title: BHLHE40 Orchestrates TL1A-Driven ILC3 Effector Programs and RORγt⁺ APC-Mediated Tolerance [ATAC-Seq]

status: Public on Jul 06 2026

first: Wei

last: Yang

state: NY

address: Belfer Research Building,Room 760B,413 E. 69th Street

department: Department of Medicine

summary: A central feature of the intestinal immune system is the ability to protect against pathogens while maintaining antigen-specific tolerance to the gut bacteria that coat its surface. Here, we identified Bhlhe40 as a central regulator of both ILC3- and ROR𝛾t⁺ APC-dependent mucosal immunity. TL1A stimulation and inflammatory bowel disease both enhance Bhlhe40 expression in intestinal ILC3s. Basal Bhlhe40 expression in ILC3s is essential for efficient transcription of cytokine effectors and maintenance of mucosal immunity, whereas TL1A-induced upregulation of Bhlhe40 further amplifies these effects. Bhlhe40 is also highly expressed in ROR𝛾t⁺ APCs, where it is required for optimal generation of antigen-specific Tregs. Together with the colonic microbiota, Bhlhe40 regulates expression of the co-stimulatory molecule Tnfsf4 (OX40L), which is necessary for the induction of Helicobacter hepaticus-specific Tregs. These findings reveal a previously unrecognized role for Bhlhe40 in orchestrating intestinal ILC3 responses and promoting Bhlhe40-dependent co-stimulatory signals in ROR𝛾t⁺ APCs that coordinate antigen-specific tolerance.

overall_design: To determine whether Bhlhe40 regulates chromatin accessibility in ILC3, we performed ATACseq for sorted intestine ILC3s from Bhlhe40+/-Rag2-/- and Bhlhe40-/-Rag2-/- mice stimulated with or without rTL1A for 18hr.

first: Randy

last: Longman


title: SpxA1 and SpxA2 Function as a Stoichiometry-Dependent Regulatory Rheostat Governing Virulence Gene Expression in Group A Streptococcus — RNA-seq dataset

status: Public on Jul 13 2026

city: Nashville

first: Anthony

last: Flores

state: TN

address: 1161 21st Avenue S, MCN D7219

country: USA

institute: Vanderbilt University Medical Center

type: Expression profiling by high throughput sequencing

summary: Group A Streptococcus (GAS) encodes two paralogs of the Spx transcriptional regulator, SpxA1 and SpxA2, which interact with RNA polymerase to modulate virulence gene expression. To define the transcriptomic consequences of SpxA1 and SpxA2 loss, we performed strand-non-specific paired-end RNA-seq in the wild-type emm3 GAS strain MGAS10870 and isogenic deletion mutants (deltaSpxA1 and deltaSpxA2) grown to mid-exponential phase in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY). Differential expression analysis identified distinct transcriptomic signatures for each paralog, with SpxA1 primarily influencing oxidative stress response genes and SpxA2 modulating CovR-regulated virulence factor-encoding genes. These data contribute to a multi-omic analysis including DIA proteomics, NanoString nCounter, and CovR ChIP-exo that defines the regulatory roles of SpxA1 and SpxA2 in GAS pathogenesis.

overall_design: Wild-type MGAS10870 (emm3) and isogenic deletion mutants deltaSpxA1 and deltaSpxA2 were grown in THY medium to mid-exponential phase (OD600 ~0.45) in biological triplicate. RNA was extracted and strand-non-specific paired-end RNA-seq libraries were prepared and sequenced by the VANTAGE core facility at Vanderbilt University Medical Center. Raw reads were aligned to the MGAS10870 reference genome (NZ_CP067090.1) using CLC Genomics Workbench v23. Differential gene expression was determined using DESeq2 with Bonferroni and Benjamini-Hochberg FDR correction. Significance thresholds: |log2FC| >= log2(1.5), padj < 0.05.

middle: R

first: Misu

middle: A

last: Sanson

first: Luis

last: Vega


title: A 3D Human Bone and Bone Marrow‐on‐a‐Chip Model for In Vitro Bone Remodeling and Immune Cell Maintenance

city: Lübeck

first: Kristian

last: Händler

address: Ratzeburger Allee 160

department: Human Genetics

country: Germany

institute: UKSH

summary: We developed a human Bone-on-a-Chip (BOAC) model that integrates autologous primary immune and bone cells on native human bone substrates within a xeno-free, perfused environment. In contrast to existing models, which focus primarily on hematopoietic or stromal compartments, our system mimics functional bone remodeling and enables the long-term maintenance of mature immune cells. Dynamic flow and sequential cell seeding facilitated osteoclast-mediated resorption, osteoblast-driven matrix formation, and the preservation of donor-specific immune profiles over several weeks. The balance between bone cell activity and immune cell maintenance was further optimized by controlled temperature modulation. The BOAC model preserves key features of bone and bone marrow physiology, including extracellular matrix formation, soluble factor signaling, and cellular heterogeneity. Single-nucleus RNA sequencing confirmed the sustained presence of donor-specific immune and bone cell populations. This 3D human in vitro system provides a robust platform for translational research and personalized medicine.

overall_design:
RNA-seq profiling was performed on a human ex vivo bone tissue biopsy (reference sample) and two in vitro Bone-on-a-Chip samples on day 42 of cultivation. The in vitro cultures were assembled using bone and immune cells from the same donor as the ex vivo biopsy.
Please note that this is single-cell RNA seq data from fixed tissue using 10X Genomics Flex chemistry. This protocol results in multiplexed fastq files that need to be demultiplexed into individual samples using cellranger.  The sample represents a mixed sample of the following three samples multiplexed in the one set of fastq files:
Patient_bone_femoral_head_biopsy (Pat2337_TC1)
scaffold_populated_with_patient_PBMC (P2337_BOAC_6w_SC121_PBMC)
scaffold_populated_with_patient_BMMNC (P2337_BOAC_6w_SC130_BMMNC)
A config.csv file to demultiplex the fastq using cellranger >=7 is uploaded as well

first: Nina

last: Stelzer

first: Melanie-Jasmin

last: Ort

first: Emily

last: Bortel

first: Ioanna

middle: M

last: Dimitriou

first: Martin

last: Textor

first: Georg

middle: N

last: Duda

first: Janosch

last: Schoon

first: Uwe

last: Marx

last: Kornak

first: Annika

last: Winter

first: Bernhard

last: Hesse

first: Stefanie

last: Donner

first: Sebastian

last: Hardt

first: Oliver

last: Klein

first: Simon

last: Reinke

first: Malte

last: Spielmann

first: Sven

last: Geißler


title: Transcriptomics of Neurochondrin (NCDN)-depleted and control U251 glioblastoma cells

status: Public on Jul 11 2026

city: Shanghai

first: Tingrong

last: Ren

address: 131 Dong'an Road, Xuhui District, Shanghai, China

country: China

institute: fudan university

summary: Pre mRNA splicing is orchestrated by the spliceosome; a dynamic and highly regulated ribonucleoprotein complex composed of five small nuclear ribonucleoprotein particles (snRNPs). Despite extensive studies, the biogenesis of snRNPs remains incompletely understood. Here, we identify neurochondrin (NCDN) as a critical regulator of pre-U5 snRNP biogenesis in the cytoplasm. NCDN directly binds to AAR2 and facilitates its release from the PRPF8−AAR2−EFTUD2 assembly intermediate, a key step required for U5 snRNP maturation. Loss of NCDN causes the accumulation of this intermediate, resulting in a decreased level of mature U5 snRNP. Spliceosome dysregulation often leads to alternative splicing abnormalities implicated in cancer. Indeed, NCDN deficiency suppresses tumor cell proliferation and induces apoptosis, while high NCDN expression promotes tumor cell growth and correlates with poor survival in glioblastoma patients. Transcriptome analysis reveals that loss of NCDN causes widespread alternative splicing defects and changes in gene expression. Aberrant splicing of tumor-associated genes may contribute to tumor progression in glioblastoma. Collectively, these results establish NCDN as an essential chaperone factor for U5 snRNP assembly and spliceosome function, and highlight NCDN as a potential therapeutic target in the treatment of glioma with elevated NCDN expression.

overall_design: To examine the role of NCDN in mRNA splicing regulation, we performed RNA sequencing on NCDN-knockdown (shNCDN) and control (shControl) U251 cells.

first: Gaigai

last: Wei

first: Haiping

last: Zhao

first: Huiling

last: Zhang

first: Yuqi

first: Jingjing

last: Yi

first: Zhihan

last: Guo


title: Expression landscape and circadian regulation of lncRNAs in the kidney [snRNA-seq]

status: Public on Jul 08 2026

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: Recent multi-omics work shows that the diurnal rhythmicity of kidney function is associated with circadian oscillations in renal mRNA, protein and metabolite abundances. Yet circadian regulation of renal lncRNAs, which are emerging as important modulators of diverse (patho)physiological processes, remains largely unexplored. Here, we provide a comprehensive characterization of renal lncRNA expression across cell types and circadian time points using bulk RNA-Seq and single-nucleus RNA-Seq (snRNA-seq) using kidney samples from male mice. Although the majority of lncRNAs are lowly expressed and only a fraction is annotated, their profiles sufficed to distinguish nearly all renal cell types. Compared with mRNAs, lncRNAs were more cell-type specific and an inverse correlation between cell-type specificity and expression level was evident. To assess the role of the circadian clock, we used mice lacking the core-clock regulator BMAL1 in renal tubules. Approximately one-sixth of lncRNAs and one-third of mRNAs were rhythmic. In contrast with mRNAs, lncRNAs exhibited an asymmetric temporal distribution between night and day, with peak expression occurring preferentially during the inactive phase of the mice. Bmal1 deletion partially disrupted rhythmicity in both biotypes and altered overall expression levels; lncRNAs were predominantly upregulated. These findings uncover the diversity of renal lncRNAs, their cellular distribution and their circadian regulation in male mice.

overall_design: Single nucleus RNAseq (scRNAseq) profiling of mouse kidney from 8 mice.  Of these, 4 were conditional knockouts of Arntl (Bmal1) in the renal tubule (cKOt), and 4 were of a control genotype (Ctrl). They were housed under 12-hours light/12-hours dark cycles and were sacrificed at two different circadian time points: zeitgeber time ZT 4 and ZT 16 (ZT 0 being the time of light on and ZT 12 the time of light off). Four replicates per genotype and time point were included.  The genotpyes and time points were the same as in our bulk RNASeq data set (GEO accession <>) , which was produced for the same study. The experiment was performed on a separate set of mouse individuals.

first: Dmitri

last: Firsov

first: Fanny

last: Durussel

first: Muriel

last: Auberson

first: Yohan

last: Bignon


title: The use of microRNA mimics to increase microRNA levels in the developing organs of newborn mice.

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: MicroRNA are emerging of important regulators of cell and tissue differentiation, organ development, and disease pathogenesis. The use of microRNA antimiRs which deplete microRNA pools is a well-established and successful intervention in both in vivo and in vitro settings, where the goal is to reduce the abundance of selected microRNA species. However, whilst efforts to increase the abundance of selected microRNA species in vitro have found widespread success in cell culture, delivering functional microRNA to the organs of living, intact experimental animals remains problematic. The objective of this study was to examine the efficacy of delivery of commercially-available microRNA mimics that are marketed for in vitro and in vivo use to multiple organs of the laboratory mouse, following parenteral administration in various protocols over the first 14 days of post-natal life. The data presented indicate that parenteral administration of a microRNA mimic is largely inefficient, with moderate delivery of a miR-497a-5p mimic noted in the liver, but not the kidneys, lungs, heart, or brain. Changes in the abundance of a limited number of mRNA and protein targets in the liver were observed, using batch RNA-Seq and proteomic screening; indicting the delivery of a miR-497a-5p mimic had functional consequences for the liver transcriptome and proteome. These data highlight the potential utility of commercially-available microRNA mimics in an in vivo setting, however, these data also highlight notable hurdles that still need to be overcome to facilitate the further use of microRNA mimics to study physiological processes in living, intact organisms.

overall_design: A chemically stabilized miR-497a-5p mimic (and an inert "scrambled" mimic in the control group) will be administered to newborn mice by intraperitoneal injection, using the highest tested "safe dose" for stabilized oligonucleotides (100 mg/kg), in a protocol that has been documented to be effective for the delivery of microRNA inhibitors constructed with the same nucleotide chemistry (intraperitoneal injections on the first and third day of post-natal life). The brain, heart, kidneys, liver, and lungs will be harvested on the fifth, seventh, and 14th days of post-natal life, and screened by real-time RT-PCR for the presence of miR‑497‑5p, and subjected to batch RNA-Seq to asses an impact of miR-497a-5p delivery on candidate mRNA targets.

last: Willen

first: Despoina

last: Myti

first: Solmaz

last: Khaghani Raziabad

first: Claudio

last: Nardiello

first: Rory

middle: E

last: Morty


title: Transcriptome profiling of ARHGAP29-depleted human embryonic palatal mesenchymal cells

status: Public on Jul 03 2026

city: Yinchuan

first: Zhumin

last: wang

state: ningxia

address: Shengli Street

department: School of Stomatology

institute: ningxia medical university

summary: ARHGAP29 is implicated in nonsyndromic cleft lip with or without cleft palate, but its role in human palatal mesenchymal cells remains incompletely understood. Human embryonic palatal mesenchymal (HEPM) cells were transfected with ARHGAP29-targeting siRNA or a non-targeting negative-control siRNA. Total RNA sequencing was performed for three independent biological replicates per group. The study was designed to identify transcriptional changes associated with ARHGAP29 depletion. Differential expression and functional enrichment analyses indicated changes in developmental and stress-responsive gene programs, including p53- and Notch-related pathways.

overall_design: Strand-specific total RNA sequencing of HEPM cells after siRNA-mediated ARHGAP29 knockdown. Three independent biological replicates transfected with ARHGAP29 siRNA (Si1, Si2 and Si3) were compared with three independent biological replicates transfected with non-targeting negative-control siRNA (NC1, NC2 and NC3). The present submission contains the six samples used for the mRNA expression analysis reported in the associated manuscript.

last: Wang

first: Ying

last: Yang

first: Lili

last: Yu

first: Chen

last: Hu

first: Wen

last: Dong

first: Di

last: Yan

first: Yongqing

last: Huang

first: Xiaoli

last: Ma

first: Jian


title: BHLHE40 Orchestrates TL1A-Driven ILC3 Effector Programs and RORγt⁺ APC-Mediated Tolerance [scRNA-seq]

city: New York

first: Wei

institute: Weill Cornell Medicine

overall_design: To determine the impact of Bhlhe40 on ROR𝛾t+ APCs, we performed scRNAseq on sorted CD45+ Lineage- MHCII+ cells from the mesenteric lymph nodes of 2 weeks old mice sufficient or deficient for Bhlhe40, treated with or without agonist DR3 for 2 days.

first: Randy

last: Longman


title: BHLHE40 Orchestrates TL1A-Driven ILC3 Effector Programs and RORγt⁺ APC-Mediated Tolerance.

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Kidney-specific deletion of the BicC family RNA binding protein 1 triggers an ADPKD-like cystogenic program

status: Public on Jun 30 2026

first: Benjamin

last: Rothé

address: Station 19

department: SV

institute: École Polytechnique Fédérale de Lausanne

summary: Autosomal dominant polycystic kidney disease (ADPKD) arises from mutations in polycystin-1/PKD1 or polycystin-2/PKD2 that induce injury-repair pathways and dysregulate cAMP and YAP/TAZ signaling to promote cyst growth. Cystic kidneys with elevated cAMP levels also develop in mouse embryos lacking the BicC family RNA-binding protein 1 (Bicc1). To prevent embryonic lethality, we flanked Bicc1 exon 4 with loxP sites for conditional knockout (cKO) in renal tubules using inducible Pax8rtTA-driven Cre in adults, or distal segment-specific deletion in utero using Ksp-Cre. Whereas Bicc1-deficient adult kidneys formed relatively few cysts within six months, distal nephron-specific deletion induced aggressive PKD-like disease. Automated Renal Tubule Cyst Quantification (ARTCyQ), a novel machine-learning pipeline to analyze immunofluorescent stainings, revealed increasing ambiguity in nephron segment identity and activation of ADPKD-related pathways, including YAP signaling. Accordingly, transcriptional profiling revealed overlap with PKD and injury-repair signatures, supporting a role for Bicc1 in polycystin signaling.

overall_design: RNA-seq of male and female BICC1 deficient mice

first: Céline

last: Gagnieux

first: Florian

last: Bernet

first: Lona

last: Kroese

first: Romain

last: Guiet

first: Allison

last: Burns

first: Roy

last: Combe

first: Ivo

last: Huijbers

first: Daniel

middle: B

last: Constam


title: STING deficiency does not rescue short-telomere mediated aging phenotypes and longevity in TERC or TERT telomerase deficient mice

status: Public on Jul 02 2026

city: Madrid

first: Elena

last: Piñeiro-Yáñez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

summary: The c-GAS-STING pathway is proposed to have a key physiological role in the response to viral genomes and other types of endogenous DNA byproducts by inducing inflammatory pathways.  More recently a role of the c-GAS-STING in senescence and in response to short telomeres has been also proposed.  To address the role of the cGAS-STING pathway in the age-related pathologies and decreased longevity associated to short and dysfunctional telomeres, here we have generated double mutant mice for STING and increasing generations of telomerase deficiency, either owing to deficiency in the telomerase RNA component, TERC, or in the reverse transcriptase component (TERT).  Our results with both telomerase-deficient mouse cohorts show that STING deficiency does not rescue any of the major phenotypes associated to short telomeres, including decreased body weight, infertility, and a plethora of degenerative pathologies.  Importantly, STING deficiency does not rescue the progressively decreased maximum and median lifespan of increasing generations of Terc or Tert deficient mice. These findings indicate that STING does not mediate aging phenotypes associated to short telomeres in mammals. Furthermore, they have profound implications for the development of therapeutic strategies based on STING inhibition for the treatment of age-related diseases associated to short or dysfunctional telomeres.

overall_design: To determine whether genome-wide expression programs derived from short telomeres are dependent on STING, we directly analyzed the cellular transcriptome through RNA sequencing  in the small intestine of Terc+/+/Sting+/+, Terc+/+/Stinggt/gt, G3 Terc-/-/Sting+/+, and G3 Terc-/-/Stinggt/gt mouse cohorts.

first: Rosa M.

last: Marión

first: José Carlos

last: González

first: Maria A.

last: Blasco


title: Bottlebrush Polymer Conjugates for Enhanced Antisense Oligonucleotide Therapy in Myotonic Dystrophy Type 1

status: Public on Jul 01 2026

city: Boston

first: Ke

last: Zhang

state: MA

address: 360 Huntington Ave

institute: Northeastern University

summary: Oligonucleotides are a promising class of genetic medicine for myotonic dystrophy type 1 (DM1), the most common adult-onset muscular dystrophy. However, poor muscle distribution of nucleic acid drugs following systemic administration has hindered drug development, and no curative treatment currently exists. DM1 pathology requires drug localization to the nucleus, where pathogenic mutant RNA is sequestered, posing additional challenges after cellular internalization regarding endosomal escape and nuclear uptake. Here, we show that a locked nucleic acid oligonucleotide targeting mutant CUG repeat RNA tracts, conjugated to a bottlebrush polymer, exhibits improved muscle distribution and potent correction of DM1-associated splicing dysregulation in a DM1 mouse model. Significant improvements in myotonia, body weight, and grip strength were observed. The conjugate was well tolerated following 12 weeks of weekly intravenous administration. These findings suggest that bottlebrush polymer conjugates may overcome key limitations of conventional oligonucleotide therapeutics for neuromuscular conditions, with potential to become a potent and cost-effective DM1 therapy.

overall_design: RNA-seq of quadriceps from FVB/N wildtype mice or myotonic dystrophy type 1 (DM1) HSA-LR20b mice (Strain #032031, Jackson Laboratory) treated with pacDNA-L9 or controls, 2 weeks after i.v. injection.

first: Yao

last: Li

first: Christopher

last: Oetheimer


title: Modeling Tay-Sachs Disease in Astrocyte-Like Cells Reveals Significant Changes in the Transcriptomic Profile

status: Public on Jul 04 2026

city: Bogotá

first: Diego

middle: Alejandro

last: Suárez-García

department: Science department

country: Colombia

institute: IEIM

summary: Tay-Sachs disease is a rare genetic disorder characterized by the accumulation of GM2 ganglioside in neuronal lysosomes due to deficient β-hexosaminidase A (HexA) activity. Progressive GM2storage leads to severe neurodegeneration, including developmental delay, motor weakness, seizures, ataxia, and early death, typically by five years of age. Although previous studies have elucidated several neuronal mechanisms, including apoptosis, endoplasmic reticulum stress, neuroinflammation, and demyelination, these investigations have focused almost exclusively on neurons. However, other components of the central nervous system, particularly astroglia, may play a critical role in disease pathophysiology as suggested by studies in related lysosomal storage disorders.To address this gap, we generated an astrocyte-like model deficient in HexA by targeted knockdown of the HEXA gene in U87MG astrocytoma cells . The resulting cell line recapitulates key pathological features, including lysosomal accumulation, increased neutral lipid content, reduced mitochondrial mass, and elevated reactive oxygen species production. Transcriptomic analysis revealed significant alterations in pathways associated with neuronal degeneration, synaptic organization, mitochondrial dysfunction, and ganglioside metabolism. In summary, this model reproduces some classical cellular alterations reported in Tay-Sachs disease and could potentially provide novel insight into astrocyte involvement in its pathophysiology. These findings support the relevance of non-neuronal cells in disease pathophysiology and establish this system as a valuable platform for screening potential novel mechanisms and therapeutic approaches. Furthermore, this approach highlights the importance of integrating cell type specific models to better understand disease heterogeneity and providing insights into the progressive neurodegeneration of Tay-Sachs disease, positioning this model as a valuable tool for studying its underlying pathophysiology

overall_design: RNA-Seq profilling of wild type U87MG cells and  U87MG cells with CRISPR-Cas9 mediated HEXA gene silencing.

last: Suárez-Garcia

first: Angela

middle: J

last: Espejo-Mojica

first: Carlos

last: Alméciga-Diaz


title: BHLHE40 Orchestrates TL1A-Driven ILC3 Effector Programs and RORγt⁺ APC-Mediated Tolerance

first: Wei

last: Yang

overall_design:
To determine the role of Bhlhe40 in ILC3, we performed RNAseq for sorted intestine ILC3s from Bhlhe40+/-Rag2-/- and Bhlhe40-/-Rag2-/- mice stimulated with or without rTL1A or IL-23 for 18hr.
To define the transcriptional programs regulated by TL1A, we performed RNA sequencing of sorted intestinal ILC3s from RorcCreRosa26Td/+Rag2-/- mice stimulated in vitro with or without TL1A for 18hr.

first: Randy

last: Longman


title: RepliSage: A Stochastic Graph-Based Framework for 3D Chromatin Modeling Across the Cell Cycle

city: Warsaw

first: Dariusz

last: Plewczynski

state: mazovia

address: Banacha 2c

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

summary: Modeling DNA replication requires capturing the interplay of multiple biophysical processes and their effects on chromatin structure. We present RepliSage, a multi-scale framework that integrates three key factors: replication timing, loop extrusion, and compartmentalization. Replication forks act as moving barriers that reorganize chromatin during S phase by interfering with loop extrusion. Our approach combines: (1) fork propagation simulated from single-cell replication timing data, (2) Monte Carlo modeling of loop extrusion and epigenetic state transitions, and (3) 3D reconstruction using OpenMM, where loops are modeled as harmonic bonds and epigenetic states drive compartmental interactions. Chromatin is represented as a graph where both the links and the node states change over time. By adjusting model parameters across cell cycle phases, we reproduce known structural transitions and explore how replication stress alters genome organization. This is the first framework to dynamically integrate all three processes for simulating chromatin architecture during the cell cycle.

overall_design: The SMC1 HiChIP experiment was performed in the GM12878 lymphoblastoid cell line under control (DMSO and water) and replication stress (APH and HU) conditions.

first: Sevastianos

last: Korsak

first: Krzysztof

middle: H

last: Banecki

first: Karolina

last: Buka

first: Abhishek

last: Agarwal

first: Joanna

last: Borkowska


title: Effect of lentivirus  pseudotyped by SARS-CoV2 S-protein  on 3D skin equivalents transcriptome

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Cell entry of SARS-CoV-2 depends on binding of the viral spike (S) glycoprotein to the host cell receptor ACE2 and its priming/cleavage by the host protease TMPRSS2. We and others showed that skin cells including keratinocytes express significant amounts of ACE2 and TMPRSS2. To uncover the potential role of skin in SARS-CoV-2 infection we infected 3D skin equivalents (HSE) made from human keratinocytes growing on collagen matrix infused with fibroblasts with lentiviral reporter pseudotyped by SARS-CoV-2 S-protein and expressing Tomato fluorescent protein. Tomato expression analysis by Q-PCR and immunofluorescence indicated that HSE were successfully infected. Here we analyzed the effect of binding of viral S-protein to ACE2 in control and inflamed by the cytokines (IL1b, IL6, TNFa and IFNg) 3D HSE on keratinocyte transcriptome.

overall_design: Mature 3D HSE with well-formed epidermis were treated with combination of cytokines (TNFa+IL1b+IL6+IFNg ,10ng/each) or vehicle (0.4% BSA) as a control and in 7 days after the development of inflammation, half of 3D HSE were infected with Tomato lentiviral reporter pseudotyped by SARS-CoV-2 S-protein applied topically on the top of HSE. In 72 hrs when we could observe Tomato fluorescenece in HSE, total RNA was extracted by Quagene meRnaeasy mini-kit. The groups (two HSE/group) are called according to the treatment: Con, Cyt, Vir, CytVir.

first: Irina

last: Budunova

first: Daria

last: Chudakova


title: DNA methylation profiling identifies long-range epigenetic silencing of clustered protocadherins as a key determinant of meningioma progression [discovery]

city: Tübingen

first: Daniel

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

type: Methylation profiling by genome tiling array

summary: Meningioma is the most common primary brain tumor in adults, but molecular drivers of progression occurring in a subset of meningiomas are poorly understood. We hypothesized that epigenomic variations are causal for the clinical heterogeneity of meningiomas and may be functionally relevant for disease progression. To test this hypothesis, we performed global DNA methylation profiling of a large cross-sectional cohort and a longitudinal cohort of human meningiomas. Our analysis identifies a DNA hypermethylation signature that is correlated with clinical outcomes and enables more accurate prognostication in intermediate-risk meningiomas than previous classification systems. Analyses of longitudinal high-grade meningioma samples in comparison to clinically benign meningiomas and normal meningeal tissue show convergent contributions, but differing plasticity of copy number variations and DNA hypermethylation along the trajectory of meningioma progression. Systematic analysis of DNA hypermethylation in high-grade meningiomas unravel a tumor suppressive role of clustered protocadherins by regulating b-catenin signaling. Together, our study provides fundamental insights into the molecular mechanisms underlying the heterogeneity of clinically benign and aggressive meningiomas and the microevolutionary adaptation during disease progression.

overall_design: DNA methylation profiling was peformed on n=237 primary and recurrent human meningioma samples. Six samples were excluded following initial quality control due to insufficient data quality. The remaining 231 samples passed quality control and constituted the cohort used for all downstream analyses reported in the associated study.

first: Ghazaleh

last: Tabatabai


title: Increased arrhythmic risk in obesity is transduced by adipose tissue-derived extracellular vesicles

first: Worawan

last: Limpitikul

address: 55 Fruit Street

institute: Massachusetts General Hospital

summary: While obesity is associated with atrial fibrillation and ventricular arrhythmias, whether direct communication from excess fat transduces this risk to the heart is unknown. Here, we demonstrate prolongation of the action potential duration (APD) is human atrial myocytes obtained from obese but not lean patients indicating obesity-associated electrical remodeling. Consistent with this observation, visceral adipose tissue-derived extracellular vesicles (VAT EVs) from obese individuals similarly prolong action potential duration (APD) and impair calcium handling in human stem cell-derived cardiomyocytes, activate human cardiac fibroblasts and drive macrophages toward a pro-inflammatory phenotype, promoting a pro-arrhythmic substrate. We observed this communication in vivo, where adipose-derived EVs directly target cardiac cells in obese mice more than in lean mice, implicating a fat-heart communication axis in obesity. Human functional genomics anchored on genes differentially expressed in human cardiomyocytes, fibroblasts, and macrophages after human obese VAT-EV exposure identified targets causally linked to both QT interval (n=117,532) and atrial fibrillation (n= 181,446). Pharmacological blockade of a VAT-EV induced ion channel TRPC3 in cardiomyocytes restored the APD toward normal. These results collectively implicate an EV-mediated direct communication pathway between adipose tissue and the heart in arrhythmogenesis that activates both known and novel pathways, offering a new paradigm to identify mediators of cardiovascular disease in obesity.

overall_design: human induced puripotent stem cell-derived atrial myocytes (iPSC-aCMs), ventricular myocytes (iPSC-vCMs), and cardiac fibroblasts (iPSC-CFs) and macrophages were treated with extracellular vesicles derived from human visceral adiopose tissue (VAT EVs) and bulk RNA-seq was performed on these 4 cell types


title: DNA methylation profiling identifies long-range epigenetic silencing of clustered protocadherins as a key determinant of meningioma progression


title: Bulk RNA sequencing of CFF-16HBEge cells following plasmid lipofection or virus-like particle transduction

city: Cork

first: Lucia

last: Nicosia

state: Co. Cork

address: College Road

country: Ireland

institute: University College Cork

summary: Delivery strategies for gene editing applications can affect editing outcomes by eliciting distinct cellular responses. This work presents bulk RNA sequencing data from human bronchial epithelial CFF-16HBEge cells, following delivery of an adenine base editor and sgRNA as plasmid DNA via lipofection or as ribonucleoprotein complexes via engineered virus-like particles (eVLPs). Differential gene expression and gene ontology analyses revealed condition-specific transcriptional profiles. This dataset provides a resource for investigating cellular responses to gene editing delivery approaches in vitro.

overall_design: RNA-seq profiling of CFF-16HBEge cells 48 hours post transfection with plasmid DNA, transduction with eVLPs or mock-treatment

first: Patrick

middle: T

last: Harrison

first: Martina

middle: F

last: Scallan


title: Expression data from colorectal cancer cells following thymoquinone and 5-Fluorouracil treatment.

city: Sosnowiec

first: Celina

last: Kruszniewska-Rajs

address: Jednosci 8

department: Molecular Biology

institute: Medical University of Silesia

summary:
The aim of this study was to comprehensively evaluate the effects of thymoquinone, alone and in combination with 5-fluorouracil, on global gene expression profiles in colorectal cancer cells following treatment.
Cells treated with thymoquinone, 5-fluorouracil or their combination were subjected to genome-wide gene expression analysis. Transcriptomic profiling was performed using an oligonucleotide microarray platform

overall_design: The human colorectal adenocarcinoma cell line RKO (ATCC® CRL-2577) was cultured in Eagle’s Minimum Essential Medium.Cells were grown in standard tissue culture flasks, and experiments were performed using cultures within six passages to ensure phenotypic stability and reproducibility. Cells were plated in six-well culture plates at a density of 3 × 10⁵ cells per well and incubated for 48 h to allow proper attachment. Following the stabilization period, cells were treated with thymoquinone, 5-fluorouracil, or their combination.

first: Natalia

last: Kurowska

first: Barbara

last: Strzałka-Mrozik


title: NICO Myriad system Improves sample quality for molecular pathology assays

city: Miami

first: Glaucia Maria

middle: de

last: Mendonça Fernandes

state: FL

address: 4060 SW 97th PL

department: HWCOM Cellular and Molecular Medicine

institute: Florida International University

summary: Meningiomas are commonly treated through surgery, radiation, or chemotherapy, based.  These decisions are guided by pathological interpretation which traditionally uses the WHO classification schema. Current diagnostic methods based on FFPE samples often fall short of providing precise treatment, and hence multiple revisions have been generated such as cImpact8. However, emerging molecular techniques, such as circular RNA (circRNA) profiling show potential to enhance diagnostic accuracy but are limited by degradation caused by FFPE process. To overcome this challenge, we tested the extent to which the NICO Myriad system enhances tissue preservation.  The NICO Myriad system extracts fresh tissue in situ using a refrigerated chamber and Ringer’s Lactate fluid. This study aims to compare the efficiency of Traditional and NICO tissue extraction protocols for meningioma resection, focusing on circRNA profiles as clinical biomarkers. We performed circRNA sequencing in 20 patients, collected under identical tumor resection conditions. We performed T-test to compare RNA extraction and sequencing quality, circRNA detection and profile between protocols. DEseq analysis was applied to circRNAs Differential Expression, and Weighted Gene Co-expression Network Analysis (WGCNA) correlated with clinical features followed by GO enrichment. NICO protocol enhances RNA integrity (p=0.0023), yielding a high-quality data (>Q30 median=95%) which reduced variation of circRNA detection. WGCNA identified two modules differentiating the protocols, while two modules were related with WHO Grade 2 associated with cellular metabolism, and epitranscriptomic regulation.  We conclude that the NICO protocol, which offers a homeostatic environment, significantly improves the precision of circRNA detection.

overall_design: This study compared Traditional and NICO Myriad tissue extraction protocols in 20 meningioma patients by performing circRNA sequencing, differential expression (DESeq2), and WGCNA analysis to assess RNA integrity, sequencing quality, and circRNA profile variation, demonstrating that the NICO protocol significantly improves RNA preservation and circRNA detection.

first: Glaucia

last: de Mendonça Fernandes

last: Pevedello

first: Jose

last: Otero


title: TERT drives liver tumorigenesis and immune reprogramming independently of telomere elongation

status: Public on Jun 29 2026

city: Marseille

first: Laura

last: BRAUD

address: 27 boulevard Leï Roure

country: France

institute: Institut Paoli Calmettes (IPC)

summary: We generated two mouse models, p21⁺/Tert and p21⁺/TertCi, that express either telomerase reverse transcriptase (TERT) or its catalytically inactive form under the control of the p21 promoter, establishing a feedback loop that restricts telomerase expression to p21-positive cells. By 18–20 months of age, approximately 15% of mice from both genotypes developed liver tumors with histopathological features resembling human hepatocellular carcinoma (HCC). Whole-exome sequencing revealed activating mutations in Ctnnb1 in p21⁺/Tert tumors, and activating HrasGln61Lys mutations in p21⁺/TertCi tumors, associated with elevated C>A transversions as well as recurrent PP1 subunit mutations in multiple tumors. Despite distinct point mutations, both models exhibited chromosomal alterations recurrent in human HCC. β-catenin–activated tumors displayed gene expression signatures characteristic of human HCC, as well as SLC1A5 overexpression, whereas MAPK-mutated tumors showed transcriptional profiles consistent with MAPK/ERK pathway activation. Both genotypes demonstrated upregulation of glycolytic enzymes and downregulation of gluconeogenic enzymes such as FBP1, but overexpressed distinct NRF2 targets.  Spatial architecture of the tumors using the Hyperion™ Imaging System revealed reduced HNF4A-positive hepatocytes in all tumors, independent of Hnf4a transcriptional changes, and markedly decreased immune cell infiltration in β-catenin–activated tumors. Together, these results uncover unanticipated roles for TERT beyond telomere elongation and identify molecular and metabolic biomarkers predictive of immunotherapy response in HCC.

overall_design: To assess the effects of p21 promoter-driven mTert and mTertCi expression on global transcription, we performed RNA-seq experiments on the liver tumor.

last: Braud

first: Julien

last: Vernerey

first: Arnaud

last: Guille

first: Pierre

last: Cordier

first: Clémence

last: Ginet

first: Tom

last: Egger

first: Manuel

last: Bernabe

first: Dmitri

last: Churikov

first: Quentin

last: Da Costa

first: Aida

last: Meghraoui

first: Chantal

last: Desdouet

first: Li

last: Gu

first: François

last: Bertucci

first: Christophe

last: Lachaud

first: Vincent

last: Geli


title: Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers

status: Public on Jun 27 2026

city: Palo Alto

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Dr

department: Genetics

institute: Stanford University

summary: Enhancers activate promoters to regulate gene expression in the human genome, but the rules by which enhancer and promoter activities combine are debated. Recent studies have developed various reporter assays to test many enhancer and promoter sequences in combination, but arrived at different conclusions and have not yet provided quantitative measurements that predict the effects of enhancers in their endogenous locations in the genome. To resolve this, we systematically compare 6 different reporter assay designs, and identify and resolve critical confounders in measuring enhancer-promoter compatibility. With redesigned reporter assays, we show that enhancers are broadly compatible with promoters, but promoters show large differences in responsiveness to enhancers (e.g. 40-fold versus <2-fold activation by a strong enhancer).

overall_design: For 3 cloned libraries of enhancer-promoter (E x P) combinations (21Ex26P, 203Ex78P, and 21Ex500P), we performed custom plasmid pool amplicon sequencing to build an enhancer-promoter-BC look-up table. We then read out enhancer-promoter pair RNA expression via sequencing of barcodes in separately extracted RNA and DNA. With the 21Ex26P library, we cloned the reporter construct in three different designs (upstream, downstream, and STARR-seq) and delivered the reporter in two different ways (plasmid or integrated into chromatin). For the latter two libraries only the upstream, integrated assay was conducted. For each upstream assay, we also captured full length transcripts and sequenced the 5’-ends to map the TSS of reporter transcripts to filter for those that initiated within the enhancer, confounding the expression readout.

first: Yingxuan

last: Tan

first: Judhajeet

last: Ray

first: Maya

middle: U

last: Sheth

first: Benjamin

last: Doughty

first: William

last: Greenleaf


title: Single-cell RNA sequencing reveals how myeloid cell reprogramming by commensal Prevotella enhances defense against Streptococcus pneumoniae lung infection

status: Public on Jun 26 2026

city: Aurora

first: Sarah

last: Clark

state: CO

address: 12700 E 19th Ave, Mail Stop 8333

institute: University of Colorado School of Medicine

summary: Streptococcus pneumoniae expresses a suite of virulence factors that modulate the innate immune response, delaying effective clearance. However, immune interactions with other bacteria influence this dynamic. Depletion of respiratory tract anaerobes including Prevotella is associated with increased mortality from pneumonia, an effect that can be replicated by pre-exposure to Prevotella melaninogenica in mice. Here, we demonstrate using single-cell RNA sequencing that P. melaninogenica shifts myeloid cell transcriptional profiles during pneumococcal infection from interferon-dominant to pro-phagocytic, correlating with increased S. pneumoniae phagocytosis and clearance from the lung. In neutrophils, improved antibacterial defense was dependent on TNF signaling through TNFR2. Prevotella-enhanced defense also required the recruitment of monocyte-derived macrophages, with selective enrichment of a Cxcl3+ population which differed from the C1qa+ population dominant during S. pneumoniae infection in unprimed mice. This work reveals an optimized innate immune defense program which may contribute to natural infection resistance mediated by respiratory tract commensal-host interactions.

overall_design: Pooled RNA seq of 16 samples; scRNA-seq

first: Sara

last: Stoner

first: Eric

middle: D

last: Larson

first: Sam

last: Fulte

first: Erin

last: Fish

first: Steve

middle: C

last: Shaw

first: Edward

last: Janoff

first: Matthias

last: Mack


title: Collagen-producing eye cell atlas reveals distinct fibroblast fates in early injury versus fibrotic subretinal disease

status: Public on Jun 23 2026

city: Schlieren

first: Said

last: Aktas

state: Zurich

address: Wagistr 10

institute: Roche Innovation Center Zurich

summary: Fibrosis is the end-stage of a maladaptive process that occurs when the body's normal wound-healing strategy becomes dysregulated. Subretinal fibrosis is the end stage of neovascular age-related macular degeneration (nAMD), the most common cause of central vision loss in people over the age of 50. The cellular sources of excess extracellular matrix contributing to subretinal fibrosis are unknown, as is the heterogeneity of cells involved in the fibrotic process. Here we identify cells contributing to subretinal fibrosis by using Col1a1-YFP reporter mice to non-invasively image collagen production in real-time in vivo in two disease models, 1) a resolving retinal injury model and 2) a fibrotic model of subretinal disease. We create a collagen-producing eye cell atlas for subretinal injury and demonstrate subretinal fibroblast heterogeneity in healthy, resolving and fibrotic tissue. We identify distinct molecular characteristics of general repair/resolving fibroblast populations versus pathogenic pro-fibrotic collagen-producing fibroblasts. Integration of this collagen-producing eye cell atlas with a published collagen-producing lung cell atlas shows conserved pro-fibrotic fibroblasts in both organs, yet also uncovers novel tissue-specific fibroblast populations unique to subretinal fibrosis. A Fap+Fgl2+ fibroblast population significantly expands in subretinal fibrosis that expresses the highest levels of collagens and distinctively expresses ECM components periostin, col15a1 and col6a5. Immunolabelling of mouse and human-donor eye tissue support the fibroblastic expression and peri-vascular location of periostin as clearly distinguishing between bona-fide fibrosis and early disease in nAMD. Our collagen-producing eye cell atlas is a valuable resource for studying distinct fibroblast subsets in homeostasis, early injury and fibrosis

overall_design: We sorted YFP+ and YFP- cells from the RPE/choroid tissue of Col1a1-YFP mice in early injury and fibrosis

first: Ema

last: Ozaki

first: Kelly

last: Mulfaul

first: Kiva

last: Brennan

last: Roubeix

last: Palko

first: Katie

last: Robb

first: Tai-Hsien

last: Ou-Yang

first: Marie-Claire

last: Schanne-Klein

first: Anna

last: Toidze

first: Avril

last: Watson

first: Mark

last: Cahill

first: Peter D

last: Westenskow

first: Derrick

last: Feenstra

first: Sarah Louise

last: Doyle


title: Xylosyltransferase-II deficiency rewires innate immune signaling and destabilizes polarization in human macrophages

city: Bad Oeynhausen

first: Isabel

last: Faust-Hinse

state: NRW

address: Georgstraße 11

department: ILTM

institute: HDZ NRW, Institut für Laboratoriums- und Transfusionsmedizin, Universitätsklinik der Ruhr-Universität Bochum

summary: Xylosyltransferase-II (XT-II), encoded by XYLT2, catalyzes the rate-limiting step of proteoglycan biosynthesis, yet its role in macrophage biology and innate immune regulation remains poorly defined. Given the central role of macrophages in inflammatory signaling and tissue homeostasis, we investigated the transcriptional consequences of XYLT2 deficiency in human primary macrophages across distinct polarization states (M0, M1, M2). Bulk mRNA sequencing revealed that XYLT2 deficiency induces a conserved and robust transcriptional reprogramming independent of polarization state. Differential expression analysis identified a shared interferon-associated gene signature, characterized by the upregulation of interferon-stimulated genes, including STAT1, IRF7, and multiple IFIT family members. Pathway enrichment analysis demonstrated significant activation of innate immune sensing pathways, including RIG-I-like, NOD-like, and Toll-like receptor signaling, alongside strong enrichment of JAK–STAT and cytokine signaling pathways. In parallel, pathways such as NF-κB, PI3K–Akt, and MAPK signaling exhibited bidirectional regulation, indicating complex network rewiring rather than uniform activation. Notably, osteoclast differentiation pathways were enriched among upregulated genes, suggesting a shift toward a pro-osteoclastogenic transcriptional state. Collectively, these findings demonstrate that XYLT2 deficiency drives a global, interferon-dominated transcriptional program associated with enhanced innate immune activation and altered macrophage functional identity, providing a mechanistic link between impaired proteoglycan biosynthesis and dysregulated immune signaling.

overall_design:
RNA-seq profiling of human primary monocyte-derived macrophages from four independent donors following siRNA-mediated XYLT2 knockdown (siXYLT2) compared to non-targeting control (siNC), analyzed across three polarization states (M0, M1, M2) after 48 h of polarization in a paired donor design.

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

first: Alina

last: Witt

first: Thanh-Diep

last: Ly

last: Kühle

first: Cornelius

last: Knabbe


title: A Transcriptional and Cellular Exploration of Obesity and Type-II Diabetes in Human Adipose Tissues [scRNA-seq]

first: William

middle: V

last: Trim

address: 25 Shuttack Street

department: Systems Biology

institute: Harvard Medical School

summary: Obesity is tightly linked to metabolic disorders such as type-II diabetes (T2D), though a sub-population of individuals with obesity do not present with such morbidities. The biological factors conferring T2D vulnerability remain incompletely understood. We recruited 58 individuals with obesity with or without a clinical diagnosis of T2D (Ob+T2D and Ob). We profiled paired samples of omental and subcutaneous adipose by scRNA-seq (n=10), flow cytometry under basal and stimulated conditions (n=42), and histology (n=17). Flow cytometry and chemokine quantification were also performed in paired whole blood. We identified depot-specific reprogramming of the omental non-haematopoietic compartment in Ob+T2D, centred on mesothelial, endothelial, innate T cells, and macrophages. Mesothelial and IGFBP2+ cells exhibited a fibrotic, EMT-like phenotype, while omental endothelial cells exhibited a lipid-overload, inflammatory, antigen presentation profile in T2D. Omental and subcutaneous adipose innate T cells exhibited an inflammatory profile akin to that identified in mice to temper macrophage inflammation during obesity. These findings reveal new insights into the pathophysiology of T2D in adipose tissue and identify compensatory networks within the tissues that could be exploited by targeted therapeutics.

overall_design:
scRNA sequencing of four cohorts:
Omental Adipose tissue Stromal Cells - Obese no type-II diabetes
Omental Adipose tissue Stromal Cells - Obese with type-II diabetes
Subcutaneous abdominal adipose stromal cells - Obese on type-II diabetes
Subcutaneous abdominal adipose stromal cells - Obese with type-II diabetes

last: Healy

first: Brenneth

last: Stevens

first: John G

last: Scanlan

first: Heather

last: Faust

first: Sara Svensson

last: Akusjarvi

middle: L

last: O'Brien

first: Donal

last: O'Shea

first: Michael

last: Brenner

first: Helen

last: Heneghan

first: Lydia

last: Lynch

first: Kseniia

last: Petrova


title: CHCHD10 alleviates Alzheimer’s Disease Pathogenesis by Modulating Epigenetic Landscape in Directly Reprogrammed Neurons

city: Cleveland

first: Tian

last: Liu

state: Ohio

address: 2103 Cornell Road

department: Pathology

institute: Case Western Reserve University

type: Methylation profiling by high throughput sequencing

summary: Alzheimer’s disease (AD) is associated with widespread epigenetic alterations, including changes in DNA methylation. CHCHD10, a mitochondrial intermembrane space protein, has been implicated in mitochondrial function and neurodegeneration, but its role in epigenetic regulation remains unclear. In this study, we performed genome-wide DNA methylation profiling in fibroblast-derived induced neurons from cognitively normal controls (NC) and AD patients, with and without CHCHD10 overexpression. We identified disease-associated differentially methylated regions (DMRs) and evaluated the extent to which CHCHD10 restoration modulates these epigenetic signatures. This dataset provides a resource for understanding mitochondrial-epigenetic interactions in AD.

overall_design:
This study investigates the role of CHCHD10 in regulating genome-wide DNA methylation in AD. Fibroblast-derived induced neurons were generated from cognitively NC and AD patients, preserving donor-specific genetic and epigenetic features. In AD neurons, CHCHD10 was ectopically expressed to evaluate its impact on AD-associated epigenetic alterations.      Genome-wide DNA methylation profiling was performed across three experimental groups: NC neurons, AD neurons, and AD neurons with CHCHD10 overexpression (AD+CHCHD10). Differentially methylated regions (DMRs) and CpG-level methylation changes were identified to assess disease-associated alterations and their potential reversal following CHCHD10 restoration.      All samples were processed using a consistent bioinformatic pipeline, including alignment to the same reference genome, methylation calling, and downstream analyses under uniform parameters. Processed data provided in this submission include CpG-level methylation values, DMR annotations, and associated genomic coordinates for all samples. Although raw sequencing data (FASTQ files) are not available, all processed methylation data for these samples are provided to enable reproducibility of the reported analyses.     Primary fibroblast lines used in this study were obtained from the Coriell Institute for Medical Research and are subject to material transfer and redistribution restrictions. These materials cannot be redistributed by the authors but may be obtained directly from Coriell, subject to their access policies.

***************************************************************
raw FASTQ files are unavailable.
***************************************************************

first: Teresa M

last: Thomas

first: Ching-Yao

last: Yang


title: The dual trxG/PcG protein ULTRAPETALA1 modulates H3K27me3 and directly enhances POLYCOMB REPRESSIVE COMPLEX 2 activity for fine-tuned reproductive transitions

status: Public on Jun 25 2026

city: Grenoble

first: Christel

last: Carles

state: Auvergne/Rhone Alpes

address: 17 rue des Martyrs, bât. C2

department: Laboratoire Physiologie Cellulaire Végétale (LPCV)

institute: University Grenoble Alpes

summary: The antagonistic POLYCOMB (PcG) REPRESSIVE COMPLEX 2 (PRC2) and trithorax (trxG) chromatin machineries play a major role in orchestrating gene expression during the development of multicellular eukaryotes. These complexes are well known for depositing and maintaining the repressive H3K27me3 and activating H3K4me3 marks, respectively. However, the mechanisms that govern the switch between these functions remains elusive, especially in plants, whose lifelong, flexible development relies heavily on this process. Here we demonstrate that the plant specific ULTRAPETALA1 (ULT1) protein, previously reported as a trxG factor that antagonizes the PRC2 enzymatic subunit CURLY LEAF (CLF), also exhibits a repressive function, increasing H3K27me3 levels at over a thousand genes. We discovered a physical interaction between ULT1 and PRC2 components, particularly the SWINGER (SWN) enzymatic subunit. We further show that in vitro ULT1 significantly enhances the enzymatic activity of PRC2SWN, and to a lesser extent also that of PRC2CLF, corroborating our epigenomic and developmental genetic data that reveal different ULT1 activity depending on the catalytic subunit of the PRC2 complex. This study provides new insights into the relative activities of CLF and SWN and introduces a novel mechanistic framework for a chromatin switch mediated by a bivalent trxG/PcG factor.

overall_design:
Eight day old seedlings of loss-of-function (ult1-2,ult-3) and gain-of-function (35S:ULT1) plants (Ler background) and loss-of-function mutants of the H3K27me3 demethylase REF6 (ref6-3) (Col-0 background) were used to perform ChIP-seq for profiling of H3K27me3 and H4K4me3 chromatin marks . Additionally, combinations of ult1-3 (Col-0 background) with PRC2 HMTs (clf-28, swn-7) were used for profiling of H3K27me3.
Eight day old seedlings of loss-of-function (ult1-2,ult-3) and gain-of-function (35S:ULT1) plants were used to perform ChIP-seq for profiling of H3K27me3 and H4K4me3 chromatin marks

first: Vangeli

last: Geshkovski

first: Julia

last: Engelhorn

first: Jean-Baptiste

last: Izquierdo

first: Hamida

last: Laroussi

first: Caroline

last: Thouly

first: Laura

last: Turchi

first: Meredith

last: Wouters

first: Marie

last: Le Masson

first: Emmanuel

last: Thévenon

first: Ambre

last: Petitalot

first: Lauriane

last: Simon

first: Manon

last: Verdier

first: Sophie

last: Desset

first: Philipp

last: Michl-Holzinger

first: Astrid

last: Bruckmann

first: Hugues

last: Parrinello

first: Klaus

last: Grasser

first: Aline

last: Probst

first: Raphaël

last: Margueron

first: Gilles

last: Vachon

first: Jan

last: Kadlec

first: Cristel


title: Coordinated RNA- and protein-templated synthesis of double-stranded DNA by a dual reverse transcriptase immune system [Tn-seq]

status: Public on Jun 22 2026

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

summary: Defense-associated reverse transcriptase (DRT) systems mediate antiviral immunity through distinct modes of cDNA synthesis: class 1 DRTs catalyze untemplated synthesis, whereas class 2 DRTs polymerize non-coding RNA-templated products. However, how these distinct modes drive defense remains unclear. Here, we report that DRT3 immunity arises when class 1 and class 2 RT activities cooperate to produce self-complementary double-stranded DNA (dsDNA). DRT3a uses a 5′-ACACAC-3′ RNA template to synthesize poly-(dTdG) repeats, whereas DRT3b synthesizes poly-(dCdA) repeats without any nucleic acid template. Cryo-electron microscopy reveals that DRT3b forms a hexamer and uses active-site-adjacent residues as deoxyadenosine and deoxycytidine gates to enforce alternating nucleotide addition, representing a unique example of amino-acid-templated DNA polymerization. DRT3 is toxic in cells lacking RecBCD, implicating host recombination machinery in limiting dsDNA accumulation, and the phage-encoded RecBCD inhibitor Gam triggers DRT3-mediated abortive infection. These findings reveal how two polymerases with distinct templating strategies generate complementary DNA for antiviral defense.

overall_design: We performed Tn-seq in a library of transposon mutated E. coli cells expressing DRT3 and Gam under and inducible promoter to assess insertion enrichment.

first: Megan

last: Wang

first: Kanta

last: Yoneyama

first: Rimantė

last: Žedaveinytė

first: Junichiro

last: Ishikawa

first: Stephen

last: Tang

first: Hoang

last: Le

first: Tanner

last: Wiegand

first: Josephine

last: Ramirez

first: Naoto

last: Nagahata

first: Yanzhe

last: Ma

first: Dennis

last: Zhang

first: Erick

last: Helmeczi

first: Mirela

last: Berisa

first: Marko

last: Jovanovic

first: Masahiro

last: Hiraizumi

first: Keitaro

last: Yamashita

first: Hiroshi

last: Nishimasu


title: Coordinated RNA- and protein-templated synthesis of double-stranded DNA by a dual reverse transcriptase immune system [miniprep-seq]

first: Samuel

last: Sternberg

overall_design: We performed miniprep-seq on E coli containing DRT3 and it's trigger Gam under an inducible promoter and perfomred a timecourse sequencing experiment to determine poly-(dCdA) and poly-(dTdG) motif change over induction time.

first: Megan

last: Wang


title: Coordinated RNA- and protein-templated synthesis of double-stranded DNA by a dual reverse transcriptase immune system [RIP-seq]

overall_design: We performed total RNA-seq in WT or ∆greA E. coli cells expressing DRT3 to assess transcript levels.

first: Kanta

last: Yoneyama

first: Rimantė

last: Žedaveinytė


title: Argonaute proteins orchestrate Meiotic Sex Chromosome Inactivation and timing of the spermatogenic transcriptional program [Multiome]

city: Ithaca

first: Andrew

last: Grimson

address: 526 Campus Rd

department: Molecular and Cell Biology

institute: Cornell University

summary: Argonaute proteins (AGO) are best known for their role in microRNA-mediated post-transcriptional gene silencing. Here, we demonstrate that AGO3 and AGO4, but not AGO2, localize to the sex chromatin of pachytene spermatocytes, where they are required for the transcriptional silencing of XY-linked genes that characterizes Meiotic Sex Chromosome Inactivation (MSCI). Previous findings showed that deletion of Ago4 (Ago4-/-) mildly impairs MSCI and normal spermatozoa production. By contrast, loss of Ago3 (Ago3-/-) does not produce these defects, while combined deletion of Ago1, Ago3, and Ago4 (Ago413-/-) leads to severely reduced fertility, accompanied by disrupted autosomal and sex chromosome gene regulation and altered chromatin accessibility in spermatocytes. In Ago413-/- mice, premature overexpression of spermiogenesis genes during prophase I results in reduced sperm production, abnormal sperm morphology, and impaired fertilization capacity. Together, AGO3 and AGO4 act during prophase I to ensure the timely expression of meiosis-related genes during prophase I while maintaining repression of spermiogenesis-associated genes. These results indicate that AGO3 and AGO4 act in a coordinated fashion in the male germline to orchestrate cell progression in spermatogenesis through temporal regulation of autosomal and sex chromosome genes.

overall_design: Germ cell suspensions were obtained from Ago413-/- and Ago413+/+ mouse testis and enriched using MACS. Single nuclei were extracted from cells and joint snRNA and snATAC libraries were prepared using the 10x Genomics platform.

first: Alexis

last: Dziubek

first: Maria de las Mercedes

last: Carro

first: Paula

last: Cohen


title: Coordinated RNA- and protein-templated synthesis of double-stranded DNA by a dual reverse transcriptase immune system [cDIP-seq]

overall_design: We performed cDIP-seq in E. coli cells expressing DRT3 and its various mutations either with or without T5 or Lambda phage infection to assess cDNA production levels.

first: Junichiro

last: Ishikawa

first: Stephen

last: Tang

first: Hoang

last: Le

first: Tanner

last: Wiegand

first: Josephine

last: Ramirez

first: Naoto

last: Nagahata


title: Clostridioides difficile stimulates CCL20 expression in human colonoid monolayers in a transwell-based co-culture system that supports its anaerobic growth

city: Boston

first: Carol

middle: A

last: Kumamoto

address: 150 Harrison Ave.

department: Department of Molecular Biology and Microbiology

institute: Tufts University

summary: The pathogenic bacterium Clostridioides difficile is a major cause of antibi-otic-associated diarrheal disease. Treatment of the disease is challenging because anti-biotics used for treatment may also perpetuate the conditions that contributed to initial susceptibility. Elucidating the mechanisms of C. difficile/intestinal epithelium interaction is needed to facilitate the development of new therapeutic options. The studies described in this communication demonstrate the development of a tissue culture system that supported the growth of C. difficile in co-culture with a model of the human intestinal epithelium produced from colonoids, organoids derived from human colonic biopsies. Epithelial cell responses to C. difficile included upregulation of CCL20, encoding a chemokine. Glucosylating toxin production by the bacteria was required for upregulation of CCL20. Additionally, bacteria associated with the monolayer in a non-toxin dependent manner. This system will support future investigation of epithelium/C. difficile interac-tions during CDI and identification of mechanisms that drive pathogenesis by C. difficile in the human intestine.

sample_organism:
Clostridioides difficile
Homo sapiens

platform_organism:
Clostridioides difficile
Homo sapiens

overall_design: We conducted a single cell RNASeq (scRNASeq) study of colonoids in co-culture with C. difficile or with buffer only (referred to as Mock). A more detailed analysis of the re-sponses of colonoids to C. difficile challenge over a time course will be presented else-where. Our analysis here focused on identifying gene markers that could be used to monitor the response of colonoids to C. difficile in co-culture. Differentiated colonoid monolayers were produced as described for Fig. 1 and in-oculated with pre-germinated spores of strain UK1 (or buffer). Two replicates of the ex-periment comparing a Cd co-culture with a mock culture after 15 hrs of incubation were performed, yielding 4 samples: Mock replicate a (Ma), Mock replicate b (Mb) C. difficile co-culture replicate a (CDa) and C. difficile co-culture replicate b (CDb). As described in Materials and Methods, single cell suspensions were produced and processed for scRNASeq using the 10x platform.

first: Paola

last: Zucchi

first: Adrianne

last: Gladden

middle: W

last: Day

first: Jules

last: Dressler

first: Revathi

last: Govind

first: Mohammad

last: Almeqdadi

first: Albert

last: Tai

first: Rebecca

last: Batorsky


title: A role for nucleosome remodellers during resection of deprotected telomeres in yeast [ChIP-seq]

city: Dortmund

first: Anja

last: Deiser

address: Otto-Hahn-Str. 6

department: DOLCE

institute: TU-Dortmund

summary: The choice between distinct DNA double-strand break (DSB) repair pathways is a central determinant of genome stability. This decision critically depends on DNA end resection, the nucleolytic processing of DSB ends that generates 3′ single-stranded DNA required for homologous recombination while simultaneously suppressing non-homologous end joining. Although the enzymatic mechanisms of resection have been well defined, its regulation by the dynamic, DSB-surrounding chromatin remains poorly understood. Here, we used the budding yeast cdc13-1 system to investigate how chromatin influences resection after telomere deprotection. Analysis of long-range resection nucleases revealed that Dna2 contributes to telomeric processing, particularly in the absence of Exo1, and acts in conjunction with the STR complex (Sgs1–Top3–Rmi1). Genetic removal of chromatin regulatory factors showed that H2A.Z incorporation did not significantly affect resection, whereas depletion of major nucleosome evictors RSC and SWI/SNF impaired telomere resection. These findings indicate that chromatin remodelling by RSC and SWI/SNF are involved in single-strand DNA formation after telomere deprotection and highlights utilisation of the cdc13-1 system to investigate chromatin regulators and their role in DSB repair pathway choice.

overall_design: Illumina-Seq of S.cerevisiae after AsiSI induced DSB induction.

first: Kim

last: Rinho

first: Caitlyn

last: Agar

first: Juan de Dios

last: Barba Tena

first: Boris

last: Pfander


title: Argonaute proteins regulate the timing of the spermatogenic transcriptional program [miRNA-seq]

first: Andrew

last: Grimson

type: Non-coding RNA profiling by high throughput sequencing

summary: Argonaute proteins are known for their role in microRNA-mediated post-transcriptional gene silencing. Using a triple Ago413-/- mouse model, we show that AGO3 and AGO4 are key regulators of spermatogenesis, orchestrating expression of meiosis-related genes during prophase I, while maintaining silencing of spermiogenesis genes. Overexpression of spermiogenesis genes during prophase I in Ago413-/- mice results in subfertility. Here, we show that AGO3, but not AGO2, localizes to the sex chromatin of pachytene spermatocytes, where together with AGO4, it is required for transcriptional silencing of XY-linked genes. We also identify BRG1, a BAF complex subunit as an AGO3 interactor, and observe that loss of AGO3 and AGO4 leads to increased BRG1 in spermatocytes, evidencing a role for AGO3 in transcriptional control during meiosis. Notably, we reveal that altered gene regulation during prophase I given by loss of AGO3 and AGO4 transcends the meiotic phase of spermatogenesis, leading to poor quality germ cells.

overall_design: smallRNA-seq of purified pachytene/diplotene spermatocytes and round spermatids from testis of Ago+/+, Ago+/-, and AGO-/- male mice, with samples paired to RNA-seq

first: Alexis

last: Dziubek

first: Maria de las Mercedes

last: Carro

first: Paula

last: Cohen

first: Jen

middle: K

last: Grenier


title: Argonaute proteins regulate the timing of the spermatogenic transcriptional program [scRNA-seq]

overall_design: Germ cell suspensions were obtained from Ago413-/- and Ago413+/+ mouse testis, flow sorted to remove sperm, and alanlyzed with scRNA-seq

middle: E


title: Phosphatase-independent suppression of mucosal inflammation and disease progression by Salmonella SopB

status: Public on Jun 21 2026

city: Aachen

first: Matthias

last: Hornef

address: Pauwellstr 30

department: Medical Microbiology

institute: Uniklinik Aachen

summary: The results of our current study show that  Salmonella oter protein (SopB)  suppresses early epithelial chemokine expression, delays mucosal immune cell recruitment, reduces barrier impairment by enterocyte necroptosis, and prevents disease progression and premature death in our neonatal S. Typhimurium infection model. To elucidate the underlying mechanism, we have conducted bulk RNA sequencing to identify alterations in gene expression.

overall_design: C57BL/6 mice are infected on day 1 after birth with 100 CFU wild-type or SopB-deficient S. Tm. (both strains are provided by Prof. Michael Hensel at Osnabrück Univerisity, Germany). Enterocytes (IECs) were isolated from total small intestinal tissues using a previously established EDTA-based protocol at d1p.i. (Lotz et al., 2006). RNA was isolated from the epithelial cell pellet or homogenized intestinal tissue using TRIzol® according to manufacturer’s recommendations. The RNA samples were handed in to Genomics Core Facility at UKA.

first: Nour

last: Diab

last: Schmitz

first: Narasimha Murthy Keshava Prasad

last: Gubbi

first: Geonomics Core Facility University Hospital RWTH

last: Aachen

first: Kaiyi

last: Zhang

first: Mathias W.


title: Activation of tumor-specific CD8+ T cells prior to radiopharmaceutical therapy improves anti-tumor response

status: Public on Jun 19 2026

city: Madison

first: Daeun

last: Shim

state: Wisconsin

address: 1111 Highland Ave

institute: Daeun Shim

summary: Previously, we found that the presence and activation of tumor-specific CD8+ T cells prior to radiopharmaceutical therapy (RPT), 90Y-NM600, enhanced anti-tumor responses. Here, we aimed to evaluate changes in the tumor immune microenvironment after E.G7-OVA tumor-bearing mice received adoptive transfer of naïve OT-I CD8+ T cells, followed by a DNA vaccine, and 90Y-NM600. Tumors were collected 7 and 14 days following 90Y-NM600, isolated total RNA, and performed gene expression analysis using the nCounter Mouse Immune Exhaustion Panel on the nCounter MAX system.

overall_design: E.G7-OVA tumor-bearing mice received naïve OT-I CD8+ T cells (day -3), followed a DNA vaccine (empty vector pTVG4 or OVA-encoding pTVG-sOVA; day -2), and 1.85MBq 90Y-NM600 (delivering 5Gy to the tumor; day 0). Tumors were collected 7 and 14 days post-90Y-NM600

first: Douglas

middle: G

last: McNeel


title: Soluble CD137 produced by Foxp3+ regulatory CD4 T cells is immunosuppressive and restrains ongoing autoimmune diabetes

city: Milwaukee

first: Yi-Guang

last: Chen

state: WI

address: 8701 Watertown Plank Rd.

institute: Medical College of Wisconsin

summary: CD137 (4-1BB) is expressed in a subset of Foxp3+ regulatory CD4 T cells (Tregs) but its role in Treg function is not completely clear. Due to alternative splicing that excises the transmembrane domain coding exon, CD137 is expressed as cell surface and soluble forms. We studied the function of CD137 in Tregs using the NOD mouse model of autoimmune type 1 diabetes (T1D). Treg-specific deletion of CD137 resulted in significant reduction of circulating soluble CD137 and considerably accelerated T1D development because of heightened clonal expansion and differentiation of effector T cells in pancreatic islets. CD137 deficiency in Tregs reduced their accumulation in islets and negatively impacted their differentiation trajectory toward a highly suppressive phenotype. Restoring Treg-derived soluble CD137 reduced islet T cell activation and delayed T1D onset without affecting the accumulation of phenotypically suppressive Tregs. Thus, as a major in vivo source, Treg-derived soluble CD137 participates in autoimmune control.

overall_design: Islet-infiltrating cells were sorted into CD4 T cells and non-CD4 T cells and analyzed by paired scRNA-seq and scTCR-seq

first: Rabia

last: Nabi

first: Chien-Wei

last: Lin

first: Yu

last: Wang

first: Ashley

last: Ciecko

first: Bardees

last: Foda

first: Amber

last: Drewek

first: Scott

last: Lieberman

first: William

last: Ridgway


title: Argonaute proteins regulate the timing of the spermatogenic transcriptional program

first: Andrew

last: Grimson

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

overall_design: Refer to individual Series


title: Argonaute proteins regulate the timing of the spermatogenic transcriptional program [RNA-seq]

overall_design: RNA-seq of purified pachytene/diplotene spermatocytes and round spermatids from testis of Ago+/+, Ago+/-, and AGO-/- male mice, with samples paired to smallRNA-seq.

first: Alexis

last: Dziubek

first: Maria de las Mercedes

last: Carro

first: Paula

last: Cohen

first: Jen

last: Grenier


title: Multimerization of ELAV is essential for directing neuronal alternative splicing and polyadenylation programs

status: Public on Jun 18 2026

first: David

middle: W. J.

last: McQuarrie

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medicine, Cornell University

summary: ELAV/Hu RNA-binding proteins (RBPs) are key regulators of neuronal alternative splicing and polyadenylation programs across animals. How ELAV/Hu RBPs achieve gene-specific regulation by recognizing spaced U-rich motifs through multimerization, remains uncertain. We determined X-ray crystal structures of ELAV RNA recognition motif 3 (RRM3) to reveal that multimerization is mediated by two evolutionary-conserved interfaces in non-RNA binding parts of the RRM to form a tetramer. Mutational probing of these two interfaces in photoreceptor neurons shows that both contribute to ELAV function in development. Although RRM3 binds RNA, this feature is not required for neuronal alternative splicing in this assay in contrast to multimerization. Notably, multimerization defective elav mutants are embryonic lethal. Genomic profiling demonstrates a requirement for multimerization to direct neuronal alternative splicing and polyadenylation programs. Our study provides molecular insights into a molecular protein-framework of ELAV/Hu proteins essential to extract gene-specific regulation from a landscape of redundant sequence motifs.

overall_design: Total RNA was isolated from 20-24 h Drosophila melanogaster embryos of wild-type, elav[null], elav[null] fne[null], and elav[WDd] mutant genotypes. Homozygous elav mutant embryos were identified by absence of GFP using the FM7 KrGFP balancer, which lacks maternal GFP contribution, combined with embryonic autofluorescence morphology. Total RNA extraction was performed using Tri-reagent from SIGMA following the manufacturer's instructions. Poly(A)-selected RNA-seq libraries were prepared from total RNA and sequenced as paired-end 150 bp reads on an Illumina NovaSeq X Plus platform.

first: Matthias

last: Soller


title: Longitudinal single-cell transcriptomic profiling of human breast milk and paired peripheral blood mononuclear cells across lactation

status: Public on Jun 17 2026

city: Singapore

first: Jia Ming

last: Low

address: NUHS Tower Block, 1E Kent Ridge Road, Singapore 119228

country: Singapore

institute: National University Hospital

summary: We performed single-cell RNA sequencing of human breast milk and paired peripheral blood mononuclear cells collected longitudinally across lactation. The study characterizes dynamic changes in epithelial and immune cell populations during the transition from colostrum to mature milk and compares breast milk immune cells with paired maternal peripheral blood immune cells.

overall_design: Human breast milk samples were collected longitudinally during colostrum, transitional, and mature lactation stages. Paired maternal peripheral blood mononuclear cells were collected from a subset of participants. Single-cell RNA sequencing was performed using the 10x Genomics platform. Cell populations were identified and annotated using standard bioinformatics workflows.

first: Shi

first: Sheau Yng

last: Lim

first: Zhou

last: Jian

first: Shu Feng Melisa

last: Ng


title: Quantitative profiling of SMG6 cleavage sites in HEK293 cells

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

summary: The nonsense-mediated mRNA decay pathway targets specific mRNAs for degradation in a translation-dependent manner. NMD can induce RNA turnover via either the bulk mRNA deadenylation and decapping machinery or via the specialized SMG6 endonuclease. SMG6 is a magnesium-dependent nuclease, leading to the presence of 5' phosphates on cleavage intermediates. These 5' phosphates can be captured by adapter ligation for identification by high-throughput sequencing. Here we adapt Akron5-seq for quantitative identification of SMG6 cleavage sites in HEK293 cells. This approach improves upon previous methods for SMG6 cleavage site mapping by using 1) RNA fragmentation and 3' adapter ligation to avoid length biases caused by low reverse transcriptase processivity, 2) unique molecular identifiers to remove PCR duplicates, and 3) triplicate measurements to enable robust statistical analyses.

overall_design: HEK-293 cells were transfected with non-targeting (siNT), SMG6, XRN1, or XRN1+SMG6 siRNAs for 72 hours.

first: Poonam

last: Thakran

first: Robert


title: Chromatin does not fully acquire the properties of post-mortem neurons during iPSCs-to-neurons differentiation.

city: Moscow

first: Anna

last: Kononkova

address: Nobel st., Building 1

department: Skoltech Center of Life Sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

summary: Induced pluripotent stem cells (iPSCs) have fundamentally advanced the field of neuroscience, offering a highly adaptable methodology for generating patient-specific neurons and modeling neurological diseases.  However, a critical question remains: how accurately do iPSC-derived neurons mimic the molecular and structural intricacies of post-mortem neurons? In this study, we embark on a comprehensive investigation of chromatin architecture in both iPSC-derived and post-mortem neurons. We collected and uniformly processed the largest collection of publicly available Hi-C datasets  for human and mouse neurons, along with our newly generated maps. The thorough analysis on the resulting data reveals that iPSC-derived neurons retain properties of non-differentiated cells and resemble developing stages of neurons rather than fully mature neurons. Our study not only provides a detailed comparison of chromatin architecture between iPSC-derived and post-mortem neurons but also offers the largest dataset of uniformly processed Hi-C data for human and mouse neurons.

overall_design:
Comparative Hi-C analysis of chromatin spatial structure in iPSC-derived neuronal cells and  NeuN+ cells isolated from human post-mortem brain samples.

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


title: Recovery of proofreading-impaired SARS-CoV-2 reveals a mutator phenotype and an ExoN activity threshold for viability

status: Public on Jun 16 2026

city: San Antonio

first: Yan

last: Xiang

state: TX

address: 7703 FLOYD CURL DR

department: Microbiology, Immunology and Molecular Genetics

institute: UT Health San Antonio

summary: Coronaviruses (CoVs) replicate unusually large RNA genomes that necessitate proofreading by the 3′-to-5′ exoribonuclease (ExoN) formed by nonstructural proteins 14 (nsp14) and 10 (nsp10). Previous studies suggested that inactivation of the ExoN catalytic site in severe acute respiratory syndrome CoV 2 (SARS-CoV-2) is lethal, leaving unresolved whether the virus can tolerate impaired proofreading activity. Here, we investigated the functional requirement for ExoN in SARS-CoV-2 replication by combining a continuous fluorescence-based biochemical assay with an optimized single-bacmid reverse genetics system. Mutational analysis of residues involved in RNA binding or catalysis revealed graded effects on ExoN activity in vitro. Alanine substitution of Lys9, a residue positioned near the RNA-binding interface, did not reduce ExoN activity, whereas charge reversal at this position (K9E) impaired activity more strongly than alanine substitutions of the catalytic motif I residues D90 and E92 (D90A/E92A). Correspondingly, recombinant SARS-CoV-2 carrying K9A was readily recovered, whereas the D90A/E92A mutant was recovered only after an extended delay and K9E could not be rescued despite repeated attempts. The D90A/E92A mutant exhibited reduced replication while maintaining the engineered ExoN substitutions during serial passage. Deep sequencing of viral populations revealed a marked increase in genome-wide sequence variation in the D90A/E92A mutant, demonstrating a stable mutator phenotype. Together, these findings indicate that SARS-CoV-2 can tolerate substantial impairment of ExoN activity but depends on a minimal activity threshold for viability. This system provides a platform for defining how SARS-CoV-2 proofreading controls genome stability, viral fitness, and sensitivity to antiviral strategies that exploit reduced replication fidelity.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design:
RNA-seq of serially passaged SARS-CoV-2 with or without NSP14 mutation in Vero cells
sequencing of two different recombinant SARS-CoV-2 viruses (WT vs nsp14 mutant)  over different passages. The processed data compare these two different recombinant SARS-CoV-2 viruses (WT vs nsp14 mutant)  in terms of loss of genomic fragments (reflected by read-depth difference)  and accumulation of viral mutations (reflected by SNPs and error rates) over passage.

first: He

last: Li

first: Xiang

last: Yan


title: Coordinated RNA- and protein-templated synthesis of double-stranded DNA by a dual reverse transcriptase immune system [RNA-seq]

first: Samuel

last: Sternberg

overall_design: We performed total RNA-seq in WT or ∆greA E. coli cells expressing DRT3 to assess transcript levels.

first: Megan

last: Wang

first: Kanta

last: Yoneyama

first: Rimantė

last: Žedaveinytė

first: Junichiro

last: Ishikawa

first: Stephen

last: Tang

first: Hoang

last: Le

first: Tanner

last: Wiegand

first: Josephine

last: Ramirez

first: Naoto

last: Nagahata

first: Yanzhe

last: Ma

first: Dennis

middle: J

last: Zhang

first: Erick

last: Helmeczi

first: Mirela

last: Berisa

first: Marko

last: Jovanovic

first: Masahiro

last: Hiraizumi

first: Keitaro

last: Yamashita

first: Hiroshi

last: Nishimasu


title: riboseq_Acute Glucose Stimulation Drives Coordinated Translational Reprogramming in Primary Pancreatic Islets: From Global Remodeling to Fine-tuned Insulin Synthesis

status: Public on Jun 15 2026

city: Tianjin

first: Xiaoxi

last: Xu

address: No. 154, Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

summary: Pancreatic β cells rapidly increase protein synthesis to maintain glucose homeostasis, but the immediate translational dynamics underlying this adaptive response remain poorly defined. In this study, high-resolution ribosome profiling (Ribo-seq) was performed on primary mouse pancreatic islets under acute low-glucose (2.5 mM) and high-glucose (25 mM) conditions. High glucose induced extensive translational reprogramming, including induction of immediate-early genes, suppression of stress-related genes, expansion of the cytosolic translation machinery, coordinated upregulation of secretory pathway components, and metabolic remodeling. Bulk RNA-seq was performed to support translation efficiency analysis. These data define glucose-responsive translational programs in primary islets and provide a resource for understanding β-cell function and insulin synthetic capacity.

overall_design: Primary pancreatic islets from 6-8-week-old male C57BL/6J mice were incubated in low glucose (2.5 mM) or high glucose (25 mM) for 2 h. Cycloheximide (100 μg/mL) was added during the last 15 minutes to fix ribosomes. Ribo-seq libraries were generated using ~500-600 islets per replicate to assess glucose-regulated translation, and RNA-seq was performed for translation efficiency analysis.

first: Yiqing

last: Wang

first: Chunyang

last: Shi

first: Yao

last: Liu

first: Wenli

last: Feng

first: Ming


title: RNAseq_Acute Glucose Stimulation Drives Coordinated Translational Reprogramming in Primary Pancreatic Islets: From Global Remodeling to Fine-tuned Insulin Synthesis


title: Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer

city: Los Angeles

first: Suhn

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Cancer Biology

institute: University of Southern California

summary:
Background: The transcription process is controlled by non-coding regulatory elements, more than 70% of which are putative enhancers. These enhancers comprise over 600,000 regions and are marked by histone modifications. However, the mechanisms by which altered enhancers in cancer cooperate within the three-dimensional chromatin architecture to drive oncogenic programs remain poorly understood.
Results: By integrating 201 H3K27ac ChIP seq datasets from prostate, we identify 3,216 high confidence prostate cancer-specific putative enhancers. Ultra high resolution chromatin interaction profiling by Region Capture Micro-C at a representative chr6q24.1 locus reveals that these enhancers form cancer specific, highly nested interactions with promoters that coalesce into a multi connected hub absent in normal prostate cells. CRISPR/Cas9 perturbations of these enhancers, examined one by one, distinguish enhancer classes within the hub. Deletion of a central enhancer collapses hub-wide enhancer activities and architecture, leading to the downregulation of target genes, impaired proliferation, and reduced clonogenic growth. In contrast, deletion of a redundant enhancer results in minimal transcriptional changes, as neighboring enhancers rescue cancer signaling through compensatory architectural rewiring that strengthens alternative enhancer-promoter interactions. We also observe that FOXA1, a pioneer transcription factor activated in prostate cancer, directly binds to these enhancers and regulates distinct enhancer classes, leading to varying degrees of chromatin accessibility and gene expression changes.
Conclusions: These findings suggest that enhancers function in a coordinated manner, forming multi-connected cancer-specific chromatin interaction hubs, with distinct enhancer classes contributing differently to gene regulation. This study advances our ability to modulate gene expression in a cell type-specific manner, opening new avenues for precision therapies.

overall_design: We performed ChIP-seq, ATAC-seq, RNA-seq, and Region Capture Micro-C in prostate cells.

first: Huan

last: Cao

first: Zexun

last: Wu

first: Baixi

last: Ji

first: Seolyn

last: Yang

first: Leonardo

last: Gonzalez-Smith


title: Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer [ChIP-Seq]


title: Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer [RNA-Seq]


title: Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer [ATAC-Seq]


title: Quantification of interaction strength between a synthetic enhancer-promoter pair with Region Capture Micro-C

city: Cambridge

first: Anders

last: Hansen

address: 32 Vassar St, Building 56-722

institute: Massachusetts Institute of Technolo

summary: To quantify the interaction strength between a synthetic enhancer-promoter (E-P) pair investigated in this study, we applied Region Capture Micro-C (RCMC) to a ~1.9 Mb region containing the engineered E-P pair. We mapped the 3D genomic structure of these loci across multiple clonal mouse embryonic stem cell (mESC) lines featuring varying E-P genomic distances and CTCF binding site configurations, along with control lines with either the enhancer or the entire E-P pair deleted. Furthermore, we profiled E-P interactions under acute depletion of CTCF and/or cohesin subunit RAD21. For the 339 kb E-P pair flanked by convergent CTCF binding sites, we assessed three perturbations: CTCF depletion (via dTAG-13), RAD21 depletion (via 5-ph-IAA), and simultaneous CTCF and RAD21 co-depletion. RAD21 depletion was also performed on the 339 kb E-P pair lacking CTCF binding sites.

overall_design: Region Capture Micro-C to quantify E-P interaction strength across different mouse embryonic stem cell (mESC) lines, including depletion of CTCF and cohesin subunit RAD21 using dTAG and AID2 systems respectively.

first: Jin

middle: H

first: Henrik

last: Pinholt

first: Jack

last: Toppen

first: Miles

last: Huseyin

first: James

middle: M

last: Jusuf

first: Christos

last: Katsifis

first: Leonid

last: Mirny

first: Christoph

last: Zechner

middle: S


title: The RNA Binding Protein ZFP36L2 Displays Tissue-Selective mRNA Targeting in Mice [RNA-seq]

city: Chapel Hill

first: Silvia

middle: B

last: Ramos

state: NC

address: 133 Medical Drive

department: Biochemistry and Biophysics

institute: UNC-Chapel Hill

summary: ZFP36L2 (zinc finger protein 36 like 2, C3H type-ZFP) is an RNA-binding protein targeting transcripts rich in adenine-uridine elements (AREs). Previous transcriptomic analysis suggested that ZFP36L2 displays a distinct transcript preference, depending on the tissue of expression. However, this analysis was restricted to a few tissues. Here, we collected RNA-seq data in six tissues and detected a remarkable transcript selectivity.  Given that ZFP36L2 accelerates the degradation of specific ARE-transcripts upon binding, we obtained differential expression transcriptomic data on a Zfp36l2 knock-out mouse model to delve into the mechanisms governing this tissue-specific targeting. Transcriptomic analyzes of up regulated ARE-transcripts in lung, liver, bone marrow, spleen, kidney, and ovary of the Zfp36l2-deficient mouse confirmed that there is high tissue preference in ZFP36L2 targets. We observed only one common up regulated gene, Apol11b, among these six different tissues. However, we do observe common trends, specifically an enrichment in protein coding genes in the up regulated genes, consistent with these RBP primarily targeting genes on their 3’ UTRs. Interestingly, we observed a significant increase in the proportion of IG (immunoglobulin) genes being up regulated. We further performed eCLIP (Enhanced Cross-Linking&ImmunoPreciptation) on a mouse cell line, MLTC-1 cells, to identify direct binding sites of ZFP36L2. AU-Rich Element score (AREscore) analysis revealed enrichment in both up regulated genes and eCLIP peaks, although some differences were observed in flanking residue composition. Our findings provide new insights into the intricate regulatory network orchestrated by ZFP36L2, opening avenues for exploring its potential roles in different tissues.

overall_design: Animals carrying both wild-type copies of Zfp36l2 (WT) were used as controls. In both groups, WT and KO, the collected tissues were derived from age-matched animals from both sexes; and in most collections, the WT and KO animal pairs were derived from the same litter. The tissues were collected from animals Day 6 to 9, thus at a short window post birth, reflecting a similar developmental stage; except for one ovarian sample collected at D13.

first: George

last: Stephenson

first: Alain

last: Laederach


title: Identification of tumor-derived T cell antigen

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: To identify Tumor-derived T cell ligands, MR1-overexpressing colon cancer cell line CT26_cl9 and its mutant CT26_cl9_M8 were compared.

overall_design: Three RNA samples prepared from each cell line were applied for comparative analysis.

first: Kensuke

last: Shibata

first: Yuka

last: Yamada


title: Single cell analysis of human peripheral blood cells

summary: In this study, we aimed to identify human T cell clonotypes ractive to tumor-associated metabolites. For this purpose, we generated tumors that lack a particular metabolite. After the tumor was cocultured with human peripheral blood mononuclear cells, proliferated cells were sorted and applied for single cell analysis. We identified 17 T cell clonotypes that underwent clonal expansion.

overall_design: Sorted human peripheral blood mononuclear cells were applied for single cell analysis. There are two samples; one cocultured with a tumor lacking a particular metabolite(KO tumor), one cocultured with the parental tumor (WT tumor). By comparing two data sets derived from two samples, we identified T cell clonotypes that underwent clonal expansion upon stimulation with a particular metabolite.


title: Effect of WDR34 and WDR60 loss of function on the transcriptome in IMCD3 cells

city: Freiburg im Breisgau

first: Sebastian

last: Arnold

address: Albertstraße 25

department: Institute of Experimental and Clinical Pharmacology and Toxicology

institute: University Freiburg

summary: Wdr34 and Wdr60 human disease causing missense alleles are responsible for ciliary chondrodysplasias including Jeune Syndrome. Resulting donwstream cell signallling effects and effect on gene expression are unknown.

overall_design: Wdr34 and Wdr60 human disease causing missense alleles were generated in IMCD3 cells using CRISPR base editing. Mutant clones were compared to controls by transcriptomics analysis

first: Miriam

last: Schmidts

first: Dinu

last: Antony

first: Gwang-Jin

last: Kim