Mycoplasma contamination of leukemic cell lines alters protein expression determined by reverse phase protein arrays

In vitro simulation of the acute lymphoblastic leukemia niche: a critical view on the optimal approximation for drug testing

Acute lymphoblastic leukemia with the worst prognosis is related to minimal residual disease. Minimal residual disease not only depends on the individual peculiarities of leukemic clones but also reflects the protective role of the acute lymphoblastic leukemia microenvironment. In this review, we discuss in detail cell-to-cell interactions in the 2 leukemic niches, more explored bone marrow and less studied extramedullary adipose tissue. A special emphasis is given to multiple ways of interactions of acute lymphoblastic leukemia cells with the bone marrow or extramedullary adipose tissue microenvironment, indicating observed differences in B- and T-cell-derived acute lymphoblastic leukemia behavior. This analysis argued for the usage of coculture systems for drug testing. Starting with a review of available sources and characteristics of acute lymphoblastic leukemia cells, mesenchymal stromal cells, endothelial cells, and adipocytes, we have then made an update of the available 2-dimensional and 3-dimensional systems, which bring together cellular elements, components of the extracellular matrix, or its imitation. We discussed the most complex available 3-dimensional systems like "leukemia-on-a-chip," which include either a prefabricated microfluidics platform or, alternatively, the microarchitecture, designed by using the 3-dimensional bioprinting technologies. From our analysis, it follows that for preclinical antileukemic drug testing, in most cases, intermediately complex in vitro cell systems are optimal, such as a "2.5-dimensional" coculture of acute lymphoblastic leukemia cells with niche cells (mesenchymal stromal cells, endothelial cells) plus matrix components or scaffold-free mesenchymal stromal cell organoids, populated by acute lymphoblastic leukemia cells. Due to emerging evidence for the correlation of obesity and poor prognosis, a coculture of adipocytes with acute lymphoblastic leukemia cells as a drug testing system is gaining shape.

Sık Kullanılan Bazı Hücre Hatları için Kalite Kontrol: Mikoplazma Kontaminasyon Tespiti, Sitokrom B ve Sitokrom Oksidaz Alt Birim I Genlerinin DNA Dizi Analizlerinin Gerçekleştirilmesi

Amaç: Laboratuvarlarda sık kullanılan serviks epitelyal karsinom (HeLa), insan periferal kan promiyelösitik lösemi (HL-60), fare C3/bağ dokusu (L929), Madin Darby köpek böbrek (MDCK), fare nöroblastom (Neuro-2a) gibi bazı hücre hatlarının mikoplazma kontaminasyon kontrollerinin yapılması, kimlik doğrulamalarının gerçekleştirilmesi ve klonalitelerinin belirlenmesidir.Yöntem: Bu çalışmada üç farklı türe ait beş hücre hattı kullanılmıştır. Çalışılan tüm hatların Bisbenzimid (Hoechst 33258) ile deoksiribonükleik asit (DNA) floresan işaretlemesi yapılarak mikoplazma kontaminasyonu kontrolleri gerçekleştirilmiştir. Hücre hatlarından DNA izolasyonları yapılmış, elde edilen DNA örneklerinden sitokrom B (CYTB) geninin bölgesel amplifikasyonu için L14816 ve H15173 primerleri; sitokrom oksidaz alt birim I (COI) geni için ise LCO 1490 and HCO 2198 primerleri kullanılmıştır. İlgili amplifikasyonların DNA dizi analiz sonuçları, biyoinformatik araçlar kullanılarak referans dizilerle karşılaştırmalı olarak değerlendirilmiştir.Bulgular: Çalışmada ilgili hücrelerin, Bisbenzimid (Hoechst 33258) ile üretici firmanın protokollerine göre belirlenen konsantrasyon ve sürede yapılan boyama sonucunda mikoplazma kontaminasyonuna rastlanılmamıştır. Ayrıca CYTB gen bölgesi için veritabanında yer alan referans dizi ile yapılan karşılaştırma sonucu HL-60 için %97; "HeLa, L929, MDCK, Neuro-2a” hücre hatları için ise %98 oranında benzerlik bulunmuştur. COI gen bölgesi için ise bu benzerlik oranları “HeLa, HL-60, L929, MDCK ve Neuro-2a” hücre hatları için sırasıyla %95, %99, %96, %96 ve %98 olarak bulunmuştur.Sonuç: Bu bağlamda, çalışmadan elde edilen Bisbenzimid (Hoechst 33258) işaretleme ve DNA dizi analiz sonuçları, pek çok araştırmada kullanılan bu hücre hatlarının kalitesi konusunda kabul edilebilir bir belirteç ve güven sağlamıştır.   

Reverse phase protein arrays in acute leukemia: investigative and methodological challenges

INTRODUCTION

Acute leukemia results from a series of mutational events that alter cell growth and proliferation. Mutations result in protein changes that orchestrate growth alterations characteristic of leukemia. Proteomics is a methodology appropriate for study of protein changes found in leukemia. The high-throughput reverse phase protein array (RPPA) technology is particularly well-suited for the assessment of protein changes in samples derived from clinical trials.

AREAS COVERED

This review discusses the technical, methodological, and analytical issues related to the successful development of acute leukemia RPPAs.

EXPERT COMMENTARY

To obtain representative protein sample lysates, samples should be prepared from freshly collected blood or bone marrow material. Variables such as sample shipment, transit time, and holding temperature only have minimal effects on protein expression. CellSave preservation tubes are preferred for cells collected after exposure to chemotherapy, and incorporation of standardized guidelines for antibody validation is recommended. A more systematic biological approach to analyze protein expression is desired, searching for recurrent patterns of protein expression that allow classification of patients into risk groups, or groups of patients that may be treated similarly. Comparing RPPA protein analysis between cell lines and primary samples shows that cell lines are not representative of patient proteomic patterns.

FTIR Microspectroscopy for the Assessment of Mycoplasmas in HepG2 Cell Culture

To assess the presence and absence of mycoplasma contamination in cell culture, Fourier transform infrared (FTIR) microspectroscopy, coupled with multivariate analysis, was deployed to determine the biomolecular changes in hepatocellular carcinoma cells, HepG2, before and after mycoplasma contamination. The contaminated HepG2 cells were treated with antibiotic BM-Cyclin to decontaminate the mycoplasma, and polymerase chain reaction (PCR) was then performed to confirm the presence or the absence of mycoplasma contamination. The contaminated and decontaminated HepG2 cells were analyzed by FTIR microspectroscopy with principal component analysis (PCA) and peak integral area analysis. The results showed that the FTIR spectra of contaminated HepG2 cells demonstrated the alteration in the IR spectra corresponding to the lipid, protein, and nucleic acid regions. PCA analysis distinguished the spectral differences between the groups of mycoplasma-contaminated and -decontaminated cells. The PCA loading plots suggest that lipid and protein are the main contributed molecules for the difference between these two cell groups. Peak integral area analysis illustrated the increase of lipid and nucleic acid and the decrease of protein contents in the contaminated HepG2 cells. FTIR microspectroscopy is, therefore, proven to be a potential tool for assessing mycoplasma removal by monitoring biomolecular alterations in cell culture.

The Lipocalin2 Gene is Regulated in Mammary Epithelial Cells by NFκB and C/EBP In Response to Mycoplasma

Lcn2 gene expression increases in response to cell stress signals, particularly in cells involved in the innate immune response. Human Lcn2 (NGAL) is increased in the blood and tissues in response to many stressors including microbial infection and in response to LPS in myeloid and epithelial cells. Here we extend the microbial activators of Lcn2 to mycoplasma and describe studies in which the mechanism of Lcn2 gene regulation by MALP-2 and mycoplasma infection was investigated in mouse mammary epithelial cells. As for the LPS response of myeloid cells, Lcn2 expression in epithelial cells is preceded by increased TNFα, IL-6 and IκBζ expression and selective reduction of IκBζ reduces Lcn2 promoter activity. Lcn2 promoter activation remains elevated well beyond the period of exposure to MALP-2 and is persistently elevated in mycoplasma infected cells. Activation of either the human or the mouse Lcn2 promoter requires both NFκB and C/EBP for activation. Thus, Lcn2 is strongly and enduringly activated by mycoplasma components that stimulate the innate immune response with the same basic regulatory mechanism for the human and mouse genes.

Direct qPCR is a sensitive approach to detect Mycoplasma contamination in U937 cell cultures

OBJECTIVE

We aim to directly detect Mycoplasma DNA in a U937 suspension cell culture without using DNA purification. In order to make Mycoplasma contamination monitoring easier, we optimized a commercially available quantitative PCR (qPCR)-based detection kit. We compared the sensitivity of direct qPCR against qPCR with a purified DNA template.

RESULTS

Our findings indicate that qPCR worked optimally with a 6 μl sample volume and a 52 °C annealing-extension temperature. We were able to decrease the annealing-extension step time from 60 to 20 s without any major decrease in reaction sensitivity. The total cycle time of optimized direct qPCR was 65 min. The optimized qPCR protocol was used to detect Mycoplasma DNA before and after DNA purification. Our findings indicate that direct qPCR had a higher sensitivity than regular qPCR. Ct levels produced by direct qPCR with 6 μl templates were almost identical to Ct levels produced by regular qPCR with DNA purified from a 60 μl cell culture sample (23.42 vs 23.49 average Ct levels, respectively). The optimized direct qPCR protocol was successfully applied to monitor the elimination of Mycoplasma contamination from U937 cell cultures.

Mycoplasma contamination affects cell characteristics and decreases the sensitivity of BV2 microglia to LPS stimulation

Mycoplasma is the most common contaminant and greatly affects host cells. The influence of mycoplasma on microglia cells remains unknown. Here, we investigated the influence of mycoplasma contamination on BV2 cells (a microglia cell line). We found that mycoplasma contamination increased the phosphorylation of NF-kB and MAPK signal pathway and induced the activation of BV2 cells. These mycoplasma-contaminated BV2 cells exhibited a transition of cell morphology and slower proliferation, as well as increased gene expression and protein secretion of inflammatory factors. Furthermore, mycoplasma-contaminated BV2 cells had decreased sensitivity to lipopolysaccharide stimulation. These findings suggested that mycoplasma contamination greatly influenced the characteristics and function of microglia cells. It is important to prevent and exclude mycoplasma contamination in our research.