Single-molecule detection of deoxyribonucleoside triphosphates in microdroplets

A new approach to single-molecule DNA sequencing in which dNTPs, released by pyrophosphorolysis from the strand to be sequenced, are captured in microdroplets and read directly could have substantial advantages over current sequence-by-synthesis methods; however, there is no existing method sensitive enough to detect a single nucleotide in a microdroplet. We have developed a method for dNTP detection based on an enzymatic two-stage reaction which produces a robust fluorescent signal that is easy to detect and process. By taking advantage of the inherent specificity of DNA polymerases and ligases, coupled with volume restriction in microdroplets, this method allows us to simultaneously detect the presence of and distinguish between, the four natural dNTPs at the single-molecule level, with negligible cross-talk.

Abstract 2198: An integrated workflow for liquid biopsy of circulating multiple myeloma cells (CMMCs) with single cell resolution reveals tumor heterogeneity

Background: Multiple myeloma (MM) is a bone marrow derived cancer of plasma cells, which remains an incurable disease. Because of the invasive and painful nature of bone biopsy, an alternate tumor monitoring strategy is needed. We have previously shown that Circulating Multiple Myeloma Cells (CMMCs) isolated by CellSearch® (CS) are prognostic and indicative of disease burden through remission and relapse. Here we report, for the first time, the molecular characterization of pure single CMMCs isolated from a multiple myeloma patient, by integrating CS and DEPArray™ (DA) NxT systems, providing access to copy-number alteration (CNA) profiling. Methods: 4.0ml of peripheral blood from a patient with multiple myeloma was tested. On CS, target CMMCs were enriched using anti-CD138 for cell capture, and stained immunofluorescently with CD38-PE, CD19 and CD45-APC. Nuclei were stained with DAPI and detected target cells counted. The enriched sample was then analyzed using the DA NxT system: single CMMCs (CD38+/CD19- and CD45-/DAPI+), along with some single White Blood Cells (WBCs: CD38-/CD19+ or CD45+/DAPI+), were isolated. The DNA of each single cell was amplified using the Ampli1™ WGA kit and used for highly-multiplexed, genome-wide single-cell CNA analysis using a Ampli1™ LowPass kit (LPCNA) on Illumina® MiSeq. Results: CS identified 128 CMMCs. From DA NxT we harvested 20 individual CMMCs for LPCNA analysis. Copy-number profiles of CMMCs confirmed their tumor origin, showing a high-level of genome instability with several gains and few losses of chromosomal segments. Moreover, an unsupervised hierarchical cluster analysis highlighted a conserved pattern of alterations, enabling the separation between CMMCs and WBCs groups. A pattern of copy-number gains shared by all CMMCs, coupled with gains and losses shared by a subset of CMMCs, suggests a branched evolution of different tumor subclones. WBC profiles were flat as expected. Conclusions: Cell enrichment by CS followed by individual cell sorting using DA NxT, enabled the isolation of single CMMCs with 100% purity. Ampli1™ single-cell analysis demonstrated CMMC molecular heterogeneity suggestive of tumor subclones presence. This platform combination provides a reliable and non-invasive method for MM characterization enabling translational research and future clinical application.

Citation Format: Mario Terracciano, Claudio Forcato, Edoardo Petrini, Alberto Ferrarini, Valentina del Monaco, Andrea Raspadori, Carrie Morano, Steven Gross, Chiara Bolognesi, Genny Buson, Thai Bui, Francesca Fontana, Gianni Medoro, Mark Connelly, Nicolò Manaresi. An integrated workflow for liquid biopsy of circulating multiple myeloma cells (CMMCs) with single cell resolution reveals tumor heterogeneity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2198.

Abstract 4579: The genetic heterogeneity and the molecular evolution of systemic metastatic castration resistant prostate cancer during therapy

Background: Circulating tumour cells (CTCs) have a significant prognostic impact in metastatic castration-resistant prostate cancer (mCRPC) and provide direct access to the systemic disease. Here, we performed genome-wide copy number analysis of CellSearchTM detected CTCs to follow the genomic evolution of mCRPC during systemic therapy.

Methods: Blood samples were collected from 13 patients with mCRPC before, during and after two different targeted therapy regimes. Single CTCs were isolated from CellSearchTM cartridges using the DEPArray™ system and the MoFlo XDP cell sorter. Genomes of sorted single cells were amplified using Ampli1™ WGA kit. Amplification products were analysed by array-based comparative genomic hybridization (aCGH) and low-pass sequencing (LPS) using Ampli1™ LowPass kit to detect somatic chromosomal copy number aberrations (CNAs) and explore the degree of genomic heterogeneity.

Results: We analysed >300 CTCs for CNAs by aCGH and/or LPS. Although most CTCs displayed CNAs typical for mCRPC, we identified three genomic CTC-groups across all cells with the EpCAMpos/CKpos/DAPIpos/CD45neg phenotype: CTCs with typical mCRPC CNAs (Type A; 80%), extremely aberrant CTCs (Type B; 11%), CNA-negative/low CTCs (Type C; 9%). The occurrence of Type B and C was almost mutually exclusive. At baseline, we noted different levels of CTC-heterogeneity and different CTC-aberration levels between the different patients. Interestingly, CTCs of patients with a relevant decrease in CTC-count under PARP-inhibition (CTC-responder) displayed significantly elevated CNAs at baseline compared to CTC-non-responders. During therapy, we could observe clonal changes among all patients.

Conclusions: Our data show that CTC-analysis enables the dissection of clinical relevant intra-patient heterogeneity and clonal evolution under therapy in mCRPC patients. Comprehensive genomic monitoring during therapy might help to tailor therapies more effectively and may pinpoint to molecular mechanism of therapeutic resistance.

Citation Format: Rui PL Neves, Streit LRF Anna, Katharina Raba, Elina-Katharina Bongers, Bianca Behrens, Guus van Dalum, Penny Flohr, Joaquin Mateo, Semini Sumanasuriya, Mateus Crespo, Berni Ebbs, Gemma Fowler, Pasquale Rescigno, Suzanne Carreira, Maryou Lambros, Edoardo Petrini, Marianna Garonzi, Nicolò Manaresi, Johann de Bono, Nikolas H. Stoecklein. The genetic heterogeneity and the molecular evolution of systemic metastatic castration resistant prostate cancer during therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4579.

Digital sorting and copy number profiling of purified, PD-L1 positive, Reed Sternberg cells in classical Hodgkin lymphoma

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Background: Classical Hodgkin Lymphoma (cHL) is one of the disease in which the check-point inhibitors have been demonstrated to be more successful. Lately, it has been reported that in malignant Reed-Sternberg Cells (RSCs), PD-1 ligands (PD-Ls) are overexpressed and that chr.9 amplification correlates with advanced stages of the disease, when the standard therapy have already failed. Unfortunately, the detection of the genetic alterations in RSCs is challenging, as one of the hallmark of cHL is the presence of a small number of malignant cells sparse in an abundant and heterogeneous immune infiltrate. Here we present a method for the isolation and the genetic characterization of purified RSCs, which overcomes the limitations posed by the low-cellularity of cHL biopsies, and could be helpful for earlier detection of genetic alterations and adoption of immunotherapy. Methods: FFPE tissue sections from cHL patients were dissociated down to single-cell suspension and stained using anti-CD30 and anti-PD-L1 antibodies. Beyond the positivity to CD30 and PD-L1, RSCs were selected according to morphological criteria such as cell size and the presence of polylobate nuclei compared to surrounding lymphocytes. Target cells were isolated using the DEPArray™ cell sorter, as single cells or in small pools of cells. Recovered cells were whole genome amplified ( Ampli1™ WGA), and genome-wide copy-number aberrations (CNAs) profiles were obtained using Ampli1™ LowPass kit on IonTorrent platform. Results: After the dissociation, RSCs maintained cell morphology and therefore, we were able to discriminate them from the heterogeneous immune infiltrate. RSCs appeared as large multinucleated cells with a big central nucleolus surrounded by a clear halo; cell diameter and ploidy were computed from the images. Pools of lymphocytes and pools of CD30+/ PD-L1+ RSCs were isolated. Sequencing results confirmed the expected flat profile for lymphocytes, while RSCs showed an aberrant profile with multiple losses and gains. Conclusions: The analysis of purified RSCs, could offer a valuable tool to uncover genetic alterations hidden by cHL immune infiltrate, for earlier adoption of more effective treatment regimens.

Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells

Global demethylation is part of a conserved program of epigenetic reprogramming to naive pluripotency. The transition from primed hypermethylated embryonic stem cells (ESCs) to naive hypomethylated ones (serum-to-2i) is a valuable model system for epigenetic reprogramming. We present a mathematical model, which accurately predicts global DNA demethylation kinetics. Experimentally, we show that the main drivers of global demethylation are neither active mechanisms (Aicda, Tdg, and Tet1-3) nor the reduction of de novo methylation. UHRF1 protein, the essential targeting factor for DNMT1, is reduced upon transition to 2i, and so is recruitment of the maintenance methylation machinery to replication foci. Concurrently, there is global loss of H3K9me2, which is needed for chromatin binding of UHRF1. These mechanisms synergistically enforce global DNA hypomethylation in a replication-coupled fashion. Our observations establish the molecular mechanism for global demethylation in naive ESCs, which has key parallels with those operating in primordial germ cells and early embryos.

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Impaired DNA methylation maintenance is the cause of global demethylation in naive ESCs

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Loss of H3K9me2 and UHRF1 lead to impaired maintenance targeting to replication foci

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TET enzymes are not required for global demethylation

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Mathematical model accurately predicts global 5mC and 5hmC during epigenetic resetting

MicroRNAs in HBV-related hepatocellular carcinoma: functions and potential clinical applications

Hepatitis B virus (HBV) infection is still a relevant problem worldwide and many cases of hepatocellular carcinoma (HCC) are related to HBV. The prognosis of HBV-related HCC is poor, particularly for advanced stage diagnosis. Although follow-up strategies were adopted for patients at risk, there is need for an optimal early biomarker for the screening purpose. MicroRNAs (miRNAs) are small non-coding RNAs, tightly connected to cell type and differentiation status and act as genetic regulator which can be involved in oncogenic processes. The alteration in miRNA expression pattern may represent a new opportunity for HBV-related HCC diagnosis and therapies. Some studies focused on miRNA polymorphism responsible for HCC susceptibility; others found several miRNAs deregulated by HBV X protein as well as miRNAs altered in HBV-related HCC tissue and cells. A high variability among results emerged, probably due to different techniques employed, biological substrates, experimental procedures, criteria of miRNAs selection and ethnic provenience of the included patients. Interestingly, circulating miRNAs have been studied as potential HCC-biomarkers but the reported accuracy is still not convincing, particularly in distinguishing patients with HCC from patients with cirrhosis. Hence, the use of miRNAs remains in an experimental phase and more studies are required to define their role in the clinical practice.

A new phosphate-starvation response in fission yeast requires the endocytic function of myosin I

Endocytosis is essential for uptake of many substances into the cell, but how it links to nutritional signalling is poorly understood. Here, we show a new role for endocytosis in regulating the response to low phosphate in Schizosaccharomyces pombe. Loss of function of myosin I (Myo1), Sla2/End4 or Arp2, proteins involved in the early steps of endocytosis, led to increased proliferation in low-phosphate medium compared to controls. We show that once cells are deprived of phosphate they undergo a quiescence response that is dependent on the endocytic function of Myo1. Transcriptomic analysis revealed a wide perturbation of gene expression with induction of stress-regulated genes upon phosphate starvation in wild-type but not Δmyo1 cells. Thus, endocytosis plays a pivotal role in mediating the cellular response to nutrients, bridging the external environment and internal molecular functions of the cell.

Highlighted Article: The endocytic machinery, including the type 1 myosin Myo1, is required to establish a quiescence response to low-phosphate stress in fission yeast.

[Initial observations on the organization of the testis of Trisopterus minutus capelanus]

Testis of the Teleostean fish Trisopterus minutus capelanus has been examined to study the organization of the seminiferous tubules and the ultrastructural features of the germ cells. The testis is shown to be composed of seminiferous tubules full of cells: only few of them have just a very narrow lumen. Each tubule is divided by thin septa of connective tissue in zones containing homogeneous cells; such an organization is confirmed by ultrastructural images showing groups of synchronously developing germ cells. By morphological characterization of the germ cells found in each zone, 6 maturation stages have been identified. During spermiogenesis, a progressive shrinkage of germ cells and a nuclear chromatin condensation have been observed. Intercellular bridges, homogeneously dispersed granules of glycogen and groups of mitochondria associated with dense granular material have been described. Such features are present in the earlier stages of spermiogenesis and are retained until the later stages of spermatid differentiation. The spermatozoon shows a lack of acrosome as in many other teleosts previously studied.

Particular ultrastructural aspects of cryptorchid testis in adult and advanced age

The authors have observed with E.M. Philips 301 some biopsies obtained from testes of cryptorchid patients aged between 38 and 72 to study the ultrastructural aspects of seminiferous tubules in this age. Tissues were fixed in 2% phosphate-buffered solution of glutaraldehyde and then postfixed in 1% osmium tetroxide, processed for routine electron microscopy. The seminiferous tubules appear strongly damaged and we have observed numerous Sertoli cells and only few dark spermatogonia. The Sertoli cells appear either normal and mature or with a cytoplasm filled with big lipid droplets and large amounts of glycogen. The basal membrane of the seminiferous tubules is thickened. Leydig cells are characterized by dilated smooth endoplasmic reticulum and numerous nuclear bodies.

Particular aspects of seminiferous tubules at early puberty

In the seminiferous tubules of patients at early puberty we have observed Sertoli cells showing an homogeneous aspect. In the cytoplasm of some of these elements dense bodies, which present a particular structure and shape, have been recognized. As far as the germ cells, we can find spermatogonia, spermatocytes and spermatids at various developmental stages. The presence of intercellular bridges among the germ cells and of binucleated spermatids with only one acrosome is a characteristic and fairly frequent finding in our specimens, obtained from normal patients.

Further contributions about the use of the horseradish peroxidase (HRP) in the ultrastructural study of the olivary neurons of cat

In order to recognize with E.M. the specific aspect of HRP in olivary neurons of cat, we have used newborn animals twenty-four, forty-eight hours old. The observation of these neurons has allowed us to see a numerous series of dense bodies various in size and density; these bodies have never been found in similar neurons from adult cats or from newborn cats not treated with HRP. These structures could represent the equivalent of an intraneuronal storage of enzyme, whose presence had been confirmed by O.M.

Ultrastructural aspects of Sertoli cells in infancy

In the present study some aspects of Sertoli cells of testicular-biopsy specimens of children from 0 to 8 years old are examined. We can distinguish two main morphological situations. In the first one, Sertoli cells with monomorphic aspect can be seen; in the second can be shown Sertoli cells with various aspects. In this polimorphic situation we can distinguish three Sertoli cell types differing in cellular shape, cytoplasme electron-density and amount of RER and Golgi complex.

[Problems in perfusion and preservation of the rat kidney isolated for the purpose of transplantation]

AA. performed an experimental trial on rats in order to demonstrate damages derived from organ perfusion (kidney) with endo- and extracellular electrolitic solutions. M/E values of structural alterations of the cells allowed the standardisation of renal perfusion methods for transplantation.