The Cancer Genome Atlas Program. On melanoma data, scSTAR improved immunotherapy-response prediction accuracy from 0.8 to 0.96.

WGCNA combined with machine learning algorithms for analyzing key genes and immune cell infiltration in heart failure due to ischemic cardiomyopathy.

Background: Ischemic cardiomyopathy (ICM) induced heart failure (HF) is one of the most common causes of death worldwide. This study aimed to find candidate genes for ICM-HF and to identify relevant biomarkers by machine learning (ML). Methods: The expression data of ICM-HF and normal samples were downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between ICM-HF and normal group were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and gene ontology (GO) annotation analysis, protein-protein interaction (PPI) network, gene pathway enrichment analysis (GSEA), and single-sample gene set enrichment analysis (ssGSEA) were performed. Weighted gene co-expression network analysis (WGCNA) was applied to screen for disease-associated modules, and relevant genes were derived using four ML algorithms. The diagnostic values of candidate genes were assessed using receiver operating characteristic (ROC) curves. The immune cell infiltration analysis was performed between the ICM-HF and normal group. Validation was performed using another gene set. Results: A total of 313 DEGs were identified between ICM-HF and normal group of GSE57345, which were mainly enriched in biological processes and pathways related to cell cycle regulation, lipid metabolism pathways, immune response pathways, and intrinsic organelle damage regulation. GSEA results showed positive correlations with pathways such as cholesterol metabolism in the ICM-HF group compared to normal group and lipid metabolism in adipocytes. GSEA results also showed a positive correlation with pathways such as cholesterol metabolism and a negative correlation with pathways such as lipolytic presentation in adipocytes compared to normal group. Combining multiple ML and cytohubba algorithms yielded 11 relevant genes. After validation using the GSE42955 validation sets, the 7 genes obtained by the machine learning algorithm were well verified. The immune cell infiltration analysis showed significant differences in mast cells, plasma cells, naive B cells, and NK cells. Conclusion: Combined analysis using WGCNA and ML identified coiled-coil-helix-coiled-coil-helix domain containing 4 (CHCHD4), transmembrane protein 53 (TMEM53), acid phosphatase 3 (ACPP), aminoadipate-semialdehyde dehydrogenase (AASDH), purinergic receptor P2Y1 (P2RY1), caspase 3 (CASP3) and aquaporin 7 (AQP7) as potential biomarkers of ICM-HF. ICM-HF may be closely related to pathways such as mitochondrial damage and disorders of lipid metabolism, while the infiltration of multiple immune cells was identified to play a critical role in the progression of the disease.

Risk prediction model construction for post myocardial infarction heart failure by blood immune B cells.

Background: Myocardial infarction (MI) is a common cardiac condition with a high incidence of morbidity and mortality. Despite extensive medical treatment for MI, the development and outcomes of post-MI heart failure (HF) continue to be major factors contributing to poor post-MI prognosis. Currently, there are few predictors of post-MI heart failure. Methods: In this study, we re-examined single-cell RNA sequencing and bulk RNA sequencing datasets derived from the peripheral blood samples of patients with myocardial infarction, including patients who developed heart failure and those who did not develop heart failure after myocardial infarction. Using marker genes of the relevant cell subtypes, a signature was generated and validated using relevant bulk datasets and human blood samples. Results: We identified a subtype of immune-activated B cells that distinguished post-MI HF patients from non-HF patients. Polymerase chain reaction was used to confirm these findings in independent cohorts. By combining the specific marker genes of B cell subtypes, we developed a prediction model of 13 markers that can predict the risk of HF in patients after myocardial infarction, providing new ideas and tools for clinical diagnosis and treatment. Conclusion: Sub-cluster B cells may play a significant role in post-MI HF. We found that the STING1, HSPB1, CCL5, ACTN1, and ITGB2 genes in patients with post-MI HF showed the same trend of increase as those without post-MI HF.

Case report: Acute ST-elevation myocardial infarction and cardiogenic shock caused by a giant right sinus of Valsalva aneurysm and right coronary artery compression.

A sinus of Valsalva aneurysm (SVA) is a rare aortic disease that may be congenital or acquired. Patients with an intact SVA are usually asymptomatic, whereas a ruptured SVA may cause acute chest pain and dyspnea. We present a rare case of acute ST-elevation myocardial infarction and cardiogenic shock in a 51-year-old man. Emergency coronary angiography revealed a giant aneurysm with an absence of flow in the right coronary artery. Both two-dimensional echocardiography and computed tomography angiography showed a giant right SVA, which ruptured into the pericardial sac and led to extrinsic compression of the right coronary artery. Surgical repair combined with coronary bypass grafting was performed. Unfortunately, the patient died from low cardiac output syndrome and postoperative multiple organ failure. This case highlights that the possibility of SVA rupture should be considered in acute myocardial infarction cases and that echocardiography and coronary computed tomography angiography are important in providing an accurate and rapid SVA diagnosis.

Ethyl Pyruvate Alleviates Pulmonary Hypertension through the Suppression of Pulmonary Artery Smooth Muscle Cell Proliferation via the High Mobility Group Protein B1/Receptor for Advanced Glycation End-Products Axis.

PURPOSE: Pulmonary arterial hypertension (PAH) is a formidable disease with no effective treatment at present. With the goal of developing potential therapies, we attempted to determine whether ethyl pyruvate (EP) could alleviate PAH and its mechanism. METHODS: Pulmonary smooth muscle cells were cultured in conventional low-oxygen environments, and cellular proliferation was monitored after treatment with either EP or phosphate-balanced solution (PBS). Expression of high mobility group protein B1 (HMGB1) and receptor for advanced glycation end-products (RAGE) protein were detected by western blot. After hyperkinetic PAH rat models were treated with EP, hemodynamic data were collected. Right ventricular hypertrophy and pulmonary vascular remodeling were evaluated. Expression of HMGB1 and RAGE protein was also detected. RESULTS: In vitro, proliferative activity increased in low-oxygen environments, but was inhibited by EP treatment. Furthermore, Western blotting showed the decreased expression of HMGB1 and RAGE protein after EP treatment. In vivo, pulmonary artery pressures were attenuated with EP. Right ventricular hypertrophy and pulmonary vascular remodeling were also reversed. Additionally, the expression levels of HMGB1 and RAGE were reduced in lung tissues. CONCLUSIONS: EP can alleviate PAH by suppressing the proliferation of pulmonary artery smooth muscle cells via inhibition of HMGB1/RAGE expression.

Is tri-port totally thoracoscopic surgery for mitral valve replacement a feasible approach?

BACKGROUND: Minimally invasive cardiac surgery is an attractive approach for both surgeons and patients. This study aims to describe the experience of mitral valve replacement (MVR) with Ma's tri-port totally thoracoscopic cardiac surgery technique (MTCST) and to prove the feasibility and safety of this technique. METHODS: A total of 490 consecutive patients undergoing MVR were divided into MTCST group (MT group, n=267) and conventional median sternotomy group (MS group, n=223). The perioperative characteristics and the follow-up information were recorded and analyzed between the two groups. RESULTS: The in-hospital mortality and re-operation rate were not significant between the two groups. Compared with the MS group, cardiopulmonary bypass time and aortic cross-clamp time were both longer in the MT group while total operative time was similar to the MS group. Patients in the MT group had less pain and required a decreased analgesic administration than that in the MS group. Intraoperative blood loss, perioperative blood transfusion and the postoperative drainage were all significantly reduced in the MT group as compared to the MS group. Mechanical ventilation time, ICU duration, hospitalization time and hospitalization cost were decreased in the MT group. Patients undergoing MVR with MTCST had a higher Medical Treatment Satisfactory Score than those with conventional sternotomy. CONCLUSIONS: MTCST for mitral valve disease was technically safe and feasible. The results showed that MTCST was a suitable minimally invasive alternative to the conventional sternotomy approach and was a desirable approach for patients with mitral valve disease.

Employing the Sirolimus-Eluting Poly (Propylene Carbonate) Mesh for the Prevention of Arteriovenous Graft Stenosis in Rats.

Poly (propylene carbonate, PPC) is a new member of the aliphatic polyester family. An outstanding feature of PPC is that it produces mainly water and carbon dioxide when degraded in vivo, causing minimal side effects. This unique property together with excellent biocompatibility and biodegradability makes PPC a promising material for drug delivery. In this study, we explored the effect of the sirolimus (an inhibitor of cell growth)-eluting PPC mesh on graft stenosis and its possible mechanisms in a rat arteriovenous grafting model. The PPC mesh was prepared by electrospinning. A jugular vein to abdominal aortic autograft transplantation model was established in rats. The graft was then treated by wrapping with the drug mesh or the drug-free mesh or left untreated. Four weeks posttransplantation, neointima was measured with hematoxylin and eosin staining, matrix metalloproteinase-2 (MMP-2), and MMP-9, and proliferating cell nuclear antigen (PCNA) in the grafts were assayed by Western blotting and immunohistochemistry, respectively. In vitro rat aortic adventitial fibroblast cell (RAAFC) migration was assessed using the Boyden chamber assay, and phospho-mammalian target of rapamycin (mTOR) levels in RAAFCs were determined by Western blotting. Animals with the drug mesh had an intimal area index of 4.87% ± 0.98%, significantly lower than that of the blank group (14.21% ± 2.56%) or the PPC group (15.03% ± 2.35%, both P < .05). The sirolimus mesh markedly suppressed MMP-2 and MMP-9 expression, decreased PCNA-positive cell numbers, inhibited RAAFC migration, and reduced phospho-mTOR levels. Our data suggest that the sirolimus-eluting PPC mesh might be potentially applied for the management of grafting stenosis.

Applicability of electrospun polypropylene carbonate polymers as a drug carrier for sirolimus.

Polypropylene carbonate (PPC), a biodegradable aliphatic polyester, exhibits one particular advantage over other polyesters, which is that following degradation in vivo, it primarily produces H2O and CO2, causing minimal side effects. Although PPC exhibits limited mechanical strength, and is therefore not able to serve as a scaffold to support tissue regeneration, it may be suitable for drug delivery; however, this requires further investigation. In the present study, electrospinning was applied to generate PPC polymers containing sirolimus, a cell growth­inhibiting drug which is used to treat restenosis. The properties of PPC­sirolimus polymers were examined using scanning electron microscopy, differential scanning calorimetry and in vitro degradation assays. Drug loading and entrapment efficiency were determined, and in vitro sirolimus­release from the polymer was assessed. Furthermore, the effect of PPC­sirolimus polymers on cell growth was measured using an MTT assay in vitro. The results of the present study demonstrated that electrospun PPC polymers formed a uniform three­dimensional, grid­intertwined, net­like structure; the surface of the polymers was smooth and the diameter was ~3 µm. Differential scanning calorimetry analysis demonstrated that sirolimus existed in an amorphous state in the polymer. Following soaking in PBS for 4 weeks, the polymer swelled and the net­like structure broke down and fragmented. Sirolimus loading and entrapment efficiency were 10.3±3.2 and 95.1±10.6%, respectively. Sirolimus­release from PPC­sirolimus polymers continued for 28 days in PBS. PPC­sirolimus markedly inhibited the growth of rat aortic adventitial fibroblast cells, an effect which was not observed with PPC alone. The results of the present study suggest that PPC polymers are a promising alternative drug carrier for sirolimus.

Transcatheter Closure Versus Repeat Surgery for the Treatment of Postoperative Left-to-Right Shunts: A Single Center 15-Year Experience.

BACKGROUND: Repeat surgery and the percutaneous approach (transcatheter closure (TCC)) have been used for the management of postoperative left-to-right shunts. In this study, we described our 15 years of experience in treating postoperative left-to-right shunts with these two approaches. METHODS: From February 2002 to February 2017, 50 patients with residual left-to-right shunts, following cardiac surgery, were treated using TCC or repeat surgery. Clinical examination, standard 12-lead electrocardiography, chest X-ray, and a transthoracic echocardiogram were performed before hospital discharge and at all follow-ups. RESULTS: The closure rate was 100% in both groups and there was no procedure-related mortality. Patients with TCC had few complications. The procedure time and duration of hospital stay for TCC patients were 58.9 ± 27.7 min and 6.1 ± 0.8 days, respectively. Eleven out of 19 patients receiving reoperation suffered serious complications after surgery, e.g., bleeding and nosocomial infections. The operation time and duration of hospital stay for reoperation patients were 256.7 ± 60.5 min and 17.0 ± 4.0 days, respectively. No other serious complications were seen at all follow-up visits for both groups. CONCLUSIONS: In conclusions, TCC is safe and effective for the management of postoperative left-to-right shunts, and is associated with few complications, which can be the favored closure strategy over repeat surgery for the management of postoperative left-to-right shunts.

Transcatheter closure of calcified patent ductus arteriosus in older adult patients: Immediate and 12-month follow-up results.

OBJECTIVE: To present our experience in transcatheter closure of calcified patent ductus arteriosus (PDA) in older adult patients, which has rarely been reported. PATIENTS: From 2009 to 2014, a total of 16 patients (median age 58 years) with calcified PDA underwent transcatheter closure in our center. All patients were symptomatic with major symptoms being exertional dyspnea (in 12), palpitations (in 8), and fatigue (in 5). A continuous murmur was heard in all patients. The median ductus diameter was 4 mm (range 3-7 mm). The median Qp/Qs was 1.6 (range 1.4-2.9). INTERVENTIONS: Transcatheter closure was performed for all patients. The size of the occluder selected was 2-3 mm greater than the narrowest portion of PDA. We experienced difficulties in advancing the multipurpose catheter through the calcified duct in about one third of patients (5/16). Considering that calcified tissue has a greater tendency to rupture, hence, to close PDA in these patients, they adopted the retrograde wire-assisted technique and modified the procedure to reduce the shear stress of sheath and avoid any sheath kinking. For the remaining 11 patients, the advancement of the multipurpose catheter through the calcified duct was smooth and the conventional antegrade approach was applied. OUTCOME MEASURES: Clinical examination, standard 12-lead electrocardiography, chest x-ray, and transthoracic echocardiography were performed before hospital discharge, at 1-, 3-, 6-, and 12-months follow-ups. RESULTS: All PDAs were successfully closed. There were no deaths. Three patients had a trivial residual shunt, with one also having intravascular hemolysis. Following pharmacological treatment, hemolysis signs vanished at 7 days postprocedure. The trivial residual shunt disappeared in all three patients at 3-month follow-up. No new-onset residual shunt, device embolization, device dislocation, infective endocarditis, or embolism was observed at all follow-up time points. CONCLUSION: Successful closure of calcified PDA with few complications in older adult patients was achieved using the duct occluder.

Successful Closure of a Ventricular Septal Defect Using a Novel Non-Prosthesis Touching Technique Following Mechanical Aortic Valve Replacement.

Percutaneous intervention is preferred over reoperation for the treatment of iatrogenic membranous ventricular septal defects (VSDs). During the standard percutaneous procedure, an arterio-venous loop is used for occluder deployment, entailing the risk of device impingement on the prosthetic aortic valve, which may cause serious complications or even death. In this report, we describe a novel non-prosthesis touching procedure for the closure of a VSD in a patient with prior aortic valve replacement. The unique feature of this technique is the use of an apex-venous loop for occluder deployment, which prevents the device impingement on the prosthetic valve, thus avoiding difficulties, lengthy operation and serious complications associated with the standard procedure. Immediate and 1-year follow-up results showed that the VSD was successfully closed and no serious complications were observed.

Intratracheal instillation of ethyl pyruvate nanoparticles prevents the development of shunt-flow-induced pulmonary arterial hypertension in a rat model.

PURPOSE: To investigate whether inhalation of ethyl pyruvate (EP) encapsulated with poly(ethylene glycol)-block-lactide/glycolide copolymer nanoparticles (EP-NPs) can prevent the development of shunt-flow-induced hyperkinetic pulmonary arterial hypertension (PAH) in a rat model. MATERIALS AND METHODS: Rats were separated into five groups: blank (ie, no treatment after shunt flow), normal control (ie, no shunt flow or treatment), EP-NP instillation, EP-only instillation, and vehicle. The animals received intratracheal instillation of EP-NPs or other treatments immediately after a shunt flow, and treatment continued weekly until the end of the experiment. Hemodynamic data were recorded, pulmonary arterial remodeling was assessed, and levels of inflammatory mediators and ET1 expression in the lung and serum were analyzed. In addition, retention of EP in the lungs of rats in the EP-NP and EP-only groups was measured using high-performance liquid chromatography. RESULTS: After 12 weeks, hemodynamic abnormalities and pulmonary arterial remodeling were improved in the EP-NP instillation group, compared with the blank, EP-only, and vehicle groups (P<0.05). In addition, the EP-NP group showed significantly decreased levels of HMGB1, IL-6, TNFα, reactive oxygen species, and ET1 in the lung during PAH development (P<0.05). Furthermore, EP-NP instillation was associated with reduced serum levels of inflammatory factors and ET1. High-performance liquid-chromatography measurement indicated that EP retention was greater in the lungs of the EP-NP group than in the EP-only group. CONCLUSION: EP-NP instillation attenuated inflammation and prevented pulmonary arterial remodeling during the development of PAH induced by shunt flow. In the future, EP-NP delivery into the lung might provide a novel approach for preventing PAH.

Pterostilbene attenuates inflammation in rat heart subjected to ischemia-reperfusion: role of TLR4/NF-κB signaling pathway.

OBJECTIVE: The aim of the present study was to investigate whether pterostilbene could modulate the TLR4/NF-κB signaling, reduce neutrophil accumulation and TNF-α induction in an ischemia/reperfusion injured rat heart model. MATERIALS AND METHODS: Rats were randomly exposed to sham operation, myocardial ischemia and reperfusion (MI/R), MI/R + pterostilbene, MI/R + pterostilbene + L-NAME. And myocardial infarct size, apoptosis, TLR4 expression, NF-κB expression, MPO level and TNF-α level were detected. RESULTS: The results demonstrated that after MI/R, the expressions of myocardial TLR4, NF-κB and caspase-3 increased significantly in ischemia area. Compared with MI/R, pterostilbene significantly attenuated the expressions of TLR4, NF-κB and caspase-3. In addition, it also reduced myeloperoxidase (MPO) levels, both serum and myocardial TNF-α production, myocardial infarct sizes (INF/AAR%) and myocardial apoptosis induced by MI/R. All the effects of pterostilbene were abolished by L-NAME, a nitric oxide synthase inhibitor. CONCLUSION: These data provide evidence that pterostilbene inhibits TLR4/NF-κB signaling and apoptosis in the rat heart subjected to MI/R, which is associated with NO production.

Combined hypoxia inducible factor-1α and homogeneous endothelial progenitor cell therapy attenuates shunt flow-induced pulmonary arterial hypertension in rabbits.

BACKGROUND: Hyperkinetic pulmonary arterial hypertension (PAH) is a common complication in congenital heart disease, and affects operations, indications, and prognoses for patients. Gene-based stem cell transplantation is an alternative treatment that can attenuate PAH. METHODS: Hyperkinetic PAH rabbit models were successfully established, using common carotid artery and jugular vein anastomosis. Endothelial progenitor cells (EPCs) were isolated from the bone marrow, cultured, and transfected with human hypoxia inducible factor-1 alpha (hHIF-1α), using lentiviruses. Two weeks after the transfected EPCs were transplanted into the rabbits, catheterization was applied to collect hemodynamic data. The hypertrophy of the right ventricle and pulmonary vascular remodeling were evaluated by measuring the right ventricle hypertrophy index, the medial wall thickness, and the medial wall area. Western blot and immunohistochemistry analyses were used to detect the expression of hHIF-1α in the pulmonary small arteries. RESULTS: Two weeks after transplantation, systolic pulmonary arterial pressure and mean pulmonary arterial pressure were both attenuated. The hypertrophy of the right ventricle, and pulmonary vascular remodeling were reversed. Expression of hHIF-1α in the hHIF-1α-transfected EPCs that had been transplanted was high, and the number of pulmonary small arteries had increased. In addition, combined HIF-1α and homogeneous EPC therapy was more effective at attenuating PAH and increasing the density of pulmonary small arteries, compared with EPC transplantation alone. CONCLUSIONS: Both the therapy with HIF-1α-transfected EPCs, and EPC transplantation, attenuated shunt flow-induced PAH, by means of an angiogenic effect. The former therapeutic method was more effective.

Adipose-derived stromal cell autologous transplantation ameliorates pulmonary arterial hypertension induced by shunt flow in rat models.

Hyperkinetic pulmonary arterial hypertension (PAH) severely influences the success of operation for congenital heart disease and deteriorates the prognosis of disease. Adipose-derived stromal cell (ADSC) is a good alternative multipotent stem cell for regeneration medicine. PAH rat models were established by arteriovenous shunt and ADSCs were isolated, cultured, and labeled in vitro. Twelve weeks after shunt operation, rats received an injection of 5 × 10(7) ADSCs. Two weeks after transplantation, hemodynamic abnormality induced by the shunt flow and the hypertrophy of right ventricle were reversed, which was confirmed by invasive measurement and echocardiography examination. The PAH rats receiving cell transplantation demonstrated decreased remodeling of small arteries in the lung; immunohistochemistry analysis showed augmented expression of hepatocyte growth factor (HGF) and increased number of pulmonary small arteries. Western blot and real-time reverse transcriptase-polymerase chain reaction indicated that the protein and mRNA levels of HGF and endothelial nitric oxide synthase increased, respectively, in the lung after cell transplantation. Our results suggested that ADSC transplantation can ameliorate PAH induced by shunt flow by enhancing the expression of HGF and subsequently promoting angiogenesis in the injured lung tissue.