Review
Biochemistry & Molecular Biology
Tapan Kumar Mohanta, Awdhesh Kumar Mishra, Ahmed Al-Harrasi
Summary: The genome is the most functional part of a cell and is organized in a compact three-dimensional structure. Despite TADs being major contributors to 3D genome organization, they are absent in Arabidopsis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Joachim Wolff, Rolf Backofen, Bjoern Gruening
Summary: The single-cell Hi-C clustering approach proposed in this study utilizes an approximate nearest neighbors method based on locality-sensitive hashing to reduce computational resources. It shows advantages in processing large-scale data compared to competitive methods.
Article
Biochemistry & Molecular Biology
Van Hovenga, Jugal Kalita, Oluwatosin Oluwadare
Summary: Chromosome conformation capture (3C) is a method for measuring chromosome topology and inferring 3D structure. The HiC-GNN method is proposed for predicting chromosome structure from Hi-C data with good generalization capability and prediction accuracy.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
David Vadnais, Oluwatosin Oluwadare
Summary: ParticleChromo3D+ is a containerized web-based genome structure reconstruction server/tool, which provides researchers with a portable and accurate tool for analyses via a graphical user interface (GUI). It saves time for researchers, eases usage pain points, and offloads computational processing/installation time.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Article
Genetics & Heredity
Brandon Collins, Oluwatosin Oluwadare, Philip Brown
Summary: With the advancement of Next Generation Sequencing and Hi-C experiments, high quality genome-wide contact data has become more accessible. The ChromeBat method based on the Bat Algorithm is proposed to solve the Chromosome and Genome Reconstruction problem using real Hi-C data with state-of-the-art performance. ChromeBat contributes algorithmic diversity to the field of Genome Reconstruction, providing an effective approach for solving the problem.
Article
Genetics & Heredity
Oleg Bylino, Airat N. Ibragimov, Anna E. Pravednikova, Yulii Shidlovskii
Summary: Chromosome conformation capture methods (C-methods) are important tools for analyzing the spatial interactions between DNA regions. Understanding the basic steps of the chromatin conformation capture procedure (3C) is crucial, and optimizing conditions for cell treatment can lead to more efficient experiments.
FRONTIERS IN GENETICS
(2021)
Review
Biochemistry & Molecular Biology
Robert S. Piecyk, Luca Schlegel, Frank Johannes
Summary: This article explores the application of Deep Learning models in gene regulation, analyzing their model accuracy, training strategies, and data preparation steps. It finds that transfer learning combined with functionally curated interactions is the most promising approach for learning cell-type specific sequence features in the future.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biology
Carolina Penaloza, Alejandro P. Gutierrez, Lel Eory, Shan Wang, Ximing Guo, Alan L. Archibald, Tim P. Bean, Ross D. Houston
Summary: A chromosome-level assembly for the Pacific oyster (C. gigas) was created and annotated, providing a valuable resource for genetics and genomics studies, as well as selective breeding in aquaculture.
Article
Oncology
Xiaoyu Huang, Yong Huang, Ping Li
Summary: This study investigated the impact of serum lipid levels on the treatment of epithelial ovarian cancer (EOC) patients receiving bevacizumab and developed a predictive model for prognosis. The study found that serum levels of total cholesterol, triglycerides, apolipoprotein A1, and free fatty acids significantly increased, while apolipoprotein B levels significantly decreased. Using machine learning, independent risk factors were identified and a predictive model for progression-free survival in EOC patients was constructed.
FRONTIERS IN ONCOLOGY
(2023)
Article
Mathematical & Computational Biology
David Vadnais, Michael Middleton, Oluwatosin Oluwadare
Summary: In this study, a novel approach called ParticleChromo3D is proposed for 3D chromosome and genome structure reconstruction from Hi-C data using Particle Swarm Optimization. Validation using multiple metrics shows that ParticleChromo3D produces more accurate results compared to existing algorithms and the constructed structures are highly consistent.
Article
Microbiology
Ignat V. Sonets, Nikita V. Dovidchenko, Sergey V. Ulianov, Maria S. Yarina, Stanislav I. Koshechkin, Sergey V. Razin, Larissa M. Krasnopolskaya, Alexander V. Tyakht
Summary: The complete genome sequence of G. lucidum strain 5.1 was obtained using high-throughput shotgun sequencing. The improved assembly process resulted in 12 chromosome-level scaffolds. Comprehensive annotation of the genome identified genes likely involved in polysaccharide biosynthesis. This study is important for elucidating the medicinal potential of Ganoderma species, discovering novel pharmaceutically valuable compounds, and understanding fungal genomic organization.
Article
Multidisciplinary Sciences
Martin Franke, Elisa De la Calle-Mustienes, Ana Neto, Maria Almuedo-Castillo, Lbai Irastorza-Azcarate, Rafael D. Acemel, Juan J. Tena, Jose M. Santos-Pereira, Jose L. Gomez-Skarmeta
Summary: CTCF plays a critical role in animal development by regulating three-dimensional chromatin structure and enhancer-promoter interactions, essential for controlling the expression of thousands of genes. The architectural protein CTCF mediates chromatin looping and is enriched at the boundaries of topologically associating domains (TADs), impacting gene regulation during development. Loss of CTCF leads to disrupted chromatin structure and affects the expression of developmental regulators, highlighting its essential role in providing structural context for enhancer-promoter interactions.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Luming Meng, Chenxi Wang, Yi Shi, Qiong Luo
Summary: There is a strong demand for methods that can efficiently reconstruct valid super-resolution intact genome 3D structures from sparse and noise single-cell Hi-C data. The authors developed the Single-Cell Chromosome Conformation Calculator (Si-C) within the Bayesian theory framework for this purpose, demonstrating its potential for visualizing and investigating interactions between all chromatin loci at the genome scale in individual cells. This method is essential in investigating chromosome folding and can reveal cell-to-cell varying domain structures and hyperfine structures in domains, such as loops.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Paul D. Waters, Hardip R. Patel, Aurora Ruiz-Herrera, Lucia Alvarez-Gonzalez, Nicholas C. Lister, Oleg Simakov, Tariq Ezaz, Parwinder Kaur, Celine Frere, Frank Gruetzner, Arthur Georges, Jennifer A. Marshall Graves
Summary: The study found that microchromosomes, as elements of an ancient animal genome, are highly conserved in birds and share synteny with certain small chromosomes in the chordate amphioxus. Turtles and squamates have independently lost microchromosomes through fusion events, resulting in different fusion patterns in different lineages. Microchromosomes are spatially separated into a central compartment in cells, showing higher interaction between microchromosomes compared to macrochromosomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Evolutionary Biology
Aryn P. Wilder, Olga Dudchenko, Caitlin Curry, Marisa Korody, Sheela P. Turbek, Mark Daly, Ann Misuraca, Gaojianyong Wang, Ruqayya Khan, David Weisz, Julie Fronczek, Erez Lieberman Aiden, Marlys L. Houck, Debra M. Shier, Oliver A. Ryder, Cynthia C. Steiner
Summary: High-quality reference genomes are essential for understanding population history and conserving biodiversity. In this study, a new genome assembly was generated for the federally endangered Pacific pocket mouse (PPM) using PacBio HiFi long reads, Omni-C and Hi-C data. The assembly revealed interesting features, such as a long heterochromatic region and variable heterozygosity across the genome. The study suggests recent inbreeding in a formerly large population. This reference genome will be valuable for future studies on outbreeding depression, inbreeding depression, and genetic load.
GENOME BIOLOGY AND EVOLUTION
(2022)
Editorial Material
Oncology
Masaya Yotsukura, Yuji Muraoka, Yukihiro Yoshida, Kazuo Nakagawa, Kouya Shiraishi, Takashi Kohno, Yasushi Yatabe, Shun-ichi Watanabe
ANNALS OF SURGICAL ONCOLOGY
(2023)
Article
Oncology
Zhuxuan Fu, Maria Mori Brooks, Sarah Irvin, Susan Jordan, Katja K. H. Aben, Hoda Anton-Culver, Elisa Bandera, Matthias W. Beckmann, Andrew Berchuck, Angela Brooks-Wilson, Jenny Chang-Claude, Linda S. Cook, Daniel W. Cramer, Kara L. Cushing-Haugen, Jennifer A. Doherty, Arif B. Ekici, Peter A. Fasching, Renee T. Fortner, Simon A. Gayther, Aleksandra Gentry-Maharaj, Graham G. Giles, Ellen L. Goode, Marc T. Goodman, Holly R. Harris, Alexander Hein, Rudolf Kaaks, Lambertus A. Kiemeney, Martin Koebel, Joanne Kotsopoulos, Nhu D. Le, Alice W. Lee, Keitaro Matsuo, Valerie McGuire, John R. McLaughlin, Usha Menon, Roger L. Milne, Kirsten B. Moysich, Celeste Leigh Pearce, Malcolm C. Pike, Bo Qin, Susan J. Ramus, Marjorie J. Riggan, Joseph H. Rothstein, Joellen M. Schildkraut, Weiva Sieh, Rebecca Sutphen, Kathryn L. Terry, Pamela J. Thompson, Linda Titus, Anne M. van Altena, Emily White, Alice S. Whittemore, Anna H. Wu, Wei Zheng, Argyrios Ziogas, Sarah E. Taylor, Lu Tang, Thomas Songer, Nicolas Wentzensen, Penelope M. Webb, Harvey A. Risch, Francesmary Modugno
Summary: The lifetime ovulatory years (LOY) are positively associated with nonmucinous epithelial ovarian cancer (EOC) risk, implicating factors beyond ovulation in the development of EOC. The protective effects of parity and oral contraceptive use may not solely depend on anovulation.
JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE
(2023)
Article
Dermatology
Catherine M. Olsen, Nirmala Pandeya, Jean Claude Dusingize, Rachel E. Neale, Stuart MacGregor, Matthew H. Law, David C. Whiteman
Summary: This cohort study compares the clinical characteristics of first and second melanomas and finds that individuals with second primary melanomas are more likely to have more nevi and higher genetic predisposition for melanoma compared to those with only one melanoma.
Article
Ophthalmology
Owen M. M. Siggs, Ayub Qassim, Xikun Han, Henry N. N. Marshall, Sean Mullany, Weixiong He, Emmanuelle Souzeau, Anna Galanopoulos, Ashish Agar, John Landers, Robert J. J. Casson, Alex W. W. Hewitt, Paul R. R. Healey, Stuart L. L. Graham, Stuart MacGregor, Jamie E. E. Craig
Summary: In this study, a high polygenic risk was associated with more rapid structural and functional progression in early POAG, despite more intensive treatment. A polygenic risk score may serve as a valuable adjunct to identify individuals who stand to benefit the most from more frequent surveillance and earlier or more intensive treatment.
JAMA OPHTHALMOLOGY
(2023)
Article
Oncology
Tomoharu Mori, Yusuke Okamoto, Anfeng Mu, Yoshimi Ide, Akiyo Yoshimura, Noriko Senda, Yukiko Inagaki-Kawata, Masahiro Kawashima, Hiroyuki Kitao, Eriko Tokunaga, Yasuo Miyoshi, Shozo Ohsumi, Koichiro Tsugawa, Tomohiko Ohta, Toyomasa Katagiri, Shigeru Ohtsuru, Kaoru Koike, Seishi Ogawa, Masakazu Toi, Hiroji Iwata, Seigo Nakamura, Keitaro Matsuo, Minoru Takata
Summary: The ALDH2 enzyme's ability to break down aldehydes is impaired by a specific gene polymorphism, leading to alcohol flushing and an increased risk of esophageal cancer in East Asians. Recent studies suggest that this gene variant may result in higher levels of DNA damage caused by naturally occurring aldehydes. However, in breast epithelial cells, this loss of function does not appear to have an impact on the initiation and development of cancer.
Letter
Oncology
Yu Okubo, Yasushi Yatabe
JOURNAL OF THORACIC ONCOLOGY
(2023)
Article
Oncology
Raphela A. Ranjan, Julienne K. Muenzner, Philipp Kunze, Carol I. Geppert, Matthias Ruebner, Hanna Huebner, Peter A. Fasching, Matthias W. Beckmann, Tobias Baeuerle, Arndt Hartmann, Wolfgang Walther, Markus Eckstein, Ramona Erber, Regine Schneider-Stock
Summary: The biological and growth characteristics of two breast cancer cell lines were investigated in a CAM model, and the results confirmed the known features of the breast cancer cell lines observed in vitro and in cells. The CAM model was found to be a reliable alternative for breast cancer research, reducing the need for murine animal experiments.
Article
Hematology
Marie Fredslund Breinholt, Lone Schejbel, Anne Ortved Gang, Torsten Holm Nielsen, Lars Moller Pedersen, Estrid Hogdall, Peter Norgaard
Summary: In this study, next generation sequencing (NGS) analysis was implemented in routine diagnostic work-up for B-cell non-Hodgkin's lymphoma (B-NHL). Mutations were detected in 94% of samples, and 50% of unclassified cases could be assigned a likely diagnostic subtype based on mutational findings. This gene sequencing approach provides potential diagnostic, prognostic, and predictive value for classification and risk-stratification of B-NHL.
EUROPEAN JOURNAL OF HAEMATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Federica Fabro, Trisha V. Kers, Kate J. Feller, Cecile Beerens, Ioannis Ntafoulis, Ahmed Idbaih, Maite Verreault, Kate Connor, Archita Biswas, Manuela Salvucci, Jochen H. M. Prehn, Annette T. Byrne, Alice C. O'Farrell, Diether Lambrechts, Gonca Dilcan, Francesca Lodi, Ingrid Arijs, Andreas Kremer, Romain Tching Chi Yen, Miao-Ping Chien, Martine L. M. Lamfers, Sieger Leenstra
Summary: Chemotherapy using temozolomide is the standard treatment for glioblastoma, but temozolomide resistance remains a challenge. This study reveals the association between resistance and heterogeneity in glioblastoma, and identifies distinct phenotypic behaviors and gene expressions in response to temozolomide. The adaptability and heterogeneity of glioblastoma cells contribute to their ability to survive and develop resistance mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Hagai Levi, Shai Carmi, Saharon Rosset, Rinat Yerushalmi, Aviad Zick, Tamar Yablonski-Peretz, Qin Wang, Manjeet K. Bolla, Joe Dennis, Kyriaki Michailidou, Michael Lush, Thomas Ahearn, Irene L. Andrulis, Hoda Anton-Culver, Antonis C. Antoniou, Volker Arndt, Annelie Augustinsson, Paivi Auvinen, Laura Beane Freeman, Matthias Beckmann, Sabine Behrens, Marina Bermisheva, Clara Bodelon, Natalia Bogdanova, Stig E. Bojesen, Hermann Brenner, Helen Byers, Nicola Camp, Jose Castelao, Jenny Chang-Claude, Maria-Dolores Chirlaque, Wendy Chung, Christine Clarke, Margriet J. Collee, Sarah Colonna, Fergus Couch, Angela Cox, Simon S. Cross, Kamila Czene, Mary Daly, Peter Devilee, Thilo Dork, Laure Dossus, Diana M. Eccles, A. Heather Eliassen, Mikael Eriksson, Gareth Evans, Peter Fasching, Olivia Fletcher, Henrik Flyger, Lin Fritschi, Marike Gabrielson, Manuela Gago-Dominguez, Montserrat Garcia-Closas, Jose Angel Garcia-Saenz, Jeanine Genkinger, Graham G. Giles, Mark Goldberg, Pascal Guenel, Per Hall, Ute Hamann, Wei He, Peter Hillemanns, Antoinette Hollestelle, Reiner Hoppe, John Hopper, Simona Jakovchevska, Anna Jakubowska, Helena Jernstrom, Esther John, Nichola Johnson, Michael Jones, Joseph Vijai, Rudolf Kaaks, Elza Khusnutdinova, Cari Kitahara, Stella Koutros, Vessela Kristensen, Allison W. Kurian, James Lacey, Diether Lambrechts, Loic Le Marchand, Flavio Lejbkowicz, Annika Lindblom, Sibylle Loibl, Adriana Lori, Jan Lubinski, Arto Mannermaa, Mehdi Manoochehri, Dimitrios Mavroudis, Usha Menon, AnnaMarie Mulligan, Rachel Murphy, Ines Nevelsteen, William G. Newman, Nadia Obi, Katie O'Brien, Ken Offit, Andrew Olshan, Dijana Plaseska-Karanfilska, Janet Olson, Salvatore Panico, Tjoung-Won Park-Simon, Alpa Patel, Paolo Peterlongo, Brigitte Rack, Paolo Radice, Gad Rennert, Valerie Rhenius, Atocha Romero, Emmanouil Saloustros, Dale Sandler, Marjanka K. Schmidt, Lukas Schwentner, Mitul Shah, Priyanka Sharma, Jacques Simard, Melissa Southey, Jennifer Stone, William J. Tapper, Jack Taylor, Lauren Teras, Amanda E. Toland, Melissa Troester, Therese Truong, Lizet E. van der Kolk, Clarice Weinberg, Camilla Wendt, Xiaohong Rose Yang, Wei Zheng, Argyrios Ziogas, Alison M. Dunning, Paul Pharoah, Douglas F. Easton, Shay Ben-Sachar, Naama Elefant, Ron Shamir, Ran Elkon
Summary: This study examined the performance of European-based breast cancer (BC) polygenic risk score (PRS) models in Ashkenazi Jewish (AJ) women. The results showed that the European-based PRS models can identify AJ women with significantly increased BC risk, offering potential improvement in BC risk assessment for this population.
JOURNAL OF MEDICAL GENETICS
(2023)
Article
Oncology
Simon Ezban Grutzmeier, Bojan Kovacevic, Peter Vilmann, Charlotte Vestrup Rift, Linea Cecilie Melchior, Morten Orebo Holmstrom, Lene Brink, Hazem Hassan, John Gasdal Karstensen, Hanne Grossjohann, Deepthi Chiranth, Anders Toxvaerd, Carsten Palnaes Hansen, Estrid Hogdall, Jane Preuss Hasselby, Pia Klausen
Summary: Pancreatic cancer is a devastating disease with a low survival rate. Patient-derived 3D cultures have shown promise for personalized treatment, but most models do not include supportive tissue cells. In this study, a co-culture model was created using cells from endoscopic biopsies, showing interaction between tumor and stromal cells. The study also highlights the need to include cancer-associated fibroblasts (CAFs) in models, as CAFs impact treatment response.
Article
Oncology
Michi Sawabe, Daisuke Kawakita, Isao Oze, Shinichi Iwasaki, Yasuhisa Hasegawa, Shingo Murakami, Hidemi Ito, Nobuhiro Hanai, Keitaro Matsuo
Summary: This study is the first to suggest an association between prediagnostic folate intake and head and neck squamous cell carcinoma (HNSCC) survival that differs based on fluorouracil (FU)-containing chemotherapy. In the FU-containing chemotherapy group, higher folate intake is associated with better overall survival, while no clear association is observed in the non-FU-containing chemotherapy group. This finding indicates that the folate status affects the heterogeneity of one-carbon metabolism in HNSCC.
Article
Cardiac & Cardiovascular Systems
Takaki Akamine, Kazuo Nakagawa, Kimiteru Ito, Hirokazu Watanabe, Masaya Yotsukura, Yukihiro Yoshida, Yasushi Yatabe, Masahiko Kusumoto, Shun-Ichi Watanabe
Summary: We evaluated the potential of preoperative fluorine-18-fluorodeoxyglucose positron emission tomography to predict invasive thymic epithelial tumours in patients with computed tomography-defined clinical stage I thymic epithelial tumours <5 cm in size who are generally considered to be candidates for minimally invasive approaches.
INTERDISCIPLINARY CARDIOVASCULAR AND THORACIC SURGERY
(2023)
Article
Medicine, Research & Experimental
Jelle Verhoeven, Kathryn A. Jacobs, Francesca Rizzollo, Francesca Lodi, Yichao Hua, Joanna Pozniak, Adhithya Narayanan Srinivasan, Diede Houbaert, Gautam Shankar, Sanket More, Marco B. Schaaf, Nikolina Dubroja Lakic, Maarten Ganne, Jochen Lamote, Johan Van Weyenbergh, Louis Boon, Oliver Bechter, Francesca Bosisio, Yasuo Uchiyama, Mathieu J. M. Bertrand, Jean Christophe Marine, Diether Lambrechts, Gabriele Bergers, Madhur Agrawal, Patrizia Agostinis
Summary: Autophagy in tumor endothelial cells plays a role in suppressing inflammatory responses and maintaining immunosuppression. The loss of autophagy in TECs enhances antitumor immunity by promoting infiltration and function of T-cells. The presence of an inflammatory TEC phenotype correlates with clinical responses to immunotherapy.
EMBO MOLECULAR MEDICINE
(2023)
Meeting Abstract
Oncology
Manuela Salvucci, Liam Poynter, Reza Mirnezami, Steven Carberry, Robert O'Byrne, James Alexander, Diether Lambrechts, Kirill Veselkov, James M. Kinross, Jochen Prehn
JOURNAL OF CLINICAL ONCOLOGY
(2023)