title: ZSTK3744, a Novel Aryl Hydrocarbon Receptor Agonist, Overcomes Chemotherapy Resistance in Triple-Negative Breast Cancer [microarray]

city: Hachioji-shi

first: Takahio

last: Ohashi

state: Tokyo

address: 7-1, Minamiosawa 4-chome

institute: Zenyaku Kogyo Co., Ltd.

summary: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by a poor prognosis owing to the lack of therapeutic targets, including hormone receptors and HER2. Systemic chemotherapy remains the primary treatment option; however, its efficacy is frequently limited by chemotherapy resistance, a substantial challenge in clinical management. In the present study, we aimed to develop a novel anticancer drug that overcomes chemotherapy resistance in TNBC. First, chemotherapy-resistant MDA-MB-468 cells derived from TNBC were developed via long-term exposure to adriamycin or paclitaxel. Compared with wild-type cells, these resistant cells exhibited reduced sensitivity to paclitaxel, adriamycin, and eribulin in the viability assays. Various compounds were screened for their cell growth-inhibitory activity against these resistant cells to identify novel therapeutic agents; ZSTK3744 was a promising candidate and showed significant anti-tumor activity in vitro and in vivo. Mechanistically, ZSTK3744 upregulated CYP1A1, CYP1B1, and TIPARP expression in MDA-MB-468 cells but exhibited no cell growth-inhibitory activity in aryl hydrocarbon receptor (AhR) knockout cells, indicating that ZSTK3744 act as an AhR agonist. Notably, ZSTK3744 demonstrated superior tumor inhibition and lower pulmonary toxicity in ex vivo and in vivo models than other AhR agonists. These results suggest that ZSTK3744 combines robust cell growth-inhibitory activity with a favorable safety profile. In conclusion, ZSTK3744 is a promising candidate for overcoming chemotherapy resistance in TNBC, addressing the urgent need for more effective treatment options for this aggressive cancer subtype. This study represents the first demonstration of the anti-tumor activity of an AhR agonist on chemotherapy-resistant TNBC.

overall_design: mRNA expression profiling was conducted to compare gene expression between wild-type MDA-MB-468 breast cancer cells and their chemo-resistant derivatives. The chemo-resistant cells were generated through long-term exposure to either adriamycin or paclitaxel.

first: Takahiro

first: Tsubasa

last: Nagasaki

first: Kayoko

last: Kawai-Asami

first: Kotomi

last: Akatsuka

first: Yuko

last: Nagata

first: Sayuri

last: Terada

first: Shinsuke

last: Hiramoto

first: Eika

last: Higashi

first: Ryuichiro

last: Ohshita

first: Kuramochi

last: Mizuki

first: Makoto

last: Furuya

first: Mai

last: Todoroki

first: Hisashi

last: Yoshimi

first: Keiko

last: Fukushima


title: ZSTK3744, a Novel Aryl Hydrocarbon Receptor Agonist, Overcomes Chemotherapy Resistance in Triple-Negative Breast Cancer [RNA-seq]

status: Public on Dec 31 2025

country: Japan

type: Expression profiling by high throughput sequencing

overall_design: RNA-seq profiling was performed to compare gene expression between wild-type MDA-MB-468 breast cancer cells and chemo-resistant derivatives. Chemo-resistant cells were generated by long-term exposure to either adriamycin or paclitaxel.


title: Driver mutation landscape of acute myeloid leukemia provides insights for neoantigen-based immunotherapy [scRNA-seq]

city: Shanghai

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

country: China

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Acute myeloid leukemia (AML) has lagged in benefiting from immunotherapies, primarily due to the scarcity of actionable AML-specific antigens. Driver mutations represent promising immunogenic targets, but a comprehensive characterization of the AML neoantigen landscape and their impact on patient outcomes and the AML immune microenvironment remain unclear. Herein, we conducted matched DNA and RNA sequencing on 304 AML patients and extensively integrated data from additional ∼2500 AML cases, identifying 49 driver genes, notably characterized by a significant proportion of insertions and deletions (indels). Neoantigen analysis showed that indels triggered a higher abundance of neoantigens both in quantity and quality compared to single nucleotide variants (SNVs) and gene fusions. By integrating peptide features pertinent to neoantigen presentation and T cell recognition, we developed two robust models of epitope immunogenicity that significantly enriched immunogenic neoepitopes. We validated 30 neoantigens through in vitro direct binding assays of predicted peptides to MHC proteins and confirmed the immunogenicity of 20 neoantigens using interferon-γ ELISpot and tetramer assays. Moreover, we demonstrated that patients with higher neoantigen loads, derived from driver mutations, exhibited poor clinical outcomes and an IFN-driven adaptive immune response, which was associated with immune suppression and tumor evasion. Through deconvolution of large-scale bulk transcriptomes, integration of single-cell RNA sequencing and multiparametric flow cytometry, we confirmed a strong association between neoantigen load and CD8+ T cell exhaustion. This study provides a comprehensive landscape of AML neoantigens derived from driver mutations, offering putative immunogenic targets and emphasizing the need for strategies to revitalize the immunosuppressive milieu.

overall_design:
Single cell RNA sequencing from 4 patient tumors enrolled in the study. Biopsies were taken from bone marrow at diagnosis.

***************************************************************
Submitter statement concerning missing raw data: Law restrictions prohibit us from publicly sharing raw sequencing data, which however can be made available upon reasonable request and permission of the local ethics committee.
***************************************************************

first: Junmin

last: Li


title: A methylome-based score to predict response to regorafenib in recurrent glioblastoma

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

type: Methylation profiling by genome tiling array

summary: Following encouraging results of the REGOMA Phase 2 trial, regorafenib is increasingly used for the treatment of recurrent glioblastoma, IDH-wildtype. Identifying predictive factors for response to regorafenib is of paramount importance. DNA methylation profiling is considered the gold standard for diagnosing and classifying central nervous system tumors. We explored the predictive value of methylation profiling in recurrent glioblastoma patients treated with regorafenib, highlighting the potential of DNA methylation profiling in guiding therapeutic strategies and warrant further validation in clinical settings.

overall_design: Thirty-three recurrent glioblastoma patients were enrolled in the study. DNA methylation profile was performed on paraffin-embedded tumor obtained at first surgery. Median progression-free survival (PFS) and overall survival (OS) following regorafenib treatment were 3 and 7.5 months, respectively, aligning with findings from the REGOMA trial. Methylation classes RTK2 and mesenchymal were associated with an improved response to regorafenib. Copy number variation analysis showed that imbalances in the p53-MDM2 and cyclin-Rb pathways negatively predict response to treatment. Multivariate analysis demonstrated that CCND2 gene gain/amplification and chromosome 13 deletion, encompassing the RB1 gene, were associated with reduced PFS, while, MDM2 gain/amplification was linked to dimished OS. We developed methylation-based scores for predicting PFS and OS outcomes. Notably, the PFS score exhibited a 100% negative predictive value, enabling precise patients’ selection. Differentially methylated region analysis suggested that resistance to regorafenib may involve disruptions in WNT signaling, cadherin-mediated adhesion, and presenilin pathways.


title: Driver mutation landscape of acute myeloid leukemia provides insights for neoantigen-based immunotherapy [RNA-seq]

overall_design:
Comprehensive transcriptome sequencing  was performed on a total of 147 AML patients  .

***************************************************************
Submitter statement concerning missing raw data: Law restrictions prohibit us from publicly sharing raw sequencing data, which however can be made available upon reasonable request and permission of the local ethics committee.
***************************************************************


title: The Role of Placental DNA Methylation in the Pathogenesis of Chronic Intervillositis of Unknown Etiology

status: Public on Dec 30 2025

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

summary: Objectives: Chronic intervillositis of unknown etiology (CIUE) is the pathological influx of maternal inflammatory cells into the intervillous space of the placenta without demonstrable cause. CIUE is associated with placental damage and increased risk of pregnancy loss, fetal demise, and growth restriction. The pathogenic mechanism is unclear, and we lack biomarkers for detection, and treatments to prevent recurrence. DNA methylation (DNAme) is a biomarker altered in association with many disease states. We hypothesized that CIUE may be associated with a distinct signature placental DNAme signature.    Methods: DNAme was profiled using the Illumina Infinium MethylationEPIC v2.0 array on fresh-frozen placental tissue. After quality control, data were available for 24 CIUE (14 high grade, 10 low grade) and 27 non-CIUE placental samples, plus six independent decidua samples. CIUE was confirmed and graded by a perinatal pathologist. Contamination was assessed using the 65 array genotyping probes, placental cell composition and epigenetic age were estimated. After processing, DNAme data were available at 855,732 CpGs.    Results: Several lines of evidence indicated maternal DNA in CIUE placentas. Genetic contamination metrics were higher in CIUE than non-CIUE cases. In XY samples, X chromosome copy number increased with CIUE grade, suggesting XX contaminating DNA. Principal components analysis placed CIUE samples closer to decidua along PC1 than non-CIUE samples, cell composition showed elevated Hofbauer cells, monocytes, and neutrophils in CIUE. Epigenetic age was higher in CIUE versus non-CIUE samples. Together, these findings suggested an increased concentration of non-self XX DNA in CIUE cases, likely originating from an adult, macrophage-rich source, suggesting a maternal origin. An epigenome-wide association study found that all significant differentially methylated loci associated with CIUE were attenuated after adjusting for cell composition.     Conclusions: Our results illustrate that placental DNAme patterns in CIUE reflect signatures of maternal infiltration rather than intrinsic DNAme alterations. This study also highlights the value of integrating the diverse molecular data outputs of DNAme arrays to explore the presence of maternal cells in placental tissue.     ***************************************************************  IDAT files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable SNP genotyping data for open access but are available upon reasonable request to JT or WPR for research use.  ***************************************************************

overall_design:
DNAme data for 51 fresh-frozen placental (chorionic villi)  samples was profiled with the Illumina Infinium MethylationEPIC v2.0  array in Vancouver, Canada. DNAme data from raw IDAT files were read into R and processed with the minfi and ewastools packages. Methylated intensity, unmethylated intensity, and detection p values were calculated for all probes. The raw data (meth/unmeth/detp) is available, as are the full beta value matrices after data processing. H&E-stained slides of correlated formalin fixed paraffin embedded tissue for each CIUE sample were reviewed by a perinatal pathologist (JT) to ensure accurate diagnosis. CIUE was defined as low grade if between 5-50% of the placental intervillous space was occupied by histiocytes (with or without associated fibrin) and high grade if 50% or more of the space was involved, as previously described. IFNγ protein level expression status (positive/negative) was assessed  in all samples. For cases in this study, aneuploidy was determined by a combination of (i) clinically performed quantitative fluorescent polymerase chain reaction (ii) chromosomal microarray performed on a research basis, and (iii) copy-number analysis performed on the DNAme data with the conumee 2.0 R package. Because placental samples used for DNAme arrays were obtained from a single small sampling location, we were unable to distinguish between whole-placenta aneuploidy and confined placental mosaicism, and all aneuploid samples were annotated with the understanding that they may in some cases be mosaic.
*** IDAT files were not available due to patient privacy concerns***

first: Amy

middle: M

last: Inkster

first: Maria

middle: S

last: Peñaherrera

middle: P

first: Jefferson

last: Terry


title: Chromatin Assembly Factor 1 is Required for Normal Gene Repression and Facultative Heterochromatin Formation in Neurospora crassa [ChIP-seq]

status: Public on Dec 26 2025

city: Athens

first: Zachary

middle: A

last: Lewis

state: GA

address: 120 E. Green St.

department: Microbiology

country: USA

institute: University of Georiga

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Formation of facultative heterochromatin by Polycomb Repressive Complex 2 (PRC2) is a well conserved epigenetic mechanism that functions to control transcriptional dynamics across eukaryotes. PRC2 catalyzes histone H3 lysine 27 tri-methylation (H3K27me3), a histone post-translational modification that helps maintain stable gene repression. Gene repression by PRC2 is important for organismal development and defects in PRC2 function are associated with human ailments, such as Weaver syndrome and various cancers. In this study, we reveal the replication-dependent histone chaperone, Chromatin Assembly Factor 1 (CAF-1), is required for normal facultative heterochromatin formation in model fungus N. crassa. CAF-1 deficiency results in widespread misregulation of gene expression, particularly within facultative heterochromatin domains, which is accompanied by a rearrangement of H3K27me3 patterns. Regional losses of H3K27me3 are associated with reduced levels of ASH-1 catalyzed H3K36 methylation, and gains of histone modifications associated with active transcription. Furthermore, analysis of a double mutant deficient for both CAF-1 and PRC2 activity revealed that these complexes play distinct roles in maintaining gene repression and facultative heterochromatin. Collectively, these results shed light on CAF-1's role in maintaining a repressive chromatin environment.

overall_design: ChIP-seq performed on mycelial tissue after overnight growth in WT and mutant strains

first: Eduardo

middle: V

last: Torres

first: Collin

middle: D

last: Link

first: Rochelle

last: Yap

first: Aileen

middle: R

last: Ferraro

first: Abigail

last: Deaven

first: Jackie

middle: F

last: Pelham


title: Selection, development and structural characterization of 2' FY-RNA aptamers for pyoverdine

city: Ames

first: Marit

last: Nilsen-Hamilton

state: Iowa

address: 2437 Pammel Dr

department: BBMB

institute: Iowa State University

summary: Pyoverdines are siderophores employed by a variety of pseudomonas species to capture essential iron by which their growth is supported in many environments in which they can be harmful or helpful to coinhabiting species or the organisms that they inhabit. Of the Pseudomonas fluorescens group, the pyoverdine of each pseudomonad species is constituted of a central chromophore and a unique peptide component that is produced by nonribosomal peptide synthetases. Pyoverdine Pf5 (PYO-Pf5) is the product of pseudomonas protegens, a species that supports plant growth, particularly in soils with limiting iron. To explore the dynamics of P. protegens activity in soil, we have selected 2’ FY modified RNA aptamers that selectively recognize PYO-Pf5 with high affinities. Two 2’FY-RNA aptamers, with different base sequences, were selected that specifically bind pyoverdine-Pf5 (PYO-Pf5) over pseudobactin (PSB), a related pyoverdine, and two other siderophores, enterobactin and ornibactin. The 2’FY-RNA aptamers were shown to be G-quadruplexes by computational prediction, N-methyl mesoporphyrin IX (NMM) binding and CD spectroscopy. They were compared with their counterparts (same base sequence) in RNA and DNA for function and structure. Whereas the 2’FY-RNA and RNA forms bound PYO-Pf5 and had circular dichroism (CD) spectra typical of a G-quadruplex, the DNA forms neither bound PYO-Pf5 nor showed diagnostic NMM binding or CD spectra for G-quadruplexes. The impact of 2’ moiety in aptamers on their structure and function have been explored and results revealed that the nature of the chemical group at the 2’ position influences binding activity and structure.The aptamers will be applied to a nanoporous aluminum oxide biosensor to detect PYO-Pf5. This sensor provides a future opportunity to track the locations around plant roots of P. protegens and to monitor PYO-Pf5 production and movement through the soil.

overall_design: SELEX was performed with PYO-Pf5 as target to select 2’FY-RNA aptamers. For the first round of selection libraries of 1015 2’ FY-RNA were used. The biotinylated capture oligos, which are complementary to the short constant region in the library sequence, were attached to streptavidin coated magnetic beads. The 2’ FY-RNA libraries were first hybridized with oligos complementary to the PCR primer regions and then immobilized on the beads by hybridization with the capture oligos. The length of the capture oligo varied with the SELEX round as did the hybridization temperature and the oligo: PYO-Pf5 ratio . The bound oligos were captured using a magnet and purified by ethanol precipitation in the presence of 2 µL linear polyacrylamide (LPA) . Purified 2’FY-RNA was reverse transcribed and amplified by low fidelity Taq polymerase. The ratio of 2’FY-RNA to PYO-Pf5 was reduced and the length of capture oligo increased in successive SELEX rounds to increase selection pressure .  Nine rounds of selection were performed, and two sequential rounds of counter selection were done after rounds 3 and 6. The targets for counter selection were enterobactin and ornibactin. All targets used in selection and counter-selection were the Fe3+-bound forms. PCR-amplified libraries were prepared for NGS using Nextera Illumina sequencing primers and the appropriate bar coding. Next generation sequencing was performed by  Novogene facility, Sacramento, California using HiSeq PE150 platform. The raw NGS data was demultiplexed and assigned to respective rounds by open-source software AptaSuite. Barcodes were used to assign DNA pools from different rounds of selection. A zero-nucleotide mismatch between the reference and matched barcodes, and two mismatches between the reference and matched primers were criteria for demultiplexing.  Further analysis was done with the sequences that met this standard. Clustering was done with 10 iterations of locality sensitive hashing, sampling 55% of the indices in the randomized regions and allowing no more than 10 nucleotide mismatches between the seed sequence of a cluster to each remaining member. Clusters were extracted for further analysis and aptamer screening.

first: Sharif

last: Anisuzzaman


title: Distinct Physiological and Transcriptomic Responses between Tolerant and Susceptible Rapeseed (Brassica napus) Germplasm to Submergence Stress

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

institute: Northwest A&F University

summary: Waterlogging and submergence are major abiotic stresses impairing rapeseed development and hence evaluation of waterlogging tolerance ability is crucial for the development of tolerant lines through breeding approaches. This study investigated submergence impact on the survival rate, physiological responses, and transcriptomic variation of the young seedlings of 706 Brassica napus germplasm. We identified 57 highly tolerant and 109 highly susceptible accessions underwent six days submergence. Most accessions originated from the downstream of Yangtze River region had higher tolerance level. SOD enzymic activity increased both in the five representative tolerant and susceptible genotypes under submergence stress. POD activity also increased in the tolerant genotypes whereas CAT activity decreased, showing a opposite trend compared to the susceptible genotypes. The tolerant genotypes showed less chlorosis and produced less malondialdehyde than that in the susceptible group, while soluble protein content increased more than that in the susceptible genotypes. Transcriptome analysis detected 5,072 and 5,063 up-regulated genes, as well as 3,512 and 3,889 down-regulated genes in the tolerant / susceptible group in comparison to their respective control. Many genes encoding the transcription factors in AP2/ERF, bHLH, MYB, WRKY, and NAC families were also significantly regulated. The differentially expressed genes shared by the two pairs comparison were mainly enriched in such KEGG pathways as circadian rhythm, tryptophan metabolism, and porphyrin and chlorophyll metabolism. The specific pathways in the tolerant group were enriched in carbon metabolism, phenylpropanoid biosynthesis, and biosynthesis of amino acid etc. while the specific pathways in the susceptible group were more distributed in hormone signal transduction, sucrose and starch metabolism, and vitamin B6 metabolism etc. The results uncovered distinct physiological and transcriptomic differences between tolerant and susceptible genotypes.

overall_design: The young seedlings of five resistant and five sensitive germplasm were divided into two groups: the control group cultivated under normal conditions and the treatment group submerged in water for 24 hours. Then equal amounts of young seedlings of each genotype were mixed for RNA extraction, with three biological replicates for each sample.

first: Xing

last: Su

first: Ronghao

last: Guo

first: Yongli

last: Fu


title: Chromatin Assembly Factor 1 is Required for Normal Gene Repression and Facultative Heterochromatin Formation in Neurospora crassa [RNA-seq]

overall_design: RNA-seq performed on mycelial tissue after overnight growth in WT and mutant strains

middle: E


title: WSTF deficiency reprograms regulatory networks by linking locus‑specific chromatin remodeling to altered isoform expression and misdirected signaling [mRNA-seq]

status: Public on Dec 24 2025

city: Tallahassee

first: Shahin

last: Behrouz Sharif

state: Florida

address: 319 Stadium Dr.

department: Biological Sciences

institute: Florida State University

summary: Loss of the chromatin remodeler WSTF (BAZ1B), a gene deleted in Williams syndrome, causes reproducible, genome-scale reprogramming of chromatin states and transcript processing that links altered chromatin composition to misprocessed transcripts and aberrant signaling. Using engineered HCT116-WSTFKO cells and patient-derived Williams syndrome cell lines, we combine transcriptome profiling, microscopy, chromatin CUT&RUN, and histone post-translational modification (HPTM)-defined chromatin state modeling to show that WSTF localizes to promoters and gene bodies of actively transcribed loci together with ASH2L and CBP. Loss of WSTF causes depletion of ASH2L/CBP, selective loss of H3K4me2 and multiple acetylation marks, and gain of Polycomb components.  This loss results in systematic conversion from a multi-mark active promoter/enhancer chromatin landscape to a hypoacetylated, H3K4me2-depleted, PRC-enriched landscape. These chromatin changes coincide with widespread isoform switching and splicing alterations in genes encoding chromatin regulators and signaling pathways. This WSTF deficiency produces Wnt/β-catenin hyperactivation. A locus-specific example at TCF7L2 demonstrates how gene body loss of active marks drives isoform switching that alters DNA binding domains and decouples stabilized nuclear β-catenin from canonical target engagement. Our results link signaling dysregulation to developmental pathway misregulation consistent with Williams syndrome phenotypes.

overall_design:
mRNAseq profiling  of wild-type HCT116 cells and two biological replicates of its WSTF knock-out derivative.
mRNAseq profiling  of Corriel-derived B-cell lines including GM14295, GM14296, and GM14297, corresponding to William's syndrome family.

first: Jonathan

middle: H

last: Dennis


title: WSTF deficiency reprograms regulatory networks by linking locus‑specific chromatin remodeling to altered isoform expression and misdirected signaling [CUT&Run]

overall_design:
CUT&RUN of WSTF, SNF2H, ASH2L, CBP, EZH2, CBX4, LaminB, H2AK119ub, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me3, H3K9ac, H3K14ac, H3K27me3, H3K27ac, H3K36me2, H4K5ac, H4K8ac, H4K12ac, and H4K20me1 in two technical replicates of HCT116 cells
CUT&RUN of SNF2H, ASH2L, CBP, EZH2, CBX4, LaminB, H2AK119ub, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me3, H3K9ac, H3K14ac, H3K27me3, H3K27ac, H3K36me2, H4K5ac, H4K8ac, H4K12ac, and H4K20me1 in two biological replicates of HCT116-WSTFKO cells


title: Synergistic Effects of High-Fiber Diet and N-Carbamylglutamate on Sow Reproductive Performance via Uterine Microbiota-PI3K/Akt Modulation

city: Nanjing

first: Yaxu

last: Liang

state: 江苏省

address: 江苏省南京市玄武区南京农业大学

institute: Nanjing agricultural university

summary: Landrace x Yorkshire sows were selected to investigate the synergistic effects of high fiber diet and 0.05% NCG on reproductive performance through transcriptomic analysis of endometrium samples.

overall_design: The sows were randomly assigned to four dietary treatment groups (n = 100 per group) as follows: low-fiber group (LF; 3.73% crude fiber); low-fiber + NCG group (L+N; 3.73% crude fiber + 0.05% NCG); high-fiber group (HF; 7.46% crude fiber); high-fiber + NCG group (H+N; 7.46% crude fiber + 0.05% NCG). The experimental was initiated on the day of breeding and continued throughout the entire gestation period of 114 days.

first: Hongyang

last: Wang

first: Yongsong

last: Tan


title: Gene expression profiles in S2-007, S2-020 and S2-028 pancreatic ductal adenocarcinoma cell lines

city: Yonago

first: Hirotoshi

last: Mochida

state: Tottori

address: 86 Nishi-cho

department: Pathology

institute: Faculty of Medicine, Tottori University

summary: To investigate the subcellular localization of maspin in pancreatic ductal adenocarcinoma (PDAC) and its functional relevance, gene expression profiles were analyzed in S2-007 (expressing nuclear and cytoplasic maspin), S2-028 (expressing cytoplasmic-only maspin), and S2-020 (expressing weakly maspin) cells. The data provides insight into the differential function of maspin in PDAC depending on its subcellular localization.

overall_design: Total RNA from these cells were recovered using Rneasy MINI Kit. To purify the strand-specific mRNA library, the mRNA was reverse transcribed into cDNA using random primers, and then the synthesized double-strand cDNA was fragmented, and the cDNA was subsequently ligated adapters. Transcriptome sequencing in strand-specific mRNA-seq library was performed using illumine NovaSeq 6000 Sequencing System.

first: Tomohiko

last: Sakabe

first: Yoshihisa

last: Umekita


title: Isw2-dependent chromatin remodeling at the CRZ1 promoter governs azole tolerance in Candida albicans

status: Public on Dec 23 2025

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

institute: Universite de Montreal

summary: Here, we conducted a quantitative analysis of transcription factor deletion mutants in Candida albicans to identify novel modulators of azole tolerance. We found that loss of ISW2, which encodes the catalytic subunit of an ATP-dependent chromatin-remodeling complex, markedly increased azole tolerance, establishing Isw2 as a negative regulator of this phenotype in C. albicans. By integrating RNA-seq and ChEC-seq analyses, we defined the Isw2 regulon and discovered that this remodeler binds and modulates nucleosome dynamics at the promoter of CRZ1, a transcription factor that acts downstream of the calcineurin pathway and is a key regulator of azole tolerance. Consistent with this, CRZ1 transcript levels were elevated in the isw2 mutant, supporting a model in which Isw2 modulates antifungal tolerance by directly restricting CRZ1 transcription.

overall_design: In this study, we identified transcripts that were differentially regulated in the isw2 mutant, which lacks the chromatin remodeler Isw2. The transcriptional profile of isw2 cells grown in the synthetic complete medium supplemented or not with the antifungal amphotericin B (0.45 µg/ml) was compared to that of the wild-type (WT) strain grown under the same conditions. For ChEC-seq, DNA cleavage profiles from Isw2-MNase cells (C-terminal MNase-tagged ISW2 at the native locus) were normalized to those from MNase-free control cells (WT cells with ectopic MNase expression).

first: Antony T.

last: Vincent

first: Maria Juliana

last: Mantilla

first: Faiza

last: Tebbji

first: Andrew

last: Chatr-aryamontri


title: Transcriptional Profiling of Zebra Finch Hypothalamus After Chronic Heat Call Exposure

status: Public on Dec 22 2025

city: Clemson

first: Prakrit

last: Subba

state: SC

address: 132 Long Hall, 230 Parkway Drive

institute: Clemson University

summary: Late-stage zebra finch embryos were exposed to chronic playback of parental heat calls or control sounds to test how acoustic cues of extreme heat reshape hypothalamic gene expression. RNA-seq of medial hypothalamic punches revealed modest changes in neuroendocrine genes but strong downregulation of muscle and cytoskeletal programs, with evidence of altered isoform usage and enrichment in neurovascular cell populations. These findings indicate that parental heat calls drive a non-neuroendocrine transcriptional program underlying early-life developmental plasticity and acoustic-mediated adaptation to environmental extremes in birds.

overall_design: Embryonic zebra finch (Taeniopygia guttata) eggs from breeding pairs were incubated at 37.5°C and, on embryonic day 10 (E10) in the morning, were randomly allocated to either heat-call playback (whine + heat calls; n=10) or control-call playback (whine + tet calls; n=9) using a within-clutch design that balanced laying order. Playbacks were delivered via speakers attached to incubators from E10-E13 for 9 h/day over 4 days, with eggs and playbacks swapped daily between incubators to minimize incubator-specific effects. On the night of E13, all embryos were transferred to a new incubator without playback so both groups experienced identical conditions immediately prior to sampling and the experimenter could be blind to treatment. On E14 (10:00-12:00), embryos were removed from the egg and decapitated, and one 1 mm medial hypothalamic punch was collected from 100 um coronal cryosections at the level where the third ventricle first became visible; punches were frozen on dry ice and stored at -80°C. RNA was sequenced on an Illumina NextSeq 500 (75 bp, paired-end) following adapter/quality trimming (Trimmomatic v0.39), and expression was analyzed to test effects of playback condition (and sex, where applicable), with downstream co-expression network, pathway enrichment, and cell-type deconvolution analyses to link transcriptional changes to hypothalamic cell populations.

first: Katerina

last: Palios

first: Michael G.

last: Emmerson

first: Elisabetta

last: Versace

first: Katherine L.

last: Buchanan

first: Mylene M.

last: Mariette

first: David F.

last: Clayton

first: Julia M.

last: George


title: Vaccine Delivery Platforms Affect Heterologous Protection by Hemagglutinin-Based Influenza Vaccines in Pigs

status: Public on Dec 19 2025

city: Lincoln

first: Hiep

last: Vu

state: Nebraska

address: 4240 Fair St

department: Animal Science and Nebraska Center for Virology

institute: University of Nebraska-Lincoln

summary: Vaccine-associated enhanced disease (VAED) poses a significant challenge in vaccine development for certain diseases. Vaccine-associated enhanced respiratory disease (VAERD), a form of VAED, has been observed in pigs vaccinated with whole-inactivated vaccine against influenza A virus (IAV) vaccines, followed by an exposure to antigenically mismatched virus strains. Similar outcomes have been reported in pigs vaccinated with a protein-based vaccine containing hemagglutinin (HA), a key viral surface antigen of IAV.  We recently developed a lipid nanoparticle encapsulated DNA vaccine encoding the HA gene of IAV, which induced robust immune responses after a single immunization and protected pigs against homologous IAV challenges. This study compared the immunogenicity and efficacy of HA-protein-based and HA-DNA-based vaccines against an antigenically mismatched IAV strain in pigs. While the HA protein-based vaccine exacerbated lung consolidation compared to non-vaccinated controls, the HA-based DNA vaccine prevented gross lung lesion development. Transcriptome analysis revealed distinct gene expression profiles, highlighting differences in host immune responses. These findings provide direct evidence that the same vaccine antigen, when delivered through different platforms, can result in different outcomes: protection versus disease enhancement. This underscores the importance of selecting appropriate delivery platforms for vaccine development. Furthermore, the IAV vaccine in pigs could be a valuable model for studying the immunological mechanisms underlying vaccine-enhanced diseases.

overall_design: A total of 18 pigs, 3 weeks old and seronegative for swine influenza A virus, were assigned to three treatment groups. After a 1-week acclimation period, Group 1 received a single intramuscular dose of the pdm09-LNP vaccine, which consisted of 500 µg of a DNA plasmid encoding the HA protein of the H1N1 pdm09 influenza virus, encapsulated in lipid nanoparticles. Group 2 received the pdm09-protein vaccine, administered as two intramuscular doses 21 days apart. This vaccine contained 10 µg of purified recombinant HA protein expressed using a baculovirus expression system and emulsified in an oil-in-water adjuvant. The doses were given at 4 and 7 weeks of age. Group 3 did not receive any treatment and served as a negative control. Peripheral blood mononuclear cells (PBMCs) were collected at 10 weeks of age and sent to Azenta Life Sciences for RNA sequencing. Total RNA was extracted, and poly(A) RNA was purified. RNA sequencing was performed on an Illumina platform with 2 × 150 bp reads, generating approximately 20 million paired-end reads per sample.

first: The

middle: N

last: Nguyen

first: Danh

middle: C

last: Lai

first: Hung

middle: Q

last: Luong

first: Sushmita

last: Kumari

first: Kassandra

last: Matinez

first: Sarah

last: Sillman


title: Different modes of engagement with the nucleosome acidic patch yield distinct functional outcomes

city: Durham

first: Michael-Christopher

last: Keogh

state: NC

address: 6 Davis Dr

institute: EpiCypher, Inc

summary: The nucleosome acidic patch is a hub of coordinated engagement by proteins that regulate genomic function. Here we report that S. cerevisiae Dot5 contains an arginine-rich HMGN-like motif that mediates nucleosome acidic patch binding and is required for the cell growth, DNA repair and heterochromatin defects that are exhibited when the protein is overexpressed. The heterologous expression of single chain antibodies to the nucleosome acidic patch confers a similar range of phenotypes, with the most severe observed when an ‘arginine-anchor’ mode of binding analogous to many endogenous factors is employed. This highlights a delicate balance between nucleosome acidic patch interactors that are critical for normal cellular functions and dysregulated in disease.

overall_design:
Genome binding/occupancy profiling by high throughput sequencing
CUT&RUN reactions performed in yeast (S. cerivisiae) cells

first: Ujani

last: Chakraborty

first: Emma

last: Saccone

first: Grisel

last: Cruz-Becerra

first: Laiba

last: Khan

first: Nina

last: Arslanovic

first: Rhiannon

last: Aguilar

first: Susan

middle: L

last: Gloor

first: Sabrina

last: Hunt

first: Heather

middle: J

last: Folkwein

first: Natalia

last: Ledo Husby

first: Keith

last: Maier

first: Matthew

last: Marunde

first: Noah

middle: K

last: Schomburg

first: Anup

last: Vaidya

first: Martis

middle: W

last: Cowles

first: Bryan

last: Venters

first: George

last: Kassavetis

first: Zu-Wen

last: Sun

first: James

middle: T

last: Kadonaga

first: Jean-Paul

last: Armache

first: Jessica

last: Tyler


title: Ancestry-Linked IL-10 Signaling and Macrophage Activation Modulate Fibroblast Responses to Oxidative Stress in a PEG-Based Microphysiological System

city: College Park

first: Erika

middle: Taylor

last: Moore

state: Maryland

address: 3102 A. James Clark Hall

department: Bioengineering

institute: University of Maryland

summary: Fibroblast responses to injury are shaped by cytokine signaling and macrophage activation, yet the extent to which these pathways vary across individuals, and how ancestry-associated immune differences influence fibrosis risk, remains poorly understood. Here, we developed a poly(ethylene glycol) (PEG)-based hydrogel microphysiological system to model fibroblast–macrophage interactions following oxidative stress and integrate donor-specific immune signals using matched macrophages and serum. Circulating monocytes from individuals of self-reported African American ancestry exhibited higher expression of CCL4 and increased serum IL-10, whereas those from European ancestry donors showed elevated OXER1 expression. Within the hydrogel, oxidative stress reduced fibroblast number while inducing Ki67 and p16. Exogenous TGF-β1 enhanced fibroblast survival and collagen 3 production but did not independently increase α-smooth muscle actin (α-SMA). Anti-inflammatory macrophages promoted fibroblast activation through mechanisms resistant to TGF-β receptor inhibition. Incorporating donor-derived macrophages and serum revealed that cultures from individuals of European ancestry demonstrated higher fibroblast α-SMA and p16 expression, despite lower systemic IL-10 levels. Pharmacologic inhibition of IL-10 further increased α-SMA, particularly in European ancestry–derived cultures, identifying IL-10 as a key protective signal limiting fibroblast activation. This hydrogel system provides a platform for dissecting inter-individual immune variation and identifying mechanisms underlying ancestry-associated fibrosis risk.

overall_design: In this study, monocytes from 24 human donors were analyzed for the expression of 269 inflammation-related genes to compare molecular profiles across sex and ancestry.

first: Nana

last: Owosu-Boaitey

last: Taylor Moore


title: Identifying membrane-bound transcriptional regulatory proteins from rare but evolutionarily conserved domain combinations

status: Public on Dec 18 2025

city: Austin

first: Muyoung

last: Lee

state: TX

address: 2506 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Transcriptional regulatory proteins, including transcription factors (TFs) and chromatin modifiers, perform their crucial cellular functions inside cell nuclei. However, unlike most TFs, membrane-bound transcription factors (MBTFs) are first anchored in membranes before nuclear translocation. Known MBTFs are vital for processes from myelin expression (MYRF) to cholesterol homeostasis (SREBP), yet their overall diversity remains uncharted. We hypothesized that additional membrane-bound transcriptional regulators (MBTRs) might exist and developed a bioinformatics screen that prioritizes membrane proteins likely to regulate transcription. Our approach leverages domain composition, assuming that surprising domain combinations suggest novel biological functions. We searched for rare but evolutionarily conserved combinations of transmembrane domains paired with domains likely involved in transcriptional regulation. Our method rediscovered known MBTFs and membrane-bound histone kinases, and identified novel MBTR candidates, including histone N-acetyltransferases and the prolactin regulatory element-binding protein PREB. Experimental validation indicates that PREB may undergo cleavage. Without its transmembrane domain, PREB exhibits nuclear localization and chromatin association in mouse embryonic stem cells. Furthermore, we identified a putative class of new MBTFs that share MYRF's DNA-binding domain. These findings underscore the utility of our method and provide a framework for investigating MBTRs that likely facilitate the integration of extracellular signals with transcriptional responses.

overall_design: bioChIP-seq was performed on PREB- and PREBΔTM-expressing ES cells treated with 0.5 µg/mL Dox for 24 hours as previously described (21). Cells were cross-linked with 1% formaldehyde (Fisher Bioreagents, BP531-500) for 7 minutes at room temperature, and the reaction was quenched by adding glycine (Fisher Scientific, BP381-1) to a final concentration of 0.125 M. The chromatin was sheared to an average fragment size of ~200 bp using a Bioruptor sonicator (Diagenode). Cross-linked chromatin was pre-cleared with Protein A agarose beads (Thermofisher, 10008D) and subsequently subjected to immunoprecipitation using Dynabeads MyOne Streptavidin T1 (Invitrogen, 65602). Immunoprecipitated complexes were washed twice with 2% SDS, once with buffer A (0.1% Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 500mM NaCl), once with buffer B (250mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1mM EDTA, 10mM Tris-Cl pH 8.1), and twice with TE buffer. The crosslinked protein-DNA complexes were reversed with an elution buffer (1% SDS, 10mM EDTA, 50mM Tris-Cl 8) to the washed beads and were incubated at 65°C overnight. RNase A (Thermo Scientific, EN0531) was then treated for 30 minutes, followed by treatment of proteinase K (NEB, P8107S) for 2 hours. DNA was extracted with phenol:chloroform:isoamyl alcohol (Invitrogen, 15593031), then precipitated and re-suspended in the TE buffer. Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit (NEB, 7103L), and sequencing was conducted on an Illumina NovaSeq 6000 platform to generate 50-bp paired-end reads. Comparison of the samples with the BirA-only control allowed identification of target-specific binding sites, and IgG ChIP served as a negative control, providing a background signal.

first: Yeejin

last: Jang

first: Qingqing

last: Guo

first: Jonghwan

last: Kim

first: Edward

middle: M

last: Marcotte


title: Hypoxia-activated scleraxis a mediates epicardial progenitor differentiation into a unique cardiac perivascular cell type

city: New York

first: Jingli

last: Cao

state: NY

department: Cell & Developmental Biology

institute: Weill Cornell Medical College

summary: The epicardium is a crucial source of progenitor cells and paracrine signals that support heart development and regeneration. However, the molecular mechanisms that guide epicardial cell fate decisions remain incompletely understood. Here, we identify the transcription factor Scleraxis a (encoded by scxa) as a key regulator of epicardial progenitor differentiation in zebrafish. Through single-cell transcriptomics, genetic lineage tracing, and cardiac injury models, we show that scxa is transiently induced in activated epicardial progenitor cells (aEPCs) during both heart regeneration and developmental coronary angiogenesis. scxa+ epicardial cells primarily give rise to a previously uncharacterized cardiac population of perivascular cells marked by col18a1a, molecularly distinct from classical pericytes and vascular smooth muscle cells. We refer to this population as epicardial-derived perivascular mesenchymal cells (Epi-PMCs). These Epi-PMCs closely associate with coronary vessels and may contribute to vascular stabilization and remodeling, potentially through the anti-angiogenic but vessel-stabilizing activity of endostatin derived from collagen XVIII. Loss of scxa increases coronary vessel density. Mechanistically, we identify hypoxia and Hif1a signaling as upstream regulators of scxa, with systemic hypoxia or Hif factor stabilization robustly inducing scxa expression in the epicardium. Together, these findings uncover a hypoxia-responsive Scxa-Col18a1a axis that drives epicardial differentiation toward a vascular-supportive fate, offering new insight into the regulation of coronary vessel development and the regenerative potential of the epicardium.

overall_design: CUT&Tag of histone modification H3K4me1 of epicardial progenitor cells. Heart amputation surgery was performed on adult fish (6 months of age) carrying tcf21:nucEGFP and ptx3a:mScarlet reporters. Hearts were isolated at 3 days post injury together with the uninjured control (2 biological replicates each). Ventricles were digested and EGFP+ cells (uninjured) and EGFP+mScarlet+ (3 dpa) cells were isolated for CUT&Tag processing.

first: Jun

last: Yao

first: Yu

last: Xia


title: Hv1 upregulation worsens spinal, spleen, and lung molecular pathology and impairs locomotion after spinal cord injury in aged male mice

status: Public on Dec 17 2025

city: Baltimore

first: Hangnoh

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

summary: Spinal cord injury (SCI) induces both intraspinal damage and systemic organ pathology, with aging as a major determinant of outcome. However, how advanced age exacerbates SCI pathology remains unclear. The voltage-gated proton channel Hv1, a regulator of immune activation, increases with age and after SCI, and its deletion is neuroprotective in young mice.  Thus, we hypothesized that age-related Hv1 upregulation worsens spinal cord, spleen, and lung pathology and hinders locomotor recovery after SCI through immune modulation. Using aged Hv1 KO and WT male mice subjected to moderate SCI, we assessed behavioral and molecular outcomes. Transcriptomic analysis revealed that Hv1 mRNA expression was higher in the brains of aged sham mice and further upregulated in injured spinal cord tissues. Spinal cord RNA-seq showed acute innate immune and cytokine activation in both genotypes. Hv1 deletion enhanced chromatin remodeling, epigenetic and Wnt signaling, while suppressing NF-κB–driven inflammation and oxidative stress–induced apoptosis. In the spleen, Hv1 depletion enhanced immune responses while suppressing mitosis. T cell and leukocyte activation increased, whereas lung cytokine signaling decreased. At 6 weeks after SCI, Hv1 KO mice showed elevated expression of genes related to circadian rhythm and T cell proliferation in the spinal cord, increased mitotic gene expression but reduced adaptive immunity in the spleen, and enhanced immune activation with decreased cilium activity in the lungs.

overall_design: RNA-Seq gene expression profiling was performed on 18–22-month-old male C57BL/6 (WT)  and Hv1 KO mice subjected to either sham treatment or SCI. Total RNA was extracted from the spinal cord, lung, and spleen tissue samples at 7 days and 6 weeks post-injury.  Transcriptomic differences between Sham and Injury, WT and KO mice were analyzed.

first: Zihui

last: Wang

first: Yun

last: Li

first: Junfang

last: Wu


title: Differential nucleosome organization in human interphase and metaphase chromosomes [ChemMap]

city: Evanston

first: Xiaozhong

state: IL

address: 2200 Campus Dr

institute: Northwestern University

summary: Mitosis induces profound changes in chromosome structure, impacting nucleosome organization. Here, we employed chemical mapping to achieve single-base-pair resolution of nucleosome positioning in human interphase and metaphase chromosomes, unveiling distinct organizing principles between the two states. During interphase, we observe greater variability in internucleosome spacing, with a higher abundance of shorter linkers compared to metaphase, reflecting the genome's adaptability in accommodating nucleosome arrays for gene expression. Local analyses further uncover differential nucleosome landscapes at key euchromatin landmarks, including promoters, enhancers, and insulators, in each state. Moreover, we analyzed the relationship between DNA cyclizability and dyad positioning during mitosis. Our results indicate that in metaphase, nucleosomes exhibit significantly higher cyclizability around the dyad, whereas during interphase, nucleosomes more frequently position DNA with higher cyclizability in the nucleosome shoulder near regulatory genomic regions. Together, this study offers novel insights into the intricate interplay between DNA mechanics and nucleosome dynamics during mitosis.

overall_design: Through PiggyBac transgenic expression of an shRNA directed against a shared DNA sequence present in all human H4 genes and RNAi-resistant H4S47C cDNA, we generated H4S47C-substituted HeLa S3 stable cell lines suitable for efficient chemical cleavage of nucleosomes. Using these cells, we performed chemical nucleosome mapping experiments in both interphase and synchronized mitotic cells, with two replicates for each condition.

first: Keren

first: Irem

last: Unlu

first: Lilien

last: Voong

first: Xiaotian

last: Ma

first: Yiren

last: Tu

first: Ji-ping


title: Differential nucleosome organization in human interphase and metaphase chromosomes [MNase-Seq]

overall_design: MNase digestion of nucleosomal DNA in interphase and metaphase HeLa S3 cells was performed as described previously.


title: Differential nucleosome organization in human interphase and metaphase chromosomes [RNA-Seq]

overall_design: Total RNA-seq of 2 clones of Hela S3 cells were performed as a complimentary data for the analysis of nuclesome mapped by chemical mapping


title: Differential nucleosome organization in human interphase and metaphase chromosomes [Chemical Mapping]


title: Differential nucleosome organization in human interphase and metaphase chromosomes [RNA-seq]

overall_design: Total RNA-seq of Hela S3 cells were performed as a complimentary data for the analysis of nuclesome mapped by chemical mapping


title: Differential nucleosome organization in human interphase and metaphase chromosomes [Mnase-seq]


title: Integrated omics revealed regulatory mechanisms governing potato (Solanum tuberosum L.) seedling growth during shade avoidance syndrome

status: Public on Dec 16 2025

first: Zexue

last: He

state: Jiangsu Province

address: Xuanwu District,1 Weigang

department: Agricultural College

institute: Nanjing Agricultural University

summary:
Background: Potato (Solanum tuberosum L.) is the fourth largest food crop worldwide with significant economic value and importance for food security. Shade avoidance syndrome (SAS) considerably affects crop architecture and productivity in high-density planting systems; however, its molecular mechanisms in potato remain poorly understood.
Methods: Potato seedlings were subjected to four light treatments simulating different shade signals: white light (control, WL), low blue light (LBL, simulating blue light attenuation by plant canopies), low red:far-red ratio (WL+FR, simulating far-red reflection from neighboring plants), and their combination (LBL+FR, simulating complete plant shade environment). We conducted a comprehensive study integrating morphological characterization, leaf anatomical analysis, hormone quantification, transcriptome sequencing, and metabolite profiling.
Results: Morphological analysis revealed that WL+FR primarily induced internode elongation (+20.0%) and leaf hyponasty, while LBL promoted stem elongation through increased node production (+36.3%). When combined, these signals (LBL+FR) synergistically enhanced stem elongation by 79.3%. Anatomical examination showed that LBL-treated leaves formed thickened palisade tissue layers (176.34 μm) with 6-7 layers of spongy tissue, whereas WL+FR resulted in thinner leaves (151.22 μm). Transcriptomic analysis identified 6,057 differentially expressed genes enriched in photosynthesis, hormone signaling, and carbohydrate metabolism pathways. A total of 1,168 differentially accumulated metabolites were detected across treatments, particularly organic acids and lipids associated with TCA (tricarboxylic acid) cycle and starch-sucrose metabolism. Weighted gene co-expression network analysis (WGCNA) identified PHYTOCHROME A (PHYA) as the central hub gene coordinating SAS responses under combined light stress, significantly diverging from the PHYB-centric model established in Arabidopsis.

overall_design:
The experiment utilized 20-day-old potato plants (Solanum tuberosum L. cv. Atlantic) provided by the Agricultural Biotechnology Research Center, Ningxia Academy of Agriculture and Forestry Sciences. This cultivar was selected for its vigorous growth and broad adaptability. Virus-free plantlets were obtained through tissue culture and subcultured for three generations before experiment. Only plants with uniform growth were selected and transferred to soil, where they were acclimated for 14 days under a 16-h light/8-h dark cycle at 60% relative humidity. The growth environment simulated artificial shading conditions, with temperature maintained at 23-25°C. The experiment was conducted with six plants per treatment group. Light treatments were implemented using combinations of different LED light sources, including white light, blue light (400-499 nm), red light (600-699 nm), and far-red light (700-750 nm). To establish low R:FR conditions, far-red light (peak wavelength 730 nm) was supplemented to white light. For low blue light conditions, white light was passed through two layers of yellow filter (#101, Lee Filters, CA, USA). Light quality and intensity were measured using a HiPoint HR-350 spectrometer (wavelength range: 380-780 nm, accuracy: ±2 nm), and R:FR ratios were calculated according to the method described by Lyu et al [30].
Four light treatments were established to assess plant responses under varying light conditions. The white light treatment (WL) applied full-spectrum white LEDs with peak wavelengths at 450 nm and 570 nm, simulating a daylight-like spectrum. In the low blue light treatment (LBL), white light filtered through yellow filters, reducing blue light intensity to 1.5 μmol·m⁻²·s⁻¹.  For low R:FR treatment (WL+FR), far-red light was added to the white light, resulting in an R:FR ratio of 0.41. The fourth treatment combined WL+FR and LBL, and was referred to as LBL+FR.
Photosynthetically active radiation (PAR) was maintained at 500 μmol m⁻²s⁻¹ to observe plant responses during the transition from etiolation to de-etiolation. Light quality parameters were monitored every 2 h throughout a 14-day treatment period， with detailed records of photon flux density (PPFD; 400-750 nm) under each treatment condition

first: Li

last: Zhang

first: Feng-Jie

last: Nie


title: Single-cell RNA-seq analysis of PDX (Patient-Derived Xenograft) tumors isolated from mouse spleens, treated with Empty CAR, anti-CD72 H24 nanoCAR or anti-CD72 NbD4.13 nanoCAR.

status: Public on Feb 23 2026

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: Single-cell RNA-seq analysis was performed on human mantle cell lymphoma PDX (Patient-Derived Xenograft) tumors isolated from mouse spleens to examine gene expression changes after treatment of Empty CAR, humanized anti-CD72 nanobody-based CAR-T (“H24 nanoCAR”) or NbD4.13-based anti-CD72 nanoCAR-T.

overall_design: Human mantle cell lymphoma PDX tumor (DFBL44685) was implanted at 1 e6 cells/mouse, mice were then treated with Empty, H24 or NbD4.13 CAR at 5e6 CAR+ cells per mouse on day 10. Spleens were collected at day 70 after tumor implantation. Tumor cells were isolated from mouse spleens and sorted with gating on human CD45+ positive cells. The samples were processed using 10X chromium platform (Chromium Next GEM Immune Profiling 5'HT kit v2, 1000374). Illumina sequencing was performed on the PDX tumor samples using Illumina NovaSeq X 1.5B platform with paired-end 150 bp reads.

first: Adila

last: Izgutdina

first: Bonell

last: Patino Escobar

first: Arun

last: Wiita


title: HIV-1 expression is heterogeneous among clones of CD4+ T cells carrying authentic intact latent proviruses

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: Antiretroviral therapy suppresses HIV-1 infection but is not curative because it fails to eliminate a reservoir of intact latent proviruses that reside primarily in CD4+ T cells. This compartment is composed of rare T cells that predominantly express memory and effector memory markers. The lack of precise understanding of the latent compartment has made it challenging to develop curative strategies for HIV-1 infection. Here we report on the properties of CD4+ T cells clones carrying intact latent proviruses, expanded in vitro from single cells obtained from the reservoir of people living with HIV-1. The latent proviruses in the clones were integrated into ZNF genes, non-genic satellite and centromeric regions, frequently associated with latency. Notably, the transcriptome of the cultured clones resembled their cells of origin. Despite their descent from single cells, only a fraction of the cells ranging from 0.4-14% expressed relatively low levels of HIV-1 that did not measurably alter host gene transcriptome. Latency reversing agents (LRAs) variably increased the number and amount of expression per cell, but the effects were modest and clone and LRA specific. The results suggest that pharmacologic and immunologic approaches to clear the reservoir should be optimized to accommodate intra- and inter-clonal diversity.

overall_design: CD4+ T cells harboring intact latent proviruses were obtained from single cells from 7 ART-suppressed individuals and expanded in vitro. These expanded clones were analyzed at baseline (resting) and after 24 hours of stimulation (activated) with anti-CD3/CD28 + IL-2. We performed 5' single-cell RNA sequencing (scRNA-seq) and T-cell receptor (scV(D)J-seq) using the 10X Genomics platform to characterize proviral expression and the host cell transcriptome.

first: Cintia

last: Bittar

first: Ana

last: Teixeira

first: Gabriela

middle: S

last: Santos

first: Klara

last: Lenart

first: Marcilio

last: Fumagalli

first: Noemi

last: Linden

first: Isabella

middle: A

last: Ferreira

first: Marina

last: Caskey

first: R. Brad

last: Jones

first: Mila

last: Jankovic

first: Michel

last: Nussenzweig


title: Regulation of the Yersinia pseudotuberculosis Type III Secretion System by the CpxAR Two-Component System

city: Santa Cruz

first: Victoria

last: Auerbuch

address: 1156 High Street

department: Microbiology and Environmental Toxicology

institute: University of California Santa Cruz

summary: The type III secretion system (T3SS) is a cell envelope-spanning injectisome found in many Gram negative pathogens. Expression of the T3SS is controlled by extracellular signals such as cell envelope stress. For example, the CpxAR two component system negatively regulates the Yersinia pseudotuberculosis Ysc T3SS, although the mechanism for this regulation remains unclear. As expected from previous studies, we found that mutations in Y. pseudotuberculosis that lock CpxR in its constitutively activated state (∆cpxA and cpxRD51E) led to decreased expression of the Ysc T3SS. CpxR did not bind to the regulatory regions of lcrF, encoding the Ysc T3SS master regulator. However, overexpression of LcrF protein rescued the T3SS expression defect of the ∆cpxA and cpxRD51E mutants, suggesting that CpxR represses lcrF through an indirect mechanism. Transcriptome analysis of Y. pseudotuberculosis showed that 101 genes were upregulated and 77 genes downregulated in both the ∆cpxA and cpxRD51E strains compared to wildtype, including seven genes known to modulate transcription. Individual deletion of these seven regulatory factors did not identify any single gene responsible for CpxR-dependent repression of LcrF, suggesting that the CpxAR system may act through multiple pathways to indirectly regulate the Ysc T3SS. However, this analysis led us to examine the role of the OmpR/EnvZ two component regulatory system, which is responsive to osmolarity, in LcrF regulation. Deletion of ompR led to a two-fold increase in LcrF and T3SS expression. These results suggest more complex regulation of the Ysc T3SS by two component regulatory systems than previously appreciated.

overall_design: Yersinia pseudotuberculosis IP2666pIB1 strains with consitutive CpxR activation were generated, one lacking the cpxA gene (delta cpxA) and one posessing a cpxR allele coding for a phosphomemetic version of the protein (cpxRD51E). Mutant and wildtype strains were grown shaking at 26°C overnight in 2ml LB media and then subcultured to an OD of 0.2 in fresh low calcium LB supplemented with 20mM sodium oxalate and 20mM magnesium cholride. These cultures were grown shaking at 26°C for 1.5 hours and then shifted to 37°C shaking for 1.5 hours to mimic host infection conditions and induce Type III Secretion. Each sample was then pelleted and RNA extracted for sequencing.

first: Karen

last: Hug

first: David

last: Balderas


title: TBP regulates transposable element expression in early mouse embryos

status: Public on Dec 15 2025

city: Munich

first: Clara

last: Hermant

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells (IES)

country: Germany

institute: Helmholtz Zentrum Munich

summary: Activation of the embryonic genome is a crucial step in development. In addition to thousands of genes, many transposable elements (TEs) are robustly transcribed during early mammalian development. However, their transcriptional regulators remain largely unexplored. Here, we set out to identify transcription factors regulating the expression of highly expressed TEs from the LINE, SINE and ERVL families during mouse preimplantation development. In particular, the MaLR family are the most abundant ERVL in the mouse genome and are also the most abundant constituent of the transcriptome in early mouse embryos. Surprisingly, we find the general transcription factor TBP directly and specifically activates MaLRs. Loss-of-function of TBP in mouse embryos leads to downregulation of MaLRs, specifically the ORR1A family, which is the youngest ORR subclass and contributes a significant portion of major zygotic genome activation transcripts. We demonstrate that TBP regulates MaLRs through direct binding. Our work contributes to the identification of regulators of TE expression in vivo and highlights a previously unrecognised role for a general transcription factor in regulating an exquisitely specific TE transcriptional programme.

overall_design: Late 2-cell stage embryos were collected and Cut&Tag was performed using TBP antibody and IGG as control.

first: Maria-Elena

last: Torres-Padilla


title: TopBP1 controls conventional dendritic cell development and Flt3L-driven cDC1 differentiation via PU.1 and IRF8 [ChIP-Seq]

city: Suwon-si

first: Minsuk

last: Cha

address: 2066, Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University

summary: DNA topoisomerase II-binding protein 1 (TopBP1) plays a vital role in V(D)J recombination during B and T cell development. However, its role in the development of conventional dendritic cells (cDCs) remains unexplored. Mice with DC-specific depletion of TopBP1 (TopBP1cKO) showed accelerated tumor progression due to impaired anti-tumor immunity, characterized by cDC deficiency and pre-DC accumulation. Notably, Flt3 ligand (Flt3L)-mediated tumor immunotherapy was ineffective in TopBP1cKO tumor-bearing mice. Our study demonstrates that TopBP1 is required not only for the steady-state differentiation of total cDCs, including both cDC1 and cDC2, but also for the terminal differentiation of XCR1⁻CD24⁺ emergency progenitors (EPs; CD11c⁺cKit⁺) into XCR1⁺CD24⁺ cDC1s in response to Flt3L. Furthermore, we revealed that TopBP1 directly interacts with PU.1 and IRF8, key transcription factors (TFs) required for cDC development, triggering the expression of their downstream target genes. These findings identify TopBP1 as a crucial factor for cDC development and Flt3L-driven EP differentiation into cDC1s, revealing that the function of key TFs for cDC development is mediated via interaction with TopBP1. Our work underscores the importance of TopBP1 in promoting cDC development and the therapeutic efficacy of Flt3L-mediated tumor immunotherapy.

overall_design: ChIP-seq profiling of CD24⁺ EP(Emergency progenitor; CD11c+CD117+)s from the spleen of TopBP1^fl/fl (littermate) mice on day 9 after Flt3L-Ig injection.

first: Min-Suk

first: Yong-Soo

last: Bae


title: Extremes on the benign-malignant tumour spectrum: Distinct transcriptomic landscapes between two common canine perianal neoplasms based on the hallmarks of cancer [nCounter®]

city: Berlin

first: Alexander

middle: F. H.

last: Haake

address: Robert-von-Ostertag-Straße 15

department: Department of Veterinary Medicine

institute: Freie Universität Berlin

summary: The hallmarks of cancer describe stepwise changes in cellular functions and molecular pathways of tumour cells that undergo malignant progression. Although 14 hallmarks have been proposed, their manifestation at the molecular level across different tumour types remains incompletely understood. Here, we hypothesised that hallmark-associated transcriptomic signatures reflect the contrasting biological behaviours of a pair of a benign and a malignant tumour. To this end, we compared the two most common canine perianal tumours, the highly malignant apocrine gland anal sac adenocarcinoma (AGASAC) and the benign hepatoid gland adenoma (HGA). Spontaneous primary tumours were analysed using RNA-Seq (AGASAC n = 11, HGA n = 10) and a direct mRNA hybridisation panel (AGASAC n = 28, HGA n = 12). Large transcriptomic differences were observed in both the number of differentially expressed genes and enriched pathways. Surprisingly, transcriptomic differences based on the hallmarks of cancer were less pronounced that anticipated, particularly for “activating invasion and metastasis” and “inducing or accessing vasculature”. Only the HGAs showed a significant enrichment for “deregulating cellular energetics”. However, our data point towards a contrasting immune landscape between the compared tumours and a subgrouping of AGASACs associated with the inflammatory landscape. Overall, the transcriptomes of these two benign-malignant tumour extremes on the tumour spectrum contrasted each other in select aspects of the hallmarks. Still, their malignant or benign behaviours could not generally be mirrored on the mRNA level.

overall_design:
FFPE tissue samples of AGASACs (n = 33; 28 primary tumours, 5 nodal metastases) and HGAs (n = 12) from pet dogs were retrospectively obtained from the archive (spanning the years 2006 to 2021) and total RNA was extracted. The RNA was hybridised to the nCounter® Canine IO Panel XT CodeSets and a 30 probe Panel Plus. Differential gene expression (DGE) was implemented in the nSolverTM 4.0 Analysis Software with the R 3.3.2-based Advanced Analysis 2.0 plug-in (version 2.0.134) for AGASAC primary tumour (PT) versus baseline of HGA and AGASAC PT versus AGASAC nodal metastases (NM).

Attention: This GEO submission only includes the nCounter® data. The 3' RNA-Seq data used in the publication were submitted separately to GEO (GSE302161). 25 samples in this submission are re-used/re-analyzed (see GSE261791), please see "Description" under each sample for the cross-reference.

first: Alina

last: Loriani Fard

first: Vladimir

last: Jovanovic

first: Michael

last: Hummel

first: Sandro

last: Andreotti

first: Achim

middle: D

last: Gruber


title: TBP regulates transposable element expression in early mouse embryos [RNA-seq]

overall_design: Mouse embryos (zygotes) were microinjected with antibodies against TBP (TBP LOF) and mIGG (CONTROL for TBP LOF) or FOXJ3 (FOXJ3 LOF) and rIGG (CONTROL for FOXJ3 LOF), cultured for 4h and microinjected with Trim21 mRNA, to finally be cultured until the late 2-cell stage and collected for Smart-Seq+5', an adaptation protocol of Smart-Seq2


title: ILC2 regulate a fibroblast progenitor niche in the pancreas (Dpp4CreERT2 lineage trace scRNA-seq)

status: Public on Jul 03 2026

city: Cambridge

first: Timotheus

last: Halim

address: University of Cambridge Li Ka Shing Centre, Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

summary: Local fibroblast development and densities greatly influence organ health and disease, although it remains unclear how tissue fibroblast topography is controlled in situ. Here we define group 2 innate lymphoid cells (ILC2) as key regulators of fibroblast homeostasis in the pancreas. ILC2 co-localise with Pi16+Dpp4+Ly6c+ fibroblasts in an interstitial niche of the exocrine pancreas, which encapsulates the organ parenchyma. ILC2 specifically regulate the expansion of Pi16+Dpp4+Ly6c+ fibroblasts, which have progenitor capacity, while paradoxically also restraining differentiated intra-parenchymal Col15a1+ fibroblasts during inflammation. These homeostatic circuits reinforce fibroblast numbers after injury and set an inflammatory threshold. The ILC2-Pi16+Dpp4+Ly6c+ fibroblast progenitor niche expands locally in cancer, and controls cancer associated fibroblast ontogeny and density. Hence, ILC2-fibroblast dialogue represents a regulatory node that locally orchestrates tissue homeostasis and pathology.

overall_design: Dpp4(CreERT2/+)Rosa26(lsl-tdTom) mice were orthopically implanted with 2838c3 PDAC tumour cells and tamoxifen administered on days 7, 8, and 9. Tumours were harvested 21 days post-implantation and processed into single cell suspensions. tdTom- and tdTom+ CD45- CD31- EpCAM- Pdgfra+ Pdpn+ fibroblasts were separately sorted from individual tumours on a BD S8 Discover sorter. Samples were loaded onto GEM-X Universal 3' Gene Expression v4 4-plex Reagent Kits for on-chip multiplexing.

first: Thomas

last: Yip

first: Charlotte

last: Simpson

first: Ashley

last: Sawle


title: Single-cell heterogeneity in interferon induction potential is heritable and governed by variation in cell state IV

status: Public on Dec 13 2025

city: Urbana

first: Elizabeth

middle: Anne

last: Thayer

address: 407 S Goodwin Ave

institute: University of Illinois at Urbana-Champaign

summary: Type I and III interferons (IFNs) are among the first lines of defense against viral infections, yet they are generally only produced by a tiny fraction of infected cells. Here, we show that variability in tonic cell signaling significantly influences cells’ ability to produce IFN upon stimulation with the synthetic double-stranded RNA, polyinosinic:polycytidylic acid (pIC). Using single-cell approaches, we found that members of the activator protein (AP)-1 transcription factor were implicated in IFNL1 expression predisposition. This guided us to investigate the role of the mitogen-activated protein kinase (MAPK) pathway, specifically the c-Jun N-terminal kinase (JNK), in IFNL1 production. We found that inhibition of JNK signaling severely altered the nature of the innate antiviral response upon pIC stimulation, independently of the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway. Together, our study emphasizes the influence of intrinsic stochasticity in cell state on heterogeneity in IFN expression.

overall_design: Bulk ATAC-seq of clonal populations dervied from a parental (WT) A549 population. These are unstimulated samples to assess their basal chromatin accessibility profiles.

first: Gabriela

last: Shipman

first: Joel

last: Rivera-Cardona

first: Tarun

last: Mahajan

first: QiWen

last: Teo

first: Sebastian

last: Paez

first: Joseph

last: Lederer

first: Jie

last: Chen

first: Nicholas

last: Wu

first: Sergei

last: Maslov

first: Christopher

middle: B

last: Brooke


title: Single-cell heterogeneity in interferon induction potential is heritable and governed by variation in cell state II

overall_design: Bulk RNA-seq of A549 cells treated with ruxolitinib, JNK-IN-8, both inhibitors, or DMSO. Cells were pretreated with the inhibitors for 4 hours before either being treated with pIC or only lipofectamine.  The cells were then incubated for 16 hours then the RNA was extracted for sequencing.


title: Single-cell heterogeneity in interferon induction potential is heritable and governed by variation in cell state I

overall_design: Bulk RNA-seq of clonal populations dervied from a parental (WT) A549 population. These are unstimulated samples to assess their basal transcriptional profiles.


title: Extremes on the benign-malignant tumour spectrum: Distinct transcriptomic landscapes between two common canine perianal neoplasms based on the hallmarks of cancer [RNA-Seq]

status: Public on Dec 14 2025

first: Alexander

last: Haake

overall_design:
FFPE tissue samples of AGASACs (n = 15; 11 primary tumours, 4 nodal metastases) and HGAs (n = 10) from pet dogs were retrospectively obtained from the archive (spanning the years 2006 to 2021) and total RNA was extracted. The RNA was sequenced with QuantSeq 3'. DESeq2 was used for differential gene expression (DGE) analysis in the comparison AGASAC primary tumours (PT) versus HGA and AGASAC primary PT versus AGASAC nodal metastases (NM). - Attention: This GEO submission only includes the 3' RNA-Seq data pertaining to 6 technical replicates, the other 24 samples are re-used samples already accessible via GEO (GSE261790). The nCounter® data used in the publication were submitted separately to GEO (GSE301538).

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

middle: F

first: Alina

last: Loriani Fard

first: Vladimir

last: Jovanovic

first: Michael

last: Hummel

first: Sandro

last: Andreotti


title: Effect of Drs2 gene knockout on gene expression in Candida glabrata

status: Public on Dec 10 2025

city: shanghai

first: Geng

last: Lv

address: huangpuqu

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: To estiamte the role lipid flippase gene Drs2 plays in Candida glabrata, a ΔDrs2 null mutant was constructed based on standard strain ATCC2001 (wild type, WT) through homologous recombination. Then, gene expression profiling analysis was performed using data obtained from RNA-seq of WT and ΔDrs2 mutant.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ATCC2001 yeasts and ΔDrs2 strain yeasts

first: Ke-Zhi

first: Jun-Tao

last: Zhao

first: Si-Jia

last: Huang

first: Lu-Ling

last: Wang

first: Jin-Yan

last: Liu


title: TRMT112 Drives A Tumor Growth and Metastasis-Promoting Program in Triple-Negative Breast Cancer

status: Public on Dec 11 2025

city: Birmingham

first: Dongquan

state: AL

address: AB1170 1720 2nd Ave. South

institute: University of Alabama at Birmingham

summary: Ribosomal RNA Modifying Proteins (RRMPs) are integral to ribosome biogenesis, executing post-transcriptional modifications that influence translation fidelity and efficiency. Dysregulation of RRMPs has been increasingly implicated in cancer progression, yet their collective role across malignancies remains largely unexplored. Here, we performed a multi-omics analysis of 22 RRMPs across diverse cancer types using The Cancer Genome Atlas, the Molecular Taxonomy of Breast Cancer International Consortium, and additional high-throughput datasets. Our analysis revealed widespread genomic alterations and transcriptional dysregulation of RRMPs across malignancies, with distinct expression patterns in breast cancer subtypes. Notably, Triple-Negative Breast Cancer (TNBC) exhibited the highest RRMPs enrichment, which correlated with increased genomic instability including elevated tumor mutational burden and aneuploidy scores, and poor survival outcomes. Among the RRMPs, tRNA methyltransferase activator subunit 11-2 (TRMT112) emerged as a key regulator of tumor progression. Functional assays demonstrated that TRMT112 knockdown in TNBC cells significantly reduced proliferation, migration, invasion, and metastatic potential, whereas its overexpression enhanced these tumorigenic properties. Polysome profiling and RNA sequencing of actively translated transcripts revealed that TRMT112 reprograms the translational landscape by promoting pro-metastatic and stromal remodeling pathways while suppressing immune-related processes. In vivo studies using an orthotopic breast cancer model further confirmed that TRMT112 depletion impairs tumor growth and reduces metastatic burden. Collectively, our findings establish RRMPs as critical modulators of cancer progression and identify TRMT112 as a key driver of aggressive phenotypes in TNBC. The dysregulation of TRMT112 across breast cancer subtypes highlights its potential as both a prognostic biomarker and a therapeutic target. These insights provide a mechanistic foundation for future interventions aimed at targeting TRMT112-driven translational programs in aggressive breast cancer.

overall_design:
To investigate how silencing or overexpressing TRMT112 affects transcript translation and associated protein networks, we performed polysome profiling in the breast cancer cell lines MDA-MB-231, SUM159, and BT-549. Polysomes were isolated from these cells using a sucrose gradient fractionation system.
RNA-seq was subsequently performed on the polysome fractions to identify transcripts actively translated by ribosomes under TRMT112 knockdown and overexpression conditions. This approach allowed us to assess how TRMT112 modulates translational activity and impacts gene expression at the level of protein synthesis.

first: Lalita

last: Samant

first: Rajeev

first: Amr

last: Elhamamsy


title: A Complete Spatial Map of Mouse Retinal Ganglion Cells Reveals Density and Gene Expression Specializations [En face Retina]

city: Aurora

first: Samuel

middle: Alexander

last: Budoff

state: co

address: RC1 North Tower, P18-7101 Mail Stop

department: Physiology & Biophysics

institute: Colorado University Anschutz Medica

summary:
Retinal ganglion cells (RGCs) transmit visual information from the eye to the brain. In mice, several RGC subtypes show nonuniform spatial distributions, potentially mediating specific visual functions. However, the full extent of RGC specialization remains unknown. Here, we used en-face cryosectioning, spatial transcriptomics, and machine learning to map the spatial distribution of all RGC subtypes identified in previous single-cell studies. While two-thirds of RGC subtypes were evenly distributed, others showed strong biases toward ventral or dorso-temporal regions associated with sky vision and the area retinae temporalis (ART), the predicted homolog of the area centralis. Additionally, we observed unexpected spatial variation in gene expression within several subtypes along the dorso-ventral axis or within vs. outside the ART, independent of RGC density profiles. Finally, we found limited correlations between the gene profiles of the ART and the primate macula, suggesting divergent specialization between the mouse and primate central vision.
Five wild-type mouse retinas sectioned en face at 20 μm followed by 10x Xenium spatial transcriptomics with a custom panel of 300 genes chosen by the GraSP algorithm. Data processed with Baysor segmentation and CuttleNet cell type prediction as detailed in github.com/sbudoff/MappingAllMurineRGCs

overall_design: Five wild-type C57BL/6 mouse retinas sectioned en face at 20 μm and analyzed with custom 300-gene Xenium panel to map spatial distribution of all RGC subtypes

first: Alon

last: Poleg-Polsky


title: A Complete Spatial Map of Mouse Retinal Ganglion Cells Reveals Density and Gene Expression Specializations [RGC_CrossSection]

summary:
Retinal ganglion cells (RGCs) transmit visual information from the eye to the brain. In mice, several RGC subtypes show nonuniform spatial distributions, potentially mediating specific visual functions. However, the full extent of RGC specialization remains unknown. Here, we used en-face cryosectioning, spatial transcriptomics, and machine learning to map the spatial distribution of all RGC subtypes identified in previous single-cell studies. While two-thirds of RGC subtypes were evenly distributed, others showed strong biases toward ventral or dorso-temporal regions associated with sky vision and the area retinae temporalis (ART), the predicted homolog of the area centralis. Additionally, we observed unexpected spatial variation in gene expression within several subtypes along the dorso-ventral axis or within vs. outside the ART, independent of RGC density profiles. Finally, we found limited correlations between the gene profiles of the ART and the primate macula, suggesting divergent specialization between the mouse and primate central vision.
Pre-dissected regional samples from wild-type mouse retinas cross-sectioned at 20 μm followed by 10x Xenium spatial transcriptomics with the 5000-gene pan-tissue panel. Data processed with Baysor segmentation and CuttleNet cell type prediction as detailed in github.com/sbudoff/MappingAllMurineRGCs

overall_design: Pre-dissected retinal regions from wild-type C57BL/6 mice cross-sectioned at 20 μm and analyzed with Xenium 5k gene panel for regional expression profiling


title: Spatial analyses of early, untreated SSc skin identify a proinflammatory vascular niche of macrophage-fibroblast signaling

status: Public on Dec 12 2025

city: Lebanon

first: Helen

middle: C

last: Jarnagin

state: NH

address: WTRB 6-84, 1 Medical Center Drive

institute: Dartmouth College

summary: Uncovering the early interactions and spatial distribution of dermal fibroblasts and immune cells in treatment-naïve diffuse cutaneous systemic sclerosis (dcSSc) patients is critical to understanding the initiating events skin fibrosis. We generated an integrated multiomic dataset of early, treatment naïve dcSSc skin. Skin biopsies were analyzed by single-nuclei multiome sequencing (snRNA-seq and snATAC-seq) and two different paired spatial transcriptomic platforms to comprehensively describe the molecular changes in these individuals. We identified a proinflammatory niche within papillary, hypodermis, and vascular niches, that are enriched for activated myeloid cells and proinflammatory fibroblasts characterized by expression of proinflammatory cytokines. Pathway analyses showed significant enrichment of PI3K-AKT-mTOR signaling pathway expression in these cellular niches, driven by profibrotic growth factor signaling networks. Macrophage subclustering showed SSc-specific macrophage activation of IL6-JAK-STAT signaling and the enrichment of oxidative phosphorylation pathways. Ligand-receptor analysis revealed that SSc macrophages secrete PDGF and TGFB to activate the inflammatory SSc-dominant fibroblast subclusters. Spatial transcriptomic analyses showed infiltrating macrophages secreted PDGF and TGFB, modulating fibroblast activation in these niches. Multiomic data integration and spatial transcriptomic neighborhood analysis showed co-localization of fibroblasts, macrophages, and T cells around the vasculature. These data suggest that interactions between activated immune cells and proinflammatory fibroblasts around vascular niches are an early event in scleroderma pathogenesis.

overall_design: 10 samples

first: Jarnagin

last: Helen

first: Whitfield

last: Michael


title: Association between blood parameters, whole-blood transcriptomic profiles, and immune-related adverse events in metastatic renal cell carcinoma during nivolumab plus ipilimumab

status: Public on Feb 14 2026

city: tsukuba

first: Satoka

last: Kinase

address: tenoudai 1-1-1

institute: University of tsukuba

summary: Pretreatment immune profiles associated with immune-related adverse events (irAEs) may inform individualized management strategies, including enhanced monitoring and early toxicity intervention, in patients with metastatic renal cell carcinoma (mRCC) treated with nivolumab plus ipilimumab. In this cohort (n = 51), we analyzed pretreatment peripheral blood parameters and whole-blood transcriptomic profiles. Higher lymphocyte and monocyte counts (odds ratios [ORs] 14.36 and 9.90, respectively) were significantly associated with an increased risk of irAEs, whereas higher neutrophil counts and C-reactive protein levels (ORs 0.08 and 0.27, respectively) were associated with a decreased risk. To characterize immune pathways associated with irAE development, we performed whole-blood transcriptomic analyses. Gene set enrichment analysis revealed upregulation of lymphocyte- and humoral immunity-related pathways and downregulation of neutrophil- and inflammatory-related pathways in patients who developed irAEs. CIBERSORTx demonstrated reduced neutrophil fractions and increased proportions of CD8⁺ T cells and activated memory CD4⁺ T cells, indicating an adaptive immune-dominant profile. Exploratory analysis identified five candidate genes (ANAPC1, CDK4, MCM6, GRAP2, and BST2) that may contribute to the immune features associated with irAE development. Collectively, these findings suggest that irAE development is associated with a distinct systemic immune profile characterized by enhanced lymphocyte-related and reduced neutrophil-related immune activity.

overall_design:
Whole-blood RNA sequencing was performed on pretreatment peripheral blood samples from 51 patients with metastatic renal cell carcinoma treated with nivolumab plus ipilimumab. Patients were stratified according to the development of immune-related adverse events (irAEs). Differential expression analysis, gene set enrichment analysis (GSEA), and immune cell deconvolution (CIBERSORTx) were conducted to characterize transcriptomic differences between irAE-positive and irAE-negative groups.Peripheral whole blood samples were collected in PAXgene Blood RNA tubes (PreAnalytiX) and processed according to the manufacturer’s protocol prior to RNA extraction and library preparation.

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

first: Yoshiyuki

last: Nagumo

first: Bunpei

last: Isoda

first: Hiromichi

last: Sakurai

first: Reo

last: Takahashi

first: Shuhei

last: Suzuki

first: Akane

last: Yamaguchi

first: Ryota

last: Yanagihashi

first: Kozaburo

last: Tanuma

first: Satoshi

last: Nitta

first: Masanobu

last: Shiga

first: Kosuke

last: Kojo

first: Atsushi

last: Ikeda

first: Takashi

last: Kawahara

first: Akio

last: Hoshi

first: Shuya

last: Kandori

first: Bryan

last: Mathis

first: Hiroyuki

last: Nishiyama


title: Gene expression analysis of murine normal mammary gland fibroblasts (mNFs) after perturbing the expression of ASPA (silencing and over-expression)

city: Santander

first: Fernando

last: Calvo

state: Cantabria

address: C. Albert Einstein, 22

country: Spain

institute: IBBTEC

summary: Metabolic reprogramming is a hallmark of cancer, and the field has predominantly focused on investigating metabolic alterations in tumour cells. However, the relevance, mechanism and consequences of metabolic adaptations in stromal cells remains largely unexplored. Here, we identify Aspartoacylase (ASPA) as a metabolic enzyme consistently repressed in tumour stroma and cancer-associated fibroblasts (CAFs). Loss of ASPA is associated with the accumulation of its substrate, N-acetylaspartate (NAA), and we corroborate the relevance of this metabolite in the control of macrophage polarization. Importantly, we report an unprecedented reciprocal crosstalk of ASPA with TGFβ signalling. TGFβ suppresses ASPA expression, whereas ASPA restrains TGFβ-dependent myofibroblast conversion and the generation of aggressive pro-tumoral responses in fibroblasts. Analyses of human specimens revealed a strong negative prognostic value for ASPA in different tumour types, associated with pro-tumoral macrophages and TGFβ signalling levels. Our findings unveil ASPA expression in fibroblasts as a previously unknown gatekeeper of TGFβ responses and activation in cancer, and shed light into the intratumoral metabolic crosstalk that governs the process of cancer progression.

overall_design: RNA-seq profiling of murine mammary normal fibroblasts (mNF1) after silencing ASPA with two independent shRNAs. Scramble shRNA (shC) and two individual shRNA targeting Aspa (Sh3-ASPA and Sh4-ASPA), under doxycyclin control, were transfected in mNF1, and selection was performed using Blasticidin at 10 μg/mL final concentration. Stable clones were cultured in subconfluency in full DMEM (10% FBS) and treated with 300ng/mL of doxycyclin for 5 days, and RNA was extracted. In addition, RNA-seq profiling of mNF1 control and over-expressing a wild-type form of ASPA, after treatment with vehicle or TGF-beta1 , on duplicates. mNF1 were stably transfected with a doxycyclin-inducible cDNA for ASPA and selected using Blasticidin at 10 μg/mL final concentration. Stable clones were cultured in full DMEM (10%FBS) and treated with Vehicle (control) or with 300ng/mL of doxycyclin for 5 days to induce ectopic ASPA expression (mNF1-ASPA). Cells were then exposed to vehicle (Vh) or to 10 ng/mL of TGF-beta1 for 24 h, and RNA extracted.

first: Catalina

last: Capó-Serra

first: Miguel

last: Juliá


title: Novel SLCO2B1 mRNA isoform acts as a noncoding RNA and drives cancer progression through FMR1-mediated protein biosynthesis

status: Public on Dec 09 2025

city: Shanghai

first: Wenying

last: Qiu

address: Dongan road 270

institute: Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences

summary: The eukaryotic 5’ untranslated region (5’ UTR) canonically influences mRNA translation efficiency. However, the role of the 5’ UTR structure in blocking mRNA translation and turning a coding RNA into a noncoding RNA remains undocumented. Herein, we discovered a novel mRNA isoform of the human solute carrier organic anion transporter family member 2B1 (SLCO2B1) gene, named SLCO2B1-isoformNovel (SLCO2B1-isoN), whose 5’ end stem‒loop abrogates its translational capacity and turns it into a noncoding RNA. The SLCO2B1-isoN noncoding isoform stabilizes fragile X messenger ribonucleoprotein 1 (FMR1) to trigger hepatocellular carcinoma (HCC) progression by facilitating de novo protein biosynthesis. Targeting SLCO2B1-isoN effectively inhibited orthotopic tumor xenograft growth in vivo. In conclusion, this study revealed a previously unrecognized noncoding isoform of SLCO2B1 mRNA with a 5’ end stem‒loop structure and highlighted the dual characteristics of mRNAs harboring protein-coding and noncoding isoforms, providing new insights into the richness of genetic information in protein-coding genes.

overall_design: CUT&Tag was performed using antibodies against ZEB1, SETD1B, H3K9ac, H3K27me3, H3K4me3 to identify the binding sites across DNA in MHCC97H or HepG2 cells.

first: Xianghuo

last: He


title: Combined inhibition of HRAS and MEK induces tumor regression and restores myogenic differentiation in HRAS-mutant rhabdomyosarcoma

status: Public on Dec 08 2025

city: Baltimore

first: Michael

last: Considine

address: 550 North Broadway

institute: Johns Hopkins University

summary: Hyperactive RAS signaling drives tumorigenesis in PAX 3/7::FOXO1 fusion-negative rhabdomyosarcoma (FN-RMS). Despite the frequency of these mutations, indirect RAS pathway-directed therapies have been ineffective for RAS-driven RMS. Farnesyltransferase (FTase) inhibitors (FTIs), such as tipifarnib, inhibit HRAS membrane localization and blunt HRAS effector signaling, leading to an antitumor effect in HRAS-mutant FN-RMS preclinical models. Response to FTase inhibition is limited by adaptive feedback reactivation of ERK signaling and upregulation of wild-type (WT) RAS. We found that the combination of HRAS suppression with FTI and MEK inhibition (MEKi) impaired ERK reactivation and reduced ERK transcriptional output in HRAS-mutant RMS models. Co-targeting FTase and MEK restrained tumor progression and induced terminal myogenic differentiation. These findings highlight an effective combinatorial strategy and support its preclinical translation for patients with HRAS-mutant RMS.

overall_design: RNA-sequencing of FN-RMS cell cells following siRNA RAS knockdown or treatment with small molecule inhibitors of RAS pathway constiuents.

first: Patience I

last: Odeniyide

first: Alyza

last: Skaist

first: Elana

last: Fertig

first: Christine A

last: Pratilas


title: Macrophage-exacerbated viral lung injury and mechanical overdistension-driven bacterial superinfection replicated in a human lung chip

status: Public on Dec 07 2025

city: Boston

first: Yuncheng

last: Man

state: MA

address: 201 Brookline Ave

institute: Wyss Institute, Harvard University

summary: Patients with severe influenza-induced lung injury exhibit disrupted alveolar barrier and persistent viral load, accompanied by hyperinflammation, immune cell recruitment, and risk of bacterial superinfection. These complications are often exacerbated in patients undergoing mechanical ventilation. Leveraging an immune-competent human lung alveolus-on-a-chip (Lung Chip) lined by human pulmonary alveolar epithelium co-cultured with monocyte-derived macrophages and interfaced with lung microvascular endothelium, we show that monocyte-derived macrophages play a central role in driving key hallmarks of severe influenza, including activated cell death programs. Physiological strain mimicking breathing motions supported alveolar homeostasis, whereas pathological strain analogous to mechanical ventilator-induced lung overdistension promoted secondary Pseudomonas aeruginosa infection. Computational gene network analysis combined with experimental validation identified SIRT1 as a key modulator of inflammation and susceptibility to bacterial superinfection, which can be mitigated using pharmacological SIRT1 activators. Together, these findings underscore the importance of incorporating macrophages into preclinical models of viral lung injury and establish an integrated workflow combining human Organ Chips and computational approaches for gaining insights into biophysical and molecular disease drivers while facilitating the identification of therapeutic targets and candidate countermeasures.

overall_design: Bulk RNA-seq analysis of human Lung Chips with or without IAV infection in the presence of macrophages, and of IAV-infected human Lung Chips in the presence or absence of macrophages.


title: NANP Targeting Radio-sensitizes Glioblastoma through TNFR1 Sialylation-Driven Mesenchymal Shift

city: New York

first: Erik

last: Sulman

address: 522 First Avenue

department: Radiation Oncology

institute: NYU Langone

summary: GBM remains a highly devasting brain tumor mainly due to the resistance to radiotherapy (RT), the most impactful first-line treatment for GBM. Our clonal evolution study reveals no dominant RT-resistant clones to target for recurrence prevention, leading us for a genome-wide CRISPR screening for radio-sensitizing targets in GBM. The screening highlighted DNA damage response genes, particularly in the non-homologous end-joining (NHEJ) pathway, such as PRKDC and NHEJ1, as potent radio-sensitizers. Additionally, NANP (N-acylneuraminate-9-phosphatase), a critical enzyme in the sialic acid synthetic pathway, was identified as a novel RT-sensitizing target associated with patient outcomes. NANP knockdown induces increased G2/M arrest and apoptosis following radiation, with γH2AX staining and comet assays indicating greater DNA damage. NANP deficiency impairs DNA repair, favoring error-prone NHEJ over homologous recombination (HR). Mechanistically, NANP modulates the sialylation of TNFR1, thereby influencing NF-kB signaling and the mesenchymal (MES) state of glioma stem cells (GSCs), which consequently affects RT sensitivity. Intracranial orthotopic xenograft experiments validate the function of NANP in vivo. In summary, our findings identify NANP as a novel radio-sensitizing target, dependent on TNFR1 sialylation and MES shift, providing a basis for developing innovative RT sensitizers for GBM.

overall_design:
To investigate the transcriptomic impact on GSCs upon NANP siliencing by shRNAs, we established control and NANP knockdown GSC20 (shCTL,shNANP-1 and shNANP-3)  and GSC11(shCTL and shNANP-1).
We then performed gene expression profiling analysis from RNA-seq of these GSCs.
Comparative analysis of gene expression were then performed using DESeq2.

first: Yingwen

last: Ding

first: Ze-Yan

last: Zhang


title: Bulk RNAseq data of white matter tissue injury

city: Suzhou

first: kaici

last: Tang

address: Renailu 199

institute: Soochow University

summary: We compared the transcriptomic responses in the mouse white matter tissue drive white matter lesions following LPC- and L-NIO-induced injury.

overall_design: Bulk RNA sequencing: The injured and contralateral tissues were isolated from the corpus callosum at 4 days after LPC-induced repair injury or L-NIO-induced WMS. The corpus callosum tissue collected from the sham-operated mice served as a control. In brief, total RNA was extracted via TRIzol reagent and quantified, after which ribosomal RNA depletion and poly(A) purification were performed. Libraries were quantified and pooled for paired-end sequencing on an Illumina NovaSeq 6000 platform.

first: Yu

last: Hu

first: Kaici

first: Hongli

first: Hongbo

last: Mi

first: Hao

last: Wang