Gene expression profiling in biliary atresia

Gene expression profiling in biliary atresia

CORRESPONDENCE 2 3 4 European Medical and Biological Engineering Conference EMBEC’02, Vienna, Austria, Dec 2002. Navarro V, Martinerie J, Le Van Qu...

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CORRESPONDENCE

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European Medical and Biological Engineering Conference EMBEC’02, Vienna, Austria, Dec 2002. Navarro V, Martinerie J, Le Van Quyen M, et al. Seizure anticipation in human neocortical partial epilepsy. Brain 2002; 125: 640–55. Litt B, Echauz J. Prediction of epileptic seizures. Lancet Neurol 2002; 1: 22–33. Schindler K, Wiest R, Kollar M, Donati F. EEG analysis with simulated neuronal cell models helps to detect pre-seizure changes. Clin Neurophysiol 2002; 113: 604–14.

Sir—We corresponded with Jacques Martinerie on May 2, 2002, sending details of the program we used (derived from his paper) and the signal to which we applied this program. Therefore, stating that we did not provide them with our data is inaccurate. In that correspondence, we wrote that we did use the SVD, so it is very strange that they think we did not. Moreover, we asked whether our code contained some errors. In his reply, Martinerie congratulated us on our code and suggested some fine-tuning of the parameters, which we tried without success. Furthermore, one of our main domains of expertise is numerical linear algebra, in which the SVD plays a major role. So if there is one thing we would not forget it would be the SVD. Wim Van Paesschen is an expert in the domain of epileptology and since reference dynamics were chosen with his help, it is hard to believe that we made a mistake at this stage. We agree that technical differences might exist between EEG recorders, but that is not the conclusion or advice that they gave us. They simply suggested that we do more measurements so that eventually we would encounter a signal that allowed for prediction. In our opinion, this indicates a method that is not robust and yields many false negatives. Contrary to what Le Van Quyen and colleagues suggest, we did apply the algorithm to all channels, with the same conclusion for each: no prediction was possible. We do not deny the possible use of non-linear methods in medicine; however, we think that although the paper by Le Van Quyen and colleagues indicates a promising method by which to analyse EEG signals, its robustness is questionable. McSharry and colleagues1 have shown, by using Le Van Quyen and co-workers’ own data, that a simple measure such as variance was almost as good at predicting seizures as their complicated non-linear approach. We still have doubts about the reproducibility of their results, and suspect that they have many false negatives when all

measurements are used, not only those allowing for predictions.

Department of Electrical Engineering, ESAT-SCD (SISTA), Katholieke Universiteit Leuven, Leuven, Belgium; and *Department of Neurology, University Hospital Gasthuisberg, 3000 Leuven, Belgium (e-mail: [email protected])

In our opinion, De Clercq and colleagues’ negative observations cannot be generalised, and their premature conclusions give a false picture of the current state of the art. Convincing proof requires a full scientific report of their results, including a methodological discussion and a larger statistical assessment.

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M Le Van Quyen, V Navarro, M Baulac, B Renault, *J Martinerie

W De Clercq, P Lemmerling, S Van Huffel, *W Van Paesschen

McSharry PE, Smith LA, Tarassenko L. Prediction of epileptic seizures: are nonlinear methods relevant? Nat Med (in review). http://www.maths.ox.ac.uk/ ~mcsharry/papers/natmededitor.pdf (accessed March 3, 2003).

Authors’ second reply Sir—In everyone’s interest, we must keep an open mind in this new field of seizure anticipation. Real progress will require collaboration between the major research groups, something that has already begun in an international programme that includes compilation of a large database and comparisons of different algorithms. De Clercq and colleagues could join us in this collective effort. Concerning the points raised in their letter, we wish, first, to see a full scientific description of their study as soon as possible. Without a precise methodological report (an e-mail containing the algorithms is not enough), there is no way to establish how the data have been processed and to compare their investigations with ours. Furthermore, assessment of these claims is difficult because they are based on small subgroups of individuals, introducing a potential source of bias. Since the publication of our original article, we have studied more than 50 patients and demonstrated the effectiveness of our non-linear method. In another population of patients with neocortical epilepsy,1 we analysed the sensitivity and specificity of our method on 41 seizures, and the correlations with electroclinical data and with linear approaches. These results showed a higher sensitivity to detect preictal changes than classical linear methods. Finally, the reference to McSharry’s letter does not justify the negative results obtained by De Clercq and colleagues. These observations, already reported by Litt and co-workers,2 suggest that some linear methods are sometimes able to detect preictal changes in a similar way to non-linear methods. Both analyses probably constitute different ways of viewing the same thing, and some combination of both will probably be a good direction in which to direct research on reliable seizure anticipation.

THE LANCET • Vol 361 • March 15, 2003 • www.thelancet.com

*CNRS/Laboratoire de Neurosciences Cognitives et Imagerie Cérébrale (MLVQ, VN, BR, JM) and Unité d’Epileptologie (MB), Hôpital de la Pitié-Salpêtrière, 75651 Paris cedex 13, France (e-mail: [email protected]) 1

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Navarro V, Martinerie J, Le Van Quyen M, et al. Seizure anticipation in human neocortical partial epilepsy. Brain 2002; 125: 640–55. Litt B, Esteller R, Echauz J, et al. Epileptic seizures may begin hours in advance of clinical onset: a report of five patients. Neuron 2001; 30: 51–64.

Gene expression profiling in biliary atresia Sir—Jorge A Bezerra and colleagues (Nov 23, p 1653),1 use gene microarrays to ascertain gene expression profiles in biliary atresia. We feel that several points deserve attention. First, bulk tissue was used for expression profiling. Strikingly different expression profiles can be obtained from the same tissue sample, depending on whether bulk tissue or a purified sample of target cells is used.2 This difference is due to heterogeneity of cell types and stage of cell differentiation in bulk tissue, particularly tumours. Laser capture microdissection,3 the current gold standard for procuring tissue, is technically demanding, but ideal for circumventing such contaminating gene expression. In this study, genes crucial to pathogenesis could have been incorrectly underestimated due to inflammatory cell infiltration. Likewise, genes found to be over-expressed might indeed be from inflammatory cells, or from the liver tissue itself. Stanton and colleagues studied expression profiles in myocardial infarction.4 They found a diverse range of cells, including infiltrating inflammatory cells, influenced the expression profile they elicited. We agree with Ramaswamy5 and others that laser capture microdissection and other approaches to pure cell populations should be promoted for gene expression profiling in clinical specimens. On a similar note, since inflammation is a known part of the disease process, osteopontin could be overexpressed secondary to parenchymal or other cell

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damage, not primarily due to release as a putative Th1 cytokine. On the basis of the data presented, we feel the interpretation should be viewed with a degree of caution, until further confirmatory profiling of the inflammatory cells and liver parenchyma is done. *M J F Smith, J C Coffey, J H Wang, T G Cotter, H P Redmond Departments of Academic Surgery and Biochemistry, University College Cork, Cork, Republic of Ireland (e-mail: [email protected]) 1

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Bezerra JA, Tiao G, Ryckman FC, et al. Genetic induction of proinflammatory immunity in children with biliary atresia. Lancet 2002; 360: 1653–59. Sugiyama Y, Sugiyama K, Hirai Y, Akyama F, Hasumi K. Microdissection is essential for gene expression profiling of clinically resected cancer tissues. Am J Clin Pathol 2002; 117: 109–16. Emmert-Buck MR, Bonner RF, Smith PD, et al. Laser capture microdissection. Science 1996; 274: 998–1001. Stanton LW, Garrad LJ, Damm D, et al. Altered patterns of gene expression in response to myocardial infarction. Circ Res 2000; 86: 939–45. Ramaswamy S, Golub TR. DNA microarrays in clinical oncology. J Clin Oncol 2002; 20: 1932–41.

In the context of genes related to immunity and inflammation, the increased expression of osteopontin in the livers of infants with biliary atresia might represent a hepatic response to biliary-atresia-associated injury. However, a potential role for effector lymphocytes in the hepatic microenvironment derives not only from the well recognised regulatory role of the cytokine in functional commitment of lymphocytes in vitro and in vivo,1,2 but also from the differential expression of other genes that regulate immunity and inflammation revealed by gene profiling, and on the expression of interferon gamma in most infants with biliary atresia. Follow-up studies will be necessary to directly determine whether these changes in gene expression result from differentiation through Th1 pathways or other related processes. *Jorge A Bezerra, Bruce J Aronow *Divisions of Pediatric Gastroenterology, Hepatology, and Nutrition (JAB) and Developmental Biology (BJA), Cincinnati Children’s Hospital Medical Center and University of Cincinnati, Cincinnati, OH 45229, USA (e-mail: [email protected]) 1

Authors’ reply Sir—M J F Smith and colleagues make relevant comments regarding the use of selected cell populations (such as by laser capture microdissection) in largescale gene expression analysis of pathophysiological processes within complex tissues. The positive aspects of whole tissue analyses are the lack of selection bias, the ability to preserve intact the molecular networks shown by diverse individual cells, the ability to detect specific signals generated by minority or unselected cell types, and perhaps a higher level of reproducibility between different biomedical facilities. Using whole tissue, we found the activation of a set of genes enriched with those regulating immunity and inflammation, thus suggesting that these genes have a role in the initiation or progression of biliary atresia. Adequately sampling the relative roles and responses of diverse hepatic microenvironments will require a comprehensive effort, with systematic tissue harvesting and amplification of RNA pools. This powerful approach could allow new insights into the relative contributions of multiple cell types that might alter the course of biliary injury and obstruction. Microniche sampling could also offer the opportunity to view the status of lesions at different stages, rather than essentially pooling a patient’s biopsy into a single sample.

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O’Regan AW, Hayden JM, Berman JS. Osteopontin augments CD3-mediated interferon-gamma and CD40 ligand expression by T cells, which results in IL-12 production from peripheral blood mononuclear cells. J Leukocyte Biol 2000; 68: 495–502. Chabas D, Baranzini SE, Mitchell D, et al. The influence of the proinflammatory cytokine, osteopontin, on autoimmune demyelinating disease. Science 2001; 294: 1731–35.

Clinical research in Europe Sir—Jean-Pierre Bassand and coworkers (Dec 7, p 1866)1 provide interesting insights into the situation of clinical research in Europe, and make suggestions by which to overcome the problems. I would like to add a further piece of information in support of their viewpoint. We asked 1036 students at Berlin’s Charité about the subject of and support for their medical dissertations. Only 11% of the clinical dissertations were financially supported, as opposed to 46% of the basic research studies (2 test, p<0·001). Furthermore, the students pursuing clinical dissertations more frequently did not receive support from their supervisors (16% vs 5%, p=0·01). As a result of these disadvantages in the planning and supervision of clinical research, significantly more students doing clinical research than doing basic research were dissatisfied (68% vs 49%, p=0·005).

These data show that the lack of resources for clinical research applies at the level of medical studies. More attention and resources must be directed at clinical research during medical training. Marc Dewey Charité, Medical School of the HumboldtUniversity, Department of Radiology, 10117 Berlin, Germany (e-mail: [email protected]) 1

Bassand JP, Martin J, Rydénc L, Simoons M. The need for resources for clinical research: the European Society of Cardiology calls for European, international collaboration. Lancet 2002; 360: 1866–69.

Equipment for Ethiopian hospitals Sir—This Autumn, I visited three hospitals during a private visit to Ethiopia, and saw for myself the conditions under which the medical staff are working. The Fistula Hospital in Addis Ababa, set up by an Australian couple in the 1950s, today treats 25% of the 8000 annual cases, and has outreach centres to offer access to those who are unable to travel to Addis. Outside Addis, however, there is acute deprivation. In the 50-year-old, overflowing 200-bed hospital at Bahir Dar, the Medical Director told me that they needed “everything”. He is sending a detailed list of their needs, but I could see that their facilities were similar to those available to my father in the early days of the NHS. From the smaller, more modern hospital at Lalibela (home to the rockhewn churches), the doctor in charge has written to ask if small instruments—an ophthalmoscope, for example—might be available. Might I ask anyone who has— or knows of—surplus instruments which might be donated to these and another hospital, in Axum, to let me know? I will be happy to provide additional information to anyone who contacts me. Roger K Ford Grove Lodge, Coat, Martock, Somerset TA12 6AR, UK (e-mail: [email protected])

DEPARTMENT OF ERROR Ellis M, Zwaan F, Hedström U, et al. Recombinant human interleukin 11 and bacterial infection in patients with haemological malignant disease undergoing chemotherapy: a double-blind placebo-controlled randomised trial. Lancet 2003; 361: 275–80—In this Article (Jan 25), the word haematological was changed to haemological throughout without the authors’ knowledge.

THE LANCET • Vol 361 • March 15, 2003 • www.thelancet.com

For personal use. Only reproduce with permission from The Lancet Publishing Group.