Cancer stemness, which covers the stem cell-like molecular traits of cancer cells, is essential for tumor development, progression and relapse. Both transcriptional and epigenetic aberrations are essentially connected with cancer stemness. The engagement of bromodomain (BrD) proteins-a family of epigenetic factors-has been presented in the pathogenesis of several tumor types, although their association with cancer stemness remains largely unknown. Here, we harnessed TCGA and GEO databases and used several bioinformatic tools (ie, Oncomine, PrognoScan, GEPIA2, TIMER2.0, TISIDB, GSEA, R2 platform) to characterize the association between the BrD family members' expression and cancer stemness in solid tumors. Our results demonstrate that significant upregulation of ATAD2 and SMARCA4, and downregulation of SMARCA2 is consistently associated with enriched cancer stem cell-like phenotype, respectively. Especially, higher-grade tumors that display stem cell-like properties overexpress ATAD2. In contrast to most BrD members, the gene expression profiles of ATAD2 HIGH expressing tumors are strongly enriched with known markers of stem cells and with specific targets for c-Myc transcription factor.For other BrD proteins, the association with cancer de-differentiation status is rather tumor-specific. Our results demonstrate for the first time the relation between distinct BrD family proteins and cancer stemness across 27 solid tumor types. Specifically, our approach allowed us to discover a robust association of high ATAD2 expression with cancer stemness and reveal its' versatility in tumors.

Cells and immune cells in the extracellular matrix: Depending on the tumor type and variety of TAAs (tumor-associated antigens), immune infiltrates are composed of many different subpopulations of immune cells. Epigenetic changes are also considered to be characteristic of cancer. Epigenetic factors taking part in the regulation of gene expression include the VII group of bromodomain proteins (BrD)—SP-family proteins. Here, we used transcriptomic data from the TCGA database, as well as immunological evidence from ESTIMATE, TIP, and TIMER2.0 databases for various solid tumor types and harnessed several publicly available bioinformatic tools (such as GSEA and GSCA) to demonstrate mechanisms and interactions between BrD proteins and immune infiltrates in cancer. We present a consistently positive correlation between the SP-family genes and immune score regardless of the tumor type. The SP-family proteins correlate positively with T cells’ trafficking and infiltration into tumor. Our results also show an association between the high expression of SP family genes and enriched transcriptome profiles of inflammatory response and TNF-α signaling via NF-κβ. We also show that the SP-family proteins could be considered good predictors of high immune infiltration phenotypes.

Background Efficient genetic material (DNA and RNA) and protein isolation are crucial for obtaining scientifically significant results in biotechnological analytical procedures. DNA mutations, gene expression determination on transcript and protein levels and high-throughput screening are core analyses in cancer studies. The most common tissue homogenisation methods include mortar and pestle usage. This study compares the classic pulverisation method with the nonconventional use of a ball mill. Methods The biological material constituted cancerous and unchanged adjacent tissues collected from five patients with head and neck squamous cell carcinoma (HNSCC). Tissues were halved for trituration using both homogenisation methods. The obtained material was used for DNA, RNA, and protein isolation and further PCR, RT-qPCR, and Western-blot analysis. Results After tissue homogenisation in a ball mill, we found significantly higher DNA concentration than mortar and pestle usage but no significant differences in RNA concentration and DNA and RNA purity ratios. However, the DNA quality assessed by gel electrophoresis and PCR was more excellent in samples ground with mortar and pestle. On the contrary, we demonstrated better RNA quality in ball-milled samples and gene expression analysis using RT-qPCR. We found no significant differences between protein concentration and quality extracted from tissues homogenised with the two compared methods. Conclusion Our results demonstrated that both methods of tissue homogenisation: ball mill versus mortar and pestle, are suitable for human tissue homogenisation to use the DNA and protein in downstream analysis. The ball mill homogenisation is more suitable for RNA extraction and gene expression analysis.

Wprowadzenie technik edycji genomu jako podstawowego narzędzia w badaniach naukowych wywołało znaczny postęp w naukach biologicznych, medycznych oraz pozwoliło zrozumieć patofizjologię wielu chorób. Jedną z najnowocześniejszych metod wprowadzania specyficznych zmian w genomie jest obecnie technologia CRISPR/Cas9, która poprzez insercję, delecję lub zamianę nukleotydów w sekwencji DNA prowadzi do inaktywacji genów docelowych, nabycia nowych cech genetycznych lub korekty niepożądanych mutacji. Ponadto, technologia CRISPR/Cas9 pozwala na tworzenie modeli in vitro i in vivo wielu chorób, a następnie dokładne badanie mechanizmów ich powstawania. Obecnie prowadzonych jest wiele badań w dziedzinie onkologii wykorzystujących technikę CRISPR/Cas9, a niniejsza praca jest ich zwięzłym podsumowaniem.