title: Sequence and structural determinants of efficacious de novo chimeric antigen receptors

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Advances in generative protein design using artificial intelligence (AI) have enabled the rapid development of binders against heterogeneous targets, including tumor-associated antigens. Despite extensive biochemical characterization, these novel protein binders have had limited evaluation as agents in candidate therapeutics, including chimeric antigen receptor (CAR) T cells. Here, we synthesize variable generative protein design workflows to screen 1,487 novel protein binders targeting BCMA, CD22, and CD19 for efficacy in scalable protein binding and T cell assays. We identify three main challenges that hinder the utility of de novo protein binders as CARs, including tonic signaling, occluded epitope engagement, and off-target activity. We develop computational and experimental heuristics to overcome these limitations, including screens of sequence variants for individual parental structures, that restore on-target CAR activation while mitigating liabilities. Together, our framework accelerates the development of AI-designed proteins for future preclinical therapeutic screening, helping enable a new generation of cellular therapies.

overall_design: Primary CAR T cells with different binder constucts were co-cultured with different target cell lines, hashed, mixed, and profiled via high-throughput single-cell RNA-seq profiling

first: Arthur

last: Chow

first: Hoyin

last: Chu


title: Sorted bulk RNA-seq profiling of human peripheral blood mononuclear cell populations across diverse in vitro immune stimuli

status: Public on Jul 06 2026

city: Oxford

first: Matt

last: Jackson-Wood

address: 9400 Business Park, Garsington Road

country: United Kingdom

institute: Gilead Sciences

type: Expression profiling by high throughput sequencing

summary: Human peripheral blood mononuclear cells (PBMCs) from healthy, de-identified donors were stimulated in vitro with a subset of immune stimuli and profiled by bulk RNA sequencing following fluorescence-activated cell sorting (FACS). Following a 48-hour assay, major immune cell populations were isolated, including monocytes, CD4+ T cells, CD8+ T cells, and B cells, and subjected to RNA-seq. This dataset captures cell type-specific transcriptional responses to B cell stimulator cells (BCS), CytoStim™, lipopolysaccharide (LPS), and IFN-α, alongside unstimulated baseline controls.

overall_design: Peripheral blood mononuclear cells isolated from 6 healthy human donors were exposed in vitro for 48 hours to B cell stimulator cells (BCS), CytoStim™, lipopolysaccharide (LPS), IFN-α, or unstimulated baseline control conditions. Following stimulation, major immune cell populations were isolated by FACS on a BD FACSAria™ Fusion using lineage markers for monocytes (CD14+), CD4+ T cells (CD3+, CD4+), CD8+ T cells (CD3+, CD8+), and B cells (CD19+, CD20+). RNA was extracted from sorted cells and transcriptomes measured by bulk RNA-seq.

first: Oliver

last: Wood

first: Adam

middle: T

last: Braithwaite

first: Matthew

middle: A


title: Dosage-dependent role of Gata3 in primitive endoderm and trophectoderm specification in embryonic stem cells [RNA-seq]

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway

country: USA

institute: University of Texas at Austin

summary: Transcription factors (TFs) are critical regulators of cell fate decisions, and their intricate balance determines lineage specification during early development. Gata3 is a well-established TF in the trophectoderm (TE) development, and its ectopic expression can reprogram mouse embryonic stem (ES) cells into trophoblast stem (TS) cells. Because of Gata3’s canonical role in TE, its potential involvement in primitive endoderm (PE) differentiation has remained unexamined, representing a previously overlooked avenue of investigation. Here, we reveal that Gata3 functions as a dosage-sensitive switch governing lineage commitment in mouse ES cells. Modulating Gata3 expression revealed that high levels (Gata3-H) drive TE specification, whereas lower levels (Gata3-L) promote PE differentiation, as evidenced by distinct morphological transitions, transcriptional profiles, chromatin-binding, and functional assays. Mapping targets of Gata3 revealed differential occupancy patterns at PE- versus TE-associated enhancers correlating with dose. In vitro 3D blastoid models confirmed that Gata3 dosage alone is sufficient to drive spatial segregation, with Gata3-L and Gata3-H cells preferentially localizing to PE- and TE-like compartments, respectively. Our findings highlight Gata3’s pioneer factor-like behavior, downregulation of pluripotency networks, and latent capacity to direct lineage specification beyond its classical TE specification. These results expand the understanding of Gata family TFs in early embryogenesis and provide mechanistic insights for stem-cell based models for lineage specification.

overall_design: RNA-seq was conducted on Gata3-overexpressed mESC at low (Gata3-Low) and high (Gata3-High) levels for 0, 1, 3, 5 days of dox treatment.

first: Yeejin

last: Jang

first: Mijeong


title: Dosage-dependent role of Gata3 in primitive endoderm and trophectoderm specification in embryonic stem cells [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq was conducted on Gata3-overexpressed mESC at low (Gata3-Low) and high (Gata3-High) levels (no induction or 2 days of dox treatment).


title: Bulk RNA-seq of young HSCs and Selp high vs Selp low HSCs in pre-aged mice

city: Tianjin

first: Chong

last: Yang

state: Tianjin

address: 288 Nanjing Rd, Tianjin 300020, China.

country: China

institute: Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Hematopoietic stem cells (HSCs) undergo functional and molecular alterations during aging that impair regenerative capacity and bias lineage output. P-selectin (Selp/CD62P) expression has been associated with inflammatory and stress-responsive hematopoietic states, but its transcriptional impact within the HSC compartment during early aging remains incompletely defined. In this study, we performed bulk RNA sequencing of phenotypically defined HSCs isolated from young mice and from pre-aged mice in which HSCs were further stratified based on Selp surface expression (Selp_high and Selp_low). Comparative transcriptomic analysis was conducted to identify gene expression programs associated with early aging and Selp-associated heterogeneity within the HSC pool. These data provide a resource for understanding molecular pathways linked to HSC functional decline and inflammatory priming during the initial stages of hematopoietic aging.

overall_design: HSCs were isolated from mouse bone marrow by fluorescence-activated cell sorting based on established immunophenotypic markers defining the SLAM HSC compartment. Three biological groups were analyzed: HSCs from young mice, and HSCs from pre-aged mice further stratified into Selp_high and Selp_low fractions according to surface Selp expression levels. Total RNA was extracted from sorted cells, and bulk RNA-seq libraries were generated and sequenced on an Illumina platform. Reads were quality controlled, aligned to the mouse reference genome.

first: Toshio

last: Suda


title: Innervated human cardiac muscle model reveals sympathetic drivers of KCNH2-associated arrhythmias

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: DZNE Göttingen

summary: Cardiac autonomic neurons control cardiac contractility. Dysregulation of the autonomic nervous system can lead to sympathetic overdrive resulting in heart failure and an increased incidence of fatal arrhythmias. Here, we introduce innervated engineered human myocardium (iEHM), a novel model of neuro-cardiac junctions, constructed by fusion of a bioengineered neural organoid (BENO) patterned to autonomic nervous system and engineered human myocardium (EHM). Projections of sympathetic neurons into engineered human myocardium formed presynaptic terminals in close proximity to cardiomyocytes and an extensive vascular network co-developing in the tissues. Contractile responses to optogenetic stimulation of the accordingly engineered neuronal component demonstrated functionality of the engineered neuro-cardiac junctions in iEHM. This model will serve as a human surrogate system to delineate neuron and cardiac cell contribution to brain and heart diseases and is an important step towards engineering a human brain to heart axis in a dish.

overall_design: Sympathetic neuronal organoids (SNO) were generated by culturing human induced pluripotent stem cells (hiPSC) in a 3D collagen matrix and step-wise addition of growth factors and small molecules to direct them toward an autonomic, predominantly sympathetic neuronal fate. The medium used for the SNO was based on neuron-specific Neurobasal-A medium. EHM were engineered by combining human foreskin fibroblasts and hiPSC-derived cardiomyocytes with bovine collagen and casting this mixture into a ring-shaped mold. EHM were matured for four weeks in an EHM-specific medium on auxotonic stretchers. After 40 days of culture, SNO were fused with EHM by placing the SNO in the center of the muscle ring to generate iEHM. From this day, iEHM were cultured in a mixture of neuron- and EHM-specific medium in a 1:1 ratio. At this time, SNO were transitioned to the same medium mixture to examine changes in the neuronal tissues unspecific neuro-cardiac interaction. At 6 weeks after fusion (SNO were 12 weeks old), one iEHM and SNO sample were snap-frozen, single nuclei were isolated, and their RNA was sequenced as described.

first: Lennart

middle: V

last: Schneider

first: Guobin

last: Bao

first: Dennis

middle: M

last: Krüger

first: Aditi

last: Methi

first: Ole

last: Jensen

first: Kea

last: Schmoll

first: Michael

middle: G

last: Setya

first: Sadman

last: Sakib

first: Aminath

middle: L

last: Fahud

first: Jürgen

last: Brockmöller

first: André

first: Norman

middle: Y

last: Liaw

first: Wolfram-Hubertus

last: Zimmermann

first: Maria-Patapia

last: Zafeiriou


title: Dosage-dependent role of Gata3 in primitive endoderm and trophectoderm specification in embryonic stem cells

first: Jonghwan

last: Kim

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

overall_design: Refer to individual Series


title: A multi-functional oral small molecule targeting energy and lipid metabolism as a treatment for diet-induced obesity [Exp 4]

city: Berkeley

first: Chi

last: Zhu

state: CA California

address: Morgan Hall, Rm238

department: Department of Nutritional Sciences & Toxicology

institute: University of California, Berkeley

summary: Obesity and related metabolic disorders have surged globally, representing a significant public health burden. These diseases are mechanistically interconnected through complex pathways involving dysregulated energy and lipid metabolism. As a result, therapeutic strategies that target a single molecule or pathway are unlikely to achieve optimal efficacy without inducing adverse effects. Here, we identified an orally bioavailable small molecule, 5-tetradecyloxy-2-furoic acid (TOFA), that effectively rebalances energy expenditure and lipid synthesis by both inhibiting acetyl-CoA carboxylases 1 and 2 (ACC1/2) and acting as a novel agonist of Peroxisome Proliferator-Activated Receptors alpha and delta (PPARɑ/δ). TOFA significantly alleviated obesity and associated metabolic dysfunctions in mouse models without side effects common to current treatments, such as muscle wasting. Moreover, TOFA acted synergistically with incretin analogs such as semaglutide and tirzepatide to improve obesity, dyslipidemia, and insulin resistance. Collectively, our findings suggest that the coordinated multi-targeting of lipid homeostasis and energy metabolism by TOFA is an effective approach to address multiple associated metabolic diseases.

overall_design: C57BL/6J wild type mice were exposed to a choline-deficient, L-amino acid-defined, high-fat diet (CDAA-HFD) for eight weeks followed by an oral dosing regimen of vehicle control or 125 mg/kg TOFA, BID for four weeks after which the hepatic transcriptome was analyzed; n=4-5/group.

first: Justin

last: Lee

first: Anders

last: Näär

first: Gracia

last: Bonilla

first: Ruslan

last: Sadreyev


title: A multi-functional oral small molecule targeting energy and lipid metabolism as a treatment for diet-induced obesity [Exp 3]

overall_design: C57BL/6J wild type mice (Jax strain 000664)or PPARɑ whole body knockout mice (Jax strain 008154) were exposed to a 60% high fat diet for ten weeks followed by an oral, daily dosing regimen of vehicle control or 200 mg/kg TOFA for two weeks after which the hepatic transcriptome was analyzed; n=4-5/group.


title: Racial discrepancies in placental gene expressions between Black and White healthy and preeclampsia patients of equivalent BMI and blood pressure in a Southeastern USA cohort

city: Augusta

first: Jessica

last: Faulkner

state: Georgia

address: 1120 15th Street

department: Physiology

institute: Augusta Univeristy

summary: Preeclampsia is a devastating hypertensive disorder of pregnancy that afflicts between 5-10% of pregnancies in the US, with a higher prevalence in the southern regions of the United States. Black pregnant women are disproportionally at higher risk for preeclampsia onset and severity of disease than other racial groups, including White women. Although this has been recognized in the maternal fetal medicine literature for many years, the underlying mechanism(s) for this racial disparity are unclear. One confounding issue with many studies of racial discrepancies in pregnant women is differences in comorbidities between racial groups. In our current study we were able to obtain a cohort of patients of self-identifying Black or White race that were overall matched for BMI, blood pressure, gestational age and parity and we hypothesized that genetic and placental markers of preeclampsia would be highest in our preeclampsia Black patients compared to healthy patients or White preeclampsia patients. We collected placenta tissue from this cohort of deliveries in Augusta, GA from both healthy and preeclamptic Black and White women (n=13-15). We measured expressions of several preeclampsia-implicated genes, as well as performed a placental morphological analysis and RNA sequencing of a subset of samples. Contrary to our hypothesis, our results from ddPCR analysis of genes associated with preeclampsia risk demonstrated that leptin, preproendothelin-1 (PPET-1) endothelial converting enzyme-1 (ECE-1) and soluble FMS-like tyrosine kinase-1 (sFlt-1) were higher in White preeclamptic women than in Black preeclamptic women. Our RNA sequencing analysis revealed that 136 genes significantly differed between White and Black normal pregnant patients, 288 genes differed between Black healthy and Black preeclampsia patients, while a striking 2394 genes significantly differed between White healthy and White preeclampsia patients and 2346 genes differed between White and Black preeclampsia patients. Placental histology analysis revealed that Black preeclampsia patients demonstrated a lower scoring of morphological pathologies associated with preeclampsia compared to White preeclampsia patients. Collectively, these data indicate that genetic predisposition to preeclampsia in White patients in the placenta differs greatly to that of Black patients, and that placental changes may be more subtle in Black patients that are at high risk for preeclampsia.

overall_design: Each group comprised a set of 6 samples, matched for BMI, which underwent RNA sequencing through Novogene (Sacramento, CA). Raw sequencing reads were obtained in FASTQ format, with adapter trimming already completed. Transcriptome alignment was performed using STAR (v2.7) with the GRCh38 human reference genome for mapping and annotation, applying default parameters. Subread (v2.0.3) was used for feature counting to create gene-level count matrices from the aligned reads. Differential expression analysis was conducted using DESeq2 in R, following standard normalization and statistical modeling procedures. Genes with a p-value < 0.05 were considered significantly differentially expressed. We used ClusterProfiler in R to perform Gene set enrichment analysis (GSEA) to identify enriched biological pathways.  PANTHER Pathway analysis online tool was conducted to further explore pathway-level functional annotations of differentially expressed genes. All computational analyses were carried out in an R-based environment, with statistical significance determined using appropriate multiple-testing corrections.

first: Madison

last: Ives

first: Gibson

last: Cooper

first: Cayman

last: Bickerstaff

first: Mona

last: Elgazzaz

first: Cassie

last: Sam

first: Amalia

last: Brawley

first: Safia

last: Ogbi

first: Elisabeth

last: Mellott

first: Desmond

last: Moronge

first: Stephanie

last: Stokes

first: Joanna

last: Hitchings

first: Luis

last: Zarate

first: Sravankumar

last: Kavuri

first: Padmashree

last: Woodham

first: James

last: Maher


title: mTORC1 activation induces B7-H3–dependent metabolic reprogramming in renal cell carcinoma (RCC)

status: Public on Jul 07 2026

city: Haining

first: Heng-Jia

last: Liu

state: Zhejiang

address: 718 East Haizhou Road

department: International Campus

institute: Zhejiang University - University of Edinburgh

summary: Renal cell carcinoma (RCC) affects over 435,000 people worldwide each year and remains a significant cause of cancer mortality. Aberrant activation of pathways such as mTORC1 is frequently observed in RCC, yet the mechanisms by which mTORC1 contributes to tumor development remain poorly understood. The lack of suitable animal models has limited progress in uncovering these mechanisms and advancing targeted treatments. Here, we performed single-cell transcriptomic, proteomic, and metabolomic profiling of kidneys from mice with embryonic Tsc2 deletion at E17.5, which revealed a distinct tumor cell population characterized by intercalated cell signatures, co-expression of Foxi1 and Rhcg, and hyperactivated mTORC1. These lesions closely resemble human chromophobe renal cell carcinoma (ChRCC), a subtype of RCC. The tumors show marked upregulation of the immune checkpoint molecule B7-H3. Mechanistically, the transcription factor NRF1 is elevated in Tsc2-deficient lesions and drives B7-H3 expression in tumor cells. In human specimens, B7-H3 is broadly expressed in both classical and sarcomatoid ChRCC and correlates with hallmark markers FOXI1, MUC2, and HEPACAM2. Strikingly, B7-H3 deletion in mice suppresses Tsc2 loss–driven cystic and tumor formation, restores amino acid metabolism, and attenuates aminoacyl-tRNA biosynthesis and proteasome activity. Collectively, these findings identify B7-H3 as a functional driver of Tsc2-mediated ChRCC and a promising therapeutic target in TSC-associated renal tumors.

overall_design: Comparative single-cell RNA expression profiling analysis of  kidneys from WT, TSC2 KO and TSC2/B7-H3 double KO mice.

first: Li

last: Keying

first: Heng

last: Du

first: Wang

last: Yifan

first: Damir

last: Khabibullin

first: Michel

last: Alchoueiry

first: Melissa

last: Daou

first: John

last: Asara

first: David

middle: J

last: Kwiatkowski

first: Elizabeth

middle: P

last: Henske


title: Single-Cell RNA Sequencing Unravels Interactions between Macrophages and Fibroadipogenic Progenitors during Ectopic Bone Formation in FOP Mice

city: Milan

first: Anna Sofia

last: Tascini

address: Via Olgettina, 60

department: Center for Omics Science

country: Italy

institute: IRCCS, Ospedale San Raffaele

summary: Fibrodysplasia ossificans progressiva (FOP) is a ultra rare disease causing the formation of extraskeletal bone in skeletal muscles and joint areas of affected patients, leading to progressive invalidation. To model the disease, we used the inducible Acvr1R206HloxP/loxP:CreERT2 mouse model. This study aims at investigating the early events occurring in FOP muscles, with a focus on unraveling if and how the interactions between macrophages and fibroadipogenic progenitors (FAPs) drive the formation of ectopic bone.

overall_design: Control (Acvr1R206HloxP/loxP:CreERT2) and FOP (Acvr1R206H/R206H:CreERT2) mice were used to characterize the transcriptomes of the regenerating muscle niche at two experimental timepoints: 5 and 7 days after muscular injury. The injury was performed by a mechanical compression of the gastrocnemius muscle in one of the two hindlimbs using a pair of tweezers. 5 and 7 days post-injury, muscles were collected, dissociated into single-cell suspensions and subjected to single-cell RNA sequencing. Each condition included three biological replicates from independent mice, generating data from a total of 12 independent samples.

first: Riccardo

last: Gamberale

first: Filipa

last: Timóteo-Ferreira

first: Cristiana

last: Barone

first: Mauro

last: Bergamaschi

first: Antonello

last: Spinelli

first: Emanuele

last: Azzoni

first: Silvia

last: Brunelli


title: RNA Sequencing Analysis of PFAS Impact on Liver Organoids

city: Beijing

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

summary: In order to gain a deep understanding of the effects of PFAS on liver organoids, we have constructed a liver organoid model based on human liver cells. We have treated liver organoids with two PFAS substances, namely PFOA and PFUnDA, and utilized transcriptomic sequencing technology. The purpose is to analyze the differentially expressed genes and the associated signal pathway changes in the liver organoids after treatment with these two substances, so as to provide molecular evidence for elucidating the role of PFAS in body metabolism.

overall_design: Hepatocyte organoids were cultured in a 24 - well plate until they reached a diameter of 100 - 200 micrometers. Then, the culture medium was replaced with differentiation medium. After 5 days of differentiation, they were exposed to PFOA (100μM) and PFUnDA (100μM) for 48 hours.

first: You

last: Lijuan

first: Ying

first: Tian

last: Yaru

first: Zhuang

last: Zhisen

first: Qiannan

last: Zhang

first: Xudong

last: Jia


title: A multi-functional oral small molecule targeting energy and lipid metabolism as a treatment for diet-induced obesity [Exp 2]

first: Chi

last: Zhu

overall_design: C57BL/6J mice were exposed to a 60% high fat diet for seven weeks followed by an oral dosing regimen of vehicle control or TOFA (one week of loading dose of 125 mg/kg followed by maintenance dosing 62.5 mg/kg, BID) for a total of three weeks after which the skeletal muscle transcriptome was analyzed; n=8/group.

first: Justin

last: Lee

first: Anders

last: Näär

first: Gracia

last: Bonilla

first: Ruslan

last: Sadreyev


title: A multi-functional oral small molecule targeting energy and lipid metabolism as a treatment for diet-induced obesity


title: A multi-functional oral small molecule targeting energy and lipid metabolism as a treatment for diet-induced obesity [Exp 1]

overall_design: C57BL/6J mice were exposed to a 60% high fat diet for seven weeks followed by an oral dosing regimen of vehicle control or TOFA (one week of loading dose of 125 mg/kg followed by maintenance dosing 62.5 mg/kg, BID) for a total of three weeks after which the hepatic transcriptome was analyzed; n=4/group.


title: UBE2N deficiency contributes to MASH development via p62-regulated mitophagy and PANoptosis

city: Osong-eup, Heungdeok-gu

first: WANG

last: FENG

state: Cheongju-si, Chungcheongbuk-do

address: Osongsaengmyeong ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, Republic of Korea

country: South Korea

institute: chungbun national university

summary: RNA-seq analysis of Liver tissue from Ubc13 flox/flox Alb negative and Ubc13 flox/flox Alb positive  mice.

overall_design: RNA_seq profiling of 2-month liver tissue of Ubc13 flox/flox Albmin negative and Ubc13 flox/flox Albmin positive mice.

first: FENG

last: Wang

first: Ekihiro

last: Seki

first: Yoon Seok

last: Roh


title: RNA-seq and ATAC-seq of Psc Su(Z)2 -/- intestinal stem cells in Drosophila

first: xi

last: rongwen

address: No. 7 Science Park Road, zhongguancun Life Science Park, Changping District,

institute: National Institute of Biological Sciences, Beijing

summary: Polycomb group (PcG) genes function as epigenetic silencers that maintain the repressive states of target genes essential for normal development. To elucidate the role of PRC1 components in the Drosophila midgut, we performed both RNA-seq and ATAC-seq analyses on intestinal stem cells (ISCs) deficient for PRC1 and Su(z)2. For RNA-seq controls, besides the esgts>GFP, we included ISCs harboring mutations in the Notch signaling pathway (N55e11) and the JAK-STAT pathway (dome468) as additional controls. What's more, ATAC-seq was also performed on pc-RNAi and E(z)-RNAi ISCs which represent other components of PRC1 and PRC2, respectively.

overall_design:
RNA-seq: Female flies with hs-flp, tubulin>GFP; Psc-Su(z)2XL26 FRT 42D, tublin>GAL80, and hs-flp, N55e11 FRT 19A, tubulin>GAL80; actin>GFP, and hs-flp, dome468 FRT 19A, tubulin>GAL80; actin>GFP genotypes were collected and cultivated at 25℃. After 4-6 days, the flies were placed in empty tubes, about 10 per tube, and heat-shocked in a 37℃-water bath for 1 hour. The flies were cultivated for another 2 weeks at 25℃, after that they would be dissected. Female flies with esgts>GFP genotype were collected and cultivated at 18℃ for 4-6 days year old, and then shifted to 29℃ for 7 days before dissecting. The GFP+ midgut epithelial cells were collected by FACS and analyzed using bulk RNA-seq.
ATAC-seq: Female flies with genotypes of hs-flp, tubulin>GFP; Psc-Su(z)2XL26 FRT 42D, tublin>GAL80 were collected and cultivated at 25℃. After 4-6 days, the flies were placed in empty tubes, about 10 per tube, and heat-shocked in a 37℃-water bath for 1 hour. The flies were cultivated for another 2 weeks at 25℃, after that they would be dissected. Female flies with esgts>GFP, esgts>PcRNAi, esgts>E(z)RNAi genotypes were collected and cultivated at 18℃ for 4-6 days year old, and then shifted to 29℃ for 7 days before dissecting. The GFP+ midgut epithelial cells were collected by FACS and analyzed using ATAC-seq .

first: Ruxue

last: Wei

first: Rongwen

last: Xi


title: Charting Novel Cellular Subpopulations in the Renal Cortex of Diabetic Nephropathy in a Mouse Model Through Single-Cell RNA Sequencing

city: Putian

first: Ruiyuan

last: Chen

state: Fujian

address: Fujian

institute: Taizhou University

summary: Type 1 Diabetes Mellitus (T1DM) is a prevalent autoimmune disorder character ized by the destruction of insulin-producing cells, often leading to diabetic kidney  disease (DKD). Despite extensive research, the cellular mechanisms underpinning  DKD remain poorly understood. This study aims to elucidate the cellular het erogeneity and specific cell populations involved in the renal cortex of diabetic  mice using single-cell RNA sequencing.  Kidney cortex cells from streptozotocin (STZ)-induced diabetic mice and healthy  controls were isolated and subjected to single-cell RNA sequencing. Statistical  analyses were performed to identify distinct cellular subsets and evaluate changes  in cell population dynamics. Immunohistochemistry and renal function evalua tions via Masson and Hematoxylin and Eosin staining were employed to validate  the sequencing data.  We first identified 11 distinct cellular subsets within the renal cortex. Diabetic  mice exhibited a significant increase in distal convoluted tubule cells compared to  controls. Additionally, a marked decrease in immune-related cells, including T and  Blymphocytes, neutrophils, and macrophages, was observed. Cell communication  analysis highlighted the role of the VISFATIN signaling pathway, particularly the  Nampt-Insr gene interaction, in the diabetic renal cortex.  Our findings reveal a unique cellular and molecular landscape in the renal  cortex of diabetic mice, emphasizing altered cell populations and signaling path ways critical in DKD progression. This study enhances our understanding of  T1DM-induced renal alterations and suggests potential targets for therapeutic  intervention to mitigate kidney complications in diabetes.

overall_design: Male C57BL/6 mice(22-25 g, 8 weeks old) were obtained from Hangzhou hangsi  Biotechnology Co., Ltd.. All animal experiments were conducted in accordance with  the Guidelines for the Care and Use of Laboratory Animals published by the National  Institutes of Health (NIH, USA), the ARRIVE guidelines, and were approved by  the Institutional Animal Care and Use Committee (IACUC) of Taizhou University  (Approval Number 20230012023002). For single-cell RNA sequencing, the mice were  divided into two groups: control (Ctrl) and diabetic (T1DM) groups. To induce dia betes, the diabetic mice received an intraperitoneal injection of 150 mg/kg of STZ,  as previously described [8]. The Ctrl mice received a similar volume of sodium cit rate [9–11]. The success of the diabetic model was confirmed by a glucose level over  16.7 mmol/L. Weekly measurements of body weight and blood glucose levels were  performed. We isolated intact cells from the renal cortex of healthy mice (group C) and mice  with streptozotocin (STZ)-induced diabetes mellitus (T1DM) (group D). Following  digestion and erythrolysis, a total of 9,021 cells from group C and 9,187 cells from group  D were procured for subsequent single-cell RNA-seq analysis.

first: Jiayue

last: Wan

first: Shi

last: Bai


title: Developmental programming of late-life proteostasis and longevity by NuA4 complex activity in early life [RNA-Seq]

city: Hangzhou

first: Lianfeng

last: Wu

state: Please select a state below

address: 600 Dunyu road

institute: Westlake University

summary: Maintaining proteostasis is essential for healthy aging and preventing neurodegenerative diseases like Alzheimer's disease, yet its collapse in late life leads to irreversible pathologies. It is unknown if there exists an early-life window where proteostasis can be programmed to confer lasting resilience, offering a preventative approach against these conditions. Leveraging short life cycle and the genetical tractability of Caenorhabditis elegans, we discover that inhibition of the TIP60/NuA4 acetyltransferase complex in early life can enhances late-life proteostasis and extends lifespan. We found that reducing early-life NuA4 activity diminishes epigenetic priming of H4K16ac, triggering compensatory activation of the XBP-1-mediated unfolded protein response (UPRER). This early-life-predominant XBP-1 activation remodels ER structure and reprograms lipid metabolism. Crucially, early-life NuA4/H4K16ac suppression boost oleic acid accumulation, which confers late-life health benefits. Overall, our study demonstrates the principle of developmental plasticity in shaping late-life proteostasis and reveals the potential for early interventions to combat neurodegeneration and aging.

overall_design: RNA-seq profiling of wild-type C. elegans at embryo 0h (E0), embryo 6h (E6) stage, L1 stage and Adult stage with control and mys-1 RNAi  treatment in parental generation

first: Yihan


title: Restoring NK cell cytotoxicity post-cryopreservation via synthetic IL-2-presenting cells

city: Homburg

first: Sijia

last: Zhang

state: Saarland

address: Saarland University. Center for Integrative Physiology and Molecular Medicine (CIPMM). Kirrberger Straße 100, 66424 Homburg, Germany.

department: Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine

institute: Saarland University

summary: Natural killer (NK) cells are critical components of the first-line immune defense, responsible for eliminating tumorigenic cells. NK cell-based adoptive immunotherapy has gained increasing attention; however, cryopreservation, a standard technique for NK cell storage,  significantly impairs NK cell cytotoxicity, particularly in physiological 3D environments. Here, we demonstrate that short-term co-culture with effector T cells markedly enhances NK cell motility and killing functionality. Notably, a brief 1-day co-culture is sufficient to restore cryopreservation-impaired NK cell functionality in 3D environments. This enhancement requires direct contact between T cells and NK cells, which facilitates localized high concentrations of IL-2 at the cell contact sites. To develop a controlled, donor-independent solution, we demonstrate that synthetic T cells with surface-bound IL-2 or IL-15 exhibit superior efficiency in revitalizing cryopreserved NK cells. These findings uncover a previously unrecognized role for physical contact-mediated local IL-2 or IL-15 signaling and provide an efficient, cost-effective, and tunable strategy to rescue NK cell functionality post-cryopreservation, paving the way for more scalable, potent, and clinically viable NK cell-based immunotherapies.

overall_design: RNA-seq of Human-NK cultured alone and Human-NK-T co-culture


title: The Znf711-Phf8 complex functions as a transcriptional rheostat essential for neutrophil development

city: Shanghai

first: Shuiyi

last: Tan

address: 197 Rui-Jin Road II, Shanghai, China

institute: CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics

summary: The development of neutrophils is regulated by various transcription factors and cofactors. In this study, we demonstrate that the zinc finger protein Znf711 and its interacting partner, the Phd finger protein Phf8, are critical for granulopoiesis. Notably, our mechanistic studies reveal that Znf711 and Phf8 no longer function synergistically as a well-characterized combination of transcriptional activator and coactivator during this process. Instead, Znf711 regulates neutrophil maturation in a DNA-binding independent manner by preventing its partner Phf8 from binding to chromatin. Furthermore, rather than solely acting as a histone lysine demethylase that activates transcription, Phf8, when SUMOylated, also plays a key role as a corepressor of the transcription factor Gfi1aa to inhibit the expression of the master myeloid regulator c/ebpα. Additionally, we identify a positive feedback loop between c/ebpα and znf711, which ensures a high level of c/ebpα expression at the early stages of terminal granulopoiesis to promote cell differentiation.

overall_design: To gain insight into the mechanism by which Znf711 regulates neutrophil development, RNA sequencing (RNA-seq) analyses were conducted on GFP+ cells enriched from wild-type Tg(mpx:eGFP) and znf711-/-//Tg(mpx:eGFP) larvae at 48 hpf

first: Huihui

last: Qian


title: Nanostring gene expression profiling in a mouse model of antibody-mediated rejection of kidney allografts

city: Cleveland

first: Karen

last: Keslar

state: OH

address: 9500 Euclid Avenue NB30

institute: Cleveland Clinic

summary: Acute and chronic antibody mediated rejection (ABMR) continues to decrease clinical kidney graft function and survival. Dysregulated donor-specific antibody (DSA) responses are induced in B6.CCR5-/- recipients of complete MHC-mismatched A/J kidney allografts with NK cells playing a critical role in the acute ABMR. We tested the role of neutrophils in ABMR by transplanting A/J kidneys to CCR5-/- mice with a deletion in the neutrophil serine protease cathepsin G. Whereas B6.CCR5-/- recipients rejected all kidney allografts between days 18-25, 70% of allografts survived beyond day 60 in B6.CCR5-/-cG-/- recipients. At days 15-17 post-transplant DSA titers in B6.CCR5-/-cG-/- recipients were 24.3-fold higher than those in wild-type C57BL/6 allograft recipients. Allografts from B6.CCR5-/-cG-/- recipients on days 45 and 60 had typical characteristics of chronic graft injury including interstitial collagen deposition and peri-glomerular fibrosis that was accompanied by a fibrogenic transcript signature and late post-transplant production of autoantibodies to many targets, including structural proteins including collagen IV and fibronectin. Depletion of B cells at the time DSA peak titers were achieved on day 14 post-transplant decreased serum autoantibodies levels, the kidney allograft fibrogenic transcript signature, and the chronic kidney allograft injury, despite maintenance of the high DSA titers. These results indicate a critical role for neutrophil cathepsin G during acute ABMR of kidney allografts and in its absence, DSA induced late appearance of autoantibodies mediating development of chronic kidney allograft injury.

overall_design: We measured gene expression in mouse kidney allografts transplanted from AJ donors to B6 recipients and compared it to that of CCR5/CG KO recipients, and recipients treated with different B cell depleting strategies to determine the role of neutrophils in antibody-mediated graft rejection.

first: Yosuke

last: Mitsui

middle: S

first: Robert

last: Fairchild


title: Advancing functional transcriptomics in zebrafish with high-accuracy full-length RNA sequencing

city: Poznan

first: Barbara

last: Uszczyńska-Ratajczak

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry, Polish Academy of Sciences

summary:
Zebrafish is an invaluable model organism due to its anatomical and genetic similarities to humans, including shared major organs and tissues. These similarities make findings from zebrafish studies more applicable to human biology than those from in vitro or non-vertebrate models. Despite having one of the best annotated genomes among model organisms, zebrafish genome annotations have seen limited updates in recent years, lagging significantly behind human annotations. This outdated information contributes to inaccuracies in RNA sequencing analysis, gene quantification, and other downstream analyses, reducing zebrafish’s effectiveness as a model. To address these issues, we implemented CapTrap-seq, a platform-agnostic approach to sequence full-length zebrafish transcriptomes across key developmental stages and adult tissues. Our findings indicate that CapTrap-seq delivers manual-quality genome annotations at high-throughput, helping to complete and expand zebrafish gene information and link it to broad biological contexts.
This dataset was generated within the project funded by the National Science Centre (NCN), Poland, PRELUDIUM no. 2022/45/N/NZ2/03622.

overall_design: Benchmarking of two library preparation methods, CapTrap‐seq and Template Switching Oligo (TSO) approach (NEB), was conducted to achieve full-length library preparation for long-read RNA sequencing and comprehensive zebrafish transcriptome analysis. The benchmark was performed on total RNA from four zebrafish samples—heart and testis from adult individuals and embryos at the 2–4 cell stage and 28 hours post-fertilization. Additionally, a size-selection step removing cDNA fragments shorter than 500 bp was incorporated to evaluate its effect on improving CapTrap‐seq performance.

first: Monika

last: Kwiatkowska

first: Marta

last: Blangiewicz

first: Tomasz

last: Mądry

first: Silvia

last: Carbonell-Sala

first: Guigo

last: Roderic

last: Uszczynska-Ratajczak


title: A connectome and transcriptome identity shift through a single transcription factor isoform

city: Waltham

first: Yerbol

last: Kurmangaliyev

state: MA

address: 415 South Street, MS 029

department: Biology

institute: Brandeis University

summary: The brain exhibits remarkable neuronal diversity. The sheer number of cell types emerging from extensive transcriptional, morphological, and connectome datasets compels the question of how the brain is capable of generating so many unique identities. Proper neuronal specification and subsequent features of identity, such as wiring, are essential for normal cognitive and behavioral function. However, we still know little about how identity and wiring are encoded within developmental programs. Here, we turn to the visual system of Drosophila melanogaster. We use its unprecedented combination of single-synapse-resolution wiring diagrams from EM connectomes and developmental gene expression profiles from single-cell transcriptomic atlases to study the molecular basis of cell-type specific terminal identity specification and downstream wiring patterns. We integrate analyses of neuronal anatomy, whole-cell electrophysiology, and single-cell RNA sequencing of genetically manipulated neurons (scRNA-Perturb-Seq) to establish that the transcription factor broad functions to control neuronal identity and subsequent wiring programs between two visual projection neuron cell types, LPLC1 and LPLC2. We demonstrate the first characterization in functional connectivity changes following changes in neuronal identity specification. We find broad acts through a single isoform (broad-z4) that is selectively expressed in LPLC1, and has the capacity to reprogram the morphology, functional connectivity, and transcriptional identity of postmitotic LPLC2 neurons into an LPLC1-like cell type. Our findings establish a single transcription factor isoform as the smallest unit required to differentiate neuronal identity, a strategy that may be conserved within developmental programs to expand the capacity for cell type diversity across animal species.

overall_design: Single-cell RNA sequencing of the developing LPLC2 neurons in control and broad overexpression conditions (broad-Z3 and broad-Z4 isoforms)

first: Natali

last: Smolin

middle: Z

first: Catherine

middle: R

last: von Reyn


title: JUP drives a PDGFB-JAK-STAT signaling axis to promote ovarian cancer progression

city: Zhenjiang

first: Lumeng

last: Rui

address: NO.301 Xuefu Road

institute: Jiangsu University

summary: The Janus kinase (JAK) signaling pathway is frequently associated with ovarian cancer (OC) progression. However, inhibition of JAK signaling has achieved limited therapeutic effects in OC patients, highlighting the need to elucidate the mechanisms underlying JAK dysregulation in OC development. Here, we demonstrate that Junction plakoglobin (JUP) acts as a positive regulator in the JAK signaling pathway in OC. Clinically, JUP expression is significantly upregulated and correlates with poor prognosis in OC patients. Phenotypically, depletion of JUP suppresses OC cell proliferation and migration, whereas overexpression of JUP yielded opposite effects. Mechanistically, JUP drives a PDGFB-JAK-STAT signaling axis through interaction with GABPA. Collectively, our findings establish an oncogenic role of JUP in OC progression via upregulation of JAK signaling and suggest that JUP represents a potential therapeutic target in JAK-driven OC.

overall_design: Total RNA was extracted from JUP-knockdown SKOV3 cells and control (shNC) SKOV3 cells from three independent biological replicates. RNA high-throughput sequencing was performed by Wuhan Benagen Tech Solutions Company Limited (Wuhan, China). Fragments per kilobase of exon per million fragments mapped (FPKM) values were calculated as the expression profiles of mRNAs using Cuffdiff software. Fold changes and P-values were derived from FPKM values to identify differentially expressed mRNAs. KEGG pathway enrichment analysis was subsequently performed on the set of differentially expressed mRNAs


title: Lariats-derived siRNA by PTGS pathway mediate endogenous gene silencing and translational repression

first: qi

last: Tang

state: Shanghai

address: 复旦大学江湾校区生命科学学院

institute: Fudan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Intron-derived lariat RNAs are generated by the spliceosome from pre-mRNAs. Typically, lariat RNAs undergo rapid elimination through DBR1-mediated debranching. There exists much stable lariats in Arabidopsis, indicating that a relatively high level of lariat RNAs would escape from the degradation by DBR1 under the physiological condition in plants. However, the mechanism underlying the biogenesis and function of those stable lariat RNAs remains elusive. Surprisingly, apart from a significant increase of lariat RNAs in a weak viable dbr1 mutant (dbr1-2), large amounts of double-stranded 21,22-nt sRNAs accumulated in the intronic regions where producing lariat RNAs, indicating that lariat RNAs may be further processed into sRNAs. Moreover, the increased 21,22-nt siRNAs in dbr1 mutant were demonstrated to be produced from lariat RNAs with the assistance of the RNA-dependent RNA polymerase 6 (RDR6) and Dicer-like proteins, implying the connection between lariat RNAs and the endogenous small RNA silencing pathway in plants. And we report the identification and characterization of a group of endogenous 22-siRNAs from lariats which could induce coding gene derived 22-nt siRNA that are generated by the DICER-LIKE 2 (DCL2) protein. When DBR1-mediated lariat RNA decay and DCL4 are deficient, the resulting massive accumulation of 22-nucleotide siRNAs from lariats which could induce coding gene derived 22-nt siRNA that are generated by the DICER-LIKE 2 (DCL2) protein restrains translation and inhibits plant growth. Thus, our research uncovers an unprecedented lariats-derived siRNA pathway which plays roles in plant development.

overall_design: small RNA-seq in dbr1-2 rdr126, AGO1_IP / dbr1-2, dbr1-2 dcl2-1, DBR1 H85A, dbr1-3, Col-0 mock, Col-0 TuMV, dbr1-2 mock, dbr1-2 TuMV, dbr1-2 dcl2-1 mock and dbr1-2 dcl2-1 TuMV was performed with 3 biological replicates each. lariats-seq in dbr1-3, DBR1 H85A, Col-0 mock, Col-0 TuMV, dbr1-2 mock and dbr1-2 TuMV were performed with 3 biological replicates each. RNA-seq in Col-0 mock, Col-0 TuMV, dbr1-2 mock, dbr1-2 TuMV, dbr1-2 dcl2-1 mock and dbr1-2 dcl2-1 TuMV were performed with 3 biological replicates each. Ribo-seq in Col-0, dbr1-2, dbr1-2 dcl4-2, Col-0 mock, Col-0 TuMV, dbr1-2 mock, dbr1-2 TuMV, dbr1-2 dcl2-1 mock and dbr1-2 dcl2-1 TuMV were performed with 3 biological replicates each. Polysome-enriched small RNA-seq Col-0 TuMV, dbr1-2 mock and dbr1-2 TuMV was performed with 3 biological replicates each.

first: Qi

first: Binglian

last: Zheng


title: Keratocyte gene expression shaped by ECM dimensionality: Evidence for enhanced quiescence in 3D culture

city: Dallas

first: Kara

last: Poole

address: 5323 Harry Hines Blvd

department: Ophthalmology

institute: UT Southwestern Medical Center

summary: In addition to soluble biochemical factors, biophysical cues from the extracellular matrix (ECM) can play an integral role in regulating cell behavior. Previous work has demonstrated that varying ECM dimensionality (3D vs. 2D) and structure (fibrillar vs. non-fibrillar) can produce distinct cell phenotypes; however, the transcriptional changes underlying how cells sense and respond to these different environments are not well understood. Here, we used bulk RNA sequencing to compare the gene expression profiles of primary rabbit corneal keratocytes cultured on collagen-coated substrates and on top of or embedded within fibrillar collagen matrices under serum-free conditions. Differential expression and functional analyses revealed distinct transcriptional profiles across the culture conditions and identified differentially expressed genes and enriched signaling pathways primarily related to the ECM, cell-matrix interactions, cell mechanics, and proliferation. Cells cultured in 3D fibrillar conditions exhibited gene expression patterns that better reflected a quiescent in vivo keratocyte phenotype, including broad suppression of proliferation and ECM synthesis-related genes. In contrast, cells cultured on 2D substrates showed higher expression of genes associated with an activated phenotype. Overall, these findings demonstrate the strong influence of biophysical cues from the ECM on keratocyte gene expression and highlight the importance of selecting physiologically relevant in vitro models for studies of corneal cell biology, wound healing, and regenerative therapies.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data from primary rabbit corneal keratocytes cultured in serum-free media on collagen-coated substrates, on top of fibrillar collagen matrices, or embedded within fibrillar collagen matrices.

last: Acevedo

first: Miguel

last: Miron-Mendoza

first: Matthew

last: Petroll


title: Myeloid Cell Replacement Therapy Enhances Brain Function in Friedreich Ataxia Mice via Intercellular Mitochondrial Transfer

city: Stanford

first: Natalia

last: Gomez-Ospina

address: 265 Campus Drive

institute: Stanford

summary: We used single-cell RNA sequencing (scRNA-seq) to analyze the therapeutic effects of mitochondrial transfer by bone marrow-derived CD45+CD11b+ microglia-like cells (MGLCs) engrafted in the brain of FRDA mice. MGLCs were engrafted into the FRDA mouse brain following preconditioning with Busulfan and PLX3397 and total bone marrow transplantation. We then compared the gene expression of mKate2+ FA brain cells (mKate2+ cells) that received mitochondria from MGLCs and mKate2- cells (mKate2- cells) that did not.

overall_design: In the brains of three different FRDA mice  transplanted bone marrow from healthy donors (DP+FA), donor cells (MGLCs) and recipient cells were isolated using FACS based on GFP expression. Mitochondrial transfer was assessed by mKate2 expression, with mKate2+ indicating brain cells that received mitochondria and mKate2- indicating those that did not. The mKate2+ and mKate2- cell samples were used for single-cell RNA sequencing (scRNA-seq).

first: Hyunmin

last: Cho

first: Ruhi

last: Sayana

first: Abhishek

last: Koladiya


title: Integrated multi-omics analysis revelas probiotic-conditioned host response induced by Streptococcus salivarius 24SMBc in Dictyostelium discoideum

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

summary: Monoclonal antibodies are widely used to treat follicular lymphoma (FL) and multiple myeloma (MM), but prolonged exposure may impair immune function and increase infection risk. Thus, probiotics are emerging as a strategy to counteract pathogenic colonization. Among them, Streptococcus salivarius 24SMB emerges as a promising oral probiotic. In this project, its beneficial activity was investigated using the amoeba model system Dictyostelium discoideum, widely used for studying host–bacteria interactions. Dictyostelium can be considered as a primitive macrophage, able to feed on bacteria. It was used to evaluate the effects of S. salivarius and the oral pathogen Streptococcus mutans through growth, viability, chemotaxis and phagocytosis assays, combined with transcriptomic and metabolomic analyses. Both S. salivarius and S. mutans reduced Dictyostelium growth compared to E. coli (control). However, S. salivarius significantly improved viability, particularly in sequential exposure experiments, where pre-culture with S. salivarius followed by S. mutans increased vitality by 30%. Moreover, while S. mutans reduced Dictyostelium chemotactic competence, S. salivarius enhanced it. Pre-culture with S. salivarius also increased phagocytosis of oral pathogens (S. mutans and E. corrodens), confirmed by higher intracellular ROS. Transcriptomic and metabolomic analyses further support obtained results, indicating a more active metabolic and phagocytic-primed state after S. salivarius-exposure. In contrast, S. mutans induced a stressed, energy-depleted profile. In conclusion, S. salivarius primed innate immune functions, enhancing Dictyostelium viability, chemotaxis and phagocytic capacity. These findings support Dictyostelium as a simple, cost-effective model for probiotic screening and pathogen-induced stress response studies.

overall_design: RNA-seq analysis of Dictyostelium discoideum grown with the probiotic S. salivarius 24 SMBc, the oral pathogen S. mutans and the standard nutrient E. coli B/r.

first: Simone

last: Rocco

first: Valentina

last: Schiavo

first: Ferrero

last: Giulio

first: Alessandro

last: Ferrando

first: Rita

last: Vacca

first: Afshin

last: Bagherzadeh

first: Maria

last: Santagati

first: Gaia

last: Vertillo

first: Santina

last: Romano

first: Gaetano

last: Isola

first: Cristina

last: Panuzzo

first: Barbara

last: Pergolizzi


title: Gene expression profiles of genes extracted from the hearts of untreated FRDA mice (FA+FA), FRDA mice transplanted with total bone marrow (DP+FA), and WT mice transplanted with total bone marrow (DP+WT)

first: Natalia

last: Gomez-Ospina

summary: We used Bulk RNA sequencing to compare gene expression from the RNA extracted from the hearts of FRDA mice transplanted with bone marrow from FRDA mice(FA+FA), FRDA mice transplanted with healthy bone marrow (DP+FA), and WT mice (DP+WT), after conditioning with Busulfan and PLX3397

overall_design: Whole heart tissue was collected from WT and YG8s800 mice at 20- and 22-weeks post-bone marrow transplantation (BMT), following conditioning with Busulfan (BU) and PLX3397. The time points corresponded to an age of 7–8 months for each group


title: Transcriptome analysis of uterine extracellular vesicles in pregnancies produced by artificial insemination and in vitro fertilization in cattle

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

summary: To understand the expression patterns of coding and non-coding transcripts during pregnancies achieved through AI and IVF, we performed a differential gene expression analysis on RNA-Seq data.

overall_design: Animal handling and sample collection were conducted at the Experimental Station Hildegard Georgina Von Pritzelwiltz in Londrina, PR, Brazil, with approval from the Animal Research Ethics Committee of ESALQ/USP (Protocol #2018.5.1252.11.5, CEUA nº 2018-21). Non-lactating Nelore cows (Bos taurus indicus) with an average body condition score (BCS) of 3.0 ± 0.04 were selected and synchronized using a timed-AI protocol with estradiol benzoate. Artificial insemination (AI) and in vitro embryo production (IVF) were performed using semen from a single Angus bull (Bos taurus taurus). On day 0, cows in the AI group were inseminated, while embryos were transferred to the IVF group on day 6.5. Slaughter took place on days 18 and 32 after AI and on days 12 and 26 post-embryo transfer (IVF group), representing key periods for maternal recognition (18 days) and early placental attachment (32 days). After slaughter, the reproductive tracts were immediately removed and kept on ice. On day 18, uterine horns were flushed with a saline solution to confirm pregnancy by embryo presence; on day 32, pregnancy was diagnosed via ultrasonography one day prior. Uterine fluid from 16 cows was collected and centrifuged to isolate extracellular vesicles, classified by size and concentration for AI and IVF on days 18 and 32. Samples from day 18 of the estrous cycle served as controls. These samples were kept in RNAlater (Thermo Fisher Scientific®) at 4ºC overnight and then stored at -80ºC. RNA extraction was performed using the mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific®), according to manufacturer’s instructions. RNA-Seq was conducted with 12 samples (n=3 treatment/grup).

first: Amanda

middle: F

last: Oliveira

first: Juliana

last: Felix

first: Isabelle

last: Santos

first: Mariana

middle: C

last: Almeida

first: Maria Fernanda


title: long read RNA-seq from large intestine (ENCSR219RPB)

status: Public on Jul 24 2026

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: snATAC-seq from heart (ENCSR242ITJ)


title: Lariats-derive siRNA by PTGS pathway mediate endogenous gene silencing and translational repression

first: qi

last: Tang

address: 复旦大学江湾校区生命科学学院

overall_design: small RNA-seq  in Col-0, dbr1-2, dbr1-2 dcl234 and dbr1-2 dcl4-2  was performed with 3 biological replicates each. lariats-seq  in Col-0 and dbr1-2 were performed with 3 biological replicates each. RNA-seq  in Col-0, dbr1-2 and dbr1-2 dcl4-2 were performed with 3 biological replicates each. Ribo-seq  in Col-0, dbr1-2 and dbr1-2 dcl4-2 were performed with 3 biological replicates each.

first: Qi

first: Binglian

last: Zheng


title: Microtranscriptome analysis of uterine extracellular vesicles in pregnancies produced by artificial insemination and in vitro fertilization in cattle

summary: We aimed to describe miRNA expression in extracellular vesicles

overall_design: Animal handling and sample collection were conducted at the Experimental Station Hildegard Georgina Von Pritzelwiltz in Londrina, PR, Brazil, with approval from the Animal Research Ethics Committee of ESALQ/USP (Protocol #2018.5.1252.11.5, CEUA nº 2018-21). Non-lactating Nelore cows (Bos taurus indicus) with an average body condition score (BCS) of 3.0 ± 0.04 were selected and synchronized using a timed-AI protocol with estradiol benzoate. Artificial insemination (AI) and in vitro embryo production (IVF) were performed using semen from a single Angus bull (Bos taurus taurus). On day 0, cows in the AI group were inseminated, while embryos were transferred to the IVF group on day 6.5. Slaughter took place on days 18 and 32 after AI and on days 12 and 26 post-embryo transfer (IVF group), representing key periods for maternal recognition (18 days) and early placental attachment (32 days). After slaughter, the reproductive tracts were immediately removed and kept on ice. On day 18, uterine horns were flushed with a saline solution to confirm pregnancy by embryo presence; on day 32, pregnancy was diagnosed via ultrasonography one day prior. Uterine fluid from 16 cows was collected and centrifuged to isolate extracellular vesicles, classified by size and concentration for AI and IVF on days 18 and 32. Samples from day 18 of the estrous cycle served as controls. These samples were kept in RNAlater (Thermo Fisher Scientific®) at 4ºC overnight and then stored at -80ºC. RNA extraction was performed using the mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific®), according to manufacturer’s instructions. Microarray was conducted with 16 samples (n=4 treatment/grup).

last: Scaramele


title: Transcriptome-wide m6A methylation profiling of penile tissues in a rat model of hypospadias

city: beijing

first: Jingmin

last: Zhang

address: Yabao Road

institute: CMU

summary: RNA modifications are an important component of epigenetic regulation and play essential roles in embryonic development. Among these modifications, N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic messenger RNA, regulates diverse physiological and pathological processes. Increasing evidence suggests that dysregulated m6A methylation contributes to congenital malformations and reproductive system disorders. In this study, methylated RNA immunoprecipitation sequencing (MeRIP-seq) was performed on penile tissues collected from normal rats and a rat model of hypospadias to characterize the transcriptome-wide m6A methylation landscape associated with hypospadias. These data provide a resource for investigating the potential role of m6A RNA methylation in the molecular mechanisms underlying hypospadias.

overall_design: Timed-pregnant Sprague–Dawley (SD) rats were generated by overnight mating, and the day on which a vaginal plug was detected was designated as gestational day 0 (GD0). Pregnant rats were randomly assigned to either the di-(2-ethylhexyl) phthalate (DEHP)-treated group or the corn oil vehicle control group. DEHP or corn oil was administered by oral gavage daily from GD12 to GD19. On GD19.5, fetuses were collected by cesarean section. Penile tissues from male fetuses with hypospadias and normal male fetuses were isolated for methylated RNA immunoprecipitation sequencing (MeRIP-seq).

first: Shan

last: Wang

first: Xianghui

last: Xie


title: DNA methylation maintenance by DNMT1 is essential for human trophoblast stem cell homeostasis and differentiation [RRBS]

city: Philadelphia

first: Sanam

last: Kavari

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

type: Methylation profiling by high throughput sequencing

summary: Proliferation of cytotrophoblasts (CTBs) and their differentiation into invasive extravillous trophoblasts (EVTs) are critical processes in early placental development. Defects in these processes are associated with adverse pregnancy outcomes, including recurrent pregnancy loss (RPL). There is evidence that reduced expression of the maintenance DNA methyltransferase DNMT1 in the placenta occurs in pregnancy loss and that RPL is associated with aberrant DNA methylation patterns. Therefore, we investigated the role of DNMT1 in human trophoblast growth and differentiation. Using human trophoblast stem cells (hTSCs), an in vitro analog to CTBs, we found that shRNA-mediated knockdown of DNMT1 led to decreased hTSC proliferation, genome-wide reductions in methylation, broad changes in gene expression, and impaired EVT differentiation. Transcriptome profiling of DNMT1-deficient hTSCs and hTSC-derived EVTs highlighted aberrant cytokine expression, drawing a connection to prior reports of immunological dysfunction in RPL. Finally, using a catalytic DNMT1 chemical inhibitor, we demonstrate the canonical methyltransferase activity of DNMT1 is essential for EVT differentiation and invasion. This study identifies new roles for DNMT1 in trophoblasts and addresses the molecular basis of the associations between DNMT1 expression, altered DNA methylation profiles, and RPL.

overall_design: RNA-seq of control and DNMT1 knockdown hTSC CT27 cells in undifferentiated and EVT differentiated conditions.

first: YuJin

last: Jang

first: Jonghwan

last: Kim

first: Winifred

last: Mak

first: Jennifer

last: Kalish


title: α-Synuclein blocks endoplasmic reticulum protein translocation in Parkinson’s disease [scRNA-seq]

city: Oxford

first: Nick

last: Gatford

address: Dorothy Crowfoot Hodgkin Building, South Parks Road

department: NDCN

institute: University of Oxford

summary: The primary mechanism and subcellular localisation of α-synuclein toxicity in Parkinson’s disease pathogenesis remain unknown. We spatially and temporally resolved proteomic and transcriptomic changes in human iPSC-derived dopaminergic neurons with increasing burden of pathological α-synuclein. We found that misfolded α-synuclein proteoforms, signified by the formation of nanoscale intraneuronal puncta, are associated with impaired translocon function at the endoplasmic reticulum (ER). We show that α-synuclein interacts with Sec61A in iPSC-derived dopaminergic neurons and in post-mortem brain tissue from patients with Parkinson’s disease. This interaction interferes with the co-translational translocation of ER-processed proteins including the vacuolar-type ATPase V0a1 subunit, glucocerebrosidase, and Cathepsin B, causing defective organelle function such as reduced lysosomal acidification, leading to increased extracellular vesicle release of α-synuclein. Defective ER-translocation was associated with increased ribosomal UFMylation and proteasomal recruitment but not activation of the unfolded protein response. Reduction of pathological α-synuclein by either CRISPRi to decrease α-synuclein expression or pharmacological activation of proteasomal degradation with repurposed drugs mitigates the ER defect. Our study offers a unifying mechanistic link between α-synuclein pathology and dysregulation of diverse organelle-associated proteins that are both Sec61A translocon substrates and genetic modifiers of Parkinson’s disease risk. Our data also provide a therapeutic rationale for proteasomal activation in early Parkinson’s disease.

overall_design: Single cell RNASeq of hiPSC-derived dopaminergic neurons with SNCA triplication (ND34391G) compared to an isogenic control (Clone 1-13) at day 73 (n=3 biological replicates per condition). This was done to identify pathways that are impacted by pathogenic α-synuclein in Parkinson’s disease. A total of 4 different human iPSC-derived neuron samples were sequenced on the Novaseq 6000 platform.

first: Chor

last: Lam

first: Nicholas

first: Ana

last: Aragón-González

first: Benedict

last: Tanudjojo

first: Anis

last: Sahoo

first: Andrew

last: Castle

first: Devika

last: Agarwal

first: Ashwin

last: Jainarayanan

first: Svenja

last: Hester

first: Navoneel

last: Sen

first: Justin

last: Benesch

first: Roman

last: Fischer

first: David

last: Sims

first: George

middle: K

last: Tofaris


title: A multi-functional oral small molecule targeting energy and lipid metabolism as a treatment for diet-induced obesity [Exp 5]

city: Berkeley

first: Chi

last: Zhu

address: Morgan Hall, Rm238

institute: University of California, Berkeley

summary: Obesity and related metabolic disorders have surged globally, representing a significant public health burden. These diseases are mechanistically interconnected through complex pathways involving dysregulated energy and lipid metabolism. As a result, therapeutic strategies that target a single molecule or pathway are unlikely to achieve optimal efficacy without inducing adverse effects. Here, we identified an orally bioavailable small molecule, 5-tetradecyloxy-2-furoic acid (TOFA), that effectively rebalances energy expenditure and lipid synthesis by both inhibiting acetyl-CoA carboxylases 1 and 2 (ACC1/2) and acting as a novel agonist of Peroxisome Proliferator-Activated Receptors alpha and delta (PPARɑ/δ). TOFA significantly alleviated obesity and associated metabolic dysfunctions in mouse models without side effects common to current treatments, such as muscle wasting. Moreover, TOFA acted synergistically with incretin analogs such as semaglutide and tirzepatide to improve obesity, dyslipidemia, and insulin resistance. Collectively, our findings suggest that the coordinated multi-targeting of lipid homeostasis and energy metabolism by TOFA is an effective approach to address multiple associated metabolic diseases.

overall_design: Major urinary protein (MUP)-urokinase-type plasminogen activator (uPA) transgenic mice were fed a 60% high fat diet for ten weeks followed by an oral dosing of vehicle control or 125 mg/kg TOFA, BID for six weeks after which the hepatic transcriptome was analyzed; n=8/group.

last: Lee

first: Anders

last: Näär

first: Gracia

last: Bonilla

first: Ruslan

last: Sadreyev


title: IFNg and IFNg mimetics prevent IFN-I-mediated TB susceptibility by regulating iron metabolism and lipid peroxidation.

city: Dublin

first: Oleksii

last: Rukhlenko

address: Systems Biology Ireland, University College Dublin

department: Systems Biology Ireland

country: Ireland

institute: University College Dublin

summary: Type I interferons (IFN-I) and IFNγ exert divergent effects during tuberculosis, but the mechanisms that determine whether macrophage activation promotes host defense or inflammatory pathology remain incompletely understood. Here, we dissect the interplay between IFN-I and IFNγ in macrophage activation using genetically susceptible B6.Sst1S macrophages. We show that, during tumor necrosis factor (TNF) stimulation, susceptible macrophages enter a persistent pathological activation state (pPAS) characterized by sustained lipid peroxidation and super-induction of IFN-I responses. This pathological state is maintained by autocrine IFN-I signaling. In contrast, IFNγ priming prevents pPAS development by enhancing macrophage resilience to oxidative stress, in part through regulation of iron metabolism and induction of ferritin expression. Computational cell state transition assessment and regulation (cSTAR) analysis identified pathways and small molecules predicted to promote the transition of susceptible macrophages toward an IFNγ-induced, Mtb-resistant state. Consistent with these predictions, the CDK4/6 inhibitor trilaciclib reduced lipid peroxidation by regulating iron metabolism, whereas retinoic acid signaling enhanced GPX4 expression and lipid biosynthesis programs. Combined CDK4/6 inhibition and retinoic acid receptor activation efficiently prevented the pathological activation state. Together, these findings delineate a mechanism of IFN-I/IFNγ crosstalk during macrophage activation and identify pharmacologic strategies to prevent IFN-I-dominant, lipid peroxidation-driven macrophage pathology.

overall_design: B6 and B6.Sst1S BMDMs were treated with TNF (10 ng/mL), IFNg (5 U/mL), and in combination of both for 12 h.

first: Prasanna

last: Babu Araveti

first: Shivraj

last: Yabaji

first: Muhammad

last: Zainul Arifin

first: Suruchi

last: Lata

first: Yuriy

middle: O

last: Alekseyev

first: Alexander

last: Gimelbrant

first: William

last: Bishai

first: Vadim

last: Zhernovkov

first: Boris

middle: N

last: Kholodenko

first: Igor

last: Kramnik


title: DNA methylation maintenance by DNMT1 is essential for human trophoblast stem cell homeostasis and differentiation [RNA-seq]

first: Sanam

last: Kavari

first: YuJin

last: Jang

first: Jonghwan

last: Kim

first: Winifred

last: Mak

first: Jennifer

last: Kalish


title: Fear-triggered reactive astrocytes orchestrate selective aversive memory decay via IL-3–CSF2RB2 signaling

first: changfei

last: tang

address: No. 1 Banxia Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Forgetting is a fundamental component of the memory system. While existing studies have primarily explored global neural network underlying active forgetting1, the intrinsic pathways impeding selective long-term memory stability remain elusive. Contemporary research has identified multiple decay mechanisms—including adult hippocampal neurogenesis2-6, microglia complement-mediated synaptic pruning7, 8, and protein degradation pathways9-13, yet these predominantly facilitate broad, nonspecific remodeling of neural networks. Whether dedicated mechanisms exist to achieve selective memory decay remains a fundamental unresolved question. Here, we identify a specialized subpopulation of astrocytes, termed Fear-Triggered Reactive Astrocytes (FTRA) in the hippocampal dentate gyrus, which are activated gradually but selectively after contextual fear memory. The FTRA serves as a chronic reducer of fear memory through uniquely release of interleukin-3 (IL-3) and its receptor CSF2RB2 mediated GPCR signaling and mitochondrial‑related energy metabolism in mossy cells. This leads to attenuated mossy cell excitability and behavior-associated calcium signals in granular cell neurons, ultimately driving memory loss. The FTRA operates independently of neurogenesis or microglial pruning, revealing IL-3 as a specific cytokine for spontaneous forgetting and establishing astrocytes as negative mediator of aversive memory maintenance.

overall_design: There were two parts to the experiment. In the first part, there were two groups: CFC-14d and Random-14d, each consisting of 10 mice. In the second part, there were three groups: WT-naive, WT-CFC, and KO-CFC, each consisting of 10 mice.

first: Chang-Fei

last: Tang

first: Xian-Dong

last: Liu

first: Wu-Bo

last: Han

first: Xin-Rong

last: Wu

first: Yi-Ning

last: Gao

first: Zheng-Kai

last: Lao

first: Han-Yu

last: Xu

first: Yulei

last: Deng

first: Yanqiang

last: Hou

first: Tian-Le

first: Zhang-Peng

last: Chen

first: Suya

last: Sun

first: Nan-Jie


title: PAR-CLIP-sequencing of PC9 lung cancer cells to identify FUS bingind sites

status: Public on Jul 05 2026

city: Guangzhou

first: Shouheng

last: Lin

address: 190 Kaiyuan Avenue

institute: Guangzhou Institutes of Biomedicine and Health

summary: The prognosis of non-small cell lung cancer (NSCLC) with leptomeningeal metastases (LM) is dismal. The regulators of LM progression remain elusive, thus impeding effective clinical intervention. Here, we discovered that Fused in sarcoma (FUS) ablation promoted LM in lung cell lines. As FUS is a multifaceted DNA-/RNA-binding protein involved in transcription, we explored how it represses CD36 with PAR-CLIP-seq (photoactivatable–ribonucleoside-enhanced cross-linking and immunoprecipitation, followed by high-throughput sequencing) in PC9 cells.

overall_design: CLIP-seq profiling of PC9 cells immunoprecipitated using FUS antibody-conjugated magnetic beads.


title: Transcriptome analysis of tumor tissues dervied from lung cancer patients

summary: The prognosis of non-small cell lung cancer (NSCLC) with leptomeningeal metastases (LM) is dismal. The regulators of LM progression remain elusive, thus impeding effective clinical intervention. Here, we performed transcriptome analysis of the molecular features of tumor tissues dervied from leptomeningeal-metastatic lung cancer patients. In patients with NSCLC, FUS downregulation and CD36 or SYP upregulation were associated with aggressive LM progression. CD36-mediated fatty acid metabolism and NED signature are crucial for LM progression in NSCLC, highlighting CD36 as a potential LM biomarker and a promising therapeutic target for LM treatment.

overall_design: RNA-seq profiling of wildtype PC9 or A549 cells and their leptomeningeal metastatic derivates, and their knockout derivates (sgFUS). PC9 cells treated with or without palmitic acid (PA).


title: α-Synuclein blocks endoplasmic reticulum protein translocation in Parkinson’s disease [bulk RNA-seq]

first: Nick

last: Gatford

overall_design: Bulk RNASeq was performed to temporally assess the  impact of SNCA gene triplication in hiPSC-derived dopaminergic neurons (SFC831-03-05) at day 52 of differentiation compared to day 60 (n=6 biological replicates per condition). This was done to identify pathways that are impacted by pathogenic α-synuclein in Parkinson’s disease. A total of 12 different human iPSC-derived neuron samples were sequenced on the Novaseq 6000 platform.

first: Chor

last: Lam

first: Nicholas

first: Ana

last: Aragón-González

first: Benedict

last: Tanudjojo

first: Anis

last: Sahoo

first: Andrew

last: Castle

first: Devika

last: Agarwal

first: Ashwin

last: Jainarayanan

first: Svenja

last: Hester

first: Navoneel

last: Sen

first: Justin

last: Benesch

first: Roman

last: Fischer

first: David

last: Sims

first: George

last: Tofaris


title: Remote ischemic conditioning mitigates diesel exhaust-induced pulmonary fibrosis by alleviating pulmonary inflammation and fibrogenesis

city: Delhi

first: Aastha

last: Mishra

state: Delhi

address: Mall Road, Delhi-110 007

department: Genomics and genome biology

country: India

institute: Council Of Scientific And Industrial Research–Institute Of Genomics And Integrative Biology (CSIR–IGIB)

summary: Remote ischemic conditioning (RIC), a promising non-pharmacological strategy, mitigates ischemia-reperfusion injury in multiple conditions. However, its potential as a therapeutic strategy in pulmonary fibrosis (PF), which is associated with poor survival outcomes and limited pharmacotherapies, remains unexplored.  Thus, the present study aimed to explore the therapeutic utility of RIC in a diesel exhaust-induced mouse model recapitulating PF pathology. The effects of RIC were comprehensively assessed by measuring physiological and molecular endpoints, including weight, heart rate variability (HRV), lung histopathology, circulating plasma biomarkers, bronchoalveolar lavage fluid cytokine profiles, and indices of pulmonary mitochondrial health, accompanied by bulk transcriptome sequencing of lung tissue of age-matched mice allocated to nine study groups. DE-induced PF groups receiving RIC showed marked improvements in weight, HRV, and lung mitochondrial function, substantial attenuation of histopathological damage, and significant decreases in inflammatory and fibrotic markers, indicating the potential of RIC to mitigate DE-induced fibrotic damage. Transcriptome analysis of lung tissue further supported these observations by revealing downregulation of PF markers in RIC-receiving groups, highlighting RIC's efficacy in attenuating PF features. Additionally, potential PF-relevant markers, including Calhm6, Hrc, Dnase1l3, Pla2g2d, Stab2 and Timd4, were identified across these groups that may be linked to therapeutic benefits conferred by RIC.

overall_design: The study comprised C57Bl/6 male mice randomly divided into eight groups, including healthy control [C], healthy control receiving remote ischemic conditioning (RIC) [RIC], diesel exhaust (DE)-induced pulmonary fibrosis (PF) model [DE], DE-induced PF model receiving pharmacotherapy pirfenidone (PFD) [DE+PFD], DE-induced PF model receiving RIC before PF induction as remote ischemic preconditioning (RIPreC) [RIC+DE], DE-induced PF model receiving RIC during PF induction as remote ischemic perconditioning (RIPerC) [DE+RIC], DE-induced PF model receiving pharmacotherapy PFD and RIPreC [RIC+DE+PFD], and DE-induced PF model receiving pharmacotherapy PFD and RIPerC [DE+PFD+RIC]. Age- and weight-matched mice acquired at 6 weeks of age and starting weight of 23g, along with time-bound interventions starting at 8 weeks of age, were used for each group throughout the experimental protocol.

first: Kumari

last: Swati

first: Mishra

last: Kaushlendra

first: Singh

last: Kanika

first: Kumar G

last: Krishna

first: Kumar

last: Rohit

first: Parihar

last: Abhishek

last: Rani

first: Nagar

last: Ekta

first: Arora

last: Naveen

first: Bansal

last: Vishal

last: Aastha


title: Neoadjuvant Botensilimab/Balstilimab for localized mismatch repair proficient and deficient colon cancer: Results of the NEST phase 2 clinical trial

city: New York

first: MAIDER

last: ASTORKIA

state: NY

address: 1300 York Ave

institute: WEILL CORNELL MEDICINE

summary:
Purpose: Effective immunotherapy for mismatch repair proficient colorectal cancer (CRC) is lacking. We examined the safety and efficacy of the novel next-generation immune activator/Fc-enhanced CTLA-4 inhibitor botensilimab (BOT) plus PD-1 inhibitor balstilimab (BAL) in the neoadjuvant setting for patients with resectable CRC.
Patients and Methods: Patients 18 years of age or older with non-metastatic CRC awaiting surgical resection were eligible. BOT/BAL was administered followed by surgical resection. In cohort A, patients received BOT 75 mg d1 and BAL 240 mg d1, 15; in cohorts B/C, patients received 2 additional BAL doses (d29, 43). The primary study objectives were safety, feasibility (based on surgery delay), and pathologic response. Exploratory analyses examined changes in the tumor microenvironment.
Results: Twenty-four eligible patients (26 tumors, n=22 pMMR; n=4 dMMR) were enrolled (two patients had synchronous primary tumors). Neoadjuvant BOT/BAL was safe and did not delay planned surgery in any patient. The major pathologic response rate was 41% (95% CI, 21%–64%) for pMMR, and 100% (95% CI, 40%–100%) for dMMR CRC. BOT/BAL was associated with significant anti-tumor effects in the tumor microenvironment, with an increase in the density and proportion of CD8+ T cells, a reduction in tumor infiltrating FOXP3+ Tregs, and evidence of increased immune cell-cell interaction in responding patients.
Conclusions: These findings demonstrate safety, feasibility, and encouraging pathological responses for BOT/BAL in both non-metastatic pMMR and dMMR CRC.  Tumor microenvironment remodeling suggests a robust anti-tumor immune response induced by immunotherapy. These data support the continued development of BOT/BAL in CRC.

overall_design: Phase 2 single arm clinical trial

first: Manish

middle: A

last: Shah

first: Erika

last: Hissong

first: Mehraneh

middle: D

last: Jafari

first: Pashtoon

last: Murtaza Kasi

first: Maider

last: Astorkia

first: Sahrish

last: Khan

first: Casey

last: Owens

first: Zhengming

last: Chen

first: Heather

last: Yeo

first: Fabio

last: Socciarelli

first: Sandipto

last: Sarkar

first: Alana

last: Nguyen

first: Despina

last: Siolas

first: Allyson

last: Ocean

first: Kelly

last: Garrett

first: Lea

last: Lowenfeld

first: Alessio

last: Pigazzi

first: Preethi

last: Guniganti

first: Sanjay

last: Patel

first: Doron

last: Betel

first: Manuel

last: Hidalgo


title: Characterization of Hypothetical Proteins Reveals Function Modules and Virulence Factors in Pseudomonas aeruginosa

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Uncharacterized hypothetical proteins (HPs) occupy 25-50 % of the bacterial genomes, known as dark matter, whose biological functions and regulatory processes remain mysterious. Pseudomonas aeruginosa is a superbug that causes a wide array of medical device-associated infection, and life-threatening acute or chronic infection in cystic fibrosis patient or immunocompromised individuals. In this study, we systematically revealed the functions of HPs using P. aeruginosa as a model strain. We constructed a HP deletion library that contains 938 deletion strains. Transcriptome profiling was performed to reveal a full picture of their differentially expressed genes (DEGs). We subsequently used independent component analysis (ICA) to cluster HPs into different modules with transcriptional regulatory network (TRN). The functions of 1087 HPs were determined by module and co-expression network. Combined with DEG-based virulence-associated network of HPs, we identified 33 novel virulence or antibiotic resistant-associated HPs using multiple methods and mice infection model, which are potential candidates to develop novel therapeutics against this superbug. We also revealed multiple groups of co-relationships between HPs and known virulence-associated transcription factors (TFs). In addition, we mapped the evolution of HPs in the Bacteria Kingdom, and highlighted a group of unique HPs with divergent functions in P. aeruginosa. Totally, this study annotated the functions of HPs in P. aeruginosa using transcriptome profiling coupled with machine learning, which provides an important HPs database for further studies on HPs in both eukaryotes and prokaryotes.

overall_design: RNA-seq for  Pseudomonas aeruginosa hypothetical portein mutants in LB medium

last: Deng


title: ZNF768 regulates expression of E2F proteins to drive G0/G1 transition and cell cycle progression.

city: Quebec

first: Sabine

last: Elowe

state: Quebec

address: CR-Nouveaux Centre Hospitalier, 1401 18e Rue, Site HEJ, Local L2.106

country: Canada

institute: Centre Integre en cancerologie

summary: Accurate and tightly coordinated cell cycle progression and cell proliferation is critical for development, growth and homeostasis of an organism. Recently, Zinc finger protein 768 (ZNF768) was identified as a transcription factor driving cellular proliferation, in both a p53 dependentt and independent manner. ZNF768 interacts with and represses p53 functions to limit cell cycle delay. Independently, ZNF768 promotes the transcriptional expression of key regulators of the cell cycle machinery, although the mechanism(s) through which this occurs are still unknown. Here, we report that ZNF768 protein levels are tightly regulated during the cell cycle, and its depletion leads to cell cycle exit and induction of quiescence. We found that ZNF768 modulates the cell cycle, at least in part, by controlling expression of the major pro-proliferative transcription factor E2F1 independently of p53 activation. Consequently, depletion of ZNF768, which also represses expression of the key mitotic transcription factor and E2F1 target FOXM1 leads to numerous mitotic errors. Supporting these findings, cancer genomics analyses reveal that ZNF768 expression levels are positively associated with E2F1 and FOXM1 expression levels in human tumors suggesting that cancer cells might use ZNF768 to override cell cycle arrest, sustain proliferation and promote cancer progression. Altogether, our results reveal that ZNF768 modulates cell cycle entry and proliferation, at least in part by regulating E2F1 expression.

overall_design: RNA-seq profiling of RPE1 following a 72h knockdown of ZNF768 in CTL cell line, SH_1 cell line, SH2 cell line.

first: Romain

last: Devillers

first: Benjamin

last: Brisebois

first: Suparba

last: Roy

first: Emeline

last: Lelong

first: Audrey

last: Poirier

first: Alona

last: Kolonohuz

first: Christophe

last: Tav

first: Danielle

last: Caron

last: Villot

first: Frederic

last: Lessard

first: Laura

last: Tribouillard

first: Chantal

last: Garand

first: Philippe

last: Joubert

first: Dmitry

last: Kretov

first: Samer

last: Hussein

first: Mathieu

last: Laplante


title: Integrated circRNA, miRNA and mRNA transcriptome profiling of IHNV-infected rainbow trout spleen and circUSP47-overexpressing rainbow trout hepatocytes.

city: Lanzhou

first: jinqiang

last: huang

address: Yintanlu Stress

institute: Gansu Agricultural University

summary: Infectious hematopoietic necrosis virus (IHNV) is a major viral pathogen threatening rainbow trout aquaculture, yet the ncRNA-mediated regulatory mechanisms underlying host antiviral immunity remain incompletely understood. This study integrated long RNA-seq, small RNA-seq and mRNA-seq datasets to investigate antiviral regulatory networks in rainbow trout. Spleen tissues were collected from uninfected control and IHNV-infected rainbow trout for long RNA sequencing to profile mRNAs, lncRNAs and circRNAs, and for small RNA sequencing to profile miRNAs. In parallel, rainbow trout hepatocytes transfected with empty vector or circUSP47 overexpression vector were subjected to mRNA sequencing to identify genes and immune-related pathways regulated by circUSP47. Differential expression and integrated ceRNA network analyses were used to identify candidate antiviral regulatory interactions, supporting the circUSP47-miR-30-5p-RNF135 axis in rainbow trout antiviral immunity.

overall_design: The study included two related experimental modules. In the in vivo IHNV infection module, rainbow trout were divided into an uninfected control group and an IHNV-infected group, with three biological replicates per group. Spleen tissues were collected at 48 h post infection and used for ribosomal RNA-depleted long RNA-seq to profile mRNAs, lncRNAs and circRNAs, and for small RNA-seq to profile miRNAs. In the in vitro circUSP47 overexpression module, rainbow trout hepatocytes were transfected with either empty vector control or circUSP47 overexpression vector, with three biological replicates per group, and mRNA-seq was performed after transfection. Differentially expressed circRNAs, miRNAs, lncRNAs and mRNAs were identified and integrated to construct ceRNA regulatory networks and to identify commonly regulated mRNAs and immune-related pathways associated with circUSP47-mediated antiviral regulation.

first: Jinqiang

last: Huang

first: Tongzhen

last: Sun


title: Circular RNA expression profiling of mouse MOVAS cells upon benzo[a]pyrene (BaP) exposure

city: Shijiazhuang

first: Hao

last: Xi

address: No. 361 Zhongshan East Road, Shijiazhuang, Hebei Province, China

institute: Hebei Medical University

summary: Circular RNA microarray was performed to profile the circular RNA transcriptome of mouse MOVAS cells with or without benzo[a]pyrene (BaP) treatment. MOVAS cells were exposed to 10 μM BaP for 72 hours, and untreated MOVAS cells were used as control, with three biological replicates for each group (6 samples in total). Total RNA extracted from all samples was digested with RNase R to eliminate linear RNAs and enrich circular RNAs, followed by amplification and Cy3 fluorescent labeling using Arraystar Super RNA Labeling Kit. Labeled cRNAs were hybridized onto Arraystar Mouse circRNA Array V2 microarrays. Slides were scanned with Agilent Scanner G2505C, and raw intensity data were extracted via Agilent Feature Extraction software v11.0.1.1. Quantile normalization was conducted using the limma package in R. This submission contains raw and normalized microarray expression data only. The data provides a complete circRNA expression baseline for subsequent exploration of molecular mechanisms underlying BaP-induced vascular cell injury.

overall_design: Six mouse cell samples were divided into three groups with three biological replicates each: Control group (con1, con2, con3), BaP treatment group (BaP1, BaP2, BaP3). circRNA expression profiles were analyzed using Arraystar Mouse circRNA Array V2. Differentially expressed circRNAs were identified through Volcano Plot filtering (fold change >= 2.0, p-value <= 0.05).

first: Lv

last: Pin

first: Li

last: Yuemin


title: Genomic and transcriptomic profiling of whole-genome-doubled triple-negative breast cancer cell populations

city: Austin

first: Amy

last: Brock

state: Texas

address: 107 W Dean Keaton St.

department: Biomedical Engineering

institute: University of Texas at Austin

summary: To investigate whether the mechanism of whole-genome doubling (WGD) results in distinct genomic and transcriptomic phenotypes, we compared three routes to WGD against their respective parental aneuploid controls across two triple-negative breast cancer (TNBC) cell lines (HCC1806 and MDA-MB-231). WGD mechanisms included naturally occurring cell-cell fusion and two drug-induced cell-cycle error mechanisms: mitotic slippage (MS) and cytokinesis failure (CF). All populations were profiled in biological triplicate by TagSeq (3' tag-based RNA-seq) for transcriptomic analysis and low-pass whole-genome sequencing (WGS) for copy-number profiling.

overall_design: TAGseq (3' tag-based RNA-seq) and low-pass whole-genome sequencing (WGS) were performed on three independently derived whole-genome doubling (WGD) populations (Fusion, Mitotic Slippage, Cytokinesis Failure) and their parental aneuploid control population in two TNBC cell lines (HCC1806, MDA-MB-231), with three biological replicates each.

first: Howland

last: Kennedy

first: Brock

last: Amy


title: Transcriptome analysis of leptomeningeal-metastatic cancer cells and FUS-deficient cancer cells

first: Shouheng

last: Lin

summary: The prognosis of non-small cell lung cancer (NSCLC) with leptomeningeal metastases (LM) is dismal. The regulators of LM progression remain elusive, thus impeding effective clinical intervention. Here, we performed in vivo genome-wide CRISPR-based screens and discovered that Fused in sarcoma (FUS) ablation promoted LM in both PC9 and A549 cell lines. FUS repressed CD36 expression by directly interacting with and destabilizing PPARA mRNA. CD36 augmented fatty acid uptake and oxidative phosphorylation in NSCLC cells. Matrix metallopeptidase 2 (MMP2) was upregulated through CD36-mediated fatty acid metabolism, which enabled NSCLC cells to disrupt the endothelial barrier. FUS-deficient NSCLC cells increased the expression of neuroendocrine differentiation (NED) related markers, including SRY-box transcription factor 2 (SOX2), microtubule associated protein 2 (MAP2), enolase 2 (NSE) and synaptophysin (SYP), exhibited neurite-like extensions, and expanded robustly in cerebrospinal fluid-supplemented medium through a CD36-dependent manner.  Mechanistically, fatty acid uptake increased acetyl-CoA and H3K27ac modifications to promote the expression of NED signature genes and MMP2 in NSCLC cells. Genetic or pharmacological inhibition of CD36, or inhibition of NED signature in NSCLC cells hindered LM and prolonged survival in mice. In patients with NSCLC, FUS downregulation and CD36 or SYP upregulation were associated with aggressive LM progression. Thus, CD36-mediated fatty acid metabolism and NED signature are crucial for LM progression in NSCLC, highlighting CD36 as a potential LM biomarker and a promising therapeutic target for LM treatment.


title: CircSSRP1 regulates SMAD3 to affect proliferation and apoptosis of human embryonic palatal mesenchymal cells in nonsyndromic cleft lip with or without cleft palate by sponging miR-708-5p

city: Beijing

first: Siyuan

last: Guo

state: Beijing

address: No. 9 Fanjiacun Road, Fengtai District

department: Department of Oral and Maxillofacial Plastic and Traumatic Surgery

institute: Beijing Stomatological Hospital, Capital Medical University

summary: Nonsyndromic cleft lip with or without cleft palate (NSCL/P) represents one of the most prevalent congenital anomalies in oral and maxillofacial region with unclear etiology. It is currently widely accepted that NSCL/P is a complex genetic disorder caused by multiple environmental and genetic factors. This study aimed to investigate the regulatory roles of circSSRP1/miR-708-5p/SMAD3 axis in NSCL/P. Using bioinformatic analysis methods, we performed an integrated analysis of the Clariom D Human Assay and GSE42589 dataset to construct the NSCL/P associated circSSRP1/miR-708-5p/SMAD3 axis. Subsequently, through validating the expressions of circSSRP1, miR-708-5p, and SMAD3 in NSCL/P tissues and matched normal control tissues, combined with in vitro experiments and other relevant approaches, we identified a novel circular RNA, circSSRP1. This molecule acts as a molecular sponge for miR-708-5p, thereby regulating the expression of SMAD3 and participating in the pathogenesis of NSCL/P.

overall_design: The experiment is divided into two groups: NSCL/P cases and the healthy control group. Peripheral blood RNA samples were used in gene expression microarrays (Clariom D Human Assay chips).

first: Xiangpu

last: Wang

first: Renji

last: Chen


title: Ontogenically distinct alveolar macrophages mediate cigarette smoke-induced inflammation and damage [RNA-Seq]

city: Basel

first: Atul

last: Sethi

address: Grenzacherstrasse 124

country: Switzerland

institute: Hoffmann-La Roche

summary: We employed bulk RNA sequencing to investigate how varying durations of cigarette smoke (CS) exposure affect alveolar macrophages (AM) of different ontogenies in mice. Chronic obstructive pulmonary disease (COPD) is often associated with CS and the third leading cause of death. While airway-recruited macrophages contribute to COPD pathogenesis, the role of embryonic AM (Em-AM) remains unclear. Using a CS-induced COPD mouse model, we found that CS-triggered lung inflammation and emphysema-like tissue damage correlated with substantial changes in the lung myeloid compartment. Using fate-mapping, we showed that, while most CS-induced AM were recruited bone marrow monocyte-derived AM (BM-AM), Em-AM persisted and underwent similar inflammation- and emphysema-associated adaptations as BM-AM upon CS. Therefore, our data support that the CS-exposed niche, rather than ontogeny, is the main determinant of AM fate in COPD, and that CS-induced AM changes may be potential therapeutic targets to mitigate AM dysfunction in COPD.

overall_design: After exposure to room air (RA) or CS for 4, 12, or a combined 12 weeks of smoke followed by 8 weeks of rest (12+8 weeks), AM were isolated from the lungs of Ms4a3-tdTomato mice using fluorescence-activated cell sorting and subsequently analyzed by bulk RNA-seq.

first: Marvin

last: Hering

first: Nina

last: Frey

first: Dilay

last: Cansever

first: Pablo

last: Hernández-Malmierca

first: Mika

last: Manser

first: Jordan

last: Poirot

first: Said

last: Aktas

first: Desiree

last: von Tell

first: Anna

last: Mechling

first: Kara

last: Lassen

first: Nikica

last: Miše-Racek

first: Thomas

last: Marichal

first: Emma

last: Doran


title: Engineering a Reversible Plant Hormone–Inducible ON-Switch Boosts Safety and Potency of CAR-T Cell Immunotherapy

city: Shenzhen

first: Chen

last: Yang

address: 1068 Xueyuan Avenue, Nanshan District, Shenzhen,China

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

summary: The ability to externally regulate chimeric antigen receptor (CAR) activity via small molecules offers a promising strategy to enhance the safety and precision of adoptive T cell therapies. We present a novel inducible ON-switch CAR design that leverages plant hormone signaling components to achieve controllable T cell activation. Specifically, we engineered a receptor system that integrated the plant auxin receptor IAA7 and its co-receptor AFB1, enabling ligand-dependent interactions in response to the plant hormone auxin. Our results demonstrated that this auxin-inducible CAR (auxCAR) mediated rapid, reversible, and dose-dependent T cell activation, leading to potent cytotoxicity against Raji B-cell lymphoma in vitro and in vivo. Notably, auxCAR-T cells maintained a favorable memory T cell phenotype and exhibited reduced exhaustion markers compared with conventional CAR-T cells, translating into improved therapeutic efficacy. This plant hormone-based control system offers a versatile and orthogonal approach for precise modulation of CAR activity, with significant implications for the development of safer, more adaptable immunotherapies.

overall_design: RNA seq profiling of wtCAR and auxCAR tranduced primary CD8+ T cells


title: RASA3 inhibits Th1 differentiation and attenuates inflammatory immune response by restricting the HCK kinase

city: wuhan

first: Jiayu

last: Song

address: wuhan

institute: WUHAN University

summary: Type I immunity is marked by IFN-γ, with Th1 cells as a key subset; however, intrinsic negative regulators of Th1 remain poorly defined. We identified RASA3 as such a regulator, whose expression declines during Th1 differentiation. T cell-specific RASA3 knockout enhances Th1 differentiation and exacerbates allergic contact dermatitis. Mechanistically, RASA3 inhibits Hck mRNA translation via RPL36A. HCK then phosphorylates STAT4 at Y693, driving STAT4 dimerization, nuclear entry, and IFN-γ expression. This RASA3–HCK–STAT4 axis reveals a novel mechanism for Th1 negative regulation and offers potential therapeutic targets.

overall_design: Naive CD4+ T cells, which were purified from spleen and lymph nodes, were cultured under Th1  polarization conditions from WT and RASA3 KO Mice for 1 day, 2 days and 4 days. Then, RNA was extracted from the Th1 cells.

first: Bing

last: Wu