The spatial position and replication timing of chromosomal domains are both established in early G1 phase

Mammalian chromosomal domains replicate at defined, developmentally regulated times during S phase. The positions of these domains in Chinese hamster nuclei were established within 1 hr after nuclear envelope formation and maintained thereafter. When G1 phase nuclei were incubated in Xenopus egg extracts, domains were replicated in the proper temporal order with nuclei isolated after spatial repositioning, but not with nuclei isolated prior to repositioning. Mcm2 was bound both to early- and late-replicating chromatin domains prior to this transition whereas specification of the dihydrofolate reductase replication origin took place several hours thereafter. These results identify an early G1 phase point at which replication timing is determined and demonstrate a provocative temporal coincidence between the establishment of nuclear position and replication timing.

Fine mapping of a replication origin of human DNA

A highly sensitive procedure was developed for the identification of the origin of bidirectional DNA synthesis in single-copy replicons of mammalian cells. The method, which does not require cell synchronization or permeabilization, entails the absolute quantification, by a competitive PCR procedure in newly synthesized DNA samples, of the abundance of neighboring DNA fragments distributed along a given genomic region. This procedure was utilized for mapping the start site of DNA replication in a 13.7-kb region of human chromosome 19 coding for lamin B2, which is replicated immediately after the onset of S phase in HL-60 cells. Within this region, DNA replication initiates in a 474-bp area corresponding to the 3' noncoding end of the lamin B2 gene and the nontranscribed spacer between this gene and the 5' end of another highly transcribed one. This localization was obtained both in aphidicolin-synchronized and in exponentially growing HL-60 cells.

Temporally coordinated assembly and disassembly of replication factories in the absence of DNA synthesis

Here we show that exposure of aphidicolin-arrested Chinese hamster ovary (CHO) cells to the protein-kinase inhibitors 2-aminopurine or caffeine results in initiation of replication at successively later-replicating chromosomal domains, loss of the capacity to synthesize DNA at earlier-replicating sites, release of Mcm2 proteins from chromatin, and redistribution of PCNA and RPA from early- to late-replicating domains in the absence of detectable elongation of replication forks. These results provide evidence that, under conditions of replicational stress, checkpoint controls not only prevent further initiation but may also be required to actively maintain the integrity of stalled replication complexes.

Sofosbuvir and daclatasvir combination therapy in a liver transplant recipient with severe recurrent cholestatic hepatitis C

Recurrent HCV infection following liver transplantation can lead to accelerated allograft injury that is difficult to treat with interferon. The aim of this study is to describe the first ever use of an interferon-free, all oral regimen in a liver transplant recipient with severe recurrent HCV. A 54-year-old male with HCV genotype 1b developed severe cholestatic HCV at 6 months posttransplant with ascites, AST 503 IU/mL, alkaline phosphatase of 298 IU/mL, HCV RNA of 12 000 000 IU/mL, and histological cholestasis with pericellular fibrosis. Sofosbuvir, an HCV polymerase inhibitor (400 mg/day), and daclatasvir, an HCV NS5A replication complex inhibitor (60 mg/day), were co-administered for 24 weeks. Within 4 weeks of initiating treatment, serum HCV RNA levels became undetectable and liver biochemistries normalized with concomitant resolution of ascites. The patient achieved a sustained virological response with undetectable HCV RNA at 9 months posttreatment. During and following treatment, the daily dose and blood level of tacrolimus remained stable and unchanged. The rapid and sustained suppression of HCV replication in this liver transplant recipient provides great promise for the use of combination oral antiviral regimens in other immunosuppressed and interferon refractory HCV patients.

BRCA1 gene promoter methylation status in high-grade serous ovarian cancer patients--a study of the tumour Bank ovarian cancer (TOC) and ovarian cancer diagnosis consortium (OVCAD)

BACKGROUND

Mutations in BRCA1/2 genes are involved in the pathogenesis of breast and ovarian cancer. Inactivation of these genes can also be mediated by hypermethylation of CpGs in the promoter regions. Aim of this study was to analyse the clinical impact of BRCA1 promoter gene methylation status in a homogenous cohort of high-grade serous ovarian cancer (HGSOC) patients.

METHODS

The cohort included 257 primary HGSOC patients treated by cytoreduction and platinum-based chemotherapy. DNA was extracted from fresh frozen tissue samples. BRCA1 gene promoter methylation rate was assessed using polymerase chain reaction (PCR).

RESULTS

14.8% of patients presented hypermethylation within a selected region of the BRCA1 promoter. The rate of hypermethylation was significantly higher in younger patients (20.8% hypermethylation in the age group ⩽ 58 years versus 8.7% hypermethylation in the age group >58 years; p = 0.008). Optimal tumour debulking could be reached in 63% of patients, without significant differences in the extent of residual disease with respect to the methylation status. No impact of BRCA1 gene promoter methylation status on progression free- and overall-survival rates was found. No significant differences within BRCA1 promoter methylation status between primary and metastatic tissue could be observed. These results on BRCA1 promoter methylation status were also confirmed in a subgroup of 107 patients found negative for BRCA1 exon 11 mutations.

CONCLUSIONS

Our data suggest that BRCA1 methylation determines the earlier onset of HGSOC. Furthermore our study supports the idea that BRCAness is not only due to mutations but also to epigenetic changes in BRCA1 promoter gene.

Haplotype analysis of hemochromatosis: evaluation of different linkage-disequilibrium approaches and evolution of disease chromosomes

We applied several types of linkage-disequilibrium calculations to analyze the hereditary hemochromatosis (hh) locus. Twenty-four polymorphic markers in the major histocompatibility complex (MHC) class I region were used to haplotype hh and normal chromosomes. A total of 169 hh and 161 normal chromosomes were analyzed. Disequilibrium values were found to be high over an unusually large region beginning 150 kb centromeric of HLA-A and extending nearly 5 Mb telomeric of it. Recombination in this region was approximately 28% of the expected value. This low level of recombination contributes to the unusually broad region of linkage disequilibrium found with hh. The strongest disequilibrium was found at locus HLA-H (delta = .84) and at locus D6S2239 (delta = .85), a marker approximately 10 kb telomeric to HLA-H. All disequilibrium methods employed in this study found peak disequilibrium at HLA-H or D6S2239. The cys282tyr mutation in HLA-H, a candidate gene for hh, was found in 85% of disease chromosomes. A haplotype phylogeny for hh chromosomes was constructed and suggests that the mutation associated with the most common haplotype occurred relatively recently. The age of the hh mutation was estimated to be approximately 60-70 generations. Disequilibrium was maintained over a greater distance for hh-carrying chromosomes, consistent with a recent mutation for hh. Our data provide a reasonable explanation for previous difficulties in localizing the hh locus and provide an evolutionary history for disease chromosomes.

Nucleolin inhibits Hdm2 by multiple pathways leading to p53 stabilization

Nucleolin is a c-Myc-induced gene product with defined roles in ribosomal RNA processing and the inhibition of chromosomal DNA replication following stress. Here we find that changes in nucleolin protein levels in unstressed cells cause parallel changes in the amount of p53 protein. Alterations in p53 levels arise from nucleolin binding to the p53 antagonist Hdm2, resulting in the inhibition of both p53 ubiquitination and Hdm2 auto-ubiquitination. Nucleolin does not alter p53 ubiquitination by human papillomavirus E6, indicating that the effect is specific for Hdm2. Although the inhibition of ligase activity would be expected to stabilize Hdm2, we instead find that nucleolin also reduces Hdm2 protein levels, demonstrating that nucleolin inhibits Hdm2 using multiple mechanisms. Increases in nucleolin levels in unstressed cells led to higher expression of p21(cip1/waf1), a reduced rate of cellular proliferation, and an increase in apoptosis. Thus, nucleolin has a number of properties in common with the tumor suppressor ARF (alternate reading frame). We propose that nucleolin, like ARF, responds to hyperproliferative signals by upregulation of p53 through Hdm2 inhibition.

Stability and nuclear distribution of mammalian replication protein A heterotrimeric complex

Replication protein A (RPA), a stable complex of three polypeptides, is the single-stranded DNA-binding protein essential for DNA replication in eukaryotic cells. Previous studies of the subcellular distribution and stability of the RPA heterotrimer during the mammalian cell cycle have produced conflicting results. Here, we present evidence that these inconsistencies can be accounted for by the presence of an extractable pool of soluble RPA within the nucleus. Indirect immunofluorescence experiments in both CHO and HeLa cells showed that all three RPA subunits associated specifically with sites of ongoing DNA synthesis, similar to the replication fork protein proliferating cell nuclear antigen. Furthermore, we found no evidence for disassembly of the chromatin-bound heterotrimeric RPA complex in vivo. Our results are consistent with a role for RPA in the initiation and elongation steps of replication, as previously defined in the viral in vitro replication systems.

In vivo protein-DNA interactions at human DNA replication origin

Protein-DNA interactions were studied in vivo at the region containing a human DNA replication origin, located at the 3' end of the lamin B2 gene and partially overlapping the promoter of another gene, located downstream. DNase I treatment of nuclei isolated from both exponentially growing and nonproliferating HL-60 cells showed that this region has an altered, highly accessible, chromatin structure. High-resolution analysis of protein-DNA interactions in a 600-bp area encompassing the origin was carried out by the in vivo footprinting technique based on the ligation-mediated polymerase chain reaction. In growing HL-60 cells, footprints at sequences homologous to binding sites for known transcription factors (members of the basic-helix-loop-helix family, nuclear respiratory factor 1, transcription factor Sp1, and upstream binding factor) were detected in the region corresponding to the promoter of the downstream gene. Upon conversion of cells to a nonproliferative state, a reduction in the intensity of these footprints was observed that paralleled the diminished transcriptional activity of the genomic area. In addition to these protections, in close correspondence to the replication initiation site, a prominent footprint was detected that extended over 70 nucleotides on one strand only. This footprint was absent from nonproliferating HL-60 cells, indicating that this specific protein-DNA interaction might be involved in the process of origin activation.

A human DNA replication origin: localization and transcriptional characterization

A single-copy 13.7 kb human DNA region (L30E) located on Ch. 19 p13.3 contains an origin of DNA replication in myeloid HL-60 cells. The origin was localized, by means of quantitative PCR within approximately 3000 bp, in a highly transcribed region containing at least two closely spaced genes with the same polarity of transcription, one encoding lamin B2 and the other an unidentified protein. The origin region overlaps an undermethylated "CpG island" at the 5'-end of the second transcription unit. A binding site (CACGTG) for basic helix-loop-helix (bHLH) DNA binding proteins such as USF/MLTF or MYC-MAX was located by DNase I footprinting analysis in the promoter of the second gene. DMSO differentiation of HL-60 cells, that completely shuts off replication, also drastically reduces the transcription of L30E region. On the other hand such treatment does not modify the methylation pattern of the CpG island and does not abolish the DNase I protection of the bHLH binding site.

Regulation of mammalian replication origin usage in Xenopus egg extract

Xenopus embryos initiate replication at random closely spaced sites until a certain concentration of nuclei is achieved within the embryo, after which fewer, more specific chromosomal sites are utilized as origins. We have examined the relationship between nucleo-cytosolic ratio and origin specification when Chinese hamster ovary (CHO) cell nuclei are introduced into Xenopus egg extracts. At concentrations of intact late-G1-phase nuclei that approximate early Xenopus embryos, the entire genome was duplicated nearly 4 times faster than in culture, accompanied by a de-localization of initiation sites at the dihydrofolate reductase (DHFR) locus. As the concentration of nuclei was increased, the number of initiation sites per nucleus decreased and initiation at the DHFR locus became localized to the physiologically utilized DHFR origin. Origin specification was optimal at nuclear concentrations that approximate the Xenopus mid-blastula transition (MBT). Higher concentrations resulted in an overall inhibition of DNA synthesis. By contrast, with intact early G1-phase nuclei, replication initiated at apparently random sites at all concentrations, despite an identical relationship between nucleo-cytosolic ratio and replicon size. Furthermore, permeabilization of late-G1-phase nuclei, using newly defined conditions that preserve the overall rate of replication, eliminated site-specificity, even at nuclear concentrations optimal for DHFR origin recognition. These data show that both nucleo-cytosolic ratio and nuclear structure play important but independent roles in the regulation of replication origin usage. Nucleo-cytosolic ratio clearly influences the number of replication origins selected. However, titration of cytosolic factors is not sufficient to focus initiation to specific sites. An independent mechanism, effecting changes within G1-phase nuclei, dictates which of many potential initiation sites will function as an origin.

Risk factors and outcomes associated with type of uterine rupture

PURPOSE

To identify risk factors associated with the occurrence of complete uterine rupture (CUR) in comparison to partial uterine rupture (PUR) to further investigate to what extent a standardized definition is needed and what clinical implications can be drawn.

METHODS

Between 2005 and 2017 cases with CUR and PUR at Charité University Berlin, Germany were retrospectively identified. Demographic, obstetric and outcome variables were analyzed regarding the type of rupture. Binary multivariate regression analysis was conducted to identify risk factors associated with CUR. In addition, the intended route of delivery (trial of labor after cesarean delivery (TOLAC) and elective repeat cesarean delivery (ERCD)), divided according to the type of rupture, was compared.

RESULTS

92 cases with uterine rupture were identified out of a total of 64.063 births (0.14%). Puerperal complications were more frequent in CUR (67.9 versus 41.1%, p = 0.021). Multiparity ≥ 3 was more frequent in CUR (31 versus 10.7%, p = 0.020). Factors increasing the risk for CUR were parity ≥ 3 (OR = 3.8, p = 0.025), previous vaginal birth (OR = 4.4, p = 0.011), TOLAC (OR = 6.5, p < 0.001) and the use of oxytocin (OR = 2.9, p = 0.036). After multivariate analysis, the only independent risk factor associated with CUR was TOLAC (OR = 7.4, p = 0.017).

CONCLUSION

TOLAC is the only independent risk factor for CUR. After optimized antenatal counselling TOLAC and ERCD had comparable short-term maternal and fetal outcomes in a high resource setting. A high number of previous vaginal births does not eliminate the risk of uterine rupture. A clear distinction between CUR and PUR is essential to ensure comparability among studies.

DNA replication and nuclear organization: prospects for a soluble in vitro system

The role of nuclear structure in the replication of eukaryotic DNA has been the subject of debate for many decades. The recent demonstration that once-per-cell-cycle replication can take place in vitro without a nucleus, providing sufficiently high concentrations of replication factors are supplied, suggests that one role of the nucleus is to concentrate essential factors. This important finding has paved the way for the establishment of a purified biochemical system for replication of eukaryotic DNA. However, this soluble system, derived from Xenopus egg extracts, initiates replication within any DNA sequence and does not recapitulate the spatial and temporal regulation of DNA replication that is observed in most cells. In both Xenopus and Drosophila embryos, site-specific initiation of replication is not observed until after nuclei become transcriptionally active at the blastula stage of development. Furthermore, programmed changes in both the locations of origins and the time during S-phase at which sequences are replicated accompany key stages of metazoan development. Recent findings indicate that these changes correlate with changes in nuclear organization and that the spatial and temporal program for replication is established early in G1-phase when nuclei are structurally and functionally reorganized after mitosis.

Presence of HLA-DR immunopositive cells in human fetal thymus

Several kinds of thymic cells express MHC class II antigens, including human-leukocyte-associated antigen-DR (HLA-DR) during postnatal development. The present study was focused on the detection and analysis of HLA-DR immunoreactivity in human fetal thymuses (6-7th month of gestation). Using monoclonal antibodies, indirect immunoperoxidase staining (IIP), immunogold electron microscopy (IGEM), enzyme-linked immunosorbent assay (ELISA) and flow cytometry, HLA-DR immunopositive (IP) thymic cells were found in samples studied. IIP and IGEM demonstrated the presence of HLA-DR IP stromal cells (SCs): epithelial cells (ECs), dendritic-like cells (DCs) and macrophages (MCs) as well as HLA-DR IP lymphocytes (Lys) in all thymic regions. HLA-DR immunoreactivity was more prominent in the medullary ECs (mECs) than in the cortical ECs (cECs). Strong staining of Hassall's corpuscles and the adjacent mECs was seen. The differences in the intracellular distribution of HLA-DR molecules were detailed by IGEM as a first attempt to analyse HLA-DR IP cells at ultrastructural level. ELISA data and two-colour flow cytometric analysis revealed the presence of HLA-DR IP and HLA-DR/CD3 double IP Lys in accordance with the immunocytochemical assays. The results presented enrich the information about HLA-DR IP components of the thymic microenvironment in developing human thymus and raise the question of their role during prenatal T cell differentiation and selection processes.

Searching for replication origins in mammalian DNA

The attempts at identifying precise replication origins (ori) in mammalian DNA have been pursued mainly through physico-chemical and biochemical approaches, in view of the essential failure of the search for autonomously replicating sequences in cultured cells. These approaches involve the mapping of short stretches of nascent DNA, the identification of the regions where either leading or lagging strands switch polarity, or the localization of replication intermediates by two-dimensional gel electrophoresis. Due to the complexity of animal cell genomes, most of these studies have been performed on amplified domains and with the use of synchronization procedures. The results obtained have been controversial. In order to avoid the use of experimental procedures potentially affecting the physiological mechanism of DNA replication, we have developed a method for the localization of ori in single-copy loci in exponentially growing cells. This method entails the absolute quantification of the abundance of selected DNA fragments along a genomic region within samples of newly synthesized DNA by competitive polymerase chain reaction (PCR); the latter is immune to all the uncontrollable variables which severely affect the reproducibility of conventional PCR. The application of this method to SV40 ori-driven plasmid replication precisely identifies the known ori localization. Using the same approach, we have mapped an ori for bi-directional DNA replication in a 13.7-kb locus of human chromosome 19 encoding lamin B2.

Isolation and cloning of putative mouse DNA replication initiation sites: binding to nuclear protein factors

By using an original two-step technique (trioxsalen crosslinking/immunoprecipitation) we were able to isolate in a single-stranded form a fraction of mouse DNA enriched in putative Replication Initiation Sequences (RIS). The isolated and purified single-strand fragments were made double-stranded in vitro and were cloned in pUC12 to prepare a confined RIS library. 30 randomly selected RIS inserts were subjected to gel mobility shift assay using nuclear extracts either from dividing, or from quiescent mouse cells. Twelve out of the 30 RIS fragments showed specific binding to proteins present in nuclear extract from dividing cells, while none were retarded by extracts from quiescent cells. RIS12, RIS18 and RIS30 were sequenced and it was found that they were A+T rich and contained different regulatory elements. By using a two step procedure (Heparin-sepharose chromatography/DNA affinity chromatography) we isolated the protein factor that specifically binds to RIS12. It appeared as a double band with apparent molecular masses of 63 and 65 kD.

Application of an immunological method to detect trace amounts of dried human semen

An immunological assay based on a monoclonal antibody was used for identification of trace amounts of dried human semen in forensic science evidence. The monoclonal antibody (Mab 4E6) produced recognizes a human sperm-coating antigen which is specific to human seminal plasma. This antigen seems to be a protein secreted by the epithelial cells of the ejaculatory duct, which is stable indefinitely at room temperature. Mab 4E6 reacts positively with semen samples from individuals independently to their ABO group or secretory status, but does not react with semen from bull, ram, boar, horse, rabbit and dog. In the assay system developed, Mab 4E6 can detect human seminal plasma at concentrations of 0.5 micrograms/ml total protein. A similar sensitivity is found when human semen stains are eluted from forensic science samples and tested by the same assay. This method shows a good correlation with the microscopic methods routinely used. The method described is very sensitive and reproducible, it is time saving and special laboratory equipment is not needed.

A modified protocol for in vivo footprinting by ligation-mediated polymerase chain reaction

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Serum sperm antibodies unrelated to mumps orchitis

In order to determine whether there is an association between mumps orchitis and serum sperm antibodies, we tested patients at the time orchitis was diagnosed (n = 7) and individuals who had had orchitis at least 1 month previously (n = 14). Data were compared with the results for a control group of blood donors (n = 20). Sperm antibodies were detected by the gelatin agglutination test of Kibrick, the tray agglutination test of Friberg and the ELISA. Clinically significant sperm antibody levels were not found in patients in the early stages of the disease. Four subjects tested post-disease were positive in the Friberg test and one was positive in the ELISA. One control serum was also positive in the latter test. Significant differences were not found between levels in patients in the early stages of the disease and levels in individuals post-disease, although the results of the Friberg test differed significantly between controls and former mumps orchitis cases. These data do not support the assumption of an involvement of humoral immunity against spermatozoa in mumps orchitis patients.

Effects of the antidepressant drug moclobemide on learning and memory in rats

Moclobemide is a well known drug with antidepressant action. The aim of this study was to investigate the effects of moclobemide on learning and memory processes in Sprague Dawley rats. Over a 5-day period, learning sessions with 30 trials per day and memory retention tests were performed. The conditioned responses (avoidances), the unconditioned responses (escapes) and the intertrial crossings were observed. An active avoidance test was carried out using a shuttle box. Two passive avoidance tests were used: step-through (using a light chamber) and step-down (using a platform). In the step-through passive avoidance test, the learning and retention sessions consisted of three trials each and the latency of reaction times (the rat remaining in the light chamber for more than 180 sec) was used as criterion. In the step-down passive avoidance test, learning and retention sessions consisted of two trials and the latency of reaction times (the rat remaining on the platform for 60 sec) was used as criterion. In the active avoidance tests, moclobemide dose-dependently increased the number of avoidances during learning sessions and maintained this number in memory retention tests. Moclobemide did not alter the number of escapes, but did increase motor activity. In the passive avoidance tests, moclobemide also increased the latency of reaction times in learning and short memory retrieval tests. These findings suggest that moclobemide improves learning and memory processes in active and passive avoidance tests and has a cognition-enhancing effect.

Influence of migrant background on patient preference and expectations in breast and gynecological malignancies (NOGGO-expression V study): results of a prospective multicentre study in 606 patients in Germany

Background

An effective cross-cultural doctor-patient communication is vital for health literacy and patient compliance. Building a good relationship with medical staff is also relevant for the treatment decision-making process for cancer patients. Studies about the role of a specific migrant background regarding patient preferences and expectations are lacking. We therefore conducted a multicentre prospective survey to explore the needs and preferences of patients with a migrant background (PMB) suffering from gynecological malignancies and breast cancer to evaluate the quality of doctor-patient communication and cancer management compared to non-migrants (NM).

Methods

This multicentre survey recruited patients with primary or recurrence of breast, ovarian, peritoneal, or fallopian tube cancer. The patients either filled out a paper form, participated via an online survey, or were interviewed by trained staff. A 58-item questionnaire was primarily developed in German and then translated into three different languages to reach non-German-speaking patients.

Results

A total of 606 patients were included in the study: 54.1% (328) were interviewed directly, 9.1% (55) participated via an online survey, and 36.8% (223) used the paper print version. More than one quarter, 27.4% (166) of the participants, had a migrant background. The majority of migrants and NM were highly satisfied with the communication with their doctors.

First-generation migrants (FGM) and patients with breast cancer were less often informed about participation in clinical trials (p < 0.05) and 24.5% of them suggested the help of an interpreter to improve the medical consultation. Second and third-generation migrants (SGM and TGM) experienced more fatigue and nausea than expected.

Conclusions

Our results allow the hypothesis that training medical staff in intercultural competence and using disease-related patient information in different languages can improve best supportive care management and quality of life in cancer patients with migrant status.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08731-6.

Purification and characterization of sperm-coating antigen, identified by a monoclonal antibody

A procedure was designed for purification of a human seminal plasma-specific antigen (HSP-antigen) identified by a monoclonal antibody produced in this laboratory (mAb 4E6). Pooled human seminal plasma was fractionated by consecutively applied methods: affinity chromatography on Lentil lectin sepharose, gel chromatography on Ultrogel AcA 34 and immunoaffinity on mAb 4E6 coupled CNBr-Sepharose 4B. The antigen-containing fraction obtained after this procedure was proved to be homogeneous when analysed by electrophoresis in polyacrylamide gel. After the consecutive purification procedures the degree of purification was 128 times as compared to the starting material. Electrophoretic analysis of the purified 4E6 antigen under reducing conditions showed that it consisted of 3 polypeptide subunits with molecular weight 70 kDa, 64 kDa and 60 kDa respectively. On the basis of the data obtained from competitive ELISA testing of sera from infertile patients it has been suggested that the identified antigen may be involved in pathogenesis of immunologic infertility.