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Epigenomes May 2024Nucleosomes are non-uniformly distributed across eukaryotic genomes, with stretches of 'open' chromatin strongly associated with transcriptionally active promoters and... (Review)
Review
Nucleosomes are non-uniformly distributed across eukaryotic genomes, with stretches of 'open' chromatin strongly associated with transcriptionally active promoters and enhancers. Understanding chromatin accessibility patterns in normal tissue and how they are altered in pathologies can provide critical insights to development and disease. With the advent of high-throughput sequencing, a variety of strategies have been devised to identify open regions across the genome, including DNase-seq, MNase-seq, FAIRE-seq, ATAC-seq, and NicE-seq. However, the broad application of such methods to FFPE (formalin-fixed paraffin-embedded) tissues has been curtailed by the major technical challenges imposed by highly fixed and often damaged genomic material. Here, we review the most common approaches for mapping open chromatin regions, recent optimizations to overcome the challenges of working with FFPE tissue, and a brief overview of a typical data pipeline with analysis considerations.
PubMed: 38804369
DOI: 10.3390/epigenomes8020020 -
Pharmacological Research Aug 2023Small-cell lung cancer (SCLC) is generally considered a 'homogenous' disease, with little documented inter-tumor heterogeneity in treatment guidance or prognosis...
Multi-dimensional characterization of immunological profiles in small cell lung cancer uncovers clinically relevant immune subtypes with distinct prognoses and therapeutic vulnerabilities.
Small-cell lung cancer (SCLC) is generally considered a 'homogenous' disease, with little documented inter-tumor heterogeneity in treatment guidance or prognosis evaluation. The precise identification of clinically relevant molecular subtypes remains incomplete and their translation into clinical practice is limited. In this retrospective cohort study, we comprehensively characterized the immune microenvironment in SCLC by integrating transcriptional and protein profiling of formalin-fixation-and-paraffin-embedded (FFPE) samples from 29 patients. We identified two distinct disease subtypes: immune-enriched (IE-subtype) and immune-deprived (ID-subtype), displaying heterogeneity in immunological, biological, and clinical features. The IE-subtype was characterized by abundant immune infiltrate and elevated levels of interferon-alpha/gamma (IFNα/IFNγ) and inflammatory response, while the ID-subtype featured a complete lack of immune infiltration and a more proliferative phenotype. These two immune subtypes are associated with clinical benefits in SCLC patients treated with adjuvant therapy, with the IE-subtype exhibiting a more favorable response leading to improved survival and reduced disease recurrence risk. Additionally, we identified and validated a personalized prognosticator of immunophenotyping, the CCL5/CXCL9 chemokine index (CCI), using machine learning. The CCI demonstrated superior predictive abilities for prognosis and clinical benefits in SCLC patients, validated in our institute immunohistochemistry cohort and multicenter bulk transcriptomic data cohorts. In conclusion, our study provides a comprehensive and multi-dimensional characterization of the immune architecture of SCLC using clinical FFPE samples and proposes a new immune subtyping conceptual framework enabling risk stratification and the appropriate selection of individualized therapy.
Topics: Humans; Small Cell Lung Carcinoma; Retrospective Studies; Neoplasm Recurrence, Local; Prognosis; Lung Neoplasms; Tumor Microenvironment
PubMed: 37392900
DOI: 10.1016/j.phrs.2023.106844 -
International Journal of Molecular... Jul 2023Salivary myeloperoxidase (MPO) is a key mediator of the oral immune system, acting as an enzyme that utilises HO to generate molecules with high bactericidal activity.... (Review)
Review
Salivary myeloperoxidase (MPO) is a key mediator of the oral immune system, acting as an enzyme that utilises HO to generate molecules with high bactericidal activity. While MPO determination in plasma is quite common, the use of saliva is still rare. Our systematic review was designed to answer the question "Are salivary levels of myeloperoxidase altered in patients with systemic diseases?". Following the inclusion and exclusion criteria, we included twenty-six studies. Altered MPO levels in saliva were most commonly found in patients with cardiovascular and gastrointestinal diseases. Most studies concerned unstimulated whole saliva, and only a few of them stimulated, mainly by chewing paraffin. Enzyme-linked immunosorbent assay (ELISA) was the most common method for determination of MPO concentrations in saliva. Increased salivary MPO levels were more often observed for inflammatory diseases, except patients with inflammatory bowel diseases who were eligible for biologic therapy. In conclusion, MPO could be altered in the saliva of patients with systematic diseases, especially cardiovascular or gastrointestinal diseases. However, further investigations are recommended to validate these outcomes.
Topics: Humans; Enzyme-Linked Immunosorbent Assay; Hydrogen Peroxide; Peroxidase; Saliva
PubMed: 37569455
DOI: 10.3390/ijms241512078 -
Genome Biology Nov 2023Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to...
Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic imbalance, and copy number alterations in Visium data. STmut is tested on fresh-frozen Visium data, formalin-fixed paraffin-embedded (FFPE) Visium data, and tumors with and without matching DNA sequencing data. Copy number is inferred on all conditions, but the chemistry of the FFPE platform does not permit analyses of single nucleotide variants. Taken together, we propose solutions to add the genetic dimension to spatial transcriptomic data and describe the limitations of different datatypes.
Topics: Humans; Formaldehyde; Transcriptome; Paraffin Embedding; Neoplasms; Gene Expression Profiling; High-Throughput Nucleotide Sequencing
PubMed: 38037084
DOI: 10.1186/s13059-023-03121-6 -
Frontiers in Cellular and Infection... 2023Corneal infections are a leading cause of visual impairment and blindness worldwide. Here we applied high-resolution transcriptomic profiling to assess the general and...
PURPOSE
Corneal infections are a leading cause of visual impairment and blindness worldwide. Here we applied high-resolution transcriptomic profiling to assess the general and pathogen-specific molecular and cellular mechanisms during human corneal infection.
METHODS
Clinical diagnoses of herpes simplex virus (HSV) (n=5) and bacterial/fungal (n=5) keratitis were confirmed by histology. Healthy corneas (n=7) and keratoconus (n=4) samples served as controls. Formalin-fixed, paraffin-embedded (FFPE) human corneal specimens were analyzed using the 3' RNA sequencing method Massive Analysis of cDNA Ends (MACE RNA-seq). The cellular host response was investigated using comprehensive bioinformatic deconvolution (xCell and CYBERSORTx) analyses and by integration with published single cell RNA-seq data of the human cornea.
RESULTS
Our analysis identified 216 and 561 genes, that were specifically overexpressed in viral or bacterial/fungal keratitis, respectively, and allowed to distinguish the two etiologies. The virus-specific host response was driven by adaptive immunity and associated molecular signaling pathways, whereas the bacterial/fungal-specific host response mainly involved innate immunity signaling pathways and cell types. We identified several genes and pathways involved in the host response to infectious keratitis, including CXCL9, CXCR3, and MMP9 for viral, and S100A8/A9, MMP9, and the IL17 pathway for bacterial/fungal keratitis.
CONCLUSIONS
High-resolution molecular profiling provides new insights into the human corneal host response to viral and bacterial/fungal infection. Pathogen-specific molecular profiles may provide the foundation for novel diagnostic biomarker and therapeutic approaches that target inflammation-induced damage to corneal host cells with the goal to improve the outcome of infectious keratitis.
Topics: Humans; Matrix Metalloproteinase 9; Keratitis; Cornea; Inflammation; Corneal Ulcer; Eye Infections, Fungal; Eye Infections, Bacterial
PubMed: 38274739
DOI: 10.3389/fcimb.2023.1285676 -
European Review For Medical and... Oct 2023Hand osteoarthritis (OA) is associated with considerable disability, especially in the elderly patient population. Paraffin wax (PW) and prolotherapy (P) are... (Randomized Controlled Trial)
Randomized Controlled Trial
OBJECTIVE
Hand osteoarthritis (OA) is associated with considerable disability, especially in the elderly patient population. Paraffin wax (PW) and prolotherapy (P) are non-pharmacological treatment methods used in this setting. This study aimed to compare the therapeutic efficacy of P and PW in hand osteoarthritis.
PATIENTS AND METHODS
This study was designed as a single-center, randomized-controlled trial conducted at our Physical Medicine and Rehabilitation Clinic between February 2019 and July 2020. Patients with bilateral hand OA were divided into PW and P treatment groups. The PW group was treated 5 days per week for 2 weeks. The P group received an injection of dextrose solution into the ligaments of painful joints once weekly for three weeks. Visual analog scale (VAS), Duruoz Hand Index (DHI) scale, hand dynamometer for grip strength, and pinch meter for lateral pinch were used for baseline and post-treatment follow-up assessments.
RESULTS
Overall, 42 patients were included. The VAS scores significantly decreased in both PW and P groups (p=0.024 and p=0.014). Baseline and third-month post-treatment VAS scores did not significantly differ (p=0.581). The DHI scores improved significantly in both groups (p<0.001 and p<0.001), being higher in the P than in the PW group (p=0.042). Right- and left-hand grip strength increased significantly in PW and P groups (p<0.001, p=0.001; p=0.013, p=0.002, respectively).
CONCLUSIONS
Both treatment methods were effective regarding pain and grip strength; however, P improved the hand functions more significantly.
Topics: Humans; Aged; Paraffin; Hand Strength; Prolotherapy; Osteoarthritis; Hand; Treatment Outcome
PubMed: 37916318
DOI: 10.26355/eurrev_202310_34124 -
Heliyon Oct 2023To address the global alarm of desertification and boost plant progress in arid and desert environments, super-hydrophobic sand has been suggested and fabricated in...
To address the global alarm of desertification and boost plant progress in arid and desert environments, super-hydrophobic sand has been suggested and fabricated in numerous researches. In the present work, sand was hydrophobized by coating with a mixture of paraffin wax and silicone oils. The contact angle (CA) of sand with 4.5 w% silicone oils increased from 143.2° to 154.2° with decreasing the chain size of silicone oil, and the further addition of 13.5 w% of paraffin wax produced a super hydrophobic sand with a CA value up to 160° comparing to 154.2° without added paraffin wax. The Fourier Transform Infrared spectra suggested the development of inter molecular forces between silicone oil and sand as well as between paraffin and silicone oil, the driving force of which was the variation in viscosity of silicone oils. The later was higher in the case of lower molecular weight silicone oil. In particular, analyzing the characteristic bands of -(CH)-in paraffin wax, i.e. the corresponding bands at 720, 730, 1460 and 1470 cm and the two bands at 1020 and 1095 cm of silicone oil revealed that two roles of paraffin were taking place. While paraffin was placed between sand and silicone oil, it coated the sand particles when lower molecular weight silicone oil was used in the first procedures, whereas it coated the higher molecular weight silicone oil in the second procedures. Molecular dynamic calculation has been performed and confirmed the previous reached conclusions and showed that paraffin molecules were encapsulated in a silicone oil shell. The average adsorption energy of paraffin and silicon oil molecules on sand particles were 29.5 and 38.9 kcal mol respectively.
PubMed: 37867885
DOI: 10.1016/j.heliyon.2023.e20874 -
The Journal of Investigative Dermatology Aug 2023Highly effective targeted therapies are available to treat noncommunicable chronic inflammatory skin diseases. In contrast, the exact diagnosis of noncommunicable...
Gene Expression-Based Molecular Test as Diagnostic Aid for the Differential Diagnosis of Psoriasis and Eczema in Formalin-Fixed and Paraffin-Embedded Tissue, Microbiopsies, and Tape Strips.
Highly effective targeted therapies are available to treat noncommunicable chronic inflammatory skin diseases. In contrast, the exact diagnosis of noncommunicable chronic inflammatory skin diseases is complicated by its complex pathogenesis and clinical and histological overlap. Particularly, the differential diagnosis of psoriasis and eczema can be challenging in some cases, and molecular diagnostic tools need to be developed to support a gold standard diagnosis. The aim of this work was to develop a real-time PCR-based molecular classifier to distinguish psoriasis from eczema in formalin-fixed and paraffin-embedded-fixed skin samples and to evaluate the use of minimally invasive microbiopsies and tape strips for molecular diagnosis. In this study, we present a formalin-fixed and paraffin-embedded-based molecular classifier that determines the probability for psoriasis with a sensitivity/specificity of 92%/100%, respectively, and an area under the curve of 0.97, delivering comparable results to our previous published RNAprotect-based molecular classifier. The psoriasis probability, as well as levels of NOS2 expression, positively correlated with the disease hallmarks of psoriasis and negatively with eczema hallmarks. Furthermore, minimally invasive tape strips and microbiopsies were effectively used to differentiate psoriasis from eczema. In summary, the molecular classifier offers broad usage in pathology laboratories as well as outpatient settings and can support the differential diagnosis of noncommunicable chronic inflammatory skin diseases on a molecular level using formalin-fixed and paraffin-embedded tissue, microbiopsies, and tape strips.
Topics: Humans; Formaldehyde; Tissue Fixation; Diagnosis, Differential; Paraffin Embedding; Psoriasis; Eczema; Gene Expression
PubMed: 36889660
DOI: 10.1016/j.jid.2023.02.015 -
Current Issues in Molecular Biology Sep 2023Colorectal cancer (CRC) is a serious public health problem known to have a multifactorial etiology. The association between gut microbiota and CRC has been widely...
Colorectal cancer (CRC) is a serious public health problem known to have a multifactorial etiology. The association between gut microbiota and CRC has been widely studied; however, the link between archaea and CRC has not been sufficiently studied. To investigate the involvement of archaea in colorectal carcinogenesis, we performed a metagenomic analysis of 68 formalin-embedded paraffin fixed tissues from tumoral ( = 33) and healthy mucosa ( = 35) collected from 35 CRC Tunisian patients. We used two DNA extraction methods: Generead DNA FFPE kit (Qiagen, Germantown, MD, USA) and Chelex. We then sequenced the samples using Illumina Miseq. Interestingly, DNA extraction exclusively using Chelex generated enough DNA for sequencing of all samples. After data filtering and processing, we reported the presence of archaeal sequences, which represented 0.33% of all the reads generated. In terms of abundance, we highlighted a depletion in methanogens and an enrichment in in the tumor tissues, while the correlation analysis revealed a significant association between the and the tumor mucosa ( < 0.05). We reported a strong correlation between , , and tumor tissues, and a weak correlation between and healthy adjacent mucosa. Here, we demonstrated the feasibility of archaeome analysis from formol fixed paraffin-embedded (FFPE) tissues using simple protocols ranging from sampling to data analysis, and reported a significant association between and tumor tissues in Tunisian patients with CRC. The importance of our study is that it represents the first metagenomic analysis of Tunisian CRC patients' gut microbiome, which consists of sequencing DNA extracted from paired tumor-adjacent FFPE tissues collected from CRC patients. The detection of archaeal sequences in our samples confirms the feasibility of carrying out an archaeome analysis from FFPE tissues using a simple DNA extraction protocol. Our analysis revealed the enrichment of , especially , in tumor mucosa compared to the normal mucosa in CRC Tunisian patients. Other species were also associated with CRC, including and , which is a methanogenic archaea; both species were found to be correlated with adjacent healthy tissues.
PubMed: 37754261
DOI: 10.3390/cimb45090477 -
International Journal of Molecular... Sep 2023Single-cell sequencing (scRNA-seq) has revolutionized our ability to explore heterogeneity and genetic variations at the single-cell level, opening up new avenues for... (Review)
Review
Single-cell sequencing (scRNA-seq) has revolutionized our ability to explore heterogeneity and genetic variations at the single-cell level, opening up new avenues for understanding disease mechanisms and cell-cell interactions. Single-nucleus RNA-sequencing (snRNA-seq) is emerging as a promising solution to scRNA-seq due to its reduced ionized transcription bias and compatibility with richer samples. This approach will provide an exciting opportunity for in-depth exploration of billions of formalin-fixed paraffin-embedded (FFPE) tissues. Recent advancements in single-cell/nucleus gene expression workflows tailored for FFPE tissues have demonstrated their feasibility and provided crucial guidance for future studies utilizing FFPE specimens. In this review, we provide a broad overview of the nuclear preparation strategies, the latest technologies of snRNA-seq applicable to FFPE samples. Finally, the limitations and potential technical developments of snRNA-seq in FFPE samples are summarized. The development of snRNA-seq technologies for FFPE samples will lay a foundation for transcriptomic studies of valuable samples in clinical medicine and human sample banks.
PubMed: 37762049
DOI: 10.3390/ijms241813744