LDLR gene rearrangements in Czech FH patients likely arise from one mutational event

BACKGROUND

Large deletions and duplications within the low-density lipoprotein receptor (LDLR) gene make up approximately 10% of LDLR pathogenic variants found in Czech patients with familial hypercholesterolemia. The goal of this study was to test the hypothesis that all probands with each rearrangement share identical breakpoints inherited from a common ancestor and to determine the role of Alu repetitive elements in the generation of these rearrangements.

METHODS

The breakpoint sequence was determined by PCR amplification and Sanger sequencing. To confirm the breakpoint position, an NGS analysis was performed. Haplotype analysis of common LDLR variants was performed using PCR and Sanger sequencing.

RESULTS

The breakpoints of 8 rearrangements within the LDLR gene were analysed, including the four most common LDLR rearrangements in the Czech population (number of probands ranging from 8 to 28), and four less common rearrangements (1-4 probands). Probands with a specific rearrangement shared identical breakpoint positions and haplotypes associated with the rearrangement, suggesting a shared origin from a common ancestor. All breakpoints except for one were located inside an Alu element. In 6 out of 8 breakpoints, there was high homology (≥ 70%) between the two Alu repeats in which the break occurred.

CONCLUSIONS

The most common rearrangements of the LDLR gene in the Czech population likely arose from one mutational event. Alu elements likely played a role in the generation of the majority of rearrangements inside the LDLR gene.

Metal-Free 1,3-Boronate Rearrangement to Ketones Driven by Visible Light

Boronate rearrangements, such as the Matteson and Petasis reactions, are valuable metal-free reactions for the transfer of the carbo group on boron to intramolecular electrophilic sites. However, only highly reactive electrophiles are suitable, and ketones are too inactive for those boronate rearrangements due to the high energy barriers. We disclose here the 1,3-boronate rearrangement to ketones, for which a high energy barrier (44.9 kcal/mol) is prohibitory for thermal reactions in the ground state. The reaction is enabled by the key keto-enol-boronate bidentate complex formation in situ, which absorbs visible light to reach the excited state for the chemoselective 1,3-boronate rearrangement to ketones. Experimental and computational investigations exclude free radical intermediates from organoboronates. The aryl, alkenyl, and alkyl boronic acids react with various 1,3-diketones driven by visible light irradiation to construct structurally diverse β-keto tertiary alcohols under metal-free conditions. The reaction demonstrates substrate diversity with 58 examples, yields up to 98 %, and it is suitable for gram-scale synthesis.

Photothermal Conversion by Carbon Black Facilitates Aryl Migration by Photon-Promoted Temperature Gradients

The Newman Kwart Rearrangement (NKR) offers an efficient and high-yielding method for producing substituted thiophenols from phenols. While an industrially important protocol, it suffers from high activation energy barriers (35-43 kcal/mol), requiring the use of extreme temperatures (>200 °C) and specialty equipment. This report details a highly efficient and straightforward method for facilitating the NKR using photothermal conversion. This underused, unique reactivity pathway arises from the irradiation of nanomaterials that relax via a non-radiative decay pathway to generate intense thermal gradients. We show carbon black (CB) can be an inexpensive and abundant photothermal agent under visible light irradiation to achieve a facile NKR under mild conditions. The scope includes a wide array of stereo- and electronically diverse substrates with increasing difficulty of rearrangement, including BHT and BINOL as effective substrates. Furthermore, we demonstrate the unique application for temporal control in a thermal reaction and tunability of thermal gradients by modulating light intensity. Ultimately, photothermal conversion enables high-temperature reactions with simple, visible light irradiation.

The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection

BACKGROUND

Accessory proteins have diverse roles in coronavirus pathobiology. One of them in SARS-CoV (the causative agent of the severe acute respiratory syndrome outbreak in 2002-2003) is encoded by the open reading frame 8 (ORF8). Among the most dramatic genomic changes observed in SARS-CoV isolated from patients during the peak of the pandemic in 2003 was the acquisition of a characteristic 29-nucleotide deletion in ORF8. This deletion cause splitting of ORF8 into two smaller ORFs, namely ORF8a and ORF8b. Functional consequences of this event are not entirely clear.

RESULTS

Here, we performed evolutionary analyses of ORF8a and ORF8b genes and documented that in both cases the frequency of synonymous mutations was greater than that of nonsynonymous ones. These results suggest that ORF8a and ORF8b are under purifying selection, thus proteins translated from these ORFs are likely to be functionally important. Comparisons with several other SARS-CoV genes revealed that another accessory gene, ORF7a, has a similar ratio of nonsynonymous to synonymous mutations suggesting that ORF8a, ORF8b, and ORF7a are under similar selection pressure.

CONCLUSIONS

Our results for SARS-CoV echo the known excess of deletions in the ORF7a-ORF7b-ORF8 complex of accessory genes in SARS-CoV-2. A high frequency of deletions in this gene complex might reflect recurrent searches in "functional space" of various accessory protein combinations that may eventually produce more advantageous configurations of accessory proteins similar to the fixed deletion in the SARS-CoV ORF8 gene.

Diastereoselective Synthesis of Monofluorocyclohexenes through Photocatalyzed Cascade Cyclization of gem-Difluoroalkenes and α,β-Unsaturated Carbonyl Compounds

Monofluoroalkenes are nonhydrolyzable mimetics of amides. Previous work focused on the synthesis of non-cyclic monofluoroalkenes. However, diastereoselective synthesis of monofluorocyclohexenes from non-cyclic substrates is challenging. Herein, we report the first photocatalyzed cascade cyclization reactions of readily available α,β-unsaturated carbonyl compounds and gem-difluoroalkenes for the synthesis of highly functionalized monofluorocyclohexenes. The reaction shows broad substrate scope with high diastereoselectivity (> 30 examples, up to 86% yield, > 20:1 dr). The post-reaction transformations of the products demonstrate the synthetic potential of this methodology.

Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae)

BACKGROUND

The cactus family (Cactaceae) has been reported to have evolved a minimal photosynthetic plastome size, with the loss of inverted-repeat (IR) regions and NDH gene suites. However, there are very limited genomic data on the family, especially Cereoideae, the largest subfamily of cacti.

RESULTS

In the present study, we assembled and annotated 35 plastomes, 33 of which were representatives of Cereoideae, alongside 2 previously published plastomes. We analyzed the organelle genomes of 35 genera in the subfamily. These plastomes have variations rarely observed in those of other angiosperms, including size differences (with ~ 30 kb between the shortest and longest), dramatic dynamic changes in IR boundaries, frequent plastome inversions, and rearrangements. These results suggested that cacti have the most complex plastome evolution among angiosperms.

CONCLUSION

These results provide unique insight into the dynamic evolutionary history of Cereoideae plastomes and refine current knowledge of the relationships within the subfamily.

Selective 3,3-Rearrangement of Azobenzenes upon Complexation by a Frustrated Lewis Pair

The reaction of the oxygen-bridged frustrated Lewis pairs (FLPs) tBu₂ P-O-Si(C₂ F₅ )₃ (1) and tBu₂ P-O-AlBis₂ (2) with azobenzene, promoted by UV irradiation, led to a selective complexation of the cis-isomer. The addition product of 2 is stable, while the adduct of 1 isomerizes in solution in an ortho-benzidine-like [3,3]-rearrangement by cleavage of the N-N bond, saturation of the nitrogen atoms with hydrogen atoms and formation of a new bond between two phenyl ortho-carbon atoms. Similar rearrangements take place with different para-substituted azobenzenes (R=Me, OMe, Cl) and di(2-naphthyl)diazene, while ortho-methylated azo compounds do not form adducts with 1. All adducts were characterized by multinuclear NMR spectroscopy and elemental analyses and the mechanism of the rearrangement was explored by quantum-chemical calculations.

Highly Enantioselective Brønsted Acid Catalyzed Heyns Rearrangement

Herein we report the first method for highly enantioselective Brønsted acid catalyzed Heyns rearrangements. These reactions, catalyzed by a chiral spiro phosphoric acid, afforded synthetically valuable chiral α-aryl-α-aminoketones which cannot be obtained by means of previously reported Heyns rearrangement methods. This method features low catalyst loadings, high yields and high enantioselectivities, making these reactions highly practical. We used the method to efficiently synthesize various chiral amines, including some biologically active molecules. We experimentally proved that these acid-catalyzed Heyns rearrangements proceeded via a proton-transfer process involving an enol intermediate and the stereocontrol was realized during the proton-transfer step.

Direct Synthesis of α-Amino Acid Derivatives by Hydrative Amination of Alkynes

α-Amino acid derivatives are key components of the molecules of life. The synthesis of α-amino carbonyl/carboxyl compounds is a contemporary challenge in organic synthesis. Herein, we report a practical method for the preparation of α-amino acid derivatives via direct hydrative amination of activated alkynes under mild conditions, relying on sulfinamides as the nitrogen source. Computational studies suggest that the reaction is enabled by a new type of sulfonium [2,3]-sigmatropic rearrangement.

Maximal total population of species in a diffusive logistic model

In this paper, we investigate the maximization of the total population of a single species which is governed by a stationary diffusive logistic equation with a fixed amount of resources. For large diffusivity, qualitative properties of the maximizers like symmetry will be addressed. Our results are in line with previous findings which assert that for large diffusion, concentrated resources are favorable for maximizing the total population. Then, an optimality condition for the maximizer is derived based upon rearrangement theory. We develop an efficient numerical algorithm applicable to domains with different geometries in order to compute the maximizer. It is established that the algorithm is convergent. Our numerical simulations give a real insight into the qualitative properties of the maximizer and also lead us to some conjectures about the maximizer.

1,5-Allyl Shift by a Sequential Achmatowicz/Oxonia-Cope/Retro-Achmatowicz Rearrangement

1,3-Allyl and 1,2-allyl shifts through [3,3]- and [2,3]-sigmatropic rearrangements are well-established and widely used in organic synthesis. In contrast, 1,5-allyl shift through related [3,5]-sigmatropic rearrangement is unknown because [3,5]-sigmatropic rearrangement is thermally Woodward-Hoffmann forbidden. Herein, we report an unexpected discovery of a formal 1,5-allyl shift of allyl furfuryl alcohol through a 2-step sequential rearrangement. Mechanistically, this formal 1,5-allyl shift is achieved through a sequential ring expansion/contraction rearrangement: 1) Achmatowicz rearrangement (ring expansion), and 2) cascade oxonia-Cope rearrangement/retro-Achmatowicz rearrangement (ring contraction). This new 1,5-allyl shift method is demonstrated with >20 examples and expected to find applications in organic synthesis and materials chemistry.

Passerini-Smiles Reaction of α-Ketophosphonates: Platform for Phospha-Brook/Smiles Embedded Cascades

The Passerini-Smiles reactions of α-ketophosphonates with nitrophenols has been used as a platform to observe complex cascades involving multiple Smiles transfers coupled with phospha-Brook rearrangement. When using 4-nitrophenols a rare 1,3-Truce-Smiles rearrangement is observed leading to diarylacetamide derivatives. 2-Nitro-derivatives lead to a completely different reactivity pattern that may be explained by a nitro to nitroso conversion followed by a σ-π metathesis. All mechanistic assumptions are confirmed by DFT calculations performed on both families of adducts. The potential of this work has been further demonstrated by the use of N-aryl α-ketoamides as alternative starting materials for these cascades as well as the disclosure of new aza-Nazarov access to hydroxy-indolones.

Transformation of Crowded Oligoarylene into Perylene-Cored Chiral Nanographene by Sequential Oxidative Cyclization and 1,2-Phenyl Migration

Synthetic innovation for constructing sophisticated nanographenes is of fundamental significance for a variety of advanced applications. Herein, we report a distinctive method to prepare π-extended chiral nanographenes with 29 benzenoid rings and two helical breaches from a highly crowded perylene-cored oligoarylene precursor. Under Scholl's conditions, the reaction predominantly involves the regioselective and sequential cyclization in the peri- and bay regions of the perylene core, and the complanation of the 1-phenyl[5]helicene intermediate module via 1,2-phenyl migration. The resulting chiral nanographenes are configurationally stable at 180 °C due to the high diastereomerization barriers of ca. 45 kcal mol^-1 . These molecules also possess globally delocalized π-systems with low HOMO/LUMO gaps, leading to nearly panchromatic absorption, intensive electronic circular dichroism signals and deep-red circularly polarized luminescence.

The potential of family-free rearrangements towards gene orthology inference

Recently, we proposed an efficient ILP formulation [Rubert DP, Martinez FV, Braga MDV, Natural family-free genomic distance, Algorithms Mol Biol 16:4, 2021] for exactly computing the rearrangement distance of two genomes in a family-free setting. In such a setting, neither prior classification of genes into families, nor further restrictions on the genomes are imposed. Given two genomes, the mentioned ILP computes an optimal matching of the genes taking into account simultaneously local mutations, given by gene similarities, and large-scale genome rearrangements. Here, we explore the potential of using this ILP for inferring groups of orthologs across several species. More precisely, given a set of genomes, our method first computes all pairwise optimal gene matchings, which are then integrated into gene families in the second step. Our approach is implemented into a pipeline incorporating the pre-computation of gene similarities. It can be downloaded from gitlab.ub.uni-bielefeld.de/gi/FFGC. We obtained promising results with experiments on both simulated and real data.

Genome diversity and instability in human germ cells and preimplantation embryos

Genome diversity is essential for evolution and is of fundamental importance to human health. Generating genome diversity requires phases of DNA damage and repair that can cause genome instability. Humans have a high incidence of de novo congenital disorders compared to other organisms. Recent access to eggs, sperm and preimplantation embryos is revealing unprecedented rates of genome instability that may result in infertility and de novo mutations that cause genomic imbalance in at least 70% of conceptions. The error type and incidence of de novo mutations differ during developmental stages and are influenced by differences in male and female meiosis. In females, DNA repair is a critical factor that determines fertility and reproductive lifespan. In males, aberrant meiotic recombination causes infertility, embryonic failure and pregnancy loss. Evidence suggest germ cells are remarkably diverse in the type of genome instability that they display and the DNA damage responses they deploy. Additionally, the initial embryonic cell cycles are characterized by a high degree of genome instability that cause congenital disorders and may limit the use of CRISPR-Cas9 for heritable genome editing.

Analysis of multiple chromosomal rearrangements in the genome of Willisornis vidua using BAC-FISH and chromosome painting on a supposed conserved karyotype

BACKGROUND

Thamnophilidae birds are the result of a monophyletic radiation of insectivorous Passeriformes. They are a diverse group of 225 species and 45 genera and occur in lowlands and lower montane forests of Neotropics. Despite the large degree of diversity seen in this family, just four species of Thamnophilidae have been karyotyped with a diploid number ranging from 76 to 82 chromosomes. The karyotypic relationships within and between Thamnophilidae and another Passeriformes therefore remain poorly understood. Recent studies have identified the occurrence of intrachromosomal rearrangements in Passeriformes using in silico data and molecular cytogenetic tools. These results demonstrate that intrachromosomal rearrangements are more common in birds than previously thought and are likely to contribute to speciation events. With this in mind, we investigate the apparently conserved karyotype of Willisornis vidua, the Xingu Scale-backed Antbird, using a combination of molecular cytogenetic techniques including chromosome painting with probes derived from Gallus gallus (chicken) and Burhinus oedicnemus (stone curlew), combined with Bacterial Artificial Chromosome (BAC) probes derived from the same species. The goal was to investigate the occurrence of rearrangements in an apparently conserved karyotype in order to understand the evolutionary history and taxonomy of this species. In total, 78 BAC probes from the Gallus gallus and Taeniopygia guttata (the Zebra Finch) BAC libraries were tested, of which 40 were derived from Gallus gallus macrochromosomes 1-8, and 38 from microchromosomes 9-28.

RESULTS

The karyotype is similar to typical Passeriformes karyotypes, with a diploid number of 2n = 80. Our chromosome painting results show that most of the Gallus gallus chromosomes are conserved, except GGA-1, 2 and 4, with some rearrangements identified among macro- and microchromosomes. BAC mapping revealed many intrachromosomal rearrangements, mainly inversions, when comparing Willisornis vidua karyotype with Gallus gallus, and corroborates the fissions revealed by chromosome painting.

CONCLUSIONS

Willisornis vidua presents multiple chromosomal rearrangements despite having a supposed conservative karyotype, demonstrating that our approach using a combination of FISH tools provides a higher resolution than previously obtained by chromosome painting alone. We also show that populations of Willisornis vidua appear conserved from a cytogenetic perspective, despite significant phylogeographic structure.

Upfront Management of ALK-Rearranged Metastatic Non-small Cell Lung Cancer: One Inhibitor Fits All?

PURPOSE OF REVIEW

Anaplastic lymphoma kinase (ALK) rearrangements represent a seldom event in non-small cell lung cancer (NSCLC). Given the oncogene alteration, ALK targeting represents the main therapeutic strategy. Here, we review evidence regarding ALK inhibitors (ALKi): clinical activity, safety profiles, financial costs, and biomarkers of efficacy.

RECENT FINDINGS

During the past 10 years, multiple ALKi have been developed, and four different compounds are currently available as upfront options for ALK+ NSCLC patients: crizotinib, ceritinib, alectinib, and brigatinib. Second-generation (2G) ALKi demonstrated superior clinical activity in terms of median progression-free survival (mPFS), objective response rate (ORR), intracranial disease control, and duration of response (DOR) when compared with crizotinib. 2G ALKi represent the current gold-standard first-line treatment for ALK-rearranged metastatic NSCLC. Among all available options, in our opinion, alectinib has likely the best profile of clinical activity and safety, thus emerging as the best upfront therapy. More insights will come from ongoing trials and analysis of biomarkers.

Ret Receptor Has Distinct Alterations and Functions in Breast Cancer

Ret receptor tyrosine kinase is a proto-oncogene that participates in development of various cancers. Several independent studies have recently identified Ret as a key player in breast cancer. Although Ret overexpression and function have been under investigation, mainly in estrogen receptor positive breast cancer, a more comprehensive analysis of the impact of recurring Ret alterations in breast cancer is needed. This review consolidates the current knowledge of Ret alterations and their potential effects in breast cancer. We discuss and integrate data on Ret changes in different breast cancer subtypes and potential function in progression, as well as the participation of distinct Ret network signaling partners in these processes. We propose that it will be essential to define a shared molecular feature of tumors with alteration in Ret receptor, be this at the genetic level or via overexpression in order to design effective therapies to target the Ret pathway. Here we review experimental evidence from basic research and pre-clinical studies concentrating on Ret alterations as potential biomarkers for recurrence, and we discuss the possibility that targeting the Ret pathway might in the future become a treatment for breast cancer.

Using Genomics to Differentiate Multiple Primaries From Metastatic Lung Cancer

INTRODUCTION

Genomic technologies present a promising mechanism of resolving the clinical dilemma of distinguishing independent primary tumors from intrapulmonary metastases in NSCLC. We evaluated the utility of discordant mapping somatic junctions from chromosomal rearrangements in diagnosing metastatic disease compared to the current standard histologic review.

MATERIAL AND METHODS

Mate-pair sequencing was performed on DNA extracted from 76 distinct tumors from 37 cases of multiple lung cancers. Discordant mapping junctions and chromosomal copy levels were assessed for each tumor. Blood-derived DNA was available on 22 of these cases for germline assessments. A lung cancer next-generation sequencing panel was additionally performed on tumor pairs from 17 patients.

RESULTS

Whereas mate-pair sequencing was able to classify lineage in all tumor pairs, histologic review appeared to misclassify lineage in 9 of 33 (27%) same-histology tumor pair comparisons. Based on disagreement between the reviewing pathologists, histopathologic lineage was classified as indeterminate in seven cases. In two cases where pathologists agreed on a metastatic call, no shared junctions were found suggesting independent primaries. Although germline junctions passing algorithmic filters were common, on average less than three were present and all had predictable structures of small focal rearrangements or transposons. Evaluation of shared chromosomal copy changes and driver mutations through a lung cancer next-generation sequencing panel, while informative, were nondefinitive in calling lineage in all cases.

CONCLUSIONS

The highly unique nature and prevalence of chromosomal rearrangement in lung cancers provide a useful and definitive technique for calling lineage in multifocal lung cancer.

Cytogenetic and molecular genotyping in the allotetraploid Festuca pratensis × Lolium perenne hybrids

BACKGROUND

Species of the Festuca and Lolium genera, as well as intergeneric Festuca × Lolium (Festulolium) hybrids, are valuable fodder and turf grasses for agricultural and amenity purposes worldwide. Festulolium hybrids can merge in their genomes agronomically important characteristics. However, in polyploid plants, especially in allopolyploids, the hybridization of divergent genomes could contribute to various abnormalities, such as variability in chromosome number, structural rearrangements, and/or disorders in inheritance patterns. Here we studied these issues in allotetraploid Festuca pratensis × Lolium perenne hybrids.

RESULTS

Cytogenetic procedures, including fluorescent in situ hybridization, genomic in situ hybridization, and molecular markers - inter-simple sequence repeats (ISSR) were exploited. This cytogenetic approach indicated the dynamics in the number and distribution of ribosomal RNA genes and structural rearrangements for both parental genomes (Festuca and Lolium) in hybrid karyotypes. The separate analysis of F. pratensis and L. perenne chromosomes in hybrid plants (F2-F3 generations of F. pratensis × L. perenne) revealed the asymmetrical level of rearrangements. Recognized structural changes were mainly located in the distal part of chromosome arms, and in chromosomes bearing ribosomal DNA, they were more frequently mapped in arms without this sequence. Based on the ISSR markers distribution, we found that the tetrasomic type of inheritance was characteristic for the majority of ISSR loci, but the disomic type was also observed. Nonetheless, no preference in the transmission of either Festuca or Lolium alleles to the following generations of allotetraploid F. pratensis × L. perenne hybrid was observed.

CONCLUSION

Our study reports cytogenetic and molecular genotyping of the F. pratensis × L. perenne hybrid and its following F2-F3 progenies. The analysis of 137 allotetraploid F. pratensis × L. perenne hybrids revealed the higher level of recombination in chromosomes derived from F. pratensis genome. The results of ISSR markers indicated a mixed model of inheritance, which may be characteristic for these hybrids.

Organoboron chemistry comes to light: recent advances in photoinduced synthetic approaches to organoboron compounds

Photoinduced synthetic approaches to organoboron compounds have attracted significant attention in the recent years. Photochemical activation of organic molecules enables generation of reactive intermediates from a variety of precursors, resulting in borylation methods with improved and broader substrate scopes. The review summarizes recent developments in the area of photoinduced reactions of organoboron compounds with an emphasis on borylation of haloarenes, amine derivatives, and redox-active esters of carboxylic acids, as well as photoinduced rearrangements of organoboron compounds and photoinduced synthesis of organoboron compounds from alkenes and alkynes.

DMD genomic deletions characterize a subset of progressive/higher-grade meningiomas with poor outcome

Progressive meningiomas that have failed surgery and radiation have a poor prognosis and no standard therapy. While meningiomas are more common in females overall, progressive meningiomas are enriched in males. We performed a comprehensive molecular characterization of 169 meningiomas from 53 patients with progressive/high-grade tumors, including matched primary and recurrent samples. Exome sequencing in an initial cohort (n = 24) detected frequent alterations in genes residing on the X chromosome, with somatic intragenic deletions of the dystrophin-encoding and muscular dystrophy-associated DMD gene as the most common alteration (n = 5, 20.8%), along with alterations of other known X-linked cancer-related genes KDM6A (n =2, 8.3%), DDX3X, RBM10 and STAG2 (n = 1, 4.1% each). DMD inactivation (by genomic deletion or loss of protein expression) was ultimately detected in 17/53 progressive meningioma patients (32%). Importantly, patients with tumors harboring DMD inactivation had a shorter overall survival (OS) than their wild-type counterparts [5.1 years (95% CI 1.3-9.0) vs. median not reached (95% CI 2.9-not reached, p = 0.006)]. Given the known poor prognostic association of TERT alterations in these tumors, we also assessed for these events, and found seven patients with TERT promoter mutations and three with TERT rearrangements in this cohort (n = 10, 18.8%), including a recurrent novel RETREG1-TERT rearrangement that was present in two patients. In a multivariate model, DMD inactivation (p = 0.033, HR = 2.6, 95% CI 1.0-6.6) and TERT alterations (p = 0.005, HR = 3.8, 95% CI 1.5-9.9) were mutually independent in predicting unfavorable outcomes. Thus, DMD alterations identify a subset of progressive/high-grade meningiomas with worse outcomes.

Molecular Subtypes of Prostate Cancer

PURPOSE OF REVIEW

This review will examine the taxonomy of PCa subclasses across disease states, explore the relationship among specific alterations, and highlight current clinical relevance.

RECENT FINDINGS

Prostate cancer (PCa) is driven by multiple genomic alterations, with distinct patterns and clinical implications. Alterations occurring early in the timeline of the disease define core subtypes of localized, treatment-naive PCa. With time, an increase in number and severity of genomic alterations adds molecular complexity and is associated with progression to metastasis. These later events are not random and are influenced by the underlying subclasses. All the subclasses of localized disease initially respond to androgen deprivation therapy (ADT), but with progression to castrate-resistant PCa (CRPC), mechanisms of resistance against ADT shift the molecular landscape. In CRPC, resistance mechanisms largely define the biology and sub-classification of these cancers, while clinical relevance and opportunities for precision therapy are still being defined.

Resolution effects in reconstructing ancestral genomes

BACKGROUND

The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions.

RESULTS

We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses.

CONCLUSIONS

We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics.

The Linum usitatissimum L. plastome reveals atypical structural evolution, new editing sites, and the phylogenetic position of Linaceae within Malpighiales

The plastome of Linum usitatissimum was completely sequenced allowing analyses of evolution of genome structure, RNA editing sites, molecular markers, and indicating the position of Linaceae within Malpighiales. Flax (Linum usitatissimum L.) is an economically important crop used as food, feed, and industrial feedstock. It belongs to the Linaceae family, which is noted by high morphological and ecological diversity. Here, we reported the complete sequence of flax plastome, the first species within Linaceae family to have the plastome sequenced, assembled and characterized in detail. The plastome of flax is a circular DNA molecule of 156,721 bp with a typical quadripartite structure including two IRs of 31,990 bp separating the LSC of 81,767 bp and the SSC of 10,974 bp. It shows two expansion events from IRB to LSC and from IRB to SSC, and a contraction event in the IRA-LSC junction, which changed significantly the size and the gene content of LSC, SSC and IRs. We identified 109 unique genes and 2 pseudogenes (rpl23 and ndhF). The plastome lost the conserved introns of clpP gene and the complete sequence of rps16 gene. The clpP, ycf1, and ycf2 genes show high nucleotide and aminoacid divergence, but they still possibly retain the functionality. Moreover, we also identified 176 SSRs, 20 tandem repeats, and 39 dispersed repeats. We predicted in 18 genes a total of 53 RNA editing sites of which 32 were not found before in other species. The phylogenetic inference based on 63 plastid protein-coding genes of 38 taxa supports three major clades within Malpighiales order. One of these clades has flax (Linaceae) sister to Chrysobalanaceae family, differing from earlier studies that included Linaceae into the euphorbioid clade.

Whole Exome Sequencing in Multiple Myeloma to Identify Somatic Single Nucleotide Variants and Key Translocations Involving Immunoglobulin Loci and MYC

Multiple myeloma is a malignancy of terminally differentiated plasma cells in the bone marrow. These plasma cells produce high levels of immunoglobulin which cause end-organ damage. Rearrangements within the immunoglobulin loci are a physiological part of B cell development, but these DNA level double-strand breaks may result in interchromosomal translocations. There are five main translocations involving the Ig loci: t(4;14) 12%, t(6;14) 1%, t(11;14) 15%, t(14;16) 3%, and t(14;20) 2%. These are primary events, found in all cells within the tumor clone and are associated with different prognosis. The t(4;14), t(14;16), and t(14;20) are associated with a poor prognosis, whereas the others are associated with a more favorable prognosis. Rearrangements at the MYC locus are also associated with a poor prognosis and increased expression of MYC. MYC rearrangements are frequent (25%) and involve interchromosomal translocations involving Ig loci or other partners, but also include intrachromosomal inversions, duplications and deletions. As such, the Ig and MYC loci are key players in the myeloma genome and including these in any genomic studies is key to understanding the relationship with other abnormalities. We have designed a custom capture of the Ig and MYC loci which can be added to exome or targeted captures to inform on these key events. This saves on performing additional tests to determine these events, which are generally mandatory for any genetic investigations in myeloma. This custom capture is also relevant to other B cell malignancies where MYC and Ig translocations occur.

On the rearrangement of N-aryl-N-Boc-phosphoramidates to N-Boc-protected o-aminoarylphosphonates

Abstract

Various arylamines were converted in two steps to N-Boc-N-arylphosphoramidates. LiTMP and LDA induced directed ortho-metalation at temperatures from −78 to 0 °C. The ensuing [1,3]-migration of the phosphorus atom with its substituents from the nitrogen to the ortho-carbanionic carbon atom gave N-Boc-protected o-aminoarylphosphonates. The nature of the substituent of 3-substituted phenylphosphoramidates strongly influenced the regioselectivity of phosphonate formation. A crossover experiment with a deuterated phosphoramidate proved the intramolecular course of the rearrangement. Three representative N-Boc-o-aminoarylphosphonates were deprotected to access the corresponding o-aminoarylphosphonic acids.

Graphical Abstract

Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family

BACKGROUND

Among the 13 families of early-diverging eudicots, only Circaeasteraceae (Ranunculales), which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addition, the phylogenetic position of Circaeasteraceae as sister to Lardizabalaceae has only been weakly or moderately supported in previous studies using smaller data sets. Moreover, previous plastome studies have documented a number of novel structural rearrangements among early-divergent eudicots. Hence it is important to sequence plastomes from Circaeasteraceae to better understand plastome evolution in early-diverging eudicots and to further investigate the phylogenetic position of Circaeasteraceae.

RESULTS

Using an Illumina HiSeq 2000, complete plastomes were sequenced from both living members of Circaeasteraceae: Circaeaster agrestis and Kingdonia uniflora . Plastome structure and gene content were compared between these two plastomes, and with those of other early-diverging eudicot plastomes. Phylogenetic analysis of a 79-gene, 99-taxon data set including exemplars of all families of early-diverging eudicots was conducted to resolve the phylogenetic position of Circaeasteraceae. Both plastomes possess the typical quadripartite structure of land plant plastomes. However, a large ~49 kb inversion and a small ~3.5 kb inversion were found in the large single-copy regions of both plastomes, while Circaeaster possesses a number of other rearrangements, particularly in the Inverted Repeat. In addition, infA was found to be a pseudogene and accD was found to be absent within Circaeaster, whereas all ndh genes, except for ndhE and ndhJ, were found to be either pseudogenized (ΨndhA, ΨndhB, ΨndhD, ΨndhH and ΨndhK) or absent (ndhC, ndhF, ndhI and ndhG) in Kingdonia. Circaeasteraceae was strongly supported as sister to Lardizabalaceae in phylogenetic analyses.

CONCLUSION

The first plastome sequencing of Circaeasteraceae resulted in the discovery of several unusual rearrangements and the loss of ndh genes, and confirms the sister relationship between Circaeasteraceae and Lardizabalaceae. This research provides new insight to characterize plastome structural evolution in early-diverging eudicots and to better understand relationships within Ranunculales .

Karyotype diversity suggests that Laonastes aenigmamus (Laotian rock rat) (Rodentia, Diatomyidae) is a multi-specific genus

Laonastes aenigmamus (Khanyou) is a recently described rodent species living in geographically separated limestone formations of the Khammuan Province in Lao PDR. Chromosomes of 21 specimens of L. aenigmamus were studied using chromosome banding as well as fluorescent in situ hybridization (FISH) techniques using human painting, telomere repeats, and 28S rDNA probes. Four different karyotypes were established. Study with human chromosome paints and FISH revealed that four large chromosomes were formed by multiple common tandem fusions, with persistence of some interstitial telomeres. The rearrangements separating the different karyotypes (I to IV) were also reconstructed. Various combinations of Robertsonian translocations or tandem fusions involving the same chromosomes differentiate these karyotypes. These rearrangements create a strong gametic barrier, which isolates specimens with karyotype II from the others. C-banding and FISH with telomere repeats also exhibit large and systematized differences between karyotype II and others. These data indicate an ancient reproductive separation and suggest that Laonastes is not a mono-specific genus.

History of chromosome rearrangements reflects the spatial organization of yeast chromosomes

Three-dimensional (3D) organization of genomes affects critical cellular processes such as transcription, replication, and deoxyribo nucleic acid (DNA) repair. While previous studies have investigated the natural role, the 3D organization plays in limiting a possible set of genomic rearrangements following DNA repair, the influence of specific organizational principles on this process, particularly over longer evolutionary time scales, remains relatively unexplored. In budding yeast S.cerevisiae, chromosomes are organized into a Rabl-like configuration, with clustered centromeres and telomeres tethered to the nuclear periphery. Hi-C data for S.cerevisiae show that a consequence of this Rabl-like organization is that regions equally distant from centromeres are more frequently in contact with each other, between arms of both the same and different chromosomes. Here, we detect rearrangement events in Saccharomyces species using an automatic approach, and observe increased rearrangement frequency between regions with higher contact frequencies. Together, our results underscore how specific principles of 3D chromosomal organization can influence evolutionary events.

Identification of rearranged sequences of HPV16 DNA in precancerous and cervical cancer cases

Integration of HPV16 DNA into the host chromosome is considered to be a crucial step towards genomic instability and cervical cancer development. Aim of the present study was to investigate the presence of HPV16 rearranged intra-viral sequences in HPV16-positive normal, precancerous and cervical cancer samples using the method of Restriction Site-PCR (RS-PCR). Sequence analysis of HPV16 integrants revealed for the first time in clinical samples two distinct rearranged intra-viral sequences, concerning the conjunction of E2 and L1 genes and the conjunction of E1 and L1 genes with inverted orientation. Furthermore mapping analysis of the E1 and E2 genes in cervical samples with rearranged intra-viral sequences of HPV16 genome was conducted in order to determine the integrity of viral genes. The identification of intra-viral rearrangements provides valuable information regarding the HPV16 DNA integration, and may be a significant biomarker for the presence of chromosomal instability and DNA damages in clinical samples.

Subtelomeric multiplex ligation-dependent probe amplification as a supplement for rapid prenatal detection of fetal chromosomal aberrations

Background

Pregnant women with high-risk indications are highly suspected of fetal chromosomal aberrations. To determine whether Multiplex Ligation-dependent Probe Amplification (MLPA) using subtelomeric probe mixes (P036-E2 and P070-B2) is a reliable method for rapid detection of fetal chromosomal aberrations. The subtelomeric MLPA probe mixes were used to evaluate 50 blood samples from healthy individuals. 168 amniocytes and 182 umbilical cord blood samples from high-risk fetuses were analyzed using the same subtelomeric MLPA probe sets. Karyotyping was also performed in all cases of high-risk pregnancies, and single nucleotide polymorphism array analysis was used to confirm submicroscopic and ambiguous results from MLPA/karyotyping.

Results

Subtelomeric MLPA analysis of normal samples showed normal result in all cases by use of P036-E2 probe mix, while P070-B2 probe mix gave normal results for all but one case. In one normal control case P070-B2 produced a duplicated signal of probe for 13q34. In the high-risk group, totally 44 chromosomal abnormalities were found by karyotyping and MLPA, including 23 aneuploidies and 21 rearrangements or mosaics. MLPA detected all 23 aneuploidies, 12 rearrangements and 1 mosaic. Importantly, MLPA revealed 4 chromosomal translocations, 2 small supernumerary marker chromosomes (sSMCs), and 3 subtelomeric imbalances that were not well characterized or not detectable by karyotyping. However, MLPA showed negetive results for the remaining 8 rearrangements or mosaics, including 3 low mosaic aneuploidies, 1 inherited sSMC, and 4 paracentric inversions.

Conclusions

Results suggest that combined use of subtelomeric MLPA and karyotyping may be an alternative method for using karyotype analyses alone in rapid detection of aneuploidies, rearrangements, and sSMCs.

Electronic supplementary material

The online version of this article (doi:10.1186/s13039-014-0096-1) contains supplementary material, which is available to authorized users.

Directed Metalation Linked to Transition Metal Catalyzed Cascade Reactions: Two Total Syntheses of Plicadin, the Alleged Coumestan from Psoralea plicata

The oxygen-rich heterocyclic compound 1-which was proposed to be the structure of plicadin, the alleged naturally occurring coumestan from the herb Psoralea plicata-was synthesized by the rational combinations of directed ortho and remote metalation reactions with cascades of Negishi, Sonogashira, Castro-Stephens, and carbamoyl Baker-Venkataraman reactions.

Stereospecific Migration of P from N to C sp 2: Ring-Expansion Reaction of Chiral Diazaphospholidine Oxides

An addition-pseudorotation-elimination pathway is proposed for the first stereospecific ring-expansion reaction of chiral diazaphospholidine oxides by a 1,3-migration of P from N to C sp 2 [Eq. (1)]. R=H, Ph; LDA=lithium diisopropylamide.

Asymmetric Total Synthesis of Fredericamycin A

Seventeen years after the isolation of the promising antitumor antibiotic fredericamycin A, the first asymmetric total synthesis of this compound has been accomplished and thereby its absolute configuration established. The key feature is the regiocontrolled [4+2] cycloaddition of 3 to 2, which was obtained by the stereospecific rearrangement of 1. Cp = (-)-camphanoyl.

Total Synthesis of (±)-Halomon by a Johnson-Claisen Rearrangement

The total synthesis of the polyhalogenated antitumour agent halomon (1) was accomplished with two novel transformations as key steps: a Johnson-Claisen rearrangement of a dichlorinated alkene for the preparation of the tertiary chlorinated C3 and a new rearrangement of bromohydrins for the regiospecific introduction of the bromine and chlorine atoms on C6 and C7, respectively.

Rhodium(I)-Catalyzed Regioselective Ring- Expanding Rearrangement of Allenylcyclopropanes into Methylenecyclopentenes

A highly regioselective C-C bond cleavage of the cyclopropane rings occurs in substituted allenylcyclopropanes in the presence of cationic rhodium(I) complexes. Thus, ring expansion of readily accessible allenylcyclopropanes can be achieved to give 3-methylenecyclopentenes, which could have applications as multifunctional synthetic building blocks.