Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR

Molecular analyses of normal and diseased cells give insight into changes in gene expression and help in understanding the background of pathophysiological processes. Years after cDNA microarrays were established in research, RNA sequencing (RNA-seq) became a key method of quantitatively measuring the transcriptome. In this study, we compared the detection of genes by each of the transcriptome analysis methods: cDNA array, quantitative RT-PCR, and RNA-seq. As expected, we found differences in the gene expression profiles of the aforementioned techniques. Here, we present selected genes that exemplarily demonstrate the observed differences and calculations to reveal that a strong RNA secondary structure, as well as sample preparation, can affect RNA-seq. In summary, this study addresses an important issue with a strong impact on gene expression analysis in general. Therefore, we suggest that these findings need to be considered when dealing with data from transcriptome analyses.

Membrane Transporters and Channels in Melanoma

Recent research has revealed that ion channels and transporters can be important players in tumor development, progression, and therapy resistance in melanoma. For example, members of the ABC family were shown to support cancer stemness-like features in melanoma cells, while several members of the TRP channel family were reported to act as tumor suppressors.Also, many transporter proteins support tumor cell viability and thus suppress apoptosis induction by anticancer therapy. Due to the high number of ion channels and transporters and the resulting high complexity of the field, progress in understanding is often focused on single molecules and is in total rather slow. In this review, we aim at giving an overview about a broad subset of ion transporters, also illustrating some aspects of the field, which have not been addressed in detail in melanoma. In context with the other chapters in this special issue on "Transportome Malfunctions in the Cancer Spectrum," a comparison between melanoma and these tumors will be possible.

Extracellular acidosis triggers a senescence-like phenotype in human melanoma cells

Acidosis of the tumor microenvironment is a characteristic of solid tumors such as malignant melanoma. Main causes of the extracellular acidification are metabolic alterations in cancer cells. While numerous studies showed that acidosis promotes tumor invasiveness, metastasis, and neoangiogenesis resulting in malignant progression, contrary data reported that acidosis induces cell apoptosis, inhibits cell proliferation, and mediates cell autophagy. Here, we show that low pH (pH 6.7) induces senescent/quiescent phenotype in melanoma cells after long-time treatment defined by induction of SA-ß-galactosidase, upregulation of p21, G₁ /G₀ cell cycle arrest, and reduction of proliferation. Moreover, we revealed that extracellular acidosis triggers the inhibition of eIF2α and subsequently the activation of ATF4 expression, a key component of the integrated stress response (ISR), indicating an acid-mediated translation reprogramming. Interestingly, we also demonstrated that acidosis represses microphthalmia-associated transcription factor (MITF) and activates the expression of the receptor tyrosine kinase AXL. This MITF^low /AXL^high phenotype is correlated with drug resistance and therapeutic outcome in melanoma. Our results suggest that acidosis is an important microenvironmental factor triggering phenotypic plasticity and promoting tumor progression.

Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles

The high‐throughput department of DKMS Life Science Lab encounters novel human leukocyte antigen (HLA) alleles on a daily basis. To characterise these alleles, we have developed a system to sequence the whole gene from 5′‐ to 3′‐UTR for the HLA loci A, B, C, DQB1 and DPB1 for submission to the European Molecular Biology Laboratory – European Nucleotide Archive (EMBL‐ENA) and the IPD‐IMGT/HLA Database. Our workflow is based on a dual redundant sequencing strategy. Using shotgun sequencing on an Illumina MiSeq instrument and single molecule real‐time (SMRT) sequencing on a PacBio RS II instrument, we are able to achieve highly accurate HLA full‐length consensus sequences. Remaining conflicts are resolved using the R package DR2S (Dual Redundant Reference Sequencing). Given the relatively high throughput of this strategy, we have developed the semi‐automated web service TypeLoader, to aid in the submission of sequences to the EMBL‐ENA and the IPD‐IMGT/HLA Database. In the IPD‐IMGT/HLA Database release 3.24.0 (April 2016; prior to the submission of the sequences described here), only 5.2% of all known HLA alleles have been fully characterised together with intronic and UTR sequences. So far, we have applied our strategy to characterise and submit 1056 HLA alleles, thereby more than doubling the number of fully characterised alleles. Given the increasing application of next generation sequencing (NGS) for full gene characterisation in clinical practice, extending the HLA database concomitantly is highly desirable. Therefore, we propose this dual redundant sequencing strategy as a workflow for submission of novel full‐length alleles and characterisation of sequences that are as yet incomplete. This would help to mitigate the predominance of partially known alleles in the database.

Acidic tumor microenvironment in human melanoma

One characteristic of solid tumors such as malignant melanoma is the acidification of the tumor microenvironment. The deregulation of cancer cell metabolism is considered a main cause of extracellular acidosis. Here, cancer cells utilize aerobic glycolysis instead of oxidative phosphorylation even under normoxic conditions, as originally described by Otto Warburg. These metabolic alterations cause enhanced acid production, especially of lactate and carbon dioxide (CO2 ). The extensive production of acidic metabolites and the enhanced acid export to the extracellular space cause a consistent acidification of the tumor microenvironment, thus promoting the formation of an acid-resistant tumor cell population with increased invasive and metastatic potential. As melanoma is one of the deadliest and most metastatic forms of cancer, understanding the effects of this extracellular acidosis on human melanoma cells with distinct metastatic properties is important. The aim of this review was to summarize recent studies of the acidification of the tumor microenvironment, focusing on the specific effects of the acidic milieu on melanoma cells and to give a short overview of therapeutic approaches.

A multi-site study using high-resolution HLA genotyping by next generation sequencing

The high degree of polymorphism at human leukocyte antigen (HLA) class I and class II loci makes high-resolution HLA typing challenging. Current typing methods, including Sanger sequencing, yield ambiguous typing results because of incomplete genomic coverage and inability to set phase for HLA allele determination. The 454 Life Sciences Genome Sequencer (GS FLX) next generation sequencing system coupled with conexio atf software can provide very high-resolution HLA genotyping. High-throughput genotyping can be achieved by use of primers with multiplex identifier (MID) tags to allow pooling of the amplicons generated from different individuals prior to sequencing. We have conducted a double-blind study in which eight laboratory sites performed amplicon sequencing using GS FLX standard chemistry and genotyped the same 20 samples for HLA-A, -B, -C, DPB1, DQA1, DQB1, DRB1, DRB3, DRB4, and DRB5 (DRB3/4/5) in a single sequencing run. The average sequence read length was 250 base pairs and the average number of sequence reads per amplicon was 672, providing confidence in the allele assignments. Of the 1280 genotypes considered, assignment was possible in 95% of the cases. Failure to assign genotypes was the result of researcher procedural error or the presence of a novel allele rather than a failure of sequencing technology. Concordance with known genotypes, in cases where assignment was possible, ranged from 95.3% to 99.4% for the eight sites, with overall concordance of 97.2%. We conclude that clonal pyrosequencing using the GS FLX platform and CONEXIO ATF software allows reliable identification of HLA genotypes at high resolution.

The inhibitory neural circuitry as target of antiepileptic drugs

Impairments and defects in the inhibitory neurotransmission in the CNS can contribute to various seizure disorders, i.e., gamma-aminobutyric acid (GABA) and glycine as the main inhibitory neurotransmitters in the brain play a crucial role in some forms of epilepsy. Recent advances in deciphering the molecular basis of the GABAergic and glycinergic systems has been achieved by means of cloning techniques and gene targeting strategies in animals, contributing to the understanding of drug action. As well, several anticonvulsive substances emerged which target key molecules of the inhibitory systems. Employment of recombinant expression systems, including, but not restricted to the inhibitory circuitry, will further facilitate drug screening and rational approaches to design novel specific antiepileptic drugs, which act highly efficiently to prevent or reduce generation and spread of seizures.

Binding of human lipoproteins (low, very low, high density lipoproteins) to recombinant envelope proteins of hepatitis C virus

Heterogeneities in the density of hepatitis C virus (HCV)-RNA-carrying material from human sera (1.03-1.20 g/ml) are partially due to the binding of lipoproteins [low density (LDL), very low density (VLDL), high density (HDL) lipoproteins] and immunoglobulins. In this study we demonstrate the binding of recombinant HCV envelope protein (El/E2) to human LDL, VLDL and HDL on a molecular basis. The binding of lipoproteins was restricted to the middle part of the El gene product (amino acids 222-336) and the C-terminal part of the E2 protein (amino acids 523-809). Lipoproteins did not bind to recombinant HCV core protein.

Molecular epidemiology of an outbreak of HCV in a hemodialysis unit: direct sequencing of HCV-HVR1 as an appropriate tool for phylogenetic analysis

Infection with hepatitis C virus (HCV) is still a serious problem in hemodialysis patients, despite screening of blood products for anti-HCV antibodies. The prevalence of HCV in HD patients is between 15% and 30% in Germany. We report the molecular epidemiology of an HCV outbreak in a hemodialysis unit in 1997 is determined. HCV hypervariable region 1 (HVR1) was amplified from serum samples of 19 patients by polymerase chain reaction (PCR) and sequenced directly. In addition, HCV isolates from 3 of these 19 patients were cloned and sequenced. 14 newly infected patients and two patients, who had been infected for several years had very closely related HCV isolates. Unrelated HCV isolates as well as sequences obtained from an HCV outbreak in a plasmapheresis center were found in different, distantly related branches. These findings provide strong evidence for nosocomial transmission of the virus, despite following strict general hygiene precautions. The production of anti-HCV antibody was delayed significantly or seroconversion did not occur at all during the period of observation in 8 out of 14 newly infected HCV RNA positive patients. Close-meshed reverse transcription-polymerase chain reaction (RT-PCR) analyses on apparently non infected patients within hemodialysis units and upon admission of new patients is strongly recommended for the early detection and prevention of outbreaks of HCV.

Low density lipoprotein receptor as a candidate receptor for hepatitis C virus

Hepatitis C virus (HCV) binds to different human cell lines in vitro. However, the efficiency of adsorption is very low due mainly to a relatively small fraction of the virus being able to bind to these cells. Free low density lipoprotein (LDL > 200 microg/ml) is able to block the attachment of HCV to human fibroblasts in vitro completely. COS-7 cells being primarily not able to bind HCV were transfected with a vector containing the entire coding sequence of the human LDL-receptor (LDLR). HCV was now bound to these cells. We propose that HCV and LDL are competitive for the cellular LDLR and that LDL in sera of patients may regulate the binding of HCV to this target.

Low density lipoprotein receptor as a candidate receptor for hepatitis C virus

Hepatitis C virus (HCV) binds to different human cell lines in vitro. However, the efficiency of adsorption is very low due mainly to a relatively small fraction of the virus being able to bind to these cells. Free low density lipoprotein (LDL > 200 microg/ml) is able to block the attachment of HCV to human fibroblasts in vitro completely. COS-7 cells being primarily not able to bind HCV were transfected with a vector containing the entire coding sequence of the human LDL-receptor (LDLR). HCV was now bound to these cells. We propose that HCV and LDL are competitive for the cellular LDLR and that LDL in sera of patients may regulate the binding of HCV to this target.

Low density lipoprotein receptor as a candidate receptor for hepatitis C virus

Hepatitis C virus (HCV) binds to different human cell lines in vitro. However, the efficiency of adsorption is very low due mainly to a relatively small fraction of the virus being able to bind to these cells. Free low density lipoprotein (LDL > 200 microg/ml) is able to block the attachment of HCV to human fibroblasts in vitro completely. COS-7 cells being primarily not able to bind HCV were transfected with a vector containing the entire coding sequence of the human LDL-receptor (LDLR). HCV was now bound to these cells. We propose that HCV and LDL are competitive for the cellular LDLR and that LDL in sera of patients may regulate the binding of HCV to this target.

Characterization of unusual escape variants of hepatitis B virus isolated from a hepatitis B surface antigen-negative subject

Hepatitis B virus DNA was extracted from serial serum samples of a hepatitis B surface antigen-negative patient with antibodies to the core protein as the only marker of an infection with hepatitis B virus. This patient showed no symptoms of hepatic injury. Sequencing of the amplified viral DNA demonstrated multiple amino acid changes clustering in surface-exposed regions of the surface protein. Synthesis and association of the middle (M) and small (S) surface proteins could be shown in vitro. The variant surface antigens were recognized neither by monoclonal antibodies to the surface antigen nor by the vaccinee's sera. Consequences for hepatitis B surface antigen testing and vaccine development are discussed.

[Endogenous digitalis-like factor in liver cirrhosis and cholestasis]

Endogenous digitalis-like factor (EDLF), an inhibitor of membrane Na+/K(+)-ATPase, is discussed to be involved in the pathogenesis of cirrhogenic portal hypertension, ascites formation and development of functional hepatorenal failure. Therefore, we investigated the serum content of this mediator in patients with liver cirrhosis Child-Pugh stage A, B, and C (n = 27) by means of enzyme immunoassay with a specific digoxin antibody. Furthermore, a correlation analysis was performed in order to find out correlations between signs of cell injury, cholestasis, synthetic cell function, ascites formation, and hepatorenal failure. Our results demonstrate that EDLF is significantly elevated in Child C cirrhosis (0.61 +/- 0.15 ng/ml) in comparison to Child A cirrhosis (0.013 +/- 0.2 ng/ml) and is also higher than in Child B cirrhosis (0.23 +/- 0.25 ng/ml). In patients without ascites EDLF (0.056 +/- 0.19 ng/ml) differs significantly from that of patients with non-complicated ascites (0.156 +/- 0.176 ng/ml) and from that of patients with therapy refractory ascites (0.66 +/- 0.17 ng/ml) or hepatorenal failure (1.56 ng/ml). There are no correlations between EDLF and renal function. Significant correlations were demonstrated for cholestasis (serum bilirubin), synthesis function (serum protein, Quick's value, cholinesterase, fibrinogen, albumin), and the degree of portasystemic encephalopathy (number connection test). We conclude that EDLF may act as a mediator in the process of progressive portal hypertension and its complications due to cirrhosis. This process of progression is caused by the inhibition of Na+/K(+)-ATPase, vasoconstriction, and endothelin secretion.

Hepatic aldehyde dehydrogenase (E.C. 1.2.1.3.) isoenzymes and malondialdehyde levels in alcoholic liver disease

To clarify the controversially discussed behaviour of hepatic ALDH isozymes in different liver diseases, 98 liver biopsy specimens were investigated as to their total ALDH and their isozyme activity. Simultaneously the malondialdehyde (MDA) content was measured in both biopsy samples and serum. The results show a significant decrease of the "low Km" isozyme E-2 activity depending on the severity of the liver disease. The tendency for the E-2 activity to decrease was greater in alcoholic than in nonalcoholic liver diseases. Although in all our diagnosis groups elevated MDA concentrations could be measured in both serum and liver tissue, a direct specific inhibitory effect on the E-2 activity could not be confirmed. The change from the low Km pathway to the high Km pathway of aldehyde detoxification, however, may contribute to the progress in alcoholic liver disease.

[Diagnostic value of molecular weight related urinary protein electrophoresis in normal total protein excretion]

The electrophoresis of urinary proteins related to the molecular weight in SDS-polyacrylamide gels stood the test for the clarification of the cause of proteinurias. Also in normal excretion of the total protein the analysis of protein is reasonable after concentration of the urine. In the electrophoretic separation of 104 urinary specimens with a maximum protein content of 0.15 g/l in 44 cases a normal protein pattern was found. In 60 cases pathological patterns occurred which in their protein composition greatly corresponded to the damage within the nephron to be expected in the different clinical diagnoses. The results show that the SDS-polyacryl amide gel electrophoresis is suitable for the early recognition and differentiation of injuries of the kidneys.

A low molecular weight alanine aminopeptidase in urine. Biochemical equivalent of tubular atrophy?

Using agarose gel electrophoresis, a faster moving alanine aminopeptidase (EC 3.4.11.2) has been demonstrated in the urine from cases of Fanconi syndrome, endemic (Balkan) nephropathy and advanced renal insufficiency. The enzyme was partially purified and its properties (isoelectric point, molecular weight, substrate specificity, influence of metal ions, Michaelis constant, antigenic behavior) were compared with those of normal kidney alanine aminopeptidase. Isoelectric points and antigenic properties are identical, but the molecular weights differ by a factor of about 2. Therefore, the greater electrophoretic mobility is due to the smaller size of the atypical enzyme.

Nature of the multiple forms of alanine aminopeptidase

Alanine aminopeptidase (particle-bound aminopeptidase, EC 3.4.11.2) isolated in a highly purified state from human liver, kidney, and pancreas were investigated with regard to their different electrophoretic mobilities. While the molecular weights are identical, different isoelectric points were found. The results of carbohydrate analysis point to N-acetylneuraminic acid as the main factor that causes the differences in electrophoretic behaviour of the alanine aminopeptidases investigated.