Integrated multi-omics profiling to establish an IGFBP-based prognostic score for pancreatic ductal adenocarcinoma: unraveling prognostic biomarkers, immune microenvironment crosst... by Xiao Guan, Yongrun Mu, Xin Jin, Chengfeng Wang

“…To explore the biological mechanisms underlying IGFBP involvement in PDAC, we further incorporated single-cell transcriptomic sequencing and spatial transcriptomic data to investigate the relationship between IGFBP expression and the tumor immune microenvironment.ResultOur prognostic model effectively stratified PDAC patients into distinct risk categories with significant survival differences. …”
Get full text

Skin Barrier in Normal and Allergic Horses: What Do We Know? by Rosanna Marsella

“…Skin dysbiosis and predominance of staphylococcus have been described in horses with pastern dermatitis. Transcriptomic studies of the epidermis of normal and allergic horses have found that lesional allergic skin has substantial transcriptomic differences when compared with healthy skin, namely downregulation of genes of tight junctions, keratins, and upregulation of serine proteases and IL-13. …”
Get full text

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. by Christopher Barry, Matthew T Schmitz, Cara Argus, Jennifer M Bolin, Mitchell D Probasco, Ning Leng, Bret M Duffin, John Steill, Scott Swanson, Brian E McIntosh, Ron Stewart, Christina Kendziorski, James A Thomson, Rhonda Bacher

“…These results suggest that downstream transcriptomic response kinetics to signaling cues are faster in mouse versus human cells, and may offer a partial account for the vast differences in developmental rates across species.…”
Get full text

Immune characteristics and SALL1 methylation as prognostic biomarkers in primary and metastasis colorectal cancer by Yiwen Zhang, Tianqi Han, Hui Zhang, Jiali Li, Jun Chu, Jiaqi Liu

“…Abstract Colorectal cancer (CRC) and its metastatic form (mCRC) demonstrate considerable biological and clinical heterogeneity. By analyzing transcriptomic data from CRC and mCRC patients, we identified significant differences in gene expression profiles between the two. …”
Get full text

Altered Epithelial Gene Expression in Peripheral Airways of Severe Asthma. by Akul Singhania, Hitasha Rupani, Nivenka Jayasekera, Simon Lumb, Paul Hales, Neil Gozzard, Donna E Davies, Christopher H Woelk, Peter H Howarth

“…Differences between central and peripheral airways were evaluated using transcriptomic analysis (Affymetrix HG U133 plus 2.0 GeneChips) of epithelial brushings obtained from severe asthma patients (N = 17) and healthy volunteers (N = 23). …”
Get full text

Prognostic Biomarkers for Papillary Thyroid Cancer: Reducing Overtreatment, Improving Clinical Efficiency, and Enhancing Patient Experience by Oliver F Bathe MD, MSc, Cynthia Stretch PhD

“…Transcriptomic-based prognostic tests, like the novel Thyroid GuidePx ® classifier, effectively stratify PTCs into distinct molecular subgroups with differing recurrence risks, surpassing traditional clinicopathological models in predictive accuracy. …”
Get full text

RNAi effector diversity in nematodes. by Johnathan J Dalzell, Paul McVeigh, Neil D Warnock, Makedonka Mitreva, David McK Bird, Pierre Abad, Colin C Fleming, Tim A Day, Angela Mousley, Nikki J Marks, Aaron G Maule

“…To test if this is due to inter-species differences in RNAi effector complements, we performed a primary sequence similarity survey for orthologs of 77 Caenorhabditis elegans RNAi pathway proteins in 13 nematode species for which genomic or transcriptomic datasets were available, with all outputs subjected to domain-structure verification. …”
Get full text

Differential ABA sensitivity of superior and inferior rice grains is linked to cell cycle entry into endoreduplication by Anil Kumar Nalini Chandran, Larissa Irvin, Balpreet K. Dhatt, Yuvraj Chopra, Steven McArtney, Marci A. Surpin, Sriram K. Reddy, Harkamal Walia

“…We found that ABA and a combination of ABA and BA (ABA+BA) applications increased the grain yield in field studies, primarily by improving the grain weight of both superior and inferior grains. Transcriptomic analysis of developing grains shows differences in the expression of core cell cycle genes between the superior and inferior grains at four days after fertilization between the control and phytohormone applications. …”
Get full text

Noninvasive biomarkers implicated in urea and TCA cycles for metabolic liver disease by Guiyan Yang, Yu-Jui Yvonne Wan

“…Machine learning approaches classified urine and serum metabolites for differential dietary intake and age difference. Additionally, the gut microbiota could predict FXR functional status. …”
Get full text

Responses to checkpoint inhibition in metastatic triple negative breast cancer driven by divergent myeloid phenotypes by Avia D. Wilkerson, Ivan Juric, Salendra Singh, Patricia A. Rayman, Paul G. Pavicic, Jennifer Powers, Prerana Bangalore Parthasarathy, Zahraa Al-Hilli, Jennifer S. Ko, Timothy Chan, Tyler Alban, Alberto J. Montero, C. Marcela Diaz-Montero

“…Differences in CD33+ cell phenotype result in functional differences in lymphocyte activities between responders and non-responders. …”
Get full text

Comparative analysis of WC1.1+ and WC1.2+ γδ T cell subset responses from cattle naturally infected with Mycobacterium bovis to repeat stimulation with mycobacterial antigens. by Alia Parveen, Sajad A Bhat, Mahmoud Elnaggar, Kieran G Meade

“…Previous studies have identified a preferential transcriptomic response in WC1.1+ cells during natural bTB infection, suggesting a subset-specific response to mycobacterial antigens. …”
Get full text

The TAAR1 Agonist PCC0105004 Regulates Amygdala Synaptic Plasticity to Alleviate Anxiety‐Like Behaviors in Rats by Yingtian Zhang, Wei Zhang, Linyao Yu, Yaoqin Shi, Min Xu, Hui Wang, Chunmei Li, Jingwei Tian

“…For the mechanistic studies, whole‐genome transcriptomic analysis revealed significant differences in the patterns of amygdala gene expression in the CUMS‐induced anxiety rat model. …”
Get full text

Single-cell RNA sequencing reveals a new mechanism of endothelial cell heterogeneity and healing in diabetic foot ulcers by Songyun Zhao, Hua Yu, Zihao Li, Wanying Chen, Kaibo Liu, Hao Dai, Gaoyi Wang, Zibing Zhang, Jiaheng Xie, Yucang He, Liqun Li

“…The study found that endothelial cells from DFU patients exhibited significant transcriptomic differences under various conditions, particularly in signaling pathways related to inflammatory responses and angiogenesis. …”
Get full text

Multi‑omics identification of a novel signature for serous ovarian carcinoma in the context of 3P medicine and based on twelve programmed cell death patterns: a multi-cohort machin... by Lele Ye, Chunhao Long, Binbing Xu, Xuyang Yao, Jiaye Yu, Yunhui Luo, Yuan Xu, Zhuofeng Jiang, Zekai Nian, Yawen Zheng, Yaoyao Cai, Xiangyang Xue, Gangqiang Guo

“…Genomics, single-cell transcriptomes, bulk transcriptomes, spatial transcriptomes, and clinical information from TCGA-OV, GSE26193, GSE63885, and GSE140082 were collected and analyzed to verify the prediction model. …”
Get full text

Divergent B-cell and cytotoxic TNK cell activation signatures in HLA-B27-associated ankylosing spondylitis and acute anterior uveitis by Eisa Mahyari, Sean Davin, Kimberly Ogle, Emma Fale-Olsen, Carley Shaut, Tammy M. Martin, Jasvinder S. Ahuja, Eric Suhler, Atul Deodhar, James T. Rosenbaum, James T. Rosenbaum, Tejpal Gill, Tejpal Gill

“…Our study identified HLA-B27- and disease-specific transcriptomic differences in AS and AAU. The immune profiles of AS+AAU closely resembled those of AS, suggesting AS plays a dominant role in immune dysregulation. …”
Get full text

Three regulatory elements upstream of LMO4 are strongly associated with intermittent fertilization intensity in Chicken by Lei Wang, Weijian Fan, Xiuping Wang, Yangming Pan, Xing Hong, Mingze Li, ShiJun Li

“…This research aims to identify key candidate genes and variants regulating IFI through transcriptomic analysis and dual luciferase assays. Our study's transcriptomic analysis of 12 individuals exhibiting extreme IFI revealed several key candidate genes. …”
Get full text

Exploring the effects of feeding methods on the growth and meat flavor of Wenchang chicken by Tieshan Xu, Qicheng Jiang, Chaohua Xu, Zhepeng Xiao, Xinli Zheng, Lihong Gu

“…This study compared cage-rearing (CR) and free-range (FR) groups in terms of growth performance, slaughter performance, meat quality, IMP (inosine monophosphate) content, AAs, FAs, serum lipid metabolites, and transcriptomic and metabolomic analyses. The CR group showed increased body weight, live weight, and abdominal fat but lower leg muscle percentage and breast muscle redness, suggesting flavor differences. …”
Get full text

A 20-feature radiomic signature of triple-negative breast cancer identifies patients at high risk of death by Humaira Noor, Yuanning Zheng, Adam B. Mantz, Ryle Zhou, Andrew Kozlov, Wendy B. DeMartini, Shu-Tian Chen, Satoko Okamoto, Debra M. Ikeda, Melinda L. Telli, Allison W. Kurian, James M. Ford, Shaveta Vinayak, Mina Satoyoshi, Vishal Joshi, Sarah A. Mattonen, Kevin Lee, Olivier Gevaert, George W. Sledge, Haruka Itakura

“…We built a prediction model that leverages breast magnetic resonance imaging (MRI) features to predict risk groups based on a 50-gene Transcriptomics Signature (TS). The TS distinguished patients with high-risk for death in multivariate survival analysis (Transcriptomic cohort: [HR] = 13.6, 95% confidence interval [CI] = 1.56-1, p = 0.02; SCAN-B cohort: HR = 1.45, CI 1.04-2.03, p = 0.02). …”
Get full text

Multi-Omics Profiling Reveals Glycerolipid Metabolism-Associated Molecular Subtypes and Identifies ALDH2 as a Prognostic Biomarker in Pancreatic Cancer by Jifeng Liu, Shurong Ma, Dawei Deng, Yao Yang, Junchen Li, Yunshu Zhang, Peiyuan Yin, Dong Shang

“…Subsequently, GLM in PC was characterized using lipidomics, single-cell RNA sequencing (scRNA-seq), and spatial transcriptomic analysis. A cluster analysis based on bulk RNA sequencing data from 930 PC samples identified GLM-associated subtypes, which were then analyzed for differences in prognosis, biological function, immune microenvironment, and drug sensitivity. …”
Get full text

A Systems Hypothesis of Lipopolysaccharide-Induced Vitamin Transport Suppression and Metabolic Reprogramming in Autism Spectrum Disorders: An Open Call for Validation and Therapeut... by Albion Dervishi

“…We propose that chronic microbial lipopolysaccharide (LPS) exposure in ASD suppresses vitamin transporter function, initiating mitochondrial dysfunction and transcriptomic reprogramming. Validation in LPS-exposed systems using integrated transcriptomic–metabolomic analysis is warranted.…”
Get full text