title: Gene expression profile at single cell level of the vein grafts

city: Hangzhou

first: Rong

last: Mou

address: 79 Qingchun Road

institute: Zhejiang University

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of non-inflammatory cells or venous graft derived cells to explore the underling mechanisms responsible for the different VGs with or without lymphatic vessels.

overall_design: CD45- non-inflammatory cells from vein grafts were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Kai

last: Chen

first: Pengwei

last: Zhu

first: Qingbo


title: Interallelic gene conversion can revert acquired single nucleotide variants associated with myeloid disease

status: Public on Sep 02 2025

city: Nashville

first: Alexander

middle: J

last: Silver

state: Tennessee

address: 2220 Pierce Ave

country: USA

institute: Vanderbilt University School of Medicine

type: Expression profiling by high throughput sequencing

summary: The purpose of this study was to examine how removal of truncating ASXL1 mutations via interallelic gene conversion affects gene transcription in models of myeloid hematologic malignancies.

overall_design: We performed a bulk RNAseq differential gene expression analysis of K562 and OCI-AML5 cells that were treated with scramble gRNA control or ASXL1-targeting gRNA. Three experimental replicates of each condition were included.

first: Michael

middle: R

last: Savona


title: Tcf7l2 is a master regulator of muscle wasting in severe cancer cachexia

city: Singapore

first: Christiane

last: Ruedl

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Hyper-activation of the canonical Wnt signalling pathway drives tumour initiation and cancer progression. Of the four TCF/LEF transcription factors that propagate Wnt signalling, TCF7L2 is believed to be relevant in colorectal cancer because it is essential for adult gut homeostasis. However, this has been challenging to verify because Tcf7l2 germline or adulthood knockouts are lethal. To circumvent lethality and mimic the systemic action of a potential drug, we generated a transgenic mouse strain that allows inducible, tuneable and reversible repression of endogenous Tcf7l2. While >95 % Tcf7l2 repression was lethal, 80 % repression rescued moribund mice from death in the ApcMin/+-DSS colon adenocarcinoma model. Unexpectedly, Tcf7l2 repression did not impact tumour growth but reversed lethal cachexia—a cancer comorbidity characterised by severe weight and muscle loss. During severe cachexia, elevated Tcf7l2 in the gastrocnemius muscle induces atrophy via the ubiquitin proteasome system (UPS) and autophagy lysosome system (ALS). Repressing Tcf7l2 in the gastrocnemius reduces the expression of UPS and ALS genes to non-cachectic levels, thereby preventing atrophy and restoring muscle mass. Therapeutic targeting of TCF7L2 could ameliorate cachexia-induced muscle atrophy. Our mice could be utilised to study conditions that involve muscle atrophy, such as aging, diabetes and neuromuscular diseases.

overall_design: 6 samples were analysed, comprising of colon tumours from cachectic APC-WT mice under doxycycline treatment for 10 days (n = 3) and recovered APC-KI mice under doxycycline treatmnet for 6 weeks (n = 3). Doxycycline treatment repressed endogenous Tcf7l2 expression in a systemic manner, but only APC-KI and not APC-WT mice.

first: Klaus

last: Karjalainen

first: Mei

middle: L

last: Leong


title: Fasting Mimicking Diet inhibits autophagy and synergizes with chemotherapy to promote T cell-dependent leukemia-free survival

city: Los Angeles

first: Valter

middle: D

last: Longo

state: CA

address: 3715 McClintock Avenue

institute: USC

summary: We have investigated the effects of FMD cycles in combination with or without chemotherapy (vincristine) in syngeneic in vivo B-ALL mouse model

overall_design: RNA-seq analyses on spleen tissue isolated from B-ALL mice at the end of the treatment

first: Roberta

last: Buono

first: Serghei

last: Mangul


title: m6A/YTHDF1 modulates CAP1-mediated actin turnover and synaptic function to regulate anxiodepressive-like behaviors [RNA methylation]

status: Public on Sep 01 2025

city: Shenzhen

first: Xidan

last: Zhou

state: Guangdong

address: No. 1068 Xueyuan Avenue, Shenzhen University Town

country: China

institute: Chinese Academy of Sciences Shenzhen Institutes of Advanced Technology

summary: Neuroplasticity and synaptic dysfunction are central to depression, yet the underlying mechanisms remain poorly understood. While m6A and its reader YTHDF1 regulate mRNA translation, neuroplasticity and learning behaviors, their role in affective disorders such as depression remains unexplored. This study identifies YTHDF1 as a key regulator of depression pathogenesis. Genetic deletion of YTHDF1 in mice caused anterior cingulate cortex (ACC) hyperactivity, heightened social stress sensitivity, and anxiodepressive-like behaviors after acute social stress. Using multi-omic approaches, we uncovered a critical role for actin cytoskeleton dynamics and identified cyclase-associated protein 1 (CAP1) as a downstream effector of YTHDF1. Loss of YTHDF1 reduced CAP1 expression from early postnatal stages, resulting in F-actin accumulation, impaired synaptic function, and behavioral deficits. Strikingly, early postnatal YTHDF1 re-expression in the ACC restored CAP1 levels, synaptic integrity, and reversed depressive-like phenotypes. These findings establish the m6A/YTHDF1/CAP1 axis as a critical pathway regulating synaptic function and depression.

overall_design: We performed MeRIP-seq (m6A-seq) on RNA isolated from the anterior cingulate cortex (ACC) of adult YTHDF1 wild-type (WT) mice to profile the global landscape of N6-methyladenosine (m6A) modification. The experiment included three biologically independent replicates, with each replicate representing a pooled ACC sample from 10 mice to ensure sufficient input material and account for biological variability.

first: Tao

first: Yihui

last: Cui

first: Si

last: Li

first: Chen

last: Guo


title: m6A/YTHDF1 modulates CAP1-mediated actin turnover and synaptic function to regulate anxiodepressive-like behaviors

overall_design: We performed high-throughput RNA sequencing of anterior cingulate cortex (ACC) of adult Ythdf1 wild-type (WT) and knockout (KO) mice. Three replicates were conducted for each genotype. The RNA libraries were sequenced on the illumina NovaseqTM 6000 platform by LC Bio Technology CO.,Ltd (Hangzhou, China).


title: m6A/YTHDF1 modulates CAP1-mediated actin turnover and synaptic function to regulate anxiodepressive-like behaviors [RIP-Seq]

overall_design: We performed YTHDF1-specific RNA immunoprecipitation followed by high-throughput sequencing (YTHDF1-RIP-seq) on anterior cingulate cortex (ACC) tissue from adult wild-type mouse. This study was designed to identify the transcriptome-wide set of mRNAs that physically interact with the m6A reader protein YTHDF1 in this brain region. The experiment included three biologically independent replicates.


title: Substantial collateral effects induced by CasRx  in mammalian cells and mice

city: Shanghai

first: Hui

last: Yang

state: Shanghai

address: 320 Yueyang Road

institute: CAS Center for Excellence in Brain Science and Intelligence Technology

summary:
CRISPR-Cas13 systems have recently been employed to silence RNAs in yeast, plants, mammalian cell lines and animals, however, collateral effects induced by Cas13 may impede their research and therapeutic applications.
Here, we found Cas13a and CasRx-mediated RNA knockdown induced substantial collateral effects on both exogenous and endogenous genes in mammalian cells.
Moreover, transgenic mice carrying CasRx, with or without targeting guide RNA, exhibited high lethality.
Therefore, our results present limitations of CasRx, requiring a solution to address its fidelity before clinical applications.

overall_design: To study the collateral effects of casRx system targeting endogenous genes in mammalian cells, we designed a  three groups experiment using HEK293T cell lines, including a control (casRx with exogenous targets) and two treatment groups (casRx with endogenous targets). Three replicates were prepared for each group for whole transcriptome sequencing. One sample in the control group was discarded due to quality issue. We finally have 8 RNAseq samples in total, two for the  control group, labeled with NT, and three for each endogenous-target groups, labeled with casRx+RPL4 g1 and casRx + RPL4 g2, respectively.

first: Bingbing

last: He

first: Jia

last: Huang

first: Yuanhua

last: Liu


title: Regulation of the NSL complex by TAF4A is critical for genome stability and quiescence of skeletal muscle stem cells [RNA-seq of MuSCs from control and Taf4asKOmice]

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: Acetylation of lamin A/C by the NSL complex, containing MOF and KANSL2, is instrumental for maintaining nuclear architecture and genome stability, but the mechanisms controlling expression of NSL complex components in different cell types are poorly characterized. Here, we describe that TAF4A, primarily known as a subunit of the general transcription factor TFIID, is critical for cell type-specific regulation of Kansl2 in MuSCs. Inactivation of Taf4a in MuSCs reduces expression of Kansl2 and alters post-translational modification of lamin A/C, thereby decreasing the stiffness of MuSC nuclei and disrupting the nuclear architecture. Using CUT&RUN technique, we found that TAF4A together with the heterotrimeric transcription factor NF-Y controls Kansl2 expression. In addition to destabilization of the nuclear architecture, reduced expression of Kansl2 in Taf4a-mutant MuSCs changes expression of numerous genes involved in chromatin regulation. The subsequent loss of heterochromatin and MuSC activation, in combination with pronounced genomic instability, activates MuSCs and impairs MuSC proliferation, which depletes the stem cell pool and abolishes skeletal muscle regeneration. We conclude that TAF4A-NF-Y-dependent transcription regulation safeguards heterochromatin and genome stability of MuSCs via the NSL complex.

overall_design: Transcriptome profiling of MuSCs from control and Taf4asKOmice

first: Angelina

middle: M

last: Georgieva

first: Stefan

last: Günther


title: Androgen receptor cell-autonomously regulates luminal cell plasticity [ATAC-Seq]

city: New York City

first: Dan

state: NY

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ATAC-seq was performed using intact, Ar knockout or castrated luminal cell after 2 weeks Ar knockout or 5 days castration

overall_design: Alive Ar knockout or castrated prostate luminal cells after 2 weeks Ar knockout or 5 days castration were sorted by Fluorescence-activated cell sorting (FACS) according to Epcam, Cd24a, EYFP and DAPI and analyzed using RNAseq.

first: Yu

last: Chen


title: Androgen receptor cell-autonomously regulates luminal cell plasticity [RNA-Seq]

summary: Comparision of transcriptome of Intact, Ar knockout or castrated luminal cell after 2 weeks Ar knockout or 5 days castration


title: Macrophage MERTK mediates pressure overload-induced heart failure via type I interferon response

city: shanghai

first: yikai

last: cui

address: xietu street 180

institute: fudan university

summary: Macrophages play a critical role in the pathogenesis and progression of heart failure, wherein sustained cardiomyocyte apoptosis is a key feature. The MER proto-oncogene tyrosine kinase (MERTK) is a critical receptor that mediates the efferocytosis of apoptotic cells by macrophages. However, the role and mechanism of action of MERTK in pressure overload-induced heart failure remains unclear. Here, we demonstrate that MERTK expression was upregulated in cardiac tissue macrophages of mice with pressure overload-induced heart failure. Deletion of MERTK ameliorated transverse aortic constriction (TAC)- and Ang II-induced cardiac hypertrophy and heart failure. This protective effect was associated with reduced type I interferon signaling and was reversed by interferon receptor activation. Efferocytosis assays were performed to demonstrate that mitochondrial double-stranded RNA from apoptotic cardiomyocytes activated Toll-like receptor 3 in macrophages, promoting Interferon beta (IFNb) expression. In vitro experiment identified that IFNb sensitized cardiomyocytes to Ang II stimulation by augmenting the P53 pathway, suppressing Ang II-induced protective mitophagy and promoting cardiomyocyte apoptosis. In conclusion, macrophage MERTK receptor exacerbated post-TAC heart failure and cardiac hypertrophy by mediating the phagocytosis of apoptotic cardiomyocytes and promoting IFNb expression. This study provides novel insights into the role of macrophage MERTK-mediated efferocytosis and type I interferon response in the pathogenesis of heart failure. These findings highlight an unrecognized function of MERTK in pressure overload-induced cardiac remodeling and identify IFNb as a key downstream effector of MERTK in this pathological process

overall_design: rna-seq profiling of hearts of wildtype and Mertk knockdown c57 mice at 8 weeks after transverse aortic constriction

first: Yikai

first: Liwei

first: Junbo

last: Ge


title: Transcriptome profile of LX-2 cells

city: Wuhan

first: An

last: Zhang

address: Aerodrome Road 13

institute: Huazhong University of Science and Technology

summary: Liver fibrosis is characterized by deposition of excessive extracellular matrix (ECM). The major source of ECM is activated hepatic stellate cells (HSCs).NAT10 is the only known acetyltransferase catalyzing ac4C RNA modification. The purpose of this transcriptome is to explore the role of NAT10 acting as ac4C acetyltransferase during HSC activation.

overall_design: RNA-seq profiling of  LX-2 cells(con) and TGF-β1 stimulated LX-2 cells (TGFB) and LX-2 cells transfected with NAT10 SiRNA(SiNAT10) and then stimulated with TGF-β1 (SiNAT10_TGFB).

first: Chunwei

last: Shi


title: Mechanisms of sexually dimorphic adipose tissue remodelling upon prolonged breastfeeding

city: Oslo

first: Damien

last: Dufour

address: Sognsvannsvein 9

country: Norway

institute: University of Oslo

summary: Understand how the transcriptome the the inguinal white adipose tissue changes between post natal 21 and 28 in regard to separation with the mother.

overall_design: We used inguinal white adipose tissue from 3- and 4-week-old male and female mice separated at p21 or kept with their mother

first: Philippe

last: Collas

first: Charlotte

last: Boccara

first: Nolwenn

last: Briand


title: Single-Cell Atlas of Neuroglial Dynamics in SNCA-A53T Parkinson's Disease Model

city: Shiyan prefecture level city in Hubei

first: Jingjing

last: Weng

address: Shiyan City, Hubei Province

institute: Hubei University of Medicine

summary: Single-cell sequencing reveals that activation of the neuroinflammatory axis triggered by mutations in the SNCA gene A53T and dysregulation of the transcriptional regulatory network in Parkinson's disease (PD) combine to shape a cell-specific pathological picture of the substantia nigra-striatal pathway

overall_design: Two samples were obtained from the midbrain tissue of A53T mice; Two samples were obtained from the midbrain tissue of wild-type mice; One sample was obtained from the striatum tissue of A53T mice; A sample is derived from the striatum tissue of wild-type mice

first: Binqing

last: Qin

first: Xiaodong

last: Sun

first: Ming

last: Sang


title: Discovery of antimicrobial peptides targeting Acinetobacter baumannii via a pre-trained and fine-tuned few-shot learning-based pipeline

first: Junjie

last: Huang

state: Zhejiang

address: 150 Dongfang Street Xiasha, Qiantang District

department: Center for AI and Intelligent Medicine

institute: Hangzhou Institute of Medicine, Chinese Academy of Sciences

summary: Acinetobacter baumannii, a robust Gram-negative bacterium known for inducing nosocomial infections and displaying multidrug resistance, remains a formidable challenge to combat. The limited arsenal of antimicrobial peptides targeting this pathogen underscores the need for innovative strategies. Here, we report a pioneering few-shot learning-based pipeline to identify potent antimicrobial peptides targeting A. baumannii. This pipeline effectively scans through the entire libraries of hexapeptides, heptapeptides, and octapeptides, encompassing tens of billions of candidates, despite the extreme scarcity of available training data. Comprising classification, ranking, and regression modules as an integration, each module is trained using a few-shot learning strategy involving pre-training and multiple fine-tuning steps while incorporating similar and true data fine-tuning. This methodology mitigates the potential overfitting concerns due to the small size of the training samples and then enhances the predictive capability of the pipeline. The results highlight the robustness and versatility of the methodology, demonstrating its effectiveness in discovering AMPs against A. baumannii and C. albicans, while demonstrating low off-target toxicity and negligible susceptibility to drug resistance. Additionally, the EME7(7) exhibits efficacy in controlling A. baumannii infections within a mouse pneumonia model, notably without inducing kidney injury — a contrast to the observed effects of polymyxin B. This work provides a paradigm for addressing the challenges posed by limited data availability.

overall_design: Bacteria suspensions (10^8 c.f.u. mL-1, dispersed in PBS) were incubated with PBS and EME7(7) at concentrations of 2×MIC for 2 h. They were pelleted in centrifuge tubes by centrifugation at 12000 rpm/min for 15 min at 4 °C and washed in PBS thrice (10^9 c.f.u. mL-1) and immediately frozen in liquid nitrogen. Thereafter, RNAs of samples were extracted and analyzed by a Real-Time PCR Detection System (CFX384, Bio-Rad, USA) for measuring concentrations.

first: Wentao

first: Aowen

last: Wang

first: Yunzhi

last: Jiang

first: Yuxian

last: Lai

first: Yanchao

last: Xu

first: Cong

last: Zhao

first: Peng


title: Expression data from tumor tissues derived from Nrf3 knockdown cells in mice fed a normal chow diet (NC) or a high-fat diet (HFD)

city: Kyotanabe

first: Tsuyoshi

last: Waku

address: 1-3 Tatara Miyakodani

country: Japan

institute: Doshisha University

summary:
A CNC-family transcription factor, Nrf3, is highly expressed in mouse renal adenocarcinoma Renca cells, although the tumorigenic function of Nrf3 in NC or HFD-fed mice remains unclear.
We used microarrays to identify Nrf3-regulated gene expression network in tumor tissues of NC or HFD-fed mice.

overall_design: For RNA extraction and hybridization on Affymetrix microarrays, we generated Renca cells stably expressing shNrf3 or control shRNA (shCtrl)

first: Akira

last: Kobayashi


title: Responses of intestinal organoids to infection by Mycobacterium avium resemble symptoms observed in Crohn’s disease

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary: Crohn’s disease (CD) is a chronic inflammatory bowel disease (IBD) in humans. Mycobacterium avium, which causes Johne’s disease in ruminants, has been suggested as a potential CD trigger due to similar pathology. However, early epithelial responses to M. avium and their relevance to CD remain unclear. This study aimed to establish a mouse small intestinal organoid (mSIO) model of M. avium infection and assess whether the resulting epithelial and immune responses resemble CD-related inflammation. M. avium-infected mSIOs were analyzed using confocal microscopy, serial block-face scanning electron microscopy, and a macrophage co-culture system to observe bacterial localization and immune cell behavior. RNA-seq and Gene Set Enrichment Analysis (GSEA) were performed to assess transcriptional changes. Comparative transcriptomic analysis was performed against a previous published RNA-seq dataset from gut tissues of germ-free mice colonized with microbiota from CD patients. M. avium efficiently infected mSIOs, disseminated through the tissue and triggered macrophage migration and clustering around infected organoids. Transcriptomic profiling revealed strong upregulation of inflammatory genes and enrichment of pro-inflammatory pathways such as TNF-α signaling. Comparative analysis revealed significant overlap in gene expression profile between M. avium-infected mSIOs and intestinal tissues of CD-humanized mice, including shared enrichment of the IBD signaling pathway. Notably, Mmp7, involved in epithelial remodeling and inflammation, emerged as a common marker in both models. This study presents a robust mSIO model of M. avium infection that replicates key features of CD-associated inflammation. The model presents a useful tool for studying host-pathogen interactions and identifies Mmp7 as a molecular link between bacterial infection and CD-like pathology.

overall_design: Mycobacterium avium-infected mouse small intestinal organoids and their uninfected control organoids were collected for RNAseq

middle: P

first: Wanbin

last: Hu


title: Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [scATAC_head]

city: kaifeng

first: Hao

state: Hainan

address: Jinming

institute: Henan University

summary: The blastema is key to forming complete tissues in regenerating Dugesia japonica (D. japonica). However, the dynamic changes in cellular compositions and transcription landscapes in blastema during regeneration are understudied. Here, through genome reannotation, 3D spatial transcriptome construction, scRNA-seq and scATAC-seq analyses of changes in gene expression and chromatin structures, we delineated key transcription factors regulating the developmental trajectories of major cell clusters in the regenerating head. Importantly, we found that the T-cell factor 4 positive (DjTcf4+) cells highly accumulated at wound areas, and its gene network is critical for proper timing of development during regeneration in multiple progenitor cells. Depletion of DjTcf4 and its target genes led to singular eye and/or dull tail phenotypes and delayed regeneration. Taken together, we built multi-omics atlases in D. japonica and revealed noncanonical function of the DjTcf4 network in developmental pattern formation, laying a foundation for studies of regeneration in D. japonica.

overall_design: Examine single cell chromatin accessibility profiles of intact and 5 dpa animals by 10X scATAC-Seq platform. The experiment was performed in duplicate, resulting in 4 samples.

first: Mengmeng

last: Lu

first: Lei

first: Xiaopeng

last: Zou

first: Hongfei

last: Liu

first: Ya

last: Gao

first: Yanming

first: Yunchao

last: Kan


title: Vertebral Bone Marrow Transplant from a Deceased Lung Transplant Donor: Durable Hematopoiesis and Immune Tolerance

city: Pittsburgh

first: Xiaohua

last: Chen

state: PA

address: 4401 Penn Ave

institute: UPMC CHP BMTCT

summary: Background: Primary immunodeficiency patients are ineligible for lung transplant (LTX) due to futility and bone marrow transplant (BMT) for lung failure. We hypothesized that using marrow extracted from the vertebral bodies (VB) of a deceased lung donor with partial HLA-match would be able to establish persistent hematopoiesis and generate immunity and tolerance. Methods: A teenager with severe combined immunodeficiency in lung failure due to recurrent pneumonias underwent LTX in 2016 from a 1/8 HLA allele-matched unrelated donor followed by reduced intensity conditioning and infusion of T cell/B cell-depleted cryopreserved VB marrow 4 months later. Results: Immune competence and donor-derived thymopoiesis were evident by six months post-BMT, while immunosuppression was withdrawn at 16-month post-BMT. Donor T cell (>95%) and myeloid chimerism (7-10%) have persisted for over nine years.  At two years post-BMT, circulating donor-derived T cells were hyporesponsive to host dendritic cells in vitro. T-cell receptor clonotyping revealed the disappearance of host-reactive clones identifiable in the marrow graft, while circulating donor T cells exhibited downmodulation of signaling pathways for cytotoxicity/rejection, paired with upregulated immunomodulatory pathways, suggesting active suppression. In parallel, circulating predominantly host monocytes upregulated signaling pathways compared to their donor-derived counterparts, indicating active interactions between post-thymic donor T cells and host monocytes. Conclusion: In summary, durable hematopoietic engraftment and protective immunity were demonstrable for the first time in a patient receiving deceased donor vertebral bone marrow graft. Moreover, tolerance exceeding 8-years without immunosuppression was attainable.

overall_design: 1. RNAseq profiling of donor T cells pre-BMT (graft T cells) in comparing to donor cells at clinical immue tolerant stage post-BMT. These T cells were either alone or in vitro stimulated with host dendritic cells. 2. RNAseq profiling of FACS sorted donor monocytes (dMONO) in comparing to host monocytes (hMONO) at clinical tolerance stage 2yrs post-BMT. The profiling also includes graft monocyte (gMONO) and host monocytes (hMONO) pre-BMT.

first: Paul

last: Szabolcs

first: Marian

last: G. Michaels

first: Memphis

last: Hill

first: Evelyn

last: Garchar

first: Zarreen

last: Amin

first: Heather

last: M. Stanczak

first: Shawna

last: McIntyre

first: Aleksandra

last: Petrovic

first: Dhivyaa

last: Rajasundaram

first: Ansuman

last: Chattopadhyay

first: Jonathan

last: E. Spahr

first: Peter

last: D. Wearden

first: Geoffrey

last: Kurland


title: Transcriptional reprogramming in mantle cell lymphoma promotes BTK inhibitor resistance

city: New york

first: Jihye

last: Paik

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

summary: Resistance to Bruton’s tyrosine kinase inhibitors (BTKi) remains a major therapeutic challenge in B-cell malignancies, limiting treatment durability. We demonstrate BRG1-mediated chromatin remodeling as a major driver of BTKi resistance. We show that cancer-associated BRG1 ATPase domain mutations protect cells from BTKi-induced ferroptosis by limiting reactive oxygen species (ROS) production and labile iron. Mechanistically, the BRG1T910M mutation activates the unfolded protein response (UPR) via ATF4, leading to upregulation of MEF2B, a key suppressor of ferroptosis. MEF2B further inhibits mitochondrial respiration and thus prevent BTKi-induced mitophagy and ferroptosis. Pharmacological inhibition of BRG1 promotes ferroptosis by suppressing pro-survival B cell receptor (BCR) signaling and the ATF4-MEF2B axis. We show that a clinical stage BRG1 inhibitor restores ferroptosis in BTKi-resistant cells and synergizes with BTKi across various MCL models. Together we propose  for co-targeting BRG1 and BTK in treatment of B-cell malignancies.

overall_design:
MINO cells expressing wildtype or mutant BRG1 or treated with FHD-286 were analyzed by RNA-seq. JEKO cells ectopically expressing MEF2B were analyzed by RNA-seq. Primary MCL cells were analyzed by RNA-seq.
MINO cells expressing wildtype or mutant SMARCA4 or treated with FHD-286 were analyzed by ATAC-seq or BRG1/H2K27Ac Cut&Run. CCMCL1 cells expressing cas9-sgROSA or cas9-sgBRG1 were analyzed by ATAC-seq. JEKO cells ectopically expressing MEF2B were analyzed by Cut&Run.

first: Hwang

last: Sooyeon

first: Nikolli

last: Helgi

first: Paik

last: Jihye


title: Metabolic Interplay in Acute Lung Injury: PARK7 Integrates PUFA Metabolism and H3K14 Lactylation to Attenuate Endothelial Ferroptosis and Dysfunction [ChIP-Seq]

first: Jian

last: Xu

address: 180 Fenglin Road

institute: Zhongshan hospital

summary: Acute respiratory distress syndrome (ARDS) is a severe clinical condition characterized by widespread inflammation and fluid accumulation in the lungs. Endothelial cell (EC) metabolic changes in acute lung injury (ALI) and their relationship to injury remain unclear. Transcriptomic and lipidomic analyses revealed downregulation of PUFA synthesis pathways, particularly omega-3 PUFAs, in pulmonary ECs during LPS-induced ALI. Activation of the PUFA metabolic pathway, through FADS1/2 overexpression or omega-3 fatty acid supplementation, protected ECs from ferroptosis and restored barrier function. Overexpression of FADS1/2 in a mouse model of ALI, combined with alpha-linolenic acid (ALA) supplementation, significantly mitigated lung injury, reduced inflammatory cytokines, and improved pulmonary edema and barrier integrity. PARK7 was identified as an endogenous regulator of FADS1/2, acting through the BMP-SMAD1/5/9 signaling. Driven by histone H3K14 lactylation, which was also promoted by the downregulation of FADS1/2, PARK7 upregulation restored FADS1/2 expression and counteracted ferroptosis, thereby forming a protective feedback loop. This study elucidates a novel regulatory axis involving the two major metabolic changes—downregulation of PUFA synthesis and upregulation of histone lactylation—in ALI pathogenesis, which are interconnected through the PARK7-BMP signaling pathway. Targeting this axis offers potential therapeutic strategies for mitigating endothelial dysfunction and ferroptosis in ARDS/ALI.

overall_design: HUVEC cells transfected with negative control and siPARK7 were used for RNA-seq. Primary mouse pulmonary microcirculation endothelial cells (MPMEC) were used for ChIP-seq experiments with H3K14la antibody.


title: Metabolic Interplay in Acute Lung Injury: PARK7 Integrates PUFA Metabolism and H3K14 Lactylation to Attenuate Endothelial Ferroptosis and Dysfunction [RNA-Seq]


title: Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [scRNA-DjTcf4]

first: Hao

last: Wang

overall_design: Examine single cell gene expression profiles of Control and DjTcf4 RNAi treatment in 5 dpa trunk fragment animals by 10X scRNA-Seq platform. The experiment was performed in 2 sample.

first: Mengmeng

last: Lu

first: Lei

last: Huang

first: Xiaopeng

last: Zou

first: Hongfei

last: Liu

first: Ya

last: Gao

first: Yanming

first: Yunchao

last: Kan


title: Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [scRNA_head]

overall_design: Examine single cell gene expression profiles of intact and 5 dpa animals by 10X scRNA-Seq platform. The experiment was performed in 2 samples.


title: Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [mRNA_DjTcf4]

overall_design: Examine gene expression profiles of control and DjTcf4 RNAi treatment in intact and 5 dpa trunk fragment animals by mRNA-Seq platform. The experiment was performed in quadruplicate of intact group and triplicate or quadruplicate of 5 dpa group, resulting in 15 samples;


title: Medicinal Food Homology in Action: Flos Sophorae Immaturus-Broccoli Seed Extract Suppresses Tumor Growth through G2/M Arrest and EMT Inhibition

first: Fuwen

last: Yuan

state: 上海

address: Cailun Road #1200, Pudong New area

institute: Shanghai University of Traditional Chinese Medicine

summary: Despite advancements in cancer therapy, metastasis and chemoresistance remain critical challenges due to tumor heterogeneity and compensatory pathways. This study investigates the synergistic anti-tumor potential of Flos Sophorae Immaturus (FSI) and broccoli seed extract (BSE), two natural products aligned with the "medicinal food homology" paradigm. Using in vitro and in vivo models of lung and prostate cancers, we demonstrate that FSI-BSE (F/B extract) co-treatment exerts supra-additive effects by concurrently inducing G2/M cell cycle arrest and suppressing epithelial-mesenchymal transition (EMT). Mechanistically, with integrative LC-MS/MS, network pharmacology, molecular docking, transcriptomic profiling, and molecular experimental validation, this study revealed that F/B extract targets and disrupts the cell cycle regulators such as cyclin-dependent kinases (CDKs) and cell division cycle 25 (CDC25), as well as the EMT effectors (e.g., Matrix metalloproteinase, Snail, and E-cadherin). Additionally, F/B extract suppressed tumor growth without toxicity in xenograft mouse models, supported by unaltered organ histology and blood parameters. These findings demonstrate a polypharmacological strategy leveraging dietary botanicals to address cancer complexity. By bridging cell cycle arrest and EMT inhibition, F/B extract treatment offers a non-toxic adjuvant approach with translational potential, underscoring the therapeutic value of medicinal food homology in oncology.

overall_design: mRNA profiles of A549 cells treated with vehicle, F/B extract were generated by deep sequencing, in triplicate, using Illumina HiSeq6000


title: Trogocytosis contributes tumor escape and limits tumoricidal activity in hPSCs-derived CAR macrophages

city: Guangzhou

first: Baoqiang

last: Kang

address: Kaiyuan Avenue 190

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Pluripotent stem cells (PSCs) derived chimeric antigen receptor macrophages (iCAR-Ms) hold great potential for immunotherapy, particularly against T-cell malignancies which are challenging in CAR-T therapy. Here, we generate human iCAR-Ms targeting CD5 for treating T-cell malignancies. iCAR-Ms display tumoricidal activities against various T- malignant cells expressing CD5 such as Jurkat, SUP-T1 and primary tumor cells. However, The iCAR-M tumoricidal activities are largely dependent on CD5 density on tumor cells. The escaped tumor cells show reversible CD5 loss without changes on its mRNA level. Meanwhile, the retrieved iCAR-Ms show little reduced tumoricidal activities against new tumor cells expressing CD5. Based on time lapse imaging and transcriptional analysis, we show that iCAR-Ms mainly medicate trogocytosis while less phagocytosis when approach tumor cells. Our data reveal trogocytosis as an important limitation factor in iCAR-M tumoricidal activities and tumor escape, providing a rational to develop enhanced CAR-M for immunotherapies.

overall_design: We compared the transcriptome of  the CAR-Mac, ∆CAR-Mac, CAR-Mac_Tumor and  ∆CAR-Mac_Tumor cells by RNA-Seq.

first: Baoiqnag

first: Shuoting

first: Guangjin

last: Pan

first: Jiajun


title: Peptidoglycan from Bifidobacterium adolescentis enhances IL-10 production in regulatory B cells to alleviate gut inflammation

city: Seoul

first: Yoonho

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: University of Ulsan College of Medicine

summary: Emerging evidence highlights the critical role of the gut microbiota in maintaining intestinal homeostasis and modulating host immune responses. However, the mechanisms remain incompletely understood. In this study, we screened Lactobacillus and Bifidobacterium strains isolated from healthy individuals to identify symbionts capable of suppressing gut inflammation. Among them, Bifidobacterium adolescentis (Bifi-94) induced IL-10 production in mononuclear cells in vitro. Oral administration of Bifi-94 to mice treated with dextran sulfate sodium attenuated weight loss and reduced colonic inflammation scores. In wild-type C57BL/6 mice, Bifi-94 increased IL-10 levels in colonic tissue homogenates without altering the frequency of regulatory T cells. Instead, CD19+CD11b+ regulatory B (Breg) cells emerged as the primary source of IL-10, with their numbers significantly increasing in the peritoneal cavity (PEC) after treatment. IL-10 secretion by PEC cells was robustly activated by live, heat-killed, and formalin-fixed Bifi-94. Peptidoglycan (PGN) purified from Bifi-94 selectively stimulated IL-10 production in CD19+CD11b+ Breg cells and upregulated key PGN synthesis enzymes, including MurE, MurD, Alr, and UppP. Mechanistically, Bifi-94-derived PGN promoted Toll-like receptor 2 (TLR2)-dependent activation of ERK and p38 MAPK signaling in Breg cells. Notably, PGN similarly enhanced IL-10 production in CD19+ B cells from human colonic tissue. These findings demonstrate that Bifi-94-derived PGN promotes IL-10 production in Breg cells via TLR2-mediated signaling, thereby contributing to the attenuation of gut inflammation.

overall_design: Inflamed intestinal tissues obtained from patients with Crohn's disease were processed for 10x xenium spatial transcriptomic analysis.

first: Sohyeon

first: Ho-Su

first: Jiyoung

last: Yu

first: Kyunggon

last: Kim

first: Tae-Young

first: Su-Hyun

first: Seungil

first: Mi-Na

last: Kweon


title: Similarities and Differences in the Intestinal Actions of Metformin and Imeglimin

city: Kobe

first: Kenji

last: Sugawara

state: Please Select

address: 7-5-1 Kusunoki-cho, Chuo-ku

institute: Kobe university graduate school of medicine

summary: We investigated the intestinal actions of metformin and imeglimin by transcriptomic profiling. Bulk RNA-seq was performed on intestinal tissues from C57BL/6J mice after single or chronic drug administration, and single-cell RNA-seq was conducted on colon samples after chronic treatment.

overall_design:
Bulk RNA-seq: Male C57BL/6J mice received (i) a single oral dose of metformin or imeglimin (600 mg/kg) with colon harvested at 6 h, or (ii) chronic exposure via drinking water (3 mg/mL) for 4 weeks, with proximal/middle/distal small intestine and colon collected.
Single-cell RNA-seq: Colonic cells from mice treated with metformin or imeglimin in drinking water for 12 weeks were dissociated and processed with 10x Genomics Chromium Fixed RNA Profiling; sequencing on NovaSeq 6000.


title: Effect of renal failure and sex on gene expression in mouse strain C57Bl/6J kidneys

city: Newark

first: Melissa

middle: B.

last: Rogers

state: NJ

address: 185 south orange ave.

department: Biochem. & Molec. Biology

institute: Rutgers NJMS

summary: Sex and genetic background are key, but sometimes overlooked factors, that profoundly impact disease susceptibility and presentation in both humans and disease models. We previously showed that deficiency of KLOTHO protein, an important renal regulator of mineral homeostasis and a cofactor for FGF23, causes different phenotypes in 129S1/SvlmJ (129) and C57BL/6J (B6) mouse strains (Kuro-o et al. Mutation of the mouse Klotho gene leads to a syndrome resembling ageing. Nature 390: 45-51, 1997; Salloum JS, Garsetti DE, Rogers MB. Genetic Background Influences the Impact of KLOTHO Deficiency. Physiological Genomics. 52, 512-516 (2020). The 129 strain was more severely affected, with decreased longevity, decreased body weight, and increased amounts of kidney calcification compared to B6 mice. Here we used RNA seq to profile messenger RNAs in kidneys from control (ctrl) healthy and Klotho homozygous deficient strain B6 mice of both sexes.   The kidney messenger RNA profiles of control and Klotho homozygous deficient strain 129 mice of both sexes has been submitted separately. Comparing and contrasting the genetic architecture leading to different phenotypes associated with specific inbred mouse strains may reveal previously unrecognized and important metabolic interactions affecting chronic kidney disease.  Both sex and kidney status modulated mRNA profiles.

overall_design: The Klotho mutation (Kuro-o et al. Mutation of the mouse Klotho gene leads to a syndrome resembling ageing. Nature 390: 45-51, 1997) was made fully congenic on the C57BL/6J (B6) by backcrossing more than 10 times. RNA was extracted from male and female mice between 46 and 59 days of age for RNA-seq profiling. Control mice with healthy kidneys were either homozygous wild type (++)  or heterozygous for the recessive Klotho mutation (Kl+).  Affected mice with renal failure were homozygous for the recessive Klotho mutation (KlKl).

middle: B

first: Tapan

middle: A

last: Shah

first: Diane

middle: E

last: Garsetti

first: Yue

first: Khushboo

last: Sahay

first: Hernandez

last: Lindsey


title: Bulk RNA-seq study 11- RNA-seq of male KOLF2.2J hiPSC-derived cortical brain organoids during different time points.

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

summary: This study aims to gather information on iPSC-derived cortical brain organoids differentiated in six different time points. Bulk RNA sequencing (RNA-seq) was performed at days 3, 4, 5, 20, 25, and 32 post-initiation of differentiation. The resulting dataset provides a foundational control reference for assessing the roles of various transcription factors previously manipulated in cortical organoid models.

overall_design: RNA-seq was conducted on 18 samples representing six differentiation time points, with three biological replicates per condition. Wildtype KOLF2.2J hiPSC lines were differentiated under uniform conditions to generate cortical brain organoids. This comprehensive design allowed for a robust analysis of previously manipulated transcription factors on brain organoid formation.

first: Juliana

last: Diniz

first: Bill

last: Skarnes

first: Paul

last: Robson


title: Retinol Binding Protein 4 reactivates latent HIV-1 via the JAK/STAT5 and JNK pathways

city: Ulm

first: Konstantin

middle: MJ

last: Sparrer

address: Meyerhofstr. 1

department: Institute of Molecular Virology

institute: Ulm University Medical Center

summary: Reactivation of the latent viral reservoirs is crucial for a cure of HIV/AIDS. However, current latency reversing agents are inefficient and the endogenous factors that have the potential to reactivate HIV in vivo remain poorly understood. To identify natural activators of latent HIV-1, we screened a comprehensive peptide/protein library derived from human hemofiltrate, representing the entire blood peptidome, using J-Lat cell lines harboring transcriptionally silent HIV-1 GFP reporter viruses.  Fractions potently reactivating HIV-1 from latency contained human Retinol Binding Protein 4 (RBP4), the carrier of retinol (vitamin A). We found that retinol-bound holo-RBP4 but not retinol-free apo-RBP4 strongly reactivates HIV-1 in a variety of latently infected T cell lines. Functional analysis revealed that this reactivation depends on the JAK/STAT5 and JNK pathways but does not require retinoic acid production. High levels of RBP4 were detected in plasma from both healthy individuals and people living with HIV-1. Physiological concentrations of RBP4 induced significant viral reactivation in latently infected cells from individuals on long-term antiretroviral therapy with undetectable viral loads. As a potent natural HIV-1 latency-reversing agent, RBP4 offers a novel approach to activating the latent reservoirs and bringing us closer to a cure.

overall_design: RNA-seq profiling of J-Lat HIV reporter cells expressing , clone 10.6 and 8.4, treated with either RBP4 for 48 hours of left untreated.

first: Chiara

last: Pastorio

first: Markus

last: Jaritz

first: Moritz

last: Gaidt

first: Frank

last: Kirchhoff


title: The function of Men1 and kmt2a gene in lung of mice

city: Xiamen

first: Aobo

last: Lian

state: No

address: Xiang'an South Road, Xiang'an District, Xiamen

institute: xiamen university

summary: To explore the target genes of Men1 and Kmt2a in lung of mice, we isolated the lung tissues from WT and Men1 knockout and Kmt2a  mouse and performed gene expression profiling analysis by RNA-seq.

overall_design: Comparative gene expression profiling analysis between Men1 knockout(KO) and Kmt2a knockout(KO) in lung of mice

first: Bangming

last: Jin

first: Guanghui


title: Bulk RNA-seq study 10- RNA-seq of male KOLF2.2J hiPSC-derived endoderm and mesoderm homozygous null for three different transcription factors.

summary: This study aims to phenotype iPSC-derived early endoderm and mesoderm that contain homozygous null alleles for the following transcription factors: ISL1, NKX2-1, and EOMES. Null alleles were generated using insertion of a premature termination codon with frameshift (PTC+1) in the case of ISL1 or full protein coding region deletion (KO) for NKX2-1 and EOMES. RNA-seq data was generated after 5 days of initiating differentiation from iPSCs. This analysis allowed the investigation of early embryonic development, cell fate mapping, and lineage analysis.

overall_design: The study involved the generation of RNA-seq on 15 samples. Two of the transcription factors were analyzed in the endoderm differentiation scheme and one in the early mesoderm scheme. Three biological replicates were run for each gene. Additionally, three biological replicates were run of wild-type KOLF2.2J cells (the parental male cell line in which the KOs were generated) under the same differentiation conditions. This comprehensive design allowed the investigation of the effects of transcription factor manipulation during early embryonic development.


title: tRNA binding and modification by the Escherichia coli dihydrouridine synthase DusA

city: Winnipeg

first: Sarah

last: Schultz

state: Manitoba

address: 144 Dysart Rd

department: Chemistry

country: Canada

institute: University of Manitoba

summary: Dihydrouridine (D) is one of the most highly conserved tRNA modifications throughout all domains of life. D20 is particularly conserved and is formed by DusA in E. coli, but its mechanisms and functions remain uncovered. Here, we characterized the molecular mechanisms of DusA in tRNA binding, cofactor oxidation, and tRNA modification, in addition to the cellular functions of DusA in tRNA maturation and mRNA translation. Thereby, we reveal DusA binds tRNA using a two-step mechanism involving local tRNA conformational changes. Although DusA can modify an unmodified tRNA substrate, it binds to previously modified tRNA with a higher affinity. In contrast to the well-studied T arm modifying enzymes TrmA and TruB, DusA does not globally increase tRNA aminoacylation levels, but does improve aminoacylation for specific tRNA species. Despite only few changes in tRNA charging, DusA improves the translation for several specific codons, suggesting a direct role for dihydrouridine in tRNA function on the ribosome. Thus, we propose DusA functions non-redundantly with TrmA and TruB to fine-tune protein synthesis.

overall_design: Total RNA samples were extracted from early log phase WT (n=3) and ΔdusA (n=3) E. coli strain BW25113 under acidic conditions (pH <5) using TRIzol. Samples were sent to MesoRNA on dry ice where they were underwent periodate oxidation/beta elimination, library preparation, and sequencing as described previously (PMID: 35513407).

middle: K

first: Nadia

last: Hossain

first: Lauren

last: Barnes

first: Kristin

last: Koutmou

first: Ute

last: Kothe


title: Glutamine influx licenses macrophage glutaminolysis for restorative functions in atherosclerosis

city: Paris

first: Sebastien

last: Dussaud

address: 91 bd de l'hopital

country: France

institute: UPMC

summary: Atherosclerotic plaque macrophages are key players at the site of disease, where metabolic reprogramming dictates whether they ameliorate or exacerbate pathogenesis. Here, we found that glutamine synthetase served as a metabolic rheostat controlling nutrient flux into cells in vitro, macrophage restorative functions in the context of atherosclerosis relied more heavily on glutamine influx and glutaminase activity. Cell-intrinsic regulation of glutaminolysis drives macrophage metabolic and transcriptional rewiring in atherosclerosis by diverting exogenous Gln flux to balance remodeling and restorative functions. Thus, we uncover a role of glutamine uptake upstream of glutaminolysis in atherosclerotic plaque development and stability.

overall_design: Bone marrow-derived macrophages were generated from Gls1-/- and control mice and cultured for the last 24h in presence or absence of interleukin-4 and glutamine synthase inhibitor (MSO). Atherosclerosis-prone Ldlr-/-  mice were backrossed with or without Gls2-/- mice and served as recipients for transplantation of Gls1-/- or control bone marrow. Then, hyperlipidemia was induced in these mice by feeding them with an atherogenic diet (Western diet, TD88137, Ssniff) for 11 weeks. Peritoneal macrophages were obtained from all four genotypes at the end of the study.

first: Saloua

last: Benhmammouch

first: Coraline

last: Borowczyk

first: Clara

last: Pierrot-Blanchet

first: Thibault

last: Barouillet

first: Florent

last: Murcy

first: Sébastien

first: Laurent

last: Yvan-Charvet


title: PFOS perturbs metabolism in C2C12 skeletal myoblasts

city: Clemson

first: William

last: Baldwin

state: SC

address: 132 Long Hall

institute: Clemson University

summary: PFOS has been shown to perturb metabolism in skeletal muscle according to previous research from our lab. To determine the transciptional changes associated with PFOS exposure, C2C12 skeletal myoblasts were exposed to PFOS for 24 hours. Changes in several metabolic pathways were seen, including amino acid and glucose metabolism.

overall_design: Cells were grown to 100% confluency in petri dishes and treated with 0, 2, or 6 micromolar PFOS for 24 hours.

first: Jazmine

last: Eccles-Miller

middle: S


title: Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Genetics and Gene Regulation

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Long-read RNA sequencing technologies offer unparalleled in- sights into transcriptomes by enabling full-length sequencing of RNA molecules, uncovering novel isoforms and alternative splicing events. While long-read sequencing platforms, such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), have historically been associated with higher error rates, recent advancements in both platforms have significantly en- hanced read accuracy, broadening their applicability for tran- scriptomic studies. With the rapid evolution of sequencing protocols and bioin- formatics tools, the trade-offs between sequencing throughput, read length, accuracy, and cost present significant challenges in selecting the optimal approach. Systematic benchmarking studies that compare these options are crucial to inform fu- ture research directions. However, many existing benchmark- ing datasets with matched data across multiple platforms have limitations, including: 1) a lack of realistic biological replicates, which may restrict the generalisability of differential analysis results to real-world scenarios, and 2) the use of earlier sequenc- ing kits, which may not reflect the latest advancements in se- quencing technology, limiting their relevance for future studies that typically use newer sequencing protocols. Here we present LongBench, a comprehensive benchmarking dataset designed to fill these critical gaps. Derived from eight lung cancer cell lines with synthetic RNA spike-ins, LongBench includes bulk, single-cell, and single-nucleus RNA-seq data from three state-of-the-art long-read sequencing platforms — ONT PCR-cDNA, ONT direct RNA, PacBio Kinnex — alongside Il- lumina short-read data for robust cross-platform comparisons. The LongBench dataset is a valuable resource for benchmarking and improving sequencing protocols and bioinformatics tools. With the LongBench dataset we present a systematic evaluation of transcript capture, quantification, and differential expression analyses, examining the strengths and limitations of each se- quencing platform in various biological contexts, enabling re- searchers to make more informed decisions on platform and method selection.

overall_design: Bulk, Single-cell & Single-nucleus RNA-seq of 8 lung cancer cell lines with synthetic RNA spike-ins sequenced across Oxford Nanopore, PacBio & Illumina platforms to generate a transcriptomics benchmark dataset.

first: Yupei

last: You

first: Ashleigh

last: Solano

first: James

last: Lancaster

first: Margaux

last: David

first: Changqing

last: Wang

first: Shian

last: Su

first: Kathleen

last: Zeglinski

first: Reza

last: Ghamsari

first: Jin

last: Ng

first: Manveer

last: Chauhan

first: Josie

last: Gleeson

first: Yair

last: Prawer

first: Bénédicte

last: Dubois

first: Isabelle

last: Cleynen

first: Marie-Liesse

last: Asselin-Labat

first: Kate. D.

last: Sutherland

first: Michael

last: Clark

first: Quentin

last: Gouil


title: Bulk RNA-seq study 8- RNA-seq of male KOLF2.2J hiPSC-derived trophoblast cell lines homozygous null for nine different transcription factors.

first: MorPhiC

last: Consortium

summary: This study aims to phenotype iPSC-derived trophoblast lines that contain homozygous null alleles for transcription factors expressed within the extra-embryonic lineage, with a focus on differentiation toward either primitive syncytium or extra-embryonic mesenchymal cells, depending on the TF being analyzed. Null alleles were generated by insertion of a premature termination codon with frameshift (PTC+1). RNA-seq data was generated after 6 days of initiating differentiation from iPSCs. The study included the homozygous null alleles for the following transcription factors: DLX3, MSX2, VGLL1, MAFB, NR2F2, ELF5, ASCL2, HIF1A, and TP63. Notably, the hypoxia-inducible factor HIF1A as well as ELF5, ASCL2, and TP63 were evaluated under both 20% oxygen and 3% (~ level present at peri-implantation) oxygen concentrations. This analysis provided insight into the impact of loss of function for these transcription factors in trophoblast lineage differentiation.

overall_design: The study involved the generation of RNA-seq on 53 samples. Eight of the transcription factors were analyzed in the primitive syncytium differentiation scheme and one in the extra-embryonic mesenchymal cell scheme. Three biological replicates were run for each gene. Additionally, three biological replicates were run of wild-type KOLF2.2J cells (the parental male cell line in which the KOs were generated) under the same differentiation conditions and under both 20% and, in some cases, 3% O₂ concentrations. This comprehensive design allowed for a robust analysis on the effects of transcription factor manipulation on cell fate decisions within the extra-embryonic lineage.

first: Juliana

last: Diniz

first: Bill

last: Skarnes

first: Paul

last: Robson


title: The tyrosine kinase inhibitor GNF-7 targets senescent cells through allosteric activation of GCN2

city: Madrid

first: Oscar

last: Fernandez-Capetillo

address: Fermin Caballero 56, 3D

country: Spain

institute: CNIO

summary: The one-two-punch approach refers to the sequential administration of two different chemotherapies, the second of which targets cancer cells that resisted the initial treatment. To find such a second punch, we performed a chemical screen to find drugs that are preferentially toxic for cells with an activated DNA damage response (DDR). This screen identified the tyrosine kinase inhibitor GNF-7 as a top hit. Subsequent work revealed that GNF-7 is a potent senolytic, even when senescence is triggered by therapies that do not activate the DDR. Consistently, GNF7 is highly efficacious to kill cancer cells previously treated with CDK4/6 inhibitors, including in patient-derived organoids and mouse xenografts. Surprisingly, the senolytic effect of GNF-7 is not mediated by the inhibition of a tyrosine kinase (TK), but rather by the allosteric activation of GCN2, an effect previously reported for other TK inhibitors. Together, our study reports the discovery of a novel senolytic agent that strongly synergizes with CDK4/6 inhibitors when applied sequentially and expands our understanding of the mechanisms behind the anticancer effects of TK inhibitors.

overall_design: RNAseq analyses of HT1080 human cancer cell lines, exposed to 1 uM of GNF7 for 6h or 24h. Where indicated, HT1080 cells were previously induced into senescence, by the expression of a dominant negative mutant of TRF2 for 6 days, which promoted telomere uncapping and cellular senescence.

first: Wareed

last: Ahmed

first: Daniela

last: Huhn

last: Fernández-Capetillo


title: Synergistic activity of caspofungin and posaconazole against Candida auris biofilms based on phenotypic, transcriptomic and in vivo insights

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

summary: The World Health Organization (WHO) had designated Candida auris as a critical public health threat due to its multidrug resistance to antifungal agents, high mortality rate, and its ability to cause nosocomial outbreaks. A matter of serious concern is that conventional antifungal monotherapies is frequently ineffective against biofilm-associated C. auris infection, highlighting the need for more effective strategies. Combination therapies have demonstrated improved efficacy and specificity, and may also slow the development of antifungal resistance. Therefore, this study aimed to evaluate the in vitro and in vivo efficacy of caspofungin (CAS) and posaconazole (POSA) in combination against sessile C. auris isolates from the South Asian clade and to characterize the associated transcriptomic responses. The CAS with POSA combination resulted in a significant reduction in median minimum inhibitory concentrations (4–32-fold for CAS and 8–64-fold for POSA) compared to monotherapies. Synergistic interactions were observed in all isolates tested, with fractional inhibitory concentration indices ranging from 0.078 to 0.31. In line with the in vitro findings, synergistic interactions were confirmed by in vivo experiments. The fungal kidney burden decreases were three log volumes in mice treated with combination of 1 mg/kg/day caspofungin and 1.5 mg/kg/day posaconazole. To investigate the gene expression changes in response to combination treatment, 612 genes showed increased expression and 465 genes were downregulated relative to the untreated control biofilms (fold change >1.5 or <–1.5). Notably, genes involved in biofilm dispersion, oxidative stress response, iron metabolism, and glycolysis were downregulated, whereas those associated with cell wall organization or biogenesis, osmotic stress response, calcium signaling, drug efflux, biofilm formation, and the biosynthesis of ergosterol and chitin were upregulated. These findings demonstrate the potent synergistic activity of CAS and POSA against C. auris biofilms and provide insight into C. auris antifungal therapeutic responses, thereby contributing to the development of more effective antifungal treatment strategies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of caspofungin and/or posaconazole treated and untreated Candida auris biofilms.

first: Fruzsina

last: Kovács

first: Andrea

last: Harmath

first: Dávid

last: Balázsi

first: Lajos

last: Forgács

first: Ágota

last: Ragyák

first: Noémi

last: Balla

first: Zoltán

last: Tóth

first: Aliz

last: Bozó

first: László

last: Majoros

first: Renátó

first: Ágnes


title: Delineation of the oncogenic potential of AKT downstream targets in murine and human hepatocellular carcinoma

city: San Francisco

first: Guofei

last: Cui

state: CALIFORNIA

institute: UCSF

summary: Aberrant activation of AKT is a key oncogenic driver in hepatocellular carcinoma (HCC). As AKT activates multiple downstream signaling pathways, the key mechanisms mediating AKT-driven tumorigenesis must be elucidated to develop optimal treatment strategies. Using an Akt/NRas-induced HCC mouse model, we found that AKT promotes tumorigenesis by targeting TSC2 and GSK3α&β rather than FOXO family members. Loss of either TSC2, leading to mTORC1 activation, or both GSK3 isoforms cooperated with activated NRAS to promote HCC formation in vivo, albeit with different latencies. Simultaneous TSC2 and GSK3α&β deletion cooperated with NRAS to rapidly induce HCC formation, mirroring observations from the Akt/NRas HCC model. RNA-seq studies indicated distinct pathways regulated by TSC2/mTORC1 and GSK3α&β during hepatocarcinogenesis, with FOXM1 functioning as a major effector of GSK3. In summary, these findings uncover AKT’s role in suppressing the TSC complex and GSK3 to drive HCC, offering mechanistic insights into oncogenic signaling and potential therapeutic targets.

overall_design: RNA-seq profilling of normal liver (NL) and liver tumor tissues from Akt/NRas-, Tsc2-/-/NRas-, sgGSK3α&β/NRas-, and Tsc2-/-/sgGSK3α&β/NRas-induced murine liver tumor models.

first: Yi

last: Zhou

first: Weiting

last: Liao

first: Eleonora

last: Cossu

first: Matthias

last: Evert

first: Shu

last: Zhang

first: Jingxiao

last: Wang

first: Shanshan

last: Deng

first: Andrew

last: Yonemura

first: Lucie

last: David

first: Meng

last: Xu

first: Juliette

last: Doumergue

first: Xinjun

last: Lu

first: Lihui

last: Yang

first: Jinghua

last: Li

first: Binyong

last: Liang

first: Haichuan

first: Hongwei

first: Sheng

last: Zhong

first: Youping

first: Diego

middle: F

last: Calvisi

first: Jinqiu

last: Zhao

first: Xin

last: Chen

first: Xue


title: RiboTag and bulk RNA sequencing using AAV-Control and AAV-shLarp1 infected sensory neurons.

city: Daegu

first: Eunsu

last: Jang

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Brain Sciences

institute: DGIST

summary: To investigate the role of the RNA-binding protein LARP1 and its interaction with ribosomal protein mRNAs in regenerating neurons, we performed total RNA and RiboTag sequencing analysis using AAV-Control or AAV-shLarp1 infected sensory neurons using RiboTag mice, RPL22HA+/+;Advillin-Cre+.

overall_design: RiboTag sequencing data from cultured sensory neurons infected with AAV-Control and AAV-shLarp1. Preconditioning through sciatic nerve injury was conducted on mice before the neuron culture to activate their regenerative state.

first: Yewon

last: Jeon

first: Jinyoung

last: Lee

first: Yeonsoo

last: Oh

first: Hoyong

last: Jin

first: Youwon

first: Bohm

first: Ju-Yeon

first: Ju-Hwan

last: Song

first: Jung-Eun

last: Shin

first: Yongcheol

last: Cho


title: RiboTag and bulk RNA sequencing using AAV-shGpr151 and AAV-shGpr151 with AAV-e5'UTR infected sensory neurons.

summary: After discovering that Gpr151 mRNA regulates the CSDE1-mediated rp-mRNA operon, we designed an engineered version of the 5'UTR of Gpr151 mRNA(e5'UTR), which has an enhanced interaction with CSDE1. To determine if this e5'UTR RNA can restore the down-regulated rp-mRNA operon formation in Gpr151 knockdowned neurons, we performed total RNA and RiboTag sequencing analysis using AAV-shGpr151 or AAV-shGpr151 with AAV-e5'UTR infected sensory neurons using RiboTag mice, RPL22HA+/+;Advillin-Cre+.

overall_design: RiboTag sequencing data from cultured sensory neurons infected with AAV-shGpr151 and AAV-shGpr151 with AAV-e5'UTR. Preconditioning through sciatic nerve injury was conducted on mice before the neuron culture to activate their regenerative state.


title: DRG tissue LARP1-IP sequencing using sciatic nerve injured and uninjured mice.

summary: To determine LARP1 associated RNAs after injury in sensory neurons, we conducted LARP1-IP sequencing analysis using dorsal root ganglion (DRG) tissues of wild type mice.

overall_design: LARP1-IP sequencing of RNAs extracted from the dorsal root ganglion (DRG) tissues. Sciatic nerve injury was conducted for the injured samples.


title: Transcriptome analysis of Aochk1 in nematode-trapping fungus Arthrobotrys oligospora

city: kunming

first: Luo

last: huan

address: wujiaying street

institute: yunnan university

summary: Transcriptomic analysis revealed that differentially expressed genes in the absence of Aochk1 were involved in  carbohydrate metabolism, amino acid metabolism, lipid metabolism, Autophagy, energy metabolism, and translation.

overall_design: Examination of differential genes in the WT and ΔAochk1 mutant strains and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Huan

last: Luo

first: Jinkui


title: RiboTag and bulk RNA sequencing using AAV-Control and AAV-shGpr151 infected sensory neurons.

summary: To investigate the role of the Gpr151 mRNA and its interaction with ribosomal protein mRNA operon in regenerating neurons, we performed total RNA and RiboTag sequencing analysis using AAV-Control or AAV-shGpr151 infected sensory neurons using RiboTag mice, RPL22HA+/+;Advillin-Cre+.

overall_design: RiboTag sequencing data from cultured sensory neurons infected with AAV-Control and AAV-shGpr151. Preconditioning through sciatic nerve injury was conducted on mice before the neuron culture to activate their regenerative state.


title: DRG tissue CSDE1-IP sequencing using sciatic nerve injured and uninjured mice.

summary: To determine CSDE1 associated RNAs after injury in sensory neurons, we conducted CSDE1-IP sequencing analysis using dorsal root ganglion (DRG) tissues of wild type mice.

overall_design: CSDE1-IP sequencing of RNAs extracted from the dorsal root ganglion (DRG) tissues. Sciatic nerve injury was conducted for the injured samples.


title: DRG tissue RiboTag and bulk RNA sequencing using sciatic nerve injured and uninjured mice.

summary: Peripheral neurons can regenerate after nerve injury. To determine the transcriptional and post-transcriptional regulation after injury, we conducted total RNA and RiboTag sequencing analysis using sensory neuron-specific RiboTag mice, RPL22HA+/+;Advillin-Cre+.

overall_design: RiboTag-Seq of sensory neurons located in the dorsal root ganglion (DRG) tissues. Sciatic nerve injury was conducted for the injured samples.


title: RiboTag and bulk RNA sequencing using AAV-Control and AAV-shCsde1 infected sensory neurons.

summary: Peripheral neurons can regenerate after nerve injury. To investigate the role of the RNA-binding protein CSDE1 and its interaction with ribosomal protein mRNAs in regenerating neurons, we performed total RNA and RiboTag sequencing analysis using AAV-Control or AAV-shCsde1 infected sensory neurons using RiboTag mice, RPL22HA+/+;Advillin-Cre+.

overall_design: RiboTag sequencing data from cultured sensory neurons infected with AAV-Control and AAV-shCsde1. Preconditioning through sciatic nerve injury was conducted on mice before the neuron culture to activate their regenerative state.


title: CSDE1-RIP and bulk RNA sequencing using primary DRG neurons infected with LV-control or LV-e5'UTR.

summary: To determine overexpression of e5'UTR can enhance injury responsive rp-mRNA operon without injury, we conducted CSDE1-IP sequencing analysis using primary dorsal root ganglion (DRG) neurons infected with LV-control and LV-e5'UTR.

overall_design: CSDE1-IP sequencing of the primary dorsal root ganglion (DRG) neurons infected with LV-control and LV-shGpr151. DRG neurons were extracted from E13 mice.


title: Investigating the molecular mechanisms underlying the therapeutic effects of Detumescence Analgesic Plaster on knee osteoarthritis through RNA sequencing technology

city: Beijing

first: Chunxia

middle: ZL

state: Beijing

address: nstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiao Street, Dongzhimennei, Dongcheng District, Beijing, China

department: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

summary: In this study, transcriptome sequencing was used to study the mechanism of Detumescence Analgesic Plaster (DAP) in the treatment of Knee Osteoarthritis. We identified the key pathways and key genes for the treatment of Knee Osteoarthritis by transcriptome sequencing of rat cartilage issue, and completed qPCR validation. The results showed that genes such as NDUFA5, NDUFA6, NDUFS6, and COX6A2 were enriched in the oxidative phosphorylation signaling pathway. DAP intervention significantly increased the mRNA levels of NDUFA5, NDUFA6, NDUFS6, COX6A2, and MYL3 in rat cartilage tissue, alleviating damage and injury. This study provides a new idea for the molecular mechanism of Detumescence Analgesic Plaster in the treatment of KOA.

overall_design: Male SD rats without specific pathogen (SPF) were randomly divided into three groups: control group, KOA model group, and anti-inflammatory and analgesic patch group (0.1470 g/kg), with 12 animals in each group. According to previous literature, a KOA model was established in rats. 0.1 mL of a prepared 4% papain solution was extracted and injected into the lateral side of the patellar ligament on days 1, 4, and 7 of the modeling process. The rats were then fed normally and treated externally for 5 weeks. Differential expression genes (DEGs) were analyzed using DESeq2, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to identify important pathways. In addition, gene set enrichment analysis (GSEA) was used to identify the key signaling pathways of Xiaozhong Zhitong Tie, STRING functional protein association network analysis was used to analyze the interaction network and weighted gene co expression network (WGCN) analysis, and CytoHubba topology was used to screen DAP candidate targets targeting KOA. We conducted qPCR experiments on 5 key core genes and confirmed the accuracy of the analysis results.

first: Weijie

first: Yue

last: Yin

first: Xiaomei

last: Xiang

first: Lu

last: Fu

first: Ping

last: Wang

first: Yanqiong

last: Zhang

first: Haiyu

last: Xu


title: RNA-seq of Immortalized RAFLS treated with TNFα for 24h and DMSO or celastrol derivatives for 4h in human

city: Macau

first: Dingqi

address: Taipa

country: Macau

institute: Macau University of Science and Technology

summary: This experiment is to explore the mechanism of anti-inflammatory activity of celastrol derivatives on Rheumatoid arthritis fibroblast-like synoviocytes (RAFLS), compared with celastrol. Immortalized RAFLS cells were simulated with 1 ng/mL TNFα for 24h, and exposed to different treatments during the last 4 hours. Total RNA was extracted with Trizol. Transcriptomic profiling was performed with an in-house, proprietary method that captures the 3’ primed end of mRNA molecules for sequencing. The data was processed with a custom script. Briefly, sequencing reads were demultiplexed based on sample barcode with idemux, trimmed with cutadapt to remove polyA, adaptor and low-quality sequences, mapped to human GRCh38 reference assembly with STAR aligner. PCR duplicates were removed based on UMI with UMI-tools. Htseq-count was used to generate read counts. The count matrix was analyzed with DESeq2 package to determine differential genes. Enrichment and GSEA was performed with clusterprofiler.

overall_design: DMSO: negative control, 3 samples. Cel: celastrol, 3 samples. Cel5, celastrol derivative 5, 3 samples. Cel6: celastrol derivative 6, 3 samples. All cells are simulated with 1 ng/mL TNFα for 24h, and exposed to different treatments during the last 4 hours.

first: Baixiong

last: Huang

first: Pak-Lam

last: Ng

first: Kam-Wai

last: Wong


title: Treatment of prostate cancer with oncolytic virus OH2 [scRNA-seq_RM-1]

city: Wuhan

first: Jinzhou

state: Hubei

address: Jiefang Avenue

institute: Tongji Hospital

summary: Prostate cancer is a major challenge due to limited treatment options in advanced stages. Immunotherapy has shown promising prospects in various cancers, but it faces obstacles in prostate cancer due to its immunosuppressive microenvironment and low response rate to current therapies. Oncolytic virus therapy provides a new immunotherapy approach by stimulating anti-tumor immune responses. This study investigated the histological changes of the novel herpes simplex virus type II (HSV-II) oncolytic virus OH2 in prostate cancer tumors.

overall_design: Prostate cancer subcutaneous transplanted tumors (RM-1, 3 vs. 3) were treated with oncolytic virus OH2 intervention

first: Ye

last: An

first: Guichen

last: Ye

first: Zhiyu

last: Xia

first: Shaogang

first: Qidong


title: Fibrillin-Related Proteins Control Calcium Homeostasis in Dystrophic Muscle Across Species

city: Normal

first: Andres

last: Vidal-Gadea

state: Illinois

address: 125 S Fell Ave

institute: Illinois State University

summary: Duchenne muscular dystrophy (DMD) involves progressive muscle degeneration associated with calcium dysregulation, but the mechanisms linking extracellular matrix (ECM) integrity to calcium homeostasis remain unclear. We investigated whether MUA-3, a fibrillin-related ECM protein in Caenorhabditis elegans, contributes to calcium regulation in dystrophic muscle. Using fluorescent calcium imaging in transgenic worms expressing muscle-specific GCaMP2, we found that downregulating mua-3 selectively elevated resting calcium levels in healthy muscle but had no effect in dystrophic (dys-1) muscle, suggesting impaired MUA-3 function in dystrophy. Despite altered calcium dynamics, mua-3 downregulation did not affect locomotor function. In human dystrophic myoblasts, we observed significantly elevated sarcoplasmic calcium levels concurrent with substantial downregulation of fibrillin genes FBN1/FBN2. These findings demonstrate that fibrillin-related proteins regulate calcium homeostasis across species, suggesting that ECM integrity directly contributes to cellular calcium control in muscle. This work identifies a conserved mechanism linking extracellular matrix stability to intracellular calcium regulation and suggests that targeting ECM-calcium coupling may offer new therapeutic approaches for muscular dystrophy.

overall_design: RNA Seq profiling of undifferentiated healthy and dystrophic human myoblasts

first: Damiano

last: Marchiafava


title: Inhibition of NLRP1 Inflammasome Activation by Tyrosine Kinase Inhibitors Restores Erythropoiesis in Diamond-Blackfan Anemia Syndrome

city: Elche

first: Alicia

last: Martinez Lopez

state: Alicante

address: Avenida Candalix 42, 5A

institute: IMIB

summary: Diamond-Blackfan Anemia Syndrome (DBAS) is characterized by impaired erythropoiesis due to dysfunctional ribosome biogenesis and aberrant cellular signaling. Here, we investigate how ribosomal stress-induced activation of the NLRP1 inflammasome modulates erythroid differentiation in DBAS. We demonstrate that FDA/EMA-approved tyrosine kinase inhibitors (TKIs) effectively mitigate defective erythropoiesis in Diamond-Blackfan anemia syndrome (DBAS) by inhibiting NLRP1 inflammasome activation. Specifically, nilotinib enhances erythroid differentiation in K562 cells through suppression of the ZAKα/P38/NLRP1/CASP1 axis, leading to increased GATA1 protein levels and upregulation of key erythroid genes involved in iron acquisition, hemoglobin synthesis, and erythrocyte structure. These effects were validated in human CD34+ hematopoietic stem and progenitor cells (HSPCs) and zebrafish models, where nilotinib, along with other TKIs (imatinib, dasatinib, and bosutinib), promoted erythropoiesis at the expense of myelopoiesis and reduced caspase-1 activity. Importantly, in RPS19-deficient zebrafish and human models and HSPCs from patients with DBAS, nilotinib, imatinib and dasatinib rescued defective erythroid differentiation and restored hemoglobin levels. These findings highlight the potential of TKIs to address the erythroid defects observed in ribosomopathies like DBAS. Given the limited treatment options available for DBAS and other congenital anemias, our study provides compelling evidence for repurposing TKIs as a novel therapeutic strategy to alleviate pathological NLRP1 activation and improve erythropoiesis. This work opens new avenues for managing ribosome-related disorders and advancing personalized medicine approaches for hematopoietic diseases.

overall_design: K562 cells were pretreated with 0.1 μM nilotinib, followed by differentiation with 50 μM hemin for 24 h. Three biological replicates (15 μl at 200 ng/μl)


title: Integrated Transcriptomic and Metabolomic Analyses for Circadian Disruption biomarker identification

city: Shanghai

first: Baoyin

last: Ren

state: -- None selected --

address: No. 500 Dongchuan Road, Minhang District, Shanghai, China

institute: East China Normal University

summary: Although the impact of circadian disruption is well recognized, definitive indicators and time windows for its detection are currently lacking. Here, by conducting transcriptomic, metabolomic, and integrated analysis, we comprehensively investigated the gene and metabolite changes on the 7th day after a single 6-hour phase advance jet lag in mice. Our findings revealed significant alterations during this post-jet lag window, especially in core clock genes Bmal1 and Cry1, and metabolites L-Arginine and SM(d18:1/18:1(11Z)), with notable differences at Zeitgeber Time 0 (ZT0), suggesting ZT0 as a key diagnostic time point. Additionally, we identified L-Serine as a potential biomarker for indexing circadian disruption irrespective of time points. Our study provides new insights into potential biomarkers for detecting circadian clock disruption.

overall_design: Experimental Design: Species/Strain: Male C57BL/6 mice (8-10 weeks old). Treatment: A single 6-hour phase advance light cycle (simulated jet lag) vs. stable light-dark controls. Time Points: Liver and serum samples collected on day 7 post-jet lag at ZT0 (lights-on) and ZT12 (lights-off). Groups: Control (n=24): Stable 12:12 light-dark cycle. Jet Lag (n=24): Phase-advanced light cycle. Omics Data: Transcriptomics: RNA-seq (Illumina NovaSeq) of liver tissue, focusing on core clock genes (Bmal1, Cry1) and circadian pathways. Metabolomics: LC-MS/MS analysis of serum metabolites, including L-Arginine, SM(d18:1/18:1(11Z)), and L-Serine. Integrated Analysis: Multi-omics network and pathway enrichment (KEGG, Reactome) to identify biomarkers.

first: Yingzhi

first: Hui

first: Haonan

last: Li

first: Changxiao

last: Ma

first: Meina

last: Guo

first: Hongmei

last: Tan

first: Jiayang

first: Huiwen

last: Zheng

first: Bingyi

last: Shen

first: Jiazhi

first: Zhaiyi

last: Liu

first: Jingwen

last: Zhu

first: Jiaxin

first: Lejia

last: Qiu

first: Xiaoyan

first: Youfei

last: Guan

first: Guangrui

last: Yang

first: Lihong

last: Chen


title: A Transcriptomic Atlas of Adult Tissues of the Sea Urchin Lytechinus variegatus Identifies Early Transitions in Gonadogenesis

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

summary: Sea urchins have been a well-used model of fertilization and of the molecular biology of embryonic development. Our understanding of the molecular identity of adult tissues, on the other hand, has lagged significantly, a deficiency all too apparent with recent successes in mutational analyses in transgenerational studies. Here we focus on the developmental timing of gonadogenesis with particular reference to developmental features of when a juvenile reaches adulthood and begins to make eggs and sperm. We find a large variation in timing of reaching fertility in Lytechinus variegatus such that in 4.5 months, animals that have reached a mass/body ratio and making eggs or sperm. This is correlated with the external metric of opening of the gonadopore, indicative of gametogenesis. We identify a sac-like structure in juveniles that by both morphological and transcriptomic analysis appears to be an indeterminant gonad that transitions into an ovary or testis. We follow this development into adulthood and compare the transcriptomes of gonads and gametes to all 16 major tissues of the adult, revealing a broad definition of the tissue types, and displaying genes that are differentially enriched, and/or specifically expressed by each tissue. These datasets serve as a guide for gene selection in traditional CRISPR/Cas9 mutagenesis, for design of integrated transposase reporters, and for parsing out unique functions in tissues that in combination give this animal its unique attributes.

overall_design: Major tissues from adult sea urchins (Lytechinus variegatus) were isolated and stored in Trizol. Total RNA was extracted for each sample and sent to Novogene for next-generation bulk RNA sequencing following the manufacturer's instructions. Libraries were sequenced by Novogene in a paired-end fashion. Gonads and presumptive gonads were isolated from Lv at 4.5 month post fertilization (4.5 mpf). These tissues were isolated and stored in Trizol. Total RNA was extracted and sent to Admera Health for next-generation bulk RNA sequencing following the manufacturer's instructions, in a paired end fashion.

first: Cosmo

last: Pieplow

first: Madison

last: Silvia

first: Gerardo

last: Reyes

first: Gary

last: Wessel


title: PXR-dependant dysregulation of glucose metabolism induced by chronic exposure to NOAEL-level pesticide mixture in mice

city: Toulouse

first: LAILA

last: LAKHAL

address: 180 chemin de Tournefeuille

department: SA

institute: INRA

summary: Pesticides are essential in modern agriculture but raise concerns about long-term metabolic effects, particularly through nuclear receptor activation. This study examines the impact of chronic exposure to a mixture of five pesticides (dieldrin, propiconazole, boscalid, bupirimate, and pendimethalin) with or without tributyltin (TBT) on glucose and lipid metabolism in mice, focusing on the role of the constitutive androstane receptor (CAR) and pregnane X receptor (PXR). TBT was included for its strong affinity for RXR, a key heterodimerization partner of CAR and PXR, to assess whether RXR activation modulates or amplifies the metabolic effects of pesticide exposure. Results showed that pesticide exposure at NOAEL levels altered CAR and PXR dependent metabolic pathways. CAR knockout mice exhibited reduced free fatty acids and fasting glycemia, while PXR activation led to lower peak glycemia in oral glucose tolerance tests. Transcriptomic analysis identified disrupted pathways linked to glucose uptake and insulin sensitivity. These findings suggest that low-dose pesticide exposure can subtly affect metabolism via nuclear receptor interactions. The inclusion of TBT emphases RXR’s role in metabolic regulation. Overall, the study underscores the need to consider cocktail effects in risk assessment.

overall_design: 3 groups of WT C56BL/6J mice exposed each to a different diet, a Control diet, a diet with 5 pesticides at the NOAEL and a diet with the 5 pesticides and Tributyltin at the NOAEL

first: Laila

last: Mselli-Lakhal

first: Yannick

last: Dauwe

first: Claire

last: Naylies

first: Anne-Marie

last: Loustau

last: Lippi


title: Designed, linked-domain proteins are pan-UBE2D inhibitors and induce proteostress and the unfolded protein response in HeLa cells

city: Stockton

first: Joseph

last: Harrison

state: CA

address: 3601 Pacific Ave

institute: University of the Pacific

summary: Ubiquitin (Ub) is a protein post-translational modification that controls proteostasis through mechanisms spanning transcription, translation, and protein degradation. Ub conjugation occurs through a cascade of three enzyme classes (E1, E2, and E3s) involving >1000 proteins that regulate the ubiquitination of cellular proteins. The E2 Ub-conjugating enzymes are the midpoint, yet their cellular roles remain under-characterized. Here, we develop highly selective, multivalent, designed protein inhibitors against all UBE2D/UBCH5 isoforms by targeting the RING- and backside-binding sites. In HeLa cells, these inhibitors phenocopy knockdown of UBE2D by enhancing chemosensitivity to cisplatin. Whole-cell proteomics reveal ~20% of the identified proteins are more abundant and most do not have altered RNA levels, suggesting their protein turnover is regulated by UBE2D. Enrichment analysis of the altered mRNAs indicates the UBE2D inhibitors trigger the unfolded protein response. These precision tools will enable new studies about UBE2D’s cellular roles and help to deconvolute complex ubiquitin regulatory network.

overall_design: These samples correspond to HeLa cells electroportated with either the UBE2D inhibitor UBOX-UBL or the UBOX-UBLcontrol. PolyA enrichment and mRNA sequencing was performed by Seqquest genomics

first: Zara

last: Bukhari


title: Single Cell RNAseq of adult and stem cell derrived iris muscle

city: Kgs. Lyngby

first: Anne

middle: Zebitz

last: Eriksen

address: Produktions Torvet 423

department: Health Technology

country: Denmark

institute: Technical University of Denamrk

summary: We performed single-cell RNA sequencing (scRNAseq) on iris tissue from three adult human donors and human embryonic stem cell (hESC)-derived whole eye organoids, termed “SEAM,” using the 10X Genomics Chromium platform.  From the adult human datasets, we identified an iris muscle population based on the co-expression of PAX6 and smooth muscle proteins (ACTA2 and TAGLN). This dataset was further used to characterize the expression profile of the non-neuronal, crest-derived iris muscle.  Additionally, we differentiated hESCs into whole eye organoids (SEAM) and performed scRNAseq after 7 weeks of differentiation. In the organoids, we identified cell populations corresponding to most ocular cell types, spanning neurons, distal optic cup, periocular mesenchyme, and ocular surface epithelium. Notably, we identified iris muscle-like cells in the developing eye organoids.  We conducted an integrated analysis using the Seurat R package to compare the hESC-derived eye organoids with one of the adult donor irises (IRIS91 and SRAM48). This analysis revealed a shared iris muscle cluster containing cells from both datasets. The hESC-derived iris muscle represents a developing tissue with lower expression of mature muscle genes and higher expression of transcription factors, such as PAX6 and LHX2.  Human globes from donors aged 50–74 years were obtained within 24 hours postmortem from the Eye-Bank for Sight Restoration, NY, and Miracle in Sight, NC, with informed consent provided by the donors or their next of kin. This study was reviewed by the Icahn School of Medicine at Mount Sinai IRB oversight and deemed not to be human subject research. We received approval for use of H9 cell lines by WiCell.

overall_design:
This study involves single-cell RNA sequencing (scRNAseq) of two sample types: adult human iris tissue from three donors and human embryonic stem cell (hESC)-derived SEAM whole eye organoids collected at week 7 of differentiation.  Sample Preparation:  Frozen vials of freshly isolated adult human iris tissue and SEAM cultures were used. Cell viability was assessed using Trypan Blue staining, and only debris-free cell suspensions with >80% viability were processed. Approximately 10,000 cells were used as input for each sample. Library Preparation:  Cells were processed using the 10X Genomics Chromium Controller (v3.16) and Chromium Single Cell 3’ Library and Gel Bead Kit (v3.0). Gel beads in oil microdroplets (GEMs) were created to encapsulate single cells. Reverse transcription was performed inside GEMs to generate cDNA tagged with unique molecular indices (UMIs) and cell barcodes. GEMs were broken, and cDNA was amplified and quantified using an Agilent Bioanalyzer High Sensitivity chip and Qubit analysis (Thermo Fisher). Sequencing:  Libraries were sequenced on an Illumina NovaSeq 6000 platform using S4 flow cells (100 bp paired-end reads). Target sequencing depth was 50,000–100,000 reads per cell. Data Processing:  FASTQ files were generated using the Cell Ranger Single-Cell Software Suite (v3.1). Reads were aligned to the GRCh38 human reference genome. Filtered matrices of unique gene counts were produced for downstream analysis. Data Filtering and Normalization:  Low-quality cells (fewer than 500 unique genes) and potential doublets (more than 5,500 unique genes) were excluded. Final analysis included an average of 1,523 cells from adult human iris tissue and 6,039 cells from SEAM organoids. Data were normalized using a global-scaling method (LogNormalize) with a scale factor of 10,000. Analysis:  Principal component analysis (PCA) was performed, and clustering was conducted. Dimensionality reduction was visualized using Uniform Manifold Approximation and Projection (UMAP). Differential expression analysis was performed to identify cluster-specific genes, and heatmaps were generated to visualize the top 20 differentially expressed genes per cluster. Annotation and Enrichment:  Cluster annotation was based on manual curation of gene expression patterns and complemented with Enrichr gene set enrichment analysis (using the GO Biological Process 2018 database).

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first: Timothy

last: Blenkinsop

first: Bar

last: Markovoz

middle: Z


title: Transcriptomic Analysis Corroborates the New Radial Model of the Mouse Pallial Amygdala

city: Murcia

first: Elena

last: Garcia-Calero

address: Avda. Buenavista

institute: University of Murcia

summary: The mammalian amygdala is located in the temporal lobe of the telencephalon and plays a key role in limbic processing. Recently, our group proposed a radial morphological model to understand the glutamatergic (pallial) part of this nuclear complex in terms of separate progenitor domains. This model explains the amygdala region as consisting of several adjacent developmental radial progenitor units, disposing their distinct periventricular, intermediate, and superficial strata from the ventricle to the pial surface. It was expected that cell populations belonging to specific progenitor domains would present greater molecular similarity to each other than to neighboring developmental units. In this work, we aim to corroborate the existence of several radial domains in the pallial amygdala at the transcriptomic level. snRNAseq experiments in the amygdala of adult mice of both sexes indicated that at low resolution, the whole pallial amygdala was found to divide into two super-radial domains distinguished by differential expression of Slc17a6 and Slc17a7; the former partly imitates molecularly the subpallial (output) amygdalar regions, whereas the rest of the pallial amygdala is molecularly more akin to the surrounding cortical areas. In addition, our snRNAseq transcriptomic analysis fully supports the postulated amygdalar radial model of four main radial domains.

overall_design: Amygdalar region was microdissected from entire whole brains from adult mice, two males, two females. We used microsurgical knives under a dissection microscope (Leica S91) in ice-cold Sigma-Aldrich Dulbecco’s Phosphate Buffered Saline, without calcium and magnesium. The dissected tissue was frozen in liquid nitrogen and stored at -80ºC until used. Nuclei were isolated using the Minute™ single nucleus isolation kit designed for neuronal tissue/cells (Cat# BN-020, Invent Biotechnologies). Nuclei suspensions from each adult sample (AMM_A, AF_2, AM_2, AM_3) was diluted to an appropriate concentration and used as input to the 10X Chromium platform, using 10x Genomics Chromium controller plus Chromium Single Cell products for snRNAseq experiments.

first: Gloria

last: Fernández

first: Lara

last: López-González

first: Eduardo

last: Pons-Fuster

first: Luis

last: Puelles


title: Transcriptomic effects of INTS1 knockout in zebrafish larvae

city: Tel Aviv

first: Shir

last: Confino

address: Chaim Levanon St 55, Tel Aviv-Yafo

department: Neurobiology, Biochemistry and Biophysics

country: Israel

institute: Tel Aviv University

summary: Precise regulation of RNA polymerase II (RNAPII) is fundamental to transcriptional fidelity in eukaryotes. The Integrator complex, a conserved multi-subunit assembly, safeguards transcriptional integrity through its interaction with RNAPII, mediating transcription initiation, nascent RNA cleavage, and 3′ end processing. INTS1, the largest subunit of the Integrator complex, is critical for its function, and its mutations are linked to human neurodevelopmental disorders, yet, the underlying transcriptional effects remain poorly defined. Here, we characterize the global transcriptional effects of INTS1 deficiency in zebrafish. INTS1 loss leads to widespread gene expression changes, including of genes linked to hyperactivity and pathways associated with Attention-Deficit/Hyperactivity Disorder. We observe mutant-specific first intron retentions and transcript extensions. These findings underscore a central role for INTS1 in coordinating transcriptional regulation, and highlight the essential function of the Integrator complex in maintaining transcriptome integrity. Together, they offer insights into how INTS1 disruption may contribute to behavioral and physiological abnormalities.

overall_design: Global transcriptomic analysis of head pools from 120 hpf INTS1 knockout zebrafish larvae and their wild-type siblings


title: Treatment of prostate cancer with oncolytic virus OH2 [bulkRNA-seq_22-Rv1]

first: Jinzhou

last: Xu

overall_design: Prostate cancer cell lines (22-Rv1, 3 vs. 3) were treated with oncolytic virus OH2 intervention

first: Ye

last: An

first: Guichen

last: Ye

first: Zhiyu

last: Xia

first: Shaogang

last: Wang

first: Qidong


title: Prenatal SMN-dependent defects in translation uncover a reversible primary ciliopathy in spinal muscular atrophy

city: Trento

first: Gabriella

last: Viero

address: Via Sommarive 18

department: Institute of Biophysics

country: Italy

institute: CNR

summary: Spinal muscular atrophy (SMA) is a neuromuscular disease caused by low levels of SMN protein resulting from mutations in the SMN1 gene. Several therapeutic approaches capable of boosting SMN are now approved for use in human patients, delivering remarkable improvements in lifespan and symptom severity. However, new and unexpected phenotypes are being reported in treated SMA patients, including growing evidence for significant neurodevelopmental comorbidities in some individuals, indicative of alterations in brain development. Here, using a mouse model of severe SMA, we reveal an underlying neurodevelopmental phenotype in SMA where prenatal SMN-dependent defects in translation drive a primary ciliopathy in the CNS. Cell proliferation was significantly reduced in the hippocampus of SMA mice at E14.5, accompanied by widespread perturbations in translation, disrupting genes associated with primary cilia. The density of primary cilia in vivo, as well as cilial length in vitro, was significantly decreased in prenatal SMA mice, revealing core morphological hallmarks of a primary ciliopathy. Prenatal transplacental therapeutic intervention with an SMN-restoring small molecule (Risdiplam) rescued primary cilia defects in SMA mouse embryos. We conclude that SMN protein is required for normal cellular and molecular development of the CNS, with low levels in SMA driving a primary ciliopathy. Early, systemic treatment with SMN-restoring therapies is likely to be required to target neurodevelopmental comorbidities.

overall_design: Ribosome profiling was obtained from control (Smn+/−; SMN2tg/0) and SMA Taiwanese mouse model (Smn−/−; SMN2tg/0, strain 005058) at embryonic day 14.5 from brain and spinal cord. Experiments were performed in biological triplicates for each tissue.

first: Federica

last: Genovese

first: Yu-Ting

last: Huang

first: Anna

last: Motyl

first: Martina

last: Paganin

first: Gaurav

last: Sharma

first: Ilaria

last: Signoria

first: Deborah

last: Donzel

first: Nicole

last: Lai

first: Marie

last: Pronot

first: Rachel

last: Kline

first: Helena

last: Chaytow

first: Kimberley

middle: J

last: Morris

first: Kiterie

last: Faller

first: Thomas

last: Wishart

first: Ewout

last: Groen

first: Michael

last: Cousin

middle: H

last: Gillingwater


title: PPT1 is a negative regulator of STING signaling in cancer cells and its inhibition reactivates immune surveillance in cold tumors

city: Worcester

first: Emma

middle: V.

last: Watson

state: MA

address: AS7-1045 Albert Sherman Center, 368 Plantation St

department: Systems Biology

country: USA

institute: UMass Chan Medical School

summary: Immunotherapy modalities have revolutionized cancer treatment for a number of metastatic and treatment-refractory tumor types. Still, many malignancies that are lacking in T cell infiltrates and immunologically “cold” fail to respond to these modalities. One approach to increase tumor immunogenicity has been to induce STING and downstream interferon signaling that is often dysregulated in “cold” tumors. Despite some early success of STING agonists in preclinical cancer models, these approaches have not been successful in the clinic due to poor tumor penetrance and systemic toxicities. Here we performed a genome-wide CRISPR screen to uncover novel therapeutic targets to activate STING expression in human tumors. We identified Palmitoyl Protein Thioesterase1 (PPT1) as a negative regulator of STING highly expressed in “cold” ovarian and prostate tumors. Genetic or pharmacological PPT1 suppression increased STING protein stability and its downstream activation of interferon and inflammatory cytokine signaling to enhance T cell migration. Treatment of preclinical prostate and ovarian cancer models expressing low levels of STING with the small molecule PPT1 inhibitor GNS561 enhanced STING expression and activation, leading to infiltration and activation of cytotoxic T cells that turned these tumors “hot” and reduced tumor growth, fibrosis, and dissemination without toxicity. Further analysis demonstrated that PPT1 is associated with reduced STING expression, CD8+ T cell numbers, overall survival, and immunotherapy outcomes in ovarian and prostate cancer patients. Thus, PPT1 inhibition may be a promising approach to activate STING and potentiate the effects of immunotherapy in “cold” tumors.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq profiling of A1847, PC3, and MycCAP;p53KO cells treated with vehicle (DMSO) or 5 µM GNS561 for 24 hrs

first: Arshia

middle: N

last: Kaur

middle: V

first: Shreya

middle: R

last: Chowdhury

first: Marcus

last: Ruscetti