Microdissected DNA Research Articles

Genomic alterations in ovarian endometriosis and subsequently diagnosed ovarian carcinoma.

Can the alleged association between ovarian endometriosis and ovarian carcinoma be substantiated by genetic analysis of endometriosis diagnosed prior to the onset of the carcinoma? The data suggest that ovarian carcinoma does not originate from ovarian endometriosis with a cancer-like genetic profile; however, a common precursor is probable. Endometriosis has been implicated as a precursor of ovarian carcinoma based on epidemiologic studies and the discovery of common driver mutations in synchronous disease at the time of surgery. Endometrioid ovarian carcinoma and clear cell ovarian carcinoma are the most common endometriosis-associated ovarian carcinomas (EAOCs). The pathology biobanks of two university hospitals in Sweden were scrutinized to identify women with surgically removed endometrioma who subsequently developed ovarian carcinoma (1998-2016). Only 45 archival cases with EAOC and previous endometriosis were identified and after a careful pathology review, 25 cases were excluded due to reclassification into non-EAOC (n = 9) or because ovarian endometriosis could not be confirmed (n = 16). Further cases were excluded due to insufficient endometriosis tissue or poor DNA quality in either the endometriosis, carcinoma, or normal tissue (n = 9). Finally 11 cases had satisfactory DNA from all three locations and were eligible for further analysis. Epithelial cells were collected from formalin-fixed and paraffin-embedded (FFPE) sections by laser capture microdissection (endometrioma n = 11) or macrodissection (carcinoma n = 11) and DNA was extracted. Normal tissue from FFPE sections (n = 5) or blood samples collected at cancer diagnosis (n = 6) were used as the germline controls for each included patient. Whole-exome sequencing was performed (n = 33 samples). Somatic variants (single-nucleotide variants, indels, and copy number alterations) were characterized, and mutational signatures and kataegis were assessed. Microsatellite instability and mismatch repair status were confirmed with PCR and immunohistochemistry, respectively. The median age for endometriosis surgery was 42 years, and 54 years for the subsequent ovarian carcinoma diagnosis. The median time between the endometriosis and ovarian carcinoma was 10 (7-30) years. The data showed that all paired samples harbored one or more shared somatic mutations. Non-silent mutations in cancer-associated genes were frequent in endometriosis; however, the same mutations were never observed in subsequent carcinomas. The degree of clonal dominance, demonstrated by variant allele frequency, showed a positive correlation with the time to cancer diagnosis (Spearman's rho 0.853, P < 0.001). Mutations in genes associated with immune escape were the most conserved between paired samples, and regions harboring these genes were frequently affected by copy number alterations in both sample types. Mutational burdens and mutation signatures suggested faulty DNA repair mechanisms in all cases. Datasets are available in the supplementary tables. Even though we located several thousands of surgically removed endometriomas between 1998 and 2016, only 45 paired samples were identified and even fewer, 11 cases, were eligible for sequencing. The observed high level of intra- and inter-heterogeneity in both groups (endometrioma and carcinoma) argues for further studies of the alleged genetic association. The observation of shared somatic mutations in all paired samples supports a common cellular origin for ovarian endometriosis and ovarian carcinoma. However, contradicting previous conclusions, our data suggest that cancer-associated mutations in endometriosis years prior to the carcinoma were not directly associated with the malignant transformation. Rather, a resilient ovarian endometriosis may delay tumorigenesis. Furthermore, the data indicate that genetic alterations affecting the immune response are early and significant events. The present work has been funded by the Sjöberg Foundation (2021-01145 to K.S.; 2022-01-11:4 to A.S.), Swedish state under the agreement between the Swedish government and the county councils, the ALF-agreement (965552 to K.S.; 40615 to I.H.; 965065 to A.S.), Swedish Cancer Society (21-1848 to K.S.; 21-1684 to I.H.; 22-2080 to A.S.), BioCARE-A Strategic Research Area at Lund University (I.H. and S.W.-F.), Mrs Berta Kamprad's Cancer Foundation (FBKS-2019-28, I.H.), Cancer and Allergy Foundation (10381, I.H.), Region Västra Götaland (A.S.), Sweden's Innovation Agency (2020-04141, A.S.), Swedish Research Council (2021-01008, A.S.), Roche in collaboration with the Swedish Society of Gynecological Oncology (S.W.-F.), Assar Gabrielsson Foundation (FB19-86, C.M.), and the Lena Wäpplings Foundation (C.M.). A.S. declares stock ownership and is also a board member in Tulebovaasta, SiMSen Diagnostics, and Iscaff Pharma. A.S. has also received travel support from EMBL, Precision Medicine Forum, SLAS, and bioMCC. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

B Chromosomes in Free-Living Flatworms of the Genus Macrostomum (Platyhelminthes, Macrostomorpha).

B chromosomes (Bs) or supernumerary chromosomes are extra chromosomes in the species karyotype that can vary in its copy number. Bs are widespread in eukaryotes. Usually, the Bs of specimens collected from natural populations are the object of the B chromosome studies. We applied another approach analyzing the Bs in animals maintained under the laboratory conditions as lines and cultures. In this study, three species of the Macrostomum genus that underwent a recent whole-genome duplication (WGD) were involved. In laboratory lines of M. lignano and M. janickei, the frequency of Bs was less than 1%, while in the laboratory culture of M. mirumnovem, it was nearer 30%. Their number in specimens of the culture varied from 1 to 14. Mosaicism on Bs was discovered in parts of these animals. We analyzed the distribution of Bs among the worms of the laboratory cultures during long-term cultivation, the transmission rates of Bs in the progeny obtained from crosses of worms with different numbers of Bs, and from self-fertilized isolated worms. The DNA content of the Bs in M. mirumnovem was analyzed with the chromosomal in situ suppression (CISS) hybridization of microdissected DNA probes derived from A chromosomes (As). Bs mainly consisted of repetitive DNA. The cytogenetic analysis also revealed the divergence and high variation in large metacentric chromosomes (LMs) containing numerous regions enriched for repeats. The possible mechanisms of the appearance and evolution of Bs and LMs in species of the Macrostomum genus were also discussed.

Germline-Restricted Chromosome (GRC) in Female and Male Meiosis of the Great Tit (Parus major, Linnaeus, 1758).

All songbirds studied so far have a germline-restricted chromosome (GRC), which is present in the germ cells and absent in the somatic cells. It shows a wide variation in size, morphology, and genetic content between the songbird species. In this paper, we analyzed GRC behavior in female and male meiosis of the great tit, using immunolocalization of meiotic proteins and FISH with GRC-derived DNA probes. We found that, despite dozens of million years of independent evolution, the great tit GRC displays a striking similarity with the GRCs of two species of martins and two species of estrildid finches examined earlier. It was usually present in two copies in females forming recombining bivalent and in one copy in males forming a condensed heterochromatic body with dotted-like axial elements of the synaptonemal complex. We observed mosaicism for the GRC copy number in the female and male great tit. This indicates that one of the GRC copies might be passively lost during premeiotic germ cell divisions. After the meiotic prophase, the GRC was ejected from most male germ cells. The reverse and interspecies FISH with GRC-specific microdissected DNA probes indicates that GRCs of the great tit, pale martin, and zebra finch differ substantially in their genetic content despite similarities in the meiotic behavior.

Abstract PD5-10: Mutational burden of the normal breast during age and pregnancy

Abstract Background: The potential for accumulation of somatic mutations in the healthy breast throughout life and pregnancy is poorly understood. In particular, the unique mutational landscape of both epithelial and stromal components of the mammary gland has not been investigated in depth. As cancer risk correlates with both age, age of first-time pregnancy and other factors including pregnancy itself, we wished to study mutational rate over time, using these landmarks. Methods: Here, using whole genome sequencing, we determined how the rate of mutations in both cancer drivers and passenger mutations are affected by both age and pregnancy. We aimed to describe for the first time how the mammary epithelium and stroma differ in their mutational burden. Results: Our analysis of epithelial and stromal laser-capture micro-dissected DNA from 25 normal breast samples of nulliparous and age-matched early- and late-parous women collected from Komen Tissue Bank, University of Indiana, shows that the mammary gland is characterised by known COSMIC signatures SBS1 and SBS5, both of which correlate with age (p&amp;lt;0.05). Using a non-negative matrix factorization approach, we identified a novel signature HB1 for a subset of samples which could not be fitted into the known signature database. Differences between the two cellular compartments were observed mostly in the enrichment pathway of mutated genes, notably a significant enrichment in mutations in the PI3K-Akt signalling pathway in the epithelium. We found that parous stroma is associated with a significant enrichment in mutations in the 3’UTR of genes, suggesting that regulation of the environment in the post-partum breast could preferably occur via these pathways. Alike other normal tissue, the mutational burden of the mammary gland significantly increases with age (P&amp;lt;0.05) and we observed parity-associated patterns of mutational burden, particularly evident in the epithelial compartment. The nulliparous epithelium is characterised by a significant increase of mutations (p&amp;lt;0.05), but mutated clones are maintained at a consistently small size. Conversely, the number of somatic mutations in the parous epithelium is not significantly affected by age, but age is positively correlated with bigger clone sizes (P&amp;lt;0.05) in this group. This trend suggests that possible cancer-associated mutations may have a lower probability of occurring but higher chance of expanding within the parous breast with age, compared to the nulliparous breast. To confirm this, we detected mutations in known driver genes in all the healthy samples, with some occurrence of known individual pathogenic variants.Conclusions: We show the mutational landscape of the healthy breast and highlight differences in the epithelial and stromal cellular compartments. We show how mutated cells, including mutations in driver genes for breast cancer, and genetic alterations change in the contest of pregnancy and age, provide a possible explanation for pregnancy-associated breast cancer risk. Citation Format: Biancastella Cereser, Neha Tabassum, Lisa Del Bel Belluz, Sladjana Zagorac, Angela Yiu, Philip Carter, Cristian Miere, Alicia R Jeffries-Jones, Justin Stebbing. Mutational burden of the normal breast during age and pregnancy [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD5-10.

Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing.

Somatic mutations accumulate in healthy tissues as we age, giving rise to cancer and potentially contributing to ageing. To study somatic mutations in non-neoplastic tissues, we developed a series of protocols to sequence the genomes of small populations of cells isolated from histological sections. Here, we describe a complete workflow that combines laser-capture microdissection (LCM) with low-input genome sequencing, while circumventing the use of whole-genome amplification (WGA). The protocol is subdivided broadly into four steps: tissue processing, LCM, low-input library generation and mutation calling and filtering. The tissue processing and LCM steps are provided as general guidelines that might require tailoring based on the specific requirements of the study at hand. Our protocol for low-input library generation uses enzymatic rather than acoustic fragmentation to generate WGA-free whole-genome libraries. Finally, the mutation calling and filtering strategy has been adapted from previously published protocols to account for artifacts introduced via library creation. To date, we have used this workflow to perform targeted and whole-genome sequencing of small populations of cells (typically 100-1,000 cells) in thousands of microbiopsies from a wide range of human tissues. The low-input DNA protocol is designed to be compatible with liquid handling platforms and make use of equipment and expertise standard to any core sequencing facility. However, obtaining low-input DNA material via LCM requires specialized equipment and expertise. The entire protocol from tissue reception through whole-genome library generation can be accomplished in as little as 1 week, although 2-3 weeks would be a more typical turnaround time.

Regions enriched for DNA repeats in chromosomes of Macrostomum mirumnovem, a species with a recent Whole Genome Duplication.

The free-living flatworm Macrostomum mirumnovem is a neopolyploid species whose genome underwent a recent Whole Genome Duplication (WGD). In the result of chromosome fusions of the ancient haploid chromosome set, large metacentric chromosomes were formed. In addition to three pairs of small metacentrics, the current karyotype of M. mirumnovem contains two pairs of large metacentric chromosomes, MMI1 and MMI2. The generation of microdissected DNA libraries enriched for DNA repeats followed by DNA probe preparation and fluorescent in situ hybridization (FISH) were performed. The DNA probes obtained marked chromosome regions enriched for different DNA repeats in the M. mirumnovem chromosomes. The size and localization of these regions varied in different copies of large chromosomes. They varied even in homologous chromosomes, suggesting their divergence due to genome re-diploidization after a WGD. Besides the newly formed chromosome regions enriched for DNA repeats, B chromosomes were found in the karyotypes of the studied specimens of M. mirumnovem. These B chromosomes varied in size and morphology. FISH with microdissected DNA probes revealed that some Bs had a distinct DNA content. FISH could paint differently B chromosomes in different worms and even in the same sample. B chromosomes could carry a bright specific fluorescent signal or could show no fluorescent signal at all. In latter cases, the specific FISH signal could be absent even in the pericentromeric region of the B chromosome. Possible mechanisms of B chromosome formation and their further evolution are discussed. The results obtained indicate an important role that repetitive DNAs play in genome re-diploidization initiating a rapid differentiation of large chromosome copies. Taking together, karyotype peculiarities (a high level of intraspecific karyotypic diversity associated with chromosome number variation, structural chromosomal rearrangements, and the formation of new regions enriched for DNA repeats) and some phenotypic features of M. mirumnovem (small body size, short lifecycle, easy maintenance in the laboratory) make this species a perspective model in the studies of genomic and karyotypic evolution in species passed through a recent WGD event.

Langerhans Cell Histiocytosis Associated With Renal Cell Carcinoma Is a Neoplastic Process: Clinicopathologic and Molecular Study of 7 Cases.

Langerhans cell histiocytosis (LCH) is a rare histiocytic disorder composed of Langerhans cells admixed with reactive mononuclear and granulocytic cells, associated with prominent eosinophils. LCH is considered a neoplasm, driven in most cases by oncogenic RAS/RAF/MEK/ERK pathway mutations. The disease predominantly affects children. Urinary system involvement has rarely been reported in a multisystem disease setting. We describe 7 patients who presented with LCH occurring within (6 cases) or after (1 case) a resected clear cell (n=6) or clear cell papillary (n=1) renal cell carcinoma (RCC), identified prospectively in our routine and consultation files (2012 to 2019). The patients included 5 women and 2 men, with a median age of 54 years (range, 39 to 73 y), none with a history of LCH or LCH manifestations before the time of RCC diagnosis. The median size of the RCC was 3.5 cm (range, 1.8 to 8.3 cm). Treatment included partial (5 cases), or radical (2 cases) nephrectomy. All RCCs on gross examination showed at least focal cystic changes and were low grade (World Health Organization [WHO]/International Society of Urologic Pathologists [ISUP] grade 1 to 2). The LCH foci were detected as incidental histological finding within the resected RCC in all six cases and they were limited to few high-power fields (<2 mm) in 5 of 6 cases, but in the sixth case, they occupied almost the entire clear cell papillary RCC (2 cm nodule). No LCH manifestations were detected in the normal kidney or in perinephric fat. The seventh patient developed LCH within inguinal deep soft tissue followed by systemic manifestations 6 years after clear cell RCC. Langerhans cell immunophenotype was supported by the reactivity for S-100, CD1a, and langerin and by the negative pankeratin. Successful pyrosequencing of microdissected LCH DNA revealed the V600E BRAF mutation in all 6 cases of LCH within RCC. To our knowledge, only 3 similar cases were published since 1980; the only case tested for BRAF mutation showed wild-type BRAF. This is the first study analyzing the morphologic and genetic features of a cohort of LCH associated with RCC. In our experience, these cases may be underrecognized in practice, or may erroneously be diagnosed as RCC dedifferentiation or high-grade sarcomatoid transformation. Finally, the detection of BRAF mutation further confirms that LCH in this setting is indeed a neoplasm, rather than a reactive lesion.

Generation of microdissected DNA probes from metaphase chromosomes when chromosome identification by routine staining is impossible.

Application of microdissected DNA libraries and DNA probes in numerous and various modern molecular cytogenetic studies showed them as an efficient and reliable tool in the analysis of chromosome reorganization during karyotypic evolution and in the diagnosis of human chromosome pathology. An important advantage of DNA probe generation by metaphase chromosome microdissection followed by sequence-independent polymerase chain reaction in comparison with the method of DNA probe generation using chromosome sorting is the possibility of DNA probe preparation from chromosomes of an individual sample without cell line establishment for the production of a large number of metaphase chromosomes. One of the main requirements for successful application of this technique is a possibility for identification of the chromosome of interest during its dissection and collection of its material from metaphase plates spread on the coverslip. In the present study, we developed and applied a technique for generation of microdissected DNA probes in the case when chromosome identification during microdissection appeared to be impossible. The technique was used for generation of two sets of Whole Chromosome Paints (WCPs) from all chromosomes of two species of free-living flatworms in the genus Macrostomum, M. mirumnovem and M. cliftonensis. The single-copy chromosome technique including separate collection of all chromosomes from one metaphase plate allowed us to generate WCPs that painted specifically the original chromosome by Chromosome In Situ Suppression Hybridization (CISS-Hybridization). CISS-Hybridization allowed identifying the original chromosome(s) used for DNA probe generation. Pooled WCPs derived from homologous chromosomes increased the intensity and specificity of chromosome painting provided by CISS-Hybridization. In the result, the obtained DNA probes appeared to be good enough for application in our studies devoted to analysis of karyotypic evolution in the genus Macrostomum and for analysis of chromosome rearrangements among the worms of laboratory cultures of M. mirumnovem.

Abstract P2-05-04: Low molecular weight cyclin E facilitates replication stress tolerance in breast cancer development

Abstract Purpose: Low Molecular Weight Cyclin E (LMW-E) are the oncogenic forms of cyclin E and were originally discovered in breast cancer (BC). LMW-E are generated from N-terminal cleavage of the 50 KDa, full-length cyclin E1 (FL-cycE). Our laboratory has established that LMW-E expression (i) correlates with poorer survival in BC patients; (ii) increases in frequency as BC progress from ductal carcinoma in situ to invasive ductal carcinoma; (iii) drives spontaneous and metastatic BC in murine transgenic models; (iii) causes human mammary epithelial cells (hMECs) to transform in vitro and form tumors in vivo. Elucidating the critical oncogenic functions and essential downstream factors of LMW-E is a current void in the field and may have important therapeutic implications. Experimental Design: Immunohistochemistry (IHC) analysis were performed using tumor specimens (n=725) from breast cancer patients diagnosed with Stage 1 or 2 disease to determine the level of LMW-E. Micro-dissected tumor DNA from these tissues were analyzed for copy number variations (CNVs) using Molecular Inversion Probe (MIP) based arrays. CCNE1(encoding Cyclin E1) knock-out 76NE6 and 76NF2V hMEC lines were generated by CRISPR, followed by transfection of lentivirus vector expressing doxycycline inducible EGFP fused LMW-E or FL-cycE. Time-lapse live cell imaging was performed to monitor the cell growth and phenotypes after induced expression of LWM-E or FL-cycE. DNA replication and replication stress were examined by BrdU labeling and immunofluorescent (IF) assays using antibodies against BrdU and Replication Protein A (RPA). IF for gamma-H2AX and western blotting for phosphor-RPA32, ATR-CHK1 and ATM-CHK2 pathways were performed to determine the DNA damage and responses. Results: Analysis of CNVs for the 725 tumors stratified by the cyclin E phenotypes reveal that the frequency of the CNVs (gains &amp; losses) were the most significant in patients whose tumors expressed LMW-E and were predictive of poor prognosis independent of BC subtypes. DNA damage signals including gamma-H2AX foci and phosphor-CHK1 were similarly enhanced in hMECs induced for FL-cycE or LMW-E over-expression. Different effects of FL-cycE and LMW-E on DNA replication and replication stress were observed. Induced FL-cycE overexpression attenuated increased RPA foci and RPA phosphorylation, inhibits DNA replication and cell growth, and ultimately lead to cell death. LMW-E overexpression facilitated DNA replication and cell proliferation with damaged DNA, resulting in multi-nuclei and micro-nuclei formation in daughter cells. Conclusion: LMW-E expression positively correlates with genomic instability in BC samples. LMW-E facilitates hMECs to by-pass replication stress induced tumor barrier and survive with damaged DNA, resulting in abnormal nuclei formation, an oncogenic phenotype. Citation Format: Mi Li, Kwang Huei Low, Tuyen Bui, Kelly K Hunt, Khandan Keyomarsi. Low molecular weight cyclin E facilitates replication stress tolerance in breast cancer development [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-05-04.

Genome and Karyotype Reorganization after Whole Genome Duplication in Free-Living Flatworms of the Genus Macrostomum.

The genus Macrostomum represents a diverse group of rhabditophoran flatworms with >200 species occurring around the world. Earlier we uncovered karyotype instability linked to hidden polyploidy in both M. lignano (2n = 8) and its sibling species M. janickei (2n = 10), prompting interest in the karyotype organization of close relatives. In this study, we investigated chromosome organization in two recently described and closely related Macrostomum species, M. mirumnovem and M. cliftonensis, and explored karyotype instability in laboratory lines and cultures of M. lignano (DV1/10, 2n = 10) and M. janickei in more detail. We revealed that three of the four studied species are characterized by karyotype instability, while M. cliftonensis showed a stable 2n = 6 karyotype. Next, we performed comparative cytogenetics of these species using fluorescent in situ hybridization (FISH) with a set of DNA probes (including microdissected DNA probes generated from M. lignano chromosomes, rDNA, and telomeric DNA). To explore the chromosome organization of the unusual 2n = 9 karyotype discovered in M. mirumnovem, we then generated chromosome-specific DNA probes for all chromosomes of this species. Similar to M. lignano and M. janickei, our findings suggest that M. mirumnovem arose via whole genome duplication (WGD) followed by considerable chromosome reshuffling. We discuss possible evolutionary scenarios for the emergence and reorganization of the karyotypes of these Macrostomum species and consider their suitability as promising animal models for studying the mechanisms and regularities of karyotype and genome evolution after a recent WGD.

Chromosome Evolution in the Free-Living Flatworms: First Evidence of Intrachromosomal Rearrangements in Karyotype Evolution of Macrostomum lignano (Platyhelminthes, Macrostomida).

The free-living flatworm Macrostomum lignano is a hidden tetraploid. Its genome was formed by a recent whole genome duplication followed by chromosome fusions. Its karyotype (2n = 8) consists of a pair of large chromosomes (MLI1), which contain regions of all other chromosomes, and three pairs of small metacentric chromosomes. Comparison of MLI1 with metacentrics was performed by painting with microdissected DNA probes and fluorescent in situ hybridization of unique DNA fragments. Regions of MLI1 homologous to small metacentrics appeared to be contiguous. Besides the loss of DNA repeat clusters (pericentromeric and telomeric repeats and the 5S rDNA cluster) from MLI1, the difference between small metacentrics MLI2 and MLI4 and regions homologous to them in MLI1 were revealed. Abnormal karyotypes found in the inbred DV1/10 subline were analyzed, and structurally rearranged chromosomes were described with the painting technique, suggesting the mechanism of their origin. The revealed chromosomal rearrangements generate additional diversity, opening the way toward massive loss of duplicated genes from a duplicated genome. Our findings suggest that the karyotype of M. lignano is in the early stage of genome diploidization after whole genome duplication, and further studies on M. lignano and closely related species can address many questions about karyotype evolution in animals.

New insights into the karyotype evolution of the free-living flatworm Macrostomum lignano (Platyhelminthes, Turbellaria)

The free-living flatworm Macrostomum lignano is a model organism for evolutionary and developmental biology studies. Recently, an unusual karyotypic diversity was revealed in this species. Specifically, worms are either ‘normal’ 2n = 8, or they are aneuploid with one or two additional large chromosome(s) (i.e. 2n = 9 or 2n = 10, respectively). Aneuploid worms did not show visible behavioral or morphological abnormalities and were successful in reproduction. In this study, we generated microdissected DNA probes from chromosome 1 (further called MLI1), chromosome 2 (MLI2), and a pair of similar-sized smaller chromosomes (MLI3, MLI4). FISH using these probes revealed that MLI1 consists of contiguous regions homologous to MLI2-MLI4, suggesting that MLI1 arose due to the whole genome duplication and subsequent fusion of one full chromosome set into one large metacentric chromosome. Therefore, one presumably full haploid genome was packed into MLI1, leading to hidden tetraploidy in the M. lignano genome. The study of Macrostomum sp. 8 — a sibling species of M. lignano — revealed that it usually has one additional pair of large chromosomes (2n = 10) showing a high homology to MLI1, thus suggesting hidden hexaploidy in its genome. Possible evolutionary scenarios for the emergence of the M. lignano and Macrostomum sp. 8 genomes are discussed.

The origin of B chromosomes in yellow-necked mice (Apodemus flavicollis)-Break rules but keep playing the game.

B chromosomes (Bs) are known for more than hundred years but their origin, structure and pattern of evolution are not well understood. In the past few years new methodological approaches, involving isolation of Bs followed by whole DNA amplification, DNA probe generation, and fluorescent in situ hybridization (FISH) or the B chromosome DNA sequencing, has allowed detailed analysis of their origin and molecular structure in different species. In this study we explored the origin of Bs in the yellow-necked wood mouse, Apodemus flavicollis, using generation of microdissected DNA probes followed by FISH on metaphase chromosomes. Bs of A. flavicollis were successfully isolated and DNA was used as the template for B-specific probes for the first time. We revealed homology of DNA derived from the analyzed B chromosomes to the pericentromeric region (PR) of sex chromosomes and subtelomeric region of two pairs of small autosomes, but lower homology to the rest of the Y chromosome. Moreover, all analysed Bs had the same structure regardless of their number per individual or the great geographic distance between examined populations from the Balkan Peninsula (Serbia) and Eastern Europe (south region of Russia and central Belarus). Therefore, it was suggested that B chromosomes in A. flavicollis have a unique common origin from the PR of sex chromosomes, and/or similar evolutionary pattern.

Origin of B chromosomes in the genus Astyanax (Characiformes, Characidae) and the limits of chromosome painting.

Eukaryote genomes are frequently burdened with the presence of supernumerary (B) chromosomes. Their origin is frequently investigated by chromosome painting, under the hypothesis that sharing the repetitive DNA sequences contained in the painting probes is a sign of common descent. However, the intragenomic mobility of many anonymous DNA sequences contained in these probes (e.g., transposable elements) adds high uncertainty to this conclusion. Here we test the validity of chromosome painting to investigate B chromosome origin by comparing its results for seven B chromosome types in two fish species genus Astyanax, with those obtained (1) by means of the physical mapping of 18S ribosomal DNA (rDNA), H1 histone genes, the As51 satellite DNA and the (AC)15 microsatellite, and (2) by comparing the nucleotide sequence of one of these families (ITS regions from ribosomal DNA) between genomic DNA from B-lacking individuals in both species and the microdissected DNA from two metacentric B chromosomes found in these same species. Intra- and inter-specific painting suggested that all B chromosomes that were assayed shared homologous DNA sequences among them, as well as with a variable number of A chromosomes in each species. This finding would be consistent with a common origin for all seven B chromosomes analyzed. By contrast, the physical mapping of repetitive DNA sequences failed to give support to this hypothesis, as no more than two B-types shared a given repetitive DNA. Finally, sequence analysis of the ITS regions suggested that at least some of the B chromosomes could have had a common origin.

Apolipoprotein C-II Deposition Amyloidosis: A Potential Misdiagnosis as Light Chain Amyloidosis.

Hereditary amyloidoses are rare and pose a diagnostic challenge. We report a case of hereditary amyloidosis associated with apolipoprotein C-II deposition in a 61-year-old female presenting with renal failure and nephrotic syndrome misdiagnosed as light chain amyloidosis. Renal biopsy was consistent with amyloidosis on microscopy; however, immunofluorescence was inconclusive for the type of amyloid protein. Monoclonal gammopathy evaluation revealed kappa light chain. Bone marrow biopsy revealed minimal involvement with amyloidosis with kappa monotypic plasma cells on flow cytometry. She was started on chemotherapy for light chain amyloidosis. She was referred to the Mayo clinic where laser microdissection and liquid chromatography mass spectrometry detected high levels of apolipoprotein C-II, making a definitive diagnosis. Apolipoprotein C-II is a component of very low-density lipoprotein and aggregates in lipid-free conditions to form amyloid fibrils. The identification of apolipoprotein C-II as the cause of amyloidosis cannot be solely made with routine microscopy or immunofluorescence. Further evaluation of biopsy specimens with laser microdissection and mass spectrometry and DNA sequencing of exons should be done routinely in patients with amyloidoses for definitive diagnosis. Our case highlights the importance of determining the subtype of amyloidosis that is critical for avoiding unnecessary therapy such as chemotherapy.

Comparative analysis of DNA homology in pericentric regions of chromosomes of wood mice from genera Apodemus and Sylvaemus

In the present study, an analysis of the DNA homology of the pericentric chromosomal regions and pericentric heterochromatin in distantly related species of wood mice (species from the Apodemus genus, as well as from the Apodemus and Sylvaemus genera) was conducted by fluorescent in situ hybridization (FISH) with microdissected DNA probes obtained from the corresponding chromosomal regions of these species. Cross-hybridization of microdissected DNA probes obtained from pericentric C-positive blocks of chromosomes of Sylvaemus species with chromosomes of Apodemus species, as well as DNA probes from pericentric C-positive blocks of chromosomes of Apodemus species with chromosomes of Apodemus and Sylvaemus species, showed that DNA repeats homologous to the pericentric regions in other species represented. dispersed repeats in C-negative chromosomal regions, as well as in several regions bordering pericentric C-positive and C-negative regions in heterochromosomes and autosomes and in distal regions in the long arms of several autosomes. The results indicate that the level of DNA homology in pericentric chromosomal regions decreases with an increase in the differentiation level and a decrease in the kinship between the compared forms and species of wood mice. Most likely, degeneration of the DNA repeats is accompanied by a gradual destruction of repeat clusters and their replacement by new, nonhomologous repeats in almost all pericentric regions (some old repetitive sequences might be "extruded" into interstitial or telomeric regions of chromosomes). These processes, which are observed in some species from Sylvaemus genus in distantly related species of Sylvaemus and Apodemus genera, have almost achieved the final stages.

Unusual chromatin state in Rhynchosciara americana (Diptera: Sciaridae).

Euchromatin and heterochromatin are usually defined by the degree of DNA compaction, gene content and combinations of histone and non-histone proteins. More recent studies on protein location have been able to specify a variety of chromatin types thus adding chromatin configurations other than the two basic reference states. Chromatin research exploiting non-model organisms has the potential to provide novel information related to epigenetic modifications and their impact on chromosome structure and function. Polytene chromosomes of Rhynchosciara americana display a particular region within the A9 sub-section characterised by lack of DNA compaction as well as an usual polytene banding pattern. DNA content in the sub-section seems to be low as deduced by DAPI staining. Antibodies to H3K4me, a conserved epigenetic transcription marker,labelled the A9 sub-section strongly. In contrast,transcriptional activity in the region, if any, seems to be low as inferred by detection of RNA polymerase II and RNA. Histone markers related to heterochromatin formation such as H3K9me and H3K27me are underrepresented in the A9 sub-section. However, a chromodomain-containing sciarid protein was detected in the region, displaying levels of fluorescence very close to those observed in pericentric heterochromatin.A plasmid micro-library constructed with microdissected DNA from the A9 sub-section was screened for repetitive DNA. The proportion of inserts containing repeats was found to be similar to that contained in another micro-library made with DNA from a single chromosome end of this species. The data suggest an unusual "chromatin colour" indicating that high levels of histone markers related to transcription coexist with a significant presence of chromodomain-containing proteins and the virtual absence of histone modifications observed in heterochromatin formation.

Abstract 3884: Genome-wide analysis of somatic mutations shared by co-occurring ovarian high-grade serous carcinomas and serous tubal intraepithelial carcinomas

Abstract INTRODUCTION Serous tubal intra-epithelial carcinoma (STIC) in the fallopian tube has been proposed as a putative precursor of ovarian high-grade serous carcinoma (HGSC)[1,2]. Association of STIC and HGSCs is seen in ∼50% of cases, and in ∼15% of women undergoing prophylactic removal of fallopian tubes. Clonal STIC-HGSC relationship is suggested by shared TP53 mutations and overexpression[3]. To further investigate the relationship, we applied genome-wide sequencing of same-patient STIC, HGSC and normal tube DNAs isolated from FFPE tumor specimens of 4 ovarian cancer patients. Here we report extended patterns of somatic alterations shared between STIC and HGSC and identify the affected homeostatic pathways. METHODS We established the STIC-HGSC co-occurrence by pathological evaluation and immunohistochemistry for TP53 and MKI67 positivity. Overlapping TP53 mutations were determined by Sanger sequencing. DNA was isolated from STIC, HGSC and normal tissue areas of paraffin sections, with laser-capture microdissection and whole-genome DNA amplification employed for STICs due to the small cellular content. 250 ng of DNA was converted to sequencing libraries (Kapa Biosystems kit) and exome enrichment done by SeqCap EZ System, Nimblegen, Roche. Exomes were sequenced on Illumina HiSeq2500 at ∼100x coverage in 100-bp paired-end run. Somatic mutations were analyzed by MuTect and FreeBayes callers to determine unique as well as overlapping STIC and HGSC alterations. RESULTS Deep sequencing expanded the number of shared STIC-HGSC mutations to 20-55 per patient. ETV5, LPAR4, MTOR, and PAK3 genes harbored recurrent mutations in HGSCs, and the shared STIC-HGSC mutations involved genes acting in the pathways of response to stress, regulation of apoptosis, autophagy, RAS and small GTPase-mediated signaling, and actin cytoskeleton organization (e.g. MTOR, NF1, BECN1, ARHGEF18, RASA1, PREX2, TTN). Our findings were corroborated for 80 STIC-HGSC-shared gene mutants by the cBioportal/The Cancer Genome Atlas data on ovarian serous carcinoma. CONCLUSIONS The broad patterns of somatic alterations shared by STIC and HGSC document a clonal relationship of these neoplastic lesions and possible origins of ovarian carcinomas in the tubal epithelium. We propose that our genome-wide strategy, once reproduced in a higher patient number, may facilitate future development of approaches to HGSC screening, treatment and prevention. ACKNOWLEDGMENTS IARC Regular Budget; IARC Postdoctoral Fellowship Program (supported by the European Commission FP7 Marie Curie Actions COFUND). NYU Genome Technology Center (supported in part by NIH/NCI P30CA016087). We thank Dr E. Kuhn for assistance with pathology evaluations. REFERENCES 1. Li HX, et al. Int J Clin Exp Pathol. 2014 Feb 15;7(3):848-57. 2. Kurman RJ. Ann Oncol. 2013 Dec;24 Suppl 10:x16-21. 3. Kuhn E, et al. J Pathol. 2012 Feb;226(3):421-6. Citation Format: Yan Song, Maude Ardin, Vincent Cahais, Christine Carreira, Reetta Holmila, Stephanie Villar, Xavier Castells, Maxime Vallee, Adriana Heguy, Pierre-Paul Bringuier, Qin Guo, Xun Zhang, Jiri Zavadil. Genome-wide analysis of somatic mutations shared by co-occurring ovarian high-grade serous carcinomas and serous tubal intraepithelial carcinomas. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3884. doi:10.1158/1538-7445.AM2015-3884

Abstract PD1-4: Somatic leukemogenic mutations associated with infiltrating white blood cells in breast cancer patients

Abstract Background: In the last few decades, theoretical models of cancer growth and progression have long focused on the aberrations of cancer cells alone, such as the abnormal mitotic and invasive characteristics of cancer cells. More recent research across multiple solid tumors suggests a critical interplay between solid tumors and immune regulating cells. Mounting evidence suggests that the immune system can tip the scales of cancer progression, eliciting either an anti-tumor or pro-tumor immune response depending upon varying stimulating and inhibitory factors. Here, we are the first to demonstrate novel mutations including leukemogenic mutations among tumor infiltrating lymphocytes in breast cancer patients. Methods: We obtained 17 primary breast cancer samples from patients who presented for either a lumpectomy or mastectomy as part of an IRB approved biospecimen protocol. Of the 17 patient samples, 13 had triple negative breast cancer, 2 had ER+, HER2+ disease, and 2 had ER+, HER2- disease. In the 17 samples, we used fluorescent activated cell sorting to separate CD45-positive hematopoietic cells from CD45-negative epithelial cells. We then performed exome sequencing of tumor-infiltrating hematopoietic cells to investigate for the presence of pathogenic mutations in tumor-associated leukocytes. In this first step, we identified candidate mutations in known cancer genes, including BCOR, NOTCH2, TET2, NF1, EZH2, and JAK1. As a validation step, we then performed capture-based sequencing of tumor-infiltrating leukocytes in 20 breast cancer samples matched to each patient’s germline DNA sample (buccal swab). In 10 of the 20 patients, we identified and validated somatic mutations. Of note, 6 of these patients harbored mutations known to be associated with leukemia, including DNTM3A, TET2, and BCOR. Most of these mutations were present in at least 5-20% of reads. This suggests that these mutations were present in enriched subclones and were not rare alleles occurring in a minority of hematopoietic stem cells. Lastly, we performed 454 deep sequencing analysis of microdissected tumor DNA samples and confirmed the absence of these mutations in breast cancer cells. Conclusion: Our data demonstrate somatic mutations in tumor infiltrating leukocytes in breast tumors which were not identified in matched germline or tumor DNA samples. Notably, some of these mutations have been implicated in the pathogenesis of lymphoid and myeloid malignancies. This observation suggests a unique relationship between cancer cells and mutant infiltrating leukocytes. We are now investigating the functional interaction between cancer cells and hematopoietic cells. Our findings reframe our understanding of carcinogenesis and offer novel opportunities for cancer detection and treatment. Citation Format: Elizabeth A Comen, Maria Kleppe, Hannah Wen, Britta Weigelt, Lennart Bastian, Brian Blum, Franck T Rapaport, Matt Keller, Nicolas Socci, Agnes Viale, Daoqi You, Robert Benezra, Edi Brogi, Jorge Reis-Filho, Michael Berger, Ross Levine, Larry Norton. Somatic leukemogenic mutations associated with infiltrating white blood cells in breast cancer patients [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr PD1-4.

Diagnostic and Prognostic Utility of a DNA Hypermethylated Gene Signature in Prostate Cancer

We aimed to identify a prostate cancer DNA hypermethylation microarray signature (denoted as PHYMA) that differentiates prostate cancer from benign prostate hyperplasia (BPH), high from low-grade and lethal from non-lethal cancers. This is a non-randomized retrospective study in 111 local Asian men (87 prostate cancers and 24 BPH) treated from 1995 to 2009 in our institution. Archival prostate epithelia were laser-capture microdissected and genomic DNA extracted and bisulfite-converted. Samples were profiled using Illumina GoldenGate Methylation microarray, with raw data processed by GenomeStudio. A classification model was generated using support vector machine, consisting of a 55-probe DNA methylation signature of 46 genes. The model was independently validated on an internal testing dataset which yielded cancer detection sensitivity and specificity of 95.3% and 100% respectively, with overall accuracy of 96.4%. Second validation on another independent western cohort yielded 89.8% sensitivity and 66.7% specificity, with overall accuracy of 88.7%. A PHYMA score was developed for each sample based on the state of methylation in the PHYMA signature. Increasing PHYMA score was significantly associated with higher Gleason score and Gleason primary grade. Men with higher PHYMA scores have poorer survival on univariate (p = 0.0038, HR = 3.89) and multivariate analyses when controlled for (i) clinical stage (p = 0.055, HR = 2.57), and (ii) clinical stage and Gleason score (p = 0.043, HR = 2.61). We further performed bisulfite genomic sequencing on 2 relatively unknown genes to demonstrate robustness of the assay results. PHYMA is thus a signature with high sensitivity and specificity for discriminating tumors from BPH, and has a potential role in early detection and in predicting survival.