Research Paper

Cell Death & Disease: Global profiling reveals common and distinct N6-methyladenosine (m6A) regulation of innate immune responses during bacterial and viral infections (Lai & Chen Labs)

March 15, 2022

Jian Feng, Teng Zhang, Océane Sorel, Wen Meng, Xinquan Zhang, Zhao Lai, Weiming Yuan, Yidong Chen, Yufei Huang & Shou-Jiang Gao Abstract N6-methyladenosine (m6A) is a dynamic post-transcriptional RNA modification influencing all aspects of mRNA biology. While m6A modifications during numerous viral infections have been described, the role of m6A in innate immune response remains unclear. [...]

eLife: Signature-scoring methods developed for bulk samples are not adequate for cancer single-cell RNA sequencing data (Zheng, Chen, & Wang Labs)

March 7, 2022

Nighat Noureen,  Zhenqing Ye,  Yidong Chen,  Xiaojing Wang,  Siyuan Zheng  Abstract Quantifying the activity of gene expression signatures is common in analyses of single-cell RNA sequencing data. Methods originally developed for bulk samples are often used for this purpose without accounting for contextual differences between bulk and single-cell data. More broadly, these methods have not [...]

Non-Coding RNA, FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis (Bishop Lab)

February 25, 2022

by Mirolyuba Ilieva 1ORCID,Henry E. Miller 2,3,4ORCID,Arav Agarwal 4,5,Gabriela K. Paulus 4,6,Jens Hedelund Madsen 1,Alexander J. R. Bishop 2,3,7ORCID,Sakari Kauppinen 1 and Shizuka Uchida 1,*ORCID Abstract Most long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes and their expression is often restricted to specific cell types, certain time points during development, and [...]

Cancers: Global Genomic and Proteomic Analysis Identified Critical Pathways Modulated by Proto-Oncogene PELP1 in TNBC (Chen & Lai)

February 25, 2022

by Zexuan Liu 1,2,†,Kristin A. Altwegg 1,3,†ORCID,Junhao Liu 1,2,Susan T. Weintraub 4,Yidong Chen 5,6,Zhao Lai 5,7,Gangadhara R. Sareddy 1,3,Suryavathi Viswanadhapalli 1,3,*ORCID and Ratna K. Vadlamudi 1,3,8,* Simple Summary The proto-oncogene PELP1 is commonly overexpressed in many cancers including triple-negative breast cancer (TNBC). In this study, we utilized global proteomic and RNA-seq approaches to elucidate the [...]

Journal of Pediatric Hematology/Oncology: Extrarenal Anaplastic Wilms Tumor A Case Report With Genomic Analysis And Tumor Models (Kurmasheva & Houghton)

February 8, 2022

Willis, Kelsi R. MS*; Sathe, Adwait A. PhD†; Xing, Chao PhD†,‡,§; Koduru, Prasad PhD*; Artunduaga, Maddy MD∥,¶; Butler, Erin B. MD#; Park, Jason Y. MD, PhD*,¶; Kurmasheva, Raushan T. PhD**,††; Houghton, Peter J. PhD**,††; Chen, Kenneth S. MD¶,#; Rakheja, Dinesh MD*,¶ Abstract Primary extrarenal Wilms tumors are rare neoplasms that are presumed to arise from [...]


Brain, Behavior, & Immunity: Sex-dependent pain trajectories induced by prolactin require an inflammatory response for pain resolution (Lai Lab)

January 24, 2022

Author links open overlay panelJenniferMecklenburga  AndiWangzhouf  Anahit H.Hovhannisyana  PriscillaBarba-Escobedoa  Sergey A.Sheinb  YiZoud  KorriWeldond  ZhaoLaideVincentGoffing  GregoryDussorf  Alexei V.Tumanovb  Theodore J.Pricef  Armen N.Akopianac   Highlights: • Prolactin treatment generates sex differences in pain trajectories in mice. • Low-dose prolactin treatment causes a non-resolving pain phenotype in females. • Pain resolution is preceded by pro-inflammatory CD11b+/CD64+ cell responses. • [...]

eLife: RNA binding to human METTL3-METTL14 restricts N6-deoxyadenosine methylation of DNA in vitro (Gupta Lab)

January 21, 2022

Shan Qi,  Javier Mota,  Siu-Hong Chan,  Johanna Villarreal,  Nan Dai,  Shailee Arya,  Robert A Hromas,  Manjeet K Rao,  Ivan R Corrêa Jr  Yogesh K Gupta  Abstract Methyltransferase like-3 (METTL3) and METTL14 complex transfer a methyl group from S-adenosyl-L-methionine to N6 amino group of adenosine bases in RNA (m6A) and DNA (m6dA). Emerging evidence highlights the role of [...]

Frontiers in Microbiology: Robust Heat Shock Response in Chlamydia Lacking a Typical Heat Shock Sigma Factor (Lai Lab)

January 20, 2022

Yehong Huang1,2†, Wurihan Wurihan2†, Bin Lu1,2†, Yi Zou3, Yuxuan Wang2†, Korri Weldon3, Joseph D. Fondell2†, Zhao Lai3,4, Xiang Wu1*†, and Huizhou Fan2*† Cells reprogram their transcriptome in response to stress, such as heat shock. In free-living bacteria, the transcriptomic reprogramming is mediated by increased DNA-binding activity of heat shock sigma factors and activation of genes normally repressed [...]

Frontiers in Genetics: Differential lncRNA/mRNA Expression Profiling and Functional Network Analyses in Bmp2 Deletion of Mouse Dental Papilla Cells (Lai Lab)

January 20, 2022

Feng Wang1,2†, Ran Tao1†, Li Zhao1, Xin-Hui Hao1, Yi Zou3, Qing Lin1, Meng Meng Liu2, Graham Goldman2, Daoshu Luo1* and Shuo Chen2* Bmp2 is essential for dentin development and formation. Bmp2 conditional knock-out (KO) mice display a similar tooth phenotype of dentinogenesis imperfecta (DGI). To elucidate a foundation for subsequent functional studies of cross-talk between [...]