Article
Veterinary Sciences
Libin Chen, Jiayu Ruan, Yiyi Chen, Wenxuan Deng, Jinyu Lai, Lei Fan, Juncheng Cai, Chan Ding, Qiuyan Lin, Bin Xiang, Tao Ren
Summary: In this study, circRNA transcriptome sequencing was used to analyze the differences in circRNA expression profiles after velogenic NDV infection in chicken embryo fibroblasts (CEFs). The results showed that NDV infection altered circRNA expression profiles in CEFs and revealed significant enrichment of differentially expressed (DE) circRNAs for metabolism-related pathways. Further analysis and validation demonstrated that circRNAs are involved in NDV replication by regulating metabolism-related genes and miRNA. These findings provide new insights into the mechanisms underlying NDV-host interactions.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Gerhard Leinenga, Liviu-Gabriel Bodea, Jan Schroder, Giuzhi Sun, Yichen Zhou, Jae Song, Alexandra Grubman, Jose M. Polo, Jurgen Gotz
Summary: Transcranial scanning ultrasound combined with intravenously injected microbubbles can transiently open the blood-brain barrier and reduce amyloid-beta pathology in an Alzheimer's disease mouse model. The response of microglial cells to this treatment is complex and has potential applications for AD therapy.
BIOENGINEERING & TRANSLATIONAL MEDICINE
(2023)
Article
Dermatology
Ronghui Zhu, Xiaoyu Pan, Shangshang Wang, Zhuoqiong Qiu, Chaoying Gu, Xu Yao, Wei Li
Summary: This study used snRNA-seq and scRNA-seq in parallel to analyze skin cells, and found that snRNA-seq had advantages in avoiding contamination from mitochondrial and ribosomal RNA, and was able to better detect transcription factors. Through Slingshot analysis, snRNA-seq identified more spatially and functionally relevant keratinocyte clusters that exhibited expected differentiation dynamics.
JOURNAL OF DERMATOLOGICAL SCIENCE
(2023)
Article
Immunology
Peiru Wei, Mingyou Dong, Yin Bi, Saiqiong Chen, Weiyu Huang, Ting Li, Bo Liu, Xiaoqian Fu, Yihua Yang
Summary: The study identified 1293 macrophage marker genes through single-cell RNA sequencing analysis, and identified seven core genes closely related to recurrent miscarriage (RM) using various algorithms. A nomogram constructed from the expression levels of these genes showed high diagnostic value for RM, suggesting potential targets for preventative treatments.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medicine, Research & Experimental
Xueshu Chen, Wei Chen, Yan Zhao, Qinrong Wang, Wenling Wang, Yining Xiang, Hang Yuan, Yuan Xie, Jianjiang Zhou
Summary: The interaction between Helicobacter pylori, fibroblasts, and cancer cells induces the expression of Serpin E1, promoting the activation of normal fibroblasts to cancer-associated fibroblasts and gastric carcinogenesis.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Environmental Sciences
Chuanxin Zhang, Xueqi Dong, Xiaoyu Yin, Xinyi Yuan, Jiawei Wang, Jinzhu Song, Zhenzhen Hou, Cheng Li, Keliang Wu
Summary: 2-bromoacetamide (BAcAm), a new class of disinfection by-products (DBPs), is commonly found in drinking water worldwide. The high cytogenetic toxicity of BAcAm has raised concerns about its toxic effects on early embryonic development. In this study, we developed an optimized in vitro culture (IVC) system for peri-and early post-implantation mouse embryos and used it to assess the developmental toxicity of BAcAm. We observed that exposure to BAcAm led to a decrease in egg cylinder formation rate and aberrant lineage differentiation in a dose-dependent manner. Transcriptomic analysis further revealed that BAcAm exposure during early developmental stages affected the abundance of transcripts related to various biological processes, indicating its toxic effects on embryonic development. Therefore, this study provides a robust tool for studying the toxicology of chemicals during early embryonic development and highlights the developmental toxicity of BAcAm in mammals.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Multidisciplinary Sciences
Weijun Jiang, Jiajia Shi, Jingjie Zhao, Qiu Wang, Dan Cong, Fenghua Chen, Yu Zhang, Yuhan Liu, Junzheng Zhao, Qian Chen, Linhao Gu, Wenjia Zhou, Chenhang Wang, Zhaoyuan Fang, Shuhui Geng, Wei Xie, Luo-Nan Chen, Yang Yang, Yun Bai, Haodong Lin, Xiajun Li
Summary: ZFP57 is a master regulator of genomic imprinting, which controls the expression of target imprinted genes by maintaining differential DNA methylation at ICRs. Mutations in Zfp57 lead to allelic expression switches in target imprinted genes and genes associated with the NOTCH signaling pathway.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Chia-Ching Chang, Min-Shu Hsieh, Mong-Wei Lin, Yi-Hsuan Lee, Yi-Jing Hsiao, Kang-Yi Su, Te-Jen Su, Sung-Liang Yu, Jin-Shing Chen
Summary: This study established a novel three-gene prognostic signature for predicting the clinical outcomes of lung adenocarcinoma by comparing differences in gene expression profiles between low- and high-grade adenocarcinomas.
Article
Clinical Neurology
Dulika Sumathipala, Petter Stromme, Zohreh Fattahi, Torben Luders, Ying Sheng, Kimia Kahrizi, Ingunn Holm Einarsen, Jennifer L. Sloan, Hossein Najmabadi, Lambert van den Heuvel, Ron A. Wevers, Sergio Guerrero-Castillo, Lars Morkrid, Vassili Valayannopoulos, Paul Hoff Backe, Charles P. Venditti, Clara D. van Karnebeek, Hilde Nilsen, Eirik Frengen, Doriana Misceo
Summary: Mutations in the ZBTB11 gene are associated with intellectual disability. The study found that patients with ZBTB11 mutations showed atrophy in multiple brain regions and had malonic and methylmalonic aciduria as disease markers. In vitro experiments indicated that ZBTB11 regulates mitochondrial functions and RNA processing.
Article
Plant Sciences
Xiaomei Dong, Haishan Luo, Wenjing Bi, Hanyu Chen, Shuai Yu, Xiaoyu Zhang, Yuxin Dai, Xipeng Cheng, Yupeng Xing, Xiaoqin Fan, Yanbin Zhu, Yanling Guo, Dexuan Meng
Summary: This study identified a large number of allele-specific imprinted genes in maize hybrids, which are involved in intercellular nutrient transport, signaling pathways, and transcriptional regulation of kernel development. Mutations and overexpression of one ASIG were shown to affect the length and width of kernels, highlighting the importance of ASIGs in optimizing seed traits in crop plants.
Article
Biochemistry & Molecular Biology
Magdalena Grill, Isaac Lazzeri, Andrijana Kirsch, Nina Steurer, Tanja Grossmann, Michael Karbiener, Ellen Heitzer, Markus Gugatschka
Summary: Reinke's edema is a voice disorder associated with smoking and voice abuse, characterized by changes in vocal fold fibroblasts. Differential expression analysis between RE and control VFF revealed upregulated genes and pathways involved in extracellular matrix remodeling, inflammation, and fibrosis, while downregulated genes and pathways were associated with ECM degradation, cell cycle control, and proliferation.
Article
Genetics & Heredity
Zhe Zhao, Wenqi Li, LiMeng Zhu, Bei Xu, Yudong Jiang, Nan Ma, LiQun Liu, Jie Qiu, Min Zhang
Summary: This study investigated the role of cancer-associated fibroblasts (CAFs) in colon cancer progression using single-cell RNA sequencing. The study identified differentially expressed genes (DEGs) in various subsets of CAFs and demonstrated the prognostic value of these subsets in colon cancer. The study also revealed the interaction between CAFs and immune cells as an important factor affecting immune score and prognosis. Additionally, the study explored the differential response to anti-cancer drugs and immunotherapy in low-risk and high-risk patients predicted by the CAF-related model.
FRONTIERS IN GENETICS
(2022)
Article
Cell Biology
Ryohei Yoshitake, Gregory Chang, Kohei Saeki, Desiree Ha, Xiwei Wu, Jinhui Wang, Shiuan Chen
Summary: Through single-cell RNA sequencing analysis, two major types of mouse mammary gland fibroblasts were identified, each exhibiting unique functional characteristics and distinct localization. Estrogen was found to alter gene expression profiles of fibroblasts in a population-specific manner, without distinct activation of estrogen receptor signaling. Integrative analysis with other datasets revealed directional differentiation among mammary gland fibroblast populations, and potential interactions between epithelial cells and fibroblasts in mammary glands were inferred based on the mouse mammary epithelium atlas.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Oncology
Daeseung Kim, Jeong Seon Kim, Inyoung Cheon, Seo Ree Kim, Sang Hoon Chun, Jae Jun Kim, Sieun Lee, Jung Sook Yoon, Soon Auck Hong, Hye Sung Won, Keunsoo Kang, Young-Ho Ahn, Yoon Ho Ko
Summary: By using single-cell RNA sequencing, this study identified several subpopulations of cancer-associated fibroblasts (CAFs) in lung adenocarcinoma with distinct gene expression patterns and functional characteristics. Some of these subpopulations may serve as potential therapeutic targets for lung cancer treatment.
Article
Biochemistry & Molecular Biology
Yi Yang, Jia-Peng He, Ji-Long Liu
Summary: The research team generated a single-cell transcriptomic atlas of embryo implantation sites in mice, identifying global gene expression changes associated with embryo implantation. They predicted signaling interactions between uterine luminal epithelial cells and mural trophectoderm of blastocysts, as well as between uterine epithelial-stromal crosstalk at implantation sites.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Ji Liao, Tie-Bo Zeng, Nicholas Pierce, Diana A. Tran, Purnima Singh, Jeffrey R. Mann, Piroska E. Szabo
Summary: BWS and SRS are imprinting disorders related to misexpression of IGF2, and prenatal diagnosis and intervention targeting IGF2 can prevent these conditions. Studies using mouse models demonstrate that normalizing IGF2 levels can correct fetal overgrowth and growth retardation.
Article
Genetics & Heredity
Tie-Bo Zeng, Nicholas Pierce, Ji Liao, Piroska E. Szabo
Summary: The study revealed that EHMT2 plays a crucial role in repressing the maternal allele in noncanonical imprinting, particularly related to the derepression of ERVK promoters. Loss of DNA methylation in Ehmt2(-/-) embryos was associated with biallelic derepression of ERVK promoters.
Article
Genetics & Heredity
Tie-Bo Zeng, Nicholas Pierce, Ji Liao, Purnima Singh, Kin Lau, Wanding Zhou, Piroska E. Szabo
Summary: EHMT2 plays a regulatory role in suppressing transcriptional and developmental variation during the transition between gastrulation and organ specification in embryos, particularly at the six-somite stage.
Article
Pediatrics
Wendy Landier, Smita Bhatia, F. Lennie Wong, Jocelyn M. York, Jessica S. Flynn, Harrison M. Henneberg, Purnima Singh, Kandice Adams, Karen Wasilewski-Masker, Brooke Cherven, Rama Jasty-Rao, Marcia Leonard, James A. Connelly, Saro H. Armenian, Leslie L. Robison, Anna R. Giuliano, Melissa M. Hudson, James L. Klosky
Summary: This study aimed to evaluate the immunogenicity and safety of HPV vaccine in young cancer survivors. The results showed that the three-dose series of HPV vaccine had similar immunogenicity and safety in cancer survivors compared to the general population, providing evidence for its use in this vulnerable population.
LANCET CHILD & ADOLESCENT HEALTH
(2022)
Article
Biophysics
Noha Sharafeldin, Jianqing Zhang, Purnima Singh, Alysia Bosworth, Yanjun Chen, Sunita K. Patel, Xuexia Wang, Liton Francisco, Stephen J. Forman, F. Lennie Wong, Akinyemi Ojesina, Smita Bhatia
Summary: The study suggests that genome-wide significant SNPs may be associated with cognitive impairment in BMT recipients. The construction of a weighted genome-wide polygenic risk score allows for the prediction of cognitive impairment risk.
BONE MARROW TRANSPLANTATION
(2022)
Article
Cell Biology
Yingying Meng, Guliang Wang, Hongjuan He, Kin H. Lau, Allison Hurt, Brianna J. Bixler, Andrea Parham, Seung-Gi Jin, Xingzhi Xu, Karen M. Vasquez, Gerd P. Pfeifer, Piroska E. Szabo
Summary: A biological process that erases Z-DNA specifically in germ cells of the mouse male foetus has been discovered, which is mediated by a previously uncharacterized zinc finger protein, ZBTB43. This process prevents DNA double-strand breaks and promotes de novo DNA methylation, ensuring genomic and epigenomic integrity.
NATURE CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Seung-Gi Jin, Yingying Meng, Jennifer Johnson, Piroska E. Szabo, Gerd P. Pfeifer
Summary: This study provides detailed analysis of two types of oxidative DNA damage and its association with inflammation and cancer. The results show that the occurrence of oxidized guanines and oxidized thymines is dependent on specific DNA sequences and may lead to cancer-related mutations.
Article
Oncology
Xuexia Wang, Purnima Singh, Liting Zhou, Noha Sharafeldin, Wendy Landier, Lindsey Hageman, Paul Burridge, Yutaka Yasui, Yadav Sapkota, Javier G. G. Blanco, Kevin C. C. Oeffinger, Melissa M. M. Hudson, Eric J. J. Chow, Saro H. H. Armenian, Joseph P. P. Neglia, A. Kim Ritchey, Douglas S. S. Hawkins, Jill P. P. Ginsberg, Leslie L. L. Robison, Gregory T. T. Armstrong, Smita Bhatia
Summary: This study identified genetic variants associated with anthracycline-related cardiomyopathy using two independent study cohorts. Two single-nucleotide polymorphisms (SNPs), rs17736312 (ROBO2) and rs113230990 (near a CCCTC-binding factor insulator), showed significant gene-environment interaction effect on anthracycline-related cardiomyopathy in the discovery cohort and rs17736312 was successfully replicated in the replication cohort. The study also identified gene-gene interaction and independent effects of TGF-beta 1 and ROBO2 on heart failure.
JOURNAL OF CLINICAL ONCOLOGY
(2023)
Editorial Material
Genetics & Heredity
Gerd P. Pfeifer, Piroska E. Szabo
Article
Oncology
Purnima Singh, David K. Crossman, Liting Zhou, Xuexia Wang, Noha Sharafeldin, Lindsey Hageman, Javier G. Blanco, Paul W. Burridge, Saro H. Armenian, Frank M. Balis, Douglas S. Hawkins, Frank G. Keller, Melissa M. Hudson, Joseph P. Neglia, A. Kim Ritchey, Jill P. Ginsberg, Wendy Landier, Smita Bhatia
Summary: A novel association between the haptoglobin 2 (HP2) allele and cardiomyopathy was discovered. Higher expression of the HP gene is associated with an increased risk of developing cardiomyopathy. The binding of HP to free hemoglobin prevents oxidative damage, providing a mechanistic basis for this observation.
JACC: CARDIOONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Purnima Singh, Liting Zhou, Disheet A. Shah, Romina B. Cejas, David K. Crossman, Mariam Jouni, Tarek Magdy, Xuexia Wang, Noha Sharafeldin, Lindsey Hageman, Donald E. McKenna, Steve Horvath, Saro H. Armenian, Frank M. Balis, Douglas S. Hawkins, Frank G. Keller, Melissa M. Hudson, Joseph P. Neglia, A. Kim Ritchey, Jill P. Ginsberg, Wendy Landier, Paul W. Burridge, Smita Bhatia
Summary: Investigation found an association between genome-wide differential methylation at CpG sites in peripheral blood DNA and anthracycline-induced cardiomyopathy. Several genes associated with cardiac dysfunction were also identified. This suggests that differential DNA methylation of certain genes could play a role in the pathogenesis of anthracycline-induced cardiomyopathy.
SCIENTIFIC REPORTS
(2023)
Article
Cardiac & Cardiovascular Systems
Purnima Singh, Disheet A. Shah, Mariam Jouni, Romina B. Cejas, David K. Crossman, Tarek Magdy, Shaowei Qiu, Xuexia Wang, Liting Zhou, Noha Sharafeldin, Lindsey Hageman, Donald E. McKenna, Saro H. Armenian, Frank M. Balis, Douglas S. Hawkins, Frank G. Keller, Melissa M. Hudson, Joseph P. Neglia, A. Kim Ritchey, Jill P. Ginsberg, Wendy Landier, Ravi Bhatia, Paul W. Burridge, Smita Bhatia
Summary: This study examined the differential blood-based mRNA expression profiles in anthracycline-exposed childhood cancer survivors with and without cardiomyopathy. The results revealed dysregulation of several genes, including LDHA, CD36, IL1R1, IL1R2, MMP8, and MMP9, that are associated with metabolic perturbations, structural remodeling, and symptomatic cardiotoxicity in these survivors.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2023)
Article
Multidisciplinary Sciences
Ji Liao, Sangmin Song, Samuel Gusscott, Zhen Fu, Ivan Vanderkolk, Brianna M. Busscher, Kin H. Lau, Julie Brind Amour, Piroska E. Szabo
Summary: This study provides experimental evidence in mice that prospermatogonia-specific broad low-level transcription plays a crucial role in the establishment of paternal methylation imprint in the male germline.