Double minute chromatin bodies in a case of ovarian ascitic carcinoma

Beyond the Chromosome: Recent Developments in Decoding the Significance of Extrachromosomal Circular DNA (eccDNA) in Human Malignancies

Extrachromosomal circular DNA (eccDNA) is a form of a circular double-stranded DNA that exists independently of conventional chromosomes. eccDNA exhibits a broad and random distribution across eukaryotic cells and has been associated with tumor-related properties due to its ability to harbor the complete gene information of oncogenes. The complex and multifaceted mechanisms underlying eccDNA formation include pathways such as DNA damage repair, breakage-fusion-bridge (BFB) mechanisms, chromothripsis, and cell apoptosis. Of note, eccDNA plays a pivotal role in tumor development, genetic heterogeneity, and therapeutic resistance. The high copy number and transcriptional activity of oncogenes carried by eccDNA contribute to the accelerated growth of tumors. Notably, the amplification of oncogenes on eccDNA is implicated in the malignant progression of cancer cells. The improvement of high-throughput sequencing techniques has greatly enhanced our knowledge of eccDNA by allowing for a detailed examination of its genetic structures and functions. However, we still lack a comprehensive and efficient annotation for eccDNA, while challenges persist in the study and understanding of the functional role of eccDNA, emphasizing the need for the development of robust methodologies. The potential clinical applications of eccDNA, such as its role as a measurable biomarker or therapeutic target in diseases, particularly within the spectrum of human malignancies, is a promising field for future research. In conclusion, eccDNA represents a quite dynamic and multifunctional genetic entity with far-reaching implications in cancer pathogenesis and beyond. Further research is essential to unravel the molecular pathways of eccDNA formation, elucidate its functional roles, and explore its clinical applications. Addressing these aspects is crucial for advancing our understanding of genomic instability and developing novel strategies for tailored therapeutics, especially in cancer.

Innovative insights into extrachromosomal circular DNAs in gynecologic tumors and reproduction

Originating but free from chromosomal DNA, extrachromosomal circular DNAs (eccDNAs) are organized in circular form and have long been found in unicellular and multicellular eukaryotes. Their biogenesis and function are poorly understood as they are characterized by sequence homology with linear DNA, for which few detection methods are available. Recent advances in high-throughput sequencing technologies have revealed that eccDNAs play crucial roles in tumor formation, evolution, and drug resistance as well as aging, genomic diversity, and other biological processes, bringing it back to the research hotspot. Several mechanisms of eccDNA formation have been proposed, including the breakage-fusion-bridge (BFB) and translocation-deletion-amplification models. Gynecologic tumors and disorders of embryonic and fetal development are major threats to human reproductive health. The roles of eccDNAs in these pathological processes have been partially elucidated since the first discovery of eccDNA in pig sperm and the double minutes in ovarian cancer ascites. The present review summarized the research history, biogenesis, and currently available detection and analytical methods for eccDNAs and clarified their functions in gynecologic tumors and reproduction. We also proposed the application of eccDNAs as drug targets and liquid biopsy markers for prenatal diagnosis and the early detection, prognosis, and treatment of gynecologic tumors. This review lays theoretical foundations for future investigations into the complex regulatory networks of eccDNAs in vital physiological and pathological processes.

Extrachromosomal circular DNA: biogenesis, structure, functions and diseases

Extrachromosomal circular DNA (eccDNA), ranging in size from tens to millions of base pairs, is independent of conventional chromosomes. Recently, eccDNAs have been considered an unanticipated major source of somatic rearrangements, contributing to genomic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. In addition, the origin of eccDNA is considered to be associated with essential chromatin-related events, including the formation of super-enhancers and DNA repair machineries. Moreover, our understanding of the properties and functions of eccDNA has continuously and greatly expanded. Emerging investigations demonstrate that eccDNAs serve as multifunctional molecules in various organisms during diversified biological processes, such as epigenetic remodeling, telomere trimming, and the regulation of canonical signaling pathways. Importantly, its special distribution potentiates eccDNA as a measurable biomarker in many diseases, especially cancers. The loss of eccDNA homeostasis facilitates tumor initiation, malignant progression, and heterogeneous evolution in many cancers. An in-depth understanding of eccDNA provides novel insights for precision cancer treatment. In this review, we summarized the discovery history of eccDNA, discussed the biogenesis, characteristics, and functions of eccDNA. Moreover, we emphasized the role of eccDNA during tumor pathogenesis and malignant evolution. Therapeutically, we summarized potential clinical applications that target aberrant eccDNA in multiple diseases.

Sei-1 promotes double minute chromosomes formation through activation of the PI3K/Akt/BRCA1-Abraxas pathway and induces double-strand breaks in NIH-3T3 fibroblasts

Sei-1 is a potential oncogene that plays an important role in promoting genomic instability. Double minute chromosomes (DMs) are hallmarks of gene amplification and contribute to tumorigenesis. Defects in the DNA double-strand break (DSB) repairing pathways can lead to gene amplification. To date, the mechanisms governing the formation of DMs induced by Sei-1 are not fully understood. We established DMs induced by Sei-1 in the NIH-3T3 cell line. RNA-sequencing was used to identify key characteristics of differentially expressed genes. Metaphase spreads were used to calculate DM numbers. Immunofluorescence was employed to detect γH2AX foci. Western blot and Akt pathway inhibition experiments were performed to reveal the role of the PI3K/Akt/BRCA1-Abraxas pathway in Sei-1-induced DMs. Luciferase reporter assay was employed to explore the regulatory mechanisms between Sei-1 and BRCA1. DM formation was associated with a deficiency in DSB repair. Based on this finding, activation of the PI3K/Akt/BRCA1-Abraxas pathway was found to increase the DM population with passage in vivo, and inhibition resulted in a reduction of DMs. Apart from this, it was shown for the first time that Sei-1 could directly regulate the expression of BRCA1. Our results suggest that the PI3K/Akt/BRCA1-Abraxas pathway is responsible for the formation of DMs induced by Sei-1.

Gemcitabine eliminates double minute chromosomes from human ovarian cancer cells

Double minute chromosomes are cytogenetic manifestations of gene amplification frequently seen in cancer cells. Genes amplified on double minute chromosomes include oncogenes and multi-drug resistant genes. These genes encode proteins which contribute to cancer formation, cancer progression, and development of resistance to drugs used in cancer treatment. Elimination of double minute chromosomes, and therefore genes amplified on them, is an effective way to decrease the malignancy of cancer cells. We investigated the effectiveness of a cancer drug, gemcitabine, on the loss of double minute chromosomes from the ovarian cancer cell line UACC-1598. Gemcitabine is able to decrease the number of double minute chromosomes in cells at a 7500X lower concentration than the commonly used cancer drug hydroxyurea. Amplified genes present on the double minute chromosomes are decreased at the DNA level upon gemcitabine treatment. Gemcitabine, even at a low nanomolar concentration, is able to cause DNA damage. The selective incorporation of double minutes chromatin and γ-H2AX signals into micronuclei provides a strong link between DNA damage and the loss of double minute chromosomes from gemcitabine treated cells. Cells treated with gemcitabine also showed decreased cell growth, colony formation, and invasion. Together, our results suggest that gemcitabine is effective in decreasing double minute chromosomes and this affects the biology of ovarian cancer cells.

Identification of amplified genes in a patient with acute myeloid leukemia and double minute chromosomes

A case of acute myeloid leukemia (M2) with double minute chromosomes and complex karyotypic abnormalities was analyzed cytogenetically and molecularly. Comparative genomic hybridization (CGH) showed that the 8q24 region that contains the MYC oncogene was not amplified. Instead, amplification of chromosomal regions 11q23-->qter and 9p11-->pter was identified. Southern blot analysis confirmed the CGH findings and showed that the ETS1, FLI1, SRPR, NFRKB, and KCNJ5 genes located at 11q23-->24 were amplified, whereas the MLL at 11q23 was not amplified. Additionally, the IFN beta 1 and CDKN2A genes at 9p were amplified, but to a lesser degree. This is the first example of a case of acute myeloid leukemia with double minute chromosomes that has not involved amplification of either the MYC or the MLL genes.

Cloning of a non-c-myc DNA fragment from the double minutes of a human colon carcinoid cell line

The cell line COLO 320 DM, derived from an untreated human colon carcinoid tumor, was subcloned to obtain a population (Cl 11) with an average of 37 double minutes (DM) per cell. Fractionation of the chromosomes by differential centrifugation yielded a fraction enriched in DM. DNA isolated from the DM-enriched fraction was inserted into the Pst I site of pBR322. One clone, p446, representative of a number of similar clones, contained a region complementary to genomic unique sequences (region p446U). Southern blot analysis using COLO 320 DNA, and DNA from two other cell lines derived from the same biopsy, COLO 320 HSR and COLO 321 HSR, demonstrated amplification and rearrangement of sequences complementary to p446U when compared with 28 different tumor and normal cell lines, some of which contained DM or homogeneously staining regions (HSR). COLO 320 DM Cl 11 had approximately 110 copies per cell of the p446U sequence, or three copies per DM. COLO 320 HSR, which contained one HSR, had 35 copies per cell, while COLO 321 HSR, which contained two HSR, had 700 copies. In addition, p446U did not hybridize with insert sequences of recombinant plasmid pHM(E + H), which includes the human c-myc coding region, 3 kb of upstream flanking sequences and 0.5 kb of downstream flanking sequences, or with an exon 3 probe, pMYC RI-CLA. Amplification of p446U was also not seen in cell lines containing amplified c-myc or N-myc genes. These results indicate that more than one sequence may be amplified in DM or HSR containing tumor cells, but that they need not be amplified together in other tumors.

Cytogenetic studies in ovarian cancer

Cytogenetic studies of ovarian cancer have been conducted in the Medicine Branch, NCI, National Institutes of Health for 5 years. A total of 72 patients were studied by direct preparation and/or 1- to 3-day short-term culture of ascites (86 samples), pleural fluid (4 samples), and tumor (2 samples). Repeat examinations (1-24 months later) were performed in 7 of the 72 patients. Forty-four patients (62%) were successfully analyzed with banding techniques: 6 patients had adenocarcinoma, 7 had serous adenocarcinoma, 13 had serous papillary adenocarcinoma, 7 had serous papillary cystadenocarcinoma, 2 had mucinous adenocarcinoma, 6 had undifferentiated or poorly differentiated adenocarcinoma, 1 had clear cell adenocarcinoma, and 2 were not classified. Of these 44 patients, 29 had received prior chemotherapy, 14 were untreated, and in 1 patient the treatment status was unknown. Aneuploidy was observed in all patients and there was considerable variation in the chromosome numbers (even within single samples), often ranging from diploidy to triploidy to tetraploidy. All 44 patients had numerical abnormalities and 39 had structural abnormalities. The chromosomes most frequently involved in structural abnormalities (in decreasing order according to the number of patients involved) were #1, #3, #2, #4, #9, #10, #15, #19, #6, and #11; the least involved chromosomes were #21 and #5. Clone formation and the number of chromosomes involved in structural abnormalities increased with duration of disease and were more extensive in patients treated with chemotherapy than in patients treated with surgery alone. Our data did not show a deletion of chromosome #6 (6q-) to be specific for ovarian cancer.

A nonrandom chromosomal abnormality, del 3p(14-23), in human small cell lung cancer (SCLC)

In order to determine whether or not there are specific chromosomal changes in small cell lung cancer (SCLC), karyotypic analyses of 16 continuous SCLC tissue culture lines, three fresh tumor specimens (bone marrow), one direct preparation of bone marrow involved with SCLC, and two lymphoblastoid lines derived from SCLC patients were studied. Cell lines were derived from primary tumor, or metastases to bone marrow, subcutaneous nodules, or pleural fluid; all 16 lines had biochemical and histologic properties characteristic of SCLC. Of the 15 males and 3 females, 6 patients had no prior treatment. All of the 16 cell lines, the 3 fresh specimens, and the direct bone marrow preparation had a common deletion of the short arm of chromosome #3. Use of the shortest region of overlap analysis showed the common deletion was of the short arm in the regions p(14-23). This specific chromosomal abnormality, del 3p, was not found in five non-SCLC cell lines studied and is of major potential biological and diagnostic importance.

Double minutes in mouse neuroblastoma cells and their hybrids

Cytogenetic studies were carried out on three clones of mouse neuroblastoma cells and six interspecific hybrid cells derived from the mouse neuroblastoma cells with either rat glioma cells and liver cells or Chinese hamster brain cells. The hybrid cells possessed characteristic karyotypes with marker chromosomes originating from the neuroblastoma cells. The parental chromosome constitution in the hybrid cells was clone-specific, even in the clones derived from the same parental cells. Double minutes (DMs) were demonstrated in the neuroblastoma cells and in all the hybrid cells studied. In addition other chromosome aberrations, such as microchromosomes and chromosome pulverization, were also observed in these cells. DMs varied in number and morphology among the cells. The number of DMs per cell correlated positively with the level of ploidy and with the karyological constitution contributed by the parental neuroblastoma cells. The results indicate that DMs have a chromosome nature and that the DMs of neuroblastoma chromosomes were transferred into the hybrid cells.

Karyotypic analysis of human ovarian carcinoma cells cloned in short term agar culture

We report detailed chromosome banding analysis of six cases of ovarian adenocarcinoma cultured 24--96 hr in a recently developed bioassay for clonogenic tumor cells. The results of G and C banding revealed a variety of chromosome changes including the observation of a simple deletion for a portion of the long arm of chromosome #6, del(6)(pter leads to q15--21:), in tumor cells from four of six patients. Our study indicates that short-term agar culture can provide a valuable tool in the study of tumor cell karyology. A comparison of our results with previously published studies suggests that in addition to alterations of chromosome #1, the deletion of 6q may represent a characteristic chromosomal aberration in ovarian carcinoma.

Cytological and cytogenetical analysis of thoracic duct lymph in patients with pulmonary carcinomas

Seven patients with squamous cell carcinomas of the lung and nodular metastases underwent Daniels' biopsy and cannulation of the thoracic duct. Lymph specimens obtained by aspiration the day after catheter insertion were examined by cytologic and cytogenetical techniques, including chromosome banding methods. In five of the seven cases maligant cells could be detected by karyotype analysis, whereas standard cytologic examinations yielded no positive diagnoses. This indicates that chromosome analysis is applicable as a diagnostic tool in lymph fluid.