Biomarkers and therapeutic strategies targeting microglia in neurodegenerative diseases: current status and future directions by Min-Young Noh, Hyuk Sung  Kwon, Min-Soo Kwon, Minyeop Nahm, Hee Kyung Jin, Jae-sung Bae, Seung Hyun Kim

“…Emerging technologies—including single-cell omics, spatial transcriptomics, and artificial intelligence (AI)-driven integration of multimodal data—offer new opportunities to align biomarker profiles with evolving disease states and improve patient stratification. …”
Get full text

Identification and Mechanistic Studies of Key Genes in Thalamic Hemorrhage Pain by Multi-omics by Chen Yang, Ju Gao, Yaqun Li, Yinggang Xiao, Tianfeng Huang

“…Comprehensive multi-omics profiling involving transcriptomics, proteomics, metabolomics, ribosome profiling (Ribo-seq), and single-cell RNA sequencing (scRNA-seq) was conducted. …”
Get full text

PRMT5 deficiency in myeloid cells reprograms macrophages to enhance antitumor immunity and synergizes with anti-PD-L1 therapy by Jian Cao, Yongyu Chen, Bingqian Zhou, Shiyu Chen, Zheyi Chen, Yiren Huang, Lisong Shen, Yingxia Zheng

“…Bulk and single-cell transcriptomics were employed to explore the mechanistic roles of PRMT5 in regulating lipid metabolism and macrophage polarization. …”
Get full text

Long-read sequencing sheds light on key bacteria contributing to deadwood decomposition processes by Etienne Richy, Priscila Thiago Dobbler, Vojtěch Tláskal, Rubén López-Mondéjar, Petr Baldrian, Martina Kyselková

“…For the first time we observed active nitrogen fixation by Steroidobacteraceae, as well as hemicellulose degradation and chitin recycling by Patescibacteria. …”
Get full text

Interferon regulates neural stem cell function at all ages by orchestrating mTOR and cell cycle by Damian Carvajal Ibañez, Maxim Skabkin, Jooa Hooli, Santiago Cerrizuela, Manuel Göpferich, Adrien Jolly, Katrin Volk, Marc Zumwinkel, Matilde Bertolini, Gianluca Figlia, Thomas Höfer, Guenter Kramer, Simon Anders, Aurelio A Teleman, Anna Marciniak‐Czochra, Ana Martin‐Villalba

“…Additionally, the molecular link between interferons and activation in neural stem cells and how this relates to progenitor production is not well understood. Here we combine single‐cell transcriptomics, RiboSeq and mathematical models of interferon to show that this pathway is important for proper stem cell function at all ages in mice. …”
Get full text

The myoblast methylome: multiple types of associations with chromatin and transcription by Sagnik Sen, Michelle Lacey, Carl Baribault, V. K. Chaithanya Ponnaluri, Pierre Olivier Esteve, Kenneth C. Ehrlich, Mia Meletta, Sriharsa Pradhan, Melanie Ehrlich

“…We generated methylomes for human myoblasts (SkM progenitor cells) and determined myoblast differentially methylated regions (DMRs) for comparison to the epigenomics and transcriptomics of diverse cell types. Analyses were from global genomic and single-gene perspectives and included reporter gene assays. …”
Get full text

Targeting myeloid cells in pancreatic ductal adenocarcinoma: from primary tumors to liver metastasis by Ruining Gong, Ying Chen, Chang Li, Huan Zhang, Zimin Liu, Qian Yu

“…Particular focus is placed on current clinical immunotherapy strategies targeting myeloid cells, and combinations with conventional chemoradiotherapy, considering contemporary knowledge and future trends. Advancements in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics have provided deeper insights into the molecular intricacies and diversity of PDAC, revealing potential therapeutic targets. …”
Get full text

KDELR1 regulates chondrosarcoma drug resistance and malignant behavior through Intergrin-Hippo-YAP1 axis by Huabin Yin, Dongjie Jiang, Yongai Li, Wenjun Chen, Jie Zhang, Xinghai Yang, Jinbo Hu, Haifeng Wei

“…To address this, we developed a single-cell transcriptional map of CS, comparing it with OS and normal cancellous bone. …”
Get full text

Unraveling the development of cutaneous neurofibromas in neurofibromatosis type 1 by Pernelle Pulh, Fanny Coulpier, Audrey Onfroy, Layna Oubrou, Wanzhen Zhang, Léa Toledano, Elie Abou Zougheib, Laura Fertitta, Pierre Wolkenstein, Piotr Topilko

“…Using a trauma-induced Nf1-KO model with scRNAseq, we designed a transcriptomic atlas of growing and mature cNFs, as well as adjacent apparently healthy skin. …”
Get full text

Longitudinal multi-omics in alpha-synuclein Drosophila model discriminates disease- from age-associated pathologies in Parkinson’s disease by Justin Moore, Timothy Wu, Justin Dhindsa, Omar El Fadel, Anh Le, Alma Perez, Bismark Amoh, Akash Tarkunde, Katy F. Zhu, Matthew Avalos, Eric B. Dammer, Duc M. Duong, Nicholas T. Seyfried, Joshua M. Shulman, Ismael Al-Ramahi, Juan Botas

“…To identify molecular changes early in the disease course and distinguish PD pathologies from aging, we generated Drosophila expressing alpha-synuclein (αSyn) in neurons and performed longitudinal bulk transcriptomics and proteomics on brains at six time points across the lifespan and compared the data to healthy control flies as well as human post-mortem brain datasets. …”
Get full text

Unveiling ac4C modification pattern: a prospective target for improving the response to immunotherapeutic strategies in melanoma by Jianlan Liu, Pengpeng Zhang, Chaoqin Wu, Binlin Luo, Xiaojian Cao, Jian Tang

“…This research integrated single-cell sequencing data and transcriptomics to pinpoint ac4C-related genes (acRG) linked to melanoma progression and evaluate their clinical implications. …”
Get full text

The spatial landscape of glial pathology and T cell response in Parkinson’s disease substantia nigra by Maxwell Ma, Fahad Paryani, Kelly Jakubiak, Shengnan Xia, Susumu Antoku, Adithya Kannan, Jaeseung Lee, Nacoya Madden, Shailesh Senthil Kumar, Juncheng Li, David Chen, Gunnar Hargus, Aayushi Mahajan, Xena Flowers, Ashley S. Harms, David Sulzer, James E. Goldman, Peter A. Sims, Osama Al-Dalahmah

“…However, the characteristics of this response within the brain are not well understood. Here, we employed single-nucleus RNAseq, spatial transcriptomics, and T cell receptor (TCR) sequencing to analyze T cell and glial cell states in post-mortem PD brain tissue. …”
Get full text

Deciphering the Complexity of the Immune Cell Landscape in Kidney Allograft Rejection by George Terinte-Balcan, George Terinte-Balcan, George Terinte-Balcan, Emilie Lebraud, Julien Zuber, Dany Anglicheau, Dany Anglicheau, Gener Ismail, Gener Ismail, Marion Rabant, Marion Rabant

“…In the last few years, multiplex IF techniques and automatic counting systems as well as transcriptomics studies (bulk, single-cell and spatial techniques) have provided invaluable clues to further decipher the complex puzzle of rejection. …”
Get full text

Cholangiocytes contribute to hepatocyte regeneration after partial liver injury during growth spurt in zebrafish by Sema Elif Eski, Jiarui Mi, Macarena Pozo-Morales, Gabriel Garnik Hovhannisyan, Camille Perazzolo, Rita Manco, Imane Ez-Zammoury, Dev Barbhaya, Anne Lefort, Frédérick Libert, Federico Marini, Esteban N. Gurzov, Olov Andersson, Sumeet Pal Singh

“…In both injuries, de novo hepatocytes emerged alongside existing ones. Single-cell transcriptomics and lineage tracing with Cre-driver lines generated by genome editing identified cholangiocytes as the source of de novo hepatocytes. …”
Get full text

DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation by Emily K.W. Lo, Adrian Idrizi, Rakel Tryggvadottir, Weiqiang Zhou, Wenpin Hou, Hongkai Ji, Patrick Cahan, Andrew P. Feinberg

“…Regions of differential methylation were enriched for motifs of KLF and AP-1 family transcription factors, as were those of human pancreatic intraepithelial neoplasia (PanIN) samples, demonstrating the relevance of this epigenetic transition state memory in human carcinogenesis. Finally, single-cell spatial transcriptomics revealed that these ADM transition cells were enriched for PI3K pathway and AP1 family members. …”
Get full text

Whole-genome bisulfite sequencing of cell-free DNA unveils age-dependent and ALS-associated methylation alterations by Yulin Jin, Karen N Conneely, Wenjing Ma, Robert K. Naviaux, Teepu Siddique, Emily G. Allen, Sandra Guingrich, Robert M. Pascuzzi, Peng Jin

“…Integration with spinal cord transcriptomics revealed that 31% of DMR-associated genes exhibited differential expression in ALS patients compared to controls, with over 20 genes significantly correlating with disease duration. …”
Get full text

Decreased expression of cell adhesion genes in cancer stem-like cells isolated from primary oral squamous cell carcinomas by Amrendra Mishra, Harshini Sriram, Pinal Chandarana, Vivek Tanavde, Rekha V Kumar, Ashok Gopinath, Raman Govindarajan, S. Ramaswamy, Subhashini Sadasivam

“…Seventy resected tumours were dissociated into single cells and stained with antibodies to CD44 as well as CD45 and CD31 (together referred as Lineage/Lin). …”
Get full text

Small extracellular vesicles: messengers at the service of breast cancer agenda in the primary and distant microenvironments by Angela Galardi, Valentina Fogazzi, Claudia Tottone, Marta Giussani, Serenella M. Pupa, Giulia Cosentino, Marilena V. Iorio

“…Finally, we explores how integrating artificial intelligence, single-cell transcriptomics, and multi-omics approaches can help overcome major challenges such as small EV heterogeneity and tracking limitations. …”
Get full text

Hypoxic Upregulation of IER2 Increases Paracrine GMFG Signaling of Endoplasmic Reticulum Stress‐CAF to Promote Chordoma Progression via Targeting ITGB1 by Tao‐Lan Zhang, Bo‐Wen Zheng, Chao Xia, Peng‐Fei Wu, Bo‐Yv Zheng, Ling‐Xiang Jiang, Jing Li, Guo‐Hua Lv, Hong Zhou, Wei Huang, Ming‐Xiang Zou

“…Abstract Currently, the oncogenic mechanism of endoplasmic reticulum stress‐CAF (ERS‐CAF) subpopulation in chordoma remains unknown. Here, single‐cell RNA sequencing, spatial transcriptomics, GeoMx Digital Spatial Profiler, data‐independent acquisition proteomics, bulk RNA‐seq, and multiplexed quantitative immunofluorescence are used to unveil the precise molecular mechanism of how ERS‐CAF affected chordoma progression. …”
Get full text

Sphingosine-1-phosphate stimulates colorectal cancer tumor microenvironment angiogenesis and induces macrophage polarization via macrophage migration inhibitory factor by Fang Wu, Zhaode Feng, Xuan Wang, Yingcong Guo, Bingcong Wu, Shuheng Bai, Ning Lan, Min Chen, Juan Ren

“…In order to elucidate the contribution of S1P to the complexity of the tumor microenvironment, we employed intercellular communication analysis and functional enrichment analysis at the single-cell transcriptome (scRNA-seq) level. The expression of Sphingosine kinase 1 (SPHK1) in human tissues was verified by immunohistochemical staining (IHC). …”
Get full text