title: Effect of deletion of PoxTMA7 in Penicillium oxalicum HP7-1 at the transcriptional level

first: Di

summary: In order to explaining the mechanism of microprotin PoxTMA7,we deleted PoxTMA7 in P. oxalicum ΔPoxKu70  ,and we want to investigating the function of deletion of PoxTMA7 at transcriptional level.

overall_design: RNA-seq profilling of  wide type and deletion mutant  ΔPoxTMA7 cultured in medium containing 1% Avicel for 24 h, in order to explaining the mechanism of POXTMA7 in regulation cellulase and xylanase production in P. oxalicum

first: Tian

last: Di

first: Zhao

last: Shuai


title: 1Arp2/3 complex controls microglial cell dynamics and homeostasis by regulating TGF-β signaling.

status: Public on Jan 31 2026

city: Freiburg

first: Maximilian

last: Frosch

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

type: Expression profiling by high throughput sequencing

summary: Microglia are the major brain-resident immune cell subsetthat areessential during pathology and physiology in the central nervous system. The regulation of functional elementsrequired for microglialhomeostasis needsto be precisely orchestrated.To date, the underlying mechanismshave not been fully investigated. Here,we show that actin network dynamics mediated by the Arp2/3 complex play a crucial role in microglial cell function. Upon interruption of Arp2/3 complex integrity in the conditional knockoutmouse model, we found significant alterations in microglial cell morphology, motility, and chemotaxisfunction.Transcriptomics analysis revealedthat Arp2/3-deficient microglia downregulatehomeostatic signature and upregulatecell activationthat isassociated with APOE induction, Ms4a7upregulation,and TGFsignaling impairment. In vitrostudies confirm that the Arp2/3 downstream actin-related molecules are required for mediating the TGFsignaling pathway in microglia. Our resultsshow that the Arp2/3complexis required for microglia cell dynamics and plays a key role in maintaining microglial cell homeostasis by regulating the TGF-β signaling.

overall_design: scRNA-seq of CD45+ cells from control and Arpc4dCx3cr1 mice

first: Shima

last: Safaiyan

first: Gianni

last: Monaco


title: miRNA Profiling shows shared Signatures in Pediatric Asthma, Obesity and their comorbidity

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

summary: Obesity is considered as a significant contributor of childhood asthma. Concerningly, obesity and asthma comorbity is found to be  associated with increased asthma symptoms and reduced response to corticosteroid therapy. In this study we investigate how the co-existence of obesity in children with asthma alter their molecular characteristics.

overall_design: We aimed to identify microRNA (miRNA) signatures associated with pediatric asthma-obesity comorbidity. We compared miRNA profiles in the RNA extracted from peripheral blood between four groups: normal weight with asthma (NW-A, n = 11), overweight/obesity with asthma (OO-A, n = 10), overweight/obesity with no asthma (OO, n = 10), and normal weight with no asthma (NW, n = 12). Downstream analysis of differentially expressed miRNAs were conducted using different bioinformatic tools. Finally, correlation of differentially expressed miRNAs with different clinical parameters and plasma cytokines were assessed using Pearson’s correlation analysis.

first: Harshita

last: Hailesh

first: Safa

last: Noor

first: Lena

last: Hayati

first: Stefan

last: Worgall

first: Ibrahim

last: Janahi


title: Cruciform-forming AT/TA repeats are acted upon by structure selective endonucleases and Rad51 prior to repositioning to the nuclear periphery for repair

status: Public on Jan 28 2026

city: New York

first: Bertrand

last: Theulot

state: NY

address: 100 WASHINGTON SQ E, Attn: Duncan Smith

country: USA

institute: NYU

summary: Structure-forming DNA repeats can pose a barrier to DNA replication and repair and create chromosomal fragile sites. An (AT/TA) 34 DNA repeat, derived from the Flex1 region of human common fragile site FRA16D, can form hairpin and cruciform structures which interfere with DNA replication. When inserted into the S. cerevisiae genome, the Flex1(AT) 34 repeat stimulates chromosome deletions in a manner dependent on the Mus81-Mms4 nuclease and the SLX4 nuclease scaffold. It was previously found that hairpin forming CAG/CTG repeats move to the nuclear periphery to maintain genomic stability. We show that the structure forming AT/TA repeat also relocalizes to the nuclear periphery in late S/G2 phase in a replication and length-dependent manner. In contrast to the CAG repeat, this shift in nuclear positioning is dependent on polySUMOylation and the activity of the Mus81-Mms4 nuclease. Thus, different replication barriers may have differing dependencies for processing and repositioning to the nuclear periphery to protect genome integrity. Processing by the Mre11 nuclease and Rad51 strand exchange occurs prior to repositioning. Replication analysis shows that the replisome likely bypasses the AT structure-induced barrier leaving an under-replicated region that requires resolution. We conclude that AT/TA repeats form post-replicative DNA structures that are targeted for nuclease cleavage and require hairpin processing and repositioning to the nuclear periphery for homologous recombination-dependent repair.

overall_design: OK-seq was performed in Saccharomyces cerevisiae strains carrying either an (AT/TA)_34 DNA repeat or a Flex1 control cassette inserted on chromosome VI or chromosome X, in RAD52+ and rad52Δ genetic backgrounds. UCSC Genome Browser session with strand-specific coverage tracks is available at: https://genome.ucsc.edu/s/bt2459/okseq%2Dboer%2D2026 . Custom analysis scripts used to generate the figures are available here: https://github.com/btheulot/ok-seq-boer-2026

first: Jan L

last: Boer

first: Sara M.

last: Crippen

first: Amelia J.

last: Kim

first: Daphne N.

last: Kramer

first: Daniel

last: Dovrat

first: Amir

last: Aharoni

first: Duncan J.

last: Smith

first: Catherine H.

last: Freudenreich


title: Single-cell multiomics uncovers an endothelial mechanosensitive PIEZO1-IL-33 axis driving pulmonary fibrosis

status: Public on Jan 30 2026

city: Chengdu

first: Bisen

last: Ding

address: Renmin South Road

country: China

institute: State Key Laboratory of Biotherapy

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pulmonary fibrosis (PF) represents a progressive interstitial lung disease marked by excessive extracellular matrix deposition and architectural distortion. Vascular endothelial cells (ECs) critically contribute to fibrogenesis through paracrine secretion of pro-fibrotic mediators, yet their mechanobiological regulation remains elusive. UsingThrough integrated single-cell multi-omics profiling of human PF specimens and experimental fibrosis models induced by bleomycin or silica (Bleomycin/SiO2-induced), we identify identified mechanosensitive Piezo1 upregulation in ECs as a hallmark of fibrotic progression. Endothelial-specific Piezo1 knockout significantly attenuates attenuated Bleomycin-induced fibrotic remodeling, establishing its pathogenic necessity. Mechanistically, Piezo1 activation promotes promoted PF development by inducing a pro-fibrotic molecule interleukin-33 (IL-33) secretion via CAPN2-mediated STAT3 phosphorylation. These findings suggest that the endothelial PIEZO1-CAPN2-STAT3-IL-33 axis is a promising therapeutic target for PF intervention.

overall_design: Lung tissues of Saline or Silica or Bleomycin induced mice were obtained for sequencing (n=3 per group).

first: Lanlan

last: Zhang

first: Ruijie

last: Hou


title: Runx1 transcriptional regulation of microglia critically modulates opioid analgesia and withdrawal in humans and rodents [ChIP-seq]

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

summary: Opioid pain-relief and adverse outcomes differ between individuals. We show that runt-related transcription factor 1 (Runx1) is a determinant of opioid responses in humans and rodents and modulates the microglial transcriptome. Electron microscopy and single-cell RNA-sequencing revealed that deletion of Runx1 from microglia produces distinct ultra-structural and transcriptomic signatures. Microglia Runx1-deficient mice have reduced morphine potency, despite having no prior opioid exposure and normal nociceptive thresholds. These mice required greater amounts of post-operative morphine and displayed robust morphine-induced hyperalgesia and exacerbated withdrawal. In humans, genome-wide linkage analyses (GWAS) revealed variations within the Runx1 gene is associated with inter-individual differences in perioperative opioid requirement and opioid withdrawal severity. Identification of Runx1 susceptibility genotypes has implications for individualizing opioid pain management and determining risk of opioid dependence.

overall_design: Spinal cord cells were isolated from male C57BL/6J mice at 8-10 weeks of age. For each immunoprecipitation, chromatin from 10 spinal cords was pooled, yielding a sample of approximately 10 µg, and incubated with 9 µg of antibody against Runx1 (rabbit polyclonal, ab23980, lot# 1017033-4, Abcam) overnight at 4 °C with rotation. ChIP-Seq library preparation and sequencing reactions were conducted by GENEWIZ, Inc/Azenta US, Inc. (South Plainfield, NJ, USA).

first: Heather

last: Leduc-Pessah

first: Sarthak

last: Sinha

first: Brendan

last: McAllister

first: Daisuke

last: Nishizawa

first: J√∫lia

last: Canet-Pons

first: Churmy

middle: Y

last: Fan

first: Marie-Kim

last: St-Pierre

first: Amyaouch

last: Bradaia

first: Manon

last: Defaye

first: Nynke

last: van den Hoogen

first: Nicole

middle: E

last: Burma

first: Jonathan

last: Damblon

first: Einer

last: Muñoz-Pino

first: Luke

middle: M

last: Healy

first: Valerio

last: Piscopo

first: Ken-ichi

last: Fukuda

first: Tatsuya

last: Ichinohe

first: Makoto

last: Nagashima

first: Masakazu

last: Hayashida

first: Emma

last: Johnson

first: Arpana

last: Agrawal

first: Louisa

last: Degenhardt

first: Nicholas

middle: G

last: Martin

first: Elliot

middle: C

last: Nelson

first: Christophe

last: Altier

first: Marie-Eve

last: Tremblay

first: Chad

last: Bousman

first: Stefano

last: Stifani

first: Yves

last: De Koninck

first: Kazutaka

last: Ikeda

last: Biernaske

first: Tuan

last: Trang


title: Danggui Niantong granules in the treatment of rheumatoid arthritis - a mechanistic approach using ceRNA networks

city: Guangzhou

first: Yisi

last: Cai

address: No. 1023 South Shatai Road, Baiyun District

department: School of Traditional Chinese Medicine

institute: Southern Medical university

summary: This project aims to explore the changes in ceRNA expression profiles of mh7a after the use of Danggui Niantong granules. In conclusion, this study provides evidence that DGNTG exhibits anti-RA effects associated with its inhibition of  synoviocyte proliferation, migration and invasion. To explore the underlying mechanism, we constructed a ceRNA network based on transcriptomic data from DGNTG-treated MH7A cells.

overall_design: CeRNA microarray analysis of MH7a cells in control group and Danggui Niantong granule-treated group

first: Yanyan

last: Song

first: Xiaoling

last: Zeng

first: Gang

last: Liu

first: Lixia

last: Yuan


title: Comprehensive immune profiling reveals IFN-γ signaling in T cells mediates parasite phagocytosis in a rodent malaria model : Spatial transcriptomics data

first: chen

last: li

institute: Sichuan Univercity

summary: Malaria-associated lung pathology, a severe and life-threatening manifestation of Plasmodium infection, involves complex immune remodeling within the pulmonary microenvironment. To resolve the spatial architecture of this immune response, we performed spatial transcriptomic analysis on lung tissues from a Plasmodium berghei NK65-induced rodent model. Our study identifies IFN-γ signaling in T cells as a pivotal regulator of the lung's spatial immune landscape. By utilizing conditional knockout (cKO) mice lacking Ifngr1 specifically in T cells, we observed that the blockade of T cell-intrinsic IFN-γ signaling attenuates lung pathology. Spatially, this protection is characterized by an enriched colocalization and enhanced interaction between T cells and monocytes. This robust interaction drives the expansion of a unique proinflammatory monocyte subset defined by CD8 and Ly6C expression within specific pulmonary niches. These CD8+ Ly6C+ monocytes exhibit significantly enhanced phagocytic capacity and elevated MHCII expression in situ. Our spatially resolved findings illustrate that the T cell-IFN-γ signaling axis dictates the spatial organization of T cell-monocyte communication, highlighting this interaction as a potential therapeutic target for mitigating malaria-induced lung injury.

overall_design: To characterize the spatial immune landscape of malaria-associated lung pathology, we performed spatial transcriptomic analysis on lung tissues from naïve, infected (day 7), and T cell-specific Ifngr1 cKO (day 7) mice, with the two infected groups multiplexed onto a single slide to generate two integrated sequencing libraries; this design enables precise in situ mapping of cellular interactions and reveals how the loss of T cell-intrinsic IFN-γ signaling reshapes the pulmonary microenvironmental niches to attenuate tissue injury.

first: Jingwen

last: Lin

first: Shasha

last: Chen

first: Qingxin

last: Yang


title: NanoString Breast Cancer 360 expression profiling of histologically normal breast lobules from NHBW and NHWW donors (BC360)

status: Public on Feb 02 2026

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

summary: Histologically normal breast lobules were obtained from non-Hispanic Black women (NHBW) and non-Hispanic White women (NHWW) (n=10 per group) matched by age, BMI, and parity. RNA extracted from FFPE sections was profiled using the NanoString Breast Cancer 360 CodeSet to characterize transcriptional programs associated with group differences in benign breast epithelium.

overall_design: Twenty histologically normal breast lobule samples (10 NHBW, 10 NHWW) were profiled on the NanoString Breast Cancer 360 panel. Raw RCC files are provided along with normalized expression values.

first: Joshua

middle: W

last: Ogony


title: In vitro cartilage tissues following overexpression of TFs

status: Public on Jan 27 2026

city: Boston

first: April

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Cartilage plays a crucial role in skeletal development and function, and abnormal development contributes to genetic and age-related skeletal disease. Compromises to the integrity of joint-lining articular cartilage in particular lead to debilitating chronic degenerative diseases including osteoarthritis. To better understand how human articular cartilage develops in vivo, we jointly profiled the transcriptome and open chromatin regions in individual nuclei recovered from distal femora at 2 fetal timepoints. We used these multiomic data to predict transcription factor-based regulatory networks that are important for articular chondrocyte differentiation. We developed a human pluripotent stem cell platform for interrogating the function of predicted transcription factors during chondrocyte differentiation and identified new biological roles for CREB5. We expect new regulatory networks we uncovered using multiomic data to be important for promoting cartilage health and treating disease, and our platform to be a useful tool for studying cartilage development in vitro.

overall_design: bulk RNA seq of in vitro derived chondrocytes following modulation of NFATC2 or CREB5

first: Divya

last: Venkatasubramanian

first: Gayani

last: Senevirathne

first: Andrew

last: Zhu

first: Terence

middle: D

last: Capellini

first: Sarah

last: Jachim


title: Single-cell transcriptomics of spinal microglia from Cx3cr1-Cre-YFP x flxRunx1 mice

first: Jeff

last: Biernaskie

summary: Runx1 is a transcription factor known to be involved in microglial reactivity in the perinatal period, but its role in regulating microglia reactivity later in life is not well understood. Transgenic mice with a conditional inducible deletion of the transcription factor Runx1 in Cx3cr1 positive cells were generated to further investigate. Immunohistochemical labelling and electron microscopy, flow cytometry and quantitative PCR showed indications of altered microglial phenotype in knock-out mice. Single-cell seq was pursused to further delineate the microglial populations in wild-type and Runx1 knock-out mice.

overall_design:
scRNA-seq of Wild type (vehicle-treated and Runx1 Knock-out (tamoxifen-treated) spinal microglia.
To knock out the transcription factor Runx1 from microglia we crossed Cx3cr1-CreER-YFP mice with floxed Runx1 mice. Mice were treated with tamoxifen 1 mg or vehicle i.p. for 5 days to induce recombination. 4 weeks were allowed for repopulation of peripheral cx3cr1 expressing cells. FACS as used to isolate YFP-positive cells from the spinal cord of tamoixfen (knock-out) or vehichle (wild type) mice. All samples were processed according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent D1000 ScreenTape System. We recovered 4,500 and 2,600 cells for wild type and knock-out conditions, respectively. Next Generation Sequencing was done using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~75,000-100,000 reads/cell.

first: Heather

last: Leduc-Pessah

first: Sarthak

last: Sinha

first: Tuan

last: Trang


title: Kupffer Cell Calibration of T Cell Responses via VSIG4-CD5 Interaction Promotes Tumor Evasion [TCR-Seq]

city: Hefei

first: xia

last: zhou

address: huang shan Road 443

institute: university of science and technology of china

summary: Liver metastasis often resists T cell-based immunotherapy, indicating an adaptation of metastatic tumors towards reduced immunogenicity in the liver. Here we demonstrate that VSIG4, an immune checkpoint molecule predominantly expressed on Kupffer cells, plays an opposing role in determining the growth of liver metastases with varying antigenicity by modulating cognate TCR signaling through its interaction with CD5. Mechanistically, VSIG4-CD5 engagement impedes activation of low-affinity CD8+ T cells while enhancing responses of high-affinity CD8+ T cells by rescuing them from activation-induced cell death. This bi-directional regulation favors growth of metastatic tumor clones with low antigenicity, and fosters an T cell-unfavorable immune landscape as metastatic liver cancer progresses. Blockade of VSIG4-CD5 interaction with a newly generated anti-VSIG4 nanoantibody sensitizes liver metastases to anti-PDL1 therapy, achieving remarkably synergistic efficacy in mice. Our findings provide mechanistic insights into cancer immunoediting in liver metastasis and propose a promising approach for treating immunologically cold tumors.

overall_design: MC38 cells were injected into WT and VSIG4 ko mice. 14 days latter, CD8+ T cells from tumor-bearing WT and VSIG4 ko mice were isolated and sorted by FACS, Further RNA-seq were performed and analyzed.

first: Xia

last: Zhou

first: Wei

last: Liu

first: Jing

last: Hu

first: Qi

last: Yao


title: Cell-specific transcriptomics and silencing reveal aquaporin function in grass stomatal movements

status: Public on Jan 26 2026

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

summary: The high efficiency of grass stomata is believed to be due to their structure and anatomy, with two dumbbell-shaped guard cells surrounded by two subsidiary cells (SCs) and an efficient functional molecular interaction between these cells. Important channels expressed in these cells are aquaporins (AQPs), which contribute to the dynamic of stomatal movement. To further investigate genes expressed in maize GCs and SCs, RNA sequencing was performed on microdissected GCs and SCs during day and night. A general transcriptomic analysis first revealed that genes upregulated in SCs compared to GCs during the day were primarily involved in lipid transport, lipid localization, and lipid metabolism, whereas genes more highly expressed in GCs were associated with photosynthesis, chloroplasts, and plastids. Interestingly, the expression of several AQP genes varied both spatially and temporally. For example, the plasma membrane aquaporin ZmPIP1;5 and ZmPIP2;5 displayed a higher expression in GCs than in SCs during the day, whereas ZmPIP1;3 and ZmPIP2;1 exhibited an opposite pattern. To examine the specific roles of AQPs in these cells, a CRISPR-based tissue-specific knockout system was successfully used to silence ZmPIPs belonging to the PIP1 subfamily in either maize GCs or SCs. The targeted knockout of ZmPIP1s in these cells impaired stomatal movements in response to light, ABA, and CO₂ compared with wild-type plants. Overall, these findings reveal transcriptomic specificities between maize GCs and SCs, providing valuable insights into the regulation of rapid stomatal movements in grasses, and highlight the role of ZmPIP1s in these processes.

overall_design: Maize B104 seeds were germinated and transferred to potting soil, as previously described. The plants were grown in a phytotron under a 16/8 h light/dark cycle (25/22 °C) and a daytime light intensity of 200 mmol. m−2. s−1 at the top of the leaves. Humidity was maintained between 60% and 70% in the growth chamber. Epidermal strips were peeled from the third leaf of two-week-old maize seedlings. They were placed on microscope glass slides (plain microscope slides 76x26mm, 0.8 mm x 1.00 mm, AGL4242) and flash-frozen with liquid nitrogen. The samples were immediately stored at -80 °C until microdissection. The samples were collected at two times, i.e., day (two hours after the light onset) and night (two hours after the light offset). Four independent collections were carried out. On the day before the microdissection, the peeled epidermal strips were freeze-dried at -40 °C for 10 h under pressure of 10 Pa in a Labconco® Free-Zone Plus freeze-drier. At the end of the process, the temperature slightly increased to room temperature for 3 h. A few drops of absolute ethanol were placed on the strips to flatten them. The samples were stored in a desiccator under vacuum at room temperature until microdissection, to avoid rehydration. Guard cells (GC) and subsidiary cells (SC) were collected using a PALM MicroBeam system (Carl Zeiss MicroImaging GmbH). GCs or SCs were selected using Zeiss software and cut using a laser. After cutting, cells were pressure catapulted and collected immediately in a tube with an adhesive cap (Carl Zeiss™ 415190-9211-000). Approximately 1500 cells were collected in one tube, and two tubes were used to collect cells for each sample.

first: Lei

last: Ding

first: Maxime

middle: J

last: Laurent

first: Stijn

last: Aesaert

first: Julien

last: Georgery

first: David

last: Cohen

first: Laurens

last: Pauwels

first: Didier

last: Le Thiec

first: Dirk

last: Inzé

first: François

last: Chaumont


title: Transcriptomic analysis in relation to adventitious rooting of different petunia species

city: Erfurt

first: Sindy

last: Chamas

address: Kuehnhaeuser Strasse 101

institute: Erfurt Research Centre for Horticultural Crops, University of Applied Sciences Erfurt

summary: Excision-induced adventitious rooting of cuttings is a key developmental process for vegetative propagation of many crops, that involves a phytohormone-controlled reprogramming and redifferentiation of specific cells in the stem base. Even though the important role of auxin as inductor of adventitious roots is widely accepted, the endogenous control of auxin action at whole cutting level and the interaction with other hormones are not completely understood. Comparing the genome-sequenced Petunia species P. axillaris and P. inflata, we monitored the transcriptome of phytohormone-related genes in different cutting sections by a phytohormone-targeted microarray. Expression of 17 selected auxin-related genes was quantified in the same RNA samples by RT-qPCR.

sample_organism:
Petunia axillaris
Petunia integrifolia subsp. inflata

overall_design: Gene expression in five different tissues (basal leaves, upper leaves, shoot apex, upper shoot and stem base) of Petunia cuttings was measured at 0, 0.5, 2, 24 and 72 hours post excision. Three replicates were taken for each time point and tissue. Cuttings from two Petunia species (P. axillaris and P. inflata) were used for this experiment.

first: Uwe

last: Druege

first: Katharina

last: Federspiel


title: APOBEC3-mediated mutagenic processes in DNA-repair-deficient HCT116 cells selectively induced by high-dose 5FdUR treatment.

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

summary: The presence of genomic uracil and its respective repair play key roles in colorectal, gastric, and other solid tumor therapies targeting thymidylate biosynthesis. Previously, we established that the treatment of HCT116 colon cancer cell lines with either raltitrexed (RTX) or 5-fluoro-2’-deoxyuridine (5FdUR), two potent inhibitors of thymidylate synthase, results in characteristic uracil patterns (PMID: 32956035). Here, we focus on drug-specific differences manifested in the drug-induced mutagenesis. Therefore, whole genome sequencing was performed in drug-treated (5FdUR or RTX) HCT116 cells that are deficient and stably express the UNG inhibitor protein, UGI. Mutational analysis revealed a significant increase in the frequency of C-to-T somatic transitions selectively upon high-dose 5FdUR treatment in DNA-repair deficient cells. The mutational spectra and the clustered nature of these transitions pointed to the action of DNA cytidine deaminases. Indeed, an induction of some APOBEC3 enzymes was experimentally confirmed upon the high-dose 5FdUR treatment, in parallel with decreased cytotoxicity, as compared to the low-dose, or any efficient doses of RTX. The observed drug-induced mutagenicity and decreased cytotoxicity might be relevant for personalized cancer therapy.

overall_design: We performed whole genome sequencing experiments from UGI expressing HCT116 cells treated with either 0.1 or 20 microM of RTX or 5FdUR for 48 hours. Samples are as follows: 5FdUR_0.1_UGI_HCT116, RTX_0.1_UGI_HCT116, 5FdUR_20_UGI_HCT116, RTX_20_UGI_HCT116, and the non-treated control: NT_UGI_HCT116). Genomic DNA was isolated from each sample and fragmented to approximately 300 bp fragments by sonication. Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, Ipswitch, MA, USA), and were sequenced by Illumina paired-end reads (PE)150 bp in a Novaseq 6000 platform by iBioScience (Pécs, Hungary). Reads were filtered and aligned to the reference human genome (GRCh38.d1.vd1, (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files)). For details, see the Supplementary Method of the related publication. Genomic variants called using mutect2 (GATK4) from treated vs. non-treated input samples in several arrangements defined in the names of each vcf file. For details, see the Supplementary Method of the related publication.

first: Eszter

last: Holub

first: Gábor

last: Papp

first: Hajnalka

middle: L

last: Pálinkás

first: Milda

middle: B

last: Szajkó

first: Richard

last: Izrael

first: Beáta

last: Vértessy

first: Angéla

last: Békési


title: Characterizing age-dependent changes in histone methylation and determine the role of Trr and Trx in histone methylation in adult fly photoreceptors

city: WEST LAFAYETTE

first: Weake

middle: Marie

last: Vikki

state: IN

address: 175 S University st

department: Biochemistry

institute: Purdue University

summary: Histone modifications are important for DNA-templated activities, such as transcription. In the first part of this study, we profiled H3K4me2/3, H3K36me3. H3K9me3 and H3K27me3in young (D10) and old (D40) fly photoreceptors using CUT&RUN to characterize global changes in histone methylation during aging. Our data show that both active and repressive marks exhibit consistently decreased levels in photoreceptors cells of old flies compared to young flies. This global decrease in histone methylation suggests an overall reduction in methylation potential in old photoreceptors. In the second part of the same manuscript, we expressed shRNA against mCherry (control), Trr and Trx, two H3K4 methyltransferases, and profile H3K4me1, H3K4me2, and H3K4me3 using CUT&RUN. Our data show that the knockdown of Trr and Trx leads to pronounced decrease in H3K4me3 levels and modest decrease in H3K4me2 and H3K4me1 in adult photoreceptors.

overall_design: Drosophila were maintained on standard fly food at 25°C under 12-h:12-h light:dark conditions. Male flies were collected at indicated age (days post-eclosion, D) ± 1 day and ZT12 ± 15 minutes. For D10/D40 CUT&RUN, Rh1-Gal4>UAS-GFPKASH flies that express GFP on the photoreceptor nuclei membrane were collected on either D10 or D40 in quadruplicates, 400 flies per replicate. Photoreceptor nuclei were immuno-enriched (NIE) by anti-GFP coated magnetic beads (Jauregui-Lozano et al., 2021). CUT&RUN was performed on bead-bound photoreceptor nuclei as described in (Meers et al., 2019). Antibodies used are: anti-H3K4me2/3 (Abcam #ab8580), anti-H3K36me3 (Abcam #ab9050), anti-H3K9me3 (Abcam #ab176916) and anti-H3K27me3 (Epicypher #13-0055) and anti-IgG negative control (Epicypher #13-0042). pAG-MNase activation/ cleavage was performed for 20 minutes upon the addition of CaCl2.  For knockdown CUT&RUN, Rh1-Gal4>UAS-GFPKASH were crossed to either control (mCherry) RNAi, Trr RNAi (BDSC #36916), or Trx RNAi (BDSC #33703) and progenies were collected on D10 in triplicates for CUT&RUN. Antibodies used are: anti-H3K4me1 (Abcam #ab8895), anti-H3K4me2 Thermo Fisher #710796), anti-H3K4me3 (EpiCypher #13-0041) and anti-IgG negative control (Epicypher #13-0042). pAG-MNase activation/ cleavage was performed for 30 minutes. CUT&RUN libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® kit. Detailed protocols for NIE-based CUT&RUN are available: dx.doi.org/10.17504/protocols.io.kxygxp1d4l8j/v2.

first: Gaoya

last: Meng

first: Makayla

middle: N

last: Marlin

first: Vikki

last: Weake


title: Sex-Based Differences in Cell Types and Gene Expression within the Anterior Cruciate Ligament

city: San Francisco

first: Brian

middle: T

last: Feeley

state: CA

address: 1700 Owens St

department: Orthopedic Surgery

institute: University of California, San Francisco

summary: ACL tear rates in females is significantly higher compared to their male counterpart. We utilized 11 patient samples to explore the biological and transcriptomic differences that exist in male and female ACL.

overall_design:
Human anterior cruciate ligament was mechanically and enzymatically digested. Live cells were sorted by FACS and then sequenced. All cells were analyzed by 10x Genomics 3' single cell RNA sequencing.

Please note that the processed data files for GSM8656015 sample have been replaced with individual files for each patient on Feb 25, 2026.

first: Justin

last: Lau

first: Steven

last: Garcia

first: Xuhui

last: Liu

first: Stephanie

last: Wong


title: Radiotherapy plus neoadjuvant and concomitant IL-13Rα2-directed immunotoxin therapy for diffuse intrinsic pontine glioma

status: Public on Jan 24 2026

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

summary: Radiotherapy (RT) is the standard-of-care for diffuse intrinsic pontine glioma (DIPG); however, it functions as a palliative treatment. Interleukin 13 receptor subunit alpha 2 (IL-13Rα2) is upregulated in most DIPG tumors, posing a promising therapeutic target. Immunotherapies harnessing IL-13Rα2 to selectively deliver cytotoxic payloads such as pseudomonas exotoxin A (PE) are safe in DIPG patients and efficacious in preclinical disease models. Here, we used DIPG cell lines and mouse models to compare RT alone with RT plus the IL-13Rα2-targeted PE immunotoxin GB13 (IL13.E13K-PE4E). DNA strand breaks were evaluated by γH2AX and apoptosis, as well as other on-target effects, by Western blot and immunofluorescence. CellTiter-Glo® and colony formation delineated cell viability and proliferation. In vivo efficacy was based on survival of mice with orthotopic tumors. Animals received fractionated focal irradiation and neoadjuvant and concomitant GB13 by convection-enhanced delivery. GB13 improved the efficacy of RT in vitro through inhibition of DNA damage repair and convergent modulation of apoptotic signaling. Combined RT and intratumoral administration of GB13 decreased tumor burden and prolonged survival in orthotopic xenograft and genetically engineered mouse models. These findings indicate that RT plus GB13 is well tolerated and effective, informing future investigation of a novel therapeutic approach for DIPG.

overall_design: Baseline gene expression of patient-derived diffuse midline glioma H3 K27 altered.

first: Julian

middle: S

last: Rechberger

first: Wouter

last: Vanbilloen

first: Leo

middle: F

last: Nonnenbroich

first: Jizhi

last: Ge

first: Randy

last: Schrecengost

first: Rachael

middle: A

last: Vaubel

first: Liang

last: Zhang

first: David

last: Daniels


title: Gene Expression Changes Induced by YTHDC1 knockdown in triple-negative breast cancer cells

first: Zheng-hao

last: Lai

address: No.107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital

summary: To investigate the role of YTHDC1 in triple-negative breast cancer, we performed YTHDC1 knockdown in triple-negative breast cancer cell lines MDA-MB-231 and Hs578T, followed by transcriptome sequencing using next-generation sequencing technology.

overall_design: We randomly divided MDA-MB-231 and Hs578T cells into two groups, each comprising three replicate samples. One group was treated with siYTHDC1, while the other received siNC treatment as the control group. Following successful knockdown of YTHDC1, total RNA was extracted using the Trizol method. After RNA quality control, transcriptome sequencing was performed.

first: Man-Li

last: Luo

first: Zheng-Hao

first: Na-Na

last: Li

first: Xue


title: Recombinant Spider Silk Membranes Promote Human Renal Epithelial Differentiation and Function

status: Public on Jan 22 2026

city: Stuttgart

first: Florian

last: Büttner

address: Auerbachstraße 112

institute: Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology

summary: Porous membranes are frequently used as supports of cell monolayers in functional studies of epithelial and endothelial barriers. However, conventional polymer-based membranes such as those made of polycarbonate do not mimic the structural and biochemical properties of native basement membranes, which may limit cellular differentiation and function. Here, we use a nanofibrillar membrane made of recombinant spider silk functionalized with the integrin-binding RGD motif of fibronectin and coated with human kidney-specific laminin-521 (LN/FN-silk) as a novel substrate for renal epithelial monolayer cultures. Cellular morphology, mRNA expression, barrier properties and transporter activity were assessed using scanning and transmission electron microscopy, RNA-sequencing, lucifer yellow permeability assays, immunofluorescence staining and fluorescent probe transport assays. Immortalized renal proximal tubular epithelial cell (RPTEC/TERT1) monolayers cultured on LN/FN-silk membranes and in co-culture with human fibroblasts (fHDF/TERT166) exhibited cuboidal morphology, reduced cell death and maintained barrier integrity with tight junction expression compared to conventional polymer-based transwell membranes. In contrast to the LN/FN-silk membranes, the polycarbonate membranes released the endocrine disrupting toxicant bisphenol A, triggering estrogen-mediated signalling. Furthermore, cells on LN/FN-silk membranes showed enhanced directional anion and cation transport, compared to cells cultured on conventional membranes. In summary, the results indicate that LN/FN-silk membranes improve differentiation and functional maintenance of renal epithelial cell cultures, thereby allowing preservation of renal epithelial transport functions.

overall_design: RNA-Seq of RPTEC/TERT1 monocultures on LN/FN-silk (SR), RPTEC/TERT1 / fHDF/TERT166  co-cultures on LN/FN-silk (SRF), RPTEC/TERT1 monocultures on LN/PC (PR), RPTEC/TERT1 / fHDF/TERT166 co-cultures on LN/PC (PRF) and fHDF/TERT166 monocultures (F).

first: Alina

last: Meyer

first: Lea-Maria

last: Mayer

first: Linnea

last: Gustafsson

first: Jens

last: Eriksson

first: Kathrin

last: Klein

first: Son

last: Vo

first: Volker

last: Lauschke

first: Mikael

last: Sellin

first: My

last: Hedhammar

first: Per

last: Artursson


title: Multiscale analysis and functional validation of the cellular and genetic determinants of skeletal disease

city: SYDNEY

first: Peter

last: Croucher

state: NSW

address: 384 VICTORIA ST, DARLINGHURST NSW 2010

country: Australia

institute: Garvan Institute of Medical Research

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Brief Pulses of High-Level Fluid Shear Stress Enhance Metastatic Potential and Rapidly Alter the Metabolism of Cancer Cells

city: Norfolk

first: Michael

last: Henry

state: Virgina

address: 700 W Olney Rd, PO Box 1980

department: Department of Biomedical and Translational Sciences

institute: Eastern Virginia Medical School at Old Dominion University

summary: Circulating tumor cells (CTCs) face challenges to their survival including mechanical and oxidative stresses that are different from cancer cells in solid primary and metastatic tumors. The impact of adaptations to the fluid microenvironment of the circulation on the outcome of the metastatic cascade are not well understood. Here we find that cancer cells (PC-3, MDA-MB-231, Myc-CaP) exposed to brief pulses of high-level FSS exhibit enhanced invasiveness and anchorage-independent proliferation in vitro and enhanced metastatic colonization/tumor formation in vivo. Cancer cells exposed to FSS rapidly alter their metabolism in a manner that promotes survival by providing energy for cytoskeletal remodeling and contractility as well as reducing equivalents to counter oxidative stress associated with cell detachment. Thus, exposure to FSS may provide CTCs an unexpected survival benefit that promotes metastatic colonization.

overall_design: RNAsequeince of PC-3  that were either briefly exposed to fluid shear stress (sheared) or not (static) and then held in suspension for 3, 12, or 24 hours after exposure. Experiment was performed such that sheared and static samples for an individual biological replicate within a timepoint can be paired as they are from an original pool of cells. Data from between timepoints are biologically independent

first: Devon

last: Moose


title: Targeting the Cancer-Retina Antigen PDE6G with mRNA-LNP Vaccine Elicits Potent Anti-Tumor Immunity Against Breast Cancer

city: 杭州

first: wei

last: zhang

state: 浙江省

address: 浙江省杭州市钱塘区下沙街道东方街150中国科学院杭州医学研究所

institute: 浙江工业大学

summary: The development of effective mRNA vaccines for breast cancer has been constrained by the lack of highly immunogenic and tumor-specific antigens. Here, we identify PDE6G, an immune-privileged retina-enriched antigen aberrantly overexpressed in breast tumors, and develop a PDE6G mRNA-LNP vaccine. Vaccination elicited robust CD8+ T cell responses, promoted clonal expansion of effector and IFN-competent T cell subsets, and suppressed tumor growth without detectable toxicity. Single-cell RNA  sequencing (scRNA-seq) revealed that vaccination of PDE6G mRNA-LNP reshapes the tumor immune microenvironment (TIME) by expanding antigen-presenting Cd74+ tumor-associated macrophages (TAMs) while reducing immunosuppressive Maf+ macrophages, and enhancing crosstalk between macrophages and CD8+ T cells. Moreover, combining PDE6G mRNA-LNP with PD-1 blockade further improved anti-tumor efficacy. These findings establish cancer-retina antigens as promising vaccine targets and demonstrate that PDE6G mRNA-LNP coordinates adaptive immunity and tumor microenvironment remodeling, providing a safe and potent strategy for breast cancer immunotherapy.

overall_design: PDE6G-expressing tumor models (experimental group) were immunized with PDE6G mRNA-LNP vaccine

first: Yue

last: Zhao

first: Yichun

last: Pan

first: Wei

last: Zhang

first: Zhao

last: Zuo


title: Gene expression analysis and proximity labeling reveal posttranscriptional functions of the yeast RNA Polymerase II regulator Def1

status: Public on Jan 21 2026

city: University Park

first: Oluwasegun

middle: Tosin

last: Akinniyi

state: PA

address: 463 North Frear

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: Def1 is a yeast protein that promotes transcription elongation and regulates the degradation of RNA polymerase II during transcription stress. Although Def1 is localized in the cytoplasm, its functions in this cellular compartment are not yet understood. Despite its well-established roles in transcription, a comprehensive genome-wide analysis of its impact on gene expression has not been conducted. Here, we performed RNA sequencing (RNA-seq) analysis on cells lacking DEF1 and surprisingly found that only a few hundred genes exhibited altered expression, both upregulated and downregulated. To evaluate mRNA synthesis and decay rates in these DEF1-deficient cells, we used a nascent transcription metabolic labeling technique called RATE-seq. As expected, we observed reduced synthesis rates across the genome in these cells. Additionally, a global decrease in mRNA decay rates was observed, suggesting that Def1 plays a role in the post-transcriptional regulation of mRNAs. The changes in synthesis and decay rates showed a strong correlation, indicating that this compensation helps buffer steady-state mRNA levels. To gain further insight into Def1's functions, we conducted proximity labeling experiments to identify its protein binding partners within the cells. Our findings revealed that Def1 primarily interacts with cytoplasmic regulators involved in post-transcriptional processes, including proteins responsible for deadenylation, decapping, and translation regulation. Using an mRNA decay reporter assay, we demonstrated that recruiting Def1 to mRNA reduces its expression and accelerates its turnover. In summary, we have identified a novel cytoplasmic function for Def1, establishing it as a key regulator of gene expression in both transcription and mRNA decay.

overall_design:
The role of Def1 in translation and in the regulation of RNA was studied by using RNA-seq, RNA metabolic labeling, and Ribo-seq
Wild type (W303) and def1△ strains were grown to log phase (OD~0.8-1) and then treated with 5mM 4-thiouracil
For metabolic labeling, cells were labeled for different times, then harvested, followed by RNA isolation and pull-down.
For Ribo-seq, RNA was isolated from monosomes
For steady-state RNA-seq, RNA was isolated at log phase
Libraries were prepared and sequenced. Analysis was carried out.

first: Aswathy

last: Sebastian

first: Joseph

last: Reese


title: Identifying the impact of H3K4 methylation on the circadian clock in aging Drosophila photoreceptors

first: Weake

last: Vikki

summary: To synchronize with environmental stimuli, predominantly light, the circadian clock directs the physiological and behavioral cycles with a periodicity of approximately 24 hours. The circadian clock is progressively dysregulated during aging, correlating with the development of many neurodegenerative diseases. Circadian disruption in the eye affects retinal development and accelerates photoreceptor degeneration during aging, which implies a protective effect of the functional circadian clock on photoreceptor neurons. At the core of the molecular clock, Clock (CLK) and Cycle (CYC), a pair of transcription activators, regulate the rhythmic transcription of output genes, including a substantial fraction of phototransduction genes. In the aging photoreceptors, CLK:CYC exhibit differential activity while the mechanisms that contribute to this change and its impact on downstream gene expression are poorly understood. H3K4me3 is a ubiquitous chromatin modification that is present at actively transcribed gene promoters. By profiling nuclear transcriptome throughout the 24h day, we identified that knockdown of any of the H3K4 methyltransferase significantly alter the rhythmic gene expression, and collectively, H3K4 methyltransferases (Set1, Trr and Trx) contribute to 90% of the rhythmic transcriptome in Drosophila photoreceptors. In addition, all of the core clock genes showed decreased expression amplitude in any of the KD conditions, indicating H3K4 methylation elevates clock-controlled transcription activation. Given that a global decrease of H3K4me3 is observed in the aging eye, our study favors the scenario where decreased H3K4me3 levels during aging reduce clock-controlled transcription.

overall_design: To knockdown H3K4 methyltransferase in Drosophila photoreceptors, we cross Rh1-Gal4 flies with UAS-RNAi lines, and use F1 progenies for RNA-seq. mCherry knockdown is used as a negative control. F1 flies are raised in 12-hour light: 12-hour dark incubators to Day 10. 400 males are collected every 4 hours spanning the 24- hour day (from ZT0 to ZT20) with a replicate of three each time point. Photoreceptor cells are extracted using nuclear-immuno enrichment (NIE) technique developed in our lab (Jauregui-Lozano et al., 2021, Genetics). Nuclear RNA is purified using ZYMO Direct-zol RNA Microprep Kits (#R2061). RNA library is prepared using Ovation® SoLo RNA-Seq System (#0502-32). mCherry and Set1 KD cDNA libraries are split into 3 laned and sequenced on HiSeq PE150. Trr and Trx KD cDNA libraries are sequenced using NovaSeq X Plus PE150.

first: Gaoya

last: Meng


title: Rapamycin Reverses the Hepatic Response to Diet-Induced Metabolic Stress That Is Amplified by Aging.

status: Public on Jan 16 2026

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

summary: Aging is associated with increased susceptibility to metabolic stress and chronic liver disease, yet the interactions between age and metabolic stressors and the potential for ameliorating interventions remain incompletely understood. Here, we examined the hepatic response of young (7-month-old) and old (25-month-old) C57BL/6 male mice to a 9-week high-fat diet (HFD) and assessed whether rapamycin, a well-established pro-longevity intervention, could mitigate age-exacerbated effects. While both age groups developed metabolic-associated steatohepatitis (MASH), older mice displayed more severe hepatic steatosis, inflammation, and transcriptional dysregulation. Transcriptomic profiling of whole livers and purified hepatocytes revealed that aging amplifies HFD-induced inflammatory and metabolic gene expression changes, including activation of immune pathways and suppression of metabolic pathways. Notably, treatment of aging mice with rapamycin reversed the majority of HFD-driven transcriptional alterations, including upregulation of pro-inflammatory regulators such as Stat1, and dysregulation of metabolic gene networks. Rapamycin also reduced hepatosteatosis, total body weight, and a tumorigenic transcriptomic signature associated with hepatocellular carcinoma risk. These findings demonstrate that aging intensifies hepatic sensitivity to dietary metabolic stress and identify rapamycin as a promising therapeutic to counteract age-related liver dysfunction and metabolic dysfunction-associated steatotic liver disease (MASLD) progression.

overall_design: Three cohorts were examined: normal diet (ND) + vehicle, high fat diet (HFD, 60% calories from fat) + vehicle and high fat diet + rapamycin (42ppm). Mice were initiated on either ND + vehicle or ND + rapamycin at 4-months of age. Once mice reached 18-months of age, they were either maintained on ND + vehicle, or HFD + vehicle, HFD + rapamycin for 9-weeks. Mice were maintained until euthanized and heptocytes were isolated using 2-step perfusion protocol.

first: Aaron

last: P. Havas

first: Adarsh

last: Rajesh

last: D. Adams


title: A Nanopore-Based HIV-1 Reference Epitranscriptome

city: Winston-Salem

first: Keith

last: Gagnon

state: NC

address: 575 Patterson Ave

institute: Wake Forest Baptist Medical Center

summary: Post-transcriptional modifications to RNA, which comprise the epitranscriptome, play important roles in RNA metabolism, gene regulation, and disease pathogenesis. However, mapping modifications and characterizing their function is often challenged by a lack of consensus on their presence and significance. The availability of reference epitranscriptomes to benchmark data would significantly advance epitranscriptomic studies. Toward this goal, we established a reference epitranscriptome for human immunodeficiency virus 1 (HIV-1), an important human pathogen. We sequenced a model HIV-1 genome from infected T cells using the latest nanopore technology. A sense and novel preliminary antisense HIV-1 epitranscriptome were generated where N6-methyladenosine, 5-methylcytosine, pseudouridine, inosine, and 2'-O-methyl modifications were mapped by multiplexed base calling at nucleotide resolution. Modification miscalling due to sequence and modification context was corrected with synthetic RNA fragments and m6A was validated with an inhibitor. Modifications were stable under combination antiretroviral therapy (cART) treatment, in primary CD4+ T cells, and in HIV-1 virions. In contrast, spliced transcript-dependent modification levels were observed. Sequencing samples from people living with HIV (PLWH) revealed substantial conservation of m6A in circulating strains. Our approach offers a benchmark reference to advance HIV-1 epitranscriptomics and provides a roadmap for the creation of reference epitranscriptomes for other viruses or pathogens.

overall_design:
Nanopore direct RNA-seq of Jurkat and CD4+ T cells, infected with HIV-1 and treated with or without cART, in order to detect changes in HIV-1 RNA modification patterns. Synthesized fragments with known RNA modifications were used as modification-calling controls.
POD5 files for these samples are available at https://zenodo.org/records/18223642 .

last: Bosmeny

first: Adrian

last: Pater

first: Li

first: Lydia

last: Larkai

first: Beverly

middle: E

last: Sha

first: Zidi

last: Lyu

first: Masad

last: Damha

first: João

middle: I

last: Mamede


title: RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing IV

status: Public on Jan 23 2026

city: Zürich

first: Giulia

middle: Arianna

last: Moro

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

summary: Many scRNAseq-based methods suffer from a high number of non-detects and a bias towards the 3' or 5' end of transcripts. We developed a method termed RoCK and ROI to address these two biases. RoCK and ROI leads to the enrichment of the transcriptome profile of cells with information on transcripts of interest

overall_design:
RoCK and ROI is based on barcoded beads of the BD Rhapsody platform. For RoCKseq specific capture, TSO oligos on BD Rhapsody beads are modified with a/ multiple capture sequence(s) specific to transcripts of interest. ROIseq, on the other hand, is based on specific primers which are spiked in during library generation, directing reads to regions of interest (ROIs). For this set of experiments, RoCK and ROI was performed to enhance the detection of BCR::ABL1 fusion transcripts in a mix of patient-derived leukemic cell lines (K562, SUP-B15, Loucy) and a  B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patient at first diagnosis.

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

first: Izaskun

last: Mallona

first: Malwine

last: Barz

first: Lorenz

last: Bastian

first: Claudia

last: Baldus

first: Mark

last: Robinson

first: Erich

last: Brunner

first: Konrad

last: Basler


title: Rational design of immune gene therapy combinations via in vivo CRISPR activation screening of tumor microenvironment modulators

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine


title: Single-cell RNA Sequencing of Wildtype and/or Dazl Mutant Mouse Ovarian Cells Across Embryonic Developmental Stages (E10.5 (Wild type), E11.5 (Wild type and Dazl-/-), E12.5 (Dazl-/-), E15.5 (Wild type)

status: Public on Jan 15 2026

city: Baltimore

first: Allan

last: Spradling

address: 3520 San Martin Dr

institute: Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science

summary: We have identified a Golgi- and microtubule-rich vesicular structure, "fusome" which resembles the Drosophila fusome and accumulates asymmetrically during germ cell cyst divisions starting at E11.5. Genes associated with fusome become enriched in presumptive oocytes during cyst divisions and early meiosis, suggesting a role in oocyte rejuvenation. To investigate this further, we performed single-cell RNA sequencing (scRNA-seq) of mouse fetal germ cells at E10.5, E11.5, and E15.5, including developmental stages not previously covered in earlier datasets (GSE136441), thereby generating a composite dataset of E10.5-P5 germ cells. Additionally, we analyzed Dazl homozygous and heterozygous mutant ovarian germ cells at E11.5 and E12.5 to study the impact of Dazl loss on cyst formation and fusome-associated gene expression dynamics. This dataset provides a comprehensive resource to explore transcriptional changes across key stages of fetal ovarian development and in the context of Dazl function.

overall_design: Embryonic ovaries were dissected, and fetal sex was identified using Quinacrine and DAPI staining of tail samples to exclude males in E10.5/E11.5 gonad samples. Female gonads were pooled and dissociated into single cells using 0.25% Trypsin at 37°C for 5–7 minutes with gentle trituration. Trypsin was neutralized with 10% FBS, and cells were filtered through a 30 μm strainer. After centrifugation and resuspension in 0.04% BSA, cell viability was assessed with trypan blue, and high-quality samples (>90% viability) were loaded (~10,000 cells) onto the 10X  (Genomics Chromium platform (v3/v4 chemistry) per manufacturer’s instructions. For mutant samples, Dazl+/- males and females were mated, and embryos collected at E11.5 and E12.5. Tail DNA was extracted using the KAPA Express Extract Kit and genotyped using standard JAX protocols (strain 035880). Identified homozygous and heterozygous fetal gonads were dissociated as above and subjected to scRNA-seq on the same 10X chromium platform.

first: Madhulika

last: Pathak

middle: C


title: Targeting Fused in Sarcoma (FUS): A Novel Antisense Strategy for Treating Idiopathic Pulmonary Fibrosis

status: Public on Jan 20 2026

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research


title: Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [Bisulfite-seq]

status: Public on Jan 13 2026

city: Cambridge

first: Bongmin

last: Bae

state: MA

address: 16 Divinity Ave

institute: Harvard University

type: Methylation profiling by high throughput sequencing

summary: Genomic imprinting is an epigenetic phenomenon in which genes exhibit restricted or biased expression from one allele according to parental origin. Imprinted gene expression plays a crucial role in the development, including the brain. Higher-order chromatin structure has long been associated with gene regulation, particularly in the context of spatial enhancer-promoter interactions. Given the characteristic parental allele-biased expression pattern of imprinted genes, a compelling question is whether the three-dimensional organization of parental genomes plays a role in imprinted gene regulation. Using a capture Hi-C approach, we identifiedparental allele-specific higher-order chromatin structures across multiple imprinted domains in the mouse brain. These allele-specific structural features largely stem from annotated imprinting control regions (ICRs), concomitant with allele-specific binding of CTCF. Detailed analysis suggests that transcriptional start sites (TSS) of active and inactive alleles of imprinted genes form distinct chromatin interactions, differing in degree and/or type. CRISPRi screeningrevealed a distal cis-regulatory element that modulates imprinted expression of the Mest-Copg2locus in neurons, and its regulatory mechanism is tightly associated with allele-specific chromatin interactions. Further investigation revealed that both a cis-acting long non-coding RNA and allele-specific enhancer-promoter architecture modulates Mest-Copg2 imprinted expression. Together, this study highlights the interplay between chromatin structure and regulatory landscapes that modulate allele-specific expression of imprinted genes.

overall_design: Targeted bisulfite sequencing using Nanopore from hybrid mESC treated with DMSO or DNMTi (GSK-3484862).

first: Katherine

last: Gu

first: Amanda

last: Whipple


title: Dynamics of phage-host interactions in Bacteroides fragilis resolved by single-cell transcriptomics [scRNA-Seq data]

city: Seattle

first: Dmitry

last: Sutormin

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: The interactions between lytic phages and their hosts are typically studied in bulk culture, which obscures cell-cell differences in infection susceptibility or expression of protective factors. Here, we use bacterial single-cell RNA sequencing to profile the transcriptomes of ~50,000 cells from cultures of a human pathobiont, Bacteroides fragilis, infected with a lytic bacteriophage. From a single sampling, we quantified the asynchronous progression of phage infection in individual bacterial cells and reconstructed the infection timeline, characterizing both host and phage transcriptomic changes as infection unfolded. Further, we discovered phenotypic subpopulations of bacteria that remained uninfected. Each cell's vulnerability to phage infection was influenced by expression of multiple genetic loci, most prominently phase-variable capsular polysaccharide (CPS) biosynthesis pathways and an operon predicted to encode fimbrial genes. These findings uncovered genome-wide phase variation and stochasticity that enable bacterial survival and re-growth without acquiring additional mutations. Overall, we establish bacterial single-cell RNA sequencing as a powerful platform for investigating the dynamics of host-phage interactions and revealing the roles of phase variation and stochasticity in bacterial defenses.

overall_design: Exponentialy growing Bacteroides fragilis NCTC 9343 culture was a) cultivated in chopped meat carbohydrate (CMC) media; b) infected with Bf12P1 phage in CMC media; c) cultivated in CMC media supplemented with 100µM bile acid DCA; d) infected with Bf12P1 phage in CMC media supplemented with 100µM bile acid DCA. Cells were fixed in 4% formaldehyde and processed via microSPLiT protocol.

first: Anika

last: Gupta

first: Norma

last: Morella

first: Anna

last: Kuchina


title: Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [CUT&Tag]

overall_design: CTCF CUT&Tag from primary cortical neurons isolated from F1 E16 embryos, including forward (BxC) and reverse (CxB) crosses. / H3K27ac CUT&Tag from hybrid KRABxCast NPC-derived neurons, treated with scramble (LV-Scrb) or enhancer-targeting (LV-E105) gRNAs. / CTCF CUT&Tag from hybrid mESC, treated with DMSO or DNMTi (GSK-3484862).


title: DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase

status: Public on Jan 12 2026

city: Chicago

first: Yang

last: Li

institute: The University of Chicago

summary: Here, we describe the DEMETER-assisted 5-Methylcytosine Nicking sequencing (DMN-seq) utilizing 5mC-specific glycosylase DEMETER to nick DNA at 5mC sites, enabling 5mC detection at the single-base resolution. Leveraging this nicking activity to deplete hypermethylated sites, we adapted DMN-seq to preferentially enrich and investigate hypomethylated regions in colorectal cancer samples. When applied to cell-free DNA as low as 0.1 ng, DMN-seq significantly expands the scope of cancer biomarkers by capturing hypomethylated regions, with high sensitivity and reproducibility even in low-input clinical samples.

overall_design: mESC gDNA supplemented with 0.1% (w:w) λ-DNA were fragmented and added with 200 bp dsDNA oligo and 164 bp dsDNA oligo as spike-in. They are subjected to DMN-seq library preparation protocol.

first: Yiding

last: Wang

first: Chang

last: Ye


title: Identification of recurrent tumor-specific markers in patient-matched ovarian cancer samples

city: Incheon

first: Mi-Ryung

last: Han

address: 265, Harmony-ro, Yeonsu-gu, Incheon, Republic of Korea

country: South Korea

institute: Incheon National University

summary: In this study, we performed a transcriptomic comparative analysis on formalin-fixed paraffin-embedded (FFPE) specimens, collecting both primary ovarian cancer tissue and recurrent ovarian cancer tissue in a series from the same patients in real-world settings. Our aim was to identify clinically significant Differentially Expressed Genes (DEGs) associated with the recurrence of HGSOC .

overall_design: We performed RNA-seq on matched primary and recurrent ovarian cancer tissues from 24 patients. This study aims to identify the genetic marker of ovarian cancer recurrence.

first: Min-A

last: Kim

first: Johyeon

last: Nam

first: Jaehoon


title: WNT7 orchestrates myofibroblast heterogeneity to induce desmoplasia

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory


title: Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [ATAC-seq]

overall_design: ATAC-seq datasets from 8-weeks-old mouse cortices, including forward (BxC) and reverse (CxB) crosses.

first: Daniel

last: Loftus


title: Sequencing DNA methylation and hydroxymethylation at co-occurring chromatin features

first: Somdutta

last: Dhir

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

summary: Epigenetic modifications govern chromatin dynamics and cell state. However, current methods cannot simultaneously resolve the presence of multiple DNA modifications at co-occurring chromatin-associated features. It is thus not clear how these features are physically coupled and how their combinations regulate genome function. To address this key question, we report 6-base-CUT&Tag, a method for simultaneous 6-base sequencing at target chromatin features. Using 6-base-CUT&Tag to profile 5mC and 5hmC at co-occurring histone modifications in mouse embryonic stem cells, we identify histone mark-specific signatures of methylation and hydroxymethylation to improve discrimination of different functional enhancer states.

overall_design: NGS sequencing DNA libraries prepared from genomic DNA from mouse ESC cells. Cells were probed using the CUT&Tag methodology using different primary antibodies against a panel of histone marks and 6-base-seq DNA libraries were prepared from the extracted gDNA (6-base-CUT&Tag). 2-3 biological replicates are included per experiment, originated from independent E14Tg2a mESC cultures. Libraries prepared from total tagmented genomic DNA from E14 cells are also included as whole-genome (WG) controls.

first: Rafael

last: C Tavares

first: Xuan

last: He

first: Jack

last: Monahan

first: Minna

last: Taipale

first: Paula

last: Golder

first: Aldo

last: Ciau-Uitz

first: Walraj

last: Gosal

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: DHODH as a Targetable Metabolic Achilles' Heel for chemo-resistant B-ALL

city: Stanford

first: Yuxuan

last: Liu

state: California

address: 265 Campus Drive

department: Pediatrics

institute: Stanford University

summary: Relapse continues to limit survival for patients with B-cell acute lymphoblastic leukemia (B-ALL). Previous studies have independently implicated activation of B-cell developmental signaling pathways and increased glucose consumption with chemo-resistance and relapse risk. Here, we connect these observations, demonstrating that B-ALL cells with active signaling, defined by high expression of phosphorylated ribosomal protein S6 (“pS6+ cells”), are metabolically unique and glucose dependent. Metabolic flux and carbon tracing confirms pS6+ cells to be highly glycolytic and notably sensitive to glucose deprivation, relying on glucose for de novo nucleotide synthesis. Uridine, but not purines or pyrimidines, rescues pS6+ cells from glucose deprivation, demonstrating uridine to be essential for their survival. Active signaling in pS6+ cells drives uridine production through activating phosphorylation of carbamoyl phosphate synthetase (CAD), the enzyme catalyzing the initial steps of uridine synthesis. Inhibition of signaling abolishes glucose dependency and CAD phosphorylation in pS6+ cells. Primary pS6+ cells demonstrate high expression of uridine synthesis proteins, including dihydroorotate dehydrogenase (DHODH), the rate-limiting catalyst of de novo uridine synthesis. Gene expression demonstrates that increased expression of DHODH is associated with relapse and inferior event-free survival after chemotherapy. Further, the majority of B-ALL genomic subtypes demonstrate activity of DHODH. Inhibiting DHODH using BAY2402232 effectively kills pS6+ cells in vitro with its IC50 correlated with the strength of pS6 signaling across 14 B-ALL cell lines and patient-derived xenografts (PDX). In vivo DHODH inhibition prolongs survival and decreases leukemia burden in pS6+ B-ALL cell line and PDX models. These findings link active signaling to uridine dependency in B-ALL cells and associate this with risk of relapse. Targeting uridine synthesis through DHODH inhibition offers a promising therapeutic strategy for chemo-resistant B-ALL as a novel therapeutic approach for relapsed disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sorted pre-B cell in comparing pS6+ and pS6- patients.

first: Jolanda

last: Sarno

first: Pablo

last: Domizi

first: Kara

last: Davis


title: Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [RNA-seq]

first: Bongmin

last: Bae

overall_design: Total RNA-seq from hybrid BxC and CxB primary cortical neurons. / Total RNA-seq from hybrid KRABxCast NPC-derived neurons treated with scramble (LV-Scrb) or enhancer-targeting (LV-E105) gRNAs.  /  mRNA-seq from hybrid mESC treated with DMSO or DNMTi (GSK-3484862).

first: Katherine

last: Gu

first: Amanda

last: Whipple


first: Yang

last: Li

overall_design: A total of 10 ng of gDNA from CRC patient cohort tumor tissue and adjacent healthy colon tissue was used as the untreated sample, whereas 40 ng was used as the DME-treated sample, 1 replicate was used for CRC cohort gDNA. All gDNA samples were prepared, fragmented, and end-repaired in the same way as those used for methylated DNA enrichment. 1 ng, 0.5 ng. A total of 0.1 ng of cfDNA from CRC patients and healthy controls was used as the untreated sample, whereas 2 technical replicates of the same input level were used as DME-treated samples.

first: Yiding

last: Wang

first: Chang

last: Ye


title: Co-translational determination of quaternary structures in chaperone factories

city: Montpellier cedex 05

first: Séverine

last: Boulon

address: 141 rue de la Cardonille

country: France

institute: CNRS

summary: The HSP90/R2TP quaternary chaperone assembles key cellular machines, including the three nuclear RNA polymerases and many non-coding RNPs. Here, we characterized the RNA associated to R2TP and found that it binds many partners co-translationally. Its co-translational interactome further reveals many novel potential clients and identifies clients bound only co-translationally, only post-translationally, or both. For pairs of subunits assembling together and bound co-translationally by R2TP, only a marginal proportion of their mRNAs is co-localized and co-translated. Instead, the HSP90 and R2TP chaperones induce the formation of condensates accumulating client mRNAs and thus favoring co-translational interactions between chaperones and clients. The R2TP then cycles between co- and post-translational steps and this is regulated by ATP: it binds co-translationally in absence of ATP and becomes released from post-translational assembly intermediates by ATP hydrolysis. Assembly of protein complexes is thus initiated early by chaperones and this mechanism, dubbed co-translational chaperone channeling (cha-cha), substitutes for the rarity of co-localized/co-translated mRNAs.

overall_design: RIP-seq analysis of RNA samples following affinity purification of proteins of interest from HCT116 cells, under different drug treatments (puromycin, CB-6644). HCT116 cells lines expressing GFP-tagged protein where constructed via CRISPR/Cas9 edition.

first: Manon

last: Philippe

first: Soha

last: Salloum

first: Jacques

last: Imbert

first: Simon

last: Georges


title: EPOP and MTF2 Activate PRC2 Activity through DNA-sequence specificity

status: Public on Jan 09 2026

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

summary: The Polycomb repressive complex 2 (PRC2) establishes transcriptionally silent chromatin by catalyzing histone H3 lysine 27 trimethylation (H3K27me3). Although cofactors such as MTF2 and JARID2 are known to direct PRC2 to nucleation sites and stimulate its catalytic activity, the role of the PRC2-associated factor EPOP has remained unclear and even controversial. Here, we combine biochemical reconstitution and a cellular EED-rescue system to define EPOP’s contribution to initial PRC2 recruitment and de novo H3K27me3 deposition. We show that EPOP, like MTF2, directly stimulates PRC2 histone methyltransferase activity in vitro. In vivo, EPOP is dispensable for initial PRC2 recruitment but promotes de novo H3K27me3 deposition in cooperation with MTF2 and JARID2. Mechanistically, electrophoretic mobility shift assays and reconstituted chromatin substrates reveal that EPOP and MTF2 enhance PRC2–nucleosome binding in a sequence- and chromatin-dependent manner: EPOP preferentially potentiates activity on GA-rich dinucleosomes, whereas MTF2 favors GCN-rich substrates. Together, these findings position EPOP as a positive regulator of PRC2 function during the establishment of H3K27me3 domains, and reveal a paradigm in which distinct cofactors confer DNA-sequence-specific control of de novo H3K27me3 deposition.

overall_design: To dissect the contribution of PRC2 accessory factors to initial PRC2 recruitment and de novo H3K27me3 deposition, we used a mouse embryonic stem cell (mESC) system in which the core PRC2 subunit EED is knocked out, eliminating PRC2 chromatin binding and H3K27me3 after passaging. Re‑expression of HA‑tagged EED (EED‑rescue) was induced and profiled at 0 h (pre‑rescue baseline) and 24 h (early de novo phase). We performed ChIP‑seq for HA‑EED (proxy for PRC2 chromatin recruitment) and ChIP‑seq for H3K27me3 (histone mark deposition) across a factorial panel of genotypes: wild‑type accessory factor background and targeted knockouts of MTF2, JARID2, EPOP, as single KOs and double KOs (MTF2/JARID2, EPOP/MTF2, EPOP/JARID2).This design enables direct comparison of initial PRC2 recruitment (HA‑EED ChIP‑seq) and de novo H3K27me3 deposition (H3K27me3 ChIP‑seq) kinetics in the presence or absence of individual cofactors during the onset of Polycomb domain formation.

first: Jeffrey

last: Granat

first: Sanxiong

first: Danny

last: Reinberg


title: scRNA-seq of induced pluripotent stem cell derived decidual natural killer cells

first: Virginia

middle: Chu

last: Cheung

address: 2880 Torrey Pines Scenic Dr.

department: Pathology

institute: Univeristy of California, San Diego

summary: Decidual natural killer (dNK) cells are the most abundant immune cells at the maternal-placental interface in early gestation. The exploration of dNK cell heterogeneity and function is currently an active area of research, particularly as these differ across gestation and different regions of the placenta. We applied proteomic and transcriptomic single cell definitions of dNK cells and subtypes to characterize these cells at the chorioamniotic membranes (CAM) and basal plate (BP, maternal surface) regions of the placenta at term. We found that there is reduced abundance of low-effector-function dNK1 and increased abundance of high-effector-function dNK3 in term decidual compartments. At term, in comparison to BP-dNK, CAM-dNK had greater abundance of moderate-effector-function dNK2, decreased abundance of dNK3, and lower expression of inhibitory receptor CD9. At the same time, using our knowledge of dNK heterogeneity, we developed a protocol to differentiate induced pluripotent stem cells (iPSC) into dNK cells. In this manuscript, we detail a protocol to differentiate iPSC into dNK-like cells as characterized by scRNA-seq analyses and CD45+CD56brightCD16- protein expression. We further developed the protocol to enrich for dNK2 – the most abundant dNK cell type in first trimester and term CAM – while inducing expression of dNK marker proteins CD9 and CD103 with the addition of TGFß. This study reveals the shift in dNK subtypes underlying functional changes in dNK cells between first trimester and term and detail a protocol with which we can methodically differentiate iPSC into dNK cells and specifically induce the dNK2 subtype for mechanistic perturbation.

overall_design: iPSC-dNK cells grown in suspension culture were collected, filtered, counted and loaded on the 10x Genomics chip.

first: Mana

last: Parast


overall_design: 200 ng of λ-DNA (NEB) or mESC gDNA supplemented with 0.1% (w:w) λ-DNA were fragmented and added with 200 bp dsDNA oligo and 164 bp dsDNA oligo as spike-in. They are subjected to DMN-seq library preparation protocol.

first: Wang

last: Yiding

first: Li

last: Yang

first: Ye

last: Chang


title: Glucocorticoid-dependence and independence of the circadian liver transcriptome

city: Manchester

first: Robert

last: Maidstone

address: Michael Smith Building, Oxford Road

institute: University of Manchester

summary: The liver, a critical metabolic organ, shows clear day-night variation in patterns of gene and protein expression, and in metabolic pathway activity. Liver cells possess molecular circadian clocks, but systemic factors also contribute to the circadian rhythmicity of liver gene expression. Here, we examine the role of glucocorticoid signalling. Glucocorticoids are essential hormones, with a strong circadian oscillation, which control multiple cellular processes via their action on the glucocorticoid receptor (GR). We first compare clock factor and GR binding at promoters and enhancers linked to rhythmic genes, and find increased clock factor binding at those elements where GR is also present. We find that genes with GR binding at the promoter are more likely to show rhythmic expression. We go to test the role of GR more directly, by examining circadian rhythms of gene expression in mice with and without hepatocyte-targeted GR deletion. Notably, we observe only a small effect of GR deletion, with the vast majority of rhythmic genes showing unchanged rhythmic expression, despite evidence for GR binding in the vicinity of these genes. We do find a small number of genes to show lost or gained rhythmicity with GR deletion, and genes which lose rhythmicity do associate with GR binding sites. However, GR appears redundant for conveying timing information to most of the rhythmic liver transcriptome, a conclusion which is supported by our re-analysis of an independent published dataset.

overall_design: Cre-mediated recombination was induced by injecting mice with 0.1mg tamoxifen i.p. (T5648, Sigma-Aldrich) each day for 5 days. 14 days after the first injection, at ZT0, all mice were transferred to light-tight cabinets, and maintained in constant darkness. After a further 24 hrs (CT0), tissue collection was commenced, with one Cre- (‘WT’) and one Cre+ (‘GR-LKO’) mouse being euthanised every 2 hrs for 48 hrs. As far as possible, the sex of the mice euthanised was alternated at each time point (e.g. males at CT0, CT4, CT8; females at CT2, CT6, CT10).

first: Louise

last: Hunter

first: Mudassar

last: Iqbal

first: Nicola

last: Begley

first: David

last: Bechtold

first: Matthew

last: Baxter

first: Andrew

last: Loudon

first: Magnus

last: Rattray

middle: W

last: Ray


title: Glucocorticoid-dependence and independence of the circadian liver transcriptome [ChIP-seq]

overall_design:
Mice were treated acutely with an intraperitoneal injection of dexamethasone or vehicle, and liver tissue harvested one hour later at ZT18. Data from ZT6 is previously published and avaliable from Array Express: E-MTAB-10224
This study includes re-analysis of samples from ArrayExpress E-MTAB-10224/ERP127680


title: Lysophosphatidic acid synergizes with 1,25-dihydroxyvitamin D to promote fibroblast growth factor-23 synthesis via MAPK signaling and induction of the IL12A gene

city: BOSTON

first: Birol

last: Ay

state: Massachusetts

address: 50 BLOSSOM STREET

institute: MASSACHUSETTS GENERAL HOSPITAL

summary: Dysregulated actions of the bone-derived phosphaturic hormone, fibroblast growth factor-23 (FGF23), underlie the pathophysiology of several diseases. FGF23 is synthesized primarily in osteocytes in response to various endogenous molecules; however, the mechanisms governing FGF23 production are incompletely understood. Glycerol-3-phosphate (G3P), a glycolytic by-product originating from the kidney, critically controls skeletal FGF23 synthesis via its conversion in bone to lysophosphatidic acid (LPA), which stimulates osteocyte FGF23 production. The bioactive vitamin D, 1,25-dihydroxyvitamin D (1,25D), also promotes FGF23 production in osteocytes. We herein demonstrated that LPA requires 1,25D action to raise FGF23 levels in mouse bone explants and mice. RNA sequencing of osteocyte-like Ocy454 cells identified differentially expressed genes (DEGs) uniquely induced by LPA/1,25D co-treatment. These unique DEGs were enriched for the ribosome biogenesis pathway. DEGs concurrently induced by individual LPA and 1,25D treatments were enriched for MAPK signaling, and inhibiting this pathway obliterated LPA/1,25D-induced FGF23 production. DEGs following LPA/1,25D co-treatment were enriched for the cytokine-cytokine interaction pathway. Moreover, LPA/1,25D co-treatment, but not individual LPA and 1,25D treatments, rapidly induced the expression of Il12a, the gene encoding the proinflammatory cytokine interleukin-12 alpha-subunit, which responded solely to 1,25D at later times and required MAPK-ERK1/2 signaling. Inhibiting cytokine signaling or knocking down Il12a inhibited, while overexpressing Il12a enhanced LPA/1,25D-induced FGF23 production. However, challenging Ocy454 cells with recombinant bioactive interleukin-12 failed to enhance FGF23 production, suggesting that Il12a plays a non-canonical role. Our results reveal a mechanism of skeletal FGF23 synthesis involving cooperative actions of LPA and 1,25D, advancing our understanding of FGF23 regulation.

overall_design: RNAseq data of Lysophosphatidic acid (LPA) and 1,25-dihydroxy vitamin D (1,25D) treated Ocy454 cells to promote skeletal fibroblast growth factor-23 (FGF23) synthesis and explore the involved signaling pathways at 2 and 8 hours.

first: Sajin

middle: M

last: Cyr

first: Yorihiro

last: Iwasaki

first: Elizabeth

last: Hill

first: Eugene

middle: P

last: Rhee

first: Nevil

last: Singh

first: Petra

last: Simic

first: Murat

last: Bastepe


title: Resistance Potential of the HLA-A2-restricted Immunodominant SARS-CoV-2 Specific CD8+ T Cell Receptor Repertoire to Antigenic Drift

city: Philadelphia

first: Ning

last: Jiang

address: 210 S 33rd St

department: Bioengineering

institute: University of Pennsylvania

summary: A major concern of COVID-19 is immune escape. While T cells are implicated in protection against severe disease, direct evaluation of their capacity to specifically target SARS-CoV-2 variants remains limited. We aim to narrow this gap by profiling the ability of CD8+ T cells to recognize SARS-CoV-2 mutations after vaccination and observe a high degree of phenotype and repertoire diversity. To better understand the breadth of antigen repertoire coverage, we interrogate the ability of SARS-CoV-2 specific TCRs to bind all point mutations of the immunodominant HLA-A2:S269-277 epitope. While mutation space coverage is surprisingly vast, specific substitutions are not recognized by the vaccine-elicited repertoire. Structural analyses reveal a TCR sequence-based antigen recognition limitation intrinsic to vaccination. Further investigation reveals that this repertoire ‘hole’ is not present in the naive repertoire, suggesting future immune escape through these potential escape mutations could be relieved by modifications to vaccines.

overall_design:
To understand the viral mutation coverage of vaccine-elicited T cell receptor repertoires in individuals that have received COVID-19 mRNA vaccines, we multiplexed DNA-barcoded pMHC multimers with single cell T cell receptor and RNA sequencing before and after vaccination.
In vitro expanded antigen specific T cell receptors were also isolated using single cell amplicon VDJ sequencing.

first: Michael

middle: J

last: Malone

first: Chao

last: Huang

first: Yong

last: Zhang

first: Yi

last: Qi

first: Lea

last: Williams

first: Laura

last: Su

first: Jizhong

last: Lou


title: Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [Capture Hi-C]

first: Bongmin

last: Bae

overall_design: Region capture Hi-C datasets from 8-weeks-old mouse cortices, including forward (BxC) and reverse (CxB) crosses. / Region capture Hi-C datasets from hybrid mESC treated with DMSO or DNMTi (GSK-3484862). / Region capture Hi-C datasets from primary cortical neurons isolated from F1 E16 embryos (BxC crosses).

first: Amanda

last: Whipple


title: SWAP70 Promotes Atherosclerosis via Endothelial CAV1 Nuclear Translocation [ATAC-seq]

status: Public on Jan 08 2026

city: Shenzhen

first: Tianyu

last: Gao

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

summary: Hemodynamic forces play a pivotal role in modulating endothelial function and contribute to the spatial distribution of atherosclerotic lesions. Here, we identify SWAP70 as a flow-sensitive gene whose chromatin accessibility is dynamically regulated by shear stress. Using ATAC-seq analysis of human endothelial cells exposed to static conditions, laminar shear stress (LSS), or oscillatory shear stress (OSS) for 72 hours, we observed that OSS markedly increased chromatin accessibility at the SWAP70 promoter compared to LSS. This enhanced accessibility under OSS suggests transcriptional activation of SWAP70 in response to disturbed flow. These findings indicate that SWAP70 may serve as a mechanosensitive regulator, epigenetically primed by atheroprone flow patterns to modulate endothelial inflammation.

overall_design: ATAC-seq profiling of HUVECs exposed to static, laminar shear stress (LSS), or oscillatory shear stress (OSS) for 72 hours to assess flow-dependent chromatin accessibility at the SWAP70 promoter.


title: Spatial characterization of the transcriptome of the adult healthy and mutant FUS mouse spinal cords [Spatial transcriptomics]

city: Leuven

first: Sandrine

last: Da Cruz

address: Herestraat 49 |

country: Belgium

institute: VIB-KUL Center for Brain & Disease Research

summary: Here we investigated the spatial transcriptome of the aged mouse spinal cord using 10X Genomics Visium platform. We produced local transcriptomes of the full spinal cord with a resolution of 100 um, characterizing ventral and dorsal horn regions, in addition to grey and white matter regions. With these spatial data, it is possible to explore the spatial transcriptome of the aged mouse spinal cord, extrapolating information on the cellular composition of this tissue.

overall_design: Eight 10-um thick sections of spinal cord tissue (4 controls and 4 mutant FUS samples) were layered on the proprietary Visium Spatial Gene Expression Slide (10X Genomics, Cat#PN-2000233) and further processed.

first: Diana

last: Piol

first: Theo

last: Killian

first: Gabriele

last: Partel

first: Nikolai

last: Hecker

first: Sam

last: Kint

first: Katy

last: Vandereyken

first: Thierry

last: Voet

first: Kristofer

last: Davie

first: Stein

last: Aerts

first: Alejandro

last: Sifrim


title: Epigenome-wide DNA Methylation Profiling in the Investigation of Treatment and Life-Course Exposures and Adverse Health Outcomes in Survivors of Childhood Cancer from the St. Jude Lifetime Cohort

city: Memphis

first: Zhaoming

last: Wang

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary:
Long-term survivors of childhood cancer experience treatment-related cardiotoxicity among a broad spectrum of chronic health conditions, which may be further aggrevated by suboptimal life-course social/behavioral/environmental exposures. Epigenetic mechanisms, particularly DNA methylation (DNAm), provide a potential link through which these exposures become biologically embedded and subsequently influence long-term health outcomes.
Epigenome-wide association studies (EWAS) identified DNAm signatures associated with both treatment effects as well as life-course exposures. In parallel, DNAm variations were also evaluated in relation to cardiometabolic risk factors, cardiovascular diseases, and other chronic health conditions, revealing individual CpG sites or genes/geomic regions where these CpGs reside linked to clinically relevant phenotypes. Together, these findings support DNAm as a molecular interface connecting diverse exposures to adverse health outcomes.
In addition, epigenetic age acceleration, assessed using DNAm-based aging biomarkers, was observed among survivors exposed to cancer treatments. Epigenetic age acceleration mediated a substantial proportion of the associations between cancer treatment exposures and cardiometabolic risk factors or cardiovascular diseases, supporting accelerated biological aging as a key pathway linking cancer treatment to long-term morbidity. Lifestyle and health behaviors, as well as social vulnerability and psychosocial stress, were also associated with variations in epigenetic age acceleration, highlighting the potential modifiability of aging-related pathways in ameliorating late-effects among childhood cancer survivors.
In conclusion, these findings establish DNAm—captured through EWAS signatures and epigenetic age acceleration—as central molecular mechanisms linking treatment effects and life-course exposures to cardiotoxicity along with other chronic health conditions in childhood cancer survivors. This integrative epigenetic framework supports the use of DNAm-based biomarkers for risk stratification and nominates modifiable pathways as potential intervention targets  to improve long-term survivorship outcomes.

overall_design:
We included childhood cancer survivors and community controls from the St. Jude Lifetime Cohort Study, a retrospective hospital-based cohort with prospective clinical follow-up. DNA methylation profiles were generated using the Illumina Infinium MethylationEPIC BeadChip from blood- or saliva-derived DNA. A subset of participants contributed DNAm profiles at more than one time point.

The data generation was supported by grant awards from the National Cancer Institute at the National Institutes of Health (R01 CA290112 and R01 CA279520 to Dr Wang, U01 CA195547 to Drs Hudson and Ness) and by grant the V-Foundation grant (DT2020-014 to Dr. Wang).


title: A stem cell knockout village reveals lineage rewiring and a non-canonical islet cell fate in monogenic diabetes

status: Public on Jan 07 2026

city: Washington

first: Bicna

last: Song

state: DC

address: 7144 13th Pl NW

institute: Children's National Hospital

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

overall_design: Refer to individual Series


title: Single-cell RNAseq of from murine pancreas tumor (KPC) and chronic pancreatitis (KC)

first: Jonathan

last: Preall

summary: Pancreatic ductal adenocarcinoma (PDA) is characterized by a desmoplastic extracellular matrix (ECM) that is produced and remodeled by myofibroblastic cancer-associated fibroblasts (myCAFs), thus promoting tumor progression and resistance to therapy. Thus, identification of the regulatory pathways that drive desmoplasia is a pressing clinical need. Transcriptional profiling of tumor resident fibroblasts across PDA progression identified a CAF subset, termed WNT-sensing myCAFs, in both mouse and human PDA. These surround WNT7A/B+ cancer cells and express genes associated with ECM deposition and remodeling. Pharmacological inhibition of ligand-dependent WNT signaling or genetic ablation of Wnt7b in PDA cells depleted the number of WNT-sensing CAFs subpopulation and reduced collagen deposition in vivo, while ectopic Wnt7b expression enhanced desmoplasia. WNT7B overexpression also led to increased metastasis, resulting in a metastatic niche presenting similar WNT-sensing myCAF architecture. Our findings establish WNT7 as a critical regulator of myCAF function and offer a targetable axis to reduce tumor desmoplasia.

overall_design: Pancreatic tumors from KPC (Kras+/LSL-G12D; Trp53+/LSL-R172H; Pdx1-Cre), or chronic pancreatitis tissue from KC (Kras+/LSL-G12D; Pdx1-Cre) mice were minced and enzymatically digested in DMEM supplemented with Collagenase D, Dispase, DNase I, and soybean trypsin inhibitor at 37°C. KPC tumor suspensions were then stained for CD45,CD31, EPCAM, and FACS sorted. Fibroblasts were enriched by sorting viable (DAPI-) cells from the population negative for all three markers (triple-negative, "TN"). Alternatively, all viable cells were enriched from the DAPI- fraction ("DN").  KC pancreata were harvested for single-cell RNAseq without sorting.  For Wnt7b targeting, Cas9-expressing mT6LOH organoid lines were first established by spinfection with LentiV-Cas9-puro vector (Addgene #108100). The single-guide RNA (sgRNA) cassette (sgRNA1-scaffold-bovineU6-sgRNA2) was synthesized as a gene block (IDT) and cloned into LRG2.1-Blast. sgRNAs targeting Wnt7b were sgRNA1= CTCGCGGAACTTAGGTAGCG,  sgRNA2= GTGCAACCGCACCTCGCCGG. For control, sgRNA1=GAAGATGGGCGGGAGTCTTC, targeting the Rosa26 locus and sgRNA2= AGATCATCATATAAGCTTTA, targeting a safe harbor region on chromosome 10 (28474669). KPC-derived mT6LOH organoids were tranduced in culture and single clones selected and verified for loss-of-function mutations by PCR. Orthotopic tumors were grown by injecting 500 cells in the pancreatic parenchyma of C57BL/6J mice, and harvest for scRNA-seq as above.

first: Youngkyu

last: Park

first: Sandeep

last: Nadella

first: Mojdeh

last: Shakiba

first: Jennifer

last: Thalapillil

first: Giuseppina

last: Caligiuri

first: Juliene

last: Hinds

first: David

last: Tuveson


title: Stc2a inhibits IGF-stimulated somatic growth in favor of organismal survival under hypoxic stress

city: Ann Arbor

first: Hui

last: Xu

state: Michigan

address: 500 S State St

institute: University of Michigan

summary: In response to hypoxia, animals reduce somatic growth to shift energy resources toward the maintenance of vital functions and survival. Although this phenomenon is widespread in the animal kingdom, the factors and mechanisms involved remain poorly understood. Here we report that hypoxia causes major changes in zebrafish transcriptomic landscapes with hormonal activity or hormonal signaling identified as most prominently up-regulated GO term and KEGG pathway. Among the top in this group is Stanniocalcin 2a (Stc2a), a secreted glycoprotein that inhibits insulin-like growth factor (IGF) signaling by binding to pappalysin metalloproteinases and inhibiting their activities. The hypoxic induction of stc2a expression is attenuated in Hif2- deficient fish. Genetic deletion of Stc2a increased the developmental speed and growth rate, resulting in enlarged adult organ and body size. Under hypoxia, stc2a-/- fish grew faster than wild-type fish but showed reduced survival rate. These phenotypes were reversed by inhibiting pappalysin activity or blocking IGF signaling. These findings suggest that Stc2a limits IGF- mediated growth in favor of survival and that the induction of Stc2a is part of a conserved mechanism regulating the trade-off between somatic growth and survival under hypoxic stress.

overall_design: RNA-seq profiling of wild-type zebrafish embryos exposed to normoxia (20.9% O₂) or hypoxia (6% O₂) from 81 to 96 hours post-fertilization (hpf). Each condition included three to four biological replicates, with 30 larvae pooled per replicate.

first: Zhengyi

first: Jinay

last: Shah

first: Shuang

last: Li

first: Shriya

last: Jaggi

first: Cunming

last: Duan


title: SWAP70 Promotes Atherosclerosis via Endothelial CAV1 Nuclear Translocation

first: Tianyu

last: Gao

summary: Endothelial inflammation is a critical contributor to atherosclerosis and is tightly regulated by mechanical and inflammatory cues. Here, we identify SWAP70 as a key mechanosensitive adaptor protein involved in endothelial inflammatory responses. Using RNA-seq analysis of human umbilical vein endothelial cells (HUVECs) under three conditions—control (KOC), TNF-α stimulation (TKOC), and TNF-α stimulation with SWAP70 knockdown (TKO)—we demonstrate that SWAP70 deficiency profoundly alters the transcriptional landscape induced by TNF-α. SWAP70 knockdown suppresses the expression of key pro-inflammatory mediators such as VCAM1, MCP1, and CXCL8. Functional enrichment analysis reveals that SWAP70 regulates inflammation-related pathways including TNF, NF-κB, and MAPK signaling. These findings suggest that SWAP70 facilitates endothelial inflammation by promoting transcriptional responses to pro-inflammatory stimuli and may serve as a regulatory hub linking disturbed flow and cytokine signaling in atherosclerosis.

overall_design: RNA-seq profiling of HUVECs transduced with control or SWAP70 shRNA under basal and TNF-α-stimulated conditions to investigate SWAP70-mediated inflammatory transcriptional responses.