Article
Cell & Tissue Engineering
Jingtao Guo, Enrique Sosa, Tsotne Chitiashvili, Xichen Nie, Ernesto Javier Rojas, Elizabeth Oliver, Kathrin Plath, James M. Hotaling, Jan-Bernd Stukenborg, Amander T. Clark, Bradley R. Cairns
Summary: This study provides insights into the complex changes in cell identity during human testis development in prenatal life, from the establishment of testicular cords to the transitioning of male primordial germ cells into cells resembling f0 spermatogonia. The analysis of single-cell transcriptomes reveals the coordinated and temporal development of embryonic, fetal, and postnatal male germline and somatic niche.
Article
Biochemical Research Methods
Jennifer Hammelman, Tulsi Patel, Michael Closser, Hynek Wichterle, David Gifford
Summary: This study compares nine computational methods for identifying reprogramming factors for cell differentiation. The researchers found that methods using chromatin accessibility performed the best, with an average identification rate of 50-60% of reprogramming factors in the top ten candidates. Among the chromatin accessibility methods, DeepAccess and diffTF showed the highest correlation with the ranked significance of transcription factor candidates. AME and diffTF were identified as optimal methods for transcription factor recovery, allowing for systematic prioritization of candidates in the design of new reprogramming protocols.
Article
Oncology
Isabel Gomez-Redondo, Benjamin Planells, Sebastian Canovas, Elena Ivanova, Gavin Kelsey, Alfonso Gutierrez-Adan
Summary: The study found that methylation reprogramming in pig germ cells follows the general dynamics shown in mice and humans, unveiling genomic elements that behave differently between male and female germ cells.
CLINICAL EPIGENETICS
(2021)
Article
Cell Biology
Xiaoju Guan, Panpan Chen, Minpeng Ji, Xin Wen, Dan Chen, Xingyi Zhao, Fu Huang, Jiexia Wang, Jingjing Shao, Jiajia Xie, Xingxing Zhao, Fenfen Chen, Jing Tian, Han Lin, Barry R. Zirkin, Ping Duan, Zhijian Su, Haolin Chen
Summary: In adult testis, stem Leydig cells (SLCs) could be involved in the regeneration of adult Leydig cells (ALCs). The proliferation and differentiation of SLCs are separately regulated, as indicated by the observation that cells proliferating after ALC loss were not the ones forming ALCs.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Physical
Yang Song, Jennifer Soto, Binru Chen, Tyler Hoffman, Weikang Zhao, Ninghao Zhu, Qin Peng, Longwei Liu, Chau Ly, Pak Kin Wong, Yingxiao Wang, Amy C. Rowat, Siavash K. Kurdistani, Song Li
Summary: Deformation of the cell nucleus boosts cell reprogramming and offers potential applications in cell engineering.
Article
Multidisciplinary Sciences
Frederik Oger, Maeva Moreno, Mehdi Derhourhi, Bryan Thiroux, Lionel Berberian, Cyril Bourouh, Emmanuelle Durand, Souhila Amanzougarene, Alaa Badreddine, Etienne Blanc, Olivier Molendi-Coste, Laurent Pineau, Gianni Pasquetti, Laure Rolland, Charlene Carney, Florine Bornaque, Emilie Courty, Celine Gheeraert, Jerome Eeckhoute, David Dombrowicz, Julie Kerr-Conte, Francois Pattou, Bart Staels, Philippe Froguel, Amelie Bonneford, Jean-Sebastien Annicotte
Summary: Histone deacetylase enzymes (HDACs) regulate gene expression by deacetylating specific histone and non-histone proteins. In this study, the researchers investigated the role of HDACs in maintaining the identity and function of insulin-producing beta cells in the pancreas. They found that HDAC inhibition altered the transcriptional program of beta cells and could lead to loss of their identity.
Article
Genetics & Heredity
Khaista Rahman, Muhammad Jamal, Xi Chen, Wei Zhou, Bin Yang, Yanyan Zou, Weize Xu, Yingying Lei, Chengchao Wu, Xiaojian Cao, Rohit Tyagi, Muhammad Ahsan Naeem, Da Lin, Zeshan Habib, Nan Peng, Zhen F. Fu, Gang Cao
Summary: In this study, the endogenous type III-A CRISPR/Cas10 system of M. tuberculosis was utilized for efficient gene editing and RNA interference. It was proven that this system can successfully and specifically knock in/out M. tuberculosis genes as confirmed by DNA high-throughput sequencing. Furthermore, genome-wide RNA interference screening was performed to identify M. tuberculosis genes regulating in vitro and intracellular growth. This system can be widely used for exploring the functional genomics of M. tuberculosis and facilitating the development of novel anti-TB drugs and vaccines.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Review
Biochemistry & Molecular Biology
Ryan L. McCarthy, Jingchao Zhang, Kenneth S. Zaret
Summary: Heterochromatin is a chromosomal region that contains repressive histone modifications and factors that compact the chromatin, thus limiting the binding of transcription factors and inhibiting gene activation and cell identity changes. While important for cell differentiation, heterochromatin presents challenges in cell reprogramming. Recent studies have shown that transient disruption of heterochromatin machinery can enhance reprogramming. This review discusses the establishment and maintenance of heterochromatin during development and explores how the regulation of H3K9me3 heterochromatin can improve our ability to direct cell identity changes.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Genetics & Heredity
Tsunetoshi Nakatani, Jiangwei Lin, Fei Ji, Andreas Ettinger, Julien Pontabry, Mikiko Tokoro, Luis Altamirano-Pacheco, Jonathan Fiorentino, Elmir Mahammadov, Yu Hatano, Capucine Van Rechem, Damayanti Chakraborty, Elias R. Ruiz-Morales, Paola Y. Arguello Pascualli, Antonio Scialdone, Kazuo Yamagata, Johnathan R. Whetstine, Ruslan Sadreyev, Maria-Elena Torres-Padilla
Summary: Totipotent cells in early mouse embryos and 2-cell-like cells have slow DNA replication fork speed. Slowing replication fork speed promotes the emergence of 2-cell-like cells and improves the efficiency of somatic cell nuclear transfer reprogramming and the formation of induced pluripotent stem cell colonies.
Article
Developmental Biology
Prim B. Singh, Assem Zhakupova
Summary: 'Age reprogramming' is a process that rejuvenates the molecular and cellular pathways of a cell without going through an embryonic stage. It helps to understand how to reverse aging while retaining cellular identity and function, which is beneficial for regenerative medicine.
Article
Biochemical Research Methods
Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek
Summary: TRTools is a Python library and suite of command line tools developed for filtering, merging and quality control of TR genotype files, utilizing an internal harmonization module to make it compatible with outputs from a wide range of TR genotypers.
Review
Oncology
Alma Jaqueline Heredia-Mendez, Gricelda Sanchez-Sanchez, Cesar Lopez-Camarillo
Summary: During the last century, 2D cell cultures have been commonly used to study cancer biology, drug discovery, genomics, and gene expression regulation. However, this approach has limitations in accurately reproducing the tumor microenvironment and cellular processes. To overcome these limitations, 3D cell cultures have been implemented to better mimic the biological and molecular features of tumors. This review discusses the application of different types of 3D cell culture models to characterize the epigenetic changes in cancer cells, particularly DNA methylation patterns, and the impact of microenvironmental factors on these changes.
Article
Multidisciplinary Sciences
Jing Wang, Cai Zhou, Shuai Gao, Xiuling Song, Xinyan Yang, Jiaqi Fan, Shaofang Ren, Linzi Ma, Jiexiang Zhao, Manman Cui, Ke Song, Mei Wang, Chaohui Li, Yi Zheng, Fang Luo, Kai Miao, Xiaochun Bai, Andrew P. Hutchins, Lin Li, Gang Chang, Xiao-Yang Zhao
Summary: Round spermatid injection (ROSI) technique shows promise for treating infertility in some men. However, the developmental potential of ROSI embryos is compromised and the mechanisms are not fully understood. This study explores the transcriptome, chromatin accessibility, and DNA methylation patterns of ROSI embryos derived from early-stage round spermatids using single-cell multiomics sequencing. It identifies reprogramming defects in ROSI embryos at the pronuclear stages, primarily associated with misexpression of a group of minor zygotic genome activation genes. The study also discovers a small compound, A366, that can improve the developmental potential of ROSI embryos by correcting epigenetic and transcriptomic states.
Article
Biochemistry & Molecular Biology
Monika Mokrzycka, Stefan Stojalowski, Miroslaw Tyrka, Przemyslaw Matysik, Barbara Zmijewska, Rafal Marcinkowski, Urszula Wozna-Pawlak, Roza Martofel, Michal Rokicki, Monika Rakoczy-Trojanowska, Pawel Krajewski
Summary: This study identified markers associated with wheat agronomic traits using genome-wide association analysis. The study also investigated the effects of markers on heterosis and their linkage disequilibrium grouping. The results revealed a large number of single nucleotide polymorphisms with significant effects, predominantly influencing protein translation modification. These findings provide valuable insights for developing new wheat varieties with desirable properties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Euxhen Hasanaj, Jingtao Wang, Arjun Sarathi, Jun Ding, Ziv Bar-Joseph
Summary: Cell type assignment is a major challenge in high throughput single cell data analysis. To address this issue, researchers have developed Cellar, a software tool that provides interactive support for cell type assignment and dataset comparison.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Karina A. Pena, Sofya Savransky, Breanna Lewis
Summary: Compartmentalization of GPCR signaling is an emerging topic that emphasizes the importance of spatial bias in signaling for physiological relevance. PTH1R was the first GPCR discovered to signal via cAMP from endosomes, challenging the conventional model of GPCR signaling. The location of cAMP generation determines the physiological outcomes of GPCR signaling.
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2024)
Article
Cell Biology
Cheng-Xu Ma, Xiao-Ni Ma, Jin-Jin Liu, Cong-Hui Guan, Ying-Dong Li, Nan Zhao, Didac Mauricio, Song-Bo Fu
Summary: The downregulation of primary cilia (PCs) due to BRAFV600E mutation contributes to the aggressiveness and lymph node metastasis of Papillary Thyroid Cancer (PTC).
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2024)
Article
Cell Biology
Kejun Wu, Cuihua Huang, Wenrong Zheng, Yubin Wu, Qintao Huang, Menghua Lin, Ruonan Gao, Liqin Qi, Guanlian He, Xiaoying Liu, Xiaohong Liu, Linxi Wang, Zhou Chen, Libin Liu
Summary: Recurrent non-severe hypoglycemia in patients with diabetes is associated with cognitive impairment. This study found that this condition is associated with reduced mitophagy in the hippocampus, leading to mitochondrial dysfunction and neurological impairment.
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2024)
Article
Cell Biology
Yifei Lv, Yizhou Huang, Huiyu Fan, Yunxiu Zhao, Linjuan Ma, Yibing Lan, Chunming Li, Peiqiong Chen, Zheng Lou, Jianhong Zhou
Summary: Before menopause, females have a lower incidence of cardiovascular disease than age-matched males, possibly due to the protective effects of sex hormones. 17 beta-E2 inhibits THBS1 expression, preventing cell senescence and apoptosis, and counteracts oxidative stress by suppressing the TGF-beta/Smad signaling pathway.
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2024)
Article
Cell Biology
Ana C. L. Camargo, Flavia B. Constantino, Sergio A. A. Santos, Ketlin T. Colombelli, Luiz M. F. Portela, Matheus N. Fioretto, Luisa A. Barata, Guilherme T. Valente, Carlos S. Moreno, Luis A. Justulin
Summary: This study examined the effects of maternal malnutrition on the transcriptomic landscape of the ventral prostate in rats. It found that changes in molecular pathways related to cellular development and tissue morphogenesis were associated with maternal malnutrition. The Abcg1 gene was found to be deregulated in both malnourished rats and prostate cancer models and patients.
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2024)
Article
Cell Biology
Sandra Romero-Cordoba, Mayel Chirinos, Nancy Noyola-Martinez, Nayeli Torres-Ramirez, Mitzi Garcia-Olivares, Juan Pablo Aragon-Hernandez, Ixchel Ramirez-Camacho, Rosa Zuniga, Fernando Larrea, Ali Halhali, David Barrera
Summary: This study analyzed the effects of calcitriol, TGF-131, and their combination on human trophoblast cells. The results showed that the combination treatment modified the transcriptional landscape and mainly affected the storage, activity, and metabolism of lipids, which may have an impact on placental development.
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2024)
Article
Cell Biology
Traver J. Wright, Richard B. Pyles, Melinda Sheffield-Moore, Rachel R. Deer, Kathleen M. Randolph, Kristen A. Mcgovern, Christopher P. Danesi, Charles R. Gilkison, Weston W. Ward, Jayson A. Vargas, Peyton A. Armstrong, Sarah E. Lindsay, Mohammed F. Zaidan, Justin Seashore, Tamara L. Wexler, Brent E. Masel, Randall J. Urban
Summary: This study investigates the persistent neurologic symptoms in COVID-19 patients after recovery and explores the association between these symptoms and disrupted growth hormone secretion and gastrointestinal discomfort.
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2024)
Article
Cell Biology
Li-Li Chen, Ya-Qin Li, Zhi-Hui Kang, Xuan Zhang, Su-Yan Gu, Na Wang, Xue-Yan Shen
Summary: Defects in trophoblastic EMT caused by dysregulation of circTNRC18's interaction with LIN28A play a vital role in the development of preeclampsia. LIN28A overexpression suppresses circTNRC18-mediated inhibition of trophoblast migration, invasion, and EMT, while LIN28A knockdown promotes them. Furthermore, circTNRC18 regulates the intracellular distribution of LIN28A and the expression of insulin-like growth factor II, affecting cell migration and invasion. Targeting the circTNRC18-LIN28A regulatory axis may provide a novel treatment approach for preeclampsia.
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2024)