title: Comparative transcriptome analysis to reveal key drought-stress responsive genes in sorghum (Sorghum bicolor (L.) Moench)

city: Nugegoda

first: Dona Vihara

middle: Sugandhika

last: Kaluthanthri

state: Western province

address: Gangodawila

department: Botany

country: Sri Lanka

institute: University of Sri Jayewardenepura

summary: Flowering pathways are accelerated for rapid production of flowers and seeds in response to drought in certain varieties of sorghum (Sorghum bicolor (L.) Moench). The objective of the present study was to identify potential drought responsive genes that affect flowering time in sorghum under drought stress. Sorghum germplasm accessions representing early, intermediate, and late flowering groups were selected, and drought stress was administered on 25-day old seedlings of the Drought-Stressed group (DS) by withdrawing water whilst the control group of plants were well-watered (WW). At anthesis, with the initiation of pollen shedding, flag leaf tissues were harvested, and total RNA was separately isolated from samples. Transcription profiles consisting of 60 base pairs, paired end reads from total RNA of each sample were explored using Illumina Genome Analyzer deep sequencing method. An average of 66,059,932 clean reads were mapped. Among 10,468 differentially expressed genes, a set of 126 genes was up-regulated, and a set of 61 genes was down-regulated in all comparisons. Pathway enrichment analysis revealed de novo purine biosynthesis and lipoate biosynthesis pathways and Wnt signaling pathway affecting differentially expressed sorghum genes in response to drought. Transcriptome level differences among early, intermediate and late flowering groups of sorghum under WW and DS conditions were efficiently explored in the present study using RNA sequence analysis tools. Candidate genes and pathways that might be used to improve drought tolerance in sorghum were identified. Findings of the present study would lead to new targets for enhancing drought stress tolerance in sorghum.

overall_design: Seeds of sorghum germplasm accessions selected for early, intermediate, and late flowering groups (‘FRANCE 6005’, ‘KURUNEGALA 421’ and ‘MONARAGALA 93’) were obtained from the seed gene bank of Plant Genetic Resources Center (PGRC), Gannoruwa, Sri Lanka. Seeds were germinated to obtain plants which were exposed to two treatments as well-watered (WW) and drought-stressed (DS) conditions. Biological replicates of each germplasm accession and treatment were maintained in a net house under controlled environment. Flag leaf tissues were harvested from three different plants in each replicate in each treatment at pollen shedding stage. Total RNA was separately isolated from frozen flag leaf samples. RNA quality and integrity were assessed prior to RNA-sequencing. Library preparation was done using a TrueSeq Stranded mRNA LT Sample prep kit. RNA was sequenced using a HiSeq 2500 (Illumina) sequencer following HCS 2.2.70 sequencing control software. Transcription profiles consisting of 60 base pair, paired-end reads from total RNA of early, intermediate and late flowering groups under well-watered (WW) and drought-stressed (DS) conditions were explored with the Illumina Genome Analyzer deep sequencing platform.

first: Dona

middle: V

first: Suriya

middle: A

last: Perera

first: Pinumkarage

middle: N

last: Dasanayaka


title: L3MBTL2 maintains MYCN-amplified neuroblastoma cell proliferation through silencing NRIP3 and BRME1 genes [NB1_NGP_KO]

status: Public on Jun 16 2026

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epigenetic alterations critically affect tumor development. Polycomb-group complexes constitute an evolutionarily conserved epigenetic machinery that regulates stem cell fate and development. They are implicated in tumorigenesis, primarily via histone modification. Canonical and non-canonical Polycomb repressive complex 1 (PRC1.1–6) mediate the ubiquitination of histone H2A on lysine 119 (H2AK119ub). Here, we studied the functional roles of L3MBTL2, one of the PRC1.6 molecules, in neuroblastoma (NB) cells. shRNA- and CRISPR/Cas9-mediated L3MBTL2 depletion caused NB cell growth inhibition, cell-cycle arrest, and γ-H2A.X upregulation. Moreover, the knockout of L3MBTL2 profoundly suppressed xenograft tumor formation. Transcriptome analysis identified Break repair meiotic recombinase recruitment factor 1 (BRME1) and nuclear receptor interacting protein 3 (NRIP3) as targets of L3MBTL2-mediated silencing. The deletion of L3MBTL2 reduced enrichment of H2AK119ub and PCGF6 at transcriptional start site proximal regions of the targets. Add-back studies unveiled the importance of L3MBTL2-BRME1 and -NRIP3 axes for NB cell proliferation. We further manifested the association of MYCN with de-repression of NRIP3 in an L3MBTL2-deficient context. Therefore, this study first revealed the significance of L3MBTL2-mediated gene silencing in MYCN-amplified NB cells.

overall_design: Doxycycline-inducible Cas9 and sgL3MBTL2 stable NGP and NB-1 cells reveal L3MBTL2 knockout-associated chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of PCGF6, MYCN, and H2AK119ub.

first: Ryu

last: Okada

first: Shunpei

last: Satoh

first: Ryuichi

middle: P

last: Sugino

first: Ritsuko

last: Onuki

first: Masayuki

last: Haruta

first: Kyosuke

last: Mukae

first: Atsuko

last: Nakazawa

first: Jesmin

last: Akter

first: Miki

last: Ohira

first: Takehiko

last: Kamijo


title: L3MBTL2 maintains MYCN-amplified neuroblastoma cell proliferation through silencing NRIP3 and BRME1 genes [NGP_parental]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for PCGF6, MYCN, RING1B and H2AK119ub in parental neuroblastoma cell line NGP.


title: microRNA expression in the prefrontal cortex, nucleus accumbens, and peripheral blood serum of adult male rats following heroin self-administration

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

country: USA

institute: Temple University

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the microRNAs differentially expressed in the prefrontal cortex, nucleus accumbens, or serum exosomes of adult male rats that self-administered 0.075 mg/kg/infusion of heroin for 10 days in 6 hour daily sessions.

overall_design: microRNA profiles in three different regions of heroin-exposed animals versus saline-exposed animals


title: PBRM1 RNA-seq

city: West Lafayette

first: Sagar

middle: M

last: Utturkar

state: IN

address: 201 S University St

department: Institute for Cancer Research

institute: Purdue University

type: Expression profiling by high throughput sequencing

summary: Mammalian SWI/SNF or BAF are multi-subunit complexes that regulate cell-type specific gene expression by modulating chromatin accessibility, in coordination with transcription factors and other chromatin regulators. PBRM1 is the complex defining subunit of PBAF class of SWI/SNF complexes. It is mutated in ~40% of clear cell renal cell carcinoma cases but also associated with cancer progression and therapy resistance, indicating context-dependent function. We have previously reported that loss of PBRM1 in normal epithelial cells results in a partial Epithelial-to-Mesenchymal Transition (EMT). In this study, we have utilized epigenomic and transcriptomic approaches to understand the mechanistic role of PBRM1 in EMT-regulated gene expression, and its relationship to genome-wide histone modifications.

overall_design: RNA-seq was performed on control and PBRM1 KO NMuMG cells with 0, 24, 48, 72h of TGFbeta treatments; control or ATF3 KD NMuMG cells with 0, 24, 48, 72h of TGFbeta treatment; control or PBRM1 KD 4T1 cells with 0 or 4 days of TGFbeta treatment

first: Emily

last: Dykhuizen

first: Alisha

last: Dhiman


title: A developmental switch in the piRNA pathway ensures stage-specific transposon silencing in Drosophila

status: Public on Jun 15 2026

city: Risskov

first: Thomas

middle: Høgsbro

last: Grønbæk

address: Broloftet 5, 4.tv

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: Transposable element (TE) mobilization poses a major threat to genome integrity and fertility. In animals, TEs are suppressed in the germline by the Piwi-interacting RNA (piRNA) pathway, which is well characterized during late-stage Drosophila oogenesis. However, it remains unclear how TEs and the piRNA pathway are regulated across the dynamic chromatin and transcriptional landscape of earlier germline development. Here, using stage-specific chromatin profiling, piRNA sequencing, and temporally controlled knockdown of piRNA pathway components, we characterize TE regulation throughout Drosophila female germline development and uncover two distinct phases of piRNA-mediated transposon defense. In the first phase, spanning primordial germ cells through mitotically dividing germline stem cells, only a subset of TE families is transcriptionally competent, driven by TE-intrinsic cis-regulatory elements. These TEs are targeted by a piRNA program that relies on promoter-driven piRNA clusters independently of Moonshiner, Kipferl, and H3K27me3. In the second phase, triggered at the transition to endocycling nurse cells, the coordinated upregulation of Moon, Kipferl, Nxf3, and Bootlegger combined with increased H3K27me3 deposition reconfigures the piRNA pathway for enhanced piRNA production from heterochromatic dual-strand clusters, targeting the additional TE families activated in the polyploid nurse cell environment. Stage-specific chromatin profiling reveals that Piwi-dependent H3K9me3 deposition at TE loci requires their transcriptional activation. Importantly, silencing established by the early piRNA program can be maintained independently of piRNA pathway activity in later development, consistent with an epigenetic lock mechanism. Our findings establish that the piRNA pathway is not merely maintained but actively remodeled across germline development to match changing TE silencing demands.

overall_design: The study aim was to investigate the TE and piRNA expression and the chromatin environment across female germline development. To this end, we conducted RNAseq on bulk RNA, RNAseq on polyA enriched RNA, small RNAseq from argonaute proteins using TRAPR, Cut&tag-seq experiments on both full ovaries and bam-/- mutant ovarian cysts. Cut&tag the experiments were conducted on sorted GSC-like cells from bam-/- ovarian cysts and on sorted nurse cell nuclei (512c).

first: Marianne

last: Yoth

first: Artem

last: Ilin

first: Anja

last: Ebert

first: Tamsin

last: Samuels

first: Marina

last: Giovannetti

first: Felipe

last: Teixeira

first: Peter

last: Andersen


title: Competition for H2A.Z Between IAP Elements and Gene Promoters is Governed by ANP32E

city: Rochester

first: Patrick

last: Murphy

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: The histone variant H2A.Z is the most evolutionarily conserved histone protein and among the most well studied chromatin factors in biology, yet several unknowns remain, including the role of H2A.Z in transcriptional regulation and its function at heterochromatic repetitive loci. We find that H2A.Z accumulates at a subset of endogenous retrotransposons, including IAP elements, upon their transcriptional activation, and this build-up occurs at the expense of H2A.Z levels over gene promoters. We also find that the H2A.Z removal chaperon ANP32E allows these changes to occur by permitting repetitive elements to gain access to surplus H2A.Z which is not installed at gene promoters. Our results are consistent with a model in which H2A.Z supports transcriptional activation of repetitive elements, and competition for H2A.Z between promoters and repetitive elements underlies transcriptome-wide response to retrotransposon reactivation.

overall_design: CUT&Tag of H2AZ in WT and ANP32E-KO MEFs, treated with decitabine (DAC) or DMSO. RNA-Seq and H3K9me3 CUT&Tag experiments are also included here. H3K27ac CUT&Tag in WT MEFs is included. All conditions had at least 2 replicates

first: Garrett

last: Ruff

first: Michael

last: Ayers


title: HCFC2 knockdown in human colorectal cancer cell lines

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

summary: There is an urgent and unmet need for improved therapeutic approaches against aggressive colorectal cancer (CRC). Host Cell Factor 2 (HCF-2) is a transcriptional coactivator with an emerging role in cancer biology. Our data suggest that HCF-2 is a critical effector of peroxisome proliferator-activated receptor-gamma coactivator 1 beta (PGC-1β) signaling in CRC, supporting its potential as a targetable vulnerability in aggressive disease. Previous findings from our lab show that shRNA-mediated depletion of HCF-2 decreases anchorage-independent growth in CRC models, indicating a role for HCF-2 in CRC cell survival. To identify transcriptional programs regulated downstream of HCF-2, we performed RNA-seq following shRNA-mediated HCF-2 knockdown in SW620 and T84 CRC cell lines. Knockdown efficiency was confirmed by western blot prior to sample submission, and RNA-seq data were provided to collaborators for downstream computational analysis. The resulting transcriptomic profile will help define HCF-2-dependent gene expression programs and potential targetable vulnerabilities in aggressive CRC.

overall_design: 18 samples: 2 cell lines (SW620, T84) x 3 conditions (non-targeting control, shHCFC2 #287, shHCFC2 #449) x 3 biological replicates. Paired-end Illumina RNA-seq.

first: Kurt

last: Fisher

first: M. Jordan

first: Hadassha

last: Tofilau

first: Kamryn

last: Reynolds

first: Robert

last: Svoboda

first: Rebecca

last: Wright


title: CD36 gates nocturnal hypertension by regulating inactive period blood pressure variation via renal AMPK/HDAC5/PER1 axis

city: Chongqing

first: Mengyue

last: Chen

state: Chongqing

address: No. 1, Medical College Road, Yuzhong District, Chongqing City

department: Department of Infectious Diseases

country: China

institute: the Second Affiliated Hospital，Chongqing medical university

summary: Nocturnal hypertension is a strong predictor of cardio cerebrovascular disease (CVD), yet its underlying mechanisms remain largely unknown. In this study, we identified CD36 as a key regulator of blood pressure (BP) rhythms and as a gatekeeper of nocturnal hypertension. Its deficiency disrupts circadian BP rhythms.We continuously monitored 48-hour BP using telemetry in CD36 global knockout (KO) mice and renal proximal tubule-specific CD36 KO mice. We also collected serum samples and ambulatory blood pressure monitoring (ABPM) data from patients with nocturnal hypertension to assess the relationship between CD36 expression and nocturnal hypertension. A comprehensive screening of various factors affecting BP and circadian rhythms was conducted to explore the molecular mechanisms involved, utilizing RNA sequencing, calorimetry, enzyme-linked immunosorbent assay (ELISA), co-immunoprecipitation, immunofluorescence assays, and echocardiography. Our telemetry data revealed significantly elevated BP during the daytime (inactive period) in both CD36 global KO and renal proximal tubule specific KO mice compared to their control counterparts. Furthermore, levels of platelet CD36 negatively correlated with the severity of nocturnal hypertension in humans. Mechanistically, CD36 modulates BP rhythms through the AMPK/HDAC5/PER1 pathway: its deficiency activates phosphorylated AMPK, leading to the dissociation of the HDAC5-PER1 complex, enhancing PER1 nuclear accumulation, and desynchronizing the oscillations of intrarenal reninangiotensin-aldosterone system (RAAS) genes and clock-controlled genes (CCGs), ultimately disrupting BP rhythm. Our findings highlight CD36 as a critical integrator that links renal clocks to BP homeostasis, establishing it as a potential predictor and therapeutic target for nocturnal hypertension.

overall_design: RNA-Seq profiling of the renal cortical tissue samples collected from CD36f/f mice and Kidney proximal tubules specific CD36 knockout mice at ZT0, ZT4, ZT8, ZT12, ZT16 and ZT20.

first: Yang

last: Zhang

first: Shuning

last: Fu

first: Miao

first: Xia

last: Li

first: Zhenyu

last: Wang

first: Mingyang

first: Danyang

first: Siqi

last: Luo

first: Li

last: Wei

first: Shuyao

first: Lihong

first: Yaxi

first: Xiong Z

last: Ruan


title: Bulk RNAseq analysis of wildtype and Pim1-/- macrophages

city: Wauwatosa

first: Yiliang

address: 8727 W Watertown Plank

institute: Versiti

summary: PIM1 is a serine/threonine kinase that modulates immune responses and cellular metabolism. To examine the function of PIM1 in macrophage gene expression, peritoneal macrophages were isolated from wild-type and Pim1-/- mice. They were treated with 20 μg/mL oxidized low-density lipoprotein for 8 hours. Total RNA was extracted and analyzed using bulk RNA sequencing to compare gene expression profiles and identify differentially regulated pathways between wild-type and Pim1-/-  macrophages.

overall_design: For RNA library preparation, the Illumina TruSeq Stranded mRNA kit (single indexed) was utilized, and sequencing was carried out on the Illumina HiSeq 2500

first: Mirza Ahmar

last: Beg

first: Quoc Quang

last: Luu

first: Vaya

first: Yaxin

first: Gang

last: Xin

first: Weiguo

last: Cui

first: Roy

middle: L

last: Silverstein


title: Human iPSC-Based Alveolus-on-Chip Reveals Immunometabolic Regulation of Influenza A Virus Infection by Butyrate

city: Jena

first: Marc Thilo

last: Figge

state: Thuringen

address: Adolf-Reichwein-Straße 23

department: Applied System Biology

country: Germany

institute: HKI-Leibniz

summary: Host–microbiota interactions critically shape susceptibility and outcome of viral respiratory infections such as influenza A virus (IAV). The short-chain fatty acid butyrate is a key microbial metabolite with established immunomodulatory properties, yet its pleiotropic effects on viral pathogenesis and immune–metabolic balance remain incompletely understood. Physiologically relevant models that recapitulate the complexity of the alveolar niche remain limited. However, induced pluripotent stem cells (iPSC)-derived cell cultures offer a unique opportunity to investigate these interactions within a structured human microenvironment and to extend them toward patient-specific applications. We developed a multicellular alveolus-on-chip platform derived from isogenic human iPSCs, integrating alveolar type II epithelial cells, endothelial cells, and macrophages under an air–liquid interface and physiological flow. Influenza A virus (IAV) infection was modelled in this system to test the influence of the short-chain fatty acid butyrate on viral replication. Single-cell RNA sequencing and cytokine profiling were used to map transcriptional dynamics and immune–metabolic responses related to viral infection and butyrate treatment. The alveolus-on-chip recapitulated key features of the human distal lung, including epithelial–macrophage crosstalk, barrier integrity, and IAV susceptibility. Macrophage plasticity and epithelial remodeling were central determinants of infection outcome. Butyrate treatment constrained host biosynthetic and metabolic programs exploited by IAV, including ribosome biogenesis, RNA processing, and mitochondrial function, while preserving type I/II interferon signaling. Cytokine profiling further demonstrated reduced IL-1β and TNF-α, elevated IL-10, and increased GM-CSF, suggesting a shift toward regulatory and tissue-supportive immunity. This study establishes an isogenic iPSC-derived alveolus-on-chip as a human-relevant platform to dissect immunometabolic regulation during viral infection. The model reveals a dual role of butyrate in dampening inflammation and metabolic activation while maintaining antiviral defense. Beyond influenza, the approach may serve as a scalable framework for patient-specific modeling of respiratory infections and for assessing nutritional or metabolite-based interventions.

overall_design: iPSC-derived alveolus-on-chip cultures from donor line BU3 were pre-treated with butyrate, infected with influenza A virus (IAV), and harvested for single-cell RNA-seq analysis.

first: Hristina

last: Koceva

first: Yann

last: Bachelot

first: Thilo

first: Maria-Joao

last: Amorim

first: Alexander

last: Mosig


title: LINEMAP: Quantitative temporal reconstruction of single-cell lineage topology and division history from evolving CRISPR barcodes

city: Houston

first: Zheng

last: Yin

state: TX

address: 6565 Fannin St, MC: F6-300

department: Systems Medicine and Bioengineering

institute: Houston Methodist Cancer Center

summary: This study generated CRISPR barcode sequencing data from a PyMT-Cas9 mammary tumor cell line engineered with integrated homing guide RNA (hgRNA) lineage barcodes. Cells were collected at day 5 and day 14 following doxycycline-induced Cas9 activation to characterize barcode mutation accumulation and lineage evolution. These data were used to evaluate LINEMAP, a computational framework for quantitative reconstruction of lineage topology and cell division history from evolving CRISPR barcodes.

overall_design: A PyMT-Cas9 mammary tumor cell line carrying integrated A21 and B25 hgRNA barcodes was established. Barcode editing was induced by doxycycline-mediated Cas9 activation. Cells were harvested at day 5 and day 14 after induction. Genomic DNA was extracted, barcode loci were PCR amplified, and amplicons were sequenced to characterize barcode mutation dynamics and lineage evolution.

first: Lin

first: Wenjuan

last: Dong

first: Dingcheng

last: Gao

first: Stephen

middle: T

last: Wong


title: Genome-wide characterization of extrachromosomal circular DNA and its functional role in colon cancer carcinogenesis and progression [RNA-seq]

city: Suzhou

first: Wenbo

last: Jia

state: Jiangsu Province

address: No.199 Ren'ai Road

institute: Soochow University

summary: Extrachromosomal circular DNAs (eccDNAs) are defined as distinct genomic entities of circular and mobile DNA molecules, but their molecular functions in and impact on breast cancer (BC) are rarely known. This study used Circle-seq to analyze eccDNAs from 19 BC tissues and 17 adjacent normal tissues. We found that eccDNAs are present on all chromosomes and enriched in seven eccDNA hotspot genes (HSGs) associated with the BC pathway. Several eccDNAs harboring entire genes (eccGenes) and eccDNAs harboring miRNAs (eccMIRs) were identified and linked to cancer-relevant pathways. Synthetic eccMIR6748, eccMIR6508, and eccMIR3142 elevated miRNA expression in MCF-7 cells, with eccMIR6748 promoting BC cell migration and invasion by upregulating miR-6748, which suppresses tumor suppressor candidate factor 5 (TUSC5) at the post-transcriptional level. eccMIR6748 also influences BC progression via the p38 mitogenactivated protein kinase (MAPK) signaling pathway. These findings suggest that eccDNAs, which contain functional genomic segments, play a role in BC initiation and progression, offering a dynamic source of genomic plasticity and potential as biomarkers and therapeutic targets.

overall_design:
This study includes three complementary sequencing assays on human samples to investigate circular DNA, microRNA, and mRNA expression profiles.A total of 6 samples were analyzed, comprising two experimental groups with 3 biological replicates per group.
A: Circle seq (circular DNA). Paired end 150 bp sequencing on Illumina NovaSeq 6000. Linear DNA was removed by exonuclease treatment, followed by rolling circle amplification. Clean reads were aligned to the reference genome (HG38) using BWA, and circular DNAs were identified with circle map. Differential expression was analyzed with edgeR.
B: miRNA seq. Single end sequencing. Small RNA libraries were constructed and sequenced. Reads were trimmed with cutadapt, aligned to miRBase pre miRNAs (v22) plus newly predicted pre miRNAs using Novoalign. miRNA expression was normalized by TPM. Novel miRNAs were predicted with miRDeep2. Differential expression was calculated using edgeR.
C: mRNA seq. Paired end 150 bp sequencing on Illumina NovaSeq 6000. mRNA was enriched via poly A selection, strand specific libraries were prepared. Raw reads were preprocessed with fastp, aligned to HG38 using HISAT2, and gene counts were obtained with featureCounts. Differential expression was analyzed with edgeR).
All differential analyses were followed by GO and KEGG pathway enrichment. Data visualization was performed with IGV, cluster heatmaps, scatter plots, and volcano plots.

first: Ji

last: Wang

first: Kehan


title: Transcriptomic profiling of PRMT2 wild-type and PRMT2 knockout KG-1a acute myeloid leukemia cells

city: Dijon

first: Laurent

last: DELVA

address: 7 boulevard Jeanne d’Arc

department: Inserm U1231 (CTM)

country: France

institute: Université de Bourgogne

summary: PRMT2 is implicated in adhesion-dependent cytoskeletal signaling and bone marrow engraftment in acute myeloid leukemia (AML). To define the transcriptional consequences of PRMT2 loss, we performed RNA sequencing of KG-1a AML cells comparing PRMT2 wild-type cells with independent CRISPR/Cas9-generated PRMT2 knockout clones. Differential expression analysis identified a common set of genes downregulated upon PRMT2 deletion. Gene ontology and gene set enrichment analyses showed that PRMT2 loss reduced transcriptional programs associated with leukocyte activation, cell adhesion, migration, and leukocyte cell-cell adhesion. These data support a role for PRMT2 in maintaining adhesion-associated transcriptional programs in AML cells and provide a transcriptomic resource linking PRMT2-dependent signaling to leukemic cell interaction with the bone marrow microenvironment.

overall_design: KG-1a human acute myeloid leukemia cells were used to compare PRMT2 wild-type cells with CRISPR/Cas9-generated PRMT2 knockout cells. Two independent PRMT2 knockout clones were generated using PRMT2-targeting crRNAs and validated at the DNA, RNA, and protein levels. Total RNA was extracted from PRMT2 wild-type and PRMT2 knockout KG-1a cells using TRIzol reagent. RNA-seq library preparation and sequencing were performed by GENEWIZ/Azenta Life Sciences using paired-end sequencing. Reads were aligned to the human reference genome GRCh38 using STAR in two-pass mode, and gene-level counts were generated. Differential gene expression analysis was performed in R using DESeq2 after filtering low-count genes. Log2 fold changes were estimated using apeglm shrinkage. Differentially expressed genes were defined using |log2 fold change| ≥ 1 and false discovery rate < 0.05. Gene set enrichment analysis was performed with clusterProfiler using Gene Ontology Biological Process gene sets, and over-representation analysis was performed on genes commonly deregulated across independent PRMT2 knockout clones.

first: Denis

last: Masnikov

first: Romain

last: Aucagne

last: Delva

first: Cyril

last: Fournier


title: Severe hyperchylomicronemia sensitizes the heart to pathological remodeling: evidence from GPIHBP1 deficient mice

city: Dalian

first: rui

last: fan

address: No. 193, Lianhe Road, Dalian City

institute: Dalian Medical University

summary: This dataset contains bulk RNA sequencing data generated from cardiac tissues of wild-type (WT) and Gpihbp1 knockout (Gpihbp1−/−) mice. GPIHBP1 deficiency disrupts intravascular triglyceride-rich lipoprotein hydrolysis and results in severe hyperchylomicronemia. To investigate the molecular changes associated with chronic triglyceride-rich lipoprotein accumulation in the heart, total RNA was isolated from cardiac tissues and subjected to high-throughput transcriptome sequencing. These data provide a resource for characterizing gene expression alterations and biological pathways associated with cardiac metabolic remodeling, mitochondrial dysfunction, and heart failure susceptibility in the setting of severe hypertriglyceridemia.

overall_design: To investigate the effects of Gpihbp1 deficiency on the hearts of mice, the hearts of wild-type (WT) mice and Gpihbp1 knockout mice were dissected, and RNA was extracted for a large-scale RNA sequencing study (n = 4 in each group).

first: Rui

last: Fan

first: Jingyi

last: Li

first: Gefan

last: Wan

first: Jiawei

last: Liao

first: Wei

last: Huang


title: Comparative transcriptomic analysis of lettuce under cadmium and selenium nanoparticle treatments

city: Chengdu

first: xiumei

last: luo

address: Shuangliu

department: Institute of Urban Agriculture

institute: Chinese Academy of Agricultural Sciences

summary: This study investigated the role of biosynthesized selenium nanoparticles (SeNPs) derived from Chlorella sorokiniana SZ2-1 in alleviating cadmium (Cd) toxicity in Lettuce (Lactuca sativa L. cv.‘Red oak-leaf’)  under hydroponic conditions.The research focused on evaluating the effects of SeNPs on Cd uptake, translocation, subcellular distribution, selenium speciation, and stress-responsive transcriptional regulation. Lettuce seedlings were exposed to Cd alone or in combination with different concentrations of SeNPs. Physiological, biochemical, ionomic, transcriptomic, and metabolomic analyses were conducted to elucidate the detoxification mechanisms induced by SeNPs.

overall_design: Lettuce (Lactuca sativa L. cv. ‘Red oak-leaf’)  seedlings were grown hydroponically in Hoagland nutrient solution under controlled conditions. After preliminary Cd toxicity screening, 10 mg/L Cd was selected for further experiments. Seedlings were treated with Cd alone or combined with different concentrations of biosynthesized SeNPs (1, 3, and 5 mg/L). Treatments included control (CK), Cd, SeNPs alone, and Cd + SeNPs, each with three biological replicates. Root and shoot samples were collected for analyses of Cd accumulation, selenium speciation, transcriptomics, metabolomics, and physiological responses associated with Cd detoxification.

first: Sawera

last: Akram


title: The scaffolding protein AKAP79/150 shapes innate immune responses to allergen

city: Durham

first: Hamed

last: Bostan

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Allergic airway inflammation involves innate immune signaling pathways that regulate inflammatory gene expression and cytokine responses. In this study, we performed RNA-seq analysis of mouse bone marrow-derived macrophages following house dust mite (HDM) allergen exposure to examine transcriptional changes associated with allergen-induced immune activation. These data provide gene expression profiles that may help define inflammatory and immune pathways regulated during HDM-driven innate immune responses.

overall_design: Bone marrow-derived macrophages isolated from  C57BL/6 mice, were treated with house dust mite (HDM) allergen or vehicle for 1 h, followed by RNA-seq analysis to identify HDM-induced transcriptional changes.

first: Suneet

last: Kaur

first: Anant

middle: B

last: Parekh


title: Functional Landscape of Zebrafish Gonadotropins and Receptors: A Comprehensive Genetic Analysis

city: Macau

first: Chu

last: ZENG

address: Avenida da Universidade Taipa

country: Macau

institute: University of Macau

summary: In vertebrates, reproduction is primarily controlled by two master hormones, or gonadotropins, from the pituitary: follicle-stimulating hormone (FSH) and luteinizing hormone (LH), which act through their cognate receptors, FSHR and LHCGR, in gonads. Like other vertebrates, zebrafish also has two gonadotropins and respective receptors. However, while zebrafish FSH activates Fshr specifically, its LH can activate both Fshr and Lhcgr, suggesting three signaling pathways – the canonical FSH-Fshr and LH-Lhcgr pathways, and a non-canonical LH-Fshr pathway. To dissect functional roles of these pathways, we generated a series of zebrafish mutants lacking one, two, three, or all four genes encoding the two ligands and their receptors: fshb, lhb, fshr, and lhcgr. Single mutants confirmed the essential roles of FSH and LH in zebrafish reproduction. Double mutants demonstrated the functionality of all three pathways, especially the non-canonical LH-Fshr pathway, and highlighted the importance of Fshr in mediating both FSH and LH actions. Transcriptome analysis of double mutant follicles (infertile lhb-/-;lhcgr-/- with FSH-Fshr pathway and fertile fshb-/-;lhcgr-/- with LH-Fshr pathway) revealed potential molecular mechanisms underlying LH stimulation of oocyte maturation and ovulation via Fshr. Triple mutants revealed spontaneous, ligand-independent activities of Fshr and Lhcgr, in supporting spermatogenesis. The quadruple mutant (fshb-/-;lhb-/-;fshr-/-;lhcgr-/-) displayed an all-male phenotype with underdeveloped, infertile gonads primarily containing spermatogonia, suggesting a critical role for gonadotropins in gonadal differentiation and development. This comprehensive genetic study provides insights into functional importance of gonadotropins in zebrafish reproduction and their signaling mechanisms.

overall_design: RNA-seq profiling of full growth follicles in control (fshb+/-;lhb+/-;fshr+/-;lhcgr+/-), fshb+/-;lhb-/-;fshr+/-;lhcgr-/- mutant, and fshb-/-;lhb+/-;fshr+/-;lhcgr-/- mutant zebrafish

last: Ge

last: Zeng


title: An intracellular amino acid scarcity sensor tunes protein hunger

first: Vincent

last: Croset

address: Department of Biosciences, South Road

country: United Kingdom

institute: Durham University

summary: Protein is a dietary macronutrient with a strong homeostatic drive, which plays a major contribution in determining total energy intake. Most animals, including Drosophila, display compensatory preference for amino acid-rich food following dietary protein scarcity. In the CNS, peptidergic cells play an important role in adaptive feeding behaviour, by mediating the satiating effects of protein consumption. We demonstrate that protein appetite and compensatory feeding following amino acid deprivation are also under peptidergic control. Using single-nucleus RNA-sequencing, we identified gene expression changes in peptidergic neurons from amino acid-deprived flies and sated controls. One of the strongly regulated genes is Lsp2, which encodes an amino acid storage protein essential for larval development and pupation. We demonstrate that in the adult brain, specific peptidergic neurons use Lsp2 levels as a gauge to scale protein intake.

overall_design: Peptidergic nuclei in the Drosophila melanogaster brain were labelled by expressing UAS-unc84-GFP with a dimm-GAL4 driver. Following three days of complete nutrition or a three day amino acid deprivation period, heads of female Drosophila were flash frozen. Nuclei were dissociated as described in McLaughlin et al (2010), and peptidergic nuelci isolated by flourescent activated cell sorting (FACS) before single-cell sequencing analysis.

first: Sophie

last: Waldron


title: Pancreatic gene expression in offspring exposed to maternal threonine deficiency

city: Tokyo

first: Xuguang

address: 1-1-1 Yayoi, Bunkyo-ku

institute: Tokyo University

summary:
This study analyzed pancreatic gene expression in mouse offspring from control and maternal threonine-deficient groups using the Affymetrix Mouse Genome 430 2.0 Array.
MAS5 signal intensities and detection calls were generated from Affymetrix CEL files and are provided as a matrix table for control and threonine-deficient samples.

overall_design: Two pooled pancreatic RNA samples were analyzed: one control offspring sample and one offspring sample exposed to maternal threonine deficiency. Each sample was hybridized to an Affymetrix Mouse Genome 430 2.0 Array.

first: Huijuan

last: Jia


title: First primary adult sheep neural screen identifies therapeutic candidates for spinal cord injury

city: Bryan

first: Manshi

last: Patel

state: Texas

address: 8447 John Sharp Pkwy

department: Neuroscience & Experimental Sciences

institute: Texas A&M University Health Science Center

summary: High content screening efforts for age-associated neurological disorders previously relied on embryonic, early neonatal, or induced pluripotent stem cell-derived neural cells. This dichotomy in age between cells in drug screens and the target adult population in the clinic likely impedes translational successes. Aging reduces regenerative potential, impeding glial process extension and neuronal neurite regeneration. Pharmacologically enhancing the extension of processes in adult glia and neurite outgrowth in adult neurons holds therapeutic value. However, no previous assay allowed for high content screening in primary adult neural cells. We previously developed a screening platform that uses primary adult neurons from rodents. Though, the limited yield in neural cells prevented true high content screening. We recently adapted this brain tissue processing method to larger mammals. It led to the development of a high content screen using primary adult sheep neural cells and the first recorded case of primary adult sheep neurons being cultured, as demonstrated by immunocytochemistry, western blotting, and single-nucleus RNA sequencing. We conducted a pilot screen of 2281 unique compounds from preselected libraries, identifying numerous compounds that have shown efficacy in the clinic for various neurological indications, validating our protocol. We identified for the first time several new molecules promoting processes/neurite growth in adult cells, including GSK180736A, PHA665752, and StemRegenin1. All three compounds were subsequently tested in a preclinical spinal cord injury model to identify neurologically beneficial hits. Altogether, we provide here a novel drug screening tool that may help identify new leads for age-associated neurological disorders.

overall_design: Single‑nucleus RNA‑sequencing was performed on cortical tissue from an adult female sheep to assess how tissue processing affects neural cell‑type composition. Cortical tissue was divided into two conditions: a pre‑processed group in which nuclei were isolated directly from dissected cortex, and a post‑processed group in which tissue underwent additional debris and red blood cell removal prior to nuclei isolation. Approximately 5,000 nuclei per condition were captured and sequenced using a commercial droplet‑based 3′ snRNA‑seq platform, and data were processed with the DRAGEN pipeline followed by Seurat for quality control, normalization, dimensionality reduction, clustering, and cell‑type annotation. Canonical marker genes were used to identify neurons, oligodendrocytes, microglia, and astrocytes, and the relative abundance and marker expression of these populations were compared between pre‑ and post‑processed samples.

first: Arthur

last: Sefiani

first: Olivia

last: Samaie

first: Adelina

first: Cedric

middle: G

last: Geoffroy


title: Fatty acid ethanolamides-producing gut bacteria alleviate gastrointestinal symptoms in diarrhea-predominant irritable bowel syndrome with coexisting insulin resistance

city: Hong Kong

first: Shujun

last: Xu

address: 7 Baptist University Road

department: Chinese Medicine

country: Hong Kong

institute: Hong Kong Baptist University

summary: We used fresh ileum tissue samples and performed single-cell RNA sequencing with the DNBelab C4 platform to investigate the mechanisms by which OEA treatment affects IBS-D-related symptoms in TNBS-treated mice. This approach enabled us to analyze cell-type-specific transcriptomic changes and to identify key cellular responses following OEA intervention in the context of TNBS-induced IBS-D symptoms

overall_design: After 19 days of OEA treatment, fresh ileum samples from control, TNBS-treated, and OEA-treated mice were collected, preserved in MACS® Tissue Storage Solution, and analyzed by single-cell RNA sequencing to assess cellular and transcriptomic changes relevant to IBS-D

first: Lixiang

last: Zhai


title: Transcriptional Response of inorganic sulphate replete and deplete condition in WT H37Rv and pe22/ppe36 KO strains.

city: seattle

first: Ashutosh

last: Tripathi

state: Washington

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children's Research Institute

summary: To investigate the outermemberane SO4 transporters proteins in WT H37Rv and monitor the expression of other SO4 responsive genes in WT and pe22/ppe36 KO strains.

overall_design: Wild-type (WT) Mycobacterium tuberculosis H37Rv was cultured in Middlebrook 7H9 medium supplemented with 10% OADC, 0.5% glycerol, 0.05% tyloxapol, and 100 µM sodium propionate until an OD₆₀₀ of 0.8 was reached. Cells were then harvested by centrifugation, washed three times with phosphate-buffered saline (PBS), and resuspended in sulfate-free HdB medium. Cultures were incubated for an additional 48 h in the presence or absence of 100 µM sodium sulfate.Total RNA were isolated. For sulfate repletion experiments, WT and pe22/ppe36 knockout (KO) strains were grown in 7H9 medium supplemented with 10% OADC, 0.5% glycerol, 0.05% tyloxapol, and 100 µM sodium propionate to an OD₆₀₀ of 0.8. Cells were harvested, washed three times with PBS, and resuspended in modified sulfate-free Sauton’s medium for 48 h to induce sulfate starvation. Following starvation, sodium sulfate was added to a final concentration of 10 mM, and cultures were incubated for an additional 24 h. Bacterial pellets were collected at the indicated time points, total RNA was isolated, and gene expression was quantified by RNA sequencing.

first: Tripathi

last: Ashutosh

first: Vishant

last: Boradia

first: Christoph

last: Grundner


title: NAT10 inhibition alleviates renal tubular epithelial cell senescence by impeding ac4C acetylation of PAPP-A mRNA in diabetic nephropathy

city: Zhengzhou

first: Mingyang

last: Hu

state: Henan

address: jinshui

institute: Department of Nephrology, First Affiliated Hospital of Zhengzhou University

summary: Cellular senescence plays a critical role in diabetic nephropathy (DN). Understanding the mechanisms underlying the senescence response is therefore essential for developing effective therapies for DN. In this study, we provide evidence that NAT10 expression was markedly elevated in the kidney tissues of patient with DN and was associated with adverse clinical outcomes. NAT10 directly bound to PAPP-A, induced ac4C acetylation modification of the PAPP-A transcript, and enhanced its stability, thereby promoting PAPP-A upregulation. Moreover, NAT10-mediated ac4C acetylation accelerated renal tubular epithelial cell senescence in DN through the PAPP-A/p53 pathway. Conditional knockout (cKO) of NAT10 attenuates renal tubular senescence in streptozotocin (STZ)-induced type 1 diabetes mellitus (T1DM) mouse models. Renal tubular-specific knockdown of NAT10 via targeted adeno-associated virus ameliorates renal tubular epithelial cell senescence in db/db mouse models of type 2 diabetes mellitus (T2DM). Pharmacological inhibition of NAT10 with Remodelin protects against renal tubular epithelial cell senescence both in vivo and in vitro. In conclusions, NAT10-mediated ac4C acetylation contributes to renal tubular epithelial cell senescence in DN and that NAT10-regulated PAPP-A could be a promising and feasible therapeutic target in DN.

overall_design: To elucidate how NAT10-mediated ac4C modification contributes to renal tubular epithelial cell senescence in DN, we performed ac4C-specific RNA immunoprecipitation followed by high-throughput sequencing (acRIP-seq) in a mouse model of DN. Integrated analysis of acRIP-seq and RNA-seq data from db/m and db/db mice was then conducted.

first: Sijie

last: Zhou


title: Microbiome-Derived Metabolites Shape CD4⁺ T-Cell Differentiation and Immune Aging in Chronic HIV-1 Infection [RNA-Seq]

city: Atlanta

first: Souheil

last: Younes

state: Georgia

address: 1750 Haygood Dr NE

department: Pathology and Laboratory Medicine

institute: Emory University

summary: The role of aromatic gut-derived bacterial metabolites (GDBMs) in shaping immune cell metabolism and function remains poorly explored. Using ex vivo metabolomic profiling of paired plasma and CD4⁺ T-cells from people living with HIV-1 (PLWH), we identified a network of aromatic GDBMs whose cell-associated abundance, rather than systemic levels, was linked to broad alterations in CD4⁺ T-cell metabolic and functional states. Among these metabolites, p- cresol sulfate (PCS) emerged as a mechanistic prototype investigated in depth. Ex vivo flow cytometry and single-cell RNA sequencing of CD4⁺ T-cells stratified by cell-associated PCS levels revealed dose-dependent enrichment of transcriptional programs associated with impaired differentiation capacity, regulatory-like identity, and cellular senescence. Consistently, in vitro transcriptomic and proteomic analyses of PCS-exposed CD4⁺ T cells demonstrated induction of cell-cycle arrest, mitochondrial dysfunction, and senescence-associated programs, including upregulation of p16 and p21. Integration of these immunometabolic features with measurements of HIV-1 reservoir size in PLWH revealed that CD4⁺ T-cell states defined by cell-associated GDBMs track with intact proviral DNA levels in vivo. Together, these findings define a microbiome-derived axis that reshapes CD4⁺ T-cell metabolism and fate and promotes immune aging–associated states in PLWH. Our data suggest that cell-associated GDBMs may foster immunometabolic CD4⁺ T-cell states previously linked to long-term HIV-1 reservoir persistence in vivo.

overall_design: PBMCs from 5 healthy donors were labeled with CTV and stimulated with anti-CD3/CD28 in the presence of PCS (0, 10, 50, 100 uM). After 6 days, CD4⁺ T-cells were sorted into proliferating (CTV low) and non-proliferating (CTV high) populations for each condition, generating 8 samples per donor (4 conditions x 2 proliferation states), followed by bulk RNA sequencing.

first: Amanda

middle: C

last: Da Silva

first: Luke

last: Flantzer

first: Souheil-Antoine


title: In vivo genome-wide CRISPR screens in human T cells to enhance T cell therapy for solid tumors

city: San Francisco

first: Qi

last: Liu

state: California

address: HSW RM 901A, 513 Parnassus Avenue

institute: UCSF Health, San Francisco , California, US

summary: Large-scale CRISPR screening in human T cells holds significant promise for identifying genetic modifications that can enhance cellular immunotherapy. However, many genetic regulators of T cell performance in solid tumors may not be readily revealed in vitro. In vivo screening in tumor-bearing mice offers greater physiological relevance but has historically been limited by low intratumoral T cell recovery. Here, we developed a new model system that achieves substantially higher human T cell recovery from tumors, enabling genome-wide in vivo screens with relatively small numbers of mice. Tumor-infiltrating T cells in this model exhibit hallmarks of dysfunction compared to matched splenic T cells, creating an ideal context for screening for genetic modifiers of T cell activity in the tumor microenvironment. Using this platform, we performed two genome-wide CRISPR knockout screens to identify genes regulating T cell intratumoral abundance and effector function, as measured by IFN-γ production. The intratumoral abundance screen uncovered the P2RY8-Gα13 GPCR signaling axis as a negative regulator of human T cell infiltration into tumors. The effector function screen identified GNAS as a key regulator of T cell dysfunction in tumors. Its protein product, Gαs, acts as a convergent signaling node downstream of multiple GPCRs that sense different suppressive ligands. Targeted GNAS knockout rendered T cells resistant to multiple suppressive cues and significantly improved therapeutic performance across diverse solid tumor models in both CAR and TCR systems. Moreover, combinatorial knockout of P2RY8 and GNAS further enhanced overall tumor control, demonstrating that complementary screens with distinct in vivo readouts can nominate gene targets addressing orthogonal barriers, and that combining such edits can improve therapeutic potency. This flexible and scalable platform can be adapted to diverse tumor models and screening modalities, enabling systematic discovery of genetic strategies to equip T cell therapies for solid tumors.

overall_design: For bulk RNA sequencing of in vivo T cells, AAVS1 control and GNAS KO B7H3-BBz CAR T cells were isolated from preclinical MES-SA tumor models using cells derived from three independent human donors 14 days post infusion. For each donor and genotype, tumor-infiltrating CAR T cells were pooled from 2-3 mice to obtain sufficient material for RNA extraction. In total, 6 biological replicates per group were included for sequencing. For in vitro experiments, T cells were cultured in the presence or absence of GPCR agonists, as described in the “Human T cell isolation and culture” section, for 24 hours. Total RNA was extracted and submitted to Novogene for library preparation and sequencing. mRNA libraries were prepared using poly(A) enrichment and sequenced on a NovaSeq X Plus platform (PE150). Raw sequencing data were processed using standard bioinformatics pipelines. Clean reads were aligned to the human reference genome (GRCh38), and gene-level counts were generated for downstream analysis. Differential gene expression analysis was performed using DESeq2.

first: Julia

last: Carnevale


title: Microbiome-Derived Metabolites Shape CD4⁺ T-Cell Differentiation and Immune Aging in Chronic HIV-1 Infection [scRNA-seq]

overall_design: CD4⁺ T-cells from PLWH with high and low cell-associated PCS concentrations were analyzed ex vivo using scRNAseq

first: Shuya

last: Kyu

first: Ana

last: Santana

first: Aarthi

last: Talla


title: Excess muscle plasma membrane leak disrupts extracellular matrix content and shifts macrophage-mediated muscle repair [scRNA-Seq]

city: Chicago

first: GaHyun

last: Lee

address: 303 E Superior

institute: Northwestern University

summary: Plasma membrane repair is critical for tissue integrity, especially for elongated contractile muscle cells. Genetically-mediated defects in plasma membrane resealing produce persistent leak, leading to a disordered extracellular matrix.  Loss of the membrane repair protein dysferlin slows sarcolemmal resealing and promotes excess leak.  Annexin A6 is also implicated in sarcolemmal repair, forming repair caps at the site of membrane disruption.  On its own, deletion of the gene for annexin A6, Anxa6, had little effect on muscle health.  In contrast, combined loss of dysferlin and annexin A6 (DysfA6) generated muscle fibers with profoundly defective membrane leak.  Strikingly, Anxa6 deletion in the context of loss of dystrophin (mdxA6) did not exacerbate muscle defects.  The persistent membrane leak in DysfA6 muscle resulted in marked macrophage infiltration with disordered macrophage polarization.  Injured muscle fibers were targets of macrophage efferocytosis.  Loss of Anxa6 was associated with increased expression of annexins A1 and A2, both of which were heavily deposited into the extracellular matrix.  In vitro, macrophages exposed to annexins A1 and A2 expressed increased Csf1, consistent with a model where excess leak results in annexins A1 and A2 in the extracellular matrix, where this protein composition elicits macrophage proliferation and efferocytosis.

overall_design: Quadriceps, abdominal and paraspinal muscles of 4-month-old female Dysf and DysfA6 mice were pooled by mouse (n=2 mouse per genotype) and digested to isolate mononuclear cells, which were sequenced to analyze for scRNA-seq

first: Lauren

last: Vaught

first: Dorothy

last: DeBiasse

first: Alexis

last: Demonbreun

first: Elizabeth

last: McNally


title: Excess muscle plasma membrane leak disrupts extracellular matrix content and shifts macrophage-mediated muscle repair

overall_design: RNA-seq profiling of myofibers from quadriceps muscle of 6-month-old Dysf and DysfA6 females, enriched by removing mononuclear cells through size selection.


title: The IKKα-regulated microRNA miR-9-5p mediates lung cancer growth and invasiveness via CDH1/Wnt/β-catenin signalling

city: Ioannina

first: Evangelos

last: Kolettas

address: School of Medicine, University of Ioannina, University Campus, 45110 ioannina, Greece

department: School of Medicine

country: Greece

institute: University of Ioannina

summary: IKKα is a serine/threonine kinase that acts as a tumour suppressor in non-small cell lung cancer (NSCLC) in an NF-κΒ-independent manner, however, little is known about its downstream signalling pathways. To interrogate the IKKα signalling network in NSCLC, we investigated the impact of IKKα silencing on the miRNA expression profile of NSCLC cells. Nanostring miRNome analysis identified miR-9-5p, a known oncomir, as the top upregulated miRNA upon IKKα depletion. We show that overexpression of miR-9-5p in human lung cancer cells increases cell migration and invasion and promotes epithelial-to-mesenchymal cell transition (EMT) through loss of E-cadherin and activation of the Akt1/β-catenin pathway. In vivo tumour xenograft models show that overexpression of miR-9-5p promotes tumour growth, and widespread transcriptomic reprogramming, altering the expression of genes related to EMT, apoptosis and NF-κB signalling. Overall, we show that miR-9-5p acts as an oncogenic effector upon IKKα loss, promoting tumour progression through EMT and Akt-1/GSK-3β/β-catenin pathway activation, leading to increased invasiveness and tumour growth.

overall_design: RNA sequencing of A549 and H1299 tumour xenografts, with miR-9-5p overexpression (MIR-9) and control samples (TWI-H1)

first: Simoni

last: Besta

first: Eugenia

last: Roupakia

first: Zoi

last: Kanaki

first: Giannis

last: Vatsellas

first: Mark

last: Samuels

first: Spyros

last: Foutadakis

first: Maria

last: Tokamani

first: Alessandro

last: Barbon

first: Raphael

last: Sandaltzopoulos

first: Dimitris

last: Kanellis

first: Jiri

last: Bartek

last: Hatziapostolou

first: Christos

last: Polytarchou

last: Thanos

first: Apostolis

last: Klinakis


title: Processing of Reversed Replication Forks is Required for the Resolution of Replication-Transcription Conflicts [WGS]

city: Nashville

first: Juan

last: Carvajal Garcia

state: TN

address: 2215 Garland Avenue

institute: Vanderbilt University

summary: DNA replication and transcription occur simultaneously on the same template, leading to conflicts between the two machineries. Conflicts stall replication forks, lead to genome instability, mutagenesis, and the formation of deleterious R-loop structures. Despite many studies across various organisms, how the replication fork structure is impacted by these encounters remains unclear. Here, we performed an unbiased genetic screen using a transposon library to identify factors essential for surviving deadly conflicts in Bacillus subtilis. Our screen identified three hits: RNase HIII, AddA and AddB. Our prior work had shown that RNase HIII, which processes R-loops, is essential for surviving conflicts. However, AddA and AddB, which function together as a complex to process blunt DNA ends, have not been previously identified as essential conflict resolution factors. Through follow-up genetic and biochemical analyses, we found that the helicase activity but not the nuclease activity of this complex is required for conflict resolution. Based on the fundamental properties of DNA, our work collectively indicates that upon conflicts, the nascent strands form a reversed fork structure, which is then unwound by AddAB, leading to re-annealing to the parental strands. This process re-establishes an intact replication fork that can be used to restart replication after conflicts.

overall_design: Eihter WT or addAB deficient cells were grown in LB to an OD of 0.5. All cells have the luxABCDE operon in the head-on orientation that is either not induced (minus IPTG) or induced (plus IPTG)

last: Carvajal-Garcia

first: Houra

last: Merrikh


title: The transcriptional cofactor Tle3 programs resident memory CD8+T cells differentiation [RNA-seq]

first: Qiang

last: Shan

address: No. 100, Chongwen Road

institute: Suzhou Institute of Systems Medicine

summary: Tissue-resident CD8+ T cells (CD8+ TRM) possess the ability to efficiently eliminate invading pathogens locally and are an essential component of the immune barrier. The upregulation of tissue residency-related genes and the downregulation of tissue egress-related genes are critical for the differentiation and long-term residency of CD8+ TRM. However, the coordinated regulatory mechanisms of these two transcriptional programs remain unclear. Tle3 is a transcriptional cofactor that promotes and maintains the differentiation of circulating memory CD8+ T cell subsets by cooperating with key transcription factors. However, its role in the differentiation of CD8+ TRM remains unknown. Our preliminary studies indicate that Tle3 promotes the differentiation of CD8+ TRM subsets in multiple tissues, including the lung, and serves as a key regulator of TRM differentiation. Transcriptomic analysis suggests that Tle3 regulates CD8+ TRM differentiation by promoting the expression of TRM-associated genes while suppressing tissue egress-related genes, highlighting its crucial role in establishing the transcriptional program of CD8+ TRM and balancing the expression of residency and egress-related genes. Nevertheless, the key downstream molecules regulated by Tle3 and how it coordinates different transcriptional networks remain unclear.

overall_design: Naïve P14 CD8+ T cells were isolated from the LNs from WT, Tle3–/–, Klf2–/–or Tle3–/–Klf2–/–, transgenic mice, and were adoptively transferred into B6.SJL recipients at 2×105 cells/mouse. The recipients were intranasal (i.n.) infection with 1×105 PFU of Influenza A virus A/WSN/33 (H1N1) on the following day. RNA-seq of the lung TRM of mice with WSN-GP33 intranasal infection in day14.

first: Xiaoyu

last: Lin


title: Processing of Reversed Replication Forks is Required for the Resolution of Replication-Transcription Conflicts [Tn-seq]

overall_design: A transposon insertion library, in which all cells have the luxABCDE operon in the head-on orientation, that is either not induced (minus IPTG) or induced (plus IPTG) was grown in LB to and OD of 0.5 and sequenced


title: The transcriptional cofactor Tle3 programs resident memory CD8+T cells differentiation [scRNA-seq]

overall_design: Naïve P14 CD8+ T cells were isolated from the LNs from WT or Tle3–/–transgenic mice, and were adoptively transferred into B6.SJL recipients at 2×105 cells/mouse. The recipients were intranasal (i.n.) infection with 1×105 PFU of Influenza A virus A/WSN/33 (H1N1) on the following day. ScRNA-seq of the lung TRM of mice with WSN-GP33 intranasal infection in day14.


title: The transcriptional cofactor Tle3 programs resident memory CD8+T cells differentiation [ChIP-seq]

overall_design: we systematically dissect the cooperative and distinct roles of Tle3 in shaping the transcriptional and epigenetic landscape of antiviral CD8⁺ T cells. Using CUT&RUN across single knockout models, we reveal that Tle3 coordinate memory differentiation through both chromatin remodeling–dependent mechanisms.


title: Comprehensive Cytogenetic and Genomic Profiling of the Murine AML12 (Alpha Mouse Liver 12) Hepatocyte Cell Line

city: Aachen

first: Ralf

last: Weiskirchen

address: Pauwelsstr. 30

department: IFMPEGKC

institute: RWTH University Hospital Aachen

summary: In our study, we aimed to provide a comprehensive cytogenetic and genomic profiling of the murine AML12 hepatocyte cell line. We established an integrated reference map that combines cytogenetics, short tandem repeat (STR) profiling, and transcriptomic analysis through RNA sequencing. Our findings reveal that AML12 maintains hepatocyte lineage identity while exhibiting partial de-differentiation and a complex karyotypic landscape characterized by a near-tetraploid chromosome set with recurrent structural rearrangements. This study serves as a valuable resource for the scientific community, enhancing the understanding of AML12's genetic characteristics and its implications for future research in liver biology and related fields.

overall_design: RNA-seq profiling of AML12 cells cultured under standard conditions.

first: Chao-Chung

last: Kuo


title: The transcriptional cofactor Tle3 programs resident memory CD8+T cells differentiation [ATAC-seq]

city: Suzhou

overall_design: Naïve P14 CD8+ T cells were isolated from the LNs from WT or Tle3–/–transgenic mice, and were adoptively transferred into B6.SJL recipients at 2×105 cells/mouse. The recipients were intranasal (i.n.) infection with 1×105 PFU of Influenza A virus A/WSN/33 (H1N1) on the following day. -seq of the lung TRM of mice with WSN-GP33 intranasal infection in day14.


title: Global Transcriptome analyses in Human Trophoblast Stem Cells (human TSCs) derived from placental tissues from patients suffering from idopathic recurrent pregnancy losses (RPLS).

city: Kansas city

first: Soumen

last: Paul

state: Kansas

address: Rainbow Blvd

department: Pathology

institute: University of Kansas Medical center

summary: We established RPL-Patient specific TSC lines from placental tissues collected after  patients undergoing procedures at the REI clinic at the University of Kansas Medical Center. Two groups of RPL-TSC lines were established. A control RPL-TSC group, which were established from placental tissues without any apparent defect in placental ultratructure and trophoblast layers and also maintained high expressions of protein arginine methyl transferase 1 (PRMT1) in villous cytotrophoblast cells (CTBs). The second group is the experimental RPL-TSC group, which were established from RPL-Placentae with defects in placental villi structure and trophoblast layers and showed strong repression of PRMT1 expression in villous CTBs. The established  RPL-TSCs were tested for PRMT1 expression. TSCs showed similar expression patterns of PRMT1 with respect to CTBs, from which they were established. Thus, RPL-TSC lines with high expression of PRMT1 are called PRMT1_high RPL-TSCs and The experimental RPL TSCs are called PRMT1_low RPL-TSCs. Four RPL-TSC lines from each group were used for global RNA-sequencing to identify global gene expression patterns.

overall_design: Total RNA from the whole placental villi was isolated using RNeasy Mini Kit (#74104) from Qiagen per the manufacturer’s protocol with on column DNase digestion.  RNA concentrations were quantified using a NanoDrop Spectrophotometer at a  wavelength of 260nm. Integrity of the total RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).cDNA libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).  Finally, deep sequencing was done using the Illumina NovaSeq 6000 sequencing system at the University of Kansas Genome Sequencing Facility to generate100 bp pair-end reads. The RNA-seq data were used for quality check, filtering and mapping to the human reference genome (hg38). Count files are generated by featureCounts tool and  downstream analysis was performed using DESeq2-Bioconductor R package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).

first: Purbasa

last: Dasgupta

first: Rajnish

last: Kumar


title: Tumor-Specific RNA Editing Nanomedicine Activated by Wnt Signaling for Methionine Metabolic Immunotherapy

first: Honglin

last: Tang

address: 866 Yuhangtang Road

institute: Zhejiang  University

summary: Tumor cells often outcompete T cells for methionine, impairing T cell function and immune surveillance. However, selectively targeting methionine metabolism in tumors remains challenging. Here, we develop a Wnt-activated RNA editing nanoplatform (TREND) to specifically disrupt the tumor methionine transporter SLC43A2 and reprogram the metabolic competition between tumor cells and CD8+ T cells. By taking advantages of aberrant Wnt signaling pathway in tumor cells, we first established a Wnt-responsive promoter which was used to control the transcription of the plasmid encoding RNA editor (CasRx) targeting SLC43A2, in order to ensure RNA editing in tumor cells with activated Wnt signaling. To further promote the accumulation and the intracellular translocation of CasRx in the tumor cells in vivo, a tumor-targeted delivery system was engineered by cloaking hybrid cell membrane over the polymeric carriers for the systemic delivery of CasRx plasmid. Such a therapeutic strategy combining tumor-targeted delivery and tumor-specific RNA editing greatly relieves the metabolic competition of methionine between tumor cells and T cells, restores H3K79me2 and STAT5 expression and increases intracellular glutathione (GSH) to suppress ROS-driven activation of the NFAT/NR4a/Tox exhaustion axis, thereby reducing immune checkpoint expression. This strategy significantly boosts the activity of T-cell effectors and suppresses the progression of tumors in multiple mouse models, providing a modular and programmable RNA-based approach for tumor-targeted metabolic immunotherapy.

overall_design: We established a Hepa1-6 tumor-bearing mouse model and treated the mice with the TREND system delivering CasRx plasmids containing either a mock sgRNA or an sgRNA targeting SLC43A2, administered via tail-vein injection. Following treatment, tumor tissues were harvested and tumor-infiltrating lymphocytes were isolated for RNA sequencing analysis.

first: Xiaojie

last: Xu

first: Lilong

last: Liu

first: Silu

last: Tan

first: Chongzhi

last: Wu

first: Zijian

last: Shen

first: Bowen

last: Li

first: Tingting

last: Yuan

first: Da

first: Shipeng

last: Ning

first: Yuan

last: Ping


title: Effects of nanodelivery system PQR NPs on gene expression regulation in antagonizing erastin-induced PC12 cell damage via ferroptosis

city: Jinzhong City, Shanxi Province

first: Chen-Long

address: No. 98, University Street, Yuci District, Jinzhong City, Shanxi Province

institute: Shanxi Medical University

summary: The coordinated and sequential interactions between drug-loaded nanocarriers and key genes within the cellular ferroptosis pathway are crucial for maintaining the survival and functional stability of PC12 neuronal cells. In this report, we demonstrate that quercetin-loaded PQR NPs serve as a key regulatory vehicle in counteracting Erastin-induced damage to PC12 cells. The absence of PQR NPs markedly heightens PC12 cells' susceptibility to Erastin-induced ferroptosis, a phenomenon reversible through exogenous administration of PQR NPs. Furthermore, PQR NPs interact both physically and functionally with core ferroptosis pathway genes (such as GPX4) and epigenetic modifiers, thereby regulating the expression levels of ferroptosis-related genes during Erastin-induced injury. Although PQR NPs are not essential for the transcriptional activity of core genes themselves, the quercetin delivery and release process mediated by PQR NPs is indispensable for scavenging excess reactive oxygen species within cells, maintaining GPX4 expression stability, and inhibiting Erastin-induced lipid peroxidation. Collectively, our data provide a molecular framework for how nanodelivery systems exert cytoprotective effects by regulating ferroptosis pathway gene expression. In this process, PQR NPs deliver quercetin and modulate the expression balance of key ferroptosis genes, thereby counteracting Erastin-induced damage in PC12 cells.

overall_design: RNA sequencing analysis was performed on PC12 cells following different treatments, including untreated controls, Erastin-induced PD models, and co-interventions with Erastin and PQR NPs.

first: ChengWu

last: Zhang


title: Elucidating the impact of chemotherapy on human bone marrow stroma [RNA-seq_human patients]

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

summary: To understand the impact of chemotherapy treatment on the bone marrow microenvironment, we accquired paired bone marrow (BM) aspirate samples from patients with acute lymphoblastic leukemia (ALL) collected at diagnosis and 4w later (end of induction therapy) at the Princess Margaret Hospital.  The BM stroma was obtained by expanding BM aspirates in culture, and profiled by RNA-sequencing.

overall_design:
RNA-sequencing was performed on mono-stromal layer obtained from BM aspirates collected at diagnosis and after ALL induction chemotherapy.

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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.
***************************************************************

first: Ximing


title: MBNL1-dependent alternative splicing of NUMA1 shapes neuronal identity during fibroblast-to-neuron reprogramming

city: Chongqing

first: BINGLIN

last: ZHU

address: 313 Jinyue Road

institute: Jinfeng Laboratory

summary: Direct neuronal reprogramming provides a powerful strategy to generate neurons from somatic cells without passing through a pluripotent state. However, the post-transcriptional mechanisms that refine neuronal identity downstream of fate induction remain poorly understood. Here, we identify alternative splicing as a critical regulator of neuronal identity during fibroblast-to-neuron reprogramming. Knockdown of the RNA-binding protein MBNL1 establishes a distinct reprogramming state (AMmnp) that enhances neuronal maturation and strongly biases induced neurons toward an inhibitory, GABAergic identity, without markedly altering overall conversion efficiency. Transcriptomic analyses revealed coordinated repression of extracellular matrix-associated gene programs together with widespread remodeling of alternative splicing. Among MBNL1-dependent splicing events, NUMA1 exon 16 emerged as a prominent target. Functional manipulation of NUMA1 isoforms demonstrated that exon 16 inclusion suppresses neuronal marker expression specifically in the AMmnp context, whereas exon skipping is permissive for neuronal differentiation. These findings establish MBNL1-dependent alternative splicing of NUMA1 exon 16 as a post-transcriptional mechanism that refines neuronal identity acquisition during direct reprogramming, highlighting alternative splicing as an active determinant of induced neuron quality and subtype specification.

overall_design: Transcriptomic profiling of induced neurons mediated by ASCL1, miR124-9/9*, p53 shRNA, PTBP2 shRNA and MBNL1 shRNA at day 14 using human skin fibroblast (HFF-1 cells).

first: Jun

first: Qiushuang

last: Long

first: Ruoqi

first: Binglin

last: Zhu


title: A single cell atlas of porcine hematopoietic development

city: Columbia

first: John

last: Driver

state: MO

address: 1201 Rollins Street

institute: University of Missouri

summary: Domestic pigs are a globally important agricultural species that are increasingly used as large animal biomedical models to bridge the gap between rodents and non-human primates. A thorough understanding of the porcine immune system is needed to safeguard pig health through therapies and vaccines and better utilize swine as preclinical models. Here, we paired single-cell transcriptomic analyses with T and B cell receptor profiling to create a cell atlas of pig hematopoietic development using cells dissociated from central lymphoid organs during embryonic, neonatal, and adult life. We highlight the connection between fetal liver and bone marrow, B cell and gd T cell differentiation trajectories, granulopoiesis in fetal liver, and T and B cell receptor recombination kinetics. Our combined data provides new insights into pig immune system development and contributes a valuable resource for advancing pigs as a model to study blood and immune-related diseases in humans.

overall_design: Fetuses were recovered from pregnant females euthanized at 41, 47, 60, 70, and 90 days of gestation (DG). Fetal liver samples were collected at 41 DG, thymus samples at 60, 75, and 90 DG, and bone marrow samples at 47, 60, 75, and 90 DG. In addition, postnatal thymus and bone marrow samples were collected from 1-day-old (DOA) piglets and 7-month-old (MOA) gilts.


title: Extinction-recruited prefrontal-hypothalamic pathway encodes positive affect to sustain extinction and prevent relapse in PTSD mice

city: Shanghai

first: Zejie

last: Lin

address: 280 South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Effective psychotherapeutic interventions for post-traumatic stress disorder (PTSD) rely on fear extinction to suppress maladaptive fear responses, yet their long-term efficacy is limited by high relapse rates. Notably, extinction involves not only fear inhibition but also affective engagement. However, whether and how internal affective components contribute to extinction retrieval and long-term persistence remain unclear. Here, we demonstrate that positive affective experiences arising during extinction govern the long-term persistence of extinction and resistance to spontaneous recovery. We identify a subpopulation of medial prefrontal cortex (mPFC) extinction neurons projecting to supramammillary nucleus glutamatergic (SuMGlu) neurons that encodes positive affective experience during extinction and selectively governs long-term extinction persistence. This ensemble is spatially, anatomically, and transcriptionally distinct from mPFC extinction neurons projecting to zona incerta somatostatin-expressing (ZISST) neurons, which primarily support extinction retrieval. Transcriptomic profiling reveals enrichment of sirtuin 1 (Sirt1) within SuM-projecting extinction ensembles, and bidirectional manipulation of SIRT1 alters extinction relapse vulnerability in a PTSD mouse model. These findings provide a cortical–hypothalamic framework incorporating molecular features that governs the long-term persistence of fear extinction and resistance to relapse through positive affective processes.

overall_design: To address the extinction experience-dependent molecular differences in ZI- and SuM-projecting mPFC populations, the mPFC tissues were extracted from TRAP2 mice, and the nuclei were isolated for 10x Genomics single-nucleus RNA sequencing (snRNA-seq) analysis.


title: SUMOylation and ubiquitination reciprocally regulate SMCHD1 antiviral activity against herpes simplex virus 1

city: Wuhan

first: Tian

last: Xuezhang

address: Donghu Road

institute: Wuhan University

summary: Host restriction factors serve as intrinsic barriers against viral infection, and are frequently counteracted by viral antagonists. Previous studies, including our own, have identified SMCHD1 as a restriction factor that suppresses the replication of multiple viruses. Here, we reveal that the antiviral activity of SMCHD1 is dynamically regulated by two different post-translational modifications. SUMOylation of the SMCHD1 hinge domain is critical for its association with viral genome and enhances its antiviral activity. In contrast, during herpes simplex virus 1 (HSV-1) infection, the viral E3 ligase ICP0 induces SMCHD1 ubiquitination and proteasomal degradation, thereby relieving viral restriction. Loss of ICP0 stabilizes SMCHD1 and leads to marked accumulation of SUMOylated SMCHD1, rendering ICP0-deficient HSV-1 more sensitive to SMCHD1-mediated inhibition. Together, our findings uncover a reciprocal SUMO-ubiquitin regulatory mechanism that governs SMCHD1 antiviral activity and highlight a refined virus-host arms race centered on biphasic modification of a single restriction factor.

overall_design: U2OS cells were infected with HSV-1 ICP0 RFm (MOI=5) for 4h, followed by CUT&Tag analysis


title: Transcriptome analysis of early human placenta and idiopathic recurrent pregnancy loss samples

city: Kansas City

first: Soumen

last: Paul

state: KS

address: Hemenway Building 3901 Rainbow Boulevard

department: Department of Pathology & Laboratory Medicine

institute: University of Kansas Medical Center

summary: The goal of this study was to test gene expression changes in developing human placenta, which are associated with idiopathic recurrent pregnancy losses (RPL). In particular, we focused on RPL placental tissues that show significant defect in villi organization. Placental samples (less that 15 weeks) were collected. 4 control placentae with normal villi structure and 4 RPL placentae with defective villi formation were collected and ensured tissue viability. Whole placental villi were used to prepare RNA using Qiagen RNeasy Mini Kit with on column DNase digestion. RNA-seq analysis were performed using a NovaSeq 6000 platform.

overall_design: Total RNA from the whole placental villi was isolated using RNeasy Mini Kit (#74104) from Qiagen per the manufacturer’s protocol with on column DNase digestion. RNA concentrations were quantified using a NanoDrop Spectrophotometer at a wavelength of 260nm. Integrity of the total RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).cDNA libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Finally, deep sequencing was done using the Illumina NovaSeq 6000 sequencing system at the University of Kansas Genome Sequencing Facility to generate100 bp pair-end reads. The RNA-seq data were used for quality check, filtering and mapping to the human reference genome (hg38). Count files are generated by featureCounts tool and downstream analysis was performed using DESeq2-Bioconductor R package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).

first: Rajnish

last: Kumar


title: Decoding stage-specific symbiotic programs in the Rhizophagus irregularis – tomato interaction using single-nucleus transcriptomics

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

summary: Arbuscular mycorrhizal fungi (AMF) establish a dynamic and asynchronous symbiosis with a wide range of land plants, involving distinct stages of root colonization and associated cellular responses that co-occur within the same root. Whilst decades of research have significantly enhanced our understanding of the plant’s symbiotic gene repertoire, this spatial and temporal complexity has hindered a detailed dissection of the molecular mechanisms underlying fungal accommodation. Here, we present the first single-nucleus RNA sequencing (snRNA-seq) dataset of Solanum lycopersicum roots colonized by Rhizophagus irregularis. Unsupervised clustering of an AM-specific cluster reveals AM-responsive root epidermal cells as well as a developmental gradient of cortical cells across distinct stages of arbuscule formation, unveiling colonization stage-specific transcriptional signatures. Moreover, using Motif-Informed Network Inference based on single-cell EXpression data (MINI-EX), we put forward candidate transcription factors orchestrating these stage-specific transcriptional programs. Together, our data support novel hypotheses on how diverse plant developmental and physiological pathways—including localized cell cycle reactivation and the integration of multiple nutritional cues—are coordinated to facilitate the establishment of a functional symbiosis. As such, this high-resolution dataset serves as a valuable resource for candidate gene prioritization and future reverse genetic studies.

overall_design: snRNA-seq dataset of three replicates of Solanum lycopersicum roots, either mock-infected or colonized by Rhizophagus irregularis.

first: Naomi

last: Stuer

first: Toon

last: Leroy

first: Thomas

last: Eekhout

first: Annick

last: De Keyser

first: Jasper

last: Staut

first: Klaas

last: Vandepoele

first: Petra

last: Van Damme

first: Judith

last: Van Dingenen

first: Sofie

last: Goormachtig


title: Preserved magnitude and breadth of T cell immunity to SARS-CoV-2 mRNA vaccination in inflammatory bowel disease patients treated with anti-cytokine biologics

first: Tania

middle: H

last: Watts

address: 1 King's College Circle

department: Immunology

institute: University of Toronto

summary: The widespread vaccination against SARS-CoV-2 offered an opporunity to investigate the effects of anti-cytokine biologics on the cellular responses to a specific vaccination. Previous research has demonstrated inflammatory bowel disease (IBD) patients treated with anti-TNF agents exhibit decreased Spike (S)-specific antibody responses compared to IBD patients treated with anti-IL-12/23 or healthy controls, even after four doses of mRNA vaccine (Cheung et al. JCI 2025). Less is known about the impacts of anti-TNF and anti-IL-12/23 therapy on T cell responses to vaccination, although previous research in our group has demonstrated that T cells responses in patients treated with anti-TNF or anti-IL-12/23 tend to wane quicker after two vaccine doses, compared to healthy controls (Dayam, Law, et al. JCI Insight 2023). To further examine the phenotype of and breadth of memory T cell responses to SARS-CoV-2 mRNA vaccination, here we performed immune profiling of S-specific memory T cells, isolated from anti-TNF treated- or anti-IL-12/23- treated IBD patients and healthy controls from timepoints after two and three vaccine doses, via 5' single cell RNA-sequencing (with CITE-sequencing for hashtags only) and TCR-sequencing.

overall_design: CITE-seq and TCR-seq: PBMCs from healthy controls (n=3), anti-TNF treated IBD patients (n=5) and anti-IL-12/23 treated IBD patients (n=4) isolated 2-4 weeks post vaccine dose 2 (Timepoint 3) and post vaccine dose 3 (Timepoint 5) were stimulated with ancestral Spike (S) peptide pools (PepMix, JPT) and antigen-reactive memory T cells were sorted based on the dual expression of activation induced markers. Prior to sorting, samples were tagged with an unique TotalSeqC hashtag antibody (HTOs) to identify each donor in downstream analyses. Sorted S-reactive memory T cells were subsequently analyzed using CITE-seq and TCR-seq. Patients were matched between timepoints, with the exception of two anti-TNF treated IBD patients (identified by TotalSeq-C hashtag #10) that were only sequenced at one timepoint: note, Timepoint 3 TotalSeq-C hashtag #10 is a different individual from Timepoint 5 TotalSeq-C hashtag #10.

first: Michelle

middle: W

last: Cheung

first: Mark

middle: S

last: Silverberg


title: Osteocyte-specific deletion of Gasdermin D drives osteoarthritis cartilage degeneration by promoting inflammation and remodeling in subchondral bone

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

institute: Hokkaido University

summary: In osteoarthritis, we discovered that the number of osteocytes in the subchondral bone is reduced. By investigating the interaction between chondrocytes and osteocytes, we aim to elucidate the underlying pathological mechanisms.

overall_design: MLO-Y4 osteocyte cell line and primary murine chondrocytes were co-cultured using transwell inserts for 24 and 48 hours. Prior to co-culture, chondrocytes were stimulated with 10 ng/mL interleukin-1β for 6 hours.

first: Yuki

last: Ogawa

first: Mohamad

first: Norimasa

last: Iwasaki


title: TMEM97 is A Cholesterol Sensing Onco-Protein and Sustains Mitochondrial Energetics Through Lipid Biosynthesis

city: Istanbul

first: Burcu

last: Yucel

address: Unalan Mah.

department: Medical Faculty

country: Turkey

institute: Istanbul Medeniyet University

summary: Despite advanced therapeutics, gastric carcinoma is still a leading cause of cancer mortality. Investigating metabolic vulnerabilities has become crucial to identify new drug targets and to develop biomarkers for monitoring disease progress. The aim of this study is to investigate the functional role of TMEM97 in the cholesterol metabolism and carcinogenesis. We demonstrated that TMEM97 ablation substantially reduced in vitro cell proliferation and impaired tumor growth in xenograft models. Furthermore, TMEM97 deficiency disrupted cholesterol homeostasis. Untargeted metabolomics identified a significant accumulation of the post-lanosterol intermediate follicular fluid meiosis-activating sterol (FF-MAS) in KO cells under both normal and lipoprotein-deficient serum (LPDS) conditions, implying a bottleneck in cholesterol biosynthesis beyond lanosterol. Notably, TMEM97 KO cells showed compensatory upregulation of key regulatory enzymes HMGCR and SQLE, alongside enhanced expression of sterol regulatory element-binding proteins (SREBP1/2), suggesting a regulatory feedback loop. Additionally, the loss of TMEM97 induced broader metabolic reprogramming as multi-omic analysis revealed impaired TCA cycle with altered levels of intermediates, gene expressions and decreased mitochondrial oxygen consumption rate (OCR), particularly under LPDS conditions. Structural analysis revealed a conserved cholesterol recognition/interaction amino acid consensus (CARC) motif in TMEM97, and the deletion of this motif substantially reduced cholesterol binding in vitro. To conclude, TMEM97 senses cholesterol availability and modulates SREBP-mediated transcriptional responses to lipid availability. Loss of TMEM97 impairs post-lanosterol cholesterol biosynthesis, alters lipid profiles, and disrupts mitochondrial bioenergetics. Given its tumorigenic role and druggability, TMEM97 delineated as a novel drug target for gastric carcinoma.

overall_design: TMEM97 KO and WT HGC27 gastric carcinoma cell lines were proliferated in either in FBS containing serum or LPDS containing serum for 3 days with 3 independent biological samples. After the incubation cells were collected and RNAs were collected.


title: Extracellular matrix reprogramming by the YAP/TAZ/TGF-ß2 axis drives immune exclusion in cholangiocarcinoma models

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

institute: Leibniz Institute on Aging

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

overall_design: Refer to individual Series


title: Transcriptomic effects of miR-21-5p on preimplantation mouse blastocysts

first: Yuehan

last: Li

address: No. 1095, Jiefang Ave.

institute: Huazhong University of Scicence and Technology

summary: Preimplantation embryos cultured in vitro exhibit increased stress and apoptosis compared with in vivo development. miR-21-5p is a conserved, highly abundant microRNA in reproductive-tract extracellular vesicles and has been implicated in cell-survival pathways. To define its transcriptomic impact on early embryos, we performed RNA-seq on mouse blastocysts generated by IVF and cultured in KSOM with either miR-21-5p agomir (50 nM) or blank control. Each biological replicate consisted of five pooled blastocysts; n=4 replicates per group. Sequencing was carried out on an Illumina NovaSeq X Plus.

overall_design: Two conditions: blank control vs miR-21-5p agomir (50 nM). Four biological replicates per condition; each library from a pool of five IVF-derived mouse blastocysts cultured to the blastocyst stage. Raw and processed files are provided.

first: Mingwei

last: Lv

first: Wenjing

last: Xiong

first: Lei

last: Jin

first: Cong

last: Sui


title: Osteocyte-specific deletion of Gasdermin D drives osteoarthritis cartilage degeneration by promoting inflammation and remodeling in subchondral bone.

summary: In osteoarthritis, we discovered that pyroptosis of osteocytes in the subchondral bone contributes to disease progression. Ongoing studies using knockout mouse models aim to elucidate the effects of inhibiting this pathological pathway on disease progression .

overall_design: To activate the NOD-like signaling pathway and induce pyroptosis, osteocytes were stimulated with lipopolysaccharide (LPS) for 3 hours, followed by aluminum hydroxide treatment for another 3 hours. Osteocytes were isolated from both wild-type mice and osteocyte-specific Gsdmd knockout mice, and differential transcriptional responses were assessed using bulk RNA sequencing.


title: Adipocytes are dispensable in shaping the ovarian cancer tumor microenvironment in the omentum

city: St Louis

first: Jichang

last: Han

address: 4905 Children's PI

institute: Washington University in St Louis

summary: The omentum, a specialized adipose tissue within the peritoneum, is a key metastatic niche for ovarian cancer (OC) dissemination during peritoneal carcinomatosis. The prevailing view is that omental adipocytes promote tumor growth by providinglipids, since global FABP4 deficiency curbs tumor growth. Here, we generated mice lacking mature adipocytes in the peritoneum and omentum. ID8p53–/–Brca2–/– , BPPNM, and KPCA OC cells retained a propensity to seed at regions typically associated with adipocytes, even without mature adipocytes. However, lack of mature adipocytes did not suppress peritoneal OC expansion, whereas removing the adipocyte-free omentum did. Murine and human single-cell RNA sequencing analysis revealed that endothelial FABP4 was high in the omentum. Indeed, endothelial cell-selective deficiency of FABP4 reduced OC growth in the peritoneum. These findings prompt a re-evaluation of adipocyte contributions to OC progression and  point to a key role of the omental vasculature in supporting OC growth metabolically.

overall_design:
scRNAseq of human omentum, seperated the membrane and fat regions.  This is a benign omentum sample from 1 patient with granuloma cell ovarian cancer. This sample was from a Black or African American patient. The sample was collected before any chemotherapy.
Please note that this dataset contains human-derived data, and the      corresponding raw sequencing files will be submitted to the      appropriate controlled-access repository (e.g., dbGaP or SRA) in      compliance with data protection policies.

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

first: Rachel

last: Mintz

first: Emily

last: Butka

first: Alexandre

last: Gallerand

first: Ayoung

last: Kim

first: Sarah

last: Ning

first: Nicole

middle: K

last: Yiew

first: Mary

last: Wohltmann

first: Wei

last: Zou

last: Zhang

first: Karen

middle: E

last: Inouye

first: Gökhan

last: Hotamişligil

first: Samantha

last: Morris

first: Bernd

last: Zinselmeyer

first: Gwendalyn

middle: J

last: Randolph


title: Differentiation of tumor-infiltrating GZMK+ effector memory T cells associates with response to neoadjuvant immunotherapy in head and neck cancer

city: Bethesda

first: Cem

last: Sievers

address: 10 Center Drive

institute: NIH

summary: We performed single-cell RNA/VDJ-sequencing of sorted T cells from pre- and post-treatment tumor biopsies of patients with HPV-unrelated head and neck squamous cell carcinoma treated with either bintrafusp alfa alone or in combination with Tri-Ad5 vaccine.

overall_design: Clinical tumor tissue specimens were collected from patients with newly diagnosed, previously untreated HPV-unrelated HNSCC treated on clinical trial NCT04247282.

first: Clint

last: Allen


title: PKM2-deficiency induced fatty acid biosynthesis activation limits the response of non-small cell lung cancer to Osimertinib

first: Ge

last: Sun

state: Hubei

address: Shizi Mountain Street No.1

institute: Huazhong Argriculture University

summary: Non-small cell lung cancer (NSCLC) - the most common form of lung cancer - is an aggressive malignancy with limited effective therapeutic options1. Osimertinib, a third-generation epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI), has revolutionized treatment for EGFR-mutant NSCLC, yet resistance significantly limits its clinical benefit to patients2. Here, using a genome-wide genetic screen, we discover that pyruvate kinase M2 (PKM2) is a novel regulator of Osimertinib resistance. Loss of PKM2 triggers fatty acid biosynthesis activation in a glycolysis-independent manner. We have shown that PKM2 interacts with KDM1A in cytosol and nuclear translocation of KDM1A is increased in both PKM2-KO and Osimertinib-persister cells. Mechanistically, KDM1A demethylates H3K9me3 in the promoter region of the key lipid synthesis enzyme, fatty acid synthase (FASN), and cooperates with transcription factor AP-2 to activate FASN transcription, thereby conferring Osimertinib resistance. Pharmacological inhibition of FASN by Orlistat induces synthetic lethality with Osimertinib in vitro and vivo Osimertinib-resistant models. Treatment of 9 NSCLC patients who were unresponsive to Osimertinib with the combination of Osimertinib plus Orlistat  resulted in meaningful clinical responses. Our data highlights metabolic vulnerabilities and provides potential therapeutic approaches for treating TKI-resistant NSCLC.

overall_design: The data include the transcriptomic, proteomic, metabolomic, and epigenomic sequencing required for this study

first: Chunguang

last: Lei

first: Li

last: Li


title: SenCat: Cataloging human cell senescence through multiomic profiling of multiple senescent primary cell types

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: There is an urgent need to comprehensively catalog senescence markers across a wide range of cell types in an organism. Here, we profiled the transcriptomes and proteomes in over 30 senescence paradigms employing 14 different primary human cell types. Our results indicate that senescent cells from all tissue types do not share a unique marker, but they do share in the activation of specific metabolic pathways and damage response pathways to elicit tissue repair. Importantly, considering combinations of some of the most widely shared senescence markers validated the presence of senescent-like cells in mice through single-cell RNA-sequencing and immunostaining approaches. The enclosed catalog represents a much-needed resource to identify senescent cells across tissues in the body.

overall_design: Doxorubicin-induced senescence was triggered by a single dose of doxorubicin (10 mg/kg, Selleckchem) in 3 months old mice and at the specified time points.

first: Carlos

last: Anerillas

first: Gisela

last: Altés

first: Katarína

last: Grešová

first: Dimitrios

last: Tsitsipatis

first: Krystyna

last: Mazan-Mamczarz

first: Reema

last: Banarjee

first: Ana

last: Cunningham

first: Martin

last: Salamini-Montemurri

first: Jen-Hao

last: Yang

first: Rachel

last: Munk

first: Martina

last: Rossi

first: Yulan

last: Piao

first: Bradley

last: Olinger

first: Quinn

last: Strassheim

first: Jennifer

last: Martindale

first: Jinshui

last: Fan

first: Chang-Yi

last: Cui

first: Delaney

middle: V

last: Rutherford

first: Ying

last: Hao

first: Ziyi

first: Jessica

last: Roberts

first: Yue

middle: A

last: Qi

first: Kotb

last: Abdelmohsen

first: Allison

last: Herman

first: Manolis

last: Maragkakis

first: Nathan

last: Basisty

first: Myriam

last: Gorospe


title: Post-treatment peripheral-blood T cells from HNSCC patients undergoing neoadjuvant immunotherapy treatment.

first: Cem

last: Sievers

summary: We performed single-cell RNA/VDJ-sequencing of sorted T cells from post-treatment blood of patients with HPV-unrelated head and neck squamous cell carcinoma treated with either bintrafusp alfa alone or in combination with Tri-Ad5 vaccine. These patients are identical to the patients from which tumor-infiltrating T cells were isolated as reflected in the sample names.

overall_design: Clinical blood specimens were collected from patients with newly diagnosed, previously untreated HPV-unrelated HNSCC treated on clinical trial NCT04247282.

first: Clint

last: Allen


title: A cross model spatial and single-cell atlas reveals the conserved involvement of osteopontin in polycystic kidney disease

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Internal Medicine

institute: University of Oklahoma Health Sciences Center

summary: Polycystic kidney disease (PKD) arises from mutations in cilia-associated genes, such as PKD1 and PKD2, expressed in renal epithelial cells, leading to progressive kidney dysfunction and end-stage kidney disease (ESKD). To elucidate the cellular and molecular consequences of these mutations, we constructed an integrated single-cell and spatial transcriptomics atlas across mouse models of PKD, mapping changes in cell type composition, gene expression, and intercellular signaling networks. Single-cell and spatial transcriptomics revealed elevated Spp1 (osteopontin) expression enhanced signaling interactions with macrophages and fibroblasts in cystic niches. Whereas deletion of Spp1 increased cyst severity in the Ift88 model, it reduced PKD severity in the orthologous Pkd1RC/RC model, concurrent with model-specific differences in Spp1 cell type expression and communication partners. We also found increased SPP1 expression and signaling in single-cell RNA sequencing data from autosomal dominant PKD (ADPKD) patients, highlighting cross-species conservation. Together, our integrated atlas identified conserved intercellular signaling networks within cystic niches, including SPP1, offering insights into PKD pathogenesis and potential therapeutic targets.Conclusion: Collectively, our data indicate that tVNS improves HFpEF by reducing Spp1 expressing CCR2+ CRM and inducing expression of pro-reparative Igf1 in TLF+/MHC2+ CRM. These effects are mediated through cholinergic signaling, highlighting a neuroimmune pathway in HFpEF.

overall_design: We performed single cell RNA sequencing (scRNAseq) on kidney tissue isolated from ~1 year old Pkd1RC/RC mice.

first: Sarah

last: Miller

first: Hua

last: Zhong

first: Anjun

last: Ma


title: TCR-stimulation of peripheral-blood CD8+ T cells.

summary: We performed single-cell RNA/VDJ-sequencing of sorted CD8+ T cells from the blood of patients with HPV-unrelated head and neck squamous cell carcinoma. The corresponding cells were cultured with or without aCD3/aCD28-mediated TCR stimulation. Importantly, these patients were not treated on a clinical trial and are distinct from the other patients included in this study.

overall_design: Clinical blood specimens were collected from patients with newly diagnosed, previously untreated HPV-unrelated HNSCC undergoing standard of care procedures following verbal and written informed consent under an IRB-approved biospecimen protocol (NCT03429036).