title: RNAseq data of liver macrophages in YFP positive and YPF negative

status: Public on Aug 10 2025

city: Beijing

first: Zhaoqi

last: Zhang

state: Beijing

address: Beijing China Institute of Zoology，Chinese Academy of Sciences

country: China

institute: University of Chinese Academy of Sciences

summary: Tissue-resident macrophages (RTMs), predominantly originating from embryonic progenitors, play a pivotal role in maintaining tissue homeostasis and immune regulation. Their functional diversity is shaped by both their developmental origins—including the yolk sac, fetal liver, and bone marrow—and the local tissue microenvironment. In this study, we identified a unique subset of RTMs in Lyz2cre-RosaYFP reporter mice that lack Lyz2 expression and persist long-term in peripheral tissues. These Lyz2-YFP- RTMs follow a distinct developmental trajectory, transitioning from Lyz2-YFP-CD117+CD45-AA4.1- early erythro-myeloid progenitors (EMPs) to Lyz2-YFP-CD117+CD45+AA4.1- intermediate EMPs in a Csf2rb-dependent manner. Transcriptional profiling reveals that yolk sac-derived Kupffer cells (KCs) lacking Lyz2 expression are enriched in genes associated with T cell chemotaxis and tumor immunity. Functionally, these Lyz2-never expressed (Lyz2-YFP-) KCs are preferentially localized within intratumoral regions, where they promote hepatocellular carcinoma progression by recruiting CD4+CD25+Foxp3+ regulatory T cells (Tregs) and inducing T cell exhaustion. Conversely, Lyz2-ever expressed (Lyz2-YFP+) KCs exhibit anti-tumor activity by enhancing effector CD8+ T cell function. Our findings unveil a long-lived subset of RTMs with sustained pro-tumorigenic potential, underscoring the critical role of their yolk sac-derived developmental trajectory in shaping their functional properties. This study provides novel insights into the ontogeny-dependent heterogeneity of RTMs and their dual roles in tumor immunity.

overall_design: Samples were sorted from YFP- and YFP+ KCs from 6-8 weeks old male and female Lyz2cre-RosaYFP reporter mice for 2×105 KCs each group. Total RNA was dissolved by Trizol lysis buffer and then sent for RNA extraction and cDNA library preparation for RNA-sequencing analysis. The RNA extraction, cDNA library preparation, and sequences were generated by CapitalBio Technology (Beijing, China).

first: Tong

last: Lei

first: Qian

first: Yong

last: Zhao


title: Conservation and alteration of mammalian striatal interneurons

status: Public on Aug 11 2025

city: San Francisco

first: Alex

last: Pollen

state: CA

country: USA

institute: University of California San Francisco

type: Expression profiling by high throughput sequencing

summary: Mammalian brains vary in size, structure, and function, but the extent to which evolutionarily novel cell types contribute to this variation remains unresolved. Recent studies suggest there is a primate-specific population of striatal inhibitory interneurons, the TAC3 interneurons. However, broader taxonomic and developmental characterization is required to address novelty in cell type evolution. Here, we examine gene expression in inhibitory neurons across 11 mammalian species, spanning 160 million years divergence from primates. We find that the initial class of newborn TAC3 interneurons specified during development represents an ancestral, MGE-derived striatal population also present in pig and ferret cortex. This discovery prompted a reexamination of the Glire clade, including mice which are thought to lack the TAC3 type. Targeted enrichment of MGE precursors in mice reveals conservation of the TAC3 initial class, camouflaged by reduced expression of Tac2 (the mouse ortholog of TAC3) and a gain of Th expression. Extending our analysis to the adult striatum further supports the homology of primate TAC3 and mouse Th striatal interneurons, while uncovering a rare Tac2 subpopulation in mouse ventromedial striatum. This study suggests that initial classes of telencephalic inhibitory neurons are largely conserved and that during evolution, neuronal types in the mammalian brain change through redistribution and fate refinement, rather than by derivation of novel precursors early in development.

sample_organism:
Mustela putorius furo
Sus scrofa
Oryctolagus cuniculus
Mus musculus
Rattus norvegicus
Monodelphis domestica
Petaurus breviceps

overall_design: 10x Genomics Chromium next GEM single cell 3' RNA-sequencing of developing ferret, pig, rat, rabbit, mouse, opossum and sugar glider developing brain.

first: Emily

middle: K

last: Corrigan


title: A novel t(5;7)(q31;q21/CDK6::IL3 in immature T-cell acute lymphoblastic leukemia with IL3 overexpression and reactive eosinophilia [WTE]

city: Perugia

first: Roberta

last: La Starza

address: Piazzale Menghini 9

department: Department of Medicine and Surgery

country: Italy

institute: University of Perugia

summary: IL3 expression and reactive eosinophils

overall_design: Copy number analysis of a case of  T-ALL, harboring the CDK6::IL3 rearrangement, by CytoScan HD Affymetrix platform

first: Valentina

last: Pierini

last: Bardelli


title: A novel t(5;7)(q31;q21/CDK6::IL3 in immature T-cell acute lymphoblastic leukemia with IL3 overexpression and reactive eosinophilia [SNP]

summary: IL3 expression and reactive eosinophils


title: Differential expression profiles of RNAs in Hep3B cells after silencing LINC01547

city: Yantai

first: Defang

last: Li

address: No. 346 Guanhai, Laishan District

institute: Binzhou Medical University

summary: We extracted the total RNA of Hep3B cells after silencing LINC01547 for 48 h and used RNA-seq technology to detect differentially expressed RNAs in Hep3B cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Hep3B cells from NC or si-LINC01547 groups.

first: Dan

last: Wang


title: Aberrant splicing exonizes C9ORF72 repeat expansion in ALS/FTD

city: New Haven

first: Suzhou

last: Yang

state: CT

address: 100 College Street, Room 225

department: Neuroscience

institute: Yale University

summary: A nucleotide repeat expansion (NRE) in the first annotated intron of the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). While C9 NRE-containing RNAs can be translated into several toxic dipeptide repeat proteins, how an intronic NRE can access the translation machinery in the cytoplasm remains unclear. By capturing and sequencing NRE-containing RNAs from patient-derived cells, we found that C9 NRE was exonized by the usage of downstream 5ʹ splice sites and exported from the nucleus in a variety of spliced mRNA isoforms. C9ORF72 aberrant splicing was substantially elevated in both C9 NRE+ motor neurons and human brain tissues. Furthermore, NREs above the pathological threshold were sufficient to activate cryptic splice sites in reporter mRNAs. In summary, our results revealed a crucial and potentially widespread role of repeat-induced aberrant splicing in the biogenesis, localization, and translation of NRE-containing RNAs.

overall_design: Conventional RNA-seq analysis cannot distinguish reads from the NRE-containing transcripts from the much more abundant C9ORF72 mRNAs without NRE. To specifically enrich the NRE-containing transcripts, we adapted the previously described RNA antisense purification (RAP) method and used 5ʹ-biotinylated (CCCCGG)3 ASOs to capture (GGGGCC)n NRE-containing transcripts from nuclear and cytoplasmic RNAs of patient-derived fibroblasts for RNA-seq analysis.

first: Denethi

last: Wijegunawardana

first: Udit

last: Sheth

first: Austin

middle: M

last: Veire

first: Juliana

last: Salgado

first: Tanina

last: Arab

first: Manasi

last: Agrawal

first: Jeffrey

last: Zhou

first: João

middle: D

last: Pereira

first: Tania

middle: F

last: Gendron

first: Junjie

middle: U

last: Guo


title: Gene expression effects of KDAC6 (HDAC6) knockout in HT1080 cells

city: New Orleans

first: Terry

middle: J

last: Watt

state: LA

address: 1 Drexel Dr.

department: Chemistry

institute: Xavier University of Louisiana

summary: To study the gene expression and phenotype roles of KDAC6, CRISPR/Cas9 was used to create knockout cell lines from wild-type HT1080 cells.  Four individual isolated knockout clones were pooled to create the line.  Comparable wild-type data is available in GSE302260.

overall_design: Gene expression profiling analysis of RNA-seq data for HT1080 cells having KDAC6 knockout, with 4 replicates.

first: Tasha

middle: B

last: Toro


title: RNA-seq of wild-type HT1080 fibrosarcoma cells

summary: Reference RNA-seq data for experiments involving treatments of HT1080 cells.

overall_design: Gene expression profiling analysis of RNA-seq data for wild-type HT1080 cells, with 4 replicates.


title: Effect of overexpressing PRDM16 in human podocytes treated with high glucose

city: Wuhan

first: Ben

last: Tang

address: JieFang Avenue

department: Department of Nephrology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: To elucidate the function of PRDM16 in high glucouse environment , we performed RNA-seq on HPC cells transfected with negative control(NC) or PRDM16 overexpressing lenti-virus when treated with high glucouse .We then performed gene expression profiling analysis using data obtained from RNA-seq above.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NC or PRDM16 overexprssing lenti-virus transfected HPCs in high glucouse environment.

first: Qian

last: Yuan

first: Beng


title: Dynamic analysis of obstructive nephropathy with prolonged obstruction duration by multi-omics

city: Qingdao

first: wei

last: jiao

state: Shandong

address: No. 16 Jiangsu Road, Qingdao 266000, Shandong Province, China

department: urology

institute: The Affiliated Hospital of Qingdao University

summary: Introduction It is necessary to study the time series of obstructive nephropathy because of different pathophysiological changes in different stages of obstructive nephropathy. Methods In order to recognize the dynamic molecular changes of obstructive nephropathy, this study applied multi-omics ways to evaluate the mRNA and metabolite in different stage of obstructive nephropathy. Results Based on Gene Ontology (GO) and KEGG pathway analyses of transcriptome and metabolism, we defined specific pathways and persistent pathways in the early, middle, and late stages of obstructive nephropathy. adipocytokine signaling pathway, PPAR signaling pathway, JAK-STAT signaling pathway and all types of amino acid metabolism receive the most attention. Conclusion Through this approach, it was discovered that targeting specific molecules, proteins, kinases and critical pathways could be a promising approach for treating obstructive nephropathy.

overall_design: We have developed a series of unilateral ureteral obstruction (UUO) animal models with varying durations of obstruction to simulate the sequential pathological changes in obstructive nephropathy. The animals were randomly divided into five groups according to the duration of ureter ligation. Group A: ureter ligation lasts for 1 day; Group B: ureter ligation lasts for 3 days; Group C: ureter ligation lasts for 7 days; Group D: ureter ligation lasts for 14 days; Group E: sham group. Rats were anesthetized with ketamine (100 mg/kg). Median laparotomy was conducted on heating pads, and the left ureter was exposed and then ligated with 4-0 silk. The sham group was established by dissecting the left ureter without ligation. The kidneys were harvested on the designated time point day after surgery of each group for transcriptomic and metabolomic analysis. All rats underwent cervical dislocation under anesthesia after the kidneys were removed.

first: Xinning

first: Shang

last: Xu

first: Guipeng

first: Jingxian

first: Zhilong

last: Liu

first: Yize

first: Yi

last: Xia

first: Yuxin

first: Wei

last: Jiao


title: Bronchial epithelial cells transcriptomics upon flagellin stimulation (Microarray)

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: Innate immune memory is a new concept describing ability of innate myeloid and lymphoid cells to gain memory characteristics after transient stimulation, resulting in an nonspecific modified response upon secondary challenge. In recent work, we demonstrated that bronchial epithelial cells, non immune cells, that are the first immune cells of the lower respiratory tract to encounter pathogens were capable of innate immune memory after pre-exposure to Pseudomonas aeruginosa flagellin. In the present study  we identified chromatin modifications induced by flagellin pre-exposure that sustain reprogramming of transcriptional patterns. We researched chromatin structure modifications responsible for the modulation of gene expression and thus of innate memory induced by the exposure of cells to flagellin.

overall_design: 15 samples, 5 conditions in triplicate

first: Jeanne

last: Bigot

first: Juliette

last: Hamroune

first: Sébastien

last: Jacques

first: Mathieu

last: Legars

first: Loïc

last: Guillot

first: Harriet

last: Corvol

first: Christophe

last: Hennequin

last: Guitard

first: Viviane

last: Balloy

first: Claudia

last: Chica


title: Human cytomegalovirus infection impairs axon formation via repressing glycogen synthase kinase-3β activity-mediated adenosine triphosphate synthesis

status: Public on Aug 09 2025

city: shenyang

first: jingxuan

last: sun

address: puhe

institute: china medical university

summary: Human cytomegalovirus (HCMV)has a global distribution and is highly prevalent. HCMV infection has been recognized as a major contributor to neural development abnormalities in embryos and children. However, the underlying mechanisms by which HCMV infection leads to neurological diseases remain incompletely understood. Our study showed that HCMV inhibits neural cell differentiation by affecting the production of adenosine triphosphate (ATP) during neural differentiation. In this work, we found that HCMV infection interferes with the neural differentiation of stem cells from human exfoliated deciduous teeth (SHEDs)and human neuroblastoma cell line (SH-SY5Ys), affects the expression of neural cell markers, and inhibits the axon formation of neural cells. Under neurogenic inductive conditions, HCMV infection of SHEDs and SH-SY5Ys caused an increase in Glycogen synthase kinase-3β(GSK-3β) phosphorylation level and a decrease in GSK-3β phosphatase activity. HCMV infection was shown to inhibits GSK-3β activity, suppresses the level of mitochondrial oxidative phosphorylation in cells, reduces ATP production, impedes energy supply during neural differentiation, and inhibits neural differentiation. Our study sheds light on a molecular mechanism by which crosstalk between protein phosphorylation and oxidative phosphorylation links HCMV infection and neural differentiation and raises a potential strategy for the therapy of congenital HCMV infection.

overall_design: RNA-seq of human SHsy5y in control and  experiment group of SHsy5y and SHsy5y_infection


title: ASNA1 CKO with XMCL-CRE+ E14.5 mouse heart RNAseq

city: San Diego

first: Zengming

last: Zhang

address: 9500 Gilman Drive, La Jolla

institute: UCSD

summary: ASNA1 (also known as TRC40) is a key component of the tail-anchored (TA) protein targeting pathway. To investigate its role in the heart, we generated cardiomyocyte-specific ASNA1 conditional knockout (ASNA1 CKO) mice. RNA-seq analysis was performed on E14.5 embryonic heart to identify transcriptional changes caused by ASNA1 deficiency. Our results reveal that ASNA1 is essential for maintaining the stability of TA proteins and regulating vesicular transport in cardiomyocytes, which are critical for normal cardiac development and function.

overall_design: To investigate the role of Asna1 in cardiac development, we generated cardiomyocyte-specific Asna1 knockout mice (Asna1^fl/fl; Xmlc2-Cre^+/−) by crossing floxed Asna1 mice with Xmlc2-Cre transgenic mice. Ventricular tissues were collected from embryonic day 14.5 (E14.5) knockout and control littermates (n = 4 biological replicates per genotype). Total RNA was extracted, and RNA integrity was assessed prior to library preparation. Strand-specific mRNA libraries were prepared using the Illumina TruSeq Stranded mRNA kit and sequenced on the Illumina HiSeq 6000 platform to generate ~30 million paired-end reads (150 bp) per sample.

first: Ju

last: Chen


title: A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [scTCR_immunotherapies]

city: Noda City Chiba

first: Mikiya

last: Tsunoda

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo university of science

summary: Effective cancer immunotherapy relies on the clonal proliferation and expansion of CD8+ T cells in the tumor.  However, our insights into clonal expansions are limited, owing to an inability to track the same clones in tumors over time. Here, we developed a multi-site tumor mouse model system to track hundreds of expanding and contracting CD8+ T cell clones over multiple timepoints in tumors of the same individual. Through coupling of clonal expansion dynamics and single-cell RNA/TCR-seq data, we identified a transcriptomic signature in PD-1+Ly108+ precursor exhausted cells that strongly predicts rates of intratumoral clone expansion. The signature correlates with expansion in mice, both with and without immunotherapies, and in patients undergoing PD-1 blockade therapy. Expression of the signature during treatment corresponds with positive clinical outcomes. Downregulation of the signature precedes clone contraction – a phase in which clones contract but maintain revivable precursor exhausted cells in the tumor. LAG-3 blockade re-activates the expansion signature, re-expanding pre-existing clones, including previously contracted clones. These findings reveal how the study of clonal expansion dynamics provide a powerful ‘pan-immunotherapy’ signature for monitoring immunotherapies with implications for their future development.

overall_design: Lewis lung carcinoma (LLC) cells (5 × 10^5 cells /mouse) were inoculated subcutaneously (s.c.) into the left flank and right flank of C57BL/6 mice (aLAG3: n=5, aPDL1/aCTLA4: n=6). Tumors were excised on day 14 and day 21. T cells obtained from each tumor were analyzed by bulk TCR-sequencing.

first: Munetomo

last: Takahashi

first: Hiroyasu

last: Aoki

first: Masaki

last: Kurosu

first: Haru

last: Ogiwara

first: Shigeyuki

last: Shichino

first: David

last: Bending

first: Shumpei

last: Ishikawa

first: James

last: Thaventhiran

first: Kouji

last: Matsushima

first: Satoshi

last: Ueha


title: Facial vein collection and ibuprofen administration in mouse serial blood collections reduce pain and inflammation

city: Seoul

first: Jeong-Hwan

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Veterinary Medicine

country: South Korea

institute: Konkuk University

summary: Blood collection is essential for assessing the physiological status of laboratory animals, however, it inflicts pain, stress, tissue damage, and behavioral disorder to the animal. The administration of analgesics is one way to reduce the distress of animals suffering after experiments. Here we compared efficacious blood collection methods from the facial vein (FV), retroorbital plexus (RP), and lateral tail vein (TV) and the effects of ibuprofen administration based on animal welfare aspects. We evaluated body condition, behavioral activity, stress, pain, immunological profiles, and genetic changes in serial blood collections with or without ibuprofen administration for 8 weeks. We found that RP method reduced body weight, food intake, and water intake. RP method increased the grimace scales of orbital tightening and ear position. RP and TV methods reduced nest-building behaviors. RP and TV methods increased the concentrations of corticosterone, prostaglandin E2, and pro-inflammatory cytokines in peripheral blood. Infiltration of effector immune cells was increased in RP methods. Gene expressions associated with stress, pain, and immune system regulation were upregulated in all RP groups and ibuprofen non-administrated TV group. In contrast, the changed features were restored in FV method and ibuprofen administration. These data indicate that the FV blood collection and ibuprofen administration are suitable methods to mitigate physiologically harmful factors for mice depending on animal welfare considerations.

overall_design: RNA-seq profilling of PBMCs from control(Non) and blood collecting groups (facial vein FV, retroorbital plexus  RP,  and tail vein TV with or without ibuprofen administration) at week 8 of blood collections.

first: Moon-Seok

first: Eunjin

last: Bae

first: Jin Soo

last: Han


title: Comparison of gene expression between natural ligand treatment and agonistic antibody treatment in a CD30+ cell line

city: Ibaraki

last: Nagata

state: Osaka

institute: Epitope Science Co. Ltd.

summary: CD30 receptor (TNFRSF8) is highly expressed in some types of lymphoma. CD30 is successfully used as a target for antibody-drug conjugate to treat CD30+ lymphoma. The agonistic activity of the anti-CD30 antibody likely contributes to tumor cell killing. However, not all antibodies exhibit agonistic activity. We found that potent agonistic antibodies recognize the N-terminus epitope cluster that is distantly located from the ligand binding site of CD30. This study compared gene expression profiles between CD30 natural ligand and agonistic antibody T104 treatment in a CD30+ ALCL Karpas 299 cell line.

overall_design: 8 samples were analyzed. CD30+ ALCL Karpas 299 cells were precultured for 16 hrs. They were subsequently treated in the used medium with CD153(CD30L)-Fc fusion protein and/or anti-CD30 agonistic T104 monoclonal antibodies for 8 hrs. Biological duplicates were prepared for (1) untreated cells, (2) CD153-Fc-treated cells, (3) T104-treated cells, (4) CD153-Fc plus T104-treated cells. Biotin-labeled cRNA was prepared from the total RNA and subjected to hybridization with the HumanHT-12 v3 Expression BeadChip (Illumina).  Data were analyzed using BeadStudio.

first: Tomoko

last: Ise


title: CD200R1 loss in CNS-associated macrophages triggers T cell-driven neurodegeneration in Parkinson’s disease

city: 北京市

first: 震

last: 张

address: 右安门西头条10号

institute: 首都医科大学

summary: Immune dysregulation is increasingly recognized as a key contributor to Parkinson’s disease (PD) pathogenesis. While microglia are established central nervous system (CNS) immune regulators, the role of CNS-associated macrophages (CAMs) and their upstream modulation by immune checkpoints remains poorly defined. Here, we identify CD200R1, a myeloid-specific inhibitory receptor, as a checkpoint selectively expressed by embryonically derived CAMs at CNS borders. CD200R1 deletion reprograms CAMs toward a proinflammatory, antigen-presenting state enriched in interferon and pyroptosis-related gene signatures. In α-synuclein–based PD models, CD200R1 loss exacerbates dopaminergic neurodegeneration, enhances CD8⁺ T cell infiltration, and promotes formation of tertiary microglial–T cell nodules. Mechanistically, it activates the caspase-8/GSDMD pyroptosis pathway in CAMs, creating a permissive environment for pathogenic T cells. Pyroptosis blockade with disulfiram attenuates T cell infiltration and neurodegeneration. Notably, pharmacological activation of CD200R1 via CD200Fc suppresses CAM activation and confers neuroprotection. These findings define a border-specific immune checkpoint that governs CAM–T cell crosstalk and represents a tractable therapeutic target in PD.

overall_design: Eighteen-month-old WT and CD200R1⁻/⁻ mice were used to investigate the role of CD200R1 in neuroinflammation and T cell–mediated neurodegeneration. Brain tissues were collected for immune profiling and transcriptomic analysis. CD11b⁺ cells were isolated using magnetic separation, and cell viability, concentration, and clumping were assessed using acridine orange/propidium iodide staining and automated fluorescence cell counting. Single-cell suspensions (18,228 cells from WT and 19,159 from CD200R1⁻/⁻) were processed with the 10x Genomics Chromium system for single-cell RNA-seq.

first: Ting

last: Zhang

first: Zhen

first: Kun

last: Niu

first: Taoying

last: Huang

first: Jiali

last: Guo

first: Xiaoli

last: Gong

first: Yunke

last: Gao

first: Qixin

last: Zhu

first: Ang

last: Zhao

first: Gongbikai

last: Xarbat

first: Yuheng

last: Liu

first: Jie

last: Shen

first: Xiannian

first: Jun

last: Jia

first: Ke

last: Wang

first: Shuying

first: Zhaoyuan

first: Florent

last: Ginhoux


title: Bronchial epithelial cells accessibility upon flagellin stimulation (ATAC-Seq)

first: Rachel

last: Legendre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Innate immune memory is a new concept describing ability of innate myeloid and lymphoid cells to gain memory characteristics after transient stimulation, resulting in an nonspecific modified response upon secondary challenge. In recent work, we demonstrated that bronchial epithelial cells, non immune cells,  that are the first immune cells of the lower respiratory tract to encounter pathogens were capable of innate immune memory after pre-exposure to Pseudomonas aeruginosa flagellin. In the present study  we identified chromatin modifications induced by flagellin pre-exposure that sustain reprogramming of transcriptional patterns. We researched chromatin structure modifications responsible for the modulation of gene expression and thus of innate memory induced by the exposure of cells to flagellin.

first: Jeanne

last: Bigot

first: Juliette

last: Hamroune

first: Sébastien

last: Jacques

first: Mathieu

last: Legars

first: Loïc

last: Guillot

first: Harriet

last: Corvol

first: Christophe

last: Hennequin

last: Guitard

first: Viviane

last: Balloy

first: Claudia

last: Chica


title: Characterization of DNA methylation and transcriptomics during early pregnancy in dairy cows [RNA-seq]

city: shihezi

first: shiyi

last: li

address: shibei 4th road

institute: shihezi university

summary: DNA methylation is an essential epigenetic mechanism involved in cell differentiation, proliferation, apoptosis, and metabolism. However, the DNA methylation changes of related genes during early pregnancy in dairy cows remain unclear . The purpose of this study was to study DNA methylation-related changes in early pregnancy cows and construct gene pools associated with pregnancy. In this study, we used peripheral blood samples from 15 healthy, productive and similar cows at 30 days post-breeding (Pre30) and 10 non-pregnant cows (Ctrl) and association analysis was performed using Reduced Representation Bisulfite Sequencing (RRBS) and transcriptomic sequencing methods. Targeted bisulfite sequencing (TBS) and Quantitative Real-time PCR (RT-qPCR) method are used to verify the Methylation differential genes. Our findings showed that DNA methylation majorly occurred in the cytosine-guanine (CG) range, and the amount of hypomethylation was higher than that of hypermethylation in 3Utrs, introns and promoters. A total of 76530 differentially methylated sites (DMCs) and 16411 differentially methylated regions (DMRs) were identified. RNA-seq identified 8858 differentially expressed genes (DEGs), with 4499 down-DEGs and 4359 up-DEGs. However, there were 44 significant differentially expressed genes, including 25 up-DEGs and 19 down-DEGs. DMC gene ontology (GO) analysis revealed significant enrichment in developmental process, cell differentitaion and nevous system development in biological processes (BP);Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant enrichment in cancer overview and cellular and Gastric cancer and Immune disease signaling pathways. DMRs GO analysis highlighted significant enrichment in the developmental process, cell differentiation and nervous system development; KEGG the results showed that significant enrichment in Signaling pathways regulating pluripotency of stem cells, Systemic lupus erythematosus，Transcriptional misregulation in cancer，Spliceosome，Herpes simplex virus 1 infection, Maturity onset diabetes of the young. DEG GO analysis results show that the main enrichment in BP differentiation of bone marrow cells, red blood cell differentiation and erythrocyte steady-state and anion during transportation and transshipment; KEGG analysis mainly concentrated in retinol metabolism, purine metabolism, cAMP signaling pathway and Gap junction pathway. Through a comprehensive analysis of RRBS and transcriptomics, 12 genes, including HBB, HBA 1, GPR 4, CPXM 2, SLC20A2, AFAP 1 and DOK 7, were different both in the methylome and the transcriptome. Early pregnancy changes in DNA methylation were significant and mainly down-regulated. These results can be the epigenetic changes in early pregnancy for cows provide new insights.

overall_design: To investigate the changes in methylation associated with early pregnancy in cows, we used peripheral blood from 15 cows 30 days post-breeding (Pre) and 10 non-pregnant cows (Ctrl).There ere two groups, each with three biological replicates.


title: NSUN2 Facilitates Dicer Cleavage of DNA Damage-Associated R-Loops to Promote Repair [ONT direct RNA sequencing]

status: Public on Aug 08 2025

city: Oxford

first: Monika

last: Gullerova

address: S Parks Rd

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

summary: DNA integrity is constantly challenged by both endogenous and exogenous damaging agents, resulting in various forms of damage. Failure to repair DNA accurately leads to genomic instability, a hallmark of cancer. Distinct pathways exist to repair different types of DNA damage. Double-strand breaks (DSBs) represent particularly severe form of damage, due to physical separation of DNA strands. Repair of DSBs requires activity of RNA Polymerase II (RNAPII) and generation of Damage-associated transcripts (DARTs). Here we show that the RNA m5C-methyltransferase NSUN2 localizes to DSBs in transcription-dependent manner, where it binds to and methylates DARTs. Depletion of NSUN2 results in an accumulation of nascent DARTs around DSBs, specifically of the de novo primary DARTs. Furthermore, we detected an RNA-dependent interaction between NSUN2 and DICER, which was stimulated by DNA damage. NSUN2 activity promoted Dicer cleavage of DARTs associated R-loops, which is required for efficient DNA repair. We report a previously unrecognized role of the RNA m5C-methyltransferase NSUN2 within RNA-dependent DNA damage response, highlighting its function as a DICER chaperone for the clearance of non-canonical substrates such as DARTs, thereby contributing to genomic integrity.

overall_design: To investigate the role of NSUN2 in regulating processing of damage associated transcripts at genome-wide level, we emplyed the ONT direct RNA sequencing of chromatin associated RNA sequencing to detect the nascent transcripts and its modifications around DSBs in both mock and NSUN2-depleted cells.

first: Adele

last: Alagia

first: Kamal

last: Ajit


title: Glycerol-3-phosphate activates ChREBP, FGF21 transcription and lipogenesis in Citrin Deficiency

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: Citrin Deficiency (CD) is caused by inactivation of SLC25A13, a mitochondrial membrane protein required to move electrons from cytosolic NADH to the mitochondrial matrix in hepatocytes. People with CD do not like sweets. We discovered that SLC25A13 loss causes accumulation of glycerol-3-phosphate (G3P), which activates carbohydrate response element binding protein (ChREBP) to transcribe FGF21, which acts in the brain to restrain intake of sweets and alcohol, and to transcribe key genes of de novo lipogenesis. Mouse and human data establish G3P-ChREBP as a new mechanistic component of the Randle Cycle that contributes to metabolic dysfunction-associated steatotic liver disease (MASLD) and forms part of a system that communicates metabolic states from liver to brain in a manner that alters food and alcohol choices. The data provide a framework for understanding FGF21 induction in varied conditions, suggest ways to develop FGF21-inducing drugs, and suggest drug candidates for both lean MASLD and support of urea cycle function in CD.

overall_design: To determine whether deletion of NADH shuttle systems and/or provision of glycerol resulted in a ChREBP transcriptional program, we harvested livers from 40 mice representing water and glycerol-exposed males of the four genotypes, prepared cDNA and performed bulk paired-end 150 base-pair RNA sequencing (RNAseq)61 using an Illumina NovaSeq X Plus sequencer at >20 million paired reads per sample.

first: Vinod

last: Tiwari

first: Byungchang

last: Jin

first: Olivia

last: Sun

first: Charles

last: Brenner


title: Efferocytic remodeling of pancreatic intra-islet macrophages by limited beta-cell death [bulk_RNASeq_mouse]

city: St. Louis

first: Pavel

last: Zakharov

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Wash.Univ in St. Louis

summary: The primary driver of Type I diabetes are the autoimmune T cells that destroy insulin-producing beta-cells within the islets of Langerhans in the pancreas. Pancreatic macrophages have also been variably linked to disease onset and progression. As macrophage-mediated removal of dying cells via ‘efferocytosis’ regulate tissue homeostasis and immune responses, we addressed whether efferocytosis by intra-islet macrophages influences the immune environment of pancreatic islets. Here, using a series of complementary omics-based and functional approaches, we identify a subset of anti-inflammatory intra-islet ‘efferocytic macrophages’ (e-Mac) within the pancreas of mice and humans. When limited beta-cell apoptosis is induced in vivo in wild type C57BL/6 mice and diabetic-prone NOD mice, islet macrophages adopt this e-Mac phenotype without an apparent increase in total intra-islet macrophage numbers. Strikingly, such induction of limited beta-cell apoptosis and increase in e-Mac numbers in NOD mice led to long-term suppression of autoimmune diabetes. These data advance a concept that efferocytosis-associated reprogramming of the islet macrophages and its subsequent influence on the adaptive immune response could be beneficial in modulating diabetic autoimmunity.

overall_design: RNA-seq profiling of CD4⁺ T cells co-cultured with islet macrophages from single low-dose STZ- or buffer-treated NOD mice.

middle: N

first: Chanchal

middle: S

last: Chowdhury

first: Orion

last: Peterson

first: Brady

last: Barron

first: Anthony

last: Vomund

first: Laurent

last: Gorvel

first: Emil

middle: R

last: Unanue

first: Eynav

last: Klechevsky

first: Xiaoxiao

last: Wan

first: Kodi

last: Ravichandran


title: Conserved facultative heterochromatin across cell types identify regulatory sequences underpinning cell identity and disease

city: Springfield lakes

first: Enakshi

last: Sinniah

state: Queensland

address: 59 Orchard Crescent

country: Australia

institute: University of Queensland

summary: Cellular diversity is a product of evolution acting to establish divergent regulatory programs from a common genome. Here, we use cross-cell-type epigenetic conservation to gain insight into the impact of selective constraints on genome function and phenotypic variation. By comparing chromatin accessibility across hundreds of diverse cell-types, we identify 1.4% of the human genome safeguarded by conserved domains of facultative heterochromatin, which we term regions under “cellular constraint”. We calculate single-base resolution cellular constraint scores and demonstrate robust prediction of functionally important coding and non-coding loci in a cell-type-, trait-, and disease-agnostic manner. Cellular constraint annotation enhances causal variant identification, drug discovery, and clinical diagnostic predictions. Furthermore, cell-constrained sequences share signals of positive and negative selection, suggesting a dynamic role in influencing human fitness and adaptation. Overall, this study demonstrates that evolutionary chromatin dynamics can be leveraged to inform the translation of genetic discoveries into effective biological, therapeutic, and clinical outcomes.

overall_design: Hashtag barcoded WTC CRISPRi (Control) and RP11-175E9.1-g1 CRISPRi WTC (NKX2-6-AS1 K/D) hiPSCs were differentiated and on day 6 were pooled together with other samples for sequencing. Single live cells were collected and FACs sorted for a multiplexed scRNA-seq run.

first: Dalia

last: Mizikovsky

first: Woo Jun

last: Shim

first: Chris

last: Chow

first: Yassine

last: Souilmi

first: Fei-Fei

last: Cheng

first: Zhili

last: Zeng

first: Jordan

last: Laurie

first: Matthew

last: Foster

first: Sonia

last: Shah

first: Mikael

last: Boden

first: Jian

first: Bastien

last: Llamas

first: Nathan

last: Palpant


title: Efferocytic remodeling of pancreatic intra-islet macrophages by limited beta-cell death [scRNASeq_human]

first: Pavel

last: Zakharov

overall_design: sc-RNASeq profiling of CD45+ cells isolated from the islets of human donors

first: Chanchal

last: Chowdhury

first: Orion

last: Peterson

first: Brady

last: Barron

first: Anthony

last: Vomund

first: Laurent

last: Gorvel

first: Emil

last: Unanue

first: Eynav


title: Transcriptional adaptation of human airway epithelium upon cigarette smoking

city: Ultimo

first: Alen

last: Faiz

state: NSW x

address: Thomas St,

institute: University of Technology Sydney

summary: Despite the well-known adverse health effects, smoking is still one of the leading causes of preventable death worldwide. Smoking has shown to significantly alter gene transcription in blood, but limited studies have assessed the effects of smoking on structural lung cells. Here, we investigated how the airway wall responds and adapts to chronic smoke exposure by changing airway epithelial transcriptional profiles in response to cigarette smoke exposure, using RNA-Seq. This study identifies panels of genes, related to the response of airway epithelial cells to cigarette smoke. Furthermore, our study shows especially luminal epithelial cells are affected by smoke and that the airways are epigenetically regulated to promote the expression of oxidative stress-response genes, which dampens the effects of chronic smoke exposure.

overall_design:
The Study to Obtain Normal Values of Inflammatory Variables From Healthy Subjects (NORM; NCT00848406) included non-COPD smokers and never-smokers. Bronchial biopsies were collected and then sequenced using RNA-Seq.
***Submitter declares that the raw data contains genetic information, and thus are not provided due to privacy concerns****

first: Maarten

last: Van Den Berge


title: Mesoscale proximity labeling at chromatin to study small molecule mechanism of action [RNAseq_4h_782]

city: Jupiter

first: Cameron

middle: James

last: Douglas

state: FL

address: 120 Scripps Way

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

summary: Proximity labeling traditionally identifies interactomes of a single protein or RNA, though this approach limits mechanistic understanding of biomolecules functioning within complex systems. Here, we demonstrate a strategy for deciphering ligand-induced changes to global biomolecular interactions by enabling proximity labelling at the mesoscale, across an entire cellular system. By inserting nanoscale proximity labelling catalysts throughout chromatin, this system, MesoMap, provided new insights into how HDAC inhibitors regulate gene expression. Furthermore, it revealed that the orphaned drug candidate, SR-1815, regulates disease-linked Syngap1 gene expression through direct inhibition of kinases implicated in both neurological disorders and cancer. Through precise mapping of global chromatin mobility, MesoMap promotes insights into how drug-like chemical probes induce transcriptional dynamics within healthy and disease-associated cellular states.

overall_design: Mouse primary cortical neurons from Syngap1 conditional rescue (Syngap1+/ls) mice were treated with either DMSO (vehicle) or SR-1815 for 4h and total RNA was collected for sequencing. N=5 for SR-1815 and DMSO.

first: Preston

last: Samowitz

first: Feifei

last: Tong

first: Alice

last: Long

first: Caitlin

last: Bradley

first: Laszlo

last: Radnai

first: David

last: MacMillan

first: Courtney

middle: A

last: Miller

first: Gavin

last: Rumbaugh

first: Ciaran

middle: P

last: Seath


title: Mesoscale proximity labeling at chromatin to study small molecule mechanism of action [RNAseq_2wk_736]

overall_design: Mouse primary cortical neurons from Syngap1 conditional rescue (Syngap1+/ls) mice were treated with either DMSO (vehicle) or SR-1815 for 2wk and total RNA was collected for sequencing. N=5 for SR-1815 and DMSO.


title: Depot-dependent effects of subclinical ketosis on visceral and subcutaneous adipose tissue transcriptional cellular diversity in dairy cows

city: Lubbock

first: Clarissa

last: Strieder-Barboza

state: Texas

address: ESB II, 1006 Canton Ave.

department: Veterinary Sciences

institute: Texas Tech University

summary: Adipose tissue plays a central role in regulating whole-body metabolic health, facilitated by the variety of cell types and their wide-ranging functions. In addition, depot-specific differences in adipose tissue have been shown to play important roles in different disease states including obesity, diabetes, and metabolic dysfunction in human and animal models. For early postpartum dairy cattle, metabolic dysfunction, triggered by a negative energy balance, is often manifested as subclinical ketosis (SCK). However, the role that subcutaneous (SAT) and visceral (VAT) adipose tissue depots, and their diverse cellular compositions, play in the response to subclinical ketosis conditions is unclear. Flank SAT and omental VAT were collected via laparotomy from five non-ketotic (NK; BHB ≤ 0.8 mmol/L) and five subclinical ketosis (SCK; 1.4 mmol/L < BHB ≤ 2.6 mmol/L) multiparous cows during early lactation. Following collection, nuclei were isolated from the tissue and subjected to single-nuclei RNA sequencing in order to investigate the transcriptional cellular heterogeneity. Distinct clusters of adipocytes (AD), adipose stem/progenitor cells (ASPC), immune cells (IMC), endothelial cells (EC), and pericyte/smooth muscle cells (PE/SMC) were identified in both adipose depots, with a greater abundance of ASPC in SAT compared to VAT. In addition, we identified a VAT-specific AD subtype characterized by higher expression of progenitor-like marker genes. While the abundance of none of the identified cell subtypes were different between SCK and NK, underlying transcriptional changes provided insight into potential effects of SCK. In general, SCK was associated with pro-lipogenic, anti-inflammatory, and pro-angiogenic transcriptional changes, possibly indicating a greater capacity for homeostatic responsiveness in SAT under conditions of enhanced negative energy balance. In contrast, SCK appeared to promote transcriptional changes indicative of impaired adipogenesis, impaired angiogenesis, and increased inflammation in VAT. Uniquely, our study presents novel insight into the cellular heterogeneity of adipose tissue in dairy cattle with subclinical ketosis. Furthering our understanding of the role of adipose tissue in response to this form of metabolic challenge has the potential to enhance efforts aimed at limiting the incidence and impact of subclinical ketosis and improving the health and productivity of dairy cattle.

overall_design: Five non-ketotic cows (NK; n = 5; BHB ≤ 0.8 mmol/L; 3.2 ± 1.6 lactations; 7.4 ± 1.8 DIM; 3.7 ± 0.2 BCS) and five cows with subclinical ketosis (SCK; n = 5; BHB > 1.4 and ≤ 2.6 mmol/L; 3.2 ± 1.2 lactations; 7.8 ± 2.0 DIM; 3.6 ± 0.4 BCS) were selected for adipose tissue sampling. Adipose tissue samples of flank subcutaneous adipose tissue (SAT) and omental visceral adipose tissue (VAT) were collected via laparotomy from each cow, and ~1g of tissue was immediately flash frozen and kept in liquid nitrogen until nuclei isolation.

first: Hunter

last: Ford


title: Effect of Myosin 10 or Jagged 1 knockout on gene expression in H1299 Non-small cell lung cancer leader cells.

city: Atlanta

first: Raaven

last: Goffe

state: GA

address: 100 Woodruff Circle

institute: Emory University School of Medicine

summary: While minimizing lung cancer metastasis can improve overall survival, few models exist where subpopulations with stable high and low metastatic potential can be easily and reliably isolated. Our previous work characterized two stable subpopulations, termed Leaders and Followers, from the H1299 Non-Small Cell Lung Cancer model. H1299 Leaders and Followers have different transcriptional profiles, biomarkers, genomic methylation patterns, metabolic states, and morphologies.Of note, H1299 Leaders express high levels of Jagged1 (JAG1) and Myosin 10 (MYO10) and drive collective invasion and metastasis. To determine how JAG1 and MYO10 contribute to Leader cell biology and lung cancer metastasis, we utilized CRISPR-Cas9 to generate edited pools of H1299 cells targeting either JAG1 or MYO10. Fluorescence-activated cell sorting using a Leader-Follower biomarker, IL13R2, was used to generate single cell derived candidate clones. Candidate clones were screened using western blot for Leader and Follower cell biomarkers (JAG1, MYO10, HTATIP2 and IL13R2) followed by Sanger sequencing of candidate clones was also conducted to confirm target gene status. Using this method, 2 JAG1 knockout, 2 MYO10 knockout, 1 MYO10 knockdown and, 2 wildtype MYO10 JAG1 H1299 single-cell derived clones were generated.

overall_design: RNA-seq profiling of  2 JAG1 knockout, 2 MYO10 knockout, 1 MYO10 knockdown and, 2 wildtype MYO10 JAG1 clonal cell lines along with H1299 parental, leader and follower cell lines.

first: Henry

last: Claussen

first: Robert

last: Aurther

first: Adam

middle: I

last: Marcus


title: Gene expression in CD30+ L540 cell line induced by different anti-CD30 antibodies that bind to different epitopes

first: Satoshi

last: Nagata

summary: CD30 receptor (TNFRSF8) is highly expressed in some types of lymphoma. Therefore, CD30 is successfully used as a target for antibody-drug conjugate to treat CD30+ lymphoma. In this study, we compared gene expression profiles induced in CD30+ L540 cell line by treating CD30 natural ligand or anti-CD30 antibodies against different epitopes.

overall_design: 12 samples were analyzed. CD30+ Hodgkin’s lymphoma L540 cells were precultured for 16 hrs. They were subsequently treated in the used medium with CD153(CD30L)-Fc fusion protein or anti-CD30 T104, T428, T427 or PW30 monoclonal antibodies for 8 hrs (not 24 hrs=the sample labels were wrong). Biological duplicates were prepared for each treatment. Biotin-labeled cRNA were prepared from the total cellular RNA and subjected to hybridization with the HumanHT-12 v3 Expression BeadChip (Illumina). Data were analyzed using BeadStudio.

first: Tomoko

last: Ise


title: FOP HO early lesion single cell sequencing

city: Tarrytown

first: Wei Keat

last: Lim

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron

summary: experiment for single cell sequencing of early FOP lesion to determine the pathogenesis of HO lesion development

overall_design: FOP mouse model will be initiated with Tamoxifen. 5 days post muscle injury, affected muscle and control muscle collected for single cell sequencing. A WT mice is used as sham.

first: Charles

last: Hwang

first: Chase

last: Pagani

first: Nanditha

last: Das

first: Simone

last: Marini

first: Amanda

last: Huber

first: LiQin

last: Xie

first: Johanna

last: Jimenez

first: Susannah

last: Brydges

first: Kalyan

last: Nannuru

first: Andrew

last: Murphy

first: Aris

last: Economides

first: Sarah

last: Hatsell

first: Benjamin

last: Levi


title: Rejuvenating macrophages by FcγR-targeted tuftsin clusters for sepsis-associated secondary infection

city: Beijing

first: Qing

last: Guangchao

address: No. 11, First North Road, Zhongguancun, Beijing, 100190, P.R. China

institute: National Center for Nanoscience and Technology

summary: Sepsis-associated secondary infection often leads to high mortality rate. Dysfunctional macrophages are the primary contributors to inadequate antimicrobial defense in patients   with sepsis-associated immunosuppression, elevating the risk of opportunistic infections. Here, a bacteria-targeted transformable macrophage nanorejuvenator, designated as BATMAN, is developed to effectively tackle sepsis-associated secondary infection by coordinating the arrest of invasive bacteria and rejuvenation of dysfunctional macrophages based on the in situ responsive transformation. The results affirm the BATMAN’s effective binding and transformation on bacterial surface. The enzymatic removal of Chems by bacterial lipase disrupts the hydrophilic-hydrophobic balance of BATMAN, triggering the inside-out rearrangement that exposes the concealed tuftsin and facilitates its assembly into polyvalent peptide clusters on trapped bacteria driven by the assembly of FFVLK. This transformation not only reduces the invasiveness of bacteria, but enhances the interaction between tuftsin clusters and macrophage Fc gamma receptor, promoting bacterial phagocytosis and driving macrophage repolarization. As a result, BATMAN rejuvenates the compromised immune response to eliminate the polymicrobial- and even multidrug-resistant pathogen-induced pulmonary infection in septic mice. Consequently, we anticipate that our in situ transformable BATMAN holds promise as a therapeutic alternative for sepsis-associated secondary infection.

overall_design: RNA-seq profiling of M2 bone marrow-derived macrophages treated with PBS or SA@BATMAN5 for 24 hours

first: Guangchao

last: Qing

first: Yuxuan

last: Zhang

first: Xing-Jie

last: Liang

first: Yang

last: Luo


title: Transcriptome and proteome reveal the effects of asmA on efflux and metabolic functions in Enterobacter cloacae ST2260

city: Guangzhou

first: Xu

last: Yang

address: Postal address, 151 Yanjiang Rd, Yuexiu District,

institute: the First Affiliated Hospital of Guangzhou Medical University

summary: Background: Efflux pumps are important cofactors for carbapenem resistance in Enterobacter cloacae. The regulatory mechanism by which asmA influences efflux pump function in this species remains unclear. This study explored the regulatory role of asmA on efflux pumps in carbapenem-resistant Enterobacter cloacae. Results: Sixteen carbapenem-resistant Enterobacter cloacae were collected. All strains carried blaNDM, 87.5% of which were blaNDM-1 and 12.5% were blaNDM-5. PAβN had weak inhibition on carbapenem resistance in ST78 and strong inhibition in ST2260. ST2260(CY-8) was still resistant to carbapenems after elimination of blaNDM and could be inhibited by PAβN. However, ST78(CY-9) lost its resistance to carbapenems. Knockout of asmA reduced the MIC of ST2260 by 16-fold. ST78 showed no such changes. Growth curves revealed impaired growth only in ST2260ΔasmA. Transcriptomics/qRT-PCR revealed no significantly altered acrAB-tolC or marA expression in either strain. Membrane proteomics detected AcrB loss specifically in ST2260ΔasmA. The loss of asmA affected a wide range of membrane proteins, especially OmpW. Molecular docking predicted that AsmA could bind to AcrB, with stronger binding energy in ST78. The buried area of the CY-8 model involved 110 contact residues, while the number of contacts of the CY-9 model increased to 144. The AsmA chain of the two models had 46 common contact residues, and the AcrB chain had 60 common contact residues. AcrB of ST78 generally carries the I277V mutation. Conclusion: asmA is highly conserved in Enterobacter cloacae. It has functional heterogeneity in different ST types. In ST2260, asmA can affect efflux pump-mediated carbapenem resistance. AsmA can regulate AcrAB-TolC not by affecting marA. It is predicted that AsmA can maintain the carbapenem resistance of Enterobacter cloacae ST2260 by helping AcrB anchor to the inner membrane. The difference in carbapenem resistance mediated by efflux pumps between ST78 and ST2260 suggests that ST78 commonly carries the AcrB I277V mutation, which is a key site for efflux of β-lactams.

overall_design: This transcriptomics study compares Enterobacter cloacae strains to investigate the role of asmA in carbapenem resistance. The design includes four groups: ST2260 ΔblaNDM (CY-8ΔN) ST2260 ΔblaNDM ΔasmA (CY-8ΔNΔA) ST78 ΔblaNDM (CY-9ΔN) ST78 ΔblaNDM ΔasmA (CY-9ΔNΔA) with three biological replicates per group (12 total samples). Bacteria were grown to logarithmic phase. Total RNA was extracted using the CTAB method, followed by rRNA depletion (RiboCop Kit) and Illumina Stranded mRNA library preparation. Sequencing was performed on Illumina NovaSeq™ (PE150) at Majorbio Cloud Platform. Reference genome: Enterobacter cloacae ATCC 13047.


title: Differential expression profiles of RNAs in Hep3B cells treated with Bufotalin

city: Yantai

first: Defang

last: Li

address: No. 346 Guanhai, Laishan District

institute: Binzhou Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: We extracted the total RNA of Hep3B cells treated with Bufotalin for 48 h and used RNA-seq technology to detect differentially expressed RNAs such as lncRNAs, miRNAs, and mRNAs in Hep3B cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Hep3B cells from Control or Bufotalin-treated groups.

first: Dan

last: Wang


title: Gene expression in Ramos human B cell line induced by treatment with anti-FCRL1 antibody treatment

first: Satoshi

last: Nagata

summary: B cell receptor CD40 and FCRL1 are highly expressed in Ramos B cell line. Therefore, these receptors are considered to cooperate in B cell activation. In this study, we compared gene expression profiles induced in Ramos cell line by combined treatments of anti-IgM antibody, anti-CD40 antibody, and anti-FCRL1 antibodies.

overall_design: 12 samples were analyzed. Ramos B cells were precultured for 16 hrs. They were subsequently treated in the used medium with anti-BCR (anti-IgM), anti-CD40 (G28-5 MAb) and anti-FCRL1 (E3 MAb) anti-IgM antibodies for 24 hrs. Biological duplicates were prepared for each treatment. Biotin-labeled cRNA was prepared from the total cellular RNA and subjected to hybridization with the HumanHT-12 v3 Expression BeadChip (Illumina). Data were analyzed using BeadStudio.

first: Tomoko

last: Ise


title: Gene expression in FCRL2+ cell lines stimulated with anti-FCRL2 antibodies

summary: Fc receptor-like 2 (FCRL2) molecule is expressed in the B cell subpopulation. Although FCRL2 has both immunoreceptor tyrosine-based activation/Inhibition motives (ITAM/ITIM) in the intracellular regions, the biological functions and roles remain unknown. In this study, we compare gene expression profiles in # FCRL2+ cell lines (HS-Sultan, RPMI8226, or SU-DHL-5) with and without treatment of a mixture of Anti-FCRL2 monoclonal antibodies.

overall_design: 12 samples were analyzed. FCRL2+ HS-Sultan, RPMI8226, or SU-DHL-5cells were precultured for 16 hrs. They were subsequently treated in the used medium with a mixture of anti-FCRL2 B24 and B62 monoclonal antibodies for 24 hrs. Biological duplicates were prepared for each treatment. Biotin-labeled cRNA was prepared from the total cellular RNA and subjected to hybridization with the HumanHT-12 v3 Expression BeadChip (Illumina). Data were analyzed using BeadStudio.


title: Gene expression effects of KDAC8 (HDAC8) knockout in HT1080 cells

city: New Orleans

first: Terry

last: Watt

address: 1 Drexel Dr.

institute: Xavier University of Louisiana

summary: To study the gene expression and phenotype roles of KDAC8, CRISPR/Cas9 was used to create knockout cell lines from wild-type HT1080 cells.  Four individual isolated knockout clones were pooled to create the line.  Comparable wild-type data is available in GSE302260.

overall_design: Gene expression profiling analysis of RNA-seq data for HT1080 cells having KDAC8 knockout, with 4 replicates.

first: Tasha

last: Toro


title: Epigenetic reprogramming involved in bronchial epithelial cells memory induced by flagellin stimulation

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

institute: Institut Pasteur

summary: Innate immune memory is a new concept describing ability of innate myeloid and lymphoid cells to gain memory characteristics after transient stimulation, resulting in an nonspecific modified response upon secondary challenge. In recent work, we demonstrated that bronchial epithelial cells that are non immune cells, the first immune cells of the lower respiratory tract to encounter pathogens were capable of innate immune memory after pre-exposure to Pseudomonas aeruginosa flagellin. In the present study  we identified chromatin modifications induced by flagellin pre-exposure that sustain reprogramming of transcriptional patterns. We researched chromatin structure modifications responsible for the modulation of gene expression and thus of innate memory induced by the exposure of cells to flagellin.

overall_design: Refer to individual Series

first: Jeanne

last: Bigot

first: Juliette

last: Hamroune

first: Sébastien

last: Jacques

first: Mathieu

last: Legars

first: Loïc

last: Guillot

first: Harriet

last: Corvol

first: Christophe

last: Hennequin

last: Guitard

first: Jean-Yves

last: Coppee

first: Viviane

last: Balloy

first: Claudia

last: Chica


title: Aberrant lncRNA and mRNA expression in patients with anti-N-methyl-D-aspartate receptor encephalitis

city: Jinan

first: Xiaoyu

last: Ma

address: 247 Beiyuan Street

institute: The Second Hospital of Shandong University

summary: Background: Anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis is a nervous autoimmune disorder discovered in the recent more than fifteen years. To understand potential involvement of epigenetic mechanisms in pathogenesis of anti-NMDAR encephalitis, we initiated a study to compare the expression profiles of long non-coding RNAs (lncRNAs) and messenger RNA (mRNAs) in patients of anti-NMDAR encephalitis and healthy controls. Methods: 11 patients who were diagnosed with anti-NMDAR encephalitis were enrolled in our observational studies. Total RNA was extracted from patients’ plasma and the expression levels of lncRNAs and mRNAswere determined. Differential expression analysis via RNA sequencing, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, as well as a co-expression network of lncRNA-mRNA were performed in 5 patients and 5 healthy controls to evaluate potential the changes in expression patterns. The expression levels of certain lncRNAs and mRNAs were further validated in 11patients and 11 healthy controls using quantitative real-time polymerase chain reaction (qRT-PCR). Results: It was found that a total of 83 lncRNAs and 2345 mRNAs were differentially expressed in five patients with anti-NMDAR encephalitis compared with five healthy controls.  Of those lncRNAs, 63 were upregulated and 20 downregulated, while 1509 mRNAs were upregulated and 836 downregulated. GO and KEGG pathway analyses showed that a wide range of biological functions were perturbed during acute anti-NMDAR encephalitis. Differentially expressed genes were found to be involved in autoimmune, B cell signaling, neuroinflammation, or synaptic plasticity. qRT-PCR was conducted in 11 patients and 11healthy controls to further confirm the levels of six lncRNAs and four mRNAs, and the results were found to be consistent with those by RNA sequencing. The co-expression networks of lncRNA-mRNA were performed in some meaningful KEGG analyses, including chemokine signaling pathway, Long-term potentiation, B cell receptor signaling pathway and MAPK signaling pathway. Conclusions: Taken together, these findings suggest the involvement of a number of molecular pathways in anti-NMDAR encephalitis, some of which could serve as potential biomarkers to assist in diagnosis, treatment and prognosis.

overall_design: RNA-seq of human plasma in health and disease group


title: A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [scTCR_untreated]

city: Noda City Chiba

first: Mikiya

last: Tsunoda

address: 2669 Yamazaki

institute: Tokyo university of science

summary: Effective cancer immunotherapy relies on the clonal proliferation and expansion of CD8+ T cells in the tumor.  However, our insights into clonal expansions are limited, owing to an inability to track the same clones in tumors over time. Here, we developed a multi-site tumor mouse model system to track hundreds of expanding and contracting CD8+ T cell clones over multiple timepoints in tumors of the same individual. Through coupling of clonal expansion dynamics and single-cell RNA/TCR-seq data, we identified a transcriptomic signature in PD-1+Ly108+ precursor exhausted cells that strongly predicts rates of intratumoral clone expansion. The signature correlates with expansion in mice, both with and without immunotherapies, and in patients undergoing PD-1 blockade therapy. Expression of the signature during treatment corresponds with positive clinical outcomes. Downregulation of the signature precedes clone contraction – a phase in which clones contract but maintain revivable precursor exhausted cells in the tumor. LAG-3 blockade re-activates the expansion signature, re-expanding pre-existing clones, including previously contracted clones. These findings reveal how the study of clonal expansion dynamics provide a powerful ‘pan-immunotherapy’ signature for monitoring immunotherapies with implications for their future development.

overall_design: Lewis lung carcinoma (LLC) cells (5 × 10^5 cells /mouse) were inoculated subcutaneously (s.c.) into the left flank and right flank of C57BL/6 mice (n=5). Tumors were excised on day 14 and day 21. T cells obtained from each tumor were analyzed by bulk TCR-sequencing.

first: Munetomo

last: Takahashi

first: Hiroyasu

last: Aoki

first: Masaki

last: Kurosu

first: Haru

last: Ogiwara

first: Shigeyuki

last: Shichino

first: David

last: Bending

first: Shumpei

last: Ishikawa

first: James

last: Thaventhiran

first: Kouji

last: Matsushima

last: Ueha


title: Reduced glutathione levels in Enterococcus faecalis trigger metabolic and transcriptional compensatory adjustments during iron exposure.

city: Santiago

first: Victor

last: Aliaga

address: Camino La Pirámide 5750

country: Chile

institute: Universidad Mayor

summary: The microarrays experiments was performed in order to identify transcriptional networks in Enterococcus faecalis. Work:Reduced glutathione levels in Enterococcus faecalis trigger metabolic and transcriptional compensatory adjustments during iron exposure

overall_design: A six chip study (two technical replicates) using total RNA recovered from four separate cultures of: Enterococcus faecalis OG1RF (N medium growth),  Enterococcus faecalis OG1RF gshΔ mutant strain (N medium growth), Enterococcus faecalis OG1RF gshΔ mutant iron treatment (N medium growth + 0.5 mM FeCl3-NTA). Each chip measures the expression level of 3,114 genome genes from Enterococcus faecalis strain V583 (A7980-00-01).


title: Characterization of DNA methylation and transcriptomics during early pregnancy in dairy cows

city: shihezi

first: shiyi

last: li

address: shibei 4th road

institute: shihezi university

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is an essential epigenetic mechanism involved in cell differentiation, proliferation, apoptosis, and metabolism. However, the DNA methylation changes of related genes during early pregnancy in dairy cows remain unclear . The purpose of this study was to study DNA methylation-related changes in early pregnancy cows and construct gene pools associated with pregnancy. In this study, we used peripheral blood samples from 15 healthy, productive and similar cows at 30 days post-breeding (Pre30) and 10 non-pregnant cows (Ctrl) and association analysis was performed using Reduced Representation Bisulfite Sequencing (RRBS) and transcriptomic sequencing methods. Targeted bisulfite sequencing (TBS) and Quantitative Real-time PCR (RT-qPCR) method are used to verify the Methylation differential genes. Our findings showed that DNA methylation majorly occurred in the cytosine-guanine (CG) range, and the amount of hypomethylation was higher than that of hypermethylation in 3Utrs, introns and promoters. A total of 76530 differentially methylated sites (DMCs) and 16411 differentially methylated regions (DMRs) were identified. RNA-seq identified 8858 differentially expressed genes (DEGs), with 4499 down-DEGs and 4359 up-DEGs. However, there were 44 significant differentially expressed genes, including 25 up-DEGs and 19 down-DEGs. DMC gene ontology (GO) analysis revealed significant enrichment in developmental process, cell differentitaion and nevous system development in biological processes (BP)；Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant enrichment in cancer overview and cellular and Gastric cancer and Immune disease signaling pathways. DMRs GO analysis highlighted significant enrichment in the developmental process, cell differentiation and nervous system development; KEGG the results showed that significant enrichment in Signaling pathways regulating pluripotency of stem cells, Systemic lupus erythematosus，Transcriptional misregulation in cancer，Spliceosome，Herpes simplex virus 1 infection, Maturity onset diabetes of the young. DEG GO analysis results show that the main enrichment in BP differentiation of bone marrow cells, red blood cell differentiation and erythrocyte steady-state and anion during transportation and transshipment; KEGG analysis mainly concentrated in retinol metabolism, purine metabolism, cAMP signaling pathway and Gap junction pathway. Through a comprehensive analysis of RRBS and transcriptomics, 12 genes, including HBB, HBA 1, GPR 4, CPXM 2, SLC20A2, AFAP 1 and DOK 7, were different both in the methylome and the transcriptome. Early pregnancy changes in DNA methylation were significant and mainly down-regulated. These results can be the epigenetic changes in early pregnancy for cows provide new insights.

overall_design: To investigate the changes in methylation associated with early pregnancy in cows, we used peripheral blood from 15 cows 30 days post-breeding (Pre30) and 10 non-pregnant cows (Ctrl).There were two groups, each with three biological replicates.


title: Spermatogenesis, hormonal fluctuations, and testicular gene expression changes in male blue catfish, Ictalurus furcatus, throughout pubescent and early adult stages of development

city: Auburn

first: Ian

last: Butts

state: Alabama

address: 203, Swingle Hall

department: School of Fisheries, Aquaculture & Aquatic Sciences

institute: Auburn University

summary: Male blue catfish (Ictalurus furcatus) mature at 4-7 years and cannot be hand-stripped, making sperm collection a lethal procedure. Sperm are also highly variable in quality/quantity. Therefore, establishing links between seasonality, aging, and reproductive success is essential. Since there are no prior studies regarding seasonal and age-related changes in the testis transcriptome of male blue catfish, we evaluated global gene expression in testicular tissue over a 34-month period (2.3 to 4.9 years old; y/o). Significant differential expressed genes and gene ontology of pairwise comparisons are presented and discussed.

overall_design: A total of 15 testis tissue samples from blue catfish males were used in this study, corresponding to ages 2.9, 3.1, 3.9 and 4.2. Three-four testis tissue samples were collected per age group and extracted for RNA-seq.

first: Jason

last: Abernathy

first: Kaylan

last: Martin


title: The ALT-LINC complex mediates cellular responses to matrix mechanics

city: St. Louis

first: Helen

last: McNeill

state: Missouri

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine in St. Louis

summary: Nuclear Envelope Membrane Protein 1 (NEMP1) is crucial for metazoan fertility; loss of Nemp1 causes primordial oocyte death, residing in the mechanically challenging ovarian cortex. Here, we show that softening the ovary rescues oocyte loss and restores fertility in NEMP1 knockout mice. In cell culture, NEMP1 depletion on stiff substrates leads to death, while cells remain viable on soft substrates. We further show that NEMP1 regulates YAP nuclear translocation, essential for mechanotransduction. Mechanistically, Nemp1-depleted cells on stiff substrates or subjected to stretching exhibit reduced nuclear YAP localization, and expressing nuclear YAP5SA restores cell viability. Loss of NEMP1 disrupts actin organization, inhibiting YAP nuclear translocation. Inducing actin polymerization rescues nuclear YAP, indicating an F-actin-dependent mechanism for NEMP1-mediated mechanotransduction. NEMP1 forms a novel complex with NESPRIN2's KASH domain, strengthening the actin cytoskeleton to withstand mechanical forces, independently of SUN proteins. Thus, NEMP1-Nesprin complex, named hereafter ALT-LINC, creates a mechanosensitive pathway parallel to the LINC complex and is crucial for YAP mechanotransduction, enabling cellular response to mechanical stress in vitro and in vivo.

overall_design: RNA-seq profiling of the human epithetial cell line (hTERT RPE-1 - CRL-4000) cultured on soft (10 kPA) and stiff (120 kPA) substrates. This dataset compares control samples and siNemp1-treated samples under both stiffness conditions.

first: Abira

last: Ganguly

first: Nattapon

last: Thanintorn


title: Mesoscale proximity labeling at chromatin to study small molecule mechanism of action [MNase-seq]

first: Cameron

last: Douglas

summary: Proximity labeling traditionally identifies interactomes of a single protein or RNA, though this approach limits mechanistic understanding of biomolecules functioning within complex systems. Here, we demonstrate a strategy for deciphering ligand-induced changes to global biomolecular interactions by enabling proximity labelling at the mesoscale, across an entire cellular system. By inserting nanoscale proximity labelling catalysts throughout chromatin, this system, MesoMap, provided new insights into how HDAC inhibitors regulate gene expression. Furthermore, it revealed that the orphaned drug candidate, SR-1815, regulates disease-linked Syngap1 gene expression through direct inhibition of kinases implicated in both neurological disorders and cancer. Through precise mapping of global chromatin mobility, MesoMap promotes insights into how drug-like chemical probes induce transcriptional dynamics within healthy and disease-associated cellular states.

overall_design: WT HEK293T and pc293T cells, which express histone constructs for proximity labeling, were evaluated by Mnase-seqencing to observe whether the histone constructs altered nucleosome distributuion throughout chromatin. N=3 replicates were used for each cell line.

first: Preston

last: Samowitz

first: Feifei

last: Tong

first: Alice

last: Long

first: Caitlin

last: Bradley

first: Laszlo

last: Radnai

last: MacMillan

first: Courtney

last: Miller

first: Gavin

last: Rumbaugh

first: Ciaran

last: Seath


title: Mesoscale proximity labeling at chromatin to study small molecule mechanism of action [CUTandTag_2]

overall_design: pc293T cells, which contained FLAG tagged histone constructs, under went CUT&Tag sequencing to confirm localization of histone constructs thoughout chromatin. N=3 samples were used for each antibody target. The antibodies included FLAG, Histone H3.3, and IgG.

first: David


title: Mesoscale proximity labeling at chromatin to study small molecule mechanism of action [CUTandTag_1]

overall_design: pc293T cells, which contained FLAG tagged histone constructs, under went CUT&Tag sequencing to confirm localization of histone constructs thoughout chromatin. N=3 samples were used for each antibody target, and n=2 for the IgG control. The antibodies included FLAG, H3K27ac, H3K27me3, and IgG.


title: Efferocytic remodeling of pancreatic intra-islet macrophages by limited beta-cell death

first: Pavel

last: Zakharov

address: 660 S Euclid Ave Box 8118

institute: Wash.Univ in St. Louis

summary: The primary driver of Type I diabetes are the autoimmune T cells that destroy insulin-producing beta-cells within the islets of Langerhans in the pancreas. Pancreatic macrophages have also been variably linked to disease onset and progression. As macrophage-mediated removal of dying cells via ‘efferocytosis’ regulate tissue homeostasis and immune responses, we addressed whether efferocytosis by intra-islet macrophages influences the immune environment of pancreatic islets. Here, using a series of complementary omics-based and functional approaches, we identify a subset of anti-inflammatory intra-islet ‘efferocytic macrophages’ (e-Mac) within the pancreas of mice and humans. When limited beta-cell apoptosis is induced in vivo in wild type C57BL/6 mice and diabetic-prone NOD mice, islet macrophages adopt this e-Mac phenotype without an apparent increase in total intra-islet macrophage numbers. Strikingly, such induction of limited beta-cell apoptosis and increase in e-Mac numbers in NOD mice led to long-term suppression of autoimmune diabetes. These data advance a concept that efferocytosis-associated reprogramming of the islet macrophages and its subsequent influence on the adaptive immune response could be beneficial in modulating diabetic autoimmunity.

overall_design: sc-RNASeq profiling of CD45+ cells isolated from the islets of non-obese diabetic (NOD) or healthy C57BL/6 mice. Mice were injected with single low-dose STZ (or control buffer) at 4 weeks of age, and analyzed 10 days later (at 5.5 weeks of age) or 8 weeks later (at 12 weeks of age)

first: Chanchal

last: Chowdhury

first: Orion

last: Peterson

first: Brady

last: Barron

first: Anthony

last: Vomund

first: Laurent

last: Gorvel

first: Emil

last: Unanue

first: Eynav

last: Klechevsky

first: Xiaoxiao

last: Wan

first: Kodi

last: Ravichandran


title: Blood transcriptional signatures of asymptomatic FDG-PET/CT-defined Subclinical TB lesions and their prediction of future TB progression

city: Melbourne

first: Dylan

last: Sheerin

state: VIC

address: 1G Royal Parade

institute: WEHI

summary: Diagnostic tests for tuberculosis (TB) infection poorly predict future incident disease risk.  We investigated a cohort of asymptomatic HIV-uninfected household contacts of TB in South Africa in which baseline lung lesions indicative of Subclinical TB identified by [18F]-fluoro-2-deoxy-D-glucose (FDG)-positron emission/computed tomography (PET/CT) had high predictive value for future TB over 5 years. RNA-sequencing analysis of whole blood samples at baseline PET/CT, 5-15m PET/CT2, and the TB diagnosis of incident TB revealed persistent enrichment of neutrophil and monocyte transcriptional modules in those with Subclinical TB and worsening and discrete lung abnormalities, while expression of a core set of type I IFN genes related to FDG-avid lymph nodes. Leveraging multiple machine learning algorithms, we derived gene signatures of various PET/CT lesion Subclinical phenotypesTB, future lesion worsening and TB diagnosis. prevalent and incident TB. Validating signatures in two independent cohorts against TB progression within 6,12,18 and fup to 24-29-months, confirmed gave AUC of 0.75-0.95 and 0.77-0.87 with performance above optimal sensitivity and wminimum specificity for the WHO target product profile for TB progression.

overall_design:
Asymptomatic, HIV uninfected, adult, household contacts of drug-resistant (at least Rifampin resistant) TB were recruited. Their sputa (induced/spontaneous) underwent Xpert MTB/RIF and culture and blood was drawn for QuantiFERON in-tube-Gold (QFT-Gold), QFT-Plus, and Tempus tubes for RNA. A baseline PET/CT was performed in 250 individuals who were Xpert negative at baseline, and a second PET/CT was performed in 112 participants after 5 to 15 months and XX participants had a third PET/CT at endpoint TB diagnosis. Participants were followed for up to five years, with repeat symptom and induced sputum screening between years 2-3 at any time when they presented to the clinical with TB signs or symptoms and at completion of follow-up via interrogation of their health service encounters via the Western Province Provincial Health Data Centre and clinic medical records. PET/CT features at baseline consistent with TB were assessed by readers blinded to clinical details and classified by prespecified radiographic and microbiologic criteria.
This repository consists of the first 131 RNA-seq samples (87 visit 1, 37 visit 2, 5 TB endpoint, 3 visit post TB treatment (Tx)), categorized primarily by PET/CT features identified at the visit, changes between visit 1 and visit 2 or visit 2and visit 3, and TB diagnosis at baseline (prevalent TB) or during folllow-up (incident TB).

first: Hanif

last: Esmail

first: Jerry

last: Ellner

first: Padmini

last: Salgame

first: Robert

last: Wilkinson

first: Anna

last: Coussens


title: MiRNA sequencing profiles of brain and intestinal tissues in mice between ischemic stroke comorbid with gut dysbiosis group and Xinqingning Tablet group

city: Nanjing

first: Yuanhao

last: Xu

state: --- Select One ---

address: Longmian Avenue 639

institute: China Pharmaceutical University

summary: We profiled microRNA expression in brain and colon tissues from a mouse model of ischemic stroke comorbid with gut dysbiosis after Xinqingning Tablet treatment.

overall_design: Male C57BL/6J mice underwent fecal-slurry-induced gut dysbiosis plus permanent middle-cerebral-artery occlusion, received Xinqingning Tablet (0.61 g/kg), and were subjected to small-RNA sequencing.

first: Shuaishuai

last: Gong


title: Analysis of the genes and mechanisms responsible for the cytotoxicity of the Legionella Ofk308 strain in the Tetrahymena host

city: Yamaguchi City

first: Istiana

middle: Nur

last: Vidayanti

state: Yamaguchi Prefecture

address: 1677-1 Yoshida

institute: Yamaguchi University

summary: Legionella pneumophila, an intracellular pathogen responsible for the pneumonia-like Legionnaires’ disease in humans, inhabits aquatic environments, including man-made water systems such as water fountains, foot spas, and tap water, and exists as part of biofilms or as a protozoan parasite. As a bacterivore, Tetrahymena thermophila provides a favorable environment for Legionella to establish a replicative niche (Legionella-containing vacuole; LCV) under environmental stress. Conversely, the L. pneumophila Ofk308 strain, isolated from an Ashiyu foot spa, has been found to be cytotoxic to the ciliate T. thermophila CU427. This study aimed to identify the cytotoxicity-related genes of Legionella and elucidate their mechanisms specific to the Tetrahymena host. A comparative analysis using RNA-sequencing was conducted with two Legionella strains, Philadelphia-1 and Ofk308, to select several candidate genes. Deletion mutants of Ofk308 were constructed by homologous recombination. Eight out of ten candidate gene deletion mutants were successfully generated. These mutants were analyzed for cytotoxicity against T. thermophila and intracellular bacterial growth at 2 h, 24 h, and 48 h postinfection. Among the deletion mutants, ∆vicinal oxygen chelate (VOC) and msrB/A exhibited reduced cytotoxicity. Furthermore, LCVs formed in T. thermophila infected with ∆VOC and msrB/A were smaller in size compared to those formed by the parental strain Ofk308, suggesting a role in both cytotoxicity and intracellular growth. Multiple factors contribute to the cytotoxicity exhibited by the Ofk308 strain in protozoan host cells, and gene expression analysis may reveal additional relevant factors.

sample_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design: Legionella pneumophila Phil-1 (control) and Ofk308 strains were cultured at 37°C to the exponential phase in AYE, then diluted and cultured again at 30°C for 24 h. The total RNA were extracted in triplicates for each strain.

first: Istiana Nur

first: Kenta

last: Watanabe

first: Ema

last: Fujino

first: Takashi

last: Shimizu

first: Masahisa

last: Watarai


title: Lactate-Driven Protein Lactylation Regulates Virulence in Plasmodium falciparum

city: Cambridge

first: Sida

last: Ye

state: Massachusetts

address: 48 CREIGHTON ST

department: Department of Mathematics

institute: UMass Boston

summary: Lactic acidosis, driven by hyperlactatemia, is a hallmark of severe Plasmodium falciparum malaria, yet its impact on parasitic life cycle and gene expression remains unclear. In mammalian cells, lactate influences transcription through histone lactylation, a novel post-translational modification. In this study, we demonstrate that P. falciparum undergoes lactate-derived lysine lactylation on nuclear proteins, including histones, histone variants, and AP2 transcription factors, with lactylation levels dynamically varying in response to physiological lactate ranges. Through CUT&RUN profiling, we show that elevated lactate enhances chromatin occupancy of lactylated proteins at promoters of genes involved in virulence and cytoadherence. Correspondingly, transcriptomic analyses demonstrated a suppression of these genes in response to elevated lactate, a pattern also evident in clinical isolates from severe malaria patients. Functionally, we demonstrate that high lactate reduces the binding ability of infected erythrocytes to CD36 receptor. Together, our findings reveal protein lactylation as a metabolite-responsive epigenetic mechanism in P. falciparum, linking host metabolic state to transcriptional reprogramming with direct implications for parasite virulence and disease pathogenesis.

overall_design: This study provides genome-wide profiling of lactylation in Plasmodium falciparum 3D7 parasites across ring, trophozoite, and schizont stages supplemented with either 0.5 mM or 8 mM exogenous sodium l-lactate using the Cleavage Under Targets and Release Using Nuclease (CUT&RUN) technique. Parasites were treated for 12 hours and then harvested at ring stage (12-16 hpi), trophozoite stage (28-32hpi) and schizont (40-44 hpi). Both panKla antibody and a site-specific H4K12la antibody were employed, alongside H3K4me3 and H4K12ac as positive controls and IgG as a negative control. These data offer insights into lactylation-mediated epigenetic regulation in malaria parasites and represent the first lactylation CUT&RUN dataset in P. falciparum.

first: Kumar

last: Manish

first: Ye

last: Sida

first: Lou

last: Jingjing

first: Zarringhalam

last: Kourosh

first: Duraisingh

last: Manoj


title: RP105 exerts hepatoprotective effects in sepsis by modulating the SOCS2/JAK2/STAT3 signaling pathway

city: wuhan

first: Hong

last: Duo

address: No. 169 East Lake Road, Wuchang District

institute: Zhongnan Hospital of Wuhan University

summary: During the occurrence of sepsis, the liver plays a crucial role in immune defense. However, the excessive immune response within the liver can also make it the main target organ for sepsis-related injuries. In this paper, our aim is to explore the protective role of RP105 in liver injury caused by sepsis and clarify its underlying molecular mechanisms. We established a cecal ligation and puncture (CLP) model using RP105 knockout mice. We observed the protective effect of RP105 on liver damage caused by sepsis. We also conducted RNA sequencing (RNA-Seq) analysis on the CLP group and the RP105 knockout CLP group. Furthermore, through in vitro and in vivo experiments, we found that RP105 alleviated liver injury caused by sepsis through the classical regulation of SOCS2 via the JAK2/STAT3 signaling pathway.

overall_design: To investigate the role of RP105 in sepsis-induced liver injury, we employed both in vivo and in vitro approaches. An in vivo mouse model of sepsis was established using the cecal ligation and puncture (CLP) technique. RP105 knockout (RP105⁻/⁻) mice and wild-type (WT) littermates were subjected to CLP surgery, and liver tissues were harvested 24 hours post-surgery for histological and molecular analyses. To elucidate the molecular mechanisms underlying the protective effects of RP105, RNA sequencing (RNA-Seq) was performed on liver samples from WT-CLP and RP105⁻/⁻-CLP groups (n=3 per group).

first: Qin

last: Deng

first: Ruoping

last: Chen

first: Zhihui

last: Fu

first: Huaqin

last: Pan

first: JianSheng

last: Xiao

first: Qifa

first: Qi


title: The role of hepatocyte R-spondin 2 in regulating hepatic steatosis and fibrosis.

city: Memphis

first: Bhupesh

last: Singla

state: TN

address: 881 Madison Ave

institute: UNIVERSITY OF TENNESSEE HEALTH SCI CTR

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) primarily results from dysregulated lipid metabolism in hepatocytes. However, the mechanisms governing hepatic lipid metabolism remain incompletely understood. Our preliminary experiments demonstrated elevated expression of R-spondin 2 (RSPO2), a matricellular protein, in steatotic livers. To investigate the role of RSPO2 in MASLD and the potential mechanisms involved, we performed bulk RNA sequencing of liver samples from Apoe knockout mice injected with either control Gfp-AAV or Rspo2-AAV to induce RSPO2 overexpression, following 12 weeks of Western diet feeding.

overall_design: Total RNA from Gfp-AAV- or Rspo2-AAV-injected mice liver samples was isolated using TRIzol reagent according to the manufacturer's instructions. The quality of RNA was determined using the Agilent 2100 Bioanalyzer System. The samples with RNA Integrity Numbers of more than 8 were sent to Novogene Corporation Inc., Sacramento, for bulk RNA-sequencing.

first: Ravi

middle: V

last: Aithabathula


title: Nuclear and cytosolic J-domain proteins provide synergistic control of Hsf1 at distinct phases of the heat shock response [steady state]

city: Heidelberg

first: Lucia

last: Svoboda

address: Im Neuenheimer Feld 345

country: Germany

institute: ZMBH

summary: The heat shock response (HSR) is the major defense mechanism against proteotoxic stress in the cytosol and nucleus of eukaryotic cells. Initiation and attenuation of the response are mediated by stress-dependent regulation of heat shock transcription factors (HSFs). Saccharomyces cerevisiae encodes a single HSF (Hsf1), facilitating the analysis of HSR regulation. Hsf1 is repressed by Hsp70 chaperones under non-stress conditions, and becomes activated under proteotoxic stress, directly linking protein damage and its repair to the HSR. J-domain proteins (JDPs) are essential for targeting of Hsp70s to their substrates, yet the specific JDP(s) regulating Hsf1 and connecting protein damage to HSR activation remain unclear. Here we show that the yeast nuclear JDP Apj1 primarily controls the attenuation phase of HSR by promoting the Hsf1’s displacement from heat shock elements in target DNA. In apj111 cells, HSR attenuation is significantly impaired. Additionally, yeast cells lacking both Apj1 and the major JDP Ydj1 exhibit increased HSR activation even in non-stress conditions, indicating their distinct regulatory roles. Apj1’s role in both nuclear protein quality control and Hsf1 regulation underscores its role in directly linking nuclear proteostasis to HSR regulation. Together these findings establish the nucleus as key stress-sensing signaling hub.

overall_design: Ribosome profiling and RNAseq data of total translatome of Saccharomyces cerevisiae wild-type (WT, reference) or mutants, grown at steady state or heat-shocked (HS) for indicated timepoints. 2-3 replicates were generated for each library

first: Carmen

last: Ruger-Herreros

first: Gurranna

last: Male

first: Aseem

last: Shrivastava

first: Markus

last: Höpfler

first: Katharina

last: Jetzinger

first: Jiri

last: Koubek

first: Günter

last: Kramer

first: Fabian

last: den Brave

first: Axel

last: Mogk

first: David

last: Gross

first: Bernd

last: Bukau


title: Analysis of N6-methyladenosine methylome (m6A) enrichment level in adipose stem and progenitor cells with or without FTO inhibition

city: Shanghai

first: Hongrui

last: Chen

address: 639 Zhizaoju Road, Shanghai 200011, P.R.China.

department: Plastic and reconstruction surgery

institute: Shanghai ninth people's hospital

summary: To investigate the function of N6-methyladenosine methylome (m6A) in adipose stem and progenitor cells isolated from facial infiltrating lipomatosis (FIL-ASPCs), we analyzed m6A enrichment level in FIL-ASPCs with or without FTO inhibitor (FTO-IN-1) treatment through methylated RNA immunoprecipitation (MeRIP) sequencing.

overall_design: Methylated RNA immunoprecipitation (MeRIP) sequencing was performed in FIL-ASPCs treated with FI or DMSO (Ctrl) to identify downstream targets of FTO in FIL-ASPCs

first: Bin

last: Sun

first: Chen

last: Hua

first: Xiaoxi

last: Lin


title: SFXN2 contributes mitochondrial dysfunction‑induced apoptosis as a substrate of Parkin

city: hengyang

first: shishi

last: luo

state: hunan

address: 28 West Changsheng Road

department: Hengyang Medical College

institute: University of South China

summary: Mitochondrial proteins and mitochondrial functions are interdependent. In this study, we confirm that the protein level of SFXN2 decreases significantly during mitochondrial damage, primarily due to proteasome-mediated degradation. Parkin, a mitochondrial E3 ligase, facilitates the polyubiquitination and proteasomal degradation of SFXN2. Reduced SFXN2 exacerbates mitochondrial damage‑induced cell death across multiple cell lines, while elevated expression of SFXN2 protects neurons from the mitochondrial stress. Taken together, this work identifies SFXN2, as a Parkin substrate, that mitigates mitochondrial damage and possesses anti‑apoptosis effect, and its reduction contributes to mitochondrial damage‑induced cell death in various cell lines, including 293T, SH‑SY5Y, and N2a cells.

overall_design: RNA-seq profiling of wildtype HEK293 cells(NC_HA) and their stable overexpressing of SFXN2(OE_HA).

first: yechuan

last: he

first: danling

last: wang


title: Nuclear and cytosolic J-domain proteins provide synergistic control of Hsf1 at distinct phases of the heat shock response

first: Lucia

last: Svoboda

first: Carmen

last: Ruger-Herreros

first: Gurranna

last: Male


title: Nuclear and cytosolic J-domain proteins provide synergistic control of Hsf1 at distinct phases of the heat shock response [time course]

first: Aseem

last: Shrivastava

first: Markus

last: Höpfler

first: Katharina

last: Jetzinger


title: Innate immune sensing of Plasmodium falciparum sporozoites and blood stages by human monocytes

city: Berlin

first: Parnika

last: Mukherjee

address: Augustenburger Platz 1

institute: Charité Universitätsmedizin Berlin

summary: Plasmodium sporozoites are potent inducers of adaptive immunity, but the underlying mechanisms of sporozoite sensing by innate cells are still unclear. To gain insights into the activation of human innate immune cells by sporozoites as opposed to activation by blood stages, we co-cultured GFP expressing P. falciparum sporozoites (PfSPZ) and blood stage parasites (PfRBC) with human monocytes. Comparing between the responses induced by PfSPZ and PfRBC revealed mostly genes with higher expression in PfSPZ-stimulated monocytes, most prominently COX-2 encoding PTGS2 and the chemokines CCL20 and CCL5. In addition, monocytes stimulated with PfSPZ displayed stronger plasma membrane injury than monocytes stimulated with PfRBC

sample_organism:
Plasmodium falciparum
Homo sapiens

platform_organism:
Plasmodium falciparum
Homo sapiens

overall_design:
NF54-HGL P. falciparum sporozoites, expressing a GFP-luciferase fusion protein under the control of the CSP promotor, were isolated from A. stephensi salivary glands, sort-purified by flow cytometry and co-cultured with primary human T and B cell depleted PBMCs at an MOI of 0.5. Additionally, we co-cultured T and B cell depleted PBMCs from the same donors with magnetically enriched P. falciparum infected erythrocytes and control uninfected erythrocytes (RBC) at an MOI of 5

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

first: Kai

last: Pohl

first: Jason

last: McGowan

first: Sophia

last: Brumhard

first: Anna

last: Hiller

first: Benedikt

last: Obermayer-Wasserscheid

first: Leif

middle: E

last: Sander

first: Ian

last: Cockburn


title: Unveiling small non-coding RNA dynamics during recombinant Adeno-associated virus production.

city: Biberach an der Riß

first: Madina

last: Burkhart

address: Hubertus-Liebrecht-Straße 35

department: Institute for Applied Biotechnology

institute: Hochschule Biberach

summary:
Recombinant adeno-associated viruses (rAAVs) are a cornerstone of modern gene therapy, offering precise delivery and stable transgene expression with minimal immunogenicity. Despite clinical advancements, large-scale rAAV production faces significant challenges such as low yield, high costs, and variability, hindering its scalability. Recent research suggests that miRNAs and snoRNAs can modulate viral replication, transcriptional regulation, and host defense mechanisms, making them attractive targets for improving rAAV production. This study examines the expression profiles of microRNAs (miRNAs) and small nucleolar RNAs (snoRNAs) during rAAV plasmid transfection and production in HEK293F cells.
We used microarrays to detail differential expression during rAAV production versus mock transfection and basal expression and identified significantly up- and down-regulated small non-coding RNAs (ncRNAs).

overall_design: HEK293F cells were either mock- or rAAV transfected and cultivated over 72 h, each in biological triplicates. During cultivation and production, samples were taken at 0 h, as well as 6, 12, 24, 48 and 72 h post-transfection to analyse cellular parameters and rAAV titers. Ultimately, RNA specimens of each sampling time point were isolated and analysed via microarray expression analysis. Differential expression was considered significant regarding difference in fold change ≥1.5, p-value <0.05 and FDR <0.1.

first: Katrin

last: Langenbach

first: Karlheinz

last: Holzmann

first: Nadine

last: Hornung

first: Jamie-Ann

last: Baiz

first: Kerstin

last: Otte


title: PML is crucial for neural stem cell differentiation, stress tolerance and mitochondrial integrity

city: Heraklion-Voutes

first: Syrago

last: Spanou

address: N.Plastira 100

country: Greece

institute: IMBB-FORTH

summary: The tumor suppressor promyelocytic leukemia protein (PML) has important roles in brain development; however, the molecular and cellular pathways regulated by PML in neuronal cells remain largely unknown. To address this issue, we analyzed gene expression changes caused by loss of PML in neural stem cells. Our findings revealed that PML-deficient cells exhibited increased mTOR (mammalian target of rapamycin) pathway activation and protein translation, as well as impaired autophagy and proteasome activity, resulting in increased formation of aggregates and stress-induced death. Loss of PML disrupted mitochondrial integrity, leading to impaired respiration, membrane potential, morphology, and production of increased reactive oxygen species. These mitochondrial defects were caused by diminished PGC-1α expression and PPARγ (peroxisome proliferator-activated receptor gamma) signaling and could be reversed using a PPAR agonist. Together, our results indicate that PML is a critical regulator of neuronal survival and protection from stress. We propose that enhancing PML expression may offer therapeutic benefits in neurological disorders.

overall_design: RNAseq profiling in mouse embryonic neural stem cells (E13.5) WT and Pml-/-.

first: Takis

last: Makatounakis

first: Elena

last: Deligianni

first: Sofia

last: Papanikolaou

first: Martina

last: Samiotaki

first: Fabien

last: Moretto

first: Christoforos

last: Nikolaou

first: Joseph

last: Papamatheakis

first: Androniki

last: Kretsovali