title: Single-cell map of the healthy human immune system across the lifespan reveals unique infant immune signatures

status: Public on May 07 2026

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

summary: The human immune system undergoes dynamic remodeling from infancy through old age. We profiled PBMCs from 167 healthy individuals (ages 2 months to 105 years): infants (n=36), children (n=26), adolescents (n=20), young adults (n=24), middle‑aged (n=16), older adults (n=33) and oldest old (n=12) using scRNA‑seq and snATAC‑seq (n=23). MAIT and γδ T cells showed a “rise and fall” pattern, rising in childhood, peaking in young adulthood, and declining with age. Conventional CD8⁺ T cells were most profoundly altered with age, with decreasing naïve and increasing GZMK⁺ and TEMRA cells. The oldest old had increased TEMRA, adaptive NK, and KLRF1⁺ γδ T cells. Infants showed increased CD16⁺ monocytes and pDCs, constitutive interferon‑stimulated gene expression, and expanded SOX4⁺ naïve T cells. Inflammatory and stress‑response pathways increased with age, while interferon pathways declined. This map provides insights into human immune system dynamics across the lifespan, emphasizing unique features of the infant immune system.

overall_design:
This study includes 95 samples generated in-house (this submission) and 72 samples obtained from four publicly available datasets, for a total of 167 samples.
Participants were grouped into seven age categories:
• Infants (2 months–2 years): n = 36
• Children (2–12 years): n = 26
• Adolescents (12–18 years): n = 20
• Young adults (18–40 years): n = 24
• Middle-aged adults (45–65 years): n = 16
• Older adults (65–85 years): n = 33
• Oldest old (85–105 years): n = 12

The public datasets are described below:
• Deng et al. (GSE231906): n = 21
• Wang et al. (syn61609846): n = 45
• Wang et al. (GSE168732): n = 3
• Zhong et al. (GSE206295): n = 3

For epigenetic analyses, single‑nucleus ATAC‑sequencing (snATAC‑seq) data from 23 healthy PBMC donors were utilized, distributed across age groups as follows:
• Infants and children: n = 9
• Adolescents: n = 3
• Young and middle‑aged adults: n = 6
• Older adults: n = 5

Supplementary files include AnnData objects (.h5ad) derived from:
• scRNA-seq: multiple immune cell subsets from 167 donors
• snATAC-seq: multiple immune cell subsets from 23 donors

Submitter declares that the raw data will be available through dbGaP (phs003259.v1 ) due to patient privacy concerns.

first: Asa

last: Thibodeau

first: George

last: Kuchel

first: Octavio

last: Ramilo

first: Jacques

last: Banchereau

first: Duygu

last: Ucar


title: CSF-1R inhibition and lenalidomide synergize to promote myeloma control after autologous stem cell transplantation

status: Public on May 01 2026

city: Seattle

first: Julie

last: Boiko

state: Washington

address: 1101 Fairview Ave N

country: USA

institute: Fred Hutchinson Cancer Center

type: Expression profiling by high throughput sequencing

summary: Autologous stem cell transplantation (ASCT) with maintenance lenalidomide remains the mainstay of consolidation therapy for eligible multiple myeloma (MM) patients but preventing disease relapse remains a critical unmet need. Here we investigated whether immunosuppressive myeloid populations in bone marrow (BM) correlated with ASCT outcomes. Using a preclinical ASCT model with suboptimal endogenous anti-myeloma activity, we demonstrated that while neither CSF-1R inhibition nor lenalidomide monotherapy significantly improved outcomes, their combination synergistically attenuated disease progression and prolonged survival. Single-cell RNA sequencing revealed that lenalidomide expanded NK-like CD8+ T-cells but paradoxically also increased the frequency of Csf1r+ macrophages. Cell-cell communication analyses identified Csf1r+ macrophages as suppressors of these NK-like and effector-like exhausted (Tphex) CD8 T-cell populations through CD94/NKG2A and PD-L1/PD-1, respectively. CSF-1R blockade depleted these immunosuppressive macrophages, which correlated with decreased expression of inhibitory receptors and enhanced expression of activation markers in Tphex.

overall_design: Vk12653-bearing recipients were transplanted with 10 x 106 BM from naïve donors and 2 x 106 T-cells from concurrent donor cohorts injected with myeloma at the same time as the recipients. Therapies were administered starting 7 days post-transplant. CRBN transgenic mice were used as donors and recipients in lenalidomide-treated groups (50mg/kg for 21 days by daily oral gavage). Anti-CSF-1R (𝛼CSF-1R) or control IgG (IgG) was administered twice weekly at a dose of 400µg per mouse for 4 weeks.

first: Simone

last: Minnie

first: Kenneth

last: Ho

first: Geoffrey

last: Hill


title: In vivo BMAL1 occupancy mapping using MACS-Calling Cards reveals disease-associated retargeting in Cln3Δex7/8 astrocytes

city: St. Louis

first: India

last: Reiss

state: Missouri

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University in St. Louis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Astrocytes maintain neuronal homeostasis through cellular programs that are frequently disrupted early in neurodegenerative disease, many of which are regulated by the circadian clock. The core clock transcription factor BMAL1 is required for normal astrocyte function, yet whether its regulatory activity is altered during neurodegeneration remains unclear. Moreover, astrocyte circadian gene expression patterns are profoundly reprogrammed in disease, yet the underlying mechanisms remain unclear, primarily due to a lack of methods for identifying DNA binding sites of BMAL1 in specific cell types in the brain. Here, we have developed an in vivo strategy to record transcription factor genomic occupancy specifically in astrocytes (MACS-Calling Cards, MACS-CC), and used it to map BMAL1 binding. We applied this strategy to the Cln3Δex7/8 mouse model of CLN3 disease, a fatal neurodegenerative disorder, which exhibits early astrocyte dysfunction prior to widespread neuronal loss as well as circadian dysregulation. This allowed us to test how the progressive pathological cascade caused by CLN3 deficiency reprograms BMAL1 binding in astrocytes. BMAL1 binding was extensively redistributed, with comparable numbers of wild-type-specific and disease-specific sites. Wild-type-specific BMAL1 binding was enriched near genes involved in circadian regulation and astrocyte differentiation, whereas disease-specific sites lacked coherent functional enrichment. Consistent with these changes, RNA-seq of sorted astrocytes revealed reduced expression of mature astrocyte markers in Cln3Δex7/8 mice. To define the mechanisms underlying BMAL1 retargeting in Cln3Δex7/8  astrocytes, we tested whether changes in chromatin accessibility could explain disease-associated gains and losses of BMAL1 binding. Although chromatin accessibility was broadly remodeled, differential accessibility did not predict BMAL1 binding gains or losses. Instead, motif analyses supported a model in which loss of normal cooperative transcription factor partnerships contributes to BMAL1 retargeting. Together, these findings demonstrate that MACS-CC enables in vivo transcription factor occupancy mapping in astrocytes and reveals the mechanisms behind early rewiring of circadian regulatory programs within a model of progressive pathology leading to neurodegeneration. Our data also shed new light on astrocyte dysfunction in CLN3 disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: BMAL1 Calling Card, Mnase-seq, and RNA-seq datasets from astrocytes (enriched from MACS), as well as BMAL1 Calling Card datasets from HepG2 cells.

first: Reiss

last: India


title: Single-cell RNA-sequencing profiles reveal the developmental landscape of hawthorn leaves.

city: Kunming

first: Guigang

last: Zhao

state: Yunnan

address: #21 Qingsong Road

country: China

institute: Kunming Institute of Zoology

summary: Hawthorn (Crataegus spp.) is an economically and medicinally important genus in Rosaceae. Its leaves accumulate valuable secondary metabolites, including flavonoids, and have long been used in traditional Chinese medicine. Despite available chromosome-level genome assemblies and bulk transcriptome data, the cellular composition of hawthorn leaves, their developmental trajectories, and the cell-type-specific distribution of biosynthetic gene expression remain uncharacterized. Here we report the first single-cell transcriptomic atlas of hawthorn leaves, generated by integrating protoplast-based scRNA-seq and nucleus-based snRNA-seq from two species (C. pinnatifida var. major N. E. Br. and C. scabrifolia (Franch.) Rehder). From four libraries, we profiled 32,292 high-quality cells, resolved sixteen transcriptional clusters, and annotated nine canonical cell types: mesophyll, pavement, guard, xylem, metaxylem, phloem parenchyma, companion, sieve element, and meristematic cells. Cell-type-resolved interspecific comparison identified 642 differentially expressed genes between species, with divergent enrichment of photosynthesis and volatile biosynthesis processes in C. pinnatifida var. major and hypoxia-response processes in C. scabrifolia. Pseudotime analysis reconstructed branched developmental trajectories converging on mesophyll dominance at late stages, consistent with classical dicotyledonous leaf organogenesis. Cell-type-resolved profiling demonstrated spatial partitioning of flavonoid biosynthetic genes across multiple cell populations, with upstream enzymes concentrated in epidermal and phloem-associated cells and downstream enzymes in mesophyll and xylem cells. This atlas provides a cellular framework for mechanistic study of tissue‑specific secondary metabolite and for future functional and breeding applications in hawthorn.

sample_organism:
Crataegus pinnatifida
Crataegus scabrifolia

overall_design: The collected leaf material was cut into approximately 1 mm fragments and placed in an ice-cold dissociation pretreatment buffer (20 mM KCl, 10 mM CaCl₂, 0.1% bovine serum albumin, 20 mM MES, 0.6 M mannitol).

first: GuiGang

first: Xien

last: Wu

first: Baozheng

last: Wang

first: Xiaolu

last: Li

first: Junjuan

last: Zheng

first: Zhaoli

last: Ding

first: Guodong

first: Ticao

last: Zhang


title: Artificial intelligence-assisted prediction of PANoptosis related molecular targets and precise screening of neuroprotective drugs for spinal cord injury

city: Guangzhou

first: Ge

state: Guangdong

address: No.106 Zhongshan Rd.2

institute: Guangdong Provincial People's Hospital(Guangdong Academy of Medical Sciences),  Southern Medical University

summary: Abstract: Spinal cord injury (SCI) is a highly disabling central nervous system disease with complex pathology, and targeted neuroprotective drugs remain clinically lacking. However, traditional molecular target screening and drug prediction methods are inefficient, costly, and poorly targeted, failing to meet clinical precision treatment needs. To address this, we introduced artificial intelligence to construct a multi-dimensional data integration framework. First, we established normal, acute- and subacute-phase SCI mouse complete transection models, and RNA-seq combined with single-cell sequencing confirmed acute-phase extensive neuronal PANoptosis. Using WGCNA and MCC algorithms, 25 candidate genes for extensive neuronal PANoptosis in the acute phase were screened out. Then, we comprehensively applied machine learning algorithms including Random Forest, Support Vector Machine, and Elastic Net Model to predict and prioritize potential molecular targets, identifying 13 core genes for extensive neuronal PANoptosis, including Tacc3, Aurka, Mcm6, Mcm5, Ripk1, etc. With the help of the Connectivity Map, drug prediction was performed on these 13 genes, and the 8 candidate drugs with neuroprotective effects were screened out. Through protein domain screening, it was verified via proof-by-contradiction assays that the drug Xaliproden can establish robust interactions with the 7XMK, 7FCZ and 7FD0 domains of Ripk1, a core molecule of the PANoptosome, via a network of multiple hydrogen bonds. This finding provides a novel screening strategy for neuroprotective drugs for spinal cord injury and is of great significance for promoting the establishment of a precision treatment system for the acute phase of injury.

overall_design: RNA sequencing was performed on the spinal cord tissue samples of mice with complete T9 spinal cord transection injury at 0 days, 3 days, and 21 days post-injury.


title: Chromatin Isolation by RNA purification (ChIRP)-followed RNA sequencing of human leukemia cell lines, MOLMO13 and OCI-AML4, folowing lncRNA CRISPR/Cas9 editing and cytosine base editing

city: Boston

first: Peng

last: Lyu

state: Massachusetts

address: 1 Blackfan Street

institute: Boston Children's Hospital

summary: The HOXA gene locus coordinates body patterning, hematopoiesis, and differentiation. While studying blood phenotype-associated variation within the HOXA locus, we identified a genetic variant, rs17437411, associated with globally reduced blood counts, protection from blood cancers, and variation in anthropometric phenotypes. We find that this variant disrupts the activity of a previously unstudied antisense long non-coding RNA (lncRNA) located between HOXA7 and HOXA9, which we have named HOTSCRAMBL. The HOTSCRAMBL variant disrupts lncRNA function and reduces human hematopoietic stem cell (HSC) self-renewal. Mechanistically, HOTSCRAMBL enables appropriate expression and splicing of HOXA genes in HSCs, most notably HOXA9, in an SRSF2-dependent manner. Given the critical role of HOXA gene expression in some blood cancers, we also demonstrate that HOTSCRAMBL variation or deletion compromises HOXA-dependent acute myeloid leukemias. Collectively, we show how insights from human genetic variation can uncover critical regulatory processes required for effective developmental gene expression.

overall_design: RNA profiling of human leukemia cell lines, MOLMO13 and OCI-AML4 under long non-coding RNA HOTSCRAMBL knockout and cytosine base edited conditons. AAVS1 KO and CBE serve as CRISPR/Cas9 and cytosine base editing controls, respectively.

first: Vijay

middle: G

last: Sankaran


title: Salvianolic acid B upregulates miR-744-5p expression in peripheral blood mononuclear cell–derived extracellular vesicles to alleviate uremic cardiomyopathy

city: Dalian

first: Wang

last: Ziran

state: Liaoning

address: No.9 West Section Lvshun South Road

institute: Dalian Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Uremic cardiomyopathy (UCM) is a severe complication of uremia that lacks effective treatments. The role of immune dysfunction in hemodialysis patients with UCM remains unclear. Peripheral blood mononuclear cells (PBMCs) are major components of the immune system; however, they do not directly contact cardiomyocytes. In general, extracellular vesicles (EVs) function as intercellular communication mediators. Therefore, in this study, we first investigated the role of PBMC-derived EVs (PBMC-EVs) in UCM and identified EV-miR-744-5p as a key molecule involved in PBMC–cardiomyocyte communication. Mechanistically, indoxyl sulfate (IS) downregulated miR-744-5p expression in PBMC-EVs, leading to IGF2R upregulation in cardiomyocytes, thereby exacerbating myocardial injury via induction of hypertrophy, apoptosis, and inflammatory pathway activation in the cardiomyocytes. These files provide sequencing results on altered miRNAs in PBMC-EVs after IS stimulation.

overall_design: Including IS-stimulated PBMC-EVs and untreated (control) PBMC-EVs.

first: Ziran

first: Jiaojiao

last: Hao

first: Yaxi

last: Shang

first: Wenli

last: Ma

first: Weidong

first: Qingzhu

last: Tang

first: Xiangning

last: Du

first: Fan

last: Yang

first: Biaojie

last: Qin

first: Kun

last: Xiao

first: Longkai

first: Xianan

last: Guo

first: Shuang

last: Meng

first: Huiyi

last: Song

first: Hongli

last: Lin


title: Transcriptomic profiling of human CD34⁺/CD45RA-/CD90+ HSCs folowing lncRNA CRISPR/Cas9 editing and cytosine base editing [bulk_RNAseq]

first: Peng

overall_design: RNA profiling of human peripherial blood derived CD34⁺CD45RA-CD90+ HSCs under long non-coding RNA HOTSCRAMBL knockout and CBE condition. AAVS1 KO and CBE as CRISPR/Cas9 and cytosine base editing controls, respectively.

first: Vijay


title: Rifamycin O as a Novel CRBN Ligand for Targeted Degradation of IKZF1/3 Proteins in Hematopoietic Malignancies

city: China

first: Jinlian

last: Wei

state: Shanghai

institute: ECUST

summary: We found that Rifamycin O could effectively suppressed the hematologic tumors growth in vitro and in vivo. The antitumor effect of Rifamycin O is first identified so far.

overall_design: Examination of Rifamycin O-treated and control group in K562 cells by RNA-seq, in triplicate

first: Liang

last: Liao

first: Qiang

last: Wang

first: Zhengyang

last: Gao

first: Jian

last: Li


title: ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment [ChIP-seq]

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Short interspersed nuclear elements (SINEs) are abundant non-autonomous transposable elements (TEs) derived from RNA polymerase III (Pol III)-transcribed short non-coding RNAs. SINEs retain sequence features recognized by the Pol III machinery and constitute a substantial portion of vertebrate genomes. Despite their impact on genome stability and evolution, the mechanisms governing SINE transcription remain poorly understood. Although DNA methylation and heterochromatin formation have been implicated in their repression, we find these pathways play only a minor role in mouse embryonic stem cells. Instead, we identify the ChAHP complex as a key repressor of SINE B2 elements. ChAHP directly inhibits Pol III transcription by blocking TFIIIB recruitment without affecting TFIIIC binding. This selective interference prevents transcription initiation and highlights a distinct regulatory mechanism. Our findings establish ChAHP as a non-canonical repressor of Pol III-dependent SINE transcription, offering new insights into the control of this pervasive class of non-coding genomic elements.

overall_design: Analysis of RNA Polymerase III transcribed SINEs in mouse embryonic stem cells (mESC) in  wild-type and under accute ADNP- and GTF3C1-depletion conditions. ChIP-seq for RNA Pol III, TFIIIB, TFIIIC, TFIIIA and ADNP were in general performed in biologically indepdenden duplicates. For ADNP ChIP in wt conditions, we included 6 replicates. All ChIPs except for Pol III were performed using endogenously tagged proteins.

first: Jakob

last: Schnabl

first: Michaela

last: Schwaiger

first: Marc

last: Bühler


title: ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment.

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

overall_design: Refer to individual Series


title: ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment [RNA-seq]

overall_design: Total RNA-seq and TT-seq analysis in mESCs after accute ADNP-depletion, GTF3C1-depletion, CTCF-depletion and combined ADNP/CTCF-depletion. RNA-seq and TT-seq experiments were performed in independent triplicates.


title: Stage-specific degradation of cyclin D3 orchestrates myelopoiesis and restrains MPN development [scRNA-seq]

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

summary: Cyclin D3 is critical for myelopoiesis, with its rapid, stage-specific degradation regulating normal granulocyte-monocyte differentiation. Using a knock-in mouse model with a degradation-resistant cyclin D3 variant (D3T283A), we show that sustained cyclin D3 levels enhance granulocyte-monocyte output, cause microcytic erythrocytes, thrombocytosis, and extramedullary hematopoiesis. Splenic HSPCs from D3T283A mice exhibit increased self-renewal and competitive repopulation advantage. Prolonged D3T283A expression drives a high-penetrance myeloproliferative neoplasm, reducing survival.

overall_design: Single-cell sequencing was performed on spleenocytes from C57BL/6J mice with a CRISPR/Cas9-induced mutation in the CCND3 gene, resulting in a Threonine 283 to Alanine substitution (D3T283A). Mice were bred and maintained as heterozygous knock-in. Specifically, two D3T283A female mice, aged 12 and 16 months, and two age- and sex-matched wild-type (WT) female mice were used. The experiment was conducted on spleenocytes from mice aged 12–16 months, when the D3T283A mouse model exhibits severe symptoms of myeloproliferative neoplasm.

first: Bartosz

last: Mucha

first: Vincenzo

last: Tarallo

first: Shuyuan

last: Zhang

first: Marganit

last: Farago

first: Polly

last: Phillips-Mason

first: Harrison

last: Lindley

first: Mark

last: Cameron

first: Chen

last: Zhao

first: Amar

middle: B

last: Desai

first: Alan

middle: J

last: Diehl


title: Systematic Profiling of Essential Fungal Transcription Factors Uncovers Ezt1 as a Central Pathobiological and Morphogenic Regulator in Cryptococcus neoformans [RNA-Seq 2]

status: Public on May 05 2026

city: Seoul

first: Yong-Sun

last: Bahn

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

department: Department of Biotechnology

country: South Korea

institute: Yonsei university

summary: Cryptococcus neoformans is a global fungal pathogen that causes fatal cryptococcosis, underscoring the urgent need for novel therapeutics given the limitations of current antifungals. Here, we systematically investigate essential transcription factors (TFs) in C. neoformans, focusing on their roles in growth and their potential as drug targets. We developed experimental pipelines to assess growth requirement, essentiality, and function using conditional gene expression, constitutive overexpression, and random spore analysis. Through these systematic analyses, we identify one quasi-essential (growth-required but non-essential) TF, Fhl1, and 13 essential TFs, including three (Ezt1, Ezt2 and Cbf1) that are highly divergent from counterparts in other eukaryotes. Notably, Ezt1 emerged as a central TF regulating over 1,200 genes, controlling growth, antifungal drug and stress responses, sexual development, and virulence. Collectively, our findings define the essential TF landscape of C. neoformans and provide a framework for leveraging these regulators, particularly Ezt1, to develop targeted therapies for cryptococcosis.

overall_design: The wild-type (H99), PH3:CBF1, PH3:EZT1, and PH3:EZT2 strains were grown in YPD liquid medium at 30°C overnight. The cultures were then transferred to fresh YPD liquid medium and incubated until the OD600 reached 0.8. Three biologically independent cultured samples were prepared for each strain, and total RNA was purified.

first: Seung-Heon

last: Lee

first: Sheng

last: Sun

first: Yu-Byeong

last: Jang

first: Seong-Ryong

last: Yu

first: Yeseul

last: Choi

first: Jin-Tae

first: Eui-Seong

last: Kim

first: Jong-Seung

first: Joseph

last: Heitman

first: Kyung-Tae


title: Stage-specific degradation of cyclin D3 orchestrates myelopoiesis and restrains MPN development [RNA-seq]

first: Ata

last: Abbas

overall_design: RNA-sequencing was performed on spleenocytes from C57BL/6J mice with a CRISPR/Cas9-induced mutation in the CCND3 gene, resulting in a Threonine 283 to Alanine substitution (D3T283A). Mice were bred and maintained as heterozygous knock-in. Specifically, three D3T283A (12-16 months), and three age-matched wild-type mice were used. The experiment was conducted on spleenocytes from mice aged 12–16 months, when the D3T283A mouse model exhibits severe symptoms of myeloproliferative neoplasm.

first: Bartosz

last: Mucha

first: Vincenzo

last: Tarallo

first: Shuyuan

first: Marganit

first: Polly


title: Small RNA Seq profiling of tissue specific MSCs derived EVs

city: Delhi

first: Sujata

last: Mohanty

state: Delhi

address: Ansari nagar

department: Stem Cell Facility

country: India

institute: AIIMS, New Delhi

summary: Small extracellular vesicles (sEV) play a pivotal role in intercellular communication and hold immense therapeutic potential. In this study, we aimed to characterize sEV derived from bone marrow mesenchymal stromal cells (BM-MSCs) and Wharton’s jelly mesenchymal stromal cells (WJ-MSCs), cultured under normoxic and hypoxic conditions for elucidating their functional inclinations. Using high-throughput miRNA sequencing, we identified distinct miRNA profiles across cell types and oxygenation states, revealing unique signatures associated with hypoxia-driven cellular adaptations.

overall_design: The small RNA sequencing of sEV derived from respective MSCs was outsourced to Eurofins Genomics India Pvt. Ltd. Briefly, RNA was extracted using the TRIzol reagent (Invitrogen, Shanghai, China) following the protocol provided by the manufacturer, and the samples were shipped in dry ice to the laboratory of Eurofins Genomics India Pvt. Ltd. (a) Illumina NextSeq Small RNA Library Preparation Quality and quantity of the received RNA samples were checked on NanoDrop followed by Agilent Tape station using High Sensitivity RNA ScreenTape. The small RNA sequencing libraries were prepared from the received total RNA samples using Illumina NEBNext® Multiplex Small RNA Library Prep Kit for Illumina (NEB) as per the manufacturer’s instruction. Approximately 1 µg of RNA was processed for 3' adapter ligation followed by 5’ adaptor ligation. The adaptor ligated RNA samples were then converted to cDNA using reverse transcriptase followed by PCR amplification using common primer and indexed primer. The enriched library was then purified using Spin column followed by AMPureXP bead-based size selection. The size selected and purified libraries were analyzed in 4200 Tape Station system (Agilent Technologies) using High sensitivity D1000 Screen tape as per manufacturer instructions. (b) Cluster Generation and Sequencing After obtaining the Qubit concentration for the libraries and the mean peak sizes from Agilent Tape Station profile, the PE Illumina libraries will be loaded onto Illumina NextSeq500 platform for cluster generation and sequencing. Paired-End sequencing allows the template fragments to be sequenced in both the forward and reverse directions on NextSeq500. The kit reagents were used in binding of samples to complementary adapter oligoes on paired-end flow cell. The adapters were designed to allow selective cleavage of the forward strands after re-synthesis of the reverse strand during sequencing. The copied reverse strand will be used to sequence from the opposite end of the fragment. (c) Read Filtering Small RNA sequencing data is known to include reads from other category of small non-coding RNAs such as tRNA, snoRNA, snRNA and piRNA ect. Sample-wise reads were mapped against the customized database of Rfam (Database built after removing miRNA and their precursor sequences from the Rfam) using Bowtie v1.3.1 aligner with default parameters. The unmapped against Rfam database were considered for downstream analysis. Reads having length less than 18 nts and greater than 30 nts were excluded from the analysis. The reads which have length between 18-30 bases were considered for miRNA identification. Reads passed above filtration steps were considered as cleaned putative miRNA population, taken further for known and novel miRNA identification. (d) miRNA Prediction and Analysis Mapper.pl and miRDeep2.pl modules of miRDeep2 tool were used to identify novel miRNAs and precursors in sample(s) using reference genome. The resulting candidate novel precursors were filtered based on: the miRDeep2 score (≥4), significant randfold p-value. Know mature and precursor miRNAs of Homo sapiens were downloaded from miRBase database. Quantifier module of miRDeep2 tool was used to quantify miRNAs in each sample using predicted novel miRNAs, and known miRNAs downloaded from miRBase as reference. The analysis was carried out for miRNAs expressed differentially with p-value < 0.05 reported between control and treated samples respectively. Log2 Fold Change (log2FC) values greater than zero were considered up-regulated whereas less than zero were down-regulated along with p-value threshold of 0.05 for statistically significant results. miRNAs were further shortlisted based on specific criteria, such as differential expression and biological relevance. To identify their functional roles, target genes regulated by the shortlisted miRNAs were predicted using the miRWalk database, and pathway enrichment analysis was performed using the Panther database to uncover key biological pathways influenced by these miRNAs. Subsequently, Venny 2.0 was used to identify common miRNAs across multiple experimental groups by comparing miRNA lists and generating Venn diagrams. The intersection of miRNAs from different groups was analysed to determine shared regulatory roles and conserved pathways. This integrated approach provided valuable insights into miRNAs' biological significance and involvement in key regulatory pathways.

first: Yashvi

last: Sharma


title: RFX5 Mediates High-order Structures to Regulate Cancer Progression-Associated Genes [Hi-C]

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

summary: RFX5 is a DNA binding protein known to regulate MHC genes expressions with little studies on its role in maintaining 3D genome architecture. Recent studies have shown its potential in mediating long-range interactions in specific regions, though the underlying mechanism remains poorly understood. Here, using genes related to cancer progression as a paradigm, we studied the role of RFX5 and found that it specifically regulates these genes. It mediates interactions between gene promoters and their distal enhancers, which can be several hundreds of kilobases apart. We also found that RFX5 regulates higher-order structures of TADs and compartments, which become unstable upon loss of RFX5. Our findings elucidate the fundamental role of RFX5 in maintaining proper chromosome architecture and shed light on the relationship between chromatin loops and gene expression.

overall_design: Hi-C experiments measuring global contact frequencies in RFX5 deleted cells and their wildtype control

first: Ge

last: Xiao

first: Zhang

last: Yijun

first: Wang

last: Yongming


title: Seeding-competent early taumultimers are associated with cell type-specific transcriptional signatures

city: London

first: Rahel

last: Feleke

address: Ducane Road

country: United Kingdom

institute: Imperial College

summary: The initial molecular alterations of Alzheimer’s disease (AD) are unknown. Established AD is characterized by profound structural and transcriptional alterations in the human brain, with the hallmark neuropathological features being beta-amyloid (Aβ) accumulation in senile plaques and hyperphosphorylated fibrillar tau in neurofibrillary tangles (NFTs). Previous evidence indicates that tau multimerization into small aggregates is one of the earliest molecular alterations, anticipating the accumulation of hyperphosphorylated tau in NFTs. In this study, we investigated the seeding capacity of these early small tau multimers and the transcriptional changes associated with them, aiming to unveil early pathogenic processes in AD-type tau pathology. Early tau multimers visualized with tau proximity ligation assay (tau-PLA) in the post-mortem temporal cortex demonstrated high seeding activity detected by real-time quaking-induced conversion (RT-QuIC) and induction of aggregates in a tau biosensor cell line. Using single-nucleus transcriptomics, we showed that brain tissue harboring seeding-competent early tau multimers, but without significant NFT pathology, is associated with substantial gene expression alterations across diverse cell types when compared to control tissue lacking either multimers or NFTs. Differentially expressed genes, such as APP, MAPT, and PSEN1, exhibited significant enrichment of AD heritability in up-regulated genes within excitatory neurons, astrocytes, and oligodendrocytes. Pseudotime analysis exposed a positive correlation between the progression of tau pathology and the expression of genes marking reactive astrocytes. In summary, our results support the hypothesis that seeding-competent tau multimerization may initiate AD-type tau pathology cascades before the accumulation of tau in NFTs. This research contributes valuable insights into the early molecular events associated with AD, with implications for future diagnostic and therapeutic strategies.

overall_design: SnRNA-seq analysis was performed on the cohort representing 16 subjects with no clinical history of AD.

first: Simona

last: Jogaudaite

first: Elisavet

last: Velentza‑Almpani

first: Jeong Hun

last: Ko

first: Javier

last: Alegre‑Abarrategui


title: Achilles tendon exhibits distinct transcriptomic changes with increased mitochondrial energy production under lunar gravity

city: Tokyo

first: Taro

last: Kasai

address: Bunkyoku Hongo7-3-1

country: Japan

institute: The University of Tokyo

summary: Gravity plays a fundamental role in maintaining the structure and function of biological tissues, particularly within the musculoskeletal system. In space, the absence or reduction of gravitational forces leads to musculoskeletal deterioration, posing significant challenges for astronauts and individuals experiencing prolonged immobilization. Consequently, the effects of microgravity on muscle and bone have been extensively studied. Recent research highlights the crucial role of tendons in force transmission and mechanical stability; however, their transcriptomic response to reduced gravity remains largely unexplored. Here, we examined the adaptations of the Achilles tendons to lunar gravity (1/6 of Earth gravity) using RNA sequencing of tissue samples obtained from mice reared in the International Space Station for 25-26 days. Compared to quadriceps femoris muscles and brown adipose tissue, a greater number of genes were upregulated in the Achilles tendons under reduced gravity. Enrichment analyses revealed a significant upregulation of mitochondrial energy production in the Achilles tendons exposed to reduced gravity. Meanwhile, genes associated with extracellular matrix organization and collagen integrity were downregulated. Although histological examination showed no obvious structural differences between the lunar and Earth gravity groups, the expression of Atp5b, a subunit of ATP synthase, was enhanced in the lunar gravity group. Our findings suggest that mechanical loading regulates tendons by influencing mitochondrial energy production and extracellular matrix composition. These insights may contribute to therapeutic strategies for tendon degeneration associated with aging and disuse-related conditions.

overall_design: RNA-seq profiling of Achilles tendon, muscle, and brown adipose tissue in wild-type mice under Earth and lunar gravity

first: Toshiya

last: Tsubaki

first: Takumi

last: Matsumoto

first: Yasuhide

last: Iwanaga

first: Asuka

last: Terashima

first: Yasunori

last: Omata

first: Sakae

last: Tanaka

first: Taku

last: Saito


title: RFX5 Mediates High-order Structures to Regulate Cancer Progression-Associated Genes [4C-Seq]

first: Xiao

last: Ge

overall_design: QHR-4C experiments to calculate contact frequencies between gene promoters and their upstream or downstream enhancer fragments


title: Longitudinal single-cell and spatial transcriptomics reveals intratumor heterogeneity, therapeutic response, and comparative value of canine marginal zone lymphoma

status: Public on Aug 12 2026

city: Minneapolis

first: Grace

last: Walker

state: Minnesota

address: 425 East River Parkway

department: Masonic Cancer Center

institute: University of Minnesota


title: Single cell transcriptomes and spatial architecture of pancreatic pre-invasive lesions reveal acinar metaplastic cells' heterogeneity

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

country: Israel

institute: Hebrew University

platform_organism:
Mus musculus
synthetic construct


title: Single cell transcriptomes of pancreatic pre-invasive lesions and cancer reveal acinar metaplastic cells’ heterogeneity [MERFISH]

summary: In this project, we utilized single-cell RNA sequencing (scRNA-seq) and MERFISH spatial transcriptomics to profile the development of pancreatic cancer in a mouse model, tracing its progression from the pre-invasive stage to full malignancy. By employing a reporter gene, we were able to dissect the heterogeneity of metaplastic acinar cells, identifying and profiling six distinct types and states of these cells. We validated their localization within pre-invasive lesions, assessed the heterogeneity across various lesions, and calculated the colocalization of different acinar metaplastic cells with stromal cells.

overall_design: Tamoxifen was injected into six-eight weeks old Ptf1a-CreER, LSL-Kras-G12D, LSL-tdTomato (PRT) mice, and the pancreas was collected for single cell purification from mice seven months post-tamoxifen injection (PTI)

first: Juan

middle: S

last: Arcila-Barrera


title: Effects of anti-CD40 agonist and Cabozantinib on the immune microenvironment of mouse hepatocellular carcinoma

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: CD45+ cells were extracted from mouse HCC model with or without treatment of anti-CD40 and cabozantinib for the scRNA-seq processing.

overall_design: scRNA-Seq

first: D

middle: L

last: Ou

first: C


title: The spatial architecture of pancreatic pre-invasive lesions reveal acinar metaplastic cells’ heterogeneity [scRNA-seq]

overall_design: Tamoxifen was injected into six-eight weeks old Ptf1a-CreER, LSL-Kras-G12D, LSL-tdTomato (PRT) mice, and the pancreas was collected for single cell purification from mice seven months post-tamoxifen injection (PTI) Tamoxifen was injected into six-eight weeks old Ptf1a-CreER, LSL-Kras-G12D, LSL-tdTomato (PRT) mice, and the pancreas was collected for single cell purification from mice seven months post-tamoxifen injection (PTI)


title: DNA-based immune profiling in murine blood with methylation cytometry deconvolution

status: Public on May 14 2026

city: LEBANON

first: Brock

last: Christensen

state: NEW HAMPSHIRE

address: 1 MEDICAL CENTER DRIVE

department: Epidemiology

institute: Dartmouth College

type: Methylation profiling by genome tiling array

summary: Cell-type-specific patterns of DNA methylation have been leveraged to develop methods for accurate and reproducible DNA-based cell typing in human blood and other biospecimens. Recently developed and standardized genome -scale DNA methylation arrays for mus musculus offer an instrument for quantifying cellular composition with epigenetic signatures specific to each cell type. We present  a novel murine immune cell deconvolution tool that leverages DNA methylation profiles FlowSorted.Blood.IlluminaMouseMethylation. Separately from BALB/c and C57BL/6 mice, we used flow cytometry to purify polymorphonuclear neutrophil (PMN), monocyte, B-lymphocyte, natural killer, and CD4+ and CD8+ T-cells. Genome-scale DNA methylation was measured with the Illumina MouseMethylation BeadChip array at >285,000 CpG loci in purified cells for reference profile development. For testing and validation, DNA methylation was measured in both eye bleed and terminal blood whole blood samples from four mouse strains. To benchmark and determine accuracy of reference libraries for DNA methylation cell type deconvolution, flow cytometry of independent whole blood samples from four mouse strains was used. The Identifying Optimal Libraries (IDOL) algorithm identified an optimal reference library of 300 CpGs for deconvolution with RMSE values across testing and validation samples of <1.7 for all cell types except B lymphocytes (RMSE<2.75). This methylation cytometry tool for mice offers the ability to conduct DNA-based immune profiling in archival samples and reduce confounding from cell type heterogeneity in molecular studies of whole blood samples.

overall_design: Major immune cell populations were isolated from peripheral blood or spleen from C57BL/6 and BALB/c mice; this included B cells (n = 8), CD4 T cells (n = 8), CD8 T cells (n = 8), natural killer cells (n = 7), and polymorphonuclear cells (n = 7). DNA was extracted from these pure cell samples and hybridized onto the Infinium Mouse Methylation BeadChip for DNA methylation profiling.

first: Samuel

middle: R

last: Reynolds

first: Hannah

last: Stolrow

first: Min Kyung

last: Lee

first: Steven

middle: C

last: Pike

first: Fred

last: Kolling

first: Jacqueline

middle: Y

last: Channon

first: Daniel

middle: W

last: Mielcarz

first: Gary

middle: A

last: Ward

first: Jennifer

last: Fields

first: Lucas

last: Salas


title: Disease-associated microglia adopt stage-specific phenotypes that regulate T cell fate and immunity in glioma

first: Jiawen

last: Qian

address: 130 Dong'an Road

institute: Fudan University

summary: Glioma microenvironment contains numerous myeloid cells, including brain-resident microglia and recruited monocytes and macrophages (Mo/Mφ). Previous researches studied these cells collectively and revealed their pro-tumor effects. Yet, little is known about the differences among these myeloid populations. Here we revealed the phenotypic characteristics, spatial variances, and dynamic changes of these relatively heterogeneous cell populations by single-cell sequencing analysis. Microglia were pro-inflammatory transiently, and soon skewed to restore the homeostasis of the central nervous system (CNS). Notably, a subset of glioma-associated microglia shared similar trait in a diverse spectrum of neuropathogenesis. Mo/Mφ, on the other hand, were responsible for various tumor-promoting effects, such as angiogenesis, tumor invasion, and immune evasion. Moreover, the Mo/Mφ subsets presented prognostic and classificatory value in clinical application. Conclusively, these results eliminate the long-existing ambiguity about the role of microglia and Mo/Mφ in glioma pathogenesis, and reveal their prognostic and therapeutic value for glioma patients.

overall_design: scRNA-seq profiles for the CD45hi/loCD11b+ cells isolated from the tumor-bearing hemispheres of the GL261 glioma model at day 10, day 20, and terminal stage.

first: Chen

last: Wang


title: Mechanisms of Differential Signaling by IFNLR1 Variants

status: Public on Apr 30 2026

city: Charleston

first: Eric

last: Meissner

state: SC

address: 135 Rutledge Ave

department: Infectious Diseases

institute: Medical University of South Carolina

summary: Introduction: Lambda interferons signal through the interferon lambda receptor-1 (IFNLR1) and IL10RB heterodimer to induce interferon stimulated genes (ISGs). We previously showed that proteins derived from distinct IFNLR1 splice isoforms uniquely influence gene expression and HBV replication in stem cell-derived hepatocytes (iHeps). Here, we evaluated the mechanisms of signal transduction by full-length IFNLR1 (variant 1) and a truncated variant missing part of the cytoplasmic JAK1-interacting domain (variant 2). Methods: We evaluated HEK293T cells, wild-type (WT), and IFNLR1 knock-out (KO) iHeps with doxycycline-inducible expression FLAG-tagged IFNLR1 variants using the Duolink proximity ligation assay, ImageStream flow cytometry, western blotting of JAK-STAT proteins, susceptibility to JAK1 and TYK2 inhibitors, and gene expression profiling. Results: Each variant demonstrated IFNL-induced colocalization with IL10RB, but variant 1 was more rapidly and extensively internalized. In WT iHeps with intact endogenous IFNLR1, overexpression of either variant 1 or variant 2 enabled higher IFNL-induced JAK1, TYK2, STAT1 and STAT2 phosphorylation, yet variant 2 supported less robust ISG induction than variant 1. In iHeps with abrogated endogenous IFNLR1 expression, variant 2 supported less JAK1 and TYK2 phosphorylation and ISG induction than variant 1 yet was not deficient in supporting STAT1 and STAT2 phosphorylation. Select ISGs had differential constitutive expression in IFNL-untreated variant-expressing iHeps. In iHeps expressing variant 1, WT-iHeps were more resistant than KO-iHeps to TYK2-inhibition of antiviral ISG induction yet conversely were more susceptible to TYK2-inhibition of proinflammatory ISG induction, suggesting endogenously produced noncanonical variants influence the TYK2-dependence of IFNL signaling. Conclusions: IFNLR1 variants promote differential utilization of signaling mediators to influence IFNL-induced gene expression patterns, indicating a putative role in pathway regulation.

overall_design: RNAseq profiling on IFNLR1 variant-expressing WT and IFNLR1-KO iHeps and EV-controls +/- doxycycline induction and +/- IFNL3

first: Laura

last: Novotny

first: Carla

last: Martinez-Morant

first: Stephen

last: Duncan

first: Paula

last: Traktman

first: Monika

last: Gooz


title: Impaired RIPK4 function interferes with the metastatic potential of melanoma cells through deregulation of their adhesive status

city: Krakow

first: Ewelina

last: Madej

address: Gronostajowa 7

department: Department of Biophysics and Cancer Biology

country: Poland

institute: Jagiellonian University

summary: Receptor-interacting protein kinase 4 (RIPK4) has been implicated in the progression of numerous tumours. In non-melanoma skin cancer, RIPK4 plays a suppressor role, whereas in melanoma it functions as an oncogene that modulates key signalling pathways involved in melanoma cell survival and expansion. Increased RIPK4 levels in metastatic melanoma biopsies prompted us to investigate the consequences of RIPK4 loss for the invasive and metastatic phenotype of melanoma cells. Using an integrated approach involving clinical samples, in vivo xenograft models, and transcriptomic and 3D functional assays, we show that RIPK4 deletion significantly reduces pulmonary metastasis formation. This reflects its role in late-stage metastatic events, such as extravasation and colonization, particularly since this phenotype correlates with extensive transcriptional reprogramming of adhesion- and motility-related genes in melanoma cells, as evidenced by next-generation sequencing and functional validation in spheroid and collagen-based models. Despite exhibiting features of a partial shift toward an amoeboid phenotype such as membrane blebbing and increased MLC2 phosphorylation, RIPK4 knockout cells display impaired motility and invasion. Re-expression of RIPK4 restores mesenchymal morphology and migratory capacity. Together, our results establish RIPK4 as a critical regulator of melanoma invasion and metastasis. Nonetheless, they also demonstrate that the loss of RIPK4 function activates compensatory phenotypic shifts in melanoma cells that fail to fully rescue their invasive potential.

overall_design: To investigate the effects of RIPK4 knockout on melanoma cell fate, we generated RIPK4-deficient A375 human melanoma cells using the CRISPR/Cas9 genome-editing system and compared them with control cells. Subsequently, we performed bulk RNA sequencing to assess transcriptional changes. The experiment was conducted with three biological replicates.

first: Norbert

last: Wronski

first: Sławomir

last: Lasota

first: Anna

last: Brożyna

first: Małgorzata

last: Szczygieł

first: Agnieszka

last: Harazin-Lechowska

first: Jan

last: Czerbniak

first: Janusz

last: Rys

first: Jaroslaw

last: Czyz

last: Wolnicka-Glubisz


title: Cutibacterium acnes inhibits Staphylococcus lugdunensis biofilm formation through inhibition of autolysis and purine biosynthesis.

city: Lawrence

first: Luis Caetano

last: Antunes

state: KS

address: 1200 Sunnyside Avenue

institute: University of Kansas

summary: Cutibacterium acnes is a predominant member of the human skin microbiome that plays a pivotal role in maintaining homeostasis and protecting the host against pathogen colonization. Staphylococcus lugdunensis, while also a resident of the skin microbiota, is an opportunistic pathogen capable of causing severe infections, associated with its ability to form biofilms. Building on our previous observation that C. acnes secretes molecules capable of inhibiting S. lugdunensis biofilm formation without inhibiting planktonic growth, we investigated the underlying molecular mechanisms of this phenomenon. Here, we demonstrate that cell-free supernatants from various C. acnes strains exhibit dose-dependent antibiofilm activity targeting the initial stages of S. lugdunensis biofilm development. Additionally, extracellular molecules from C. acnes cultures significantly reduced the ability of S. lugdunensis to adhere to and invade human epithelial cells (A549) and to adhere to keratinocytes (HaCaT). Transcriptomic analysis revealed that C. acnes-derived molecules significantly repressed the expression of genes involved in purine biosynthesis in S. lugdunensis, while inducing the expression of the negative regulators of autolysis, lrgA and lrgB. Functional assays confirmed that C. acnes-derived molecules inhibit autolysis and extracellular DNA (eDNA) release by S. lugdunensis. Crucially, the addition of exogenous guanine suppressed the effect of C. acnes molecules on both biofilm formation and lrgA gene expression. Collectively, our data indicate that C. acnes molecules inhibit S. lugdunensis biofilm formation by depleting the intracellular guanine pool, which leads to repression of autolysis, thereby reducing the release of eDNA essential for biofilm structural integrity. These findings underscore the potential of exploiting interspecies microbiome interactions to better understand their role in pathogen exclusion.

overall_design: RNA-seq profiles of Staphylococcus lugdunensis ATCC 43809 grown in the absence or presence of cell-free conditioned media of Cutibacterium acnes ATCC 11827.

first: Rosana

last: Ferreira


title: Gene expression profile at single cell level of B16 and MC38 tumor infiltrating CD45+ TILs isolated from Gpr65-deficient and WT mice

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. of Immunology

country: Germany

institute: University Medical Center Mainz

summary: We used single cell RNA sequencing to analyze the composition of the tumor microenvironment of B16 and MC38 tumors in Gpr65-deficient and WT mice

overall_design: B16 or MC38 tumor cells were inoculated s.c. into Gpr65-deficient and WT mice. At day 17 (B16), respectively day 16 (MC38), single cell suspensions were prepared from excised whole tumors, and CD45+ cells were enriched by magnetic bead separation and flow cytometry-based cell sort.

first: Toszka

last: Bohn

first: Jean-Fred

last: Fontaine

first: Natalia

last: Truong


title: Stress accelerates hepatocellular carcinoma progression via a gut microbial-metabolite axis

status: Public on May 13 2026

city: Chengdu

first: Pengfei

last: Yue

state: Sichuan

address: No. 37 Guoxue Alley, Wuhou District

institute: West China Hospital, Sichuan University

summary: Hepatocellular carcinoma is one of the most prevalent malignancies worldwide, and the role of stress in hepatocellular carcinoma progression remains incompletely understood. In this study, we integrated clinical and preclinical models to investigate how stress-associated gut microbiota remodeling contributes to hepatocellular carcinoma progression. Stress profoundly altered the gut microbiota, with Phocaeicola vulgatus significantly reduced. Restoration of Phocaeicola vulgatus or administration of its tryptophan-derived metabolite indole-3-propionic acid attenuated hepatocellular carcinoma progression in vivo. Single-cell RNA sequencing was performed to characterize changes in the hepatocellular carcinoma tumor microenvironment. Indole-3-propionic acid treatment reduced endothelial JAM2 expression and was associated with reduced JAM2-F11R-mediated endothelial-macrophage crosstalk. These findings support a role for the stress-gut microbiota-metabolite-tumor microenvironment axis in hepatocellular carcinoma progression and suggest potential translational targets for microbiome-based therapeutic strategies.

overall_design: Comparative single-cell RNA sequencing analysis was performed on hepatocellular carcinoma samples from control and stress-associated experimental groups to investigate stress-induced changes in the tumor microenvironment and to explore the role of the gut microbiota-derived metabolite indole-3-propionic acid in hepatocellular carcinoma progression.

first: Zhe

last: Hu

first: Minlan

last: Yuan

first: Zhenjie

last: Zhang

first: Biao

last: Yang

first: Zhongwei

last: Cao


title: Human germline biallelic loss-of-function OSMR variants cause severe allergic disease

city: Vancouver

first: Stuart

middle: E

last: Turvey

state: BC

address: 938 W 28th Ave

country: Canada

institute: BC Children's Hospital Research Institute

summary: OSMRβ (Oncostatin M receptor beta), a member of the IL-6 superfamily of cell surface receptors, binds OSM and IL-31 and plays a critical role in human immunity. We identified probands from four kindreds with biallelic damaging variants in OSMR, which encodes OSMRβ. Patients had a unifying phenotype for severe widespread, early-onset atopic dermatitis, peripheral eosinophilia, and elevated serum IgE. Patient OSMRβ variants were not appropriately expressed on the cell surface compared to OSMRβWT. Patient OSMR variants showed significantly reduced OSM-mediated activation of STAT1, STAT3, and STAT5 and distinct transcriptional changes in primary dermal fibroblasts, including loss of interferon and inflammatory signatures. These defects were rescued upon lentiviral transduction of WT-OSMR. Together, these data establish that human germline biallelic loss-of-function OSMR variants cause severe allergic disease. We anticipate that this discovery will facilitate the recognition of additional affected individuals and the full definition of this novel primary atopic disorder.

overall_design: Bulk RNAsequencing on unstimulated primary patient fibroblast and healthy control fibroblasts

first: Sharma

last: Mehul

first: Samra

last: Simran

first: Turvey

last: Stuart


title: Paired mutation calling and spatial transcriptomics identify cellular neighbourhoods dictating the neoplastic outcome of colitis

city: Cambridge

first: Elisa

last: Moutin

address: Robinson Way

department: CRUK Cambridge Institute

institute: University of Cambridge

summary: In the progression from Inflammatory Bowel Disease to associated cancer, the clonal mutational landscape shifts from selection of mutations in inflammatory genes to selection of cancer-driver mutations1–4. How prevalence and expansion of either type of mutated clones could be impacted by the cellular environment in which they arise, and how this affects the neoplastic outcome of colitis is unknown. Here, we combine in vivo lineage tracing, in-silico modelling, mutational profiling and spatial transcriptomics in a mouse model of colitis-associated tumorigenesis to capture clone fates associated with chronic inflammation. We identify epithelial- and immune-enriched neighbourhoods and propose a model in which establishment of a reparative tissue environment facilitates tumour initiation by promoting the selection and expansion of pro-oncogenic clones, reducing the span of inflammation-resistant neighbourhoods containing non-oncogenic clones.

overall_design: RNAseq profilling of fresh colon tissue samples from N=3 colitic Muc2hom mice compared to fresh colon tissue samples from N=3 control Muc2het mice (3 samples x 3 mice per condition)

first: Linus

last: Chang

first: Giada

last: Giavara

first: Shenay

last: Mehmed

first: Mathilde

last: Colombe

first: Filipe

last: Lourenco

first: Maria

middle: N

last: Skoufou-Papoutsaki

first: Richard

last: Kemp

first: Philippe

last: Gascard

first: Thea

last: Tlsty

first: David

last: Tourigny

first: Douglas

last: Winton


title: Transcriptomic profiling of pancreatic cancer cells and tissues from genetically engineered mouse models

city: Ulm

first: Thomas

last: Wirth

address: Albert-Einstein-Allee 11

institute: Institute of Physiological Chemistry, University of Ulm

summary: This study investigates transcriptomic alterations associated with pancreatic ductal adenocarcinoma (PDAC) progression in genetically engineered mouse models. Total RNA was extracted from two types of samples: (1) pancreatic cancer cells isolated from KPC and KPNiC tumors, and (2) whole pancreatic tissue lysates from WT, NiC, KC, and KNiC mice. RNA-seq libraries were polyA-selected and strand-specific, sequenced on the DNBSEQ-G400 platform (BGI Genomics). Bioinformatic analyses included read alignment (HISAT2), quantification (RSEM), differential gene expression (DESeq2), and gene set enrichment analysis (GSEA). This dataset provides insights into the impact of NIK deletion on pancreatic tumor biology.

overall_design: Mouse pancreatic cancer models were used to evaluate the role of NIK (NF-κB-inducing kinase) in tumor biology. Tumor cells were isolated from KPC and KPNiC tumors (n=3 per group), and whole pancreas tissues were harvested from saline-treated WT, NiC, KC, and KNiC mice (n≥3 per group). Total RNA was extracted using the RNeasy Mini Kit and sequenced using paired-end 150 bp reads on the DNBSEQ-G400 platform. The design includes both tumor-intrinsic and tissue-wide transcriptomic analyses to assess NIK-associated changes in gene expression and pathway activation.

first: Ziwei

last: Du

first: Miltiadis

last: Tsesmelis


title: LINE1 RNA demethylation represses chromatin accessibility and sensitizes cancer cells to blockage of DNA damage repair ChIP-seq

city: Beijing

first: Jun

last: Liu

address: Haidian District

department: School of Life Sciences

institute: Peking University

summary: Repression of DNA damage repair by PARP inhibitors (PARPi) has shown great efficacy in cancer treatment. However, therapy resistance remains a significant clinical challenge. Here, we demonstrated that the N6-methyladenosine (m6A) modification of long interspersed nucleotide element-1 (LINE1, or L1) facilitates DNA damage repair in cancer cells, whereas removal of L1 m6A modifications enhances the sensitivity of both BRCA-wild-type and BRCA-mutant cells to PARPi. Specifically, following olaparib treatment, METTL3 accumulates on chromatin, which results in increased chromatin accessibility. Knockdown of METTL3 or removal of m6A on L1 RNAs increases METTL3 levels, leading to reduced chromatin accessibility. This, in turn, inhibits DNA end resection at damage sites and prevents PARP1 dissociation, ultimately impairing homologous recombination repair and enhancing tumor sensitivity to PARPi. Our findings unveil a novel regulatory mechanism of L1 m6A that governs the DNA damage repair response, providing a potential strategy of targeting METTL3 in combination with PARPi for cancer therapy.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K9me3 in LOVO and RKO cells, with or without METTL3 knockdown.

Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for METTL3 in LOVO and RKO cells

first: Zihong

last: Kang

first: Ruimeng

last: Li


title: LINE1 RNA demethylation represses chromatin accessibility and sensitizes cancer cells to blockage of DNA damage repair [ATAC-seq]

summary: Repression of DNA damage repair by PARP inhibitors (PARPi) has shown great efficacy in cancer treatment. However, therapy resistance remains a significant clinical challenge. Here, we demonstrated that the N6-methyladenosine (m6A) modification of long interspersed nucleotide element-1 (LINE1, or L1) facilitates DNA damage repair in cancer cells, whereas removal of L1 m6A modifications enhances the sensitivity of both BRCA-wild-type and BRCA-mutant cells to PARPi. Specifically, following olaparib treatment, METTL3 accumulates on chromatin, which results in increased chromatin accessibility. Knockdown of METTL3 or removal of m6A on L1 RNAs increases H3K9me3 levels, leading to reduced chromatin accessibility. This, in turn, inhibits DNA end resection at damage sites and prevents PARP1 dissociation, ultimately impairing homologous recombination repair and enhancing tumor sensitivity to PARPi. Our findings unveil a novel regulatory mechanism of L1 m6A that governs the DNA damage repair response, providing a potential strategy of targeting METTL3 in combination with PARPi for cancer therapy.

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) in control and METTL3-knockdown LOVO and RKO cells, with or without olaparib treatment.


title: Cross-Species Comparison between Mouse Kidney Multi-Omics and Human Genome-Wide Association Studies Highlights Molecular Features Associated with Oxalate Nephropathy

city: Nagoya

first: Ryosuke

last: Chaya

state: Aichi

address: Kawasumi 1, Mizuho-cho, Mizuho-ku

department: Nephro-urology

institute: Nagoya City University Graduate School of Medical Sciences

summary: Urolithiasis, a recurrent and increasingly prevalent disease globally, has a complex pathophysiology that impedes comprehensive understanding. This study sought to identify new pathogenetic molecules linked to urolithiasis through multi-omics analysis of a urolithiasis mouse model's kidneys and human genome-wide association analysis (GWAS). In the multi-omics analysis of urolithiasis mouse kidneys using RNA-seq, whole cell proteome, and phosphoproteome, we identified 1,173 genes, 342 proteins, and 516 phosphorylated peptides which were differentially expressed (DE) when comparing model with control mice. We employed large-scale urolithiasis GWAS resources from BioBank Japan, UK Biobank, and FinnGen through a meta-analysis, which provided 343 urolithiasis-related genes by gene enrichment analysis. Integrating the results of mouse and human analyses, we identified 46 urolithiasis-associated candidate molecules shared across species. We then further validated relevance of these 46 molecules in human urolithiasis. DE analysis comparing gene expression of the human renal papilla with and without stones found upregulation of CRYAB and SHROOM3, which are specifically expressed in collecting duct principal cells. Colocalization analysis between urolithiasis GWAS and expression quantitative trait loci (eQTL) data of human renal tubules revealed colocalization for GLUD1, UMOD, SLC34A1, and TCEA3. Colocalization analysis between the urolithiasis GWAS and 51 urolithiasis-related human phenotype GWAS found that SNX17 and UMOD showed prominent genetic pleiotropy. This study not only highlights novel urolithiasis-related molecules such as CRYAB, SHROOM3, TCEA3, and SNX17 but also elucidates cell types harboring the effects of known urolithiasis-related molecules. Consequently, successful mapping of renal effectuating molecules in urolithiasis has been achieved.

overall_design: RNA-seq analysis was performed on kidney tissues from C57BL/6 mice in a urolithiasis model induced by intraperitoneal administration of glyoxylate (100 mg/kg). Groups include control (no treatment) and glyoxylate-treated mice for 1, and 6 days.

first: Kazumi

last: Taguchi

first: Takahiro

last: Yasui


title: Nicotinamide N-Methyltransferase as a Therapeutic Target in Taxane-Resistant Castration-Resistant Prostate Cancer

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

summary: Drug resistance in patients remains a significant obstacle to successful treatment, even with improvements in cancer treatment strategies. Resistance to taxanes, such as docetaxel (Dtx) and cabazitaxel (Cbz), frequently emerges in Castration Resistant Prostate Cancer (CR-PCa). Through pulse selection of the parental cells (Du145), we established Dtx- and Cbz-resistant CR-PCa cell models and integrated different omic approaches, including transcriptomics and proteomics, to determine the molecular signatures underlying taxane resistance. Interestingly, several genes were regulated in the same direction (up- or down-regulation) at both the gene and protein expression levels in resistant cells compared to parental cells, suggesting that alterations primarily occur at the transcriptional level and manifest at the protein level. Among the differentially regulated genes, CRIP2, a gene associated with tumor suppressor function, has been found to be the most downregulated in taxane-resistant cells. Conversely, NNMT exhibited top-ranked significant upregulation and has been validated in the context of taxane resistance. Its overexpression was shown to promote taxane resistance, whereas depletion via siRNA or gRNA has resensitized the cells. RNA-sequencing of NNMT-knockout cells has indicated involvement of TGFβ signaling, and suppressing this pathway has further increased the taxane sensitivity. EMT was another pathway depleted upon knockout, and subsequent analysis revealed a significant correlation between NNMT and EMT-related genes (VIM, CDH2, FN1, TGFB1, and ZEB2) in both the cell line panel (CCLE) and patient data. Additionally, in cancers other than PCa, NNMT has been observed to predict treatment outcomes, and notably, among the patients with a high EMT signature, elevated NNMT levels were associated with decreased overall survival. More importantly, NNMT-high patients were found to be non-responders to taxane-containing chemotherapy regimens. Collectively, our findings suggest that targeting NNMT and the pathways it affects, such as TGFβ, offers a viable approach for addressing taxane-resistant PCa.

overall_design:
To gain insight into the molecular mechanisms underlying NNMT-mediated reversion of drug resistance, we aimed to examine the transcriptome of docetaxel-resistant (DtxR) Du145 cells treated with gRNA-NNMT
We performed a gene expression profiling analysis using data obtained from RNA-seq of NonTargeting (NT) Control and gRNA-NNMT treated docetaxel-resistant (DtxR) Du145 cells.

first: Buse

last: Cevatemre

first: Ezgi

last: Karyemez

first: İpek

last: Bulut

first: Mehmet

last: Gonen

first: Ahmet Tarik

last: Baykal

first: Tugba

last: Bagci-Onder

first: Ceyda

last: Acilan


title: LINE1 RNA demethylation represses chromatin accessibility and sensitizes cancer cells to blockage of DNA damage repair [MeRIP-seq]

overall_design:
Chromatin-associated RNA m6A profiles of METTL3 knockdown cells (LOVO and RKO) and its control were generated by deep sequencing, in duplicate.

Chromatin-associated RNA m6A profiles of METTL3 knockdown cells (OVCAR8 and SKOV3) and its control were generated by deep sequencing, in duplicate.


title: Successive waves of transcriptional repression and de-repression license the cell cycle progression in an archaeon [ChIP-Seq]

status: Public on Apr 29 2026

city: Qingdao

first: yunfeng

last: yang

address: State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China

institute: shandong university

summary: Archaea of the order Sulfolobales execute a well-structured cell cycle program similar to that of eukaryotic cells. However, the mechanism of cell cycle regulation remains enigmatic. Here, we show that three essential ribbon-helix-helix domain transcription factors, aCcr1, aCcr2, and aCcr3, play pivotal roles in controlling the cell cycle progression in the thermoacidophilic archaeon Saccharolobus islandicus by licensing the timely transcription of the key genes that define the cell cycle phases. The three transcription factors act as repressors and recognize similar regulatory sequences. However, their expression timing during the cell cycle differs: aCcr1 is expressed immediately after the cell division, aCcr3 during the transition between the G1 and genome replication (S) phase, whereas aCcr2 is expressed throughout the cell cycle. The disengagement of aCcr2 from the recognized promoters prior to the M phase is controlled through its phosphorylation by the cyclically-expressed eukaryotic-like kinase aCcrK (archaea cell cycle regulatory kinase). The synergy between aCcr1, aCcr2, and aCcr3 is also achieved through their differential affinities for the promoters and the levels of protein expression. The global regulation of the Sulfolobales cell cycle may be achieved not through transcriptional activation, but rather by repression of the key genes during strategic moments of the cell cycle. We propose a phosphorylation-assisted braking point model for the cell cycle control in Sulfolobales, which may represent a simple evolutionary intermediate on the way to the more complex cell cycle regulation in eukaryotes.

overall_design: Chromatin immunoprecipitation (ChIP-Seq) was performed according to Takemata et al.(39) with slight modifications. Briefly, the cells were collected 3 hours after synchronization, cross-linked by adding 1% formaldehyde for 15 minutes, and quenched with a final concentration of 125 mM glycine. The cells were pelleted by centrifugation at 5,000 g for 10 minutes and washed with PBS. The cells were then resuspended in TBS-TT buffer (20 mM Tris, 150 mM NaCl, 0.1% Tween-20, 0.1% Triton X-100, pH 7.5) and fragmented by sonication until the DNA fragments were of 200-500 bp. After centrifugation (10,000 g for 15 minutes), a 100 µl aliquot of the DNA-containing supernatant was kept apart to be uses as an input control and the remaining sample was divided into two aliquots. One aliquot was incubated with anti-aCcr2,3 antibody-coated protein A beads (Cytiva) and the other was incubated with pre-immune serum-coated protein A beads, which served as a nonspecific binding control (Mock control). After incubation at 60 °C for 10 hrs, the samples were collected and the captured DNA was purified by using the DNA Cycle-Pure Kit (Omega) according to the manufacturer's instruction. The input samples were treated as above without the addition of antiserum and beads. The purified DNA was used for ChIP-Seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system

first: Yunfeng

last: Yang

first: Shikuan

last: Liang

first: Zixin

last: Geng

first: Jinfeng

last: Ni

first: Qunxin

last: She

first: Mart

last: Krupovic

first: Yulong

last: Shen


title: Gene expression profiing of C28/I2 Human Chondrocyte Cell Line with control and FGF9 shRNA

city: Taichung

first: Ya

middle: Huey

last: Chen

address: No. 100號, Section 1, Jingmao Road, Beitun District, Taichung City, 406

department: Cancer Center

institute: China Medical University

summary: Osteoarthritis (OA) is an age-related degenerative joint disease. Ccartilage gradually degraded underlying joint bones during OA development. Gene expression profiling analysis was conducted on human OA primary chondrocytes and their normal counterparts. We identified the downregulation of FGF9 in OA primary chondrocytes compared to normal counterparts. Depletion of FGF9 expression by specific FGF9 shRNA in chondrocytes significantly exacerbates senescence and ROS level.

overall_design: To investigate the role of FGF9 in chondrocytes involved in osteoathritis (OA) progressiion, human normal chondrocytes cell lines, C28/I2, was infected with lentiviral based control and FGF9 shRNA. Total RNA was harvested and conducted RNA sequencing.   The gene expression profiling was obtained from RNA-seq of C28/I2-shvoid and shFGF9.

first: Ya-huey

first: Yu-Chia

last: Liu


title: Successive waves of transcriptional repression and de-repression license the cell cycle progression in an archaeon [RNA-Seq]

overall_design: The control group consists of empty plasmid strains, while the experimental group comprises strains overexpressing transcription factors aCcr2 and aCcr3, induced by arabinose.

first: Miguel V

last: Gomez-Raya-Vilanova

first: Wenying

last: Xia

first: Junfeng

first: Qihong

last: Huang


title: Loss of FAM60A disrupts Sin3/HDAC control of the Hippo signaling and promotes oncogenic YAP1 activation

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

summary: FAM60A (also known as SINHCAF) is a subunit of the Sin3/HDAC histone deacetylase complex with established roles in chromatin remodeling, yet its broader cellular functions remain largely undefined. Using immunological, biochemical, CRISPR/Cas9, genomic, and proteomic approaches, we mapped the FAM60A interaction network and its functional impact. We reveal that FAM60A binds directly to HDAC1 to recruit Sin3/HDAC to SIN3A, while a dual domain architecture mediates additional associations with RNA and DNA binding proteins. CRISPR/Cas9–mediated HDAC1 knockout abolishes the FAM60A–SIN3A interaction, confirming this dependency. Loss of FAM60A triggers widespread transcriptional rewiring, including downregulation of WWC3—a scaffold for LATS1/2 activation. Consequently, YAP1 dephosphorylation and nuclear accumulation shifted cell-cycle dynamics toward G₁ enrichment and conferred resistance to metabolic stress. Restoration of FAM60A or exogenous WWC3 reactivated Hippo “off” signaling, normalized cell-cycle distribution, and reversed stress resistance. These findings establish FAM60A as a pivotal epigenetic tuner linking histone deacetylation to Hippo pathway regulation and nominate the FAM60A–HDAC1–WWC3 axis as a potential therapeutic target to restore growth control in YAP-driven cancers.

overall_design: This study explores the diverse roles of FAM60A in addition to its interaction with the Sin3/HDAC complex. We applied immunological, biochemical, and CRISPR/Cas9 techniques alongside genomics, proteomics, and computer-based molecular modeling.

first: Mojnu

last: Miah

first: Md

last: Nazmul Huda

last: Islam

first: Dayebgadoh

last: Gerald

first: Khator

last: Sneha

first: Jahangir

last: Alam

first: Thornton

last: Janet

first: Gies

last: Allen

first: Bauer

last: Michael

first: Stephens

last: Kimberly

first: Nagalo

middle: M

last: Bolni

first: Mohammad

last: Alinoor Rahman

first: Michael

middle: P

last: Washburn

first: Sayem


title: Monoclonal antibodies targeting PCDH7 inhibit tumor growth and enhance targeted therapy response in non-small cell lung cancer

city: Dallas

first: Nicole

last: Novaresi

state: TX

address: 6000 Harry Hines Blvd

institute: UTSW

summary: We identified a critical oncogenic role for Protocadherin 7 (PCDH7), a cell surface protein and member of the Cadherin superfamily in NSCLC. PCDH7 is frequently overexpressed in lung adenocarcinoma (LUAD) and associates with poor clinical outcome. Depletion of Pcdh7 reduces lung tumor burden and prolongs survival in mouse models of high-grade NSCLC, demonstrating that this protein is an actionable therapeutic target. Here we report the development and characterization of high affinity anti-PCDH7 monoclonal antibodies (mAbs) that inhibit downstream MAPK pathway activation and suppress tumor growth in multiple mouse models, including KRAS- and EGFR-mutant models. A lead mAb (mAb7) sensitized tumors to the FDA-approved MEK inhibitor trametinib. Moreover, the humanized mAb7-IgG1 exhibited antibody dependent cellular cytotoxicity (ADCC) and Fc-mediated immune effector killing of tumor cells in vivo.  These findings provide an important step towards the clinical development of PCDH7-targeting antibodies for the treatment of NSCLC and other tumor types with high PCDH7 expression.

overall_design: To exploit PCDH7 as a potential vulnerability in NSCLC, we developed and characterized high affinity anti-PCDH7 monoclonal antibodies (mAbs) with the goal of identifying those that: 1, have high affinity for the PCDH7 extracellular domain; 2, inhibit downstream MAPK pathway activation and cell viability in multiple LUAD cell lines; 3, suppress tumor growth in multiple mouse models, including KRAS- and EGFR-mutant models; 4. engage the anti-tumor immune response in an Fc-dependent manner.

first: Poorva

last: Ghosh

first: Kathryn

last: O'Donnell


title: Conserved roles of GATA4 and its target gene TBX2 in regulation of human cardiogenesis

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

institute: University of Exeter Medical School

summary: The transcription factor (TF) GATA4 is a key mediator of cardiogenesis. GATA4 regulates cardiogenesis through the expression of its target genes, only some of which have been identified. We have used a gain of function model based on pluripotent embryonic ectoderm explants from Xenopus embryos expressing GATA4, to identify a set of downstream targets of GATA4 which are also regulated by Nodal, a known cardiogenic signal. GATA4 was shown to be required for the expression of target genes tbx2 and prdm1 in vivo, likely acting in a direct fashion by interacting with their regulatory regions. In addition, tbx2 and prdm1 are shown to have roles of their own in vivo, as downregulation of tbx2, a positive target, and overexpression of prdm1, a negative target, interferes with cardiac development in Xenopus embryos.

overall_design: Gene expression measured with RNA-seq timecourse in X.laevis animal caps with induced GATA4 and Nodal, at 2.5, 5.0, 7.5, and 24h post treatment

first: Branko

last: Latinkic

first: Pavel

last: Kirilenko

first: Ilya

last: Patrushev

last: Gilchrist


title: Disease-associated genetic variants can cause missense effects in tissue-specific protein isoforms

city: Edinburgh

first: Giovanna

last: Weykopf

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

summary: Genetic variants can cause protein-coding mutations that result in disease. Variants are typically interpreted using the reference transcript for a gene. However, most human multi-exon genes encode alternative isoforms. Here, we show that coding exons in alternative isoforms harbour more population variants than exons of reference isoforms, consistent with their reduced evolutionary constraint, and that these variants are more likely to cause nonsynonymous coding mutations. Common and rare disease-associated variants mapping to alternative transcripts can lead to amino acid substitutions predicted to be structurally damaging in the corresponding protein isoform. The alternative transcripts to which disease-associated variants map demonstrate high tissue-specific expression, with many unannotated in reference human genomes, revealed only by long-read RNA-sequencing. As an example, we report an unannotated alternative transcript of the inflammasome regulator DPP9 that is lung epithelium-specific and which harbours a common genetic variant associated with severe COVID-19 and lung fibrosis. The variant causes a p.Leu8Pro missense mutation in an alternative first exon, predicted to disrupt the encoded alpha helix. These findings highlight the importance of considering alternative isoforms, their tissue-specific expression, and full-length transcripts in variant interpretation, with implications for uncovering underappreciated mechanisms of both common and rare disease.

overall_design: Target-enriched long-read Nanopore-sequencing of  WT barrier epithelial cell lines (A549, H358, HBEC3, HSAEC1-KT, N/TERT-1), enriched for genes of interest (DPP9, MYDGF, FEM1A and SAFB) using custom exon probes.

first: Simon

last: Biddie


title: Clinical cure of chronic hepatitis B is associated with priming and perpetuation of hepatic CD4+ T cell responses

city: San Francisco

first: Ravi

last: Patel

state: CA

address: 513 Parnassus Ave

department: CoLabs

institute: University of California San Francisco

summary: Hepatitis B virus (HBV) is a major global pathogen that often leads to immune-mediated progressive liver injury and liver cancer. While seroclearance of the surface antigen (HBsAg) defines clinical cure and reduces disease-associated risks, HBsAg clearance is rarely observed and remains therapeutically elusive. Here we overcome some of the challenges to studying immune mechanisms of HBsAg clearance in chronic hepatitis B (CHB) using our mouse model of age-dependent HBsAg clearance and persistence, and samples from our BeNEG-DO trial that provided longitudinal PBMCs from patients who either cleared HBsAg or retained stable HBsAg levels after stopping nucleos(t)ide analog therapy. We show that young mice fail to clear HBsAg and have an impaired ability to efficiently initiate and sustain an HBV-specific CD4+ T cell response. We also demonstrate a role for CD4+ T cells in hepatic leukocyte organization, HBV-specific CD8+ T cell cytotoxicity, and ultimately HBsAg clearance. Upstream of the CD4+ T cell response, we reveal that hepatic dendritic cells, particularly cDC2s, direct effective CD4+ T cell activation and differentiation. Studies in CHB patients identified immune features of HBsAg clearance that overlap with the mouse model, including Th1 and cytotoxic CD4+ T cell activation and CD8+ T cell cytotoxic effector function. These findings identify an important role for potent CD4+ T cell activation in the clinical cure of CHB, and illuminate potential immunotherapeutic targets for enhancing CD4+ T cell responses to achieve greater HBsAg clearance rates.

overall_design:
PBMC samples were collected from HBeAg-negative CHB patients prior stopping long-term antiviral therapy (AVT) - baseline and at the follow up visits after stopping AVT. Surface protein and gene expresssion was analyzed using CITE-seq. Patients were grouped into two groups:  HBsAg clearance or persistence based on the status of HBsAg after 48 months of follow up post end of treatment .

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

last: Jespersen

first: Lia

last: Avanesyan

middle: K

first: Gabriela

last: Fragiadakis

first: Stewart

last: Cooper

first: Jody

last: Baron


title: Psilocybin Elicits a Conserved Glucocorticoid-Responsive Gene Signature Across Five 5-HT2A Receptor-Rich Brain Regions in the Male Rat

city: Tehran

first: Ashkan

last: Veysi

state: Tehran

address: 16 Azar avenue

department: Cell and molecular biology

country: Iran

institute: University of Tehran

summary: psychedelics are a class of substances best known for their extraordinary mind-altering effects, psychoactive properties that give them both opportunities and risks towards people’s mental health. Based on evidence from clinical trials, psilocybin, a widely used psychedelic for research purposes, appears to produce long-lasting therapeutic effects with minimal physical side effects in patients with a range of mood and addictive disorders. However, as psilocybin profoundly impacts perception, emotion, cognition and the sense of self, it is difficult to use it in the same way that ordinary candidate compounds with therapeutic potential are tested in routine daily clinical trials. Preclinical experiments can therefore provide valuable insights into the molecular mechanisms underlying the reported clinical effectiveness of the compound. Several lines of evidence strongly suggest that psilocybin exerts its effects through 5-HT2A receptors located postsynaptically to serotonergic neurons, particularly concentrated in the frontal cortex, parts of the limbic system (i.e., amygdala and hippocampus), and striatum. In an attempt to improve our knowledge of regional patterns of gene expression in the brain induced by psilocybin, we have generated a global map of gene expression in selected regions of adult rat brain (medial prefrontal cortex, cingulate cortex, hippocampus, and striatum; both right and left sides) using 3prime-RNASeq technology. While our findings revealed a few differentially expressed genes (DEGs) to be present in two or more regions, others had a region-specific profile. Additionally, pathways normally activated by glucocorticoids were found to be enriched in all the examined brain regions following psilocybin treatment.

overall_design: We treated 12 male rats each with 2 mg/kg of psilocybin and 12 male rats in control group with saline. In the next step, samples from five regions of the rats brains, including mPFC, cingulate cortex, striatum, amygdala, and hippocampus, were subjected to RNA extraction, library preparation and RNA-sequencing.

first: Daniela

last: Atanasovski

first: Maryam

last: Ardalan

first: Nasrin

last: Motamed

first: Elias

last: Eriksson


title: Enhancer regulation of OSR2 in mandibular incisor agenesis susceptibility [CUT&Tag]

status: Public on Apr 28 2026

city: Nanjing

first: Liwen

last: Fan

address: Hanzhong Road 140

institute: Nanjing Medical University

summary: Mandibular incisors are the most frequently congenitally absent teeth in Asian populations, affecting mastication, speech, aesthetics, and oral and maxillofacial functions over the long term. However, the genetic etiology of mandibular incisor agenesis (MIA) remains obscure. In this study, we conducted the first genome-wide association study on MIA in a Chinese population and identified an enhancer variant rs71514987 associated with an increased risk of MIA (odds ratio = 2.18, 95% confidence interval = 1.83-2.58, P = 3.62×10-19). Functional characterization indicated that rs71514987 C allele reduced the binding affinity of GATA4 to the OSR2 promoter, leading to increased OSR2 expression via remote regulation. Notably, elevated OSR2 levels promoted cell proliferation but diminished cell differentiation, migration, and apoptosis capabilities in stem cells from human exfoliated eciduous teeth (SHED), as well as abnormal development of pharyngeal teeth in zebrafish models. Mechanistic experiments further revealed that OSR2 bound to the promoter region of CXCR4, promoting its transcription level in the GPCR pathway, thereby influencing odontogenic differentiation during tooth development. Our findings provide novel insights into the molecular etiology of MIA.

overall_design: human exfoliated deciduous teeth (SHED) cells at passage 3 were collected and subjected to CUT&Tag assays using anti-OSR2 antibody (sc-393516X, Santa Cruz). Briefly, cells were incubated with ConA beads, followed by primary antibody, secondary antibody, and pG-Tn5 transposase to tag DNA adjacent to OSR2-bound loci. Tagmentation was performed at 37°C for 1 hour, and the reaction was stopped with EDTA, SDS, and proteinase K. DNA was extracted using phenol-chloroform and ethanol precipitation. A matched IgG control (SHED_IgG) was included as a negative control. Libraries were sequenced on the Illumina NovaSeq 6000 platform (Shanghai Jiayin Biotechnology Ltd). Raw reads were processed with Trimmomatic, and clean reads were aligned to hg19 using BWA-MEM. This experiment aimed to identify genome-wide OSR2 binding sites in SHED cells to understand its transcriptional regulatory mechanisms in mandibular incisor agenesis.

first: Xinyu

last: Zhang

first: Ji

last: Mao

first: Barbara

last: Vona

first: Xinze

last: Xu

first: Mulong

last: Du

first: Lan

last: Ma

first: Yongchu

last: Pan


title: The embryonic origins of site-specific arthritis; Bulk RNA sequencing of CD34+(Pi16+) fibroblasts stimulated with TNF and IL1b.

city: Oxford

first: Sarah

last: Davidson

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

institute: University of Oxford

summary: The cellular basis for site-specific inflammation remains unclear. In human fingers, proximal interphalangeal (PIP) joints are preferentially affected by inflammatory arthritis, whereas distal interphalangeal (DIP) joints are spared, providing a model to investigate the predilection of inflammation to distinct sites. We combine single-cell RNA sequencing, imaging and X-ray tomography to examine cellular composition, spatial organization and structure of finger joints during foetal development. PIP joints were enriched for Pi16+ fibroblasts, which are located in perivascular regions and at tendon–ligament interfaces. To investigate whether Pi16+ fibroblasts have a specific response to inflammatory cytokines Pi16+ and Pi16- cells were sorted from foetal fingers using the co-expressed marker CD34. Thes cells were cultured in vitro with and without TNF and IL1b and analyzed using bulk RNA sequencing.

overall_design: Embryonic fibroblast populations were isolated from fingers of n=3 donors (16-17pcw) provided by the Joint MRC/Wellcome Trust (grant# MR/X008304/1 and 226202/Z/22/Z) Human Developmental Biology Resource (www.hdbr.org).  Skin was removed, leaving all tendon, ligaments, capsule and synovium intact. DIP and PIP joints were excised, pooled and enzymatically digested for each donor individually. CD45-CD31-PDPN+ fibroblast populations were FACs sorted into Thy1+CD34+ and Thy1+CD34- populations for in vitro culture. For each donor, cells were stimulated +/- TNF and IL1b (in duplicate, total n=6 per condition), for 24h prior to bulk RNA sequencing.

first: Christopher

last: Buckley

first: Mark

last: Coles


title: Single cell analysis of clinically resolved epidermal skin from nickel-challenged individuals treated with either anakinra or placebo

city: Copenhagen

first: Kelvin

last: Yeung

address: Blegdamsvej 3B

country: Denmark

institute: LEO SIC

summary: Background: Topical corticosteroids are used as a standard treatment option in allergic contact dermatitis (ACD). However, the treatment doesn’t inhibit the generation of skin-resident memory T (TRM) cells. These cells play an important role in the pathogenesis of skin flare ups in ACD. Currently, findings in murine models suggest interleukin (IL)-1 inhibition can suppress the immune response to contact allergens. Objectives: To determine if IL-1 inhibition can attenuate acute skin flare-ups and restrict the development of TRM cells. Methods:  A murine model was used to investigate the role of IL-1 on epidermal TRM cells by measuring changes in ear thickness and T cell composition. Next, we conducted a randomized, double-blinded, placebo-controlled trial (RCT) [H-22001652; EudraCT number: 2021-004750-39]. Nickel allergic participants were patch-tested at 1) baseline, 2) while being treated with either anakinra or placebo, 3) and 21 days after treatment. The primary outcome was the International Contact Dermatitis Research Group (ICDRG) score 48 hours after patch test application. While secondary outcomes were a reduction of immune cells in clinically cleared and actively inflamed skin. Results: In mice, IL-1 inhibition decreased the number of epidermal CD8+ TRM cells and attenuated skin flare-ups upon re-exposure. Twenty participants were enrolled and completed the RCT, but anakinra failed to improve ICDRG scores. Conclusions: Although IL-1 inhibition has been proven successful in murine models for ACD, there is currently no clinical evidence that suggest it being efficacious as a short-term treatment option for acute skin flare-ups in humans.

overall_design:
Analysis of epidermal skin cells obtained by punch biopsies from preiovusly nickel-challenged clinically cleared skin taken 21 days after challenge. Individuals were either treated with anakinra or placebo for six consecutive days during the challenge.

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>>>Raw data are unavailable due to patient privacy concerns<<<
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title: Dynamic expression of CD9 protein in T-cell acute lymphoblastic leukemia [bulk RNA-seq]

status: Public on Apr 27 2026

city: Marseille

first: Dominique

last: Payet Bornet

address: 27bd Lei Roure

country: France

institute: CRCM

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy affecting both children and adults. Given its persistently poor prognosis, there is a critical need to identify additional factors involved in T-ALL oncogenesis and progression. CD9, a membrane protein of the tetraspanin family implicated in diverse cellular processes, has been associated with prognosis in several cancers, yet its role in T-ALL remains poorly understood. In this study, using first a mouse model, we found that CD9 overexpression is associated with leukemic T cells that have migrated outside the thymus into peripheral tissues. Then, analysis of a human T-ALL cohort shows that CD9 expression is heterogeneous, tends to increase at relapse and is enriched in the TAL1⁺ molecular subtype. We further demonstrate that CD9⁺ cells display enhanced migratory capacity compared with CD9⁻ counterparts, and that CD9 levels affect extracellular vesicle biogenesis. Altogether our findings support a role for CD9 in T-ALL leukemogenesis and highlight its potential involvement in relapse.

overall_design:
RNA-seq profiling of Patient-Derived Xenograft of primary human T-ALL samples in immunodeficient NSG mice and Jurkat cells.
Submitters state "Raw sequencing data correspond to Patient-Derived Xenografts (PDX) and are therefore subject to privacy restrictions (PDX* samples)."

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Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.
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first: Julie

last: Quessada

first: Mathis

last: Nozais

first: Charlotte

last: Savey

first: Julien

last: Rey

first: Delphine

last: Potier

first: Marie

last: Loosveld


title: Transcriptomic Profiling of the Sex-linked Biological Pathways of Severe Pulmonary Arterial Hypertension associated with Endothelial Cell Caveolin-1 Depletion and Chronic Hypoxia

city: Chicago

first: Richard

middle: D.

last: Minshall

state: IL

address: 835 S Wolcott Ave - E709C MSB (M/C 868)

department: Anesthesiology & Pharmacology and Regenerative Medicine

institute: University of Illinois Chicago

summary: Pulmonary arterial hypertension (PAH) is distinguished by elevated blood pressure and vascular resistance in the arteries of the lungs.  Patients with PAH demonstrate pulmonary vascular remodeling, wall thickening, and a high rate of morbidity due to right heart failure.  Notably, while female patients are more likely to develop PAH, male patients suffer from higher morbidity rates after diagnosis.  The molecular mechanism(s) underlying PAH development is poorly understood, though heritable PAH linked to mutations in bone morphogenic protein receptor 2 (BMPR2) and caveolin-1 (CAV1) may provide novel insights into the disease’s pathophysiology.  To interrogate this dynamic, we utilized a global CAV1 knockout (CAV1-KO) mouse model (CAV1-/-) in conjunction with chronic hypoxia to induce symptoms of PAH as demonstrated by hemodynamic and ECHO cardiography recordings.  Both female and male CAV1-/- mice in chronic hypoxia demonstrated elevated right ventricular systolic pressure (RVSP) of 48.49mmHg and 47.78mmHg respectively.  Female knockout mice started to die earlier in hypoxic conditions (4 wks), though male mice showed greater total mortality by the end of the 8 wks of hypoxia.  In addition to wildtype controls, we compared this knockout mouse to endothelial-specific CAV1 reconstituted (CAV1-RC) knockouts and found that restoration of CAV1 expression only in endothelial cells (ECs) is sufficient to ameliorate PAH symptoms, highlighting the importance of vascular CAV1 in maintaining pulmonary artery function.  RNA-sequencing of the lungs revealed that CAV1-/- is associated with downregulation of biological process gene pathways involved in cilium assembly in normoxic conditions for both sexes.  In hypoxic conditions, CAV1 knockout in females leads to downregulation of BMP signaling, while male hypoxic CAV1-/- led to a significant increase in muscle cell development genes.  Reconstitution of CAV1 in ECs lead to upregulation of immune signaling pathways, muscle cell development, and various cell differentiation pathways in both sexes.  Females showed a unique upregulation of cilia-related pathways, while males demonstrated increased BMP signaling.  These data indicate that muscle cell development, angiogenesis, cilia assembly, immune response, and BMP signaling pathways undergo sex-specific transcriptional regulation during PH development that may underlie sex differences in PH patient outcome.

overall_design: This experiment contains bulk RNA-sequencing data from mouse lungs exposed to 6 weeks of normal oxygen levels (Normoxia, Nx) or chronic 10% oxygen (Hypoxia, Hx).  Males (M) and Females (F) were treated as separate groups to investigate sex differences. Genotypes studied were wildtype control (B6/129SJ2), global Caveolin-1 knockout (Cav1(tm1Mls/)J), and a Cav1-knockout model with Cav1 specifically reconstituted and expressed in endothelial cells (Cav1-RC) obtained from William Sessa at Yale University.

first: Joseph

last: Leasure

first: Samuel

last: Lee

first: Kayla

last: Yerlioglu

first: Maricela

last: Castellon

first: Haibin

last: Li

first: Andres

last: Fantuzzi

first: Sunny

last: Chen

first: Sami

last: Muslmani

first: Arnav

last: Sharma

first: Jiwang

middle: D


title: scRNA-seq analyses of cerebrospinal fluid (CSF) cells in older adults with or without Alzheimer's disease after Bacillus Calmette Guerin (BCG) vaccination.

city: Charlestown

first: Mahesh Chandra

last: Kodali

state: MA

department: Neurology

institute: Massachusetts General Hospital / Harvard Medical School

summary: Cerebrospinal Fluid cells collected from older adults before and after BCG vaccination were studied. This database is part of the following. NCT04507126 - A Pilot Study of the Effects of Bacillus Calmette-Guérin (BCG) Immunization on Cerebrospinal Fluid and Blood-based Biomarkers in Older Adults - ClinicalTrials.gov. https://clinicaltrials.gov/ct2/show/NCT04507126 NCT05004688 - A Trial to Evaluate the Effects of BCG in Adults With MCI and Mild-to-Moderate AD - - ClinicalTrials.gov. https://clinicaltrials.gov/ct2/show/NCT05004688

overall_design: Briefly, In the present study, Cerebrospinal Fluid (CSF) Cells were collected and cryopreseved from subjects before (Baseline, 0 months or BL) and after (3 months and 12 months) BCG Vaccination. The cells at each of the time points (i.e. BL, 3mo and 12mo) were thawed followed by scRNA-seq on 10x.

first: Marc

last: Weinberg

first: Steven

last: Arnold