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Hammerling, Ulf
Publications (10 of 10) Show all publications
Herman, S., Emami Khoonsari, P., Aftab, O., Krishnan, S., Strömbom, E., Larsson, R., . . . Gustafsson, M. G. (2017). Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions.. Metabolomics, 13(7), Article ID 79.
Open this publication in new window or tab >>Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions.
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2017 (English)In: Metabolomics, ISSN 1573-3882, E-ISSN 1573-3890, Vol. 13, no 7, article id 79Article in journal (Refereed) Published
Abstract [en]

INTRODUCTION: Mass spectrometry based metabolomics has become a promising complement and alternative to transcriptomics and proteomics in many fields including in vitro systems pharmacology. Despite several merits, metabolomics based on liquid chromatography mass spectrometry (LC-MS) is a developing area that is yet attached to several pitfalls and challenges. To reach a level of high reliability and robustness, these issues need to be tackled by implementation of refined experimental and computational protocols.

OBJECTIVES: This study illustrates some key pitfalls in LC-MS based metabolomics and introduces an automated computational procedure to compensate for them.

METHOD: Non-cancerous mammary gland derived cells were exposed to 27 chemicals from four pharmacological classes plus a set of six pesticides. Changes in the metabolome of cell lysates were assessed after 24 h using LC-MS. A data processing pipeline was established and evaluated to handle issues including contaminants, carry over effects, intensity decay and inherent methodology variability and biases. A key component in this pipeline is a latent variable method called OOS-DA (optimal orthonormal system for discriminant analysis), being theoretically more easily motivated than PLS-DA in this context, as it is rooted in pattern classification rather than regression modeling.

RESULT: The pipeline is shown to reduce experimental variability/biases and is used to confirm that LC-MS spectra hold drug class specific information.

CONCLUSION: LC-MS based metabolomics is a promising methodology, but comes with pitfalls and challenges. Key difficulties can be largely overcome by means of a computational procedure of the kind introduced and demonstrated here. The pipeline is freely available on www.github.com/stephanieherman/MS-data-processing.

Keywords
Batch effects, Data handling, Drug metabolism, Mass spectrometry, Metabolomics
National Category
Bioinformatics (Computational Biology)
Research subject
Bioinformatics
Identifiers
urn:nbn:se:uu:diva-323946 (URN)10.1007/s11306-017-1213-z (DOI)000403779800002 ()28596718 (PubMedID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish Research Council
Available from: 2017-06-11 Created: 2017-06-11 Last updated: 2019-04-29Bibliographically approved
Hammerling, U., Laurila, J. B., Grafstrom, R. & Ilbäck, N.-G. (2016). Consumption of Red/Processed Meat and Colorectal Carcinoma: Possible Mechanisms Underlying the Significant Association. Critical reviews in food science and nutrition, 56(4), 614-634
Open this publication in new window or tab >>Consumption of Red/Processed Meat and Colorectal Carcinoma: Possible Mechanisms Underlying the Significant Association
2016 (English)In: Critical reviews in food science and nutrition, ISSN 1040-8398, E-ISSN 1549-7852, Vol. 56, no 4, p. 614-634Article, review/survey (Refereed) Published
Abstract [en]

Epidemiology and experimental studies provide an overwhelming support of the notion that diets high in red or processed meat accompany an elevated risk of developing pre-neoplastic colorectal adenoma and frank colorectal carcinoma (CRC). The underlying mechanisms are disputed; thus several hypotheses have been proposed. A large body of reports converges, however, on haem and nitrosyl haem as major contributors to the CRC development, presumably acting through various mechanisms. Apart from a potentially higher intestinal mutagenic load among consumers on a diet rich in red/processed meat, other mechanisms involving subtle interference with colorectal stem/progenitor cell survival or maturation are likewise at play. From an overarching perspective, suggested candidate mechanisms for red/processed meat-induced CRC appear as three partly overlapping tenets: (i) increased N-nitrosation/oxidative load leading to DNA adducts and lipid peroxidation in the intestinal epithelium, (ii) proliferative stimulation of the epithelium through haem or food-derived metabolites that either act directly or subsequent to conversion, and (iii) higher inflammatory response, which may trigger a wide cascade of pro-malignant processes. In this review, we summarize and discuss major findings of the area in the context of potentially pertinent mechanisms underlying the above-mentioned association between consumption of red/processed meat and increased risk of developing CRC.

Keywords
Dietary patterns, red/processed meat, intestinal carcinogenesis, morphogenetic pathways, haem, nitrosyl-haem, N-nitroso compounds, fat peroxidation
National Category
Nutrition and Dietetics Cancer and Oncology
Identifiers
urn:nbn:se:uu:diva-299091 (URN)10.1080/10408398.2014.972498 (DOI)000373125300005 ()25849747 (PubMedID)
Available from: 2016-07-14 Created: 2016-07-14 Last updated: 2017-11-28Bibliographically approved
Aftab, O., Fryknäs, M., Hammerling, U., Larsson, R. & Gustafsson, M. (2015). Detection of cell aggregation and altered cell viability by automated label-free video microscopy: A promising alternative to endpoint viability assays in high throughput screening. Journal of Biomolecular Screening, 20(3), 372-381
Open this publication in new window or tab >>Detection of cell aggregation and altered cell viability by automated label-free video microscopy: A promising alternative to endpoint viability assays in high throughput screening
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2015 (English)In: Journal of Biomolecular Screening, ISSN 1087-0571, E-ISSN 1552-454X, Vol. 20, no 3, p. 372-381Article in journal (Refereed) Published
Abstract [en]

Automated phase-contrast video microscopy now makes it feasible to monitor a high-throughput (HT) screening experiment in a 384-well microtiter plate format by collecting one time-lapse video per well. Being a very cost-effective and label-free monitoring method, its potential as an alternative to cell viability assays was evaluated. Three simple morphology feature extraction and comparison algorithms were developed and implemented for analysis of differentially time-evolving morphologies (DTEMs) monitored in phase-contrast microscopy videos. The most promising layout, pixel histogram hierarchy comparison (PHHC), was able to detect several compounds that did not induce any significant change in cell viability, but made the cell population appear as spheroidal cell aggregates. According to recent reports, all these compounds seem to be involved in inhibition of platelet-derived growth factor receptor (PDGFR) signaling. Thus, automated quantification of DTEM (AQDTEM) holds strong promise as an alternative or complement to viability assays in HT in vitro screening of chemical compounds.

Keywords
time-lapse microscopy, video microscopy, phase contrast microscopy, differentially time evolving morphologies, high throughput screening (HTS), cell aggregation, PDGFR signalling.
National Category
Bioinformatics (Computational Biology) Social and Clinical Pharmacy
Research subject
Bioinformatics; Clinical Pharmacology
Identifiers
urn:nbn:se:uu:diva-234561 (URN)10.1177/1087057114562158 (DOI)000350310000007 ()25520371 (PubMedID)
Available from: 2014-10-21 Created: 2014-10-21 Last updated: 2018-01-11Bibliographically approved
Aftab, O., Fryknäs, M., Hassan, S., Nygren, P., Larsson, R., Hammerling, U. & Gustafsson, M. (2015). Label free quantification of time evolving morphologies using time-lapse video microscopy enables identity control of cell lines and discovery of chemically induced differential activity in iso-genic cell line pairs. Chemometrics and Intelligent Laboratory Systems, 141, 24-32
Open this publication in new window or tab >>Label free quantification of time evolving morphologies using time-lapse video microscopy enables identity control of cell lines and discovery of chemically induced differential activity in iso-genic cell line pairs
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2015 (English)In: Chemometrics and Intelligent Laboratory Systems, ISSN 0169-7439, E-ISSN 1873-3239, Vol. 141, p. 24-32Article in journal (Refereed) Published
Abstract [en]

Label free time-lapse video microscopy based monitoring of time evolving cell population morphology has potential to offer a simple and cost effective method for identity control of cell lines. Such morphology monitoring also has potential to offer discovery of chemically induced differential changes between pairs of cell lines of interest, for example where one in a pair of cell lines is normal/sensitive and the other malignant/resistant. A new simple algorithm, pixel histogram hierarchy comparison (PHHC), for comparison of time evolving morphologies (TEM) in phase contrast time-lapse microscopy movies was applied to a set of 10 different cell lines and three different iso-genic colon cancer cell line pairs, each pair being genetically identical except for a single mutation. PHHC quantifies differences in morphology by comparing pixel histogram intensities at six different resolutions. Unsupervised clustering and machine learning based classification methods were found to accurately identify cell lines, including their respective iso-genic variants, through time-evolving morphology. Using this experimental setting, drugs with differential activity in iso-genic cell line pairs were likewise identified. Thus, this is a cost effective and expedient alternative to conventional molecular profiling techniques and might be useful as part of the quality control in research incorporating cell line models, e.g. in any cell/tumor biology or toxicology project involving drug/agent differential activity in pairs of cell line models.

Keywords
Time evolving morphology, quality control, iso-genic cell line, cancer pharmacology, time-lapse microsopcy, video microscopy
National Category
Computer Sciences Cancer and Oncology
Identifiers
urn:nbn:se:uu:diva-234563 (URN)10.1103/PhysRevC.91.024602 (DOI)000350096200003 ()
Available from: 2014-10-21 Created: 2014-10-21 Last updated: 2018-01-11Bibliographically approved
Kashif, M., Andersson, C., Åberg, M., Nygren, P., Sjöblom, T., Hammerling, U., . . . Gustafsson, M. G. (2014). A Pragmatic Definition of Therapeutic Synergy Suitable for Clinically Relevant In Vitro Multicompound Analyses. Molecular Cancer Therapeutics, 13(7), 1964-1976
Open this publication in new window or tab >>A Pragmatic Definition of Therapeutic Synergy Suitable for Clinically Relevant In Vitro Multicompound Analyses
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2014 (English)In: Molecular Cancer Therapeutics, ISSN 1535-7163, E-ISSN 1538-8514, Vol. 13, no 7, p. 1964-1976Article in journal (Refereed) Published
Abstract [en]

For decades, the standard procedure when screening for candidate anticancer drug combinations has been to search for synergy, defined as any positive deviation from trivial cases like when the drugs are regarded as diluted versions of each other (Loewe additivity), independent actions (Bliss independence), or no interaction terms in a response surface model (no interaction). Here, we show that this kind of conventional synergy analysis may be completely misleading when the goal is to detect if there is a promising in vitro therapeutic window. Motivated by this result, and the fact that a drug combination offering a promising therapeutic window seldom is interesting if one of its constituent drugs can provide the same window alone, the largely overlooked concept of therapeutic synergy (TS) is reintroduced. In vitro TS is said to occur when the largest therapeutic window obtained by the best drug combination cannot be achieved by any single drug within the concentration range studied. Using this definition of TS, we introduce a procedure that enables its use in modern massively parallel experiments supported by a statistical omnibus test for TS designed to avoid the multiple testing problem. Finally, we suggest how one may perform TS analysis, via computational predictions of the reference cell responses, when only the target cell responses are available. In conclusion, the conventional error-prone search for promising drug combinations may be improved by replacing conventional (toxicology-rooted) synergy analysis with an analysis focused on (clinically motivated) TS. 

National Category
Cancer and Oncology Engineering and Technology
Research subject
Engineering Science with specialization in Solid State Physics
Identifiers
urn:nbn:se:uu:diva-229737 (URN)10.1158/1535-7163.MCT-13-0430 (DOI)000338710100026 ()24755197 (PubMedID)
Available from: 2014-08-18 Created: 2014-08-12 Last updated: 2017-12-05Bibliographically approved
Hammerling, U., Freyhult, E., Edberg, A., Sand, S., Fagt, S., Knudsen, V. K., . . . Gustafsson, M. G. (2014). Identifying Food Consumption Patterns among Young Consumers by Unsupervised and Supervised Multivariate Data Analysis. European Journal of Nutrition & Food Safety, 4(4), 392-403
Open this publication in new window or tab >>Identifying Food Consumption Patterns among Young Consumers by Unsupervised and Supervised Multivariate Data Analysis
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2014 (English)In: European Journal of Nutrition & Food Safety, ISSN 2347-5641, Vol. 4, no 4, p. 392-403Article in journal (Refereed) Published
Abstract [en]

Although computational multivariate data analysis (MDA) already has been employed in the dietary survey area, the results reported are based mainly on classical exploratory (descriptive) techniques. Therefore, data of a Swedish and a Danish dietary survey on young consumers (4 to 5 years of age) were subjected not only to modern exploratory MDA, but also modern predictive MDA that via supervised learning yielded predictive classification models. The exploratory part, also encompassing Swedish 8 or 11-year old Swedish consumers, included new innovative forms of hierarchical clustering and bi-clustering. This resulted in several interesting multi-dimensional dietary patterns (dietary prototypes), including striking difference between those of the age-matched Danish and Swedish children. The predictive MDA disclosed additional multi-dimensional food consumption relationships. For instance, the consumption patterns associated with each of several key foods like bread, milk, potato and sweetened beverages, were found to differ markedly between the Danish and Swedish consumers. In conclusion, the joint application of modern descriptive and predictive MDA to dietary surveys may enable new levels of diet quality evaluation and perhaps also prototype-based toxicology risk assessment.

National Category
Nutrition and Dietetics
Identifiers
urn:nbn:se:uu:diva-229925 (URN)10.9734/EJNFS/2014/9082 (DOI)
Available from: 2014-08-18 Created: 2014-08-18 Last updated: 2014-09-10Bibliographically approved
Aftab, O., Nazir, M., Fryknäs, M., Hammerling, U., Larsson, R. & Gustafsson, M. G. (2014). Label free high throughput screening for apoptosis inducing chemicals using time-lapse microscopy signal processing. Apoptosis (London), 19(9), 1411-1418
Open this publication in new window or tab >>Label free high throughput screening for apoptosis inducing chemicals using time-lapse microscopy signal processing
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2014 (English)In: Apoptosis (London), ISSN 1360-8185, E-ISSN 1573-675X, Vol. 19, no 9, p. 1411-1418Article in journal (Refereed) Published
Abstract [en]

Label free time-lapse microscopy has opened a new avenue to the study of time evolving events in living cells. When combined with automated image analysis it provides a powerful tool that enables automated large-scale spatiotemporal quantification at the cell population level. Very few attempts, however, have been reported regarding the design of image analysis algorithms dedicated to the detection of apoptotic cells in such time-lapse microscopy images. In particular, none of the reported attempts is based on sufficiently fast signal processing algorithms to enable large-scale detection of apoptosis within hours/days without access to high-end computers. Here we show that it is indeed possible to successfully detect chemically induced apoptosis by applying a two-dimensional linear matched filter tailored to the detection of objects with the typical features of an apoptotic cell in phase-contrast images. First a set of recorded computational detections of apoptosis was validated by comparison with apoptosis specific caspase activity readouts obtained via a fluorescence based assay. Then a large screen encompassing 2,866 drug like compounds was performed using the human colorectal carcinoma cell line HCT116. In addition to many well known inducers (positive controls) the screening resulted in the detection of two compounds here reported for the first time to induce apoptosis.

Keywords
Apoptosis, high throughput screening, cancer
National Category
Cancer and Oncology
Research subject
Bioinformatics
Identifiers
urn:nbn:se:uu:diva-229069 (URN)10.1007/s10495-014-1009-9 (DOI)000340518000010 ()
Funder
Swedish Society for Medical Research (SSMF)
Available from: 2014-07-29 Created: 2014-07-29 Last updated: 2018-01-09Bibliographically approved
Aftab, O., Fryknäs, M., Zhang, X., De Milito, A., Hammerling, U., Linder, S., . . . Gustafsson, M. G. (2014). Label-free detection and dynamic monitoring of drug-induced intracellular vesicle formation enabled using a 2-dimensional matched filter. Paper presented at High Content Anlaysis. Autophagy, 10(1), 57-69
Open this publication in new window or tab >>Label-free detection and dynamic monitoring of drug-induced intracellular vesicle formation enabled using a 2-dimensional matched filter
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2014 (English)In: Autophagy, ISSN 1554-8627, E-ISSN 1554-8635, Vol. 10, no 1, p. 57-69Article in journal (Refereed) Published
Abstract [en]

Analysis of vesicle formation and degradation is a central issue in autophagy research and microscopy imaging is revolutionizing the study of such dynamic events inside living cells. A limiting factor is the need for labeling techniques that are labor intensive, expensive, and not always completely reliable. To enable label-free analyses we introduced a generic computational algorithm, the label-free vesicle detector (LFVD), which relies on a matched filter designed to identify circular vesicles within cells using only phase-contrast microscopy images. First, the usefulness of the LFVD is illustrated by presenting successful detections of autophagy modulating drugs found by analyzing the human colorectal carcinoma cell line HCT116 exposed to each substance among 1266 pharmacologically active compounds. Some top hits were characterized with respect to their activity as autophagy modulators using independent in vitro labeling of acidic organelles, detection of LC3-II protein, and analysis of the autophagic flux. Selected detection results for 2 additional cell lines (DLD1 and RKO) demonstrate the generality of the method. In a second experiment, label-free monitoring of dose-dependent vesicle formation kinetics is demonstrated by recorded detection of vesicles over time at different drug concentrations. In conclusion, label-free detection and dynamic monitoring of vesicle formation during autophagy is enabled using the LFVD approach introduced.

Keywords
phase-contrast microscopy, automated microscopy, vesicle detection, autophagy, image processing
National Category
Clinical Medicine
Identifiers
urn:nbn:se:uu:diva-216046 (URN)10.4161/auto.26678 (DOI)000328812400006 ()
Conference
High Content Anlaysis
Available from: 2014-01-20 Created: 2014-01-17 Last updated: 2017-12-06Bibliographically approved
Aftab, O., Engskog, M., Haglöf, J., Elmsjö, A., Arvidsson, T., Pettersson, C., . . . Gustafsson, M. (2014). NMR spectroscopy based metabolic profiling of drug induced changes in vitro can discriminate between pharmacological classes. Journal of chemical information and modeling, 54(11), 3251-3258
Open this publication in new window or tab >>NMR spectroscopy based metabolic profiling of drug induced changes in vitro can discriminate between pharmacological classes
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2014 (English)In: Journal of chemical information and modeling, ISSN 1549-9596, Vol. 54, no 11, p. 3251-3258Article in journal (Refereed) Published
Abstract [en]

Drug induced changes in mammalian cell line models have already been extensively profiled at the systemic mRNA level and subsequently used to suggest mechanisms of action for new substances as well as to support drug repurposing, i.e. identifying new potential indications for drugs already licensed for other pharmacotherapy settings. The seminal work in this field, which includes a large database and computational algorithms for pattern matching, is known as the “Connectivity Map” (CMap). The potential of similar exercises at the metabolite level is, however, still largely unexplored. Only recently the first high throughput metabolomic assay pilot study was published, involving screening of metabolic response to a set of 56 kinase inhibitors in a 96-well format. Here we report results from a separately developed metabolic profiling assay, which leverages 1H NMR spectroscopy to the quantification of metabolic changes in the HCT116 colorectal cancer cell line, in response to each of 26 compounds. These agents are distributed across 12 different pharmacological classes covering a broad spectrum of bioactivity. Differential metabolic profiles, inferred from multivariate spectral analysis of 18 spectral bins, allowed clustering of most tested drugs according to their respective pharmacological class. A more advanced supervised analysis, involving one multivariate scattering matrix per pharmacological class and using only 3 spectral bins (three metabolites), showed even more distinct pharmacology-related cluster formations. In conclusion, this kind of relatively fast and inexpensive profiling seems to provide a promising alternative to that afforded by mRNA expression analysis, which is relatively slow and costly. As also indicated by the present pilot study, the resulting metabolic profiles do not seem to provide as information rich signatures as those obtained using systemic mRNA profiling, but the methodology holds strong promise for significant refinement.

National Category
Cancer and Oncology
Identifiers
urn:nbn:se:uu:diva-234564 (URN)10.1021/ci500502f (DOI)000345551000021 ()25321343 (PubMedID)
Available from: 2014-10-21 Created: 2014-10-21 Last updated: 2015-02-03Bibliographically approved
Schaal, W., Hammerling, U., Gustafsson, M. G. & Spjuth, O. (2013). Automated QuantMap for rapid quantitative molecular network topology analysis. Bioinformatics, 29(18), 2369-2370
Open this publication in new window or tab >>Automated QuantMap for rapid quantitative molecular network topology analysis
2013 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 29, no 18, p. 2369-2370Article in journal (Refereed) Published
Abstract [en]

SUMMARY:

The previously disclosed QuantMap method for grouping chemicals by biological activity used online services for much of the data gathering and some of the numerical analysis. The present work attempts to streamline this process by using local copies of the databases and in-house analysis. Using computational methods similar or identical to those used in the previous work, a qualitatively equivalent result was found in just a few seconds on the same dataset (collection of 18 drugs). We use the user-friendly Galaxy framework to enable users to analyze their own datasets. Hopefully, this will make the QuantMap method more practical and accessible and help achieve its goals to provide substantial assistance to drug repositioning, pharmacology evaluation and toxicology risk assessment.

AVAILABILITY:

http://galaxy.predpharmtox.org

CONTACT:

mats.gustafsson@medsci.uu.se or ola.spjuth@farmbio.uu.se

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

National Category
Bioinformatics and Systems Biology
Research subject
Bioinformatics
Identifiers
urn:nbn:se:uu:diva-204704 (URN)10.1093/bioinformatics/btt390 (DOI)000323943200024 ()23828784 (PubMedID)
Funder
eSSENCE - An eScience CollaborationSwedish Research Council, 2011-6129
Available from: 2013-08-08 Created: 2013-08-08 Last updated: 2018-03-05Bibliographically approved
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