title: Microsomal triglyceride transfer protein restricts progesterone production in Leydig Cells by regulating SREBP2 activity [RNA-Seq]

overall_design: RNA sequencing of 48h old culture of wildtype and MTP knockout MA10 cells after stimulation with 8-BrcAMP for 3h

middle: J


title: ATF7ip inhibits the tumor immune response by promoting terminal CD8+ T cell Exhaustion

status: Public on Apr 13 2026

city: San Francisco

first: Jun Hyung

last: Sin

state: CA

address: 513 Parnassus Ave S-1076

department: Pediatrics

country: USA

institute: University of California, San Francisco

type: Expression profiling by high throughput sequencing

summary: CD8+ T cell exhaustion limits the immune response to tumors because of ineffective T cell effector functions. Thus, therapies that inhibit T-cell exhaustion are critical for optimizing cancer treatment. Recent studies have implicated epigenetic proteins in T-cell exhaustion. Here, we identified activating transcription factor 7 interacting protein (ATF7ip) as an epigenetic protein critical for inducing T cell exhaustion. Loss of Atf7ip in CD8+ T cells results in decreased terminal exhaustion and increased numbers of progenitor-exhausted cells in both chronic viral infections and cancer. Owing to decreased exhaustion, Atf7ip-deficiency in CD8+ T cells leads to an enhanced immune response to tumors. Mechanistically, ATF7ip functions to stimulate the deposition of repressive H3K9me3 at critical immune-effector gene loci, such as Il7r and Il2 leading to enhanced exhaustion. Our data suggest that ATF7ip may be a rational target for deletion in adoptive T-cell therapies to reduce CD8+ T-cell exhaustion.

overall_design: TCRb+CD3+ T cells from 3-4 Atf7ip-sufficient and Atf7ip-deficient mice were pooled and FACS sorted into 1.5 ml tubes containing DMEM with 2 FBS. About 20,000 cells per 100 ul were sent out for 10X sequencing. Single cells were captured using the 10X chromium microfluidics system and barcoded and sequenced on the Illumina NovaSeq.

first: Sujit

last: Kashyap

first: Michael

middle: R

last: Waterfield


title: H3K9me3 controls epidermis development by repressing RNA Pol II activity on key promoters and enhancers [bulk RNA-Seq]

city: Ithaca

first: Chris

middle: Ke

last: Bai

state: NY

address: 526 Campus Rd

department: MBG

institute: Cornell University

summary: Histone H3 lysine 9 trimethylation (H3K9me3) is a heterochromatin mark important for silencing repetitive DNA elements and for repressing lineage-inappropriate genes during early murine development, but its role in later organogenesis remains understudied. Here, we simultaneously target three histone methylases, Suv39h1, Suv39h2 and Setdb1, to deplete H3K9me3 specifically in developing epidermis. H3K9me3 loss blocks epidermis morphogenesis, resulting in defective cell differentiation, impaired barrier function, disrupted hair follicle formation, and failed Merkel cell specification. Single cell transcriptomic analysis reveals epidermal cells with mixed lineage identity and perturbed cell-type specific gene programs, including cell cycle, extracellular matrix, cytoskeleton, and metabolism. Using our recently developed approach, PReCIS-seq, we present the first cell-type specific, genome-wide landscape of transcriptionally engaged RNA polymerase II (RNA Pol II) in intact tissue following H3K9me3 depletion. We find that H3K9me3-enriched islands restrict inappropriate RNA Pol II activity at select developmentally regulated enhancers and promoters. This work highlights the indispensable role of H3K9me3, mediated by its three major histone methyltransferases, in regulating lineage diversification and developmental progression during mouse organogenesis.

overall_design: Suv39h1,SUv39h2,Setdb1 triple knockout was induced in embryonic basal cells to deplete H3K9me3 and then bulk RNA-seq profiling was performed on sorted Epcam+α6+ double positive basal cells at E16.5

middle: K

first: Tudorita

last: Tumbar


title: H3K9me3 controls epidermis development by repressing RNA Pol II activity on key promoters and enhancers [CUT&Run]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Suv39h1,SUv39h2,Setdb1 triple knockout was induced in embryonic basal cells to deplete H3K9me3 and then CUT&RUN was performed on sorted Epcam+α6+ double positive basal cells at E15.5, using H3K9me3 antibodies and IgG as control


title: Maternal IntS11 primes embryonic totipotency by organizing early zygotic transcription initiation [RNA-seq]

city: Kunming

first: Liangliang

last: Wang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

country: China

institute: Yunnan University

summary: Zygotic genome activation (ZGA) marks the first transcriptional milestone and establishes embryonic totipotency. Although pioneer factors have been reported to initiate this process, how chromatin is primed for the totipotent state, allowing the binding of pioneer factors for successful ZGA, remains unclear. Here, we identify IntS11, the catalytic subunit of the Integrator complex, as a totipotent determinant of embryonic chromatin governing ZGA in Drosophila. We show that IntS11 functions upstream of pioneer factors in early embryos: maternal IntS11 depletion substantially impairs RNA polymerase II (Pol II) recruitment, thereby preventing pioneer factors Zelda and GAGA factor (GAF) from accessing regulatory elements and initiating genome-wide zygotic transcription. Mechanistically, IntS11 exerts dual roles: its canonical endonuclease activity is required to sustain major-wave zygotic transcription, while a distinct enzyme-independent function drives de novo Pol II loading and pioneer factor engagement. These findings uncover a fundamental maternal-specific mechanism whereby IntS11 establishes transcriptional competence, ensuring totipotent chromatin states and successful ZGA.

overall_design: To investigate the effect of IntS11 on the zygotic gene activation of drosophila embryo, we established a variety of mutants. We then performed gene expression profiling analysis using data from RNA-seq of mutant embryos and wild-type embryos at 2-3 time points.

first: Yiru

first: Yaqi

last: Miao

first: Yuan

last: Song

first: Jialiang

last: Zhou

first: Yuanxiang

last: Zhu

first: Ying

last: Cheng

first: Wenxin

last: Zhang

first: Qinmiao

last: Sun

first: Fan

last: Lai

first: Guoqiang

first: Dahua

last: Chen


title: Comprehensive transcriptome analysis of influenza A virus-infected MDCK cells treated with Mel56

city: Tokushima

first: Takashi

last: Kuzuhara

address: Yamashiro-cho

department: Faculty of Pharmaceutical Sciences

country: Japan

institute: Tokushima Bunri University

summary: To identify the genes involved in the anti-influenza activity of Mel56, we performed an RNA sequencing (RNA-seq) analysis of IAV-infected MDCK cells treated with Mel56. A total of 1,767 differentially expressed genes (DEGs) were identified using |fold-change (FC)| ≥ 2 and raw p-value < 0.05 as thresholds for the comparison between Mel56-treated and DMSO-treated MDCK cells infected with A/PR/8/34 virus. Among these DEGs, 1,062 were upregulated and 705 were downregulated (≥2-FC) in response to Mel56 treatment.

overall_design:
RNA-seq analysis
MDCK cells were seeded in a 96-well plate (1 × 10E4 cells/well). Mel56 (10 μM) was mixed with or without A/PR/8/34 (MOI 0.01) virus in growth medium containing 10% FBS and incubated for 30 min at 37 °C with 5% CO2. DMSO (0.1%) was used as the negative control. The resulting mixture was added to the cells. After a 24 h incubation at 37 °C with 5% CO2, total RNA was extracted from cell lysates using an RNeasy Mini Kit (Qiagen).
  Total RNA concentrations were calculated using Quant-IT RiboGreen (Thermo Fisher Scientific). To assess the integrity of total RNA, samples were run on a TapeStation RNA Screentape (Agilent Technologies, Santa Clara, CA, USA). Only high-quality RNA preparations (RIN greater than 7.0) were used for RNA library construction. A library was independently prepared with 1 µg of total RNA for each sample using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA). The first step in the workflow involved purifying the poly-A-containing mRNA molecules using poly-T-attached magnetic beads. Following purification, mRNA was fragmented into small pieces using divalent cations at elevated temperatures. Cleaved RNA fragments were copied into first-strand cDNA using SuperScript II Reverse Transcriptase (Thermo Fisher Scientific) and random primers. This was followed by the synthesis of second-strand cDNA using DNA Polymerase I, RNase H, and dUTP. These cDNA fragments underwent an end-repair process, followed by the addition of a single ‘A’ base and ligation of the adapters. The products were purified and enriched using PCR to create a final cDNA library. Libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, Wilmington, MA, USA) and qualified using a TapeStation D1000 ScreenTape (Agilent Technologies). Indexed libraries were then submitted to Illumina NovaSeqX (Illumina), and paired-end (2×150 bp) sequencing was performed by Macrogen, Inc.

RNA-seq data processing and analysis
Paired-end sequencing reads were generated using an Illumina NovaSeqX sequencing platform. Trimmomatic v0.38 was used to remove adapter sequences and trim poor-quality bases. The cleaned reads were aligned to the Canis lupus familiaris (CanFam3.1) genome using HISAT v2.1.0. Reference genome sequences and gene annotation data were downloaded from the NCBI Genome Assembly and RefSeq databases, respectively. The aligned data (in SAM file format) were sorted and indexed using SAMtools v1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b. Gene-level and transcript-level quantifications were performed as raw read counts, Fragments Per Kilobase of transcript per million mapped reads, and TPM.

Differential gene expression analysis of RNA-seq data
Differential gene expression was analyzed using DESeq2 v1.38.3 with raw counts as input. In the QC step, genes with non-zero counts in all samples were selected. Principal component analysis and multidimensional scaling plots were generated to confirm similarity in expression between samples. The filtered dataset was subjected to RLE normalization to correct for variations in library sizes among samples. The statistical significance of DEGs was determined using DESeq2 nbinom WaldTest. FC and p-values were extracted from Wald test results. All p-values were adjusted using the Benjamini–Hochberg algorithm to control the false discovery rate. |FC| ≥ 2 and adjusted p-value < 0.05 were the thresholds for significance. Hierarchical clustering of the log-transformed values for significant genes was performed using distance metric = Euclidean distance and linkage method = complete. Gene enrichment and functional annotation analyses for significant genes were performed using gProfiler (https://biit.cs.ut.ee/gprofiler/orth) against the GO database and the in-house KEGG viewer script against the KEGG pathway database (https://www.genome.jp/kegg/pathway.html). Adjusted p-values obtained using gProfiler were derived using a one-sided hypergeometric test and corrected using the Benjamini–Hochberg method. Adjusted p-values from the KEGG viewer results were derived using a two-sided modified Fisher’s exact test and corrected using the Benjamini–Hochberg method.

first: Masaki

last: Shoji


title: Ki-67 promotes circulating tumor cell intravasation and metastasis in breast cancer

city: Basel

first: Yongzhan

address: Otto-Stern-Weg 7 HPL H17.2

country: Switzerland

institute: ETH Zurich

summary: Hematogenous dissemination by circulating tumor cells (CTCs) drives metastatic spread. However, the molecular features that empower these cells to colonize distant organs remain unclear. We profiled single CTCs and CTC clusters from three breast cancer xenograft models by single-cell RNA sequencing and uncovered a shared transcriptional program marked by broad upregulation of cell-cycle genes. A targeted CRISPR loss-of-function screen identified MKI67 as an essential regulator of CTC abundance, particularly of cluster abundance, and metastatic progression. MKI67 disruption markedly reduced CTC numbers and decreased the fraction ofCTC clusters, leading to diminished lung metastases. CRISPRa-mediated re-expression of downstream adhesion genes CD47 and KLF4 restored both cluster prevalence and metastatic burden. Our findings link cell-cycle upregulation to enhanced metastatic capacity and position MKI67-dependent adhesion signals as tractable targpendent adhesion signals as tractable targets against metastatic spread.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To compare gene expression profiles of CTCs with their primary and metastatic counterparts, we performed single-cell RNA sequencing using the 10X Genomics Chromium platform. We sequenced single CTCs, CTC clusters (both homo- and heterotypic), primary tumor cells and lung metastatic tumor cells from three orthotopic breast cancer models: two models in immunodeficient NOD.Cg-Prkdcscid-Il2rgtm1Wjl/SzJ (NSG) mice  (a human breast cell line xenograft (LM2-NSG) and a patient-derived CTC xenografts (BR16-CDX-NSG)) and one immunocompetent syngeneic breast cancer model (a mouse breast cell line xenograft (FVB-MVT1)).

first: Jianwen

first: Karin

last: Strittmatter

first: Yu-Wei

first: Maria

last: Waldmeier

first: Selina

last: Budinjas

first: Massimo

last: Saini

first: Ece-Su

last: Ildiz

first: Ana

last: Gvozdenovic

first: Werner

last: Kovacs

first: Francesc

last: Castro-Giner

first: Nicola

last: Aceto


overall_design: LM2-GFP-Luc cells were transduced at low MOI (<1) with a lentiviral vector carrying inducible Cas9 (Edit-R system) and selected with blasticidin. A custom sgRNA library targeting 214 genes (1,413 sgRNAs plus 129 non-targeting controls) was cloned into pLCKO2, verified by sequencing, and packaged into lentivirus using HEK293T cells. LM2-GFP-Cas9-P2A-TurboRFP cells were transduced with the library at MOI = 0.3 and selected with puromycin, then expanded and injected into NSG mice. Doxycycline was administered at day 39 to induce Cas9. At day 42, CTCs and tumors were collected, and TurboRFP-positive cells were isolated by FACS. Genomic DNA was extracted, and sgRNAs were amplified via nested PCR and sequenced on an Illumina MiSeq platform.

last: Zhou


title: Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [RIP-Seq]

city: Montreal

first: Marc

last: Fabian

state: Quebec

address: 3755 Côte Ste-Catherine Road

department: Department of Oncology

country: Canada

institute: McGill

summary: The CCR4-NOT complex is a central regulator of gene expression, orchestrating mRNA destabilization and decay through interactions with RNA-binding proteins (RBPs) and the miRNA-induced silencing complex (miRISC). However, identifying which RBP and miRNA target sites actively recruit this complex to engender mRNA turnover remains challenging, due in part to the multiple modes by which the CCR4-NOT can be recruited to targets. Here, to address this, we developed TRACER (Targeted RNA Association of CCR4-NOT and  Element Recovery), a crosslinking approach that enables high-throughput mapping of cis-acting RNA elements that recruit the CCR4-NOT complex to target RNAs. TRACER analysis of a human epithelial cell line uncovers thousands of CCR4-NOT target elements, including many of which map to known and/or predicted RBP binding motifs, as well as miRNA target sites. Importantly, we show that CCR4-NOT recruitment elements identified by TRACER play important roles in promoting mRNA decay. Taken together, our approach provides the first high-resolution transcriptome-wide map of CCR4-NOT targeting elements in human cells that engender mRNA decay.

overall_design: RIP-seq of HEK293 to capture CCR4-NOT-associated RNAs by immunoprecipitation with V5-tagged CNOT7 subunit harboring a D40A mutation to impair catalytic activity of the complex.

first: Zijun

last: Luo

first: William

last: Brothers

first: Aldo

last: Hernandez-Corchado

first: Justin

last: Zhao

first: Zara

last: Aryampour

first: Connor

last: Campbell-Smith

first: Hamed

last: Najafabadi


title: MAPS-seq of small RNA sLLM1042+ in Lactococcus cremoris subsp. cremoris MG1363

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Life sciences center

country: Lithuania

institute: Vilnius Universitye

summary: The contribution of small RNAs to the regulation of cell wall defense mechanisms, which play a central role in protecting bacteria from environmental insults, remains poorly understood in Lactococcus cremoris, a paradigmatic organism for studying lactic acid bacteria. Analysis of the profiles of 193 putative sRNAs, including 131 newly identified in this study, revealed altered expression of 20 and 25 sRNAs following treatment with major cell wall-targeting antimicrobials lysozyme and penicillin G, respectively. Further analysis and genome-wide functional screening identified four sRNAs that modulate the lysozyme response in opposite directions, with sLLM1042+, sLLM2-, and sLLM1993+ conferring increased, and sLLM461+ decreased, resistance. Moreover, elevated expression of sLLM2- or sLLM1042+ promoted the sensitivity of cells to penicillin G and certain abiotic stresses, and had pleiotropic effects on gene regulation at both RNA and protein levels, positioning them as key elements in regulatory networks. Notably, the sLLM2- mediated decrease in four putative tellurium resistance proteins resulted in L. cremoris sensitivity to tellurite stress. As sLLM2- mutations, altering lysozyme and penicillin responses, reduce the expression of alanine racemase Alr, we suggest that its upregulation possibly modulates D-alanine levels, thereby affecting lipoteichoic acid modification or peptidoglycan synthesis. Our findings underscored the broad roles of sRNAs in defensive responses to cell wall-targeting antimicrobials in lactic acid bacteria.

overall_design: The MS2-affinity purification protocol coupled with RNA sequencing (MAPS) was applied to identify interaction partners of the small RNA sLLM1042+ in Lactococcus cremoris subsp. cremoris MG1363 (formerly classified as Lactococcus lactis subsp. cremoris MG1363).

first: Renatas

last: Krasauskas

first: Dominyka

last: Keturauskaitė

first: Kotryna

last: Kvederavičiūtė


title: Effect of sRNAs sLLM2- and sLLM1042+ overexpression on the L. cremoris subsp. cremoris MG1363 transcriptome

overall_design: The transcriptome of Lactococcus cremoris subsp. cremoris MG1363 (formerly classified as Lactococcus lactis subsp. cremoris MG1363) was analyzed at the mid-exponential growth stage under control conditions and upon increased expression of two small RNAs, sLLM2- and sLLM1042+.

first: Milda

last: Mickutė


title: SIRT6 Overexpression Counteracts Chromatin Aging

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

type: Methylation profiling by high throughput sequencing

summary: Aging is associated with detrimental changes in chromatin structure and gene expression, contributing to inflammation, metabolic decline and tissue dysfunction. SIRT6, a histone deacetylase, plays a key role in maintaining chromatin integrity and promoting longevity. Here, we show that aging leads to increased chromatin accessibility in the murine liver, accompanied by upregulation of inflammation and downregulation of metabolic pathways. Remarkably, SIRT6 overexpression reversed these changes, reducing inflammation and enhancing metabolic function. Notably, ETS family members were enriched in regions with increased accessibility during aging, while liver-enriched transcription factors (LETFs) were enriched in regions with reduced accessibility. ChIP-seq analyses of H3K9ac and H3K56ac binding showed that H3K9ac, but not H3K56ac, is associated with increased accessibility during aging, and that SIRT6 can reverse this effect. Furthermore, AAV-mediated SIRT6 overexpression in aged mice demonstrated that SIRT6 not only slows age-related chromatin changes but can also reverse them, rejuvenating chromatin accessibility to a youthful state.

overall_design: Methylome of liver from WT and SIRT6 tg, young (3-4 mo) and old (23-24 mo) mice

first: Ron

last: Nagar

first: Zacharia

last: Scwartz

first: Haim

middle: Y

last: Cohen


title: sRNA sequencing of Lactococcus cremoris in response to penicillin and lysozyme stress

overall_design: Small RNA (sRNA) expression in Lactococcus cremoris subsp. cremoris MG1363 (formerly classified as Lactococcus lactis subsp. cremoris MG1363) was analyzed during the exponential growth phase under control conditions and following treatment with penicillin G or lysozyme, as well as throughout all stages of bacterial growth under untreated conditions.


title: Loss of WWOX Drives Cutaneous Squamous Cell Carcinoma (cSCC) through Regulating EMT [RNA-Seq]

city: Jerusalem

first: Rami

last: Aqeilan

address: Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem

summary: Cutaneous Squamous Cell Carcinoma (cSCC) is the second most common skin cancer, with a rising incidence in recent years. Through protein-protein interactions, the WW domain-containing oxidoreductase (WWOX) has been found to be a key player in many cellular processes, including DNA repair, apoptosis, metabolism, and transcriptional regulation. WWOX loss has been reported in many malignancies, including cSCC, suggesting a tumor suppressor role, but its function as a skin cancer antagonist and the underlying molecular mechanisms are not yet fully understood. To better understand WWOX's role in cSCC, we generated K14-Cre;Wwox;Trp53 conditional knock-out mice, leading to the development of cSCC. Strikingly, mice with ablated WWOX developed cSCC with increased penetrance and earlier onset. Characterization of cSCC morphology, immune markers, and transcriptional signatures revealed poorly differentiated cSCC with epithelial-to-mesenchymal transition (EMT) traits in tumors lacking WWOX compared to their controls. The hyperplastic phenotype of the epidermis in conditionally Wwox-knock-out mice was observed at an early age and impacted the surrounding microenvironment as well. Based on WWOX's known interaction with and stabilization of the transcription factor p63, we proposed that epidermal WWOX loss reduces p63 levels, destabilizing the tissue's epithelial integrity. Indeed, our findings confirmed this mechanism, demonstrating that diminished p63 impairs the epidermal protective barrier and accelerates the progression of aggressive cSCC. The WWOX-p63 correlation was also observed in human cSCC samples, inversely related to tumor stage. These findings were further supported in keratinocytes and cSCC human cell line models, where WWOX deficiency led to reduced p63 expression, concomitant with enhanced tumorigenic potential and migratory capacity.

overall_design: RNA profiles of dtTomato+ cells of cSCC, old epidermis and young epidermis samples from K14cre;Wwoxfl/fl;p53fl/fl mouse model

first: Tirza

last: Bidany-Mizrahi

first: Jonathan

last: Monin

first: Abed

last: Nasereddin

middle: I


title: H3K9me3 controls epidermis development by repressing RNA Pol II initiation on key promoters and enhancers [scRNA-seq]

first: Chris

last: Bai

overall_design: Suv39h1,SUv39h2,Setdb1 triple knockout was induced in embryonic basal cells to deplete H3K9me3 and then single cell RNA-seq profiling was performed on sorted Epcam+α6+ double positive basal cells at E16.5

first: Tudorita

last: Tumbar


title: SIB1-SEC23A undergo ER to chloroplast relocalization to mediate immunity in Arabidopsis thaliana

city: HKSAR

first: Jialin

last: Peng

address: Kowloon Tong Kowloon, Hong Kong

institute: Hong Kong Baptist University

summary: Inter-organellar communication has emerged as a critical factor in maintaining cellular homeostasis under stress conditions. Chloroplasts function not only as central organelles for energy production but are also increasingly recognized as stress sensors and signal integrators. SIGMA FACTOR-BINDING PROTEIN 1 (SIB1), encoded by a nuclear gene, has been identified as a positive regulator of plant immunity, with localization in both chloroplasts and the nucleus. In this study, we identified Arabidopsis SEC23A, a COPII complex component known to mediate membrane trafficking between the endoplasmic reticulum (ER) and the Golgi apparatus, as a novel interactor of SIB1. Our findings reveal that under normal conditions, both SIB1 and SEC23A localize to the ER, while SIB1 is also localized in the nucleus. Upon ER stress and/or treatment with the immunity inducer salicylate, both proteins are relocated from the ER to the chloroplasts. Notably, SEC23A, similar to SIB1, also functions as a positive regulator of disease resistance. In response to pathogen infection, SIB1 and SEC23A downregulate expression of chloroplast- and nucleus-encoded genes associated with photosynthesis while enhancing expression of defense-related genes. Together, our findings reveal a previously uncharacterized pathway of ER–chloroplast communication mediated by SIB1 and SEC23A during plant stress responses and immunity, providing novel insights into the intricate regulatory networks that govern inter-organellar communication under stress in plants.

overall_design: The plants were infected with the avirulent P. syringae strain DC3000 expressing the avirulent gene avrRpm1 (Pst avrRpm1).The leaves were collected 3 hours after pathogen infection and mock treatment for RNA extraction for analysis

first: Huan

last: Zhong

first: Yiji

last: Xia


title: Loss of WWOX Drives Cutaneous Squamous Cell Carcinoma (cSCC) through Regulating EMT [ChIP-Seq]

overall_design: ΔNp63 ChIP-seq for untreated A431 shp53 cells: WWOX WT, WWOX KO and WWOX rescue

first: Osama

last: Hidmi


title: Comprehensive analysis of gene expression in visceral fat of morbidly obese patients undergoing bariatric surgery [Human]

city: Kobe

first: Yusei

last: Hosokawa

state: Hyogo

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

department: 1Division of Diabetes and Endocrinology, Department of Internal Medicine

institute: Kobe University graduate school of medicine

summary: This data is part of the data being used to search for factors associated with the treatment effects of bariatric surgery in patients with severe obesity and is the result of RNA-seq analysis of 40 samples of visceral adipose tissue obtained during bariatric surgery. The research for factors is ongoing and has not been published.

overall_design: The study participants were patients who underwent Laparoscopic Sleeve Gastrectomy (LSG) at Chibune General Hospital between January and August 2020 for the treatment of primary obesity. One patient who underwent LSG with duodenojejunal bypass was included. Blood samples were collected before and one year after surgery, and approximately 8 to 10 cm3 of visceral white adipose tissue (vWAT) was obtained from the subjects during surgery and stored in liquid nitrogen. At the beginning of the study, the number of participants was designed 40, but 5 self-interrupted their visits, so the number of completers was 35. The number of vWAT samples was 40, so that of RNA-seq data was also 40.  Sample numbers 11.35.42 are missing numbers assigned to patients for whom surgery was not performed or samples were not collected after informed consent was obtained. This retrospective observational study was approved by the Institutional Review Boards of Kobe University Hospital (approval no. B230036) and Chibune General Hospital (approval no. 20230502A), and it conformed to the provisions of the Declaration of Helsinki (as revised in 2013).

first: Yushi

last: Hirota

first: Seiji

last: Nishikage

first: Wataru

last: Ogawa


title: Glycogen metabolism in Sertoli cells sustains germ cell survival through lactate shuttling

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

summary: Sertoli cells accumulate glycogen within a specific developmental window, peaking at embryonic day (E) 12.5 and rapidly depleting by E13.5. Using immunofluorescence and single-nuclei RNA-seq, we identified the regulatory mechanisms underlying this transient glycogen storage. Glycogen accumulation correlates with elevated PPP1R3C expression, while its degradation coincides with increased glycogen phosphorylase (PYGB) levels. Functional assays revealed that glycogen metabolism is not required for Sertoli cell differentiation but is essential for germ cell survival. Pharmacological inhibition of glycogen breakdown resulted in germ cell loss, which could not be rescued by exogenous lactate or glucose, highlighting a critical metabolic dependency. Glycogen-derived lactate is transported via the MCT4/MCT1 shuttle from Sertoli cells to germ cells, supporting their survival. These findings establish glycogen metabolism as a key determinant of germ cell viability, emphasizing a metabolic coupling between Sertoli and germ cells during testis development with implications for reproductive health.

overall_design: Two E12.5 gonadal pairs (control or Ppp1r3c cKO) were pooled per sample, for a total of 3 samples per group.

first: Humphrey H-C

first: Martin

middle: A

last: Estermann

first: Joseph

last: Sheheen

first: Sara

last: Grimm

first: Boris

last: Tezak

first: Yu-Ying

last: Chen

first: Karina

middle: F

last: Rodriguez

first: Tsuyoshi

last: Morita

first: Blanche

last: Capel


title: Maternal IntS11 primes embryonic totipotency by organizing early zygotic transcription initiation [Micro-C]

first: Liangliang

last: Wang

overall_design: To investigate the effects of IntS11 on Drosophila embryos, we generated various mutants. Subsequently, we performed Micro-C analysis using both mutant and wild-type embryos.

first: Yiru

first: Yaqi

last: Miao

first: Yuan

last: Song

first: Jialiang

last: Zhou

first: Yuanxiang

last: Zhu

first: Ying

last: Cheng

first: Wenxin

last: Zhang

first: Qinmiao

last: Sun

first: Fan

last: Lai

first: Guoqiang

first: Dahua


title: Lung mucosal and systemic responses at single-cell resolution in an aerosolised Mycobacterium bovis BCG human challenge model

city: Oxford

first: Shuailin

last: Li

address: Old Road Campus Research Building

country: United Kingdom

institute: University of Oxford

summary: The development of an effective vaccine against tuberculosis (TB) is hindered by the limited understanding of the dynamics of cellular responses to Mycobacterium tuberculosis infection in humans. Here, in our aerosolised Mycobacterium bovis BCG human challenge study, we used single-cell and bulk immune profiling of bronchoalveolar lavage and blood samples to temporally resolve the dynamics of immune responses in BCG-naïve individuals. We observed a rapid change in cellular composition and gene expression in both the lung mucosa and blood. TB-specific gene signatures were observed on days 2 and 7 following aerosol challenge. T cell receptor (TCR) clones that expanded in the blood seven days post-challenge (BCG-expanded TCR clones) persisted in the lung mucosa for up to 56 days post-challenge, with most of these detectable in the blood prior to challenge.  Pre-existing BCG-expanded TCR clones were more likely to be activated CD4⁺ T cells and were more enriched in the lung mucosa than newly expanded TCR clones. Only a small proportion of mycobacterial antigen-reactive TCR clones in the blood, detected by the activation-induced marker assay, were enriched in the lung mucosa. Several public BCG-expanded TCR clones across individuals were identified in the lung mucosa and shown to be reactive to mycobacterial antigens using artificial antigen-presenting cells and reporter T cells. Overall, our study provides crucial insights into the dynamics of human mucosal and systemic immunity following aerosolised BCG challenge, informing the design of more effective TB vaccines.

relation:
Reanalysis of: GSM8636641
Reanalysis of: GSM8636642
Reanalysis of: GSM8636643
Reanalysis of: GSM8636644
Reanalysis of: GSM8636645
Reanalysis of: GSM8636646
Reanalysis of: GSM8636647
Reanalysis of: GSM8636648
Reanalysis of: GSM8636649
Reanalysis of: GSM8636650
Reanalysis of: GSM8636651
Reanalysis of: GSM8636652

overall_design:
Three BAL samples were collected from three volunteers on days 2, 7, 14, 28 and 56 post-aerosol BCG infection, respectively. Three BAL samples were collected from three volunteers on days 2, 7, 14, 28 and 56 post saline inhalation, respecitvely. Samples from the Groups 1 and 2 (Batch 1, days 2 and 7) were processed using the Chromium Next GEM Single Cell V(D)J Reagent kits v1.1 (10x Genomics) and sequenced using a single index configuration. Due to changes in reagents availability, the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10x Genomics) were used for library construction for Groups 3-5 (Batch 2, days 14, 28 and 56) samples. Each BAL sample was loaded to either one or two GEM wells and the FASTQ files were combined together. The target number of cells per well was 5,000. FASTQ files should first be split into one or two samples according to the index sequences for analysis. PBMCs from six donors (14,000 cells each) challenged with aerosol BCG in the group 3 (only three of them had BAL samples profiled by single-cell RNA sequencing (scRNA-seq)) collected on days 0, 2, 7 and 14 following aerosol BCG challenge were pooled and processed using the Chromium Next GEM Single Cell 5’ HT Reagent Kit (v2) to generate gene expression, surface protein, and V(D)J libraries, following the manufacturer’s protocols. PBMC samples from days 0, 2, 7, 14, 28, 56 or 84 were processed using the SMART-Seq Human TCR (with UMIs) kit for bulk TCR sequencing (TCR-seq). PBMC samples collected on day 7 following aerosol BCG challenge were stimulated with either PPD, M.bovis lysate or BCG and AIM+ CD4⁺ or CD8⁺ T cells, identified by co-expression of CD134 and CD137, CD154 and CD134, CD154 and CD137, CD69 and CD134, CD69 and CD137, or CD69 and CD154 were sorted and processed using the SMART-Seq Human TCR (with UMIs) kit for bulk TCR-seq. The gene expression data of the BAL samples collected on days 2 and 7 (12 sample in total) were already published in GSE282132 and were reanalysed here to make it possible to compare the following time points with these two time points. The GSM of these reanalysed data from GSE282132 are GSM8636641, GSM8636642, GSM8636643, GSM8636644, GSM8636645, GSM8636646, GSM8636647, GSM8636648, GSM8636649, GSM8636650, GSM8636651, GSM8636652. The reanalysed processed data include: TBT04301005A_filtered_feature_bc_matrix.h5, TBT04301005B_filtered_feature_bc_matrix.h5, TBT04301006_filtered_feature_bc_matrix.h5, TBT04301007_filtered_feature_bc_matrix.h5, TBT04301011_filtered_feature_bc_matrix.h5, TBT04301020A_filtered_feature_bc_matrix.h5, TBT04301020B_filtered_feature_bc_matrix.h5, TBT04301021A_filtered_feature_bc_matrix.h5, TBT04301021B_filtered_feature_bc_matrix.h5, TBT04301026A_filtered_feature_bc_matrix.h5, TBT04301026B_filtered_feature_bc_matrix.h5, TBT04301029A_filtered_feature_bc_matrix.h5, TBT04301029B_filtered_feature_bc_matrix.h5, TBT04301030A_filtered_feature_bc_matrix.h5, TBT04301030B_filtered_feature_bc_matrix.h5, TBT04301025A_filtered_feature_bc_matrix.h5, TBT04301025B_filtered_feature_bc_matrix.h5, TBT04301034A_filtered_feature_bc_matrix.h5, TBT04301034B_filtered_feature_bc_matrix.h5, TBT04301038A_filtered_feature_bc_matrix.h5, TBT04301038B_filtered_feature_bc_matrix.h5.

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

last: Morrison

first: Julia

last: Marshall


title: Low inflammation correlates with protumor Tim4+ TREM1+ resident macrophage expansion and limited monocyte-derived macrophage formation during peritoneal colorectal cancer

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Research based essentially on mouse models of ovarian cancer peritoneal metastasis have revealed that peritoneal macrophages, that include resident peritoneal macrophages (resMØs) and monocyte-derived non-resident macrophages, promote peritoneal tumor growth, through the induction of tumor cell proliferation and migration, and immunosuppression. However, the mechanisms controlling the expansion and differential contribution of resMØs and monocyte-derived non-resident macrophages to the pool of peritoneal macrophages present in tumor-bearing mice, and to promote tumor growth, remains to be addressed. Using a mouse model of colorectal cancer (CRC) peritoneal metastasis, based on the intraperitoneal injection of mouse tumor organoids, derived from primary tumors arising in genetically engineered mice, bearing mutations in Apc, Kras, Tgfbr2 and Trp53,  and developing human-like metastatic CRC tumor growth, in the present report, the origin, expansion and function of peritoneal macrophages during peritoneal CRC tumor growth, has been investigated. Our data support that the low inflammatory status of the peritoneal cavity associated to CRC peritoneal tumor growth, restrained Ly6Chi monocyte recruitment and formation of Tim4- resMØs and moMØs, while enabling a marked cell proliferation-driven expansion of Tim4+ resMØs. Tumor-induced Tim4+ resMØs displayed a migratory and protumor transcriptomic signature, involving the activation of genes controlling the expression of important protumor molecules, such as A2A/A2B, ARG1, IDO, IL-6, IRG1, MMP12, PD-L1/2, SPP1, TREM1 and VEGFa. Correspondingly, during peritoneal CRC tumor growth, Tim4+ TREM1+ resMØs migrated to the omentum, the main peritoneal target organ for peritoneal metastasis, and promoted CRC peritoneal tumor progression.

overall_design: RNA-seq profiling of Tim4+ resident macrophages isolated from peritoneal fluid in steady state (Ctrl x3 replicates) and 12 days after MTO injection (12d x4 replicates)

first: Margarita

last: Ferriz

first: Natalia

last: Álvarez-Ladrón

first: Alejandra

last: Gutiérrez-González

first: Marta

last: H. Fernández-Sesma

first: Adrián

last: Vega-Pérez

middle: C

first: Ana

last: Cayuela López

first: Eduard

last: Batlle

first: Daniele

last: Tauriello

first: Carlos

last: Ardavín


title: Maternal IntS11 primes embryonic totipotency by organizing early zygotic transcription initiation [ATAC-seq]

first: Liangliang

last: Wang

overall_design: To investigate the role of IntS11 in Drosophila embryos, we generated multiple mutant lines. Subsequently, we performed ATAC-seq analyses using both mutant and wild-type embryos.

first: Yiru

first: Yaqi

last: Miao

first: Yuan

last: Song

first: Jialiang

last: Zhou

first: Yuanxiang

last: Zhu

first: Ying

last: Cheng

first: Wenxin

first: Qinmiao

last: Chen


title: Maternal IntS11 primes embryonic totipotency by organizing early zygotic transcription initiation [ChIP-seq]

overall_design: To investigate the role of IntS11 in Drosophila embryos, we generated multiple mutant lines. Subsequently, we performed ChIP-seq analyses with multiple antibodies using both mutant and wild-type embryos.

last: Zhang

last: Sun

first: Fan

last: Lai

first: Guoqiang

first: Dahua


title: Association of miR-29 with postoperative neurological complications in acute type A aortic dissection patients

city: Fuzhou

first: xiaochai

last: lv

address: Xin-quan Road

institute: Fujian Medical University Union Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Objectives. Postoperative neurological complications (PONC), associated with substantial morbidity and mortality, represent a prevalent clinical challenge following surgical repair of  acute type A aortic dissection (AAD). This study aimed to identify novel biomarkers for early diagnosis of PONC to facilitate timely clinical intervention. Methods. We established deep hypothermic circulatory arrest (DHCA) rat models, extracted total RNA from the hippocampus of rats (DHCA group and control group), performed miRNA sequencing, screened for differentially expressed genes (DEGs) between the two groups, and analyzed their associated biological processes (BP) and pathways. A cohort of 95 patients diagnosed with AAD was enrolled in this study. Comprehensive clinical assessments and a standardized neuropsychological test battery were systematically conducted. Serum miR-29 levels were quantified via reverse transcription quantitative real-time polymerase chain reaction. Results. Transcriptomic profiling of rat hippocampus under deep hypothermic circulatory arrest / cardiopulmonary bypass (DHCA/CPB) identified 37 differentially expressed miRNAs (|log2FC|≥1.3, P<0.05), with miR-29a-5p and miR-29b-3p showing the most significant dysregulation. Functional enrichment implicated MAPK signaling and junctional pathways in blood-brain barrier modulation. In a clinical cohort of 95 aortic dissection patients, the PONC group exhibited prolonged CPB time (164.00 (137.00, 193.00) vs. 140.00 (120.25, 161.00), P=0.012), elevated inflammatory biomarkers (pre-op interleukin-6: 106.60 vs. 47.00, P<0.001), and altered miR-29 expression profiles. Multivariate analysis confirmed preoperative miR-29b-3p (OR=2.53, 95%CI 1.17-5.47) and postoperative miR-29a-5p (OR=0.21, 95%CI 0.05-0.96) as independent PONC predictors. The nomogram demonstrated robust discrimination (AUC=0.867, 95%CI 0.771-0.963) and clinical utility (net benefit=0.23), with 30-day survival analysis revealing miR-29b-3p-associated mortality risk (HR=4.372, 95%CI 0.928-20.596, P=0.041). Conclusions. Dual-phase miR-29 dysregulation predicts PONC post-AAD repair, validated by a nomogram and miR-29b-3p-associated mortality risk, guiding early intervention strategies.

overall_design: Establishment of DHCA/CPB animal model A rodent model utilizing cardiopulmonary bypass (CPB) and deep hypothermic circulatory arrest (DHCA) was developed based on a previously described methodology[19]. After 6-hour preoperative fasting, rats were weighed and anesthetized via 3% sevoflurane inhalation. Following supine fixation, tracheal intubation was performed using a 16G catheter connected to a rodent ventilator (100% oxygen with 3% sevoflurane). Mechanical ventilation was paused during DHCA and resumed post-arrest with parameters set at 60-70 breaths/min and tidal volume of 8-10 mL/kg, adjusted based on arterial blood gas analysis. Core temperature was monitored via a paraffin-lubricated rectal probe. Venous drainage was established through a silicone catheter in the jugular vein. Arterial pressure monitoring and perfusion were achieved via left femoral artery and tail artery cannulation, respectively (membrane oxygenator and circuits from Xi'an Xijing Medical Supplies Co., Ltd.). Vascular access points were secured by distal ligation and proximal fixation. In the DHCA group: (1) Normothermic CPB maintained for 5 min; (2) Gradual cooling to target temperature over 30 min; (3) 30-min circulatory arrest; (4) 60-min rewarming to >35°C; (5) Post-CPB ventilator support for 30 min (Fig. 1). Sham-operated controls underwent identical procedures excluding CPB/DHCA. At 24 h post-modeling, rats were euthanized via pentobarbital sodium (50 mg/kg) for tissue harvesting. Hippocampus was subsequently processed for transcriptomic profiling via RNA sequencing (RNA-seq).

first: Xiaochai

last: Lv

first: Yong

last: Lin

first: Yanting

last: Hou

first: Minxia

last: Xie

first: Liangwan


title: Persistent dopamine-dependent remodeling of the neural transcriptome in response to pregnancy and postpartum [CUT&RUN]

city: New York

first: Jennifer

last: Chan

state: New York

address: 1470 Madison Ave 9-201

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Pregnancy and postpartum experiences represent transformative physiological states that impose lasting demands on the maternal body and brain, resulting in lifelong neural adaptations. However, the precise molecular mechanisms driving these persistent alterations remain poorly understood. Here, we used brain-wide transcriptomic profiling to define the molecular landscape of parity-induced neural plasticity, identifying the dorsal hippocampus (dHpc) as a key site of transcriptional remodeling. Combining single-cell RNA sequencing with a maternal separation paradigm, we additionally demonstrated that chronic postpartum stress significantly disrupts dHpc adaptations by altering dopamine dynamics, leading to dysregulated transcription, altered cellular plasticity, and impaired behavior. We further established the sufficiency of dopamine modulation in the regulation of these parity-induced adaptations via chemogenetic suppression of dopamine release into dHpc, which recapitulated key transcriptional and behavioral features of parity in virgin females. In sum, our findings establish dopamine as a central regulator of parity-induced neuroadaptations, revealing a fundamental transcriptional mechanism by which female reproductive experiences remodel the maternal brain to sustain long-term behavioral adaptations.

overall_design: 4 bulk CUT&RUN-seq-seq experiments conducted: 1) in dHpc examining effect of stress (NP, Control PP, Stress PP), and 2) in dHpc examining effect of chemogenetic suppression in NP (NP-mCherry, NP-hM4Di), 3) in human subiculum examining effect of parity; 4) specificity of antibody by examining HeLa cell line with writer TG2 KO

first: Giuseppina

last: di Salvo

first: Ashley

last: Cunningham

first: Sohini

last: Dutta

first: Elizabeth

last: Brindley

first: Weekley

last: Benjamin

first: Ethan

last: Wan

first: Cindy

first: Turecki

last: Gustavo

first: Ian

last: Maze


title: Evaluation of gene expressions in epididymal white adipose tissue (eWAT) of adipocyte-specific LTA4H overexpression mice.

first: Yusei

last: Hosokawa

summary: To investigate the alteration of eWAT gene expression in adipocyte-specific Lta4h overexpression mice(A-LTA4HOE mice), we collected the eWAT of control mice and A-LTA4HOE mice fed high-fat diet for 4 weeks or 16weeks after weaning at 4 weeks old. We performed gene expression profiling analysis using data from RNA-seq of these 4 groups.

overall_design: Male A-LTA4HOE mice and their control mice at 4 weeks of age were randomized to individual diet groups and given free access to tap water and the HFD diet [60 kcal% fat (HFD22, CLEA Japan)] for 4 weeks or 16 weeks. We collected eWAT, and total RNA was extracted from the eWAT using an RNeasy Mini Kit (Qiagen, Hilden, Germany) and subjected to RNA sequencing analysis.

first: Wataru

last: Ogawa

first: Tetsuya

last: Hosooka


title: Mitochondria isolated from male skeletal muscle contain a small and distinct population of microRNA that are differentially expressed following acute endurance exercise [miRNA-seq]

city: Burwood

first: Danielle

last: Hiam

state: Vic

address: 221 Burwood Hwy

department: IPAN

country: Australia

institute: Deakin University

summary: Initially thought to localise at the cytosol and nucleus only, emerging evidence indicates that miRNAs also localise within the mitochondria where they could regulate diverse pathological and physiological processes. Therefore, the aim of the current study was to use small RNA sequencing to profile the entire population of miRNAs in human skeletal muscle of healthy males in isolated mitochondria and whole-tissue in response to acute endurance exercise. Twelve healthy males (age 26 ± 4 years, mean ± SD) cycled for 60 min at 70% VO2peak and muscle biopsies were collected at rest, immediately after and 3 h after exercise. The mitochondria were isolated by immunoprecipitation, further purified, then the resident RNA was sequenced to assess the mitochondrial transcriptome. Small RNA sequencing revealed that mitochondria isolated from male skeletal muscle tissue contain a small and distinct population of miRNAs. Of the approximately 110 mature miRNAs detected in skeletal muscle mitochondria at each time-point, the canonical myo-miRs miR-1, miR-133 and miR-206 families constituted on average 45% of total mitochondria miRNA reads. However, none of the canonical myo-miRs were differentially expressed in mitochondria following endurance exercise. Future research is now required to investigate miRNA-mRNA interactions in the mitochondria of skeletal muscle tissue.

overall_design: Participants (n=12) completed 60 mins of continuous cycling at 70% VO2peak. Whole skeletal muscle samples were obtained pre-exercise, immediately post-exercise and 3h post-exercise, and immediately processed for the isolation of mitochondria.

first: Jessica

last: Silver

first: Stella

last: Loke

first: Larry

last: Croft

first: Megan

last: Soria

first: Soren

last: Nielsen

first: Severine

last: Lamon

first: Glenn

last: Wadley


title: Persistent dopamine-dependent remodeling of the neural transcriptome in response to pregnancy and postpartum [snRNA-seq]

first: Jennifer

last: Chan

overall_design: snRNA-seq conducted on 4 dorsal hippocampal mouse tissues punches, with 3 groups (6 NP, 4 Control PP, 5 Stress PP)

first: Giuseppina

last: di Salvo

first: Ashley

last: Cunningham

first: Sohini

last: Dutta

first: Elizabeth

last: Zhang


title: Time-series RNA-Seq of Drosophila fat body during wing disc tumor development

city: Hong Kong

first: Yan

last: Yan

address: HKUST, Clear Water Bay

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: Here, we performed time-series RNA-Seq of Drosophila fat body during wing disc tumor growth to explore how the fat body responds to distant tumor growth at the transcriptomic level.

overall_design: We induced wing disc tumors by knocking down scrib with C855a-Gal4, an epithelial specific driver. These larvae cannot pupate and will grow into giant larvae until 14 days. Normal larvae fat body at 4 and 5 days after egg laying (AEL) were dissected as control. We collect embryos within 3 hours and raise them until 4, 5, 8, 11 days AEL to dissect the fat body and perform RNA-Seq. For each time point, 4 replicates of 50 larvae fat body were dissected.


title: Reconstructing signaling histories of single cells via perturbation screens and transfer learning

city: Cambridge

first: Nicholas

middle: T

last: Hutchins

state: MA

address: 455 Main St.

institute: Massachusetts Institute of Technology

summary: Manipulating the signaling environment is an effective approach to alter cellular states for broad-ranging applications, from engineering tissues to treating diseases. Such manipulation requires knowing the signaling states and histories of the cells in situ, for which high-throughput discovery methods are lacking. Here, we present an integrated experimental-computational framework that learns signaling response signatures from high-throughput in vitro perturbation atlas and infers combinatorial signaling activities in in vivo cell types with high accuracy and temporal resolution. Specifically, we generated signaling perturbation atlas across diverse cell types/states through multiplexed sequential combinatorial screens on human pluripotent stem cells. Using the atlas to train IRIS, a neural network-based model, and predicting on mouse embryo scRNAseq atlas, we discovered global features of combinatorial signaling code usage over time, identified biologically meaningful heterogeneity of signaling states within each cell type, and reconstructed signaling histories along diverse cell lineages. We further demonstrated that IRIS greatly accelerates the optimization of stem cell differentiation protocols by drastically reducing the combinatorial space that needs to be tested. This framework leads to the revelation that different cell types share robust signal response signatures, and provides a scalable solution for mapping complex signaling interactions in vivo to guide targeted interventions.

overall_design: hESCs were first differentiated into the middle primitive streak using the protocol from Loh et al. 2016 and Kishimoto et al. 2022. Following combinatorial signaling ligand stimulation (using RA, TGFB, WNT, FGF, BMP)  for 3 days, cells were differentiated into a variety of cell states. They were collected and barcoded with Multi-Seq reagents then pooled and sequenced.

first: Miram

last: Meziane

first: Claire

last: Lu

first: Maisam

last: Mitalipova

first: David

last: Fischer

first: Pulin

last: Li


title: Gene expression analysis of Subperitoneal Fibroblast (SPF) by knockdown of Transgelin.

city: Kashiwa-shi

first: Okamoto

last: Ryuji

address: 6-5-1 Kashiwanoha

institute: National cancer center east

summary: Transgelin expression in colorectal cancer has been reported to correlate with patient prognosis. The aim of this study was to investigate the function of Transgelin in fibroblasts of colorectal cancer. As a method, we assessed whether knockdown of Transgelin alters the expression of the gene.

overall_design: Gene expression analysis of SPF was performed by RNA sequence. Three SPFs, each established from separate cancer tissue samples, were transfected with sh luc or sh Transgelin#1. After introduction of the sh vector, RNA derived from stimulated and unstimulated cells was extracted by addition of cancer cell culture supernatant. The final analysis was performed using 3 (SPF type) × 2 (2 vectors) × 2 (with or without cancer cell culture supernatant added) for a total of 12 Samples.


title: Incorporation of genome-bound cellular proteins into HIV-1 particles regulates viral infection

first: Jeffrey

last: Lee

address: Dorothy Hodgkin Road

summary: The initial steps of the human immunodeficiency virus 1 (HIV-1) lifecycle are regulated by cellular RNA-binding proteins (RBPs). To understand the scope of these early host-virus interactions, we developed in virion RNA interactome capture (ivRIC), which allowed the comprehensive and systematic profiling of the proteins that interact with the HIV-1 genomic (g)RNA inside viral particles. ivRIC identified 104 cellular RBPs within the encapsidated HIV-1 ribonucleoprotein, many of which are typically found in the cellular nucleus. Notably, these nuclear RBPs interact with the HIV-1 RBP Rev, suggesting that they associate with HIV-1 gRNA during its nuclear life. Functional assays show that ivRBPs are important for HIV-1, including PURA and PURB, which control viral gene expression and infectivity through interaction with critical sequences in the gRNA. Our characterisation of the composition of the encapsidated ribonucleoprotein of HIV-1 uncovers new host-virus interactions that invokes new mechanisms for controlling HIV-1 infection.

overall_design: iCLIP of PURA and PURB Jurkat Flp-In T-REx cells with or without HIV-1 (1 MOI) for 48 hours. 3 replicates each for immunoprecipitate and size-mated input samples.

first: Manuel

last: Garcia-Moreno

first: Marko

last: Noerenberg

first: Louisa

last: Iselin

first: Alfredo

last: Castello


title: A novel triple-action Pt(IV) prodrug presents multiple anti-cancer effects and overcomes cisplatin resistance [XR-seq]

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

summary: Cisplatin is a widely used chemotherapeutic agent that is cytotoxic to cancer cells primarily by damaging their DNA.  However, drug resistance limits its efficacy and significantly restricts its use. Cisplatin resistance is complex and multifactorial, as it involves numerous cellular pathways and activities. Among these are the constitutive activation of the nuclear factor erythroid 2 (NF-E2)-related factor 2 / Kelch-like erythroid cell-derived protein with CNC homology (ECH)-associated protein 1 (Nrf2/Keap1) pathway, overexpression of histone deacetylases (HDACs), and increased nucleotide excision repair (NER). Simultaneous inhibition of both the Nrf2/Keap1 pathway and HDAC activity could be beneficial for addressing the challenge of cisplatin resistance and retrieve chemo-sensitivity. In this study, we synthesized a novel Pt(IV) derivative that is assembled from cisplatin, an Nrf2 inhibitor, and an HDAC inhibitor. This triple-action prodrug, cct-[Pt(NH3)2Cl2(VPA)(PhB)] (cPVP), enabled the parallel-targeting of multiple cancer-related pathways using a single agent. Compared to cisplatin, cPVP exhibited significantly enhanced damage-formation and cytotoxicity, and presented inhibitory effects on the Nrf2/Keap1 pathway, HDAC activity, and NER. Furthermore, the prodrug demonstrated improved efficacy against cisplatin-resistant cells. Most importantly, cPVP prevented the development of resistance to both cisplatin and itself in cancer cells. Together, our results suggest that the triple-action cPVP could be a feasible alternative to cisplatin in the clinic.

overall_design: We performed XR-seq in A2780 cells, treated with either 200 µM of cisplatin or 30 µM of cPVP for 3h, with 2 replicates for each treatment.

first: Ya'ara

last: Negev-Korem

first: Hadar

last: Golan-Berman

first: Elisheva

last: Heilbrun

first: Subhendu

last: Karmakar

first: Yoram

last: Soroka

first: Marina

last: Frušić-Zlotkin

first: Ofer

last: Chen

first: Hiba

last: Hassanian

first: Dan

last: Gibson

first: Ron

last: Kohen


title: Age-related transcriptomic differences in peripheral blood of adolescents with major depressive disorder

city: Chongqing

first: Xinyu

last: Zhou

address: 1 Youyi Road, Yuzhong District

department: Department of Psychiatry

institute: The First Affiliated Hospital of Chongqing Medical University

summary: In this study, we collected peripheral blood samples of a typical large population, including MDD cases and healthy controls from children and adolescents, and aimed to apply RNA-seq sequencing to comprehensively analyze the transcriptomic characteristics in adolescent depression patients. In comparison to healthy patients, we discovered that several immune response-associated genes were dysregulated in MDD patients, with the majority of these differential genes strongly correlated with the HAMD-17 and HAMA scores. Furthermore, we investigated the effects of drug therapy on transcription variations in teenagers with MDD and discovered that changes in these differentially expressed genes and immune cell types were unaffected by drug use, implying that the current medication has a lower effect on the MDD population. Notably, these transcriptional differences may disrupt the immune system's coordinated function during adolescent and adult depression, resulting in distinct changes in immune cells that contribute to the pathophysiology of depression in adolescents. Our findings may shed new light on the pathogenesis of depression in children and adolescents, potentially leading to more precise and effective treatment strategies.

overall_design: We collected peripheral blood samples of MDD cases and healthy controls from children and adolescents, and applied RNA-seq sequencing to comprehensively analyze the transcriptomic characteristics in adolescent depression patients.

first: Kai

last: Guo

first: Xueer

last: Liu

first: Fang

last: Huang


title: Nicotinic acid-induced histone nicotinylation suppresses hepatocellularcarcinoma metastasis by regulating PPFIA1 gene expression.

city: beijing

first: li

middle: yi

last: xiao

state: State...

address: road of xueyuan 38

institute: peking university

summary:
Histone post-translational modifications (PTMs) controls the gene expression profile via transcriptional regulation．Aberrant histone PTMs chromatin structures lead to dysregulated gene expression and cancer progression. Nicotinic acid (vitamin B3 or vitamin PP), one of the thirteen essential vitamins, has a wide range of uses, helping to function digestive system, skin and nervous system. Here we show nicotinic acid (NA) induces histone and non-histone lysine nicotinylation, and identify 17 nicotinylation sites on core histones in HeLa cells. Also, NA-derived nicotinylation of histone lysine residues is an epigenetic modification that regulates gene transcription via altering the chromatin accessibility by generating nicotinyl-CoA. Knic inactivates oncogene PPFIA1 transcription by inhibiting its combination with transcription factors HOXB9, and PPFIA1 was found as an important role in promoting cells spreading on the extracellular matrix and is required for migration and invasion in human breast tumor cells
However, the role and the molecular mechanisms of PPFIA1 control hepatocellularcarcinoma (HCC) initiation and progression are poorly understood. Here we demonstrate PPFIA1 promotes proliferation, migration, invasion and tumorigenesis of HCC in vivo and in vitro. It is worth noting that the expression of PPFIA1 is upregulated in multiple human carcinomas, including HCC. Our study also suggests that PPFIA1 is a promising potential target of NA for the future treatment strategies of HCC

overall_design: Yixiao,Li

first: Yuhan

last: jiang

first: Haoyi

last: Yan

first: Ziheng

last: Qin


title: Mitochondria isolated from male skeletal muscle contain a small and distinct population of microRNA that are differentially expressed following acute endurance exercise

first: Danielle

last: Hiam

overall_design: Participants (n=12) completed 60 mins of continuous cycling at 70% VO2peak. Whole skeletal muscle samples were obtained pre-exercise, immediately post-exercise and 3h post-exercise, and immediately snap frozen in liquid nitrogen for future analyses.

first: Jessica

last: Silver

first: Stella

last: Loke

first: Larry

last: Croft

first: Megan

last: Soria

first: Soren

last: Nielsen

first: Severine

last: Lamon

first: Glenn

last: Wadley


title: A forward genetic screen identifies Sirtuin1 as a driver of neuroendocrine prostate cancer.

city: New York City

first: Alessandro

last: Vasciaveo

address: 1130 Saint Nicholas Ave., 910

department: Department of Systems Biology

institute: Columbia University

summary: Although most prostate tumors are relatively indolent, advanced disease can progress to aggressive, often lethal variants, including neuroendocrine prostate cancer (NEPC). To identify drivers of aggressive prostate cancer, we used Sleeping Beauty (SB) transposon mutagenesis in a mouse model having prostate-specific loss of Pten and Tp53 (NPp53 mice). Compared with control NPp53-SB(—) mice, experimental NPp53-SB(+) mice developed more aggressive tumors with increased metastasis. Notably, NPp53-SB(+) mice exhibited NEPC phenotypes with transcriptomic features that recapitulate human NEPC. Analysis of recurrent common insertion sites (CIS) and associated genes (CIS-genes) identified genes differentially expressed between NEPC and non-NEPC tumors. Analysis of NEPC-enriched CIS genes by cross-species integration of genomic and transcriptomic data prioritized Sirtuin 1 (Sirt1) as a candidate mechanistic determinant of NEPC. Gain- and loss-of-function studies in human prostate cancer cells and mouse NEPC organoids confirmed that SIRT1 promotes NEPC, while pharmacological inhibition suppresses it. Thus, integration of cross-species analyses with an unbiased forward genetic screen uncovered novel drivers of NEPC.

overall_design: Refer to individual Series


title: Mesenchymal WNT2B is required for the maintenance of the human small intestinal epithelium

city: Cincinnati

first: Abid Al

last: Reza

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: In this study, we compare the transcriptional patterns of tHIOs derived from a control stem cell line with those derived from a patient with Diarrhea-9. We also compare the transcriptional patterns of enteroids derived from control patient biopsies and from the biopsies of patients with Diarrhea-9

overall_design: tHIOs from both lines were harvested at 10 weeks post-transplant. RNA was extracted, and was processed for bulk RNA sequencing. Bulk RNA was also extracted from enteroids from both types of patients.

first: Akaljot

last: Singh

first: Holly

last: Poling

first: Abid

last: Al Reza


title: A forward genetic screen identifies Sirtuin1 as a driver of neuroendocrine prostate cancer

summary: Advanced prostate cancer is often associated with the emergence of more aggressive disease phenotypes, including neuroendocrine prostate cancer (NEPC), which are currently incurable. To identify drivers of aggressive prostate cancer, we conducted a Sleeping Beauty (SB) transposon mutagenesis screen based on a mouse model having conditional loss of function of Pten and Tp53 prostate (NPp53). Compared with the control mice (NPp53-SB(—)), the experimental mice (NPp53-SB(+)) develop aggressive prostate cancer phenotypes that are highly heterogeneous and highly metastasis. Most notably, a high percentage of NPp53-SB(+) prostate tumors have features of NEPC, which are conserved with human prostate cancer. To identify and prioritize drivers of NEPC in these NPp53-SB(+) tumors, we used a novel integrative approach that combines (i) genomic analyses of common insert sites (CIS) for the SB transposon, (ii) VIPER analyses of control NPp53-SB(+) prostate tumors to identify master regulators (MRs) enriched in NEPC, and (iii) comparative transcriptomic analyses with data from human prostate cancer patients followed by integrative analyses using of these data using a CINDy algorithm to identify CIS-associated genes that modulate the NEPC phenotypes. Among these the nicotinamide adenosine dinucleotide (NAD)-dependent deacetylase, sirtuin 1 (Sirt1). Loss- and gain-of-function studies in human prostate cancer cell lines showed that SIRT1 promotes NEPC, while its depletion or inhibition reduces NEPC. Overall, this integrative phenotypic and systems analyses have identified of candidate drivers of NEPC and may be generalizable to analyzing and interpreting data from analogous in vivo mutagenesis screens.

overall_design: To perform the Sleeping beauty (SB) mutagenesis screen, we used the NPp53 mice (for Nkx3.1CreERT2/+; Ptenflox/flox; Trp53flox/flox). These mice develop prostate adenocarcinoma that progresses to CRPC following androgen deprivation (via castration) and that can further progress to advanced prostate cancer phenotypes, including NEPC, following treatment with second generation the anti-androgens. We, therefore, reasoned that this GEMM would serve as an excellent model to screen for drivers of advanced prostate cancer. As a control, we used the NP mice (for Nkx3.1CreERT2/+; Ptenflox/flox), which develop well-differentiated prostate adenocarcinoma that develops CRPC following androgen deprivation but does not progress to more advanced phenotypes following treatment with second generation anti-androgens (ref). Activation of the Nkx3.1CreERT2 allele via tamoxifen induction leads to temporal and spatial recombination of Pten and/or Trp53 specifically in the prostatic epithelium

first: Francisca

middle: N

last: de Almeida

first: Andrea

last: Califano

first: Cory

last: Abate-Shen


title: Persistent dopamine-dependent remodeling of the neural transcriptome in response to pregnancy and postpartum [bulk RNA-seq]

first: Jennifer

last: Chan

overall_design: 8 bulk RNA-seq experiments conducted: 1) across 11 brain regions (NP vs. PP), 2) across reproductive events (NP, MatingOnly, PregnancyOnly, PupSensitized,PP), 3) across reproductive timepoints in dHpc (7.5dpc, 17.5dpc, 2dpp, 21dpp, NP, PP), 4) across reproductive timepoints in mPFC (7.5dpc, 17.5dpc, 2dpp, 21dpp, NP, PP), 5) across reproductive timepoints in vHpc (7.5dpc, 17.5dpc, 2dpp, 21dpp, NP, PP), 6) in dHpc examining effect of stress (NP, Control PP, Stress PP), and 7) in dHpc examining effect of chemogenetic suppression in NP (NP-mCherry, NP-hM4Di, PP-mCherry, PP-hM4Di), 8) human dorsal subiculum tissue between subjects with 0 births (NP) vs. 1-2 births (Parous)

first: Giuseppina

last: di Salvo

first: Ashley

last: Cunningham

first: Sohini

last: Dutta

first: Elizabeth

last: Brindley

first: Ethan

last: Wan

first: Cindy

last: Zhang

first: Ian

last: Maze


title: Targeting CBX3 by a dual BET/PLK1 inhibitor enhances the anti-tumor efficacy of CDK4/6 inhibitors in prostate cancer

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

summary: Castration-resistant prostate cancer (CRPC) after commencement of Androgen deprivation therapy (ADT) seriously shorten the life span of patients with prostate cancer. The BET inhibitors and CDK4/6 inhibitors have shown efficacy in preclinical models of prostate cancer. We previously reported that CDK4/6 inhibitors overcome the resistance of CRPC to BET inhibitors by destabilizing BRD4, which indicates that the combination of CDK4/6 inhibitors and BET inhibitors is also promising for the treatment of CRPC. In this study, we attempted to exploit the candidates affecting the antitumor activity of CDK4/6 inhibitors and BET inhibitors in CRPC. Our data demonstrated that CBX3 is almost positively correlated with the cell cycle of multiple malignancies and is downregulated by BET inhibitors. Then, we showed that CBX3 is transcriptionally upregulated by BRD4 in CRPC cells. Moreover, we demonstrated that CBX3 modulates the sensitivity of CRPC to CDK4/6 inhibitors through binding with RB1 to release E2F1. Furthermore, we revealed that PLK1 phosphorylates CBX3 to enhance the interaction between RB1 and CBX3, and desensitized CRPC cells to CDK4/6 inhibitors. Given that BRD4 regulates CBX3 expression and PLK1 affects the binding between RB1 and CBX3, we proposed that a dual BRD4/PLK1 inhibitor could increase the sensitivity to CDK4/6 inhibitors partially through CBX3 in CRPC cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the prostate cancer after inhibition, knockdown and overexpression of CBX3 by siRNA, plasmids and BRD4/PLK1 dual inhibitor (BI-2536).

first: Xin

last: Jin


title: A forward genetic screen identifies Sirtuin1 as a driver of neuroendocrine prostate cancer [RNA-Seq]

first: Alessandro

last: Vasciaveo

overall_design: To perform the Sleeping beauty (SB) mutagenesis screen, we used the NPp53 mice (for Nkx3.1CreERT2/+; Ptenflox/flox; Trp53flox/flox) (Fig. 1A). These mice develop prostate adenocarcinoma that progresses to CRPC following androgen deprivation (via castration) and that can further progress to advanced prostate cancer phenotypes, including NEPC, following treatment with second generation the anti-androgens (ref). We, therefore, reasoned that this GEMM would serve as an excellent model to screen for drivers of advanced prostate cancer. As a control, we used the NP mice (for Nkx3.1CreERT2/+; Ptenflox/flox), which develop well-differentiated prostate adenocarcinoma that develops CRPC following androgen deprivation but does not progress to more advanced phenotypes following treatment with second generation anti-androgens (ref). Activation of the Nkx3.1CreERT2 allele via tamoxifen induction leads to temporal and spatial recombination of Pten and/or Trp53 specifically in the prostatic epithelium


title: Lnc-DC in differentiated keratinocytes

city: ChongQing

first: Xue-ting

last: Hu

address: No. 10, Changjiang Branch Road, Yuzhong District

institute: Daping Hosptial，Army Medical University

summary: Lnc-DC knockdown in HaCaT cells leads to decreased expression of terminal differentiation genes. Results indicate that lnc-DC modulates keratinocytes differentiation.

overall_design: To determine the differentiation signature for HaCaT keratinocytes, with lnc-DC gene silencing, total RNA was isolated in biological replicates from cells induced to differentiate and performed RNA-seq

first: Xiao-feng

last: Wu


title: 15 neurodevleopmenal disorder associated genes in development and differntiation of brain organoids [Ampliconseq]

status: Public on Apr 12 2026

city: New Haven

first: Huanyao

last: Gao

state: Connecticut

address: 300 George St., Suite 901

institute: Yale University

summary: Associated with dataset "A CRISPR screen in human iPSC-derived neurons reveals convergent transcriptomic effects of neurodevelopmental disorder genes"

overall_design: H1-hESC-iCas9 cells were transduced with a pooled gRNA library containing four gRNAs per target gene with 20% of the library comprising non-targeting gRNAs. Following selection with 1 µg/mL puromycin, the established cell line was used to generate cortical organoids following a well-established protocol151 with slight modifications, The organoids were maintained in culture for ~80 days, at which DNA was extracted and sgRNA site was PCR cloned and submitted for Ampliconseq.

first: Meilin

last: Garcia

first: Kayla

last: Retallick-Townsley

first: April

last: Pruitt

last: Davidson

first: Novin

last: Balafkan

first: Jonathan

last: Warrell

first: Tzu-Chieh

last: Huang

first: Alfred

last: Kibowen

first: Zhiyuan

last: Chu

first: Yi

last: Dai

first: Sarah

middle: E

last: Fitzpatrick

first: Ran

last: Meng

first: Annabel

last: Sen

first: Sophie

last: Cohen

first: Olivia

last: Livoti

first: Suha

last: Khan

first: Charlotte

last: Becker

first: Andre

middle: L

last: Silva

first: Jenny

last: Liu

first: Grace

last: Dossou

first: Jen

last: Cheung

first: Susanna

first: Sadaf

last: Ghorbani

first: Peter

middle: M

last: Deans

first: Marisa

last: DeCiucis

first: Prashant

last: Emani

first: Hongying

last: Shen

first: Mark

last: Gerstein

first: Zuoheng

last: Wang

first: Laura

last: Huckins

first: Ellen

last: Hoffman

first: Kristen

last: Brennand


title: B12 promotes gut dysbiosis and an inflammatory microenvironment that potentiates myeloid biased Tet2-deficient hematopoiesis [dataset 1]

city: Miami

first: Luisa

last: Cimmino

state: Florida

address: 1501 NW 10th Ave, BRB 711

institute: University of Miami

summary: Recent studies have linked elevated vitamin B12 serum levels with the presence of Clonal Hematopoiesis (CH) and an increased risk of developing myeloid malignancy. High B12 supplementation increases serum levels, alters gut microbial composition, and reduces the production of short-chain fatty acids (SCFAs), which help maintain gut barrier function and mucosal integrity. TET2 mutation is a frequent driver of CH that progresses in a positive feedback loop in response to microbial signals suggesting that B12 may influence CH via the gut microbiome. We evaluated the microenvironmental effects of B12 supplementation in a Tet2-deficient model of CH and found that B12 enhances myelopoiesis, heightens the responses of myeloid cells to bacterial stimuli, and increases the levels of circulating inflammatory cytokines. B12 supplementation also induced gut dysbiosis and reduced the levels of SCFA-producing bacteria in both wild-type and Tet2-deficient mice. Importantly, the effects of excess B12 were reversible upon oral supplementation with the SCFA butyrate. These findings suggest that B12 may promote CH progression by disrupting microbiome-derived SCFA metabolism, highlighting a potential therapeutic role for SCFA supplementation in mitigating CH.

overall_design: scRNAseq of mouse splenic CD45.2+CD11b+ Cells treated with Low B12 or High B12

last: Lyon

first: Luis

last: Nivelo

first: Molly

last: Dalzell

first: Alejandro

last: Villarino


title: Construction of MeTA-inducible system in pancreatic cancer cell lines as well as a normal pancreatic ductal cell line

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

institute: Tohoku University Graduate School of Medicine

summary: Epigenetic gene silencing by aberrant DNA methylation is one of the important mechanisms leading to the loss of key cellular pathways in tumorigenesis. In order to identify critical hypermethylated and silenced genes in cancer cells, we have developed the method called methyl-CpG targeted transcriptional activation (MeTA), which can globally reactivate hypermethylated genes in the genome. In MeTA, a fusion gene comprised of the MBD from MBD2 protein and the NFkB transcriptional activation domain (AD) is transfected into cancer cells. Then MBD specifically binds to the promoter regions of hypermethylated genes, and NFkB (AD) recruits p300/CREB-binding protein (CBP) and reactivates epigenetically silenced genes. We have constructed a tetracycline-inducible NFkB (AD)-MBD (MeTA) expressing system using pancreatic cancer cell lines MIA PaCa-2, PK-1, and PK-9 as well as one normal pancreatic epithelial cell line HPDE. MeTA induction significantly suppressed cell growth and caused apoptosis in both PK-1 and PK-9.

overall_design: Three pancreatic cancer-derived cell lines, PK-1_MeTA#17, PK-9_MeTA#15 and MIA PaCa-2_MeTA#3 and a normal pancreatic ductal epithelial cell line HPDE_MeTA#1, that allow tetracycline-regulated NFkB(AD)-MBD expression were constructed. The RNAs from these cell lines with (4 days tetracycline treatment) or without tetracycline were prepared and analyzed by using Agilent whole human genome microarray (4×44K).

first: Shunichi

last: Tsuge


title: Micro RNA expression in human skeletal muscle mitochondria

first: Jessica

last: Silver

address: 221 Burwood Highway

summary: MiRNAs are non-coding RNAs that regulate gene expression. MiRNAs mostly localise within the cytosol but are also found in the mitochondria where they can regulate the expression of mitochondrial-encoded transcripts. Aberrant miRNA expression is linked to mitochondrial dysfunction in chronic metabolic conditions. However, the role of miRNAs in the regulation of mitochondrial function in healthy tissue, such as in response to exercise, is not known. The aim of this study was to use a small RNA library preparation approach to profile the entire population of miRNAs in human skeletal muscle mitochondria and investigate if mitochondrial miRNA expression was altered following an acute endurance exercise.

overall_design: Participants (n=12) completed 60 mins of continuous cycling at 70% VO2 peak. Mitochondria were isolated from skeletal muscles obtained pre-exercise, immediately post-exercise and 3h post-exercise.

first: Stella

last: Loke

first: Larry

last: Croft

first: Adam

last: Trewin

first: Danielle

last: Hiam

first: Severine

last: Lamon

first: Glenn

last: Wadley


title: In vivo RNA sequencing identifies the lncRNA ReLoV critical for morphological transition and virulence in Candida albicans I

city: Wuhan

first: Hao

last: Cui

address: Wuhan University, 299 Bayi Road, Wuchang District, Wuhan, Hubei, P.R. China

institute: Wuhan University

summary: Candida albicans is the most prevalent fungal pathogen of humans responsible for nosocomial infections with high mortality rates. Despite its clinical importance, mechanisms governing C. albicans pathogenicity are incompletely understood. To identify long noncoding RNAs (lncRNAs) implicated in the pathogenicity of C. albicans, we performed in vivo Strand-specific RNA sequencing (RNA-seq) in a murine model of systemic infection. We found that hundreds of lncRNAs were expressed by C. albicans during invasive infection, among which 170 were unannotated so far. We further showed that a considerable number of lncRNAs were differentially expressed in fungal cells that invade into murine kidneys relative to uninfected (UI) cells. Differential expression of lncRNAs was validated by qRT-PCR assay. We identified ReLoV, an uncharacterized lncRNA, whose expression was significantly induced upon in vivo infection. The relov Δ/Δ mutant failed to develop elongated filaments in murine kidneys and displayed an attenuated virulence in a systemic infection model. The expression of ReLoV was also increased in response to multiple filament-inducing stimuli, including serum, neutral pH (Lee’s) and rapamycin. ReLoV was critical for hyphal maintenance, but is dispensable to initiate hypha formation. The lack of ReLoV reduced the transcript of UME6, a hypha-specific transcriptional activator that controls the level and duration of hypha-specific transcription, during hyphal elongation but not initiation. We suggest that misregulation of UME6 level in the relov Δ/Δ mutant causes its defects in hyphal development during invasive infection, as well as under in vitro hypha-inducing conditions. Collectively, these data uncover the lncRNA ReLoV as an additional layer of genetic regulation of morphogenesis and pathogenesis in C. albicans.

overall_design: To investigate the functional differences between the newly identified lncRNA Relov and its adjacent gene UME6 during Candida albicans hyphal development, we obtained gene expression profiles of the Relov deletion mutant, ume6 deletion mutant, and wild-type strain under hyphal induction conditions, with the wild-type group serving as the control.

first: Yi

last: Wang

first: Youzhi

last: Zhao

first: Tianxu

first: Gang

last: Luo

first: Yang

last: Lu

first: Chang

last: Su


title: RNAseq validation of Neurodevelopmental disorder associated genes knockout efficiency [RNAseq]

first: Huanyao

last: Gao

overall_design: The H1 hESC line with iCas9 (NIHhESC-10-0043) was used to assess the editing efficiency of the gRNAs and conduct the mitochondrial pooled and arrayed experiments. NPCs were generated using the dual SMAD inhibition approach per the STEMdiff SMADi Neural Induction Kit protocol (STEMCell Technologies, #08581). To validate gene KO, NPCs were transduced with LV particles carrying four gRNAs per target gene. After 48 h of selection with 1 µg/mL puromycin, Cas9 expression was induced by adding dox at 2 µg/mL for 72 h. Following induction, cells were collected for bulk RNA-seq.

first: Meilin

last: Garcia

first: Kayla

last: Retallick-Townsley

first: April

last: Pruitt

first: Elizabeth

last: Davidson

first: Novin

last: Balafkan

first: Jonathan

last: Warrell

first: Tzu-Chieh

last: Huang

first: Alfred

last: Kibowen

first: Zhiyuan

last: Chu

last: Dai

first: Sarah

last: Fitzpatrick

first: Ran

last: Meng

first: Annabel

last: Sen

first: Sophie

last: Cohen

first: Olivia

last: Livoti

first: Suha

last: Khan

first: Charlotte

last: Becker

first: Andre

last: Silva

first: Jenny

last: Liu

first: Grace

last: Dossou

first: Jen

last: Cheung

first: Susanna

first: Sadaf

last: Ghorbani

first: Peter

last: Deans

first: Marisa

last: DeCiucis

first: Prashant

last: Emani

first: Hongying

last: Shen

first: Mark

last: Gerstein

first: Zuoheng

first: Laura

last: Huckins

first: Ellen

middle: J

last: Hoffman

first: Kristen

last: Brennand


title: A novel triple-action Pt(IV) prodrug presents multiple anti-cancer effects and overcomes cisplatin resistance [ATAC-seq]

city: Jerusalem

first: Sheera

last: Adar

institute: Hebrew University of Jerusalem

overall_design: We performed ATAC-seq in A2780 cells, treated with either 200 µM of cisplatin or 30 µM of cPVP for 2h, with 2 replicates for each treatment.

first: Ya'ara

last: Negev-Korem

first: Hadar

last: Golan-Berman

first: Elisheva

last: Heilbrun

first: Subhendu

last: Karmakar

first: Yoram

last: Soroka

first: Marina

last: Frušić-Zlotkin

first: Ofer

last: Chen

first: Hiba

last: Hassanian

first: Dan

last: Gibson

first: Ron

last: Kohen


title: Comparison of induced pluripotent stem cells derived neurons from patient with heterozygous GBA mutation N370S and controls

city: Tübingen

first: Dina

last: Ivaniuk

address: Otfried Müller Str. 23

country: Germany

institute: DZNE

summary:
We performed global gene expression profile to investigate impact of GBA mutation on cellular function of dopaminergic neurons
Pathway analyses of differentially regulated genes revealed mitochondrial function as one of the most dysregulated pathways in patient neurons, thus confirming the impact of GBA mutations on mitochondria

overall_design:
Control (n=3) and GBA-PD iPSCs with heterozygous N370S mutations (n=3) were differentiated into dopaminergic neurons, enriched by FACS sorting at DIV55 based on a surface marker code CD24high CD29− CD184− CD44− CD15− and subjected to microarray analysis

Contributor: Atlas Biolabs

first: David

last: Schöndorf


title: In vivo RNA sequencing identifies the lncRNA ReLoV critical for morphological transition and virulence in Candida albicans II

first: Hao

last: Cui

overall_design: To determine whether lncRNAs play a role during Candida albicans infection, we performed RNA-seq to obtain expression profiles at 24 hours and 48 hours post-infection, with an uninfected group serving as the control. The RNA-seq analysis was applied on the kidney, which is frequently the most heavily infected organ with hematogenously disseminated candidiasis.

first: Yi

last: Wang

first: Youzhi

last: Zhao

first: Tianxu

first: Gang

last: Luo

first: Yang

last: Lu

first: Chang

last: Su


title: Transcriptomic profiling of splenic CD4+ T cells in DSS-induced colitis mice treated with Akkermansia muciniphila

city: chengdu

first: Mingshan

last: Jiang

institute: west china hospital

summary: This study provides a transcriptomic dataset of splenic CD4+ T cells isolated from a DSS-induced colitis mouse model. Mice were treated with Akkermansia muciniphila or PBS as control. RNA sequencing was performed to characterize gene expression changes associated with microbial intervention. The dataset includes gene-level raw count matrices and normalized expression values (FPKM), providing a resource for investigating host–microbiome interactions and immune regulation in inflammatory bowel disease.

overall_design: Splenic CD4+ T cells were isolated from DSS-induced colitis mice. Two groups were analyzed: mice treated with Akkermansia muciniphila and control mice treated with PBS. RNA-seq was performed on three biological replicates per group. Gene expression profiles were generated and quantified at the gene level.


title: Effect of overexpression of PPFIA1 on gene expression in HepG2 cells

first: li

last: xiao

summary:
To investigate the  function PPFIA1 protein in the regulation of HepG2 cells, we established HepG2 cell lines in which PPFIA1 target gene has been overexpressed.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2different cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for overexpression  Flag- cells and Flag-PPFIA1cells

first: Yixiao

last: Li


title: A novel triple-action Pt(IV) prodrug presents multiple anti-cancer effects and overcomes cisplatin resistance [Damage-seq]

first: Sheera

last: Adar

overall_design: We performed Damage-seq in A2780 cells, treated with either 200 µM of cisplatin or 30 µM of cPVP for 2h, with 2 replicates for each treatment.

first: Ya'ara

last: Negev-Korem

first: Hadar

last: Golan-Berman

first: Elisheva

last: Heilbrun

first: Subhendu

last: Karmakar

first: Yoram

last: Soroka

first: Marina


title: Higher basal tumor immune activity coupled with a systemic immune response improves liver cancer outcomes

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

institute: Westmead Institute of Medical Research

summary: This study examines how systemic immune responses and liver immune activity influence liver tumor development. In a diethylnitrosamine (DEN)‑induced mouse model of hepatocellular carcinoma, mice were fed different diets for 26 weeks to assess the impact of metabolic and inflammatory conditions on tumor progression. Tumor burden varied across diets, with increased tumor formation in some diets and a diet with combined cholesterol and cholic acid showing tumor burdens similar to controls. Flow cytometry revealed that mice on the combined diet exhibited the strongest expansion and activation of bone marrow hematopoietic stem and progenitor cells (HSPCs). RNA‑seq was performed on tumor and non‑tumor liver tissues to profile diet‑associated transcriptional changes, and weighted gene co‑expression network analysis (WGCNA) identified conserved immune‑related gene expression modules. Enhanced systemic hematopoietic responses were associated with stronger liver immune gene expression and increased innate immune cell infiltration, correlating with reduced tumor burden. These findings highlight a link between systemic hematopoietic activation, hepatic immune responses, and liver tumor outcomes.

overall_design: Male C57BL/6 mice were injected intraperitoneally with 25 mg/kg body weight of diethylnitrosamine (DEN) at 14 days of age. These mice were then given the diets containing 34% Sucrose (HS diet), cholic acid (0.5%) added diet (CA diet), or a cholesterol rich diet (2%) which contained high sucrose (34%), 2% cholesterol and 0.5% cholic acid (ChR diet) starting from week 22 for 14 weeks. The control group was fed with the normal chow (NC) diet throughout the experiment. The mice were harvested at 34 weeks after injection (at the age of 36 weeks).

first: Esmaili

last: Saeed


title: Bile acids mediate liver-bone marrow crosstalk

summary: This study examines the impact of tumor presence on bone marrow hematopoiesis in mouse models of liver cancer. Using a Hepa1-6 xenograft model in C57BL/6 mice, hematopoietic stem and progenitor cell populations were analyzed by flow cytometry. Although overall HSPC frequencies did not differ between tumor-bearing and control mice, tumor size positively correlated with HSPC numbers. RNA-seq comparison between xenograft and DEN-induced liver tumors revealed distinct transcriptomic profiles, indicating that xenograft tumors do not fully recapitulate the liver tumor microenvironment.

overall_design: Hepa1-6 mouse hepatoma cells were cultured in DMEM supplemented with 10% FBS, penicillin-streptomycin, and GlutaMAX. Cells were resuspended at 1×10⁷ cells/mL, mixed 1:1 with growth factor-reduced Matrigel, and 1×10⁶ cells were injected subcutaneously into the flanks of 6–8-week-old C57BL/6 mice. Tumors were harvested after 4 weeks or when tumor weight reached ~1 g.


title: Leucine, Autoimmune Diseases, and Circulating Mediators Shape the Causal Landscape of Lymphoid Malignancies

city: Bonn

first: Jingjing

last: Pu

address: Auf dem Hügel 41, 2.0G

institute: Universitätsklinikum Bonn

summary: This study investigated environmental and metabolic determinants of lymphoid malignancies (LM) using a systematic Mendelian randomization analysis of 10,090 GWAS traits from the IEU OpenGWAS database. Autoimmune diseases, including hyperthyroidism and membranous nephropathy, were identified as risk factors for LM, and mediation analysis suggested circulating promotilin, monounsaturated fatty acids, and glucose as potential mediators. Leucine was identified as a protective factor. Findings were evaluated in large epidemiological cohorts and UK Biobank multi-omics data, and further examined in lymphoid malignancy cell lines and an MH/NRASG12D B-cell precursor acute lymphoblastic leukemia mouse model. High-leucine conditions suppressed cell proliferation and induced apoptosis in vitro, while a high-leucine diet prolonged survival in vivo. Higher plasma leucine levels were also associated with improved clinical outcomes in B-ALL and CAR-T-treated B-cell lymphoma cohorts.

overall_design: Human B-cell precursor acute lymphoblastic leukemia cell line NALM-6 was cultured under normal leucine (50 mg/L) or high leucine (550 mg/L) conditions. Total RNA was extracted from NALM-6 cells using Vazyme RNA Isolator (R401-01), and RNA-seq libraries were subjected to paired-end sequencing on the BGI-2000 platform. This study was designed to compare transcriptomic changes in NALM-6 cells under different leucine conditions and identify leucine-responsive genes/pathways.

first: Dongguo

last: Liang

first: Yan

last: Ren

first: Qiong

first: Amit

last: Sharma

first: Ingo

middle: G

last: Schmidt-Wolf


title: hnRNPC specifically promotes SARS-CoV-2 frameshifting

city: Beijing

first: Jinchen

last: Xu

address: Tiantan xili

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: We analyzed whether hnRNPC facilitates the expression of viral non-structural proteins, which are essential for viral RNA replication. Ribosome profiling was performed on Vector, hnRNPC1, hnRNPC2 and HSD17B13 overexpressing Huh7 cells infected with HCoV-229E

overall_design: Ribosome profiling was performed onVector, hnRNPC1, hnRNPC2 and HSD17B13 overexpressing Huh7 cells infected with HCoV-229E. Ribosome profiling was performed by CloudSeq Inc. (Shanghai, China) following the GenSeq Ribo Profile Kit manual (GenSeq, Inc.).

first: Jingchen

first: Zonggen

last: Peng


title: Single cell RNA and DNA profiling of aged rat kidney

city: Philadelphia

first: Hanzhi

last: Wang

address: 422 Curie Blvd

institute: University of Pennsylvania

summary: We have employed a novel technology based on 10X platform to simultaneously detect DNA and expression following nucleosome depletion (DEFND-seq) to kidney cortex samples of rats from different age groups. This study characterized somatic copy number alteration of rat chromosomes during aging and associated gene expression changes during aging, especially in an injured proximal tubule cell population.

overall_design: We performed DEFND-seq and single-cell multiome ATAC+ gene expression on nuclei isolated from kidney cortex of Wistar male rats of age 16, 30, 56 and 82 weeks.

last: Verma

first: Xiao

last: Xiao

first: Wilson

last: Parker


title: Integrated single-nucleus RNA-seq dataset of mouse brain from a multi-factorial benchmarking study

city: Xi'an

first: Jin

last: Ning

state: --- Select One ---

address: Yanta Road 76, Yanta District

institute: Xi'an Jiaotong Univeristy

summary: Single-nucleus RNA sequencing (snRNA-seq) is pivotal for dissecting cellular heterogeneity in the brain, yet the individual and interactive effects of technical variables on cell composition and gene expression remain poorly quantified. Here we present the first multi-factorial benchmarking study of snRNA-seq technical confounders in the adult mouse brain, by performing a systematic evaluation of tissue harvest methods (post-mortem vs. in vivo) and nuclear fixation (methanol-fixed vs. fresh), using the identical sequencing platforms (SeekOne Digital Droplet). We find that standard post-mortem harvest induces a rapid, selective loss of metabolically active glutamatergic neuron subpopulations, which obscures transcripts related to advanced cognitive functions while preserving overall cellular proportions. While methanol fixation minimally alters cell-type composition, it introduces cell-type-specific gene expression shifts that preferentially stabilize structural and core functional transcripts. We validated these technical artifacts to provide a systematic map of confounders, identifying glutamatergic neurons as uniquely vulnerable to workflow-induced bias. Our study offers a robust experimental and analytical framework to separate technical noise from true biological signal. These findings establish that precise reporting and control of workflow variables are prerequisites for building reproducible, integrative brain cell atlases and ensuring accurate biological discovery in single-cell transcriptomics.

overall_design: The study presents a four-arm benchmarking pipeline utilizing the SeekOne Digital Droplet platform to isolate the effects of tissue harvest and nuclear fixation on the adult mouse brain transcriptomic landscape. To evaluate these technical variables, we employed a singleton design without biological replicates (n=1 per group). A single distinct sample was processed for each protocol combination, utilizing either standard post-mortem harvest or in vivo stabilization, and subsequently processed either fresh (no fixation) or subjected to methanol fixation prior to library preparation.

first: Ye

last: Li

first: Minxi

last: Shi

first: Xuzhao

last: Bian

first: Shiquan

last: Sun


title: Blocking NKp46-CCR6-ILC3 autophagy alleviates necrotizing enterocolitis by restoring energy metabolism balance [ATAC-Seq]

city: Guangzhou

first: Junyu

last: He

address: School of Basic Medicine, Southern Medical University, Guangzhou

institute: School of Basic Medical Sciences, Southern Medical University

summary: Group 3 innate lymphoid cells (ILC3s) play a crucial role in intestinal inflammatory disorders such as necrotizing enterocolitis (NEC) in neonates; however, the mechanisms by which ILC3s contribute to NEC remain unclear. In this study, single-cell transcriptomics, in vivo experiments on T cell-deficient mice, and targeted cell interventions demonstrated that NKp46−CCR6− (double-negative, DN) ILC3 autophagy significantly impacts NEC development by regulating intracellular metabolism. Mice lacking ATG5 or treated with autophagy inhibitors exhibited reduced ILC3 abundance and impaired ILC3 function, alleviating NEC. Mechanistically, ATG5 deficiency enhanced fatty acid metabolism while reducing glycolysis. Conversely, inhibiting fatty acid oxidation or supplementing with lactate restored the quantity and functionality of ATG5-deficient DN ILC3s, exacerbating NEC. Lipid metabolism analyses combined with a mouse model of NEC indicated that phosphatidylcholine supplementation alleviated intestinal inflammation by inhibiting DN ILC3 autophagy. Clinically, patients with NEC showed elevated ILC3 levels and significant enrichment of autophagy genes. These findings highlight the importance of DN ILC3 autophagy in metabolic adaptation, suggesting potential strategies for managing NEC.

overall_design: Comparison of chromatin accessibility for DN ILC3 genes between Atg5fl/fl mice and RorccreAtg5fl/fl mice

first: Yumei

first: Yuxiong

last: Guo

first: Kai

last: Wu

first: Laiqin

first: Qiqiong


title: Blocking NKp46-CCR6-ILC3 autophagy alleviates necrotizing enterocolitis by restoring energy metabolism balance [scRNA-seq]

overall_design: Breastfeeding mice and NEC model mice intestinal ILC cell proportions and gene expression

first: Xinyao