Data File Standard for Flow Cytometry, version FCS 3.1.

The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. In 1984, the first Flow Cytometry Standard format for data files was adopted as FCS 1.0. This standard was modified in 1990 as FCS 2.0 and again in 1997 as FCS 3.0. We report here on the next generation flow cytometry standard data file format. FCS 3.1 is a minor revision based on suggested improvements from the community. The unchanged goal of the standard is to provide a uniform file format that allows files created by one type of acquisition hardware and software to be analyzed by any other type.The FCS 3.1 standard retains the basic FCS file structure and most features of previous versions of the standard. Changes included in FCS 3.1 address potential ambiguities in the previous versions and provide a more robust standard. The major changes include simplified support for international characters and improved support for storing compensation. The major additions are support for preferred display scale, a standardized way of capturing the sample volume, information about originality of the data file, and support for plate and well identification in high throughput, plate based experiments. Please see the normative version of the FCS 3.1 specification in Supporting Information for this manuscript (or at http://www.isac-net.org/ in the Current standards section) for a complete list of changes.

Promising combination therapies with gemcitabine.

Because treatment regimens for breast cancer commonly include gemcitabine, we evaluated two promising combinations in preclinical studies: gemcitabine (Gemzar; Eli Lilly and Company, Indianapolis, IN) with either ionizing radiation or docetaxel (Taxotere; Aventis Pharmaceuticals, Inc, Parsippany, NJ). In breast cancer cell lines that expressed either wild-type p53 (MCF-7) or mutant p53 (MCF-7/Adr), sensitivity to the cytotoxic effects of gemcitabine during a 24-hour incubation was similar (IC(50) values 80 and 60 nmol/L in MCF-7 and MCF-7/Adr, respectively). Both cell lines were well radiosensitized by gemcitabine at the corresponding IC(50), with radiation enhancement ratios of 1.6 to 1.7. Although the MCF-7 cells accumulated nearly twice as much gemcitabine triphosphate compared with the MCF-7/Adr cells, a similar reduction in 2'-deoxyadenosine 5'-triphosphate pools was observed. While the number of dying cells, as measured by sub-G1 DNA content or S-phase cells unable to replicate DNA, differed between the wild-type p53 or mutant p53-expressing cell lines, neither parameter correlated with radiosensitization. Docetaxel was a more potent cytotoxic agent than gemcitabine in MCF-7 cells (IC(50) = 1 nmol/L). Strong synergistic cytotoxicity was observed in cells treated with gemcitabine (24 hours) followed by docetaxel (24 hours) or the reverse sequence. However, simultaneous addition of the two drugs was antagonistic. To determine whether synergy with radiation or docetaxel was mediated by increased DNA damage, DNA double-strand breaks (double-strand breaks) were measured by immunostaining for phosphorylated H2AX. Ionizing radiation produced more double-strand breaks than gemcitabine alone, while no significant double-strand breaks formed with docetaxel alone. The addition of docetaxel or ionizing radiation to gemcitabine-treated cells did not increase H2AX foci formation. These results show that the combination of gemcitabine with ionizing radiation or docetaxel produces strong, schedule-dependent synergy in breast cancer cells that is not mediated through increasing DNA double-strand breaks.

Laboratory and clinical evidence of synergistic cytotoxicity of sequential treatment with gemcitabine followed by docetaxel in the treatment of sarcoma.

PURPOSE: A recent report of the combination of gemcitabine and docetaxel described favorable results in patients with uterine leiomyosarcoma. The objective of this report is to describe experience with this combination in a variety of histologic subtypes of sarcoma. Additionally, cell-culture studies were performed to assess the effect of the sequence of drug administration on colony formation. PATIENTS AND METHODS: A medical record review of 35 patients receiving the gemcitabine/docetaxel combination was undertaken. Gemcitabine 675 mg/m(2) intravenously was administered over 90 minutes on days 1 and 8, and docetaxel 100 mg/m(2) intravenously was administered over 60 minutes on day 8 of a 21-day cycle. Cell culture studies using the SAOS-2 osteosarcoma cell line and MCF-7 breast cancer cell line were also performed. Gemcitabine and docetaxel were added to cells either simultaneously for 24 hours, gemcitabine for 24 hours followed by docetaxel for 24 hours, or the reverse sequence. RESULTS: Thirty-five patients were treated. Five complete responses and 10 partial responses were observed for an overall response rate of 43%. Responses occurred in uterine, extremity, and retroperitoneal leiomyosarcoma, osteosarcomas, angiosarcomas, malignant fibrous histiocytomas, malignant peripheral-nerve sheath tumors, and Ewing's sarcoma. In the cell culture studies, gemcitabine followed by docetaxel provided synergy. In contrast, the administration of drugs simultaneously resulted in antagonism, and docetaxel followed by gemcitabine provided mixed results. CONCLUSION: The combination of gemcitabine and docetaxel seems to be active in a variety of sarcomas. A multicenter, randomized clinical trial in soft tissue sarcoma comparing gemcitabine alone with this combination, is ongoing.

The role of DNA synthesis inhibition in the cytotoxicity of 2',2'-difluoro-2'-deoxycytidine.

PURPOSE: Cytotoxicity from the anticancer drug 2',2'-difluoro-2'-deoxycytidine (dFdCyd) has been correlated with its incorporation into DNA. However, cytotoxicity may also result from inhibition of DNA synthesis, due to either (1) dFdCyd diphosphate-mediated inhibition of ribonucleotide reductase, or (2) direct inhibition of DNA polymerases by the 5'-triphosphate of dFdCyd (dFdCTP). To elucidate the role of DNA synthesis inhibition in the cytotoxicity of dFdCyd, we compared dFdCyd to hydroxyurea (HU), a ribonucleotide reductase inhibitor, and aphidicolin, an inhibitor of DNA polymerases, in the U251 and D54 human glioblastoma cell lines. METHODS: Sensitivity to dFdCyd, HU, and aphidicolin were determined using a colony formation assay. The effects of these drugs on DNA synthesis were measured by dual parameter flow cytometry, while the effects on nucleotide pool levels were analyzed by high-performance liquid chromatography. RESULTS: HU and aphidicolin elicited substantially less cytotoxicity than the multi-log killing with dFdCyd. When used at equitoxic concentrations (24-h IC50 values), dFdCyd and HU decreased purine dNTP pools primarily, but dFdCyd was less effective than HU. dFdCyd had decreased dATP by about 80% after 4-12 h, and required 8-24 h to decrease DNA synthesis by 50%. In contrast, HU rapidly depleted dATP by >98% within 2 h, which resulted in >90% inhibition of DNA synthesis. Aphidicolin at a concentration similar to its Ki values for DNA polymerases (1 microM) decreased DNA synthesis by >70% within 2 h. However, this decreased cell survival by only 10% (U251 cells) and 40% (D54 cells). CONCLUSIONS: These results demonstrate that HU and aphidicolin produced a more rapid and profound inhibition of DNA synthesis than dFdCyd, but resulted in significantly less cytotoxicity. This suggests that inhibition of DNA synthesis accounted for less than one log of the multi-log cytotoxicity observed with dFdCyd, whereas incorporation of dFdCTP into DNA is a more lethal event.