Log2 FC Research Articles

Comprehensive analysis of exosomal circRNA, lncRNA, and mRNA profiles to identify the potential RNAs involved in the pathogenesis of venous malformation.

Venous malformation (VM) is a kind of congenital vascular anomaly with a high incidence of recurrence, detailed pathogenesis and standard treatment of VM still lack now. Increasing evidence showed exosomal RNA plays a pivotal role in various diseases. However, the underlying mechanism of VM based on the potential differentially exosomal RNAs remains unclear. Comparative high-throughput sequencing with serum exosomes from three VM patients and three healthy donors was used to explore differentially expressed (DE) circRNAs, DE lncRNAs, and DE mRNAs involving the formation of VM. We identified and verified DE circRNAs, DE lncRNAs, and DE mRNAs via qRT-PCR assay. We explored the potential functions of these exosomal DE non-coding RNAs via performing further Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Besides, circRNA/lncRNA-miRNA-mRNA linkages were also constructed to find their potential relationships in VM. A total of 121 circRNAs, 53 lncRNAs, and 42 mRNAs (|log2 FC| ≥ 2.0, FDR <0.05, n=3) were determined to be differentially expressed. QRT-PCR validated that these top-changed DE circRNAs, lncRNAs, and mRNAs had significant expression changes. Functional studies demonstrated that DE circRNAs play a pivotal role in thyroid hormone signaling pathway, DE lncRNAs function as a key regulator in MAPK signaling pathway and DE miRNAs participate in the process of hepatocellular carcinoma mostly. Our study comprehensively depicted exosomal DE non-coding RNAs networks related to the pathogenesis of VM which can provide new insight into, a novel target for treating VM.

Transcriptome Profiling during Sequential Stages of Cryopreservation in Banana (Musa AAA cv Borjahaji) Shoot Meristem.

Cryopreservation approaches have been implemented in gene banks as a strategy to back up plant genetic resource collections that are vegetatively propagated. Different strategies have been employed to effectively cryopreserve plant tissue. There is little information on the cellular processes and molecular adjustments that confer resilience to the multiple stresses imposed during a cryoprotocol. In the present work, the cryobionomics of banana (Musa sp.), a non-model species, was investigated through the transcriptomic approach using RNA-Seq. Proliferating meristems of in vitro explants (Musa AAA cv 'Borjahaji') were cryopreserved using the droplet-vitrification technique. Transcriptome profiling analysis of eight cDNA libraries including the bio-replicates for T0 (stock cultures (control tissue), T1 (high sucrose pre-cultured), T2 (vitrification solution-treated) and T3 (liquid nitrogen-treated) meristem tissues was carried out. The raw reads obtained were mapped with a Musa acuminata reference genome sequence. A total of 70 differentially expressed genes (DEGs) comprising 34 upregulated and 36 downregulated were identified in all three phases as compared to control (T0). Among the significant DEGs (>log FC 2.0), during sequential steps, 79 in T1, 3 in T2 and the 4 in T3 were upregulated and 122 in T1, 5 in T2 and 9 in T3 were downregulated. Gene ontology (GO) enrichment analysis showed that these significant DEGs were involved in the upregulation of biological process (BP-170), cellular component (CC-10) and molecular function (MF-94) and downregulation of biological process (BP-61), cellular component (CC-3) and molecular function (MF-56). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs were involved in the biosynthesis of secondary metabolites, glycolysis/gluconeogenesis, MAPK signaling, EIN 3-lke 1 protein, 3-ketoacy-CoA synthase 6-like, and fatty acid elongation during cryopreservation. For the first time, a comprehensive transcript profiling during four stages of cryopreservation in banana were carried out, which will pave the way for devising an effective cryopreservation protocol.

Abstract P6-11-03: Lipid-rich environment induces epigenetic reprogramming in non-transformed breast epithelial cells enhancing a mammary cell plasticity

Abstract Introduction. The identification of women specifically at risk for estrogen receptor negative breast cancer (ER- BC) and the targeted treatment of this disease are significantly unmet clinical needs. We analyzed the gene expression profiles of epithelial cells from the contralateral unaffected breasts (CUBs) of BC patients and identified a lipid metabolism gene signature enriched in the CUBs of women with ER- BC (PMID: 28263391). Subsequently, we observed that exposure of non-transformed breast epithelial cells to lipids results in significant changes in gene expression and histone posttranslational modifications; and increased flux through multiple metabolic reactions, including those of serine and methionine (PMID: 35508495). Interestingly, the upregulated genes are involved in neural development, axon guidance, neural crest pathways and stemness. Neural genes are highly expressed in Triple Negative Breast Cancers (TNBCs) especially in the C2 cluster. Given that mammary stem/progenitor cells have distinct metabolic properties compared to other mammary cell subsets, we hypothesized that upon lipid exposure, stem-like cells have a survival advantage, and that lipid induces epigenetic reprogramming into neural-like cells which may foster a malignant transformation. Methods. To interrogate potential mechanisms linking lipids and epigenetic reprogramming, we performed CUT&amp;RUN for H3K4me3 and H3K27me3 in non-transformed, estrogen and progesterone receptor negative MCF-10A cells cells exposed to vehicle or octanoic acid (OA) for 24 hrs. Peaks were called using MACS2 and differential peaks identified with DiffBind. Differentially expressed genes affected by OA (PMID: 28263391) were compared with target genes from the CUT&amp;RUN. To determine the contribution in OA exposed cells of serine and methionine metabolism to S-adenosyl methionine (SAM), 13C-glucose tracing was performed. The Aldefluour assay was used to identify stem-like (ALDH+) cells in lipid-exposed MCF-10A cells. To determine if lipid-exposed cells adopt a neural-like phenotype, MCF-10A cells were grown on Poly-D-Lysine/Laminin (PDL/LM) coated plates. Results. A total of 661 differential peaks were identified for H3K4me3 (FDR &amp;lt; 0.05) encompassing TNBC C2 markers (NRTN, CHRM3) and genes involved in neuron differentiation, axonogenesis (NGFR, NGF, FOXA2), neural crest migration (NTRK2, MMP2) and EMT (DLL4, MMP15). Approximately 73% of H3K4me3 OA-associated peaks encompass regulatory regions of genes that experienced a significant increase in gene expression with OA exposure (FDR &amp;lt; 0.01), including NGFR (log2 FC = 11.7), FOXA2 (log2 FC = 11.6), NGF (log2 FC = 8). Twelve H3K27me3 peaks were significantly enriched in vehicle (FDR &amp;lt; 0.05) and associated with increased gene expression in OA, among them were the stem cell markers LGR6 (log2 FC = 1.9) and PLAG1 (log2 FC = 2.8). 13C stable isotope tracing revealed that in presence of OA, glucose contributes to increased fractional abundance of the SAM M+1 isotopologue (adj p = 0.003) indicating that carbons derived from the serine synthesis pathway are used for re-methylation of homocysteine to methionine. Vehicle treated cells growing on PDL/LM plates assumed an epithelial phenotype while OA-treated cells adopted a neurite-like phenotype. Upon OA treatment the percentage of ALDH+ cells increased by a minimum of 10%. Conclusions. The increase of fractional abundance of SAM and the upregulation of neural genes regulated by H3K4me3 as well as the enrichment of ALDH+ cells and the development of a neural-like phenotype in a rich lipid environment, suggests that lipid exposure affects the production of SAM, which results in epigenetic fostered plasticity, leading to reprogramming/selecting cells with a multi-potential embryonic or stem-like state and/or differentiation to a neural/neural crest-like state. Citation Format: Mariana Bustamante Eduardo, Gannon Cottone, Seema Khan, Susan Clare. Lipid-rich environment induces epigenetic reprogramming in non-transformed breast epithelial cells enhancing a mammary cell plasticity [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-11-03.

Abstract PD2-11: Human Cytomegalovirus Reactivation in Immunosuppressive Th2 Tumor Microenvironment Facilitates Brain Metastatic Outgrowth

Abstract Background Brain metastases is a fatal consequence of advanced breast cancer with a poor prognosis. Both tumor intrinsic molecular underpinning of the primary tumor and microenvironmental brain niche factors have been reported to allow invading cancer cells to colonize and outgrow into the brain. A systemic investigation of these tumor intrinsic and microenvironmental factors using same patient paired primary breast and brain metastatic tumor samples are warranted. Methods Nine pairs of primary breast and brain metastatic tumor samples were collected for RNA sequencing. Pairwise differential gene expression analysis and gene set enrichment analysis (GSEA) were conducted. TCGA-BRCA (n=1222) dataset and a combined breast cancer cohort (n=2,765) were used for clinical and immune-infiltration correlation analysis. GSE12276 (n=204) dataset was used for brain-metastasis free survival correlation. Immunohistochemistry staining of HCMV was conducted on a total of 16 primary breast and brain metastatic tumor sections including 2 pairs. Two patient-derived xenograft (PDX) models were used for antiviral treatment and mechanism investigation. Results 371 up-regulated and 2,153 down-regulated genes in the 9 paired brain metastatic tumors vs. breast tumors (P&amp;lt; 0.05; log2 FC&amp;gt;1 or ←1) were identified from the RNAseq data. Reactome Human cytomegalovirus (HCMV) early and late events was the top enriched pathway for the 371 brain metastasis up-regulated genes, and Reactome IL4 and IL5 signaling was the top enriched pathway for the 2,153 primary breast tumor up-regulated genes. Among the 371 brain metastasis up-regulated genes, 287 genes are also up-regulated in primary breast cancer vs. normal breast in the TCGA 1222 cohort (P&amp;lt; 0.05). High expression of 23 out of the 287 genes are significantly associated with shorter distant metastasis-free survival (DMFS) in a combined breast cancer cohort of 2,765 patients (Logrank P&amp;lt; 0.05), and 19 of the 23 genes are associated with poor brain metastasis-free survival (BMFS) in the GEO dataset GSE12276 (n=204)(Logrank P&amp;lt; 0.05). We further identified that elevated expression of 12 out of the 19 genes are consistently associated with Th2 cell activation and NK cell deactivation in the TCGA 1222 cohort, for which the immunosuppressive Th2 cells are defined by secretion of IL4 and IL5 signature cytokines. Immunoreactive HCMV immediate early proteins indicating virus infection were examined in all the 16 patient tumor tissues, and strong positive signals were seen in both the paired breast tumor and brain metastatic specimens. Preventive treatment of anti-HCMV drug ganciclovir by suppressing viral DNA replication inhibited tumor colonization in the mouse brain in the two HCMV-positive PDX models. Conclusions Our systemic analysis of paired primary breast and brain metastatic tumor tissues identified a causal relationship between HCMV infection and reactivation, immunosuppressive Th2 cell activation and NK cell deactivation, and brain metastatic outgrowth. Since HCMV reactivation frequently induce encephalopathy during chemotherapy or radiation therapy, anti-HCMV agents may represent an effective strategy in preventing and controlling brain metastases. Citation Format: Xin Wang, Akshjot Puri, Amna Irfan, Kun Han, Wei Qian, Liliana Guzman, Roberto Rosato, Hong Zhao, Jenny Chang, Stephen Wong. Human Cytomegalovirus Reactivation in Immunosuppressive Th2 Tumor Microenvironment Facilitates Brain Metastatic Outgrowth [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD2-11.

Abstract PD10-05: PD10-05 Neoadjuvant tamoxifen therapy reactivates tumor suppressor protein p53 in luminal breast cancer patients: Results from a window-of-opportunity clinical trial

Abstract Therapeutic effect of tamoxifen (Tam) against ER+ breast cancer (BC) is known to be mediated by its binding to estrogen receptor-alpha (ERά/ESR1) and inhibiting estrogen signaling leading to altered gene expression. Besides this canonical mode of function, our pre-clinical studies had revealed a novel mechanism wherein ESR1 directly binds wild type p53 (wt TP53) resulting in repression of its tumor suppressor functions, and Tam blocks this inactivation of TP53. Although patients with Luminal Tumors expressing wt TP53 are known to be more responsive to tamoxifen therapy, the underlying mechanism in tumors has remained unknown. To test the hypothesis that abrogation of the ESR1-mediated functional inactivation of TP53 is one of the major mechanisms that underlie the early effects of Tam therapy, we conducted a window of opportunity clinical trial in newly diagnosed luminal breast cancer patients undergoing surgical therapy. Methods: 59 women with ER+ invasive BC were randomized to 20mg Tam daily for 28 days prior to surgery or standard of care (SOC). TP53 status was confirmed by massively parallel sequencing. ER+ wt TP53 tumors were included in the study. IHC was performed on FFPE tissue from tumors to compare expression of ESR1 and TP53 along with their selected downstream targets. ESR1–TP53 interaction in situ was determined by Proximity Ligation Assay (PLA).17β-estradiol and Tam metabolites were measured in the plasma, tumor, and surrounding normal tissue using LC-MS/MS. Global transcriptome analysis in tumors was conducted by RNA-seq. Proteome expression in resected tumors was analyzed by reverse phase protein array (RPPA) with 216 proteins. Findings: Importantly, IHC on tumor tissues showed that the levels of ESR1 and TP53 were not altered in response to Tam therapy, whereas ESR1–TP53 interaction was considerably disrupted by Tam (in situ PLA data). Differential gene expression (DGE) analysis using DESeq2 R package followed by GSEA pathway analysis showed that 307 genes were differentially expressed (p&amp;lt; 0.05) (log FC&amp;gt;1.5) in tumors from Tam-treated versus untreated patients in response to Tam therapy. Pathways representing TP53 signaling, stem cells, and low-grade luminal breast cancer were upregulated in the Tam treated group while those representing adipogenesis, invasive breast cancer, estradiol response, ras signaling, and E2F targets were downregulated. “Master Regulators” identified by iRegulon included several p53 targets. Integration of RNA-seq and RPPA data revealed that DEGs fall into three categories: (i) regulated by TP53, (ii) regulated by ESR1, and (iii) regulated by both TP53 and ESR1. Together, the data demonstrated that in addition to its conventional effects mediated by its binding to ESR1 and inhibiting estrogen signaling leading to altered gene expression, Tam disrupted the ESR1–TP53 interaction leading to functional reactivation of TP53 and reprogramming of gene expression. Conclusions: Our data 1) support ESR1–TP53 crosstalk in tumors as a novel mechanism underlying endocrine therapy response of luminal BC patients, and 2) highlight the importance of factoring TP53 into therapeutic strategies for ER+ BC patients, and 3) have implications in stratifying ER+ BC patients to those who will or will not be responsive to Tam therapy. Citation Format: Gokul M. Das, Swati A. Kulkarni, Chetan Oturkar, Spencer Rosario, Stephen B. Edge, Jianmin Wang, Wendy M. Swetzig, Alan D. Hutson, Benny Kaipparettu, Adrienne Groman, Araba Adjei, Andrew K. Goey, Carl D. Morrison, Shicha Kumar. PD10-05 Neoadjuvant tamoxifen therapy reactivates tumor suppressor protein p53 in luminal breast cancer patients: Results from a window-of-opportunity clinical trial [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD10-05.

Bile metabolites as diagnostic biomarkers for perihilar cholangiocarcinoma

It is difficult to directly obtain pathological diagnosis of perihilar cholangiocarcinoma (pCCA). Analysis of bile in the pCCA microenvironment, based on metabolomics and statistical methods, can help in clinical diagnosis. Clinical information, bile samples, blood liver function, blood CA199, CEA, and other indicators were collected from 33 patients with pCCA and 16 patients with gallstones. Bile samples were analyzed using untargeted metabolomics methods. A combination of multivariate and univariate analyses were used to screen for potential differential metabolites Through Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and differential metabolite remodeling, we explored changes in the pCCA pathway and potential therapeutic targets. There were significant differences in patient blood TBIL, ALT, AST, TBA, CA19-9, and CEA indices (p < 0.05, |log2(fc)| ≥ 1) between two groups. A significant correlation was found between these different indicators by Spearman's analysis. The clinical parameters were correlated with mass-to-charge ratios of 305 (Positive Ion Mode, POS) and 246 (Negative Ion Mode, NEG) in the metabolic group (|r| ≥ 0.7, P ≤ 10−7). The result of this study indicated that bile untargeted metabolomics combined with statistical analysis techniques may be used for diagnose and treatment of pCCA.

Identification of protein candidates in spermatozoa of water buffalo (Bubalus bubalis) bulls helps in predicting their fertility status.

The water buffalo (Bubalus bubalis) is an indispensable part of the Indian dairy sector and in several instances, the farmers incur economic losses due to failed pregnancy after artificial insemination (AI). One of the key factors for the failure of conception is the use of semen from the bulls of low fertilizing potential and hence, it becomes important to predict the fertility status before performing AI. In this study, the global proteomic profile of high fertile (HF) and low fertile (LF) buffalo bull spermatozoa was established using a high-throughput LC-MS/MS technique. A total of 1,385 proteins (≥1 high-quality PSM/s, ≥1 unique peptides, p < 0.05, FDR < 0.01) were identified out of which, 1,002 were common between both the HF and LF groups while 288 and 95 proteins were unique to HF and LF groups respectively. We observed 211 and 342 proteins were significantly high (log Fc ≥ 2) and low abundant (log Fc ≤ 0.5) in HF spermatozoa (p < 0.05). Gene ontology analysis revealed that the fertility associated high abundant proteins in HF were involved in spermatogenesis, sperm motility, acrosome integrity, zona pellucida binding and other associated sperm functions. Besides this, the low abundant proteins in HF were involved in glycolysis, fatty acid degradation and inflammation. Furthermore, fertility related differentially abundant proteins (DAPs) on sperm viz., AKAP3, Sp17, and DLD were validated through Western blotting and immunocytochemistry which was in coherence with the LC-MS/MS data. The DAPs identified in this study may be used as potential protein candidates for predicting fertility in buffaloes. Our findings provide an opportunity in mitigating the economic losses that farmers incur due to male infertility.

Identification and Functional Characterization of WRKY, PHD and MYB Three Salt Stress Responsive Gene Families in Mungbean (Vigna radiata L.).

WRKY-, PHD-, and MYB-like proteins are three important types of transcription factors in mungbeans, and play an important role in development and stress resistance. The genes' structures and characteristics were clearly reported and were shown to contain the conservative WRKYGQK heptapeptide sequence, Cys4-His-cys3 zinc binding motif, and HTH (helix) tryptophan cluster W structure, respectively. Knowledge on the response of these genes to salt stress is largely unknown. To address this issue, 83 VrWRKYs, 47 VrPHDs, and 149 VrMYBs were identified by using comparative genomics, transcriptomics, and molecular biology methods in mungbeans. An intraspecific synteny analysis revealed that the three gene families had strong co-linearity and an interspecies synteny analysis showed that mungbean and Arabidopsis were relatively close in genetic relationship. Moreover, 20, 10, and 20 genes showed significantly different expression levels after 15 days of salt treatment (p < 0.05; Log2 FC > 0.5), respectively. Additionally, in the qRT-PCR analysis, VrPHD14 had varying degrees of response to NaCl and PEG treatments after 12 h. VrWRKY49 was upregulated by ABA treatment, especially in the beginning (within 24 h). VrMYB96 was significantly upregulated in the early stages of ABA, NaCl, and PEG stress treatments (during the first 4 h). VrWRKY38 was significantly upregulated by ABA and NaCl treatments, but downregulated by PEG treatment. We also constructed a gene network centered on the seven DEGs under NaCl treatment; the results showed that VrWRKY38 was in the center of the PPI network and most of the homologous Arabidopsis genes of the interacted genes were reported to have response to biological stress. Candidate genes identified in this study provide abundant gene resources for the study of salt tolerance in mungbeans.

P104 Exploring the transcriptomic miRNA signatures of Egyptian Inflammatory Bowel Disease patients

Abstract Background Inflammatory Bowel Disease (IBD) is a chronic autoimmune gastrointestinal disease, sub-classified into Crohn’s disease (CD) and ulcerative colitis (UC). The two subclasses are characterized by a relapsing-remitting course with an increasingly high incidence and prevalence worldwide. Molecular mechanisms guarding the pathogenesis of these diseases remain, to the present day, ambiguous to researchers. MicroRNAs are 22 nucleotides long small noncoding RNAs that have been recently described as essential participants in immune cell development and the immune response to pathogens. During the past decade, genetic and epigenetic studies in IBD have been labeled as essential; since endoscopic assessment and biopsies provide limited data concerning early disease activity, factors for relapse, and response to treatment. To the best of our knowledge, IBD research has never addressed miRNA profiles in Egyptian CD and UC patients as compared to unaffected controls. Methods Therefore, this study aims to profile miRNAs in Egyptian patients suffering from UC and CD, using RNA-seq of total RNA extracted from colonoscopically obtained tissue pinch biopsies. Results The sequencing results showed that 30 miRNAs were uniquely expressed in tissue biopsies obtained from the CD patients, as compared to only 14 uniquely expressed in UC patients. Further web-based functional enrichment analysis showed that the miRNAs- in both disease groups- are mainly involved in six interlinked molecular pathways; including the JAK/STAT, WNT, PI3K/AKT, FOXO, MAPK, and NF-κB signaling pathways. One of the most interesting findings of the current study is the fact that the downregulation of the miR-204-5p in UC patients (log2 FC= 5.05)-as compared to CD patients- may be caused by the sponging effect of the MALAT1 long non-coding RNA (lncRNA); affecting related signaling pathways such as the Wnt/β-catenin signaling. This suggests an essential interplay between miRNAs and lncRNAs in shaping the molecular pathogenesis of UC vs. CD. Conclusion The results of the current study revealed explicit-previously undetermined- differences in the miRNA profiles of patients suffering from UC and CD. Such results are expected to impact the understanding of the difference in the molecular pathogenesis of IBD subtypes affecting patients’ response to treatment.

Nafion by-product 2 disturbs lipid homeostasis in zebrafish embryo

As a novel polyfluoroalkyl substance, Nafion by-product 2 (Nafion BP2) has been detected widely in environmental matrix as well as human samples. However, its toxicity remains poorly recognized. Here, we investigated the toxic effects of Nafion BP2 by use of zebrafish model and highlighted its toxicity on lipid homeostasis. Large sized-lipid droplets (LDs) have been revealed to gather in pericardium and anterior yolk sac region of zebrafish larvae by Oil Red O staining after a 120 h Nafion BP2 exposure. Meanwhile, the total cholesterol (TC) concentrations were significantly disrupted. Lipidomic analysis uncovered a dramatical alterations on lipid profiles. Significant reductions were observed for a set of lipids including phosphatidylinositol (PI), phosphatidylcholine (PC), phosphatidylethanolamine (PE), sphingolipid (SM) and triglyceride (TG) in zebrafish. Transcriptome analyses further confirmed genes involved in LDs biosynthesis, lipid transportation and lipid metabolism, were significantly disrupted. Especially for APOA4 and CIDEC genes, fold changes (Log2 FC) of gene expression level by up to 17.8 and 3.5, respectively, were observed. Together, these findings demonstrated the disturbance of Nafion BP2 on lipid homeostasis of zebrafish and provided an unprecedented insight into the health risk assessments of emerging fluorochemicals.

Differential Urinary Proteomic Analysis of High-Risk Cervical Intraepithelial Neoplasia.

Human papillomavirus (HPV)-associated lesions and malignancies exhibit alterations in the composition and functionality of the extracellular matrix (ECM) that represent the complex molecular pathways present between infection and disease. A total of 20 urine samples were used, including from 10 patients with cervical intraepithelial neoplasia grade 3 (CIN3) and 10 healthy controls to perform the label-free quantitative analysis using the nano-HPLC and ESI-MS ion trap mass analyzer and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) fast screening. Among 476 identified/quantified proteins, 48 were significantly changed (log2-fold change ≥1.0 or ≤-1.0, -log10 (bbinominal, p-value ≥ 1.3), of which were 40 proteins (down-regulated) and 8 proteins (up-regulated) in CIN3, in comparison to healthy controls. The biological function and key pathway enrichment of the gene set using gen set enrichment analysis (GSEA) were analyzed. The ECM-receptor interaction pathway (NES = -1.64, p = 0.026) was down-regulated by 13 proteins (HSPG2, COL6A1, COL6A3, SPP1, THBS1, TNC, DAG1, FN1, COMP, GP6, VTN, SDC1, and CD44; log2 FC range from -0.03 to -1.48) for the CIN3 group in the KEGG database. The MALDI-TOF/MS screening showed the difference of protein profiles between the control and CIN3 groups, i.e., using the scatter plot with a well-separated shape, as well as effectively distinguishing both groups (control and CIN3) using genetic algorithms (GA) with cross-validation (51.56%) and recognition capability (95.0%). Decreased levels of ECM-receptor interaction proteins may cause disturbances in the interactions of cells with the ECM and play an important role in the development and progression of cervical cancer.

Capture, Release, and Identification of Newly Synthesized Proteins for Improved Profiling of Functional Translatomes

New protein synthesis is regulated both at the level of mRNA transcription and translation. RNA-Seq is effective at measuring levels of mRNA expression, but techniques to monitor mRNA translation are much more limited. Previously, we reported results from O-propargyl-puromycin (OPP) labeling of proteins undergoing active translation in a 2-h time frame, followed by biotinylation using click chemistry, affinity purification, and on-bead digestion to identify nascent proteins by mass spectrometry (OPP-ID). As with any on-bead digestion protocol, the problem of nonspecific binders complicated the rigorous categorization of nascent proteins by OPP-ID. Here, we incorporate a chemically cleavable linker, Dde biotin-azide, into the protocol (OPP-IDCL) to provide specific release of modified proteins from the streptavidin beads. Following capture, the Dde moiety is readily cleaved with 2% hydrazine, releasing nascent polypeptides bearing OPP plus a residual C3H8N4 tag. When results are compared side by side with the original OPP-ID method, change to a cleavable linker led to a dramatic reduction in the number of background proteins detected in controls and a concomitant increase in the number of proteins that could be characterized as newly synthesized. We evaluated the method’s ability to detect nascent proteins at various submilligram protein input levels and showed that, when starting with only 100 μg of protein, ∼1500 nascent proteins could be identified with low background. Upon treatment of K562 cells with MLN128, a potent inhibitor of the mammalian target of rapamycin, prior to OPP treatment, we identified 1915 nascent proteins, the majority of which were downregulated upon inhibitor treatment. Repressed proteins with log2 FC <-1 revealed a complex network of functionally interacting proteins, with the largest cluster associated with translational initiation. Overall, incorporation of the Dde biotin-azide cleavable linker into our protocol has increased the depth and accuracy of profiling of nascent protein networks.

CD163 as a Potential Biomarker in Colorectal Cancer for Tumor Microenvironment and Cancer Prognosis: A Swedish Study from Tissue Microarrays to Big Data Analyses.

(1) Background: CD163, a specific macrophage receptor, affects the progression of malignant tumors. Unfortunately, the regulation and expression of CD163 are poorly understood. In this study, we determined the expressions of CD163 in TMA samples from CRC patients and combined them with patient data from several Swedish hospitals. (2) Methods: The expressions of CD163 in tissue samples from CRC patients were examined. After combining 472 CRC patients' gene expression and 438 CRC patients' clinical data with the TCGA database, 964 cases from the GEO database, and experimental expression data from 1247 Swedish CRC patients, we selected four genes (PCNA, LOX, BCL2, and CD163) and analyzed the tumor-infiltrating immune cells (TICs) and CRC prognosis. (3) Results: Based on histopathological TMA analysis, CD163 was strongly expressed in the stroma of both normal and cancer tissues, and the expressions in normal and cancer cells varied from negative to strong. The results from public databases show decreased expression of CD163 in cancer tissue compared to normal mucosa (|log FC| &gt; 1 and FDR &lt; 0.01), and it is a negative prognostic factor for CRC patients (p-value &lt; 0.05). Through tumor microenvironment (TME) analysis, we found a potential influence of CD163 on immune cell infiltration. Furthermore, the enrichment analysis indicated the possible interaction with other proteins and biological pathways. (4) Conclusions: CD163 is expressed differently in CRC tissue and is a negative prognostic factor. Its expression is associated with the TME and tumor purity of CRC. Considering all results, CD163 has the potential to be a predictive biomarker in the investigation of CRC.

Tear Proteome Revealed Association of S100A Family Proteins and Mesothelin with Thrombosis in Elderly Patients with Retinal Vein Occlusion.

Tear samples collected from patients with central retinal vein occlusion (CRVO; n = 28) and healthy volunteers (n = 29) were analyzed using a proteomic label-free absolute quantitative approach. A large proportion (458 proteins with a frequency > 0.6) of tear proteomes was found to be shared between the study groups. Comparative proteomic analysis revealed 29 proteins (p < 0.05) significantly differed between CRVO patients and the control group. Among them, S100A6 (log (2) FC = 1.11, p < 0.001), S100A8 (log (2) FC = 2.45, p < 0.001), S100A9 (log2 (FC) = 2.08, p < 0.001), and mesothelin ((log2 (FC) = 0.82, p < 0.001) were the most abundantly represented upregulated proteins, and β2-microglobulin was the most downregulated protein (log2 (FC) = −2.13, p < 0.001). The selected up- and downregulated proteins were gathered to customize a map of CRVO-related critical protein interactions with quantitative properties. The customized map (FDR < 0.01) revealed inflammation, impairment of retinal hemostasis, and immune response as the main set of processes associated with CRVO ischemic condition. The semantic analysis displayed the prevalence of core biological processes covering dysregulation of mitochondrial organization and utilization of improperly or topologically incorrect folded proteins as a consequence of oxidative stress, and escalating of the ischemic condition caused by the local retinal hemostasis dysregulation. The most significantly different proteins (S100A6, S100A8, S100A9, MSLN, and β2-microglobulin) were applied for the ROC analysis, and their AUC varied from 0.772 to 0.952, suggesting probable association with the CRVO.

Predictors of response of rituximab in rheumatoid arthritis by weighted gene co-expression network analysis.

The purpose of this study was to identify a biomarker that can predict the efficacy of rituximab (RTX) in the treatment of rheumatoid arthritis (RA) patients. Utilized weighted gene co-expression network analysis (WGCNA) and LASSO regression analysis of whole blood transcriptome data (GSE15316 and GSE37107) related to RTX treatment for RA from the GEO database, the critical modules, and key genes related to the efficacy of RTX treatment for RA were found. The biological functions were further explored through enrichment analysis. The area under the ROC curve (AUC) was validated using the GSE54629 dataset. WGCNA screened 71 genes for a dark turquoise module that were correlated with the efficacy of RTX treatment for RA (r = 0.42, P < 0.05). Through the calculation of gene significance (GS) and module membership (MM), 12 important genes were identified; in addition, 21 important genes were screened by the LASSO regression model; two key genes were obtained from the intersection between the important genes. Then, BANK1 (AUC = 0.704, P < 0.05) was identified as a potential biomarker to predict the efficacy of RTX treatment for RA by ROC curve evaluation of the treatment and validation groups. BANK1 gene expression was significantly decreased after RTX treatment, and a statistically significant difference was found (log FC = - 2.08, P < 0.05). Immune cell infiltration analysis revealed that the infiltration of CD4 + T cell memory subset was increased in the group with high BANK1 expression, and a statistically significant difference was found (P < 0.05). BANK1 can be used as a potential biomarker to predict the response of RTX treatment in RA patients. Key Points • Identifying the hub genes BANK1 as a potential biomarker to predict the response of RTX treatment in RA patients and confirming it in validation data. • Using the WGCNA approach and LASSO analyses to identify the BANK1 in a data set consisting of two GEO data merged and assessing the correlations between BANK1 and immune infiltration by CIBERSORT algorithm.

Cancer cell intrinsic TIM-3 induces glioblastoma progression

Glioblastoma (GBM) is identified to share common signal pathways between glioma and immune cells. Here, we find that Tcell immunoglobulin domain and mucin domain protein 3 (TIM-3) is one of the most common co-inhibitory immune checkpoints in GBM shared by tumor and non-tumor cells. Glioma cell-intrinsic TIM-3 is involved in not only regulating malignant behaviors of glioma cells but also inducing macrophage migration and transition to anti-inflammatory/pro-tumorigenic phenotype by a TIM-3/interleukin 6 (IL6) signal. In mechanism, as one of the major regulators of IL6, TIM-3 regulates its expression through activating NF-κB. Blocking this feedback loop by Tocilizumab, an IL6R inhibitor, inhibited the above effects and repressed the tumorigenicity of GBM invivo. Our work identifies glioma cell-intrinsic functions of TIM-3/IL6 signal mediating the crosstalk feedback loop between glioma cells and tumor-associated macrophages (TAMs). Blocking this feedback loop may provide a novel therapeutic strategy for GBM.

Co-Expression Network Analysis of Soybean Transcriptome Identify Hub Genes Under Saline-Alkaline and Water Deficit Stress.

Soybean is an important oilseed crop that its development and production are affected by environmental stresses (such as saline-alkaline and water deficit). This experiment was performed with the aim of identifying candidate genes in saline-alkaline stress and water-deficit stress conditions using transcriptome analysis and to investigate the expression of these genes under water deficit stress conditions using RTqPCR. In this experiment, soybean transcriptome data under saline-alkaline and water-deficit stress were downloaded from the NCBI website, and then the co-expression modules were determined for them and the gene network was plotted for each module, and finally, the hub genes were identified. To compare the expression of genes in saline-alkaline and water deficit conditions, soybean plants were subjected to water deficit stress and their gene expression was determined using RTqPCR. The filtered (Log FC above +2 and below -2) genes of soybean were grouped under saline-alkaline stress in 15 modules and under water-deficit stress in 2 different modules. Within each module, the interaction of genes was identified using the gene network, then three genes of ann11, cyp450 and zfp selected as hub genes. These hub genes are highly co-expression with other network genes, which not only display differential expression but also differential co-expression. The results of RT-PCR indicated that cyp450 gene expression was not significantly different from the control, while ann11 gene expression significantly increased under water deficit stress, but zfp gene expression decreased significantly under water deficit stress. We identified three genes, ann11, cyp450 and zfp, as hub genes. According to our results, ann11 gene had a significant increase in expression under water deficit stress, which can indicate the importance of this gene under drought conditions. Therefore, according to the results of this experiment as well as other researchers, we introduce this gene as a key gene in water deficit tolerance and recommend its use in genetic engineering to increase the tolerance of other plants.

Noninvasive nasopharyngeal proteomics of COVID-19 patient identify abnormalities related to complement and coagulation cascade and mucosal immune system.

Serum or plasma have been the primary focus of proteomics studies for COVID-19 to identity biomarkers and potential drug targets. The nasal mucosal environment which consists of lipids, mucosal immune cells, and nasal proteome, has been largely neglected but later revealed to have critical role combating SARS-CoV-2 infection. We present a bottom-up proteomics investigation of the host response to SARS-CoV-2 infection in the nasopharyngeal environment, featuring a noninvasive approach using proteins in nasopharyngeal swabs collected from groups of 76 SARS-CoV-2 positive and 76 negative patients. Results showed that 31 significantly down-regulated and 6 up-regulated proteins were identified (p < 0.05, log2 FC > 1.3) in SARS-CoV-2 positive patient samples as compared to the negatives; these proteins carry potential value as markers for the early detection of COVID-19, disease monitoring, as well as be drug targets. The down-regulation of coagulation factor 5 indicates a thrombotic abnormality in COVID-19 patients and the decreased IgG4 suggests an abnormal immune response at the point of entry in human nasopharyngeal environment, which is in consistent with KEGG and GO pathway analysis. Our study also demonstrated that mass spectrometry proteomics analysis of nasopharyngeal swabs can be used as a powerful early approach to evaluate host response to SARS-CoV-2 viral infection.

MicroRNA sequence and function analysis in peri-implantitis and periodontitis: An animal study.

To compare miRNA expression levels and predict relevant target genes and signaling pathways in peri-implantitis and periodontitis. There are many differences between periodontitis and peri-implantitis. An understanding of the similarities and differences in the transcriptional patterns of these diseases, as well as the molecular mechanisms, is beneficial for the development of management strategies. Rat models of periodontitis (PD, n= 6) and peri-implantitis (PI, n= 5) were established by ligation. Implantation without ligation (PIC, n= 5) and normal rats (PDC, n= 6) were used as controls. Micro-CT was used to confirm the successful establishment of the model. Gingiva was harvested for miRNA transcriptome sequencing, and the results were confirmed by qRT-PCR. miRNA target genes were predicted with miRTarBase. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. Sixty-nine miRNAs were differentially expressed in PI vs. PD, 105 were differentially expressed in PI vs. PIC, and 70 were differentially expressed in PD vs. PDC (log2 FC ≥1 and padj <0.05). The upregulated genes in all three comparisons were mostly involved in the biological process response to stimulus, whereas most of the downregulated genes were involved in nervous system development (p< .01). The upregulated genes in PI vs. PD and PI vs. PIC were involved in Toll-like receptor signaling and RIG-I-like signaling. The upregulated genes in PI vs. PD were involved in T- and B-cell receptor signaling, apoptosis, and osteoclast differentiation. Focal adhesion was downregulated in all three comparisons, and adherens junction was downregulated in PI vs. PD and PD vs. PDC (p< .1). This study showed differences in the miRNA expression profiles between peri-implantitis and periodontitis and annotated the possible target genes and molecular mechanisms; this study could lay a foundation for the development of management strategies.

496 Differential chromatin accessibility and gene expression suggest Th17 polarization in activated and skin-homing T cells

We generated 1,090 ATAC-seq and 1,057 T-cell RNA-seq libraries from 153 subjects, derived from 8 flow-sorted T-cell subsets (defined by CD4/CD8, CLA+/ CLA-, and 0/24h CD3/CD28 stimulation). Effects of activation and skin-homing were analyzed by DESeq2. After peak calling, 78,234 consensus peaks were present in ≥ 30 ATAC-seq libraries. A Wald test examining simple main effects identified 9,072, 3,934, and 21,174 consensus peaks as differentially accessible regions (DAR; FDR < 0.05, |log2 FC|≥ 0.585) in CD4 vs CD8, CLA+ vs CLA-, and resting vs.