Systematic analysis of cuproptosis abnormalities and functional significance in cancer

BACKGROUND

Cuproptosis is a recently discovered type of cell death, but the role and behavior of cuproptosis-related genes (CuRGs) in cancers remain unclear. This paper aims to address these issues by analyzing the multi-omics characteristics of cancer-related genes (CuRGs) across various types of cancer.

METHOD

To investigate the impact of somatic copy number alterations (SCNA) and DNA methylation on CRG expression, we will analyze the correlation between these factors. We developed a cuproptosis index (CPI) model to measure the level of cuproptosis and investigate its functional roles. Using this model, we assessed the clinical prognosis of colorectal cancer patients and analyzed genetic changes and immune infiltration features in different CPI levels.

RESULTS

The study's findings indicate that the majority of cancer-related genes (CuRGs) were suppressed in tumors and had a positive correlation with somatic copy number alterations (SCNA), while having a negative correlation with DNA methylation. This suggests that both SCNA and DNA methylation have an impact on the expression of CuRGs. The CPI model is a reliable predictor of survival outcomes in patients with colorectal cancer and can serve as an independent prognostic factor. Patients with a higher CPI have a worse prognosis. We conducted a deeper analysis of the genetic alterations and immune infiltration patterns in both CPI positive and negative groups. Our findings revealed significant differences, indicating that CuRGs may play a crucial role in tumor immunity mechanisms. Additionally, we have noticed a positive correlation between CuRGs and various crucial pathways that are linked to the occurrence, progression, and metastasis of tumors.

CONCLUSIONS

Overall, our study systematically analyzes cuproptosis and its regulatory genes, emphasizing the potential of using cuproptosis as a basis for cancer therapy.

Absorbed dose of secondary neutrons from galactic cosmic rays inside the International Space Station

In this paper, we present the results of Monte-Carlo simulations of the flux and energy spectra of neutrons generated as a result of galactic cosmic ray proton interactions with the material of International Space Station (ISS) inside Zvezda Service Module, the Airlock between Russian and USA segments and one of Russian Research Modules for a full configuration of ISS. Calculations were made for ISS orbit for the energy ranges <10 and >10 MeV for both maximum and minimum of solar activity. To test the accuracy of the calculations the same simulations were made for MIR orbital station and for CORONAS-I satellite and compared with the results of measurements. Calculated and measured fluxes are in reasonable agreement.

In vivo tropism of hepatitis C virus genomic sequences in hematopoietic cells: influence of viral load, viral genotype, and cell phenotype

Extrahepatic sites capable of supporting hepatitis C virus (HCV) replication have been suggested. We analyzed the influence of virological factors such as viral genotype and viral load, and cellular factors such as cell phenotype, on the detection rate of HCV sequences in hematopoietic cells of infected patients. Thirty-eight chronically infected patients were included in the study: 19 infected by genotype 1 isolates (1a and 1b), 13 by nongenotype 1 isolates (including genotypes 2 a/c, 3a, and 4), and 6 coinfected by genotype 1 and 6 isolates. Polymerase chain reaction (PCR) detection efficiency of viral genomic sequences, both the positive and negative strand RNA, was evaluated using RNA transcripts derived from genotype 1, 2, 3, and 4 cloned sequences and found to be equivalent within one log unit. The serum viral load, ranging from less than 2 x 10(5) Eq/mL to 161 x 10(5) Eq/mL, did not influence the detection rate of either strand of RNA in patients' peripheral blood mononuclear cells (PBMCs). Positive and negative strand RNA were found in PBMCs of all 3 cohorts of patients with a detection rate ranging from 15% to 100% and from 8% to 83.3% for the positive and negative strand RNA, respectively. Coinfected patients showed a detection rate in all cases greater than 80%. Patients infected with genotype 1 isolates showed a higher detection rate of either strands of RNA when compared with patients infected with other genotypes (P <.001 and P <.04). Both strands were found restricted to polymorphonuclear leukocytes, monocytes/macrophages, and B (but not T) lymphocytes. These data show that HCV genomic sequences, possibly reflecting viral replication, can be detected in PBMCs of chronically infected patients independent of the viral load and that specific associated cell subsets are implicated in the harboring of such sequences.

Patterns of intermediate filaments, VLA integrins and HLA antigens in a new human biliary epithelial cell line sensitive to interferon-gamma

BACKGROUND/AIMS

Intra-hepatic bile ducts are the primary site of damage in several immunologically mediated liver diseases. However, immunological processes underlying biliary epithelial cell recognition by T lymphocytes are poorly understood. Therefore, a convenient in vitro model that could mimic these immunologic disorders would be of great interest.

METHODS

A human cell line (HuGB) was established from a metastasis of gallbladder adenocarcinoma in the liver. Intermediate filament expression was analysed by immunostaining, and gamma-glutamyl transpeptidase and albumin secretion were measured. VLA integrin expression pattern, expression of HLA class I and II antigens and ICAM-1 protein were analysed by flow cytometry and their modulation by interferon-gamma was quantitated using a QIFIKIT commercial kit.

RESULTS

Histological analysis showed high similarity between the initial gallbladder adenocarcinoma and the established cell line. Cytokeratins 8 and 19 and vimentin showed strong positive staining in the established cell line. Gamma-glutamyl transpeptidase was secreted by these cells while albumin expression was negative. HuGB cells also expressed VLA-alpha2, VLA-alpha3, VLA-alpha6, VLA-beta1, but not VLA-alpha1, VLA-alpha4 and NCAM, a pattern of adhesion molecule expression compatible with the biliary epithelium. Also, similar to the biliary epithelium found in normal liver, HuGB cells expressed abundant HLA class I but few HLA class II antigens. We found that the expression of HLA antigens and ICAM-1 protein were increased during interferon-gamma treatment of HuGB cell line.

CONCLUSIONS

Both phenotypic and morphological characteristics of HuGB cells suggested their biliary origin. Sensitivity of HuGB cells to interferon-gamma suggests that this new cell line could represent a suitable model to investigate the up-regulation of membrane antigens occurring in immune diseases involving biliary epithelial cells.

Long-term productive episomal hepatitis B virus replication in primary cultures of adult human hepatocytes infected in vitro

We have previously increased the efficiency of hepatitis B virus (HBV) infection of human hepatocytes in vitro by using polyethylene glycol. After further documenting by neutralization experiments, this in vitro infection, we used this model to define new culture conditions that would maintain stable episomal replication for several weeks. We found that in the presence of 10% porcine serum and 2% dimethyl sulphoxide (DMSO), high-density cultures survived more than 3 months, while addition of hydrocortisone instead of DMSO resulted in survival of less than 1 month. HBV episomal replication was maintained without any evidence of viral integration into the host genome. The maintenance of HBV replication was demonstrated by: first, stability of the covalently-closed-circular DNA in the nucleus and relaxed circular and single-stranded replicative intermediates in the cytoplasm; second, detection of two major transcripts of 3.5 and 2.1-2.4 kb corresponding to the pregenomic and surface genes respectively; and third, continuous secretion of mature viral particles in the supernatant of infected cells. We showed that under these culture conditions, hepatocytes were blocked in the G1 phase of the cell cycle and did not spontaneously proliferate. Upon hepatocyte growth factor (HGF) stimulation, however, the ability of hepatocytes to divide was demonstrated and was compared in infected and non-infected cells. No change in proliferative capacity and no variation in c-myc and c-jun levels could be found. Hepatocyte survival was not modified in infected cells, confirming that HBV is not cytopathic for normal human hepatocytes. These new culture conditions represent substantial progress in the study of HBV-host cell interactions.

Myristylation of the hepatitis B virus large surface protein is essential for viral infectivity

The hepatitis B virus (HBV) envelope contains equimolar amounts of three viral proteins: the major (S), middle, and large (L) polypeptides. Their roles in the adsorption and penetration of the virus have not yet been elucidated. We have used a highly efficient in vitro model that permits reproducible HBV infection to investigate whether N-myristylation, a posttranslational modification of the L protein, was essential for viral infectivity. A point mutation abolishing myristylation was introduced into the HBV genome. Mutant virions were produced by transfecting viral DNA into hepatoma cells and their infectivity was evaluated on primary human hepatocyte cultures. No difference between mutant and wild-type viral RNA production could be observed. Furthermore, intermediate DNA replicative forms were observed in transfected cells demonstrating replication competence of mutant viral genomes. In addition, complete virions were produced in the cell supernatant. However, we found that mutant viral particles contained viral DNA with a reduced mean size, probably corresponding to a larger single-stranded region in the relaxed circular DNA form. We have evidenced the presence of pre-S1, pre-S2, and S epitopes at the outer surface of these virions by using immunoprecipitation with specific monoclonal antibodies. This result confirmed that mutant viruses were normally assembled. By contrast, myristylation-defective mutants completely lost their infectivity for human hepatocytes in primary cultures as shown by the absence of HBs antigen production and viral intermediate replicative forms in hepatocytes. In conclusion, the myristylation of the L protein is not required for the production of Dane-like particles but it is absolutely necessary for HBV infectivity.

A study of the effect of ABO incompatible plasma in platelet concentrates transfused to bone marrow transplant recipients

Bone marrow transplant recipients at Huddinge Hospital have routinely received single-donor platelet concentrates (PC) from blood group O donors. These PC contain approximately 350 ml plasma, which is incompatible with patients of group A, B and AB. In 27 patients transplanted with an ABO-identical bone marrow, serological investigations have been performed every week after transplantation (median 6 weeks, range 3-14). Nine of 11 recipients with blood group A developed a positive direct antiglobulin test (DAT) after PC transfusions, while none of 15 patients of blood group O developed a positive DAT. Anti-A could be eluted in DAT-positive cases. In no case was there any clinical sign of hemolysis. Nor did recipients of groups A, B or AB (n = 34) require more red blood cells or PC transfusions compared to recipients of group O (n = 47).