title: A PLETHORA3/7 transcription factor shapes cucumber shoot architecture [RNA-Seq]

city: Wageningen

first: Merijn

last: Kerstens

address: Droevendaalsesteeg 1

department: Plant Developmental Biology

institute: Wageningen University & Research

summary: PLETHORA transcription factors (PLTs) are master regulators of plant development. In Arabidopsis, loss of shoot meristematic PLTs leads to destabilised phyllotaxis, but whether these factors have similar functions in more distantly related species, is not known. Here, we investigated the role of PLTs in shaping cucumber shoot architecture. Through transcriptional analysis, we determined that two of the four homologs - CsPLT3/7 and CsPLT5 - are expressed in complementary domains in the shoot apex. In situ hybridisation showed that whereas CsPLT3/7 was expressed in the shoot apical meristem summit and leaf axils, CsPLT5 transcripts localised beneath the CsPLT3/7 domain and to the adaxial side of leaf primordia. Both transcription factors recognised an ANT-like consensus motif and bound to SAM organising genes in vitro. Using a panel of TILLING mutants of each of the four CsPLT homologs, we only identified strong phenotypic defects for Csplt3/7 mutants. The combination of Csplt1/2 and Csplt3/7 proved embryonic lethal. In young seedlings, loss of CsPLT3/7 caused absence of a shoot apical meristem, which regenerated de novo shoot from a flat shoot apex during subsequent seedling development. Mature Csplt3/7 shoots exhibited defects in internode length stabilisation, revealing both extremely short and long internodes, stem architecture, flower morphology, and axillary organ initiation. Moreover, phyllotactic patterns were slightly shifted from a spiral towards a distichous orientation. We thus provide the first evidence of a role for PLTs in shoot development outside of Arabidopsis.

overall_design: RNA profiling of 6 dpg shoot apices of cucumber '9930' seedlings grown on soil plates and in germination pouches

first: Kelvin

last: Adema

first: Olga

last: Kulikova

first: Florian

last: Müller

first: Magdalena

last: Lastdrager

first: Ben

last: Scheres

first: Viola

last: Willemsen


title: scRNA-seq analysis of lung metastatic microenvironment in Tmem175 KO and WT mice.

status: Public on Jan 19 2026

city: Chengdu

first: Ziqi

last: Zhang

state: Sichuan

address: No. 17, Block 3, Southern Renmin Road

department: National Clinical Research Center for Geriatrics,

country: China

institute: West China Hospital, Sichuan University

type: Expression profiling by high throughput sequencing

summary: A 10X Genomics scRNAseq of Tmem175-/- and WT B16-F10 lung matastatic model. The main purpose of this research is to explore the transcriptome changes in different immune cells.

overall_design: Three Tmem175-/- and WT mice were injected with B16-F10 i.v. then the lungs were applied for the scRNA-seq.

first: Lei

last: Chen

first: Xuejiao

last: Han


title: The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis

city: Heidelberg

first: Günter

last: Kramer

address: Im Neuenheimer Feld 329

country: Germany

institute: Center for Molecular Biology of Heidelberg University (ZMBH)

summary: Natural proteins are structurally diverse and often form intricate multidomain, oligomeric architectures. This presents a prima facie challenge to cellular homeostasis, as topologically complex proteins seldom refold efficiently in vitro. How cells overcome sequence-intrinsic folding limitations to optimize protein biogenesis is incompletely understood. Here, we show that efficient folding and assembly of a model 5-domain homotetramer is obligatorily coupled to its synthesis on the ribosome, and define the underlying mechanisms. During refolding of full-length protein from denaturant, maturation of the catalytic TIM barrel domain is frustrated. Assembly outpaces monomer folding, and non-native oligomers accumulate. The ribosome directs the order of folding events and specifies the pathway of oligomer assembly. Efficient de novo folding is characterised by segmental folding of the TIM barrel, shaped by binding of a nascent amphipathic helix to a cryptic pocket on the ribosome surface. Homomer assembly initiates cotranslationally via recruitment of a full-length subunit to the nascent polypeptide, and the failure to do so results in misassembly. Our results reveal how the ribosome can dictate the timing of folding and assembly to enable efficient biogenesis of a topologically complex protein.

overall_design: Probing cotranslational assembly of beta-galactosidase by selective ribosome profiling (https://doi.org/10.1038/s41586-018-0462-y) and disome selective profiling (DOI: 10.1126/science.abc7151).

first: Alžběta

last: Roeselová

first: Santosh

last: Shivakumaraswamy

first: Gabija

last: Jurkeviciute

first: Josef

last: Auburger

first: Jaro

last: Schmitt

first: Bernd

last: Bukau

first: Jessica

last: Zhiyun He

first: Radoslav

last: Enchev

first: David

last: Balchin


title: Disruption of ARID1B recruitment to the nuclear pore complex as a new anticancer therapeutic strategy [ATAC-seq]

status: Public on Jan 20 2026

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

country: USA

institute: Emory University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Triple-negative breast cancer (TNBC), a highly aggressive subtype, currently lacks potent targeted therapies. ARID1B, a key SWI/SNF chromatin remodeling complex subunit, is linked to high-grade malignancies and poorer prognosis, making it a potential biomarker and therapeutic target. However, its function and regulation remain unclear. Here, we found that uncontrolled accumulation of ARID1B and its nuclear import promoted oncogenesis and drug resistance. ARID1B negatively regulates ARID1A, impairing SWI/SNF-mediated tumor suppression and enhancing tumor survival. Using protein complex purification and mass spectrometry, we identified KPNA2-KPNB1-RANBP2 as a critical protein cascade that facilitates ARID1B nuclear import. Replacing R1518, H1519, and D1522 residues on ARID1B with T1518, G1519, and G1522 attenuated the ARID1B-KPNA2 interaction, preventing recruitment of ARID1B to the nuclear pore complex. Pharmacological inhibition of KPNB1 suppressed ARID1B translocation, thereby limiting its nuclear levels. Our RNA-seq and ATAC-seq analyses indicated that KPNB1 inhibition also mimicked the effects of the SWI/SNF inhibitor on chromatin accessibility and gene expression, likely due to the reduced nuclear levels of ARID1B. In TNBC mouse models, ARID1B knockout significantly reduced tumor growth and enhanced PARP inhibitor efficacy. Collectively, our findings reveal that disrupting ARID1B nuclear translocation could be a new therapeutic strategy for TNBC.

overall_design: 1. To investigate the role of KPNB1 in breast cancer, we examined the effect of KPNB1 inhibition using importazole (IPZ) on chromatin accessibility and gene expression in MDA-MB-468 cellls. 2. To investigate whether KPNA2-KPNB1-RANBP2-mediated ARID1B nuclear translocation affects chromatin accessibility and gene expression through the SWI/SNF complex, we conducted RNA-seq and ATAC-seq analysis in MDA-MB-468 cells treated with BRM014 (BRMi). BRMi is a commonly used small-molecule inhibitor that selectively targets the BRG1/BRM ATPase activity of the SWI/SNF complex.

first: Olena

last: Odnokoz

first: Xiaodong

last: Lu

first: Jonathan

last: Zhao

first: Yong

last: Wan


title: A PLETHORA3/7 transcription factor shapes cucumber shoot architecture [DAP-seq]

first: Merijn

last: Kerstens

country: Netherlands

overall_design: CsPLT3/7 and CsPLT5 DAP-seq on gDNA derived from 6 dpg cucumber (Rijk Zwaan proprietary parental line) shoot apical meristems grown in germination pouches

first: Kelvin

last: Adema

first: Olga

last: Kulikova

first: Florian

last: Müller

first: Magdalena

last: Lastdrager

first: Ben

last: Scheres

first: Viola

last: Willemsen


title: CA1 significantly aggravats atherosclerosis and MTZ, a inhibitor of CA1, can alleviate the disease.

city: Qingdao

first: XIAOTIAN

last: CHANG

state: Shandong

address: 1677 Wutaishan road

institute: The Affiliated Hospital of Qingdao University

summary: Aortic calcification is essential for atherosclerosis (AS). Carbonic anhydrase I (CA1) can promote calcification in aortic tissues to stimulate AS plaque formation, and methazolamide (MTZ), a CA inhibitor, can be used to treat AS by inhibiting CA1-mediated calcification. This study used an established a CA1 [+/+] KI Apoe [-/-] mice to confirm stimulatory role of CA1 on AS and the therapeutic effect of MTZ and investigate the mechanism. In this study, Apoe [-/-] mice with CA1 overexpression were induced to AS by administrating high-fat food. The present study confirmed that CA1 is AS-therapeutic target by mediating the proportions of B1/MZB-1 cells, CD8+T cells, CD11c+ macrophages and CD11c- macrophages as well as their AS-related gene expressions and focal adhesion pathway. MTZ can be used for AS therapy.

overall_design: CA1 knockin ApoE-/- mice were fed a high-fat diet to establish an AS model and then treated with MTZ. The aortic tissues were analyzed using single-cell sequencing.

first: Xiaotian

last: Chang

first: Kehua

last: Fang


title: microRNA microarray in dental pulp stem cells treated with cigarette smoke condensate

city: San Franciscco

last: Xiao

state: CA

address: 155 5th Street

department: Biomedical Sciences

institute: Arthur A. Dugoni School of Dentistry, University of the Pacific

summary: Expression profile of microRNA(miRNAs) in human dental pulp stem cells treated with cigarette smoke condensate in comparison to control.

overall_design:
In this study, commercially available human dental pulp stem cells were treated with cigarette smoke condensate. Total mRNA and miRNAs were collected for detection of miRNAs on microfludic chip based microarray.
Total RNA was spotted on chemically modified nucleotide coding segment complementary to target microRNA (miRBase ver. 22) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.

first: Xiao

first: Tahrani

middle: H

last: Leyla


title: A pivotal contribution of proteostasis failure and mitochondria dysfunction to Chromosomal Instability-induced microcephaly

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: Mosaic variegated aneuploidy (MVA), a rare human congenital disorder that causes microcephaly, is characterized by extensive abnormalities in chromosome number and caused by mutations in genes involved in accurate mitotic chromosome segregation. Here we generated a Drosophila model of microcephaly caused by depletion of a single spindle assembly checkpoint (SAC) gene in the neural stem cell (NSC) compartment to characterize the cellular mechanisms underlying this disease. We present evidence that loss of stemness of NSCs – compromised identity and proliferative capacity - is the underlying cause of the disease and results in a reduced number of neurons and glial cells. We show that loss of stemness is a consequence of the accumulation overtime of an unbalanced number of gains and losses of more than one chromosome, rather than a direct consequence of chromosomal instability-induced DNA damage or the production of simple aneuploidies. We unravel a contribution of proteostasis failure, most probably as a consequence of the imbalance in the whole protoeome, and mitochondria dysfunction to the negative impact of complex aneuploidies on stem cell identity. We identify autophagy activation -either directly or through TOR depletion –, overexpression of Radical Oxygen Species scavengers, or restoration of mitochondria proteostasis as genetic interventions capable of dampening the deleterious effects of aneuploidy on NSC identify and brain development

overall_design: The samples used for this study are late L3 larvae from Drosophila melanogaster (96 hours after egg laying at 29 ºC). For the control, we have used w; worniu-gal4, UAS-gfp-i larvae. For the experimental condition, we have used w; worniu-gal4, UAS-bub3-i larvae. 3 replicates from different days were performed and 3 brains were dissected per each genotype and per replicate. All the larvae used were females.

last: Stephan-Otto Attolini

first: Marco

last: Milan

first: Amanda

last: González


title: Effect of TMEM175 knockout on bone marrow-derived macrophages

first: Ziqi

last: Zhang

summary: To investigate the effect of TMEM175 on bone marrow-derived macrophages, bone marrow-derived macrophages from WT or Tmem175flox/flox Lyz2-Cre+/- mice were cultured. The cells were then lysed for RNA-seq.

overall_design: Primary WT or Tmem175flox/flox Lyz2-Cre+/- bone marrow-derived macrophages were cultured in 6 plates. Three wells was WT bone marrow-derived macrophages, while the other three wells were Tmem175flox/flox Lyz2-Cre+/- bone marrow-derived macrophages. The cells were lysed for RNA-seq.

first: Lei

last: Chen


title: Editing of two heat shock protein 70 genes enhances resistance of soybean to soybean cyst nematode

city: Beijing

first: Chao

last: Xiang

address: No. 2 Yuanmingyuan West Road, Haidian District

institute: Institute of plant protection, Chinese academy of agriculture sciences

summary: Heat shock protein 70 (HSP70) usually functions in maintaining protein homeostasis, and is also involved in regulating plant immunity, but mediation of plant-parasitic nematode resistance by HSP70s has rarely been reported. In this work, two high similarity soybean GmHSP70s [GmHSP70-13a (Glyma.13g254900) and GmHSP70-15a (Glyma.15g059900)] were studied in soybean cyst nematode (SCN) resistance, which is a devastating pathogen in soybean. Both GmHSP70-13a and GmHSP70-15a were significantly suppressed in resistant soybeans, compared to susceptible soybeans, at 0 day and 3 days post inoculation (dpi) of SCN. In soybean hairy roots, CRISPR/Cas9-editing of these two genes resulted in enhanced SCN resistance; accordingly, overexpressing either GmHSP70-13a or GmHSP70-15a suppressed SCN resistance. Both GmHSP70-13a and GmHSP70-15a interacted with GmSHMT08, which is one major SCN-resistant protein in soybeans and a key enzyme in one-carbon metabolism pathway. Compared to 0 dpi of SCN, at 3 dpi, GmHSP70-13a overexpression did not alter and GmHSP70-15a overexpression significantly suppressed, in contrast, the control remarkably promoted, GmSHMT08 expression in soybean. Furthermore, either GmHSP70-13a or GmHSP70-15a overexpression abnormally down-regulated expression of 4 one-carbon metabolism-associated genes (Glyma.06g235500, Glyma.12g015300, Glyma.15g071000, and Glyma.15g071200). Taken together, both GmHSP70-13a and GmHSP70-15a negatively mediated soybean SCN resistance likely by interacting with GmSHMT08, leading to GmSHMT08 suppression, along with impact of one-carbon metabolism pathway in soybean. This work provides 2 GmHSP70s gene-editing targets for soybean SCN resistance breeding.

overall_design: RNA-seq profiling of soybean wildtype ‘Williams 82’ hairy roots (WT) and their over-expression lines (OE-Empty vector, OE-GmHSP70-13a and OE-GmHSP70-15a) at Day0 and Day3 of soybean cyst nematode infection.

first: Shiming

last: Liu

first: Liuping


title: Evolutionarily divergent transcriptomic programs in ovarian folliculogenesis across mice, monkeys and humans

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Rapid production of precisely edited cattle and mice via a single AAV delivered miniature IscB#/ωRNA# [dataset 2]

city: Hohhot

last: Yang

state: Inner Mongolia Autonomous Region

address: 24 Zhaojun Rd.

department: State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock

institute: Inner Mongolia University

summary: Utilising adeno-associated virus (AAV) to deliver CRISPR/Cas has enhanced the generation of knock-out mice, but single-AAV delivery of Cas and homology-directed-repair (HDR) templates in livestock remains a challenge. Here, we introduce all-in-one AAV vectors containing shortened IscB#, the progenitor of Cas9, along with either miniature ωRNA#, or ωRNA# with a large HDR-template. Encouragingly, we efficiently generated knock-out and knock-in cattle and mice by infecting zygotes with AAV::IscB#/ωRNA#-HDR without costly micromanipulators.

overall_design:
The novel strategy to generate genetically modified mice and ruminant cattle by transduction of engineered IscB and its ωRNA (termed IscB#-ωRNA#) components into pre-implantation embryos via co-culture with adeno-associated viruses (AAVs).
To evaluate the specificity of IscB-ωRNA, the Cas-OFFinder was used to predict the potential off-target sites. Off-target sites of each group were selected from the lower number of mismatches to the higher number of mismatches. Sites with TAM were retained for IscB. Off-target sites of each guide sequence were selected in order from the lowest number of mismatches to the highest number of mismatches.


title: Multi-omic profiling unveils molecular landscapes and heterogeneous tumor microenvironment in sinonasal squamous cell carcinoma

city: Cheongju

first: Chaelin

last: You

address: Chungdae-ro 1, Seowon-Gu

country: South Korea

institute: Chungbuk National University

type: Methylation profiling by genome tiling array


status: Public on Jan 18 2026

city: Rehovot

first: Simon

last: Fishilevich

address: 234 Herzl St

country: Israel

institute: Weizmann Institute of Science

summary: This GEO submission accompanies the study “Best Practices for Massively Parallel Reporter Assays – Analyses, Diagnostics, and Interpretation” and includes five MPRA datasets used as illustrative examples in the manuscript figures. The datasets represent common MPRA experimental designs and are provided to demonstrate recommended analytical workflows, quality-control diagnostics, and interpretation strategies. These data serve as reference resources for analysis benchmarking, rather than for deriving new biological conclusions.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: This submission contains data for five MPRA experiments. MPRA1 was conducted on 79,812 oligos in human NGN2-induced neurons, in three replicates. MPRA2 was conducted on 11,243 oligos in human fetal chondrocytes, in three replicates. MPRA3 includes DNA association data for a library of 79,812 oligos. MPRA4 was conducted on 24,137 oligos in human osteoblasts, in three replicates. MPRA5 was conducted on 238,456 oligos in human HEK293 cells, in three replicates.

first: Omer

last: Ronen

first: Nadav

last: Mishol

first: Ryder

last: Easterlin

first: Nitzan

last: Haim

first: Katharina

last: Lange

last: Ahituv

first: Irene

last: Gallego Romero

first: Fumitaka

last: Inoue

first: Martin

last: Kircher

first: Michael

middle: I

last: Love

first: Max

last: Schubach

first: David

last: Gokhman


title: MRTFA-SRF driven gene expression promotes cellular stiffness by controlling cytoplasmic Ca2+ and K+ levels in cancer cells

city: CHICAGO

first: Ekrem Emrah

last: Er

state: IL

address: 909 S  WOLCOTT AVE

department: Physiology and Biophysics

institute: The University of Illinois at Chicago

summary: Cellular stiffness, the inverse of compliance, is a biophysical property of cells that fundamentally impacts homeostatic functions and pathological states and understanding how these properties are controlled can provide novel insights into tissue homeostasis and disease mechanisms. A prominent regulator of cellular stiffness is the filamentous actin (F-actin) cytoskeleton that forms aligned stress fibers during cellular contraction. It has been recently shown that F-actin polymerization and the subsequent cortical stiffening of cancer cells is regulated by the myocardin-related transcription factor A (MRTFA) and this results in dramatic changes in the ability of cancer cells to evade anti-tumor immune surveillance. However, the precise mechanism by which MRTFA regulated cortical stiffness remained unknown. Here, we demonstrate that cancer cell stiffening occurs as a consequence of MRTFA binding to its cofactor serum response factor (SRF). Specifically, MRTFA-SRF promotes the expression of Ca2+ and K+ handling genes and the flux of these ions are critically needed for cortical stiffening. Finally, we show the results of a series of rigorous gain-of-function and loss-of-function studies that reveal the large conductance K+ channel auxiliary subunit, KCNMB1, as an MRTFA-SRF target that regulates cell stiffness and F-actin organization. Collectively, these findings point to previously unrecognized MRTFA-SRF targets in cellular stiffness, including a novel druggable ion channel.

overall_design: To investigate the role of MRTFA-SRF binding on cancer cell stiffness phenotypes, using 2 cell lines with doxycycline-inducible overexpression of wildtype MRTFA or SRF-binding deficient MRTFA (Y238A), data is from 3 separate replicate sets.

first: Alexa

middle: M

last: Gajda

first: Mark

middle: A

last: Sanborn

first: Ekrem

middle: E


title: Transcriptomic profiling of dental epithelium and mesenchyme of the third deciduous molar of miniature pigs at embryonic day 50 and 60

first: Jiangyi

last: Wang

state: None Selected

address: NO. 4 Tiantanxili, Dongcheng District, Beijing, China

institute: Beijing Stomatological Hospital, Capital Medical University

summary: Reciprocal epithelial–mesenchymal interactions play a fundamental role in ectodermal organogenesis. The tooth is a typical ectodermal organ for studying epithelial–mesenchymal interactions. The dental epithelium (DE) is considered to possess the original inductive odontogenic signals rather than the dental papilla (DP) derived from mesenchyme. At the bell stage, the outer layer of the DP that is adjacent to the DE starts to differentiate into odontoblasts first, implying potential induction by DE. Epithelial signals are requisite inducers for dental cusp formation and odontoblast differentiation. However, conflicting roles for these signals have been reported. Here, we separated DE and dental mesenchyme at early and late bell stage (embryonic day 50 and 60) of the third deciduous mandibular molars(DM3) in miniature pigs and mRNA sequencing was carried out. KEGG analysis and GO enrichment showed that PI3K/AKT was one of the most enriched pathways in DE from E50 to E60. We screened out 198 genes of secreted proteins that were expressed at higher levels in DE than in DP at E50. Function experiments supported the idea that PI3K/AKT signaling from DE to DP promotes odontoblast differentiation via COL4A6 secretion.

overall_design: Transcriptomic profiles in E50 and E60 DM3 of miniature pigs using RNA sequencing (RNAseq)

first: Xiaoyu

last: Lin

first: Zongshan

last: Shen

first: Guoqing

last: Li

first: Lei

last: Hu

first: Qiong

first: Yang

first: Jinsong

first: Chunmei

last: Zhang

first: Songlin

first: Xiaoshan

last: Wu


title: KMT2D maintains Treg homeostasis and protects against inflammatory diseases by regulating the purinergic channel P2X7 [CUT&Tag]

city: Zhengzhou

first: Peng

address: Science Avenue

institute: Zhengzhou University

summary: Regulatory T (Treg) cells are essential for maintaining immune homeostasis and tolerance through the prevention of inflammatory and autoimmune responses. The histone methyltransferase KMT2D is indispensable for induced Treg (iTreg) cell differentiation, its role in the differentiation and function of Treg cells in vivo has remained largely unknown. Here, we demonstrate that KMT2D is critical for the differentiation and function of effector activated Treg (aTreg) cells. We found that KMT2D deficiency in Treg cells impairs aTreg generation and exacerbates inflammatory conditions, such as allergic airway inflammation and colitis. Mechanistically, KMT2D regulates aTreg differentiation through TCR signaling. Furthermore, KMT2D modulates Ca2+ influx by promoting the expression of purinergic receptor P2X7 through H3K4me3 deposition. Collectively, our fundings highlight a pivotal role for KMT2D in Treg cell homeostasis and function, potentially offering a new therapeutic strategy for treating inflammatory diseases.

overall_design: Sorted Treg cells of the spleen form Foxp3YFP-CreKmt2dfl/fl(cKO) and Foxp3YFP-CreKmt2d+/+ mice to perform CUT&Tag (H3K4me3) assay.


title: Zinc accumulation-induced integrated stress response triggers β-cell identity loss

city: shanghai

first: xuan

last: wang

address: 1239 Siping Road

institute: TONGJI UNIVERSITY

summary: Pancreatic β cell identity loss is increasingly recognized as a critical pathogenic contributor to β cell failure in type 2 diabetes (T2D), but the specific mechanism remains to be elucidated. In this study, we demonstrate that zinc accumulation contributes to the β cell identity loss during diabetes progression in both human and mouse islets. Using a model of human embryonic stem cell-derived islets (SC-islets), we reveal that accumulated zinc triggers the integrated stress response (ISR) with elevated ATF4 expression in SC-β cells. This, in turn, initiates α cell-specific transcription factor ARX expression, resulting in the conversion from β cells to α cells, forming a regulatory axis of zinc-ATF4-ARX. Moreover, similar to primary β cells, SC-β cells also undergo identity loss after transplantation into diabetic animals, which can be prevented by using an ISR inhibitor, resulting in improved glycemic control. Furthermore, both genetic depletion and chemical inhibition of zinc accumulation effectively safeguard SC-β cells from identity loss and enhance their efficacy in diabetic animals. Pioneeringly, our study unveils a pathogenic mechanism of accumulated zinc-induced β cell identity loss through lineage-tracing approaches and proposes a protective strategy to counteract this process.

overall_design: We first generated human embryonic stem cell derived islet (SC-islet) with reporter gene labeling β cell from hESCs by stepwise pancreatic differentiation. Next, we performed single-cell RNA sequencing (scRNA-seq) on SC-islets with or without zinc treatment with high glucose to mimic hyperglycemia in diabetes.

first: Qing

last: Ma

first: Wenjun

last: Xu

first: Xuan

first: Rui

first: Xiangyi

last: Chen

first: Zhaoyue

first: Minglu

first: Weida

first: Haoyu

last: Nie


title: Cut&Tag-seq for HER1 location using α-HER1  antibody, and Cut&Tag-seq for WT and her1 using α-H3K9me2 antibody

first: Daiming

last: Guo

address: 211 Huimin Road, Wenjiang

department: Rice Research Institute

institute: Sichuan Agricultural University

summary: To investigate the effect of the HER1 and identity its downstream targets, we analysed HER1 binding regions and genome-wide H3K9me2 levels in WT and the mutant her1 using Cut&Tag-seq.

overall_design: Cut&Tag-seq for HER1 location used the α-HER1  antibody, and Cut&Tag-seq for WT and her1 used the α-H3K9me2 antibody.

first: Kangxi

last: Du

first: Xianjun

first: Yongxiang

last: Liao


title: MAPK14 Governs Mammalian Müller glia Fate Determination between Gliosis and Reprogramming

city: Hengyang

first: Houjian

state: Hunan

address: Shigu District Chuanshan Road

institute: The First Affiliated Hospital of University of South China

summary: Irreversible loss of retinal neurons is the leading cause of blindness. Harnessing the latent stem cell potential of mammalian Müller glia offers a promising strategy for endogenous retinal regeneration. Shifting the Müller glia response from gliosis to regeneration after retinal injury is a critical step in promoting the orderly entry of Müller glia into a regenerative program. However, the molecular switch governing this divergent fate decision remains elusive. Here, through RNA-seq and scRNA-seq, we confirm the upstream determinant of Müller glia fate after retinal injury.

overall_design: RNA sequencing was performed on MIO-M1 cells following MAPK14 or control siRNA treatment, as well as MAPK8+9 or control siRNA treatment, according to the manufacturer’s instructions, to identify downstream signaling changes. To characterize the types of neurons regenerated in Adezmapimod-treated mice, we performed scRNA-seq) on fluorescence-activated cell sorting (FACS)-purified MG and their neuronal progeny 1 month after NMDA and Adezmapimod treatment.

first: Yuli

first: Wenxin

last: Sun

first: Wei

last: Zha

first: Xuechun

first: Zuguo

last: Liu


title: FBXO3-mediated DUSP9 ubiquitination reprograms MAPK signaling to eradicate tyrosine kinase inhibitor-resistant CML stem cells

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

summary: Discovering new therapeutic targets to overcome tyrosine kinase inhibitors (TKIs) resistance and clear leukemic stem cells (LSCs) is an urgent clinical need for chronic myeloid leukemia (CML) treatment. In the present study, we report that the F-box protein 3 (FBXO3) is upregulated in CD34+ CML stem cells from patients with TKI treatment failure and is regulated by BCR-ABL. Single-cell RNA sequencing (scRNA-seq) analysis indicated that FBXO3+ HSCs from CML patients have significant LSC signatures. Genetic depletion of FBXO3 significantly increased apoptosis and decreased proliferation of both imatinib-sensitive/resistant CML cell lines and CML stem cells in vitro and in vivo, with minimal effects on normal CD34+ HSCs. Mechanistically, FBXO3 interacts with DUSP9 and mediates its ubiquitination. DUSP9 knockdown partially counteracts the elimination of CML stem cells mediated by FBXO3 depleting in vitro and in vivo. RNA-seq results indicates that FBXO3-mediated ubiquitination of DUSP9 activates MAPK signaling pathway in CML cells.  Moreover, FBXO3 inhibitor alone or in combination with imatinib significantly clear CML stem cells and overcome TKI resistance in murine and human CML, with minimal effects on normal hematopoiesis.  Overall, our findings uncover novel roles of FBXO3 in CML progression and provide a rationale for combining FBXO3 inhibitors with TKIs to induce durable elimination of CML-LSCs.

overall_design: RNA-seg profiling of wildtype K562 cells and their knockdown derivatives(shDUSP9)

first: Xudong

first: Shiyu

last: Zuo

first: Yongping

last: Song

first: Zhilei

last: Bian


title: Single-Cell Profiling and Cell-Cell Communication Analysis of Splenic CD11c⁺ Cells in Wild-Type Mice

city: Mainz

first: Xinyuan

address: Langenbeckstraße 1

department: Institute for Molecular Medicine

institute: University Medical Center, Johannes Gutenberg University Mainz

summary: Single-Cell  RNA-sequencing and Cell-Cell Communication analysis of Splenic CD11c⁺ Cells from Wild-Type Mice

overall_design: We conducted single-cell analysis of splenic CD11c⁺ cells from wild-type mice to characterize immune cell heterogeneity and intercellular communication. CD11c⁺ cells were enriched using MACS beads and labeled with a multiplexing kit before capture on the BD Rhapsody Single-Cell Analysis System. Mouse macrophages (MMMs) and Langerin⁺ cDC1s were identified and subsetted using Seurat, and cell-cell communication networks were inferred using the CellChat R package. This approach enables detailed mapping of immune interactions within the splenic microenvironment.

first: Ari

last: Waisman


title: MAPK14 Governs Mammalian Müller glia Fate Determination between Gliosis and Reprogramming [scRNA-Seq]

last: Zhang

last: Wang


title: Single-Cell Transcriptomics Reveals FXR1 as an Actionable Target for siRNA Therapy in Ovarian Cancer

city: Milwaukee

first: Masaki

last: Lin

state: Wisconsin

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

summary: Ovarian cancer is one of the leading causes of cancer-related mortality among women and remains exceptionally difficult to manage and treat effectively in the clinic. Fragile X-related protein 1 (FXR1) is significantly amplified and overexpressed in ovarian and various other cancers. We have shown that FXR1 acts as a key regulator of the stability and translation of multiple oncogenic mRNAs, establishing it as an excellent therapeutic target for ovarian cancer. Our Single-cell RNA sequencing (scRNA-seq) analysis demonstrates a complex involvement of FXR1 in cancer progression mainly due to its dual role attributed through its autonomous actions in tumor cells and the modulation of tumor microenvironment (TME). Recent advances in RNA interference (RNAi) therapies have enabled targeting previously undruggable genes. In this study, we developed a locked nucleic acid (LNA)-based small interfering RNA (siRNA) to target FXR1 for ovarian cancer therapy. Compared to native siRNA, siFXR1-LNA demonstrates resistance to RNase degradation, improved tumor tissue uptake, and robust inhibition of its target FXR1. siFXR1-LNA inhibited proteins essential for tumor growth and survival while increasing the levels of pro-apoptotic proteins. Importantly, the polyethylenimine-mediated delivery of siFXR1-LNA effectively reduced tumor growth and peritoneal metastasis in ovarian cancer models, without causing toxicity in both immunocompromised and immunocompetent mice. scRNA-seq further revealed that siFXR1-LNA treatment not only suppressed FXR1 in cancer cells but also disrupted translation mechanisms linked to oncogenesis. In TME, siFXR1-LNA diminished tumor cell proliferation, reduced tumor-promoting M2-like macrophages, increased tumor inhibitory T and NK cells and increased dendritic cells with anti-tumor characteristics. Given the autonomous role of FXR1 in tumor cells and TME for oncogenesis, targeting FXR1 with siFXR1-LNA presents a unique opportunity for treating ovarian cancer and other cancers express high levels of FXR1.

overall_design: For scRNA-seq, mouse ascites from siCont(n=2) and siFXR1-LNA (n=2) was harvested and processed for scRNA-seq was performed using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index).

first: Jasmine

last: George

first: Xiaolong

last: Ma

first: Ishaque

last: Pulikkal Kadamberi

first: Ajay

last: Nair

first: Sonam

last: Mittal

first: Elaheh

last: Hashemi

first: Sudhir

last: Kumar

first: Mona

last: Singh


title: Bulk RNA-seq detects cMPC HO signature in hip arthroplasty patients

city: Boston

first: Nezihi Murat

last: Karabacak

state: Massachusetts

address: 51 Blossom St

institute: Massachusetts General Hospital

summary: Heterotopic ossification (HO), the aberrant bone in soft tissues, is one of the most debilitating complications associated with severe burn and traumatic injuries as well as joint replacement surgeries due to its insidious development. Currently, no technologies exist to either support early HO detection or to guide early prophylactic strategies. Furthermore, no technologies exist to assess treatment efficacy. In this study, we used microfluidic iChip, designed to isolate circulating rare non-hematopoietic cells from whole blood, to isolate and analyze circulating mesenchymal progenitor cells (cMPCs) released in patients that underwent hip artroplasty. RNA sequencing of cMPCs revealed the unique expression of HO-associated MPC genes observed post operation day 1, weeks earlier than gold standard radiographic diagnostic strategies.

overall_design: iChip enriched cells were lysed with RLT buffer (Qiagen Micro kit) and stored at -80C. Before proceeding to library preparation, RNA was purified with Qiagen micro kit. Total RNA libraries were prepared using Seqwell Rapid kit using manufacturer instructions.

first: Matilda

last: Holtz

first: Sneha

last: Korlakunta

first: Johanna

last: Nunez

first: Hanil

last: Kang

first: Benjamin

last: Levi

first: Murat

first: Florence


title: Cross-species identification of DLPFC-specific miR-130a-3p as a causal driver of major depressive disorder implicating microglial neuroimmune suppression

city: Hong Kong

first: Yiwen

last: Pan

address: Pokfulam Road

country: Hong Kong

institute: The University Of Hong Kong

summary: MicroRNAs (miRNAs) are postulated as pivotal epigenetic regulators in Major Depressive Disorder (MDD), yet distinguishing causal drivers from secondary associations remains a significant challenge due to cross-species barriers and tissue specificity. Here, we present a cross-species integrative framework rooted in human genetics and functionally validated in rodents to identify pathogenic miRNAs. By integrating large-scale cis-eQTLs and MDD GWAS data using Mendelian Randomization, we identified miR-130a-3p as a robust causal risk factor. Multivariable MR and neuroimaging integration further pinpointed the Dorsolateral Prefrontal Cortex (DLPFC) as the primary mediator of its pathogenic effects, characterized by disrupted related functional connectivity. Validating these findings, viral-mediated overexpression of miR-130a-3p in the murine medial prefrontal cortex (the functional homolog of human DLPFC) was sufficient to induce core depressive-like behaviors, including anhedonia and despair. Transcriptomic profiling revealed that miR-130a-3p predominantly downregulated genes enriched in immune-related pathways and specifically in microglia, suggesting a suppression of local neuroimmune signaling and an interruption of microglia-driven homeostasis. Finally, integrating these results with human Transcriptome-Wide Association Studies (TWAS) revealed that the expression levels of some miR-130a-3p downstream genes in the human DLPFC are significantly associated with MDD risk, completing a translational closed-loop that reinforces the relevance of the identified pathway. Collectively, our study identifies miR-130a-3p as a causal neuroimmune modulator in MDD and demonstrates the utility of a genetics-anchored, cross-species pipeline for dissecting the molecular etiology of psychiatric disorders.

overall_design: Bulk RNA sequencing was performed to investigate transcriptomic changes induced by miR-130a-3p overexpression in the mouse medial prefrontal cortex (mPFC). Samples consisted of mPFC tissue from mice receiving AAV-mediated overexpression of miR-130a-3p and matched control mice injected with control AAV.

first: Jiesi

first: Li

last: Zhang

first: Zhen

last: Liang

first: Shing-Chow

last: Chan


title: YBX1 Drives Post-Myocardial Infarction Angiogenesis via an m⁶A-IGF2BP1/3 Dependent Stabilization of HIF-1α mRNA

city: Xiamen

first: Yuhong

last: Zhou

state: Fujian

address: No. 1999, Guankou Middle Road, Jimei District

department: Department of Basic Medicine

institute: Xiamen Medical College

summary: Angiogenesis plays a vital role in myocardial repair following myocardial infarction (MI). Y-box binding protein 1 (YBX1), an RNA-binding protein known for its role in cancer, is found to be significantly upregulated in endothelial cells within the peri-infarct zone and in hypoxic human umbilical vein endothelial cells (HUVECs). Using in vitro and in vivo models, we demonstrate that YBX1 enhances endothelial cell viability, proliferation, migration, and tube formation. Endothelial-specific overexpression of YBX1 in a murine MI model improved cardiac function and angiogenesis, while YBX1 knockdown aggravated cardiac injury. Transcriptome (RNA-seq) analysis revealed that YBX1 deficiency disrupts HIF-1α signaling. Mechanistically, YBX1 forms a complex with IGF2BP1/3 to stabilize HIF-1α mRNA through N⁶-methyladenosine (m⁶A) modification, thereby promoting angiogenesis and cardiac repair.

overall_design: RNA-seq was performed to analyze global gene expression changes in human umbilical vein endothelial cells (HUVECs) under YBX1 knockdown and control conditions. HUVECs were transfected with siRNA targeting YBX1 (siYBX1) or negative control (siNC). Total RNA was extracted using Trizol reagent, and sequencing libraries were prepared using standard Illumina protocols. Each group contained two biological replicates. Differential expression analysis was conducted using DESeq2 to identify YBX1-dependent transcripts, with particular focus on the HIF-1α signaling pathway.

first: Fangfang

last: Bi

first: Tong

last: Yu

first: Hanyu

last: Liu

first: Miao

last: Cao

first: Yijie

last: He

first: Jin

last: Li

first: Haoshu

last: Wang

first: Chengyu

last: Kong

first: Hongwen

last: Xiao

first: Hua

last: Tian

first: Fu

first: Yun

last: Wu

first: Hongli

last: Shan


title: Characterization of a gut-restricted LXR agonist and its utility in ameliorating liver injury in experimental short gut syndrome

city: Saint Louis

first: Gwendalyn

middle: J

last: Randolph

state: Missouri

address: 425 S. Euclid

institute: Washington University in St.Louis

summary: Short bowel syndrome (SBS) results from the surgical removal of extensive portions of the small intestine and is associated with high morbidity, including intestinal failure-associated liver disease (IFALD). We aim to identify effective, targeted therapies to combat IFALD while promoting small intestinal remodeling that optimizes intestinal health and nutrient absorption. Following previous findings that an LXR agonist administered orally suppresses liver injury in a mouse model of SBS, we sought application of a gut-restricted LXR agonist to avoid potential for systemic activation of LXR. We synthesized and characterized WUSTL0717 as a potential gut-restricted hydrophobic derivative of the well-known LXR agonist GW3965and tested its ability to improve outcomes in a mouse model of SBS. Pharmacokinetic analysis in mice revealed overwhelming intestinal retention of WUSTL0717.  The  compound activated a panoply of LXR target genes, including Abca1, in the small intestine but not the liver. It also increased ileal transcript levels of Apoa1 that encodes the core protein of high-density lipoprotein (HDL) and raised HDL levels in plasma. WUSTL0717 was efficacious in protecting against IFALD. Additionally, WUSTL0717 improved nutrient absorption after small intestinal resection and promoted restoration of body weight. These data identify the LXR agonist WUSTL0717 as a gut-restricted drug that may provide therapeutic benefits for treating SBS-associated IFALD while avoiding unwanted effects of systemic LXR agonists.

overall_design: The 8-week-old C57BL/6 male mice underwent either 50-60% small bowel resection or sham surgeries. Three weeks after the operation, the mice received daily treatments of WUSTL0717 (30 mg/kg) or vehicle for 7 weeks. They were then sacrificed, and the duodenum, ileum, and liver were collected and processed for RNA sequencing.

first: Ayoung

last: Kim

first: Lingaiah

last: Maram

first: Hannah

last: Phelps

first: Jichang

last: Han

first: Rachel

middle: L

last: Mintz

first: Brad

middle: W

last: Warner

first: Bahaa

last: Elgendy


title: Locoregional delivery of autologous PD-1 knockout T cell in patients with failed first-line therapy in advanced hepatocellular carcinoma

city: changsha

first: Muqi

last: Liu

address: No.138 Tongzipo Road, Yuelu District, Changsha

department: Institute for Cell Transplantation and Gene Therapy

institute: the 3rd Xiangya Hospital of Central South University

summary: The study aims to evaluate the efficacy and safety of a novel cell-based therapy for advanced hepatocellular carcinoma (HCC). Current guidelines for advanced HCC recommend systemic therapies, such as tyrosine kinase inhibitors (TKIs) and immune checkpoint inhibitors (ICIs); however, their combined efficacy as first-line treatments remains suboptimal. This study reports findings from a first-in-human phase I clinical trial involving 3 patients with advanced HCC who had previously demonstrated poor responses to first-line therapies. The treatment involved local intratumoral injection of CRISPR-edited, PD1-deleted T lymphocytes, engineered to enhance antitumor immunity (ClinicalTrials.gov NCT04417764).  Key outcomes include a treatment response rate of 90% among assessable patients, with a median survival after enrolment of 17.2 months and an overall median survival after HCC diagnosis of 46.9 months. As of December 31, 2023, the three-year survival rate was 20%, and one patient exhibited an exceptional survival duration of 43.6 months. Secondary outcomes revealed that patients receiving the engineered T-cell therapy reported a significantly improved quality of life compared to the observation group.  The tumor immune microenvironment was analyzed pre- and post-therapy using single-cell RNA sequencing, which demonstrated that tumor-infiltrating lymphocytes (TILs) developed an effector-like phenotype following therapy.  In conclusion, this study provides strong evidence supporting the viability of CRISPR-edited, PD1-deleted T lymphocytes as a therapeutic option for advanced HCC, addressing an urgent need for more effective treatment strategies in this patient population.

overall_design: This study investigates the therapeutic potential of CRISPR-edited, PD1-deleted T lymphocytes in advanced hepatocellular carcinoma (HCC). The experimental design involved the collection of tumor biopsy samples from 3 patients with advanced HCC before and after treatment. Pre-treatment tumor samples were used to assess the baseline immune microenvironment, while post-treatment samples were analyzed to evaluate the impact of therapy on the tumor microenvironment. All samples were obtained following the local intratumoral injection of engineered T cells.

first: Wei

first: Qi

last: Liang

first: Xiaoqian

last: Ma


title: Decreased S100A7 expression is linked to altered differentiation-, autophagy- and senescence-related programs during skin aging

city: Bunkyo-Ku

first: Ge

last: Peng

state: Tokyo

address: 2-1-1 Hongo

institute: Juntendo University Graduate School of Medicine

summary: To investigate the role S100A7, a skin-derived antimicrotial peptide (AMP) in skin aging, we knockdowned S100A7 in normal human keratinocytes, which induced senescence markers, impaired autophagy, and partially recapitulated aging-associated transcriptional changes. Conversely, supplementation with physiological levels of S100A7 restored autophagic flux and attenuated senescence in D-galactose–induced aging models. These findings identify S100A7 as a molecular link between epidermal differentiation, autophagy, and cellular senescence, establishing an AMP–autophagy axis in skin aging.

overall_design:
Primary keratinocytes from human donors were matched for gender, ethnicity, and body site. Young cells were obtained from two donors aged 12 and 14 years (n = 2), and aged cells were obtained from two donors aged 77 and 79 years (n = 2). Additionally, young cells were transfected with either an siRNA duplex targeting S100A7 (n = 2) or a scrambled control siRNA (n = 2) for 24 hours. All cells were cultured in the same media and maintained at similar cell densities. RNA was then extracted for RNA sequencing analysis.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Fumihiro

last: Hattori

first: Hideoki

last: Ogawa

first: Ko

last: Okumura

first: François

last: Niyonsaba


title: Bulk RNA Sequencing of MCMV-Specific M45 Tetramer-Positive CD8⁺ T Cells from Wild-Type and  B cell-deficient JHT mice

first: Xinyuan

summary: To assess the impact of B cell deficiency on MCMV-specific CD8⁺ T cells, equal numbers of M45 tetramer-positive CD8⁺ T cells were sorted from wild-type and B cell–deficient JHT mice. The isolated antigen-specific CD8⁺ T cells were subjected to bulk RNA sequencing to compare transcriptional profiles between the two groups.

overall_design: Wild-type and B cell–deficient JHT mice were infected with murine cytomegalovirus (MCMV). At 7 days post infection, MCMV-specific M45 tetramer-positive CD8⁺ T cells were isolated by flow cytometric sorting. Equal numbers of tetramer-positive CD8⁺ T cells from each group were collected to control for differences in cell frequency. Total RNA was extracted from the sorted cells and subjected to bulk RNA sequencing to compare transcriptional profiles between wild-type and JHT mice.

first: Ari

last: Waisman


title: Bulk RNA-seq detects cMPCs HO signature in B/T mouse blood samples - dataset #1

first: Nezihi Murat

last: Karabacak

summary: Heterotopic ossification (HO), the aberrant bone in soft tissues, is one of the most debilitating complications associated with severe burn and traumatic injuries as well as joint replacement surgeries due to its insidious development. Currently, no technologies exist to either support early HO detection or to guide early prophylactic strategies. Furthermore, no technologies exist to assess treatment efficacy. In this study, we used microfluidic iChip, designed to isolate circulating rare non-hematopoietic cells from whole blood, to isolate and analyze circulating mesenchymal progenitor cells (cMPCs) released in a clinically relevant mouse model of traumatic HO. RNA sequencing of cMPCs revealed the unique expression of HO-associated MPC genes observed as soon as 6 hours post HO-inducing injury, 41 days earlier than gold standard radiographic diagnostic strategies. Using multiple lineage tracing systems, we determined that the cMPCs derived from the periosteum rather than the bone marrow. We then formulated a cMPC HO score and evaluated the diagnostic ability of the liquid biopsy approach for the early detection of HO. By using Youden’s J Statistic for optimizing sensitivity and specificity, our score yielded a sensitivity of 82% and specificity of 100% for detecting HO in mice.

first: Sneha

last: Korlakunta

first: Johanna

last: Nunez

first: Hanil

last: Kang

first: Chase

last: Pagani

first: Benjamin

last: Levi

first: Murat


title: Cardiac adventitial leptin receptor-expressing fibroblasts have a unique epigenetic landscape [mouse ATAC-Seq]

city: Milan

first: Paola

last: Cattaneo

address: Via Fantoli 16/15

department: Institute of Genetic and Biomedical Research

country: Italy

institute: National Research Council of Italy

summary: We performed ATAC (Assay for Transposase-Accessible Chromatin) sequencing of interstitial (LepR-Cre-) and adventitial (LepR-Cre+) cardiac fibroblasts in both the neonatal period (P7) and adulthood (P56). These ATAC-seq studies revealed that at P7 adventitial LepR-Cre+ cardiac fibroblasts and interstital LepR-Cre- cardiac fibroblasts exhibited abundant epigenomic differences.

overall_design: ATAC-seq analyses were performed on FACS purified LepR-Cre+ and LepR-Cre- cardiac fibroblasts at P7 and P56.

first: Veronica

last: Larcher

first: Nuno

last: Guimaraes-Camboa

first: Simone

last: Serio


title: Fibrosis-memory is mediated by IL-3-producing T cells and drives progression of fibrosis

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

summary: Repetitive injuries are an important trigger of progressive fibrosis. To study if repetitive injuries induce an accelerated pro-fibrotic process, also called “fibrosis-memory”, we established an experimental system with two consecutive, clearly separated insults in a model of renal fibrosis with reversible ureteral obstruction of the right kidney (from day 0-6) and irreversible unilateral ureteral obstruction of the left kidney (from day 17-22).

overall_design: 5' end sequencing of Tcrb mRNAs in T cells from spleen and left UUO-kidney on day 22

first: Matthias

last: Mack

last: Buchtler

first: Sophia

last: Neumayer

first: Claudia

last: Gebhard


title: Bioinformatics analysis of differentially expressed genes and pathways in the development of Juvenile-Onset Recurrent Respiratory Papillomatosis

city: Urumqi

first: Ayiheng

last: Qukuerhan

state: Xinjiang

address: No.137, Liyuoshan South Road, Xincheng District, Urumqi

institute: Xinjiang Medical University Affiliated First Hospital

summary: Background. Juvenile-Onset Recurrent Respiratory Papillomatosis (JORRP) is the most common form of benign respiratory tract tumor in children that characterized by high recurrence and aggressiveness. The purpose of this study was to screen the key genes and pathways of JORRP by biological information analysis and to investigate the molecular mechanisms of JORRP progression. Methods. RNA sequencing (RNA-seq) was used to identify differentially expressed genes (DEGs) in three JORRP tissues and two adjacent non-tumor tissues, which were first analyzed for gene ontology (GO) and Kyoto Gene and Genome Encyclopedia (KEGG) pathway enrichment.The protein-protein interaction (PPI) network of these DEGs was next constructed with STRING and visualized with Cytoscape software. The central genes were subsequently screened using CytoHubba, a plug-in in Cytoscape software, and finally evaluated using gene function enrichment analysis. Results. A total of 1795 DEGs were screened, including 876 up-regulated genes and 919 down-regulated genes. The up-regulated DEGs were mainly enriched in cornification, cell cycle, steroid biosynthesis and HIF-1 signaling pathway, and the down-regulated DEGs were associated with cilium movement, cell projection organization, metabolism of xenobiotics by cytochrome P450 and chemical carcinogenesis. VEGFA, CDH1, CDK1, IL1B, KIF11, HIF1A, ASPM, AURKA, CENPE, MKI67 were identified as hub genes from the PPI network, and these genes were mainly associated with spindle organization, cancers-related pathways, Th17 cell differentiation and HIF-1 signaling pathway. Conclusion. The key genes and pathways screened in this study may play a pivotal role in the development of JORRP and provide a scientific basis for future related studies.

first: Meili

last: Nuerbolati

first: Li

last: Ning


title: Cardiac fibrosis

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: RNA-sequencing comparing the transcriptome of adventitial LepR+ fibroblasts versus their interstitial LepR- counterparts. [mouse RNA-Seq]

summary: In this study, we investigated the role of LepR-Cre+ cardiac fibroblasts (CFs). Our results reveal a specific gene expression profile of LepR-Cre+ CFs cells compared with LepR-Cre- CFs in both the postnatal period (P7) and adulthood (P56). Our findings support a model in which adventitial fibroblasts, being characterized by upregulation of genes involved in critical functions, including hedgehog signaling, blood pressure regulation, and interaction with the immune system, are major contributors in cardiac fibrosis.

overall_design: RNA-seq analyses were performed on FACS purified LepR-Cre+ and LepR-Cre- cardiac fibroblasts at P7 and P56.

first: Omar

last: Almolla


title: Gene regulatory landscape dissected by single-cell four-omics sequencing

city: Beijing

first: Jiayu

last: Liu

address: Yiheyuan road

department: School of Life Sciences, Peking University

institute: Biomedical Pioneering Innovation Center (BIOPIC)

summary: Enrichment libraries and Hi-C libraries were processed using identical scripts. Initially, different read types were demultiplexed based on identification sequences in the R2 read. For RNA data, we first removed reads containing no poly-A sequence following GAT5-RT primer sequence. We then aligned Read 1 to the GRCm38 reference genome using STAR. Duplicates were removed based on UMIs with UMI-tools. RNA count matrix was generated by FeatureCounts with parameters “-O -M --fraction”. We used RNAsnpSplit for phasing of allele- specific RNA counts.For HiC data, reads were mapped to the GRCm38 reference genome with BWA-mem2 in “5SP” mode. Contacts and 3D genome structures were generated with Hickit software using default parameters. To remove potential contamination from RNA reads, we cleaned contacts between two exons from the same transcript, which accounted for ~0.04% of all contacts. For quality control of reconstructed 3D genome structures, five replicates were generated with random seeds, and median RMSD for each combination of 3 replicates was calculated. The first replicate in the combination with the minimum median RMSD value (if < 1.5) was used for downstream analysis. 3D proximity and 3D distance maps were generated as previously described with custom codes. For accessibility reads and histone modification reads, R2 reads, which represent Tn5 insertion sites, were aligned using BWA-mem2 with default parameters. Afterward, a custom Python script was employed to remove PCR duplicates, generating single-cell signal fragment files. For haplotype phasing, fragments were first assigned to a haplotype using SNP information from the R2 read. If the haplotype could not be determined from R2, SNP information from the R1 read was then utilized. All reads were mapped to the mm10 reference genome. All these processing steps were organized and implemented using Snakemake, and are available at https://github.com/skelviper/CHARM.

overall_design:
CHARM-seq
The RNA modality comprises three gene-by-cell expression matrices for both mESC and brain samples: one phased with CAST/EiJ (cast), one with C57BL/6J (b6), and one representing the total genome (unphased).
Histone modification modality comprises fragments with H3K27me3 and H3K27ac for mESC and brain, respectively.
Accessibility modality comprises open chromatin fragments.
HiC modality comprises 5k/20k tdg files(reconstructed 3D structures) and pairs files.
Cell names starting with 'R1' ,'R2','R3' belong to mouse_R1(rep1), mouse_R2(rep2) and mouse_R3(rep3) respectively. Cell names starting with 'P' belong to mESCs.
**Please note that the SRR_README.txt file contains the SRR accessions corresponding to each sample (as there are a total of 10,749 unique SRR accessions in PRJNA1284811) and demultiplexing details.

first: Yujie

last: Chen

first: Zhiyuan


title: Bulk RNA-seq detects cMPCs HO signature in B/T mouse blood samples - dataset #2

first: Nezihi Murat

last: Karabacak

first: Sneha

last: Korlakunta

first: Johanna

last: Nunez

first: Hanil

last: Kang

first: Chase

last: Pagani

first: Benjamin


title: RNAseq for WT and her1 rice

city: Chengdu

first: Daiming

last: Guo

state: Sichuan

summary: To investigate the effect of the HER1, we performed RNA-seq and differential expression  analyses on stigmas from WT and the her1 mutant.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and her1.

first: Kangxi

last: Du

first: Xianjun

last: Wu

first: Yongxiang

last: Liao


title: Single cell RNA-seq detects cMPCs expressing HO gene expression signature in B/T mouse blood samples

overall_design: iChip enriched cells were captured and barcoded via 10X Chromium at MGH Nextgen Core Facility.

last: Levi

first: Murat


title: Effect of Serendipita indica on gene expression in Arabidopsis thaliana seedlings under control and salt stress conditions

status: Public on Jan 17 2026

city: Pozuelo de Alarcón

first: Begoña

last: Benito-Casado

state: Madrid

address: Campus de Montegancedo, Autovía M-40 (km 38)

department: Centro de Biotecnolgía y Genómica de Plantas (UPM-INIA/CSIC)

institute: Universidad Politécnica de Madrid

summary: Serendipita indica, a widely studied beneficial root fungal endophyte, promotes plant growth under saline conditions by reducing Na⁺ accumulation in host plants, including Arabidopsis thaliana. This reduction in Na⁺ levels likely contribute to salt detoxification, though the underlying mechanisms remain unclear. Previous studies have demonstrated that SOS1, a key Na+ transporter and major determinant of salt tolerance in plants, is not involved in this reduction. To explore whether other plant transporters might participate in Na+ reduction, we first characterized the full Arabidopsis transportome, with putative substrates and subcellular localizations, and performed a comprehensive transcriptomic analysis of the full set of transporter proteins. In this study, we investigated and ruled out the possible contribution of HKT1, another relevant Na+ transporter implicated in salt adaptation in Arabidopsis. By examining differentially expressed transporters under salt stress, we identified a subset of candidate genes potentially involved in Na⁺ transport. Among these, we evaluated the role of CNGC10 and CNGC13 using mutant lines under both S. indica- and non-colonized conditions. Interestingly, both transporters appeared to be involved in the endophyte-induced decrease in Na⁺ accumulation although, other, yet-unidentified transporters may also contribute to this phenomenon, warranting further functional investigation of the candidate genes highlighted in our analysis.

overall_design: RNA-seq profiling of wild-type Columbia-0 Arabidopsis thaliana seedlings inoculated or non-inoculated with Serendipita indica in salt stress (50 mM NaCl) or control conditions (0 mM NaCl).

first: Adrián

last: González Ortega-Villaizán

first: Lorena

last: Blázquez-Conchillo

first: Carmen

last: Guerrero-Galán

first: Stephan

last: Pollmann

first: Rosario

last: Haro-Hidalgo


title: Decoding plant defense signaling using the defenseless mutant

city: Helsinki

first: Bikash

last: Baral

address: Pallaksentie 4C, 33

country: Finland

institute: University of Helsinki

summary: Despite extensive disruption of immune signaling in the defenseless mutant, residual resistance to A. alternata and Pst DC3000 persisted at levels exceeding those of known defense-compromised controls. Our RNA-seq analysis revealed a largely preserved transcriptional response, with comparable differential gene expression profiles in both Col-0 and defenseless backgrounds. These results further emphasize that full immune suppression necessitates the concurrent disruption of multiple, potentially redundant pathways (beyond our current understanding). The persistence of some resistance further implies the presence of unidentified immune mechanisms, highlighting the complexity and resilience of the plant immune system, which we are still highly unfamiliar with.

overall_design: RNAseq-profiling of Col-0 (WT) and defenseless mutant (mutation in 6 different defense genes) in control and ozone conditions, with three replicates of each.

first: Mikael

last: Brosché


title: Evidence that chaperone 4-PBA treatment alleviates the renal phenotype in Alport syndrome mouse models

city: Nicosia

first: Constantinos

last: Deltas

state: Aglantzia

address: Palaios dromos Lefkosias Lemesou No.215/6

department: Biology

country: Cyprus

institute: University of Cyprus

summary: Total RNA was extracted from glomeruli as described above. RNA quality and quantity were determined by the 2100 Bioanalyzer. RT2 Profiler PCR Array (QIAGEN) is the method used for qPCR assay. This technique takes advantage of real-time PCR performance and combines it with the ability of microarrays to detect the expression of many genes related to UPR pathway simultaneously. Total RNA that was purified from glomeruli which were extracted from mutant and wild type kidneys was measured and then converted into first strand cDNA. qPCR was followed by using the instrument-specific and ready-to-use RT2 qPCR Master Mixes and gene specific primer sets. Determination of the relative expression was done by ddCt

overall_design: We have performed the RNA arrays in whole mRNA that was isolated from glomerular lysates harvested from knockin (KI) and compound heterozygous (n=3) (EKO) mice (n=3) , that both bear the misssense mutation Col4a3:G1332E, in order to test whether the unfolded protein response (UPR) pathway is activated in the glomerular podocytes. mRNA from Wild type glomeruli was used as control (n=3). The analysis showed no upregulation of UPR in mutant mice.

first: Pavlos

last: Ioannou

first: Christoforos

last: Odiatis

first: Rania

last: Hadjisavva

first: Kyriaki

last: Antoniadou

first: Myrtani

last: Pieri

first: Apostolos

last: Malatras

first: Gregory

last: Papagregoriou

first: Antrea

last: Aristotelous

first: Paris

last: Skourides

first: Martina

last: Samiotaki

first: Matija

last: Horaček

first: Danica

last: Galešić Ljubanović

first: Kostas

last: Stylianou


title: Targeted citrullination enables p53 binding to non-canonical sites [180]

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: TP53 encodes for the transcription factor p53, which binds to a diverse set of target genes in response to stress.  Activation of p53 results in highly specific transcriptional responses, but the regulation of promoter selectivity by p53 is poorly understood.  Here we report that sequence-specific binding of p53 is regulated by its target gene and binding partner PADI4.  PADI4 enzymatically converts peptidyl-arginine to peptidyl-citrulline in a process known as citrullination.  We show p53 is citrullinated in vitro at the C-terminus by PADI4, and we confirm two citrullination events in vivo (R306, R363).  ChIP-seq reveals that PADI4 expression causes a redirection of p53 away from canonical binding sites to target genes associated with the ETS transcription factor and the interferon response.  Chromatin profiling using citrullination-specific p53 antibodies supports this conclusion.  These findings link citrullination to p53 function and illustrate how chromatin modifiers like PADI4 can redirect the p53 transcriptional response.

overall_design: Chromatin immunoprecipitation followed by DNA-sequencing (ChIP-seq) of H3K27ac, p53, PADI4, and citH3 (citrullinated histone H3 at R2, R8, and R17) in HCT116 cells transfected with a tetracycline-inducible system to induce PADI4-D350A expression. Cells were either treated with vehicle (untreated), nutlin, doxycycline, or the combination of nutlin and doxycyline for 24 hours.

first: Alexandra

last: Indeglia

first: Andrea

last: Valdespino

first: Giulia

last: Pantella

first: Sarah

last: Offley

first: Connor

last: Hill

first: Alessandro

last: Gardini

first: Maureen

last: Murphy


title: Drug Repurposing Identifies Proteasome Inhibitors as Antiproliferative Agents Counteracting Inflammation-Driven Chemoresistance in Triple-Negative Breast Cancer Organoids

city: Bangkok

first: Jakkrit

last: Khamjerm

address: 270 Rama VI Rd, Thung Phaya Thai, Ratchathewi

country: Thailand

institute: Faculty of Medicine Ramathibodi Hospital

summary: Background: Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options, characterized by high relapse rates and poor survival outcomes due to chemoresistance. This study aimed to repurpose FDA-approved drugs for TNBC and investigate their mechanisms of action in inhibiting cancer cells and counteracting  chemoresistance. Methods: Patient-derived TNBC organoids were generated from residual tumors of patients  with disease progression despite receiving standard-of-care chemotherapy. A high throughput screen of 133 FDA-approved anticancer drugs was performed on the organoids to identify potent cytotoxic agents using image-based analysis and drug-sensitivity assays. Drug response dynamics were analyzed to evaluate the efficacy of these agents in counteracting clinical drug resistance. The molecular and functional effects of the identified agents were investigated through proteomic and transcriptomic analyses, as well as translation and cell cycle assays. Results: Proteasome inhibitors bortezomib (BTZ) and carfilzomib (CFZ) were identified as potent candidates for inhibiting TNBC organoids. These drugs significantly downregulated ribosomal protein expression, suppressing translation and disrupting cell cycle progression. While TNBC organoids exhibited resistance to conventional chemotherapeutics, they were susceptible to proteasome inhibitors. Transcriptomic profiling revealed that proteasome inhibitors counteracted inflammation-driven resistance to doxorubicin (DXR) by exerting dual anti-inflammatory and anti-proliferative effects. Conclusions: This study identifies proteasome inhibition as a promising therapeutic strategy for TNBC, offering a novel approach to address unmet clinical needs. Using patient-derived organoids, this work highlights inflammation as a driver of DXR resistance and establishes it as a therapeutic target effectively counteracted by proteasome inhibitors.

overall_design: RNA-seq profile of FDA-approved anticancer drugs was performed on TNBC organoids reveals drug resistance mechanisms.

first: Rossukon

last: Kaewkhaw


title: RNA-sequencing transcriptome analysis suggested Gdf10 expression in adventitial CFs represents a mechanism for crosstalk with a distinct cardiac cell type [human RNA-seq]

first: Paola

last: Cattaneo

summary: Gdf10 encodes growth and differentiation factor 10, a member of the bone morphogenetic protein (BMP)/transforming growth factor-β (TGFβ) superfamily. Cardiac fibroblasts are known to express high levels of these receptors (used to transduce TGFβ signaling, a central pathway in fibroblast activation). In this study, we showed that adventitial fibroblasts express Gdf10 at higher levels than interstitial fibroblasts at both neonatal level and in adulthood, suggesting that it might represent a cell autonomous signaling mechanism. To test this, we conducted RNA-seq experiment in primary human cardiac fibroblasts subjected to recombinant GDF10. Whole transcriptome analysis revealed minimal alterations (only 4 moderately modulated genes), suggesting that rather than a cell autonomous mechanism, Gdf10 expression in adventitial CFs represents a mechanism for crosstalk with a distinct cardiac cell type.

overall_design: RNA-seq analyses were performed on human cardiac fibroblasts treated with vehicle or GDF10.

first: Veronica

last: Larcher

first: Nuno

last: Guimaraes-Camboa

first: Lukas

last: Tombor


title: Targeted citrullination enables p53 binding to non-canonical sites


title: An In Vivo Model of a-Synuclein Spread from Gut to Brain

city: Los Angeles

first: Bronstein

last: Jeff

state: California

address: 710 Westwood Plaza

department: Department of Neurology, David Geffen School of Medicine

institute: University of California, Los Angeles

summary: Background: Parkinson’s disease is a progressive neurodegenerative disorder characterized by the presence of pathological aggregation of the protein -synuclein and the loss of dopaminergic neurons in the substantia nigra. There is evidence that misfolding and propagation of -synuclein aggregates through networks of interconnected neurons is responsible for the pathological spread and progressive neuron loss. However, in vivo models demonstrating such pathological progression remain elusive. Results: This study utilizes a zebrafish model in order to interrogate the mechanisms of -synuclein toxicity and spread. We describe the development of a zebrafish model of neuronal human -synuclein overexpression that causes, in young fish, behavioral and neuronal changes as well as microglia activation. In aged fish, -synuclein expression induces a slow but progressive pathological phenotype manifesting in neuron loss within the gut and the CNS. This model is further utilized to seed gut pathology by incorporating a novel method of feeding human -synuclein preformed fibrils in order to initiate protein misfolding at an early age. The combination of neuronal expression of -synuclein and the exogenous addition of misfolded protein facilitates the development of brain pathology and subsequent neuron loss in the CNS. In addition to the pathological alterations induced with the fibril feeding model, genetic changes were identified by single cell RNA sequencing. These transcriptomic changes resulted in pathway alteration that implicate neurodegenerative disease processes. Conclusion: This model of -synuclein pathology is useful for understanding mechanisms underlying disease initiation and can replicate the progressive development of pathological synuclein accumulation. It has the potential to induce neuron to neuron spread and also offers a way to explore what interventions may prevent such pathological progression.

overall_design: This study investigates the impact of human alpha-synuclein (aSyn) overexpression and exogenous fibril exposure on neuronal function and transcriptomic changes in zebrafish (Danio rerio). We generated a transgenic zebrafish model expressing human aSyn in neurons using the UAS-Gal4 system (Tg[HuC:Gal4] × Tg[UAS:aSyn-T2A-eGFP]). Larvae were categorized into four groups: (1) aSyn-negative control, (2) aSyn-positive, (3) aSyn-negative + PFF-fed, and (4) aSyn-positive + PFF-fed.  At 5 days post-fertilization (dpf), zebrafish larvae were fed either control diet or food enriched with sonicated human alpha-synuclein preformed fibrils (PFFs) daily until 4 weeks post-fertilization (wpf). For transcriptomic profiling, brains from 5dpf (aSyn+ and aSyn–) and 4wpf (aSyn+ fed control or PFF food) larvae were dissected, dissociated, and processed for single-cell RNA-sequencing (scRNA-seq) using the 10X Genomics Chromium platform. CellRanger and Seurat were used for alignment, clustering, and downstream differential expression analysis.  In total, three biological replicates per condition were processed. The study design allows for assessment of cell-type-specific transcriptional responses to aSyn expression and PFF-induced seeding, with a focus on neuronal and microglial changes relevant to Parkinson’s disease progression.

first: Lisa M.

last: Barnhill

first: Sataree

last: Khuansuwan

first: Wael

last: El Nachef

first: Sung Min

last: Ha

first: Marisol

last: Arellano

first: Kazi Md Mahmudul

last: Hasan

first: Aaron

last: Kim

first: Jeff M.

last: Bronstein


title: Blood-brain barrier disrupting stimuli induce production of extracellular vesicles with distinct protein cargoes and functionality

city: Manhasset

first: Betty

last: Diamond

state: NY

address: 350 Community Drive

institute: Feinstein Institutes for Medical Research

summary: The blood-brain barrier (BBB) protects the brain from substances in the circulation; yet, this barrier can be breached. Systemic lupus erythematosus is a disease in which over 50% of patients experience manifestations of neuropsychiatric lupus (NPSLE), with many displaying BBB dysfunction. High levels of TNFα, IL-1b, C5a, and epinephrine, which have all been shown to cause BBB permeability, may be present in the serum of SLE patients. Brain microvascular endothelial cells (BMVECs) are a major structural element of the BBB. We asked whether BMVECs stimulated with barrier-disrupting factors release extracellular vesicles (EVs) which might participate in autocrine signaling or might have utility as diagnostic biomarkers of BBB permeability. We analyzed proteins in EVs secreted by unstimulated and stimulated BMVECs by mass spectrometry and used secreted EVs for further BMVEC stimulation. We subjected BMVECs to bulk RNA-seq to identify response signatures to the initial stimulus and to secondary stimulation with EVs. We show that there are agent-specific EV-associated protein profiles. EVs from BMVECs subjected to BBB-breaching stimuli alter the BMVEC transcriptional program, representing a potential feed-forward mechanism. Finally, we suggest that the proteins associated with EVs might be markers of BBB disruption.

overall_design: RNA-seq profiling of hCMEC/D3 immortalized human brain endothelial cells treated with TNFα at 25 ng/mL, IL-1β at 10 ng/mL, C5a at 50 ng/mL, epinephrine at 200 nM, or serum-free medium alone for 12 hours. Additionally, RNA-seq profiling of the same cell line following treatment with extracellular vesicles enriched from the supernatants of the cells stimulated as previously described.

first: Alec

middle: Z

last: Xiang

first: Zara

last: Adeel

first: Andrew

last: Shih


title: Targeted citrullination enables p53 binding to non-canonical sites [178]

first: Priyankara

last: Wickramasinghe

overall_design: Chromatin immunoprecipitation followed by DNA-sequencing (ChIP-seq) of H3K27ac, p53, PADI4, and citH3 (citrullinated histone H3 at R2, R8, and R17) in Yumm1.7 cells transfected with a CRISPR control system or CRISPRactivation system for PADI4 expression. Cells were either treated with vehicle (untreated), or nutlin for 24 hours.

first: Alexandra

last: Indeglia

first: Andrea

last: Valdespino

first: Giulia

last: Pantella

first: Sarah

last: Offley

first: Connor

last: Hill

first: Alessandro

last: Gardini

first: Maureen

last: Murphy


title: Targeted citrullination enables p53 binding to non-canonical sites [168]

overall_design: Chromatin immunoprecipitation followed by DNA-sequencing (ChIP-seq) of H3K27ac, H3R17me2, p53, PADI4, and citH3 (citrullinated histone H3 at R2, R8, and R17)


title: Targeted citrullination enables p53 binding to non-canonical sites [179]

overall_design: Chromatin immunoprecipitation followed by DNA-sequencing (ChIP-seq) of H3K27ac, p53, PADI4, and citH3 (citrullinated histone H3 at R2, R8, and R17), or H3R17me2 in M93-047 cells transfected with a tetracycline-inducible system to induce PADI4 expression, or tet-inducible system to knock out PADI4. Cells were either treated with vehicle (untreated), nutlin, doxycycline, or the combination of nutlin and doxycyline for 24 hours.


title: Targeted citrullination enables p53 binding to non-canonical sites [164]

overall_design: Isolation of RNA for Quantseq (RNA-seq) in HCT116 cells transfected with a tetracycline-inducible system to induce PADI4 expression, the catalytically dead version of PADI4 (D350A), an inducible knock-out of PADI4, and an empty vector. Cells were either treated with vehicle (untreated), nutlin, doxycycline, or the combination of nutlin and doxycyline for 24 hours.


title: Disease Associated Microglial TLR4-Lyn kinase is a critical regulator of neuroinflammation, Aβ phagocytosis, neuronal damage and cell survival in a 5XFAD mouse model.

city: Camden

first: Khalid

last: Hanafy

state: NJ

address: 401 Broadway,

institute: Cooper Medical School of Rowan Univ

summary: Disease-Associated Microglia (DAM) are a focus in Alzheimer's disease (AD) research due to their central involvement in the response to amyloid-beta plaques. Microglial Toll-like receptor 4 (TLR4) is instrumental in the binding of fibrillary amyloid proteins, while Lyn kinase (Lyn) is a member of the Src family of non-receptor tyrosine kinases involved in immune signaling. Increased expression of protective Syk kinase was observed, enhanced microglial Aβ phagocytosis, decreased neuronal dystrophy, and a further increase in the cell survival signaling and protective DAM population was noted. Lyn can be activated in response to TLR4 stimulation, leading to phosphorylation of various substrates and modulation of inflammatory and phagocytosis signaling pathways.

overall_design: WT, APP, 5xFAD and 5xFAD x LynKO animal groups were used for spatial transcriptomics experiment. Each brain slices were assayed with Tmem119 (microglia) and GFAP (astrocyte) markers using 6 ROIs each. In our study we have analysed the microglial gene expressions in the WT, 5xFAD and 5xFAD x LynKO groups.

first: Rezwanul

last: Islam


title: Targeted citrullination enables p53 binding to non-canonical sites [165]

overall_design: Isolation of RNA for Quantseq (RNA-seq) in M93-047 cells transfected with a tetracycline-inducible system to induce PADI4 expression, the catalytically dead version of PADI4 (D350A), an inducible knock-out of PADI4, and an empty vector. Cells were either treated with vehicle (untreated), nutlin, doxycycline, or the combination of nutlin and doxycyline for 24 hours.


title: Targeted citrullination enables p53 binding to non-canonical sites [163]

overall_design: Chromatin immunoprecipitation followed by DNA-sequencing (ChIP-seq) of H3K27ac, p53, PADI4, and citH3 (citrullinated histone H3 at R2, R8, and R17) in HCT116 cells transfected with a tetracycline-inducible system to induce PADI4 expression. Cells were either treated with vehicle (untreated), nutlin, doxycycline, or the combination of nutlin and doxycyline for 24 hours.


title: Direct reprogramming of human dermal fibroblasts into functional osteoblasts using cell-permeable Oct4-30Kc19 and Cbfβ-30Kc19

city: Chuncheon-si

first: Manho

address: Kangwondaehakgil 1

department: Biomedical science

institute: Kangwon National University

summary: This study aimed to induce the direct reprogramming of human dermal fibroblasts (HDFs) into osteoblast-like cells using the recombinant fusion proteins Oct4-30Kc19 and Cbfβ-30Kc19. Oct4 is a transcription factor known to play a crucial role in the direct reprogramming of various cell types, while Cbfβ facilitates the differentiation of bone marrow-derived mesenchymal stem cells into osteogenic lineages. To enable intracellular delivery, both transcription factors were fused with 30Kc19, a bombyx mori-derived cell-permeable protein, and expressed using an Escherichia coli system. Oct4-30Kc19 and Cbfβ-30Kc19 were successfully delivered into HDFs, and the treated cells exhibited calcium deposition, a hallmark of functional osteoblasts. RNA sequencing was performed on control, treatment, and positive control (osteoblast) groups, revealing that Oct4-30Kc19 and Cbfβ-30Kc19 treatment shifted the gene expression profile of HDFs toward an osteoblast-like state. These findings suggest that recombinant fusion protein-based transcription factor delivery may serve as a potential strategy for direct cell reprogramming into osteogenic lineages.

overall_design: Oct4-30Kc19 and Cbfβ-30Kc19 were applied to induce the direct reprogramming of human dermal fibroblasts (HDFs) into osteoblasts. To achieve this, HDFs (Gibco) were cultured in osteogenic medium supplemented with Oct4-30Kc19 and Cbfβ-30Kc19, and their gene expression profiles were analyzed by RNA sequencing (RNA-seq) and compared with those of human osteoblasts.

first: Jaeyoung

last: Lee

first: Wijin

first: Songrae

first: Ju Hyun

last: Park


title: Genetically encoded fluorescent reporters to visualize Lewy pathology in live brain

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

summary: Lewy bodies, a pathological hallmark of Parkinson’s disease, are α-synuclein-enriched cytoplasmic inclusions that drive progressive neurodegeneration these reporters provide an opportunity to directly visualize α-synuclein inclusions in live brains and support various applications for measuring their pathological effects on individual neurons.

overall_design: After anesthesia with tribromoethanol (200 mg/kg), the mice were transcardially perfused with ice-cold oxygenated sucrose-based ACSF and decapitated. Their brains were removed and placed into ice-cold oxygenated sucrose-ACSF, then were cut into slices (300 μm) in ice-cold oxygenated sucrose-ACSF with a  vibratome (Leica VT 1200S). The slices were subsequently incubated in oxygenated ACSF at 34 °C for 30 min, then at roomtemperature for 1 h. To pick the α-Syn-6H-EGFP inclusion+ neurons in the SNc, glass capillaries (2.0 mm OD, 1.16 mm ID, Sutter Instruments) were autoclaved before pulling patch-seq pipettes. All environmental surfaces were kept clean and RNase-free with DNA-OFF (Takara Cat# 9036) and RNase Zap (Life Technologies Cat# AM9780), and great care was taken to maintain an RNase-free environment during sample collection. The patch-seq pipettes were pulled using a micropipette puller (Sutter Instrument, MODEL P-97), and the resistance was 2–4 MΩ. Cells were absorbed into patch-seq pipettes and the tips of the pipettes were broken and left in the RNase-free PCR tube containing 4 μl of lysis buffer consisting of 0.1% Triton X-100, 5 mM (each) dNTPs, 2.5mM Oligo-dT30, 1 U/ml RNase inhibitor, and ERCC RNA Spike-In Mix (Life Technologies Cat# 4456740). The samples were transferred to −80 °C until further processing (Cadwell et al., 2016; Xie et al., 2021).

first: Li

last: Zhang

first: Qian

last: Wu

first: Xiaoqun

last: Wang

first: Peng

last: Cao


title: AURKA/PHB2 signaling drives acquired resistance to KRAS G12C inhibitors in KRAS G12C -mutant NSCLC

city: Fuzhou

first: xiandong

last: lin

state: fujian

address: No. 420 Fuma Road, Jinan District

institute: Fujian Cancer Hospital and Fujian Medical University Cancer Hospital

summary: Patients with non-small cell lung cancer (NSCLC) who initially respond to Sotorasib, a drug targeting the KRAS G12C mutation, eventually develop acquired resistance. However, the mechanisms driving this acquired resistance remain largely unclear. This study explored the role of AURKA in mediating resistance to Sotorasib in NSCLC. The expression levels of AURKA mRNA and protein in NSCLC cell lines (H358 and Calu-1) were assessed using qPCR and Western blot. To further elucidate the role of AURKA in the biological alterations of Sotorasib-resistant cells and its association with the PI3K/AKT signaling pathway, a comprehensive set of assays were conducted, including MTS, colony formation, Transwell migration, luciferase reporter assays, fluorescent in situ hybridization (FISH), molecular docking analyses, and immunoprecipitation. The key findings include: (1) Long-term Sotorasib treatment led to upregulation of AURKA; (2) Overexpression of AURKA induced Sotorasib resistance, suppressed apoptosis and promoted migratory potential in Calu-1 and H358 cells, while AURKA knockdown increased the sensitivity, enhanced apoptosis and inhibited migratory capacity of H358-SR and Calu-1-SR cells to Sotorasib; (3) Immunoprecipitation and luciferase reporter assays demonstrated a physical interaction between AURKA and PHB2, establishing a positive feedback loop that sustained malignant behaviors, potentially explaining how Sotorasib-resistant cells survived despite KRAS pathway inhibition; (4) AURKA stabilizes PHB2, activating the PI3K/AKT pathway and allowing cancer cells to bypass the KRAS blockade, thus restoring malignant behavior. (5) The combination of AURKA inhibitor and Sotorasib alleviates the acquired drug resistance in vitro and in vivo. These data suggest that resistance to Sotorasib in NSCLC is associated with a positive feedback loop involving AURKA, PHB2, and PI3K/AKT signaling. AURKA may serve as a biomarker for predicting the therapeutic efficacy of Sotorasib in KRAS G12C-targeted therapies and as a potential therapeutic target to overcome Sotorasib resistance in NSCLC.

overall_design: AURKA knockdown cell lines were generated using a lentiviral transduction approach. Cells were adjusted to a final concentration of 1 × 10⁶ cells/mL. Total RNA was extracted and assessed for quality and quantity by agarose gel electrophoresis and NanoDrop spectrophotometry. Poly(A)+ mRNA was enriched using oligo(dT) magnetic beads; for degraded RNA samples or prokaryotic samples, rRNA depletion kits were used instead. RNA sequencing libraries were constructed using commercial kits. Briefly, RNA was fragmented and reverse-transcribed into first-strand cDNA using random primers, followed by second-strand cDNA synthesis incorporating dUTP. The resulting double-stranded cDNA underwent end repair, A-tailing, and ligation with Illumina-compatible adapters, followed by PCR amplification to generate the final libraries. The constructed libraries were quality-checked using an Agilent 2100 Bioanalyzer, quantified by qPCR, and subsequently sequenced on an Illumina NovaSeq 6000 platform.

first: Jinrong

last: Liao

first: Xin

last: Lan

first: Zeng

last: Chen

first: Dan

last: Hu

first: Doudou

last: Luo

first: Zhiyi

last: Huang

first: Huocong

last: He

first: Yunpeng

last: Bai

first: Xingguang

first: Xiandong

last: Lin

first: Hongyu

last: Yu

first: Longbin


title: A bacterial YopJ-family acetyltransferasesuppresseshost immune response by Nε-acetylation of JAK1

status: Public on Jan 16 2026

city: Xiamen

first: Guosheng

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

summary: A common host response to pathogen infection involves the production of robust interferons or proinflammatory cytokines to activate the JAK-STAT pathway, thereby limiting pathogen replication. The bacterial pathogen Legionella pneumophila creates an intracellular niche and evades host immunity utilizing a cohort of effectors by diverse biochemical activities, thereby permissive for its intracellular replication. However, roles of the JAK-STAT pathway during bacterial infection remain elusive. Here, we identify for the first time that L.pneumophila acetyltransferase effector Lem17 acts as a negative regulator of the JAK-STAT signaling. Lem17 directly interacts with JAK1 through a JAK1-binding Box1-like motif, preventing its recruitment by cytokine receptors. As a YopJ-family acetyltransferase, Lem17 catalyzes Nε-lysine acetylation of JAK1 and impairs its kinase activity, thereby disrupting JAK1-mediated signaling transduction. Our findings provide new insights into the mechanism by which L. pneumophila subverts host immunity through acetylation and underscore the role of the JAK-STAT pathway against bacterial infection.

overall_design: RNA-sequencing (RNA-seq) analysis on IFN-β-primed HeLa cells ectopically expressing Lem17 or an empty vector.

first: Tao-Tao

first: Si-Ru

last: Zheng


title: Longitudinal Methylomic changes in PTSD following Sub-Anaesthetic Oral Ketamine Administration

city: Birtinya

first: Nathan

last: Wellington

state: QLD

address: 12 Innovation Pkwy,

department: Thompson Institute

country: Australia

institute: University of the Sunshine Coast

summary: This study is part of an investigation into the differential gene expression and methylation patterns in response to sub-anaesthetic oral ketamine treatment of PTSD to identify key molecular markers in building a predictive profile in determining longer term treatment outcomes. The data from this study is included in a number of articles and highlights the utility of combining gene expression data with epigenetic data and clinical outcomes to elucidate molecular profils receptive to ketamine’s sustained therapeutic effects as a step towards precision medicine.

overall_design: Building on clinical data gathered from the sub- anaesthetic Oral Ketamine Trial of PTSD (OKTOP) (Prince Charles Hospital (PCH) Human Research Committee ethics number: HREC/18/QPCH/288. USC ethics number: A181190), a six week open-label, dose-ranging clinical trial conducted between 2021 and 2024 by the Thompson Institute (QLD, Australia) we collected and processed blood samples from the same participants at Baseline (BAS), 1 Week post ketamine treatment (Week 7) and 4 weeks post ketamine treatment (Week 10) Twenty three Adult male and female participants, aged 18 and above, diagnosed with PTSD were recruited. Eligibility was confirmed using the Clinician-Administered PTSD Scale for DSM-5 (CAPS-5). Baseline assessments, including a physical examination, urinalysis, standard clinical blood tests, and medical history, were completed within 14 days prior to the ketamine treatment. Participants received a sub-anaesthetic dose of oral ketamine weekly, monitored by a psychiatrist and health clinician. The initial dose was set at 0.5 mg/kg and gradually increased by 0.1-0.5 mg/kg each week based on individual tolerance, with a maximum dose of 3.0 mg/kg. Samples were collected within 24 hours of post administration, processed into whole blood, serum, plasma, and peripheral blood mononuclear cells (PBMCs). DNA was extraced, bisulphite converted and processed on an Illumina Human Methylation EPIC v2.0 Bead Chip utilising the Illumina Infinium HD Methylation assay protocol. All methylation samples met the requirement of ≥96% detected CpG sites (p<0.05), based on non-cancer samples. Genome Studio v2011.1 with the Methylation module 1.9.0 software and Illumina EPIC-8v2-0_A1 manifest file was used to generate intensity data (IDAT) files.


title: Claudins interact with LILRB immune inhibitory receptors to promote myeloid immunosuppression in cancer

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

summary: The mechanisms underlying tumor cell-myeloid cell interactions within the tumor microenvironment (TME) remain unclear, and predictive biomarkers for patient response to myeloid checkpoint blockade are lacking. This study identified specific binding between tight-junction claudins (CLDNs) and leukocyte immunoglobulin-like receptor subfamily B members LILRB2 and LILRB5. In multiple human cancer cohorts, the spatial proximity of LILRB2⁺ macrophages to CLDN-expressing cancer cells correlated with clinical outcomes, nominating this spatial relationship as a potential biomarker. In syngeneic LILRB2-transgenic and humanized mouse models, CLDN18.2–LILRB2 interaction triggered bidirectional signaling, enhanced the immunosuppressive activity of myeloid cells, and accelerated tumor progression. These effects were reversed by LILRB2 blockade. Mechanistically, the CLDN-LILRB2 axis sustained immunosuppression by regulating NF-κB and STAT signaling pathways. Our findings reveal a novel tight junction protein-mediated mechanism of myeloid cell regulation in the TME, offering a rationale for targeting this pathway in cancer therapy.

overall_design: NSG-SGM3 mice that had received total body irradiation (250 cGy) were transplanted with 3 x 104 human cord blood CD34+ cells (STEMCELL, # 70008). After 6 weeks, when human immune cell engraftment in mouse peripheral blood was detected, 1 × 106 SK-MEL-5 or 2 × 106 MIA PaCa-2 cells were injected subcutaneously into the right flanks of each mouse. After tumor volumes reached 50 to 60 mm3, mice were randomized into groups and intraperitoneally injected with antibodies (LALAPG-mutated anti-LILRB2 antibody or isotype control) at a dose of 10 milligram per kilogram of bodyweight twice weekly. Liver and spleen metastases were observed 6 to 8 weeks post-tumor implantation. Live, single, tumor-infiltrating human CD45+ cells and  peripheral blood engrafted human CD45+ cells were FACS-enriched at 8 weeks post-implantation and subsequently used for single-cell RNA-sequencing analysis.

first: Xiaoye

last: Liu

first: Alec

last: Zhang

first: Kenian


title: Evolutionarily divergent transcriptomic programs in ovarian folliculogenesis across mice, monkeys and humans

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Understanding the mechanisms for human ovarian folliculogenesis is fundamental to reproductive biology and medicine. Here, we investigated transcriptomic dynamics in individual oocytes and their associated granulosa cells (GCs) during folliculogenesis in mice, monkeys and humans. Unlike mouse oocytes, which exhibited stage-specific, stepwise transcriptomic maturation, monkey and human oocytes showed minimal transcriptomic changes until the secondary follicle stage and could be broadly categorized as either immature or mature. In all three species, most highly variable genes (HVGs) during oocyte growth displayed monotonic up- or downregulation, with limited overlap in HVGs across species. GCs exhibited similarly species-specific transcriptomic trajectories. Correspondingly, intercellular communication pathways, including ligand–receptor signaling, gap junctions, and metabolic coupling between oocytes and GCs, demonstrated substantial species-specific differences. Nonetheless, X-chromosome dosage compensation and repression of evolutionarily young transposons were conserved across species. We established in vitro culture systems supporting preantral to antral follicle development in monkeys and humans, revealing relatively normal oocyte transcriptome maturation but aberrant GC profiles. By delineating interspecies differences in folliculogenesis, this study provides a framework for understanding human ovarian development and advancing its in vitro reconstruction.

first: Baku

last: Nakakita

first: Ken

last: Mizuta

first: Yoshitaka

last: Katou

first: Hidetaka

last: Tasaki

first: Tomonori

last: Nakamura

first: Chizuru

last: Iwatani

first: Hideaki

last: Tsuchiya

first: Ikuo

last: Kawamoto

first: Tomoyuki

last: Tsukiyama

first: Xun

first: Guillaume

last: Bourque

first: Junko

last: Otsuki

first: Mikiya

last: Nakatsuka

first: Akihito

last: Horie

first: Masaki

last: Mandai

first: Mitinori

last: Saitou

first: Hiroshi

last: Ohta