Przetoki tętnic wieńcowych. Lokalizacja anatomiczna i różnorodność objawów klinicznych

Wstęp: Przetoki tętnic wieńcowych są rzadkimi anomaliami. U dorosłych najczęściej powodują objawy kliniczne występujące w chorobie wieńcowej. W niniejszej pracy analizie poddano stwierdzone w koronarografii przypadki obecności tej anomalii. Materiał i metody: Przeanalizowano 4100 koronarografii. Przetoki stwierdzono u 11 chorych (0,27%). U 1 osoby przyczyną koronarografii była wada serca, u pozostałych 10 podejrzenie choroby wieńcowej. Spośród tej grupy u 3 osób stwierdzono istotne zmiany miażdżycowe, u 7 oprócz przetok nie obserwowano zmian organicznych w tętnicach wieńcowych. Oceniono stopień nasilenia dolegliwości podmiotowych i współistnienie innych schorzeń. U wszystkich chorych wykonano badania elektrokardiograficzne spoczynkowe i wysiłkowe oraz badanie echokardiograficzne. Szczególnej analizie poddano 7-osobową grupę pacjentów bez towarzyszących innych zmian w tętnicach wieńcowych. Wyniki: W 5 przypadkach przetoki rozpoczynały się w początkowym odcinku tętnicy zstępującej przedniej (LAD), także w 5 przypadkach - w początkowym odcinku prawej tętnicy wieńcowej (RCA), w 4 przypadkach - na obwodzie RCA, a w 1 przypadku - na obwodzie LAD. W 1 przypadku przetoki uchodziły do lewego przedsionka, w 5 - do tętnicy płucnej, w 5 - do prawej komory, a w 2 przypadkach - do prawego przedsionka. U wszystkich 7 chorych bez zmian miażdżycowych stwierdzono nadciśnienie tętnicze. Jedna osoba przebyła zawał serca w zakresie tętnicy, od której odchodziła przetoka. Wnioski: Przetoki tętnic wieńcowych występują w różnorodnym układzie anatomicznym i mogą powodować objawy charakterystyczne dla choroby wieńcowej. Nie można wykluczyć, że nadciśnienie tętnicze sprzyja pojawieniu się objawów klinicznych u chorych z przetokami. Dokładniejsza ocena znaczenia przetok wymaga przeprowadzenia badań w większej grupie pacjentów. (Folia Cardiol. 2004; 11: 27-32

Przetoki tętnic wieńcowych. Lokalizacja anatomiczna i różnorodność objawów klinicznych

Wstęp: Przetoki tętnic wieńcowych są rzadkimi anomaliami. U dorosłych najczęściej powodują objawy kliniczne występujące w chorobie wieńcowej. W niniejszej pracy analizie poddano stwierdzone w koronarografii przypadki obecności tej anomalii. Materiał i metody: Przeanalizowano 4100 koronarografii. Przetoki stwierdzono u 11 chorych (0,27%). U 1 osoby przyczyną koronarografii była wada serca, u pozostałych 10 podejrzenie choroby wieńcowej. Spośród tej grupy u 3 osób stwierdzono istotne zmiany miażdżycowe, u 7 oprócz przetok nie obserwowano zmian organicznych w tętnicach wieńcowych. Oceniono stopień nasilenia dolegliwości podmiotowych i współistnienie innych schorzeń. U wszystkich chorych wykonano badania elektrokardiograficzne spoczynkowe i wysiłkowe oraz badanie echokardiograficzne. Szczególnej analizie poddano 7-osobową grupę pacjentów bez towarzyszących innych zmian w tętnicach wieńcowych. Wyniki: W 5 przypadkach przetoki rozpoczynały się w początkowym odcinku tętnicy zstępującej przedniej (LAD), także w 5 przypadkach - w początkowym odcinku prawej tętnicy wieńcowej (RCA), w 4 przypadkach - na obwodzie RCA, a w 1 przypadku - na obwodzie LAD. W 1 przypadku przetoki uchodziły do lewego przedsionka, w 5 - do tętnicy płucnej, w 5 - do prawej komory, a w 2 przypadkach - do prawego przedsionka. U wszystkich 7 chorych bez zmian miażdżycowych stwierdzono nadciśnienie tętnicze. Jedna osoba przebyła zawał serca w zakresie tętnicy, od której odchodziła przetoka. Wnioski: Przetoki tętnic wieńcowych występują w różnorodnym układzie anatomicznym i mogą powodować objawy charakterystyczne dla choroby wieńcowej. Nie można wykluczyć, że nadciśnienie tętnicze sprzyja pojawieniu się objawów klinicznych u chorych z przetokami. Dokładniejsza ocena znaczenia przetok wymaga przeprowadzenia badań w większej grupie pacjentów. (Folia Cardiol. 2004; 11: 27-32

Identification of candidate enhancers controlling the transcriptome during the formation of interphalangeal joints

The formation of the synovial joint begins with the visible emergence of a stripe of densely packed mesenchymal cells located between distal ends of the developing skeletal anlagen called the interzone. Recently the transcriptome of the early synovial joint was reported. Knowledge about enhancers would complement these data and lead to a better understanding of the control of gene transcription at the onset of joint development. Using ChIP-sequencing we have mapped the H3-signatures H3K27ac and H3K4me1 to locate regulatory elements specific for the interzone and adjacent phalange, respectively. This one-stage atlas of candidate enhancers (CEs) was used to map the association between these respective joint tissue specific CEs and biological processes. Subsequently, integrative analysis of transcriptomic data and CEs identified new putative regulatory elements of genes expressed in interzone (e.g., GDF5, BMP2 and DACT2) and phalange (e.g., MATN1, HAPLN1 and SNAI1). We also linked such CEs to genes known as crucial in synovial joint hypermobility and osteoarthritis, as well as phalange malformations. These analyses show that the CE atlas can serve as resource for identifying, and as starting point for experimentally validating, putative disease-causing genomic regulatory regions in patients with synovial joint dysfunctions and/or phalange disorders, and enhancer-controlled synovial joint and phalange formation

Zeb2 DNA-Binding Sites in Neuroprogenitor Cells Reveal Autoregulation and Affirm Neurodevelopmental Defects, Including in Mowat-Wilson Syndrome

Functional perturbation and action mechanism studies have shown that the transcription factor Zeb2 controls cell fate decisions, differentiation, and/or maturation in multiple cell lineages in embryos and after birth. In cultured embryonic stem cells (ESCs), Zeb2’s mRNA/protein upregulation is necessary for the exit from primed pluripotency and for entering general and neural differentiation. We edited mouse ESCs to produce Flag-V5 epitope-tagged Zeb2 protein from one endogenous allele. Using chromatin immunoprecipitation coupled with sequencing (ChIP-seq), we mapped 2432 DNA-binding sites for this tagged Zeb2 in ESC-derived neuroprogenitor cells (NPCs). A new, major binding site maps promoter-proximal to Zeb2 itself. The homozygous deletion of this site demonstrates that autoregulation of Zeb2 is necessary to elicit the appropriate Zeb2-dependent effects in ESC-to-NPC differentiation. We have also cross-referenced all the mapped Zeb2 binding sites with previously obtained transcriptome data from Zeb2 perturbations in ESC-derived NPCs, GABAergic interneurons from the ventral forebrain of mouse embryos, and stem/progenitor cells from the post-natal ventricular-subventricular zone (V-SVZ) in mouse forebrain, respectively. Despite the different characteristics of each of these neurogenic systems, we found interesting target gene overlaps. In addition, our study also contributes to explaining developmental disorders, including Mowat-Wilson syndrome caused by ZEB2 deficiency, and also other monogenic syndromes.</p

Targeted chromatin conformation analysis identifies novel distal neural enhancers of ZEB2 in pluripotent stem cell differentiation

The transcription factor zinc finger E-box binding protein 2 (ZEB2) controls embryonic and adult cell fate decisions and cellular maturation in many stem/progenitor cell types. Defects in these processes in specific cell types underlie several aspects of Mowat-Wilson syndrome (MOWS), which is caused by ZEB2 haplo-insufficiency. Human ZEB2, like mouse Zeb2, is located on chromosome 2 downstream of a ±3.5 Mb-long gene-desert, lacking any protein-coding gene. Using temporal targeted chromatin capture (T2C), we show major chromatin structural changes based on mapping in-cis proximities between the ZEB2 promoter and this gene desert during neural differentiation of human-induced pluripotent stem cells, including at early neuroprogenitor cell (NPC)/rosette state, where ZEB2 mRNA levels increase significantly. Combining T2C with histone-3 acetylation mapping, we identified three novel candidate enhancers about 500 kb upstream of the ZEB2 transcription start site. Functional luciferase-based assays in heterologous cells and NPCs reveal co-operation between these three enhancers. This study is the first to document in-cis Regulatory Elements located in ZEB2's gene desert. The results further show the usability of T2C for future studies of ZEB2 REs in differentiation and maturation of multiple cell types and the molecular characterization of newly identified MOWS patients that lack mutations in ZEB2 protein-coding exons

Regulation of transcription and 3D chromatin architecture in instructed cell differentiation

Our genome contains an estimated number of 400,000 to 1.4 million enhancers. These are regulatory sequences mostly located outside exons of protein-coding genes either close to or far away from the transcription start site(s) of genes on the chromosome. Together with gene promoters, they are principal cell-intrinsic genomic elements assuring the activity and accurate regulation of transcription of genes, in terms of the steady-state mRNA levels and spatio-temporal precision. During early embryogenesis and subsequent organogenesis, enhancers co-regulate decisions in cell fate and differentiation, and thus creation of cell diversity. Such regulatory sequences operate often in a context of extrinsic cell stimulation by polypeptide growth factors, the signaling cascade of which is interpreted and further executed in the nucleus by transcription factors, assuring RNAPol2-mediated activation of sets of genes by their binding to promoter and enhancer sequences. These precise molecular actions must take place in a cell nucleus of 6-μm diameter average, and wherein 2m of DNA is highly compacted and present as architecturally ordered chromatin (DNA and bound proteins), as individual chromosomes. This chromatin in general, as well as its typical nucleosomes, but also enhancer and promoter sequences, are epigenetically marked (biochemically modified, in various ways). This collectively assures that the chromatin opens locally when gene transcription activation is needed, and gene-specific enhancers must thereby achieve physical proximity, which can be documented by chromatin conformation capture (3C) analyses, with the promoter of their cognate gene. At the same time, a set of biochemical marks, including those modifying histone-3 (H3) in the nucleosome, facilitates the identification of candidate enhancers. Importantly, like key protein-coding genes, sequence variation or mutation of enhancers can lead or contribute to congenital syndromes and chronic disease. Hence, both experimental studies of enhancers (including their identification in small population of embryonic cells) and key developmental transcription factors (including how their own level and activity are regulated, but also which genes and regulatory sequences they bind to), are fundamental to understanding cell-based health and disease of the entire organism. The research in this PhD thesis addresses these fundamental aspects of genetic and molecular control of embryogenesis, and at the same time investigates the mechanisms of gene regulation. It presents two lines of experimental as well as bio-informatics work, one in vivo and one in cell culture, specifically in the formation of flexible joints in developing limbs and chondrogenesis in the latter, and neural differentiation of pluripotent embryonic cells, respectively. The mechanisms of gene regulation most relevant to this PhD research are described in Chapter 1, which also includes an overview of these molecular regulations as well as mutations in regulatory elements that link to selected human limb malformations. The experimental part of research line-1 reports on the production, for the first time, of a genome-wide candidate-enhancer atlas of the joint interzone and adjacent phalanges, respectively. This work includes integrative analysis of transcriptomic data from RNA-sequencing together with H3K27ac and H3K4me1 signatures obtained by ChIP-sequencing (Chapter 3). It then reports on contribution to the establishment of a low-T2C (a targeted 3C-assay) protocol applicable to cell populations or in vivo samples available as low cell numbers, like for synovial joints (Chapter 4). Then, this low-T2C protocol is used to investigate the genomic region encompassing the Dact2 and Smoc2 genes, and identify and characterize their enhancers in the interzone during synovial joint development, which were also validated using a zebrafish larvae enhancer assay (Chapter 5). In research line-2, using neural differentiation of embryonic stem cells (ESCs), the thesis reports on the demonstration of dynamic DNA-loops in and around the human ZEB2 locus (including its 3.5 Mb-long gene desert), and co-operation between the newly identified enhancers, including in human neuroprogenitor cells (NPCs) (Chapter 6). The DNA-binding transcription factor ZEB2 is studied by many teams in different fields, but maps of its genome-wide binding sites are urgently needed. This PhD thesis therefore also includes ChIP-sequencing of Zeb2 (endogenously tagged in mouse ESCs, guaranteeing normal levels of Zeb2 production) in ESC-derived cultures of NPCs (Chapter 7). This work aims at identifying Zeb2-dependent, directly controlled target genes, as well as candidate TFs that regulate Zeb2 gene expression via its identified enhancers, and illustrates for the first time how critical the identified autoregulation of Zeb2. This PhD research as a whole combines two experimental models, multi-omics methods, and functional assays to investigate multiple regulatory mechanisms, in genome-wide as well as locus-specific studies. It documents dynamic changes in 3D chromatin architecture, enhancer signatures and activity, to reveal the underlying principles of precise control of gene expression during development and differentiation

Mutations in gene regulatory elements linked to human limb malformations

Most of the human genome has a regulatory function in gene expression. The technological progress made in recent years permitted the revision of old and discovery of new mutations outside of the protein-coding regions that do affect human limb morphology. Steadily increasing discovery rate of such mutations suggests that until now the largely neglected part of the genome rises to its well-deserved prominence. In this review, we describe the recent technological advances permitting this unprecedented advance in identifying non-coding mutations. We especially focus on the mutations in cis-regulatory elements such as enhancers, and trans-regulatory elements such as miRNA and long non-coding RNA, linked to hereditary or inborn limb defects. We also discuss the role of chromatin organisation and enhancer-promoter interactions in the aetiology of limb malformations.status: publishe

TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure

In recent years great progress has been made in identification of structural variants (SV) in the human genome. However, the interpretation of SVs, especially located in non-coding DNA, remains challenging. One of the reasons stems in the lack of tools exclusively designed for clinical SVs evaluation acknowledging the 3D chromatin architecture. Therefore, we present TADeus2 a web server dedicated for a quick investigation of chromatin conformation changes, providing a visual framework for the interpretation of SVs affecting topologically associating domains (TADs). This tool provides a convenient visual inspection of SVs, both in a continuous genome view as well as from a rearrangement’s breakpoint perspective. Additionally, TADeus2 allows the user to assess the influence of analyzed SVs within flaking coding/non-coding regions based on the Hi-C matrix. Importantly, the SVs pathogenicity is quantified and ranked using TADA, ClassifyCNV tools and sampling-based P-value. TADeus2 is publicly available at https://tadeus2.mimuw.edu.pl

Low Input Targeted Chromatin Capture (Low-T2C)

Targeted chromatin capture (T2C) is a 3C-based method and is used to study the 3D chromatin organization, interactomes and structural changes associated with gene regulation, progression through the cell cycle, and cell survival and development. Low input targeted chromatin capture (low-T2C) is an optimized version of the T2C protocol for low numbers of cells. Here, we describe the protocol for low-T2C, including all experimental steps and bioinformatics tools in detail

Evidence that recent climatic changes have expanded the potential geographical range of the Mediterranean fruit fly

Abstract The species distributions migration poleward and into higher altitudes in a warming climate is especially concerning for economically important insect pest species, as their introduction can potentially occur in places previously considered unsuitable for year-round survival. We explore the expansion of the climatically suitable areas for a horticultural pest, the Mediterranean fruit fly (medfly) Ceratitis capitata (Diptera, Tephritidae), with an emphasis on Europe and California. We reviewed and refined a published CLIMEX model for C. capitata, taking into consideration new records in marginal locations, with a particular focus on Europe. To assess the model fit and to aid in interpreting the meaning of the new European distribution records, we used a time series climate dataset to explore the temporal patterns of climate suitability for C. capitata from 1970 to 2019. At selected bellwether sites in Europe, we found statistically significant trends in increasing climate suitability, as well as a substantial northward expansion in the modelled potential range. In California, we also found a significant trend of northward and altitudinal expansion of areas suitable for C. capitata establishment. These results provide further evidence of climate change impacts on species distributions and the need for innovative responses to increased invasion threats