title: Targeted Activation of JAML+ CD8+ T Cells Enhances Immunotherapy in Hepatocellular Carcinoma

city: hangzhou

first: huan

last: chen

state: Zhejiang

address: Hangzhou, Zhejiang Province, China

institute: Zhejiang Chinese Medical University

summary: Objective: Cytotoxic T lymphocytes (CTLs) are pivotal in the therapeutic approach to hepatocellular carcinoma (HCC). Recent research has shown that junctional adhesion molecule-like protein (JAML) is capable of promoting the antitumor activity of CD8+ T cells. Our research investigates the role of JAML+ CD8 T cells in HCC. Methods: We employed time-of-flight mass cytometry (CyTOF) and an orthotopic mouse model of HCC to investigate histone modifications in tumor-infiltrating immune cells undergoing immunotherapy. Flow cytometry was used to assess CD4+ T cell differentiation and the expression of JAML in CD8+ T cells infiltrating HCC. Correlation analysis demonstrated a strong positive correlation between LDHA+ CD4 T cells and JAML+ CD8 T cells. Subsequently, we evaluated the therapeutic effects of agonistic anti-JAML antibody, both in conjunction with and without immunotherapy. Finally, RNA sequencing was performed to uncover potential regulatory mechanisms. Results: Immunotherapy substantially elevated the percentage of CD8+ T cells infiltrating HCC and altered histone modifications such as H3K18la in CD4+ T cells. Flow cytometry revealed that lactate promotes the differentiation of CD4+ T cells into Th1 cells. Lactate dehydrogenase A (LDHA) converts pyruvate to lactate. Correlation analysis revealed a strong positive relationship between LDHA+ CD4+ T cells and JAML+ CD8+ T cells in patients responsive to immunotherapy. High expression of JAML in CD8+ T cells is linked to a more favorable prognosis. In vivo experiments, the agonistic anti-JAML antibody therapy reduced tumor volume and significantly prolonged the survival of tumor-bearing mice, independent of the benefit of αPDL1-mediated immunotherapy. Pathway enrichment analysis revealed that JAML enhances CTLs responses through the oxidative phosphorylation pathway. Conclusions: Agonizing JAML can enhance the response of CTLs in treating HCC, and this effect is independent of the benefits provided by αPDL1-mediated immunotherapy, thereby offering a more effective treatment strategy for advanced HCC.

overall_design: Comparative gene expression profiling analysis based on RNA-seq data: A comparison of gene expression profiles between JAML+CD8 T cells and JAML-CD8 T cells infiltrating mouse hepatocellular carcinoma.


title: PLCG2 modulates TREM2 expression and signaling in response to Alzheimer’s disease pathology

status: Public on May 14 2025

city: Indianapolis

first: Evan

last: Messenger

state: IN

address: 320 W 15th St

country: USA

institute: Stark Neuroscience Research Institute

type: Expression profiling by high throughput sequencing

summary: Phospholipase C gamma 2 (PLCG2) is an intracellular effector of microglial cell surface receptors, including TREM2. Variants which alter PLCG2 activity impact Alzheimer’s disease (AD) risk, but the effects of PLCG2 deficiency in AD remain unclear.

overall_design: 5xFAD mice were crossed with PLCG2 and TREM2 deficient mice to assess the role of PLCG2 in response to amyloid pathology. Bulk RNA-Seq of cortices from 7.5-month-old mice was conducted for murine transcriptomic analyses.

middle: J

first: Gary

middle: E

last: Landreth

first: Bruce

middle: T

last: Lamb

first: Stephanie

last: Bissel


title: Multi-omics analysis reveals tissue-specific biosynthesis and accumulation of diterpene alkaloids in Aconitum japonicum

city: Chiba

first: Mami

last: Yamazaki

state: Chiba

address: 1-8-1 Inohana, Chuo-ku, Chiba City Pharmaceutical Research Building II

department: Department of Molecular Biology and Biotechnology

country: Japan

institute: Chiba University

summary: In this study, we performed LC-QTOF-MS-based metabolomics and RNA-seq based transcriptome analysis using four tissues of A. japonicum.

overall_design: Examination of 4 tissues of Aconitum japonicum

first: Kazuki

last: Saito

first: Hideyuki

last: Suzuki

first: Marsheige

last: Kojoma

first: Hiroki

last: Takahashi

first: Michimi

last: Nakamura

first: Ryo

last: Nakabayashi

first: Tetsuya

last: Mori

first: Amit

last: Rai

first: Megha


title: OCT-2 is associated with pro-metastatic epigenomic properties of triple-negative breast cancer cells

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

summary: Triple-negative breast cancer (TNBC) is a malignant type of breast cancer. Owing to the lack of expression of receptors that serve as molecular targets for standard therapy for breast cancer, conventional cytotoxic chemotherapy is the primary treatment option for TNBC. However, TNBC exhibits a high degree of genomic heterogeneity, rendering it resistant to chemotherapy. Therefore, there is an urgent need to identify novel therapeutic targets for the treatment of TNBC. Advances in massively parallel sequencing technology have enabled the identification of cancer cell-specific gene expression patterns and epigenetic alterations that regulate their expression. Cancer cell-specific super-enhancers (SEs) have been identified as effective therapeutic targets for cancer. In this study, we identified the functional roles of epigenetic changes and their regulatory mechanisms in TNBC cells. TNBC cell-specific SEs were formed near several genes that contribute to malignant cancer cell acquisition. We found that the transcription factor OCT-2 (encoded by POU2F2) was responsible for the formation of SEs and the expression of genes encoded in the vicinity of the SE regions. Overexpression of POU2F2 enhances the metastasis of TNBC cells in mice and their expression is highly correlated to poor prognosis of TNBC patients. Our findings provide a new insight into cancer cell-specific epigenetic changes induced by OCT-2, which trigger the progression of TNBC, and suggest possible candidates that could be targeted for the treatment of TNBC.

overall_design: RNA-seq analysis was performed in breast cancer cell lines, MDA-MB-231 (231Pa) and its highly metastatic clone, MDA-231-D. RNA-seq was also performed in 231Pa cells with forced OCT2 expression.

last: Ogikubo

first: Masato

last: Morikawa

first: Kohei

last: Miyazono


title: Learning the sequence code for mRNA and protein abundance in human immune cells [SONAR_MPRA]

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

country: Netherlands

institute: Sanquin

summary: mRNA and protein abundance are defined by transcriptional and post-transcriptional regulatory mechanisms.  Here, we develop a machine learning pipeline, termed SONAR, to decipher the endogenous sequence code that determines mRNA and protein abundance in human cells. SONAR models predict up to 62% of mRNA and 63% of protein abundance independent of promoter or enhancer information, and reveal a strong—yet dynamic—cell-type specific sequence code. We also find that the effect of sequence features is dependent on their location within the mRNA transcript. Using SONAR, we design synthetic 3’UTRs, with which protein expression levels can be manipulated and tailored to a specific cell-type. Beyond its fundamental findings, our work provides novel means to improve immunotherapies and biotechnology applications.

overall_design: A parallel reporter assay was performed to test the effect of synthetic 3'UTR sequences on GFP protein expression. HEK cells, CD8+ T cell and CD4+ T cells were transduced with a GFP-3'UTR retroviral library containing ±500 distinct synthetic 3'UTR sequences. Transduced cells were subsequently sorted for GFPhi or GFPlo cells. gDNA was isolated from these populations, 3'UTR sequences were amplified and sequenced to asses abundances

first: Benoît

middle: P

last: Nicolet


title: OCT-2 is associated with pro-metastatic epigenomic properties of triple-negative breast cancer cells [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: H3K27ac ChIP-seq analysis was performed to identify superenhancers in breast cancer cell lines, MDA-MB-231 (231Pa) and its highly metastatic clone, MDA-231-D. MDA-MB-436 and ex vivo culture of its xenograft were also evaluate by H2K27ac ChIP-seq. POU2F2/OCT2 binding regions were also identified in 231Pa cells with forced OCT2 expression and in MDA-231-D cells to compare with superenhancers.


title: Microvascular endothelial cells license APS vasculopathy through YAP1- and CCN2-mediated signaling

city: Ann Arbor

first: hui

last: shi

address: 5560 Medical Science Research Building-II 1150 W Medical Center Drive

institute: Division of Rheumatology, Department of Internal Medicine, University of Michigan

summary: Antiphospholipid syndrome (APS)-associated vasculopathy is heralded by abnormal proliferation of endothelial and smooth muscle cells, leading to small blood vessel occlusion in the skin, kidneys, and heart, amongst other organs. The underlying mechanisms remain unclear, and targeted treatment options for patients with APS are lacking. To identify and analyze APS microvascular endothelial cells (MVECs), skin biopsies of patients with APS complicated by livedo racemosa were characterized using single-cell RNA sequencing (scRNA-seq). Increased expression of CCN1 and CCN2 were discovered and further confirmed in APS skin by microscopy, and in APS plasma by ELISA. Exposure of healthy MVECs to patient IgG triggered CCN1 and CCN2 upregulation via yes-associated protein (YAP1)-mediated signaling. CCN2 originating from APS IgG-stimulated MVECs led to the proliferation and migration of vascular smooth muscle cells, which were blocked by the anti-CCN2 antibody, pamrevlumab. We further observed increased expression of CCN1 and CCN2, along with evidence of YAP1 nuclear translocation, in kidney vessels of APS nephropathy biopsies. Finally, CCN2 inhibition with pamrevlumab significantly reduced neointima thickening and cell proliferation in a mouse model of APS IgG-accelerated neointima formation. Together, this study revealed activation of YAP1-mediated signaling in APS dermal microvessels and demonstrated that the YAP1 target CCN2 plays a role in facilitating pro-proliferative communication between MVECs and VSMCs. These findings offer insights into the cellular and molecular mechanisms underlying APS vasculopathy and provide potential therapeutic targets for patients.

overall_design: Epidermal and dermal cells were isolated from skin biopsies from the upper thighs of three APS patients and four healthy volunteers, mixed 1:1 and analyzed using scRNA-seq.

first: Hui

last: Shi

first: Jason S

last: Knight


title: Inhibitory effect of Alantolactone against varicella-zoster virus in vitro

city: Hangzhou

first: xinna

last: wu

address: Yuhangtang Road

country: China

institute: zhejiang university

summary: Background : Varicella-zoster virus (VZV), a member of the α-herpesvirus family, is known for causing two distinct diseases: chickenpox (varicella) during the primary infection and shingles (zoster) due to reactivation of the virus later in life. Currently, there were vaccines available to prevent VZV infection, but it is not universally effective, and antiviral treatments for VZV are limited and may come with significant side effects. Thus, development of novel therapeutics is urgently needed. Methods: In the current study, we identified a naturally occurring ALT that inhibits replication of recombinant  VZV in human diploid fibroblast (WI-38 cells) and Adult Retinal Pigment Epithelial cell line-19 (ARPE-19 cells) through Western blotting, qPCR and plaque assays. The time-of-addition experiment was carried out to identify the stage at which ALT acted. Meanwhile, the transcriptome was applied for the initial exploration of the mechanism underlying anti-VZV activity. Results : We established a screening model for anti-VZV compounds from which we screened ALT with good antiviral efficacy. Our findings revealed that ALT alleviated cytopathic changes, reduced viral titres, and inhibited the expression of viral genes and proteins in WI-38 cells and ARPE-19 cells. Furthermore, our data showed that ALT inhibits VZV infection at both early and late stages of the viral life cycle. Finally, according to RNA-seq data, multiple inflammatory pathways were involved in this antiviral process, and IL-6 was one of the most critical hub genes. Conclusion : Together, our findings identify ALT as a anti-VZV agent that may prove useful in the treatment of VZV replication.

overall_design: Samples include WI-38 cells grouped as Mock (uninfected), DMSO+VZV (solvent control with infection), and ALT+VZV (treatment with infection), harvested at 3dpi. 3 replicates exist for each group.

first: Xinna

last: Wu

first: Genxiang

last: Mao

first: Sanying

last: Wang

first: Ping

last: Lin

first: Dongli

last: Pan

first: Zhiwei

last: Ding

first: Yunchuang

last: Chang


title: Identification of key genes associated with circadian rhythm as potential diagnostic biomarkers for cytomegalovirus infection in very low birth weight infants

city: Xuzhou

first: qianqian

last: Li

address: No.46 Heping Road

institute: Xuzhou maternal and child Health care hospital

summary: After HCMV infection, most individuals have no obvious symptoms. However, HCMV infection in very low birth weight infants can cause liver function damage, thrombocytopenia, hearing damage, cholestasis and so on. Cytomegalovirus is generally thought to lurk and activate in monocytes. In this study, we performed transcriptomic analysis of RNA-seq on peripheral blood mononuclear cells of very low birth weight infants infected with HCMV, bringing new insights into a comprehensive understanding of the immune mechanisms involved during their infection.

overall_design: In order to detect CMV infection, urine CMV-DNA-PCR was routinely performed on very low birth weight infants (birth weight < 1500g) during hospitalization. In order to explore the transcriptome changes after HCMV infection in very low birth weight infants, we randomly selected 3 patients with persistent urine CMV-DNA-PCR negative as the control group, and 3 patients with urine CMV-DNA-PCR positive as the HCMV infection group. Blood samples were collected between 9 am and 10 am, and peripheral blood monocytes were extracted and sent for RNA-seq. Enrichment analysis was performed using transcript results.

first: Qianqian

first: Junmei

last: Yan


title: Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3-/- zebrafish via enhancing Arachidonic acid/leukotriene metabolism

city: Mannheim

first: Xin

last: Zhang

address: Ludolf-Krehl-Str. 13-17

country: Germany

institute: Medical Faculty Mannheim

summary: Acrolein (ACR) is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo-keto reductase (AKR) enzyme system. The accumulation of ACR is associated with several health issues, including inflammation, oxidative stress, and cardiovascular diseases. In this study, an akr7a3 mutant zebrafish with the Tg(fli1: EGFP) signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3-/- zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature, as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses, followed by validation experiments, revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion, our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR, which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response.

overall_design: akr7a3-/-zebrafish were generated using CRISPR/Cas9 technology.  Multiple experiments are performed regarding vasculature alterations, transcriptome, and metabolomics in Tg(fli1:EGFP) zebrafish.

first: Gschwind

last: Johannes

first: Erben

last: Vanessa

first: Xiaogang

first: Bennewitz

last: Katrin

first: Jens

last: Kroll


title: Transcriptomic analysis of peaches and nectarines reveals alternative mechanism for trichome formation

city: Taichung City

first: Yuan-Kai

last: Tu

address: No.189, Zhongzheng Rd., Wufeng Dist.

department: Crop Genetic Resources and Biotechnology

country: Taiwan

institute: Taiwan Agricultural Research Institute, Ministry of Agriculture

summary: Trichomes in Prunus persica (L.) Batsch are crucial specialized structures that play a protective role against both biotic and abiotic stresses. The fruits with and without trichomes are respectively named as peach and nectarine. At the genetic level, the formation of trichome in peach is controlled by a single gene, PpMYB25, at the G locus. Peach (GG or Gg) is dominant to nectarine (gg), but such regulatory role was reported in a small-scale accessions. In this study, we performed large-scale genotype and phenotype screening on 295 accessions. Almost all accessions supported the casual relationship between trichome formation and PpMYB25. However, a peach to nectarine mutant, named Maravilha Nectarine Mutant (MN), was discovered to possess a putative functional PpMYB25 gene sequence (Gg) but revealed nectarine phenotype. Comparative transcriptomic analyses revealed that PpMYB25 transcript was absent in MN. Correlation analyses also demonstrated that the PpMYB25-mediated regulatory network was abolished in MN. In summary, our results demonstrated an alternative mechanism beyond genetic regulation on trichome formation.

overall_design: transcriptomic analyses on the fruits of this MN cultivar (Gg) together with that of other three cultivars (TN11 peach as GG, TN7 peach as Gg, Sunraycer nectarine as gg) to investigate the regulatory mechanisms of trichome development, especially on this MN cultivar.

first: Chun-Che

last: Huang

first: Han-Wei

last: Chen

first: Jo-Wei

middle: A

last: Hsieh

first: Yen-Chun

first: Yi-Pei

first: Chunxian

first: Yen-Fang

last: Song

first: Gung-Chian

last: Yin

first: Te-Lun

last: Mai

first: Ying-Chung


title: EYA3 regulation of NF-κB and CCL2 suppresses cytotoxic NK cells in the pre-metastatic niche to promote TNBC metastasis

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

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

overall_design: Refer to individual Series


title: Effect of Eya3 knockdown and constitutively-active NF-kB add-back (IKK2-SE) in 66cl4 cells in vitro

summary: To investigate gene expression changes associated with Eya3 knockdown and add-back of constitutively-active NF-kB (IKK2-SE) in 66cl4 cells

overall_design: Comparative gene expression profiling of 66cl4 SCR + Empty Vector, shEya3 KD + Empty Vector, and shEya3 KD + IKK2-SE cells in biological triplicates

first: Connor

last: Hughes

first: Sheera

middle: R

last: Rosenbaum

first: Heide

middle: L

last: Ford


title: Effect of PDCD11 silencing on gene expression in MDA-MB-231 cells

city: Yangzhou

first: Li

last: Ding

state: Jiangsu

address: No. 88, Daxuenan Road

department: College of Bioscience and Biotechnology

institute: Yangzhou University

summary: We here reported that PDCD11 deletion results in G1/S arrest and inhibited proliferation and migration of MDA-MB-231 cells. To investigate how does PDCD11 regulate the malignant phenotype of cancer cells, we performed RNA-sea analysis and found that PDCD11 knockdown leads to reduced transcriptional levels of C-MYC target genes such as E2F1, MCM2, MCM4, MCM5, MCM6, MCM7, CCNE2, CCNA2, and SKP2. Taken together, our data indicate that PDCD11 facilitates G1/S transistion, proliferation, and migration of cancer cells by regulating C-MYC pathways.

overall_design: To investigate wether and how PDCD11 regualtes the malignant phenotype of cancer cells, we established MDA-MB-231 cells with shRNA-mediated PDCD11 silencing.


title: CRISPR/Cas12 genome editing of TXNIP in human pluripotent stem cells to generate hepatocyte-like cells and insulin-producing islet-like aggregates.

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

summary: Background: Thioredoxin-interacting protein (TXNIP) regulates endoplasmic reticulum (ER) and oxidative stress, impairing glucose homeostasis in diabetes. However, it is unclear if TXNIP deficiency can improve differentiation or functionality of human stem cell-derived somatic metabolic cells. Methods: Using CRISPR-Cas12a genome editing, we generated TXNIP-deficient (TXNIP-/-) H1 human embryonic stem cells (H1-hESCs). These cells were differentiated into hepatocyte-like cells (HLCs) and stem-cell-derived insulin-producing islets (SC-islets). TXNIP-/- and TXNIP+/+ SC-islet maturation and functionality was assessed by implantation under the kidney capsule of NOD-SCID mice. Results: TXNIP deficiency significantly increased H1-hESC proliferation without affecting pluripotency, viability, or differentiation potential into HLCs and SC-islets. Bulk RNA-sequencing of thapsigargin-treated TXNIP-/- and TXNIP+/+ hESCs revealed differential expression of stress-responsive genes, with enriched apoptosis-related pathways in TXNIP+/+ cells but minimal transcriptional changes specific to TXNIP deficiency. In HLCs, TXNIP deletion reduced albumin secretion and insulin signalling, as indicated by decreased AKT phosphorylation, while showing no differences in glycolytic activity or lipid metabolism markers. Under thapsigargin-induced ER stress, TXNIP-/- HLCs exhibited transiently reduced eIF2α phosphorylation and lower BiP expression, suggesting compromised adaptive responses to prolonged stress. SC-islets derived from TXNIP-/- hESCs showed comparable viability, endocrine cell composition, and cytokine responses to TXNIP+/+ islets. Upon IFNα and IFNγ treatment, STAT1 phosphorylation was increased in TXNIP-/- SC-islets, indicating that IFN signalling remains active despite TXNIP deficiency. TXNIP-/- or TXNIP+/+ islets SC-islets implanted into NOD-SCID mice produced human C-peptide and responded to glucose stimulation. However, TXNIP-/- SC-islets showed no enhancement in glycaemic control or glucose-stimulated insulin secretion compared to controls. Conclusions: Our study demonstrates that TXNIP deficiency does not improve the differentiation of HLCs and SC-islets. We report the generation and characterization of TXNIP-/- and TXNIP+/+ H1-hESCs, HLCs and SC-islets as robust models for future studies of TXNIP’s role in metabolic cell biology.

overall_design: Bulk RNA-sequencing of stem well of wild type and TXNIP knockout cells with or without thapsigargin treatment

first: Leonardo

last: Traini

first: Javier

last: Negueruela

first: Wadsen

last: St-Pierre-Wijckmans

first: Carlos

last: Buss

first: Ao

last: Li

first: Israel

last: Perez-Chavez

first: Francisco

last: Ribeiro-Costa

first: Bernat

last: Elvira

first: Mariana

last: Nunes

first: Joris

last: Messens

first: Daria

last: Ezeriņa

first: David

last: Hay

first: Mayank

last: Bansal

first: Esteban

last: Gurzov


title: Gene expression profile at single cell level  of Drug-tolerant persister cells induced by targeted therapy in lung adenocarcinoma.

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Drug-tolerant persister (DTP) stage is viewed as a major source of non-genetic drug resistance. We use single cell RNA seq to reveal the transcriptomic heterogeniety of DTP stage

overall_design: PC9 cells were treated with 150nM Osimertinib for 4 days or 11 days to induce DTP stage. NCI-H358 cells were treated with 500nM Sotorasib for 8 days to induce DTP stage. All DTP cells (3 samples) and untreated control cells (2 samples) were collected, undergo cell hashing with barcoded antibodies and subsequently pooled in one sc-RNA seq run.

first: Yang

last: Tian

first: Feng

last: Jiang


title: Repressive chromatin regions of Osimertinib-treated PC9 cells with H3K27me3 or H3K9me3 modifications through H3K27me3 ChIP-seq or H3K9me3 ChIP-seq

summary: Drug tolorent persister cells induced by target therapy are marked by elevated level of compressed chromatin structure. We use ChIP seq against H3K27me3 or H3K9me3 antibody to reveal the repressive chromatin regions of osimertinib-treated PC9 cells.

overall_design: PC9 cells transfected with non-target sgRNAs were treated with 150nM Osimertinib for 4 days to generate the drug tolorent persister cells. Cell samples were collected and undergo ChIP seq using H3K27me3 or H3K9me3 antibody respectively.


title: Exploration of circRNA Expression Modifications and Functional Roles in a Mouse Model of OSA-induced Liver Injury: Fresh Perspectives on Pathogenic Mechanisms

city: 泉州

first: 清石

last: 陈

state: 福建省

address: 福建省泉州市鲤城区中山北路34号

institute: 医科大学附属第二医院

summary: The aim of this current study is to identify the global changes of circRNAs expression in OSA-induced liver damage.

overall_design: The APOE mice were randomly divided into a control group and a CIH group. Briefly, the mice designated for the CIH group were situated in a custom chamber fitted with 3 oxygen sensors to assess the O2 levels. A gas control delivery system connected to the chamber managed the injection of pure nitrogen which reduced the O2 concentration to 6% for 60 seconds. Afterward the system facilitated rapid replacement of O2 leading to quick reoxygenation and after another 60 seconds, the O2 concentration rose to 21%.The CIH cycle lasting 2 minutes was repeated 30 times hourly accumulating to 8 hours of each day totaling 8 weeks. After 8 weeks of CIH exposure, liver tissues were collected following cervical dislocation euthanasia performed by a trained professional under isoflurane anesthesia.

first: Qingshi

last: Chen


title: Impact of Fibrin Networks Formed by Macroporous Hydrogels with Varied Protein Absorption Capacities on Macrophage Function

first: Yani

address: No. 268, Kaixuan Rd.

institute: Zhejiang University

summary: Over the last decade, several materials strategies - such as anti-fouling hydrogels, surface coatings, and alterations in physical properties have been developed to reduce FBR by minimizing fibrotic encapsulation, though it remains inevitable. To investigate the mechanisms by which the early formation structure of host proteins (i.e. fibrin network) affects macrophage function. We developed a model system to investigate the effects of different fibrin network structures on macrophages by modifying sodium methacrylate alginate with zwitterionic (sulfobetaine) or dopamine (hereafter MSA-ZW/MSA-DA). Our data elucidated alterations in macrophage gene expression, offering insights into the potential mechanisms by which fibrin network structures influence macrophage biological processes.

overall_design: RNA-Seq profilling of macrophages cultured for 24 hours on MSA-ZW and MSA-DA hydrogels.

first: Bicong

last: Gao

first: Haifeng

last: Ni

first: Junhong

last: Lai

first: Ning

first: Xinxin

last: Luo

first: Ying

last: Wang

first: Jiaying

last: Zhao

first: Jing

last: Zhang

first: Wenjin

last: Cai

first: Guoli

last: Yang


title: The effects of sorafenib treatment on the CD4+T cell population

first: Shuowang

address: Yuhang Tang Street No.866

summary: To investigate the impact of sorafenib treatment on gene expression in CD4+T cells, we performed RNA sequencing on CD4+T cells treated with sorafenib and on control CD4+T cells that were not treated with sorafenib. Specifically, our study focused on the expression of immune related genes, and we observed an downregulation in the expression of TCR genes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sorafenib treated Treg cell and non-sorafenib treated cell.


title: A basigin antibody modulates MCTs to impact tumor metabolism and immunity

city: Shanghai

first: Dongxi

last: Xiang

address: No. 25, Lane 2200, Xietu Road

institute: Shanghai Cancer Institute

summary: Lactate metabolism and signaling intricately intertwine in the context of cancer and immunity. Basigin, working alongside monocarboxylate transporters MCT1 and MCT4, orchestrates the movement of lactate across cell membranes. Despite promising potential in treating aggressive tumors, the impact of basigin antibodies on these interactions remains unclear. Our research sheds light on this complex interplay: basigin positively modulates MCT activity. A basigin antibody transforms basigin into a negative regulator of MCTs. The antibody suppresses lactate transport and enhances anti-tumor immunity in vitro and in vivo. Furthermore, antibody alters metabolic profiles in PDOs-NSCLCs and T cells. Cryo-EM structure analysis and molecular dynamics simulations unveil that MCT1’s turnover rate is influenced by the flexibility of basigin’s Ig2 domain. By restricting Ig2 flexibility, antibody reduces MCT1 turnover. These findings underscore the promise of basigin antibodies in tumor combat by influencing metabolism and immunity and the value of shared ancillary subunits in targeting heteromeric transporters.

first: Shan

first: Yiqin

first: Jun

last: Liao


title: Complete Remission with Conventional Chemoradiotherapy in Radiation-Induced Glioma  Harboring Co-amplification of PDGFRA, KIT, and KDR: A Case Report and Literature Review

city: Hidaka

first: Mitsuaki

middle: Shirahata

last: Shirahata

state: Saitama

department: Neurosurgery/Neuro-oncology

institute: Saitama Medical University International Medical Center

summary: Background: One of the most serious complications of cranial radiotherapy is the development of radiation-induced glioma, which is estimated to occur in 1 to 4% of patients who have received cranial irradiation and has a worse prognosis than sporadic glioblastoma. To date, owing to its rarity, no standard of care has been established for radiation-induced glioma. Although comprehensive genetic analysis has recently uncovered the molecular characteristics of radiation-induced glioma, the full picture remains unclear, and the molecular features associated with treatment response and prognosis are poorly understood.   Case presentation: A 45-year-old man presented with generalized seizures caused by multiple brain tumors involving the right frontal lobe, thalamus, and brainstem. The patient had a history of whole-brain radiotherapy for the recurrence of Burkitt's lymphoma at the age of 12. He underwent craniotomy, and the histological diagnosis was a high-grade glioma with isocitrate dehydrogenase-wildtype, which was presumed to be a radiation-induced glioma that developed 33 years after whole-brain irradiation. The Heidelberg DNA-methylation brain classifier most closely matched diffuse pediatric-type high-grade glioma, receptor tyrosine kinase-1 subtype, which is a typical methylation class of radiation-induced glioma. Methylation-specific polymerase chain reaction showed that the O6-methylguanine-DNA methyltransferase gene promoter was unmethylated. Next-generation sequencing identified CDKN2A/B deletion as well as co-amplification of several receptor tyrosine kinase-encoding genes including PDGFRA, KIT, and KDR, which are all located on chromosome 4q12. Amplification of this region is present broadly across cancers and is associated with a poor prognosis in sporadic glioblastoma. Nevertheless, the patient received conventional chemoradiotherapy with temozolomide. Subsequent multimodal imaging with magnetic resonance imaging and 11C-methionine positron emission tomography revealed complete remission of all lesions. Two years later, the patient is currently alive with a favorable performance status.  Conclusions: Despite radiation-induced glioma with molecular features suggestive of an aggressive phenotype, our patient unexpectedly responded well to conventional chemoradiotherapy, resulting in complete remission that is exceptional in sporadic glioblastoma. Our case indicates that some of the radiation-induced gliomas may have distinct molecular characteristics involved in the therapeutic response that differ from those of sporadic glioblastomas.

overall_design: We aimed to identify the DNA methylation profile of radiation-induced glioma patient. The DNA was extracted from the resected tumor tissue and analyzed using the  Illumina Infinium MethylationEPIC v2.0 Kits (Illumina, Inc., San Diego, CA).


title: Autism-associated mutations in Kdm6b affect its role as a chromatin regulator in brain development

city: Durham

first: Rebecca

last: Li

state: North Carolina

address: 311 Research Drive

department: Neurobiology

institute: Duke University

summary: The regulation of gene expression in the developing brain is coordinated by changes in chromatin regulation. Chromatin regulation involves the deposition and removal of molecular modifications on the histone proteins that give structure to and control the function of genomic DNA. The trimethylation of histone H3 at lysine 27 (H3K27me3) is a chromatin mark that recruits transcriptional repressors, silencing gene transcription. The JmjC family lysine demethylase KDM6B has been identified as an enzyme that removes H3K27me3, allowing for expression of genes critical for brain development. Genetic variants in human KDM6B have been found to be  associated with intellectual disability and autism spectrum disorder (ASD); however, the molecular mechanisms by which these genetic variants affect KDM6B function remain unknown. We mapped these variants into the structure of KDM6B, and computationally assessed their likely effects on KDM6B protein function. To  experimentally determine how ASD-associated sequence variants in KDM6B affect the function of this protein in cells, we generated ASD-associated mutations into a KDM6B expression construct and assessed their effects on the enzymatic function of this protein as well as its stability and nuclear localization. We found that several  ASD-associated mutations occur in the H3K27me3 binding pocket of KDM6B and impair the ability of this enzyme to demethylate histones. In parallel, through RNA sequencing experiments in cerebellar granule neurons from mouse, we found that expression of the enzymatically active form but not the enzymatically dead form of  KDM6B was sufficient to rescue synaptic gene expression following knockdown of endogenous KDM6B. Together, these findings elucidate a novel role of KDM6B in controlling gene expression in maturing neurons, and they expand our knowledge on how chromatin dysregulation can lead to neurodevelopmental disorders like ASD.

overall_design:
To determine whether the enzymatic activity of Kdm6b is sufficient to rescue synaptic gene expression upon  knock down of endogenous mouse Kdm6b, we first knocked down endogenous mouse Kdm6b in cerebellar granule neurons using an shRNA targeted against mouse Kdm6b. We then re-expressed either an active human Kdm6b enzymatic domain or a dead human Kdm6b enzymatic domain in the same cerebellar granule neurons. Neurons were co-infected with shRNA against mouse Kdm6b and active or dead human Kdm6b enzymatic domain on DIV1, treated with AraC on DIV2, and harvested using RNAqueous Micro Kit on DIV7.
We then looked at differential gene expression across four conditions: control, shKdm6b, shKdm6b + active enzymatic domain rescue, shKdm6b + dead enzymatic domain rescue

first: Urann

last: Chan

first: Vijyendra

last: Ramesh

first: Andrew

last: Aldridge

first: Anne

last: West


title: Scanning and Mining of High Fecundity Genes by Oxford Nanopore Technologies (ONT) in Sheep (Ovis aries) Pituitary

city: taian

first: dejie

last: zhu

address: Shandong Agricultural University

institute: Shandong Agricultural University

summary: The pituitary gland is an important endocrine organ that regulates estrus and reproduction in sheep mainly through hormone synthesis and secretion. In present study, Small-tailed Han sheep (high-reproduction group, HP group), and Wadi sheep (lower-reproduction group, LP group), were used as the experiment materials, and the differential expressed genes (DEGs) were scanned and mined by Oxford Nanopore Technologies (ONT) in pituitary. A total of 7123 DEGs were found, including 3551 genes that were upregulated and 3572 genes that were downregulated in HP group. Go and KEGG related to pituitary function and reproduction were enriched, including reproductive processes, responses to stimuli, and synapses. mTOR signaling pathway, PI3K-Akt signaling pathway, cAMP signaling pathway, ERK1/2 signaling pathways and MAPK signaling pathways. The DEGs detected in this study were involved in the development of tissues and organs and the secretion of hormones in the endocrine system. These findings suggest that these genes might be related to growth, development and the reproduction regulation in sheep, which could provide a scientific basis for elucidating the genetic mechanisms of high reproduction in sheep.

overall_design: In this study, three healthy small-tailed Han sheep and three healthy Wadi sheep with similar body composition, were selected to form a high-reproduction group (HP group, small-tailed Han sheep) and a lowreproduction group (LP group, Wadi sheep). Oxford Nanopore Technologies (full-length transcriptome sequencing technology) was used for mRNA identification, screening, and functional analysis of the different groups. The pituitary tissue expression trends of eight genes were verified by Quantitative Rreal-time PCR

first: Xue

last: Xiao

first: Lin

last: Ju

first: Zhibin

last: Ji

first: Tong

first: Dejie

last: Zhu

first: Zhonghui

first: Xinming

last: Xu

first: Tianle

last: Chao

first: Jinliang

first: Fen

first: Jianmin


title: Isolation, Structure Elucidation, and Biological Activity of the Selective TACR2 Antagonist Tumonolide and its Aldehyde from a Marine Cyanobacterium

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary: A cyanobacterium secondary metabolite was discovered and in order to determine the effect of the comnppound on transcript levels we carried out an RNAseq experiment using HCT116 colorectal carcinoma cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells, treated with tumonolide (20 µM)  or vehicle control

first: Sofia

last: Kokkaliari

first: Hendrik

last: Luesch


title: Episodic ozone exposure in Long-Evans rats has limited effects on cauda sperm motility and non-coding RNA populations.

city: Research Triangle Park

first: Colette

last: Miller

state: NC

address: 109 TW Alexander

institute: U.S. Environmental Protection Agency

summary: The effects of air pollutants on the sperm ncRNA population have not been comprehensively studied, however, there is growing evidence that tobacco smoke exposure can alter the contents of mature sperm in both humans and rodents. Subsequently, we proposed that identification of specific ncRNA populations would reveal novel insights into the factors that may contribute to the hypothesized ozone-induced impairments in sperm quality.

overall_design: Cauda sperm were collected from rats exposed to air or 0.4 ppm or 0.8 ppm ozone (n=8/group) for RNA isolation of non-coding RNAs. Samples were sequenced using the Illumina NextSeq 500 platform.

middle: N


title: Gene expression profiles at single cell level of CD4 T Cells infected with HIV Nano Cre

city: New York City

first: Benjamin

last: Chen

state: New York

address: 1468 Madison Avenue

department: Infectious Disease

summary: To study the mechanisms of early HIV latency establishment, we used EHILT to infect primary CD4+ T cells and test the ability of the system to track similar EHILT phenotypes in primary CD4+ T cells

overall_design: We examined EHILT actively infected, latently infected, and dsRed uninfected phenotypes for their transcriptional profiles at single cell resolution using scRNAseq methods.

first: Donald

middle: V

last: Doanman

first: Gerrit

last: Schmidt

middle: K


title: Transcriptome study of Alzheimer's disease on post-mortem human brain

city: Belmont

first: Weiqian

last: Jiang

state: MA

address: 115 Mill St

institute: McLean Hospital

summary:
INTRODUCTION: Neuropsychiatric symptoms are common in people with Alzheimer’s disease (AD) across all severity stages. Their heterogeneous presentation and variable temporal association with cognitive decline suggest shared and distinct biological mechanisms. We hypothesized that specific patterns of gene expression associate with distinct NIMH Research Domain Criteria (RDoC) domains in AD.

METHODS: Post-mortem bulk RNAseq on the insula and anterior cingulate cortex from 60 brain donors representing the spectrum of canonical AD neuropathology combined with natural language processing approaches based on the RDoC Clinical Domains.

RESULTS: Distinct sets of >100 genes (pFDR<0.05) were specifically associated with at least one clinical domain (Cognitive, Social, Negative, Positive, Arousal). In addition, dysregulation of immune response pathways was shared across domains and brain regions.

DISCUSSION: Our findings provide evidence for distinct transcriptional profiles associated with RDoC domains suggesting that each dimension is characterized by specific sets of genes providing insight into the underlying mechanisms.

overall_design: We performed RNA sequencing of two brain regions (BA16 and BA32) from both AD patients and controls, and performed dimensional regression analysis of gene expression profiles over different RDoC scores.

first: Jonathan

last: Vogelgsang

first: Shu

last: Dan

first: Sabina

last: Berretta

first: Torsten

last: Klengel


title: Chromasome accessibility profiles at single cell level of Drug-tolerant persister cells induced by targeted therapy in lung adenocarcinoma.

first: Hideo

last: Watanabe

summary: Drug-tolerant persister (DTP) stage is viewed as a major source of non-genetic drug resistance. We use single cell ATAC seq to reveal the epigenetic heterogeniety of DTP stage

overall_design: PC9 cells were treated with 150nM Osimertinib for 11 days to induce DTP stage. NCI-H358 cells were treated with 500nM Sotorasib for 8 days to induce DTP stage. DTP cells and untreated control cells were collect and undergo sc-ATAC seq.

first: Yang

last: Tian

first: Feng


title: Targeted bisulfite sequencing in PTC

city: Seoul

first: Yeongun

last: Lee

state: State...

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei university

type: Methylation profiling by high throughput sequencing

summary: This study illuminates the critical advancement in the personalized management of papillary thyroid cancer (PTC) through the identification and validation of epigenetic biomarkers. We discovered the two distinct PTC subgroups with varying prognoses through TBS and observed the clues that PTC1 may related to immune signatures through multi-omics sequencing analysis. Then, we introduce FNAB, a minimally invasive preoperative test, for prognostication and therapeutic decision-making. Utilizing FNAB coupled with real-time digital PCR, our methodology not only facilitates the sensitive detection of seven pivotal biomarkers, including CD37, but also integrates seamlessly with the established TNM staging system to significantly refine survival predictions. This approach heralds a new era in the precise, personalized treatment of PTC, promising improved patient outcomes through the strategic application of epigenetic insights in clinical practice.

overall_design: Targeted bisulfite sequencing was performed on 55 Korean patients with PTC to investigate epigenetic variations among them.

first: Hyojin

last: Park


title: RARa restrains CD8 T cell effector program [CHIP-seq]

city: Ann Arbor

first: Chang

last: Kim

address: 109 Zina Pitcher

institute: University of Michigan

summary: We investigated the binding of RARa and BATF to the chromatin of activated CD8 T cells.  Distnctive and co-binding of the two factors in RA-depletd and replte conditions were revealed.

overall_design: WT CD8 T cells, activated for 24 h with anti-CD3, anti-CD28, and IL-2 and then rested for 24 h in IL-2 (100 U/ml), were further treated with or without RA (50 nM) for 1 h.

first: Patrick

last: Niekamp


title: RARa restrains CD8 T cell effector program [scRNA-seq]

summary: ScRNA-seq for tumor-bearing  RARα-KO, or RARα-TG mice bearing MC38 tumors was performed.

overall_design: T cells and other cells from WT, RARα-KO, or RARα-TG mice bearing MC38 tumors were compared on day 16 post tumor cell-injection.


title: M2 macrophage promoting IL-10+B cell production and contribute to alleviate asthma in mouse

first: Baichao

last: Yu

state: Shanghai

address: NO.130,  Dong'an Road , Xuhui District

institute: Fudan University

summary: B cells play a crucial regulatory role in diseases. Macrophages exist in the disease microenvironment and interact with tissue cells as well as various immune cells, but their relationship with B cells has never been reported. Using an asthma animal model and macrophage depleting agents, we found that macrophage removal significantly aggravated asthma symptoms and significantly reduced the expression of IL-10+ B cells in the asthma model. We further analyzed and found that the macrophages interacting with IL-10+ B cells in the asthma microenvironment were M2 macrophages. Moreover, through sequencing, we preliminarily found that M2 macrophages promote B cell production of IL-10 through oxidative phosphorylation pathways. Together, the results indicate that M2 macrophages act on IL-10+ B cells, thereby alleviating asthma in mouse models.

overall_design: To investigate the underlying mechanism about how M2 macrophages skew B cell towards regulatory profile, we collected naïve B cells(UN), anti-CD40 stimulated B cells(B) and M2-educated B cells(M) for RNA-seq.

first: Xueqi

last: Wang

first: Yongkun

last: Zheng

first: Yue

last: Cao

first: Mingxing

last: Wei

first: Ying

last: Fu

first: Luman

first: Yiwei

last: Chu


title: miRNA Cargo of Matrix-Bound Extracellular Vesicles Isolated from Human Left Ventricular Tissue Differs with Heart Failure

city: Pittsburgh

first: Heth

last: Turnquist

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh

type: Non-coding RNA profiling by high throughput sequencing

summary: Matrix-bound extracellular vesicles were isolated from the left ventricle tissue of de-identified patients with non-failing (healthy) hearts or with non-ischemi heart failure. mIRNA sequencing was performed on the miRNA cargo sequestered within the extracellular vesicles. Differences in the miRNA signature of healthy versus failing-tissue derived extracellular vesicles suggests that disease progression to heart failure is associated with dynamic changes in vesicular cargo.

overall_design: miRNA sequencing was performed on the cargo of extracellular vesicles isolated from left ventricle tissue of patients with non-failing hearts (healthy) or with non-ischemic heart failure (failing).

first: Chandran

last: Uma

first: Schwarzmann

last: William

first: Soman

last: Vishal


title: Single-cell dynamics of breakthrough toxicities following anakinra prophylaxis for axicabtagene ciloleucel treatment in lymphoma

city: CAMBRIDGE

first: Nicholas

last: Haradhvala

address: 75 Ames St

institute: Broad Institute

summary: Chimeric antigen receptor T cells have transformed the treatment of multiple hematologic malignancies, but are limited in application due to treatment-related toxicities. Cytokine release syndrome (CRS) and neurotoxicity (NT) are the primary toxicities associated with these therapies and are thought to be mediated by broad immune activation due to robust T-cell expansion. Current treatment of these toxicities utilize anti-IL-6 directed therapy and/or systemic glucocorticoids to mitigate the consequences of this complex inflammatory cascade. We sought to use anakinra, an IL-1R antagonist, as a prophylactic strategy to prevent clinically meaningful CRS/NT, defined as grade 2 or higher toxicity necessitating clinical intervention. Although our study, in line with others, demonstrated that IL-1R antagonism is insufficient to prevent such toxicities entirely, we were able to gain insight into the molecular immune signaling associated with breakthrough CRS & NT in the presence of anakinra prophylaxis using our scRNA dataset of patients treated with and without IL-1R antagonism. We demonstrate that IL-4 and IL-10 anti-inflammatory pathways in infused CAR-T products of both anakinra and non-anakinra cohorts were negatively associated with grade 2+ toxicities. We also found that expression of IFNg pathways and ligand-receptor activities, as well as cytokine levels of IFNg and CXCL10 in CD14+ monocytes, were significantly enriched in patients with breakthrough toxicity in the anakinra cohort. This correlated with an increase in IFNg in the peripheral blood of patients with breakthrough toxicities, among other cytokines. These data identify IFNg as a potential key mechanism in the development of CAR-T cell-associated toxcities and suggest that this pathway is also targetable and not inhibited by anakinra alone.

overall_design:
Cryopreserved infusion product was provided by Kite Pharma. PBMCs from day 7 (± 1 day) after CAR-T cell infusion or cryopreservd infusion product were thawed and resuspended in staining buffer for flow cytometry (PBS consisting of 2% FBS). Human Fc block (5 mL) was added per sample (BD Bioscience catalog no. 564219). After 5 minutes, the following antibodies (in BD brilliant stain buffer, BD Bioscience catalog no. 566349) were added for 20 minutes at 4°C: CD45 (BV786 BD Biosciences catalog no. BD563716) at a dilution of 1 in 167, CD3 (APC BD Biosciences catalog no. 340661) at a dilution of 1 in 83.5, CD4 (V450 BD Bioscience catalog no. 651850) at a dilution of 1 in 83.5, CD8 (V500c BD Bioscience catalog no. 647458) at a dilution of 1 in 83.5, CD14 (FITC BD Bioscience catalog no. 347493) at a dilution of 1 in 83.5 and Kip1 (PE conjugated, Yescarta product provided by Kite) at a dilution of 1 in 150. After washing twice, cells were resuspended in FACS buffer (2% FBS in PBS) followed by the addition of 7-AAD (Thermo Fisher Scientific). Using a BD FACSAria sorting system, live CAR-T cells and non-CAR-T cells were acquired separately. The gating strategy was based on healthy non-CAR transduced donor PBMC and was prepared separately for each group as previously performed by Haradhvala et al. (2022). Before loading on a 10x Genomics Chromium platform, samples were resuspended in 0.04% ultrapure bovine serum albumin (BSA) in PBS at 1,000 cells per μl density. Day 7 samples and infusion product were thawed similarly and combined into groups of up to five samples per 10x channel loaded at a density of 3,000 cells per μl as previously performed by Haradhvala et al. (2022).

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Submitter states that missing raw data are being made available for controlled access in dbGaP.
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first: Matthew

last: Frigault

first: Ning

last: Yao

first: Gad

last: Getz

first: Marcela

last: Maus


title: Longitudinal prediction of DNA methylation to forecast epigenetic outcomes

city: Singapore

first: Dennis

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

type: Methylation profiling by genome tiling array

summary: We introduce a probabilistic and longitudinal machine learning framework based on multi-mean Gaussian processes (GPs), accounting for individual and gene correlations across time. This method provides future predictions of DNA methylation status at different individual ages while accounting for uncertainty.

overall_design: Our model is trained on a birth cohort of children with methylation profiled at ages 0-4, and we demonstrated that the status of methylation sites for each child can be accurately predicted at ages 5-7.

first: Ai Ling

last: Teh


title: RARa restrains CD8 T cell effector program [bulk RNA-seq]

first: Chang

last: Kim

summary: The roles of RARα and BATF on CD8 T cell gene expression have been determined.

overall_design: For bulk RNA sequencing, CD8 T cells were cultured on anti-CD3-coated (1µg/ml) 96-wells in RPMI medium supplemented with 10% charcoal-stripped FBS, anti-CD28 (2 ug/ml), and IL-2 (100 U/ml) for 20 h with or without RA (15 nM). RNA was isolated using the RNAeasy kit (Qiagen #74104) according to manufacturers’ instructions and processed for poly-A-enrichment-based library preparation for paired-end 150 bp-sequencing (300 cycle) in a NovaSeq S4 Shared Flowcell at the University of Michigan Advanced Genomics core. Duplicated samples were prepared for each group. BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files. In general, Snakemake was used to manage the bioinformatics workflow 66. The reads were trimmed, examined for quality of data, and screened for various types of contamination. Reads were mapped to the reference genome GRCm38 (ENSEMBL) and assigned count estimates to genes with RSEM v1.3.3 using STAR v2.7.8a 67. Hierarchical clusters were generated using the Gene Cluster software (3.0) with a cut-off of ≥1.5 log2 fold-change and data was presented using the Java TreeView software.

first: Patrick

last: Niekamp


title: Metastatic site influences driver gene function in pancreatic cancer [scMultiome]

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Driver gene mutations can increase the metastatic potential of the primary tumor, but their role in sustaining tumor growth at metastatic sites is poorly understood. A paradigm of such mutations is inactivation of SMAD4 – a transcriptional effector of TGFβ signaling – which is a hallmark of multiple gastrointestinal malignancies. SMAD4 inactivation mediates TGFβ’s remarkable anti- to pro-tumorigenic switch during cancer progression and can thus influence both tumor initiation and metastasis. To determine whether metastatic tumors remain dependent on SMAD4 inactivation, we developed a mouse model of pancreatic ductal adenocarcinoma (PDAC) that enables Smad4 depletion in the pre-malignant pancreas and subsequent Smad4 reactivation in established metastases. As expected, Smad4 inactivation facilitated the formation of primary tumors that eventually colonized the liver and lungs. By contrast, Smad4 reactivation in metastatic disease had opposite effects depending on the tumor’s organ of residence: suppression of liver metastases and promotion of lung metastases. Integrative multiomic analysis revealed organ-specific differences in the tumor cells’ epigenomic state, whereby the liver and lungs harbored chromatin programs respectively dominated by the KLF and RUNX developmental transcription factors, with Klf4 depletion being sufficient to reverse Smad4’s tumor-suppressive activity in liver metastases. Our results show how epigenetic states favored by the organ of residence can influence the function of driver genes in metastatic tumors. This organ-specific gene–chromatin interplay invites consideration of anatomical site in the interpretation of tumor genetics, with implications for the therapeutic targeting of metastatic disease.

overall_design: To assess whether chromatin states that pre-exist in the primary tumor are linked to organ-specific metastasis, we performed coupled single-cell multiomics (ATAC/RNA-seq) on three independent KC-shSmad4 primary tumors (on Dox).

first: Kaloyan

middle: M

last: Tsanov

first: Scott

middle: W

last: Lowe


title: Metastatic site influences driver gene function in pancreatic cancer [RNA-seq]

overall_design: SMAD4 acts as a transcription factor (TF) by forming a complex with the SMAD2/3 TFs to activate gene expression programs downstream of TGFβ receptors. Hence, we performed RNA sequencing (RNA-seq) to explore the transcriptional basis of the observed organ-specific phenotypes. Leveraging the mKate2 reporter in our model, we used fluorescent-activated cell sorting (FACS) to isolate tumor (mKate2+) cells 7 and 14 days after Dox withdrawal, which allowed for assessment of Smad4 output kinetics.


title: Granulosa cell lineage undergo a transition from ERα- to ERβ-expressing cells during follicular development

city: Urbana

first: CheMyong

middle: Jay

last: Ko

state: Illinois

address: 2001 S. Lincoln Ave.

department: Comparative Biosciences

institute: University of Illinois at Urbana Champaign

summary: Estrogen receptors alpha (ERα, ESR1) and beta (ERβ, ESR2) are co-expressed in most estrogen-responsive tissues, but their expression tends to be mutually exclusive at the cellular level. In the adult ovary, ESR2 is expressed in granulosa cells (GCs) but not in theca cells or ovarian surface epithelium (OSE), whereas ESR1 is expressed in theca and OSE cells. Interestingly, recent studies showed that subpopulation of GCs is of OSE origin, suggesting that GC lineage cells lose ESR1 expression and gain ESR2 expression during the OSE cell-to-GC transition. In this study, we report that GC lineage cells initially express ESR1 but later lose their expression and gain ESR2 expression and that endothelial cell-derived TGFβ1 promotes such ESR1-to-ESR2 change in the developing ovary.

overall_design: To investigate the ovarian differential gene expression in individual cells, WT ovaries were collected from ED 16.5, PND 7, and PND 14. For single-cell RNA-seq analyses, ovaries were dissociated. Ovaries were removed, cut into small pieces, transferred to 2 ml of collagenase digestion solution containing 3.5 U of collagenase type I, 1000 U of deoxyribonuclease I, and 40 mg of BSA in H-199 media, then placed in a water bath at 37 °C for 30 min. After incubation, tissues were further dissociated by repeatedly passing them through an 18-G needle attached to a 3-ml syringe. Then, the digested tissue suspension was filtered through a 40-μm filter, centrifuged at 300 × g for 5 min, then resuspended in 1 ml of PBS containing 1% BSA. Single-cell suspensions with a viability of >90% by Trypan Blue staining were converted into individually barcoded cDNA libraries with the Single-Cell 3’ Chromium kit version 2 from 10X Genomics following the manufacturer’s protocols.

first: Chan

last: Park

first: Ji-Eun

last: Oh

first: Po-Ching

last: Lin

first: Sherry

last: Zhou

first: Emmanuel

last: Bikorimana

first: Michael

last: Spinella

first: Hyunjung

last: Lim


title: Avelumab induces superior Fc-Fc receptor-dependent natural killer cell stimulation and dendritic cell cross-talk compared to durvalumab

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

institute: CLEVELAND CLINIC LERNER COM-CWRU

summary: Natural killer cells and dendritic cells are instrumental in controlling cancer. However, the impact of PD-L1 blockade therapy on these immune cell types is not well understood. Furthermore, across many clinical trials, different anti-PD-L1 antibodies have produced varying levels of efficacy in patients, and the basis of these differences are obscure.  Avelumab, a native Fc IgG1 antibody, and durvalumab, a mutant-Fc IgG1 antibody, are two of the most commonly used anti-PD-L1 agents for cancer immunotherapy.  We compared the mechanistic effects of these agents.  Our study shows the robust impact of Fc-signaling on NK cells by avelumab. In contrast, durvalumab failed to induce NK cell activation or promote NK-DC cross-talk.

overall_design: We investigated impact of two PD-L1 inhibitors (avelumab and durvulumab) in (1) PCI-15B tumor cells, (2) NK+PCI-15B coculture, and  (3) NK+DC+PCI-15B coculture. Each treatment group has data in triplicates. We performed differential gene expression analysis and GSEA to show the differences between two groups. Normalized data was used to show differences.    In condition (1) PCI-15B tumor cells differences were identified between any two groups: no_ab_1, no_ab_2, no_ab_3; Durva_1, Durva_2, Durva_3; Ave_1, Ave_2, Ave_3.   In condition (2) NK+PCI-15B coculture differences were identified between two groups: No_ab_1, No_ab_2, No_ab_3; NK_Durva_1, NK_Durva_2, NK_Durva_3.   In condition (3) NK+DC+PCI-15B coculture differences were identified between two groups: R20001_IgG1, R20001_IgG2, R20001_IgG3; R20002_Durv_1, R20002_Durv_2, R20002_Durv_3.

first: Nicole

last: Osborne

first: Amit

last: Rupani

first: Timothy

last: Chan

first: Raghvendra

last: Srivastava


title: Analysing environmentally induced genome-wide frameshift in S. cerevisiae using SLAM-Seq

city: stockholm

first: yujie

last: zhang

address: Tomtebodavägen 23

country: Sweden

institute: Karolinska institutet

summary: In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation. To measure the RNA degradation, we utilized  SLAM-seq (Herzog, et.al, 2017, PMID: 28945705) in S.cerevisiae in wildtype and NMD mutant (upf1Δ). Our goal with SLAM-seq is to quantify the fraction of the transcriptome that is directly degraded as a result of environmentally induced ribosome frameshifts through an NMD-dependent mechanism.

overall_design: To perform pulse and chase experiment, RNA molecules were labelled with 4tU for 1h during cell grown at mid exponential phase. Cells were washed and resuspend in prewarmed medium (YPD with MES buffer or CSM with MES buffer) without  4tU and time points were collected at 0, 15 and 30 mins.

first: Yujie

last: Zhang

first: Vicent

last: Pelechano


title: Analysing environmentally induced genome-wide frameshift in S. cerevisiae using ribosome profiling

summary: In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation. To explore this process, we utilized Ribosome profiling (Ingolia, et.al 2009, PMID: 19213877), in S.cerevisiae in low nutrients condition. Our goal with Ribosome profiling was to identify gene- and codon-specific features that contribute to genome-wide frameshifting events.

overall_design: Ribosome profiling and RNA-seq was carried out on S. cerevisiae grown in CSM medium (3 replicates).


title: Analysing environmentally induced genome-wide frameshift

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

sample_organism:
Bacillus subtilis
Saccharomyces cerevisiae

overall_design: Refer to individual Series


title: Analysing environmentally induced genome-wide frameshift in S. cerevisiae and bacteria  using 5PSeq

summary: In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation.To explore this process, we utilized HT-5PSeq (Zhang & Pelechano, 2021, PMID:35474692) to measure the ribosome footprint of co-translationally degraded mRNAs in S.cerevisiae under different stresses in YPD and CSM (poor nutrients).  To show the mechanism is conserved in bacteria, we performed HT-5PSeq in  B.subtilis upon starvation .Our goal with HT-5PSeq is to identify gene- and codon-specific features that contribute to genome-wide frameshifting events.

platform_organism:
Bacillus subtilis
Saccharomyces cerevisiae

overall_design: HT5P-seq was carried out on S. cerevisiae and B. subtilis 168 (trpC2) under various environmental conditions (3 replicates). Stress-induced S. cerevisiae cells were subjected to heat shock , oxidative stress, and amino acid deprivation. S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium.  For B. subtilis,  cells were grown in both LB and minimal media.


title: Novel ex vivo culture of purified mouse mesenchymal stromal cells reveals tissue-dependent niche heterogeneity in bone marrow and functional interaction with macrophages

city: Rochester

first: Laura

last: Calvi

address: 601 Elmwood Avenue

institute: University of Rochester

summary: Mesenchymal stem/stromal cells (MSCs) are skeletal stem cells capable of regenerating bone, cartilage, and adipose tissues, while also serving as an essential immunosupportive cell for the hematopoietic stem cell pool. Therefore, the isolation and purification of murine MSCs is essential to understanding the differentiation capabilities necessary for skeletal regeneration, hematopoietic support, and immunomodulatory roles of MSCs within the bone marrow microenvironment (BMME). While many protocols on isolation from bone marrow (BM-MSCs) and bone associated cells (BAC-MSCs) have been published, none achive purity from macropahge contamination and many do not address heterogeneity of MSCs between these two compartments. To ensure a pure MSC isolation, we established a new strategy to exclude macrophages and their precursors by targeting F4/80/Ly6C/CD45. By analyzing MSC transcriptional profiles from both compartments with and without our purification strategy, we demonstrated distinct functional characteristics of MSCs by compartment, as well as functional impacts on the MSC transcriptional profile as a result of macrophage interaction.

overall_design: Four populations were collected in total from two different compartments: Bone marrow derived (BM) and bone associated cells (BAC). Bone marrow derived mesenchymal cells (MSC) were harvested from bilateral hind limbs and pelvis whole bone marrow and plated on collagen-I coated plates. After the first passage, samples were either used directly (BM-nonS) or sorted to purely isolate CD31-/CD45-/Ly6C-/F4/80-/CD51+/Sca-1+ cells (BM-S) for bulk RNAseq. BAC derived MSCs were isolated from collagenase-I treated bone fragments from bilateral hind limbs. After harvest these cells were either used directly without depletion (BAC-nonD) or depleted by magnetic separation to remove CD45+/Ly6C+/F4/80+ cells (BAC-D) for bulk RNAseq.

first: Yuko

last: Kawano

first: Hiroki

first: Stephanie

last: Busch

first: Allison

last: Li

first: Noah

last: Salama

first: Emily

last: Quarato

first: Chunmo

last: Chen

first: Mary

last: Georger

first: Mitra

last: Azadniv

first: Daniel

last: Byun

first: Elizabeth

last: LaMere

first: Mark

first: Jane

last: Liesveld

last: Becker


title: Effect of a natural product derivative on gene expression signatures in 5xFAD transgenic mice

status: Public on May 13 2025

city: shanghai

first: jiaxue

last: cha

address: Siping Road 1239

institute: Tongji university

summary: To investigate how a natural product analog mitigates AD, cortical transcriptomes from WT and 5xFAD mice were analyzed. Comparing vehicle-treated groups revealed extensive differential expression associated with neuroinflammation in 5xFAD mice. This was attenuated in the 5xFAD mice treated with the natural product, whose profiles resembled WT controls. RNA seq suggested the natural product regulated the nervous and immune systems.

overall_design: RNA-seq was employed to profile the effects of a natural product derivative on gene expression signatures in 5xFAD transgenic mice. Cortical tissues from five experimental groups, namely WT Veh, WT High P, 5xFAD Veh, 5xFAD Low P, and 5xFAD High P, were collected. Tissues from five mice per group underwent RNA extraction and subsequent transcriptome sequencing (RNA-Seq).

first: Jiaxue

last: Cha


title: U3 - acute UUO kidneys

city: Fuzhou

first: Zhimin

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

summary: Kidney single cell sequencing results from acute unilateral ureteral obstruction mice

overall_design: We performed single-cell transcriptome sequencing on acute UUO kidneys

first: Yanfang

last: Xu


title: Metastatic site influences driver gene function in pancreatic cancer [ATAC-seq]

city: New York

first: Yu-Jui

last: Ho

overall_design: Given the organ-specific transcriptional responses, we hypothesized that liver and lung metastases may harbor distinct chromatin states that afford different accessibility to SMAD4’s target genes. To test this, we performed ATAC-seq (assay for transposase-accessible chromatin using sequencing) on FACS-isolated tumor cells from the pancreas, liver, and lungs +/- Smad4 restoration (for 14 days).

first: Kaloyan

last: Tsanov

first: Scott

last: Lowe


title: Targeted bisulfite sequencing in PTC [ATAC-Seq]

first: Yeongun

last: Lee

summary: This study illuminates the critical advancement in the personalized management of papillary thyroid cancer (PTC) through the identification and validation of epigenetic biomarkers. We discovered the two distinct PTC subgroups with varying prognoses through TBS and observed the clues that PTC1 may related to immune signatures through multi-omics sequencing analysis. Then, we introduce FNAB, a minimally invasive preoperative test, for prognostication and therapeutic decision-making. Utilizing FNAB coupled with real-time digital PCR, our methodology not only facilitates the sensitive detection of seven pivotal biomarkers, but also integrates seamlessly with the established TNM staging system to significantly refine survival predictions. This approach heralds a new era in the precise, personalized treatment of PTC, promising improved patient outcomes through the strategic application of epigenetic insights in clinical practice.

overall_design: To check the impact of DNA methylation in our candidate targets, we treated the thyroid cancer cell line BCPAP with the demethylating agent 5-Azacytidine (5-Aza), followed by ATAC-seq analysis to observe which regions exhibit the most significant changes in chromatin accessibility.

first: Sumin

last: Kim

first: Sohee

last: Dho

first: Wonjin

last: Woo


title: The novel ZBTB5::JAK2 fusion gene reveals a new mechanism of kinase activation in Ph-like acute lymphoblastic leukemia

city: Chengdu

first: Qiang

last: Qiu

state: Sichuan

address: No. 17, the Third Part of Renmin South Road

institute: SKLB

summary: Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a distinct subtype of B-ALL, exhibiting a kinase-activated gene expression profile similar to Philadelphia chromosome-positive (Ph+) ALL, yet lacking the BCR::ABL fusion. Despite the identification of numerous genetic aberrations and chromosomal rearrangements, particularly those involving the ABL-class or CRLF2/JAK pathways, as drivers and therapeutic targets, the genetic diversity and underlying pathogenic mechanisms of Ph-like ALL remain incompletely understood, posing challenges for diagnosis and treatment. Here, we identified a novel JAK2 fusion, ZBTB5::JAK2, in a Ph-like ALL patient, accompanied by a frequent KRAS12D mutation. Single-cell RNA sequencing (scRNA-seq) analysis suggests that the cell population with both high JAK2 and RAS signals may represent the leukemia stem cells in this patient.

overall_design: To better understand molecular characteristics and pathogenic mechanisms of Ph-like ALL, we performed scRNA-seq on all leukocytes isolated from patients’ PB at initial diagnosis and complete remission (after CART treatment).

first: Juan

first: Tong

last: Chen

first: Ting

last: Liu


title: 5R 16S rRNA Gene Sequencing Technology in Analyzing Blood Microbiota Structure in Patients with Acute Gastrointestinal Injury

city: Shanghai

first: Li

last: Cheng

address: 500 Quxi Road, Shanghai 200011

department: Department of Rehabilitation Medicine

institute: The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: Changes in blood microbiota after AGI

overall_design: Changes in blood microbiota after AGI

first: Jin

last: Wang


title: RNA seq of human colon cancer cell line HT29 treated with nanocurcumin

city: Tabriz

first: Esmaeil

last: Babaei

state: East Azerbaijan

address: 29th Bahman Blvd.,

department: Biology

country: Iran

institute: University of Tabriz

summary: This study explores the transcriptomic effects of Gemini-curcumin (Gemini-Cur), a nano formulated version of curcumin, on HT-29 colorectal cancer cells. RNA sequencing was performed on treated and control samples to identify differentially expressed RNAs. The dataset provides insights into the molecular mechanisms of Gemini-Cur and its potential in modulating gene expression.

overall_design: Four total samples were analyzed, including two biological replicates of untreated HT-29 cells (Control) and two replicates of Gemini-Cur treated cells (Treatment). Cells were treated for 48 hours, after which total RNA was extracted for sequencing.

first: Hewa

last: Jalal Azeez

first: Zohre

last: Zibaei


title: A new IDH-independent hypermethylation phenotype is associated with astrocyte-like cell state in glioblastoma

city: Heidelberg

first: Anna-Sophie

last: Spreng

address: INF 280

institute: DKFZ

summary: DNA methylation plays a crucial role in cancer development and progression and has been linked to genetically and clinically distinct tumor classes, including IDH-mutated and IDH-wildtype adult-type diffuse gliomas. Here, we identified a CpG-island methylator phenotype (CIMP) that characterizes the receptor tyrosine kinase 2 (RTK2) subtype of IDH-wildtype glioblastoma. This RTK2-CIMP affects genomic locations and cell functions distinct from those of IDH mutation-associated IDH-CIMP and suppresses the expression of its target genes. The RTK2-CIMP-region chromatin is characterized by a combination of repressive and activating marks, including polycomb-associated H3K27me3 and enhancer-associated H3K4me1, consistent with DNA methylation-mediated silencing of genes with bivalent-state promoters in neural progenitor cells. Functionally, RTK2-CIMP affects neuronal lineage genes and is significantly associated with astrocyte (AC)-like glioblastoma, suggesting that RTK2-CIMP is an epigenetic signature of the AC-like cell state. Furthermore, we demonstrated that RTK2-CIMP can be induced by genetic manipulation in glioblastoma cells, suggesting that RTK2-CIMP is a key contributor to cell-state plasticity in glioblastoma.

overall_design: In mGB1 cells, Sox10 was stably knocked down using short hairpin RNA (shRNA). Briefly, nonoverlapping target sequences of shRNA sequences (sh1: TRCN0000018985; sh2: TRCN0000244290; Table EV1) were cloned and inserted into pLKO.1-puro (Sigma, SHG002). For the delivery of shRNAs, lentiviruses of pLKO.1-non target control, sh1 and sh2 were produced and transduced into mGB1 cells. Transduced cells were selected with 1 µg/ml puromycin for 48 h, and the K.D. efficiency was checked by both qPCR and Western blot.


title: Tumor-derived Apolipoprotein E induces Tip endothelial cell to remodel tumor stroma ratio and promote pancreatic neuroendocrine tumor progression

first: Xin

last: Lou

address: 688 Hongqu Road

department: Department of Pancreatic Surgery

institute: Fudan University Shanghai Cancer Center

summary: A low tumor stroma ratio (TSR) in patients with pancreatic neuroendocrine tumors (pNETs) is associated with a significantly poorer tumor prognosis. However, current clinical trials have shown that administration of a single drug targeting a matrix component does not improve tumor prognosis. The investigation of treatments targeting matrix components in combination with other therapies is crucial for effectively managing the TSR in pNETs. LCM analysis revealed that stroma-rich tumors excessively secrete APOE relative to stroma-poor tumors, with the specific receptor SCARB1 predominantly located on ECs. Single-cell analysis revealed a greater proportion of endothelial tip cells (TipECs) in stroma-rich tumors, because tumor-derived APOE could induce the transformation of other types of ECs into TipECs. These TipECs played crucial roles in driving pNETs progression by facilitating cancer-associated fibroblasts (CAFs) recruitment and remodeling the TSR. Mechanistically, APOE promoted the uptake of palmitic acid by ECs, and subsequently activated the transcription factor ATF6 to promote the PDGF pathway in vitro. Clinically, screening of 6 commonly used drugs for pNETs in vivo revealed that treatment with mTOR inhibitors suppressed the secretion of APOE by tumor cells and the subsequent effects of APOE on the stromal microenvironment, including the proportions of TipECs and CAFs. Importantly, mTOR inhibitors synergistically enhanced the effects of stroma-targeting PEGPH20 in vivo in pNETs. Overall, our study revealed that tumor-derived APOE could induce TipECs to remodel the TSR, and that mTOR inhibitors could increase the efficacy of the stroma-targeting drug PEGPH20.

overall_design: The aim of this study is to explore how tumor-derived Apolipoprotein E (APOE) induces Tip endothelial cells to remodel the tumor stroma ratio and promote pancreatic neuroendocrine tumor progression. In the experiment, human umbilical vein endothelial cells (HUVECs) are treated with APOE for 48 hours, while another group is treated with DMSO for 48 hours as a control. For in vivo studies, mice bearing subcutaneous pancreatic neuroendocrine tumors are divided into six drug treatment groups (everolimus, octreotide, rapamycin, sunitinib, surufatinib, temozolomide) and a PBS control group. Tumor growth, including volume and weight, is monitored, and related indicators of Tip endothelial cells and tumor stroma in HUVECs, as well as changes in tumor tissues in mice, are analyzed through various methods such as immunohistochemistry.


title: Type 1 Classical Dendritic Cells Govern Long-Term Cardiac Allograft Acceptance

city: St. Louis

first: Macee

last: Owen

state: MO

address: 660 S Euclid

institute: Washington University School of Medicine

summary: Acute and chronic rejection continue to represent serious challenges in transplant medicine. Current medical regimens focus on suppressing T-cell responses, lack effectiveness for some patients and impose significant risks of infection and malignancy. Recent studies have suggested that inhibition of co-stimulation pathways between antigen presenting cells (dendritic cells, macrophages, B-cells) and T-cells may serve as an effective strategy to prevent rejection by promoting allograft tolerance as opposed to simply suppressing immune responses. This concept has garnered excitement across the transplant community and demonstrated promising results in human renal transplant studies. A commonly used approach is inhibition of B7-CD28 and CD40-CD40L costimulatory pathways. Blocking these pathways leads to prolonged allograft survival in fully HLA-mismatched mouse heart transplantation models and non-human primates. There are important gaps in knowledge pertaining to mechanisms by which co-stimulation blockade modulates the recipient immune responses and confers donor organ tolerance. The precise immune cell populations and mechanisms responsible for induction and maintenance of donor organ tolerance remain incompletely understood. We have leveraged single cell RNA sequencing to dissect how traditional immunosuppression (cyclosporine) and co-stimulation blockade (CTLA-4 Ig, anti-CD40L neutralizing antibodies) differentially impact the immune landscape of the transplanted heart using a fully HLA-mismatched mouse model (Balb/c donor heart à B6 recipient). Analysis of these datasets demonstrated striking differences between these treatment regimens. Mice that received co-stimulation blockade displayed a marked increase in the abundance of classical dendritic cells (cDC1s and cDC2s). Compared to the cyclosporine treated group, these cells expressed negative regulators of T-cell stimulation including PDL1. Using recipient mice that lack either cDC1s or cDC2s, we found that cDC1s are absolutely required for co-stimulation blockade to confer long-term allograft survival and prevent recipient immune responses against the transplanted donor heart.

overall_design: Hearts from a BALB/c donor were transplanted into B6 (Zbtb46gfp/+) recipients treated with conventional immunosuppression (cyclosporine) or co-stimulation blockade (MR1, CTLA4-Ig). After 7 days, allografts were harvested, digested, and single cell suspensions were prepared. 3 allografts from each condition (cyclosporine and co-stimulation blockade) were pooled, and mononuclear phagocytes (MNP) (CD45+Ly6G-CD64+/-Ly6Chi/low) and dendritic cells (CD45+GFP+) were sorted by flow cytometry. 4 separate libraries were generated for single cell RNA sequencing (cyclosporine MNP, cyclosporine GFP+, co-stimulation blockade MNP, co-stimulation blockade GFP+). In a second experiment, hearts from a BALB/c donor were transplanted into B6 recipients (wildtype control or Irf8 +32-/-) treated with co-stimulation blockade. 14 days after transplant, allografts were harvested, digested, and single cell suspensions were prepared. 3 allografts from each condition (wildtype and Irf8 +32-/-) were pooled, and CD45+ DAPI- Ly6G- CD45 IV- immune cells were sorted by flow cytometry. 2 separate libraries were generated for single cell RNA sequencing (WT, IRF8).

first: Vinay

last: Penna

first: Hao

last: Dun

first: Benjamin J

last: Kopecky

first: Wenjun

last: Li

first: Kenneth M

last: Murphy

first: Daniel

last: Kreisel

first: Kory J

last: Lavine


title: Dissecting the functional differences and clinical features of R-spondin family members in metastatic prostate cancer

city: Minneapolis

first: Aiden

middle: James

last: Deacon

state: Minnesota

address: 425 East River Parkway

institute: University of Minnesota

summary: This study investigates the R-spondin family of genes (RSPO1/2/3/4), a group of secreted proteins that act as Wnt regulators, and their subsequent role in advanced prostate cancer (PC). When evaluating transcriptomic data from primary and metastatic PC patients, we found that alterations in RSPO2 were more prevalent than in other RSPO family members or Wnt-regulating genes APC and CTNNB1. Further, we found that RSPO2 alterations in PCs were significantly associated with worse disease-free survival. Through our in silico modeling, RSPO2 exhibited strong positive associations with genes regulating epithelial-mesenchymal transition (EMT) and double-negative prostate cancer (DNPC), but had negative correlations with androgen receptor (AR) and AR-associated genes. Furthermore, 3D modeling of RSPO2 revealed structural differences between itself and other RSPOs. In cell lines, RSPO2 overexpression caused up-regulation of EMT pathways, including EMT-regulatory transcription factors ZEB1 and TWIST2. Conversely, this was not observed when CTNNB1 was overexpressed in the same models. These findings highlight that, in PC, RSPO2 functions as a unique member of the R-spondin family by promoting genes and signaling pathways associated with aggressive PC and RSPO2 amplifications are associated with poor outcomes in PC patients.

overall_design: To investigate the regulatory abilities of RSPO2 in prostate cancer progression, we established RSPO2, Luciferase, and CTNNB1 overexpressed cell lines in LNCaP and PC3 cell lines using lentiviral transduction

first: Ava

last: Gustafson

first: Allison

last: Makovec

first: Ella

last: Boytim

first: David

last: Moline

first: Elin

last: Kairies

first: Sam

last: Kellen

first: Gabriella

last: von Dohlen

first: Khalid

last: Ishani

first: Megan

last: Ludwig

first: Emily

last: John

first: Alexis

last: Anike

first: Hai Dang

last: Nguyen

first: Scott

last: Dehm

first: Justin

last: Drake

first: Emmanuel

last: Antonarakis

last: Hwang


title: Epigenetic modifiers to treat retinal degenerative diseases.

city: Hershey

first: Lisa

last: Schneper

address: 700 HMC Crescent Rd

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University College of Medicine

summary: We have previously demonstrated the ability of inhibitors of LSD1 and HDAC1 to block rod degeneration, preserve vision, maintain rod-specific transcripts and downregulate those involved in inflammation, gliosis, and cell death in the rd10 mouse model of Retinitis Pigmentosa (RP). To extend our findings we tested the hypothesis that broad range of inhibitors of chromatin condensation can prevent photoreceptor degeneration in the rd10 mouse model. We used inhibitors for G9A/GLP that catalyzes methylation of H3K9, for EZH2 that catalyzes trimethylation of H3K27 and compared them to the actions of LSD1 and HDAC inhibitors. All the inhibitors decondense chromatin and all preserve, to different extents, retinas from degeneration in rd10mice, but they act through different metabolic pathways. One group of inhibitors, modifiers for LSD1 and EZH2, demonstrate a high level of maintenance of rod-specific transcripts, activation of Ca+2 and Wnt signaling pathways with inhibition of antigen processing and presentation, immune response and microglia phagocytosis. Another group of inhibitors, modifiers for HDAC and G9A/GLP work through upregulation of NGF-stimulated transcription, while down-regulating genes belong to immune response, extracellular matrix, cholesterol signaling and programmed cell death.

overall_design: Total 26 samples of mouse retina at PN24 in 5 groups: 1). 3 controls  B6.CXB1-Pde6brd10/Jrd10 (rd10) and 3 rd10 treated with HDAC inhibitor Romidepsin from PN9 till PN24; 2). 2 rd10 controls and 2 rd10 treated with G9A/GLP inhibitor UNC0642 from PN9 till PN24; 3). 4 rd10 controls and 2 rd10 treated with EZH2 inhibitor DZNep from PN9 till PN24; 4). 3 rd10 controls and 3 rd10 treated with EZH2 inhibitor UNC1999 from PN9 till PN24; 5). 2 controls FACS sorted rod photoreceptors from homozygotes mice of cross between rd10 and B6.Cg-Tg(Nrl-EGFP)1Asw/J and 2 littermates treated from PN9 till PN24 with LSD1 inhibitor GSK2879552.

first: Evgenya

last: Popova

first: Aswathy

last: Sebastian

first: Istvan

last: Albert

first: Colin

last: Barnstable


title: Spatial transcriptomics advances the use of canine patients in cancer research: a study of tumor-bearing pet dogs enrolled in an osteosarcoma clinical trial

city: Bethesda

first: Anjali

last: Garg

state: Maryland

address: Building 10, Room 1B53

department: Comparative Oncology Program,NCI

institute: National Institute of Health

summary: Pet dogs spontaneously develop many of the same tumor types as humans including osteosarcoma. Utilizing the canine patient model facilitates the study of novel therapeutics and biomarkers within the context of spontaneous carcinogenesis, inclusive of treatment resistance, metastatic progression and immune responses that mirror that observed in human cancers. Recent advances in spatial transcriptomics have improved our ability to utilize formalin-fixed paraffin-embedded tissues collected at canine autopsy. These techniques allow the canine model to be investigated alongside murine models to inform human cancer research. Herein we present the first application of the GeoMx Canine Cancer Atlas to outcome-linked samples from canine patients enrolled in an osteosarcoma clinical trial.

overall_design: A tissue microarray (TMA) of primary osteosarcoma samples was assayed using the GeoMx Digital Spatial Profiler. Samples were stratified by disease-free interval (DFI). Patients within the upper and lower tertiles were assigned to the High (n = 8) and Low DFI (n = 8) groups, respectively. Analyses included the identification of differentially expressed genes, pathway enrichment, and cell deconvolution.

first: Jessica

last: Beck

first: Church

last: Sarah

first: Christina

last: Mazcko

first: Amy

last: LeBlanc


title: The Effect of Reduced Dietary Protein on Adipose Tissue in Local Krškopolje Pigs

city: Ljubljana

first: Klavdija

last: Poklukar Žnidaršič

state: Ljubljana

address: Hacquetova ulica 17

department: Animal Science department

country: Slovenia

institute: Agricultural Institute of Slovenia

summary: The main objective of this study was to evaluate the effect of low-protein (LP) diet on adipose tissue deposition in Krškopolje pigs reared either in organic outdoor (n=2x12) or conventional indoor (n=2x12) system. In the outdoor system, RNA-sequencing revealed the upregulation of 28 genes and downregulation of 37 genes. Upregulated genes were mainly involved in lipid metabolism (ACLY, FASN, ACACA, MOGAT2), oxidative stress, and mitochondrial function. In the indoor system, RNA-sequencing revealed 30 upregulated and 28 downregulated genes. Among the upregulated genes, heat shock proteins (HSP70.2, HSPA6) were detected in pigs on LP diet, while genes involved in the innate immune system (MSR1, TREM2, CSF3R) were downregulated.

overall_design: A total of 48 animals of the Krškopolje pig breed were assigned to 4 treatment groups and reared either in the indoor (n = 2 x 12) or in the outdoor conditions (fenced open area with trees and shelter) (n = 2 x 12). Animals from the outdoor system were reared according to the organic standards and received organic feed ad libitum, while the animals reared in the indoor system received the same amount of feed based on the same ingredients, but of conventional origin. In both systems, animals received either standard (HP group, fed 15% crude protein from 20 to 80 kg, 12.5 % crude protein from 80 to 100 kg and 10 % crude protein from 100 to slaughter) or reduced protein diet (LP group, fed 15% crude protein from 20 to 60 kg and 10% crude protein from 60 kg to slaughter). After slaughter, backfat was collected at the level of the last rib and  freezed at -80 °C. Afterwards, RNA was extracted and equal amounts of total RNA from two individuals were pooled together generating 6 pools within each treatment group.

last: Poklukar

first: Marjeta

last: Čandek Potokar

first: Martin

last: Škrlep


title: Pulmonary Megakaryocytes Orchestrate Host Defense via PcrV-Induced NF-κB Signaling in Pseudomonas aeruginosa Infection

city: Chongqing,China

first: Hongli

last: Zhou

state: --- Select One ---

address: No. 83 Xinqiao Main Street, Shapingba District, Chongqing, China

institute: The Second Affiliated Hospital of the Army Medical University

summary: Megakaryocytes, traditionally known for their role in platelet production, have recently emerged as key players in immune responses during infections. In this study, we explore the involvement of pulmonary Megakaryocytes in the response to P. aeruginosa infection, with a specific focus on the mechanistic activation of Megakaryocytes via bacterial toxins. We demonstrate that P. aeruginosa infection triggers significant alterations in chemokine signaling and NF-κB pathways in pulmonary Megakaryocytes, leading to the upregulation of pro-inflammatory cytokines and chemotactic factors. Activated pulmonary Megakaryocytes effectively promote the recruitment of phagocytes, enhancing the host's resistance to P. aeruginosa infection. we identify PcrV as a key NF-κB activator in Mmegakaryocytes, evidenced by elevated expression of inflammatory markers and chemokines in response to PcrV. Inhibition of NF-κB signaling dampens this inflammatory response, confirming its critical role in megakaryocyte activation. Our findings provide novel insights into the immune function of megakaryocytes as active modulators during bacterial infections. This research highlights the complex interaction between megakaryocytes and phagocytes, suggesting a new approach for managing infectious diseases by modulating megakaryocyte activity to control bacterial pneumonia.

overall_design: After constructing an acute pneumonia mouse model with or without PAO1 strain, RNA seq analysis was performed to sort lung MKs using flow cytometry. Two samples were sent to each group for SMART sequencing.

first: Xiaolong

last: Guo

last: Liao


title: Abscisic acid and GIGANTEA signalling converge to regulate the recruitment of CONSTANS to the FT promoter and activate floral transition

city: Milano

first: Lucio

last: Conti

address: Via Celoria 26

country: Italy

institute: Università degli Studi di Milano

summary: Plants align flowering with optimal seasonal conditions to increase reproductive success. This process depends on modulating signalling pathways that respond to diverse environmental and hormonal inputs, thereby regulating the transition to flowering at the shoot apical meristem. In Arabidopsis, long-day photoperiods (LDs) stimulate the transcription of FLOWERING LOCUS T (FT), encoding the main florigenic signal. FT activation is mediated by the transcriptional regulator CONSTANS (CO), which binds to the CO responsive elements (COREs) located in the proximal FT promoter region. The phytohormone abscisic acid also (ABA) contributes to FT activation together with GIGANTEA (GI) to regulate drought escape (DE). Whether CO is a target of ABA and GI actions for the regulation of FT is, however, unknown. Here we report that ABA and its signalling components promote CO recruitment to the COREs, without causing clear effects on the diel pattern of CO protein accumulation. We also found that GI promotes CO recruitment to the COREs region, and that CO recruitment is required for the accumulation of RNAPol II at the TRANSCRIPTION START SITE of FT. Finally, we show that GI and ABA signalling pathways are largely epistatic in the control of flowering time, suggesting their involvement in the same molecular process. Taken together, these observations suggest that varying water deficit conditions modulate CO recruitment and FT expression, thus dictating DE strategies in Arabidopsis.

overall_design: ChIP-seq of transgenic SUC2::CO:CIT Arabidopsis thaliana plants in Col-0 background, with a wild type or mutant allele (aba1-6) at the ABA1 locus, resulting in two genotypes: SUC2::CO:CIT and SUC2::CO:CIT aba1-6. Two input replicates and two immuoprecipitated replicates were produced for each genotype.

first: Alice

last: Robustelli Test

first: Giorgio

last: Perrella

first: Beatrice

last: Landoni

first: Sara

last: Colanero

first: Aldo

last: Sutti

first: Paolo

last: Korwin Krukowski

first: Tianyuan

last: Xu

first: Elisa

last: Vellutini

first: Giulia

last: Castorina

first: Massimo

last: Galbiati

first: Damiano

last: Martignago

first: Eirini

last: Kaiserli

first: Chiara

last: Tonelli