title: Mitochondrial translation termination, recycling, and rescue in in-frame and out-of-frame contexts

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

institute: RIKEN

summary: Originating from a bacterial ancestor, the mitochondrial mRNAs have unique characters, including noncanonical stop codons and polycistronic ORFs. However, the molecular mechanisms of how mitochondrial ribosomes terminate the translation and are recycled remain obscure. Harnessing the high-resolution mitochondrial Ribo-Seq and Disome-Seq, here we showed that mtRF1L is a universal release factor for all stop codons, whereas mtRF1 only recognizes AGA/AGG noncanonical stop codons. mtRF1 also terminates mitoribosomes translating out-of-frame ORFs ended with AGA/AGG, explaining the presence of this protein in some vertebrates that do not possess the noncanonical stops in the main ORFs. We also found that mtRRF and mtIF3 require the mitoribosome recycling on stop codons and also reinitiation of internal ORF translation; mitoribosomes stalled at start codons are major substrates of rescue factors of ICT1, mtRF-R, and mtRES1; HEMK1-methylation of release factors enhances the termination reaction on the stop codons. Our results provide an overview of the dynamics of mitoribosomes ending protein synthesis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: MitoIP-Thor-Ribo-Seq and MitoIP-Thor-Disome-Seq were performed in cells depleting mitochondrial release factors, resucue factors, and recycling factors.

first: Mari

last: Mito

first: Qi

last: Fang

first: Yuzuru

last: Itoh

first: Yoichi

last: Shinkai

first: Shintaro

last: Iwasaki


title: Systemic and breast chronic inflammation and hormone disposition promote a tumor-permissive environment for breast cancer in older women (Rat snRNA-Seq)

status: Public on Jun 05 2026

city: Pittsburgh

first: Neil

last: Carleton

state: PA

address: 5051 Centre Ave

department: Pharmacology & Chemical Biology

country: USA

institute: University of Pittsburgh

type: Expression profiling by high throughput sequencing

summary: Estrogen receptor positive (ER+) breast cancer, the most common subtype of breast cancer, is an age-related disease, with the peak incidence of diagnosis occurring around age 70 despite low circulating levels of estradiol. Despite the hormone sensitivity of these age-related tumors, our understanding of the interplay between the systemic and local hormonal disposition and chronic inflammaging is limited. We show that aged F344 rats treated with the DMBA/MPA carcinogen develop more tumors at faster rates than their younger counterparts, suggesting that the aged environment accelerates tumor growth. snRNA-seq of the tumors showed broad local immune dysfunction that was associated with circulating chronic inflammation. Across a broad cohort of specimens from patients with ER+ breast cancer and age-matched donors of normal breast tissue, we observe that even with E1-predominant estrogen disposition in the systemic circulation, tumors in older patients upregulate HSD17B7 expression to convert E1 to E2 in the TME. Age-related accumulation of tumor-associated macrophages serve as signaling hubs that integrate the E2 and chemokine-driven chronic inflammatory signaling in the TME, which polarize TAMs towards a CD206+/PD-L1+, immunosuppressive phenotype. Overall, these findings suggest that the host’s chronic inflammation and hormonal disposition shape the local tumor microenvironment and are critical contributors to the age-related nature of ER+ breast cancer development and growth.

overall_design: This dataset contains the single-nuclei RNA-seq (snRNA-seq) from the six rat tumors (three tumors from younger rats and three tumors from older rars) that were sequenced as a part of the larger study. In brief, Fischer 344 (F344) rats aged 6-8 weeks old were purchased from Envigo and served as the “young” rats in the study. Aged F344 rats were obtained from the National Institutes of Aging (NIA) Rodent Colonies at 19-21 months old and served as the “older” rats in the study. To investigate the effect of age on tumor incidence and growth, we used a chemical carcinogen model. All rats were surgically implanted with a 50mg MPA pellet in a subcutaneous fashion (90 day continuous release; Innovative Research of America, #NP-161). One week following pellet implant, rats were dosed with a single oral gavage of DMBA (65mg/kg; Thermo Scientific Chemicals, #408181000) dissolved in sesame oil (Thermo Scientific Chemicals, #241002500). All rats recovered fully from pellet implant surgery and tolerated the DMBA dose. We performed 3’v3.1 Nuclei Isolation and GEX library preparation with the 10X Genomics Platform. Snap frozen tissues are dissociated with the 10X Genomics Nuclei Isolation Kit. After dissociation, nuclei suspension concentration and nuclei integrity are assessed using AOPI on the Nexcelom Cellometer Auto 2000. Libraries are then prepared according to the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) protocol using the 10X Genomics Chromium iX Instrument. The resulting full-length cDNA is checked for size and concentration on the Agilent Tapestation 4150 before proceeding with gene expression library preparation and sample indexing. Final libraries are checked for size on the Agilent Tapestation and concentration using the Invitrogen Qubit 2.0. Libraries are pooled and sequenced on the Illumina NovaSeq 6000 Instrument.

first: Sanghoon

last: Lee

first: Steffi

last: Oestereich

first: Adrian


title: Systemic and breast chronic inflammation and hormone disposition promote a tumor-permissive environment for breast cancer in older women (Human Bulk RNA-Seq)

overall_design: We used the standard procedure of RNeasy kit to extract total RNA from ER+ breast cancer samples of 83 tumor or 85 tumor-adjacent normal tissue obtained from Pitt Biospecimen Core (PBC) and grouped them by chronological age. These are the same samples present throughout the study. The NovaSeq 6000 library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the protocol provided by the manufacturer. Library size and quality were checked using Fragment Analyzer (Agilent) and fluorescent quantification on the Infinite F Nano + (Tecan). The libraries were normalized and pooled, and then sequenced using the NovaSeq 6000 Platform (Illumina) to an average of 25M 101 PE reads. Sequencing data was given as raw data with a Phred Q30 score of 80 or better. For processing, we used Rsubread (Bioconductor release 2.16) to align sequence reads to reference genome and used edgeR and limma R packages (Bioconductor release 4.0 and 3.58 respectively) to normalize gene expression level to log2 transcripts per million (TPM). We aligned sequence reads to GRCh38 release 14 human genome reference sequence and mapped the aligned sequences to Entrez Genes. After normalization, we removed genes of which expression level is zero across all samples to get 39,404 genes for further pathway analysis.


title: Systemic and breast chronic inflammation and hormone disposition promote a tumor-permissive environment for breast cancer in older women (Rat Bulk RNA-Seq)

overall_design: This dataset contains the bulk RNA-seq data from the six rat tumors (three tumors from younger rats and three tumors from older rars) that were sequenced as a part of the larger study. In brief, Fischer 344 (F344) rats aged 6-8 weeks old were purchased from Envigo and served as the “young” rats in the study. Aged F344 rats were obtained from the National Institutes of Aging (NIA) Rodent Colonies at 19-21 months old and served as the “older” rats in the study. To investigate the effect of age on tumor incidence and growth, we used a chemical carcinogen model. All rats were surgically implanted with a 50mg MPA pellet in a subcutaneous fashion (90 day continuous release; Innovative Research of America, #NP-161). One week following pellet implant, rats were dosed with a single oral gavage of DMBA (65mg/kg; Thermo Scientific Chemicals, #408181000) dissolved in sesame oil (Thermo Scientific Chemicals, #241002500). All rats recovered fully from pellet implant surgery and tolerated the DMBA dose. Bulk RNASeq sequencing was done via Azenta Life Sciences on an Illumina 2 x 150bp configuration. We used FastQC/0.11.7 to check the quality of reads followed by Trimmomatic/0.38 to remove the adapter contents. High quality reads(Q>30) were used for alignment using Star/2.7.9a followed by Picard/2.18.12 to mark duplicate and then run HTSeq/0.13.5 to count the reads and then DESeq2 to identify differentially expressed genes.


title: Systematic metabolome analysis of hematopoietic cells identified uridine as a vital anti-aging factor in hematopoiesis

city: Hangzhou

first: Xiangjun

last: Zeng

address: Zhejiang univerisity

country: China

institute: Zhejiang univerisity

summary: In this study, we employed immunomagnetic enrichment and fluorescence-activated cell sorting (FACS) to isolate 15 hematopoietic cell types, over 9×10^8 hematopoietic cells from 200 young and 150 aged mice, ranging from HSPCs to mature blood cells. UPLC-MS/MS untargeted analysis identified about 2000 metabolites in each cell population, which contributed to define cell-specific signatures and depict aging landscape of blood cells. We further validated our findings by experimentally screening metabolites delaying senescence and identified uridine as potential regulator to rejuvenate aged HSPCs. To enable public access to our dataset, we have constructed an open-source platform (MetaB, www.XXX.com) for easy data browsing and analysis. Collectively, our study developed a solid reference benchmark for metabolic studies in hematopoietic system and provided additional clarity to the mechanisms underlying hematopoietic aging.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for aged HSPCs treated with vehicle or uridine.

first: Xiaoqing

last: Li

first: Pengxu

last: Qian

first: He

last: Huang


title: The effect of glutamine on EMT and lung cancer metastasis

city: shanghai

first: Yinrui

last: Lei

state: 固态

address: 800 Dong chuan Road

department: Shanghai Center for Systems Biomedicine

institute: shanghai jiaotong university

summary: To investigate the effect of glutamine on lung cancer cell EMT and metastasis, we used TGFbeta to treat A549 cells for 24 hours, which were cultured under glutamine depletion or 0.2 mM or 0.5 mM glutamine. RNA-seq was performed to analyze the EMT signature of A549 cells with or without glutamine.

overall_design:
A549 cells were cultured under 0, 0.2mM or 0.5mM glutamine, treated with or without TGFbeta for 24 hours.
contributor: Major-bio Bio-Pharm Technology

last: LEI

first: Zilong

last: Geng


title: Myelin development in the peripheral nervous system of Trachemys scripta

status: Public on Jun 04 2026

city: Toluca

first: Rodolfo Daniel

last: Avila Aviles

address: Intituto Literario

country: Mexico

institute: Universidad Autonoma del Estado de Mexico

summary: Myelin is one of the most important features of the vertebrate nervous system, formed by glial cells. In the peripheral nervous system, Schwann cells produce myelin. While much is known about the molecules and processes involved in mammalian myelination, little is known about it in other vertebrate groups. In this study, we examined myelin development in the peripheral nerves of the turtle Trachemys scripta using qPCR, RNA sequencing, immunofluorescence, and TEM. Our findings indicate that in T. scripta, myelination begins during the late stages of embryonic development and continues beyond hatching. Expression profiles reveal both conservation and divergence of core myelination components between mammals and amphibians; however, direct gene-level comparisons across species require further investigation given our small sample size. The upregulation of orthologous myelin genes in the turtle PNS supports the idea that these components are conserved, although their timing, regulation, or network structure may differ across tetrapods. We based our inference of conservation on orthology and the coordinated expression of key myelin genes (e.g., ErbB2, Mag, Mpz, Mbp, Pmp22) in T. scripta. TEM analysis of turtle sciatic nerves shows myelin rings in a few axons starting at stage 21, increasing significantly by stage 24, and becoming prominent in most axons of the adult nerve. Furthermore, antibodies against MPZ, DRP2, and Kv1.1 indicate that T. scripta adult peripheral nerves at various axial levels contain myelin segments with structures consistent with appositions and Schmidt-Lanterman incisures. Overall, this is the first study of PNS myelin development in a reptile, demonstrating that myelination is a highly conserved process in vertebrates.

overall_design: Preliminary RNA sequencing (RNA-seq) profiling analysis of peripheral nerves from Trachemys scripta embryos at developmental stages 19 (st.19) and 21 (st.21)

first: Ricardo

last: Lara-Ramírez

first: Nikolas

last: Yousefi

first: Martin

last: van der Plas

first: Mayra

last: Sánchez-Hernández

first: Monserrat

last: Suárez-García

first: Carolina

last: Martínez-López

first: Alejandra

last: Valdés-Aviña

last: Ávila-Avilés

first: Torben

last: Ruhwedel

first: Wiebke

last: Moebius

first: Maria Elena

last: de Bellard


title: cGAS-mediated IFN-I signaling contributes to disease progression in drug-refractory epilepsy

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: Epilepsy is a prevalent neurological disease with a third of patients becoming non-responsive to antiepileptic drugs and developing drug-refractory epilepsy (DRE). Here we report that DRE disease progression is contributed by overactive cyclic GMP-AMP synthase (cGAS), a double-stranded DNA sensor that induces type I interferon (IFN-I) signaling. In human DRE microglia, we observe a robust IFN-I signature and the activation of upstream cGAS-STING signaling. Further, in mouse models of Dravet syndrome, a genetic form of DRE, we observe the activation of the cGAS pathway. We show that microglial cGAS can be activated by DNA released from hyperexcitable neurons. Genetic reduction and pharmacological inhibition of cGAS reduces epileptic phenotypes, glial inflammatory signatures, and neuronal transcriptomic changes, underscoring the therapeutic potential of targeting cGAS for DRE treatment.

overall_design: Droplet-based single nuclear RNA sequencing of cortex (CTX) and hippocampus from mice with PV Cre/+, Scn1a +/+ (n=3); and PV Cre/+, Scn1a F/+ (n=3). Droplet-based single nuclear RNA sequencing of hippocampus from mice with Scn1a +/-; cGAS +/- (n=4), Scn1a +/-; cGAS +/+ (n=4), Scn1a +/+; cGAS +/- (n=4), Scn1a +/+; cGAS +/+ (n=4), ctrl-treated Scn1a +/+ (n=4), ctrl-treated Scn1a +/- (n=4), TDI-treated Scn1a +/+ (n=4), and TDI-treated Scn1a +/- (n=4).

first: Yige

last: Fan

first: Man Ying

last: Wong

first: Zhuofan

first: Balaji

last: Krishnamachary

first: Daphne

last: Zhu

first: Mika

middle: P

last: Cadiz

first: Ravi

middle: K

last: Nagiri

first: Kendra

last: Norman

first: Pearly

last: Ye

first: Maitreyee

last: Bhagwat

first: Young Jae

last: Lee

first: Hui

last: Li

first: Jingjie

first: Sadaf

last: Amin

first: Kelli

last: Lauderdale

first: Hao

last: Chen

first: Wenjie

last: Luo

first: Shiaoching

last: Gong

first: Benjamin

middle: L

last: Liechty

first: Jorge

middle: J

last: Palop

first: Subhash

middle: C

last: Sinha

first: Junfang

last: Wu

first: Mingrui

last: Zhao


title: RPL27 promotes gastric cancer progression by enhancing oxidative phosphorylation via FMC1

city: hefei

first: yan

last: zheng

state: anhui province

address: Anhui Medical University

institute: Anhui Medical University

summary: Gastric cancer remains one of the leading causes of cancer-related mortality worldwide, highlighting the urgent need for novel biomarkers and therapeutic targets. Ribosomal proteins have emerged as critical regulators of tumorigenesis beyond their canonical roles in protein synthesis. In this study, we investigated the expression, functional role, and underlying mechanism of RPL27 in gastric cancer. RPL27 was significantly upregulated in gastric cancer tissues compared with adjacent normal tissues, as demonstrated by Western blot and immunohistochemistry. High RPL27 expression correlated with poor overall survival and showed potential as a prognostic biomarker. Functional assays revealed that RPL27 knockdown significantly suppressed gastric cancer cell proliferation, migration, and invasion. Transcriptomic analysis identified FMC1 as a key RPL27-downstream molecule, to regulate mitochondrial function, including membrane potential, morphology, DNA copy number, and ATP5A expression. Rescue experiments demonstrated that knockdown of FMC1 or treatment with the OXPHOS inhibitor oligomycin A partially reversed the malignant phenotypes induced by RPL27 overexpression. Furthermore, RPL27 knockdown significantly inhibited tumor growth in a xenograft mouse model. Collectively, our findings establish RPL27 as a novel oncogenic driver in gastric cancer and reveal that RPL27 promotes tumor progression through FMC1-dependent oxidative phosphorylation, suggesting that the RPL27-FMC1-mitochondrial function axis may represent a promising vulnerability for further investigation in gastric cancer.

overall_design: To investigate the transcriptional changes downstream of RPL27 knockdown in gastric cancer cells, we performed RNA-sequencing (RNA-seq) analysis. Two human gastric cancer cell lines, AGS and HGC-27, were separately transfected with small interfering RNA targeting RPL27 (siRPL27) or a negative control siRNA (siNC). Total RNA was extracted 48 hours post-transfection. For each cell line and condition, three independent biological replicates were prepared. RNA-seq libraries were constructed and sequenced on an Illumina NovaSeq 6000 platform.

first: Yan

last: Zheng


title: PDE5a Inhibition Restricts Cancer Metastasis by Disrupting NPC1-Mediated Cholesterol Trafficking Through a Non-canonical cGMP-Dependent Pathway

city: Frederick

first: Yongmei

state: MD

address: Post Office Box B

department: Advanced Biomedical Computational Science

institute: Frederick National Labroatory for Cancer Research

summary: To evaluate the effects of Sildenafil Citrate on the transcriptome, we performed differential gene expression profiling on three different cancer cell lines: 4T1 (breast carcinoma), MC38 (colon adenocarcinoma), and LLC (Lewis lung carcinoma) post-treatment

overall_design: The sequencing cohort comprised 18 samples across three murine cancer cell lines (4T1, MC38, and LLC). For each cell line, differential gene expression was evaluated between vehicle-treated controls (n=3) and Sildenafil Citrate-treated cells (n=3). Treatment durations were 24 hours for 4T1 and MC38, and 48 hours for LLC

first: Yarden

last: Ariav

first: Ray

last: Lipika

first: Sinha

last: Sanju

first: Ruppin

last: Eytan

first: Crawford

last: David

first: Erez

last: Ayelet


title: Gene expression during overexpression of ArPHR2/4 in Anoectochilus roxburghii Leaves

first: Shuguang

last: Wang

state: zhejiang

address: Zhejiang A&F University

institute: Zhejiang A&F University

summary: ArPHR2/4 acts as the core transcription factors in response to phosphorus starvation. They regulate the responsive signaling pathways, especially the phosphorus signaling cascade, thereby modulating the metabolic activities of downstream phosphate transporters. Overexpression of ArPHR2/4 in Anoectochilus roxburghii leaves markedly enhances the transcriptional activation of phosphorus-responsive genes. This finding provides valuable insights for exploring the phosphorus signaling pathway and associated metabolic processes.

overall_design: Leaves of Anoectochilus roxburghii with ArPHR2/4 overexpression and empty vector control were collected at 3 days after treatment and subjected to RNA-seq.

first: Aimin

last: Lv

first: Yi

last: Zhang

first: Hao

last: Li


title: Spatial Glyco-Codes Define Human Liver Pathology and Progression

city: New Haven

first: Xiaolong

last: Tian

state: CT

address: 55 Prospect St Rm 103

institute: yale university

summary: Glycosylation is a relatively underexplored aspect of the central dogma of biology, yet a key determinant of biological function and encodes disease-associated cellular states. However spatial glycomics is limited primarily by workflows that are costly, specialized, or insufficiently informative for conformation-dependent motifs. To address the need for a deep, cost-effective, and portable spatial glycomics technology, we developed spatial-GPT, a multimodal lectin-based platform for the simultaneous profiling of glycans, proteins, and transcripts from same-slide archival FFPE tissues. By combining DBiT-GPT sequencing with CODEX-GP imaging, spatial-GPT provides robust glycan detection in long-stored specimens, cost-effective multiplexing, and ascription of glycan motifs to cellular identity, pathology, and gene-regulatory programs at subcellular spatial resolution. Applied to human liver disease, spatial-GPT resolved glyco-codes of steatosis, fibrosis, cirrhosis, and hepatocellular carcinoma (HCC) subtypes, identified tumor-like glycan remodeling in premalignant regions, revealed conserved HCC-associated glycan programs, and uncovered glycan-defined immune and stromal neighborhoods across tissue microarrays. Spatial-GPT offers a practical extension of pathology, unlocking the glycan dimension on the same tissue section to expose a granularity that may be otherwise obscured by morphology, protein markers, or transcriptomics alone.

overall_design: We applied DBiT-GPT to 16 HCC FFPE blocks: 6 tumor regions and 4 matched non-tumor background liver regions from 6 patients with non–metabolic dysfunction-associated steatohepatitis hepatocellular carcinoma (non–MASH-HCC), and 6 tumor regions from another 6 patients with MASH-associated HCC. These blocks had been archived for 2 to 8 years before profiling.


title: STK25 m6A modification regulates CD4+ T cell glycolysis mediated immune imbalance in systemic lupus erythematosus

city: Hefei

first: Jingjing

last: Hu

address: NO.117 Meishan Road

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

summary: Systemic lupus erythematosus (SLE) is a complex autoimmune disease with an incompletely understood pathogenesis. N6-methyladenosine (m6A) has been implicated in immune regulation and disease progression, yet its role in disrupting immune homeostasis in SLE, particularly in CD4+ T-cell differentiation, remains poorly understood. In the present study, m6A-modified RNA immunoprecipitation sequencing (m6A-seq) and RNA sequencing (RNA-seq) of peripheral blood mononuclear cells from patients with SLE identified serine/threonine protein kinase 25 (STK25) as a candidate gene exhibiting abnormal m6A modification, and its expression was subsequently validated using reverse transcription-quantitative (RT-q)PCR. CD4+ T cells isolated from MRL/lupus-prone mice underwent lentiviral-mediated STK25 knockdown, and glycolytic activity was evaluated through measuring glucose uptake and lactate production. Western blotting and RT-qPCR demonstrated that STK25 knockdown reduced the expression of glycolysis-associated genes (glucose transporter 1, hexokinase 2, pyruvate kinase M2 and lactate dehydrogenase A) and the Treg-specific transcription factor Foxp3, while increasing the expression of the Th17- and Th2-associated transcription factors, RORγt and Gata3. Flow cytometry further confirmed enhanced differentiation of Th17 and Th2 cells accompanied by a reduction in Treg cells, indicating disruption of immune homeostasis. Collectively, these findings suggested that aberrant m6A modification contributes to the downregulation of STK25 expression, thereby promoting glycolytic reprogramming and CD4+ T-cell subset imbalance in SLE. STK25 may therefore represent a potential therapeutic target for restoring immune homeostasis in SLE.

overall_design: A total of five patients with SLE were enrolled as the observation group, while five healthy volunteers were recruited as the control group. Peripheral blood mononuclear cells (PBMCs) were collected from all participants for methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) analyses.

first: Ming

first: Yunfei

first: Lijun

last: Pang

first: Junjie

last: Chen

first: Shuangshuang

last: Shang

first: Chuanbing

last: Huang


title: Small RNA sequencing reveals placental miRNAs linked to congenital transmission of Trypanosoma cruzi

city: Lima

first: Carla

middle: Angelica

last: Apaza-Quiroz

address: Honorio Delgado 430 San Martin de Porres

country: Peru

institute: Universidad Peruana Cayetano Heredia

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Congenital transmission remains an important source of new Chagas disease cases. This study aimed to identify placental microRNAs (miRNAs) associated with congenital transmission of Trypanosoma cruzi. Methods: Placental samples from T. cruzi-infected mothers were classified according to congenital transmission status and analyzed by small RNA sequencing. Differential expression was assessed using DESeq2 with Benjamini-Hochberg false discovery rate correction. Nine candidate miRNAs were subsequently assessed by RT-qPCR. Results: Small RNA sequencing was performed in 31 placental samples, including 13 from transmitting mothers and 18 from non-transmitting mothers. hsa-miR-155-5p was the only miRNA significantly upregulated in placentas from transmitting mothers after multiple-testing correction and was selected as a candidate for further validation. Seven additional miRNAs (hsa-miR-193a-5p, hsa-miR-187-3p, hsa-miR-512-5p, hsa-miR-515-5p, hsa-miR-526a-5p, hsa-miR-99b-3p, and hsa-miR-455-5p) were selected based on nominal p-value, expression abundance, and differences in mean normalized counts between groups. RT-qPCR assessment in 15 placental samples, including 5 from transmitting mothers and 10 from non-transmitting mothers, showed higher normalized expression of hsa-miR-193a-5p and hsa-miR-187-3p in transmitting mothers.Conclusion: Placental miRNA profiling identified hsa-miR-155-5p, hsa-miR-193a-5p, and hsa-miR-187-3p as candidates for further investigation in congenital transmission of T. cruzi. These findings require confirmation in larger cohorts.

overall_design: miRNA-seq profiling of human placental tissue samples from Trypanosoma cruzi-infected mothers classified according to congenital transmission status: transmitting mothers with newborns positive for T. cruzi by qPCR and non-transmitting mothers with newborns negative for T. cruzi by qPCR.

first: Andrea

last: Diestra

first: Alejandra

last: Pando-Caciano

first: Fredy

last: Tinajeros

middle: A

first: Viviana

last: Pinedo

first: Vanessa

last: Adaui

first: Robert

last: Gilman

first: Natalie

last: Bowman

first: Mónica

last: Pajuelo-Travesaño


title: Mitochondria Directly Interact with the Nuclear Pore Complex

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: Mitochondria regulate cellular processes through direct and indirect interactions with other organelles. A well-studied example is contact with the endoplasmic reticulum at mitochondrial-associated ER membranes (MAMs)1, which control pathways including redox and calcium homeostasis2,3. Recent studies also reported direct mitochondria–nuclear membrane contacts in cancer cells and yeast that promote pro-survival signaling4,5. Here, we identify direct interactions between mitochondria and nuclear pores.  Using two unbiased proteomic screens, GST pulldown and BioID, we found that VDAC1 was the top mitochondrial candidate that interacts with the filamentous nuclear pore protein RANBP2. In vitro RANBP2 CRISPR knock-out, RANBP2 truncation, or site directed mutagenesis of RANBP2-VDAC1 interacting amino acids resulted in reduced mitochondria-nucleus proximity and decreased nuclear ATP and phosphocreatine levels. This was accompanied by a decline in levels of the nuclear phosphoproteome, and downregulation of pathways involved in histone modification, cellular differentiation and transcriptional regulation in vitro. Moreover, deletion of RANBP2 C-terminal domain in vivo in mice resulted in embryonic lethality due to cardiac and neural crest differentiation defects.  Collectively, these results describe a mechanism by which mitochondria directly interact with the NPC, a phenomenon critical for regulation of nuclear energetics and cellular differentiation. Undoubtedly, additional roles of this interact remain to be revealed.

overall_design: 3 biological replicates per group. Groups were WT and Ranbp2 KO 10T1/2 cells. Ranbp2 KO were generated in the same study using CRISPR/Cas9. Complete deletion was analyzed by qPCR, WB, and staining.

first: Ivan

last: Menendez-Montes

first: Hesham

last: Sadek


title: Transcriptomic analysis of GKB202-treated circulating tumor cells isolated from patients with lung cancer and pancreatic cancer

city: Taichung

first: Ruey-Hwang

last: Chou

address: No. 350, Section 1, Jingmao Road, Xinpeng Village, Beitun District

department: The Ph.D. Program of Biotechnology and Biomedical Industry Associate Professor

country: Taiwan

institute: China medicine univercity

summary: Circulating tumor cells (CTCs) are associated with metastatic dissemination and adaptive stress responses in cancer. In this study, patient-derived CTCs isolated from lung cancer and pancreatic cancer samples were treated with GKB202, a natural compound derived from Antrodia cinnamomea, to investigate treatment-associated transcriptomic changes. Bulk RNA sequencing was performed to compare untreated/control and GKB202-treated CTC samples. This dataset provides raw sequencing reads and processed gene-level expression matrices for evaluating the effects of GKB202 on CTC-related transcriptional programs, including stress-response and cancer-associated pathways.

overall_design: This study included matched vehicle-treated and GKB202-treated patient-derived CTC samples from lung cancer and pancreatic cancer. Lung cancer CTCs were derived from two patient samples (R24082001 and R24091001), and pancreatic cancer CTCs were derived from three patient samples (318, 414, and 531). For each matched pair, CTCs were treated with vehicle control or 2 µg/mL GKB202 for 3 days before bulk RNA sequencing. The experimental design enabled paired transcriptomic comparison of GKB202-treated CTCs against their corresponding vehicle-treated controls.

first: Long-Sheng

last: Lu

first: Tsung-Ju

last: Li

first: Chin-Chu

first: Ying-Yu

first: Ting-Wei

last: Lin

first: Yu-Fang

last: Hu


title: The alx gene family confers segmental identity to frontonasal cranial neural crest cells

city: Aurora

first: James

middle: T

last: Nichols

state: CO

department: Craniofacial Biology

institute: University of Colorado Anschutz Medical Campus

summary: Cranial neural crest cells in the pharyngeal arches give rise to vertebrate head skeletal structures. Hox genes confer segmental identity to the different arches, and Hox mutations result in mirror-image homeotic duplications. Frontonasal cranial neural crest cells reside anterior to the first pharyngeal arch, give rise to the midface skeleton, and are not considered part of the segmental series. Here, we demonstrate that alx genes confer segmental identity to this anterior-most population in zebrafish; alx mutations result in mirror-image homeotic transformations. We define the boundary between the frontonasal and arch populations and demonstrate that Alx expression is restricted to the anterior-most cranial neural crest cells in zebrafish and lamprey, suggesting these expression patterns were present early in the vertebrate lineage. We propose that frontonasal neural crest cells represent the anterior-most segment of the pharyngeal arch meristic series, and that Alx genes function as homeotic selector genes conferring their segmental identity.

overall_design: Zebrafish containing the transgenes sox10:mRFP and fli1:EGFP were genotyped for alx3 and alx4a. Animals were raised to 48 hours post fertalization and pooled by genotype. Pooled animals were dissociated and FACS was used to isolate GFP/RFP double positive cells (cranial neural crest cells). These cells were sequenced using Chromium 10x Genomics.

first: Abigail

last: Mumme-Monheit

first: Jennyfer

middle: M

last: Mitchell

first: Raisa

last: Bailon-Zambrano

first: Nadia

last: Wright

first: Lindsey

last: Neukirch

first: Margaret

last: Keating

first: Colette

last: Hopkins

first: Kent

last: Reimondy

first: Grace

middle: E

last: Gustafson

first: Nicole

middle: D

last: Moss

first: Daniel

last: Medeiros


title: Identification of novel CD52+ fibroblasts in nodular prostatic hyperplasia

city: Indianapolis

first: Oliver

last: Strobel

state: IN

address: A418 VanNuys Medical Sciences Building, 635 Barnhill Drive

department: Biochemistry and Molecular Pharmacology

institute: Indiana University School of Medicine

summary:
Benign prostatic hyperplasia (BPH) and lower urinary tract symptoms are strongly associated with chronic prostate inflammation and stromal remodeling, yet the stromal cell programs that emerge during inflammatory, nodular remodeling remain incompletely defined. A Toxoplasma gondii infection model produces persistent inflammation and nodular formations, providing an experimentally tractable system to map inflammation-linked stromal states.
We performed single-cell RNA sequencing of prostates from control and chronically infected male CBA/J mice harvested at 28 days post-infection (DPI). Stromal subset reprogramming was assessed by cluster-resolved pseudobulk differential expression and Ingenuity Pathway Analysis. Stromal expansion and Cd52⁺ fibroblast subset changes were validated by whole-section immunofluorescence at 28 and 60 DPI using a CellposeSAM-based tissue cytometry pipeline. To assess human relevance, CD52⁺ fibroblasts were evaluated in FFPE human prostate sections by comparing inflamed versus non-inflamed stromal regions.
Whole-prostate single-cell profiling resolved stromal, epithelial, immune, and seminal vesicle compartments. Infection increased immune-cell abundance and increased stromal representation among non-immune cells (53.1% in controls to 69.0% in infected prostates). Stromal reclustering identified eight subsets, including a Cd52⁺/Ccl5⁺ immune-reactive fibroblast population that showed the strongest selective expansion during infection. Whole-section imaging supported overall stromal expansion over time and Cd52⁺ fibroblasts increased during infection (trend at 28 DPI; borderline significance at 60 DPI (270% increase,  p = 0.0507), whereas Cxcl13⁺ fibroblasts remained rare and stable across conditions. Pathway analysis indicated immune-like stromal reprogramming during infection, with antigen-presentation programs enriched in larger fibroblast subsets and interferon/JAK–STAT signaling most consistently concentrated in the Cd52⁺/Ccl5⁺ subset. In human prostate tissue, CD52⁺ VIM⁺ CD45⁻ fibroblasts were significantly enriched in inflamed regions compared with paired non-inflamed regions within the same specimen (paired Wilcoxon p=0.0026).
Chronic, pathogen-driven inflammation produces selective, program-specific stromal remodeling rather than uniform fibroblast activation. An interferon-reactive Cd52⁺ fibroblast state expands during infection in mice and marks inflamed stromal microenvironments in human prostate, supporting discrete immune-reactive fibroblast programs as a prominent feature of inflammation-associated prostate remodeling.

overall_design: scRNA-seq conducted on 4 control CBA/J mouse prostates and 4 CBA/J mice that were infected with Toxoplasma gondii. Infected mice were ifected for 28 days before harvesting prostate. Mice age was 8-12 weeks for both control and experimental. Only sample numbers 3-5 (control and infected) were used for the analysis.

first: Hanyu

last: Xia

last: Ropa

first: Douglas

last: Strand

first: Travis

last: Jerde

first: Gustavo

last: Arrizabalaga


title: m6A reader IGF2BP3 promotes endometrial cancer progression through modification circ-EPB41L2

city: Guangzhou

first: Shanrong

last: Shu

address: 613 West Huangpu Avenue, Tianhe District

institute: The First Affiliated Hospital of Jinan University

summary: Endometrial cancer ranks as the primary contributor to cancer related fatalities on a global scale. IGF2BP3 is a reader protein of m6A modification and plays an important role in the carcinogenesis of many solid tumors. Here, we explored the role and underlying mechanism of IGF2BP3 on endometrial cancer.

overall_design: Bioinformatics methods were applied for detection of the expression of m6A reader protein and its effect on survival. qRT-PCR and western-blot were used to determine the expression of IGF2BP3 in cancer or para-cancer tissue. After down-regulation of IGF2BP3 expression, cell proliferation and migration were examined. The significantly expressed genes were identified through KEGG and GO assays. Additionally, the CLIP-seq database and MeRIP techniques were employed to ascertain the targets of IGF2BP3.


title: Renal mRNA sequencing of SLE mouse model treated with Qihuang Jianpi Zishen decoction

first: Jingjing

last: Hu

summary: Lupus nephritis (LN) is a severe manifestation of systemic lupus erythematosus in which immune dysregulation, metabolic reprogramming and gut dysbiosis converge on the kidney. Qihuang Jianpi Zishen decoction (JPZS), a spleen- and kidney-tonifying prescription used in traditional Chinese medicine, has shown renal protective effects, but its metabolism-centred modes of action remain unclear. Here, we combined an MRL/lpr lupus-prone mouse model with multi-omics profiling to delineate how JPZS modulates the gut–kidney axis. Female MRL/lpr mice were randomised to JPZS or vehicle, with C57BL/6 mice as healthy controls. Renal outcomes, serological autoimmunity and immune-inflammatory indices were assessed alongside 16S rRNA sequencing of faecal microbiota, untargeted serum metabolomics and renal transcriptomics, followed by integrative network analyses and targeted validation of glycolytic pathways. JPZS markedly alleviated proteinuria, serum creatinine elevation, glomerular IgG deposition and histopathological damage, and partially normalised circulating cytokines in MRL/lpr mice. JPZS reshaped lupus-associated gut dysbiosis, prominently enriching Akkermansia and restoring microbial pathways linked to carbohydrate metabolism. Concordantly, JPZS remodelled serum metabolites involved in amino-acid and central carbon metabolism and dampened a renal glycolytic gene signature centred on hexokinase 3 (HK3). Targeted assays confirmed reduced renal lactate content, a lower lactate/pyruvate ratio and down-regulation of HK3 and Ldhal6b after JPZS treatment. These findings indicate that JPZS ameliorates lupus nephritis, at least in part, by enriching Akkermansia and suppressing HK3-driven glycolysis in the kidney, highlighting a metabolism-focused mechanism linking a traditional formula to the gut–kidney axis.

overall_design: 12 SLE mouse models were randomly divided into a model group and a traditional Chinese medicine intervention group, with an additional 6 healthy control mice. After intervention, kidney tissue was taken, RNA was extracted, and polyA library sequencing was performed

first: Ming

last: Li

first: Lijun

last: Pang

first: Yunfei

first: Shuangshuang

last: Shang

first: Chuanbing

last: Huang


title: Ketogenic Diet Alleviates Acute Radiation-Induced Intestinal Injury through JAK2/STAT3/RORγt/IL-17A Signaling Pathway via Gut Microbiome

city: Yangzhou

first: Yefei

last: Zhu

address: No. 45, Taizhou Road

institute: Yangzhou University

summary: This study demonstrates that ketogenic diet (KD), a high-fat and low-carbohydrate dietary regimen, exerts protective effects against RIII through dual mechanisms involving microbial regulation and inflammatory pathway inhibition.

overall_design: After 16 weeks of intervention with ketogenic diet, high-fat diet, and normal diet on mice, a single radiation was administered to establish the RIII mouse model. One week later, the mice were sacrificed and the colon tissues were collected for RNAseq sequencing. Each group consisted of 3 mice.

last: Yang

first: Zhi

last: Ling

last: Zhou

first: Mingyang

last: Tao

first: Jingxian

last: Mao

first: Xuebing

last: Yan


title: NK2R signaling governs intestinal lipid mobilization and mucosal inflammation

city: La Jolla

first: Supriya

last: Srinivasan

state: CA

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

summary: Neuropeptidergic control of lipid metabolism is conserved and increasingly implicated in metabolic diseases, but receptor-level mechanisms remain unclear. Here we identify the neurokinin-2 receptor (NK2R) as a central node linking tachykinin signals to intestinal lipid mobilization, epithelial composition, and mucosal inflammation. Across complementary genetic and pharmacological perturbations, modulation of NK2R drives bidirectional effects. Loss or blockade of NK2R increases postprandial triglyceridemia and expands intestinal lipid stores, whereas agonism suppresses chylomicron output, reduces adiposity, and improves glycemia in diet-induced obesity. Transcriptomic and cellular analyses indicate coordinated upregulation of lipid-metabolic programs with a concomitant dampening of immune pathways in the absence of NK2R, accompanied by sex-specific remodeling of secretory lineages and male-biased protection from colitis. NK2R signaling also shaped the fecal microbiota in a genotype- and diet-dependent manner, highlighting crosstalk among neuropeptide signaling, epithelial physiology, and host-microbe interactions. These findings position NK2R as a molecular switch for intestinal lipid handling and mucosal inflammation and suggest that NK2R-targeted agonists or antagonists could be deployed as context- and sex-dependent therapeutic strategies for metabolic disease and inflammatory bowel disease.

overall_design: RNA-seq profiling of intestinal epithelial cells and perigonadal white adipose tissue of wild type and Tacr2null male and female mice fed a control low fat diet, fed a high fat diet for one week (acute), and fed a high fat diet for 12 weeks (chronic)

first: Pedro

last: Perez

first: Chung-Chih

last: Liu

first: Alessandra

last: Ferrari

first: Nicole

last: Littlejohn

first: John

last: Kennelly

first: Emma

last: Robinson

first: Van

last: Nguyen-Tran

first: Jon

last: Athanacio

first: Sean

middle: B

last: Joseph

first: Zaid

last: Amso

first: Peter

last: Tontonoz


title: Swi-Snf and Tup1-Cyc8 cooperate to antagonistically regulate gene transcription in yeast.

city: Dublin 2

first: Alastair

last: Fleming

address: College Green

department: Microbiology Dept.

country: Ireland

institute: Trinity College Dublin

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Saccharomyces cerevisiae Swi-Snf co-activator complex was the first ATP-dependent chromatin remodelling complex discovered which functions by altering promoter chromatin structure to enable gene transcription. Conversely, the yeast Tup1-Cyc8 complex was identified as the first global co-repressor which can repress transcription by establishing ordered arrays of hypoacetylated nucleosomes across gene promoters. Although studies have indicated potential cooperation between these archetypal complexes upon transcription regulation, the precise mechanism and global extent of this antagonistic interplay remains unclear. We have identified all of the genes subject to repression by Tup1-Cyc8 and activation by Swi-Snf in glucose-grown yeast. These antagonistically regulated genes are enriched for those involved in cell wall structure and sugar metabolism. The data reveals that some co-regulated genes are kept inactive by Tup1-Cyc8 in wt and are de-repressed in the absence of CYC8 in a SNF2-dependent manner. Conversely, other co-regulated genes are actively transcribed in wt at levels mediated by the net negative influence of CYC8 and the positive influence of SNF2. In all cases, co-regulated genes located nearest to telomeres are subject to the most robust regulation by Swi-Snf and Tup1-Cyc8. ChIP analysis suggests that Snf2p and Cyc8p are present at both the active and inactive co-regulated genes in wt, where SNF2 is required for full Tup1p occupancy. We show that Snf2p and Cyc8p can directly interact with each other, most likely in the context of their respective complexes, suggesting that Swi-Snf and Tup1-Cyc8 are present together at co-regulated genes. We demonstrate that the nucleosome remodelling activities by Swi-Snf and Tup1-Cyc8 are specific to each target gene and extend over the available upstream intergenic region, the length of which is dependent upon the genes chromosomal context. Together, these data/ provide a deeper insight into the interplay between Tup1-Cyc8 and Swi-Snf upon transcription regulation and /suggest their occupancy and activity are intimately intertwined to yield the target gene transcriptional outcome via chromosomal location-dependent chromatin remodelling covering the available upstream gene regions.

overall_design: ChIP-seq analysis of RNA pol II in wt and a CYC8 deletion mutant using antibody from Covance (MMS-126R). Data is from biological duplicate experiments.

first: Xuyuan

last: Guo

first: Mohamed

last: Al Hussain

first: Brenda

last: Lee

last: Byrne

first: Hadel

last: Aljaeed

first: Reham

last: Alnajjar

first: Karsten

last: Hokamp

first: Nicholas A

last: Kent

first: Michael

last: Church

first: Alastair B

first: Zain

last: M. F. Baazeem

first: Georgina

last: Smethurst

first: Carsten

last: Kröger

first: Charles

last: A. S. Banks

first: Jerry L.

last: Workman


title: scRNA-seq of vascular endothelial cells from multiple mouse tissues and human limb muscle

city: Kanazawa

first: Tomohiro

last: Iba

state: Ishikawa

address: 13-1, Takara-machi

country: Japan

institute: Kanazawa University School of Medicine

summary: In this study, we analyzed vascular endothelial cells (ECs) from multiple mouse tissues, liver, limb, and lung as well as from human limb muscle. We demonstrate that CD157-positive ECs exhibit a conserved transcriptional profile across tissues, including gene signatures associated with angiogenesis. By integrating mouse and human scRNA-seq datasets, we identified EC clusters in human tissue that display gene expression profiles similar to those of mouse CD157-positive ECs. These cells were localized to the intima of large vessels and were found to express newly identified, specific marker genes.

overall_design: Single cell RNA sequencing of vascular endothelial cells from multiple mouse tissues and human limb muscle

first: Hisamichi

last: Naito


title: Cellular Senescence in the Absence of Galactic Cosmic-Ray Muons

city: Salt

first: Javier

middle: Abel

last: Menendez

state: Girona

address: Dr Castany s/n. Parc hospitalari Marti i Julia

institute: Girona Biomedical Research Institute

summary: Cellular senescence is a protective stress-response that halts cell proliferation to prevent the accumulation of damage. Life on Earth evolved in the presence of constant, low-dose, unavoidable genotoxic stress caused by highly penetrating muons generated by cosmic rays. However, how cosmic background radiation (CBR) shapes senescence remains unclear. We exploited the Canfranc Deep Underground Laboratory (LSC-DUL), which is located 850 meters beneath the Spanish Pyrenees, to compare senescence phenomena in near-surface versus muon-depleted deep underground environments. The LSC-DUL provides 2,450 meters of water-equivalent shielding, reducing the flux of cosmic-ray muons by five orders of magnitude. Human cancer and noncancer cells were subjected to replicative, mitotic, and oxidative insults with diverse DNA damage response (DDR) activation potencies. Muon deprivation modestly but significantly reduced progression to late, lysosome-dependent SA--gal-positive states after low-DDR replicative stressors. However, high-DDR regimens were largely insensitive to the environment. Transcriptomic signatures of senescent states and the qualitative composition of senescence-associated secretory phenotypes (SASPs) were broadly conserved. Conceptually, stressed cells enter a shallow transcriptional and SASP-positive senescent basin that is permissive across CBR conditions. However, they cross a “CBR barrier” into a deeper SA--gal+ attractor less efficiently when ambient radiogenic noise is depleted and DDR amplitude is low. The robust inertia of high DDR damage readily overrides this barrier, ensuring the immediate occupation of the SA--gal+ fate regardless of the muonic environment. Our findings identify cosmogenic muons as evolutionary radiobiological calibrators of senescence decision-making in the near-surface biosphere. They also generate testable predictions for senescence operability in habitats lacking Earth’s characteristic muon flux, such as the Moon and Mars.

overall_design: RNA-seq profiling of A549 cells treated with well-established senescence inducers (bleomycin, alisertib, and palboclib) at days 1, 3, and 7 in a Deep Underground Laboratory (DUL), wich provides a near-zero CBR environment or in the equally elevated aboveground (AGL) and unshielded with natural CBR exposure.

first: Llop-Hernández

last: Àngela

first: López

last: Júlia

first: Verdura

last: Sara

first: Hernández-Antolin

last: Rebecca

first: Cid-Barrio

last: Laura

first: Peña-Garay

last: Carlos

first: Alarcón

last: Tomás

first: Cuyàs

last: Elisabet

first: Menendez

last: Javier A.


title: No evidence of the presence of dystrophin protein in rodent muscle stem cell

city: paris

first: gaspard

last: macaux

address: 24, rue du Faubourg Saint-Jacques

country: France

institute: INSERM

summary: The polarized distribution of dystrophin in muscle stem cells (MuSCs) has been found to regulate asymmetric cell division and maintain the balance between stem cell self-renewal and myogenic commitment. In Duchenne muscular dystrophy, which is associated with dystrophin deficiency, MuSC dysfunction is believed to contribute to fatal muscle wasting. This study investigated the dynamics of the polarized dystrophin distribution during MuSC activation. To this end, we used live fluorescence imaging to visualize EGFP-labeled dystrophin in muscle fibers and MuSCs in the DmdEGFP reporter mouse model. We also investigated this phenomenon in rats to assess the existence of interspecies consistency. Dystrophin was nearly absent on the apical side of quiescent MuSCs, whereas it rapidly accumulated near a subset of activated mouse MuSCs and 100% of rat MuSCs following enzymatic myofiber isolation and culture. Surprisingly, dystrophin that accumulated near MuSCs accumulated in membranes, and it was always found in continuity with the sarcolemma. Live imaging revealed that MuSCs could move from the condensed dystrophin, which remained attached to the myofiber. Additionally, we detected no dystrophin protein in MuSCs using different techniques, including immunocytochemistry capillary electrophoresis and fluorescence-activated cell sorting, whereas it was present in primary myoblasts and myotubes. Our findings indicate that dystrophin attached to activated MuSCs represents condensed sarcolemmal membranes. Our data suggest that dystrophin protein in MuSCs is not required for normal muscle regeneration.

overall_design: Nuclei were extrated from wild type mice aged of 2 months. Nuclei extraction was performed with the nuclei isolation from 10X Genomics kit. SnRNAseq library was prepared using Genomics platform.

first: Gaspard

last: Macaux

first: Stéphanie

last: Backer


title: The promyelocytic leukemia PML protein is a key immune suppressor in triple-negative breast cancer [RRBS]

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

type: Methylation profiling by high throughput sequencing

summary: Triple-negative breast cancer (TNBC) is an aggressive malignancy with limited treatment options and frequent resistance to immunotherapy. Here, we identify the targetable protein PML as a key mediator of immune evasion in TNBC via independent and converging mechanisms. We demonstrate that PML promotes the establishment of an immunosuppressive tumor microenvironment while concurrently impairing antigen presentation by tumor cells. Mechanistically, we find that PML partakes to the chronic activation of inflammatory and interferon-γ-responsive signaling, leading to constitutive activation of immunosuppressive genes, including PD-L1. Additionally, PML collaborates with DNMT1 to repress HLA gene expression, thus limiting tumor recognition and killing by cytotoxic T cells. Analysis of human TNBC datasets links high PML expression to impaired immune activation and poor responses to chemotherapy. As PML-targeting therapies are already clinically available for leukemia, our findings position PML as a promising actionable target to enhance immune responses and improve outcomes for patients with TNBC.

overall_design: MDA-MB-231 cells where infected with lentiviral vectors containing shRNA against PML and mock control.  Further analysis of DNA methylation was performed using as positive control cells  transduced with mock shRNA  with Decetabine.

first: Martina

last: Uggè

first: Cristina

last: Fracassi

first: Valentina

last: Giansanti


title: Swi-Snf and Tup1-Cyc8 directly cooperate to antagonistically regulate gene transcription in yeast.

first: Alastair

last: Fleming

overall_design:
AA-ChIP-seq; performed anchor away (AA) of Cyc8p and subsequent ChIP analysis of HA-tagged Snf2p in this strain. As a control, ChIP-seq and anaysis on Cyc8-AA strain without rapamycin addition was performed. Thus, monitoring Snf2-HA occupancy after Cyc8p depletion from nucleus.
Cyc8-AA-ChIP-seq; performed anchor away (AA) of Cyc8p and subsequent ChIP analysis of HA-tagged Snf2p in this strain (+/-Rap). Thus, monitoring Snf2-HA occupancy after Cyc8p depletion from nucleus versus the control (no Rap: Cyc8p remains in nucleus).

first: Xuyuan

last: Guo

first: Mohamed

last: Al Hussain

first: Brenda

last: Lee

first: Nicole

last: Byrne

first: Hadel

last: Aljaeed

first: Reham

last: Alnajjar

first: Karsten

last: Hokamp

first: Nicholas A

last: Kent

first: Michael

last: Church

first: Alastair B

first: Zain

last: M. F. Baazeem

first: Georgina

last: Smethurst

first: Carsten

last: Kröger

first: Charles

last: A. S. Banks

first: Jerry L.

last: Workman


title: Changes in RNA expression underlying sustained antidepressant effects

city: Yokohama City

first: Waki

last: Nakajima

state: Kanazawa-Ku

address: 3-9, Fukuura

department: Physiology

institute: Yokohama City University

summary: We performed RNA-seq profiling of the medial prefrontal cortex (mPFC) in Wistar Kyoto (WKY) rats, an animal model of treatment-resistant depression. The WKY rats were treated for 7 days with either K-4, a novel positive allosteric modulator of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR), or racemic ketamine. After a 7-day drug withdrawal period, mPFC tissues were collected and subjected to RNA-seq analysis. This study contributes to a understanding of the molecular mechanisms underlying the sustained antidepressant effects of ketamine.

overall_design: RNA-seq profiling of Wistar Kyoto rats in the medial prefrontal cortex (mPFC) on day 15 (7th days withdrawal after 7 days of daily administration of K-4 or ketamine.

first: Takuya

last: Takahashi


title: Targeting ATR signaling in sarcoma with homologous recombination deficiency

city: Zurich

first: Lara

last: Planas-Paz

address: Schmelzbergstrasse 12

department: Pathology and Molecular Pathology

country: Switzerland

institute: University Hospital Zurich

summary: Homologous recombination deficiency (HRD) has emerged as a key vulnerability in selected cancer types and is associated with response to platinum and PARPi-based treatment strategies. However, additional biomarkers and targeted therapy options are needed to broaden the range of patients that could benefit from this therapeutic niche. Here, we show that the SARC-HRD signature, composed of ten genes of the homologous recombination repair pathway, stratifies a cohort of sarcoma patients, and associates with genomic biomarkers of HRD, with disease progression and with the CINSARC prognostic signature. Equivalently to CINSARC, high levels of SARC-HRD are associated with poor metastasis-free survival, underscoring the potential of SARC-HRD to predict disease outcome. By pharmacotyping patient-derived cell models, we identified promising drug targets within the DNA damage response for sarcoma with HRD traits. Inhibition of ATR, CHK1 and WEE1 elicited synthetic lethality in sarcoma cells with HRD, which concomitantly showed an upregulation of ATR signaling. Combinatorial drug testing further revealed synergistic drug combinations between ATRi, WEE1i, PARP1/2i and chemotherapeutic agents with potential clinical impact. Mechanistically, targeting ATR signaling at multiple levels induced a replication defect and apoptotic cell death. Taken together, our results demonstrate the therapeutic benefit of targeting DDR mechanisms in sarcoma with HRDness traits and their potential clinical utility for treating a broader spectrum of tumor types.

overall_design: RNAseq of USZ sarcoma patient cohort including 12 leiomyosarcoma, 12 synovial sarcoma, 13 undifferentiated pleomorphic sarcoma, 14 myxofibrosarcoma and 11 malignant peripheral nerve sheath tumors

first: Chantal

last: Pauli


title: From degraded to deciphered: Applying ATAC-seq to forensic molecular diagnosis under degradation conditions

city: Chengdu

first: Weibo

last: Liang

address: Renmin South Road

institute: Sichuan University

summary: Current molecular diagnostic techniques in forensic science are significantly hindered by DNA degradation, underscoring the urgent need for robust molecular tools with resistance to degradation. In our previous study using a murine traumatic brain injury (TBI) model, we were the first to propose the feasibility of using ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) to identify trauma-related chromatin changes under early postmortem degradation conditions (2 hours). However, its applicability to human forensic samples remains insufficiently evaluated. This study aims to systematically assess the utility of ATAC-seq in identifying chromatin accessibility changes induced by TBI in human samples, with a particular focus on its stability and reliability under late-stage postmortem degradation. Cortical brain tissues from three human TBI cases and three matched controls were collected and subjected to sampling at 0 and 24 hours postmortem. Standard ATAC-seq protocols were used for library construction and sequencing. Downstream analyses included quality control, differential accessibility analysis, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment, and transcription factor motif analysis. All 12 samples exhibited high-quality sequencing metrics. Numerous differentially accessible chromatin regions (peaks) were identified between TBI and control groups, demonstrating the sensitivity of ATAC-seq in detecting trauma-associated chromatin alterations. Notably, no significant differences were observed between samples degraded for 0 and 24 hours, indicating the method’s robustness to degradation. Enrichment analyses revealed that differential peaks were significantly associated with biological processes and pathways relevant to TBI pathology, including axon development, synaptic signaling, and neurotrophin signaling pathways. The SOX transcription factor family emerged as a dominant motif, consistent with known mechanisms of TBI pathophysiology. This study provides compelling evidence that trauma-induced chromatin accessibility changes remain stable even in degraded forensic brain tissues, including those subject to late postmortem intervals. The high sensitivity and specificity of ATAC-seq support its potential application in forensic pathology, offering both a theoretical foundation and empirical validation for its broader use in forensic diagnostics.

overall_design: This study included six human cerebral cortex tissue samples, comprising three from patients with clinically confirmed traumatic brain injury (TBI) and three from uninjured brain tissue (Con), serving as normal controls . Informed consent was obtained from the legal guardians of all donors, and the study protocol was approved by the Ethical Committee of Sichuan University (Approval No. K2021024) and Ethics Committee of West China Hospital. (Approval No. 2022–153). To evaluate the stability and applicability of ATAC-seq in samples under different postmortem conditions, each tissue was processed under two standardized conditions: immediately after extraction (0 hours, fresh) and following controlled degradation for 24 hours in a 25 °C incubator. ATAC-seq library preparation was conducted using the TruePrep DNA Library Prep Kit V2 for Illumina TD501(Vazyme, China). A volume of 15 μl of Tn5 reaction mix (10 μl of 5 × TTBL and 5 μl of TTE Mix V50) was added following the kit instructions and thoroughly mixed. The mixture was incubated at 37 °C for 30 min. The resulting product was purified using a MinElute column (MinElute PCR Purification Kit, Qiagen, Germany). The PCR reaction setup included the purified fragmented DNA (24 μl), 5 × TAB (10 μl), PPM (5 μl), N5** (5 μl), N7** (5 μl), and TAE (1 μl). PCR amplification was carried out according to the recommended protocol in the manual. The number of cycles was determined based on pre-experiment qPCR, set at 12 cycles, calculated as the cycle number at which the curve reaches the plateau phase in qPCR plus 5. Subsequently, the DNA product was purified again using a MinElute column (MinElute PCR Purification Kit, Qiagen, Germany). DNA sorting was performed using VAHTS DNA Clean Beads (N411 Vazyme) according to the 0.55 × /1.0 × scheme. Fragmentation analysis of the DNA was conducted using a Cartridge Kit (BiOptic, Taiwan). Finally, the libraries were sequenced using Illumina NovaSeq 6000 sequencing.


title: Gene expression changes in response to acute and chronic in vitro treatment with selpercatinib and pralsetinib in a murine Trim24-Ret cell line, TR.1

first: Lynn

last: Heasley

institute: University of Colorado, Anschutz Medical Campus

summary: The TKIs selpercatinib and pralsetinib represent first line therapies for RET-positive lung cancer patients. Most patients exhibit responses, but treatment failure eventually occurs. To study acquired resistance in RET+ lung cancer, a novel murine lung cancer cell line was generated from C57BL/6 mice using an intratracheally injected Adeno-virus that contains Cas9 and guide RNAs targeting the Trim24 and Ret genes. This induces a gene rearrangement producing the Trim24-Ret fusion gene and the development of lung tumors. A cell line, TR.1 was derived from a resulting lung tumor. In an effort to understand how TR.1 cells respond to selpercatinib and pralsetinib, we treated TR.1 cells in vitro for 1-5 days with either 100nM selpercatinib or DMSO-control. In addition, TR.1 cells were made resistant to selpercatinib and pralsetinib through established dose-escalation in vitro until cultures that were resistant to ~500 nM TKI were established. TR.1 cells cultured in 0.1% DMSO over the same timeframe were used as controls.  At each time point or condition, RNA was isolated and submitted to bulk RNA-seq. These data will allow a deeper understanding of mechanisms mediating acquired resistance in RET fusion-positive patients

overall_design:
In Vitro RNA was collected from novel Trim24-Ret fusion lung adenocarcinoma cell lines treated for 1, 2, 3, 5 days with DMSO or 100nM selpercatinib and submitted to RNAseq (samples 1-8)
In Vitro RNA was collected from novel Trim24-Ret fusion lung adenocarcinoma cell lines from replicate selpercatinib and pralsetinib-resistant in vitro cultures as well as DMSO-treated TR.1 cells as a control (samples 9-14)

first: Trista

last: Hinz

first: Tristan

last: Doan

first: Abby

last: Ast


title: The Paradoxical protective effect of chronic stress on advanced Alzheimer's disease pathology

city: Jerusalem

first: Tamir

last: Ben-Hur

address: Hadassah Hospital

department: Department of Neurology

country: Israel

institute: Hadassah – Hebrew University Medical Center

summary: Background: Core pathology in Alzheimer’s disease (AD) includes amyloid-β (Aβ) deposition, gliosis, and eventual neuronal loss. Depression during midlife increases the risk of developing AD at late life. Late-life depression is highly prevalent among AD patients, but its role in AD pathogenesis is unclear, and specifically whether it pushes the brain with established AD pathology towards degeneration. CNS myeloid cells (Microglia and CNS associated macrophages) clear Aβ early on; however, in advanced disease stages, they adopt a neurotoxic phenotype that exacerbates neurodegeneration. It is unclear whether and how stress and depression influence CNS myeloid cells' dysfunction in AD and the neurodegenerative process. Methods: To investigate the impact of chronic stress on microglial function and on neurodegeneration, we utilized the 5xFAD mouse model, which exhibits extensive Aβ pathology but no neuronal loss at age 7 months, representing a late preclinical AD stage. We used a six-week chronic mild stress (CMS) paradigm to induce depressive behavior, after which CNS myeloid cell activation state was evaluated by transcriptomic analysis, activation marker expression and oxidation function. Neuronal and microglial densities were assessed histologically. Results: Transcriptomic analysis of freshly isolated CNS myeloid cells showed a basal hyper-activated state in non-stressed 5xFAD mice, whereas CMS suppressed multiple immunologic and metabolic pathways. CMS reduced CD68 expression, and reduced oxidative function in CNS myeloid cells. CMS did not induce neurodegeneration in the (behavioral-relevant) pre-frontal, primary motor, hippocampal and Amygdalar cortices in 5xFAD mice. Rather, CMS protected these regions from microglia-mediated neurodegeneration, caused by a microbial TLR2 agonist. Conclusion: Chronic stress and depression attenuate CNS myeloid cells. While this has been shown to promote amyloid pathology at early stages, similar attenuation of CNS myeloid cells at the stage of established AD pathology may interfere with their transition into fully neurotoxic microglia which cause neurodegeneration. These findings highlight the importance of tailoring microglial-targeted therapies to the stage-dependent roles of these cells during AD progression.

overall_design: RNA-Seq profiling of CD11b+ cells isolated from whole brains of stressed and non-stresssed, wild type and 5xFAD mice.

first: Yoel

last: Shor

first: Yuval

last: Nevo


title: Transcriptomic Profiling of HRMVPC and HRMEC Co-culture Under Normal and High Glucose Conditions

city: Luzhou

first: Xiaoqin

last: Shi

state: Sichuan

address: No. 1, Xianglin Road, Longmata District, Luzhou City,

institute: The Affiliated Hospital of Southwest Medical University

summary: We investigated the transcriptomic alterations in human retinal microvascular pericytes (HRMVPC-Immortalized) exposed to normal and high glucose conditions, with or without co-culture with human retinal microvascular endothelial cells (HRMEC-Immortalized). The study aimed to elucidate how glucose levels and endothelial interaction influence pericyte gene expression, providing insights into the cellular mechanisms potentially involved in diabetic retinopathy.

overall_design: HRMVPCs were cultured in DMEM (Gibco), and HRMECs were maintained in Endothelial Cell Medium (ScienCell). Co-culture experiments were conducted using 6-well culture plates (Corning, Costar® 3412) under standard conditions (37°C, 5% CO₂) for 24 hours. Three experimental groups were established: 1.Normal Glucose Co-culture Group (NG): HRMVPCs and HRMECs co-cultured in 5.5 mM glucose medium for 24 hours. 2.High Glucose Co-culture Group (HG): HRMVPCs and HRMECs co-cultured in 25 mM glucose medium for 24 hours. 3.High Glucose Pericyte-only Group (HG-P): HRMVPCs cultured alone in 25 mM glucose medium for 24 hours. After incubation, pericytes from the lower compartment were collected, washed, and lysed using TRIzol reagent. Total RNA was extracted, and libraries were prepared by a commercial sequencing service provider for whole transcriptome sequencing.

first: Siyan

last: Liu

first: Hongmei

last: Deng

first: Zhiyuan

last: Wang

first: Hongbin

last: Lv


title: Targeting transcriptional addiction to pro-proliferative programs in pancreatic cancer [ChIPmentation]

city: Göttingen

first: Adi

last: Mackay

address: Robert-Koch-Straße 40

department: Pathology

country: Germany

institute: University Medical Center Göttingen

summary: The pancreas is a special organ which is considered both endocrine and exocrine. The exocrine pancreas gives rise to pancreatic ductal adenocarcinoma (PDAC), which accounts for the majority of pancreatic cancer cases. In recent years, various new therapeutic options for cancer patients have resulted in increased survival, but these advancements do not include PDAC patients, who still present with a 5-year survival rate of only 13%. Therefore, there is an increasing need for finding new therapeutic targets to treat PDAC. Here, we identify the chromatin binding protein HMGB2 as a promising option. HMGB2 is overexpressed in multiple cancer types and correlates with their replicative potential. Using multiple models from patient tissue to organoids and mice, we assign a key role to HMGB2 in the proliferation control of PDAC. Using single-cell multiomics, we uncover how HMGB2 affects chromatin accessibility at a plethora of cell cycle-related gene loci, thereby directly controlling their expression. We further demonstrate how HMGB2 pharmacological targeting constrains cell proliferation and accordingly propose that it represents a ubiquitous and attractive anti-proliferative target in the fight against PDAC.

overall_design: Genomic approaches like single cell transcriptomics, RNA-seq and ChIPmentation were used in different PDAC models (cell line- Panc1, Patient derived organoids and transplanted mice) under ICM treatment, HMGB2 knockdown or control conditions.


title: Targeting transcriptional addiction to pro-proliferative programs in pancreatic cancer

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

overall_design: Refer to individual Series


title: Targeting transcriptional addiction to pro-proliferative programs in pancreatic cancer [ChIPmentation organoid]

overall_design:
Genomic approaches like single cell transcriptomics, RNA-seq and ChIPmentation were used in different PDAC models (cell line- Panc1, Patient derived organoids and transplanted mice) under ICM treatment, HMGB2 knockdown or control conditions.

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


title: Targeting transcriptional addiction to pro-proliferative programs in pancreatic cancer [scATAC organoids]


title: Targeting transcriptional addiction to pro-proliferative programs in pancreatic cancer [scRNA organoids]


title: Targeting transcriptional addiction to pro-proliferative programs in pancreatic cancer [scRNA mouse]


title: Targeting transcriptional addiction to pro-proliferative programs in pancreatic cancer [scATAC_Mice]


title: Gene Expression Profiling of the L4-stage Nematode Caenorhabditis elegans Following Ethanol Exposure

city: Duarte

first: Ching

last: Ouyang

address: 1500 E. Duarte Rd.

institute: City of Hope National Medical Center

summary: Previous studies have suggested that low to moderate alcohol exposure can extend Caenorhabditis elegans (C. elegans) lifespan, but early molecular mechanisms linking ethanol exposure to longevity have not been fully characterized. Here, we investigated how ethanol treatment affects transcriptional networks in L4-stage C. elegans by time-resolved RNA-seq. L4-stage C. elegans were exposed to 5% ethanol and time-resolved RNA-seq was performed after 1, 4, and 20 hours in solution cultures, followed by differential gene expression and KEGG pathway-based Gene Set Enrichment Analysis. At 1 hour, GSEA analysis showed significant enrichment of genes in the Longevity regulating pathway (worm) with elevated expression. Core-enrichment genes exhibited coordinated upregulation of redox-defense modules, including glutathione S-transferases (gst) and p38 MAPK components (pmk-2/pmk-3), consistent with upregulation of SKN-1/Nrf2-related stress-response genes. Detoxification (gpx and fmo families) and lipid-remodeling genes were enriched at 1 hour. By 4 hours, sod-3, a canonical DAF-16/FOXO target, was clearly upregulated, suggesting engagement of DAF-16-associated antioxidant responses, whereas Peroxisome and TGF-β signaling pathways were significantly downregulated. Together, these findings provide transcriptomic insights into a temporally structured longevity-associated response to ethanol exposure, in which early detoxification and antioxidant programs, together with membrane-lipid remodeling, are followed by DAF-16-associated gene induction and repression of peroxisome- and development-related signaling. These pathway-level changes highlight candidate biological processes potentially associated with ethanol-linked lifespan modulation in C. elegans.

overall_design: Time‑course RNA‑seq on synchronized L3 larvae of C. elegans (N2). Worms were exposed to 0% (control) or 5% (v/v) ethanol in S-basal buffer for 1, 4, and 20 hours.

first: Masaki

last: Miyazawa

first: Yoko

last: Fujita-Yamaguchi


title: The promyelocytic leukemia PML protein is a key immune suppressor in triple-negative breast cancer

first: Rosa

last: Bernardi

overall_design: Sorted CD45+ cells from tumoral tissues were counted and assessed for viability and prepared for single-cell RNA sequencing using the 10x Chromium platform (10x Genomics) following the manufacturer's protocol.

first: Martina

last: Uggè

first: Cristina

last: Fracassi

first: Anna

middle: S

last: Tascini

first: Matteo

last: Dugo

first: Francesca

last: Giannese


title: Targeting transcriptional addiction to pro-proliferative programs in pancreatic cancer [RNAKD]


title: Single cell RNA sequencing of different Kupffer cell subsets in a mycobacterial infection

city: Freiburg

first: Philipp

last: Henneke

state: Baden-Württemberg

address: Breisacher Straße 115 B

department: Institute for Infection Prevention and Control (IIK)

institute: University Hospital Freiburg

summary: Kupffer cells can be distinguished in three subpopulations during mycobacterial infection based on the expression of Tim4 and the fluorochrome tdTomato within Clec4fCre-tdTomato-NLS: ROSA26EYFP mice. These subpopulations differ in their origin and tissue localization. The aim of this scRNA sequencing was to understand the heterogeneity of macrophages and monocytes during the peak of the infection (4 weeks) and the resolution (10 weeks) and understand their dynamics.

overall_design:
Kupffer cell subsets from Clec4fCre-tdTomato-NLS: ROSA26EYFP mice 4 or 10 weeks after i.v. injection of BCG or PBS were isolated and sorted by flow cytometry.
** Please note that processed data files generated from both Gex and Hash raw data are linked to the correponding Gex sample records.

first: Jana

last: Neuber

first: Sagar

last: Sagar


title: Butyrate is anti-inflammatory at low and pro-inflammatory at high concentrations

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: Butyrate is a four-carbon short-chain fatty acid produced from microbial fermentation of dietary fibers present at high millimolar concentrations in the colonic lumen.However, in an intact epithelium, macrophages residing in the lamina propria areexposed to only sub-millimolar butyrate concentrations. Current studies show antiinflammatoryproperties of butyrate and suggest that it might have therapeuticapplications in inflammatory bowel disease and colonic cancer. We now show that theeffect of butyrate on human macrophages is strongly concentration dependent. At lowconcentrations (0.1–1 mM), butyrate suppresses LPS-induced production ofproinflammatory cytokines potentially through a combination PPAR-γ signaling andincreased histone acetylation. At high concentrations (10 mM), butyrate promotesproduction of inflammatory cytokines in a mechanism that involves G protein-coupledreceptor GPR109A, the lipid transporter CD36, and the kinase SRC. We propose thatbutyrate is a crucial signaling molecule for intestinal integrity, since intestinaldisruption exposes macrophages to high butyrate concentrations.

overall_design: RNA-seq analysis of human macrophages treated with different concentrations of butyrate

first: Muwei

last: Jiang

first: Rutger

last: Modderman

first: Aina

last: Altimira Lazaro

first: Iris

middle: H

last: Jonkers

first: Frans

last: Bianchi

first: Geert

last: van den Bogaart


title: Effects of autologous muscs transplantation on endogenous muscle stem cells and hindlimb muscles in mice.

city: Beijing

first: xupeng

last: liu

state: Beijing

address: No.3 Datun Road, Chaoyang District

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

summary: Skeletal muscle is not only the main motor organ, but also plays a vital role in secreting factors regulating systematic metabolism and aging. It has become an area of interest for new solutions to address metabolic diseases and aging associated muscle dysfunction. In this study, we proposed a new method of subcutaneous transplantation of synthetic and regenerated autologous myocytes to overcome natural physical limitations and increase latent exercise capacity. Engineered myografts exhibited mature, vascularized structures that contract continuously in the body and effectively transport therapeutic proteins. Our results suggest that whole-body muscle mass and functions are enhanced, and both metabolic and regenerative outcomes are improved in aging and obesity mouse models.

overall_design: We isolated muscle stem cells from mice by biopsy, and then isolated autologous muscle stem cells from the non-transplanted area by biopsy after autologous transplantation. On the one hand, we observed the changes in gene expression of endogenous MuSCs before and after autologous transplantation of MuSCS by RNA sequencing, and on the other hand, we also analyzed the differences in gene expression in the lower hindlimb muscles of transplanted and non-transplanted mice.

first: Xupeng

last: Liu

first: Shyh-Chang

last: Ng


title: Clonal replacement and differentiation of HIV-specific T-cells in people with HIV following anti-PD-1 in vivo

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

summary: Antiretroviral therapy (ART) in people with HIV (PWH) is highly effective but treatment is required lifelong given the persistence of virus in a latent form as well as ongoing immune dysfunction characterized by elevated expression of the exhaustion marker Programmed cell Death protein- 1 (PD-1) on HIV-specific T cells. We isolated tetramer+ HIV-specific CD8+ T-cells from PWH on ART with cancer who received anti-PD-1 (nivolumab) every 2 weeks. and observed rapid changes following the first dose of anti-PD1, including a marked increase in the frequency of HIV-tetramer+ TEX cells in a subset of participants. Using single cell RNAseq on tetramer+ cells, we observed a distinct transcriptomic signature in tetramer+ central memory T (TCM) cells and the recruitment of multiple unique TCR clones. These findings are consistent with reinvigoration and rejuvenation of HIV-specific T-cells and evidence of clonal replacement of HIV-specific cells by anti-PD-1.

overall_design: CD8 HIV antigen specific cells were sorted using a panel of 10 tetramers presenting dominant HIV epitopes of the gag, nef, vif and pol protein in the context of HLA-A2, -B7, -B8, or A3. One timepoint sample from 8-9 donors were pooled into the reaction, additionally each sample had been labelled with hash tagging antibodies. We used the Chromium Next GEM Single Cell 5’v2 kit, including TCR amplification and feature barcoding technology.

first: Celine

last: Gubser

last: Schröder

first: Sharon

last: Lewin


title: The restricted N-glycome of neurons is programmed during differentiation

city: Chapel Hill

first: Robert

middle: G

last: Mealer

state: NC

address: 120 Mason Farm Road, 5023F

institute: University of North Carolina at Chapel Hill

summary: The protein glycome of individual cell types in the brain is unexplored, despite the critical function of these modifications in development and disease. In aggregate, the most abundant asparagine (N-) linked glycans in the adult brain are high mannose structures, and specifically Man5GlcNAc2 (Man-5), which normally exits the ER for further processing in the Golgi. Mannose structures are uncommon in other organs and often overlooked or excluded in most studies. To understand cell-specific contributions to the unique brain N-glycome and its abundance of Man-5, we performed RNA-seq and MALDI-MS TOF protein N-glycomics at several timepoints during differentiation of multiple cell types. To this end, homogeneous cultures of glutamatergic neurons, GABAergic neurons, and brain-specific endothelial cells were generated from monoclonal human inducible pluripotent stem cells (hiPSCs) through cellular reprogramming. Small molecule induction of stably integrated synthetic transcription units driving morphogen expression generated differentiated cells with distinct patterns mirroring intact tissue. Comparing uninduced hiPSCs for each cell type revealed identical transcriptomic and glycomic profiles before differentiation, with low quantities of Man-5. In differentiated glutamatergic and GABAergic neurons, the most abundant N-glycans became Man-5 and its immediate precursor Man-6, despite the presence of transcripts encoding enzymes for their subsequent modification. Differentiation to brain-specific endothelial cells showed an opposite effect, with the N-glycome displaying an abundance of complex N-glycans and terminal modifications of the late secretory pathway. These results confirm that the restricted N-glycome profile of brain is programmed into neuronal differentiation, with regulation independent of the transcriptome and under tight evolutionary constraint.

overall_design: RNA-seq and MALDI-TOF MS Glycomics analysis of hiPSC derived neurons and endothelial cells

first: Cetinbas

last: Murat

first: Sadreyev

last: Ruslan

first: Mealer

last: Robert


title: Function of primary human mast cells (huMCs) in cholangiocarcinoma tissue.

city: JiNan

first: Anda

last: Shi

address: Culture West Road num 107

institute: Qilu Hospital

summary: The tumor microenvironment of cholangiocarcinoma involves mast cells playing a crucial role. Given that cholangiocarcinoma is frequently associated with biliary obstruction and cholestasis, mast cells might exhibit distinctive pathological functions under conditions of heightened bile stimulation.

overall_design: Genomic expression in human primary mast cells following cholangiocarcinoma (CCA) and calculusofcommonbileductsbile (CBDS) bile stimulation.

first: Zongli

last: Zhang


title: The functional impact of CCL17 on cholangiocarcinoma cells.

summary: The cytokine CCL17 is a potential signaling molecule in the microenvironment of cholangiocarcinoma. The downstream mechanisms of its action on tumor cells are yet to be studied.

overall_design: Assess the gene expression changes in cholangiocarcinoma cells following stimulation with CCL17 and its inhibitor C-021.


title: Pcbp1 is crucial for Naïve-to-Primed pluripotency transition due to regulation of amino acid metabolism

city: Haifa

first: Evgeny

last: Potapenko

address: Abba Khoushy Ave 199

department: Institute of Evolution

institute: University of Haifa


title: Pcbp1 is crucial for Naïve-to-Primed pluripotency transition due to regulation of amino acid metabolism [ChIP-seq]

summary: Embryo implantation coincides with the Naïve-to-Primed pluripotency transition. From fertilization to implantation only a number of cleavages is observed without significant embryo growth. Embryo-uterine connection provides necessary nutrients for further development while metabolism intensification is occurred. We have found that in vitro Naïve-to-Primed pluripotency transition of ESCs with Pcbp1 knockout is worsened – reduction of proliferation and cell death is observed. By using ChIP-seq, RNA-seq and Mass-spectrometry we show that Pcbp1 is detrimental for pluripotent properties, but is crucial for amino acid metabolism intensification. According to this, functional approaches showed protein synthesis decline, while embryos deficient for Pcbp1 demonstrated growth absence after implantation.

overall_design: ChIP-seq for Pcbp1 protein in two conditions of murine pluripotent stem cells - Naïve embryonic stem cells (Naïve) and Primed epiblast-like stem cells (EpiLC).

last: Bakhmet

first: Nadezhda

last: Vorobyeva


title: Pcbp1 is crucial for Naïve-to-Primed pluripotency transition due to regulation of amino acid metabolism [RNA-seq]

overall_design: To investigate molecular mechanisms affected in ESCs with Pcbp1 knockout during Naïve-to-EpiLC transition, RNA-seq of three independent control (Scr) clones and three independent Pcbp1-ko clones in two culture conditions (Naïve and EpiLC) was performed.


title: snRNAseq of mouse kidney from proximal tubule ACE KO mice

city: Los Angeles

first: Jonathan

middle: William

last: Nelson

address: 1333 San Pablo St.

department: Medicine

institute: University of Southern California

summary: ACE2, a membrane-bound monocarboxypeptidase with high affinity for angiotensin II (AngII), is highly expressed in the renal proximal tubule (PT). Previously, we reported elevated renal AngII levels associated with enhanced hypertension in mice globally lacking ACE2 and a role for soluble ACE2 in hypertension. Using a new mouse model, we now test the hypothesis that the PT of the kidney is a critical site for ACE2 in BP regulation acting via the intra-renal renin angiotensin system. Mice with specific deletion of ACE2 from the PT (PT ACE2 KO) have an exaggerated, initial BP response to AngII infusion, sufficient to cause cardiac hypertrophy. During this early period, reductions in key sodium transporters are observed in PT ACE2 KO mice in contrast to control mice, which instead increase renal ACE2 expression and urinary ACE2 excretion to reduce renal AngII accumulation. Quantitative molecular profiling of sodium transporters reflects impact of ACE2 deletion on homeostasis and offers mechanisms underlying AngII hypertension. Loss of ACE2 from the renal PT is sufficient to cause an exaggerated BP response and concomitant alterations in sodium reabsorption along the entire nephron. These studies reveal a dynamic pattern of intra-renal RAS regulation aimed at mitigating hypertension.

overall_design: Kidney nuclei from PT ACE2 KO and Control mice treated with Saline or AngII were isolated and purified by Fluorescence-activated nuclei sorting (FANS) and sequenced on the 10X Chromium Controller.

first: Jacqueline

last: Emathinger

first: Susan

last: Gurley


title: Butyrate blocks specific histone acetylation

first: Danny

last: Incarnato

summary: Butyrate, a short-chain fatty acid (SCFA) produced by microbial fermentation of dietary fiber, exerts beneficial metabolic and immunomodulatory functions through inhibition of histone deacetylases (HDAC) and hyperactivation of the histone acetylase (HAT) p3004. These effects are widely believed to result in the acetylation of distinct histones that regulate specific genes. However, we show that this is not the case, as butyrate dose-dependently increases the acetylation of histones throughout the entire genome regardless of their position at transcription starting sites (TSS). Mechanistically, we found that, although butyrylated p300 has increased acetylation activity as reported, it is no longer recruited to acetylated histones through its bromodomain, and thereby likely cannot maintain the acetylation of specific histones through positive feedback. Thus, butyrate does not regulate specific genes at the epigenetic level, but increases histone acetylation globally resulting in opening of the entire chromatin structure.

overall_design: ChIP-seq analysis of H3K27ac in human peripheral blood CD14+ monocytes differentiated to macrophages, treated for 24 hr with 0, 0.1 or 10 mM butyrate

first: Muwei

last: Jiang

first: Rutger

last: Modderman

first: Iris

last: Jonker

first: Geert

last: van den Bogaart


title: Single cell RNA sequencing of neutrophils enriched from the bronchoalveolar fluid and peripheral blood of pneumonic mice

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

summary: The objective of this study was to examine the potential transcriptional heterogeneity of alveolar and peripheral blood neutrophils during acute bacterial pneumonia.

overall_design: Mice were infected with S. Pneumoniae, (serotype 3) for 24 hours. Bronchoalveolar lavage fluid and peripheral blood were harvested from infected mice. Neutrophils were enriched from BALF and blood using a magnetic bead negative selection kit.

first: Katrina

last: Traber


title: Targeting one-carbon metabolic vulnerabilities of metastasis with therapeutic potential

status: Public on Jun 03 2026

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Evidence has shown that tumor progression is associated with the acquisition of growing autonomy and the creation of a complex signaling network through various signal pathways. Which particular signaling pathway is involved in the metastasis of a specific cancer is unclear. Here, we applied metastatic functional screening and identified that one-carbon and SSP metabolism pathways, as well as related genes, are associated with tumor metastasis inhibition. We engineered the cancer cells with poorly or highly metastatic potential to confirm the metabolism pathways regulating the ability to colonize different tissue sites. We also asked whether the restriction of the metabolism pathways by known inhibitors. We then identified three new compounds that can inhibit the expression of these genes and block tumor metastasis. Our findings uncovered a mechanism by which tumor cells reprogram their metabolism to promote migration, invasion, and survival at distant sites in tumor metastasis, offering a rational strategy to guide clinical treatment. The identified novel molecular proteins and pathways represent a promising therapeutic target for metastatic disease.

overall_design:
B16F10 is mouse melanoma cells, RMS14 is mouse rhabdomyosarcoma cells
Identification of genes expressed in 10 groups (three replications per group):
B16F10: DMSO
B16F10: CalC: treated with 100 nM calphostin C for 48 hours
B16F10: Rap: treated with 10nM Rapamycin for 48 hours
B16F10: LY24: treated with 10µM PI3K/AKT inhibitor LY294002 for 24 hours
B16F10: LY48: treated with 10µM PI3K/AKT inhibitor LY294002 for 48 hours
RMS14: DMSO
RMS14: CalC: treated with 100 nM calphostin C for 48 hours
RMS14: Rap: treated with 10nM Rapamycin for 48 hours
RMS14: PD24: treated with PD, 20µM MAPK inhibitor PD98059 for 24 hours
RMS14: PD48: treated with PD, 20µM MAPK inhibitor PD98059 for 48 hours

first: Yanling

last: Yu

first: Weiping

first: Glenn

last: Merlino


title: Gonadal single-cell RNA-seq analysis reveals genes important for germ cell development and sexual differentiation in sea lamprey (Petromyzon marinus)

city: East Lansing

first: Stephanie

middle: Lepp

last: Hickey

state: Michigan

address: 612 Wilson Rd

institute: Michigan State University Bioinformatics Core

summary: The sea lamprey (Petromyzon marinus) is a jawless vertebrate species that develops through larval, juvenile, and adult life stages. The mechanism of sex determination in this species is unknown and thought to be regulated by several environmental factors. During its lengthy larval stage that lasts between 3-20 years, the gonad usually contains both female and male germ cells before metamorphosis. To seek insights for sex determination and sexual differentiation in this agnathan species, we profiled gene expression patterns of gonadal cells from larvae (sex-labile) and recently metamorphosed juvenile transformers (sex-determined). We used flow cytometric cell sorting (BD FACS Aria IIu) and PIPseqTM (single-cell RNA-seq technique by Fluent BioSciences/now part of Illumina) to capture expressed genes in individual gonadal cells. Primordial germ cells expressed many specific cell markers, such as HOXA4, HOXA5A, HOXA10, KDM1A, LHX8, PAX7, POU2F2, SOX1, and SOX14. Male germ cells expressed specific cell marker ADGB, whereas gonadal macrophages expressed specific cell marker CD115/CSF1R. Interestingly, germ cells are enriched with ribosomal proteins, some can interact with heat-shock proteins or hormone receptors, and others are sensitive to sugar or lipid metabolisms. These ribosomal genes may provide a link between environmental factors such as temperature and nutrients to cellular functions, leading to changes in germ cell fate. Germ cells in the larvae expressed many transcription factors involving in DNA replication, transcription, translation, apoptosis, autophagy, cell cycles, cell differentiation, cell adhesion and migration, cell survival, chromatin remodeling and proliferation. In particular, TGF?, and Wnt signaling pathways were involved in sexual differentiation in other species. We also examined the pseudotime trajectory of top 50 gene expression patterns for female and male sexual differentiation pathways. Further analysis is required to confirm the functions of these genes and pathways in sex determination and sexual differentiation in the sea lamprey.

overall_design: single-cell RNA-seq from 4 sea lamprey gondal samples: 2 replicates of undifferentiated gonads from larvae, 1 from female transformer, and 1 from male transformer

first: Yu-Wen

last: Chung-Davidson

first: Matthew

middle: P

last: Bernard

first: Ciro

last: Amato

first: Martin

last: Estermann

first: Jacob

last: Kimmel

first: Lily

last: Gorman

first: Tyler

last: Buchinger

first: Braden

last: Idalski

first: Nicholas

last: Johnson

first: Humprey

last: Yao

first: Weiming

last: Li


title: Identification of genomic features that uniquely impact estrogen receptor alpha binding and its effects on gene expression in endometrial cancer [RNA-seq]

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

summary: Estrogen receptor alpha (ER) is an established oncogenic transcription factor in breast and endometrial cancer; however, more is known about the mechanisms controlling ER behavior in breast cancer, and therapies targeting ER have been much more successful in breast cancer. To address this disparity, we seek to identify genomic features that control ER in endometrial cancer and determine to what extent these factors differ from those in breast cancer. We focus on the locations of estrogen response elements (EREs), ER’s preferred DNA binding motif, throughout the human genome. To identify factors that predict ER genomic binding and effects on target gene expression, we apply machine learning to genomic data for each ERE in Ishikawa cells (ER+ endometrial cancer) and T-47D cells (ER+ breast cancer). Many of these factors, such as chromatin accessibility and histone modifications, are predictive of ER activity in both cell lines. However, the transcription factors that predict ER activity are found to be cell type-specific, including FOXA1 and GATA3 in T-47D cells, and ETV4 and SOX17 in Ishikawa cells. In addition, the features that predict ER binding and effects on gene expression differ, with transcription at EREs in the absence of estrogen being predictive of regulatory activity.  To verify our findings in the Ishikawa cells, we perform a CRISPR knockout screen, which confirms the discovery that SOX17 controls ER activity in endometrial cancer cells. These results identify important genomic features of ER binding and regulatory activity and how these features differ between endometrial cancer and breast cancer cells.

overall_design: RNA-seq analysis on control Ishikawa cells and SOX17KO with and without estrogen to determine estrogen-responsive gene changes in the absence of SOX17

first: Alexandra

last: Richey

first: Noel

last: Kitchen


title: Identification of genomic features that uniquely impact estrogen receptor alpha binding and its effects on gene expression in endometrial cancer [ChIP-seq]

overall_design: ChIP-seq analysis on wildtype HCI-EC_23 cells (SOX17 and H3K4me1), control Ishikawa cells (ER) and SOX17 knockout Ishikawa cells (ER)

first: Craig

last: Rush