Similar Gene Expression Patterns Research Articles

Short chain fatty acids prime colorectal cancer cells to activate antitumor immunity.

Colorectal cancer (CRC) is a leading cause of death worldwide and its growth can either be promoted or inhibited by the metabolic activities of intestinal microbiota. Short chain fatty acids (SCFAs) are microbial metabolites with potent immunoregulatory properties yet there is a poor understanding of how they directly regulate immune modulating pathways within the CRC cells. We used engineered CRC cell lines, primary organoid cultures, orthotopic in vivo models, and patient CRC samples to investigate how SCFA treatment of CRC cells regulates their ability to activate CD8+ T cells. CRC cells treated with SCFAs induced much greater activation of CD8+ T cells than untreated CRC cells. CRCs exhibiting microsatellite instability (MSI) due to inactivation of DNA mismatch repair were much more sensitive to SCFAs and induced much greater CD8+ T cell activation than chromosomally instable (CIN) CRCs with intact DNA repair, indicating a subtype-dependent response to SCFAs. This was due to SCFA-induced DNA damage that triggered upregulation of chemokine, MHCI, and antigen processing or presenting genes. This response was further potentiated by a positive feedback loop between the stimulated CRC cells and activated CD8+ T cells in the tumor microenvironment. The initiating mechanism in the CRCs was inhibition of histone deacetylation by the SCFAs that triggered genetic instability and led to an overall upregulation of genes associated with SCFA signaling and chromatin regulation. Similar gene expression patterns were found in human MSI CRC samples and in orthotopically grown MSI CRCs independent of the amount of SCFA producing bacteria in the intestine. MSI CRCs are widely known to be more immunogenic than CIN CRCs and have a much better prognosis. Our findings indicate that a greater sensitivity to microbially produced SCFAs contributes to the successful activation of CD8+ T cells by MSI CRCs, thereby identifying a mechanism that could be therapeutically targeted to improve antitumor immunity in CIN CRCs.

Cultured Renal Proximal Tubular Epithelial Cells Resemble a Stressed/Damaged Kidney While Supporting BK Virus Infection.

BK virus (BKV; human polyomavirus 1) infections are asymptomatic in most individuals, and the virus persists throughout life without harm. However, BKV is a threat to transplant patients and those with immunosuppressive disorders. Under these circumstances, the virus can replicate robustly in proximal tubule epithelial cells (PT). Cultured renal proximal tubule epithelial cells (RPTE) are permissive to BKV and have been used extensively to characterize different aspects of BKV infection. Recently, lines of hTERT-immortalized RPTE have become available, and preliminary studies indicate they support BKV infection as well. Our results indicate that BKV infection leads to a similar response in primary and immortalized RPTE. In addition, we examined the patterns of global gene expression of primary and immortalized RPTE and compared them with uncultured PT freshly dissociated from human kidney. As expected, PT isolated from the healthy kidney express a number of differentiation-specific genes that are associated with kidney function. However, the expression of most of these genes is absent or repressed in cultured RPTE. Rather, cultured RPTE exhibit a gene expression profile indicative of a stressed or injured kidney. Inoculation of cultured RPTE with BKV results in the suppression of many genes associated with kidney stress. In summary, this study demonstrated similar global gene expression patterns and responses to BKV infection between primary and immortalized RPTE. Moreover, results from bulk transcriptome sequencing (RNA-seq) and SCT experiments revealed distinct transcriptomic signatures representing cell injury and stress in primary RPTE in contrast to the uncultured, freshly dissociated PT from human kidney. IMPORTANCE Cultured primary human cells provide powerful tools for the study of viral infectious cycles and host virus interactions. In the case of BKV-associated nephropathy, viral replication occurs primarily in the proximal tubule epithelia in the kidney. Consequently, cultured primary and immortalized renal proximal tubule epithelial cells (RPTE) are widely used to study BKV infection. In this work, using bulk and single-cell transcriptomics, we found that primary and immortalized RPTE responded similarly to BKV infection. However, both uninfected primary and immortalized RPTE have gene expression profiles that are markedly different from healthy proximal tubule epithelia isolated directly from human kidney without culture. Cultured RPTE are in a gene expression state indicative of an injured or stressed kidney. These results raise the possibility that BKV replicates preferentially in injured or stressed kidney epithelial cells during nephropathy.

The interferon-rich skin environment regulates Langerhans cell ADAM17 to promote photosensitivity in lupus

Abstract Photosensitivity, a sensitivity to ultraviolet radiation, is a hallmark symptom of systemic and cutaneous lupus erythematosus (SLE and CLE). We have previously shown that photosensitivity in SLE models is caused by reduced function of Langerhans cells (LC) disintegrin and metalloprotease 17 (ADAM17), a sheddase that normally limits UVR-induced skin inflammation by activating epidermal growth factor receptor (EGFR) ligands. We also showed that LC ADAM17 activity is reduced in murine models and human SLE and that this LC ADAM17 dysfunction contributed to photosensitivity. The aim of this study is to understand why lupus LCs are dysfunctional and how type I interferon (IFN-I) in lupus skin contributes to LC ADAM17 dysregulation. In this study we utilize multiple photosensitive SLE models and skin obtained from healthy human volunteers. LC ADAM17 activity and expression was measured by flow cytometry. We found IFN-I signatures in non-lesional skin of MRL/lpr and B6.Sle1yaa photosensitive SLE models in addition to that of CLE patients, suggesting the similarities in gene expression patterns between human and mouse lupus skin. We also showed that IFN-I inhibits murine and human LC ADAM17 activity, and anti-IFNAR1 in SLE models restores LC ADAM17 function and reduces photosensitivity in EGFR− and LC ADAM17-dependent manners. Together our findings suggest a model whereby the IFN-I-rich microenvironment in non-lesional lupus skin inhibits UVR-induced ADAM17 activity, leading to photosensitivity. These results suggest that the beneficial effects of the recently FDA-approved anifrolumab on human lupus skin may be attributable to effects on improving LC ADAM17 activity.

Abstract LB283: ARC2-001 inhibits cancer-associated fibroblast-dependent cancer stem cell populations by disrupting cancer-stroma interactions

Abstract ARC2-001, a natural product and FDA-approved anti-leukemic drug, has shown anticancer effects in hematological malignancies. This study investigates the inhibitory effect of ARC2-001 on cancer-associated fibroblasts (CAFs). CAFs promote cancer progression and directly stimulate cancer cell proliferation. In addition, CAFs act as therapeutic barriers to prevent the penetration of anticancer drugs and immune cells in the treatment of solid tumors such as colorectal cancer. In our previous study, we found a master transcription factor PRRX1 of stromal fibroblasts for myofibroblastic lineage progression in the cancer microenvironment. After deleting the expression of PRRX1 in various CAFs using the CRISPR-CAS9-sgRNA system, we confirmed changes in gene expression patterns and performed in silico screening to derive drugs showing similar gene expression patterns. These drugs were investigated through a gel contraction assay and indirect co-culture/direct 3D spheroid co-culture systems using various cancer cells and CAFs. Among them, ARC2-001 treatment not only significantly reduced the ECM remodeling ability of CAFs but also showed strong anticancer effects in the co-culture systems. In addition, the response to ARC2-001 was much more sensitive in CAFs than in cancer cells: the IC50 values in cancer cells were30-50nM, and the IC50 values in CAFs were 10-20nM. We produced HCT116 (colon cancer cell)-Colon CAFs spheroids, treated them with ARC2-001at low concentrations that could only affect CAFs, and analyzed RNA transcriptome changes by RNA-SEQ. We confirmed that HCT116 cells underwent EMT as well as observed an increase in the cancer stem cell (CSC) population by CAFs through co-culture of HCT116-CAFs spheroids. Interestingly, treatment with a concentration of ARC2-001 sufficient to inhibit only CAFs had no significant effect on HCT116-only spheroids, and little change occurred in gene expression patterns, but in HCT116 cells in spheroid co-culture with CAFs, the aforementioned changes (EMT and CSC population increase) all collapsed. This indicates that ARC2-001 interferes with the interactions between cancer cells and CAFs. ARC2-001 damages the cancer stem cell population of HCT116 through CAFs inhibition, indicating that the CSC subpopulation of HCT116 cells is dependent on CAFs. We further hypothesized that co-administration of ARC2-001 and commonly used anticancer drugs could be a very effective strategy, considering the ineffectiveness of commonly used anticancer drugs on the CSC subpopulation. Thus, we transplanted colon CAFs together with HCT116 cells into NOD/SCID mice and then administered 5FU, an existing anticancer drug, together with ARC2-001. For the combined treatment in the in vivo experiment, we treated ARC2-001 and 5FU at half of the commonly used concentrations. Surprisingly, we observed that both tumor growth and cancer metastasis were suppressed in the combination treatment group. This indicates that ARC2-001 dramatically increases the effectiveness of existing anticancer drugs and can be used as an additional combination therapy for colorectal cancer chemotherapy. Citation Format: Keun-Woo Lee, So-Young Yeo, InSuk Sohn, Seok-Hyung Kim. ARC2-001 inhibits cancer-associated fibroblast-dependent cancer stem cell populations by disrupting cancer-stroma interactions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB283.

Dynamic changes in transcriptome during orthodontic tooth movement.

The objective of this study was to determine global changes in gene expression with next generation sequencing (NGS) in order to assess the biological effects of orthodontic tooth movement (OTM) on alveolar bone in a rat model. Thirty-five Wistar rats (age 14 weeks) were used in the study. The OTM was performed using closed coil Nickel-Titanium spring to apply a mesial force on maxillary first molars of 8-10g. Three hours, 1, 3, 7 and 14 days after the placement of the appliance, rats were killed at each time point respectively. The alveolar bone, around left maxillary first molar, were excised on compression side. The samples were immediately frozen in liquid nitrogen for subsequent RNA extraction. Total RNA samples were prepared for mRNA sequencing using the Illumina kit. RNA-Seq reads were aligned to the rat genomes using the STAR Aligner and bioinformatic analysis was performed. A total of 18 192 genes were determined. Day 1 has the highest number of differentially expressed genes (DEGs) observed with more upregulated than downregulated genes. A total of 2719 DEGs were identified to use as input for the algorithm. Six distinct clusters of temporal patterns were observed representing proteins that were differentially regulated indicating different expression kinetics. Principal component analysis (PCA) showed distinct clustering by time points and days 3, 7 and 14 share similar gene expression pattern. Distinct gene expression pattern was observed at different time points studied. Hypoxia, inflammation and bone remodelling pathways are major mechanisms behind OTM.

Abstract 3124: Identification of sub-clonal loss of heterozygosity (LOH) in glioblastomas analyzed with spatial transcriptomics

Abstract We propose a method to leverage spatial transcriptomics and bioinformatic analysis to identify sub-clonal loss of heterozygosity that could otherwise be missed by standard bulk sequencing in glioblastoma tumors. Glioblastomas are highly invasive and aggressive brain tumors with a low five-year survival rate of less than 10%. Current treatment strategies are not sufficient for long term disease outcome, and innovative approaches to analyze glioblastoma are imperative for future improved options. Many factors contribute to difficulty of treatment, though one critical consideration is the diffuse nature and known intratumoral heterogeneity of this cancer. It is important to determine LOH heterogeneity, as this genomic alteration is associated with copy number variation and specific classifications of gliomas. Loss of heterozygosity is an irreversible deletion of DNA that is a common alteration in cancer. Application of spatial transcriptomics can increase our understanding of genomic complexity across a tissue, and unsupervised graph clustering can computationally separate spatial regions with similar gene expression patterns. Our method investigates spatial clusters individually at known heterozygous SNP sites to identify evidence for LOH with Bayesian inference and a hidden Markov model. Our analysis centers on the balance of reference (A) and non-reference (B) spatial transcriptomics read counts at SNPs of interest. B allele frequency is the number of reads aligned to the alternative allele divided by the total number of reads counted at the SNP. At a normal two-copy state at a heterozygous site, B allele frequency is ideally 50 percent. LOH can be identified as this value deviates toward 0 or 100, and copy number alterations impact this frequency. Our method utilizes Bayes factor values, or likelihood ratios between two models, using allele counts to provide support for either LOH or a heterozygous event. For our analysis, spatial transcriptomics BAMs are processed with a graph clustering algorithm and split into cluster-specific BAMs. We calculate allele count coverage for each cluster at pre-selected heterozygous SNP positions identified through germline exome sequencing. Bayes factor values are then calculated at each SNP, resulting in evidence for LOH or a heterozygous event. Chromosomal regions are segmented by a hidden Markov approach. Cumulative metrics for each segment are evaluated to determine a “state” label of heterozygous, LOH, or undefined. We tested our method on three WHO grade 4 IDH wild-type EGFRvIII positive fresh frozen glioblastoma tissue samples. Sub-clonal heterogeneity was identified in two samples and confirmed by bulk exome sequencing, bulk RNA sequencing, and analysis of initial clinical reports. Citation Format: Michelle G. Webb, Frances Chow, Carmel McCullough, Bohan Zhang, Kyle Hurth, John Carpten, Gabriel Zada, David W. Craig. Identification of sub-clonal loss of heterozygosity (LOH) in glioblastomas analyzed with spatial transcriptomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3124.

Comparative Transcriptomic Analysis Reveals the Functionally Segmented Intestine in Tunicate Ascidian.

The vertebrate intestinal system consists of separate segments that remarkably differ in morphology and function. However, the origin of intestinal segmentation remains unclear. In this study, we investigated the segmentation of the intestine in a tunicate ascidian species, Ciona savignyi, by performing RNA sequencing. The gene expression profiles showed that the whole intestine was separated into three segments. Digestion, ion transport and signal transduction, and immune-related pathway genes were enriched in the proximal, middle, and distal parts of the intestine, respectively, implying that digestion, absorption, and immune function appear to be regional specializations in the ascidian intestine. We further performed a multi-species comparison analysis and found that the Ciona intestine showed a similar gene expression pattern to vertebrates, indicating tunicates and vertebrates might share the conserved intestinal functions. Intriguingly, vertebrate pancreatic homologous genes were expressed in the digestive segment of the Ciona intestine, suggesting that the proximal intestine might play the part of pancreatic functions in C. savignyi. Our results demonstrate that the tunicate intestine can be functionally separated into three distinct segments, which are comparable to the corresponding regions of the vertebrate intestinal system, offering insights into the functional evolution of the digestive system in chordates.

Sex differences in skeletal muscle-aging trajectory: same processes, but with a different ranking

Sex differences in muscle aging are poorly understood, but could be crucial for the optimization of sarcopenia-related interventions. To gain insight into potential sex differences in muscle aging, we recruited young (23 ± 2 years, 13 males and 13 females) and old (80 ± 3.5 years, 28 males and 26 females) participants. Males and females in both groups were highly matched, and vastus lateralis muscle parameters of old versus young participants were compared for each sex separately, focusing on gene expression. The overall gene expression profiles separated the sexes, but similar gene expression patterns separated old from young participants in males and females. Genes were indeed regulated in the same direction in both sexes during aging; however, the magnitude of differential expression was sex specific. In males, oxidative phosphorylation was the top-ranked differentially expressed process, and in females, this was cell growth mediated by AKT signaling. Findings from RNA-seq data were studied in greater detail using alternative approaches. In addition, we confirmed our data using publicly available data from three independent human studies. In conclusion, top-ranked pathways differ between males and females, but were present and altered in the same direction in both sexes. We conclude that the same processes are associated with skeletal muscle aging in males and females, but the differential expression of those processes in old vs. young participants is sex specific.

Transcriptionally imprinted glycomic signatures of acute myeloid leukemia

BackgroundAcute myeloid leukemia (AML) is a genetically and phenotypically heterogeneous disease that has been suffering from stagnant survival curves for decades. In the endeavor toward improved diagnosis and treatment, cellular glycosylation has emerged as an interesting focus area in AML. While mechanistic insights are still limited, aberrant glycosylation may affect intracellular signaling pathways of AML blasts, their interactions within the microenvironment, and even promote chemoresistance. Here, we performed a meta-omics study to portray the glycomic landscape of AML, thereby screening for potential subtypes and responsible glyco-regulatory networks.ResultsInitially, by integrating comprehensive N-, O-, and glycosphingolipid (GSL)-glycomics of AML cell lines with transcriptomics from public databases, we were able to pinpoint specific glycosyltransferases (GSTs) and upstream transcription factors (TFs) associated with glycan phenotypes. Intriguingly, subtypes M5 and M6, as classified by the French-American-British (FAB) system, emerged with distinct glycomic features such as high (sialyl) Lewisx/a ((s)Lex/a) and high sialylation, respectively. Exploration of transcriptomics datasets of primary AML cells further substantiated and expanded our findings from cell lines as we observed similar gene expression patterns and regulatory networks that were identified to be involved in shaping AML glycan signatures.ConclusionsTaken together, our data suggest transcriptionally imprinted glycomic signatures of AML, reflecting their differentiation status and FAB classification. This study expands our insights into the emerging field of AML glycosylation and paves the way for studies of FAB class-associated glycan repertoires of AML blasts and their functional implications.

Rapid direct conversion of bovine non-adipogenic fibroblasts into adipocyte-like cells by a small-molecule cocktail.

Introduction: The molecular regulation mechanism of fat deposition in bovine and its improvement on beef quality are important research directions in the livestock industry. The research of molecular mechanisms that govern the regulation and differentiation of adipocytes may conduct to understand the mechanism of obesity, lipid disorders, and fat deposition. In the recent decade, small-molecule compounds have been widely used in reprogramming and transdifferentiation fields, which can promote the induction efficiency, replace exogenous genes, or even induce cell fate conversion alone. Furthermore, small-molecule compound induction is expected to be a novel approach to generate new cell types from somatic cells in vitro and in vivo. Methods: In this study, we established rapid chemically induced platform for transdifferentiation of bovine ear fibroblasts into adipocyte-like cells using a small-molecule cocktail (Repsox, VPA, TTNPB). The chemically induced adipocytes (CiADCs) were characterized by lipid staining, qRT-PCR and WB. Bovine natural adipocytes were used as positive control, and the expression of adipocyte-related marker genes in CiADCs were analyzed. Moreover, RNA-Seq explore the mechanism of RVB in the regulation of Bovine adipocyte transdifferentiation. Results: In this study, the chemically induced adipocytes (CiADCs) could be identified as early as day 6. The CiADCs appeared to be circular and rich of lipid droplets. The adipocyte-specific genes of LPL, PPARγ, IGF1, GPD1, C/EBPδ, ADIPOQ, PCK2, FAS, C/EBPβ, PPARGC1A, C/EBPα, and CFD were detected to be significantly upregulated in both CiADCs and natural adipocytes. Western blot analysis also confirmed the increase C/EBPα and PPARγ protein level in induced adipocytes (CiADCs-6d) treated with RVB. In addition, we also found that the signaling pathways (PPAR signaling pathway, PI3K-Akt signaling pathway, p53 signaling pathway, MAPK signaling pathway, and ECM-receptor interaction) regulated by the DEGs played a vital role in adipogenesis. Discussion: In the present study, a combination of small-molecule compounds RVB was used to transdifferentiate bovine ear fibroblasts into the chemically-induced adipocyte cells (CiADCs) that have a large number of lipid droplets. Importantly, the small-molecule cocktail significantly shortened the reprogramming turnaround time. The morphology of CiADCs is close to the "ring type" of natural differentiated adipocytes on sixth day. And, the CiADCs showed similar adipocyte-specific gene expression patterns to natural adipocytes. Furthermore, RVB increased protein expression of PPARγ and C/EBPα in the chemically-induced adipocytes (CiADCs-6d). Our findings reveal that the signaling pathways of C/EBPα and PPARγ play pivotal roles in this transdifferentiation process. In addition, we also found that the signaling pathways (PPAR signaling pathway, PI3K-Akt signaling pathway, p53 signaling pathway, MAPK signaling pathway, and ECM-receptor interaction) regulated by the DEGs played a vital role in adipogenesis. In general, this study provides valuable evidence to deepen our understanding of the molecular mechanism of small molecule cocktails in regulating adipogenesis.

Spatial Transcriptomic Profiling of Cutaneous Melanoma Progression

Background and Objective:In 2022, an estimated 99,780 new melanomas will be diagnosed in the United States. As incidence rates continue to rise, identification of biomarkers for disease progression is urgently needed to prevent overdiagnosis and provide therapeutic targets. The purpose of this project was to determine if spatial transcriptomics can be used to identify transcript changes during melanoma progression.
 Methods:For this study and after specimen quality control (via DV200 values), four archival formalin fixed paraffin embedded (FFPE) human melanoma specimens were processed using the Visium Spatial Gene Expression platform. In Loupe Browser v6.0.0. (10x Genomics Inc.), K-means clustering was used as an unbiased approach in addition to manual selection of areas of melanoma adjacent to and distant from (i.e. nonadjacent) the epidermis to determine regions of interest for identification of differentially expressed genes (DEGs)
 Results:Expression of PAEP was significantly increased in a micrometastasis (~7.2 fold; Log2 scale) versus the primary melanoma in one specimen. Other DEGs also distinguished the micrometastasis (SLC16A3, CCND1, SCML4, and CSAG3) from this primary melanoma (S100A14, TRIM29, PTPRZ1, and BCAN). In the other specimens, a similar pattern of differential gene expression was seen between areas of melanoma adjacent to and nonadjacent to the epidermis. In addition, K-means clustering identified a region of differential gene expression suggestive of an inflammatory cell infiltrate next to the PAEP-enriched micrometastasis.
 Conclusions and Potential Impact:This study demonstrates the feasibility of using spatial transcriptomics to investigate transcriptional changes during melanoma progression. Increased PAEP transcripts and the immunosuppressive functions of PAEP suggest PAEP may be an important mediator of melanoma progression. The current study suggests increased PAEP transcript levels are associated with inflammatory cell infiltrates. Understanding mechanistic links between increased PAEP and inflammation during melanoma progression could provide prognostic and therapeutic insights and thus, improved care for melanoma patients.

Comparative transcriptome analyses of immune responses to LPS in peripheral blood mononuclear cells from the giant panda, human, mouse, and monkey.

Gram-negative bacteria are major pathogens that can cause illnesses in giant pandas. Lipopolysaccharides (LPS), components of Gram-negative bacteria, can activate immune responses in mammals (i.e., humans and mice) through recognition by toll-like receptors (TLRs). However, the giant pandas' immune response to LPS stimulation and the differences between the giant panda and other mammals are not fully known. In this study, we administrated peripheral blood mononuclear cells (PBMCs) from giant pandas, humans, C57BL/6 mice, and rhesus monkeys by LPS treatment at 6h followed by RNA sequencing (RNA-seq), respectively, with control of non-stimulation. KEGG analyses of differentially expressed genes (DEGs) pathways indicated that LPS could activate the classic signaling pathway of NF-κB in PBMCs from those four tested species. Thus, similar to the other three species, NF-κB is an LPS-responsive regulator of innate immune responses in giant pandas. Furthermore, the expression patterns of adapter genes, inflammatory cytokine genes, chemokines, interferon genes, cytokine genes related to cell growth and development, costimulatory molecules, Th1/Th2 cytokine genes, Th17 cytokine genes, Th9, and Th22 cytokine genes were compared among giant pandas and three other species. Our data indicated that in addition to the similar expression patterns of certain genes among giant pandas and other species, the unique expression pattern response to LPS in giant pandas was also discovered. Furthermore, Th9, Th17, and Th22 cells might be involved in the response to LPS in giant pandas at this tested time point. This study reveals that LPS-induced immune responses have different sensitivities and response timelines in giant pandas compared with other mammals. This study facilitates further understanding of the role of the TLR signaling pathway and the immune system in giant pandas, which might be helpful for disease prevention and protection.

Comparative transcriptomic evidence of physiological changes and potential relationships in vertebrates under different dormancy states.

Dormancy represents a fascinating adaptive strategy for organisms to survive in unforgiving environments. After a period of dormancy, organisms often exhibit exceptional resilience. This period is typically divided into hibernation and aestivation based on seasonal patterns. However, the mechanisms by which organisms adapt to their environments during dormancy, as well as the potential relationships between different states of dormancy, deserve further exploration. Here, we selected Perccottus glenii and Protopterus annectens as the primary subjects to study hibernation and aestivation, respectively. Based on histological and transcriptomic analysis of multiple organs, we discovered that dormancy involved a coordinated functional response across organs. Enrichment analyses revealed noteworthy disparities between the two dormant species in their responses to extreme temperatures. Notably, similarities in gene expression patterns pertaining to energy metabolism, neural activity, and biosynthesis were noted during hibernation, suggesting a potential correlation between hibernation and aestivation. To further explore the relationship between these two phenomena, we analyzed other dormancy-capable species using data from publicly available databases. This comparative analysis revealed that most orthologous genes involved in metabolism, cell proliferation, and neural function exhibited consistent expression patterns during dormancy, indicating that the observed similarity between hibernation and aestivation may be attributable to convergent evolution. In conclusion, this study enhances our comprehension of the dormancy phenomenon and offers new insights into the molecular mechanisms underpinning vertebrate dormancy.

Microtomographic, histomorphometric, and molecular features show a normal alveolar bone healing process in iNOS-deficient mice along a compensatory upregulation of eNOS and nNOS isoforms.

Inducible nitric oxide synthase (iNOS) is one of the enzymes responsible for the synthesis of nitric oxide (NO), which is an important signaling molecule with effects on blood vessels, leukocytes, and bone cells. However, the role of iNOS in alveolar bone healing remains unclear. This study investigated the role of iNOS in alveolar bone healing after tooth extraction in mice. C57Bl/6 wild type (WT) and iNOS genetically deficient (iNOS-KO) mice were subjected to upper incision tooth extraction, and alveolar bone healing was evaluated by micro-computed tomography (μCT) and histological/histomorphometric, birefringence, and molecular methods. The expression of iNOS had very low control conditions, whereas a significant increase is observed in healing sites of WT mice, where iNOS mRNA levels peak at 7d time point, followed by a relative decrease at 14d and 21d. Regarding bone healing, both WT and iNOS-KO groups showed the usual phases characterized by the presence of clots, granulation tissue development along the inflammatory cell infiltration, angiogenesis, proliferation of fibroblasts and extracellular matrix synthesis, bone neoformation, and remodeling. The overall micro-computed tomography and histomorphometric and birefringence analyses showed similar bone healing readouts when WT and iNOS-KO strains are compared. Likewise, Real-Time PCR array analysis shows an overall similar gene expression pattern (including bone formation, bone resorption, and inflammatory and immunological markers) in healing sites of WT and iNOS-KO mice. Moreover, molecular analysis shows that nNOS and eNOS were significantly upregulated in the iNOS-KO group, suggesting that other NOS isoforms could compensate the absence of iNOS. The absence of iNOS does not result in a significant modulation of bone healing readouts in iNOS-KO mice. The upregulation of nNOS and eNOS may compensate iNOS absence, explaining the similar bone healing outcome in WT and iNOS-KO strains.

Comparative <i>in vitro</i> activity of various antibiotic against planktonic and biofilm and the gene expression profile in <i>Pseudomonas aeruginosa</i>

P. aeruginosa is an opportunistic pathogen that is commonly found in nosocomial infections. The purpose of this study was to investigate the effects of seven antibiotics on P. aeruginosa planktonic growth, biofilm formation, and the expression of virulence factors. These antibiotics included Ciprofloxacin (CP), Amikacin (AMK), Vancomycin (VAN), Tetracycline (TET), Gentamicin (GEN), Erythromycin (Ery), and Clindamycin (CLI). Antibiotic susceptibility testing, Minimum Bactericidal Concentration (MBC), Minimum Inhibitory Concentration (MIC), growth curve, time-kill curve, biofilm inhibition and reduction assay, and RT-qPCR were used to assess the effects of these antibiotics on P. aeruginosa planktonic and biofilm. The clear zones of inhibition against P. aeruginosa for the CP, AMK, VAN, TET, GEN, Ery, and CLI were 26 mm, 20 mm, 21 mm, 22 mm, 20 mm, 25 mm and 23 mm, respectively. The MIC values for CP, AMK, VAN, TET, GEN, Ery and CLI against P. aeruginosa ranged from 0.25 to 1 µg/mL while the MBC values ranged from 1 and 0.5 to 2 µg/mL respectively. The growth, total viable counts (TVCs), bacterial adhesion and biofilm formation of P. aeruginosa were reduced after exposure to all the tested antibiotics in a dose-dependent manner. The RT-qPCR analysis showed that all the tested antibiotics share a similar overall pattern of gene expression, with a trend toward reduced expression of the virulence genes of interest (lasR, lasI, fleN, fleQ and fleR, oprB and oprC) in P. aeruginosa. The results indicate that all of the tested antibiotics possess antimicrobial and anti-biofilm activities, and that they may be multiple inhibitors and moderators of P. aeruginosa virulence via a variety of molecular targets. This deduction requires to be investigated in vivo.

Novel Algorithm for Diagnosis of Arrhythmogenic Cardiomyopathy and Dilated Cardiomyopathy: Key Gene Expression Profiling Using Machine Learning.

It is difficult to distinguish between arrhythmogenic cardiomyopathy (ACM) and dilated cardiomyopathy (DCM) because of their similar clinical manifestations. This study aimed to develop a novel diagnostic algorithm for distinguishing ACM from DCM. Two public datasets containing human ACM and DCM myocardial samples were used. Consensus clustering, non-negative matrix factorization, and principal component analysis were applied. Weighted gene co-expression network analysis and machine learning methods, including random forest and least absolute shrinkage and selection operator, were used to identify candidate genes. Receiver operating characteristic curves and nomograms were performed to estimate diagnostic efficacy, and Spearman's correlation analysis was used to assess the correlation between candidate genes and cardiac function indices. ACM and DCM showed highly similar gene expression patterns in the clustering analyses. Hub gene modules associated with cardiomyopathy were obtained using WGCNA. Thirteen candidate genes were selected using machine learning algorithms, and their combination showed a high diagnostic value (Area under the ROC curve = 0.86) for determining ACM from DCM. In addition, TATA-box binding protein associated factor 15 showed a negative correlation with cardiac index (R = -0.54, p = 0.0054) and left ventricular ejection fraction (R = -0.48, p = 0.0015). Our study revealed an effective diagnostic model with key gene signatures, which indicates a potential tool to differentiate between ACM and DCM in clinical practice. In addition, we identified several genes that are highly related to cardiac function, which may contribute to our understanding of ACM and DCM.

Transcriptomic Landscape and Functional Characterization of Human Induced Pluripotent Stem Cell-Derived Limbal Epithelial Progenitor Cells

Limbal stem cell deficiency (LSCD) is a complex, multifactorial disease affecting limbal epithelial progenitor cells (LEPC), which are essential for maintaining corneal stability and transparency. Human induced pluripotent stem cell-derived (hiPSC-) LEPC are a promising cell source for the treatment of LSCD. However, their similarity to native tissue-derived (T-) LEPC and their functional characterization has not been studied in detail. Here, we show that hiPSC-LEPC and T-LEPC have rather similar gene expression patterns, colony-forming ability, wound-healing capacity, and melanosome uptake. In addition, hiPSC-LEPC exhibited lower immunogenicity and reduced the proliferation of peripheral blood mononuclear cells compared with T-LEPC. Similarly, the hiPSC-LEPC secretome reduced the proliferation of vascular endothelial cells more than the T-LEPC secretome. Moreover, hiPSC-LEPC successfully repopulated decellularized human corneolimbal (DHC/L) scaffolds with multilayered epithelium, while basal deposition of fibrillary material was observed. These findings suggest that hiPSC-LEPC exhibited functional properties close to native LEPC and that hiPSC-LEPC-DHC/L scaffolds might be feasible for transplantation in patients suffering from LSCD in the future. Although hiPSC-LEPC-based stem cell therapy is promising, the current study also revealed new challenges, such as abnormal extracellular matrix deposition, that need to be overcome before hiPSC-LEPC-based stem cell therapies are viable.

Endothelial cell malfunction in unruptured intracranial aneurysm lesions revealed using a 3D-casted mold.

Intracranial aneurysms (IA) are major causes of devastating subarachnoid hemorrhages. They are characterized by a chronic inflammatory process in the intracranial arterial walls triggered and modified by hemodynamic force loading. Because IA lesion morphology is complex, the blood flow conditions loaded on endothelial cells in each portion of the lesion in situ vary greatly. We created a 3D-casted mold of the human unruptured IA lesion and cultured endothelial cells on this model; it was then perfused with culture media to model physiological flow conditions. Gene expression profiles of endothelial cells in each part of the IA lesion were then analyzed. Comprehensive gene expression profile analysis revealed similar gene expression patterns in endothelial cells from each part of the IA lesion but gene ontology analysis revealed endothelial cell malfunction within the IA lesion. Histopathological examination, electron microscopy, and immunohistochemical analysis indicated that endothelial cells within IA lesions are damaged and dysfunctional. Thus, our findings reveal endothelial cell malfunction in IA lesions and provided new insights into IA pathogenesis.

Single-Cell Transcriptome Analysis Reveals Stem Cell-like Subsets in the Progression of Waldenström's Macroglobulinemia

Waldenström's macroglobulinemia (WM) is an uncommon lymphoproliferative disorder characterized by monoclonal immunoglobulin M protein production and bone marrow infiltration by lymphoplasmacytoid cells. It remains an incurable disease. IgM monoclonal gammopathy of undetermined significance (MGUS) is the premalignant condition and is associated with the risk of developing WM. MYD88L265P is a recurrent mutation found in more than 90% of WM patients, and this genetic event is detectable in at least half of IgM MGUS patients. However, the precise cellular landscape and the mechanisms of progression from IgM MGUS to WM remain unclear. Single-cell RNA sequencing (scRNA-seq) provides us a powerful approach to explore tumor heterogeneity and identify rare malignant cells. Anti-CD38 monoclonal antibodies have been introduced into the therapeutic arsenal for plasma cell diseases. Therefore, we analyzed CD38+ immune microenvironment together with B cells and plasma cells to illustrate the first cellular landscape of IgM MGUS and WM in single cell resolution. We isolated bone marrow CD19+ and CD19-CD38+ cells from WM patients(n=3), IgM MGUS patients(n=3) and healthy donors(n=3) and employed the 10x Genomics platform to perform single-cell transcriptomic sequencing. After quality control, our dataset contained a total of 73024 cells. We used UMAP to visualize the cell superclusters and identified clusters including B cells, plasma cells, CD3+CD20+ (CD19+) cells, T cells and NK cells based on the expression of canonical lineage markers and cluster-specific markers. We found that healthy donors had the highest percentage of B cells (72.7% in healthy donors, 19.0% in IgM MGUS patients, 60.5% in WM patients; p<0.001) and that IgM MGUS and WM patients had more NK and T cells than healthy controls (0.06% and 17.7%, respectively, in healthy donors; 24.1% and 20.5% in IgM MGUS patients; 8.5% and 24.0% in WM patients; p<0.001). We also noticed that CD3+CD20+(CD19+) cells were present in both IgM MGUS and WM patients. First, we investigated the cell clusters correlated with WM pathology including B cells and plasma cells. We compared the B-cell gene expression profiles after removing the early B cells. Compared with those of IgM MGUS patients, mature B cells of WM patients showed upregulation of PIM1, DUSP22, HES1, NEAT1, RGS1, RGS16, and GADD45B. Light chain restriction and higher CNV levels were found in B cells of WM patients. SCENIC analysis showed that FOS, FOSB, EGR1 and JUNB were downregulated in B cells from WM and IgM MGUS patients. REL, a proto-oncogene promoting the survival and proliferation of B lymphocytes, was upregulated in B cells of WM patients, and IRF8 and ELF1 were upregulated in B cells of IgM MGUS patients. Nevertheless, plasma cells of WM patients, IgM MGUS patients and healthy donors were colocalized in one cluster, which might indicate their similar gene expression patterns. Next, we further determined the characteristics of B-cell subpopulation with aberrant T-cell antigen expression. Trajectory analysis revealed that CD3+CD20+(CD19+) cells and pro-B cells were located at the same end of the branched structure and were then directed toward mature B cell and plasma cell fates, respectively (Figure. 1A). This inferred developmental trajectory suggested that CD3+CD20+(CD19+) cells may be tumor stem cell-like subset. Using flow cytometry, we validated that CD3 was expressed in a fraction of CD19+ cells (mean: 3.69%, range: 0.28%-15.10%) of bone marrow samples from 8 WM patients. In addition, targeted gene sequencing was performed on CD3+CD19+ and CD3-CD19+ cells from 6 WM patients. MYD88 were proved to be the most frequently mutated gene in this cell subset. And we inferred that MYD88 mutation might be the early events in tumorigenesis by VAF analysis (Figure. 1B). Additional subclonal hits, such as CXCR4 and MAP2K1 mutations, could be acquired during tumor progression. In conclusion, our study provides comprehensive insights into mechanisms of progression from IgM MGUS to WM. We identified the rare CD19+ cell subpopulation with T-cell antigen expression in WM patients. It will be interesting to explore novel therapeutic strategies targeting rare potential cancer-initiating cells in future. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

A Transcriptional Classifier Identifies Pediatric T-Cell Acute Lymphoblastic Leukemias at High Risk for End of Induction Minimal Residual Disease

Upfront risk stratification with incorporation of risk-adapted therapy continues to be a pressing need for pediatric T-ALL. However, robust molecular or cytogenetic biomarkers are currently lacking. Instead, initial response to therapy, measured as end of induction minimal residual disease (MRD), is the only prognostic factor used in most cooperative groups. This inability to stratify patients at diagnosis limits the early introduction of rationally-designed therapies that may better achieve long-term remissions. To address this, we asked whether gene expression profiling performed at diagnosis may identify patients at high risk for future MRD+, enabling earlier therapeutic intervention. To test this, we used a training dataset of RNA-seq data from diagnostic samples from patients enrolled on the Children's Oncology Group (COG) AALL0434 trial. Using leave-one-out cross-validation, we defined a risk score (RS) for MRD+ based on the expression of 119 genes. This RS indicates the probability of being MRD+ for a given gene expression pattern. Gene ontology analysis of the genes in our model demonstrated enrichment for genes involved in signal transduction, lymphocyte differentiation and activation, and cell death. Using this model, we found that early T-cell precursor (ETP) samples (n=19), of which 79% were MRD+, had uniformly high RS, with an average of 78 (SD=17). In contrast, non-ETP samples (n=146), of which 26% were MRD+, had an average RS of 26 (SD=21), with MRD+ patients having a significantly higher RS relative to MRD- patients (p<0.0001). When we analyzed the expression pattern of the 119 genes, we found that ETP samples had a relatively uniform pattern, consistent with their high rate of MRD+. Non-ETP samples with RS<50 had a pattern that was inverted relative to the ETP samples, while those with RS>50 closely mirrored the ETP samples. Using a RS cutoff of 50 to identify patients at high risk for MRD+ gives a 97% specificity in this training cohort. Given the similar gene expression pattern between ETPs and RS>50 non-ETPs, we hypothesized that this RS classification may relate to differences in developmental stage. We found that ETP and RS>50 non-ETP samples were significantly enriched for the LMO2/LYL1, HOXA, and TLX3 subgroups of T-ALL, with the subgroup distribution in the RS>50 non-ETP samples differing significantly from the RS<50 non-ETP samples (p=0.001). Furthermore, we found that the RS>50 non-ETP samples, relative to the RS<50 samples, were enriched for lacking a TCRb rearrangement (p<0.0001), indicative of an earlier developmental stage. To determine the generalizability of our gene expression classifier, we applied our fixed model to an independent validation cohort of 826 non-ETP samples from the same COG AALL0434 trial. Here, we again found that RS>50 non-ETP samples (n=130) were significantly enriched for MRD+ relative to RS<50 samples (n=696; p<0.0001). Next, we applied our classifier model to a pilot cohort of samples from patients enrolled on COG AALL1231, which used dexamethasone rather than prednisone as the induction steroid. In this group of 31 diagnostic non-ETP samples, RS>50 samples were similarly enriched for MRD+ (p=0.05), suggesting that this classifier may retain its prognostic value across multiple induction steroids. Finally, to facilitate clinical implementation of this prognostic tool, we transitioned to the NanoString nCounter platform, a more rapid and cost-effective means of performing targeted gene expression analysis. Using 364 samples from COG AALL0434 for which we had corresponding RNA-seq data, we assessed the performance of our custom NanoString assay and found a strong correlation between the RS calculated using each of the two platforms (concordance correlation coefficient = 0.98), suggesting that the prognostic value of the classifier is retained on the NanoString assay. In conclusion, while ETP samples are commonly MRD+ and are readily identifiable by their unique cell surface immunophenotype, non-ETP samples lack a surface immunophenotype that correlates with MRD+. Here, we present a targeted gene expression classifier, validated on a clinically-tractable platform, that identifies at diagnosis a subset of non-ETP T-ALLs with a gene expression pattern that resembles that of ETP T-ALLs and that are at high risk for future MRD+.