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Lee, Jung-Seok, Goran Mitulović, Layla Panahipour, and Reinhard Gruber. "Proteomic Analysis of Porcine-Derived Collagen Membrane and Matrix." Materials 13, no. 22 (2020): 5187. http://dx.doi.org/10.3390/ma13225187.
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Collagen membranes and matrices being widely used in guided bone regeneration and soft tissue augmentation have characteristic properties based on their composition. The respective proteomic signatures have not been identified. Here, we performed a high-resolution shotgun proteomic analysis on two porcine collagen-based biomaterials designed for guided bone regeneration and soft tissue augmentation. Three lots each of a porcine-derived collagen membrane and a matrix derived from peritoneum and/or skin were digested and separated by nano-reverse-phase high-performance liquid chromatography. The peptides were subjected to mass spectrometric detection and analysis. A total of 37 proteins identified by two peptides were present in all collagen membranes and matrices, with 11 and 16 proteins being exclusively present in the membrane and matrix, respectively. The common extracellular matrix proteins include fibrillar collagens (COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL5A3, COL11A2), non-fibrillar collagens (COL4A2, COL6A1, COL6A2, COL6A3, COL7A1, COL16A1, COL22A1), and leucine-rich repeat proteoglycans (DCN, LUM, BGN, PRELP, OGN). The structural proteins vimentin, actin-based microfilaments (ACTB), annexins (ANXA1, ANXA5), tubulins (TUBA1B, TUBB), and histones (H2A, H2B, H4) were also identified. Examples of membrane-only proteins are COL12A1 and COL14A1, and, of matrix only proteins, elastin (ELN). The proteomic signature thus revealed the similarities between but also some individual proteins of collagen membrane and matrix.
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Li, Zhaoxing, Zhao Liu, Zhiting Shao, et al. "Identifying multiple collagen gene family members as potential gastric cancer biomarkers using integrated bioinformatics analysis." PeerJ 8 (May 25, 2020): e9123. http://dx.doi.org/10.7717/peerj.9123.
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Background Gastric cancer is one of the most common malignant cancers worldwide. Despite substantial developments in therapeutic strategies, the five-year survival rate remains low. Therefore, novel biomarkers and therapeutic targets involved in the progression of gastric tumors need to be identified. Methods We obtained the mRNA microarray datasets GSE65801, GSE54129 and GSE79973 from the Gene Expression Omnibus database to acquire differentially expressed genes (DEGs). We used the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to analyze DEG pathways and functions, and the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape to obtain the protein–protein interaction (PPI) network. Next, we validated the hub gene expression levels using the Oncomine database and Gene Expression Profiling Interactive Analysis (GEPIA), and conducted stage expression and survival analysis. Results From the three microarray datasets, we identified nine major hub genes: COL1A1, COL1A2, COL3A1, COL5A2, COL4A1, FN1, COL5A1, COL4A2, and COL6A3. Conclusion Our study identified COL1A1 and COL1A2 as potential gastric cancer prognostic biomarkers.
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Li, Jingyi, Nating Huang, Xun Zhang, Ci Sun, Jiarui Chen, and Qing Wei. "Changes of collagen content in lung tissues of plateau yak and its mechanism of adaptation to hypoxia." PeerJ 12 (October 1, 2024): e18250. http://dx.doi.org/10.7717/peerj.18250.
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Collagen is crucial for tissue structure, functional maintenance, and cellular processes such as proliferation and differentiation. However, the specific changes in collagen expression and its associated genes in the lung tissues of yaks at high altitudes and their relationship with environmental adaptation remain poorly understood. Studying differences in the content of collagen fibers and gene expression between yaks at high (4,500 m) and low (2,600 m) altitudes, as well as between cattle at low altitudes (2,600 m). Using Masson staining, we found that the collagen fiber content in the lung tissues of yaks at low altitude was significantly higher compared to yaks at high altitude and cattle at the same altitude (P < 0.05). It was revealed through transcriptomic analyses that genes differentially expressed between high and low altitude yaks, as well as between low altitude yaks and cattle, were notably enriched in pathways related to cell adhesion, collagen synthesis, focal adhesion, and ECM-receptor interactions. Specifically, genes involved in mesenchymal collagen synthesis (e.g., COL1A1, COL1A2, COL3A1), basement membrane collagen synthesis (e.g., COL4A1, COL4A2, COL4A4, COL4A6), and peripheral collagen synthesis (e.g., COL5A1, COL6A1, COL6A2, COL6A3) were significantly upregulated in the lung tissues of yaks at low altitude compared to their high altitude counterparts and cattle (P < 0.05). In conclusion, yaks at lower altitudes exhibit increased collagen synthesis by upregulating collagen gene expression, which contributes to maintaining alveolar stability and septal flexibility. Conversely, the expression of collagen genes in yak lung tissues was down-regulated with the increase in altitude, and it was speculated that the decrease in collagen may be used to constrain the function of elastic fibers that are more abundant at high altitude, so as to enable them to adapt to the harsh environment with hypoxia and high altitude. This adaptation mechanism highlights the role of collagen in environmental acclimatization and contributes to our understanding of how altitude and species influence collagen-related physiological processes in yaks.
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Susanti, Nelly. "Peningkatan Hasil Belajar Siswa dalam Mata Pelajaran Biologi melalui Penerapan Model Gagnon and Collay Kelas Xi MIPA2SMAN 6 Kerinci." Jurnal Ilmiah Dikdaya 12, no. 2 (2022): 426. http://dx.doi.org/10.33087/dikdaya.v12i2.335.
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Application of Learning Model Gagnon and Colay in eye lesson Biologyon student class XI MIPA 2 SMA Negeri 6 Kerinci , where is the Gagnon and Collay Modelthisis a structured learning model based on theory constructivist who emphasizes on liveliness students , independence as well as development study team by intensive . Study this is study action class (Classroom Action Research), which consists of from four component in every cycle that is planning (planning), action (action), observation (observation), and reflection (refleck), done for know is with Application of Learning Model Gagnon and Collay results study student class XI MIPA2 Public High Schools 6 Kerinci could increase. Subject in study this is student class XI MIPA2 Public High Schools 6 yang totaling 20 people. In collecting the data, this research use test on every cycle and sheet observation. As for technique data analysis that is with technique descriptive data analysis qualitative and descriptive quantitative. Descriptive qualitative used in analyze result data observation or observation, while descriptive quantitative used for give description or take conclusion based on results test learning done on every cycle.Results analysis test results study student on every cycle show that level ability student class XI MIPA2 Public High Schools 6 Kerinci experience increas, thing this seen after Application of Learning Model Gagnon and Collay, lookon cycle I average value student as big as 60 and on cycle II an average of 84. This thing show that results study biology increase after Application of Learning Model Gagnon and Collay.
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Cardoso, Victor Menezes, Gustavo Henrique Brasil Rodrigues, Kayo Felipe Barbosa Lima, et al. "Gastric adenocarcinoma: bioinformatic analysis and its relationship to perineural invasion." CONTRIBUCIONES A LAS CIENCIAS SOCIALES 18, no. 5 (2025): e17672. https://doi.org/10.55905/revconv.18n.5-097.
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This article aims to evaluate some important molecular aspects of gastric adenocarcinoma (STAD), and to evaluate its relationship with Schwann cells and other factors associated with perineural invasion. It is an analysis of open access genomic and proteomic data. Our study allowed us to identify differentially expressed genes in STAD, 1382 increased genes and 1490 decreased genes. These genes are associated with a total of 66 altered pathways, of which we selected 7 for further analysis (“PI3K-Akt”, “cytochrome P450 drug metabolism”, “renin secretion”, “renin-angiotensin system”, “PPAR”, “circadian entrainment”, and “neuroactive ligand-receptor interaction”). Of these pathways, 58 genes with an impact on survival were identified, with a negative impact on survival: COL1A1, COL1A2, COL3A1, COL4A1, COL5A1, COL5A2, COL5A3, COL6A3, ITGA11, ALDH3A1 and ALDH3B2. Other genes were also evaluated for survival and mutations. We identified frequent alterations in the SMAD4, CDH1 and MSH6 genes associated with some syndromes that have an increased risk for the development of gastric cancer. The evaluation of Schwann and STAD cells identified 47 increased and 85 decreased. These genes resulted in 3 significantly altered pathways, however with a small number of genes involved. We identified some genes related to perineural invasion that were reported in the literature, such as the NTN1 and SLIT2 genes, which revealed little evidence of perineural invasion, but evidence of dedifferentiation of Schwann cells in STAD.
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Molano Tobar, Nancy Janneth, Alejandra Rocio Rodriguez Ortiz, and Felipe García Vallejo. "Differential expression of genes associated with sports injuries." International Journal of Molecular Biology Open Access 5, no. 4 (2020): 154–58. http://dx.doi.org/10.15406/ijmboa.2020.05.00142.
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Candidate gene studies in sports injuries pose a valid new approach to investigate the genetic basis of these. In this context, our objective was to analyze the differential expression and interaction of genes associated with sports injuries using a bio informatic approach. For this study, we analyzed 31 genes associated with sports injuries previously reported in the literature. Expression analysis was performed using the Z-ratio and a protein-protein interaction network was constructed in STRING 10.0. The GO categories associated with outstanding biological processes in the network were also taken from STRING 10.0. The expression network obtained allowed establishing three clusters with a significant number of interactions, the highest interactions were found in the genes COL1A1, COL1A2, COL3A1, COL4A1, COL6A1 and COL5A1. According to the Z-ratio, the most over expressed genes were ITGB6 (z-ratio 4.32), COL1A2 (z-ratio 4.07), COL6A2 (z-ratio 3.99) and TIMM17A. In conclusion, the over-expression of genes is presented, which according to the current literature has been analyzed very little, from the sports field associated with sports injuries, a fact that merits further research. Also, we highlight the importance of bioinformatics as a complementary tool to the analysis of sports genomic data.
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Wang, Shuoshan, Xiansheng Yang, Chang Liu, et al. "Identification of key genes associated with poor prognosis and neoplasm staging in gastric cancer." Medicine 102, no. 40 (2023): e35111. http://dx.doi.org/10.1097/md.0000000000035111.
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Background: Gastric cancer (GC) is highly biologically and genetically heterogeneous disease with poor prognosis. Increasing evidence indicates that biomarkers can serve as prediction and clinical intervention. Therefore, it is vital to identify core molecules and pathways participating in the development of GC. Methods: In this study, GSE54129, GSE56807, GSE63089, and GSE118916 were used for identified overlapped 75 DEGs. GO and Kyoto Encyclopedia of Genes and Genomes pathway analysis showed DEGs mainly enriched in biological process about collagen-containing extracellular matrix and collagen metabolic. Next, protein-protein interaction network was built and the hub gene was excavated. Clinicopathological features and prognostic value were also evaluated. Results: Hub genes were shown as below, FN1, COL1A2, COL1A1, COL3A1, COL4A1, COL6A3, COL5A2, SPARC, PDGFRB, COL12A1. Those genes were upregulation in GC and related to the poor prognosis (except COL5A2, P = .73). What is more, high expression indicated worse T stage and tumor, node, metastasis stage in GC patients. Later, the results of 25 GC tumor specimens and 34 normal tissues showed that FN1, COL3A1, COL4A1, SPARC, COL5A2, and COL12A1 were significantly upregulated in cancer samples. Conclusion: Our study systematically explored the core genes and crucial pathways in GC, providing insights into clinical management and individual treatment.
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Pedro, A. Carretero Poblete. "A propósito de un sitio arqueológico puruhá del periodo Formativo Tardío en el cerro Collay de Yaruquíes (Riobamba, Ecuador)." Arqueologia Iberoamericana 44 (December 26, 2019): 66–68. https://doi.org/10.5281/zenodo.3595481.
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Con este breve aporte se realizan unas consideraciones sobre un reciente estudio publicado por Beckwith, entre 2018 y 2019, sobre el cerro Collay de Yaruquíes (Riobamba, Ecuador) que obvia los estudios que ya se realizaron en 2016 en dicho cerro, publicados en 2017, acerca de su adscripción al Formativo Tardío de Ecuador. ENGLISH: About the Puruha Archaeological Site of the Late Formative Period in the Collay de Yaruquies Hill (Riobamba, Ecuador). With this brief contribution, some considerations are made about a recent study published by Beckwith, between 2018 and 2019, on the Collay of Yaruquies hill (Riobamba, Ecuador) which ignores the studies that were already carried out in 2016 in the aforementioned hill, published in 2017, about its ascription to the Late Formative of Ecuador.
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Pedro, A. Carretero Poblete, and M. Samaniego Erazo William. "Prospección arqueológica en el sitio Puruhá de Collay, Riobamba, Ecuador." Arqueologia Iberoamericana 33 (February 11, 2017): 18–26. https://doi.org/10.5281/zenodo.1319093.
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Durante el año 2016 realizamos prospecciones arqueológicas en el cerro Collay de Riobamba, Ecuador. Entre el material recuperado, destaca la cerámica de los estilos Puruhá, Cañari y Costeña, pertenecientes a las fases finales del Formativo Tardío (<em>ca.</em> 800 a. C.) e inicios del periodo de Desarrollo Regional (<em>ca.</em> 500 d. C.). La cerámica recuperada en el cerro Collay sugiere la presencia de un importante centro Puruhá, muy próximo a la llanura de Tapi, con importantes conexiones con los Cañari de la Sierra Centro del Ecuador. ENGLISH: Archaeological Survey at the Site of Puruha Collay, Riobamba, Ecuador. In 2016, we carried out archaeological surveys on the Collay mountain of Riobamba, Ecuador. Among the recovered materials, there are Puruhá, Cañari and Costeño style pottery, all belonging to the end of the Late Formative Period (ca. 800 BC) and the Regional Development Period (ca. 500 AD). The discovery of these ceramic styles suggests the presence of an important Puruhá settlement, very near the Llanura de Tapi, that maintained important connections with the Cañari of Ecuador´s central highland region.
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Novaretti, João Victor, Diego Costa Astur, Davi Casadio, et al. "Higher Gene Expression of Healing Factors in Anterior Cruciate Ligament Remnant in Acute Anterior Cruciate Ligament Tear." American Journal of Sports Medicine 46, no. 7 (2018): 1583–91. http://dx.doi.org/10.1177/0363546518760577.
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Background: Anterior cruciate ligament (ACL) reconstruction with remnant preservation has been described and related to potential advantages. Literature is lacking regarding gene expression of potential factors related to ligament healing in the ACL remnant and its relation to time from injury. Hypothesis: The mRNA expression of ligament healing factors in the ACL remnant would be higher in acute tears (<3 months from injury) than in intermediate (3-12 months) and chronic (>12 months) injuries. Study Design: Controlled laboratory study. Methods: Gene expression of 21 genes related to ligament healing factors was analyzed in 46 ACL remnants biopsied during surgical reconstruction with quantitative real-time polymerase chain reaction technique. Specimens were divided into 3 groups according to time from injury: acute (<3 months from injury; n = 19), intermediate (3-12 months; n = 12), and chronic (>12 months; n = 15). Histological and immunohistochemical evaluation was performed by analysis of hematoxylin and eosin, CD-34, and S-100 staining. Results: Expression of COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, COL12A1, LOX, PLOD1, and TNC genes in ACL remnant was greater in acute compared with chronic injuries. COL1A1, COL5A1, COL12A1, and TNC genes were also expressed more in the acute group compared with the intermediate group. Furthermore, expression of the genes COL1A1 and COL5A2 was significantly higher in female than in male patients. No difference in the number of blood vessels and mechanoreceptors among groups was observed in the microscopic evaluation. Conclusion: The present study demonstrates that expression of COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, COL12A1, LOX, PLOD1, and TNC genes in ACL remnant is greater in acute (<3 months from injury) compared with chronic (>12 months) injuries. Furthermore, COL1A1, COL5A1, COL12A1, and TNC genes were expressed more in the acute group compared with the intermediate group (3-12 months from injury). Clinical Relevance: ACL reconstructions with remnant preservation should be performed in patients with acute injuries, as in these cases the ACL remnant may present the greatest healing potential.
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Mariesi, Anci, Maryam Zand Vakili, and Khder Niazi Nooraldeen Chalabi. "Application of the Gagnon and Collay Model in Improving High School Students' Learning Outcomes in Biology Subjects." Indonesian Journal of Education Research (IJoER) 5, no. 3 (2024): 76–83. http://dx.doi.org/10.37251/ijoer.v5i3.989.
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Purpose of the study: This research aims to investigate the effectiveness of applying the Gagnon and Collay Model in improving Biology learning outcomes for class XI students at Public Senior High School 1 Bone-Bone, North Luwu Regency. Methodology: This research is classroom action research which involves four components in each cycle. The research subjects consisted of 32 students of class XI Science 1 at Public Senior High School 1 Bone-Bone, North Luwu Regency. Data collection is carried out through tests and observation sheets in each cycle. Data analysis methods include qualitative and quantitative descriptive techniques. Main Findings: From the analysis of student learning outcomes tests in each cycle, it can be observed that the abilities of class XI Science 1 students at Public Senior High School 1 Bone-Bone, North Luwu Regency, have increased. After implementing the Gagnon and Collay Learning Model, the students' average score increased from 63.5 in cycle I to 90.38 in cycle II. This shows an increase in biology learning outcomes after implementing the Gagnon and Collay Learning Model. Novelty/Originality of this study: This research makes a significant contribution to the educational context by exploring and applying the Gagnon and Collay Model in improving student learning outcomes in Biology subjects. Through this approach, this research seeks to provide innovation in Biology teaching methods, aiming to create a learning environment that is more interactive, creative, and appropriate to the development of class XI Science 1 students.
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Mardiyanti, Mardiyanti, Ida Royani, and Taufik Samsuri. "Penerapan Model Pembelajaran Gagnon And Collay Berbantuan Games Dalam Meningkatkan Motivasi Dan Prestasi Belajar Siswa." Reflection Journal 2, no. 1 (2022): 34–45. http://dx.doi.org/10.36312/rj.v2i1.857.
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Tujuan penelitian ini adalah mengidentifikasi penerapan model pembelajaran Gagnon and Collay berbantuan games dalam meningkatkan motivasi dan prestasi belajar siswa pada materi karakteristik makhluk hidup. Subyek penelitian ini adalah siswa kelas VII SMP Muhammadiyah Mataram. Jenis penelitian yang digunakan adalah Penelitian Tindakan Kelas (PTK) yang dilaksanakan dalam dalam dua siklus. Data motovasi belajar siswa dikumpulkan dengan quisioner dan data hasil belajar dikumpulkan dengan tes. Data yang diperoleh dianalisis mengunakan statistik deskriptif. Berdasarkan hasil analisis data menunjukan bahwa pada siklus I rata-rata motivasi belajar siswa sebesar 62,5% dengan kategori termotivaasi dan meningkat pada siklus II menjadi 75,6% dengan kategori sangat termotivasi. Kondisi tersebut memperlihatkan adanya peningkatan sebesar 13,18%. Sementara data rata-rata prestasi belajar siswa pada siklus 1 sebesar 74.2% dan meningkat pada siklus II sebesar 80,9% dengan nilai rata-rata peningkatan yaitu 14,9% setelah dilakukan tindakan pada setiap siklusnya. Berdasarkan analisis data penelitian dapat disimpulkan bahwa penerapan model pembelajaran Gagnon and Collay berbantuan games dapat meningkatkan motivasi dan prestasi belajar siswa kelas VII pada mata pembelajaran IPA-Biologi SMP Muhammadiyah Mataram. The Application Of The Gagnon And Collay Learning Model Helps Games In Increasing Student Motivation And Learning Achievement The purpose of this study is to identify the application of the Gagnon and Collay learning model assisted by games in increasing student motivation and learning achievement on material characteristics of living beings. The subject of this study was a grade VII student of Muhammadiyah Mataram Junior High School. The type of research used is Classroom Action Research (PTK) which is carried out in two cycles. Student learning data were collected with questionnaires and learning outcomes data were collected with tests. The data obtained were analyzed using descriptive statistics. Based on the results of data analysis, it shows that in cycle I the average student learning motivation was 62.5% with the category of termivation and increased in cycle II to 75.6% with the category of highly motivated. This condition showed an increase of 13.18%. Meanwhile, the average data on student learning achievement in cycle 1 was 74.2% and increased in cycle II by 80.9% with an average score of 14.9% after actions were taken in each cycle. Based on the analysis of research data, it can be concluded that the application of the Gagnon and Collay learning model assisted by games can increase the motivation and learning achievement of grade VII students in the science-biology learning course of Muhammadiyah Mataram Junior High School.
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Skov, Vibe, Mads Thomassen, Lasse Kjær, et al. "Extracellular Matrix-Related Genes Are Deregulated in Peripheral Blood from Patients with Myelofibrosis and Related Neoplasms." Blood 132, Supplement 1 (2018): 5491. http://dx.doi.org/10.1182/blood-2018-99-117122.
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Abstract Introduction: The Philadelphia-negative chronic myeloproliferative neoplasms (MPNs) which include essential thrombocythemia (ET), polycythemia vera (PV) and primary myelofibrosis (PMF) are characterized by varying degrees of bone marrow fibrosis and endothelial proliferation. We and others have previously reported that these stromal alterations are reflected by increased serum levels of matrix derived metabolites, striated collagens type I/III and basement membrane components. The existence of a prefibrotic seromarker profile in MPNs is further evidenced by reports on increased serum levels of matrix metalloproteinase-3 (MMP-3) and decreased tissue inhibitor of metalloproteinase- I (TIMP-I). Using whole blood gene expression profiling, we aimed to provide a comprehensive gene signature of extracellular matrix-related proteins in MPNs with particular focus on genes associated with the regulation of major stromal proteins and MMPs. Methods: Gene expression profiling was performed on whole blood from 21 control subjects, 19 patients with ET, 41 patients with PV, and 9 patients with PMF. RNA was converted to biotin labeled amplified RNA (aRNA) using the MessageAmpTM III RNA amplification kit, and fragmented aRNA was hybridized to Affymetrix HG-U133 Plus 2.0 microarray chips recognizing 54,675 probe sets (38,500 genes). The R statistical software was applied to perform data preprocessing and statistical analysis of microarray data. Results: We identified 20,439, 25,307, and 17,417 probe sets that were differentially expressed between controls and patients with ET, PV, and PMF, respectively (FDR£0.05). These genes included 116 genes encoding extracellular matrix and adhesion molecules (ECM) important for cell-cell and cell-matrix interactions. These genes are represented on the Qiagen Human ECM panel, and in addition, all remaining collagen genes have been included. In patients with ET, COL1A1, COL1A2, COL3A1, COL4A2, COL4A5, LAMA2, LAMB1, MMP1, MMP7, MMP11, MMP12, MMP14, AND TIMP3 were among the 42 upregulated ECM genes (FDR<0.05). In patients with PV, 53 ECM genes were upregulated including COL1A1, COL1A2, COL3A1, COL4A2, LAMA2, LAMB1, MMP1, MMP7, MMP8, MMP9, MMP11, MMP12, MMP14, and TIMP3 (FDR<0.05). In PMF, COL1A2, COL3A1, COL4A2, COL4A5, LAMA2, MMP1, MMP8, MMP9, MMP14, and TIMP3 were among the 26 upregulated genes (FDR<0.05) (Table 1). 17, 14, and 13 ECM genes were significantly downregulated in ET, PV, and PMF, respectively (FDR<0.05) (data not shown). ITGA7, ITGB3, and MMP1 were significantly upregulated from ET over PV to PMF, whereas ITGAL, SPG7, and TGFBI were significantly downregulated from ET over PV to PMF. ADAMTS8, ADAMTS13, COL10A1, COL14A1, COL1A2, COL29A1, COL3A1, COL4A2, COL6A1, ITGA7, ITGB3, ITGB5, LAMA2, MMP1, MMP14, NCAM1, THBS2, and TIMP3 were significantly upregulated in both ET, PV, and PMF (FDR<0.05). COL4A3BP, COL6A2, ITGA4, ITGA5, ITGAL, ITGB1, PECAM1, SPG7, and TGFBI were significantly downregulated in both ET, PV, and PMF (FDR<0.05). In table 2a-b are shown the 10 most significantly up- and downregulated genes. Discussion and conclusions: Bone marrow fibrosis and endothelial proliferation in MPNs are elicited due to the release of fibrogenic and angiogenic growth factors primarily from hyperproliferating megakaryocytes. The connective tissue components of the bone marrow in MPNs include type III collagen, which is deposited in the early disease stages (ET/PV) as "reticulin fibrosis" being accompanied and substituted by mature Van Giesson positive collagen (type I collagen) in the advanced myelofibrosis stage. Increased endothelial cell proliferation is followed by the development of continuous sheets of basement membrane material beneath endothelial cells as assessed by increased deposition of type IV collagen and laminin. Using whole blood gene expression profiling, we provide evidence that abnormal extracellular matrix metabolism is reflected in the gene signature of peripheral blood cells from patients with MPNs. Further studies are needed to determine whether these changes represent local bone marrow fibrogenesis and/or systemic disease manifestations. Disclosures Hasselbalch: Novartis: Research Funding.
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Lipp, Sarah N., Kathryn R. Jacobson, David S. Hains, Andrew L. Schwarderer, and Sarah Calve. "3D Mapping Reveals a Complex and Transient Interstitial Matrix During Murine Kidney Development." Journal of the American Society of Nephrology 32, no. 7 (2021): 1649–65. http://dx.doi.org/10.1681/asn.2020081204.
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BackgroundThe extracellular matrix (ECM) is a network of proteins and glycosaminoglycans that provides structural and biochemical cues to cells. In the kidney, the ECM is critical for nephrogenesis; however, the dynamics of ECM composition and how it relates to 3D structure during development is unknown.MethodsUsing embryonic day 14.5 (E14.5), E18.5, postnatal day 3 (P3), and adult kidneys, we fractionated proteins based on differential solubilities, performed liquid chromatography–tandem mass spectrometry, and identified changes in ECM protein content (matrisome). Decellularized kidneys were stained for ECM proteins and imaged in 3D using confocal microscopy.ResultsWe observed an increase in interstitial ECM that connects the stromal mesenchyme to the basement membrane (TNXB, COL6A1, COL6A2, COL6A3) between the embryo and adult, and a transient elevation of interstitial matrix proteins (COL5A2, COL12A1, COL26A1, ELN, EMID1, FBN1, LTBP4, THSD4) at perinatal time points. Basement membrane proteins critical for metanephric induction (FRAS1, FREM2) were highest in abundance in the embryo, whereas proteins necessary for integrity of the glomerular basement membrane (COL4A3, COL4A4, COL4A5, LAMB2) were more abundant in the adult. 3D visualization revealed a complex interstitial matrix that dramatically changed over development, including the perinatal formation of fibrillar structures that appear to support the medullary rays.ConclusionBy correlating 3D ECM spatiotemporal organization with global protein abundance, we revealed novel changes in the interstitial matrix during kidney development. This new information regarding the ECM in developing kidneys offers the potential to inform the design of regenerative scaffolds that can guide nephrogenesis in vitro.
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Guo, Changgang, Ting Shao, Dadong Wei, et al. "Bioinformatic Identification of Potential Hub Genes in Muscle-Invasive Bladder Urothelial Carcinoma." Cell Transplantation 29 (January 1, 2020): 096368972096517. http://dx.doi.org/10.1177/0963689720965178.
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Despite aggressive treatment approaches, muscle-invasive bladder urothelial carcinoma (MIBC) patients still have a 50% chance of developing general incurable metastases. Therefore, there is an urgent need for candidate markers to enhance diagnosis and generate effective treatments for this disease. We evaluated four mRNA microarray datasets to find differences between non-MIBC (NMIBC) and MIBC tissues. Through a gene expression profile analysis via the Gene Expression Omnibus database, we identified 56 differentially expressed genes (DEGs). Enrichment analysis of gene ontology, Kyoto Encyclopedia of Genes and Genomes, and Reactome pathways revealed the interactions between these DEGs. Next, we established a protein-protein interaction network to determine the interrelationship between the DEGs and selected 10 hub genes accordingly. Bladder urothelial carcinoma (BLCA) patients with COL1A2, COL5A1, and COL5A2 alterations showed poor disease-free survival rates, while BLCA patients with COL1A1 and LUM alterations showed poor overall survival rates. Oncomine analysis of MIBC versus NMIBC tissues showed that COL1A1, COL5A2, COL1A2, and COL3A1 were consistently among the top 20 overexpressed genes in different studies. Using the TCGAportal, we noted that the high expression of each of the four genes led to shorter BLCA patient overall survival. It was evident that BLCA patients with an elevated high combined gene expression had significantly shorter overall survival and relapse-free survival than those with low combined gene expression using PROGgeneV2. Using Gene Expression Profiling Interactive Analysis, we noted that COL1A1, COL1A2, COL3A1, and COL5A2 were positively correlated with each other in BLCA. These genes are considered as clinically relevant genes, suggesting that they may play an important role in the carcinogenesis, development, invasion, and metastasis of MIBC. However, considering we adopted a bioinformatic approach, more research is crucial to confirm our results. Nonetheless, our findings may have important prospective clinical implementations.
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Simard, Mélissa, Alexe Grenier, Geneviève Rioux, et al. "Remodeling of the Dermal Extracellular Matrix in a Tissue-Engineered Psoriatic Skin Model by n-3 Polyunsaturated Fatty Acids." Biomedicines 10, no. 5 (2022): 1078. http://dx.doi.org/10.3390/biomedicines10051078.
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Psoriasis is an inflammatory skin disease mainly associated with an epidermal disorder. However, the involvement of the dermal extracellular matrix (ECM) composition in psoriasis is still poorly understood. This study aimed to investigate the expression of ECM components in psoriatic skin substitutes (PS−) compared with healthy skin substitutes (HS−), as well as the effect of an n-3 polyunsaturated fatty acid, namely α-linolenic acid (ALA), on the psoriatic dermal compartment (PSALA+). Liquid chromatography tandem mass spectrometry analyses revealed that the lipidome of PS− contained higher amounts of n-6 derived prostaglandins (PGE2) and lipoxygenase products (9-HODE and 15-HETE). ALA supplementation increased the levels of PGE3, 13-HOTrE, 15-HEPE, and 18-HEPE, and decreased the levels of PGE2, 15-HETE, and 9-HOPE compared with PS−, indicating that ALA modulates the dermal lipidome of psoriatic skin substitutes. Gene expression profiling showed that several genes encoding for different ECM proteins were overexpressed in PS− compared with HS−, namely COL1A1 (4.2-fold), COL1A2 (3-fold), COL3A1 (4.4-fold), COL4A1 (2.3-fold), COL4A2 (6.3-fold), COL5A1 (3.3-fold), COL5A2 (5.2-fold), and COL5A3 (4.6-fold). Moreover, the expression of collagen IV (Col IV), collagen VII (Col VII), and laminin was found to be increased in PS− compared with HS−, and to be restored with ALA (PSALA+) according to immunofluorescence staining, while only the collagen I to collagen III ratio was altered according to dot blot analyses. Linear regression analysis revealed several positive correlations, including Col III with 14-HDHA levels, fibronectin with 12-HETE and 15-HETE levels, the dermo-epidermal junction Col IV with PGF2α, 9-HODE, and 13-HODE levels, and laminin with levels of PGF2α, 9-HODE, 13-HODE, 5-HETE, 12-HETE, and 15-HETE. These results suggest that the ECM plays an underestimated role in the pathogenesis of psoriasis and that ALA supplementation can regulate the ECM composition.
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Danilo, Fabián Mejía Calderón, and A. Carretero Poblete Pedro. "Análisis de paisajes arqueológicos de cuenca visual (viewshed) en el sitio Puruhá de Collay." Arqueologia Iberoamericana 36 (November 17, 2017): 43–47. https://doi.org/10.5281/zenodo.1478266.
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El análisis de paisajes arqueológicos mediante la técnica de cuenca visual (<em>viewshed</em>) es una aplicación SIG que ha supuesto un punto de inflexión en el estudio de sitios arqueológicos mediante la arqueología del paisaje. En el caso de Ecuador, este tipo de estudios está en una fase incipiente. Para el caso que nos ocupa, surge como trabajo inicial para la realización de otros más específicos, como la distribución espacial de los sitios arqueológicos Puruhá en la región de Chimborazo. En este paso previo de la investigación, se ha pretendido corroborar la influencia del sitio ceremonial/ritual de Collay sobre otros sitios de su entorno y los alrededores de la ciudad de Riobamba, así como el acceso a fuentes de aprovisionamiento y rutas de acceso. ENGLISH: Archaeological Landscapes Analysis of Basin Viewshed at the Puruha Site of Collay. The study of archaeological landscapes using viewshed analysis is a GIS application that has been a turning point in the study of archaeological sites through landscape archaeology. In the case of Ecuador, this type of study is in an incipient phase. For the case that concerns us, it emerges as an initial work for the realization of more specific ones, such as the spatial distribution of Puruhá archaeological sites in the Chimborazo region. In this prior investigation step, we have attempted to corroborate the influence of the ceremonial/ritual site of Collay on other sites of its environment and the surroundings of the city of Riobamba, as well as access to supplies and access routes.
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Fang, Yang, Pingping Wang, Lin Xia, et al. "Aberrantly hydroxymethylated differentially expressed genes and the associated protein pathways in osteoarthritis." PeerJ 7 (February 25, 2019): e6425. http://dx.doi.org/10.7717/peerj.6425.
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Background The elderly population is at risk of osteoarthritis (OA), a common, multifactorial, degenerative joint disease. Environmental, genetic, and epigenetic (such as DNA hydroxymethylation) factors may be involved in the etiology, development, and pathogenesis of OA. Here, comprehensive bioinformatic analyses were used to identify aberrantly hydroxymethylated differentially expressed genes and pathways in osteoarthritis to determine the underlying molecular mechanisms of osteoarthritis and susceptibility-related genes for osteoarthritis inheritance. Methods Gene expression microarray data, mRNA expression profile data, and a whole genome 5hmC dataset were obtained from the Gene Expression Omnibus repository. Differentially expressed genes with abnormal hydroxymethylation were identified by MATCH function. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the genes differentially expressed in OA were performed using Metascape and the KOBAS online tool, respectively. The protein–protein interaction network was built using STRING and visualized in Cytoscape, and the modular analysis of the network was performed using the Molecular Complex Detection app. Results In total, 104 hyperhydroxymethylated highly expressed genes and 14 hypohydroxymethylated genes with low expression were identified. Gene ontology analyses indicated that the biological functions of hyperhydroxymethylated highly expressed genes included skeletal system development, ossification, and bone development; KEGG pathway analysis showed enrichment in protein digestion and absorption, extracellular matrix–receptor interaction, and focal adhesion. The top 10 hub genes in the protein–protein interaction network were COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL6A1, COL8A1, COL11A1, and COL24A1. All the aforementioned results are consistent with changes observed in OA. Conclusion After comprehensive bioinformatics analysis, we found aberrantly hydroxymethylated differentially expressed genes and pathways in OA. The top 10 hub genes may be useful hydroxymethylation analysis biomarkers to provide more accurate OA diagnoses and target genes for treatment of OA.
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Chen, Shixi, Ning Li, Fardous Mohammad Safiul Azam, et al. "Comparative transcriptome analysis of albino northern snakehead (Channa argus) reveals its various collagen-related DEGs in caudal fin cells." PLOS ONE 19, no. 12 (2024): e0315996. https://doi.org/10.1371/journal.pone.0315996.
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The albino northern snakehead (Channa argus) is an aquaculture species characterized by heritable albino body color, in contrast to the typical coloration. Additionally, there are gray- and golden-finned individuals, which exhibit distinct coloration in their caudal fins. We performed RNA-seq to profile the transcriptome of caudal fin tissues in albino gray-finned and golden-finned C. argus, contrasting these with normal morphs to elucidate the differences between the two groups. A total of 137,130 unigenes were identified in this study. Gene Ontology (GO) analysis showed that the identified DEGs were significantly enriched in cellular components related to cytoplasm. So far, 379 common DEGs have been identified in all three groups. Notably, we observed more DEGs in golden-finned individuals compared to gray-finned individuals. We also revealed that golden-finned individuals were enriched in collagen-related pathways compared with normal individuals. The enriched DEGs of collagen components include collagen I of COL1A1 and COL1A2, collagen II of COL2A1, collagen V of COL5A1 and COL5A2, collagen VI of COL6A1 and COL6A3, collagen IX of COL9A3, collagen X of COL10A1, collagen XI of COL11A2, collagen XII of COL12A1, collagen XVI of COL16A1, collagen XVIII of COL18A1 and decorin (DCN), all of which play a role in modulating the collagen matrix. In golden-finned albino fish, collagen-related genes were downregulated, suggesting that despite the abundance of collagen types in their caudal fin cells, gene expression was slightly limited. This work provides valuable genetic insights into collagen variation in albino C. argus, lays the foundation for research on collagen genes and is crucial for the development and utilization of fish-derived collagen as a biomaterial for tissue engineering and biomedical applications.
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Videman, Tapio, Janna Saarela, Jaakko Kaprio, et al. "DISC SIGNAL IS ASSOCIATED WITH POLYMORPHISMS IN AGC1, COL1A1, COL2A1, COL5A1, COL9A1, COL9A2, IL1A, IL18R1 AND IL18RAP GENES." Spine &NA; (August 2008): 106. http://dx.doi.org/10.1097/01.brs.0000320265.47947.91.
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Atmaja, Indah Sulistia Wardana, and Sutikno Sutikno. "Application of the Constructivism Model to Improve Vocabulary and Communication of Class III Students at SPF State Elementary School Number 104244 Jati Sari Lubuk Pakam, Deli Serdang District, School Year 2023-2024." International Journal of Educational Research Excellence (IJERE) 3, no. 1 (2024): 145–55. http://dx.doi.org/10.55299/ijere.v3i1.803.
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The purpose of this study is to (1) find out whether the application of Gagnon and Collay's constructivism model can increase the vocabulary of grade III students of UPT SPF State Elementary School Number 104244 Jati Sari Lubuk Pakam using newspaper media. (2) To find out there is an interaction between the application of Gagnon and Collay's constructivism model with vocabulary. (3). To find out whether the application of the constructivism model of Gagnon and Collay can improve public communication of grade III students of UPT SPF State Elementary School Number 104244 Jati Sari Lubuk Pakam by using newspaper media. (4) To find out there is an interaction between the application of Gagnon and Collay's constructivism model with public communication. The research design used in this study is quantitative research. The population in this study is the entire class III UPT SPF State Elementary School Number 104244 Jati Sari Lubuk Pakam. The data collection technique uses Test Essay and Observation techniques. The research found that the constructivism model of Gagnon and Collay could increase vocabulary in grade III students of UPT SPF SDN No 104244 Jati Sari using newspaper media. However, the null hypothesis (Ho) was accepted, meaning there was no interaction between the model and vocabulary. In public communication, the alternative hypothesis (Ha) was accepted, and the null hypothesis (Ho) was accepted, indicating no interaction between the model and public communication.
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Junkiert-Czarnecka, Anna, Maria Pilarska-Deltow, Aneta Bąk, et al. "Next-Generation Sequencing of Connective Tissue Genes in Patients with Classical Ehlers-Danlos Syndrome." Current Issues in Molecular Biology 44, no. 4 (2022): 1472–78. http://dx.doi.org/10.3390/cimb44040099.
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Background: Ehlers-Danlos syndrome (EDS) is a common non-inflammatory, congenital connective tissue disorder. Classical type (cEDS) EDS is one of the more common forms, typically caused by mutations in the COL5A1 and COL5A2 genes, though causative mutations in the COL1A1 gene have also been described. Material and methods: The study group included 59 patients of Polish origin, diagnosed with cEDS. The analysis was performed on genomic DNA (gDNA) with NGS technology, using an Illumina sequencer. Thirty-five genes related to connective tissue were investigated. The pathogenicity of the detected variants was assessed by VarSome. Results: The NGS of 35 genes revealed variants within the COL5A1, COL5A2, COL1A1, and COL1A2 genes for 30 of the 59 patients investigated. Our panel detected no sequence variations for the remaining 29 patients. Discussion: Next-generation sequencing, with an appropriate multigene panel, showed great potential to assist in the diagnosis of EDS and other connective tissue disorders. Our data also show that not all causative genes giving rise to cEDS have been elucidated yet.
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Konstantis, Georgios, Georgia Tsaousi, Chryssa Pourzitaki, et al. "Identification of Key Genes Associated with Tumor Microenvironment Infiltration and Survival in Gastric Adenocarcinoma via Bioinformatics Analysis." Cancers 16, no. 7 (2024): 1280. http://dx.doi.org/10.3390/cancers16071280.
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Objective: Gastric carcinoma (GC) is the fifth most commonly diagnosed cancer and the third leading cause of cancer-related deaths globally. The tumor microenvironment plays a significant role in the pathogenesis, prognosis, and response to immunotherapy. However, the immune-related molecular mechanisms underlying GC remain elusive. Bioinformatics analysis of the gene expression of GC and paracancerous healthy tissues from the same patient was performed to identify the key genes and signaling pathways, as well as their correlation to the infiltration of the tumor microenvironment (TME) by various immune cells related to GC development. Methods: We employed GSE19826, a gene expression profile from the Gene Expression Omnibus (GEO), for our analysis. Functional enrichment analysis of Differentially Expressed Genes (DEGs) was conducted using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes database. Results: Cytoscape software facilitated the identification of nine hub DEGs, namely, FN1, COL1A1, COL1A2, THBS2, COL3A1, COL5A1, APOE, SPP1, and BGN. Various network analysis algorithms were applied to determine their high connectivity. Among these hub genes, FN1, COL1A2, THBS2, COL3A1, COL5A1, and BGN were found to be associated with a poor prognosis for GC patients. Subsequent analysis using the TIMER database revealed the infiltration status of the TME concerning the overexpression of these six genes. Specifically, the abovementioned genes demonstrated direct correlations with cancer-associated fibroblasts, M1 and M2 macrophages, myeloid-derived suppressor cells, and activated dendritic cells. Conclusion: Our findings suggest that the identified hub genes, particularly BGN, FN1, COL1A2, THBS2, COL3A1, and COL5A1, play crucial roles in GC prognosis and TME cell infiltration. This comprehensive analysis enhances our understanding of the molecular mechanisms underlying GC development and may contribute to the identification of potential therapeutic targets and prognostic markers for GC patients.
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Dawood, Ali Adel. "Uneven Expression of 20 Human Papillomavirus Genes Associated with Oropharyngeal Carcinoma." Rambam Maimonides Medical Journal 14, no. 4 (2023): e0020. http://dx.doi.org/10.5041/rmmj.10508.
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Background: Human papillomavirus HPV is considered to be responsible for 95% of virus-related cancers in many organs. Oropharyngeal carcinoma (OC) is distinguished by the transformation of the healthy epithelium into precancerous cells. Aim: The current study sought to examine the uneven gene expression of 20 genes among those scanned by microarray for oropharyngeal cancer patients. Materials and Methods: GSE56142 dataset was extracted from the GEO in NCBI. 24 specimens were evaluated. Gene Ontology (GO), KEGG, and the protein-protein interaction (PPI) were used to depict the biological roles of the genes under investigation using types of software. Results: Six genes out of 20 in invasive patients had a binding correlation with high expression (PDGFRS, COL6A3, COL1A1, COL3A1, COL2A1, and COL4A1), and only two genes with low expression (CRCT1 and KRT78). The expression levels of 20 genes were examined between patients with OC and head and neck squamous cell carcinoma (HNSCC). The correlation coefficient between highly expressed genes was statistically significant at the p < 0.05 level. Conclusions: It is crucial to evaluate the high expression of particular genes as diagnostic tumor markers, particularly in the early stages.
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Caprara, Carlotta, Valentina Corradi, Matteo Rigato, et al. "ADPKD and Collagen Genes (COL4A3, COL4A4, COL4A5)." Journal of the American Society of Nephrology 34, no. 11S (2023): 943. http://dx.doi.org/10.1681/asn.20233411s1943b.
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Li, Jianxin, Xin Wang, Yinchun Wang, and Qingqiang Yang. "H19 promotes the gastric carcinogenesis by sponging miR-29a-3p: evidence from lncRNA–miRNA–mRNA network analysis." Epigenomics 12, no. 12 (2020): 989–1002. http://dx.doi.org/10.2217/epi-2020-0114.
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Aim: To identify novel competing endogenous RNA (ceRNA) network correlated with the prognosis of gastric cancer (GC) patients. Materials & methods: We systematically analyzed the aberrantly expressed genes in human GC to construct a ceRNA network by using multiple bioinformatic tools. Results: Aberrantly expressed mRNAs in GC were identified. By means of stepwise reverse prediction and validation from mRNA to lncRNA, a ceRNA network comprised of H19, miR-29a-3p, COL3A1, COL5A2, COL1A2 and COL4A1 was constructed, and all genes in the network are significantly correlated with the prognosis of GC patients. Conclusion: The present study successfully constructed a GC related ceRNA network, and provided potential targets for GC clinical treatment.
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Liu, Chuncheng, Lei Li, Mengxu Ge, et al. "Overexpression of miR-29 Leads to Myopathy that Resemble Pathology of Ullrich Congenital Muscular Dystrophy." Cells 8, no. 5 (2019): 459. http://dx.doi.org/10.3390/cells8050459.
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Ullrich congenital muscular dystrophy (UCMD) bring heavy burden to patients’ families and society. Because the incidence of this disease is very low, studies in patients are extremely limited. Animal models of this disease are indispensable. UCMD belongs to extracellular matrix-related diseases. However, the disease models constructed by knocking out some pathogenic genes of human, such as the Col6a1, Col6a2, or Col6a3 gene, of mice could not mimic UCMD. The purpose of this study is to construct a mouse model which can resemble the pathology of UCMD. miR-29 is closely related to extracellular matrix deposition of tissues and organs. To address this issue, we developed a mouse model for overexpression miR-29 using Tet-on system. In the muscle-specific miR-29ab1 cluster transgenic mice model, we found that mice exhibited dyskinesia, dyspnea, and spinal anomaly. The skeletal muscle was damaged and regenerated. At the same time, we clarify the molecular mechanism of the role of miR-29 in this process. Different from human, Col4a1 and Col4a2, target genes of miR-29, are the key pathogenic genes associating with these phenotypes. This mouse model simulates the human clinical and pathological characteristics of UCMD patients and is helpful for the subsequent research and treatment of UCMD.
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Christner, P. J., and S. Ayitey. "Extracellular matrix containing mutated fibrillin-1 (Fbn1) down regulates Col1a1, Col1a2, Col3a1, Col5a1, and Col5a2 mRNA levels in Tsk/+ and Tsk/Tsk embryonic fibroblasts." Amino Acids 30, no. 4 (2006): 445–51. http://dx.doi.org/10.1007/s00726-005-0265-y.
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Li, Ang, Ying-Xia Cui, Xing Lv, et al. "The COL4A3 and COL4A4 Digenic Mutations in cis Result in Benign Familial Hematuria in a Large Chinese Family." Cytogenetic and Genome Research 154, no. 3 (2018): 132–36. http://dx.doi.org/10.1159/000488163.
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Mutations in the COL4A5 gene result in X-linked Alport syndrome, homozygous or compound heterozygous mutations in COL4A3 or COL4A4 are responsible for autosomal recessive Alport syndrome, and heterozygous mutations in COL4A3 or COL4A4 cause autosomal dominant Alport syndrome or benign familial hematuria. Recently, the existence of a digenic inheritance in Alport syndrome has been demonstrated. We here report heterozygous COL4A3 and COL4A4 digenic mutations in cis responsible for benign familial hematuria. Using bioinformatics analyses and pedigree verification, we showed that COL4A4 c.1471C>T and COL4A3 c.3418 + 1G>T variants in cis are pathogenic and co-segregate with the benign familial hematuria. This result suggests that COL4A3 and COL4A4 digenic mutations in cis mimicking an autosomal dominant inheritance should be considered as a novel inheritance pattern of benign familial hematuria, although the disease-causing mechanism remains unknown.
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Asadi, Shahin, and Hossein Amjadi. "The Role of Genetic Mutations in Genes COL2A1, COL11A1, COL11A2, COL9A1, COL9A2, COL9A3 in Stickler Syndrome." Archives of Immunology and Allergy 3, no. 1 (2020): 18–24. http://dx.doi.org/10.22259/2639-1848.0301004.
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Wang, Xinrui, Wei Ren, Yongdong Peng, et al. "Elucidating the Role of Transcriptomic Networks and DNA Methylation in Collagen Deposition of Dezhou Donkey Skin." Animals 14, no. 8 (2024): 1222. http://dx.doi.org/10.3390/ani14081222.
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DNA methylation represents a predominant epigenetic modification with broad implications in various biological functions. Its role is particularly significant in the process of collagen deposition, a fundamental aspect of dermal development in donkeys. Despite its critical involvement, the mechanistic insights into how DNA methylation influences collagen deposition in donkey skin remain limited. In this study, we employed whole genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) to investigate the epigenetic landscape and gene expression profiles in the dorsal skin tissues of Dezhou donkeys across three developmental stages: embryonic (YD), juvenile (2-year-old, MD), and mature (8-year-old, OD). Our analysis identified numerous differentially methylated genes that play pivotal roles in skin collagen deposition and overall skin maturation, including but not limited to COL1A1, COL1A2, COL3A1, COL4A1, COL4A2, GLUL, SFRP2, FOSL1, SERPINE1, MMP1, MMP2, MMP9, and MMP13. Notably, we observed an inverse relationship between gene expression and DNA methylation proximal to transcription start sites (TSSs), whereas a direct correlation was detected in regions close to transcription termination sites (TTSs). Detailed bisulfite sequencing analyses of the COL1A1 promoter region revealed a low methylation status during the embryonic stage, correlating with elevated transcriptional activity and gene expression levels. Collectively, our findings elucidate key genetic markers associated with collagen deposition in the skin of Dezhou donkeys, underscoring the significant regulatory role of DNA methylation. This research work contributes to the foundational knowledge necessary for the genetic improvement and selective breeding of Dezhou donkeys, aiming to enhance skin quality attributes.
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Kononikhin, Alexey S., Natalia V. Zakharova, Viktoria A. Sergeeva, et al. "Differential Diagnosis of Preeclampsia Based on Urine Peptidome Features Revealed by High Resolution Mass Spectrometry." Diagnostics 10, no. 12 (2020): 1039. http://dx.doi.org/10.3390/diagnostics10121039.
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Preeclampsia (PE) is a severe pregnancy complication, which may be considered as a systemic response in the second half of pregnancy to physiological failures in the first trimester, and can lead to very serious consequences for the health of the mother and fetus. Since PE is often associated with proteinuria, urine proteomic assays may represent a powerful tool for timely diagnostics and appropriate management. High resolution mass spectrometry was applied for peptidome analysis of 127 urine samples of pregnant women with various hypertensive complications: normotensive controls (n = 17), chronic hypertension (n = 16), gestational hypertension (n = 15), mild PE (n = 25), severe PE (n = 25), and 29 patients with complicated diagnoses. Analysis revealed 3869 peptides, which mostly belong to 116 groups with overlapping sequences. A panel of 22 marker peptide groups reliably differentiating PE was created by multivariate statistics, and included 15 collagen groups (from COL1A1, COL3A1, COL2A1, COL4A4, COL5A1, and COL8A1), and single loci from alpha-1-antitrypsin, fibrinogen, membrane-associated progesterone receptor component 1, insulin, EMI domain-containing protein 1, lysine-specific demethylase 6B, and alpha-2-HS-glycoprotein each. ROC analysis of the created model resulted in 88% sensitivity, 96.8% specificity, and receiver operating characteristic curve (AUC) = 0.947. Obtained results confirm the high diagnostic potential of urinary peptidome profiling for pregnancy hypertensive disorders diagnostics.
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Zaitseva, Ekaterina L., Alla Y. Tokmakova, Iya A. Voronkova, Vasily M. Petrov, Anatoly N. Tiulpakov, and Marina V. Shestakova. "Genetic parameters of wound healing in patients with neuropatic diabetic foot ulcers." Diabetes mellitus 20, no. 5 (2017): 344–49. http://dx.doi.org/10.14341/dm9291.
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Background. Tissue repair processes are impaired in diabetic foot ulcers (DFUs). Previous research has shown that glycaemic control, cytokines and growth factors play an important role in wound healing. Emerging evidence also suggests that genes play a role via their regulation of cell proliferation, collagen synthesis and granulation tissue formation.
 Aim. To evaluate collagen genes expression in different stages of wound healing in patients with DFUs.
 Materials and methods. Prospective study included four patients with neuropathic DFUs after surgical debridement. Tissue samples were taken for morphological and genetic tests on days 0, 10 and 15 of local treatment to evaluate expression of collagen genes (i.e. COL1A1, COL1A2, COL3A1) and to perform morphological tests.
 Results. The present study confirmed that the size of wounds decreased by 8.8 7% after 10 days of local treatment and by 18.3 8% after 15 days of local treatment. According to histological examination of wound biopsies at day 10, all patients showed a tendency for lower levels of inflammatory infiltrate, increased number of fibroblast-like cells, presence of maturing granulation tissue and emergence of connective tissue fibres. After 15 days, we detected inflammatory infiltration in the wounds, despite the formation of mature granulation tissue. According to results of genetic analysis on day 10 of local wound treatment, we found a tendency for increased expression of collagen genes relative to the baseline: COL1A1 increased by 3.2 1.3 times, COL1A2 by 2.0 1.0 times and COL3A1 by 1.25 1.1 times. On day 15 of local treatment, in contrast, we found a tendency for decreased expression of COL1A1, COL1A2 and COL3A1 relative to the baseline (1.7 0.6, 2.5 2 and 20.0 3 times, respectively).
 Conclusions. The expression of collagen genes (COL1A1, COL1A2, COL3A1) is more pronounced in proliferation phase and is subsequently reduced towards the end. These data were confirmed by morphological study and clinical pictures.
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Savige, Judy, Beata S. Lipska-Zietkiewicz, Elizabeth Watson, et al. "Guidelines for Genetic Testing and Management of Alport Syndrome." Clinical Journal of the American Society of Nephrology 17, no. 1 (2021): 143–54. http://dx.doi.org/10.2215/cjn.04230321.
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Genetic testing for pathogenic COL4A3–5 variants is usually undertaken to investigate the cause of persistent hematuria, especially with a family history of hematuria or kidney function impairment. Alport syndrome experts now advocate genetic testing for persistent hematuria, even when a heterozygous pathogenic COL4A3 or COL4A4 is suspected, and cascade testing of their first-degree family members because of their risk of impaired kidney function. The experts recommend too that COL4A3 or COL4A4 heterozygotes do not act as kidney donors. Testing for variants in the COL4A3–COL4A5 genes should also be performed for persistent proteinuria and steroid-resistant nephrotic syndrome due to suspected inherited FSGS and for familial IgA glomerulonephritis and kidney failure of unknown cause.
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Shaffer, Peg. "Constructivist Learning Design: Key Questions for Teaching to Standards – By George W. Gagnon Jr. and Michelle Collay." Teaching Theology & Religion 11, no. 3 (2008): 167. http://dx.doi.org/10.1111/j.1467-9647.2008.00436.x.
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Nagel, Mato, Sylvia Nagorka, and Oliver Gross. "Novel COL4A5, COL4A4, and COL4A3 mutations in Alport syndrome." Human Mutation 26, no. 1 (2005): 60. http://dx.doi.org/10.1002/humu.9349.
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Changez, Mah I. Kan, Afsheen Nasir, Alexandra Sonsino, et al. "Genetic Overlap of Thoracic Aortic Aneurysms and Intracranial Aneurysms." Genes 16, no. 2 (2025): 154. https://doi.org/10.3390/genes16020154.
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Objective: Thoracic aortic aneurysms (TAAs) and intracranial aneurysms (ICAs) share overlapping genetic and pathophysiological mechanisms, yet the genetic interplay between these conditions remains insufficiently explored. This study aimed to identify common genetic factors underlying TAA and ICA. Methods: A comprehensive review of genome-wide association studies (GWASs) and retrospective clinical studies was conducted using PubMed, Orbis, and Web of Science. Articles addressing the genetic etiologies of TAA and ICA were analyzed. Separate lists of causative genes were compiled, and commonalities were identified. A Venn diagram was constructed to illustrate genetic overlap and shared physiological pathways. Results: We identified 24 overlapping genes associated with TAA and ICA, including LTBP2, TGFB2, TGFB3, TGFBR1, TGFBR2, SMAD2, SMAD3, COL1A2, COL3A1, COL4A1, COL5A1, COL5A2, FBN1, FBN2, ELN, LOX ACTA2, MYH11, MYLK, ABCC6, NOTCH1, MED12, PKD1, and PKD2. These genes are involved in pathways related to connective tissue biology, contractile elements, extracellular matrix components, and transforming growth factor-β signaling. While vascular endothelium and cell cycle pathways were unique to ICA, TAA pathways predominantly involved extracellular matrix remodeling. Conclusions: This study highlights the significant genetic overlap between TAA and ICA, shedding light on shared molecular mechanisms. These findings underscore the importance of interdisciplinary awareness: neurologists, neurosurgeons, and neurointerventional radiologists should monitor ICA patients for potential TAA, while cardiologists, cardiac surgeons, vascular surgeons, and vascular interventionalists should consider ICA risks in TAA patients. Further research into these genetic pathways could enhance the understanding and management of both conditions.
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Cao, Ling, Yan Chen, Miao Zhang, et al. "Identification of hub genes and potential molecular mechanisms in gastric cancer by integrated bioinformatics analysis." PeerJ 6 (July 2, 2018): e5180. http://dx.doi.org/10.7717/peerj.5180.
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Objective Gastric cancer (GC) is the fourth most common cause of cancer-related deaths in the world. In the current study, we aim to identify the hub genes and uncover the molecular mechanisms of GC. Methods The expression profiles of the genes and the miRNAs were extracted from the Gene Expression Omnibus database. The identification of the differentially expressed genes (DEGs), including miRNAs, was performed by the GEO2R. Database for Annotation, Visualization and Integrated Discovery was used to perform GO and KEGG pathway enrichment analysis. The protein–protein interaction (PPI) network and miRNA-gene network were constructed using Cytoscape software. The hub genes were identified by the Molecular Complex Detection (MCODE) plugin, the CytoHubba plugin and miRNA-gene network. Then, the identified genes were verified by Kaplan–Meier plotter database and quantitative real-time PCR (qRT-PCR) in GC tissue samples. Results A total of three mRNA expression profiles (GSE13911, GSE79973 and GSE19826) were downloaded from the Gene Expression Omnibus (GEO) database, including 69, 20 and 27cases separately. A total of 120 overlapped upregulated genes and 246 downregulated genes were identified. The majority of the DEGs were enriched in extracellular matrix organization, collagen catabolic process, collagen fibril organization and cell adhesion. In addition, three KEGG pathways were significantly enriched, including ECM-receptor interaction, protein digestion and absorption, and the focal adhesion pathways. In the PPI network, five significant modules were detected, while the genes in the modules were mainly involved in the ECM-receptor interaction and focal adhesion pathways. By combining the results of MCODE, CytoHubba and miRNA-gene network, a total of six hub genes including COL1A2, COL1A1, COL4A1, COL5A2, THBS2 and ITGA5 were chosen. The Kaplan–Meier plotter database confirmed that higher expression levels of these genes were related to lower overall survival, except for COL5A2. Experimental validation showed that the rest of the five genes had the same expression trend as predicted. Conclusion In conclusion, COL1A2, COL1A1, COL4A1, THBS2 and ITGA5 may be potential biomarkers and therapeutic targets for GC. Moreover, ECM-receptor interaction and focal adhesion pathways play significant roles in the progression of GC.
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Bulbul, Alpay, Erdal Ari, Necdet Apaydin, and Gokhan Ipekoglu. "The Impact of Genetic Polymorphisms on Anterior Cruciate Ligament Injuries in Athletes: A Meta-Analytical Approach." Biology 12, no. 12 (2023): 1526. http://dx.doi.org/10.3390/biology12121526.
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This meta-analysis aimed to investigate the association between genetic polymorphisms in Collagen type 1 alpha-1 (COL1A1), Collagen type 3 alpha-1 (COL3A1), Collagen type 5 alpha-1 (COL5A1), and Collagen type 12 alpha-1 (COL12A1) genes and anterior cruciate ligament (ACL) injuries in athletes. A systematic search was diligently conducted on the PubMed and Web of Science databases to identify relevant studies on 5–9 September 2023. Only case–control studies were included in the meta-analysis. A total of 19 studies were reviewed, involving the analysis of 3522 cases and 6399 control subjects. Data relevant to the study objectives were extracted from these chosen studies and subsequently analyzed using either a random-effects or fixed-effects model. It indicates that individuals carrying the G allele in the COL1A1 (rs1107946) gene have a decreased risk of anterior cruciate ligament injuries (OR: −0.27, 95% CI: −0.42 to −0.12, p < 0.001). A similar relationship was observed in the dominant model, but this relationship was reversed in the recessive model (OR: 0.69, 95% CI: 0.33 to 1.05, p < 0.001). However, no significant associations were found in the COL3A1 (rs1800255) and COL5A1 (rs12722) genes. In the COL12A1 (rs970547) gene, the A allele was associated with an increased risk of anterior cruciate ligament injuries (OR: 0.18, 95% CI: 0.01 to 0.36, p = 0.041). This meta-analysis suggests that genetic variants in COL1A1 (rs1107946) and COL12A1 (rs970547) may be associated with ACL injuries in athletes. However, COL3A1 rs1800255 and COL5A1 rs12722 gene variants do not appear to have a significant association with these injuries.
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Yao, Guorong, Kaiyue Zhao, Kaikai Bao, and Jing Li. "Radiation increases COL1A1, COL3A1, and COL1A2 expression in breast cancer." Open Medicine 17, no. 1 (2022): 329–40. http://dx.doi.org/10.1515/med-2022-0436.
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Abstract Background Radiotherapy-associated secondary cancer is an important issue for the treatment of breast cancer (BCa). This study aimed to investigate the molecular mechanism and genetic risk factors for radiation-associated secondary diseases in BCa. Methods The differentially expressed genes (DEGs) between preradiation and postradiation BCa samples in the GSE65505 dataset were obtained. The pathways related to the radiation-associated DEGs in the protein–protein interaction (PPI) network modules were identified. miRNAs targeted to the key genes in the PPI network were identified, and their association with BCa prognosis was analyzed. Results A total of 136 radiation-associated DEGs preradiation and postradiation BCa samples were screened out. The PPI network consisted of a significant module that consisted of 21 upregulated DEGs that were associated with “hsa04512: ECM–receptor interaction,” “hsa04151: PI3K-Akt signaling pathway,” and “hsa04115: p53 signaling pathway.” Sixteen DEGs, including three collagen genes collagen type I alpha 1 chain (COL1A1), COL3A1, and COL1A2, were enriched in 17 radiation-associated pathways. The three genes were upregulated in BCa tissues compared with controls and were also elevated by radiation. They were targeted by hsa-miR-29a/c, and the expression levels of hsa-miR-29a/c were associated with a poor prognosis of BCa. Conclusions The upregulation of COL1A1, COL3A1, and COL1A2 might be genetic risk factors for radiation-associated secondary diseases in BCa.
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Baumert, P., C. E. Stewart, M. J. Lake, B. Drust, and R. M. Erskine. "Variations of collagen-encoding genes are associated with exercise-induced muscle damage." Physiological Genomics 50, no. 9 (2018): 691–93. http://dx.doi.org/10.1152/physiolgenomics.00145.2017.
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We investigated whether single nucleotide polymorphisms (SNPs) within genes encoding the alpha-1 chain of type I ( COL1A1, rs2249492 ; rs1800012 ), type II ( COL2A1, rs2070739 ), and type V (COL5A1, rs12722 ) collagen were associated with the variable response to exercise-induced muscle damage (EIMD). Knee extensor muscle strength and soreness were assessed pre-, post-, and 48 h post-EIMD (120 maximal eccentric knee extensor contractions) in 65 young healthy participants, who were genotyped for the aforementioned SNPs. We found that COL1A1 (minor) T-allele carriers ( rs1800012 ) and (major) T-allele homozygotes ( rs2249492 ) were generally weaker ( P ≤ 0.019); and (minor) A-allele carriers of COL2A1 ( P = 0.002) and (major) T-allele carriers of COL5A1 ( P = 0.004) SNPs reported greater muscle soreness, all compared with their respective major ( rs1800012 ; rs2070739 ) and minor ( rs2249492 ; rs12722 ) allele homozygote counterparts. To conclude, the risk alleles of these four SNPs appear to negatively influence muscle strength and post-EIMD recovery, possibly via a dysregulated collagen network affecting the muscle’s mechanical properties.
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Savige, Judy, Helen Storey, Elizabeth Watson, et al. "Consensus statement on standards and guidelines for the molecular diagnostics of Alport syndrome: refining the ACMG criteria." European Journal of Human Genetics 29, no. 8 (2021): 1186–97. http://dx.doi.org/10.1038/s41431-021-00858-1.
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AbstractThe recent Chandos House meeting of the Alport Variant Collaborative extended the indications for screening for pathogenic variants in the COL4A5, COL4A3 and COL4A4 genes beyond the classical Alport phenotype (haematuria, renal failure; family history of haematuria or renal failure) to include persistent proteinuria, steroid-resistant nephrotic syndrome, focal and segmental glomerulosclerosis (FSGS), familial IgA glomerulonephritis and end-stage kidney failure without an obvious cause. The meeting refined the ACMG criteria for variant assessment for the Alport genes (COL4A3–5). It identified ‘mutational hotspots’ (PM1) in the collagen IV α5, α3 and α4 chains including position 1 Glycine residues in the Gly-X-Y repeats in the intermediate collagenous domains; and Cysteine residues in the carboxy non-collagenous domain (PP3). It considered that ‘well-established’ functional assays (PS3, BS3) were still mainly research tools but sequencing and minigene assays were commonly used to confirm splicing variants. It was not possible to define the Minor Allele Frequency (MAF) threshold above which variants were considered Benign (BA1, BS1), because of the different modes of inheritances of Alport syndrome, and the occurrence of hypomorphic variants (often Glycine adjacent to a non-collagenous interruption) and local founder effects. Heterozygous COL4A3 and COL4A4 variants were common ‘incidental’ findings also present in normal reference databases. The recognition and interpretation of hypomorphic variants in the COL4A3–COL4A5 genes remains a challenge.
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Henney, A. M., P. Tsipouras, R. C. Schwartz, A. H. Child, R. B. Devereux, and G. J. Leech. "Genetic evidence that mutations in the COL1A1, COL1A2, COL3A1, or COL5A2 collagen genes are not responsible for mitral valve prolapse." Heart 61, no. 3 (1989): 292–99. http://dx.doi.org/10.1136/hrt.61.3.292.
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Li, Ai, Yan Li, Yueyue Li, Mingming Zhang, Hong Zhang, and Feixue Chen. "Identification and validation of key genes associated with pathogenesis and prognosis of gastric cancer." PeerJ 11 (October 16, 2023): e16243. http://dx.doi.org/10.7717/peerj.16243.
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Background Gastric cancer (GC) is the fourth leading cause of cancer-related death worldwide. However, the precise mechanisms and specific biomarkers of GC have not been fully elucidated. We therefore sought to identify and validate the genes associated with GC. Methods RNA sequencing was performed on gastric tissue specimens from 10 cases each of non-atrophic gastritis (NAG), intestinal metaplasia (IM), and GC. Validation of gene expression was conducted through immunohistochemistry (IHC) staining. The Kaplan–Meier Plotter database was utilized to screen genes associated with prognosis, while protein–protein interaction analysis was conducted to identify hub genes. Results In GC-IM, the differentially expressed genes (DEGs) were predominantly enriched in pathways related to ECM-receptor interaction, focal adhesion, PI3K-Akt pathway, and pathways in cancer. Conversely, in IM-NAG, the DEGs were primarily enriched in pathways associated with fat digestion and absorption, pancreatic secretion, and retinol metabolism. IHC staining revealed elevated expression levels of KLK7 and KLK10 in GC. Specifically, KLK7 expression was found to be correlated with differentiation (P = 0.025) and depth of invasion (P = 0.007) in GC, while both KLK7 and KLK10 were associated with the overall survival (P < 0.05). Furthermore, a total of ten hub genes from DEGs in GC-NAG (COL6A2, COL1A1, COL4A1, COL1A2, SPARC, COL4A2, FN1, PCOLCE, SERPINH1, LAMB1) and five hub genes in IM-NAG (SI, DPP4, CLCA1, MEP1A, OLFM4) were demonstrated to have a significant correlation with the prognosis of GC. Conclusions The present study successfully identified and validated crucial genes associated with GC, providing valuable insights into the underlying mechanisms of this disease. The findings of this study have the potential to inform clinical practice.
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Gibson, Joel, Rachel Fieldhouse, Melanie M. Y. Chan, et al. "Prevalence Estimates of Predicted Pathogenic COL4A3–COL4A5 Variants in a Population Sequencing Database and Their Implications for Alport Syndrome." Journal of the American Society of Nephrology 32, no. 9 (2021): 2273–90. http://dx.doi.org/10.1681/asn.2020071065.
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BackgroundThe reported prevalence of Alport syndrome varies from one in 5000 to one in 53,000 individuals. This study estimated the frequencies of predicted pathogenic COL4A3–COL4A5 variants in sequencing databases of populations without known kidney disease.MethodsPredicted pathogenic variants were identified using filtering steps based on the ACMG/AMP criteria, which considered collagen IV α3–α5 position 1 Gly to be critical domains. The population frequencies of predicted pathogenic COL4A3–COL4A5 variants were then determined per mean number of sequenced alleles. Population frequencies for compound heterozygous and digenic combinations were calculated from the results for heterozygous variants.ResultsCOL4A3–COL4A5 variants resulting in position 1 Gly substitutions were confirmed to be associated with hematuria (for each, P<0.001). Predicted pathogenic COL4A5 variants were found in at least one in 2320 individuals. p.(Gly624Asp) represented nearly half (16 of 33, 48%) of the variants in Europeans. Most COL4A5 variants (54 of 59, 92%) had a biochemical feature that potentially mitigated the clinical effect. The predicted pathogenic heterozygous COL4A3 and COL4A4 variants affected one in 106 of the population, consistent with the finding of thin basement membrane nephropathy in normal donor kidney biopsy specimens. Predicted pathogenic compound heterozygous variants occurred in one in 88,866 individuals, and digenic variants in at least one in 44,793.ConclusionsThe population frequencies for Alport syndrome are suggested by the frequencies of predicted pathogenic COL4A3–COL4A5 variants, but must be adjusted for the disease penetrance of individual variants and for the likelihood of already diagnosed disease and non-Gly substitutions. Disease penetrance may depend on other genetic and environmental factors
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Vora, Hemangini Hasit. "Identification of Extra Cellular Matrix (ECM) Genes in Triple Negative Breast Cancer." Asian Pacific Journal of Cancer Biology 10, no. 2 (2025): 301–7. https://doi.org/10.31557/apjcb.2025.10.2.301-307.
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Introduction: Extracellular Matrix (ECM) is often abnormally produced, degraded, and remodelled, which creates a pro-tumorigenic environment in cancer and leads to tumor growth, angiogenesis, invasion and metastasis. This study aimed to investigate ECM genes by microarray-based transcriptome analysis and miRNA that target ECM genes in triple-negative breast cancer (TNBC). Materials and Methods: The current study evaluated 682 TME-related genes using Array Comparative Genomic Hybridization (aCGH) in 55 patients with TNBC. Results: 266 ECM genes were studied by transcriptome analysis, and it was observed that 132 ECM genes were up-regulated and 25 ECM genes were down-regulated in TNBC. Regarding upregulated genes, the majority of the genes were of Collagen family genes. Regarding downregulated genes, 14 genes were of Integrin family genes. PPI network analysis of upregulated genes using the STRING database, five hub genes identified were FN1, COL3A1, COL1A2, COL1A1, and COL6A2. Five of eight ranking methods identified FN1 and COL1A1 as the top most upregulated hub genes. The top 5 significant down-regulated hub genes were ITGB2, ITGAM, ITGAX, ITGB3, and ITGA4. Of 8 ranking methods, 7 ranking methods identified ITGB2, ITGAM and ITGAX as the most significant down-regulated hub genes. Further, target gene - miRNA regulatory networks using the miRTargetLink 2.0 tool. Conclusion: ECM genes FN1, COL1A1, ITGB2, ITGAM and ITGAX may be involved in disease progression in TNBC and, after validation, may be considered therapeutic targets for TNBC
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Liu, Chuncheng, Linan Liu, Jinlai Bo, et al. "Hypoxia-Induced Downregulation of miR-29 in Renal Tumor Cells Affects Collagen IV Subunit Expression through Multiple Sites." Biomedicines 10, no. 12 (2022): 3286. http://dx.doi.org/10.3390/biomedicines10123286.
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Multiple tumor exacerbations and treatment procedures, such as extracellular matrix remodeling, metabolic reprogramming, immunological evasion, and resistance to chemotherapy and radiotherapy, are influenced by intratumoral hypoxia. It is becoming increasingly clear how hypoxia interacts with the extracellular matrix and how this affects the growth of cancer. We analyzed the published sequencing results of hypoxia-stressed mouse kidney tumor cells and found that the expression of miR-29b was significantly downregulated. There are several sites that are complementary to the miR-29 seed sequence in the 3’ non-coding regions (3’UTRs) of various extracellular matrix-related genes, including collagen IV. We analyzed the sequences of the 3’UTRs of different subunits of collagen IV in different species and constructed the corresponding phylogenetic trees. We found that the 3’UTRs of Col4a1 and Col4a4 may have been subjected to particular evolutionary pressures. By cloning the 3’UTRs of collagen IV subunits into the psiCHECKTM-2 vector, we found that seven of the eight sites in the Col4a3–Col4a6 gene complementary to miR-29 were significantly repressed by miR-29a, b (except for the 7774–7781 of Col4a3 gene). The inhibitory efficiency of miR-29a, b on these seven sites was between 27% and 57%. The research on the regulation of miR-29 and extracellular matrix by hypoxia can provide a theoretical basis for tumor and fibrosis research and treatment.
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Rao, Dipti, Rutger J. Maas, Elisabeth A. Cornelissen, Jack F. Wetzels, and Michel van Geel. "Trigenic COL4A3/COL4A4/COL4A5 Pathogenic Variants in Alport Syndrome: A Case Report." Journal of the American Society of Nephrology 33, no. 11S (2022): 443–44. http://dx.doi.org/10.1681/asn.20223311s1443d.
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Wu, Weidan, and Linlin Zheng. "Comprehensive Analysis Identifies COL1A1, COL3A1, and POSTN as Key Genes Associated with Brain Metastasis in Patients with Breast Cancer." Evidence-Based Complementary and Alternative Medicine 2022 (August 12, 2022): 1–7. http://dx.doi.org/10.1155/2022/7812218.
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Objective. Brain metastasis (BM) is associated with a high mortality in patients with breast cancer (BC). Nevertheless, the molecular mechanisms of BM in BM remain uncertain. The study aims to identify the key genes in BC in relation to BM and to assess their prognostic value. Methods. Two microarray datasets GSE125989 and GSE100534 were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs) between primary BC and BM samples. The function enrichment analysis and protein-protein interaction (PPI) network were performed. We mapped hub genes into the Kaplan–Meier database for their correlations with BC survival. Results. Venn diagram analysis showed an overlapped upregulated DEG and 18 overlapped downregulated ones between primary BC and BM samples. We constructed the PPI network, and top 5 hub genes were sorted out according to the node degree, including type I collagen α1 chain (COL1A1), lumican (LUM), type III collagen α1 chain (COL3A1), type V collagen α2 chain (COL5A2), and periosteal protein (POSTN). The Kaplan–Meier database analysis found that COL1A1, COL3A1, and POSTN were significantly correlated with overall survival of BC patients. Conclusion. The study suggests that COL1A1, COL3A1, and POSTN may be key genes associated with BM in patients with BC.
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Khafid, Syaiful. "Pengembangan Desain Pembelajaran Geografi dengan Pendekatan Konstruktivistik." Jurnal Ilmiah Ilmu Sosial 5, no. 1 (2019): 01. http://dx.doi.org/10.23887/jiis.v5i1.18774.
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Tujuan penelitian pengembangan ini untuk menghasilkan desain pembelajaran geografi dengan pendekatan konstruktivistik meliputi: (1) model desain pembelajaran konstruktivistik (DPK), (2) rencana pelaksanaan pembelajaran (RPP), (3) bahan ajar geografi (BAG), (4) lembar kegiatan siswa (LKS), dan (5) lembar evaluasi belajar (LEB). Model penelitian pengembangan yang digunakan ialah R2D2, yaitu rekursif, desain, dan pengembangan. Model R2D2 memiliki tiga fokus yakni: (1) penetapan, (2) desain dan pengembangan, dan (3) desiminasi. Revisi model DPK di antaranya (1) ditambah uraian filsafat konstruktivisme dan filsafat pembelajaran konstruktivistik, dan (2) sintaks model DPK diadopsi dari model CLD Gagnon dan Collay. Revisi RPP antara lain: (1) dilengkapi lembar observasi aspek spiritual dan sosial, (2) skenario di RPP dibuat secara realistik, dan (3) tes uraian disertai kisi-kisi soal dan penskoran. Uji coba pembelajaran konstruktivistik berdasarkan hasil observasi aktivitas guru dan siswa di SMAN 1 Sidayu masing-masing mencapai 86,67%, sedangkan aktivitas guru di SMAN 1 Kebomas mencapai 100% dan aktivitas siswa mencapai 86,67%. Supaya proses dan hasil mencapai optimal, siswa harus menguasai prinsip belajar konstruktivistik dan peran guru sebagai motivator, fasilitator, dan konsultan. Perkembangan nilai tim dari 16 tim belajar sebanyak 14 tim belajar memperoleh rerata perkembangan nilai ≥ 25 dengan predikat super dan 2 tim belajar mendapatkan nilai berkisar 20-24 dengan predikat hebat. Respon mayoritas siswa terhadap pembelajaran konstruktivistik adalah menyenangkan.