Human LINE retrotransposons generate processed pseudogenes

Long interspersed elements (LINEs) are endogenous mobile genetic elements that have dispersed and accumulated in the genomes of higher eukaryotes via germline transposition, with up to 100,000 copies in mammalian genomes. In humans, LINEs are the major source of insertional mutagenesis, being involved in both germinal and somatic mutant phenotypes. Here we show that the human LINE retrotransposons, which transpose through the reverse transcription of their own transcript, can also mobilize transcribed DNA not associated with a LINE sequence by a process involving the diversion of the LINE enzymatic machinery by the corresponding mRNA transcripts. This results in the 'retroposition' of the transcribed gene and the formation of new copies that disclose features characteristic of the widespread and naturally occurring processed pseudogenes: loss of intron and promoter, acquisition of a poly(A) 3' end and presence of target-site duplications of varying length. We further show-by introducing deletions within either coding sequence of the human LINE-that both ORFs are necessary for the formation of the processed pseudogenes, and that retroviral-like elements are not able to produce similar structures in the same assay. Our results strengthen the unique versatility of LINEs as genome modellers.

Fine organization of Bombyx mori fibroin heavy chain gene

The complete sequence of the Bombyx mori fibroin gene has been determined by means of combining a shotgun sequencing strategy with physical map-based sequencing procedures. It consists of two exons (67 and 15 750 bp, respectively) and one intron (971 bp). The fibroin coding sequence presents a spectacular organization, with a highly repetitive and G-rich (approximately 45%) core flanked by non-repetitive 5' and 3' ends. This repetitive core is composed of alternate arrays of 12 repetitive and 11 amorphous domains. The sequences of the amorphous domains are evolutionarily conserved and the repetitive domains differ from each other in length by a variety of tandem repeats of subdomains of approximately 208 bp which are reminiscent of the repetitive nucleosome organization. A typical composition of a subdomain is a cluster of repetitive units, Ua, followed by a cluster of units, Ub, (with a Ua:Ub ratio of 2:1) flanked by conserved boundary elements at the 3' end. Moreover some repeats are also perfectly conserved at the peptide level indicating that the evolutionary pressure is not identical along the sequence. A tentative model for the constitution and evolution of this unusual gene is discussed.

Linkage and association between Plasmodium falciparum blood infection levels and chromosome 5q31-q33

We have previously mapped a locus controlling Plasmodium falciparum blood infection levels (PFBI) to chromosome 5q31-q33. We genotyped 19 microsatellite markers on chromosome 5q31-q33 in a new sample of 44 pedigrees comprising 84 nuclear families and 292 individuals living in a P. falciparum endemic area. Using a nonparametric multipoint variance-component approach (by GENEHUNTER), we evidenced a peak of linkage close to D5S636 (P=0.0069), with a heritability of 0.46. Using a variance-component method for linkage-disequilibrium mapping of quantitative traits (by QTDT) and the Bonferroni correction for multiple testing, we further detected allelic association in the presence of linkage between blood infection levels and D5S487 (P=6 x 10(-5); P(c)=0.0011), which is located on the distal part of the peak. These results confirm the importance of chromosome 5q31-q33 in the genetic control of PFBI levels.

Electrochemistry and reactivity of surface-confined catechol groups derived from diazonium reduction. Bias-assisted Michael addition at the solid/liquid interface

We have designed a novel catechol-modified electrode that could be used for bias-assisted Michael addition at the solid/liquid interface. The glassy carbon electrode was modified by the electrochemical reduction of a catechol para-substituted phenyldiazonium salt. The electrochemistry of surface-confined catechol moieties was investigated by cyclic voltammetry. The transfer coefficient and apparent surface standard electron-transfer rate constant were obtained using Laviron's theory. We demonstrate that o-quinone moieties linked to the surface remain quite reactive with nucleophilic species by Michael addition at the solid/liquid interface. To demonstrate the versatility of this procedure, 4-nitrobenzyl alcohol, (4-nitrobenzyl)amine, and a ferrocenealkylamine were chosen as nucleophile models due to their well-known redox properties. Electrochemically triggered Michael addition was validated, leading to redox headgroup-tethered surfaces.

DNA and protein changes in the spermatozoa of bulls treated orally with ethylene dibromide

Oral treatment of bulls with ethylene dibromide caused a temporary reduction of the DNA and protein content and head area of epididymal and ejaculated spermatozoa.

Selective alteration of mitochondrial function by Ditercalinium (NSC 335153), a DNA bisintercalating agent

The bifunctional intercalator Ditercalinium (NSC 335153) demonstrates an anti-tumoral cytotoxicity markedly different from other intercalating agents. A delayed toxicity is observed in eucaryotic cells, both in vitro and in vivo, at drug concentrations far below those required to observe immediate toxic effects. Fluorescence microscopy demonstrates that Ditercalinium and the mitochondrial-staining fluorophore DiOC2(5) are concentrated in the same cellular organelles of L1210 cells. Electron microscopy of Ditercalinium-treated cells reveals extensive and progressive swelling of mitochondria, with no other ultrastructural changes observed. Ditercalinium uptake and toxicity are in part related to mitochondrial membrane potential. However, drug accumulation itself does not immediately alter the mitochondrial membrane potential. Cellular ATP pool levels and the rate of respiration fall progressively after drug treatment. Nucleotide pools in DC3F cells, measured between drug treatment and death, show marked drops in pyrimidine levels while purine nucleotide levels decline more slowly. Addition of uridine or cytidine partially rescues Ditercalinium-treated cells, while toxicity is increased in the presence of 2-deoxyglucose. The combined evidence indicates that the toxicity of Ditercalinium to murine leukemia cells (L1210) and Chinese Hamster lung cells (DC3F) is due to disruption of mitochondrial function.

Synthesis and pyrogenic effect of 3 alpha, 7 alpha-dihydroxy-5 beta-androstan-17-one and 3 alpha-hydroxy-5 beta-androstane-7, 17-dione

The first chemical synthesis of 3 alpha, 7 alpha-dihydroxy-5 beta-androstan-17-one and 3 alpha-hydroxy-5 beta-androstane-7, 17-dione is reported. In this method, the 17 beta-side chain of commercial chenodesoxycholic acid was degraded in 6 steps after selective protection of the hydroxyl groups: 3 alpha-OH by a tert-butyldimethylsilyl group and 7 alpha-OH by an acetoxy group. The capacity of 3 alpha, 7 alpha-dihydroxy-5 beta-androstan-17-one and 3 alpha-hydroxy-5 beta-androstane-7, 17-dione to release a pyrogen by human leukocytes was investigated by two independent methods: supernatants from leukocytes incubated with a steroid are injected to rabbits whose fever is measured, or tested by the Limulus Test (a pyrogen detection technique). The 7-keto substituted etiocholanolone still possessed pyrogenic activity, while the 7 alpha-hydroxyl substituted one did not.

Electrodes for Membrane Surface Science. Bilayer Lipid Membranes Tethered by Commercial Surfactants on Electrochemical Sensors

Commercial surfactants, which are inexpensive and abundant, were covalently grafted to flat and transparent electrodes, and it appears to be a simple functionalization route to design biomembrane sensors at large-scale production. Sparsely tethered bilayer lipid membranes (stBLM) were stabilized using such molecular coatings composed of diluted anchor-harpoon surfactants that grab the membrane with an alkyl chain out of a PEGylated-hydrogel layer, which acts as a soft hydration cushion. The goal of avoiding the synthesis of complex organic molecules to scale up sensors was achieved here by grafting nonionic diblock oligomers (Brij58 = C _xH_{2 x+1}(OCH₂CH₂) _nOH with x = 16 and n = 23) and PEO short chains ((OCH₂CH₂) _nOH with n = 9 and n = 23) from their hydroxyl (-OH) end-moiety to a monolayer of -Ar-SO₂Cl groups, which are easy to form on electrodes (metals, semiconducting materials, ...) from aryl-diazonium salt reduction. A hybrid molecular coating on gold, with scarce Ar-SO₂-Brij58 and PEO oligomers, was used to monitor immobilization and fusion kinetics of DOPC small unilamellar vesicles (SUV) by both quartz crystal microbalance (QCM) and surface plasmon resonance (SPR) techniques. Using flat and transparent thin chromium film electrodes, we designed biosensors to couple surface sensitive techniques for membranes, including X-ray reflectivity (XRR), atomic force microscopy (AFM) with subnanometer resolution, and optical microscopy, such as fluorescence recovery after photobleaching measurements (FRAP), in addition to electrochemistry techniques (cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS)). The advantages of this biomembrane-sensing platform are discussed for research and applications.

Adcitmer® , a new CD56-targeting monomethyl auristatin E-conjugated antibody, is a potential therapeutic approach in Merkel cell carcinoma

BACKGROUND

Merkel cell carcinoma (MCC) is an aggressive skin cancer, whose tumour cells often express CD56. While immune checkpoint inhibitors constitute a major advance for treating patients with MCC with advanced disease, new therapeutic options are still urgently required.

OBJECTIVES

To produce and evaluate the therapeutic performance of a new antibody-drug conjugate (Adcitmer^® ) targeting CD56 in preclinical models of MCC.

METHODS

CD56 expression was evaluated in a MCC cohort (immunohistochemistry on a tissue microarray of 90 tumour samples) and MCC cell lines. Interaction of an unconjugated CD56-targeting antibody with CD56⁺ MCC cell lines was investigated by immunohistochemistry and imaging flow cytometry. Adcitmer^® product was generated by the bioconjugation of CD56-targeting antibody to a cytotoxic drug (monomethyl auristatin E) using the McSAF Inside^® bioconjugation process. The chemical properties and homogeneity of Adcitmer^® were characterized by hydrophobic interaction chromatography. Adcitmer^® cytotoxicity was evaluated in vitro and in an MCC xenograft mice model.

RESULTS

Similar to previous reports, CD56 was expressed by 66% of MCC tumours in our cohort, confirming its relevance as a therapeutic target. Specific binding and internalization of the unconjugated CD56-targeting antibody was validated in MCC cell lines. The high homogeneity of the newly generated Adcitmer^® was confirmed by hydrophobic interaction chromatography. The CD56-mediated cytotoxicity of Adcitmer^® was demonstrated in vitro in MCC cell lines. Moreover, Adcitmer^® significantly reduced tumour growth in a MCC mouse model.

CONCLUSIONS

Our study suggests that Adcitmer^® should be further assessed as a therapeutic option in patients with MCC, as an alternative therapy or combined with immune checkpoint inhibitors.

A simple method of surface functionalisation for immuno-specific immobilisation of proteins

We present a new and advanced methodology, developed for surface functionalisation of gold and to study immobilisation of an immuno-specific system of proteins. A combination of electrochemical quartz crystal microbalance and Raman spectroscopy techniques allowed a complete understanding of the system starting from surface functionalisation and progressing to the functional structure analysis of immobilised proteins. A simple electrochemical procedure was formulated to prepare sulphonyl chloride terminated gold surfaces that form a strong sulphonamide bond with the receptor protein staphylococcal protein A (SpA). On the SpA grafted surfaces, the immobilisation of a human IgG and consecutive binding of an immuno-specific anti-human IgG was observed. The surface functional groups form a strong interaction with SpA without disturbing its functional properties. The native functional structure of SpA and also the IgGs was found to be retained in their immobilised state.

Microdosimetry in low energy proton beam at therapeutic-equivalent fluence rate with silicon 3D-cylindrical microdetectors

In this work we show the first microdosimetry measurements on a low energy proton beam with therapeutic-equivalent fluence rates by using the second generation of 3D-cylindrical microdetectors. The sensors belong to an improved version of a novel silicon-based 3D-microdetector design with electrodes etched inside silicon, which were manufactured at the National Microelectronics Centre (IMB-CNM, CSIC) in Spain. A new microtechnology has been employed using quasi-toroid electrodes of 25μm diameter and a depth of 20μm within the silicon bulk, resulting in a well-defined cylindrical radiation sensitive volume. These detectors were tested at the 18 MeV proton beamline of the cyclotron at the National Accelerator Centre (CNA, Spain). They were assembled into an in-house low-noise readout electronics to assess their performance at a therapeutic-equivalent fluence rate. Microdosimetry spectra of lineal energy were recorded at several proton energies starting from 18 MeV by adding 50μm thick tungsten foils gradually at the exit-window of the cyclotron external beamline, which corresponds to different depths along the Bragg curve. The experimentalyF¯values in silicon cover from (5.7 ± 0.9) to (8.5 ± 0.4) keV μm^-1in the entrance to (27.4 ± 2.3) keV μm^-1in the distal edge. Pulse height energy spectra were crosschecked with Monte Carlo simulations and an excellent agreement was obtained. This work demonstrates the capability of the second generation 3D-microdetectors to assess accurate microdosimetric distributions at fluence rates as high as those used in clinical centers in proton therapy.

The epigenetic regulation of HsMar1, a human DNA transposon

BACKGROUND

Both classes of transposable elements (DNA and RNA) are tightly regulated at the transcriptional level leading to the inactivation of transposition via epigenetic mechanisms. Due to the high copies number of these elements, the hypothesis has emerged that their regulation can coordinate a regulatory network of genes. Herein, we investigated whether transposition regulation of HsMar1, a human DNA transposon, differs in presence or absence of endogenous HsMar1 copies. In the case where HsMar1 transposition is regulated, the number of repetitive DNA sequences issued by HsMar1 and distributed in the human genome makes HsMar1 a good candidate to regulate neighboring gene expression by epigenetic mechanisms.

RESULTS

A recombinant active HsMar1 copy was inserted in HeLa (human) and CHO (hamster) cells and its genomic excision monitored. We show that HsMar1 excision is blocked in HeLa cells, whereas CHO cells are competent to promote HsMar1 excision. We demonstrate that de novo HsMar1 insertions in HeLa cells (human) undergo rapid silencing by cytosine methylation and apposition of H3K9me3 marks, whereas de novo HsMar1 insertions in CHO cells (hamster) are not repressed and enriched in H3K4me3 modifications. The overall analysis of HsMar1 endogenous copies in HeLa cells indicates that neither full-length endogenous inactive copies nor their Inverted Terminal Repeats seem to be specifically silenced, and are, in contrast, devoid of epigenetic marks. Finally, the setmar gene, derived from HsMar1, presents H3K4me3 modifications as expected for a human housekeeping gene.

CONCLUSIONS

Our work highlights that de novo and old HsMar1 are not similarly regulated by epigenetic mechanisms. Old HsMar1 are generally detected as lacking epigenetic marks, irrespective their localisation relative to the genes. Considering the putative existence of a network associating HsMar1 old copies and SETMAR, two non-mutually exclusive hypotheses are proposed: active and inactive HsMar1 copies are not similarly regulated or/and regulations concern only few loci (and few genes) that cannot be detected at the whole genome level.

Grafting Commercial Surfactants (Brij, CiEj) and PEG to Electrodes via Aryldiazonium Salts

Grafting commercial surfactants appears to be a simple way to modify electrodes and conducting interfaces, avoiding the synthesis of complex organic molecules. A new surface functionalization route is presented to build surfactant coatings with monolayer thickness grafting molecules considered as nonreactive. A monolayer of -SO₂Cl functions (from a p-benzenesulfonyl chloride) was first electrografted. It showed a high reactivity toward weak nucleophiles commonly found on surfactant end-moieties such as hydroxyl groups (-OH), and it was used to covalently graft the following: (1) nonionic diblock oligomers (Brij or CiEj, C_xH_2x + (OCH₂CH₂)_nOH with x = 16 and n = 23 for Brij58, x = 16 and n = 10 for Brij C10, and x = 16 and n = 2 for Brij52); (2) poly(ethylene glycol) (PEG) short chains (PEO₉ for (OCH₂CH₂)_nOH with n = 9) and mixed formula. The surface modification due to these molecular coatings was investigated in terms of wetting properties and interfacial electrochemistry characteristics (charge transfer resistivity, capacity, and ions dynamics). Built on flat and transparent thin chromium films, Brij and PEO mixed coatings have been proven to be promising coatings for electrochemical biosensor application such as for stabilizing a partially tethered supported biomimetic membrane.

Structure and organization of a stable extrachromosomal element in human cells

We have determined the structure and organization of a 630-kb extrachromosomal element (amplisome) containing the dihydrofolate reductase-encoding gene (DHFR) in a methotrexate (MTX)-resistant human cell line, HeLa-Bu25-10B3. The size and copy number of amplisomes have previously been found to remain remarkably stable with or without selection. Both linear and open circular 630-kb amplisomes are present in these cells. We have been able to isolate the linear amplisomes after pulsed-field gel electrophoresis (PFGE), and transfect the amplisomes into MTX-sensitive recipient cells by electroporation, thus demonstrating that DNA as large as 630 kb can be transfected into mammalian cells. The NotI restriction site immediately upstream from DHFR on the circular amplisome is devoid of methylation, suggesting that it is transcriptionally active. Restriction mapping by PFGE reveals that there is only one copy of DHFR per amplisome and no repetitive structure is observed. The small size of the amplisomes, their stability and our ability to transfect large DNA molecules provide the necessary ingredients for the development of mammalian cloning vectors for large DNA fragments.

Assessment of DNA binding to human Rad51 protein by using quartz crystal microbalance and atomic force microscopy: effects of ADP and BRC4-28 peptide inhibitor

The interaction of human Rad51 protein (HsRad51) with single-stranded deoxyribonucleic acid (ssDNA) was investigated by using quartz crystal microbalance (QCM) monitoring and atomic force microscopy (AFM) visualization. Gold surfaces for QCM and AFM were modified by electrografting of the in situ generated aryldiazonium salt from the sulfanilic acid to obtain the organic layer Au-ArSO3 H. The Au-ArSO3 H layer was activated by using a solution of PCl5 in CH2 Cl2 to give a Au-ArSO2 Cl layer. The modified surface was then used to immobilize long ssDNA molecules. The results obtained showed that the presence of adenosine diphosphate promotes the protein autoassociation rather than nucleation around DNA. In addition, when the BRC4-28 peptide inhibitor was used, both QCM and AFM confirmed the inhibitory effect of BRC4-28 toward HsRad51 autoassociation. Altogether these results show the suitability of this modified surface to investigate the kinetics and structure of DNA-protein interactions and for the screening of inhibitors.

Feulgen-DNA changes in the germ cells of the male vole (Microtus agrestis) during their development

Consistent with changes in ploidy during germ cell maturation, the quantity of Feulgen DNA in round spermatids of voles is approximately a quarter of that in primary spermatocytes. The amount increases slightly in elongated spermatids, and then declines in spermatozoa from the testis, epididymis and vas deferens, below the level of round spermatids. Simultaneously nuclear area decreases so that in spermatozoa it is about one tenth that of primary spermatocytes. The rise in Feulgen DNA in elongated spermatids above the level found in round spermatids, and the decline in spermatozoa below this level, is probably caused by altered affinity of the desoxyribose for the leucofuchsin. This may be brought about by the complex physico-chemical changes occurring in chromatin and elsewhere in the nucleus and cell as they acquire their highly specialised final form.