title: Genome writing to dissect consequences of SVA retrotransposon disease X-Linked Dystonia Parkinsonism [RNA-Seq]

overall_design: Stranded RNA seq for converted mESCs, and nestinCre conditionally converted mouse striata


title: Transcriptomic Analysis of Potency Associated Genes in Hematopoietic Stem and Progenitor Cells

status: Public on Jul 01 2026

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

country: USA

institute: Indiana University

type: Expression profiling by high throughput sequencing

summary: Allogeneic hematopoietic cell transplantation is a potentially curative treatment for malignant and non-malignant hematologic disorders, wherein healthy hematopoietic stem (HSC) and progenitor cells (HSCs) reconstitute a functional blood and immune system following ablation of diseased cells. Functionally potent HSCs/HPCs from bone marrow, mobilized peripheral blood, or umbilical cord blood drive recovery of the hematopoietic system following transplantation. Improving initial characterization of the engraftment potential of donor grafts and recovery time will lead to improved patient outcomes, particularly in the case of umbilical cord blood transplantation, which is limited by low total numbers of cells. However, we still lack a complete understanding of the molecular programs that regulate potency, which is the ability of cells to home to and engraft in a hematopoietic niche, then self-renew and differentiate driving multi-lineage repopulation. Here, we use transcriptomic approaches to elucidate gene programs associated with hematopoietic cell potency in CD34+ cells derived from umbilical cord blood, which are enriched for HSCs/HPCs. We compare the transcriptomes of immunophenotypically defined HSCs/HPCs and correlate HSC transcriptomes with engraftment outcomes.

overall_design:
Immunophenotypically defined HSCs/HPCs from three distinct cord blood units were sorted by flow cytometry and harvested for RNA-sequencing. Separately, HSCs from six distinct cord blood units were immunophenotypically defined and sorted by flow cytometry while concurrently CD34+ enriched cells isolated by magnetic separation from these same six cord blood units were used in extreme limiting dilution transplantation experiments to immune deficient NSG mice. Repopulating frequencies were determined by Poisson modeling using engraftment outcomes at 4 months post-transplantation, and transcriptomes from the HSCs were correlated with these long-term engraftment frequencies (high=above average frequency; low=below average frequency).

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The table below lists GEO accessions reused/reanalyzed for this study.
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title: Single-cell transcriptomes and T cell receptor sequences of CD4 or CD8 single positive T lymphocytes from peripheral blood or urine of lupus nephritis patients at flare.

city: Berlin

first: Christopher

middle: Mark

last: Skopnik

address: Charitéplatz 1

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary: Proliferative lupus nephritis (LN) is triggered by deposition of autoantibodies in glomeruli and paralleled by a T cell-rich kidney infiltrate. Although these T cells have been attributed with propagation of tissue injury, it is unclear how they are activated and whether T cell autoreactivity drives the local inflammation. Kidney-infiltrating T cells are also observed in urine, where they have high resemblance with interstitial T cells. Therefore, urinary T cells are a proxy to investigate tissue pathogenesis. Here, we analyzed urinary T cells to elucidate if a kidney-specific T cell autoimmune reaction contributes to tubulointerstitial inflammation in LN. Using single cell RNA sequencing, we compared transcriptomes and clonotypes of T cells from blood and urine of patients with active LN and show that urinary T cells were mostly activated CD8 effector memory cells recruited from a circulating CX3CR1+ subset. Several urinary CD8 T cell clones were expanded. However, upon in vitro testing of their T cell receptors, we did not observe autoreactivity against autologous tubular epithelial cells. Instead, approximately 20% of expanded clonotypes were Epstein-Barr virus- or cytomegalovirus specific, but respective viral antigens were undetectable in kidney biopsies or urine. Conversely, kidney-infiltrating T cells had access to interleukin-15 and interferon (IFN) β and stimulation with these cytokines was sufficient to trigger degranulation and production of tumor necrosis factor, IFN γ and granzyme K. Together, these results show that CD8+CX3CR1+ T cells are recruited into the kidney in LN, where they are activated by cytokines enabling them to contribute to local inflammation.

overall_design: T cells were sorted by FACS from fresh PBMC or fresh urine of patients who were hospitalized at Charité – Universitätsmedizin Berlin due to acute lupus flares with renal involvement. Voided urine samples were diluted in PBS/BSA and put on ice as quickly as possible. Patient (Pat) 2 – 6 were paired blood and urine samples, Pat0 and Pat1 unpaired urine samples. (Paired) samples with an absolute sorted event count from urine of 3000 or above were subjected to single cell capturing with the Chromium Controller (10X Genomics). Libraries of gene expression (GEX) or T cell receptor sequences (VDJ) were prepared with kits from 10X Genomics. Sequencing was performed with Illumina NextSeq reagents and sequenced reads were aligned with the Cell Ranger pipeline (version 7.1.0) against human genome 38 (hg38) as provided by 10X Genomics (GRCh38-2020-A).

middle: M

first: Jan

last: Klocke

first: Paul

last: Freund

first: Diana

last: Metzke

first: Kai-Uwe

last: Eckardt

first: Falk

last: Hiepe

first: Mir-Farzin

last: Mashreghi

first: Philipp

last: Enghard


title: A developmentally regulated long-range enhancer-promoter contact mediates human neural development [scRNA-seq]

city: New York

first: Devin

last: Bready

state: NY

address: Placantonakis Lab, 33rd and East River Drive, Smilow 1306H

department: Neurosurgery

institute: NYU School of Medicine

summary: SOX2 is a core pluripotency factor in human embryonic stem cells (hESCs), but upon differentiation to the three germ layers, its expression is preserved selectively in neuroectoderm. The mechanisms regulating SOX2 transcription in distinct developmental stages remain incompletely understood. Here, we demonstrate that a distant enhancer 550 kb from the human SOX2 locus is selectively activated in neural stem cells (NSCs) and establishes long-range contact with the SOX2 gene. CRISPR-Cas9 excision of the enhancer has no effect in hESCs but reduces SOX2 transcription in NSCs and impairs neuroectodermal differentiation and forebrain specification in teratomas and cerebral organoids. CRISPR excision of a CTCF recognition motif adjacent to the enhancer does not affect enhancer activation in neuroectoderm but reduces chromatin looping and SOX2 transcription to partially reproduce phenotypes seen with enhancer deletion. Our findings indicate that the development of the human nervous system depends on a developmentally regulated long-range contact between a distant enhancer and the SOX2 locus.

overall_design: 4C-Sequencing of hESCs and rosette NSCs transduced with excision of nMotif or without excision expressing ROSA26 control gRNAs

first: Bready

last: Devin

first: Wang

last: Shuai

first: Sabio

last: Jonathon

first: Tsirigos

last: Aristotelis

first: Skok

last: Jane

first: Placantonakis

last: Dimitris


title: Transcriptome profiling by RNA-seq was performed on HCCLM3 cells stably transfected with a PON1-overexpressing lentivirus (PON1-OE) and its negative control (PON1-NC).

city: xi'an

first: Haolin

last: Wei

address: No. 169, Changle West Road

department: Department of Cell Biology

country: China

institute: Air Force Medical University

summary: The full-length human PON1 coding sequence was cloned into a lentiviral overexpression vector and used to infect low-expressing HCCLM3 cells. Stable overexpression clones (PON1-OE) and empty vector control clones (PON1-NC) were selected and maintained using puromycin.Each group is set up with three biological replicates.

overall_design: The HCCLM3 cells with overexpressed PON1 (PON1-OE) and the empty vector lentivirus (PON1-NC) were routinely cultured in RPMI-1640 medium containing 15% fetal bovine serum at 37°C and 5% CO2. Cell lysis was performed using the same extraction solution 24 hours after transfection.

first: Zhice

last: Tan

first: Chuheng

last: Gou

first: Zekun

last: Liu

first: Huijie

last: Bian


title: Time-course transcriptome profiling of sugarcane hybrid (ZZ1) leaves in response to Fusarium sacchari infection

city: Nanning

first: Yixue

last: Bao

address: No. 100 Daxue East Road, Xixiangtang District

institute: Guangxi university

summary: Pokkah boeng disease, caused by the fungal pathogen Fusarium sacchari, is a significant threat to sugarcane production worldwide. To elucidate the molecular defense mechanisms of sugarcane against this pathogen, we performed a comprehensive transcriptomic analysis using the hybrid cultivar ZZ1 (Saccharum officinarum x Saccharum spontaneum). Leaf tissues were collected at multiple time points (0, 12, 24, 48, 72, 120, and 144 hours) following inoculation with F. sacchari. Total RNA was extracted and sequenced using the Illumina Novaseq platform. This study aims to identify key differentially expressed genes and regulatory pathways involved in the sugarcane-pathogen interaction, providing valuable genomic resources for breeding disease-resistant sugarcane varieties.

overall_design: A temporal infection experiment was designed to study the interaction between sugarcane hybrid ZZ1 and the pathogen Fusarium sacchari. The treatment group consisted of sugarcane leaves inoculated with F. sacchari, with samples harvested at seven time points: 0h (control), 12h, 24h, 48h, 72h, 120h, and 144h post-inoculation. For each time point, three independent biological replicates were processed to ensure data reproducibility. Total RNA was isolated using the RNAprep Pure Plant Kit. The integrity and quality of the constructed cDNA libraries were rigorously evaluated using the Agilent Bioanalyzer 2100 system. Sequencing was performed on the Illumina Novaseq platform, generating high-quality raw sequence reads for downstream bioinformatic analysis.

first: Muqing

last: Zhang


title: Single Cell Transcriptomic Analysis Demonstrating Oxygen Dependence of Human Hematopoietic Stem and Progenitor Cells

first: James

last: Ropa

summary: Hematopoietic stem and progenitor cells support a lifetime supply of blood and immune cells, can become neoplastic when dysregulated, and constitute a powerful cell therapy vehicle for hematologic diseases. We demonstrated that human hematopoietic cell numbers, growth, biochemical properties, and functional potency is affected by variation in physiologically and clinically relevant local oxygen tensions. Lineage defined progenitor cells showed increased expansion in high oxygen, while primitive cells and those with in vivo potency were maintained at higher frequencies in low physiologic oxygen. Here we present a novel hematopoietic cell oxygen-dependent single cell transcriptomic profile to determine changes in gene expression induced by exposure to various physiologically relevent oxygen tensions.

overall_design: CD34+ cells derived from human umbilical cord blood were isolated using magnetic separation technology. Purified CD34+ cells were cultured in serum free media in the presence of growth factors in variable oxygen conditions using controlled oxygen incubators. Cells were grown in 1%, 3%, 5%, 14%, and 21% oxygen and were harvested two days or seven days following seeding or were isolated fresh as input control. Cells were subjected to single cell RNA-sequencing library preparation in an oxygen controlled chamber or in ambient air using PIPseq T20 kits, using TotalSeq cell hashing antibodies to multiplex.


title: Glucose Transport Dependency Defines a Therapeutic Vulnerability in Myeloproliferative Neoplasms

city: Aachen

first: Patrick

last: Weiand

state: NRW

address: Pauwelsstraße 19

department: Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation

institute: RWTH Aachen University

summary: Philadelphia chromosome-negative myeloproliferative neoplasms (MPN) comprise a heterogenous group of hematologic malignancies that include polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). The most prevalent driver mutation, JAK2V617F, is present in over 90% of PV and approximately 60% of ET and PMF cases. Current therapeutic strategies rely on cytoreductive approaches that mitigate disease burden and thromboembolic risk but are not curative. Allogeneic stem cell transplantation remains the only curative option, underscoring the need for novel therapeutic strategies. We previously identified hypoxia–inducible factor 1 (HIF-1) as a selective vulnerability in JAK2V617F–positive cells, but the underlying metabolic mechanisms remain incompletely defined. CRISPR-Cas9 knockout clones targeting the HIF-1–regulated glucose transporters GLUT1 and GLUT3 were generated in Jak2WT and Jak2V617F backgrounds to charaterize glucose uptake depletion by RNA sequencing.

overall_design: RNA-seq profile of wildtype and GLUT1 / 3 KO Jak2WT and Jak2V617F 32D cells cultured in RPMI1640 with approxiamtely physiological nutrient supplementation, foregoing any pyruvate.

first: Julian

last: Baumeister


title: Efficient in vivo pharmacological inhibition of ∆FOSB with YL-0441 in brain

first: Molly

middle: S

last: Estill

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ΔFOSB, an unusually stable member of the AP-1family of transcription factors, mediates long-term maladaptationsthat play a key role in the pathogenesis of drug addiction, cognitive decline, dyskinesias, and several other chronic neurological and psychiatric conditions. We have recently identified that 2-phenoxybenzenesulfonic acid-containing compounds disrupt the binding of ΔFOSB to DNA in vitroin cell-based assays. We show that one such analog, YL0441, disrupts the binding of ΔFOSB to DNA in vitroand in vivo, and suppresses ΔFOSB-function in cell-based assays. Importantly, infusion of YL0441 into the hippocampus of APP mice (a mouse model for Alzheimer's diseaseneuropathology) leads to virtually complete loss of ΔFOSB bound to genomic DNA as detected by CUT&RUN sequencing. Our findings corroborate that the binding/release of AP1 transcription factors to DNA can be controlled via small moleculesin vivo, even by analogs of a compound that binds to a groove outside of the DNA-binding cleft, and that our lead can be optimized via medicinal chemistry to yield a much moreefficacious inhibitor of ΔFOSB function in vivo. These findings define a strategy to design small-molecule inhibitors for other AP-1and AP-1-related transcription factors, in particular, those involved in neuropsychiatric and neurological disorders.

overall_design: In vivo studies were performed in 2–3-month-old heterozygous transgenic male and female mice expressing human amyloid precursor protein (APP) carrying Swedish (K670N, M671L) and Indiana (V717F) mutations linked to familial Alzheimer’s disease. After three days of intra-hippocampal infusion of YL0441 or vehicle, brains were removed for analysis of ΔFOSB binding. Nuclei were assessed with CUT&RUN for ΔFOSB binding.

first: Sean

last: McNeme

first: Anil

last: Kumar

first: Yun

last: Young Yim

first: Brandon

last: Hughes

first: Corey

last: St Romain

first: Yi

last: Li

first: Ashwani

first: Qichao

first: Shanghua

last: Fan

first: Nadeen

last: Takatka

first: Earnest

middle: P

last: Chen

first: Matthew

last: Rivera

first: Haiying

first: Alfred

middle: J

last: Robison

first: Mischa

last: Machius

first: Stephen

last: Haggarty

first: Jeannie

last: Chin

first: Eric

last: Nestler

first: Jia

last: Zhou

first: Gabrielle

last: Rudenko


title: Expression data from control and LRRC8A knockdown cells

city: Shanghai

first: ye

last: qing

address: Dongchuan road

institute: cancer institute

summary: To investigate the biological function of LRRC8A and its underlying molecular mechanisms, we performed high-throughput sequencing to analyze the gene expression profiles of control and LRRC8A-knockdown cells.

overall_design: To explore the functional role of LRRC8A, SW1990 cells were transfected with shRNA targeting LRRC8A. Subsequently, transcriptome profiling by RNA-seq was conducted using three biological replicates of control and LRRC8A-knockdown cells.

first: Xiaomei

last: Yang

first: Qing

last: Ye

first: Hongzhi

last: Liu

first: Xiaoqi

last: Wang

first: Lipeng

last: Hu

first: Hui

first: Shengzhe

last: Gong

first: Yitian

last: Tao

first: Zheng

last: Wu

first: Wangwang

first: Feng

last: Han

first: Lei

last: Zhu

first: Dongxue

first: Xueli

last: Zhang

first: Shuheng

last: Jiang

first: Zhigang

first: Yanmiao

last: Huo

first: Qi

last: Wo

first: Qili

last: Peng


title: RNA-seq of tumors from mice treated with FPC (5-FU, anti-PD-1 antibody, and anti-CTLA-4 antibody), mRNA–LNP and KDM5B inhibitors.

city: Suita

first: Tomoaki

last: Hara

address: Yamadaoka 2-2

country: Japan

institute: The University of Osaka

summary: Chimeric antigen receptor (CAR) T cell therapy is a highly effective cancer treatment that harnesses immune cells. However, significant challenges remain, particularly with respect to its application to solid tumours and the high cost of manufacturing. To address these limitations, the development of mRNA–lipid nanoparticle (LNP) therapeutics capable of generating CAR-T cells in vivo has attracted increasing attention. In this study, we administered LNP-formulated mRNA encoding a fibroblast activation protein (FAP)-targeting CAR in a mouse tumour model and investigated how tumour-resident cells alter their gene expression profiles in response. We further examined how KDM5B inhibition influences the antitumor effect in combination with in vivo CAR-T therapy.

overall_design: C57BL/6J mice were subcutaneously implanted with MC38 and FAP-expressing 3T3 cells and treated intravenously four times. Experiments were conducted under four treatment conditions. Mice in the FPC group received 5-fluorouracil (5-FU), an anti–PD-1 antibody, and an anti–CTLA-4 antibody. The FPCRC group received FPC in combination with mRNA-LNP and CPI-455. The FPCRJB161 group received FPC in combination with mRNA-LNP and JB-161. Control mice received phosphate-buffered saline (PBS). CPI-455 and JB-161 are KDM5B inhibitors

first: Sikun

last: Meng

first: Masamitsu

last: Konno

first: Naohiro

last: Nishida

first: Jun

last: Koseki

first: Kanji

last: Meguro

first: Yasuhiko

last: Kawano

first: Toshiya

last: Morie

first: Shingo

last: Dan

first: Taroh

last: Satoh

first: Shuji

last: Akai

first: Kazutake

last: Tsujikawa

first: Hidetoshi

last: Eguchi

first: Masaki

last: Mori

first: Yutaka

last: Miura

first: Nishiyama

last: Nobuhiro

first: Hideshi

last: Ishii


title: RNA-seq analysis of tumors derived from a xenograft model treated with the KDM5B inhibitors JB-157 or JB-161.

first: Tomoaki

last: Hara

summary: KDM5B, a member of the KDM5 family of histone demethylases, functions as a key epigenetic regulator by removing di- and trimethyl groups from H3K4 (H3K4me2/3), thereby promoting transcriptional repression. It is involved in fundamental biological processes, including development, stem cell maintenance, and tumorigenesis, and its dysregulation has been associated with multiple cancer types. Given its critical role in cancer biology, KDM5B has emerged as an attractive target for therapeutic intervention. Therefore, we conducted a screening campaign to identify novel KDM5B inhibitors. In this study, we investigated whether the KDM5B inhibitors JB-157 and JB-161, identified through our screening, exert antitumor effects.

overall_design: HT-29 human colorectal cancer cells were subcutaneously inoculated into the dorsal flank of NOD/SCID mice. On days 4 and 7 after implantation, the mice were administered intraperitoneal injections of JB-157 or JB-161 (6.69 mg/kg body weight) or 5-fluorouracil (5-FU; 100 mg/kg body weight) in a total volume of 0.2 mL.


title: ChIP-seq analysis of HT-29 cells treated with the KDM5B inhibitors JB-157 or JB-161

summary: KDM5B, a member of the KDM5 family of histone demethylases, functions as a key epigenetic regulator by removing di- and trimethyl groups from H3K4 (H3K4me2/3), thereby promoting transcriptional repression. It is involved in fundamental biological processes, including development, stem cell maintenance, and tumorigenesis, and its dysregulation has been associated with multiple cancer types. Given its critical role in cancer biology, KDM5B has emerged as an attractive target for therapeutic intervention. Therefore, we conducted a screening campaign to identify novel KDM5B inhibitors. In this study, we investigated whether the KDM5B inhibitors JB-157 and JB-161, identified through our screening, induce chromatin remodeling in HT-29 cells.

overall_design: HT-29 cells were plated in 15-cm dishes and maintained in DMEM supplemented with 10% FBS. JB-157 or JB-161 (100 µg in 30 µL) was added to the culture medium, while control cells were treated with an equal volume (30 µL) of DMSO. Following overnight incubation at 37 °C, the cells were collected, and histones were isolated from 1 × 10⁷ cells using the EpiQuik Total Histone Extraction Kit (EpigenTek) in accordance with the manufacturer’s protocol. The extracted chromatin was incubated with Histone H3 (D1H2) rabbit monoclonal antibody (Cell Signaling Technology) pre-coupled to Dynabeads Protein G (Invitrogen). Immunoprecipitated DNA was then purified according to the kit instructions and subsequently subjected to next-generation sequencing.

first: Sikun

last: Meng


title: Chromatin accessibility in human colonic fibroblasts

city: Suwon-si

first: min jung

last: sung

state: Gyeonggi-do

address: 206, World cup-ro, Yeongtong-gu

country: South Korea

institute: ajou university

summary: We investigated genome-wide chromatin accessibility changes associated with replicative senescence in human colonic fibroblasts (HCoFs). A replicative senescence model was established by serial passaging of HCoFs, and cells at different stages of aging were collected: young (passage 6), mid-old (passage 15), and old (passage 23). To characterize age-associated alterations in chromatin structure, Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) was performed. Comprehensive epigenomic profiling revealed progressive remodeling of chromatin accessibility during replicative aging. Comparative analysis across young, mid-old, and old cells enabled identification of senescence-associated regulatory regions and dynamic changes in accessible chromatin landscapes. These data provide a valuable resource for understanding the epigenetic mechanisms underlying replicative senescence in human colonic fibroblasts and offer insight into how age-dependent chromatin reorganization contributes to transcriptional regulation during cellular aging.

overall_design: Human colonic fibroblasts (HCoFs; Catalog No. 2880, ScienCell Research Laboratories, Carlsbad, CA, USA) were used in this study. Cells were cultured in Fibroblast Medium (Cat. No. 2301, ScienCell Research Laboratories, Carlsbad, CA, USA) according to the manufacturer’s instructions. A replicative senescence model was generated by serial passaging of HCoFs up to passage 23, with routine subculture approximately every three days; for old cells, passaging was performed at least weekly to maintain viability. Three cellular age groups were defined based on passage number: young (passage 6), mid-old (passage 15), and old (passage 23). ATAC-seq libraries were prepared from cells at each age stage to profile chromatin accessibility changes associated with replicative senescence. Two biological replicates per condition were used for sequencing and downstream analysis.

first: Min-Jung

last: Sung

first: Young-Kyoung

last: Lee

first: Won-Been

last: Kang

first: Soon-Sang

last: Park


title: RNA-seq profiling of post-hypoxic head and neck cancer cell lines

city: Leuven

first: Sandra

last: Nuyts

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary: Hypoxia is an important cause of radiotherapy resistance in head and neck squamous cell carcinoma (HNSCC). To investigate the transcriptional expression associated with post-hypoxic survival, we performed RNA-seq profiling of HPV-negative (FADU) and HPV-positive (SCC154) hypoxia-fate-mapped cell lines, hereafter called FADU-hfm and SCC154-hfm. Non-hypoxic (DsRed-positive) and post-hypoxic (GFP-positive) cells were sorted from 3D hfm-spheroids using fluorescence-activated cell sorting (FACS) and analyzed under normoxic conditions. The resulting dataset provides gene expression profiles of non-hypoxic and post-hypoxic cells.

overall_design: This study investigates transcriptional changes in sorted non-hypoxic (DsRed-positive) and post-hypoxic (GFP-positive) FADU-hfm and SCC154-hfm head and neck cancer cell lines using RNA-seq. The HPV-positive SCC154 and HPV-negative FADU cells were transduced with the hypoxia-fate mapping system from Godet et al. (PMID: 31649238). Spheroids from hfm-cells were established and non-hypoxic and post-hypoxic cells were sorted using fluorescence-activated cell sorting (FACS). The sorted cells were cultured under normoxic conditions. Total RNA was extracted using RNeasy Mini Kit (Qiagen) and libraries were prepared with the QuantSeq 3′ mRNA-Seq V2 Library Prep Kit (Lexogen). Sequencing was performed on an Illumina NextSeq 2000.

first: Marilyn

last: Wegge

first: Ruveyda

last: Dok

first: Ludwig

last: Dubois


title: A developmentally regulated long-range enhancer-promoter contact mediates human neural development

first: Devin

last: Bready

first: Shuai

last: Wang

first: Jonathon

last: Sabio

first: Aristotelis

last: Tsirigos

first: Jane

last: Skok

first: Dimitris

last: Placantonakis


title: A developmentally regulated long-range enhancer-promoter contact mediates human neural development [ATAC-Seq]

first: Bready

last: Devin

first: Lhoumaud

last: Priscillia

first: Tsirigos

last: Aristotelis

first: Skok

last: Jane

first: Placantonakis

last: Dimitris


title: ChREBP Is Dispensable for Myofiber Type-switch but Promotes Skeletal Muscle Regeneration

first: Lu

last: Junyu

address: 800th Xiangyin Street, shanghai,China

institute: Naval Medical University

summary: Muscle performance and fatigability are determined by the structural and metabolic properties of the specialized myofibers. Skeletal muscle demonstrates significant plasticity, with myofiber types and energy metabolic functions undergoing adaptive remodeling in response to physiological or pathophysiological stimuli. The transcription factor carbohydrate-responsive element-binding protein (ChREBP) is recognized as a crucial glucose-sensing regulator involved in glucose and lipid metabolism. However, However, the precise role of ChREBP in influencing myofiber composition and energy metabolism within muscle tissue remains ambiguous. Here, utilizing skeletal muscle-specific knockout mice, we demonstrated that ChREBP deletion did not substantially alter muscle fiber composition or metabolic function, nor did it play a role in skeletal muscle adaptive remodeling under hypoxic or high-fructose dietary conditions. Interestingly, the absence of ChREBP was associated with a modest enhancement in aerobic exercise capacity, although it markedly impaired lipid transport function and led to a reduction in triglyceride content. Furthermore, we observed that upregulation of ChREBP expression significantly increased the number of newly formed myofibers and their cross-sectional area. Taken together, this study elucidates the role of ChREBP in skeletal muscle and its adaptive remodeling, while also identifying a significant promotive function of ChREBP in the repair of skeletal muscle injuries.

overall_design:
1. RNA-seq analysis of gastrocnemius and soleus muscles from F/F mice and ChREBP skeletal muscle-specific knockout mice (ChMKO) under regular feeding conditions
2. RNA-seq analysis of gastrocnemius muscles from F/F mice and ChREBP skeletal muscle-specific knockout mice (ChMKO) after hypoxia exposure and high-fructose diet feeding
3. RNA-seq analysis of gastrocnemius tissues with ChREBP overexpression from C57BL/6J mice injected with AAV-CON and AAV-ChREBP
4. RNA-seq analysis of wildtype C2C12 cells and their overexpression derivative cell line (ChREBP overexpression) at Day 7 of myogenic differentiation

first: Junyu

last: Lu

first: Jian

last: Chen

first: Guanyu

last: Zhang

first: Wenlin

last: Li


title: Sleep Homeostasis Ensembles in the Hypothalamic PVN Reprogram Systemic Fuel Utilization via Adipose Lipolysis II

city: Beijing

first: Hong

last: Jiang

address: No. 38, Xueyuan Road, Haidian District, Beijing

institute: School of Basic Medical Sciences Peking University

summary: Here,we performed transcriptomic analyses of WAT collected during the rebound sleep phase.We revealed that upregulated genes were primarily associated with cell differentiation, whereas downregulated genes were enriched in pathways related to lipid and glucose metabolism.

overall_design: Animals were handled for 2 mins each day and habituated in deprivation chamber for 3 successive days before treatment. Sleep deprivation was initiated at lights on ZT2 by switching on the motors, choosing the continuous sweeping mode (approximately 6 s cycle time), and stopped after 10 hr at lights off (ZT12). After the deprivation, a 4-hour rebound sleep is performed in the chamber. The WAT tissues were collected during rebound sleep stage in the dark phase (ZT16).

first: Feng

last: Cao

first: Ruoyu

first: Awuti

last: Abudusalamu


title: Bulk liver mRNA-seq of Cep72 knockout and wild-type mice in Schistosoma japonicum infection–induced and CCl4-induced liver fibrosis models

city: Wuhan

first: RUI

last: Zhou

address: Donghu Road 185

institute: Wuhan University

summary: Liver fibrosis is a common pathological outcome of chronic liver injury triggered by diverse etiologies. To investigate the role of CEP72 in fibrogenesis under distinct fibrotic settings, we performed bulk mRNA sequencing of whole-liver total RNA from wild-type (WT) and Cep72 knockout (Cep72-KO) mice in two experimental models: Schistosoma japonicum (Sj) infection–induced liver fibrosis and carbon tetrachloride (CCl4)–induced liver fibrosis.  For the Sj model, mice were percutaneously infected with 17 ± 1 Schistosoma japonicum cercariae per mouse and analyzed at 8 weeks post infection, generating four groups: 8W-NC (WT control), 8W-KO-NC (Cep72-KO control), 8W-Sj (WT + Sj infection), and 8W-Sj-KO (Cep72-KO + Sj infection) (n = 2 mice per group). For the CCl4 model, mice were treated for 8 weeks with intraperitoneal injections of 10% CCl4 at 10 μL/g body weight, twice per week, and samples were collected from 8W-CCL4 (WT + CCl4) and 8W-KO-CCL4 (Cep72-KO + CCl4) groups (n = 2 mice per group).  Paired-end Illumina mRNA-seq was performed on extracted total RNA from whole liver tissue. This dataset enables comparative transcriptomic analyses to identify CEP72-associated gene expression programs and pathways involved in liver injury, inflammation, and fibrosis across parasitic and chemical models.

overall_design: This study includes two bulk liver RNA-seq experiments to evaluate genotype effects (WT vs Cep72-KO) under fibrotic and control conditions.  Schistosoma japonicum infection model (8-week timepoint): A 2 × 2 factorial design with factors Genotype (WT vs Cep72-KO) and Treatment (NC vs Sj infection). Mice in infection groups were percutaneously infected with 17 ± 1 Schistosoma japonicum cercariae per mouse and livers were collected at 8 weeks post infection, generating four groups: 8W-NC, 8W-KO-NC, 8W-Sj, and 8W-Sj-KO (n = 2 biological replicates per group; whole liver tissue).  CCl4-induced fibrosis model (8-week treatment): A genotype comparison under CCl4 challenge: 8W-CCL4 (WT) vs 8W-KO-CCL4 (Cep72-KO) (n = 2 biological replicates per group; whole liver tissue). Mice received intraperitoneal injections of 10% CCl4 at 10 μL/g body weight twice weekly for 8 weeks, followed by liver collection.  For all samples, total RNA was extracted from whole liver and subjected to paired-end Illumina mRNA sequencing for downstream differential expression and pathway analyses.


title: Quantitative analysis of Tat-dependent and host-driven HIV transcription by ChIP-seq and RNA-seq

city: Jupiter

first: CHUAN

last: LI

state: FL

address: 130 Scripps Way

institute: University of Florida

summary: HIV transcription is initiated by host transcriptional machinery prior to the production of the viral transactivator Tat, yet the magnitude and regulatory features of this Tat-independent transcriptional state remain poorly defined. In this study, we performed integrated chromatin and transcriptional profiling to quantitatively compare Tat-dependent and host-driven regulation of HIV and cellular gene expression.  Jurkat T cells were infected with isogenic HIV constructs expressing functional Tat (TatWT) or lacking Tat expression (TatNull) and analyzed under non-stimulated and stimulated conditions. Genome-wide chromatin occupancy of Tat and transcriptional machinery was measured by ChIP-seq, and corresponding transcriptional output from both the HIV provirus and host genome was quantified by RNA sequencing. These datasets define the baseline host-driven transcriptional state of HIV in the absence of Tat and enable direct comparison with Tat-amplified transcriptional responses.  Together, this integrated ChIP-seq and RNA-seq resource provides a quantitative framework for dissecting Tat-dependent and Tat-independent mechanisms of HIV transcriptional regulation in chromatin.

overall_design: Jurkat T cells were infected with isogenic HIV constructs expressing either functional Tat (TatWT) or lacking Tat expression (TatNull). Cells were maintained under non-stimulated conditions or treated with transcriptional stimulation as indicated. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) was performed to measure genome-wide occupancy of Tat and transcriptional machinery. In parallel, RNA sequencing (RNA-seq) was used to quantify transcriptional output from the HIV provirus and host genes.  Biological replicates were generated for each condition. ChIP-seq and RNA-seq datasets were integrated to enable quantitative comparison of Tat-dependent and Tat-independent transcriptional regulation at the HIV locus and across the host genome.

first: Chuan

first: Susana

middle: T

last: Valente


title: ZDHHC8-mediated β-catenin palmitoylation promotes WNT signaling activation and drives cisplatin resistance in osteosarcoma

first: Yangbai

last: Sun

address: No.270 Dongan Road

department: Department of Musculoskeletal Oncology

institute: Fudan University

summary: Chemoresistance remains a major challenge in osteosarcoma therapy, severely limiting the efficacy of cisplatin-based chemotherapy. Here, we identify the palmitoyltransferase ZDHHC8 as a critical determinant of cisplatin resistance and uncover a lipid modification–dependent mechanism that stabilizes β-catenin and sustains WNT signaling. ZDHHC8 expression was markedly upregulated in chemoresistant osteosarcoma tissues, and its knockdown significantly enhanced cisplatin-induced apoptosis both in vitro and in vivo. Transcriptomic profiling and functional assays revealed that ZDHHC8 depletion suppressed WNT/β-catenin signaling and diminished cancer stem cell–like properties. Mechanistically, ZDHHC8 directly interacted with β-catenin and catalyzed its C381-specific palmitoylation, which prevented proteasomal degradation and maintained protein stability. Mutation of C381 abolished β-catenin palmitoylation, resulting in reduced WNT activity and impaired stemness maintenance. Conversely, ZDHHC8 overexpression stabilized β-catenin and conferred cisplatin resistance. Collectively, our findings reveal a previously unrecognized ZDHHC8–β-catenin palmitoylation axis that governs WNT pathway activation and osteosarcoma chemoresistance. Targeting ZDHHC8 or disrupting β-catenin palmitoylation offers a promising therapeutic strategy to overcome drug resistance and improve osteosarcoma outcomes.

overall_design: RNA-seq was performed using human osteosarcoma 143B cells in a 2 × 2 factorial design to define transcriptional programs regulated by ZDHHC8 and to determine how ZDHHC8 depletion reshapes the cisplatin response. Stable cells expressing a non-targeting control shRNA (shCtrl) or ZDHHC8-targeting shRNA (shZDHHC8) were treated with vehicle or cisplatin, generating four experimental groups: Control (shCtrl + vehicle), Cisplatin (shCtrl + cisplatin), shZDHHC8 (shZDHHC8 + vehicle), and shZDHHC8 + Cisplatin (shZDHHC8 + cisplatin).


title: Sleep Homeostasis Ensembles in the Hypothalamic PVN Reprogram Systemic Fuel Utilization via Adipose Lipolysis

summary: While sleep homeostasis is fundamental, its causal contribution on systemic metabolism remains incompletely understood. By decoupling sleep homeostasis from circadian influences, this study identifies a previously unrecognized neural mechanism linking compensatory sleep to whole-body metabolism. Using a minimally confounded sleep homeostasis model, spatial transcriptomics revealed the paraventricular nucleus of the hypothalamus (PVN) as the most transcriptionally active region during rebound sleep. TRAP-tagging and functional manipulations demonstrated that PVN sleep-homeostasis ensemble neurons promote NREM sleep while simultaneously shifting whole-body energy utilization toward lipid oxidation. Activation of these neurons reduced respiratory exchange ratio, downregulated systemic glucose metabolism, and enhanced sympathetic-driven lipolysis in white adipose tissue (WAT), particularly inguinal depot. Stable isotope tracing confirmed suppressed glucose metabolic flux in WAT during recovery sleep. These findings uncover a neural substrate through which sleep homeostasis regulates peripheral energy balance, revealing a metabolic trade-off that may underlie the increased diabetes risk associated with sleep disruption.

overall_design: BacTRAP based RNA sequencing.To identify potential molecular markers of ensemble clusters in the PVN during sleep homeostasis, we compared translational profiles between PVN samples from rebound sleep and control sleep conditions. We injected an AAV virus (ROSA-STOP-L10a-bacTRAP) into the PVN region of TRAP2 mice, allowing for Cre-dependent expression of the fusion protein of the ribosomal protein L10a tagged with GFP specifically in rebound sleep ensemble. Subsequently, we harvested PVN samples from L10a-bactrap animals, and used an anti-GFP antibody to precipitate ribosomes of PVN neuronal ensembles (7 pooled animals per sample). Deep mRNA sequencing of RNA associated with immunopurified ribosomes from PVN neuronal ensembles yielded a detailed translational profile of PVN ensemble cells.


title: Loss of PMR4 callose synthase confers jasmonic acid-dependent resistance to the clubroot disease in Arabidopsis and Brassica napus

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

summary: Clubroot caused by the protist pathogen Plasmodiophora brassicae Woronin is a major disease in Brassica crops. Growing clubroot-resistant cultivars is the most effective and practical control strategy, but resistance genes can often be overcome by emerging pathotypes. In this study, we identified PMR4 as a potential host susceptibility factor that can be targeted as a novel genetic resource for durable clubroot resistance. Recessive PMR4 mutations in Arabidopsis thaliana conferred strong resistance to multiple P. brassicae pathotypes, independent of salicylic acid-mediated plant immunity. Using CRISPR/Cas9, we edited two PMR4 orthologs in the Brassica napus genome, and the resulting homozygous mutants exhibited resistance to both powdery mildew and clubroot diseases. While PMR4 is known to mediate callose deposition at wound and powdery mildew infection sites in leaves, this study reveals that P. brassicae infection induces callose deposition in Arabidopsis and B. napus roots in a PMR4-dependent manner. The Arabidopsis pmr4-1 mutation does not affect P. brassicae primary infection but blocks the pathogen entry from epidermal cells to stele in a jasmonic acid signaling-dependent manner, which is also correlated with enriched lignin-like and suberin compounds in periderm cell walls. Together, these findings establish PMR4-encoded callose synthase as a host susceptibility factor that facilitates P. brassicae secondary infection in host roots and demonstrate its potential as a gene-editing target for enhancing resistance to both powdery mildew and clubroot diseases as well as other possible biotic and abiotic stresses in Brassicaceae crops.

overall_design: RNA-seq profiling of Col-0 and pmr4-1 roots with or without the inoculation of Plasmodiophora brassicae pathotype 3H resting spores at 14 day-post-inoculation.

first: Runbang

last: Luo

first: Rui

last: Wen

first: Lipu

last: Wang

first: Tim

last: Dumonceaux

first: Wei

last: Xiao


title: GNPs-pIL-4 reprograms macrophage polarization and activates the OSM/GSNOR/ENG axis to improve angiogenesis and tissue repair in murine ischemic limbs

status: Public on Jul 03 2026

first: peng

last: zhang

state: Beijing

address: Peking University Medical Industrial Park

institute: Peking University

summary: Therapeutic angiogenesis based on gene therapies is a potential peripheral artery disease (PAD) treatment approach. Here, we developed a graphene nanoparticle-based IL-4 plasmid delivery system (GNPs-pIL-4) to reprogram macrophage polarization and activate the OSM/GSNOR/ENG axis to improve angiogenesis and tissue repair in ischemic limbs. Single-cell RNA sequencing analysis revealed that GNPs-pIL-4 treatment significantly enhanced the number and strength of intercellular communications in ischemic tissues, with enrichment of pathways associated with endothelial sprouting and neovascularization.

overall_design: Single-cell RNA sequencing of gastrocnemius muscle from murine hindlimb ischemia model with GNPs-pIL-4 treatment. Fourteen days after HLI surgery and GNPs-pIL-4 treatment, mice were euthanized, and gastrocnemius muscle tissues were harvested. Single-cell suspensions were prepared using a tissue dissociation system and single-cell transcriptome libraries were constructed using the 10x Genomics 3' single-cell RNA-seq platform.

first: Juan

last: Feng


title: Distinct Immune Signatures of Steroid Responsiveness in Childhood Nephrotic Syndrome

city: Seoul

first: Chaeyoon

last: Kim

address: 103, Daehak-ro, Jongno-gu

department: Department of Biomedical Sciences

institute: Seoul National University

summary: Idiopathic nephrotic syndrome (INS) is the most common primary glomerular disorder in children, yet the immunopathogenesis underlying steroid responsiveness remains incompletely understood. Here, we applied single-cell RNA sequencing to peripheral blood mononuclear cells obtained from three treatment-naïve children with steroid-sensitive nephrotic syndrome (SSNS) and one child with secondary steroid-resistant nephrotic syndrome (SRNS) at first relapse, all prior to immunosuppressive therapy.

overall_design: PBMC were isolated from the blood of four nephrotic syndrome children and were analyzed by single-cell RNA-sequencing (scRNAseq).


title: Diminished pro-inflammatory characteristics in murine bone marrow derived macrophages with impaired thyroid hormone receptor alpha signaling

city: Amsterdam

first: Esmée

last: Hoen

address: Meibergdreef 9

department: Department of Laboratory Medicine

country: Netherlands

institute: Amsterdam UMC

summary: Macrophages are versatile phagocytes of the innate immune system with functions ranging from pro-inflammatory to immunomodulatory. Macrophages are receptive to signals from thyroid hormones (THs). Here, we studied the role of the TH receptor (TR)α1 in macrophage function. Using wild type and transgenic mice with a mutation in the T3 binding domain of the TRα1 (TRα1PV), we generated bone marrow derived macrophages (BMDMs) and subsequently polarized them into pro-inflammatory or immunomodulatory phenotypes. The phenotype and function of the unpolarized, pro-inflammatory and immunomodulatory TRα1PV BMDMs was compared to the respective wild type BMDMs. The pro-inflammatory TRα1PV BMDMs displayed decreased pro-inflammatory markers, while marker expression of unpolarized and immunomodulatory TRα1PV BMDMs was unaltered. Glycolysis, a characteristic of proinflammatory macrophages, was reduced in all three TRα1PV macrophage phenotypes. Moreover, RNA sequencing revealed different expression profiles and alterations of biological pathways, including immune functions in all TRα1PV BMDMs phenotypes. Altogether, we observed that the TRα1PV mutation results in phenotypical and functional different BMDMs, with most striking changes in the pro-inflammatory phenotype, underlining the significance of adequate T3-TRα1 signaling in pro-inflammatory macrophage responses.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data of TRα1PV compared to wild type BMDMs. Unpolarized WT BMDMs were compared to unpolarized TRα1PV BMDMs, pro-inflammatory WT BMDMs to pro-inflammatory TRα1PV BMDMs, and immunomodulatory WT BMDMs to immunomodulatory TRα1PV BMDMs.

first: Kim

last: Falize

first: Aldo

last: Jongejan

first: Sheue-yann

last: Cheng

first: Xuguang

last: Zhu

first: Eveline

last: Bruinstroop

first: Anne

middle: H

last: van der Spek

first: Anita

last: Boelen


title: Bcl11a orchestrates multilineage integrity in aging hematopoiesis by regulating multipotent progenitor fate decisions

first: Linlin

last: Zhang

address: siping road

institute: Tongji university

summary: Aging hematopoiesis is characterized by myeloid skewing and impaired lymphoid output, a phenomenon traditionally attributed to intrinsic deterioration of hematopoietic stem cells (HSCs). Here, we demonstrate that aging-associated hematopoietic dysfunction is critically shaped at the level of multipotent progenitors (MPPs). We show that aging drives coordinated functional alterations across the MPP compartment, with expansion and reinforced myeloid output of MPP3 accompanied by functional attrition of lymphoid-primed MPP4, collectively exacerbating lineage imbalance. We identify Bcl11a as a dose-dependent regulator of MPP fate that preserves progenitor quiescence and lineage plasticity. Mechanistically, Bcl11a restrains premature myeloid activation by maintaining MPP3 quiescence through repression of the tyrosine kinase Fer, while simultaneously sustaining latent lymphoid potential via activation of the Irf8–Ebf1 transcriptional axis. Importantly, enhancing Bcl11a expression in aged mice restores balanced myeloid and lymphoid output, reprograms aging-associated transcriptional signatures, and rejuvenates multilineage hematopoietic function. Together, these findings establish Bcl11a as a central regulator of progenitor resilience during aging and identify MPPs as critical control points for preserving immune competence across the lifespan.

overall_design: To investigate the intrinsic role of Bcl11a in MPP3 function and the cell-autonomous effects of Bcl11a overexpression on wild-type MPP3 function, T1 and T2 MPP3 from KO-iMOS and WT-iMOS mice at the age of 3 months and 24 months were flow cytometry sorted for RNA-Seq analysis. To investigate the intrinsic role of Bcl11a in MPP4 function, T1 and T2 MPP4 from WT-iMOS mice at the age of 3 months and 24 months were flow cytometry sorted for RNA-Seq analysis.


title: Transcriptome analysis of molting variation in dominant trimolter silkworms, Bombyx mori

city: Ya, an

first: Qin

state: Sichuan

address: xinkang road No.46

department: College of Life Sciences

institute: Sichuan Agricultural University

summary: Silkworm (Bombyx mori) is a holometabolous insect that plays a significant economic role in the production of silk. The trimolter silkworms have garnered significant interest among sericulturists owing to their superior filament fineness, shorter larval duration, and reduced labor inputs. These traits render the trimolter silkworms suitable for specialized raw silk manufacturing. However, some individuals from trimolter strains may undergo an additional molt, resulting in tetramolter silkworms. The cause of this change is unclear and is the focus of this study. The trimolter silkworm variety ‘Guangri 3’, characterized by stable molting traits, is a bivoltine strain, though occasional individuals may exhibit increased molting number. Thus, the research subjects were the ‘Guangri 3’ trimolter silkworms raised at 25°C in spring (Group A: trimolter individuals as TA and tetramolter variants with increased moltinism as FA) and at 30°C in autumn (Group B: the trimolter individuals as TB and tetramolter variants with increased moltinism as FB). Statistical analysis revealed that the incidence rates of FA and FB were 1.10% and 16.10%, respectively. Subsequently, RNA-seq analysis was conducted on distinct groups. The results showed that: In group A (FA vs TA), 1,044 genes were upregulated and 846 were downregulated. In the group B (FB vs TB), 808 genes were upregulated and 707 were downregulated. GO and KEGG enrichmentanalyses of the differentially expressed genes (DEGs) in both FA vs TA and FB vs TB comparisons revealed pathways associated with insect molting, such as chitin catabolism, which encompassed key gene families including CYP, CPR, and Rp. Furthermore, PPI network analysis of the FB vs TB group identified hub genes (e.g., Hsp83), whose potential role in molting alteration under high temperature warrants further investigation.

overall_design: The study was conducted in two seasons: spring and autumn. During the entire rearing period, fresh and tender mulberry leaves were uniformly fed at fixed times every day. The spring group (group A) utilized diapause eggs of six moths from the silkworm variety ‘Guangri 3’, which were reared at a temperature of 25°C, 80%–90% RH (young instars, relative humidity) and 70%–80% RH (mature instars). The autumn group (group B) also utilized six moths of silkworm eggs. The environmental temperature for autumn silkworms under natural conditions is 30°C ± 2°C, 70%–90% RH. In addition, photoperiod exerts an influence on natural rearing in spring and autumn. Given the vital role of temperature on insects, the autumn group was reared at a higher temperature than the spring group and thus designated as the autumn high-temperature rearing group. Upon hatching, larvae (each from a single female moth) were reared individually (each from a single female moth) until the third instar molting stage. The moltinism morphology was investigated, and pooled head and thorax tissue (cephalothorax) samples of the ‘Guangri 3’ strain were collected. This sampling strategy was employed because JH is biosynthesized in the corpora allata and 20E is synthesized in the prothoracic glands, both of which are located in the cephalothorax. Three trimolter silkworms and three silkworms with increased molting number (hereinafter referred to as tetramolter silkworms) were collected from each of the spring and autumn groups for transcriptomic sequencing.

first: Lishan

last: Xu

first: Fan

last: Yan

first: Shijun

last: Yang

first: Han

first: Xinling

first: Zhiyong

first: Junfeng

last: Liu


title: Bcl11a orchestrates multilineage integrity in aging hematopoiesis by regulating multipotent progenitor fate decisions [ATAC-seq]

overall_design: To investigate the intrinsic role of Bcl11a in MPP3 function, T1 and T2 MPP3 from WT-iMOS mice at the age of 3 months were flow cytometry sorted for ATAC-Seq analysis.


title: Bcl11a orchestrates multilineage integrity in aging hematopoiesis by regulating multipotent progenitor fate decisions [CUT&Tag]

overall_design: To understand the molecular mechanism underlying Bcl11a function in MPP3. KO-iMOS and WT-iMOS mice bone marrow MPP3 cells were sorted for CUT&Tag libraries construction and sequencing.


title: Albiflorin Alleviates Osteoporosis through Suppression of Osteoclast Mitophagy via the Rap1a/ERK Signaling Pathway

city: Zhangjiagang

first: Cheng

last: Tang

state: Jiangsu

address: Zhugangxiang Road No.1

institute: Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine

summary:
Objectives：Dysregulated mitophagy coupled with osteoclast activation orchestrates the development and progression of osteoporosis.Although albiflorin (ALB) exhibits bone-protective effects through anti-inflammatory and antioxidant activities, its precise mechanism—particularly regarding mitochondrial regulation—remains unknown. This study therefore investigates ALB as a novel osteoclast inhibitor by examining its molecular mechanism in regulating mitophagy via the Rap1a/ERK signaling pathway.
Materials and Methods: ALB was evaluated using murine models of postmenopausal osteoporosis. Key methodologies included RNA sequencing (RNA-seq) for gene expression pathway analysis, transmission electron microscopy (TEM) for visualization of mitochondrial and autophagic structures, MitoTracker/LysoTracker co-staining for assessment of mitophagy, and Western blotting for protein signaling validation. The effects of ALB on osteoclast differentiation and bone loss mitigation were assessed both in vitro and in vivo.
Results:ALB significantly inhibited osteoclastogenesis and osteoclast differentiation, thereby effectively reducing osteoporosis in murine models. RNA-seq analysis revealed that ALB modulated mitophagy by regulating the expression of Rap1a and components of the ERK signaling pathway. Validation through TEM demonstrated suppressed mitochondrial autophagy, while MitoTracker/LysoTracker co-staining confirmed a reduction in mitophagy. Furthermore, Western blot analysis showed that ALB inhibited osteoclast activation via the Rap1a/ERK signaling axis.
Conclusion:ALB mitigates postmenopausal osteoporosis by suppressing osteoclast activation through Rap1a/ERK-dependent inhibition of mitophagy. These findings identify ALB as a promising therapeutic strategy for osteoporosis, addressing the need for safer long-term treatment options.

overall_design: Compartive gene expression profiling analysis of RNA-seq data for RAW264.7 cells under RANKL intervention and albiflorin intervention conditions

first: Jingxian

last: Yu

first: Dong

last: Sheng


title: Treatment of regenerating axolotl embryos with A-485

city: Lexington

first: Jeramiah

middle: James

last: Smith

state: KY

address: 101 Morgan Building

department: Biology

institute: University of Kentucky

summary: The drug A-485 was used to block the acetyltransferase activity of Crebbp/Ep300, resuling in inhibition of tail regeneration and alteration of transcription

overall_design: Developmental stage 42 (Bordzilovskaya et al 1989) embryos were anesthetized in 0.02% benzocaine and then administered tail amputations to remove 2 mm of the distal tail tip. Embryos were treated for seven days in either 0.1% DMSO (N = 11), 15 mM A-485 (N = 10), or 20 mM A-485 (N = 12) and then imaged using an Olympus dissecting microscope and DP28 camera. Additional embryos were subsequently treated after amputation in either 0.1% DMSO or 20 mM A-485 for 24 hours. At 24 HPA, 1 mm tail pieces were collected from embryos and pooled to prepare 3 replicate samples per treatment (12 tail tips per replicate). These samples were immediately flash frozen on dry ice and stored in a -80 C freezer until the time of RNA isolation. RNA was isolated using TRIzol (Invitrogen) and syringe needles for initial tissue disruption, and then following instructions included with a Monarch Total RNA Isolation Kit (NEB). RNA samples were submitted to a commercial vendor (Novogene) to generate approximately 25-30 million raw reads per sample on an Illumina sequencer. RNA-seq reads were aligned to the reference genome using HISAT2 v2.2.1 (Kim et al. 2019). Gene expression estimates were obtained from these alignments using StringTie v2.2.3 (Pertea et al. 2015), and differential expression analysis was conducted using the DEseq2 R package v1.42.1 (Love et al. 2014).

first: Nataliya

last: Timoshevskaya

first: Raissa

middle: F

last: Cecil

first: James

last: Schwartz

first: Adin

last: Kersch

first: S.

middle: R

last: Voss


title: Mesenteric inflammation-associated fibroblasts promote intestinal epithelial dysfunction and Crohn’s disease progression

first: Young-Ho

last: Ahn

address: 25 Magokdong-ro 2-gil, Gangseo-gu

department: College of Medicine

institute: Ewha Womans University

summary: The mesentery contributes to Crohn’s disease (CD) progression, promoting immune cell infiltration and fibrosis. Mesenteric fibroblasts, activated by pro-fibrotic cytokines such as TGF-β, stimulate fibrosis through excessive extracellular matrix (ECM) deposition, leading to intestinal thickening and stricture formation. In this study, we aim to explore the specific role of the mesenteric inflammation-associated fibroblasts in the development of CD. Mesenteric inflammation-associated fibroblasts (IAFs) and normal fibroblasts (NFs) were isolated from the mesenteries of patients with Crohn’s disease (CD) and individuals with non-cancerous colonic polyps (control samples) using magnetic-activated cell sorting. Phenotypic differences between the fibroblast populations were analyzed using cell viability, invasion, and collagen contraction assays. Co-culture systems, including transwell and 3D Matrigel co-cultures, were employed to evaluate the effects of NFs and IAFs on the behavior of colonic epithelial cancer cell lines (Caco-2 and HT-29). RNA-seq followed by gene set enrichment and gene ontology analyses identified IAF-specific genes associated with CD progression. Candidate genes were further validated by immunofluorescence staining in mesenteric tissues from CD patients. IAFs exhibited higher cell growth, wound healing, invasion, and collagen contraction activities compared with NFs. In a 3D Matrigel co-culture system, IAFs induced abnormal lumen formation and invasive structures in Caco-2 spheres. Consistently, IAFs promoted epithelial barrier disruption in a fluorescein transport assay using a transwell co-culture system. Conditioned media from IAFs upregulated mesenchymal markers in Caco-2 cells. Furthermore, transcriptomic analyses revealed enrichment of ECM organization chemokine- and cytokine-mediated signaling pathways in IAFs. These findings indicate that mesenteric IAFs actively contribute to epithelial barrier dysfunction and disease progression in CD. Targeting IAF-derived chemokines may represent a novel therapeutic strategy.

overall_design: RNA-seq of IAFs and NFs isolated from the mesentery of CD patients and non-CD control

first: Jihye

last: Park

first: Yang Hee

last: Joo

first: Eun Mi

last: Song

first: Sung-Ae

last: Jung


title: CRISPR/Cas9 Screen Reveals PRKCB-Mediated Phosphorylation of YBX1 Promotes Oxaliplatin Resistance in Colorectal Cancer

city: Hangzhou

first: Sheng

last: Biao

address: jiefang road

institute: Zhejiang University

summary: Chemotherapy resistance remains a major obstacle in colorectal cancer (CRC) treatment. To systematically identify genes conferring resistance to oxaliplatin, a first-line chemotherapeutic agent, we performed a genome-wide CRISPR/Cas9 knockout screen in the murine CRC cell line CT26. We used a library targeting 1,412 drug-related genes with 11,396 unique sgRNAs. Cells were treated with either vehicle control or oxaliplatin for 7 days under selection pressure. Genomic DNA was then harvested and the abundance of each sgRNA was determined by deep sequencing. Comparison between treatment groups revealed significant depletion of sgRNAs targeting 67 genes in oxaliplatin-treated cells, indicating their potential role in promoting survival and resistance. The top-ranked candidate, PRKCB (Protein Kinase C Beta), was subsequently validated. This dataset provides a comprehensive resource of genetic determinants of oxaliplatin resistance in CRC.

overall_design: A genome-wide CRISPR/Cas9 knockout screen was performed in CT26 cells. Cells transduced with the sgRNA library were split into two groups: one treated with oxaliplatin and the other with vehicle control (DMSO). After 7 days of drug selection, genomic DNA was extracted from both pools. The sgRNA regions were amplified and sequenced on an Illumina platform. Differential abundance analysis of sgRNAs between the two conditions was conducted to identify genes whose knockout sensitizes cells to oxaliplatin.


title: Fibrosis process activation in patients with acute cardiac rejection: A novel noninvasive diagnostic approach

city: Valencia

first: Estefanía

last: Tarazón

address: Avenida Fernando Abril Martorell 106

country: Spain

institute: Instituto de investigación Sanitaria La Fe

type: Non-coding RNA profiling by high throughput sequencing

summary: Cardiac allograft fibrosis is an important limiting factor for long-term graft survival. However, the fibrotic process operating in patients with acute cellular rejection (ACR) remains unclear. We aimed to identify serum mRNAs related to cardiac fibrosis whose relative abundance become altered in patients with ACR and to evaluate their diagnostic accuracy in detecting rejection episodes. A total of 40 serum samples from recipients of transplants undergoing routine endomyocardial biopsies were included in an RNA sequencing analysis that included 28 diagnosed with ACR (grade 1R, n=16; and grade ≥2R, n=12) and 12 without cardiac rejection. We detected several altered mRNAs associated with fibrosis in patients with ACR. Specifically, the activators of fibroblasts and myofibroblasts (TNS1, FAP and ACTA2; p<0.05), TGF-β signaling (TGFBR1 and JAK1; p<0.05) and WNT signaling (WNT7A and WLS; p<0.01) pathways showed significant differences in their relative abundance when we compared grade ≥2R ACR and/or grade 1R ACR groups with the nonrejection group. Further, TNS1 and WLS presented an area under the curve value >0.90 for identifying patients with moderate and severe grades of cardiac rejection. In conclusion, we found alterations in the relative abundance of circulating activators of fibroblasts and myofibroblasts, such as FAP or ACTA2, as well as in major profibrotic pathways, including TGF-β and WNT signaling, especially in clinically relevant cardiac rejection. These findings may contribute to improving the surveillance of patients with cardiac transplant and provide new therapeutic strategies for targeting fibrosis. Future studies in larger cohorts are needed to better understand the potential impact of confounding variables.

overall_design: We analyzed 40 human serum samples from heart transplant patients diagnosed with acute cellular rejection (grade 1R, n=16; and grade ≥2R, n=12) and 12 without cardiac rejection.

first: Esther

last: Roselló-Lletí


title: Aortic Single-Cell Transcriptome Analysis Reveals ApoE Isoform-Specific Effects in Vascular Disease Modulation

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: University of Cincinnati, 160 Panzeca Way

institute: University of Cincinnati

summary: The human APOE gene is polymorphic with 3 major alleles that encode apolipoprotein (apo) E2, apoE3, and apoE4. Both apoE2 and apoE4 are associated with increased atherosclerosis risk. This study uses Human APOE2, APOE3, and APOE4 gene replacement mice and scRNA-seq to delineate the mechanisms underlying this association, with a focus on how the various apoE isoforms influence the cell repertoire in the vessel wall.

overall_design: Human APOE2, APOE3, and APOE4 gene replacement mice were fed a Western type high fat-cholesterol diet. Plasma lipid levels and atherosclerosis were assessed after 16 weeks. Single cells were isolated from the aorta for single cell-RNA sequencing to determine cell composition.

first: David

middle: Y

last: Hui

first: Jeyashree

last: Alagarsamy

first: April

last: Haller

first: Anja

last: Jaeschke


title: CD44 antagonizing oHSV promotes the formation of tertiary lymphoid structures and improves anti-tumor immunity

city: Tuscaloosa

first: Sergei

last: Bombin

state: AL

address: 739 University Blvd

institute: The University of Alabama

summary: Oncolytic HSV (oHSV) therapy is currently approved for melanoma (in USA and EU) and recurrent brain tumors (conditional approval in Japan). To understand opportunities to improve therapeutic index, we analyzed transcriptomic changes in patients with recurrent brain tumors before and after treatment with CAN-3110. Gene set pathway analysis showed a significant enrichment of glycosaminoglycan (GAG) synthesis and extracellular matrix (ECM) interactions in patients after oHSV treatment. CD44 is a cell surface receptor that engages with receptors and also with ECM to orchestrate cell-ECM interactions. To evaluate the significance of the multiple CD44 regulated ECM interactions during virotherapy, we created an oHSV that encodes for the secreted extracellular CD44 (Ox44) which functions as a decoy receptor to inhibit cell-ECM interactions. Treatment with Ox44 also destabilized SLC7A11 (xCT) inducing oxidative stress and inhibiting antiviral STING signaling in infected tumor cells. Interestingly the ensuing increased viral burst and immunogenic cell death amplified innate immune activation in immune cells. This correlated with the induction of inflammatory cytokines like interferon (IFN) and IL-1 and the formation of tertiary lymphoid structures (TLS) in intracranial tumors. Single cell sequencing uncovered that Ox44-treated tumors had increased antigen presentation and increased T cell diversity and anti-tumor efficacy. To our knowledge, this is the first report to show that CD44 presents a barrier to both oncolytic virus replication as well as anti-tumor immunity.

overall_design: CD45+ immune cells isolated from 005 GSC tumor bearing hemisphere of C57BL/6 mice 5 days post oHSV treatment with or without Ferrostatin-1 and analyzed using sc-seq.

first: Upasana

last: Sahu

first: Matthew

last: Mullarkey

first: Kimberly

middle: A

last: Rivera-Caraballo

first: Adam

last: Chadli

first: Tae

last: Lee

first: Rafal

last: Pacholczyk

first: Ravindra

last: Kolhe

first: Michael

last: Caligiuri

last: Markert

first: Bangxing

last: Hong

first: Balveen

last: Kaur


title: The degradation of maternal RNA-binding protein 4E-T regulates translational activation to ensure maternal-to-zygotic transition in mouse embryos

city: Nanjing

first: Pinhua

last: Wang

address: 101 Longmian Avenue, Jiangning District, Nanjing.

institute: Nanjing Medical university

summary: The maternal-to-zygotic transition (MZT) is essential for early embryonic development, comprising zygotic genome activation (ZGA) as well as the degradation of maternal RNAs and proteins. Current research on MZT has primarily focused on the maternal activators, while the role of repressors in this process remains largely unexplored. In our study, we inhibited protein degradation at the one-cell stage using the proteasome inhibitor MG132 and observed impaired pre-implantation development and defective ZGA. Proteomic analysis of MG132-treated embryos showed that significantly up-regulated proteins in abundance were enriched for RNA-binding proteins (RBPs). Further functional screening highlighted one critical factor, 4E-T (EIF4ENIF1), whose overexpression caused two-cell stage arrest and failure of ZGA initiation. Moreover, the abnormal accumulation of 4E-T repressed translational activation and decreased ZBED3, KDM4A, etc., key factors expression in 1-cell embryo, which connected with interactions of 4E-T with eIF4E and eIF4E1B. These findings suggest that specific maternal RBP may act as repressors that require precise degradation post-fertilization to relieve translational repression and ensure successful MZT.

overall_design: For the transcriptome, we selected seven stages of oocyte and embryo when we treated embyo with MG132 and selected four stages of embryo when we overexpressed 4E-T.For the Ribo-seq of 4ET-overexpressing embryo, only late 1-cell stage embryo was used.

first: Siqi

first: Haojie

last: Yin

first: Maosheng

last: Ye

first: Qiang

first: Yue

last: Hu

first: Ran

last: Huo


title: Hormone-dependent protection against oxidative stress in uterine leiomyoma

city: Chicago

first: J. Julie

last: Kim

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: Context. Uterine leiomyomas exist in a chronically pro-oxidant environment characterized by reduced antioxidant capacity, yet they persist and grow, suggesting the activation of adaptive stress-tolerance mechanisms. Although estrogen and progesterone are central drivers of leiomyoma growth, their role in regulating mitochondrial function under oxidative stress remains incompletely understood. Objective. To investigate how estrogen and progesterone signaling modulate oxidative stress–induced transcriptional programs and mitochondrial metabolic function in uterine leiomyoma cells. Design. Primary patient-derived leiomyoma spheroids were exposed to paraquat-induced oxidative stress in the presence of estradiol, progestins, or hormone receptor antagonists. Transcriptomic responses were assessed by RNA sequencing followed by differential expression and gene set enrichment analyses. Functional mitochondrial metabolism was evaluated using Seahorse extracellular flux assays, and cellular outcomes including senescence and cell death were quantified. Patients. Uterine leiomyoma tissues were obtained from patients undergoing hysterectomy, and primary patient-derived leiomyoma cells were used to generate three-dimensional spheroid cultures. Results. Estradiol and progesterone modulated oxidative stress–responsive transcriptional programs associated with senescence, apoptosis, and mitochondrial regulation. Hormone receptor antagonism induced the most pronounced transcriptomic disruption and was associated with increased senescence and cell death. Consistent with these findings, Seahorse analyses demonstrated that hormonal signaling preserved mitochondrial maximal respiration and spare respiratory capacity under oxidative stress, whereas hormone blockade impaired mitochondrial reserve capacity without compensatory glycolytic upregulation. Progesterone receptor isoform–specific effects further supported a role for differential PR signaling in regulating mitochondrial adaptability. Conclusions. Estrogen and progesterone promote mitochondrial adaptability in leiomyoma cells, enabling survival under sustained oxidative stress. These findings identify mitochondria as a key mediator of hormone-dependent stress resilience and highlight mitochondrial metabolism as a potential therapeutic vulnerability in leiomyomas.

overall_design: RNA-seq profiling of uterine leiomyoma spheroids treated with estradiol and R5020, anti-hormones, ICI and ZK, and paraquat for 96h.

first: Ji-Yong


title: Inflammatory Monocytes Constrain YAP-Induced Cell Proliferation

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Inflammatory Monocytes Constrain YAP-Induced Cell Proliferation [MERFISH]

summary: YAP and its paralog, TAZ are transcriptional co-activators of the Hippo pathway that regulate cell growth. Their structural distinctiveness suggests important independent functional differences. To investigate this further, we generated YAP- and TAZ-predominant clones in the liver and followed their long-term behavior. YAP clones rapidly de-differentiate cells into a stem cell-like state with inflammatory immune cell recruitment followed by their clearance. In contrast, TAZ clones promote an anti-inflammatory immune environment resulting in their long-term maintenance, massive organ growth and increased mortality. YAP clones recruit inflammatory blood-derived monocytes, which if inhibited permits YAP clonal growth. Consistent with these results, YAPHigh colorectal cancer (CRC) patients had a 67% 5-year survival rate, while TAZHigh CRC patients did not survive to 5 years. Similar trends were seen in hepatocellular carcinoma patients. These findings underscore the importance of understanding the intrinsic differences in YAP and TAZ biology as independent drivers of disease.

overall_design: MERFISH on mice liver on different conditions and time points: wild-type (WT); YAP 1 weak; YAP 4 weaks; Lats 1 weak; Lats 4 weaks

first: Serrena

last: Singh

first: Nareh

last: Tahmasian

first: Jia-Jun

first: Wenjia

first: Lucas

last: Haas

first: Silvia

first: Brian

last: Kalish

first: Dean

last: Yimlamai


title: Inflammatory Monocytes Constrain YAP-Induced Cell Proliferation [bulk RNA-seq]

overall_design: bulk RNA-seq on mouse liver tissue, with wild type, Lats KO, and Yap over expression


title: Inflammatory Monocytes Constrain YAP-Induced Cell Proliferation [snRNA-seq]

overall_design: snRNA-seq on mouse liver tissue, with wild type, Lats, and Yap at different time points


title: Repurposing Trazodone for Alzheimer's Disease to Modulate Soluble ST2 Levels and Alleviate Alzheimer's Pathology

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

summary: Alzheimer’s disease (AD) is a multifactorial disorder involving various pathological mechanisms, such as amyloidosis, immune dysfunctions and synaptic impairments, which are important therapeutic targets. Repurposing drugs to target these mechanisms offers a promising approach to reduce the costs and duration of drug development. Notably, genetic studies underscore the role of microglial clearance of amyloid-beta (Aβ) in AD pathogenesis, with soluble ST2 (sST2) identified as a disease-modifying factor that impairs microglial clearance functions. In this study, we investigated drug repurposing opportunities to modulate sST2 levels and alleviate AD pathologies. Unbiased screening of common medications in AD patients and validation in model systems identified trazodone, an anti-depressant used to treat major depressive disorder, as a leading negative regulator of sST2. Trazodone primarily regulates sST2 expression through its antagonistic effects on adrenergic signaling. Importantly, trazodone treatment enhanced microglial interaction with Aβ and alleviated Aβ pathology in the APP/PS1 transgenic mouse model of AD. Furthermore, trazodone treatment reduced neurodegeneration and rescued synaptic deficits in APP/PS1 mice. Comprehensive molecular profiling of APP/PS1 mouse brains showed that trazodone restores the expression of synaptic proteins involved in synaptic integrity and plasticity. Collectively, these findings demonstrate that trazodone is a promising repurposing agent for AD that targets the underlying immune dysfunctions and synaptic deficits.

overall_design: Trazodone-treated APP/PS1 mouse cortices

first: Nancy Yuk-yu

last: IP

first: Daniel Yew Kit

last: WONG


title: Single cell RNAseq of Tumour Endothelial Cell from response or partial response tumors to Doxorubicin treatment

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: To investigate the effects of Dox treatment on Tumor Endothelial Cell (TEC) dynamics at single-cell resolution, we carried out 10X single-cell RNA sequencing. Doxorubicin exposure triggers a significant reprogramming of the tumour vasculature, substantially altering the angiocrine landscape and shaping treatment outcomes

overall_design: MMTV tumours were treated with Doxorubicin.  Placebo, acute treated, or chronic treated showing response or partial response tumours, were digested andTEC enrichment was achieved combining MACS and fluorescence-activated cell sorting (FACS) for CD31+CD45- viable cells. Cells were loaded and processed on the 10X Chromium Controller using the CG000331 Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) User guide enabled us to process the gene expression and immune profiling of the samples. Each library can be recognized by its unique sample index. Sample sequencing was performed at Novogene using a Novaseq 6000 platform and PE150 sequencing strategy.

first: Jesus

last: Gomez-Escudero

first: Gabriela

last: D'Amico

first: KM

last: Hodivala-Dilke


title: Activating transcription factor 6α governs stress-adaptive pancreatic β-cell mass expansion through the coordination of proliferation and survival

city: Kyoto

first: Takaaki

last: Murakami

state: 選択してください

address: 25 Shogoin-Kawahara-cho, Sakyo-ku

department: Department of Diabetes, Endocrinology and Nutrition

institute: Kyoto University Graduate School of Medicine

summary: We have employed a single cell RNA sequencing analysis using 10x Genomics scRNA-seq to investigate the role of ATF6α in pancreatic β-cells under chronic metabolic stress.ATF6α initiates a key branch of the unfolded protein response and has been implicated in β-cell survival, apoptosis, insulin secretory function, and glucose homeostasis. This study provides new insights into how ATF6α coordinate stress-adaptative transcriptional networks of β-cells leading to β-cell mass expansion under chronic metabolic stress, that contributes to the better understanding of preservation strategy of functional β-cell mass in diabetes.

overall_design: Pancreatic islets were isolated from 22-week-old ATF6αfl/fl and ATF6αβKO mice under normal or high-fat diet feeding and analyzed using scRNA-seq.

first: Daisuke

last: Otani

first: Sho

last: Sekito

first: Yasuhiro

last: Murakawa

last: Yabe


title: ZAK-alpha is a sensor of mRNA stasis at the ribosomal exit channe

city: Lausanne

first: David

last: Gatfield

address: Genopode building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary: Despite growing interest in the ribotoxic stress response (RSR), it remains unknown how the upstream p38 and JNK-activating MAP3 kinase ZAK-alpha senses translational impairment. Combining Alphafold3 prediction and RNA crosslinking and immunoprecipitation (CLIP), we uncover that ZAK-alpha dynamically monitors the mRNA exit channel of elongating ribosomes for mRNA stasis. This is accomplished by ZAKa via its direct interactions with the ribosomal proteins RACK1 and RPS27 as well as with the 18S rRNA helix-26. In this conformation, four mRNA-binding peptides in ZAK-alpha span across the path of ribosome-exiting mRNA. Progressive elongation effectively threads ZAK-alpha off the ribosome, while mRNA stasis stabilizes the interaction allowing for kinase activation. Prolonged binding of ZAK-alpha to slow_x0002_elongating, stalled and collided ribosomes is associated with sequestration of the inhibitory SAM domain on RACK1. We propose that compromised ribosome processivity constitutes a common ribotoxic stress signal and that ZAK-alpha is a ribosome collision-agnostic sensor of such perturbations

overall_design: Ribosome profiling from U2OS cells mock-treated or incubated for 15 min with 0.19 µM or 76 µM of anisomycin.

first: Sébastien

last: Chamois

first: Virginie

last: Ricci

first: Simon

last: Bekker-Jensen


title: Mapping the ISR Landscape in Cognitive Disorders via single-cell multi-omics

city: San Francisco

first: Kristof

last: Torkenczy

state: CA

address: 1437 S Van Ness Ave, apt 1

institute: Altos Labs

summary: Persistent activation of the integrated stress response (ISR) is a central driver of cognitive decline in both neurodevelopmental and neurodegenerative disorders. However, the cell-type-specific mechanisms underlying these deficits remain poorly understood. Here, by integrating single-cell RNA-seq and single-cell ATAC-seq, we generated an ISR atlas of the brain using Ppp1r15bR658C mice, a clinically relevant model of intellectual disability characterized by selective and persistent ISR activation. Unexpectedly, our analysis revealed that distinct brain cell types differentially engage transcriptional and chromatin remodeling programs. Notably, selective deletion of the major ISR downstream effector ATF4 in GABAergic neurons—but not in glutamatergic neurons—impacts ISR-mediated cognitive decline in Ppp1r15bR658C mice, demonstrating that different neuronal subtypes have different dependencies for ISR effectors. Finally, we defined a molecular single-cell signature of persistent ISR activation that serves as a metric of ISR-mediated cellular vulnerability, and as a biomarker for cognitive dysfunction across human cogntive disorders. These findings dissect the cell-type-specific architecture of the ISR in the brain, providing new insights into the biological mechanisms driving ISR-dependent cognitive decline.

overall_design: We performed single-cell (10X) multi-omic sequencing (scRNA-seq and scATAC-seq) of cortical tissue from Wild Type (WT) and Ppp1r15b-R658C mice. Samples were processed in two batches (n = 14 total), balanced by genotype and sex (7 WT and 7 Mutant).

first: Lucas

middle: C

last: Reineke

first: Sean

middle: W

last: Dooling

first: Benjamin

last: Henderson

last: Yang

first: Dongze

last: He

first: Richard

last: Myers

first: Peter

last: Walter

first: Stefka

last: Tyanova

first: Mauro

last: Costa-Mattioli


title: Prime Editing Enables Isogenic Modeling of PNPLA3-I148M-Associated Lipotoxicity in Hepatocytes

city: Yufu

first: Takuro

last: Uchida

state: Oita

address: 1-1 Idaigaoka, Hasama

institute: Oita University

summary: We demonstrate that prime editing enables a precise approach for modeling PNPLA3-I148M in human hepatocytes, offering a platform to investigate genotype-specific cellular responses. By combining precise genome editing with human cell modeling, this study provides new insight into the biology of a key risk allele and establishes a platform for personalized therapeutic strategies targeting genetically defined subgroups of liver disease.

overall_design: We generated HepG2 cell lines in which the PNPLA3-I148M genotype was edited to CC, GC, or GG. Using RNA-seq, we analyzed transcriptional changes in each genotype in response to palmitic acid treatment.

first: Haruna

last: Noguchi

first: Naoki

last: Wakita

first: Mitsumasa

last: Takenaga

first: Tetshushi

last: Sakuma


title: Complement Protease C1s Drives Immunosuppression in Mesenchymal Glioblastoma by Rewiring Microglia Metabolism

city: Guangzhou

first: Wang

last: Yinglun

address: 15th Floor, School of Basic Medical Sciences

institute: Southern Medical University

summary: The mesenchymal (MES) subtype of glioblastoma (GBM) exhibits a highly immunosuppressive tumor microenvironment (TME) and poor prognosis, but the underlying mechanism remains largely unclear. Herein, we demonstrate that the MES-GBM cells-derived complement protease C1s plays a crucial role in suppressing anti-tumor immunity and fostering resistance to immunotherapy in GBM. Complement components C1s and C1r are highly expressed in MES-GBM via the IL-1β/NF-κB signaling pathway. C1s binds to FGFR1 on microglial cells and cleaves FGF2, thereby inhibiting the FGFR1 pathway. This inhibition promotes mitochondrial oxidative phosphorylation and M2 microglial polarization. Depletion of C1s in MES-GBM cells restores CD8+ T cell anti-tumor immunity and inhibits GBM tumorigenesis. Furthermore, the inhibition of C1s with BCX1470 reduces tumor growth and enhances GBM sensitivity to anti-PD-L1 immunotherapy in mice. Therefore, our study reveals the pivotal function of C1s in MES-GBM immunosuppression and immunotherapy resistance, indicating a promising therapeutic target for GBM.

overall_design: RNA-seq profiling of HMC3 cells following treatment with the C1s-CM or control

first: Aidong

last: Zhou

first: Shangbiao

last: Li

first: Yuxin

last: Xie

first: Yinglun

last: Wang


title: Muscone eliminates sepsis through promotes mitochondrial autophagy during NLRP3 inflammasome activation

city: hangzhou

first: Ziwei

last: Yan

state: zhejiang

address: zhejiang university

institute: zhejiang university

summary: Musk from male deer (genus Moschus) is used in traditional Chinese medicine for thousands of years due to its anti-inflammatory effects. Muscone, as the main substance of musk, is used in chronic inflammation after myocardial infarction and susceptibility to ventricular arrhythmia by means of controlling inflammation. And previous studies reveal that muscone has a bioactivity of anti-NLRP3 inflammasome activation especially. However, how muscone suppress NLRP3 inflammasome activation is still unclear. In the current study, LPS-primed peritoneal macrophages were employed for validation of muscone suppressing NLRP3 inflammasome activation in vitro. Secondly, we found the occurrence of mitophagy in muscone treatment group by means of RNA-seq. Thirdly, we conducted fluorescence co-localization and electron microscopic analysis to verify whether muscone promote mitophagy during NLRP3 inflammasome activation. Next, we used LPS-induced sepsis mice to examine muscone promoting mitophagy in vivo. Finally, we further inquired the target of muscone promoting mitophagy with help of docking tools. We found that muscone suppressed NLRP3 inflammasome activation both in priming and activation stages in vitro. For priming stage, muscone downregulated the production of NLRP3 and pro-IL-1β with inhibiting NF-κB signaling pathway. For activation stage, muscone disturbed assembly of NLRP3 inflammasome with suppressing ASC oligomerization, interaction of ASC-pro-caspase1. Based on RNA-seq data, we speculated that muscone may promote mitophagy during NLRP3 inflammasome activation. Then we found evidences that muscone promoted mitophagy both in NLRP3 inflammasome activated macrophages and LPS-induced sepsis mice. Finally, molecular docking results displayed that muscone had strong hydrophobic interaction with TSPO, which may one of reasons for muscone promoting mitophagy. Muscone promoted mitophagy both in NLRP3 inflammasome activated macrophages and LPS-induced sepsis mice. Muscone shows a superb potential as a NLRP3 inflammasome inhibitor and a mitophagy agonist for further optimization of structure and application in clinic in trap future.

overall_design: Gene expression profiling analysis of RNA-seq data from LPS-primed peritoneal macrophages which were treated with muscone for 0.5 h prior to ATP.

first: Yufei

first: Jing

last: Qian


title: METIMMOX: Colorectal Cancer METastasis - Shaping Anti-tumor IMMunity by OXaliplatin

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231

summary:
This study aims to determine the efficacy, safety, and tolerability of the sequential addition of immune-modulating therapy to standard-of-care therapy of microsatellite-stable (MSS)/mismatch repair-proficient (pMMR) metastatic colorectal cancer (mCRC).
Patients with MSS/pMMR-mCRC harbor tumor that can be transformed into an immunogenic disease by short-course oxaliplatin-based therapy, and may thereby benefit from the addition of immune-modulating therapy to improve outcome of the current oxaliplatin-based standard-of-care. Primary objective: To determine progression-free survival (PFS), in terms of failure of treatment strategy, of sequential treatment with the Nordic FLOX (5-Fluorouracil, oxaliplatin and leucovorin) regimen and nivolumab compared with the standard-of-care Nordic FLOX regimen in previously untreated MSS/pMMR-mCRC. Secondary objectives: To determine safety and tolerability of sequential treatment with the Nordic FLOX regimen and nivolumab compared with the standard-of-care Nordic FLOX regimen. To monitor and compare quality-of-life (QoL) alterations during therapy courses.

overall_design: RNA-seq profiling.

first: Paula Anna

last: Bousquet

first: Kjersti

last: Flatma

first: Anne Hansen

last: Ree

first: Sebastian

last: Meltzer


title: Transcriptomics Identifies Mild Hyperthermia-Conditioned Tumor Supernatant as an Inducer of HepG2 Maturation

city: Shijiangzhuang

first: li

last: Zheng

address: 河北省石家庄市中山东路361号

institute: Hebei Medical University

summary: This study aimed to explore whether tumor supernatant (TSN) under mild hyperthermia induces the transformation of HepG2 cells into mature hepatocyte-like cells and to identify the underlying mechanisms involved in this process. HepG2 cells were treated at a mild hyperthermic temperature of 42.5°C for 60 minutes, and the resulting supernatant was collected and labeled as 42.5TSN. As a control, HepG2 cells were also treated at a normal temperature of 37°C for 60 minutes, and the supernatant was collected and labeled as 37TSN. The collected TSN was then concentrated and applied to untreated normal HepG2 cells to detect differential gene expression.

overall_design: This study included two groups: an experimental group (42.5TSN) and a control group (37TSN). Each group consisted of three independent biological replicates using the human hepatocellular carcinoma cell line HepG2, resulting in a total of six samples.

first: Li

first: Yan

middle: N

first: Yi

last: Ding

first: Yu

last: Ma

first: Xin

first: Jins

last: Qi

first: Jian

last: Liu


title: The extra-terminal domain drives the role of BET proteins in transcription -- SLAM-seq following 25 min depletion of Bdf1/Bdf2 and overexpression of the Bdf1 ET domain

city: Oklahoma City

first: John

middle: B

last: Ridenour

state: OK

address: 825 NE 13th St.

department: Cell Cycle and Cancer Biology Research Program

institute: Oklahoma Medical Research Foundation

summary: BET proteins facilitate transcription of most eukaryotic genes, but the specific mechanisms by which BET proteins perform their functions remain poorly understood. As chromatin readers, BET proteins use their tandem bromodomains to interact with acetylated lysine residues on histones and other protein partners. However, recent findings illustrate that bromodomain activity does not fully explain the role of BET proteins in transcription, highlighting the significance of other BET protein domains. We evaluated the importance of all conserved domains of BET proteins and determined that the extra-terminal (ET) domain is essential for cell viability, genome-wide transcription and BET protein chromatin occupancy. Furthermore, we provide evidence that the ET domain performs these functions by serving as a hub for interactions with other factors involved in transcription regulation. Our findings expand current understanding of the complex biology of BET proteins and suggest a potential mechanism by which cells can bypass bromodomain inhibition in pathologic states.

overall_design: Saccharomyces cerevisiae cells were grown in YPD medium. Cultures were treated with 3-indoleacetic acid (IAA) for 25 min to degrade target proteins then treated with 4-thiouracil (4tU) for 4 min to label newly transcribed RNA. Cells were fixed in cold methanol and stored at –80°C. Total RNA was purified under reducing conditions and treated with iodoacetamide for 15 min to alkylate 4tU-labeled RNA. 3ʹ mRNA-seq libraries were constructed and sequenced on a NovaSeq 6000 (Illumina) at the Oklahoma Medical Research Foundation Clinical Genomics Center. Paired-end 150 bp reads were processed using fastp, bbduk, and SLAM-DUNK. A minimum of three biological replicates were collected in all experiments.

first: Iwona

last: Pasionek

first: Agnieszka

last: Machowska

first: Magdalena

last: Donczew

first: Kevin

last: Boyd

first: Michael

last: Kinter

first: Rafal


title: The extra-terminal domain drives the role of BET proteins in transcription


title: The extra-terminal domain drives the role of BET proteins in transcription -- SLAM-seq following 3 h depletion of Bdf1/Bdf2 and expression of Bdf1 variants

overall_design: Saccharomyces cerevisiae cells were grown in YPD medium. Cultures were treated with 3-indoleacetic acid (IAA) for 3 h to degrade target proteins then treated with 4-thiouracil (4tU) for 6 min to label newly transcribed RNA. Cells were fixed in cold methanol and stored at –80°C. Total RNA was purified under reducing conditions and treated with iodoacetamide for 15 min to alkylate 4tU-labeled RNA. 3ʹ mRNA-seq libraries were constructed and sequenced on a NovaSeq 6000 (Illumina) at the Oklahoma Medical Research Foundation Clinical Genomics Center. Paired-end 150 bp reads were processed using fastp, bbduk, and SLAM-DUNK. A minimum of three biological replicates were collected in all experiments.


title: The extra-terminal domain drives the role of BET proteins in transcription -- SLAM-seq following 25 min depletion of Bdf1/Bdf2 and expression of Bdf1 variants


title: NUDT21 CUT&Tag in neuroblastoma

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

summary: Alternative polyadenylation (APA) generates mRNAs with distinct 3′-untranslated regions (3′ UTRs) to regulate post-transcriptional gene expression and is critical in many tumors. However, the role of alternative 3′ UTRs in neurolastoma (NB) remains elusive. Here, we show that NUDT21 knockdown inhibits NB cell proliferation, induces cycle arrest/apoptosis in vitro, and suppresses xenograft growth in nude mice. Mechanistically, NUDT21 silencing triggers global APA dynamics, with ∼85% of APA genes switching to proximal poly(A) sites, shortening 3′ UTRs. Integrative PAS-seq/RNA-seq analyses reveal that NUDT21 regulates E2F targets (e.g., MKI67) via APA. Additionally, NUDT21 occupies gene regulatory regions to directly activate E2F target transcription. Our findings demonstrate NUDT21 sustains NB proliferation through dual APA-dependent and APA-independent mechanisms, highlighting targeting NUDT21 or its downstream pathways as a promising therapeutic strategy.

overall_design: CUT&Tag profiles of SK-N-BE(2) cells NUDT21 were generated by CUT&Tag sequencing, in double, using Illumina NovaSeq X plus.

first: Yang

last: Yang

last: Pan


title: Plastic additives differentially affect the transcriptome of MCF-7 breast cancer cells

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: Humans are exposed to chemicals leaching from plastics, yet many remain data-poor and lack toxicological evaluation. High-throughput transcriptomics (HTTr) offers a scalable approach to screen chemicals of concern and derive mechanistic insights for human health risk assessment. We applied HTTr in MCF-7 breast cancer cells to evaluate plastic additives and dyes effects. Transcriptomic points of departure (tPODs) were derived from global gene perturbations, pathway-specific, and estrogen receptor α (ERα)–specific measures of gene expression. Transcriptomic biomarkers were also used to assess ERα activity and stress responses. Most plastic additives showed similar toxicological potencies, with the majority producing tPODs within one order of magnitude. Bisphenol K (BPK) was the most potent chemical tested, activating ERα at the lowest concentrations, followed by plastic additive 08 (PA08), and bisphenol A (BPA). Despite similar potencies, transcriptomic biomarkers revealed mechanistic differences: plastic additives that shared similar chemical features as BPA activated the ERα, whereas several others with different functional groups inhibited the biomarker. Pathway and upstream regulator analyses further showed that BPA-like plastic additives perturbed ERα–related pathways, while other plastic additives enriched fewer and often of opposing directionality gene sets. At the highest concentrations tested, many plastic additives also activated stress biomarkers and inhibited proliferation. These findings suggest that while many plastic additives display broadly similar in vitro potencies, they diverge in ERα regulation and downstream pathways. This study demonstrates the reproducibility and utility of HTTr for chemical screening, supports grouping of ERα-active plastic additives for read-across, and highlights the need for further screening of plastic additives.

overall_design:
MCF-7 cells were exposed to 12 chemicals across eight concentrations (0.001 – 50 µM) for 48 h, as well as BPA, a solvent control (0.1% DMSO) and a positive control (17β-estradiol, 0.1 and 1 nM).
After chemical exposure, samples underwent TempO-Seq library building and NextGeneration sequencing.
Gene expression data underwent benchmark concentration modeling to derive transcriptomic points of departure to compare toxicological potency and compare mechanism of action by doing upstream regulator and biological pathway analysis.

first: Geronimo

last: Matteo

first: Dave C.

last: Eickmeyer

first: Lauren M

last: Bradford

first: Matthew J

first: Andrew

last: Williams

first: Tara

last: Barton-Maclarenm

first: Christopher J

last: Corton

first: Carole L

last: Yauk

first: Ella

last: Atlas