Article
Biochemistry & Molecular Biology
Chunjin Ke, Xuguang Liu, Jie Wan, Zhiquan Hu, Chunguang Yang
Summary: This study explores the application value of FISH in carcinoma of non-urothelial lineages (CNUL) for the first time. The results suggest that positive urine FISH tests not only indicate urothelial carcinoma (UC), but also CNUL. CNUL and UC show different genetic changes in FISH.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Entomology
Francisco Panzera, Angeles Cuadrado, Pablo Mora, Teresa Palomeque, Pedro Lorite, Sebastian Pita
Summary: This study analyzed the distribution of microsatellites in the holocentric chromosomes of Triatominae, which are vectors of Chagas disease. The results showed that there are differences in microsatellite distribution between Triatomini and Rhodniini species, with higher abundance and diversity in Triatomini. Additionally, a high abundance of GATA repeats was found in the Y chromosome of all Triatomini species, suggesting it is an ancestral trait specific to Triatomini.
Article
Oncology
Jing Feng, Ye Guo, Wenyu Yang, Yao Zou, Li Zhang, Yumei Chen, Yingchi Zhang, Xiaofan Zhu
Summary: CDKN2A/B deletions are associated with distinct characteristics in pediatric ALL, and serve as a poor prognostic factor, especially in carriers of TP53 deletions.
FRONTIERS IN ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Lauren S. Godwin, Joanna M. Bridger, Helen A. Foster
Summary: The DNA halo method uses high salt concentrations and nonionic detergents to generate DNA loops that remain anchored to structures within nuclei, providing increased resolution and facilitating physical mapping. This technique allows for studying genomic interactions with all the structures that the genome is anchored by, revealing gene loci, whole chromosomes, alpha satellite, telomeres, and even RNA. HALO-FISH provides insight into nuclear organization and function in normal cells and in disease progression such as with cancer.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Biochemistry & Molecular Biology
Dandan Wu, Namei Yang, Qian Xiang, Mingkun Zhu, Zhongyan Fang, Wen Zheng, Jiale Lu, Lina Sha, Xing Fan, Yiran Cheng, Yi Wang, Houyang Kang, Haiqin Zhang, Yonghong Zhou
Summary: This study investigated the chromosomes of the Pseudoroegneria libanotica and identified its characteristics and intraspecific polymorphism. The findings provide important information for the study of the evolution of the P. libanotica genome. The study also suggested the heterozygosity and adaptation as factors influencing the polymorphism in P. libanotica.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Alexei A. Sazanov, Anna L. Sazanova, Mikhail D. Nefedov, Darren K. Griffin, Michael N. Romanov
Summary: We investigated a pair of gametologous genes UBE2R2/UBE2R2L in the domestic chicken genome using bioinformatic, molecular, and cytogenetic techniques. By mapping these genes on the Gallus gallus W chromosome, we found their co-localization with the UBAP2L2 gene. Fine mapping of these genes also provided insights into comparative cytogenetics in birds. Our findings suggest that bird genomes undergo moderate changes during evolution and can be successfully used for interspecies hybridization using various techniques.
Article
Biochemical Research Methods
Jenny M. Vo-Phamhi, Kevin A. Yamauchi, Rafael Gomez-Sjoberg
Summary: This paper introduces an open-source toolkit and framework that incorporates crowdsourced and expert annotations as a source of ground truth for in situ transcriptomics image analysis. Through exploring and demonstrating the use of crowdsourced annotations for validating spot-calling algorithms and tuning parameters, it confirms that consensus crowdsourced annotations can substitute expert-generated ground truth. Advancements in in situ methods deepen our understanding of spatial organization in biological processes within tissues.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Environmental Sciences
Jianpeng Zhang, Jingyi Xie, Bo Liu, Zhiyong Wang, Yilei Wang, Yonghua Jiang, Jing Zhang, Mingyi Cai
Summary: This study demonstrated the use of BAC clones and FISH techniques to identify chromosomes in large yellow croaker and study chromosome evolution in related species. The results provided a set of chromosome-specific FISH probes that will be valuable for cytogenetics and genomics research in the family.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Microbiology
Jill Jasmine Dalimot, Ilka Mc Cormick Smith, Jasmin Gerkrath, Sylvia Hartmann, Oliver A. Cornely, Soo Chan Lee, Joseph Heitman, Volker Rickerts
Summary: This study focused on improving the accuracy of mucormycosis diagnosis from tissue samples using fluorescence in situ hybridization (FISH) targeting specific regions of fungal ribosomal RNA (rRNA) of Mucorales. While the probe combination showed success in targeting Mucorales and enhancing diagnosis, autofluorescence and variations in physiological states of fungi and antifungal therapy may impact the FISH signal obtained. Further studies are needed to determine the value of FISH in diagnosing mucormycosis from different clinical samples.
Review
Biochemistry & Molecular Biology
Yu-Sheng Wang, Jia Guo
Summary: The ability to quantify a large number of varied transcripts in single cells in their native spatial context is crucial for understanding health and disease, and recent advances in multiplexed FISH methods have enabled comprehensive RNA profiling in individual cells.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Pathology
Sudarat Ainthachot, Prakasit Sa-ngiamwibool, Malinee Thanee, Sasithorn Watcharadetwittaya, Yaovalux Chamgramol, Chawalit Pairojkul, Raksawan Deenonpoe
Summary: This study investigates the association between chromosomal aberrations, clinical data, and overall survival time in patients with cholangiocarcinoma (CCA). The results show that polysomy of chromosomes 3 and 7 is significantly associated with shorter survival time, and the presence of polysomy of chromosomes 3, 7, and 17 along with heterozygous loss of 9p21 is associated with even shorter survival time. Multivariate analysis identifies polysomy of chromosomes 3 and 7, as well as polysomy of chromosomes 3, 7, and 17 with heterozygous loss of 9p21, as independent predictive factors of poor overall survival in CCA patients.
Article
Chemistry, Multidisciplinary
Bowen Zhang, Taoran Tian, Dexuan Xiao, Shaojingya Gao, Xiaoxiao Cai, Yunfeng Lin
Summary: A DNA-enhanced HCR detection system (T-probe system) is introduced for the detection of cancer-related targets, demonstrating its versatility and efficiency by detecting miRNA-21 and nucleolin. The T-probe system shows high detection rate and rapid recognition of both membrane and intracellular cancer-related targets, and exhibits superior fluorescence for imaging tumor-related biomarkers in vitro and in vivo, indicating its great potential for clinical diagnosis and therapeutic applications.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Microbiology
Demosthenes P. Morales, Aaron J. Robinson, Andrew C. Pawlowski, Caitlyn Ark, Julia M. Kelliher, Pilar Junier, James H. Werner, Patrick S. G. Chain
Summary: This study evaluates the challenges in resolving bacterial-fungal interactions and proposes the use of fluorescence in situ hybridization (FISH) for microscopy imaging to obtain more conclusive evidence on the nature of specific relationships between bacteria and fungi.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Cell Biology
Lu Xiao, Joshua Labaer, Jia Guo
Summary: A high sensitivity and specificity multiplexed in situ RNA profiling approach was developed, allowing for successful analysis of multiple RNA species in various types of tissues through cycles of RNA staining, signal amplification, and probe stripping.
Article
Plant Sciences
Yahui Xuan, Sheng Wang, Siwei Li, Jianglian Yuan, Qiming Zhou, Ningjia He
Summary: This study used cGISH and self-GISH methods to investigate the chromosome constitution and genetic relationships of 40 mulberry accessions. Multiple homozygous and heterozygous signal patterns were discovered, and five mulberry sections and their genetic relationships were defined. These findings are important for guiding hybrid breeding of perennial crops like mulberry.
Article
Oncology
Katia Ramos Moreira Leite, Leonardo Lima Borges, Leopoldo Ribeiro Filho, Daher Chade, Rafael Ferreira Coelho, Mauricio Cordeiro, Miguel Srougi, Willian Carlos Nahas
Summary: This study found that the presence of divergent histological differentiation and the immunexpression of CAIX in muscle invasive urothelial carcinoma predict no response to cisplatin based neoadjuvant chemotherapy. These findings can be easily used in clinical practice to select patients for upfront surgery.
CLINICAL GENITOURINARY CANCER
(2022)
Article
Andrology
Amaro N. Duarte-Neto, Thiago A. Teixeira, Elia G. Caldini, Cristina T. Kanamura, Michele S. Gomes-Gouvea, Angela B. G. dos Santos, Renata A. A. Monteiro, Joao R. R. Pinho, Thais Mauad, Luiz F. F. da Silva, Paulo H. N. Saldiva, Marisa Dolhnikoff, Katia R. M. Leite, Jorge Hallak
Summary: Pathological findings in testes from fatal COVID-19 cases showed a combination of orchitis, vascular changes, basal membrane thickening, Leydig and Sertoli cell scarcity, and reduced spermatogenesis associated with local SARS-CoV-2 infection, which may impair hormonal function and fertility in men.
Article
Oncology
Gabriel Arantes dos Santos, Nayara I. Viana, Ruan Pimenta, Juliana Alves de Camargo, Vanessa R. Guimaraes, Poliana Romao, Patricia Candido, Vitoria Ghazarian, Sabrina T. Reis, Katia Ramos Moreira Leite, Miguel Srougi
Summary: This study investigates the role of the CST complex in various types of cancer and reveals its importance in genetic stability, nucleic acid metabolism, and immune regulation. The study identifies potential interactors, transcription factors, and microRNAs associated with CST, as well as drugs that may disrupt CST pathways.
Article
Medicine, General & Internal
Gustavo N. C. Inoue, Ruan Pimenta, Juliana A. Camargo, Nayara Viana, Vanessa R. Guimaraes, Miguel Srougi, William C. Nahas, Katia R. M. Leite, Sabrina T. Reis
Summary: The combination of spinal and general anesthesia may attenuate the suppression of innate tumor immunity and it may be related to a reduction in the neuroendocrine response to surgery.
ANNALS OF MEDICINE AND SURGERY
(2022)
Article
Biochemistry & Molecular Biology
Claudio B. Murta, Tatiane K. Furuya, Alexis G. M. Carrasco, Miyuki Uno, Laura Sichero, Luisa L. Villa, Sheila F. Faraj, Rafael F. Coelho, Giuliano B. Guglielmetti, Mauricio D. Cordeiro, Katia R. M. Leite, William C. Nahas, Roger Chammas, Jose Pontes
Summary: This study aimed to identify potential biomarkers for lymph node metastasis and prognosis in penile cancer (PeC). The study found miRNA and gene expression profiles associated with metastasis and prognosis, as well as revealed the disruption of mRNA-miRNA regulation during disease progression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Urology & Nephrology
Victor Srougi, Rodolfo Anisio Santana de Torres Bandeira, Sabrina Thalita Reis, Gabriel Arantes dos Santos, Hiury da Silva Andrade, Katia Ramos Moreira Leite, David Hamilton-Cho, Anuar Ibrahim Mitre, Marco Antonio Arap, Miguel Srougi, Ricardo Jordao Duarte
Summary: Patients with high ICC density experience significant improvement in hydronephrosis following pyeloplasty, but ICC density is not associated with functional outcomes.
Editorial Material
Urology & Nephrology
Kenneth A. Iczkowski, Mariel Molina, Lars Egevad, David G. Bostwick, Geert J. L. H. van Leenders, Francisco G. La Rosa, Theodorus van der Kwast, Daniel M. Berney, Andrew J. Evans, Thomas M. Wheeler, Katia R. M. Leite, Hemamali Samaratunga, John Srigley, Murali Varma, Toyonori Tsuzuki, Marshall Scott Lucia, Elward David Crawford, Richard G. Harris, Philip Stricker, Nathan Lawrentschuk, Henry H. Woo, Neil E. Fleshner, Neal D. Shore, John Yaxley, Ola Bratt, Peter Wiklund, Matthew Roberts, Liang Cheng, Brett Delahunt
Article
Pathology
Hemamali Samaratunga, Lars Egevad, Michelle Thunders, Kenneth A. Iczskowski, Theodorus van der Kwast, Glen Kristiansen, Chin-Chen Pan, Katia R. M. Leite, Andrew Evans, David Clouston, Diane N. Kenwright, Peter B. Bethwaite, Greg Malone, Simon Wood, John W. Yaxley, Brett Delahunt
Summary: The classification of malignant tumors is influenced by immunohistochemical and molecular genetic findings. Renal oncocytoma, a benign tumor, can occasionally exhibit malignant behavior as a variant called hybrid oncocytic chromophobe tumor. Two new entities, low-grade oncocytic tumor (LOT) and eosinophilic vacuolated tumor (EVT) with varying nuclear pleomorphism, have been proposed. The diagnosis of these apparently benign tumors is based on morphological, immunohistochemical features, and mutations in the mTOR pathway. However, the importance and specificity of these tumors are still debatable.
Article
Cell Biology
Lars Egevad, Brett Delahunt, Kenneth A. Iczkowski, Theo van der Kwast, Geert J. L. H. van Leenders, Katia R. M. Leite, Chin-Chen Pan, Hemamali Samaratunga, Toyonori Tsuzuki, Nita Mulliqi, Xiaoyi Ji, Henrik Olsson, Masi Valkonen, Pekka Ruusuvuori, Martin Eklund, Kimmo Kartasalo
Summary: There is evidence that cribriform morphology is associated with a worse prognosis for prostatic adenocarcinoma. This study aimed to investigate the reproducibility of cribriform cancer diagnosis in prostate needle biopsies. A panel of nine prostate pathology experts independently reviewed 304 digitised biopsies and achieved a 2/3 consensus diagnosis of cribriform and noncribriform cancer in 90% of the cases. Strict diagnostic criteria were used to identify cribriform patterns and generate a set of consensus cases for standardization.
Article
Surgery
Maira Suzuka Kudo, Vinicius Meneguette Gomes de Souza, Carmen Liane Neubarth Estivallet, Henrique Alves de Amorim, Fernando J. Kim, Katia Ramos Moreira Leite, Matheus Cardoso Moraes
Summary: The study utilized artificial intelligence methods to construct a CNN for classifying Gleason patterns with high accuracy. In the test phase, the true positive ratio between pathologist and computer method reached 85% to 96%. Precision, sensitivity, and specificity all reached up to 97%.
PATIENT SAFETY IN SURGERY
(2022)
Article
Biochemistry & Molecular Biology
Ruan Pimenta, Carolina Mie Mioshi, Guilherme L. Goncalves, Patricia Candido, Juliana A. Camargo, Vanessa R. Guimaraes, Caroline Chiovatto, Vitoria Ghazarian, Poliana Romao, Karina Serafim da Silva, Gabriel A. dos Santos, Iran A. Silva, Miguel Srougi, William C. Nahas, Katia R. Leite, Nayara I. Viana, Sabrina T. Reis
Summary: This study aimed to evaluate the suppressive effect of miR-137 in prostate cancer, regardless of diet-induced hypercholesterolemia. The results showed that miR-137 could inhibit the transcription and translation of the p160 family, SRC-1, SRC-2, and SRC-3, and indirectly reduce the expression of AR. It also inhibited cell migration and invasion, reduced proliferation, and increased apoptosis rates. In vivo experiments demonstrated that tumor growth was arrested after intratumoral restoration of miR-137, with a more significant response in the hypercholesterolemic group.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Isadora Oliveira Ansaloni Pereira, Glenda Nicioli da Silva, Tamires Cunha Almeida, Ana Paula Braga Lima, Andre Luiz Ventura Savio, Katia Ramos Moreira Leite, Daisy Maria Favero Salvadori
Summary: Long non-coding RNAs are frequently dysregulated and have been associated with carcinogenesis, aggressiveness, and chemoresistance in tumors. In this study, we investigated the combined expression of JHDM1D and JHDM1D-AS1 in bladder tumors, and found that it can distinguish between low-grade and high-grade tumors. We also discovered that silencing JHDM1D-AS1 can reduce the growth and proliferation of high-grade bladder tumor cells and increase their sensitivity to gemcitabine treatment.
Meeting Abstract
Oncology
Diogo Assed Bastos, Rafael Coelho, Leonardo Cardili, Felipe Galiza, Eder Nisi Ilario, Ublio Viana, Claudio Bovolenta Murta, Giuliano Guglielmetti, Mauricio Cordeiro, Jose Pontes, David Queiroz Borges Muniz, Jamile Almeida Silva, Jose Mauricio Mota, Guilherme Fialho De Freitas, Katia Ramos Moreira Leite, Carlos Alberto Buchpiguel, William Carlos Nahas
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Meeting Abstract
Urology & Nephrology
C. B. Murta, T. K. Furuya, M. Uno, A. G. M. Carrasco, L. Sichero, L. L. Villa, S. F. Faraj, R. F. Coelho, G. B. Guglielmetti, M. D. Cordeiro, K. R. M. Leite, W. C. Nahas, R. Chammas, Jr J. Pontes
Meeting Abstract
Urology & Nephrology
Vasconcelos F. Ordones, L. F. Takano De Araujo, L. F. Fornazieri, B. A. Olivetti Artioli, P. K. Roberto Kawano, J. L. Amaro, K. R. Leite