Enzymatic and chromosomal characterization of HeLa variants

Multi-omic measurements of heterogeneity in HeLa cells across laboratories

Reproducibility in research can be compromised by both biological and technical variation, but most of the focus is on removing the latter. Here we investigate the effects of biological variation in HeLa cell lines using a systems-wide approach. We determine the degree of molecular and phenotypic variability across 14 stock HeLa samples from 13 international laboratories. We cultured cells in uniform conditions and profiled genome-wide copy numbers, mRNAs, proteins and protein turnover rates in each cell line. We discovered substantial heterogeneity between HeLa variants, especially between lines of the CCL2 and Kyoto varieties, and observed progressive divergence within a specific cell line over 50 successive passages. Genomic variability has a complex, nonlinear effect on transcriptome, proteome and protein turnover profiles, and proteotype patterns explain the varying phenotypic response of different cell lines to Salmonella infection. These findings have implications for the interpretation and reproducibility of research results obtained from human cultured cells.

PRC1-labeled microtubule bundles and kinetochore pairs show one-to-one association in metaphase

In the mitotic spindle, kinetochore microtubules form k‐fibers, whereas overlap or interpolar microtubules form antiparallel arrays containing the cross‐linker protein regulator of cytokinesis 1 (PRC1). We have recently shown that an overlap bundle, termed bridging fiber, links outermost sister k‐fibers. However, the relationship between overlap bundles and k‐fibers throughout the spindle remained unknown. Here, we show that in a metaphase spindle more than 90% of overlap bundles act as a bridge between sister k‐fibers. We found that the number of PRC1‐GFP‐labeled bundles per spindle is nearly the same as the number of kinetochore pairs. Live‐cell imaging revealed that kinetochore movement in the equatorial plane of the spindle is highly correlated with the movement of the coupled PRC1‐GFP‐labeled fiber, whereas the correlation with other fibers decreases with increasing distance. Analysis of endogenous PRC1 localization confirmed the results obtained with PRC1‐GFP. PRC1 knockdown reduced the bridging fiber thickness and interkinetochore distance throughout the spindle, suggesting a function of PRC1 in bridging microtubule organization and force balance in the metaphase spindle.

A clathrin coat assembly role for the muniscin protein central linker revealed by TALEN-mediated gene editing

Clathrin-mediated endocytosis is an evolutionarily ancient membrane transport system regulating cellular receptivity and responsiveness. Plasmalemma clathrin-coated structures range from unitary domed assemblies to expansive planar constructions with internal or flanking invaginated buds. Precisely how these morphologically-distinct coats are formed, and whether all are functionally equivalent for selective cargo internalization is still disputed. We have disrupted the genes encoding a set of early arriving clathrin-coat constituents, FCHO1 and FCHO2, in HeLa cells. Endocytic coats do not disappear in this genetic background; rather clustered planar lattices predominate and endocytosis slows, but does not cease. The central linker of FCHO proteins acts as an allosteric regulator of the prime endocytic adaptor, AP-2. By loading AP-2 onto the plasma membrane, FCHO proteins provide a parallel pathway for AP-2 activation and clathrin-coat fabrication. Further, the steady-state morphology of clathrin-coated structures appears to be a manifestation of the availability of the muniscin linker during lattice polymerization.

DOI:http://dx.doi.org/10.7554/eLife.04137.001

Cells can take proteins and other molecules that are either embedded in, or attached to, their surface membrane and move them inside via a process called endocytosis. This process often involves a protein called clathrin working together with numerous other proteins. Early on, a complex of four proteins, called the adaptor protein-2 complex, interacts with both the ‘cargo’ molecules that are to be taken into the cell, and the cell membrane. Clathrin molecules then assemble into an ordered lattice-like coat, on top of the adaptor protein complex layer. This deforms a small patch of the cell membrane and curves it inwards. The clathrin molecules coat this pocket as it grows in size, until it engulfs the cargo. The pocket quickly pinches off from the membrane to form a bubble-like structure called a vesicle, which is brought into the cell.

A family of proteins termed Muniscins were thought to be involved in the early stages of endocytosis and have to arrive at the membrane before the adaptor protein-2 complex and clathrin. But experiments to test this idea—that reduced, or ‘knocked-down’, the production of Muniscins—had given conflicting results. As such, it remained unclear how the small patches of membrane carrying cargo molecules are marked as being destined to become clathrin-coated vesicles.

Now Umasankar et al. have studied the role that these proteins play in the early stages of endocytosis in human cells grown in a laboratory. A gene-editing approach was used to precisely disrupt a gene that codes for a Muniscin protein called FCHO2. Umasankar et al. observed that these ‘edited’ cells formed clathrin coats that were more irregular compared with those that form in normal cells. Nevertheless, clathrin-mediated vesicles still formed when this protein was absent, though the process of endocytosis was slower.

Similar results were seen when Umasankar et al. used the same approach to disrupt the gene for a related protein called FCHO1 in the same cells. A short fragment of the Muniscin proteins, called the linker, was shown to bind to, and activate, the adaptor protein-2 complex. The linker then recruits this complex to the specific regions of the cell membrane where clathrin-coated vesicles will form. Several dozen other proteins also accumulate where clathrin pockets form; as such, one of the next challenges will be to investigate if this mechanism of locally activating the cargo-gathering machinery is common in living cells.

DOI:http://dx.doi.org/10.7554/eLife.04137.002

Creation of an open-access, mutation-defined fibroblast resource for neurological disease research

Our understanding of the molecular mechanisms of many neurological disorders has been greatly enhanced by the discovery of mutations in genes linked to familial forms of these diseases. These have facilitated the generation of cell and animal models that can be used to understand the underlying molecular pathology. Recently, there has been a surge of interest in the use of patient-derived cells, due to the development of induced pluripotent stem cells and their subsequent differentiation into neurons and glia. Access to patient cell lines carrying the relevant mutations is a limiting factor for many centres wishing to pursue this research. We have therefore generated an open-access collection of fibroblast lines from patients carrying mutations linked to neurological disease. These cell lines have been deposited in the National Institute for Neurological Disorders and Stroke (NINDS) Repository at the Coriell Institute for Medical Research and can be requested by any research group for use in in vitro disease modelling. There are currently 71 mutation-defined cell lines available for request from a wide range of neurological disorders and this collection will be continually expanded. This represents a significant resource that will advance the use of patient cells as disease models by the scientific community.

Parkinson's disease induced pluripotent stem cells with triplication of the α-synuclein locus

A major barrier to research on Parkinson's disease is inaccessibility of diseased tissue for study. One solution is to derive induced pluripotent stem cells from patients and differentiate them into neurons affected by disease. Triplication of SNCA, encoding α-synuclein, causes a fully penetrant, aggressive form of Parkinson's disease with dementia. α-Synuclein dysfunction is the critical pathogenic event in Parkinson's disease, multiple system atrophy and dementia with Lewy bodies. Here we produce multiple induced pluripotent stem cell lines from an SNCA triplication patient and an unaffected first-degree relative. When these cells are differentiated into midbrain dopaminergic neurons, those from the patient produce double the amount of α-synuclein protein as neurons from the unaffected relative, precisely recapitulating the cause of Parkinson's disease in these individuals. This model represents a new experimental system to identify compounds that reduce levels of α-synuclein, and to investigate the mechanistic basis of neurodegeneration caused by α-synuclein dysfunction.

Analysis of variability in albumin content of sister hepatoma cells and a model for geometric phenotypic variability (quantitative shift model)

A model (quantitative shift model) is presented that can account for the phenomenon termed geometric phenotypic variability in which quantitative variation occurs along a square root 2-fold geometric series. The model is based on data for variability in albumin content in hepatoma cells and has three basic assumptions: (i) The albumin genes on each chromosome are active and under independent quantitative regulation. (ii) The rate of albumin gene transcription per cell is the sum of the rates of transcription of the genes of each chromosome. (iii) The mechanism that controls the rate of transcription is highly variable so that at each cell cycle there is a high probability (P = 0.1-0.3) that on the newly synthesized chromatid the rate of transcription of the albumin gene will be different from that of the old chromatid. However, if the rate is different, it will usually be either half or twice the levels of the old chromatid. A computer program was developed based on the model that can generate quantitative diversity in single cells that mimics the pattern of variability in albumin content between sister hepatoma cells, among cells in clonal colonies, and in cell populations where the periodicities in single-cell distributions are compared by Fourier transform analysis. It was determined that the rate of phenotypic variability is indirectly proportional to the magnitude of the quantitative shift in albumin content and that it can be as high as 0.3 per cell per generation. Also, the square root 2 factor in geometric phenotypic variability appears to be an average of a family of values and not the actual value of the smallest quantal shift.

The widespread nature of phenotypic variability in hepatomas and cell lines, in the form of a geometric series

The phenomenon of geometric phenotypic variability is described and its widespread occurrence is established by a new analysis of data from a literature survey of quantitative variation in 39 different enzymes and other cell products in hepatomas and cell lines. The range of variation from hepatoma to hepatoma or from cell line to cell line was between 3- and 700-fold, depending on the particular cell product. By collating together and normalizing the data for the enzymes and other cell products surveyed, it was demonstrated in a statistically valid manner that the quantitative variation for most, if not all, of the enzymes and serum albumin was not random, but followed a geometric series, the consecutive terms of which differed by a factor of square root 2. In addition, examples are presented to show that quantitative inheritance in normal tissues also occurs along this geometric series.

Placental alkaline phosphatase isoenzyme expression by the non-HeLa DoT cervical-carcinoma cell line

Expression of the oncodevelopmental protein, placental alkaline phosphatase, was observed in DoT cells, an epidermoid cell line derived from cervical carcinoma. Under normal conditions of growth in vitro, biochemical inhibition, cytochemical and immunological studies revealed that these cells express the term-placental (Regan) isoenzyme. Thus alkaline phosphatase activity was observed to be heat-stable and inhibited by L-phenylalanine. These properties, supported by immunoelectrophoretic analysis using antisera specific for liver, intestinal or term-placental isoenzymes, identified the isoenzyme as placental type. DoT cells treated with prednisolone (1 microgram/ml) increased total alkaline phosphatase specific activity. This activity was also identified as term-placental phosphatase isoenzyme. On the other hand, treatment of the same cells with sodium butyrate (1 mM) did not induce increased activity of the term-placental isoenzyme, an unexpected observation. As a result of these studies, DoT cells are proposed as a representative cell line for studies of the regulation of oncodevelopmental gene expression in human tumour cells of cervical origin.

Analysis of growth dynamics and the relationship to the fluctuations in alkaline phosphatase in two strains of cells of HeLa S3 derivation

Studies have been carried out to determine an association between glucocorticoid-induced changes in the pattern of growth and the fluctuations of alkaline phosphatase in two HeLa strains. The results showed that growth arrest in steroid-treated cells did not have the characteristics of density-induced growth inhibition. Alkaline phosphatase increased with increased cell density, the increase being greater than control in steroid-treated cells of the "inducible" strain (HeLa S3G, HeLa65) and less than control in the "suppressible" strain (HeLa S3K, HeLa71). Increased serum concentration in the growth medium (0 to 20%) caused an increase in alkaline phosphatase in S3G strain and a decrease in the S3K strain.

Variability of short-term cultures of HeLa S-3 cells: changes in DNA distributions and rates of DNA synthesis

DNA distributions of HeLa S-3 cells in spinner culture exhibit significant time-dependent changes. The major differences appear to occur in the S-phase region. Significant changes in the rates of DNA synthesis in several S-phase subcompartments correlated well with the changes in the DNA distributions. It is proposed that fluctuations in these rates of DNA synthesis are a reflection of the inherent instability of these abnormal, heteroploid cells.

Evidence for a high molecular weight factor(s) in serum which increases alkaline phosphatase specific activity in HeLa

HeLa (substrain Ho) grown in serum free medium showed an increase in the specific activity of alkaline phosphatase when fetal calf serum (10%) was added to the medium (9.7 nmoles/sec/mg protein to 86.8). Under the same conditions, eight intracellular enzymes showed no increase in activity. Similar results were obtained using a different serum or medium, and with a second strain of HeLa (substrain ATC). For a given set of growth conditions, the effect of serum was dependent on its concentration and required one or more culture generations to develop. The type of isozyme expressed did not change. Neither zinc nor a total serum lipid extract would substitute for serum. The enzyme expressed by HeLaHo was not induced by prednisolone, while that in HeLaATC was. However, for cells grown in excess prednisolone without serum, the specific activity was 25% of that found for cells grown with prednisolone and serum. Cortexolone, an antagonist of prednisolone, was without effect for HeLaHo grown in A3 medium with or without serum. The serum factor had the following characteristics. It was not lost on dialysis, treatment with DNase and RNase, or removal of lipoproteins. It was reduced after heating by 65% and after treatment with Pronase by 82%. The data are interpreted to indicate the presence of a factor (s) in serum, probably a protein, which is involved in stimulating alkaline phosphatase specific activity.

Regulation of the synthesis of human chorionic gonadotropin by strains of HeLa cells in culture

Thirty-seven strains of HeLa cells were examined for their ability to synthesize human chorionic gonadotropin (hCG) and its alpha subunit (hCG-alpha) in culture. Synthesis of hCG-alpha and hCG also was investigated in the presence of sodium butyrate and 5-bromo-2'-deoxyuridine (BrdUrd). All HeLa strains synthetized hCG-alpha in culture. Sodium butyrate increased the synthesis of hCG-alpha in all HeLa cells; BrdUrd increased synthesis in 32 of the 37 strains examined. Although few HeLa strains synthesized hCG in the absence of inducers, hCG was detected in most strains in the presence of sodium butyrate. The synthesis of hCG and its alpha subunit is, therefore, a stable genetic characteristic of HeLa cells.

Expression of liver and placental alkaline phosphatases in Chang liver cells

This paper presents evidence that a protein characteristic of differentiated liver cells, liver alkaline phosphatase is synthesized by the Chang liver cell line. Liver alkaline phosphatase was demonstrated by immunochemical assay, 32P-labeling and polyacrylamide gel electrophoresis, immunofluorescence microscopy, and the fluorescence-activated cell sorter. The synthesis of the liver enzyme by the Chang liver cells is interpreted to indicate fidelity of the Chang cells to their origin from human liver tissue. Chang liver cells also synthesize a phosphatase which is similar if not indentical to the placental alkaline phosphatase. Since a placental-type alkaline phosphatase has been observed in a number of non-trophoblastic cell lines and also in some neoplasms, it does not seem reliable as an index of the origins of the cell line. Because of the claims that Chang liver cells are actually HeLa cells, HeLa cells were studied in tandem with the Chang cells. The results showed that the HeLa cells do not make the liver type phosphatase. The data are discussed in relation to the question of HeLa cell contamination of the Chang cell line and the validity of criteria normally used to identify cell lines.

Banded karyotypes of H-4-IIE-C3 rat hepatoma cells grown in vitro

Mitotic cells from the H-4-IIE-C3 rat hepatoma tissue culture line showed a range of 45 to 53 chromosomes per cell with 75% of the cells displaying a chromosome mumber between 49 and 52. Analysis of Wright's-Giemsa banded karyotypes of 22 cells revealed considerable cell to cell variation. Twenty-one structurally abnormal chromosomes were identified in these cells; the origin of nine of the 21 chromosomes were identified in these cells; the origin of nine of the 21 chromosomes could be determined. Of the structurally abnormal chromosomes detected, only one (M-1) occurred with a sufficiently high frequency to be of general use as a marker for these cells. This marker appears to be a Robertsonian translocation involving chromosome number 2 and chromosome number 10.

Synchronization of some human cell strains by serum and calcium starvation

A technique was investigated for producing parasynchronous growth of some established, aneuploid human cell strains. Removal of both serum and calcium from exponentially growing monolayer cells tended to inhibit their growth. After 20 hr, a high percentage of the cell population was arrested in or near mitosis. Readdition of serum and calcium caused parasynchronous growth of the cells of three human strains studied. All three strains incorporated tritiated thymidine maximally 10 to 15 hr after serum and calcium were added, and cell numbers increased rapidly 17 to 25 hr after the growth medium was reconstituted. Population-doubling ranged from 80% to 100% of the theoretical. The yield of parasynchronous cells is high with this technique and may produce a significant amount of nontemporally distorted biological material upon which direct biochemical analysis can be performed at various times within the generation cycle.

Cortisol modification of HeLa 65 alkaline phosphatase. Decreased phosphate content of the induced enzyme

Alkaline phosphatase activity of HeLa cells is increased 5-20-fold during growth in medium with cortisol. The increase in enzyme activity is due to an enhanced catalytic efficiency rather than an increase in alkaline phosphatase protein in induced cells. In the present study the chemical composition of control and induced forms of alkaline phosphatase were investigated to determine the enzyme modification that may be responsible for the increased catalytic activity. HeLa alkaline phosphatase is a phosphoprotein and the induced form of the enzyme has approximately one-half of the phosphate residues associated with control enzyme. The decrease in phosphate residues of the enzyme apparently alters its catalytic activity. Other chemical components of purified alkaline phosphatase from control and induced cells are similar; these include sialic acid, hexosamine and sulfhydryl residues.

Regulation of growth and morphological modulation of HeLa65 cells in monolayer culture by dibutyryl cyclic AMP, butyrate and their analogs

N6-O2'-Dibutyryl adenosine-3',5' monophosphate (DBcAMP) markedly altered the morphology of HeLa cells by increasing average cell size with an increase in total cell protein and RNA. Such effects were not caused by adenosine 3',5' monophosphate (cAMP) or related nucleosides and nucleotides. Butyrate, an enzyme catalyzed hydrolysis product of DBcAMP, induced a jagged spindle shape in HeLa cells within 8 hours and then caused them to enlarge and resemble those grown with DBcAMP. These effects were specific for butyrate (C4) and pentanoate (C5) and were not observed with isomers, substituted analogs, or other fatty acid derivatives. These morphological effects were prevented by blocking protein synthesis or by altering the cytoskeleton with Colcemide or cytochalasin B.

Variation of stemline karyotype in a HeLa cell line

100 karyotypes of a HeLa cell line (modal number 69) were studied in details. It was observed that the stemline cells of this "triploid" somatic cell population showed high degree of chromosomal polymorphism. It has been discussed that the stemline cells have number of extra chromosomes (or parts of chromosomes) which are not essential for the genetic integrity of this cell population. A loss of some of these chromosomes (or their parts) does not induce any appreciable change in the genetic make-up of these cells. The broken chromosomes lose their identity and are grouped together with the non-homologues, when the Denver system of classification is followed. However, it has been argued that in absence of any other acceptable system for classification, the Denver system can still be employed for analyzing human chromosomes both at diploid and abnormal heteroploid level. It has been held in contrast to the pseudo-stemline concept that these cells in general, have the essential genes in common and are responsible for the genetic make-up of this cell line and constitute together the stemline of this somatic cell population.

Isolation and characterization of alkaline phosphatase-constitutive variants from Chinese hamster ovary cells (CHO-k1)

Pure clones with high alkaline phosphatase (ALP) activity were isolated from Chinese hamster ovary (CHO-K1) cells which showed no detectable ALP activity. ALP-positive cells appeared at the frequency of 10(-4) in the N-methyl-N'-nitrosoguanidine-treated cell population. With respect for cellular morphology, plating efficiency and several other enzymatic activities, no distinct difference was found between the original CHO-K1 cells and its ALP-positive variants, although some alterations in karyotype were found. Levels of ALP activity in these clones was stably maintained during serial cultivation. Some of the enzymological properties of ALP in the isolated clones were similar to those in bone or kidney.

Neuraminidase activity in hela cells: effect of hydrocortisone

Homogenates of HeLa cells contain neuraminidase activity. This enzyme is particle-bound, and it has a pH optimum of 4.2. Hydrocortisone-regulated cells contain two to three times as much neuraminidase as the corresponding controls. The hydrocortisone treatment also causes an increase in the cell content of beta-glucuronidase and acid deoxyribonuclease.

Spontaneous in vitro neoplastic transformation of adult human prostatic epithelium

The possible significance of spontaneous transformation of epithelium from a benign prostatic adenoma containing glandular hyperplasia is discussed.