title: Viral transcriptional regulators extensively rewire host pathways through diverse mechanisms

first: Juan

middle: Ignacio

last: Fuxman Bass

address: 5 Cummington mall

department: Biology

institute: Boston University

summary: Viral transcriptional regulators (vTRs) reprogram host gene regulatory networks to promote replication, persistence, and immune evasion. Despite the identification of hundreds of vTRs in human viruses, how they rewire host pathways remains unclear. Here, we systematically profiled 95 vTRs from diverse human viruses across multiple functional assays. vTRs perturb immune, cell proliferation/death, and signaling pathways through various mechanisms; some bind DNA directly, others cooperate or antagonize human transcription factors (hTFs), and some remodel chromatin. vTRs can act as activators or repressors and recruit similar but not identical repertoires of proteins as hTFs. These findings reveal vTRs as versatile transcriptional modulators that converge on conserved host “pressure points” while diversifying across pathways to promote viral replication and persistence. Notably, many vTR dysregulate genes within autoimmune, neurological, and cardiovascular risk loci, revealing mechanistic links to disease. Together, we provide a comprehensive resource for understanding and targeting viral control of human transcription.

overall_design: HEK293T cells were transfected with expression constructs encoding individual viral transcriptional regulators (vTRs), empty vector controls, or left untransfected. Samples were generated in quadruplicate. Twenty-four hours after transfection, cells were either infected with Sendai virus or left untreated. RNA was collected two days post-transfection and gene expression profiles were measured using Bulk RNA Barcoding and Sequencing (BRB-seq). Libraries were prepared using the MERCURIUS DRUG-seq kit (Alithea Genomics) and sequenced on an Illumina NovaSeq platform.  The dataset contains six experimental batches comprising vTR-expressing samples, empty vector controls, and non-transfected controls under Sendai virus-infected and uninfected conditions. An additional seventh batch was generated in HEK293 cells and included selected vTRs together with vector and non-transfected controls under Poly(dA:dT)-stimulated and water-treated conditions to characterize transcriptional responses to innate immune pathway activation.  Sequencing reads were aligned to a custom GRCh38 reference augmented with viral transcriptional regulator sequences. Gene-level expression quantification was performed using STARsolo, and differential expression analyses were carried out relative to matched vector controls.

first: Jaice

last: Rottenberg

first: Xing

last: Liu

first: Mohamed

middle: Y

last: ElSadec

first: Anna

last: Berenson

first: Luis

middle: F

last: Soto-Ugaldi

first: Clarissa

last: Santoso

first: James

last: Corban

first: Phillip

middle: J

last: Dexheimer

first: Berkay

last: Engin

first: Ryan

last: Lane

first: Sakshi

last: Shah

first: Kerstin

last: Spirohn-Fitzgerald

first: Shubham

last: Khetan

first: Cheng-Che

last: Lee

first: George

last: Munoz-Esquivel

first: Zhaorong

last: Li

first: Lucia

last: Martinez-Cuesta

first: Yunwei

last: Lu

first: Philipp

last: Trollmann

first: Tong

last: Hao

first: S. Stephen

last: Yi

first: Nidhi

last: Sahni

first: Martha

last: Bulyk

first: Michael

last: Calderwood

first: Matthew

last: Weirauch

first: Marc

last: Vidal

first: Srivatsan

last: Raman

middle: I


title: Decoding the genomic identity of candidate tumor-leukocyte hybrid cells in circulation [RNA]

status: Public on Aug 09 2026

city: Charlestown

first: Doga

middle: C.

last: Gulhan

state: MA

address: 149 13th Street, Room 7.011

country: USA

institute: Mass General Brigham

type: Expression profiling by high throughput sequencing

summary: The fusion of circulating tumor cells (CTCs) with white blood cells (WBCs) has been proposed to generate hybrid cells with carcinogenic properties and metastatic potential. However, existing evidence relies on staining, and without molecular profiling, their prevalence, true identity, and the extent of their immune-like features remain unclear. To address this, we developed a mouse melanoma model with distinct fluorescent markers introduced into cancer and host cells, enabling isolation of dual-positive (DP) cells as candidates for fusion. We characterized these cells using imaging FACS to visualize cytoplasmic merging together with single-cell whole-genome and transcriptome co-profiling to detect tumor or host-specific genomic variants and gene-expression profiles. Among 500 profiled DPs, we found no clear evidence of fusion events. Only two cells in lung-metastases displayed both macrophage- and tumor-features, consistent with potential fusion but also with early stages of phagocytosis. The remaining DPs arose from non-fusion mechanisms: in tumors, they were mainly macrophages that engulfed tumor material, while in circulation, they corresponded to platelet-coated CTCs. CTCs from melanoma patients also manifested substantial platelet-coating, resulting in reduced ribosome and protein translation and increased platelet-activation and cell adhesion in both species. Overall, we conclude that dual-positive cells are already explained by parsimonious biological mechanisms without fusions.

overall_design:
Matched scDNAseq of single cells isolated from blood, lung, and cell culture/ cell lines. Sequencing done on CTCs, DPs, and WBC, along with control cells
Matched scRNAseq of single cells isolated from blood, lung, and cell culture/ cell lines. Sequencing done on CTCs, DPs, and WBC, along with control cells

first: Ezgi

last: Antmen

first: Reid

last: McNeil

first: Ankit

last: Singh

first: Shih-Bo

last: Huang

first: Min

last: Yang

first: Ji-Eun

last: Kwak

first: Ben

last: Ouyang

first: Quinn E

last: Cunneely

first: Victor R

last: Putaturo

last: Wittner

first: Weikun

last: Xia

first: Cem

last: Tanriover

first: Eujin

last: Hong

first: Douglas

last: Micalizzi

first: Lloyd

last: Bod

first: Daniel

last: Haber

first: Mehmet

last: Toner

first: Shyamala

last: Maheswaran

first: Doga C


title: Decoding the genomic identity of candidate tumor-leukocyte hybrid cells in circulation [DNA]

first: Doga

last: Gulhan

first: Ezgi

last: Antmen

first: Reid

last: McNeil

first: Bem


title: EZH2 cooperates with SREBP2 to establish the epigenomic, transcriptomic and metabolic programs for driving oncogenesis [CUT&Tag II]

city: Durham

first: Arum

last: Kim

state: NC

address: Medical Sciences Research Building III  3 Genome Ct

institute: Duke University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Enhancer of Zeste Homolog 2 (EZH2) is recurrently overexpressed in cancers, correlating with adverse clinical outcomes. How exactly EZH2 overexpression contributes to tumorigenicity is far from clear. We here report an unexplored tumor-promoting axis involving the EZH2 association with SREBP2, a master regulator of lipid metabolism. EZH2 and SREBP2 act together to potentiate the expression of mevalonate pathway genes, thereby enhancing cholesterol biosynthesis to sustain aggressive tumor growth. The partially disordered transcriptional activation domains (tADs) of EZH2 and SREBP2 directly bind and recruit p300 to mediate the proto-oncogene activation. Additionally, we employed Proteolysis Targeting Chimeras (PROTACs) to block such a noncanonical function of EZH2 in cancer. Independent EZH2-targeting PROTACs degraded EZH2 and SREBP2 both and downregulated the SREBP2-associated gene-expression program, leading to inhibition of tumor growth. Altogether, this study unveils the existence of an EZH2:SREBP2 axis in cancers, which operates to sustain tumorigenesis via promoting cholesterol metabolism, paradigm-shifting the current understanding of EZH2’s oncogenic functions.

overall_design: CUT&Tag for H3K27me3 and H3K27ac in MV4;11 acute leukemia cells.

first: Greg

last: Wang


title: OsIDD7 integrates signaling networks for arbuscular mycorrhizal symbiosis [DAP-seq]

city: Taipei

first: Shu-Yi

last: Yang

address: Life Science Building, NTU. No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: Institute of Plant Biology

summary: Arbuscular mycorrhizal (AM) symbiosis is an ancient and widespread mutualism between plant roots and Glomeromycotina fungi that enables nutrient exchange through arbuscules. Here, we identify the rice INDETERMINATE DOMAIN (IDD) transcription factor IDD7 as a key regulator of AM symbiosis. IDD7 expression is strongly induced in arbusculated cells, and loss of IDD7 markedly reduces fungal colonization and disrupts arbuscule development. IDD7 is involved in regulating genes involved in fatty acid biosynthesis, nutrient transport, and symbiotic signaling, and interacts with the transcription factors SLR1 and PHR2 through its conserved TQDFLG domain. Electrophoretic mobility shift assays show that IDD7 binds multiple promoter motifs and, together with SLR1 and PHR2, synergistically activates the promoters of PT11, PHR2, RAM1, WRI5a, and CYCLOPS. Moreover, IDD7 is required for PHR2 expression in arbusculated cells. These results identify IDD7 as a central transcriptional regulator in arbusculated cells that coordinates AM-induced gene expression and promotes arbuscule development.

overall_design: We performed DNA affinity purification sequencing (DAP-seq) to identify genome-wide binding sites of OsIDD7. Purified transcription factor proteins were incubated with genomic DNA libraries, followed by high-throughput sequencing. Peaks were identified using MACS2.

first: Wan-Ning

last: Kuo

first: Yu-Ting

last: Chang

first: Pei-Jung

last: Chen


title: EZH2 cooperates with SREBP2 to establish the epigenomic, transcriptomic and metabolic programs for driving oncogenesis [CUT&RUN II]

overall_design: CUT&RUN for EZH2 and SREBP2 in the 22Rv1 prostate cancer cells and the MV4;11 acute leukemia cells.


title: OsIDD7 integrates signaling networks for arbuscular mycorrhizal symbiosis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for rice (Oryza sativa ssp. Japonica cv. Dongjin) Azygous and idd7 mutant that were colonized with AM fungi Rhizophagus irregularis and harvested at 5 wpi and 7 wpi

first: Man-Chi

last: Ho


title: Chronoregulation of innate immune cell fibrinolytic activity

city: Dublin

first: Paula

middle: Austra

last: Klavina

address: 123 St Stephens Green

department: School of Pharmacy and Biomolecular Sciences

country: Ireland

institute: Royal College of Surgeons in Ireland

summary: Peritoneal macrophages are important for pathogen clearance, forming cell-pathogen aggregates held together by fibrin. This can be beneficial in limiting the spread of pathogens, however, persistent fibrin deposits can lead to abdominal adhesions which give rise to multiple comorbidities. How this process is regulated is poorly understood. Under inflammatory conditions, macrophages secrete PAI-1, a potent inhibitor of fibrinolysis. We found that macrophage fibrinolytic activity is dependent on the time of day. PAI 1 secretion by peritoneal macrophages was increased at the onset of activity (ZT13) compared to at the onset of rest (ZT1), both basally and following in vivo LPS stimulation. Furthermore, the fibrinolytic response was reduced at ZT13 compared to ZT1. We also establish a novel role for the Rev-erbα agonist SR9009 in reversing macrophage anti-fibrinolytic activity. The chrono-dependency of macrophage fibrinolytic activity was confirmed using SR9009, which potently inhibited PAI-1 and PAI-2 secretion from LPS-stimulated macrophages, boosting plasmin generation and fibrin clot lysis in the presence of both macrophages and endothelial cells. Moreover, SR9009 promoted intraperitoneal fibrinolysis in LPS-administered mice. Collectively, these data highlight a novel role for circadian regulation of macrophage fibrinolytic activity.

overall_design: Mouse bone marrow-derived macrophages isolated from four male C57BL6 mice treated with 10 µM SR9009 for 16 hours followed by 100 ng/mL LPS for 6 hours.

middle: A

first: Roger

last: Preston

first: Annie

middle: M

last: Curtis


title: EZH2 cooperates with SREBP2 to establish the epigenomic, transcriptomic and metabolic programs for driving oncogenesis [RNA-seq II]

overall_design: Examination of transcriptomic profiles in the SUDHL6 lymphoma cells post-treatment with the EZH2 PROTAC (MS8815), the matched SET enzymatic inhibitor (EPZ-6438), or non-PROTAC analog controls (MS8815N), relative to DMSO.


title: Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming [GZF1_snp]

city: rehovot

first: irina

last: miodownik

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

summary: Genomic imprinting secures parent-specific gene expression through differential DNA methylation at imprinted control regions (ICRs). However, how unmethylated imprinted alleles resist de novo methylation remains unclear. Using an allelic methylation reporter at the Dlk1-Dio3 ICR and a genome-wide loss-of-function screen, we identify that the zinc finger protein GZF1 specifically binds the unmethylated maternal ICR and protects it from de novo methylation in mouse embryonic stem cells, early development, and oocytes. We further show that this protection occurs independently of Tet-mediated demethylation. A regulatory element containing GZF1 and ZFP57 motifs mediates mutually exclusive, methylation-dependent binding. Loss of either factor causes reciprocal imprinting failure: Gzf1 loss induces maternal allele methylation, H3K4me3 depletion, and silencing of maternal transcripts, whereas Zfp57 loss erases paternal methylation, causing locus maternalization. Gzf1-null mice exhibit postnatal growth retardation, contextualizing cis-deletions of this region and illustrating how imprinting phenotypes may differ when studied through epigenetic perturbation versus genetic deletion. Together, our findings define a reciprocal mechanism by which sequence- and methylation-sensitive factors actively memorize parental epigenetic asymmetry through opposing waves of developmental reprogramming.

overall_design: The design contains sequences taken from a 200 bp ChIP-seq peak and divided into four distinct 60 bp segments (1–4), each containing the corresponding SNPs distinguishing the CAST and 129 alleles. Sequences named methylated and unmethylated, depicted by the Flag=1 values, were excluded from this analysis.

first: Arik

last: Toren

first: Liron

last: Hoffman

first: Irina

last: Miodownik

first: Yoav

last: Mayshar

first: Raz

last: Ben-Yair

first: Ayelet-Hashahar

last: Orenbuch

first: Hernan

last: Rubinstein

first: Aviezer

last: Lifshitz

first: Roni

last: Stock

first: Alexander

last: Wainstein

first: Daoud

last: Sheban

first: Liran

last: Shlush

first: Amos

last: Tanay

first: Ariel

last: Afek

first: Yonatan

last: Stelzer


title: Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming [GZF1]

overall_design: The design contains de Bruijn sequences representing all possible 9-mers, with a constant 3' end, and was used to determine the DNA binding specificity of mouse full-length Gzf1.


title: Truncation of the p300/CBP TAZ2 domain promotes tumor progression

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: The histone acetyltransferase activity of p300/CBP is negatively regulated by the TAZ2 domain. Truncating mutations in the TAZ2 domain have been identified in several cancer types. Here, we show that truncation of p300/CBP at the TAZ2 domain inhibits tumor cell growth in vitro, while accelerating tumor progression in a xenograft mouse model. Importantly, tumors harboring TAZ2 truncations are vulnerable to histone deacetylase inhibitors (HDACis). We performed transcriptomic analysis to investigate the molecular changes driven by TAZ2 truncation during tumor progression and in response to HDAC inhibition.

overall_design: RNA-seq profiling was performed on A549 parental and p300 TAZ2-truncated isogenic cells, xenograft tumors collected at day 30, and tumors treated with vehicle or SAHA for 4 weeks.

first: Longxia

last: Xu

first: Hongwen

last: Xuan


title: Stroma-oriented tumor microenvironment facilitates intraosseous ameloblastoma tumor growth [multiome]

city: Taipei City

first: Ting-Han

last: Chang

address: No. 155, Sec. 2, Linong St., Beitou Dist.

department: Institute of Oral Biology, College of Dentistry

institute: National Yang Ming Chiao Tung University

summary: Ameloblastoma is a locally aggressive odontogenic epithelial tumor with poorly understood intraosseous pathogenesis due to a lack of physiologically relevant models. Here, we established an orthotopic intraosseous mouse model using ameloblastoma epithelial cells in combination with ameloblastoma-derived mesenchymal stromal cells (AMMSCs) or their secretome. AMMSC-derived extracellular vesicle-enriched secretome enhances stemness, epithelial-mesenchymal transition (EMT) phenotypes, and tumorigenic ability of ameloblastoma epithelial cells. A unique signature of microRNAs in AMMSC-derived secretome is functionally associated with the upregulation of EMT-regulatory transcription factors in tumor epithelial cells. Single-nucleus ATAC and RNA sequencing revealed a dynamic EMT trajectory in primary human AM-derived epithelial cells activated by paired AMMSC-derived secretome. This study suggests that AMMSCs and their secretome drive orthotopic AM tumor development by promoting tumor epithelial cell proliferation, EMT, and vascular formation in the tumor microenvironment. This stromal-oriented orthotopic model provides a clinically relevant platform for dissecting tumor-stroma crosstalk and identifying therapeutic vulnerabilities in ameloblastoma.

overall_design: Bulk RNA-seq was used to assess gene expression changes in AM-1 cells following treatment with AMMSC-derived secretome, GMMSC-derived secretome, or vehicle control. MicroRNA-seq was performed to profile microRNAs present in AMMSC- and GMMSC-derived secretomes. Single-nucleus multiome sequencing (snRNA-seq and snATAC-seq) was conducted on primary ameloblastoma epithelial cells treated with paired AMMSC-derived secretome for 3 days. Nuclei were isolated and processed using the 10x Genomics Chromium platform to generate transcriptomic and chromatin accessibility profiles.

first: Da-Yo

last: Yuh

first: Jian-Liang

last: Chou


title: A combinatorial EVs-miRNA signature mediates the anti-tumoral activity of NFAT3- regulated extracellular vesicles in aggressive cancers.

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Aggressive cancers such as triple-negative breast cancer (TNBC) and pancreatic cancer remain difficult to treat because their malignant behavior is driven by complex gene networks rather than single oncogenic targets. Our study identifies a NFAT3 transcription factor-dependent miRNAs signature that suppresses tumor aggressiveness through extracellular vesicles (EVs). Functional analyses demonstrated that a specific combination of fifteen miRNAs (miR-Comb 15) is required to inhibit cancer cell proliferation and invasion across TNBC and pancreatic cancer models, whereas individual miRNA are insufficient to reproduce the full anti-tumoral effect. To enable therapeutic translation, we engineered EVs derived from HEK 293T, a non- tumoral and scalable vesicle source. Using an optimized exogenous pH-gradient loading strategy, miR-Comb 15 was efficiently incorporated into EVs without altering their integrity or intrinsic bioactivity. Among multiple delivery platforms tested, miR-Comb 15 loaded HEK 293T EVs consistently exhibited superior anti-tumoral efficacy both in vitro and in vivo. Together, these findings establish a strong mechanistic link between transcriptional regulation and EVs-mediated RNA delivery and demonstrates that rationally designed RNA combinations delivered by EVs represent a promising therapeutic strategy for aggressive cancers.

overall_design: T-47D-derived extracellular vesicles (EVs) were isolated by differential centrifugation and ultracentrifugation. Briefly, cells were cultured to ~70% confluence and incubated for 48 h in EV-depleted medium. Conditioned medium was sequentially centrifuged at 300 g, 2,000 g, and 10,000 g to remove cells and debris, followed by ultracentrifugation at 120,000 g for 90 min at 4°C. EV pellets were washed twice in PBS and re-pelleted under identical conditions. Final EVs preparations were resuspended in PBS, aliquoted, and stored at -80°C. Particle size distribution and concentration were assessed by nanoparticle tracking analysis (NTA) using ZetaView instruments (Particle Metrix). EV preparations were used within one freeze–thaw cycle

first: Guénolé

last: Tossou

first: Sébastien

last: Jauliac


title: Stroma-oriented tumor microenvironment facilitates intraosseous ameloblastoma tumor growth [miRNA-Seq]


title: Single cell multiomic profiling of heterogenous PROCR+ cells in mouse mammary gland [scATAC-Seq]

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Pl

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

summary: PROCR has been identified as a surface marker on cyclic mammary stem cells (MaSCs) in the basal layer of the mouse mammary gland. Due to their limited numbers, this population has not been clearly characterized. We performed single-cell multi-omics profiling of mammary epithelial cells enriched for PROCR+ cells. With an unprecedented number of PROCR+ cells, we found that this population is highly heterogeneous and identified the subpopulation most likely to resemble MaSCs. By integrating scRNA-seq and scATAC-seq data, we constructed the transcriptional regulatory network of mammary development and uncovered potential master regulators involved in lineage commitment. Motivated by the connection between PROCR's roles in normal mammary gland development and tumorigenesis, we further investigated this subpopulation in a cohort of breast cancer patients. As PROCR is a therapeutic target for a subset of TNBC, our study clarifies the nature of PROCR+ MaSCs and suggests the need for additional markers for patient stratification.

overall_design: We performed scATAC-seq on 4 sorted populations of mammary epithelial cells (MEC).

first: Erin

last: Nekritz

first: Koon-Kiu

last: Yan

first: Jose

last: Silva


title: Stroma-oriented tumor microenvironment facilitates intraosseous ameloblastoma tumor growth [RNA-Seq]


title: Heterologous expression of the C-terminus of voltage gated sodium channel Nav1.2 in neuroblastoma N1E115 cells

city: Tlalnepantla

first: Ana

middle: Victoria

last: Vega

state: Mexico

address: Avenida de los Barrios No. 1, Colonia Los Reyes Iztacala, C.P. 54090, Tlalnepantla de Baz, Estado de México

department: physiology

country: Mexico

institute: Universidad Nacional Autónoma de México

summary: Transcriptional profile in neuroblastoma cells expressing a fusion protein between green fluorescent protein(EGFP) and amino acids 1778 to 2006 of mouse voltage-gated sodium channel alpha subunit NaV1.2 (uniprot id B1AWN6). Cells N15-115 expressing EGPF were use as control. Voltage-gated sodium channels alfa-subunit NaV1.2 has a nuclear localization signal in the C-terminus region. The aim of the experiment was to learn if heterologous expression of the NaV1.2CT was able to modify the overall mRNA expresion profile.

overall_design: 2 experimental conditions: N1E-115 transfected with control plasmid pEGFP-C1 or plasmid pEGFP-NaV1.2CT. Glucose concentration in culture media was 5 mM (Low glucose). RNA from 3 dishes were pooled. Same experiment was repeated twice using 20 mM of glucose in cultures media (High glucose). Two replicates per array.

first: Julio

middle: C

last: Luna-Rojas

first: Luis

last: Arratia-Cortés

first: Erik A

last: Romero-Macias

middle: V


title: Heterogeneity in B- and epithelial-cell senescence in the pathogenesis of COPD/emphysema [scRNA-seq]

city: Rochester

first: Gagandeep

last: Kaur

address: 601 Elmwood Ave

department: Environmental Medicine

institute: University of Rochester Medical Center

summary: Increased cellular senescence leading to premature lung aging is a key mechanism for chronic inflammation and airway remodeling in emphysematous-COPD. However, the cell-specific changes resulting in ‘senescent microenvironment’ in COPD remains elusive. To bridge this gap, we used single-cell multiomics approach to identify the differentially regulated cell types, genes/pathways and spatial organization of senescence phenotype in smoke-induced emphysema in humans. Dimensionality reduction and clustering of 121,885 cells in lung tissues from emphysematous COPD patients and healthy controls (n = 6/ group) with and without a smoking history revealed a significant enrichment (p<0.01) in the senescence associated gene sets in B-lymphocytes and multi-ciliated non-nasal (MNN) epithelial cell clusters from COPD patients. Senescent B cells were found to have dysfunctional development and maturation as denoted by alterations in expression of targets including BMP6, CCNB2, MCM4, PTEN and DDIT4 in diseased state. The senescence phenotype in MNN cells was closely linked to increased expression of senescence effector genes (p16 and p21) through both single cell and spatial transcriptomic approaches. Outcomes from single-cell techniques were validated by conducting cell intervention studies using small airway epithelial cells (SAEC; submerged) and diseased-human bronchial epithelial (D-HBE; ALI) cells in vitro.  We observed increased level of p16, but not p21, in cultured SAEC cells from COPD donors. The disease-induced upregulation of p16 was attenuated upon treatment with various senolytic interventions in SAECs, but not D-HBEs. Overall, our study defines the senescence landscape of various cell types in COPD/emphysema and identified potential genes/pathways that could be targeted for interventions in future.

overall_design: Performing single cell RNA sequencing (scRNA seq) on age- and sex-matched healthy non-smokers, smokers and COPD donors. The scRNA seq results were validated using Visum CytAssist and Xenium platforms from 10X. We also used GeoMx Protein profiler to get the spatial distribution of relevant proteins in select tissue sections from COPD donors and healthy non-smokers

first: Qixin

last: Wang

first: Felix

last: Effah

first: Sadiya

last: Bi Shaikh

first: Calla

last: Fahey

first: Ariel

last: Tjitropronoto

first: Hoshang

last: Unwalla

first: Manoj

last: Mammen

first: Irfan

last: Rahman


title: Heterogeneity in B- and epithelial-cell senescence in the pathogenesis of COPD/emphysema [Xenium]

overall_design: Performing single cell RNA sequencing )scRNA seq) on age- and sex-matched healthy non-smokers, smokers and COPD donors. The scRNA seq results were validated using Visum CytAssist and Xenium platforms from 10X.


title: M2 type tumor associated macrophage-derived CCL-18 promotes glioma cell proliferation but not mediates glioma recurrence after radiotherapy

city: Xuzhou

first: Xiuping

last: Zhou

state: Jiangsu

address: Huaihaixi Road 84#

country: China

institute: Xuzhou Medical University

summary: Most of glioma patients still experience relapse after radiotherapy owing to the formation of tumor immunosuppressive microenvironment. However, the comprehensive landscape of immune cell infiltration and the molecular mechanisms mediating glioma recurrence remains unclear. Bulk RNA-seq analysis revealed the significant changes in the immune system including increased total tumor-associated macrophages (TAMs) and elevated M2-TAMs in recurrent glioma accepting radiotherapy. Meanwhile, C-C motif chemokine 18 (CCL-18) was the highest elevated molecule after radiotherapy. Consistently, the above results were confirmed in tissue microarray containing 23 paired gliomas. In vitro, radiation promoted TAM polarization into M2-TAMs, accompanying CCL-18 secretion. However, CCL-18 promote non-irradiated glioma proliferation, but did not mediate glioma recurrence after radiotherapy. Mechanistically, the pro-tumor effect of CCL-18 was weakened by the down-regulation of CCL-18 receptors on glioma accepting radiotherapy. Our study indicates CCL-18 does not mediate glioma recurrence, but has the potential to serve as a biomarker for recurrent gliomas.

overall_design:
The human glioma samples were all from the neurosurgery department of the Affiliated Hospital of Xuzhou Medical University. The tissue samples were quickly obtained during operation, cleaned with cold sterile PBS, and frozen at -80 ℃. After operation, all patients were diagnosed as glioma by the pathology department of the Affiliated Hospital of Xuzhou Medical University. In addition, all patients with recurrent glioma had received the same postoperative radiotherapy regimen. Each patient provided a written consent for the use of glioma tissues. The study has been approved by the Institutional Review Board or Ethics Committee.

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Submitter states that missing raw files are due to file loss.
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first: Jiangpeng

last: Fan

first: Yufei

last: Mao

first: Li

last: Liu

first: Zhongyu

last: Ren

first: Zidong

first: Yuanqi

last: Ma

first: Xiangrong

last: Lu

first: Guimei

last: Cui

first: Xu

last: Zhang


title: EZH2 cooperates with SREBP2 to establish the epigenomic, transcriptomic and metabolic programs for driving oncogenesis [CUT&Tag I]

first: Arum

last: Kim

overall_design: CUT&Tag for Ezh2, H3K27me3, H3K27ac, and Srebp2 in WEHI-231 cells.

first: Greg

last: Wang


title: Exploring transcriptomic change in CM-Leukemia

city: MONROVIA

first: Yahuei

last: Kuo

state: CA

address: 1218 S 5TH AVE

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

summary: To explore the transcriptome change in CM-leukemia, we performed RNA-seq for bone marrow mononuclear cells from CM mice at the leukemic stage and control littermate.

overall_design: Bone marrow mononuclear cells were harvested from CM mice at the leukemic stage and control littermate and were subjected to total RNA extraction.

first: Lianjun

first: Yu-Hsuan

last: Fu

first: Ya-Huei


title: RNA-seq of bone marrow-derived macrophages(BMDMs) coclutured with mEC25 cancer cell lines

city: Shanghai

first: Chen

last: Kun

address: DonganRoad 270

institute: Shanghai Cancer Center

summary: Our findings revealed that when BMDMs cocultured with cancer cell lines in contact, auch as mEC25,their SIRPαexpression would upregulated compared with their coculture in a non-contact manner.To investigate the underlying mechanism and the altered signaling pathway involved in the SIRPα upregulation in BMDMs when their co-culture with cancer cell lines.We conduct RNA-seq based on sorting BMDMs after their co-culture with cancer cell lines in a direct or indirect way.

overall_design: RNA-seq based on sorting BMDMs after their co-culture with mEC25 in a direct or indirect way.

first: Kun

last: Chen

first: Peng

last: wang

first: Zhengfei

last: Zhu


title: RNA-seq for CMK and M07E cell line in either the absence or presence of GNE987

city: Suzhou

first: Fang

last: Fang

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare RNA-seq results for CMK and M07E cell line in either the absence or presence of GNE987.

overall_design: 2 CMK samples with no treatment and 2 CMK samples with GNE987, 2 M07E samples with no treatment and 2 M07E samples with GNE987

first: Jian

last: Pan

first: Ailian

last: Guo

first: Zhiheng

last: Li


title: Kidney collecting duct cell type composition is regulated by Notch signaling via modulation of mTORC1 activity (ChIP-Seq)

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

summary: The kidneys play an essential role in water and electrolyte homeostasis that is dependent on maintenance of intermingled epithelial cell types within tubular collecting duct segments. Notch signaling, a regulator of cell fate selection, ensures urine concentrating capacity in adult organisms by preventing water reabsorbing principal cell types in the kidney collecting duct segments from converting into mitochondria rich intercalated cell types. Here we identify that Hes1, a target of Notch signaling, allows for the maintenance of functionally different epithelial cell types with differing metabolic states within the same microenvironment by regulating mechanistic target of rapamycin complex 1 (mTORC1) activity. Hes1 directly represses mTOR pathway components, such as Irs1, and suppresses mTORC1 activity in principal cells. Increasing mTORC1 activity in mature principal cells is sufficient to initiate the acquisition of intercalated cell type properties. These findings reveal that diversity of mature epithelial cell types within collecting duct segments is dependent on the level of mTORC1 activity, and likely allows for the epithelial cell type plasticity to be regulated by physiologic cues and the ability to sense and transduce metabolic cues.

overall_design: Chromatin immunoprecipiation was performed in  mpkCCDc14 cells transfected with Hes1-FLAG under a Tet-responsive element and  reverse tetracycline transactivator (rtTA) after doxycycline treatment for 72 hours. FLAG antibody was used for ChIP and precipitated DNA fragments were sequenced.

first: Kameswaran

last: Surendran


title: EZH2 cooperates with SREBP2 to establish the epigenomic, transcriptomic and metabolic programs for driving oncogenesis [CUT&RUN I]

overall_design: CUT&RUN for EZH2, H3K27me3, H3K27ac and SREBP2 in HepG2 and Huh7 cells and the human HCC patient sample. CUT&RUN for SREBP2 in 22Rv1 cells. HepG2 and Huh7 cells were stably expressed with HA-tagged EZH2 for HA CUT&RUN.


title: Kidney collecting duct cell type composition is regulated by Notch signaling via modulation of mTORC1 activity  (RNA-Seq).

overall_design: Pax8->rtTA; TRE->Cre; Hes1 f/f mice (Hes1 cKO) and control littermate mice  were given doxycycline (1mg/mL; Sigma-Aldrich) in drinking water containing 5% sucrose for one week starting at 3 weeks of age. RNA was extracted from whole adult mouse kidneys from Hes1 cKO (9 samples) and control littermates (7 samples). The purpose was to identify genes differentially expressed in Hes1cKO versus control littermate mouse kidneys.


title: EZH2 cooperates with SREBP2 to establish the epigenomic, transcriptomic and metabolic programs for driving oncogenesis [RNA-seq I]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of transcriptomic profiles in the HepG2 or Huh7 cells post-treatment with the EZH2 PROTAC (MS7126), the matched SET enzymatic inhibitor (C24), or non-PROTAC analog controls (MS7126N1 or MS7126N2) relative to DMSO, or after shRNA-mediated depletion of EZH2 (shEZH2) or SREBP2 (shSREBP2), relative to the scramble control (shControl). Examination of transcriptomic profiles in the WEHI-231 cells post-treatment with the EZH2 PROTAC (MS8815), the matched SET enzymatic inhibitor (EPZ-6438), or non-PROTAC analog controls (MS8815N) relative to DMSO.


title: Single-cell analysis identifies TCF4 and ID3 as a molecular switch of mammary epithelial stem cell differentiation [hg_scRNAseq]

first: Jiyang

last: Yu

summary: Mammary epithelial stem cells (MaSCs) generate the various types of epithelial cells that make up the mammary gland. However, the molecular mechanisms that regulate the differentiation of MaSCs are not well understood. We conducted a comprehensive scRNA-seq profiling of murine mammary epithelial cells, and identified a unique cell population that displays molecular characteristics of MaSCs. Upon further purification and detailed analysis, we discovered that these cells are not homogeneous. Instead, we identified three distinct subpopulations that represent the initial stages of lineage commitment. We inferred the developmental trajectory and found that one of these subpopulations represents bipotent MaSCs, from which luminal and basal lineages diverge. Using a network approach, we further identified E2-2 (Tcf4) and ID3 as potential molecular switches that could influence MaSC differentiation. Finally, we verified the existence of these novel MaSCs subpopulations in human breast tissue and examined their signatures in various breast cancer subtypes.

overall_design: We performed scRNA-seq on unsorted and sorted mammary epithelial cells (MEC).

first: Erin

last: Nekritz

first: Koon-Kiu

last: Yan

first: Jose

last: Silva


title: Steroid receptor crosstalk in granulosa cells during ovulation

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

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

overall_design: Refer to individual Series


title: Single-cell analysis identifies TCF4 and ID3 as a molecular switch of mammary epithelial stem cell differentiation [mm_bulkRNAseq]


title: Single-cell analysis identifies TCF4 and ID3 as a molecular switch of mammary epithelial stem cell differentiation [mm_scRNAseq]


title: In situ targeted gene expression analysis of postnatal mouse cortex of LgDel model 22q11.2 deletion sydnrome, including treatment with antioxidant

status: Public on Aug 08 2026

city: Roanoke

first: Thomas

last: Maynard

state: VA

address: 2 Riverside Circle

institute: Virginia Tech Carilion/FBRI

summary: The antioxidant N-acetyl cysteine (NAC) restores growth and connectivity of developing upper layer cortical projection neurons and improves cognitive performance in the LgDel mouse model of 22q11.2 Deletion Syndrome. This Xenium dataset includes cortical sections of WT and LgDel cortex at postnatal day 6 (P6), with and without NAC treatment.

overall_design: Spatial transcriptomic profiling was performed on postnatal day 6 (P6) mouse cortical sections from wild-type (WT) and LgDel (22q11.2 Deletion Syndrome model) mice, with and without in vivo N-acetylcysteine (NAC) antioxidant treatment, using a customized 347-gene Xenium probe panel to characterize Layer 2/3 cortical projection neuron and neighboring cell-type transcriptional states. NAC (900 mg/L) was administered to pregnant dams via drinking water beginning at embryonic day 14 and continued to offspring through tissue collection at P6.

first: Shah

last: Rukh

first: Daniel

middle: W

last: Meechan

first: Zachary

middle: D

last: Erwin

first: A

middle: S

last: LaMantia


title: BRANCHED1 acts as a rheostat of Nuclear Factor Y-dependent epigenetic regulation in axillary bud development

city: Beijing

first: Hao

last: Zhu

address: No. 37 Xueyuan Road, Haidian District, Beijing, China

institute: Beihang University

summary: Shoot branching exhibits significant plasticity and is largely regulated by BRANCHED1 (BRC1), a key integrator of endogenous and environmental cues that acts locally to control axillary bud development. Despite its central role, the gene regulatory networks governed by BRC1 and the mechanisms underlying its regulation remain poorly understood. This study identified a cluster of transcription factor-encoding genes (C4 genes) that are dynamically responsive to multiple branching pathways (e.g., decapitation and strigolactone signalling), inversely correlated in expression with BRC1 levels, and functionally enriched in pathways related to floral organ development (FOD) and shoot system morphogenesis. Mechanistically, we demonstrate that the heterotrimeric Nuclear Factor Y (NF-Y) complex is required for transcriptional activation of representative C4 genes (e.g., the FOD genes FRUITFULL and CAULIFLOWER), functioning through chromatin looping and H3K27me3 demethylation to establish active chromatin states at target loci. In contrast, BRC1 inhibits NF-Y complex assembly and its epigenetic regulatory effects in a dose-dependent, decapitation-responsive manner, thereby enabling tunable FOD gene expression and plastic bud development. These findings position BRC1 as a molecular rheostat of NF-Y-dependent epigenetic regulation, providing mechanistic insights into the dynamic control of axillary bud development.

overall_design: RNA-seq and H3K27me3 CUT&Tag in Arabidopsis. RNA-seq compared WT seedlings under rac-GR24 vs DMSO (7 d), and axillary tissues of intact WT, intact brc1-2, and decapitated WT. CUT&Tag profiled H3K27me3 in axillary tissues of WT vs BRC1-OE12 (anti-H3K27me3, with IgG control). All in Col-0 background.

first: Mai

last: Yang

first: Jinping

last: Zhao

first: Xiaofeng

last: Shi

first: Wenzhi

last: Lan

first: Sheng

last: Luan

first: Yongbiao

last: Zhang

first: Chun


title: Changes in gene expression after astrocytes PTBP1 knockdown

city: hangzhou

first: Mengran

state: zhejiang

address: shilongshan street

institute: westlake university

summary: To test how Ptbp1 knockdown in vitro, we employed RNA-seq analysis.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of astrocyte cells ,which were treated with NCsiRNA and Ptbp1siRNA

first: Liu

first: Wenlong

first: Yunlong


title: Characterization of an Antagonistic Antibody reactive to human and mouse TNFR2 with Anti-tumor Capacity

city: Macau

first: Yang

last: Gao

address: University of Macau Research Building (N22), Avenida Avenida, University of Taipa, Macau, SAR

institute: University of Macau

summary: Accumulating evidence indicate that tumor necrosis factor receptor type II (TNFR2) is a promising target for cancer immunotherapy, but the species-restricted reactivity of anti-human TNFR2 antibodies limits their mechanistic study in mouse tumor models.

overall_design: To overcome this limitation, we developed a novel humanized antibody, designated as UM-h101, which could bind to both human and mouse TNFR2. UM-h101 inhibited TNFR2-dependent NF-κB activation and TNF-induced proliferative expansion of human and mouse regulatory T cells (Tregs), demonstrating its antagonistic property. In immunocompetent mouse tumor models, UM-h101 markedly inhibited the growth of tumors, accompanied by the reduction of Tregs and increase in the activated CD8 CTLs in tumor. Single-cell RNA sequencing revealed that UM-h101 altered the tumor microenvironment to enhance its inflammatory response against the tumor. Furthermore, CD8 CTLs from UM-h101-treated tumors displayed enhanced oxidative phosphorylation and improved mitochondrial fitness. Further mechanistic analyses showed that UM-h101 downregulated expression levels of arginase-2 (ARG2), increased availability of intracellular arginine, and thereby restored mitochondrial fitness and sustained effector function in CD8 CTLs. This study collectively identified UM-h101 as a TNFR2 antagonist that is reactive across species, which may be valuable for therapeutic development and for exploring the mechanisms of TNFR2-targeted cancer immunotherapy.


title: Transcriptomic profiling of tumor-associated macrophages following pharmacological SYK inhibition in a human breast cancer co-culture model

city: Oeiras

first: Gonçalo

last: Trindade

address: Edifício iBET BioFarma, Av. da República

country: Portugal

institute: iBET

summary: Tumor-associated macrophages contribute to immunosuppression in breast cancer. To investigate the transcriptional effects of pharmacological SYK inhibition, primary human monocytes from three healthy donors were co-cultured with BT474 breast cancer cells for 7 days in the presence of vehicle or 0.2 µM R406. CD45-positive tumor-associated macrophages were isolated by fluorescence-activated cell sorting and analyzed by bulk RNA sequencing. The dataset enables paired analysis of R406-induced transcriptional remodeling across independent donors.

overall_design: Paired bulk RNA-seq profiling of sorted tumor-associated macrophages from BT474-monocyte co-cultures established with three independent healthy donors. For each donor, cultures were treated with vehicle or 0.2 µM R406 for 7 days, yielding six libraries in total.

first: Giacomo

last: Domenici

first: Miguel

last: Pinto

first: Viviana

last: Correia

first: Sofia

last: Batalha

first: Nádia

last: Duarte

first: Angelina

last: Palma

first: Inês

last: Isidro

first: Catarina

last: Brito


title: Integrated transcriptomic and bioelectrical profiling of stem-like cellular states in a colorectal cancer using SdFFF and UHF-DEP

city: LIMOGES

first: Stéphanie

last: DURAND

address: 2 rue du Dr Marcland

department: UMR 1308 INSERM

institute: University of Limoges / INSERM

summary: Cancer stem-like cells (CSCs) enrichment and characterization remain an analytical challenge, as conventional marker-based approaches are often time-consuming and can alter cellular properties. Here, we develop a complete label-free protocol for the enrichment and characterization of cellular states associated to stemness properties in colorectal cancer model, based on the coupling adjustment of sedimentation field-flow fractionation (SdFFF) and ultra-high-frequency dielectrophoresis (UHF-DEP). To this end, the operating conditions of SdFFF were adapted to a low conductivity dielectrophoresis buffer while maintaining the hyperlayer elution regime. Fractionated cellular subpopulation exhibits phenotypic differences in proliferative status, clonogenic potential, stem-cell related protein levels and UHF-DEP highlights significantly different high-frequency crossover distributions. Transcriptome sequencing revealed dysregulation of pathways associated with stemness, cell adhesion, membrane organization, calcium signaling and ion-channel activity, that can be linked to dielectric signatures. Overall, UHF-DEP coupling to SdFFF permit to enrich, characterize and quantify stem cell-like subpopulation within heterogeneous population of cancer cells.

overall_design: RNA-seq profiling of PT, F1 and F3 subpopulations of SW480 colorectal cell line sorted by SdFFF (sedimentation field-flow fractionation), from four independant cultures.

first: Charlotte

last: Jemfer

first: Stephanie

last: Durand

first: Elisa

last: Blin

first: Gaelle

last: Begaud

first: Serge

last: Battu


title: Multi-tissue transcriptomic landscape reveals synergistic mechanisms of exercise and GLP-1 agonist in ameliorating diabetic phenotypes in db/db mice

city: Wuhan

first: Zhenghong

last: Kang

state: Hubei

address: 461 Luoyu Road, Hongshan District, Wuhan City, Hubei Province

department: School of Sports Medicine

institute: Wuhan Sports University

summary: Type 2 diabetes mellitus (T2DM) involves coordinated multi-organ metabolic dysfunction, yet the systems-level effects of combined pharmacological and exercise interventions remain unclear. Male db/db mice received semaglutide, high-intensity interval training (HIIT), or both for eight weeks. Multi-organ bulk RNA-seq with qPCR validation and CellChat analysis was performed in heart, kidney, liver, hippocampus, and skeletal muscle. Combined treatment produced the greatest reductions in food intake, body weight, and fasting glucose. Transcriptomic responses were organ-dependent, most pronounced in skeletal muscle and liver. Under combination therapy, DEGs in hippocampus and liver no longer reached thresholds relative to single interventions, consistent with unchanged hippocampal Glp1r and hepatic Plpp7 by qPCR, whereas heart, kidney, and skeletal muscle retained concordant regulation with further reductions in cardiac Cyp2ab1 and renal/muscle Apoa1. Cross-organ analysis identified coordinated modulation of the PPARα–Plin4 axis and suppression of lipid metabolic pathways, confirmed by qPCR. Inter-organ network analysis revealed increased communication numbers but reduced interaction strength under combination therapy. These findings demonstrate organ-specific transcriptional adaptation to combined HIIT and semaglutide.

overall_design: In this study, db/db mice underwent an 8-week intervention of HIIT, semaglutide administration, or their combination. Phenotypic assessments included food intake, body weight, and fasting blood glucose. Multi-organ transcriptomic profiling (heart, liver, kidney, hippocampus, skeletal muscle) was performed, followed by differential expression analysis, integrative intersection analysis, and GO/KEGG pathway enrichment to identify intervention-specific and shared molecular signatures.

first: Hua

last: Liu

first: Shijie

last: Lai

first: Jianting

last: Sun

first: Zhiyu

last: Wang

first: Yanzhi

last: Xu


title: TH-positive pulmonary nerve fiber-epithelial interaction promotes adipose thermogenesis in male mice [C22_RNA-seq]

first: Junkun

last: Jiang

address: 500 Zhennan Road, Putuo District

institute: Tongji University

summary: Cold exposure activates sympathetic neurons in adipose tissue to maintain thermal homeostasis. However, whether sympathetic activation in non-adipose tissues contributes to cross-organ regulation of adipose thermogenesis remains unclear. Here, we demonstrate the activation of TH-positive pulmonary nerve fibers (TPNFs) by cold exposure, which further promotes adipose thermogenesis. Specifically, cold exposure activates TPNFs that innervate bronchial Club cells in the lung and leads to a reduction in Secretoglobin family 3A member 1 (SCGB3A1) expression via Adrenergic Receptor β2 (ADRB2). SCGB3A1, a Club cell-specific secretory factor, binds the choline transporter SLC44A2 on adipocytes to restrict choline uptake and impair thermogenic activation. Meanwhile, TPNFs activation induces NGF secretion from Club cells, which in turn strengthens TPNFs innervation of Club cells in a feedforward loop. Importantly, the stimulation of this mechanism via tracheal infusion of the ADRB2 agonist norepinephrine (NE) enhances thermogenesis in mice.

overall_design: RNA-seq profiling of C22 cells treated with norepinephrine (NE, 10 μM) for 3 h and untreated control cells.

first: Bing

last: Luan


title: Spatial transcriptomic profiling of the larval complete intestine of Cyrtotrachelus buqueti by Stereo-seq

city: 乐山

first: 瀚宇

last: 汪

state: 四川省

address: 四川省乐山市市中区滨河路778号

department: 林竹科技创新产业研究院

institute: 乐山师范学院

summary: Stereo-seq was used to generate a spatial transcriptomic profile of one complete larval intestine of Cyrtotrachelus buqueti. The sample was collected from Leshan, Sichuan, China in July 2023. The processed data file CY_A02600D6.h5ad contains the processed spatial transcriptomic expression matrix and associated annotations.

overall_design: One complete larval intestine from a single individual was profiled by Stereo-seq. The sample was not pooled and had no biological or technical replicate. Raw sequencing files were split into multiple CY_*.fq.gz files and are submitted by GEO FTP.

first: Hanyu

first: Wencong

last: Long

first: Xuebing

last: Han

first: Wenli

last: Xin

first: Yaojun

last: Yang


title: A conserved HAND2-HAND2_OE-SMAD1/5/9 axis drives hepatic stellate cell activation and extracellular matrix overproduction in multiple fibrotic etiologies

city: Urumqi

first: Ning

state: Xinjiang

address: Liyushan South Road 138#

department: The First Affiliated Hospital

institute: Xinjiang medical univerisity

summary: The transcription factor HAND2 plays critical roles in development, but its function in hepatic stellate cells remains largely unexplored. To elucidate the transcriptional landscape modulated by HAND2, we performed RNA‑sequencing on human LX‑2 cells transduced with a lentivirus overexpressing HAND2, compared with cells transduced with empty‑vector control. Each group comprised five independent biological replicates. This dataset enables the identification of HAND2‑regulated genes and signaling pathways, providing a valuable resource for understanding the molecular actions of HAND2 in liver fibrosis.

overall_design:
LX‑2 cells were transduced with lentivirus at a multiplicity of infection (MOI) of 50. Two groups were established: Control (empty‑vector lentivirus) and HAND2‑OE (lentivirus overexpressing HAND2). At 48 hours post‑transduction, cells were harvested for RNA extraction. Each group contained five independent biological replicates (n = 5 per condition).

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

last: Lin

first: Xiaojuan

last: Bi


title: A conserved HAND2-BMP5-SMAD1/5/9 axis drives hepatic stellate cell activation and extracellular matrix overproduction in multiple fibrotic etiologies

summary: Hepatic stellate cell (HSC) activation is a key driver of liver fibrogenesis, but the transcriptional response to bone morphogenetic protein 5 (BMP5) in these cells has not been systematically characterized. To address this, we performed RNA‑sequencing on the human LX‑2 hepatic stellate cell line following stimulation with recombinant BMP5 protein, compared with vehicle‑treated controls. Each condition included five independent biological replicates to ensure statistical robustness. Total RNA was extracted, and strand‑specific libraries were prepared for high‑throughput sequencing. This dataset enables the genome‑wide identification of differentially expressed genes, pathway enrichment analyses, and the delineation of BMP5‑regulated networks in HSCs. Our transcriptomic profiles provide a comprehensive resource for understanding the molecular actions of BMP5 in hepatic fibrosis and may reveal potential targets for therapeutic intervention.

overall_design: Human hepatic stellate LX‑2 cells were divided into two groups: a treatment group stimulated with recombinant BMP5 at 100 ng/mL for 48 hours, and an untreated control group. Each group consisted of five independent biological replicates (n = 5 per condition).


title: Single-cell RNA-seq atlas of the intestine of Cyrtotrachelus buqueti

address: 四川省乐山市市中区滨河路778号

summary: Single-cell RNA sequencing was performed on gut tissues of Cyrtotrachelus buqueti, including larval anterior midgut, larval posterior midgut, larval hindgut, and adult hindgut, to characterize intestinal cell-type composition and transcriptomic heterogeneity associated with bamboo digestion.

overall_design: Four pooled biological samples were prepared for scRNA-seq. Each pooled sample consisted of tissues from eight individuals from a specific gut region or developmental stage. No independent biological replicates were prepared. Run-level FASTQ files represent technical sequencing replicates from the corresponding pooled sample.


title: 5β-Dihydrotestosterone and mutant androgen receptor vulnerability in prostate cancer

city: Notre Dame

first: Jianneng

last: Li

state: IN

address: 271 Galvin Life Sciences, Galvin building

institute: University of Notre Dame

summary: BACKGROUND Bipolar androgen therapy (BAT) exploits the paradoxical vulnerability of castration-resistant prostate cancer (CRPC) to supraphysiologic androgen, but current BAT uses testosterone (T), which broadly activates wild-type androgen receptor (AR) in normal androgen-responsive tissues and can cause systemic androgenic effects. 5β-Dihydrotestosterone (5β-DHT), a naturally occurring T metabolite, has been considered androgenically inactive because of weak wild-type AR activity. Here, we examined whether 5β-DHT and related 5β-reduced metabolites activate mutant AR signaling and reproduce BAT-like growth suppression. METHODS Six 5β-reduced T metabolites were evaluated in C4-2 and LNCaP prostate cancer cells under androgen-depleted and BAT-like conditions. AR dependence and mutant-specific activity were assessed using enzalutamide, AR-null PC-3 cells, and PC-3 cells expressing AR-W742C or AR-H875Y. Cell proliferation, AR-responsive reporter activity, RT-qPCR, RNA sequencing with gene set enrichment analysis, immunoblotting, and senescence-associated β-galactosidase staining were used to characterize ligand responses. RESULTS At nanomolar concentrations, 5β-DHT and 3β-etiocholanediol (3β-ecdiol) induced AR target genes and promoted AR-dependent C4-2 and LNCaP growth, although less potently than T. RNA sequencing showed that both metabolites activated the T-regulated AR transcriptional program with smaller differentially expressed gene footprints. At high concentrations, 5β-DHT, but not the weaker agonist 3β-ecdiol or progesterone-class steroids, suppressed C4-2 and LNCaP proliferation. High-dose 5β-DHT also activated AR and suppressed growth in PC-3 cells expressing AR-W742C or AR-H875Y, whereas AR-null PC-3 cells were unaffected. High-dose 5β-DHT enriched androgen-response and senescence programs, suppressed G2M, E2F, and MYC-associated pathways, increased p21, p27, and p57, reduced RB phosphorylation and SKP2, and induced senescence-associated β-galactosidase activity.

overall_design: Two independent bulk RNA-seq experiments in C4-2 human castration-resistant prostate cancer cells (harboring endogenous AR T878A). Experiment 1 (low-dose, androgen-depleted): cells adapted to 10% charcoal-stripped FBS (csFBS) were treated with vehicle, 10 nM testosterone (T), 10 nM 5beta-dihydrotestosterone (5beta-DHT), or 10 nM 3beta-etiocholanediol (3beta-ecdiol) for 24 h; n=3 biological replicates per condition (12 samples total). Experiment 2 (high-dose, BAT-like conditions): cells in 10% FBS were treated with vehicle, 100 nM T, or 100 nM 5beta-DHT for 1 day (24 h) or 3 days (72 h); n=3 biological replicates per condition per time point (18 samples total). Total: 30 libraries.

first: Samual

last: Adams

first: Lindsey

last: Phelan

first: Therese

last: Lewis

first: Josie

last: Behm

first: Aggie

last: Law

first: Xianglin

last: Shi

first: Guangyuan


title: Whole-transcriptome sequencing of NT2.5, NT2.5LM, and NT2.5LV: a HER2-positive murine breast cancer cell line series with lung- and liver-preferential metastasis

city: Los Angeles

first: Evanthia

middle: T

last: Roussos Torres

institute: University of Southern California

summary: The NT2.5 cell line and its lung-preferential (NT2.5LM) and liver-preferential (NT2.5LV) metastatic derivatives constitute an isogenic HER2-positive murine breast cancer model derived from neu-N transgenic FVB/N mice. To define the transcriptional programs associated with organ-preferential metastatic colonization, we performed bulk poly(A) RNA-sequencing on the three cell lines grown in vitro. Differential expression analysis identified divergent, organ-correlated transcriptional programs distinguishing the lung- and liver-preferential derivatives on a conserved genomic background. These data accompany the whole-genome sequencing of the same cell line series deposited under the same BioProject.

overall_design: Bulk poly(A) RNA-sequencing of three HER2-positive murine breast cancer cell lines grown in vitro: the parental NT2.5 line (3 biological replicates), the lung-preferential derivative NT2.5LM (2 biological replicates), and the liver-preferential derivative NT2.5LV (3 biological replicates). Paired-end 150 bp libraries were sequenced on an Illumina NovaSeq X Plus and analyzed by STAR alignment, featureCounts quantification, and edgeR TMM normalization.

first: Batul

last: Al-Zubeidy

first: Edgar

last: Gonzalez

first: Aaron

last: Baugh

first: Marqus

last: Dela Cruz

first: Cheol

last: Park

first: Matthew

last: Jacobo

first: Isaac

last: Chan

first: Michael

last: Press


title: Strain-specific modulation of host growth, biomass composition, and transcriptomic responses in Spirodela polyrhiza by duckweed-associated bacteria

city: Kofu

first: Tadashi

last: Toyama

country: Japan

institute: University of Yamanashi

summary: Duckweed-associated plant growth-promoting bacteria (PGPB) have attracted considerable attention for enhancing duckweed biomass production; however, the mechanisms underlying strain-specific plant growth promotion remain largely unknown. Here, we compared the effects of two duckweed-associated bacterial strains, Terrimicrobium sp. PS02 and Aeromicrobium sp. PS05, on the growth, biomass composition, colonization behavior, and transcriptomic responses of Spirodela polyrhiza. While both strains enhanced duckweed biomass, PS02 yielded a 1.2-fold increase, whereas PS05 induced a statistically significant increase (1.4-fold) compared with the uninoculated control. Markedly, PS05 established approximately one order of magnitude higher bacterial populations than PS02 and formed dense extracellular polymeric substance (EPS)-mediated microcolonies on duckweed surfaces. Transcriptome analysis revealed that PS05 induced 1,108 differentially expressed genes, compared with 454 genes for PS02, indicating substantially greater host transcriptomic reprogramming. Functional enrichment analyses demonstrated that PS05 preferentially regulated carbohydrate biosynthesis and central carbon metabolism. Consistently, both transcriptomic and RT-qPCR analyses showed up-regulation of key genes involved in starch biosynthesis and carbon allocation, resulting in significantly enhanced starch accumulation and turion formation without reducing protein or photosynthetic pigment content. This study provides the first integrated evidence linking bacterial colonization strategy, host transcriptomic regulation, carbon allocation, and biomass production in duckweed, thereby establishing a mechanistic basis for engineering high-performance duckweed–microbiome systems for sustainable biomass production.

overall_design: RNA-seq profiling of Spirodela polyrhiza strain UY001 to investigate strain-specific modulation by duckweed-associated bacteria. The study compares three experimental groups: a Control group, a PS05-treated group, and a PS02-treated group. Each group consists of 3 distinct biological replicates, for a total of 9 samples.

first: Karnjana

last: Ruenpham

first: Kazuhiro

last: Mori

first: Yasuhiro

last: Tanaka

first: Arinthip

last: Thamchaipenet

first: Masaaki

last: Morikawa


title: Host-derived bile acids drive dysbiosis by selecting bile-resistant epimerizing bacteria in inflammatory bowel disease

city: Vienna

first: Maximilian

last: Baumgartner

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine

summary: The gut microbiome is a key regulator of intestinal homeostasis. Although dysbiosis is pervasively reported in inflammatory bowel diseases (IBD), its drivers and impact in disease pathophysiology are not yet fully understood. By integrating public metagenomic and metabolomic datasets from >5000 individuals across 12 ethnically diverse cohorts with independent validation cohorts and using neural-network based feature attribution, we identified epimerized bile acids (BAs) produced by microbial hydroxysteroid dehydrogenases (HSDHs) as a novel hallmark of IBD-associated dysbiosis. This shift occurs alongside previously reported changes including a depletion of microbe-derived C7-dehydroxylated BAs and an accumulation of host-derived C7-hydroxylated BAs. We show that increased levels of host-derived BA lead to epithelial remodelling during disease and are sufficient to recapitulate key features of IBD-related dysbiosis, including reduced microbial diversity and expansion of bile-resistant bacteria such as Mediterraneibacter gnavus and Escherichia coli. HSDHs found in IBD-enriched bacteria facilitate growth under high host-derived BA conditions by converting these molecules into urso- and iso-forms. While epimerized 7α-dehydroxylated BA have established immunoregulatory properties, the function of host-derived BA epimers remain poorly understood. We demonstrate that epimerized host-derived BAs exhibit reduced FXR agonist activity and that increased levels of these metabolites, or the bacteria that produce them, are associated with diminished ileal FXR signaling and altered circulating FGF19 and C4 levels in IBD patients. Our findings identify enhanced BA epimerization as a defining metabolic feature of IBD-associated dysbiosis and reveal a mechanism by which bile-resistant bacteria reshape BA signaling, linking microbial adaptation, impaired host-microbiome feedback regulation, and intestinal inflammation.

overall_design: Intestinal organoid monolayers derived from human large or small intestinal biopsies were treated 24h with chenodeoxycholic acid (150 uM), GW4064 (10 uM) or DMSO control (vehicle), followed by RNA-sequencing to define bile acid-exposure and FXR-activation signatures.

first: Clarissa

last: Campbell

first: Georg

last: Busslinger


title: Immunogen-Sponge Hydrogel Reverses TIM-3–Mediated Dendritic-Cell Exhaustion in Alveolar Echinococcosis

city: xiamen

first: YESI

last: SHI

address: xiangan south road

institute: Xiamen University

summary: Alveolar echinococcosis (AE) induces profound dendritic-cell dysfunction characterized by elevated TIM-3 expression and impaired antigen presentation. To overcome parasite-induced immunosuppression, we developed a SHIFT-engineered Immunogen-Sponge hydrogel vaccine incorporating protoscolex-derived antigens (PSAs). Bone marrow-derived dendritic cells (BMDCs) were treated with saline, PSA, F127@PSA, or SHIFT-F127@PSA and subjected to transcriptome sequencing. Comparative transcriptomic analyses were performed to investigate dendritic-cell activation, antigen presentation, immune signaling pathways, and TIM-3-associated regulatory mechanisms.

overall_design: Mouse bone marrow-derived dendritic cells (BMDCs) were cultured and treated with saline, PSA, F127@PSA, or SHIFT-F127@PSA. Total RNA was extracted after treatment and subjected to bulk RNA sequencing. Three biological replicates were included for each treatment group. Differential gene expression, pathway enrichment, and immune-related transcriptomic analyses were performed.

first: Yesi

last: Shi

first: Fan

last: Dai

first: Xuqi

last: Peng

first: Gang

last: Liu


title: Strong sustained type I IFN signaling acts cell intrinsically to impair IFNγ responses and cause tuberculosis susceptibility

city: Berkeley

first: Stefan

last: Fattinger

state: California

address: 415 Weill Hall

institute: UC Berkeley

summary: Mycobacterium tuberculosis (Mtb) causes over one million deaths annually, but most infected individuals never exhibit symptoms. Type I interferons (IFNs) have emerged as a major factor driving susceptibility to Mtb, but how type I IFNs impair immunity to Mtb is a key unresolved question. Here we show that an early effect of type I IFN during Mtb infection is the cell-intrinsic impairment of IFNγ signaling. IFNγ signaling was selectively impaired in the subset of infected macrophages experiencing high and sustained levels of type I IFN signaling. Genetic elimination of RESIST, a recently described positive regulator of type I IFN production, specifically eliminated the high and sustained type I IFN response, fully restored IFNγ signaling, and rescued susceptibility to Mtb without affecting basal type I IFN responses. Our results demonstrate that strong and sustained type I IFN responses specifically and cell intrinsically impair responsiveness to IFNγ to cause susceptibility to Mtb.

overall_design: Bulk RNAseq of B6 mouse bone marrow derived macrophages exposed to IFNβ, IFNγ, TNF, TGFβ and IFNβ/γ

first: Bianca

last: Parisi

first: Roberto

last: Chavez

first: Marian

middle: R

last: Fairgrieve

first: Ophelia

last: Lee

first: Kristen

last: Witt

first: Jesse

last: Rodriguez

first: Elizabeth

last: Turcotte

first: Ella

last: Brydon

first: Harmandeep

last: Dhaliwal

first: Angus

first: Dmitri

last: Kotov

first: Russell

middle: E

last: Vance


title: FKBP8 connects the Hsp70-Hsp90 chaperone machinery to the folding of membrane proteins

city: Shanghai

first: Jia

last: Ji

address: 386 Bibo Rd, Pudong New District

department: Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry

institute: Chinese Academy of Sciences

summary: The folding of membrane protein cytoplasmic domains on the endoplasmic reticulum (ER) surface, and their coordination with transmembrane and exoplasmic regions, remains poorly understood. Through a genome-wide CRISPR-Cas9 screen, we identified the ER-anchored FK506 binding protein 8 (FKBP8) as a chaperone essential for membrane protein folding and assembly. Using ABC transporters as model substrates, we show that FKBP8 cooperates with Hsp70-Hsp90 machinery to remodel nascent or misfolded cytosolic domains into their native conformations. Cryo-EM analysis reveals that FKBP8 employs a conserved hydrophobic ϕ94ϕ96ϕ97/ϕ158ϕ162 cluster to help form a large client-binding cavity within the FKBP8–Hsp90 complex that captures folding intermediates. FKBP8 deficiency, disruption of this cluster, or disease-associated mutations within FKBP8 abolish substrate maturation, leading to ER retention and degradation. Reconstitution with purified components demonstrates that FKBP8 and Hsp40-Hsp70-HOP-Hsp90 constitute a minimal machinery capable of restoring the native structure of a misfolded ABC transporter. These findings uncover a dedicated folding module at the ER-cytosol interface that bridges cytosolic chaperones with membrane protein quality control, suggesting a broad role for FKBP8 in safeguarding the biogenesis of complex membrane proteins.

overall_design: mCherry-2A-EGFP-ABCG2(E211Q)-Cas9-Flp-In HEK293T cells transduced with a pooled CRISPR-Cas9 sgRNA library were subjected to two rounds of flow cytometry-based sorting to enrich cell populations with reduced GFP/mCherry signals. Genomic DNA was collected from control and sorted populations, and sgRNA abundance was analyzed by NGS.

first: Man-Xi

last: Ge

first: Ming-Zhi

last: Wu

first: Zhao-Peng

last: Li

first: Zhongjian

last: Bai

first: Jieyan

last: He

first: Josefa

last: Chuh

first: Yixiao

last: Zhang

first: Jing

first: Zai-Rong


title: A host-co-opted Harbinger transposase engages multiple trihelix DNA-binding factors and controls pleiotropic phenotypes

city: Shenzhen

first: Jian-Kang

last: Zhu

state: Guangdong

address: 1088 Xueyuan Blvd, Nanshan

department: Institute of Advanced Biotechnology, Institute of Homeostatic Medicine, and School of Medicine

institute: Southern University of Science and Technology

summary: Transposase domestication is a recurring theme in eukaryotic genome evolution, yet it remains unresolved whether transposase-derived proteins can be co-opted to assemble multi-partner regulatory modules with phenotypic consequences. Here we show that a PIF/Harbinger-derived protein, HDP3, associates with multiple trihelix DNA-binding factors across tissues in Arabidopsis thaliana, and that these associations are modulated by abscisic acid (ABA). Genetic studies indicate that HDP3 and a representative trihelix partner act together in promoting germination and intersect with ABA signaling to influence seedling establishment, but diverge in their contributions to leaf development and flowering time. Transcriptome profiling reveals largely overlapping regulatory effects with concordant transcriptional directionality for both induced and repressed gene sets, while highlighting a notable exception at FLOWERING LOCUS C consistent with differential timing of the vegetative-to-reproductive transition. Together, these findings suggest that HDP3 supports context-dependent transcriptional outputs – likely via dynamic partnering with these trihelix factors – thereby contributing to pleiotropic developmental outcomes.

overall_design: To assess whether HDP3 and ASIL1 exert overlapping transcriptional effects, we generated RNA-seq datasets from 2-week-old seedlings of Col-0, hdp3-2, and asil1-2. The Col-0 RNA-seq dataset used as the wild-type control has been deposited in the GEO database under accession number GSE306349.

first: Lingrui

first: Kai

last: Tang


title: Modelling mouse embryogenesis from chemically induced totipotent stem cells

first: Hua

address: Zhongguancun Street

institute: Tsinghua University

summary: The ability to faithfully initiate embryogenesis from a single, induced non-germline cell type, akin to the totipotent blastomeres, remains a significant challenge in developmental and synthetic biology. In this study, we established conditions that enabled the continuous ex utero development of mouse embryo models (EMs), starting solely from the very beginning of chemically induced totipotent-like stem cells (ciTotiSCs) and spanning the pre-implantation morula, blastocysts, and post-gastrulation stages with both embryonic and extraembryonic compartments. These ciTotiSCs self-organized into blastocyst-like structures that closely resembled natural blastocysts in both morphology and lineage segregation. The resulting ciTotiSC-derived EMs (ciToti-EMs) successfully progressed through key developmental milestones, including gastrulation, embryonic axis formation, hematopoiesis and early organogenesis, closely resembling E8.5 natural embryos (NEs). Furthermore, extended culture led to the development of functional cardiac tissues in ciToti-EMs, highly comparable to that of E10.5-NEs. These findings demonstrate an extraordinary ability of a single induced cell type, ciTotiSCs, to autonomously recapitulate the complete spectrum of early mouse embryogenesis. Our ciToti-EM system provides a powerful new model for investigating mammalian embryonic development and opens new avenues for creating multicellular organisms from non-germline cells.

overall_design: Single-cell RNA-seq of natural mouse embryos, ciTotiSCs, and ciTotiSCs-derived mouse embryo models


title: APOE genotype modifies the gene signature of microglial and astrocytic responses to aging

city: Jacksonville

last: Zhao

state: FL

address: 4500 San Pablo Rd S

department: Neuroscience

institute: Mayo Clinic

summary: To determine how APOE genotypes impact the gene signature of microglia and astrocytes during aging at single cell level, we isolated brain cells from young (3 month of age) and aged (24 month of age) APOE2 and APOE3 and APOE4 mice, and conducted single cell RNA sequencing (scRNAseq) (4 mice/age/genotype). We annotated all the cells based on their gene markers and then focused on microglia and astrocytes for further downstream analysis. We functionally annotated each subcluster with microglia and astrocytes, based on the expression pattern of the widely accepted typical maker genes from multiple publications. Further, we identified the differentially expressed genes (DEG) in the comparison between young and aged mice for each subcluster in each APOE genotype and characterized the pathways related to these DEGs. Taken together, our dataset provided comprehensive resources to understand the APOE-regulated microglial and astrocytic responses to aging.

overall_design: We isolated brain cells from young (3 month of age) and aged (24 month of age) APOE2 and APOE3 and APOE4 mice (2 mice/sex/age/genotype), and subjected them to single cell RNA sequencing.

first: Wenhui

last: Qiao

first: Tadafumi

last: Ikezu


title: Persistent ER stress in macrophages fuels age-related inflammation and vulnerability to infection

city: Beijing

first: Jialiang

last: Guan

address: No. 5 Yiheyuan Road, Haidian District

institute: Peking University

summary: Aging is accompanied by a state of chronic, low-grade inflammation known as inflammaging that underlies increased susceptibility to infection and many age-related pathologies. Although macrophages are central to immune regulation and inflammation, the molecular mechanisms driving their age-associated dysfunction remain incompletely defined. Here, we performed bulk RNA-sequencing on FACS-sorted peritoneal macrophages from young and aged mice. Analysis of differentially expressed genes revealed that genes upregulated in aged macrophages were significantly enriched for pathways related to "response to interferon-beta" and "response to interferon-gamma". Further investigation of our RNA-seq data for upstream mediators of these genes showed that Stat1 was markedly upregulated in aged macrophages. These transcriptomic findings suggest that the chronic activation of ER UPR in aged macrophages drives an enhanced ISG program, representing a potential mechanism for inflammaging.

overall_design: To investigate the molecular mechanisms underlying age-related macrophage dysfunction, we performed bulk RNA sequencing on peritoneal macrophages isolated from young (n=4) and aged (n=4) mice. This allowed for a comparison of gene expression profiles to identify pathways dysregulated during aging.

first: Tianyu

first: Ying

last: Liu


title: Identification of novel vulnerable antimalarial targets

city: Pathum Thani

first: Philip

middle: James

last: Shaw

state: Pathum Thani

address: 113 Thailand Science Park

country: Thailand

institute: BIOTEC, NSTDA

summary: To counter the threat of drug resistant malaria parasites, drug discovery efforts should be focused on compounds with novel modes of action. Furthermore, drug candidates acting on vulnerable targets should be triaged as they are most likely to be fast-acting antimalarials and have a lower propensity to resistance. Vulnerable targets can be validated by phenotypic assessment of conditional loss of function mutants. Here, we created mutants for 17 genes with the glmS ribozyme tool. Target knockdown was assessed by RNA-seq and western blotting. Target vulnerability assay of the mutants identified MDR1, UGT1, DHFS-FPGS, and GAT as vulnerable targets.

overall_design: Clonal transgenic parasites with the target gene under the control of the glmS ribozyme were treated with 2.5 mM glucosamine to induce knockdown of target gene expression. Controls were established by treatment of the same parasites with PBS. Ring-stage synchronized parasites were treated for 24 h before harvesting for RNA-seq.   Gene expression profiles of wild-type and mutant conditions were obtained from the data.


title: RNA-Seq analysis LPCAT3 knockdown effect on primary human endometrial stromal cells(HESC).

first: Jia

last: Qi

state: Shanghai

address: No.845 Lingshan Road, Pudong District, Shanghai

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

summary: Decidualization of human endometrial stromal cells (HESCs) is a critical process in the establishment of uterine receptivity and successful pregnancy. It involves profound cellular and molecular changes, including alterations in energy metabolism, which are necessary to support the increased metabolic demands of the decidualizing cells. The enzyme lysophosphatidylcholine acyltransferase 3 (LPCAT3), known for its role in lipid remodeling, is hypothesized to influence the metabolic shifts occurring during HESC decidualization. To explore this hypothesis, we employed RNA sequencing (RNA-Seq) to assess the transcriptomic changes in HESCs following LPCAT3 knockdown during the decidualization process.

overall_design: To investigate the role of LPCAT3 in regulating endometrial stromal cell function, we cultured HESCs in which LPCAT3 has been knockdown by siRNA.


title: Proof-of-concept pilot study on the biopsy transport medium (BTM) of clinical biopsies using the Banff Human Organ Transplant (B-HOT) panel

city: Leiden

first: Ziyang

address: Albinusdreef

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

summary: The proof-of-concept study demonstrated that BTM has great potential for reflecting the status of the transplanted kidney.

overall_design: Twelve random anonymized BTM samples from clinical renal allograft biopsies with delayed graft function (DGF) were used for NanoString measurements to investigate whether gene expression profiling can discriminate between these clinical scenarios.

first: Marij

last: Welters

first: Aiko

middle: P

last: de Vries

first: Hans

last: Baelde

first: Jesper

last: Kers


title: Effects of NSUN2 deficiency on the mRNA 5-methylcytosine modification of NCI-H226 cells

first: Yang

last: Jiang

address: Xincun Rd. 389

institute: Shanghai tongji hospital

type: Methylation profiling by high throughput sequencing

summary: Aim: To study the biological function of NSUN4 in mRNA 5-methylcytosine modification. Materials & methods: The NSUN4 gene was knocked down in NCI-H226 cells via shRNA. mRNA 5-methylcytosine modification were assessed using RNA-BisSeq.

overall_design:
To investigate the function of NSUN4 in mRNA 5-methylcytosine modification, we established NCI-H226 cell lines in which NSUN4 gene has been knocked down by shRNA.
Materials & methods: The NSUN4 gene was knocked down in NCI-H226 cells via shRNA. mRNA 5-methylcytosine modification were assessed using RNA-BisSeq.


title: Effect of depletion of NSUN4 on gene expression of NCI-H226 cells [RNA-seq]

summary: Aim: To study the biological function of NSUN4 in regulating gene expression and cell proliferation.

overall_design:
To investigate the function of NSUN4, we established NCI-H226 cell lines in which NSUN4 gene has been knocked down by shRNA.
Materials & methods: The NSUN4 gene was knocked down in NCI-H226 cells via shRNA. Gene expression were assessed using RNA-Seq.


title: Molecular characterization of Wilms' Tumor: insights from single nucleus analystics on Wilms' Tumor development and oncogenesis

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: Wilms tumors are known to arise from and maintain features of the embryonic kidney associated with a surprisingly heterogenous genetic and molecular landscape. To further investigate both intra-tumor and inter-tumor variability, single nucleus RNA-sequencing (snRNA-seq) was performed on favorable histology Wilms tumors capturing blastema, epithelial, and stromal components, which were analyzed in comparison to a normal kidney reference atlas established from kidney samples (including patient-matched adjacent kidney) as well as publicly available single-cell RNA-seq from 18-week human fetal kidney. The transcriptomic profiles from Wilms tumor nuclei were shown to recapitulate its known triphasic histology, with similar gene expression signatures corresponding to nephron progenitor cells as well epithelial and stromal cells from human fetal kidneys. Tumors additionally show a high percentage of cycling cells in the G2/S phase, including tumor samples with blastemal cells both resembling “uninduced” nephron progenitors as well as tumor samples with blastema expressing more “differentiated” signatures of early proximal tubules, podocytes, as well as stromal/muscle genes. Furthermore, pathway enrichment analyses in the blastemal components show nephron/kidney epithelial development as expected, but interestingly also show neuronal/axon signatures across the majority of tumor samples. Additionally, enriched pathways in a subset of the tumors include WNT and TGF-beta signaling in the non-cycling blastema and polycomb repressive complex in cycling blastemal cells, suggesting that Wilms tumor blastema not only shows significant heterogeneity in its differentiation state/trajectory but also in its potential biological pathways/drivers.

overall_design: The transcriptional profiile of Wilms' tumor diseased kidneys were compared to non-diseased kidney tissue using single-nucleus RNAseq

first: James

last: Geller


title: Using the Banff Human Organ Transplant (B-HOT) panel to profile the characteristics of BTM, along with the corresponding FFPE and frozen materials

last: Li

summary:
High correlation coefficients across the B-HOT panel (770 genes) suggested negligible effects of storage times within 24 hours on gene expression analysis.
The BTM group displayed a higher proportion of immune cell gene expression than FFPE.

overall_design: The B-HOT code set, comprising 770 genes, was employed to analyze gene expression in RNA isolated from BTM mimics, corresponding frozen and FFPE samples, and real BTM.

middle: J


title: RNA-seq for iPSC-derived macrophages with/without Lipopolysaccharide (LPS) stimulation.

city: Jeddah

first: xuan

last: zhou

address: Thwal

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Wiskott-Aldrich syndrome (WAS) is an immunodeficiency disorder caused by the dysfunction of the Wiskott-Aldrich syndrome protein (WASP). Although the effect of WASP on actin -polymerization is well studied, less is known about its role in other intracellular systems. Here we show that WASP interacts with the nucleolus in macrophages. Using induced pluripotent stem cells and the CRISPR-Cas system, we show that knocking out WASP results in reduced nucleolar size, loss of roundness, decreased sub-nucleolar structure percentage, and impaired ribosomal RNA transcription. Furthermore, we identified interactions between WASP and two nucleolar proteins, including nucleophosmin 1 (NPM1) and fibrillarin (FBL). Previous research has demonstrated that a loss of NPM1 results in heightened cytokine expression following lipopolysaccharide (LPS) stimulation. We found that WASP-deficient cells presented less NPM1 and more cytokine expression in response to LPS stimulation, providing new insights on the role of the nucleolus in immune functions. Together, our study provides new information on WASP in nucleolar function and its control of inflammatory cytokine expression in response to inflammatory stimuli.

overall_design: 0.5 million WT iMPs (WT) and WASP-KO iMPs (Mut) were treated with/without 100 μg/ml Lipopolysaccharide (LPS) for 6 hours. RNA was extracted using the Direct-zol RNA Miniprep Plus Kits (R2073) for sequencing. The experiments were repeated two times.

first: Mo

first: Xuan

last: Zhou

first: Baolei

last: Yuan


title: The vacuolar sorting protein AoVps18 regulates mycelial growth, secondary metabolism, and trap formation by modulating the morphology of vacuoles, mitochondria, and lipid droplets in Arthrobotrys oligospora

city: Kunming

first: yankun

state: Yunnan

address: Yunnan University

institute: Yunnan university

summary: The vacuolar sorting protein AoVps18 is a subunit shared between the HOPS and CORVET complexes and plays essential regulatory roles in vacuole formation. Arthrobotrys oligospora is a common nematode-trapping (NT) fungus that immobilizes and degrades nematodes by forming ingenious traps. In this study, we characterized the function of AoVps18 using gene knockout, phenotypic analysis, transcriptome, and untargeted metabolomics. The ∆Aovps18 mutants exhibited increased mycelial septa and reduced nuclei, disrupting the cell cycle and consequently slowing mycelial growth. Deletion of Aovps18 impaired the morphology of vacuoles, mitochondria, and lipid droplets, resulting in downregulated ATP contents. Both sporulation and trap formation were absent in the mutants, leading to a complete loss of pathogenicity. In the ΔAovps18 mutant strain, 6965 compounds were downregulated and 4044 compounds were upregulated, including reduced levels of three nematode chemotaxis agents: BA, SA, and 6-MOSA. Co-analysis of the transcriptome and metabolome revealed 15 KEGG pathways regulated by AoVps18. By integrating phenotypic analysis, gene expression data, and protein-protein and DNA-protein interactions, we found that AoVps18 is positively regulated by AoSte12 and negatively regulated by AoFus3. This study elucidates the function of Aovps18 in A. oligospora, explores multiple factors affecting pathogenicity, identifies several nematodes chemokines, and provides new insights into the pathogenic mechanisms of NT fungi. These findings offer a theoretical basis for developing biocontrol agents against nematodes.

overall_design: The WT and ΔAovps18 mutant strains were cultured in PDA medium at 28 °C, 180 rpm for 3 days, and mycelium was collected. The mycelium was divided and induced with about 300 nematodes for 0, 12 and 36 h, respectively. Three replicates were performed for each sample.

first: Yankun

first: Meichen

last: Zhu

first: Wenjie

last: Wang


title: RNA-seq and Cut & Tag analyses of mouse 2-cell embryos in which lamin B1 dissociation from the nuclear envelope is inhibited

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

institute: Kyushu University

summary: We have found that lamin B1 is dissociated from the nuclear envelope transiently at the 2-cell stage during mouse embryonic development. This lamin B1 dissociation is mediated by autophagy and can be inhibited by interfering with lamin B1’s binding to LC3, a factor responsible for early autophagosome formation. In order to block interaction between lamin B1 and LC3, we injected mRNA harboring the LC3-binding domain of lamin B1 to mouse embryos and examined transcriptomes of the injected embryos by RNA sequencing (RNA-seq) analysis. In addition, embryos expressed with full-length lamin B1 mRNA harboring two different types of mutations (flLB1(F454A/L457A) and flLB1(5A)) were analyzed by RNA-seq, together with non-injection control (Non2). Another injection control (flLB1(F454A/L457A)ΔC) was also performed, together with a non-injection control (Non3). Furthermore, the effect of nuclear stiffening was examined by expressing the molecular tether-anchor system (tWT), together with a mutant carrying LaG165A (tMut) and a non-injection control (Non4). Chromatin states of such embryos were analyzed by Cut & Tag using anti-H3K4me3 antibody.

overall_design: Dissociation of lamin B1 from the nuclear envelope at the 2-cell stage was inhibited by overexpressing the LC3-binding domain of lamin B1 (LC3 or sfLB1: short fragment of lamin B1) in mouse embryos. As controls, the truncated LC3-binding domain was overexpressed (tLC3 or sfLB1Δ) or non-injected embryos were used (Non). In addition, full-length lamin B1 carrying two different types of mutations (flLB1(F454A/L457A) and flLB1(5A)), together with a non-injection control (Non2), were subjected to RNA-seq analyses. Furthermore, another injection control (flLB1(F454A/L457A)ΔC), together with a non-injection control (Non3), was also subjected to RNA-seq analyses. For the molecular tether-anchor system, the tether (an elastic I27 module of titin37 whose ends were fused to a pair of GFP nanobodies, LaG16) and the anchor proteins (mEGFP-KASH-TM) were expressed in mouse 2-cell embryos by mRNA injection. Such embryos (tWT and tMut) were analyzed by RNA-seq, together with a non-injection control (Non4). RNA-seq was performed using the mouse 2-cell stage embryos, collected at 28 hours post insemination (hpi). Embryos expressed with sfLB1 were also collected at 28 hpi and H3K4me3 distribution was examined by Cut & Tag.

first: Masahito

last: Tanaka

first: Rin

last: Sakanoue

first: Kai

last: Otsuka

first: So

last: Maezawa

first: Yuta

last: Shimamoto


title: Senescent activated naive B cells promote anti-citrullinated antigen T cell responses and the transition to clinical rheumatoid arthritis

status: Public on Aug 07 2026

city: Stanford

first: Mengrui

last: Zhang

address: 291 Campus Drive

department: Division of Immunology and Rheumatology

institute: Stanford University

summary: This study profiles peripheral B cells from individuals at risk for rheumatoid arthritis (RA), including ACPA-positive converters to clinical RA, ACPA-positive non-converters, and healthy controls, at paired pre and post time points. Using 10x Genomics Chromium single-cell gene expression (scRNA-seq), antibody-derived tag / CITE-seq surface protein profiling, and B cell receptor (BCR) V(D)J sequencing, we characterize activated naive B cell states associated with progression toward clinical RA.

overall_design: Matched scRNA-seq (GEX), CITE-seq (ADT), and BCR-seq libraries were generated from enriched peripheral B cells for 26 samples (3 healthy controls, 5 ACPA+ non-converters, and 5 ACPA+ converters; each with paired pre/post draws). Raw sequencing data are available under BioProject PRJNA1344838. Processed outputs are Cell Ranger filtered feature-barcode matrices (GEX), ADT UMI count matrices (CITE-seq), and Cell Ranger BCR contig annotation files.

first: Xiaohao

last: Wu


title: Disease context dictates the cellular targets of IL-17 in inflammatory skin disease

city: San Diego

first: Kellen

last: Cavagnero

address: 9500 Gilman Dr

institute: Univeristy of California, San Diego

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

overall_design: Refer to individual Series


title: Development-inspired approach for the derivation of functional and transplantable salivary gland organoids from human pluripotent stem cells [scRNA-Seq]

city: Buffalo

first: Stelios

middle: T.

last: Andreadis

state: NY

address: 908 Furnas Hall

department: Chemical and Biological Engineering

institute: University at Buffalo

summary: Salivary gland (SG) hypofunction significantly affects the life quality of patients with hyposalivation. Current treatment options for these conditions are limited and often result in undesirable side effects. To address this issue, we developed a novel and developmentally inspired strategy to derive salivary gland epithelial progenitor (SGEP) cells from human pluripotent stem cells (PSC). Then we employed SGEP cells derived from human iPSC with a SOX10::GFP reporter to engineer three-dimensional lumenized SG organoids, with well-defined lumens and secretory function, reminiscent of human salivary glands. Upon transplantation into the submandibular gland of athymic nude mice, mCherry+ salivary gland organoids (SGO) integrated into the gland and differentiated into salivary gland phenotypes, including acinar, ductal and myoepithelial structures. Our findings suggest that SG organoids may hold promise for studying SG development, disease progression and drug screening, as well as to develop cell therapies for salivary gland regeneration.

overall_design: We have utilized a single cell sequencing method with 10x Genomics scRNAseq to study salivary gland epithelial progenitor cells (SGEPs) derived from induced pluripotent stem cells (iPSCs). Due to the lack of treatments for patients with xerostomia (hyposalivation), we have turned to regenerative medicine with a development-inspired differentiation approach. Before seeding the SGEPs into 3D scaffolds for organoid growth, we needed to assess the cell types we had in culture after differentiating from stem cells. This study represents the first analysis of SGEPs derived from iPSCs without gene overexpression or microsurgery, and demonstrating the bipotent nature of these cells to provide insights into the intricacies of salivary gland development as seen in native tissue.

first: Sai Harsha

last: Bhamidipati

first: Laura

last: Sherwood

first: Ronel

middle: Z

last: Samuel

first: Stylianos


title: Development-inspired approach for the derivation of functional and transplantable salivary gland organoids from human pluripotent stem cells [RNA-Seq]

overall_design: We have utilized bulk sequencing with 10x Genomics RNAseq to study differentiation of iPSCs through several developmental stages through surface ectoderm, oral epithelium, salivary gland epithelial progenitor cells, and three organoid stages to both verify that our cells are undergoing differentiation through specific pathways and understand at what stages the cells are proliferating or maturing. We have identified several markers of all the above-mentioned developmental stages of the salivary gland and applied them to our study, effectively demonstrating the sequential upregulation and downregulation of these genes as the cells and organoids are pushed through differentiation with different cocktails of growth factors and inhibitors. Through sequencing analysis, we can see the downregulation of pluripotency markers and upregulation of surface ectoderm (SE) markers as we begin differentiation, and the subsequent downregulation of SE markers as we continue the process. Our analysis also demonstrates early gland markers present in the organoids at beginning 3D stages, until they are downregulated with the simultaneous upregulation of mature or late-stage salivary gland markers. This study aids understanding of salivary gland development through analysis of temporal gene modulation as the cells and organoids respond to growth factors and inhibitors in the media without the use of viral gene overexpression and microsurgery.