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121 results on '"Huch, M."'

1. Criteria for preclinical models of cholangiocarcinoma: scientific and medical relevance

Author

Calvisi, D, Boulter, L, Vaquero, J, Saborowski, A, Fabris, L, Rodrigues, P, Coulouarn, C, Castro, R, Segatto, O, Raggi, C, van der Laan, L, Carpino, G, Goeppert, B, Roessler, S, Kendall, T, Evert, M, Gonzalez-Sanchez, E, Valle, J, Vogel, A, Bridgewater, J, Borad, M, Gores, G, Roberts, L, Marin, J, Andersen, J, Alvaro, D, Forner, A, Banales, J, Cardinale, V, Macias, R, Vicent, S, Chen, X, Braconi, C, Verstegen, M, Fouassier, L, Scheiter, A, Selaru, F, Evert, K, Utpatel, K, Broutier, L, Cadamuro, M, Huch, M, Goldin, R, Gradilone, S, Saito, Y, Calvisi D. F., Boulter L., Vaquero J., Saborowski A., Fabris L., Rodrigues P. M., Coulouarn C., Castro R. E., Segatto O., Raggi C., van der Laan L. J. W., Carpino G., Goeppert B., Roessler S., Kendall T. J., Evert M., Gonzalez-Sanchez E., Valle J. W., Vogel A., Bridgewater J., Borad M. J., Gores G. J., Roberts L. R., Marin J. J. G., Andersen J. B., Alvaro D., Forner A., Banales J. M., Cardinale V., Macias R. I. R., Vicent S., Chen X., Braconi C., Verstegen M. M. A., Fouassier L., Roberts L., Scheiter A., Selaru F. M., Evert K., Utpatel K., Broutier L., Cadamuro M., Huch M., Goldin R., Gradilone S. A., Saito Y., Calvisi, D, Boulter, L, Vaquero, J, Saborowski, A, Fabris, L, Rodrigues, P, Coulouarn, C, Castro, R, Segatto, O, Raggi, C, van der Laan, L, Carpino, G, Goeppert, B, Roessler, S, Kendall, T, Evert, M, Gonzalez-Sanchez, E, Valle, J, Vogel, A, Bridgewater, J, Borad, M, Gores, G, Roberts, L, Marin, J, Andersen, J, Alvaro, D, Forner, A, Banales, J, Cardinale, V, Macias, R, Vicent, S, Chen, X, Braconi, C, Verstegen, M, Fouassier, L, Scheiter, A, Selaru, F, Evert, K, Utpatel, K, Broutier, L, Cadamuro, M, Huch, M, Goldin, R, Gradilone, S, Saito, Y, Calvisi D. F., Boulter L., Vaquero J., Saborowski A., Fabris L., Rodrigues P. M., Coulouarn C., Castro R. E., Segatto O., Raggi C., van der Laan L. J. W., Carpino G., Goeppert B., Roessler S., Kendall T. J., Evert M., Gonzalez-Sanchez E., Valle J. W., Vogel A., Bridgewater J., Borad M. J., Gores G. J., Roberts L. R., Marin J. J. G., Andersen J. B., Alvaro D., Forner A., Banales J. M., Cardinale V., Macias R. I. R., Vicent S., Chen X., Braconi C., Verstegen M. M. A., Fouassier L., Roberts L., Scheiter A., Selaru F. M., Evert K., Utpatel K., Broutier L., Cadamuro M., Huch M., Goldin R., Gradilone S. A., and Saito Y.

Abstract

Cholangiocarcinoma (CCA) is a rare malignancy that develops at any point along the biliary tree. CCA has a poor prognosis, its clinical management remains challenging, and effective treatments are lacking. Therefore, preclinical research is of pivotal importance and necessary to acquire a deeper understanding of CCA and improve therapeutic outcomes. Preclinical research involves developing and managing complementary experimental models, from in vitro assays using primary cells or cell lines cultured in 2D or 3D to in vivo models with engrafted material, chemically induced CCA or genetically engineered models. All are valuable tools with well-defined advantages and limitations. The choice of a preclinical model is guided by the question(s) to be addressed; ideally, results should be recapitulated in independent approaches. In this Consensus Statement, a task force of 45 experts in CCA molecular and cellular biology and clinicians, including pathologists, from ten countries provides recommendations on the minimal criteria for preclinical models to provide a uniform approach. These recommendations are based on two rounds of questionnaires completed by 35 (first round) and 45 (second round) experts to reach a consensus with 13 statements. An agreement was defined when at least 90% of the participants voting anonymously agreed with a statement. The ultimate goal was to transfer basic laboratory research to the clinics through increased disease understanding and to develop clinical biomarkers and innovative therapies for patients with CCA.

Published
2023

5. Organoids

Author

Zhao, Z, Zhao, Z, Chen, X, Dowbaj, AM, Sljukic, A, Bratlie, K, Lin, L, Fong, ELS, Balachander, GM, Chen, Z, Soragni, A, Huch, M, Zeng, YA, Wang, Q, Yu, H, Zhao, Z, Zhao, Z, Chen, X, Dowbaj, AM, Sljukic, A, Bratlie, K, Lin, L, Fong, ELS, Balachander, GM, Chen, Z, Soragni, A, Huch, M, Zeng, YA, Wang, Q, and Yu, H

Abstract

Organoids are simple tissue-engineered cell-based in vitro models that recapitulate many aspects of the complex structure and function of the corresponding in vivo tissue. They can be dissected and interrogated for fundamental mechanistic studies on development, regeneration and repair in human tissues, and can also be used in diagnostics, disease modelling, drug discovery and personalized medicine. Organoids are derived from either pluripotent or tissue-resident stem (embryonic or adult) or progenitor or differentiated cells from healthy or diseased tissues, such as tumours. To date, numerous organoid engineering strategies that support organoid culture and growth, proliferation, differentiation and maturation have been reported. This Primer highlights the rationale underlying the selection and development of these materials and methods to control the cellular/tissue niche; and therefore, the structure and function of the engineered organoid. We also discuss key considerations for generating robust organoids, such as those related to cell isolation and seeding, matrix and soluble factor selection, physical cues and integration. The general standards for data quality, reproducibility and deposition within the organoid community are also outlined. Lastly, we conclude by elaborating on the limitations of organoids in different applications, and the key priorities in organoid engineering for the coming years.

Published
2022

6. SP2 - Test, Reliability and Functional Safety Trends for Automotive System-on-Chip

Author

Angione, F., Appello, D., Aribido, J., Athavale, J., Bellarmino, N., Bernardi, P., Cantoro, R., De Sio, C., Foscale, T., Gavarini, G., Guerrero, J., Huch, M., Iaria, G., Kilian, T., Mariani, R., Martone, R., Ruospo, A., Sanchez, E., Schlichtmann, U., Squillero, G., Sonza Reorda, M., Sterpone, L., Tancorre, V., Ugioli, R., Angione, F., Appello, D., Aribido, J., Athavale, J., Bellarmino, N., Bernardi, P., Cantoro, R., De Sio, C., Foscale, T., Gavarini, G., Guerrero, J., Huch, M., Iaria, G., Kilian, T., Mariani, R., Martone, R., Ruospo, A., Sanchez, E., Schlichtmann, U., Squillero, G., Sonza Reorda, M., Sterpone, L., Tancorre, V., and Ugioli, R.

Abstract

This paper encompasses three contributions by industry professionals and university researchers. The contributions describe different trends in automotive products, including both manufacturing test and run-time reliability strategies. The subjects considered in this session deal with critical factors, from optimizing the final test before shipment to market to in-field reliability during operative life.

Published
2022

7. Test, Reliability and Functional Safety trends for Automotive System-on-Chip

Author

Angione, F., Appello, D., Aribido, J., Bellarmino, N., Bernardi, P., Cantoro, R., de Sio, C., Foscale, T., Gavarini, G., Huch, M., Kilian, T, Mariani, R., Martone, R., Ruospo, A., Sanchez, E., Schlichtmann, U., Squillero, G., Sonza Reorda, M., Sterpone, L., Tancorre, V., and Ugioli, R.

Published
2022

8. LifeTime and improving European healthcare through cell-based interceptive medicine

Author

Rajewsky, N., Almouzni, G., Gorski, S., Aerts, S., Amit, I., Bertero, M., Bock, C., Bredenoord, A., Cavalli, G., Chiocca, S., Clevers, H., Strooper, B., Eggert, A., Ellenberg, J., Fernández, X., Figlerowicz, M., Gasser, S., Hubner, N., Kjems, J., Knoblich, J., Krabbe, G., Lichter, P., Linnarsson, S., Marine, J., Marioni, J., Marti-Renom, M., Netea, M., Nickel, D., Nollmann, M., Novak, H., Parkinson, H., Piccolo, S., Pinheiro, I., Pombo, A., Popp, C., Reik, W., Roman-Roman, S., Rosenstiel, P., Schultze, J., Stegle, O., Tanay, A., Testa, G., Thanos, D., Theis, F., Torres-Padilla, M., Valencia, A., Vallot, C., van Oudenaarden, A., Vidal, M., Voet, T., Alberi, L., Alexander, S., Alexandrov, T., Arenas, E., Bagni, C., Balderas, R., Bandelli, A., Becher, B., Becker, M., Beerenwinkel, N., Benkirame, M., Beyer, M., Bickmore, W., Biessen, E., Blomberg, N., Blumcke, I., Bodenmiller, B., Borroni, B., Boumpas, D., Bourgeron, T., Bowers, S., Braeken, D., Brooksbank, C., Brose, N., Bruining, H., Bury, J., Caporale, N., Cattoretti, G., Chabane, N., Chneiweiss, H., Cook, S., Curatolo, P., de Jonge, M., Deplancke, B., de Witte, P., Dimmeler, S., Draganski, B., Drews, A., Dumbrava, C., Engelhardt, S., Gasser, T., Giamarellos-Bourboulis, E., Graff, C., Grün, D., Gut, I., Hansson, O., Henshall, D., Herland, A., Heutink, P., Heymans, S., Heyn, H., Huch, M., Huitinga, I., Jackowiak, P., Jongsma, K., Journot, L., Junker, J., Katz, S., Kehren, J., Kempa, S., Kirchhof, P., Klein, C., Koralewska, N., Korbel, J., Kühnemund, M., Lamond, A., Lauwers, E., Le Ber, I., Leinonen, V., Tobon, A., Lundberg, E., Lunkes, A., Maatz, H., Mann, M., Marelli, L., Matser, V., Matthews, P., Mechta-Grigoriou, F., Menon, R., Nielsen, A., Pagani, M., Pasterkamp, R., Pitkänen, A., Popescu, V., Pottier, C., Puisieux, A., Rademakers, R., Reiling, D., Reiner, O., Remondini, D., Ritchie, C., Rohrer, J., Saliba, A., Sanchez-Valle, R., Santosuosso, A., Sauter, A., Scheltema, R., Scheltens, P., Schiller, H., Schneider, A., Seibler, P., Sheehan-Rooney, K., Shields, D., Sleegers, K., Smit, A., Smith, K., Smolders, I., Synofzik, M., Tam, W., Teichmann, S., Thom, M., Turco, M., van Beusekom, H., Vandenberghe, R., den Hoecke, S., de Poel, I., van der Ven, A., van der Zee, J., van Lunzen, J., van Minnebruggen, G., Paesschen, W., van Swieten, J., van Vught, R., Verhage, M., Verstreken, P., Villa, C., Vogel, J., von Kalle, C., Walter, J., Weckhuysen, S., Weichert, W., Wood, L., Ziegler, A., Zipp, F., HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany., Medical Research Council (MRC), UK DRI Ltd, TWINCORE, Zentrum für experimentelle und klinische Infektionsforschung GmbH,Feodor-Lynen Str. 7, 30625 Hannover, Germany., Barcelona Supercomputing Center, LifeTime Community Working Groups, Cardiology, Neurology, Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Human genetics, Rajewsky N., Almouzni G., Gorski S.A., Aerts S., Amit I., Bertero M.G., Bock C., Bredenoord A.L., Cavalli G., Chiocca S., Clevers H., De Strooper B., Eggert A., Ellenberg J., Fernandez X.M., Figlerowicz M., Gasser S.M., Hubner N., Kjems J., Knoblich J.A., Krabbe G., Lichter P., Linnarsson S., Marine J.-C., Marioni J.C., Marti-Renom M.A., Netea M.G., Nickel D., Nollmann M., Novak H.R., Parkinson H., Piccolo S., Pinheiro I., Pombo A., Popp C., Reik W., Roman-Roman S., Rosenstiel P., Schultze J.L., Stegle O., Tanay A., Testa G., Thanos D., Theis F.J., Torres-Padilla M.-E., Valencia A., Vallot C., van Oudenaarden A., Vidal M., Voet T., Alberi L., Alexander S., Alexandrov T., Arenas E., Bagni C., Balderas R., Bandelli A., Becher B., Becker M., Beerenwinkel N., Benkirame M., Beyer M., Bickmore W., Biessen E.E.A.L., Blomberg N., Blumcke I., Bodenmiller B., Borroni B., Boumpas D.T., Bourgeron T., Bowers S., Braeken D., Brooksbank C., Brose N., Bruining H., Bury J., Caporale N., Cattoretti G., Chabane N., Chneiweiss H., Cook S.A., Curatolo P., de Jonge M.I., Deplancke B., de Witte P., Dimmeler S., Draganski B., Drews A., Dumbrava C., Engelhardt S., Gasser T., Giamarellos-Bourboulis E.J., Graff C., Grun D., Gut I., Hansson O., Henshall D.C., Herland A., Heutink P., Heymans S.R.B., Heyn H., Huch M., Huitinga I., Jackowiak P., Jongsma K.R., Journot L., Junker J.P., Katz S., Kehren J., Kempa S., Kirchhof P., Klein C., Koralewska N., Korbel J.O., Kuhnemund M., Lamond A.I., Lauwers E., Le Ber I., Leinonen V., Tobon A.L., Lundberg E., Lunkes A., Maatz H., Mann M., Marelli L., Matser V., Matthews P.M., Mechta-Grigoriou F., Menon R., Nielsen A.F., Pagani M., Pasterkamp R.J., Pitkanen A., Popescu V., Pottier C., Puisieux A., Rademakers R., Reiling D., Reiner O., Remondini D., Ritchie C., Rohrer J.D., Saliba A.-E., Sanchez-Valle R., Santosuosso A., Sauter A., Scheltema R.A., Scheltens P., Schiller H.B., Schneider A., Seibler P., Sheehan-Rooney K., Shields D., Sleegers K., Smit A.B., Smith K.G.C., Smolders I., Synofzik M., Tam W.L., Teichmann S., Thom M., Turco M.Y., van Beusekom H.M.M., Vandenberghe R., Van den Hoecke S., Van de Poel I., van der Ven A., van der Zee J., van Lunzen J., van Minnebruggen G., Van Paesschen W., van Swieten J., van Vught R., Verhage M., Verstreken P., Villa C.E., Vogel J., von Kalle C., Walter J., Weckhuysen S., Weichert W., Wood L., Ziegler A.-G., Zipp F., Center for Neurogenomics and Cognitive Research, Functional Genomics, Rajewsky, N, Almouzni, G, Gorski, S, Aerts, S, Amit, I, Bertero, M, Bock, C, Bredenoord, A, Cavalli, G, Chiocca, S, Clevers, H, De Strooper, B, Eggert, A, Ellenberg, J, Fernández, X, Figlerowicz, M, Gasser, S, Hubner, N, Kjems, J, Knoblich, J, Krabbe, G, Lichter, P, Linnarsson, S, Marine, J, Marioni, J, Marti-Renom, M, Netea, M, Nickel, D, Nollmann, M, Novak, H, Parkinson, H, Piccolo, S, Pinheiro, I, Pombo, A, Popp, C, Reik, W, Roman-Roman, S, Rosenstiel, P, Schultze, J, Stegle, O, Tanay, A, Testa, G, Thanos, D, Theis, F, Torres-Padilla, M, Valencia, A, Vallot, C, van Oudenaarden, A, Vidal, M, Voet, T, Cattoretti, G, Alliance for Modulation in Epilepsy, Pharmaceutical and Pharmacological Sciences, Experimental Pharmacology, RS: Carim - H02 Cardiomyopathy, MUMC+: MA Med Staf Spec Cardiologie (9), and Cardiologie

Subjects
0301 basic medicine, Male, Artificial intelligence, Legislation, Medical, [SDV]Life Sciences [q-bio], Molecular datasets, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Cell- and Tissue-Based Therapy, Diseases, LifeTime Community Working Groups, Disease, Biomarkers, Systems biology, Health data, Pharmacology, Toxicology and Pharmaceutics(all), 0302 clinical medicine, Conjunts de dades, ethics [Delivery of Health Care], Health care, Pathology, Medicine, European healthcare, BRAIN, Single-cell multi-omics, GENE-EXPRESSION, Multidisciplinary, methods [Medicine], Education, Medical, Settore BIO/13, Intel.ligència artificial, 3. Good health, ALZHEIMERS-DISEASE, Europe, Health, Management system, Perspective, Female, ddc:500, Single-Cell Analysis, Biomarkers, Diseases, Systems biology, Complex diseases, Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], medicine.medical_specialty, General Science & Technology, Cells, MEDLINE, cell-based interceptive medicine, LifeTime Initiative, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Clinical datasets, Artificial Intelligence, REVEALS, LifeTime Community, standards [Medicine], Humans, OMICS, RECONSTRUCTION, Intensive care medicine, trends [Medicine], trends [Delivery of Health Care], business.industry, Disease progression, standards [Delivery of Health Care], methods [Delivery of Health Care], 030104 developmental biology, lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4], single cell, personalized therapy, machine learning, bioinformatics, systems biology, disease, cell-based interceptive medicine, Early Diagnosis, Cardiovascular and Metabolic Diseases, Human medicine, business, Delivery of Health Care, 030217 neurology & neurosurgery, Cell based
Abstract

Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade., The LifeTime initiative is an ambitious, multidisciplinary programme that aims to improve healthcare by tracking individual human cells during disease processes and responses to treatment in order to develop and implement cell-based interceptive medicine in Europe.

Published
2020
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9. List of contributors

Author

Alessandria, V., primary, Bianchini, A., additional, Bisson, L.F., additional, Brandt, M.J., additional, Brányik, T., additional, Buckenhueskes, H.J., additional, Chambers, P.J., additional, Cocolin, L., additional, Corsetti, A., additional, Csapó, J., additional, Curtin, C.D., additional, de Vos, W.M., additional, Derkx, P.M.F., additional, Dolci, P., additional, Ewe, J.A., additional, Flahaut, N.A.L., additional, Foerst, P., additional, Franz, C.M.A.P., additional, Holzapfel, W.H., additional, Huch, M., additional, Johansen, E., additional, Korhonen, H., additional, Kuda, T., additional, Kyselová, L., additional, López, P., additional, Lücke, F.-K., additional, Mohedano, M.L., additional, Nout, R., additional, Øregaard, G., additional, Ouwehand, A.C., additional, Perpetuini, G., additional, Pihlanto, A., additional, Pretorius, I.S., additional, Rantsiou, K., additional, Röytiö, H., additional, Russo, P., additional, Santivarangkna, C., additional, Sørensen, K.I., additional, Spano, G., additional, Todorov, S.D., additional, Tofalo, R., additional, Varga-Visi, É., additional, Walker, G.A., additional, Welman, A.D., additional, and Yeo, S.K., additional

Published
2015
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11. Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine (Nature, (2020), 587, 7834, (377-386), 10.1038/s41586-020-2715-9)

Author

Rajewsky, N. Almouzni, G. Gorski, S.A. Aerts, S. Amit, I. Bertero, M.G. Bock, C. Bredenoord, A.L. Cavalli, G. Chiocca, S. Clevers, H. De Strooper, B. Eggert, A. Ellenberg, J. Fernández, X.M. Figlerowicz, M. Gasser, S.M. Hubner, N. Kjems, J. Knoblich, J.A. Krabbe, G. Lichter, P. Linnarsson, S. Marine, J.-C. Marioni, J.C. Marti-Renom, M.A. Netea, M.G. Nickel, D. Nollmann, M. Novak, H.R. Parkinson, H. Piccolo, S. Pinheiro, I. Pombo, A. Popp, C. Reik, W. Roman-Roman, S. Rosenstiel, P. Schultze, J.L. Stegle, O. Tanay, A. Testa, G. Thanos, D. Theis, F.J. Torres-Padilla, M.-E. Valencia, A. Vallot, C. van Oudenaarden, A. Vidal, M. Voet, T. Alberi, L. Alexander, S. Alexandrov, T. Arenas, E. Bagni, C. Balderas, R. Bandelli, A. Becher, B. Becker, M. Beerenwinkel, N. Benkirane, M. Beyer, M. Bickmore, W.A. Biessen, E.E.A.L. Blomberg, N. Blumcke, I. Bodenmiller, B. Borroni, B. Boumpas, D.T. Bourgeron, T. Bowers, S. Braeken, D. Brooksbank, C. Brose, N. Bruining, H. Bury, J. Caporale, N. Cattoretti, G. Chabane, N. Chneiweiss, H. Cook, S.A. Curatolo, P. de Jonge, M.I. Deplancke, B. de Witte, P. Dimmeler, S. Draganski, B. Drews, A. Dumbrava, C. Engelhardt, S. Gasser, T. Giamarellos-Bourboulis, E.J. Graff, C. Grün, D. Gut, I.G. Hansson, O. Henshall, D.C. Herland, A. Heutink, P. Heymans, S.R.B. Heyn, H. Huch, M. Huitinga, I. Jackowiak, P. Jongsma, K.R. Journot, L. Junker, J.P. Katz, S. Kehren, J. Kempa, S. Kirchhof, P. Klein, C. Koralewska, N. Korbel, J.O. Kühnemund, M. Lamond, A.I. Lauwers, E. Le Ber, I. Leinonen, V. López-Tobón, A. Lundberg, E. Lunkes, A. Maatz, H. Mann, M. Marelli, L. Matser, V. Matthews, P.M. Mechta-Grigoriou, F. Menon, R. Nielsen, A.F. Pagani, M. Pasterkamp, R.J. Pitkänen, A. Popescu, V. Pottier, C. Puisieux, A. Rademakers, R. Reiling, D. Reiner, O. Remondini, D. Ritchie, C. Rohrer, J.D. Saliba, A.-E. Sanchez-Valle, R. Santosuosso, A. Sauter, A. Scheltema, R.A. Scheltens, P. Schiller, H.B. Schneider, A. Seibler, P. Sheehan-Rooney, K. Shields, D.J. Sleegers, K. Smit, A.B. Smith, K.G.C. Smolders, I. Synofzik, M. Tam, W.L. Teichmann, S.A. Thom, M. Turco, M.Y. van Beusekom, H.M.M. Vandenberghe, R. Van den Hoecke, S. van de Poel, I. van der Ven, A. van der Zee, J. van Lunzen, J. van Minnebruggen, G. van Oudenaarden, A. Van Paesschen, W. van Swieten, J.C. van Vught, R. Verhage, M. Verstreken, P. Villa, C.E. Vogel, J. von Kalle, C. Walter, J. Weckhuysen, S. Weichert, W. Wood, L. Ziegler, A.-G. Zipp, F. LifeTime Community Working Groups

Subjects
ComputingMethodologies_DOCUMENTANDTEXTPROCESSING
Abstract

In this Perspective, owing to an error in the HTML, the surname of author Alejandro López-Tobón of the LifeTime Community Working Groups consortium was indexed as ‘Tobon’ rather than ‘López-Tobón’ and the accents were missing. The HTML version of the original Perspective has been corrected; the PDF and print versions were always correct. © 2021, The Author(s).

Published
2021

12. Voices of biotech research

Author

Annabi, N., Baker, M., Boettiger, A., Chakraborty, D., Chen, Y., Corbett, K.S., Correia, B., Dahlman, J., de Oliveira, T., Ertuerk, A., Yanik, M.F., Henaff, E., Huch, M., Iliev, I.D., Jacobs, T., Junca, H., Keung, A., Kolodkin-Gal, I., Krishnaswamy, S., Lancaster, M., Macosko, E., Martínez-Núñez, M.A., Miura, K., Molloy, J., Cruz, A.O., Platt, R.J., Posey, A.D., Shao, H., Simunovic, M., Slavov, N., Takebe, T., Vandenberghe, L.H., Varshney, R.K., Wang, J., Annabi, N., Baker, M., Boettiger, A., Chakraborty, D., Chen, Y., Corbett, K.S., Correia, B., Dahlman, J., de Oliveira, T., Ertuerk, A., Yanik, M.F., Henaff, E., Huch, M., Iliev, I.D., Jacobs, T., Junca, H., Keung, A., Kolodkin-Gal, I., Krishnaswamy, S., Lancaster, M., Macosko, E., Martínez-Núñez, M.A., Miura, K., Molloy, J., Cruz, A.O., Platt, R.J., Posey, A.D., Shao, H., Simunovic, M., Slavov, N., Takebe, T., Vandenberghe, L.H., Varshney, R.K., and Wang, J.

Abstract

What will be the most important areas of research in biotech over the coming years? Which technologies will be most important to advance knowledge and applications in these areas? Nature Biotechnology reached out to a set of faculty doing outstanding work in research areas representative of the journal’s remit and asked them to contribute their vision of where their fields are going.

Published
2021

13. Long-term live imaging and multiscale analysis identify heterogeneity and core principles of epithelial organoid morphogenesis

Author

Hof, L, Moreth, T, Koch, M, Liebisch, T, Kurtz, M, Tarnick, J, Lissek, SM, Verstegen, Monique, van der Laan, Luc, Huch, M, Matthaus, F, Stelzer, EHK, Pampaloni, F, Hof, L, Moreth, T, Koch, M, Liebisch, T, Kurtz, M, Tarnick, J, Lissek, SM, Verstegen, Monique, van der Laan, Luc, Huch, M, Matthaus, F, Stelzer, EHK, and Pampaloni, F

Abstract

Background: Organoids are morphologically heterogeneous three-dimensional cell culture systems and serve as an ideal model for understanding the principles of collective cell behaviour in mammalian organs during development, homeostasis, regeneration, and pathogenesis. To investigate the underlying cell organisation principles of organoids, we imaged hundreds of pancreas and cholangiocarcinoma organoids in parallel using light sheet and bright-field microscopy for up to 7 days. Results: We quantified organoid behaviour at single-cell (microscale), individual-organoid (mesoscale), and entire-culture (macroscale) levels. At single-cell resolution, we monitored formation, monolayer polarisation, and degeneration and identified diverse behaviours, including lumen expansion and decline (size oscillation), migration, rotation, and multi-organoid fusion. Detailed individual organoid quantifications lead to a mechanical 3D agent-based model. A derived scaling law and simulations support the hypotheses that size oscillations depend on organoid properties and cell division dynamics, which is confirmed by bright-field microscopy analysis of entire cultures. Conclusion: Our multiscale analysis provides a systematic picture of the diversity of cell organisation in organoids by identifying and quantifying the core regulatory principles of organoid morphogenesis.

Published
2021

14. Multi-site Neurogenin3 Phosphorylation Controls Pancreatic Endocrine Differentiation

Author

Azzarelli, R., Hurley, C., Sznurkowska, M., Rulands, S., Hardwick, L., Gamper, I., Ali, F., McCracken, L., Hindley, C., McDuff, F., Nestorowa, S., Kemp, R., Jones, K., Goettgens, B., Huch, M., Evan, G., Simons, B., Winton, D., Philpott, A., Rulands, Steffen [0000-0001-6398-1553], Gottgens, Berthold [0000-0001-6302-5705], Huch Ortega, Meritxell [0000-0002-1545-5265], Evan, Gerard [0000-0003-0412-1216], Simons, Benjamin [0000-0002-3875-7071], Winton, Douglas [0000-0001-6067-7927], Philpott, Anna [0000-0003-3789-2463], and Apollo - University of Cambridge Repository

Subjects
Homeodomain Proteins, endocrine system, proneural bHLH transcription factors, diabetes, Cell Differentiation, Nerve Tissue Proteins, insulinoma, neurogenin3, β cells, digestive system, Cyclin-Dependent Kinases, Living matter, Islets of Langerhans, Mice, endocrine differentiation, pancreatic development, pancreatic organoids, Animals, Basic Helix-Loop-Helix Transcription Factors, Humans, Insulin-Secreting Cells, Pancreas, Phosphorylation, Signal Transduction
Abstract

The proneural transcription factor Neurogenin3 (Ngn3) plays a critical role in pancreatic endocrine cell differentiation, although regulation of Ngn3 protein is largely unexplored. Here we demonstrate that Ngn3 protein undergoes cyclin-dependent kinase (Cdk)-mediated phosphorylation on multiple serine-proline sites. Replacing wild-type protein with a phosphomutant form of Ngn3 increases a cell generation, the earliest endocrine cell type to be formed in the developing pancreas. Moreover, un(der)phosphorylated Ngn3 maintains insulin expression in adult beta cells in the presence of elevated c-Myc and enhances endocrine specification during ductal reprogramming. Mechanistically, preventing multi-site phosphorylation enhances both Ngn3 stability and DNA binding, promoting the increased expression of target genes that drive differentiation. Therefore, multi-site phosphorylation of Ngn3 controls its ability to promote pancreatic endocrine differentiation and to maintain beta cell function in the presence of pro-proliferation cues and could be manipulated to promote and maintain endocrine differentiation in vitro and in vivo.

Published
2017

15. Mouse Model of Alagille Syndrome and Mechanisms of Jagged1 Missense Mutations.

Author

Andersson, ER, Chivukula, IV, Hankeova, S, Sjöqvist, M, Tsoi, YL, Ramsköld, D, Masek, J, Elmansuri, A, Hoogendoorn, A, Vazquez, E, Storvall, H, Netušilová, J, Huch, M, Fischler, B, Ellis, E, Contreras, A, Nemeth, A, Chien, KC, Clevers, H, Sandberg, R, Bryja, V, Lendahl, U, Andersson, ER, Chivukula, IV, Hankeova, S, Sjöqvist, M, Tsoi, YL, Ramsköld, D, Masek, J, Elmansuri, A, Hoogendoorn, A, Vazquez, E, Storvall, H, Netušilová, J, Huch, M, Fischler, B, Ellis, E, Contreras, A, Nemeth, A, Chien, KC, Clevers, H, Sandberg, R, Bryja, V, and Lendahl, U

Abstract

BACKGROUND & AIMS: Alagille syndrome is a genetic disorder characterized by cholestasis, ocular abnormalities, characteristic facial features, heart defects, and vertebral malformations. Most cases are associated with mutations in JAGGED1 (JAG1), which encodes a Notch ligand, although it is not clear how these contribute to disease development. We aimed to develop a mouse model of Alagille syndrome to elucidate these mechanisms. METHODS: Mice with a missense mutation (H268Q) in Jag1 (Jag1+/Ndr mice) were outbred to a C3H/C57bl6 background to generate a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice). Liver tissues were collected at different timepoints during development, analyzed by histology, and liver organoids were cultured and analyzed. We performed transcriptome analysis of Jag1Ndr/Ndr livers and livers from patients with Alagille syndrome, cross-referenced to the Human Protein Atlas, to identify commonly dysregulated pathways and biliary markers. We used species-specific transcriptome separation and ligand-receptor interaction assays to measure Notch signaling and the ability of JAG1Ndr to bind or activate Notch receptors. We studied signaling of JAG1 and JAG1Ndr via NOTCH 1, NOTCH2, and NOTCH3 and resulting gene expression patterns in parental and NOTCH1-expressing C2C12 cell lines. RESULTS: Jag1Ndr/Ndr mice had many features of Alagille syndrome, including eye, heart, and liver defects. Bile duct differentiation, morphogenesis, and function were dysregulated in newborn Jag1Ndr/Ndr mice, with aberrations in cholangiocyte polarity, but these defects improved in adult mice. Jag1Ndr/Ndr liver organoids collapsed in culture, indicating structural instability. Whole-transcriptome sequence analyses of liver tissues from mice and patients with Alagille syndrome identified dysregulated genes encoding proteins enriched at the apical side of cholangiocytes, including CFTR and SLC5A1, as well as reduced expression of IGF1. Exposure of Notch-expressing cells to JAG

Published
2018

17. Human primary liver cancer-derived organoid cultures for disease modeling and drug screening

Author

Broutier, L. (Laura), Mastrogiovanni, G. (Gianmarco), Verstegen, M.M.A. (Monique), Francies, H.E. (Hayley E.), Gavarró, L.M. (Lena Morrill), Bradshaw, C.R. (Charles R.), Allen, G.E. (George E.), Arnes-Benito, R. (Robert), Sidorova, O. (Olga), Gaspersz, M.P. (Marcia), Georgakopoulos, N. (Nikitas), Koo, B.-K. (Bon-Kyoung), Dietmann, S. (Sabine), Davies, S.E. (Susan E.), Praseedom, R.K. (Raaj K.), Lieshout, R. (Ruby), IJzermans, J.N.M. (Jan), Wigmore, S.J. (Stephen J.), Saeb-Parsy, K. (Kourosh), Garnett, M.J. (Mathew J.), Laan, L.J.W. (Luc) van der, Huch, M. (Meritxell), Broutier, L. (Laura), Mastrogiovanni, G. (Gianmarco), Verstegen, M.M.A. (Monique), Francies, H.E. (Hayley E.), Gavarró, L.M. (Lena Morrill), Bradshaw, C.R. (Charles R.), Allen, G.E. (George E.), Arnes-Benito, R. (Robert), Sidorova, O. (Olga), Gaspersz, M.P. (Marcia), Georgakopoulos, N. (Nikitas), Koo, B.-K. (Bon-Kyoung), Dietmann, S. (Sabine), Davies, S.E. (Susan E.), Praseedom, R.K. (Raaj K.), Lieshout, R. (Ruby), IJzermans, J.N.M. (Jan), Wigmore, S.J. (Stephen J.), Saeb-Parsy, K. (Kourosh), Garnett, M.J. (Mathew J.), Laan, L.J.W. (Luc) van der, and Huch, M. (Meritxell)

Abstract

Human liver cancer research currently lacks in vitro models that can faithfully recapitulate the pathophysiology of the original tumor. We recently described a novel, near-physiological organoid culture system, wherein primary human healthy liver cells form long-term expanding organoids that retain liver tissue function and genetic stability. Here we extend this culture system to the propagation of primary liver cancer (PLC) organoids from three of the most common PLC subtypes: hepatocellular carcinoma (HCC), cholangiocarcinoma (CC) and combined HCC/CC (CHC) tumors. PLC-derived organoid cultures preserve the histological architecture, gene expression and genomic landscape of the original tumor, allowing for discrimination between different tumor tissues and subtypes, even after long-term expansion in culture in the same medium conditions. Xenograft studies demonstrate that the tumorogenic potential, histological features and metastatic properties of PLC-derived organoids are preserved in vivo. PLC-derived organoids are amenable for biomarker identification and drug-screening testing and led to the identification of the ERK inhibitor SCH772984 as a potential therapeutic agent for primary liver cancer. We thus demonstrate the wide-ranging biomedical utilities of PLC-derived organoid models in furthering the understanding of liver cancer biology and in developing personalized-medicine approaches for the disease.

Published
2017
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18. Long-Term Adult Feline Liver Organoid Cultures for Disease Modeling of Hepatic Steatosis

Author

Kruitwagen, H.S. (Hedwig S.), Oosterhoff, L.A. (Loes A.), Vernooij, I.G.W.H. (Ingrid G.W.H.), Schrall, I.M. (Ingrid M.), Wolferen, M.E. (Monique) van, Bannink, F. (Farah), Roesch, C. (Camille), van Uden, L. (Lisa), Molenaar, M.R. (Martijn R.), Helms, J.B. (J. Bernd), Grinwis, G.C.M. (Guy C.), Verstegen, M.M.A. (Monique), Laan, L.J.W. (Luc) van der, Huch, M. (Meritxell), Geijsen, N. (Niels), Vries, R.G.J. (Robert), Clevers, H.C. (Hans), Rothuizen, J. (J.), Schotanus, B.A. (Baukje A.), Penning, C. (Corine), Spee, B. (B.), Kruitwagen, H.S. (Hedwig S.), Oosterhoff, L.A. (Loes A.), Vernooij, I.G.W.H. (Ingrid G.W.H.), Schrall, I.M. (Ingrid M.), Wolferen, M.E. (Monique) van, Bannink, F. (Farah), Roesch, C. (Camille), van Uden, L. (Lisa), Molenaar, M.R. (Martijn R.), Helms, J.B. (J. Bernd), Grinwis, G.C.M. (Guy C.), Verstegen, M.M.A. (Monique), Laan, L.J.W. (Luc) van der, Huch, M. (Meritxell), Geijsen, N. (Niels), Vries, R.G.J. (Robert), Clevers, H.C. (Hans), Rothuizen, J. (J.), Schotanus, B.A. (Baukje A.), Penning, C. (Corine), and Spee, B. (B.)

Abstract

Hepatic steatosis is a highly prevalent liver disease, yet research is hampered by the lack of tractable cellular and animal models. Steatosis also occurs in cats, where it can cause severe hepatic failure. Previous studies demonstrate the potential of liver organoids for modeling genetic diseases. To examine the possibility of using organoids to model steatosis, we established a long-term feline liver organoid culture with adult liver stem cell characteristics and differentiation potential toward hepatocyte-like cells. Next, organoids from mouse, human, dog

Published
2017
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19. Long-Term Adult Feline Liver Organoid Cultures for Disease Modeling of Hepatic Steatosis

Author

Kruitwagen, HS, Oosterhoff, LA, Vernooij, I, Schrall, IM, van Wolferen, ME, Bannink, F, Roesch, C, van Uden, L, Molenaar, MR, Helms, JB, Grinwis, GCM, Verstegen, Monique, van der Laan, Luc, Huch, M, Geijsen, N, de Vries, RG, Clevers, H, Rothuizen, J, Schotanus, BA, Penning, LC, Spee, B, Kruitwagen, HS, Oosterhoff, LA, Vernooij, I, Schrall, IM, van Wolferen, ME, Bannink, F, Roesch, C, van Uden, L, Molenaar, MR, Helms, JB, Grinwis, GCM, Verstegen, Monique, van der Laan, Luc, Huch, M, Geijsen, N, de Vries, RG, Clevers, H, Rothuizen, J, Schotanus, BA, Penning, LC, and Spee, B

Published
2017

20. Chromosomal abnormalities in hepatic cysts point to novel polycystic liver disease genes

Author

Wills, E.S., Cnossen, W.R., Veltman, J.A., Woestenenk, R.M., Steehouwer, M., Salomon, J., Morsche, R.H.M. te, Huch, M., Hehir-Kwa, J.Y., Banning, M.J., Pfundt, R.P., Roepman, R., Hoischen, A., Drenth, J.P.H., Wills, E.S., Cnossen, W.R., Veltman, J.A., Woestenenk, R.M., Steehouwer, M., Salomon, J., Morsche, R.H.M. te, Huch, M., Hehir-Kwa, J.Y., Banning, M.J., Pfundt, R.P., Roepman, R., Hoischen, A., and Drenth, J.P.H.

Abstract

Contains fulltext : 167652.pdf (publisher's version ) (Closed access), Autosomal dominant polycystic liver disease (ADPLD) is caused by variants in PRKCSH, SEC63, and LRP5, whereas autosomal dominant polycystic kidney disease is caused by variants in PKD1 and PKD2. Liver cyst development in these disorders is explained by somatic loss-of-heterozygosity (LOH) of the wild-type allele in the developing cyst. We hypothesize that we can use this mechanism to identify novel disease genes that reside in LOH regions. In this study, we aim to map abnormal genomic regions using high-density SNP microarrays to find novel PLD genes. We collected 46 cysts from 23 patients with polycystic or sporadic hepatic cysts, and analyzed DNA from those cysts using high-resolution microarray (n=24) or Sanger sequencing (n=22). We here focused on regions of homozygosity on the autosomes (>3.0 Mb) and large CNVs (>1.0 Mb). We found frequent LOH in PRKCSH (22/29) and PKD1/PKD2 (2/3) cysts of patients with known heterozygous germline variants in the respective genes. In the total cohort, 12/23 patients harbored abnormalities outside of familiar areas. In individual ADPLD cases, we identified germline events: a 2q13 complex rearrangement resulting in BUB1 haploinsufficiency, a 47XXX karyotype, chromosome 9q copy-number loss, and LOH on chromosome 3p. The latter region was overlapping with an LOH region identified in two other cysts. Unique germline and somatic abnormalities occur frequently in and outside of known genes underlying cysts. Each liver cyst has a unique genetic makeup. LOH driver gene BUB1 may imply germline causes of genetic instability in PLD.

Published
2016

23. Long-Term Culture of Genome-Stable Bipotent Stem Cells from Adult Human Liver

Author

Huch, M, Gehart, H, van Boxtel, R, Hamer, K, Blokzijl, F, Verstegen, Monique, Ellis, E, van Wenum, M, Fuchs, SA, de Ligt, J, van de Wetering, M, Sasaki, N, Boers, SJ, Kemperman, H, de Jonge, Jeroen, IJzermans, J.N.M., Nieuwenhuis, EES, Hoekstra, R, Strom, S, Vries, RRG, van der Laan, Luc, Cuppen, E, Clevers, H, Huch, M, Gehart, H, van Boxtel, R, Hamer, K, Blokzijl, F, Verstegen, Monique, Ellis, E, van Wenum, M, Fuchs, SA, de Ligt, J, van de Wetering, M, Sasaki, N, Boers, SJ, Kemperman, H, de Jonge, Jeroen, IJzermans, J.N.M., Nieuwenhuis, EES, Hoekstra, R, Strom, S, Vries, RRG, van der Laan, Luc, Cuppen, E, and Clevers, H

Abstract

Despite the enormous replication potential of the human liver, there are currently no culture systems available that sustain hepatocyte replication and/or function in vitro. We have shown previously that single mouse Lgr5+ liver stem cells can be expanded as epithelial organoids in vitro and can be differentiated into functional hepatocytes in vitro and in vivo. We now describe conditions allowing long-term expansion of adult bile duct-derived bipotent progenitor cells from human liver. The expanded cells are highly stable at the chromosome and structural level, while single base changes occur at very low rates. The cells can readily be converted into functional hepatocytes in vitro and upon transplantation in vivo. Organoids from alpha 1-antitrypsin deficiency and Alagille syndrome patients mirror the in vivo pathology. Clonal long-term expansion of primary adult liver stem cells opens up experimental avenues for disease modeling, toxicology studies, regenerative medicine, and gene therapy.

Published
2015

25. Identification of PRMT5 as a therapeutic target in cholangiocarcinoma.

Author

Elurbide J, Colyn L, Latasa MU, Uriarte I, Mariani S, Lopez-Pascual A, Valbuena E, Castello-Uribe B, Arnes-Benito R, Adan-Villaescusa E, Martinez-Perez LA, Azkargorta M, Elortza F, Wu H, Krawczyk M, Schneider KM, Sangro B, Aldrighetti L, Ratti F, Casadei Gardini A, Marin JJG, Amat I, Urman JM, Arechederra M, Martinez-Chantar ML, Trautwein C, Huch M, Cubero FJ, Berasain C, G Fernandez-Barrena M, and Avila MA

Subjects
Humans, Animals, Mice, Cell Line, Tumor, Cell Proliferation drug effects, Purine-Nucleoside Phosphorylase antagonists & inhibitors, Purine-Nucleoside Phosphorylase metabolism, Purine-Nucleoside Phosphorylase genetics, Organoids drug effects, Deoxycytidine analogs & derivatives, Deoxycytidine therapeutic use, Deoxycytidine pharmacology, Cisplatin therapeutic use, Cisplatin pharmacology, Gemcitabine, Antineoplastic Agents therapeutic use, Antineoplastic Agents pharmacology, Disease Models, Animal, Cholangiocarcinoma drug therapy, Cholangiocarcinoma genetics, Cholangiocarcinoma pathology, Protein-Arginine N-Methyltransferases antagonists & inhibitors, Protein-Arginine N-Methyltransferases metabolism, Protein-Arginine N-Methyltransferases genetics, Bile Duct Neoplasms drug therapy, Bile Duct Neoplasms pathology, Bile Duct Neoplasms genetics
Abstract

Background: Cholangiocarcinoma (CCA) is a very difficult-to-treat cancer. Chemotherapies are little effective and response to immune checkpoint inhibitors is limited. Therefore, new therapeutic strategies need to be identified., Objective: We characterised the enzyme protein arginine-methyltransferase 5 (PRMT5) as a novel therapeutic target in CCA., Design: We evaluated the expression of PRMT5, its functional partner MEP50 and methylthioadenosine phosphorylase (MTAP)-an enzyme that modulates the sensitivity of PRMT5 to pharmacological inhibitors-in human CCA tissues. PRMT5-targeting drugs, currently tested in clinical trials for other malignancies, were assessed in human CCA cell lines and organoids, as well as in two immunocompetent CCA mouse models. Transcriptomic, proteomic and functional analyses were performed to explore the underlying antitumoural mechanisms., Results: PRMT5 and MEP50 proteins were correlatively overexpressed in most CCA tissues. MTAP was absent in 25% of intrahepatic CCA. PRMT5-targeting drugs markedly inhibited CCA cell proliferation, synergising with cisplatin and gemcitabine and hindered the growth of cholangiocarcinoma organoids. PRMT5 inhibition blunted the expression of oncogenic genes involved in chromatin remodelling and DNA repair, consistently inducing the formation of RNA loops and promoting DNA damage. Treatment with PRMT5-targeting drugs significantly restrained the growth of experimental CCA without adverse effects and concomitantly induced the recruitment of CD4 and CD8 T cells to shrinking tumourous lesions., Conclusion: PRMT5 and MEP50 are frequently upregulated in human CCA, and PRMT5-targeting drugs have significant antitumoural efficacy in clinically relevant CCA models. Our findings support the evaluation of PRMT5 inhibitors in clinical trials, including their combination with cytotoxic and immune therapies., Competing Interests: Competing interests: MAA is editor of Gut. All other authors have no conflict of interest., (© Author(s) (or their employer(s)) 2025. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ Group.)

Published
2024
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26. In vitro human cell-based models: What can they do and what are their limitations?

Author

Lutolf MP, Radisic M, Beekman J, Huh DD, Huch M, Turco MY, Birgani ZNT, Gao D, Yao R, Lin H, and Takebe T

Abstract

Competing Interests: Declaration of interests M.R. is an inventor in multiple patents covering Biowire heart-on-a-chip technology that are licensed to Valo Health. She receives royalty from these inventions. M.R. holds equity in and receives consulting fees from Quthero, Inc. She is an inventor on patents and patent applications describing regenerative peptides and biomaterials that have been licensed to Quthero, Inc. D.D.H. is a founder of Vivodyne, Inc., and holds equity in Vivodyne, Inc., and Emulate Bio, Inc. D.D.H. has a number of patent applications and issued patents related to in vitro models of human tissue. M.H. is an inventor on several patents related to organoid work. J.B. is an inventor on a patent related to organoid technology, has received consultation fees, and is principal investigator on an industry-sponsored project related to the work (Proteostasis, Eloxx Pharmaceuticals). He cofounded and has shares <5% in FAIR Therapeutics. Full disclosures can be found at https://www.umcutrecht.nl/en/research/researchers/beekman-jeffrey-jm.

Published
2024
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27. Effects of pectin methyl-esterification on intestinal microbiota and its immunomodulatory properties in naive mice.

Author

Steigerwald H, Blanco-Pérez F, Macías-Camero A, Albrecht M, Huch M, Bender C, Schülke S, Keller J, Krause M, Barbas C, Gonzalez-Menendez I, Quintanilla-Martinez L, Toda M, Barber D, Kulling S, Bunzel M, Vieths S, Villaseñor A, Stoll D, and Scheurer S

Subjects
Mice, Animals, Esterification, Dietary Fiber pharmacology, Dietary Fiber metabolism, Fermentation, Pectins chemistry, Gastrointestinal Microbiome
Abstract

Pectins are dietary fibers that are attributed with several beneficial immunomodulatory effects. Depending on the degree of esterification (DE), pectins can be classified as high methoxyl pectin (HMP) or low methoxyl pectin (LMP). The aim of this study was to investigate the effects of pectin methyl-esterification on intestinal microbiota and its immunomodulatory properties in naive mice. Supplementation of the diet with LMP or HMP induced changes in the composition of the intestinal microbiota in mice toward Bacteroides, which was mainly promoted by HMP. Metabolome analysis of stool samples from pectin-fed mice showed a different effect of the two types of pectin on the levels of short-chain fatty acids and bile acids, which was consistent with highly efficient in vivo fermentation of LMP. Analysis of serum antibody levels showed a significant increase in IgG and IgA levels by both pectins, while FACS analysis revealed a decrease of infiltrating inflammatory cells in the intestinal lamina propria by HMP. Our study revealed that the structural properties of the investigated pectins determine fermentability, effects on microbial composition, metabolite production, and modulation of immune responses. Consumption of HMP preferentially altered the gut microbiota and suppressed pro-inflammatory immune responses, suggesting a beneficial role in inflammatory diseases., Competing Interests: Declaration of competing interest The authors do not have a conflict of interest. CoI statement was provided using https://declarations.elsevier.com/ or the ICMJE disclosure form. SV received honoraria as Associate Editor of JACI from AAAI, support from AAAI and EAACI and royalties from Schattauer Allergologie Handbuch Elsevier Nahrungsmittelallergien und Intoleranzen Karger Food Allergy: Molecular Basis and Clinical Practice., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Published
2024
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28. Bosea rubneri sp. nov. Isolated from Organically Grown Allium cepa.

Author

Stoll DA, Grimmler C, Hetzer B, Masoura A, Kulling SE, and Huch M

Subjects
Genome, Bacterial, Phospholipids analysis, Bacterial Typing Techniques, Sequence Analysis, DNA, Nucleic Acid Hybridization, Onions microbiology, RNA, Ribosomal, 16S genetics, Phylogeny, DNA, Bacterial genetics, Fatty Acids metabolism, Fatty Acids analysis, Fatty Acids chemistry, Base Composition
Abstract

Strain ZW T0&#95;25 T was isolated from an onion sample (Allium cepa var. Hytech F1) within a storage trial and proofed to be a novel, aerobic, Gram-stain negative, rod-shaped bacterial strain. Analyses of the 16S rRNA gene sequence and of the whole draft genome sequences, i.e., digital DNA-DNA hybridization (dDDH), Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) showed that this strain represents a new species of the genus Bosea. The genome size of strain ZW T0&#95;25 T is 6.19 Mbp, and the GC content is 66.9%. As whole cell sugars, rhamnose, ribose and glucose were identified. Ubiquinone Q-10 is the major respiratory quinone with 97.8%. Polar lipids in strain ZW T0&#95;25 T are composed of one phosphatidylethanolamine, one phosphatidylglycerol, one aminophospholipid, two aminolipids, one glycolipid and two phospholipids whereas the fatty acid profile predominantly consists of C18:1 w7c (63.3%), C16:1 w7c (19.5%) and C16:0 (7.1%). Phenotypic traits were tested in the wet lab as well as predicted in silico from genome data. Therefore, according to this polyphasic approach, the new name Bosea rubneri sp. nov. with the type strain ZW T0&#95;25 T (= DSM 116094  T  = LMG 33093  T ) is proposed., (© 2024. The Author(s).)

Published
2024
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29. ICAM-1 nanoclusters regulate hepatic epithelial cell polarity by leukocyte adhesion-independent control of apical actomyosin.

Author

Cacho-Navas C, López-Pujante C, Reglero-Real N, Colás-Algora N, Cuervo A, Conesa JJ, Barroso S, de Rivas G, Ciordia S, Paradela A, D'Agostino G, Manzo C, Feito J, Andrés G, Molina-Jiménez F, Majano P, Correas I, Carazo JM, Nourshargh S, Huch M, and Millán J

Subjects
Animals, Mice, Humans, Epithelial Cells metabolism, Hepatocytes metabolism, Liver metabolism, Actin Cytoskeleton metabolism, Leukocytes metabolism, Cell Polarity, Actomyosin metabolism, Intercellular Adhesion Molecule-1 genetics, Intercellular Adhesion Molecule-1 metabolism
Abstract

Epithelial intercellular adhesion molecule (ICAM)-1 is apically polarized, interacts with, and guides leukocytes across epithelial barriers. Polarized hepatic epithelia organize their apical membrane domain into bile canaliculi and ducts, which are not accessible to circulating immune cells but that nevertheless confine most of ICAM-1. Here, by analyzing ICAM-1&#95;KO human hepatic cells, liver organoids from ICAM-1&#95;KO mice and rescue-of-function experiments, we show that ICAM-1 regulates epithelial apicobasal polarity in a leukocyte adhesion-independent manner. ICAM-1 signals to an actomyosin network at the base of canalicular microvilli, thereby controlling the dynamics and size of bile canalicular-like structures. We identified the scaffolding protein EBP50/NHERF1/SLC9A3R1, which connects membrane proteins with the underlying actin cytoskeleton, in the proximity interactome of ICAM-1. EBP50 and ICAM-1 form nano-scale domains that overlap in microvilli, from which ICAM-1 regulates EBP50 nano-organization. Indeed, EBP50 expression is required for ICAM-1-mediated control of BC morphogenesis and actomyosin. Our findings indicate that ICAM-1 regulates the dynamics of epithelial apical membrane domains beyond its role as a heterotypic cell-cell adhesion molecule and reveal potential therapeutic strategies for preserving epithelial architecture during inflammatory stress., Competing Interests: CC, CL, NR, NC, AC, JC, SB, Gd, SC, AP, GD, CM, JF, GA, FM, PM, IC, JC, SN, MH, JM No competing interests declared, (© 2023, Cacho-Navas et al.)

Published
2024
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30. Tissue Organoid Cultures Metabolize Dietary Carcinogens Proficiently and Are Effective Models for DNA Adduct Formation.

Author

Caipa Garcia AL, Kucab JE, Al-Serori H, Beck RSS, Bellamri M, Turesky RJ, Groopman JD, Francies HE, Garnett MJ, Huch M, Drost J, Zilbauer M, Arlt VM, and Phillips DH

Subjects
Humans, Carcinogens toxicity, Carcinogens metabolism, Liver metabolism, Organoids metabolism, DNA Adducts, Neoplasms
Abstract

Human tissue three-dimensional (3D) organoid cultures have the potential to reproduce in vitro the physiological properties and cellular architecture of the organs from which they are derived. The ability of organoid cultures derived from human stomach, liver, kidney, and colon to metabolically activate three dietary carcinogens, aflatoxin B 1 (AFB 1 ), aristolochic acid I (AAI), and 2-amino-1-methyl-6-phenylimidazo[4,5- b ]pyridine (PhIP), was investigated. In each case, the response of a target tissue (liver for AFB 1 ; kidney for AAI; colon for PhIP) was compared with that of a nontarget tissue (gastric). After treatment cell viabilities were measured, DNA damage response (DDR) was determined by Western blotting for p-p53, p21, p-CHK2, and γ-H2AX, and DNA adduct formation was quantified by mass spectrometry. Induction of the key xenobiotic-metabolizing enzymes (XMEs) CYP1A1, CYP1A2, CYP3A4, and NQO1 was assessed by qRT-PCR. We found that organoids from different tissues can activate AAI, AFB 1 , and PhIP. In some cases, this metabolic potential varied between tissues and between different cultures of the same tissue. Similarly, variations in the levels of expression of XMEs were observed. At comparable levels of cytotoxicity, organoids derived from tissues that are considered targets for these carcinogens had higher levels of adduct formation than a nontarget tissue.

Published
2024
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31. Apical bulkheads accumulate as adaptive response to impaired bile flow in liver disease.

Author

Mayer C, Nehring S, Kücken M, Repnik U, Seifert S, Sljukic A, Delpierre J, Morales-Navarrete H, Hinz S, Brosch M, Chung B, Karlsen T, Huch M, Kalaidzidis Y, Brusch L, Hampe J, Schafmayer C, and Zerial M

Subjects
Mice, Animals, Liver, Bile Canaliculi, Hepatocytes, Bile, Liver Diseases
Abstract

Hepatocytes form bile canaliculi that dynamically respond to the signalling activity of bile acids and bile flow. Little is known about their responses to intraluminal pressure. During embryonic development, hepatocytes assemble apical bulkheads that increase the canalicular resistance to intraluminal pressure. Here, we investigate whether they also protect bile canaliculi against elevated pressure upon impaired bile flow in adult liver. Apical bulkheads accumulate upon bile flow obstruction in mouse models and patients with primary sclerosing cholangitis (PSC). Their loss under these conditions leads to abnormally dilated canaliculi, resembling liver cell rosettes described in other hepatic diseases. 3D reconstruction reveals that these structures are sections of cysts and tubes formed by hepatocytes. Mathematical modelling establishes that they positively correlate with canalicular pressure and occur in early PSC stages. Using primary hepatocytes and 3D organoids, we demonstrate that excessive canalicular pressure causes the loss of apical bulkheads and formation of rosettes. Our results suggest that apical bulkheads are a protective mechanism of hepatocytes against impaired bile flow, highlighting the role of canalicular pressure in liver diseases., (© 2023 The Authors. Published under the terms of the CC BY 4.0 license.)

Published
2023
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32. Generation of liver mesenchyme and ductal cell organoid co-culture using cell self-aggregation and droplet microfluidics.

Author

Dowbaj AM, Kohler TN, Cordero-Espinoza L, Hollfelder F, and Huch M

Abstract

Within the peri-portal region of the adult liver, portal fibroblasts exist in close proximity to epithelial ductal/cholangiocyte cells. However, the cellular interactions between them are poorly understood. Here, we provide two co-culture techniques to incorporate liver portal mesenchyme into ductal cell organoids, which recapitulate aspects of their cellular interactions in vitro. We integrate several techniques from mesenchyme isolation and expansion to co-culture by microfluidic cell co-encapsulation or 2D-Matrigel layer. The protocol is easily adaptable to other cells from other organs. For complete information on the generation and use of this protocol, please refer to Cordero-Espinoza et al. 1 ., Competing Interests: Declaration of interests M.H. is an inventor in several patents on organoid technology., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Published
2023
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34. Time-dependent fermentation of different structural units of commercial pectins with intestinal bacteria.

Author

Bender C, Stoll D, Huch M, Weinert C, Dötsch A, Dräger H, Keller J, Kulling S, and Bunzel M

Subjects
Humans, Fermentation, Feces microbiology, Bacteria metabolism, Rhamnogalacturonans, Pectins chemistry
Abstract

Many of the proposed health-related properties of pectins are based on their fermentability in the large intestine, but detailed structure-related studies on pectin fermentation have not been reported so far. Here, pectin fermentation kinetics were studied with a focus on structurally different pectic polymers. Therefore, six commercial pectins from citrus, apple, and sugar beet were chemically characterized and fermented in in vitro fermentation assays with human fecal samples over different periods of time (0 h, 4 h, 24 h, 48 h). Structure elucidation of intermediate cleavage products showed differences in fermentation speed and/or fermentation rate among the pectins, but the order in which specific structural pectic elements were fermented was comparable across all pectins. Neutral side chains of rhamnogalacturonan type I were fermented first (between 0 and 4 h), followed by homogalacturonan units (between 0 and 24 h) and, at last, the rhamnogalacturonan type I backbone (between 4 and 48 h). This indicates that fermentation of different pectic structural units might take place in different sections of the colon, potentially affecting their nutritional properties. For the formation of different short-chain fatty acids, mainly acetate, propionate, and butyrate, and the influence on microbiota, there was no time-dependent correlation regarding the pectic subunits. However, an increase of members of the bacterial genera Faecalibacterium, Lachnoclostridium, and Lachnospira was observed for all pectins., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Mirko Bunzel reports financial support and equipment, drugs, or supplies were provided by Karlsruhe Institute of Technology., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Published
2023
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35. Rathayibacter rubneri sp. nov. isolated from Allium cepa var. Rijnsburger, an onion landrace.

Author

Stoll DA, Grimmler C, Hetzer B, Kulling SE, and Huch M

Subjects
Onions, RNA, Ribosomal, 16S genetics, DNA, Bacterial genetics, Base Composition, Phylogeny, Bacterial Typing Techniques, Sequence Analysis, DNA, Fatty Acids chemistry, Actinomycetales
Abstract

The novel, aerobic, Gram-stain-positive, rod-shaped bacterial strain, ZW T2&#95;19 T , was isolated from an onion sample ( Allium cepa var. Rijnsburger). Analyses of the 16S rRNA gene sequence revealed that ZW T2&#95;19 T represented a member of the genus Rathayibacter but may represent a novel species of this genus. Analyses of the whole draft genome sequences, i.e. digital DNA-DNA hybridisation (dDDH) and average nucleotide identity (ANI) of ZW T2&#95;19 T and all type strains of species of the genus Rathayibacter confirmed that ZW T2&#95;19 T represents a novel species of the genus Rathayibacter . The genome size of ZW T2&#95;19 T is 4.01 Mbp and the DNA G+C content is 71.8 mol%. Glucose, mannose, rhamnose and ribose were detected as whole-cell sugars of ZW T2&#95;19 T . The major respiratory quinone of ZW T2&#95;19 T is menaquinone MK-10, at 78.9 %. The detected peptidoglycan type in ZW T2&#95;19 T is a variant of type B2γ with {Gly} [l-diaminobutyric acid (l-DAB)/l-homoserine (l-Hse)] d-Glu-l-DAB. Polar lipids in ZW T2&#95;19 T consisted of one diphosphatidylglycerol, one phosphatidylglycerol, seven glycolipids, one phospholipid and one lipid. The fatty acid profile of ZW T2&#95;19 T predominantly consisted of anteiso-C 15 : 0 (53 %), iso-C 16 : 0 (21 %) and anteiso-C 17 : 0 (18 %). In addition, API 20NE, API 50CH, API Coryne, API ZYM, antibiotic susceptibility, haemolysis and growth at different temperatures and with different supplements was investigated. On the basis of the results obtained using this polyphasic approach, including molecular, phenotypic and biochemical analyses, we propose the novel species Rathayibacter rubneri with the type and only strain ZW T2&#95;19 T (= DSM 114294 T = LMG 32700 T ).

Published
2023
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36. Metabolic Activation of Benzo[ a ]pyrene by Human Tissue Organoid Cultures.

Author

Caipa Garcia AL, Kucab JE, Al-Serori H, Beck RSS, Fischer F, Hufnagel M, Hartwig A, Floeder A, Balbo S, Francies H, Garnett M, Huch M, Drost J, Zilbauer M, Arlt VM, and Phillips DH

Subjects
Humans, Activation, Metabolic, Cytochrome P-450 CYP1A1 metabolism, Liver metabolism, Benzo(a)pyrene toxicity, DNA Adducts metabolism, Organoids drug effects, Organoids metabolism
Abstract

Organoids are 3D cultures that to some extent reproduce the structure, composition and function of the mammalian tissues from which they derive, thereby creating in vitro systems with more in vivo-like characteristics than 2D monocultures. Here, the ability of human organoids derived from normal gastric, pancreas, liver, colon and kidney tissues to metabolise the environmental carcinogen benzo[ a ]pyrene (BaP) was investigated. While organoids from the different tissues showed varied cytotoxic responses to BaP, with gastric and colon organoids being the most susceptible, the xenobiotic-metabolising enzyme (XME) genes, CYP1A1 and NQO1 , were highly upregulated in all organoid types, with kidney organoids having the highest levels. Furthermore, the presence of two key metabolites, BaP- t -7,8-dihydrodiol and BaP-tetrol-l-1, was detected in all organoid types, confirming their ability to metabolise BaP. BaP bioactivation was confirmed both by the activation of the DNA damage response pathway (induction of p-p53, pCHK2, p21 and γ-H2AX) and by DNA adduct formation. Overall, pancreatic and undifferentiated liver organoids formed the highest levels of DNA adducts. Colon organoids had the lowest responses in DNA adduct and metabolite formation, as well as XME expression. Additionally, high-throughput RT-qPCR explored differences in gene expression between organoid types after BaP treatment. The results demonstrate the potential usefulness of organoids for studying environmental carcinogenesis and genetic toxicology.

Published
2022
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37. Organoids as tools for fundamental discovery and translation-a Keystone Symposia report.

Author

Cable J, Lutolf MP, Fu J, Park SE, Apostolou A, Chen S, Song CJ, Spence JR, Liberali P, Lancaster M, Meier AB, Pek NMQ, Wells JM, Capeling MM, Uzquiano A, Musah S, Huch M, Gouti M, Hombrink P, Quadrato G, and Urenda JP

Subjects
Animals, Humans, Stem Cells, Models, Animal, Organoids metabolism, Models, Biological
Abstract

Complex three-dimensional in vitro organ-like models, or organoids, offer a unique biological tool with distinct advantages over two-dimensional cell culture systems, which can be too simplistic, and animal models, which can be too complex and may fail to recapitulate human physiology and pathology. Significant progress has been made in driving stem cells to differentiate into different organoid types, though several challenges remain. For example, many organoid models suffer from high heterogeneity, and it can be difficult to fully incorporate the complexity of in vivo tissue and organ development to faithfully reproduce human biology. Successfully addressing such limitations would increase the viability of organoids as models for drug development and preclinical testing. On April 3-6, 2022, experts in organoid development and biology convened at the Keystone Symposium "Organoids as Tools for Fundamental Discovery and Translation" to discuss recent advances and insights from this relatively new model system into human development and disease., (© 2022 New York Academy of Sciences.)

Published
2022
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38. Once upon a dish: the next frontier in engineering multicellular systems.

Author

Huch M and Gouti M

Subjects
Bioengineering, Organogenesis, Morphogenesis, Organoids, Tissue Engineering
Abstract

In June 2022, the second meeting on 'Engineering Multicellular Systems', organized by the European Molecular Biology Laboratory and the Institute of Bioengineering of Catalonia, took place in Barcelona. Stem cell and systems biologists, physicists and engineers from all over the world gathered to discuss how recent breakthroughs in organoid technologies, engineering and mechanobiology are boosting our understanding of early morphogenesis, organogenesis and organ function with applications in tissue engineering, disease modeling and drug screening. The meeting was organized with sustainability in mind, and included an ethics session and an outreach public activity., (© 2022. Published by The Company of Biologists Ltd.)

Published
2022
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39. Anniversary reflections: Inspiring discoveries and the future of the field.

Author

Lancaster M, Morris SA, Takebe T, Qian L, Gao S, and Huch M

Subjects
Anniversaries and Special Events
Abstract

Cell Stem Cell was launched in 2007, and this year marks its 15 th anniversary. To recognize this occasion, we asked six advisory board members to reflect on inspiring discoveries reported in Cell Stem Cell and how these breakthroughs connect to their vision for the future of the field., Competing Interests: Declaration of interests M.H. has an additional academic affiliation with Physics of Life Excellence Cluster, Dresden, and is an inventor of several patents on organoid technology. M.L. is also an inventor on patents related to brain organoid technology and is a founder of a:head bio and a member of its scientific advisory board. M.L., S.A.M., T.T., L.Q., S.G., and M.H. are members of Cell Stem Cell's advisory board., (Copyright © 2022. Published by Elsevier Inc.)

Published
2022
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40. Metabolism of glyphosate by the human fecal microbiota.

Author

Huch M, Stoll DA, Kulling SE, and Soukup ST

Subjects
Glycine analogs & derivatives, Humans, Isoxazoles, Suspensions, Tetrazoles, Glyphosate, Herbicides toxicity, Microbiota
Abstract

Glyphosate is the most frequently used herbicide worldwide and its application is under discussion due to health concerns. As humans may be exposed to glyphosate, the present study investigated the metabolism of glyphosate by the human fecal microbiota in vitro. Human fecal samples were collected from 15 different volunteers and fecal suspensions were prepared. The human fecal suspension samples were incubated with glyphosate under strictly anaerobic conditions and glyphosate degradation was investigated. Neither a degradation of glyphosate, nor a formation of AMPA (aminomethylphosphonic acid), the known microbial metabolite in soil, was detected. In conclusion, the microbiota of human fecal suspensions did not metabolize glyphosate under the conditions used in our study which hints at the assumption that transformation of glyphosate by the gut microbiota seems to be negligible in humans., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Published
2022
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41. Hepatobiliary tumor organoids for personalized medicine: a multicenter view on establishment, limitations, and future directions.

Author

van Tienderen GS, Li L, Broutier L, Saito Y, Inacio P, Huch M, Selaru FM, van der Laan LJW, and Verstegen MMA

Subjects
Humans, Precision Medicine, Gastrointestinal Neoplasms, Organoids
Abstract

Reliable establishment of tumor organoids is paramount to advance applications of organoid technology for personalized medicine. Here, we share our multi-center experience on initiation and tumorigenic confirmation of hepatobiliary cancer organoids. We discuss current concerns, propose potential solutions, and provide future perspectives for improvements in hepatobiliary cancer organoid establishment., Competing Interests: Declaration of interests M.H. is an inventor in a patent on liver organoids. F.M.S. is an inventor in a patent for liver cancer treatment (PCT/US2021/016849, 17/623,060, 16/479,652). The other authors declare no conflict of interest., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Published
2022
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42. Fasting improves therapeutic response in hepatocellular carcinoma through p53-dependent metabolic synergism.

Author

Krstic J, Reinisch I, Schindlmaier K, Galhuber M, Riahi Z, Berger N, Kupper N, Moyschewitz E, Auer M, Michenthaler H, Nössing C, Depaoli MR, Ramadani-Muja J, Usluer S, Stryeck S, Pichler M, Rinner B, Deutsch AJA, Reinisch A, Madl T, Chiozzi RZ, Heck AJR, Huch M, Malli R, and Prokesch A

Abstract

Cancer cells voraciously consume nutrients to support their growth, exposing metabolic vulnerabilities that can be therapeutically exploited. Here, we show in hepatocellular carcinoma (HCC) cells, xenografts, and patient-derived organoids that fasting improves sorafenib efficacy and acts synergistically to sensitize sorafenib-resistant HCC. Mechanistically, sorafenib acts noncanonically as an inhibitor of mitochondrial respiration, causing resistant cells to depend on glycolysis for survival. Fasting, through reduction in glucose and impeded AKT/mTOR signaling, prevents this Warburg shift. Regulating glucose transporter and proapoptotic protein expression, p53 is necessary and sufficient for the sorafenib-sensitizing effect of fasting. p53 is also crucial for fasting-mediated improvement of sorafenib efficacy in an orthotopic HCC mouse model. Together, our data suggest fasting and sorafenib as rational combination therapy for HCC with intact p53 signaling. As HCC therapy is currently severely limited by resistance, these results should instigate clinical studies aimed at improving therapy response in advanced-stage HCC.

Published
2022
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43. RNF43/ZNRF3 loss predisposes to hepatocellular-carcinoma by impairing liver regeneration and altering the liver lipid metabolic ground-state.

Author

Belenguer G, Mastrogiovanni G, Pacini C, Hall Z, Dowbaj AM, Arnes-Benito R, Sljukic A, Prior N, Kakava S, Bradshaw CR, Davies S, Vacca M, Saeb-Parsy K, Koo BK, and Huch M

Subjects
Adult, Animals, Carcinoma, Hepatocellular pathology, Cell Differentiation, Cell Proliferation, Fatty Liver pathology, Gene Deletion, Gene Expression Regulation, Hepatocytes metabolism, Hepatocytes pathology, Hepatomegaly pathology, Humans, Hyperplasia, Lipid Droplets metabolism, Lipid Metabolism genetics, Lipidomics, Liver pathology, Liver Neoplasms pathology, Mice, Prognosis, Carcinoma, Hepatocellular metabolism, Liver metabolism, Liver Neoplasms metabolism, Liver Regeneration, Ubiquitin-Protein Ligases metabolism
Abstract

RNF43/ZNRF3 negatively regulate WNT signalling. Both genes are mutated in several types of cancers, however, their contribution to liver disease is unknown. Here we describe that hepatocyte-specific loss of Rnf43/Znrf3 results in steatohepatitis and in increase in unsaturated lipids, in the absence of dietary fat supplementation. Upon injury, Rnf43/Znrf3 deletion results in defective hepatocyte regeneration and liver cancer, caused by an imbalance between differentiation/proliferation. Using hepatocyte-, hepatoblast- and ductal cell-derived organoids we demonstrate that the differentiation defects and lipid alterations are, in part, cell-autonomous. Interestingly, ZNRF3 mutant liver cancer patients present poorer prognosis, altered hepatic lipid metabolism and steatohepatitis/NASH signatures. Our results imply that RNF43/ZNRF3 predispose to liver cancer by controlling the proliferative/differentiation and lipid metabolic state of hepatocytes. Both mechanisms combined facilitate the progression towards malignancy. Our findings might aid on the management of those RNF43/ZNRF3 mutated individuals at risk of developing fatty liver and/or liver cancer., (© 2022. The Author(s).)

Published
2022
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44. Organoids.

Author

Zhao Z, Chen X, Dowbaj AM, Sljukic A, Bratlie K, Lin L, Fong ELS, Balachander GM, Chen Z, Soragni A, Huch M, Zeng YA, Wang Q, and Yu H

Abstract

Organoids have attracted increasing attention because they are simple tissue-engineered cell-based in vitro models that recapitulate many aspects of the complex structure and function of the corresponding in vivo tissue. They can be dissected and interrogated for fundamental mechanistic studies on development, regeneration, and repair in human tissues. Organoids can also be used in diagnostics, disease modeling, drug discovery, and personalized medicine. Organoids are derived from either pluripotent or tissue-resident stem (embryonic or adult) or progenitor or differentiated cells from healthy or diseased tissues, such as tumors. To date, numerous organoid engineering strategies that support organoid culture and growth, proliferation, differentiation and maturation have been reported. This Primer serves to highlight the rationale underlying the selection and development of these materials and methods to control the cellular/tissue niche; and therefore, structure and function of the engineered organoid. We also discuss key considerations for generating robust organoids, such as those related to cell isolation and seeding, matrix and soluble factor selection, physical cues and integration. The general standards for data quality, reproducibility and deposition within the organoid community is also outlined. Lastly, we conclude by elaborating on the limitations of organoids in different applications, and key priorities in organoid engineering for the coming years., Competing Interests: Declaration of competing interests: MH is inventor in several patents on organoid technology. A.So and LL are inventors on a patent on organoid technology. A.So is a founder and owner of Icona BioDx. HY is inventor in several patents on cell-based models. The remaining authors declare no competing interests.

Published
2022
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45. Metabolism of Daidzein and Genistein by Gut Bacteria of the Class Coriobacteriia .

Author

Soukup ST, Stoll DA, Danylec N, Schoepf A, Kulling SE, and Huch M

Abstract

The intake of isoflavones is presumed to be associated with health benefits in humans, but also potential adverse effects of isoflavones are controversially discussed. Isoflavones can be metabolized by gut bacteria leading to modulation of the bioactivity, such as estrogenic effects. Especially bacterial strains of the Eggerthellaceae, a well-known bacterial family of the human gut microbiota, are able to convert the isoflavone daidzein into equol. In addition, metabolization of genistein is also described for strains of the Eggerthellaceae . The aim of this study was to identify and investigate gut bacterial strains of the family Eggerthellaceae as well as the narrowly related family Coriobacteriaceae which are able to metabolize daidzein and genistein. This study provides a comprehensive, polyphasic approach comprising in silico analysis of the equol gene cluster, detection of genes associated with the daidzein, and genistein metabolism via PCR and fermentation of these isoflavones. The in silico search for protein sequences that are associated with daidzein metabolism identified sequences with high similarity values in already well-known equol-producing strains. Furthermore, protein sequences that are presumed to be associated with daidzein and genistein metabolism were detected in the two type strains ' Hugonella massiliensis ' and Senegalimassilia faecalis which were not yet described to metabolize these isoflavones. An alignment of these protein sequences showed that the equol gene cluster is highly conserved. In addition, PCR amplification supported the presence of genes associated with daidzein and genistein metabolism. Furthermore, the metabolism of daidzein and genistein was investigated in fermentations of pure bacterial cultures under strictly anaerobic conditions and proofed the metabolism of daidzein and genistein by the strains ' Hugonella massiliensis ' DSM 101782 T and Senegalimassilia faecalis KGMB04484 T .

Published
2021
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46. Dynamic cell contacts between periportal mesenchyme and ductal epithelium act as a rheostat for liver cell proliferation.

Author

Cordero-Espinoza L, Dowbaj AM, Kohler TN, Strauss B, Sarlidou O, Belenguer G, Pacini C, Martins NP, Dobie R, Wilson-Kanamori JR, Butler R, Prior N, Serup P, Jug F, Henderson NC, Hollfelder F, and Huch M

Subjects
Animals, Cell Proliferation, Epithelium, Liver, Mice, Epithelial Cells, Mesoderm
Abstract

In the liver, ductal cells rarely proliferate during homeostasis but do so transiently after tissue injury. These cells can be expanded as organoids that recapitulate several of the cell-autonomous mechanisms of regeneration but lack the stromal interactions of the native tissue. Here, using organoid co-cultures that recapitulate the ductal-to-mesenchymal cell architecture of the portal tract, we demonstrate that a subpopulation of mouse periportal mesenchymal cells exerts dual control on proliferation of the epithelium. Ductal cell proliferation is either induced and sustained or, conversely, completely abolished, depending on the number of direct mesenchymal cell contacts, through a mechanism mediated, at least in part, by Notch signaling. Our findings expand the concept of the cellular niche in epithelial tissues, whereby not only soluble factors but also cell-cell contacts are the key regulatory cues involved in the control of cellular behaviors, suggesting a critical role for cell-cell contacts during regeneration., Competing Interests: Declaration of interests M.H. is inventor in a patent on liver organoids and is on the advisory board of the journal Cell Stem Cell., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Published
2021
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47. Adlercreutzia rubneri sp. nov., a resveratrol-metabolizing bacterium isolated from human faeces and emended description of the genus Adlercreutzia .

Author

Stoll DA, Danylec N, Soukup ST, Hetzer B, Kulling SE, and Huch M

Subjects
Actinobacteria isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Germany, Humans, Male, Nucleic Acid Hybridization, Phospholipids chemistry, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 chemistry, Actinobacteria classification, Feces microbiology, Resveratrol
Abstract

The novel, anaerobic, Gram-positive, rod-shaped bacterial strain, ResAG-91 T , was isolated from a faecal sample of a male human volunteer. Analysis of the 16S rRNA gene sequence revealed that strain ResAG-91 T showed high similarity to the type strains of Adlercreutzia equolifaciens subsp. equolifaciens and Adlercreutzia equolifaciens subsp. celatus . Analysis of the whole draft genome sequences, i.e. digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI), of strain ResAG-91 T and the type strains of Adlercreutzia species revealed that strain ResAG-91 T represents a novel species of the genus Adlercreutzia . The genome size of strain ResAG-91 T is 2.8 Mbp and the G+C content is 63.3 mol%. The major respiratory quinone of strain ResAG-91 T was MMK-5 (methylmenaquinone). Major cellular fatty acids were C15 : 0 anteiso, C14 : 0 iso and C14 : 0 2-OH. Galactose and ribose were detected as major whole cell sugars. Furthermore, the peptidoglycan type of strain ResAG-91 T was A1γ with meso-diaminopimelic acid. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid, three unidentified phospholipids and five unidentified glycolipids. Strain ResAG-91 T was able to metabolize the stilbene resveratrol into dihydroresveratrol. On the basis of this polyphasic approach, including phenotypical, molecular (16S rRNA gene and whole genome sequencing) and biochemical (fatty acids, quinones, polar lipids, peptidoglycan, whole cell sugars, Rapid ID32A and API20A) analyses, we propose the novel species Adlercreutzia rubneri sp. nov. with the type and only strain ResAG-91 T (=DSM 111416 T =JCM 34176 T =LMG 31897 T ).

Published
2021
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48. Liver regeneration and inflammation: from fundamental science to clinical applications.

Author

Campana L, Esser H, Huch M, and Forbes S

Subjects
Cell Transplantation, Epithelial Cells cytology, Epithelial Cells transplantation, Hepatic Stellate Cells metabolism, Hepatocytes cytology, Hepatocytes pathology, Hepatocytes transplantation, Humans, Inflammation, Macrophages cytology, Macrophages pathology, Macrophages transplantation, Signal Transduction, Liver Cirrhosis pathology, Liver Cirrhosis therapy, Liver Regeneration physiology
Abstract

Liver regeneration is a complex process involving the crosstalk of multiple cell types, including hepatocytes, hepatic stellate cells, endothelial cells and inflammatory cells. The healthy liver is mitotically quiescent, but following toxic damage or resection the cells can rapidly enter the cell cycle to restore liver mass and function. During this process of regeneration, epithelial and non-parenchymal cells respond in a tightly coordinated fashion. Recent studies have described the interaction between inflammatory cells and a number of other cell types in the liver. In particular, macrophages can support biliary regeneration, contribute to fibrosis remodelling by repressing hepatic stellate cell activation and improve liver regeneration by scavenging dead or dying cells in situ. In this Review, we describe the mechanisms of tissue repair following damage, highlighting the close relationship between inflammation and liver regeneration, and discuss how recent findings can help design novel therapeutic approaches., (© 2021. Springer Nature Limited.)

Published
2021
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49. Application of human liver organoids as a patient-derived primary model for HBV infection and related hepatocellular carcinoma.

Author

De Crignis E, Hossain T, Romal S, Carofiglio F, Moulos P, Khalid MM, Rao S, Bazrafshan A, Verstegen MM, Pourfarzad F, Koutsothanassis C, Gehart H, Kan TW, Palstra RJ, Boucher C, IJzermans JN, Huch M, Boj SF, Vries R, Clevers H, van der Laan LJ, Hatzis P, and Mahmoudi T

Subjects
Hep G2 Cells, Hepatitis B complications, Hepatitis B virus pathogenicity, Humans, Liver pathology, Liver virology, Living Donors, Models, Biological, Virus Replication, Carcinoma, Hepatocellular virology, Hepatitis B virology, Liver Neoplasms virology, Organoids virology
Abstract

The molecular events that drive hepatitis B virus (HBV)-mediated transformation and tumorigenesis have remained largely unclear, due to the absence of a relevant primary model system. Here we propose the use of human liver organoids as a platform for modeling HBV infection and related tumorigenesis. We first describe a primary ex vivo HBV-infection model derived from healthy donor liver organoids after challenge with recombinant virus or HBV-infected patient serum. HBV-infected organoids produced covalently closed circular DNA (cccDNA) and HBV early antigen (HBeAg), expressed intracellular HBV RNA and proteins, and produced infectious HBV. This ex vivo HBV-infected primary differentiated hepatocyte organoid platform was amenable to drug screening for both anti-HBV activity and drug-induced toxicity. We also studied HBV replication in transgenically modified organoids; liver organoids exogenously overexpressing the HBV receptor sodium taurocholate co-transporting polypeptide (NTCP) after lentiviral transduction were not more susceptible to HBV, suggesting the necessity for additional host factors for efficient infection. We also generated transgenic organoids harboring integrated HBV, representing a long-term culture system also suitable for viral production and the study of HBV transcription. Finally, we generated HBV-infected patient-derived liver organoids from non-tumor cirrhotic tissue of explants from liver transplant patients. Interestingly, transcriptomic analysis of patient-derived liver organoids indicated the presence of an aberrant early cancer gene signature, which clustered with the hepatocellular carcinoma (HCC) cohort on The Cancer Genome Atlas Liver Hepatocellular Carcinoma dataset and away from healthy liver tissue, and may provide invaluable novel biomarkers for the development of HCC and surveillance in HBV-infected patients., Competing Interests: ED, TH, SR, FC, PM, MK, SR, AB, MV, FP, CK, HG, TK, RP, CB, JI, MH, SB, RV, HC, Lv, PH, TM No competing interests declared, (© 2021, De Crignis et al.)

Published
2021
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50. Dual Targeting of G9a and DNA Methyltransferase-1 for the Treatment of Experimental Cholangiocarcinoma.

Author

Colyn L, Bárcena-Varela M, Álvarez-Sola G, Latasa MU, Uriarte I, Santamaría E, Herranz JM, Santos-Laso A, Arechederra M, Ruiz de Gauna M, Aspichueta P, Canale M, Casadei-Gardini A, Francesconi M, Carotti S, Morini S, Nelson LJ, Iraburu MJ, Chen C, Sangro B, Marin JJG, Martinez-Chantar ML, Banales JM, Arnes-Benito R, Huch M, Patino JM, Dar AA, Nosrati M, Oyarzábal J, Prósper F, Urman J, Cubero FJ, Trautwein C, Berasain C, Fernandez-Barrena MG, and Avila MA

Subjects
Animals, CCAAT-Enhancer-Binding Proteins metabolism, Cell Line, Tumor, DNA Methylation drug effects, DNA Methylation physiology, Epigenesis, Genetic drug effects, Gene Expression Regulation, Neoplastic drug effects, Histone Code drug effects, Histone Code physiology, Humans, Mice, Treatment Outcome, Ubiquitin-Protein Ligases metabolism, Xenograft Model Antitumor Assays methods, Bile Duct Neoplasms drug therapy, Bile Duct Neoplasms metabolism, Cell Proliferation drug effects, Cholangiocarcinoma drug therapy, Cholangiocarcinoma metabolism, DNA (Cytosine-5-)-Methyltransferase 1 antagonists & inhibitors, DNA (Cytosine-5-)-Methyltransferase 1 metabolism, Enzyme Inhibitors pharmacology, Histocompatibility Antigens metabolism, Histone-Lysine N-Methyltransferase antagonists & inhibitors, Histone-Lysine N-Methyltransferase metabolism
Abstract

Background and Aims: Cholangiocarcinoma (CCA) is a devastating disease often detected at advanced stages when surgery cannot be performed. Conventional and targeted systemic therapies perform poorly, and therefore effective drugs are urgently needed. Different epigenetic modifications occur in CCA and contribute to malignancy. Targeting epigenetic mechanisms may thus open therapeutic opportunities. However, modifications such as DNA and histone methylation often coexist and cooperate in carcinogenesis. We tested the therapeutic efficacy and mechanism of action of a class of dual G9a histone-methyltransferase and DNA-methyltransferase 1 (DNMT1) inhibitors., Approach and Results: Expression of G9a, DNMT1, and their molecular adaptor, ubiquitin-like with PHD and RING finger domains-1 (UHRF1), was determined in human CCA. We evaluated the effect of individual and combined pharmacological inhibition of G9a and DNMT1 on CCA cell growth. Our lead G9a/DNMT1 inhibitor, CM272, was tested in human CCA cells, patient-derived tumoroids and xenograft, and a mouse model of cholangiocarcinogenesis with hepatocellular deletion of c-Jun-N-terminal-kinase (Jnk)-1/2 and diethyl-nitrosamine (DEN) plus CCl 4 treatment (Jnk Δhepa + DEN + CCl 4 mice). We found an increased and correlative expression of G9a, DNMT1, and UHRF1 in CCAs. Cotreatment with independent pharmacological inhibitors G9a and DNMT1 synergistically inhibited CCA cell growth. CM272 markedly reduced CCA cell proliferation and synergized with Cisplatin and the ERBB-targeted inhibitor, Lapatinib. CM272 inhibited CCA tumoroids and xenograft growth and significantly antagonized CCA progression in Jnk Δhepa + DEN + CCl 4 mice without apparent toxicity. Mechanistically, CM272 reprogrammed the tumoral metabolic transcriptome and phenotype toward a differentiated and quiescent status., Conclusions: Dual targeting of G9a and DNMT1 with epigenetic small molecule inhibitors such as CM272 is a potential strategy to treat CCA and/or enhance the efficacy of other systemic therapies., (© 2020 by the American Association for the Study of Liver Diseases.)

Published
2021
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