title: Construction of a Transferable NGS Algorithmic Model for Predicting EBV-Associated Nasopharyngeal Cancer and  High-risk Mutation

city: Shanghai

first: xiao

last: xiao

state: Shanghai

address: Ganhe road

institute: Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine

summary: Abstract Background: Epstein-Barr virus (EBV) infection is closely associated with the occurrence of nasopharyngeal carcinoma (NPC). The latent membrane protein 1 (LMP1) gene, known for its high heterogeneity, plays a crucial role in determining the oncogenic potential of NPC. This study aimed to develop a universal transferable algorithm for analyzing fragmented viral genome data using next generation sequencing (NGS), construct EBV associated NPC (EBVaNPC) prediction models, and investigate the functional significance of key mutation in LMP1. Method: EBV public whole genome sequencing data was collected and divided into a training and a test set in a 2:1 ratio. Using 26 clinical EBV-positive subjects, EBV LMP1 region (aa1-118) was sequenced with amplicon-based sequencing. An improved algorithm was developed to extract features and construct the EBVaNPC machine learning (ML) prediction modesl. The biological implications of predicted key mutation on tumor cell biological behaviors were investigated through qRT-PCR, EdU and transwell invasion assay, RNA-seq and gene ontology fingerprint (GOF) anslysis. Result: For randomly disrupted NGS data, different read length had minimal impact on the performance of models, with all six ML models achieving F1 scores above 0.8 on training dataset. On the test dataset, random forest (RF) and naive Bayes demonstrated superior performance using mutation and entropy features, respectively. The model was further validated on clinical cohorts to assess its transferability and generalizability to amplicon-based NGS data. Using differential features instead of all, data dimension was reduced while the model performance was improved. Interestingly, RF model revealed that H101R mutation in LMP1 emerged as the top significant feature, and its oncogenic implication was confirmed through proliferation and invasion experiments in HNE-1MUT-LMP1 cells. By integrating EBVaNPC GOF and RNA-seq data, the differentially expressed genes linked to the H101R mutation were involved primarily in immune regulation processes. Both approaches indicated a notable association between FOXP3-T cell anergy and WNT7A-stem cell population maintenance in HNE-1MUT-LMP1 cells. Conclusion: This study integrates algorithm design and experimental investigations to uncover the biological significance of EBV carcinogenesis, offering a clinically suitable technology for high risk NPC identification in EBV infected subjects.

overall_design: To elucidate the biological implications of the LMP1 H101R mutation, we employed an in vitro model using the NPC cell line HNE-1 transfected with the mutant LMP1. The HNE-1 cells were divided into two groups: HNE-1MUT-LMP1 and HNE-1WT-LMP1 To explore the impact of the EBV LMP1 H101R mutation on host gene expression and biological functions, we further performed RNA sequencing on HNE-1MUT-LMP1 and HNE-1WT-LMP1 cells.


title: Effect of ferroptosis on downstream gene activation in mouse macrophages

status: Public on Dec 03 2025

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

type: Expression profiling by high throughput sequencing

summary: Ferroptosis has long been debated whether it is pro- or anti-inflammatory. Here we provide the transcriptional activation levels of macrophages that have been incubated with non-ferroptotic and ferroptotic supernatants.

overall_design: Mouse primary bone marrow derived macrophages were incubated with non-ferroptotic or ferroptotic supernatants for 24h and RNA is isolated.

first: Fatma

middle: I

last: Yapici

first: Silvia

last: von Karstedt


title: Ageing-induced cell type-specific transcriptomic changes in the skin are associated with abnormal early healing responses to injury

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

summary: The progression of wound healing is delayed in aged skin. Previous studies have demonstrated that early healing responses are  the most impacted upon ageing. However, cellular changes that drive a perturbed wound microenvironment have not been fully defined. To glean a comprehensive understanding of cell-intrinsic changes that are acquired during ageing and may perhaps impact early responses to wounds, we performed single-cell RNA sequencing of 78670 cells from young and aged C57BL6/J wild-type mouse skin and Day 3 wounds. Our data underscore substantial changes in the mean proportional distribution and transcriptomic state of skin resident subpopulations in aged but not young tissues. We found that in comparison to young skin, aged skin was characterised by a global increase in basal inflammation sustained by an altered signalling environment driven by impaired keratinocyte differentiation, loss of fibroblast identity and defective macrophage function. Further, we showed that acquired changes in aged skin resident cells persisted after injury resulting in impaired and exacerbated inflammatory responses.

overall_design: Single cell sequencing was performed on live cells from whole intact skin and whole Day 3 wounds from 3 female C57BL/6J wild-type young (8-12 weeks) and 3 aged (22-24 months) mice.

last: Oguz

first: Christabel

last: Dube

first: Yasmin

last: Ong Hui Bin

first: Samydurai

last: Sudhagar

first: Shyam

last: Prabhakar

first: Matthew

last: Ronshaugen

first: Adaikalavan

last: Ramasamy

first: Lim

middle: C

last: Yan

first: Kimberly

last: Mace


title: mRNA-seq of phalanges at stages E16 and E17 of the mouse

city: Shenyang

first: Wanyi

last: Dang

state: Liaoning

address: 120 Dongling Rd, Shenyang, China

country: China

institute: Shenyang Agricultural University

summary: We used next-generation sequencing to study the skeletal development process of digits in the fore- and hindlimbs by comparing transcriptomes generated from phalanges of digits 1 and 2 from the mouse.

overall_design: Mouse phalangeal samples of digits 1 and 2 were pooled from 20 individuals at E16 and 10 individuals at E17, and mRNA-seq data were obtained by Illumina NovaSeq 6000.

first: Junnan

last: Chen

first: Dali

last: Gao

first: Zhe

last: Wang


title: Hepatic GPNMB aggravates NASH through binding to RYK [RNA-Seq]

city: Wuhan

first: Yue

last: Xi

state: Hubei

address: 81 St

department: College of life sciences

institute: Wuhan University

summary: The goals of this study are to define the moelcular events in NASH and to determine the role of GPNMB and RYK in NASH development

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq analysis on mouse livers treated with HFHC, AMLN or ND and on Huh7 cells stably transfected with RYK and treated with GPNMB ECD for 8 h

first: Waner

last: Zeng

first: Bao-Liang

last: Song


title: CapP mediates the structural formation of biofilm-specific pili in the opportunistic human pathogen Bacillus cereus.

city: Málaga

first: Ana

last: Álvarez Mena

address: IHSM, Avenida Louis Pasteur 49

country: Spain

institute: University of Málaga

summary: We report the application of a high-throughput technique, RNA-Seq to study the transcriptomic response of Bacillus cereus to the bc1280 locus deletion.

overall_design: B. cereus bc1280 mutant strain planktonic cells compared with the wild-type strain at 24 and 48 hours.

first: A

last: Álvarez-Mena

first: D

last: Romero


title: Transcription Factor 4 Maintains Endothelial Cell Identity by Inhibiting Endothelial to Mesenchymal Transition

city: BOSTON

first: Min

state: Massachusetts

address: 300 Longwood Ave

department: Department of Cardiology

country: USA

institute: Boston Children's Hospital

summary: The goal of this study is to understand the role of TCF4 and its underlying mechanism in safeguarding the endothelial identity. Methods: In this study, by integrating ChIP-Seq, DNase-Seq, RNA-Seq, single-cell RNA sequencing (scRNA-seq), and experimental investigations, we identify TCF4 as an critical EC identity gene that maintains the phenotype and function of vascular ECs. Conclustion: Our results reveal a key role of TCF4 in safeguarding EC identity and preventing EndoMT, suggesting a therapeutic potential of TCF4 for EndoMT-related vascular diseases.

overall_design:
The manipulation of TCF4 expression in HUVECs was achieved through transfection with either control or shTCF4 RNAs (resulting in TCF4 knockdown) and control or TCF4 overexpressed plasmids (resulting in TCF4 overexpression).
This submission corresponds to RNA-Seq component of study.

first: Jie

last: Lv


title: Impact of desiccation on the global transcription of Acinetobacter baumannii AB5075

city: Uxbridge

first: Rubén

last: de Dios

state: Middlesex

address: Kingston Lane

department: Life Sciences

country: United Kingdom

institute: Brunel University London

summary:
We perform RNA-seq comparing A. baumannii AB5075 cells resuspended in water or diluted M9-succinate and desiccated during 24 h (relative humidity 8-12%) to cells resuspended in water before desiccation.
A. baumannii AB5075 cultures (3 independent biological replicates) were grown overnight (approx. 16 h) in M9 minimal medium supplemented with Na-succinate 20 mM. Cultures were split in two and each half was washed 3 times either with distilled water or with M9-succinate 20 mM diluted 1:250 (v:v). OD600 of the cell supensions was adjusted to 1.0 and 1 ml from the water-suspended cells was withdrawn as a control comparison, washed with RNAlater and stored at -80 C until further processing. 1 ml of the OD-adjusted water- and M9-suspended cells were spotted on polystyrene Petri dishes and left to air-dry in a laminar flow hood. Once dried, the plates were placed in a chamber with Drierite until reaching a relative humidity of 8-12% and were incubated during 24 h. Finally, cells were harvested by directly resspending them in RNAlater and stored at -80 C. After that, total RNA was extracted from each sample and cDNA libraries were generated and sequenced.
The different comparisons showed that: i) 309 and 279 genes were upregulated and downregulated, respectively, in cells ressupended in water and desiccated compared to the control; ii) 435 and 512 genes were upregulated and downregulated, respectively, in cells resuspended in diluted M9-succinate and desiccated compared to the control; iii) 327 and 242 genes were upregulated and downregulated, respectively, in the cells resupended in water and desiccated compared to the cells resuspended in diluted M9-succinate and desiccated.

overall_design: Three independent replicates of A. baumannii AB5075 were grown overnight in M9 minimal medium supplemented with Na-succinate 20 mM, split in two equal volumes, washed 3 times with either distilled water or M9-succinate diluted 1:250 (v:v) and the OD600 was adjusted to 1.0. Then, 1 ml of each sample was spotted on a Petri dish and was left to air-dry. When dry, the Petri dishes were placed in a chanber with 8-12% relative humidity and were icubated for 24 h. 1 ml of the water suspended cells were withdrawn as control condition.

first: Lyuboslava

middle: G

last: Harkova

first: Ronan

middle: R

last: McCarthy


title: NIH-3T3 cell line response to chemotheraputic agents.

city: Richmond

first: Senthil

last: Radhakrishnan

state: VA

address: 1101 E Marshall St

institute: Virginia Commonwealth University

summary: In this study, we treated NIH-3T3 cells with various chemotherapy drugs and RNA sequencing analysis was carried out.

overall_design: Comparative gene expression profililng analysis of RNA-seq data for NIH/3T3 after treatment with Carfilzomib (CFZ), Doxorubicin (DOX), a combination of CFZ-DOX, or DMSO.

first: Janakiram

last: Vangala

middle: K


title: Open chromatin, HIF binding and mRNA expression analysis in primary tubule and ccRCC cells

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

institute: RWTH Aachen University Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series

first: Johannes

last: Schödel


title: In vivo CRISPR screening identifies SAGA complex members as a key regulators of hematopoiesis [RNA]

status: Public on Dec 02 2025

city: Philadelphia

first: Michael

last: Haney

state: PA

address: 422 Curie Boulevard

institute: University of Pennsylvania, Perelman School of Medicine, Department of Pathology

summary: The biological mechanisms that sustain the vast blood production required for healthy life remain incompletely understood. To search for novel regulators of hematopoiesis, we performed a genome-wide in vivo hematopoietic stem and progenitor cell (HSPC)-based CRISPR knockout screen for regulators of hematopoiesis. We discovered SAGA complex members, including Tada2b and Taf5l, as key regulators of hematopoiesis. Loss of Tada2b or Taf5l strongly inhibited hematopoiesis in vivo, causing a buildup of immature hematopoietic cells in the bone marrow. The SAGA complex deposits histone H3 lysine 9 acetylation (H3K9ac) and removes histone H2B ubiquitination (H2Bub). Loss of Tada2b led to reductions in H3K9ac levels and altered H2Bub enrichment in HSPCs, implicating disruption of SAGA complex activity. This was associated with upregulation of interferon pathway genes, reduced mitochondrial activity, and increased megakaryocyte progenitor cell commitment. Loss of these factors also enhanced the cell outgrowth and the interferon pathway in an in vivo human myelodysplastic syndrome cell line model. In summary, this study has identified the SAGA complex as an important regulator of hematopoiesis.

overall_design: Bulk RNA-seq of HSPCs

first: Adam

last: Wilkinson

first: Leonid

last: Olender


title: Transcription termination counteracts DNA damage after WEE1 inhibition

city: Oslo

first: Randi

last: Gussgard Syljuåsen

address: Ullernchausseen 70

department: Department of Radiation Biology, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

summary: Transcription termination is a key regulatory step in transcription and a potential target for cancer therapy, but how it can be exploited for treatment is incompletely understood. Here we show that transcription termination plays a crucial role in mitigating DNA damage and cell death upon WEE1 inhibition by adavosertib. Depleting five different transcription termination factors (WDR82, PNUTS, XRN2, DDX5 or CPSF73) increased adavosertib-induced DNA damage in S-phase. Conversely, inhibiting active transcription with DRB or triptolide, or co-depleting CDC73, a component of the PAF1 transcription elongation complex, reduced such damage. Additionally, read-through transcription following WDR82 depletion was partially inhibited by co-depletion of CDC73, supporting that read-through transcription contributes to DNA damage in response to WEE1 inhibition. Moreover, combining adavosertib with the CPSF73 inhibitor JTE-607, an anticancer compound which promotes read-through transcription, increased DNA damage during S-phase. Elevated expression of CPSF73 is associated with aggressive disease in prostate cancer patients, and combining JTE-607 with adavosertib synergistically reduced prostate cancer cell survival. Our findings suggest that transcription termination helps prevent toxic conflicts between transcription and replication following increased replication initiation caused by WEE1 inhibition.

overall_design: chromatin RNA sequencing experiment of HeLa cells 48h after transfection with scr, siWDR82, siCDC73 and siWDR82 + siCDC73


title: CSNK1A1 phosphorylates ITGB5 to decrease the sensitivity of hepatocellular carcinoma to the multi-target tyrosine kinase inhibitor by disrupting the EPS15/EGFR complex

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

summary: Oral multi-target tyrosine kinase inhibitors (TKIs), such as sorafenib, suppressing tumor-cell proliferation and tumor angiogenesis have been approved to treat patients with hepatocellular carcinoma (HCC). Of note, only approximately 30% of patients can benefit from TKIs, and this population usually acquires drug resistance within 6 months. Here, we intend to explore the mechanism that associated with the regulating the sensitivity of HCC to TKIs. We revealed that the ITGB5 was abnormally expressed in HCC and contributed to decreasing the sensitivity of TKIs in HCC. Mechanically, the unbiased mass spectrometry analysis by using the ITGB5 antibodies reveals that ITGB5 interacted with EPS15 to prevent the degradation of EGFR in HCC cells, which activated the AKT-mTOR signaling and MAPK pathway to reduce the sensitivity of TKIs in HCC cells. In addition, the mass spectrometry analysis also showed that CSNK1A1 bound with ITGB5 in HCC cells. The further study indicated that ITGB5 increased the protein level of CSNK1A1 through the EGFR-AKT-mTOR pathway in HCC. And the upregulated CSNK1A1 phosphorylate ITGB5 to enhance the interaction between ITGB5 and EPS15 and activate the EGFR in HCC cells. Thus, we identified a positive feedback loop between ITGB5-EPS15-EGFR-CSNK1A1 in HCC cells. This finding provided a theory basis for the future development of therapeutic strategies to improve the anti-HCC efficacy of TKI.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the Huh7 cells after knockdown of ITGB5.

first: Xin

last: Jin


title: Multi-omics integration identifies diverse transcripts and chromatin accessibility profiles in Monopterus albus gonads

first: Yuan

last: Zhao

address: Donghu Road 7th

institute: Institute of Hydrobiology, Chinese Academy of Sciences


title: Gene expression profiling of the whole brain of the normal littermate control for Huntington disease model mouse R6/2 at 5 weeks post-natal age using transcriptome tomography

city: Wako-shi

first: Yuko

last: Okamura-Oho

state: Saitama

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

summary: We developed a novel framework to assess comprehensive endogenous gene expression maps in a broad and isotropic 3D-anatomical context using a relatively small number of original data points: transcriptome tomography. Using this method, we produced a dataset of gene expression maps of the whole brain of the normal control mouse at 5 weeks after birth, computationally reconstructed from fraction data.

overall_design: A total of 43 fraction samples obtained with body axes-based slicing preparation conjugated with anatomical image acquisition were analysed. There are sets of body axes-based preparation series: the S series, composed of10 fractions/ C of 12 fractions/ H of 6 fractions/ L of 8 fractions/ R for 7 fractions.

first: Y

first: H

last: Yokota


title: Effect of zinc supplementation on gene expression of Rhizopus arrhizus NCCPF 710004

city: Chandigarh

first: Rachna

last: Singh

state: Chandigarh

address: Department of Microbial Biotechnology, Technology Block, Panjab University (South Campus), Sector 25

department: Microbial Biotechnology

country: India

institute: Panjab University

summary: Rhizopus arrhizus is the predominant causative agent of mucormycosis worldwide. During COVID-19 pandemic, an upsurge of this disease was noted in many countries including India. Many clinical/epidemiological studies reported that the excessive intake of nutritional supplements, especially that of zinc, owing to self-medication and over-prescription, was one of the risk factors for the emergence of Covid-19 associated mucormycosis. However, the experimental evidence remains limited. This study evaluates the changes in gene expression of Rhizopus arrhizus upon culturing under zinc-enriched conditions.

overall_design: mRNA was sequenced from Rhizopus arrhizus NCCPF 710004 after culturing in RPMI-1640 for 6 h without or with 45 µM zinc by Illumina NovaSeq 6000 technology, with 150bp paired end reads.

first: Anjna

last: Kumari

first: Pavneet

last: Kaur

first: Jasdeep


title: Identification of differentially expressed genes associated with endotracheal intubation-induced tracheal injury in a rabbit model of septic shock

city: Shijiazhuang

first: pei

last: zhang

state: He

address: No. 215, Heping West Road, Xinhua District,

department: Intensive Care Unit of Department of Anesthesiology

institute: HeBei Medical University

summary: To identify differentially expressed genes (DEGs) potentially involved in the development of endotracheal intubation-induced tracheal injury in septic shock.

overall_design: Eighteen New Zealand white rabbits were randomized to control, septic shock model, and treatment (n = 6/group). The model and treatment groups were injected with lipopolysaccharide to induce septic shock. The treatment group was administered Ringer lactate with norepinephrine to maintain the normal blood pressure. All animals underwent cuffed endotracheal intubation for 2 h. The injured tracheal segment was harvested. RNA sequencing was performed to identify the DEGs, followed by bioinformatics analysis.

first: Pei

last: Zhang

first: Huaihai

last: Lu

first: Xuze

last: Li

first: Ye

last: Tian

first: Wenbin

first: Shuxian

last: Ma

first: Chao

last: Liu

first: Xvefang

first: Lining

last: Huang


title: Curcumin impacts on cisplatin sensitivity determining apoptotic boost in mesothelioma

city: Napoli

first: Stefania

last: Crispi

address: Via Pietro Castellino,111

department: DISBA

country: Italy

institute: CNR

summary:
We analysed the molecular effects on gene modulation exerted by Curcumin C3 complex (CBP) in mesothelioma. Previous results allowed to demonstrate that CBP determined apoptosis in three different mesothelioma cell lines including one resistant to conventional chemotherapeutic treatment. CBP also affected tumor growth in vivo in a xenograft model of mesothelioma
We used microarrays to idendify gene deregulated by CBP in mesothelioma and responsible of the apoptosis induction

overall_design: Human malignant mesothelioma MSTO-211H cells were treated with 20 micromolar of CBP  for 24 hours. Cells treated with the vehicle (DMSO) were used controls. RNA extracted from  treated and control cells were used for transcriptomic analysis using Clariom S Array

first: M

last: Piccioni

first: E

last: Caputo

first: R

last: Cuciniello

first: F

last: Di Meo

first: A

last: Valentino

first: G

last: Petillo

last: Rinaldi

first: O

last: Baldi

first: S

last: Filosa

first: P

last: Bergamo


title: Investigating and correcting a rare pathogenic mutation in GDF11

city: West Hartford

first: Sean

last: Congdon

state: CT

address: 200 Bloomfield Rd

institute: University of Hartford

summary: Single nucleotide variants (SNVs) and small insertions or deletions (indels) underlie most rare monogenic disorders, yet therapeutic strategies to precisely correct these mutations remain limited. Prime Editing enables repair of such pathogenic variants without introducing double-stranded breaks. Here, we applied CRISPR Prime Editing to model and correct a de novo GDF11 nonsense mutation (Tyr336*) identified in a participant from the Undiagnosed Diseases Network (UDN) with growth delay and multisystem abnormalities. Using HEK293T cells, we generated heterozygous GDF11 Tyr336* clones, which exhibited reduced GDF11 protein levels due to post-translational degradation likely mediated by ER- and Golgi-associated quality control pathways.  These cells displayed marked Golgi abnormalities, including an increased number of compact, irregularly shaped Golgi structures, findings consistent with Golgi fragmentation and stress. Transcriptomic profiling of HET cells revealed broad dysregulation of gene networks, including downregulation of metabolic and Golgi-linked biosynthetic genes, and upregulation of cell-adhesion and extracellular matrix genes. These transcriptional shifts paralleled the participant’s developmental, neural, and cardiovascular phenotypes. To correct the mutation, we tested multiple bespoke Prime Editing strategies and identified PE7, in combination with a pegRNA designed by Pridict, as the most effective ribonucleoprotein complex for rescue. Editing efficiency was further enhanced by introducing an additional silent PAM-disrupting mutation, likely preventing both Cas9 re-binding and mismatch repair. Together, these findings support a haploinsufficiency mechanism for the GDF11 Tyr336* allele and establish a generalizable framework for disease modeling and allele-specific correction of pathogenic variants in human cells.

overall_design: This study used CRISPR prime editing in HEK293T cells to generate a heterozygous line carrying the GDF11 Tyr336* allele on two of the three chromosomes, and we compared its transcriptomic profile to that of wild-type HEK293T cells

first: John

last: Bennett

first: Rhoddean

last: Opinya

first: Amara

last: Agosto

first: Olivia

last: Dossias

first: Christopher

last: Kokko

first: Aime

middle: A

last: Levesque

first: Andrew

middle: O

last: Koob

first: Adam

last: Silver

first: Cindy

last: Thomas-Charles


title: Protective Effects of Recombinant Depolymerase Dep44 Against K64-CRKP-Induced Pulmonary Infection in a Murine Infection Model

city: hefei

first: Chengcheng

last: Ma

address: jixi road

institute: anhui chest hospital

summary: Carbapenem-resistant Klebsiella pneumoniae (CRKP), particularly the K64 serotype, poses a severe clinical threat due to its high virulence and multidrug resistance. In this study, we investigated the gene expression profiles of host lung tissues to understand the pathogenesis of K64-CRKP infection and the therapeutic mechanism of Dep44, a capsule-degrading depolymerase. An acute pneumonia mouse model was established via intranasal infection with K64-CRKP. We performed high-throughput RNA sequencing (RNA-seq) on lung tissues from four experimental groups: the negative control group (healthy mice), the positive control group (K64-CRKP infected model), the treatment group (infected mice treated with Dep44), and the drug control group (healthy mice treated with Dep44). The analysis aims to elucidate the host immune response to K64-CRKP infection and evaluate how Dep44 treatment modulates these transcriptomic changes to exert its therapeutic effect.

overall_design: Lung tissue samples were collected from BALB/c mice to analyze gene expression changes. The study design included four groups: (1) Negative Control Group: Mice were mock-infected with PBS to serve as a healthy baseline. (2) Positive Control Group (Model): Mice were intranasally infected with K64-CRKP to induce acute pneumonia, serving as the disease model for comparison. (3) Treatment Group: Mice were intranasally infected with K64-CRKP and subsequently treated with Dep44. (4) Drug Control Group: Healthy mice were administered Dep44 alone to evaluate the potential off-target effects of the drug itself. Total RNA was extracted from the lung tissues of each group. Libraries were constructed and subjected to high-throughput sequencing on the Illumina platform to compare the transcriptomic differences among these groups.

first: Tao

last: Yan


title: A transcriptomic signature that predicts pre-hypertension in adolescence and higher systolic blood pressure in childhood

city: Manchester

first: Terence

middle: S

last: Garner

address: St Mary's Hospital, Oxford Road

department: Division of Developmental Biology and Medicine

institute: University of Manchester

summary: Suboptimal fetal growth (SFG), being born small-for-gestational-age (SGA), and catch-up (CU) growth are individually and together linked to cardiometabolic (CM) risks. However not all develop adverse outcomes. This study aimed to validate a transcriptomic signature to identify individuals at greatest CM risk. Using National Heart Lung and Blood Institute criteria to define CM risk, healthy and prehypertensive 17-year-olds were identified in the ALSPAC (UK) childhood cohort. Epigenomic and transcriptomic differences were analysed. A hypernetwork identified functionally related genes, which were used in random forest classification to predict prehypertensive phenotypes. The BabyGRO (UK) cohort included 80 children aged 3–7 years, born at term following pregnancies with SFG risks. Anthropometric, CM markers and transcriptomic profiles were collected, fetal and childhood weight trajectories and their relationship to CM markers assessed, and transcriptome used for prediction. CU-SGA individuals in ALSPAC were 1.6 times more likely than all others to be prehypertensive at 17 years (p<1x10⁻⁵). A 42-gene hypernetwork cluster was highly predictive of prehypertension (AUC 0.984, error rate 5.4%). In BabyGRO, 20 of these genes accurately predicted higher systolic blood pressure (AUC 0.971, error rate 3.6%). This transcriptomic signature could help identify children with adverse pre- and postnatal growth who may develop prehypertension.

overall_design: RNA-seq profiling of blood samples from children aged three-to-seven following detection of risk of FGR

first: Reena

last: Perchard

first: Philip

last: Murray

first: Amirul

last: Roslan

first: Lucy

middle: E

last: Higgins

first: Edward

middle: D

last: Johnstone

last: Stevens

first: Peter

last: Clayton


title: Melanin Nanoparticles Alleviates Thalamic Stroke Damage by Modulating Glial Activation and Neuroinflammation

city: Tianjin

first: Libo

last: Su

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

summary: Thalamic strokes represent a major cause of post-stroke cognitive impairment, characterized by glial activation and disrupted iron homeostasis. Microglia and astrocytes play pivotal roles in the inflammatory response, but the mechanisms connecting glial activation to ferroptotic cell death remain unclear. This study explores the neuroprotective effects of melanin nanoparticles (MMPP) in thalamic stroke, focusing on glial activation and neuronal ferroptosis. Using a photothrombotic stroke model, MMPP nanoparticles suppress microglial activation, which subsequently mitigates astrocytic reactivity. Transcriptomic analysis reveals that MMPP nanoparticles regulate the MKK4/JNK signaling pathway, linking glial activation to ferroptosis. Reactive astrocytes secrete lipocalin-2 (LCN2), which triggers ferroptosis in neurons through the 24p3 receptor, causing iron accumulation and ROS production. Additionally, MMPP restores key ferroptosis markers by upregulating GPX4 and downregulating PTGS2, interrupting the pathological cascade, preserving neuronal antioxidant defenses, and reducing ferroptotic cell death. These findings highlight MMPP’s dual antioxidant and anti-inflammatory effects, particularly through modulation of the microglia-astrocyte-LCN2 axis. This study suggests that MMPP provides a promising therapeutic strategy to alleviate neuroinflammation and promote functional recovery following ischemic stroke.

overall_design: Seven days following photothrombotic surgery and melanin nanozyme injection in C57/BL mice, the thalamus was harvested for RNA sequencing.

first: Yulong

last: Shen


title: Effect of Nakaseomyces glabratus on BM-MDSCs

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

summary: Recent studies demonstrate that the gut mycobiota plays a key role in several tumors’ development. However, the contribution of commensal fungi to prostate cancer initiation and progression remains understudied. Here, we find that Nakaseomyces glabratus (N.glabratus), is enriched in fecal, blood, and tumor samples of a subset of CRPC patients, positively correlating with patients’ poor overall survival. Oral administration of N.glabratus to castrated mice accelerated CRPC development by controlling polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs). Mechanistically, androgen deprivation therapy (ADT) increases intestinal permeability, resulting in the leakage of N.glabratus from the gut to the tumor site, where it activates PMN-MDSCs by binding to the Dectin-2 receptor. Treatment of mice with a negatively charged hydrogel blocks N.glabratus translocation to the tumor site, reducing PMN-MDSCs intratumoral infiltration and activation. Taken together, these findings reveal that the gut-to-tumor translocation of commensal fungi contributes to endocrine resistance in CRPC by enhancing the immunosuppressive microenvironment of these tumors.

overall_design: After 4 days of differentiation of BM-derived MDSCs, we treated with Nakaseomyces glabratus or not for 24h. After the treatment the RNA was isolated for sequencing.

first: Troiani

last: Martina

first: Alimonti

last: Andrea


title: Symptomatic SARS-CoV-2 breakthrough infections broaden the repertoire of Spike-reactive CD4 T cells

city: La Jolla

first: Emil

last: Johansson

state: California

address: 9420 Athena Cir

department: Center for Autoimmunity and Inflammation

institute: La Jolla Institute for Immunology

summary: SARS-CoV-2 breakthrough infections (BTI) are relatively common, but little is known in terms of differentiating responses associated with asymptomatic BTI (ABTI) versus symptomatic BTI (SBTI). Here, we investigated the impact of ABTI and SBTI on antibody and T cell responses towards Spike. SBTI donors had significantly higher plasma anti-Spike RBD IgG titers compared to both ABTI and SARS-CoV-2 vaccinated donors with no signs of previous infection (VAX) donors. While no impact of ABTI or SBTIs was found in the magnitude of Spike-specific CD4 and CD8 T cell responses, both ABTI and SBTI donors had significantly higher CD4 T cell responses towards non-Spike antigens. In-depth characterization of Spike-specific CD4 and CD8 T cells at scRNA/TCRseq level revealed that ABTI and SBTI induced different alterations of the CD4 compartment. These included a IFNGhigh skewed response among cytokine-producing cells, and a concurrent expansion of type II IFN-responsive TH17-like cells in SBTI. SBTI donors were further found to have an increased CD4 TCR repertoire diversity compared to VAX donors. ABTI-associated alterations of the Spike-specific compartment were intermediate between SBTI and VAX groups, likely reflecting lower antigen exposure and less inflammatory environment during ABTIs versus SBTIs.

overall_design: Here, we used single-cell RNA sequencing (scRNAseq) and T cell receptor sequencing (scTCRseq) to characterize Spike (S)-specific T cell responses in VAX, ABTIs, and SBTIs, to define distinct immunological signatures related to T cell functionality and T cell subsets responding to antigen stimulation. We performed scRNAseq and scTCRseq on S-reactive CD4 T cells by sorting AIM+ (OX40+CD137+) cells following S megapool  stimulation.

first: Johansson

last: Emil

first: da Silva Antunes

last: Ricardo

first: Sette

last: Alessandro


title: Mitochondrial double stranded RNA Dependent Lipid Repropgramming in Non-Small Cell Lung Cancer

city: Los Angeles

first: Matthew

last: Krieger

state: CA

address: 10833 Le Conte Avenue

institute: University of California Los Angeles

summary: Transcription of the mitochondrial genome results in the generation of double stranded RNA. Escape of mitochondrial double stranded RNA (mtdsRNA) into the cytosol is harmful and functions as a class of damage associated molecular pathogen (DAMP) that elicits activation of an MDA5 driven anti-viral response in cells [PMID:30046113,38955468]. To mitigate the deleterious consequences of excess cytosolic mtdsRNA, mammalian cells rely on the mitochondria localized exonuclease polynucleotide phosphorylase (PNPase) to degrade excess mtdsRNA [PMID:20691904,38955468]. Little is known about the role of PNPase in cancer or the cellular consequences that PNPase inhibition and cytosolic mtdsRNA have on tumour cells. Here, we demonstrate that PNPase inactivation in a therapy-resistant Kras-driven, Lkb1 (KL) mutant genetically engineered mouse model (GEMM) of lung cancer resulted in a significant extension in overall survival of mice and reduced tumour cell proliferation. PNPase loss activated a robust interferon-stimulated viral mimicry response in lung tumours that triggered reprograming of lipid metabolism and upregulation of lipid droplet biogenesis in tumour cells. Tumours that escaped PNPase loss transformed into fatty lesions characterized by a massive accumulation of lipid droplets enriched for polyunsaturated fatty acids (PUFAs). Importantly, PNPase null KL tumours were highly sensitive to ferroptosis, a non-canonical form of cell death, which resulted in the near complete clearance of tumours from the lung of mice. Similarly, human lung and pancreatic tumour cells were equally sensitive to targeted pharmacological inhibition of PNPase in combination with ferroptosis induction. These findings identify PNPase as a critical regulator of tumour fate through control of mitochondrial regulated innate immunity and lipid droplet biogenesis, uncovering a new therapeutic vulnerability that may be exploited in therapy resistant lung and pancreatic tumours..

overall_design: RIP-Seq of two different mouse NSCLC cell lines with and without PNPase knockdown (1969B and L3161C) in three replicates.

first: Sandy Che-Eun

last: Lee

first: Maya Cielo

last: Cornejo

first: Kevin

middle: L

last: He


title: Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations [xenograft]

city: San Francisco

first: Hani

last: Goodarzi

department: Department of Biochemistry and Biophysics

institute: UCSF

summary: Heterogeneity between patients poses a significant challenge in cancer drug development. Although success of a drug candidate in the clinic depends on efficacy across large numbers of diverse patients, only a few in vivo preclinical models are used for assaying a preclinical drug candidate due to the lack of scalability of traditional xenograft models. To address this limitation, we developed GENEVA, a scalable platform that enables the measurement of molecular and phenotypic responses to drug perturbations at single-cell resolution, both in 3D and in vivo. GENEVA models the genetic diversity of cancer by combining multiple patient-derived cell lines and cancer cell lines into pooled 3D cultures and xenograft models, allowing us to study drug responses across a wide range of genetic backgrounds within a single experiment. This platform integrates high-resolution transcriptomics with multiplexed single-cell profiling, providing a unique ability to uncover the interplay between cancer genotypes and drug responses. In this study, we apply GENEVA to investigate KRAS G12C inhibitors and demonstrate that mitochondrial activation is a key driver of cell death following KRAS inhibition. Additionally, we identify epithelial to mesenchymal transition (EMT) as a prominent resistance mechanism to KRAS G12C inhibition using in vivo GENEVA mice. These findings highlight the utility of GENEVA in identifying novel therapeutic targets and optimizing combination therapies, while underscoring its potential to bridge the gap between preclinical cancer models and patient outcomes by modeling the complexity of tumor heterogeneity in a scalable and robust assay.

overall_design: A total of 11 cancer cell lines with varying genetic backgrounds, including BRAF(V600E) and KRAS G12C mutations, were pooled together into a single experimental setup. These pooled cells were cultured in 3D conditions and then split into three treatment groups:   Vehicle control (DMSO),  Vemurafenib (0.8 µM) targeting BRAF(V600E) mutants,  ARS-1620 (1 µM) targeting KRAS G12C mutants.  After six days of treatment, cells were harvested and subjected to scRNA-seq

first: Johnny

middle: X

last: Yu

first: Jung

middle: M

last: Suh

first: Katerina

last: Popova

first: Kristle

last: Garcia

first: Tanvi

last: Joshi

first: Bruce

last: Culbertson

first: Jessica

middle: B

last: Spinelli

first: Vishvak

last: Subramanyam

last: Lou

first: Kevan

last: Shokat

first: Jonathan

last: Weissman


title: Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations [scRNA-seq]

overall_design: Lung cancer patient-derived organoids from four genetic backgrounds (KRAS G12C, KRAS G12D, EML4-ALK fusion, and EGFR L858R) were pooled and grown in 3D Matrigel culture. These pooled PDOs were exposed to an ARS-1620 dosage series. After treatment, cells were dissociated and processed using 10x Genomics Chromium Single Cell 3' v3.1 chemistry. Libraries were demultiplexed using SNP-based assignment from scRNA-seq reads and hashed sample tags (MULTI-seq). Single-cell transcriptomes were quantified using Cell Ranger and integrated into downstream analyses to assess differential drug responses.


title: Gene expression profiling of the whole brain of the Huntington disease model mouse R6/2 at 5 weeks post-natal age using transcriptome tomography

first: Yuko

last: Okamura-Oho

summary: We developed a novel framework to assess comprehensive endogenous gene expression maps in a broad and isotropic 3D-anatomical context using a relatively small number of original data points: transcriptome tomography. Using this method, we produced a dataset of gene expression maps of the whole brain of the Huntington disease model mouse R6/2 at 5 weeks after birth, computationally reconstructed from fraction data.

overall_design: A total of 42 fraction samples obtained with body axes-based slicing preparation conjugated with anatomical image acquisition were analysed. There are sets of body axes-based preparation series: the S series, composed of10 fractions/ C of 12 fractions/ H of 6 fractions/ L of 7 fractions/ R for 7 fractions.

first: Y

first: H

last: Yokota


title: LSD1 Performs Demethylase-Independent and Context-Specific Roles in Ewing Sarcoma

city: Columbus

first: Rachel

last: Dreher

state: OH

address: 575 Children's Crossroad

institute: Nationwide Children's Hospital

summary: Lysine specific demethylase 1 (LSD1), encoded by the gene KDM1A, is overexpressed and correlates with poor patient prognosis in Ewing sarcoma. LSD1 colocalizes with the FET-fusion (EWSR::FLI1, EWS::ERG, etc) throughout the genome and has therefore been considered a critical co-regulator driving the progression of Ewing sarcoma. However therapeutic targeting of LSD1 by irreversible and noncompetitive inhibitors has yielded mixed results. Irreversible, enzymatic inhibition seems ineffective, but reversible noncompetitive inhibition has predominant off target mechanisms, leaving open the question of LSD1 function in Ewing sarcoma. Here we take a robust approach through multiple methods of depletion in multiple cell lines to define LSD1 function, both enzymatic and nonenzymatic, in Ewing sarcoma cell lines. We define a core set of 22 genes that are commonly repressed by LSD1 in all cell lines and that repression of these genes downregulates synapse functioning and e-cadherin target genes. De-repression of these genes with LSD1 loss is an early and sustained genotype in all cell lines tested. Furthermore, we define distinct gene sets in each cell line that are regulated by the enzymatic and nonenzymatic functions of LSD1 and find repression of e-cadherin target genes to be nonenzymatically regulated. This finding supports the growing body of evidence that in addition to their canonical catalytic activity, enzymes serve essential noncanonical roles as well. Lastly, we uncovered evidence through use of the irreversible inhibitor OG-L002 that 2D cytotoxicity and proliferation assays may be insufficient to determine how Ewing sarcoma responds to LSD1 inhibition.

overall_design: To evaluate the transcriptomic changes resulting from loss of LSD1 by CRISPR KO, UM171 degredation at 6hrs, 24hrs, and 96hrs, and OG-L002 inhibition in 3 Ewing sarcoma cell lines. In addition, we rescued LSD1 KO cell lines in A673 with empty vector, HA and twinstrep tagged full wild type LSD1 and HA and twinstrep tagged K661Q/A539 enzymatically dead mutant LSD1.

first: Cenny

last: Taslim

first: Ira

last: Miller

first: John

middle: W

last: Sherman

first: Emily

last: Theisen


title: Spatial transcriptomic based, endocapillary hypercellularity in IgA nephropathy

city: Seuol

first: Hwajin

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

summary: Immunoglobulin A nephropathy (IgAN) is a leading cause of chronic kidney disease, marked by mesangial IgA1 immune-complex deposition and a multi-hit pathogenesis. The Oxford classification grades histopathological lesions such as endocapillary hypercellularity (E0 and E1), which are associated with disease severity and prognosis. Despite advances in single-cell and spatial transcriptomics, the molecular basis of endocapillary hypercellularity in human IgAN remains unclear. Spatial transcriptomic data obtained using the GeoMx DSP platform were analyzed to compare gene expression profiles across normal, E0, and E1 groups.

overall_design: Human kidney tissues from control subjects and IgA nephropathy patients classified as E0 or E1 were analyzed using spatial transcriptomics to characterize classification-dependent transcriptomic alterations.

first: Jin Sug

last: Kim

first: Hyeon Do

last: Jeon

first: Kyung Hwan

last: Jeong

first: Hyeon Seok

last: Hwang

first: Ji-Youn

last: Sung

first: Kyungsik

last: Ha

first: Woochang

last: Choi


title: Stiffness-mediated Paracrine Signaling Enhances Induction of EMT in Oral Squamous Cell Carcinoma

first: Adam

middle: Jeffrey

last: Engler

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

summary: Oral Squamous Cell Carcinoma (OSCC) contains diverse communities of cells within the oral mucosa. A subset of the epithelia is highly responsive to changing niche conditions, resulting in their loss of polarity, epithelial-to-mesenchymal transition (EMT), and invasion in tumor-adjacent stroma. Given the range of cell states, we sought to understand how cytokine-mediated signaling from mesenchymal SCC25 cells or stiffness induced-mesenchymal (simCal27) cells caused EMT in naïve Cal27 epithelial cells. Media conditioned by SCC25 enhanced Cal27 cell migration, nuclear localization of EMT markers, and caused transcriptomic changes related to cytokine response ontological terms. SCC and simCal27 cells have unique cytokine profiles–which when regressed against transcriptomic changes–suggested that higher expression of IL-1a, IL-6, IL-8, Angiogenin and PAI-1 in conditioned media could drive EMT; upregulation of these cytokines also appears impactful for overall survival and progression-free interval. However, depletion and supplementation assays clearly show that the presence of these specific cytokines is critical to induce a migratory phenotype and that naïve Cal27’s motility is regulated by MAPK and AKT signaling pathways; loss or inhibition of these pathways reduced migration. These data suggest that paracrine signals from stiffness induced-mesenchymal cells act via distinct kinase pathways and may be necessary for cooperative dissemination of OSCC.

overall_design: RNA from Cal27 cells cultured with SCC25-CM for 3 days versus those cultured with fresh DMEM/F12 1:1 media for a day.

first: So Youn

last: Moon

first: Marcelo

last: Lamers

middle: J


title: RNAseq of gingival fibroblasts exposed to activated platelets

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

summary: Platelet-rich fibrin (PRF) contains not only platelets but also leucocytes and the coagulated plasmatic fraction of centrifuged blood. Conclusions about the contribution of platelets to the overall PRF activity are, therefore, indirect. To overcome this limitation, we have used washed leucocyte-depleted platelets in our bioassays. The platelets were activated with thrombin to release the contents of their granules into the serum-free culture medium. Gingival fibroblasts were exposed to this platelet-released supernatant (PRS), and transcriptional changes were identified by RNA sequencing. Under the strict criteria of a minimal 2.0-log2 fold-expression change and a significance level of 3.0-log10, we could identify 147 up-regulated and 39 down-regulated genes. Among the genes recently identified with PRF lysates were IL11 and CXCL8, and a series of genes that indicate the mitogenic activity of PRS such as centromere-associated proteins (CENPA, E, F, M, U, W), cell division cycle proteins (CDCA2, A3, A5, A8, 6, 20, 25A, 25C, 45), kinesin-like proteins (KIF11, 14, 18A, 18B, 20A, 23, 4A, C1), and shugoshin 1 and 2, as supported by gene ontology. Verification by RT-PCR and immunoassays further confirmed the significant increase of IL11 and CXCL8 when gingival fibroblasts were exposed to PRS. Consistently, PRS provokes TGF-β but not NF-κB signaling, based on Smad2/3 and p65 translocation, respectively. In summary, our in vitro data provide support for the contribution of platelets in PRF, independent of leukocytes and plasma components, to elicit a robust response from gingival fibroblasts.

overall_design: We used washed leucocyte-depleted platelets in our bioassays. The platelets were activated with thrombin to release the contents of their granules into the serum-free culture medium. Gingival fibroblasts were exposed to this platelet-released supernatant (PRS), and transcriptional changes were identified by RNA sequencing. Verification by RT-PCR and immunoassays further confirmed the significant increase of IL11 and CXCL8 when gingival fibroblasts were exposed to PRS.

first: Panahipour

last: Layla


title: 5-methylcytosine and 5-hydroxymethylcytosine are synergistic biomarkers for early detection of colorectal cancer

city: Cambridge

first: Fabio

last: Puddu

address: The Trinity Building

institute: biomodal

type: Methylation profiling by high throughput sequencing

summary: Background Early cancer detection has the potential to significantly improve treatment outcomes and survival rates. This study investigates the roles of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) as biomarkers for early-stage colorectal cancer (CRC) detection in cell-free DNA (cfDNA).  Methods We analyzed cfDNA from 37 treatment-naive CRC patients and 32 healthy controls using duet evoC 6-base whole genome sequencing (A, C, T, G, 5mC, 5hmC). We then built CRC classifiers using differentially methylated regions identified in stage IV CRC tissue samples. We compared the performance of models using 5mC-only, 5hmC-only, modified cytosine, or 5mC and 5hmC features.  Results Here we show that models combining measurements of 5mC and 5hmC significantly enhance diagnostic accuracy (AUC = 0.95) compared to traditional approaches that conflate these markers (modified C, AUC = 0.66). Notably, of all the DMRs considered, almost half show an increase in 5hmC at stage I and a corresponding decrease in 5mC at stage IV, suggesting that 5hmC can effectively track regions undergoing demethylation during tumor development.   Conclusions These results support the hypothesis that distinguishing between 5mC and 5hmC improves the sensitivity of liquid biopsy tests for early-stage cancer detection.

overall_design: biomodal evoC epigenetic sequencing of 69 cfDNA samples from healthy individuals or individuals at different stages of CRC progression

first: Annelie

last: Johansson

first: Aurélie

last: Modat

first: Jamie

last: Scotcher

first: Riccha

last: Sethi

first: Shirong

last: Yu

first: Nick

last: Harding

first: Mark

last: Hill

first: Ermira

last: Lleshi

first: Casper

last: Lumby

first: Jean

last: Teyssandier

first: Michael

last: Wilson

first: Robert

last: Crawford

first: Tom

last: Charlesworth

first: Páidí

last: Creed

first: Shankar

last: Balasubramanian

last: Osborn


title: Single-cell transcriptional profiling of cancer cells in hairy cell leukemia (HCL) patients

city: Bethesda

first: Chi-Ping

last: Day

state: Maryland

address: Bldg 15C1, NIH-Bethesda

department: National Cancer Institute

institute: National Institutes of HEalth

summary: This single-cell RNA sequencing (scRNA-seq) dataset profiles human HCL cells from two patients with Hairy Cell Leukemia (HCL) and varient subtype of HCL (HCLv), both expressing unmutated IGHV4-34. scRNA-seq was performed on isolated CD19⁺ and CD3⁺cells from peripheral blood mononuclear cells (PBMC) (n=2). The dataset enables the characterization of expressed mutation and transcriptional profiles of human HCL cells and supports investigations into cellular lineage and pathways associated with pathologic activation leading to HCL and variant form of HCL (HCLv).

overall_design: This study (protocol# 10C0066) was approved by the National Institutes of Health Institutional Review Board (IRB). Fresh peripheral blood were collected from 2 patients diagnosed with HCL undergoing standard-of-care therapeutic treatment. All patients signed IRB-approved informed consent permitting the use of their blood for research. PBMCs were purified from peripheral blood, and cells positive for either CD19 or CD3 were isolated for full-length single-cell sequencing. The expressed mutations and transcriptional profiles were analyzed for identifying the lienage and developmental state of the single cells.

last: Kreitman

first: Evgeny

last: Arons

first: Chih-Hao

last: Wu

first: Suleyman

last: Sahinalp


title: Apoptotic Cell Clearance Triggers Epithelial Fate Reprogramming During Prostate Regression [ChIP-seq]

city: Montreal

first: Luke

last: McCaffrey

state: Quebec

address: 1160 Pine Ave Ouest

department: Oncology

country: Canada

institute: McGill University

summary: Androgen deprivation induces extensive tissue remodeling in the prostate, characterized by epithelial cell attrition and acquisition of a progenitor-like state in residual luminal epithelial cells. The mechanisms driving differentiated epithelial cells toward a progenitor fate remain unclear. Here, we identify that prostate regression is mediated by the engulfment of apoptotic neighbors by epithelial cells and that efferocytosis promotes acquisition of a progenitor-like state.   We show that epithelial cells are the predominant phagocytes during regression, engaging in temporally coordinated waves of apoptotic cell clearance. This process is accompanied by marked metabolic reprogramming, including increased aerobic glycolysis and lactate production. This coincides with enhanced histone lysine-lactylation at promoters of genes involved in autophagy, apoptosis regulation, and luminal progenitor identity. Blockade of efferocytosis in vivo via epithelial-specific expression of the dominant negative phosphatidylserine binding protein MFGE8-D89E impaired prostate regression and compromised the induction of the luminal progenitor marker Tacstd2. These findings reveal that epithelial efferocytosis is an essential mechanism that couples cell clearance and epithelial plasticity. This work establishes epithelial efferocytosis as a determinant of cell state transitions in the prostate, with implications for a direct role in castration-resistant prostate cancer and other regenerative or remodeling processes.

overall_design: Genome binding/occupancy profiling by high throughput sequencing in mouse prostate

first: Adda-Lee

last: Graham-Paquin


title: TFIIIB roadblocks control alternative cleavage and polyadenylation site selection

first: Guillaume

last: Chanfreau

address: 607 Charles E Young Dr E

institute: University of California, Los Angeles

summary: To test the functional impact of Pol III on controlling alternative CPA site selection, we depleted, Rna15p, a component of the cleavage and polyadenylation factor I, Bdp1p, a core component of TFIIIB, and Bdp1p/Rna15p together, from the nucleus and assessed the effect on 3´ UTR lengths of genes nearby tRNAs. Many genes show changes in 3’ ends after Bdp1p depletion indicating that transcripts can transcription termination can be due to TFIIIB roadblocks rather than transcript cleavage by cleavage and polyadenylation factors.

overall_design: Oxford Nanopore Direct RNA sequencing performed, in triplicate, on wild-type, Bdp1, and Bdp1 Rna15 anchor away strains.

first: Kevin

last: He

middle: F


title: TFG p.G269V mutation disrupts motor neuron function in iPSC-derived models via Wnt signaling dysregulation

city: Xi 'an

first: Kun

last: Chen

address: No.169 Changle West Road

institute: Fourth Military Medical University

summary: Charcot-Marie-Tooth disease (CMT), an inherited neuropathy characterized by progressive distal muscle weakness and atrophy, is associated with axonal impairment. Although mutations in the TRK-fused gene (TFG) have been linked to both CMT and hereditary spastic paraplegia, their pathogenic mechanisms remain poorly understood. Previously, we have demonstrated that the TFG p.G269V mutation causes progressive muscle weakness in patients, impairs neurite outgrowth in primary cultured mouse neurons, and induces neuronal apoptosis in zebrafish, suggesting a conserved role in neurodevelopment. To investigate its effects in human models, we established induced pluripotent stem cells (iPSCs) from patients carrying the mutation and generated homologous correction lines using CRISPR/Cas9 editing. Both cell lines differentiated into motor neurons (MNs). Although neuronal differentiation and the expression of maturation markers were comparable, the patient-derived MNs exhibited significant axonal shortening and accumulated insoluble aggregates. Electrophysiological assessment revealed functional deficits, including reduced spontaneous and evoked action potential frequencies and elevated rheobase. Transcriptomic analysis revealed dysregulation of Wnt signaling, and pharmacological inhibition of this pathway further exacerbated the loss of neuronal excitability. Our findings indicate that the TFG p.G269V mutation autonomously disrupts MN morphology and function and that these defects can be reversed using genetic correction. Moreover, dysregulated Wnt signaling may contribute to the pathophysiology of TFG-associated neuropathy.

overall_design: iPSC differentiation into MNPs and subsequently to differentiated neurons

first: Mu

last: Zhiqiang

first: Jielin

last: Wang

first: Chen

last: Kun

last: Jing

first: Wu

last: Yuanming

first: Liu

last: Fangfang


title: Crucial roles of mesenchymal Gata2 in murine epididymal development

city: Madison

first: Fei

last: Zhao

state: Wisconsin

address: 2015 Linden Dr

department: Comparative Biosciences

institute: University of Wisconsin-Madison

summary: Androgens drive the morphogenesis and differentiation of the Wolffian duct (WD) into the epididymis, an essential organ for male reproduction, by binding to the androgen receptor (AR). However, it remains unclear whether other transcriptional programs operate beyond the central androgen/AR signaling in promoting WD development. We discovered that mesenchyme-specific deletion of the transcription factor Gata2 resulted in defective epididymal coiling in the corpus and caudal regions. The defective coiling in the absence of mesenchymal Gata2 did not result from androgen production deficiency, as there were no abnormalities in androgen production or AR/Ar expression, and dihydrotestosterone supplementation did not restore epididymal coiling in cultured WDs. Instead, Gata2 deletion might disrupt mesenchymal identity, as indicated by the significant downregulation of Itga4, an mesenchymal epididymal marker. This loss of mesenchymal identity was accompanied by reduced expression of the mesenchyme-derived morphogen Inhba and decreased epithelial proliferation, both of which are critical for proper epididymal coiling. The developmental defects persisted into adulthood, with the uncoiled corpus and caudal epididymis exhibiting abnormal epithelial morphology and luminal environments, ultimately creating conditions unsuitable for sperm storage and leading to infertility. Notably, in adult knockouts, the epididymal epithelium aberrantly expressed αSMA, further indicating a failure to properly establish epithelial differentiation. Our findings reveal an androgen-independent role for mesenchymal GATA2 in maintaining mesenchymal identity during epididymal development, highlighting the importance of proper fetal mesenchymal specification for male reproductive function.

overall_design: To explore the functional role of mesenchymal Gata2 in Wolffian duct development, we generated a tissue-specific conditional knockout model by crossing Gata2-flox mice with Osr2-Cre. We prepared 3 Gata2cKO and 3 control mesonephroi from mouse embryos at embryonic day (E) 16.5. The mesonephroi used in this study included mesonephric tubule region. Embryonic day (E16.5) mesonephroi were snap frozen and then extracted for RNA.

first: Allyssa

last: Fogarty


title: RNA-seq profiling following a 5’ isomiR  transfection

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: Annotated canonical miRNAs (anomiRs) are critical regulators of COVID-19 pathogenesis. 5’ isomiRs, which exhibit a shifted 5’ end and distinct seed region compared to their cognate anomiRs, represent an essential component of the miRNAome. However, little is known about their repertoire and expression dynamics following SARS-CoV-2 infection. Herein, we performed an integrative analysis to investigate the expression and regulation of 5’ isomiRs in SARS-CoV-2-infected human lung cells. Using Argonaute (AGO) immunoprecipitated small-RNA sequencing data, we established a repertoire of AGO-loaded 5’ isomiRome encompassing 826 5’ isomiRs from SARS-CoV-2-infected lung cells. A total of 54 5’ isomiRs were differentially expressed, with the majority showing dysregulation 24 hours after SARS-CoV-2 infection. Compared to anomiRs, 5’ isomiRs were preferentially induced at 24 hours post SARS-CoV-2 infection, including six 5’ isomiRs derived from miR-4485 precursor. By focusing on a 5’ isomiR of miR-4485-3p exhibiting one nucleotide downstream shift of the 5’ end (miR-4485-3p|+1), we demonstrated that miR-4485-3p|+1 overexpression significantly repressed genes involved in cellular processes relating to cell cycle, cytoplasmic translation, and carbohydrate derivative metabolic process. Importantly, transcriptome integration further revealed that these cellular processes repressed by miR-4485-3p|+1 overexpression were strongly downregulated at 24 hours following SARS-CoV-2 infection. Moreover, 26 out of 43 (60.5%) hub genes co-repressed by miR-4485-3p|+1 and SARS-CoV-2 infection in these three cellular processes have reported association with COVID-19 in the literature. Taken together, our findings reveal the repertoire and expression alterations of AGO-loaded 5’ isomiRs in SARS-CoV-2-infected lung cells. The identified regulatory effects of miR-4485-3p|+1 highlight potential roles of 5’ isomiRs in COVID-19 pathogenesis.

overall_design: RNA-Seq profiling from Calu-3 cells  transfected with miR-4485-3p|+1 mimics or control mimics

first: Ming-Ju

last: Lyu

first: Munire

last: Maimaiti

first: Ziwei

last: Zhong


title: Beyond amyloid-β and tau: A cell-based multivariate blood test (iCAP) for early Alzheimer’s detection

city: Potomac

first: Jennifer

last: Smith

address: Windsor View Dr

institute: PreCyte, Inc.

summary: Abstract: Background: With amyloid-β (Aβ) therapies for Alzheimer’s disease (AD) under active debate, there is a need for diagnostic tools that reflect disease biology beyond Aβ and tau for early detection and for patient stratification. The indicator cell assay platform (iCAP) is a tool for blood-based diagnostics that uses standardized cells as biosensors to transduce complex circulating signals into gene-expression readouts, which are then used to train multivariate disease classifiers for precision medicine. We developed an iCAP for early detection of Alzheimer’s disease (AD-iCAP). Methods: In a retrospective study, AD-iCAP was developed by incubating banked plasma samples from patients with early-stage AD (mild cognitive impairment or mild dementia) and age-matched controls with standardized neurons; whole-transcriptome responses were measured and used train disease classifiers by machine learning. The assay was optimized and analytically validated. Patient AD-iCAP data were separated into a training set, external validation set and an independent test set and used to parameterize and test models. To minimize bias, modeling features were selected from a predefined (a priori) 84-gene panel derived from an independent AD-iCAP dataset generated using plasma from 5xFAD mice. Results: We developed AD-iCAP using 191 banked plasma samples across three cohorts. Performance was assessed in two held-out sets: an external validation set (n=82; AUC 0.64, 95% CI 0.51–0.78) and an independent test set (n=23, AUC 0.77, 95% CI 0.57–0.96). Systems biology analyses of differential response profiles showed concordance with postmortem AD brain transcriptomes and enrichment of AD-relevant pathways beyond amyloid, including cholesterol biosynthesis, synaptic structure/neurotransmission and NGF/TrkA signaling (FDR < 0.05). The final model’s features included AD-linked genes AKT3, GPR50, PALLD and RGMA, related to neuronal signaling and cytoskeletal/axon-guidance processes. Conclusions: AD-iCAP is a blood-based diagnostic for early-stage detection of AD. It outputs cell-based transcriptional profiles with disease-relevance that are induced by circulating factors. In retrospective, multi-cohort testing, it showed modest-to-good discrimination, supporting prospective confirmation in larger cohorts. Because its readout captures biology beyond amyloid and tau, it may provide complementary information for combined testing. The multivariate readout supports further development for patient stratification as Aβ-targeted therapies and alternatives evolve.

overall_design:
Overview. The goal of the study was to develop a biosensor-based diagnostic assay whereby cultured cells (iCell neurons) detect and respond to Alzheimer's disease (AD) signals in human blood samples and machine learning tools are used to develop disease classification models based on the cellular gene expression profiles of the cells. We exposed human indicator cells (iCell Neurons (Fujifilm)  to plasma from patients and measured their gene expression response. Plasma samples were from patients who were either cognitively normal or who had early stage Alzheimer's disease. The differential gene expression pattern between the two conditions was used to predict presence of Alzheimer's disease in the patients using machine learning tools.  The study included retrospective analysis of 470 human plasma samples from 3 cohorts (See data file 1 of teh manuscript for complete description). Plasma was from either affected patients (preclinical AD (preAD) or MCI stage) or from unaffected control subjects (normal). In addition, a limited number of plasma samples from patients with non-AD dementia were also included as controls in some experiments. Samples were from three different cohorts, each with a ~1:1:1 ratio of samples from each preAD, MCI and normal class, with gender and age were roughly balanced between classes. Plasma samples were exposed to indicator cells, and total RNA was isolated and analyzed by RNA-seq. RNA-seq data from affected and unaffected samples were used to train and test machine learning classifiers to detect early-stage AD. Before classifier development, sample QC and RNA-seq data QC were performed and samples were excluded that failed quality check. For classifier development, only samples of MCI vs normal class were used.  For feature selection for model development, plasma samples from a mouse model of Alzheimer's disease (5xFAD) was analyzed in the AD-iCAP and genes with AD versus normal differential expression were selected as candidate features.  For the mouse study: Longitudinal AD-iCAP data were generated from mice at 3, 5, and 7 months, spanning pre-symptomatic and MCI stages,34,35 under nine assay conditions (3 mouse ages x 3 neuron pre-culture times). After RNA-seq and data processing using two different GC bias correction methods, we obtained 18 differential expression datasets. From these data, we derived two feature sets: 398 genes detected in ≥1 dataset (Set 1) and 84 genes detected in ≥3 datasets (Set 2), all with adjusted p ≤ 0.05 (see Data File 4 of the manuscript).
Human plasma samples were processed in the iCAP in 24 experimental batches and each batch included four technical replicates of "reference control plasma samples", which were technical replicates of plasma from a non-affected individual at 40 years of age. These referece control samples were used for quality control and normalization only.

first: Yijun

last: Qi

first: Leslie

last: Miller

first: Mark

last: D'Ascenzo

first: Jason

last: Berndt

first: George

last: Whitney

first: Fergal

last: Duffy

first: Samuel

last: Danziger

first: Elaine

last: Peskind

first: Ge

last: Li

first: Colin

last: Masters

first: Christopher

last: Fowler

first: AIBL

last: group

first: Rob

last: Lipshutz

first: John

last: Aitchison


title: Hypoxia-driven histone modifications govern gene regulation for mature eye lens formation

city: Boca Raton

first: Marc

last: Kantorow

state: FL

address: 777 Glades Rd

department: Biomedical Science

institute: Florida Atlantic University

summary: Evidence suggests that the hypoxic environment of the lens regulates the expression of genes required for lens formation and function. Here, we tested the hypothesis that hypoxia regulates these genes through induction of specific histone modifications. Global levels of hypoxia induced histone modifications were determined in cultured day 13 chick lenses exposed to 1% oxygen. The genome-wide localizations of H3K27ac and H3K4me3 were identified by CUT&RUN analysis and mapped to within 5kb of the transcriptional start sites of genes activated or repressed by hypoxia identified by RNA Seq. The requirement for these histone modifications for hypoxia induced gene expression was determined using inhibitors of histone writers and erasers. The levels of activating modifications H3K4me3, H3K9ac, H3K14ac and H3K27ac in hypoxia treated lenses increased while levels of repressive modifications H3K9me3 and H3K27me3 remained unchanged. Hypoxia-specific H3K4me3 and/or H3K27ac regions were detected within 5 kb of the transcriptional start sites of over 900 fiber cell genes with increased expression upon hypoxia exposure and 350 genes with decreased expression. Inhibition of histone writers and erasers resulted in altered levels of key fiber cell genes upon hypoxia exposure. The results provide evidence that hypoxia induced histone modifications regulate genes required for mature lens formation and they provide a framework for understanding the role of hypoxia specific histone modifications in the regulation of genes in more complex tissues.

overall_design: Whole embryonic chick lenses were incubated under normoxia (21% O2) or hypoxia (1% O2) conditions for 2H or 8H. Following incubation lenses were microdissected into epithelial and fiber cell portions and the fiber cells used for downstream analysis. CUT&RUN analysis was used to mapp genome wide histone marks resulting from exposure to hypoxia. RNAseq was used to determine gene expression changes over 8H of hypoxia treatment.

first: Lisa

last: Brennan

first: Joshua

last: Disatham


title: Functional screening of transmembrane proteins identifies dolichyl pyrophosphate phosphatase CAX-4 as a key regulator of ergosterol biosynthesis and azole resistance in Neurospora crassa

city: Beijing

first: Shuting

last: Ye

address: No.1 Beichen West Road, Chaoyang District,

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Ergosterol, a key lipid component of fungal membranes, has its homeostasis predominantly maintained through membrane-associated mechanisms, yet the role of the many transmembrane proteins in regulating sterol homeostasis remains poorly understood. Here, we systematically screened 1,042 viable transmembrane protein mutants in Neurospora crassa, and identified 180 that exhibited altered sensitivity to one or more sterol biosynthesis inhibitors. Further analysis pinpointed three genes, cax-4, chol-6 and NCU01826, as required for the upregulation of erg11 upon azole treatment. CAX-4, a conserved dolichyl pyrophosphate phosphatase, was further characterized. Deletion of this gene leads to hypersensitivity to ketoconazole and amorolfine, and impairs the proper expression of membrane and extracellular proteins. Notably, CAX-4 was required for the transcriptional induction of core ergosterol biosynthetic genes (e.g., erg11, erg6, erg24) and sterol metabolism under azole stress. This phenotype was linked to reduced levels of NcSR, a key transcription factor in sterol biosynthesis regulation, at both the mRNA and protein level. Mechanistically, CAX-4 maintains protein homeostasis via N-glycosylation, as Tunicamycin treatment phenocopied its deletion. Above all, by characterizing key transmembrane protein in sterol biosynthesis regulation, our study unveils a CAX-4 integrated crosstalk between dolichol-mediated protein N-glycosylation and sterol biosynthesis regulation, thus offering novel insights into sterol homeostasis and pointing to potential targets for the development of antifungal strategies.

overall_design: The samples used for RNA-seq were prepared as described above. After RNA extraction, total RNA was sequenced on a BGISEQ-500 platform. After quality control, the clean reads were mapped to the reference genome of N. crassa (https://fungidb.org/common/downloads/Current_Release/NcrassaOR74A/). Gene expression levels were subsequently quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM). To ensure robustness, genes with an FPKM value of less than 1 in all samples were excluded from further analysis. Differentially expressed genes (DEGs) were identified as those exhibiting a fold change greater than 2 or less than 0.5 between two samples.

first: Pengju

last: Yu

first: Xianyun

last: Sun

first: Shaojie

first: Chengcheng

last: Hu


title: Molecular determinants of neoadjuvant chemotherapy resistance in breast cancer: An analysis of gene expression and tumor microenvironment

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: Neoadjuvant chemotherapy (NAC) is a critical component of breast cancer treatment, but the molecular mechanisms underlying resistance remain poorly understood. This study aimed to identify transcriptomic changes associated with NAC resistance across four breast cancer subtypes: Luminal A, Luminal B/HER2-positive, Luminal B/HER2-negative, and Triple-Negative Breast Cancer (TNBC). RNA-seq analysis was performed on paired pre- and post-NAC breast cancer samples from 35 non-responders. Differentially expressed genes (DEGs) were identified, and functional enrichment analyses were conducted. Protein-protein interaction (PPI) networks were constructed to identify hub genes. Tumor microenvironment (TME) infiltration was estimated using deconvolution algorithms. The results revealed distinct gene expression profiles between pre- and post-NAC samples, with FOS and NR4A1 being common DEGs across all subtypes. Enriched pathways varied among subtypes, including signal transduction, estrogen biosynthesis, extracellular matrix organization, dendritic cell activation, and B cell activation. TME analysis showed increased infiltration of specific immune cell populations after NAC, including CD4 memory T cells, regulatory T cells, neutrophils, macrophages, and mast cells, varying by subtype. These findings suggest that NAC modulates gene expression, cellular activity, and TME interactions, potentially contributing to treatment resistance. Understanding the molecular determinants of NAC resistance is crucial for developing targeted therapeutic strategies and improving outcomes for breast cancer patients.

overall_design: After obtaining informed consent, patients with a histologically confirmed diagnosis of breast cancer and scheduled chemotherapy were recruited for this study. Histopathological review of pre- and post-chemotherapy biopsies was performed by an expert pathologist who reviewed the slides and outlined the tumor tissue. Following completion of the neoadjuvant regimen, treatment response was evaluated using surgical specimens obtained by a pathologist. A pCR was established according to the most accepted definition: the absence of infiltrating components in the breast and lymph nodes (ypT0/is or ypN0). Patients were classified as responders if they showed pCR and non-responders if they did not present with pCR. RNA sequencing was performed on formalin-fixed paraffin-embedded pretreatment (baseline) and posttreatment (FollowUp) tissues from 35 non-responder patients . Differentially expressed genes (DEGs) were identified between the FollowUp and Baseline samples for molecular subtypes.

first: Hedda

last: Guevara-Nieto

first: Carlos

last: Orozco

first: Rafael

last: Parra Medina

first: Jone

last: Garai

first: Liliana

last: Lopez-Kleine

first: Alba

last: Combita


title: Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations [CRISPR screen]

first: Hani

last: Goodarzi

summary: Heterogeneity between patients poses a significant challenge in cancer drug development. Although success of a drug candidate in the clinic depends on efficacy across large numbers of diverse patients, only a few in vivo preclinical models are used for assaying a preclinical drug candidate due to the lack of scalability of traditional xenograft models. To address this limitation, we developed GENEVA, a scalable platform that enables the measurement of molecular and phenotypic responses to drug perturbations at single-cell resolution, both in 3D and in vivo. GENEVA models the genetic diversity of cancer by combining multiple patient-derived cell lines and cancer cell lines into pooled 3D cultures and xenograft models, allowing us to study drug responses across a wide range of genetic backgrounds within a single experiment. This platform integrates high-resolution transcriptomics with multiplexed single-cell profiling, providing a unique ability to uncover the interplay between cancer genotypes and drug responses. In this study, we apply GENEVA to investigate KRAS G12C inhibitors and demonstrate that mitochondrial activation is a key driver of cell death following KRAS inhibition. Additionally, we identify epithelial to mesenchymal transition (EMT) as a prominent resistance mechanism to KRAS G12C inhibition using in vivo GENEVA mice. These findings highlight the utility of GENEVA in identifying novel therapeutic targets and optimizing combination therapies, while underscoring its potential to bridge the gap between preclinical cancer models and patient outcomes by modeling the complexity of tumor heterogeneity in a scalable and robust assay.

overall_design: Lung cancer cell lines (H358, H2122, H23, H441) transduced with dCas9-KRAB and pooled dual sgRNA libraries targeting approximately 100 genes were injected into the flanks of NSG mice to form mosaic xenografts. Two days post-implantation, mice were treated with Sotorasib ($100~mg/\text{kg}$) or vehicle. Dosing was performed by daily oral gavage for 13 days. Tumors were excised on day 14, and genomic DNA (gDNA) was extracted for subsequent guide RNA sequencing to quantify gene enrichment/depletion (Rho scores) and determine genetic dependencies.

first: Johnny

first: Jung

last: Suh

first: Katerina

last: Popova

first: Kristle

last: Garcia

first: Tanvi

last: Joshi

first: Bruce

last: Culbertson

first: Jessica

last: Spinelli

first: Vishvak

last: Subramanyam

first: Kevin

last: Lou

first: Kevan

last: Shokat

first: Jonathan

last: Weissman


title: Hypoxia-driven histone modifications govern gene regulation for mature eye lens formation [CUT&Run]

first: Marc

last: Kantorow

overall_design: Whole embryonic chick lenses were incubated under normoxia (21% O2) or hypoxia (1% O2) conditions for 2H . Following incubation lenses were microdissected into epithelial and fiber cell portions and the fiber cells used for downstream analysis. CUT&RUN analysis was used to mapp genome wide H3K4me3 and H3K27ac regions resulting from exposure to hypoxia. RNAseq was used to determine gene expression changes over 8H of hypoxia treatment.

first: Lisa

last: Brennan

first: Joshua

last: Disatham


title: Single-cell transcriptomic analysis reveals epithelial and microenvironmental heterogeneity in small cell carcinoma of the esophagus

city: Shijiazhuang

first: Xiaolei

last: Yin

address: No. 169, Tianshan Road

institute: Fourth Hospital of Hebei Medical University

summary: Small cell carcinoma of the esophagus (SCCE) is a rare and aggressive malignancy with limited treatment options and poor prognosis. To better characterize its biological features, we performed single-cell RNA sequencing on SCCE alongside esophageal squamous cell carcinoma, esophageal adenocarcinoma, and adjacent normal tissues. Integrative transcriptomic analysis revealed that SCCE was dominated by malignant epithelial cells displaying high chromosomal instability and could be divided into three transcriptionally distinct subtypes with divergent differentiation trajectories. The tumor microenvironment exhibited profound immune suppression with reduced immune infiltration and downregulation of immune checkpoint genes, while the stromal compartment was enriched in extracellular matrix fibroblasts with elevated ELF3 activity and inflammatory fibroblasts mediating collagen-driven signaling. Notably, SCCE displayed the most intricate cell–cell communication network among esophageal cancer subtypes. This single-cell atlas highlights the unique tumor architecture, immune exclusion, and stromal reprogramming of SCCE, providing a valuable resource for understanding its biology and guiding future mechanistic studies.

overall_design: Single-cell RNA sequencing was performed on tumor tissues from small cell carcinoma of the esophagus (SCCE) to investigate cellular heterogeneity and tumor microenvironmental features.

first: xiaolei

first: xiaopeng

last: Li

first: lili

last: Mi

first: jiaojiao

last: Hou

first: fei


title: Forced intensity-controlled endurance training on a small-animal treadmill machine inducing murine cardiac hypertrophy

city: Munich

first: Maximilian

last: Fischer

address: Marchioninistr. 15

institute: LMU University

summary: Endurance training is associated with decreased cardiovascular-related morbidity and mortality. Cardiac hypertrophy is an adaptive mechanism of the heart in response to volume and pressure overload. Nonetheless, murine exercise models for cardiac hypertrophy are still under discussion. Using a small-animal treadmill, a forced intensity controlled training model was conducted to characterize cardiac hypertrophy in mice utilizing multimodal analyses. Wild-type male C57BL/6 mice age between 5-8 weeks old were subjected to 8 weeks of forced endurance training using a small-animal treadmill or sedentary age-matched control. Transcriptomic analysis of 8-week training hearts was evaluated using RNA sequencing. RNA sequencing revealed several genes involved in the cell cycle, apoptosis, contractile protein expression, and organ growth that were among the most differentially regulated genes after 8-weeks of exercise.

overall_design: Wild-type mice were randomly assigned to forced endurance training or sedentary counterparts. Forced exercise training was performed using a dedicated small-animal treadmill (Panlab Harvard Apparatus, Holliston, Massachusetts).

first: Bartolo

last: Ferrara

first: Ludwig

last: Weckbach

first: Tobias

last: Straub


title: RNA-seq profiling of resting naive and CD27bright memory B cells and in vitro activated CD27bright memory B cells reveals differences in B-cell activation patterns in common variable immunodeficiency (CVID)

first: Ola

last: Grimsholm

address: Wahringer Gurtel 18-20

department: Pathophysiology and Allergy Research

institute: Medical University of Vienna

summary: To investigate the transcriptional differences during resting state and B-cell activation in healthy donors and patients with CVID, we sorted naive B cells and CD27bright memory B cells from the two groups and examined the resting state and TLR9 agonist (CpG)-activated CD27bright memory B cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data derived from resting naive B cells and CD27bright memory B cells, as well as from in vitro-activated CD27bright memory B cells of health controls and patients with common variable immunodeficiency (CVID).

first: Anna

last: Pousas Navarro

first: Shirin

last: Pour Akaber

first: José

last: Basílio

first: Vanda

last: Friman

first: Jesper

last: Waldenström

first: Barbara

last: Bohle

first: Ahmed

last: Mohamed


title: Cell composition and gene-expression dynamics of skeletal muscle regeneration after contraction-induced injury

city: Copenhagen N

first: NNF CBMR

last: Single-Cell Omics Platform

address: Blegdamsvej 3B

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

summary: Small-molecule activators targeting the allosteric drug and metabolite (ADaM) site of AMPK enhance insulin-independent glucose uptake in skeletal muscle and promote blood glucose lowering in preclinical models of hyperglycemia. The regulatory AMPKγ subunit plays a central role in energy sensing, and the skeletal muscle-selective γ3 isoform is essential for AMP/ZMP-induced glucose uptake, but not for ADaM site activators. We hypothesized that the predominant γ1 isoform is required for ADaM site activator-stimulated glucose uptake in skeletal muscle.

overall_design:
Single-nucleus RNA sequencing (snRNA-seq) was applied to human and mouse skeletal muscle to characterise the expression patterns of AMPK subunit isoforms across resident cell types

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

middle: N

last: Schou

first: Charline

last: Jomard

first: Danial

last: Ahwazi

first: Dipsikha

last: Biswas

first: Emilie

last: Dalbram

first: Ever

last: Espino-Gonzalez

first: Jean

last: Farup

last: Just

first: Jonas

last: Jensen

middle: T

last: Treebak

first: Jordana

last: Freemantle

first: Julien

last: Gondin

first: Kei

last: Sakamoto

first: Marc

last: Foretz

first: Marianne

last: Agerholm

first: Niels

last: Jessen

first: Rémi

last: Mounier


title: IL-22 induces Paneth cell metaplasia in the colonic epithelium of ulcerative colitis, promoting wound healing via REG3A

city: Kiel

first: Joana

middle: P.

last: Bernardes

state: SH

address: Am Botanischen Garten 11

department: Systems Immunology

institute: IKMB

summary: Paneth cell metaplasia (PCM) is a phenomenon in which Paneth cells, typically found in the small intestine, appear in the colonic epithelium of patients with ulcerative colitis (UC). Our study demonstrates that the PCM occurrence correlates with disease duration and active inflammation. Furthermore, we reveal that the inflammation-induced cytokine IL-22 suppresses Notch signaling, thereby promoting PCM formation in the colonic epithelium while simultaneously inducing REG3A expression in metaplastic niches. In vitro, we show that Reg3a directly enhances cell proliferation and promotes wound healing using mouse colonic organoids. In vivo, Reg3aΔIEC mice in both acute and chronic DSS-induced colitis models exhibit delayed wound healing. Additionally, studies conducted with patient-derived human colonic organoids revealed that REG3A administration stimulates cell proliferation and accelerates wound healing. These findings underscore a novel protective role of PCM-mediated REG3A in the colonic epithelium of patients with UC.

overall_design: RNA-seq analysis comparing Reg3afl/fl and Reg3aΔIEC colonic organoids. Treated or not with IL22.

first: Muto

last: Tomohiro

first: Go

last: Ito

first: Hiromune

last: Katsuda

first: Yui

last: Hiraguri

first: Satoru

last: Fujii

first: Kurara

last: Yamamoto

middle: P

first: Finn

last: Hinrichsen

first: Uchida

last: Hitoshi

first: Yasuhiro

last: Nemoto

first: Mayumi

last: Kinoshita

first: Eri

last: Ooshina

first: Kouhei

first: Shuji

last: Hibiya

first: Sayaka

last: Nagata

first: Fenja

last: Schuran

first: Shiro

last: Yui

first: Penelope

last: Pelczar

first: Samuel

last: Huber

first: Stefan

last: Schreiber

first: Philip

last: Rosenstiel

first: Mamoru

last: Watanabe

first: Ryuichi

last: Okamoto


title: HMGN3 ChIP-seq in AC16 cells and Bulk-RNAseq in AC16 cell with and without HMGN3 knockdown

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

summary: Chromatin structure plays a central role in regulating gene expression and maintaining cellular identity, yet the structural factors driving these processes in cardiac disease remain poorly defined. To investigate whether these factors can distinguish healthy from diseased cardiac cell populations, we generated a comprehensive list of chromatin structural genes based on an extensive literature review. Applying this list to a published single-cell RNA sequencing (scRNA-seq) dataset from human hearts with and without dilated cardiomyopathy (DCM), we found that chromatin structural gene expression effectively stratified cardiomyocyte and fibroblast populations by disease status. Diseased cardiomyocytes exhibited reduced expression of contractile genes and increased expression of cardiomyopathy markers, while fibroblasts showed enhanced activation signatures. Among these factors, HMGN3 emerged as a candidate of interest, showing consistent downregulation in cardiomyocytes from human patients, as well as in mouse (pressure overload) and pig (myocardial infarction) models of heart failure. Functional studies in AC16 cells revealed that HMGN3 depletion reduced proliferation, increased apoptosis, and decreased active chromatin marks (H3K27ac, H3K4me1), accompanied by increased chromatin compaction. These findings identify HMGN3 as a potential regulator of chromatin architecture in diseased cardiomyocytes, highlight the utility of chromatin structural gene expression in distinguishing pathological cardiac states, and reinforce the role of chromatin organization in shaping the cardiac phenotype. In this dataset, HMGN3 ChIP-seq and Bulk-RNAseq data with and without HMGN3 knockdown were generated using AC16 cells.

overall_design: ChIP-seq and Bulk-RNA-seq data were generated from AC16 cells treated by siRNA carrying HMGN3 knockdown and scramble (control) sequence. Cells were harevested 72hr after treatment. For Bulk-RNA seq

first: Xiaoxiao

last: Geng

first: Rujula

last: Pradeep

first: Min

last: Xie

first: Adam

last: Wende

first: Jianyi

last: Zhang

first: Cobo

last: Isidoro

first: Manuel

last: Rosa-Garrido


title: Research on the Inhibitory Effect of DMSO on the Treatment Process of Coal Mine Dust and Its Molecular Mechanism

city: Anhui

first: Yukang

last: Zhu

address: No. 203,Huai Bin Road, Huainan City,Anhui Province

institute: The First Hospital of AUST

summary: This study aims to investigate the anti-inflammatory and anti-fibrotic effects of Dimethyl Sulfoxide in a murine model of silicosis, and further explore its potential therapeutic effects.

overall_design: Silica suspension was administered to mice by nasal drops, followed by DMSO solution on the second day. After 30 days, the lung tissues of the mice were collected for transcriptome sequencing.

first: Guoling

last: Yao

first: Deyong

last: Ge


title: Peripheral nerve injury-induced remodeling of the tumor-associated macrophages promotes immune evasion in breast cancer

city: Guangzhou

first: Penghan

last: Huang

address: 107 Yan Jinag West Road

institute: Sun Yat-Sen University

summary: Peripheral nerve damage is intricately linked to the progression of various solid tumors and play a pivotal role in the tumor ecosystem. However, its effect on antitumor immunity and precise underlying mechanisms remain poorly understood. This study aimed to elucidate the effect of peripheral nerve damage and subsequent immune modulation on breast cancer progression.

overall_design: The experimental design involves culturing purified mouse CD8⁺ T cells in two distinct conditions: (1) control group - CD8⁺ T cells cultured with supernatant from untreated macrophages, and (2) experimental group - CD8⁺ T cells cultured with supernatant from NF-L (neurofilament light chain)-activated macrophages. Mouse CD8⁺ T cells will be isolated from spleens by mechanical dissociation followed by density gradient centrifugation using Mouse Lymphocyte Separation Medium and positive selection with REAlease® CD8a MicroBead Kit (Miltenyi). Macrophages will be derived from CD11b⁺ monocytes isolated from spleen using EasySep™ Mouse CD11b Positive Selection Kit II (Stemcell) and differentiated with M-CSF (50 ng/mL) for 7 days. For NF-L activation, macrophages will be stimulated with 5 μg/mL NF-L (prepared from sciatic nerve lysate via three freeze-thaw cycles in liquid nitrogen) for 24 hours before supernatant collection. Both control and NF-L-activated macrophage supernatants will be filtered (0.22 μm) and used at 50% concentration in fresh RPMI-1640 medium supplemented with 2% FBS for CD8⁺ T cell culture.

first: Yongxue

last: Jiang

first: Wenfeng

last: Zeng

first: Xiaoting

last: Deng

first: Jianing

last: Chen


title: ALKBH5-IGF2BP2 Axis Mediates Prostate Cancer Progression and Docetaxel Resistance via m6A-Stabilized CLSPN RNA

city: Tianjin

first: Yutong

address: Pingjiang road, tianjin

institute: tianjin medical university

summary: Prostate cancer (PCa) often progresses to castration-resistant PCa (CRPC), where docetaxel (DTX) resistance is a major challenge. We investigated the role of the m6A demethylase ALKBH5 in this resistance. ALKBH5 expression was significantly reduced in CRPC clinical samples. Functionally, overexpressing ALKBH5 inhibited PCa cell proliferation and migration, while its knockdown enhanced these effects and increased DTX resistance. Conversely, restoring ALKBH5 or knocking down the m6A reader IGF2BP2 reversed resistance. Multi-omics analysis identified CLSPN, a DNA replication stress regulator, as a key downstream target. Mechanistically, ALKBH5-mediated m6A demethylation reduces CLSPN mRNA stability in an IGF2BP2-dependent manner. Low ALKBH5, therefore, stabilizes CLSPN via IGF2BP2, promoting resistance. These findings, validated in clinical samples and organoid models, demonstrate that the ALKBH5-IGF2BP2 axis modulates DTX resistance in mCRPC through m6A-dependent regulation of CLSPN. Targeting this pathway represents a promising therapeutic strategy to overcome DTX resistance.

overall_design:
The C4-2 cells in the empty vector control group (NC) and the ALKBH5 overexpression group were subjected to m6A sequencing to analyze the differential patterns of m6A methylation modification.
RNA sequencing was performed to analyze the differential mRNA expression in C4-2 cells following overexpression of the empty vector control (NC) and ALKBH5 (i.e. *-input samples)

first: Yang

last: Li

first: Zongzhu

last: Liang

first: Zhao

last: Yang

first: Haotian

last: Ren

first: Wanqing

last: Wei

first: Yuanjie

last: Niu

first: Zhiqun

last: Shang


title: Loss of brain insulin production impairs learning and memory in female mice

city: Vancouver

first: Howard

last: Cen

state: BC

address: 2350 Health Sciences Mall

institute: University of British Columbia

summary: Diabetes is a metabolic disorder characterized by dysfunctional insulin release and action, and it is a risk factor for Alzheimer’s disease, the most common form of dementia. Alterations in brain insulin signalling and metabolism have been linked with Alzheimer’s disease in multiple studies. It has been previously shown that the ancestral insulin gene, Ins2, is transcribed locally within the brain. Here we demonstrate that Ins2 mRNA is higher in females than males, and modulated by diet. Moreover, we demonstrate that the Ins2 protein is prominently expressed within the hippocampus, a brain region with established roles in learning and memory. To specifically determine how insulin produced locally in the brain influences hippocampal function, learning and memory, and adult neurogenesis, we used mice with germline Ins2 knockout (Ins2-/-) and the normal complement of wildtype Ins1 alleles. Compensation from the Ins1 gene, results in normal glucose tolerance, normal insulin sensitivity, normal fasting insulin, and normal body weight under these dietary conditions. We assessed visuo-spatial learning and memory in male and female Ins2-/- and wild-type littermate control mice using the Morris water maze (MWM). Learning and memory performance of female Ins2-/- mice was significantly impaired relative to wild-type mice, whereas the performance of male Ins2-/- and wild-type mice did not differ. We profiled isolated hippocampi from female Ins2-/- and littermate control mice using RNA sequencing to provide an unbiased analysis of gene expression differences that underlie these behavioural changes. Cyclin D1 (Ccnd1) was significantly reduced in Ins2-/- mice, prompting us to examine adult neurogenesis using exogenous mitotic marker EdU and the immature neuronal marker doublecortin (DCX). Collectively, our data demonstrate female-specific role for brain-derived Ins2 on learning and memory function in mice.

overall_design: RNA-seq of hippocampus from Ins2+/+ and Ins2-/- mice.

first: James

last: Johnson