Molecular Pathway Activation Markers Are Associated with Efficacy of Trastuzumab Therapy in Metastatic HER2-Positive Breast Cancer Better than Individual Gene Expression Levels.

Increased expression or amplification of HER2 receptor tyrosine kinase gene ERBB2 is well-known and widely used as a prognostic biomarker of breast cancer (BC) response to the targeted treatment with trastuzumab and its analogs. Considering that part of the BC patients overexpressing HER2 does not respond to trastuzumab, clinical trial NCT03521245 was initiated to identify additional gene expression and molecular pathway activation response biomarkers to trastuzumab treatment in HER2-positive BC. Using RNA sequencing gene expression in 23 formalin-fixed, paraffin embedded HER2 positive BC tissue blocks from patients who either responded or not responded to trastuzumab treatment was profiled. Differentially regulated genes and molecular pathways were identified in the groups of trastuzumab responders and non-responders. These results were next compared with the 42 previously published BC trastuzumab responder and non-responder RNA sequencing profiles from the clinical trials NCT00513292 and NCT00353483. No correlation was observed between the response status and the expression levels of ERBB2 gene in the HER2 positive BC samples. Analysis of the differentially expressed genes and molecular pathways in the combined dataset revealed 15/27 commonly up/down regulated genes and 15/25 pathways, respectively. However, only the intersection of molecular pathways upregulated in trastuzumab responders vs non-responders was statistically significantly enriched compared to the random expectation model. A classifier built using the most significantly upregulated molecular pathway - cAMP Pathway Protein Retention - demonstrated the best performance for prediction of the HER2 positive BC response to trastuzumab for both our experimental and previously reported data. This pathway also predicted time to recurrence in the combined dataset with Log-rank p-value 0.041.

Identification of intracellular Spiroplasma melliferum metabolites by the HPLC-MS method.

In contrast to the abundance of systems-oriented approaches describing changes on the transcriptome or proteome level, relatively few studies have employed the metabolome. The goal of the presented research was to identify as many intracellular metabolites as possible in a Spiroplasma melliferum extract by flow injection time-of-flight mass spectrometry. The Mollicutes class bacterium S. melliferum is a member of a unique category of bacteria that have in common the absence of a cell wall, a reduced genome, and simplified metabolic pathways. Metabolite identification was confirmed by fragmentation of previously detected ions by target mass spectrometry. The selected liquid chromatography approach, hydrophilic interaction chromatography with amino and silica columns, effectively separates highly polar cellular metabolites prior to their detection on a high accuracy mass spectrometer in positive and negative acquisition mode for each column. Here we present reliable measurement of 76 metabolites, including components of sugar, amino acid, and nucleotide metabolism. We have identified about a third of the possible intracellular S. melliferum metabolites predicted by genome annotation.

Purification and functional analysis of recombinant Acholeplasma laidlawii histone-like HU protein.

HU is a most abundant DNA-binding protein in bacteria. This protein is conserved either in its heterodimeric form or in one of its homodimeric forms in all bacteria, in plant chloroplasts, and in some viruses. HU protein non-specifically binds and bends DNA as a hetero- or homodimer and can participate in DNA supercoiling and DNA condensation. It also takes part in some DNA functions such as replication, recombination, and repair. HU does not recognize any specific sequences but shows some specificity to cruciform DNA and to repair intermediates, e.g., nick, gap, bulge, 3'-overhang, etc. To understand the features of HU binding to DNA and repair intermediates, a fast and easy HU proteins purification procedure is required. Here we report overproduction and purification of the HU homodimers. The method of HU purification allows obtaining a pure recombinant non-tagged protein cloned in Escherichia coli. We applied this method for purification of Acholeplasma laidlawii HU and demonstrated that this protein possesses a DNA-binding activity and is free of contaminating nuclease activity. Besides that we have shown that expression of A. laidlawii ihf_hu gene in a slow-growing hupAB E. coli strain restores the wild-type growth indicating that aclHU can perform the basic functions of E. coli HU in vivo.

The histone-like protein HU binds specifically to DNA recombination and repair intermediates.

The heterodimeric HU protein associated with the Escherichia coli nucleoid shares some properties with histones and HMG proteins. HU binds DNA junctions and DNA containing a nick much more avidly than double-stranded (ds-) DNA. Cells lacking HU are extremely sensitive to gamma irradiation and we wondered how HU could play a role in maintaining the integrity of the bacterial chromosome. We show that HU binds with high affinity to DNA repair and recombination intermediates, including DNA invasions, DNA overhangs and DNA forks. The DNA structural motif that HU specifically recognizes in all these structures consists of a ds-DNA module joined to a second module containing either ds- or single-stranded (ss-) DNA. The two modules rotate freely relative to one another. Binding specificity results from the simultaneous interaction of HU with these two modules: HU arms bind the ds-DNA module whereas the HU body contacts the 'variable' module containing either ds- or ss-DNA. Both structural motifs are recognized by HU at least 1000-fold more avidly than duplex DNA.

Tramtrack protein-DNA interactions. A cross-linking study.

Interaction of the Tramtrack protein from Drosophila melanogaster with DNA was analyzed by a cross-linking method. Tramtrack residues cross-linkable to the partially depurinated DNA were identified by direct sequencing. The N-terminal alpha-amino group of the protein DNA-binding domain was found to be the major product of cross-linking. The location of the N terminus on the DNA was determined by identification of the DNA bases that were cross-linked to the protein alpha-amino group. We conclude that accessory N-terminal peptide preceding the first zinc finger of Tramtrack directly interacts with DNA, both in specific and nonspecific DNA-protein complexes. Our finding explains the role in the protein binding of the DNA bases outside of the direct interaction with the zinc fingers.

[Analysis of peculiarities in nucleotides disposition in the origin of chromosome replication-oriC from Escherichia coli]. / Analiz osobennostei raspredeleniia nukleotidov na uchastke nachala replikatsii khromosomy-oriC iz Escherichia coli.

Along with symmetrical features (palindromes, direct and inverted repeats), periodicities in the disposition of nucleotides in the origin of chromosome replication oriC from E. coli were studied by means of Fourier analysis. Peaks corresponding to the periods T = 2, 17, 95-100 nucleotides are the highest in the Fourier spectrum of oriC. Peaks corresponding to the periods T = 3, 11, 19, 13, 24, 27, 28, 41, 79-81 nucleotides are also prominent, but not so high. Thus, the main periodicities of the oriC spectrum of are not multiple of the B-DNA sugar-phosphate backbone period, which destabilize DNA at oriC and contributes to the spontaneous unwinding of DNA. The differences between the Fourier spectrum of oriC and those of regions adjacent to oriC are demonstrated.

The binding motif recognized by HU on both nicked and cruciform DNA.

The heterodimeric HU protein, highly conserved in bacteria and involved in transposition, recombination, DNA repair, etc., shares similarity with histones and HMGs. HU, which binds DNA with low affinity and without sequence specificity, binds strongly and specifically to DNA junctions and DNA containing single-strand breaks. The fine structure of these specific complexes was studied by footprinting and HU chemically converted into nucleases. The positioning of HUalphabeta on nicked DNA is asymmetrical and specifically oriented: the beta-arm binds the area surrounding the break whereas the alpha-arm lies on the 3' DNA branch. This positioning necessitates a pronounced bend in the DNA at the discontinuous point, which was estimated by circular permutation assay to be 65 degrees. At junctions, HU is similarly asymmetrically positioned in an identical orientation: the junction point plays the role of the discontinuous point in the nicked DNA. The HU binding motif present in both structures is a pair of inclined DNA helices.

Mechanism of Lac repressor switch-off: orientation of the Lac repressor DNA-binding domain is reversed upon inducer binding.

Lac repressor's DNA-binding domains contain helix-turn-helix motif which, though similar to those of phage lambda Cro protein, are oriented differently with respect to DNA: in the specific complexes with Lac operator, N termini of the repressor's subunits are facing inwards. We demonstrate that, in the presence of an inducer, the repressor's N termini cross-link to the operator's outermost nucleotides. We suggest that the inducer fixes the repressor's DNA-binding domains in the Cro-type configuration and thus garbles its recognition surface. Since the Cro-type configuration is perfectly suitable for binding the DNA, this also explains how the switched-off repressor retains its non-specific DNA-binding.

[Effect of an inducer on orientation of the DNA-binding domain of the Lac repressor]. / Vliianie induktora na orientatsiiu DNK-sviazyvaiushchikh domenov Lac-repressora.

We have identified the lac repressor amino acids which form cross-links with partially depurinated DNA and hence are proximate to it. Only lysine-33 is cross-linkable in specific complex with lac operator. At the presence of inducer molecules lysine-33 remains cross-linkable. However, the N-terminal alpha-aminogroup was additionally cross-linked with the boundaries of lac operator. We conclude that orientation of the DNA-binding domain of the repressor is reversed by inducer binding.

[Electrostatic interaction and differences in specific and nonspecific interactions of the Lac-repressor with DNA]. / Elektrostaticheskie vzaimodeistviia i razlichiia v spetsificheskom i nespetsificheskom vzaimodeistviiakh Lac-repressora s DNK.

To investigate the complexes of lac-repressor with specific and non-specific DNA sequences method of covalent cross-linking of proteins to partially depurinated DNA was used. We have identified the amino acid resides which form cross-links and hence are proximate to DNA. Only lysine 33 is cross-linkable in specific complex. In the case of non-specific complex (at the presents of inducer molecules) lysine 33 remains cross-linkable. Some consequences of these phenomena in aspects of the physical backgrounds of protein-DNA interactions have been discussed.