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1. Kidney organoids recapitulate human basement membrane assembly in health and disease

Author

Mychel RPT Morais, Pinyuan Tian, Craig Lawless, Syed Murtuza-Baker, Louise Hopkinson, Steven Woods, Aleksandr Mironov, David A Long, Daniel P Gale, Telma MT Zorn, Susan J Kimber, Roy Zent, and Rachel Lennon

Subjects
extracellular matrix, basement membrane, kidney organoid, fetal kidney, glomerular development, Medicine, Science, Biology (General), QH301-705.5
Abstract

Basement membranes (BMs) are complex macromolecular networks underlying all continuous layers of cells. Essential components include collagen IV and laminins, which are affected by human genetic variants leading to a range of debilitating conditions including kidney, muscle, and cerebrovascular phenotypes. We investigated the dynamics of BM assembly in human pluripotent stem cell-derived kidney organoids. We resolved their global BM composition and discovered a conserved temporal sequence in BM assembly that paralleled mammalian fetal kidneys. We identified the emergence of key BM isoforms, which were altered by a pathogenic variant in COL4A5. Integrating organoid, fetal, and adult kidney proteomes, we found dynamic regulation of BM composition through development to adulthood, and with single-cell transcriptomic analysis we mapped the cellular origins of BM components. Overall, we define the complex and dynamic nature of kidney organoid BM assembly and provide a platform for understanding its wider relevance in human development and disease.

Published
2022
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2. Correction: Consensus statement on standards and guidelines for the molecular diagnostics of Alport syndrome: refining the ACMG criteria

Author

Judy Savige, Helen Storey, Elizabeth Watson, Jens Michael Hertz, Constantinos Deltas, Alessandra Renieri, Francesca Mari, Pascale Hilbert, Pavlina Plevova, Peter Byers, Agne Cerkauskaite, Martin Gregory, Rimante Cerkauskiene, Danica Galesic Ljubanovic, Francesca Becherucci, Carmela Errichiello, Laura Massella, Valeria Aiello, Rachel Lennon, Louise Hopkinson, Ania Koziell, Adrian Lungu, Hansjorg Martin Rothe, Julia Hoefele, Miriam Zacchia, Tamara Nikuseva Martic, Asheeta Gupta, Albertien van Eerde, Susie Gear, Samuela Landini, Viviana Palazzo, Laith al-Rabadi, Kathleen Claes, Anniek Corveleyn, Evelien Van Hoof, Micheel van Geel, Maggie Williams, Emma Ashton, Hendica Belge, Elisabeth Ars, Agnieszka Bierzynska, Concetta Gangemi, and Beata S. Lipska-Ziętkiewicz

Subjects
Genetics, Genetics (clinical)
Published
2023
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4. Guidelines for genetic testing and management of Alport syndrome

Author

Judy Savige, Beata S. Lipska-Zietkiewicz, Elizabeth Watson, Jens Michael Hertz, Constantinos Deltas, Francesca Mari, Pascale Hilbert, Pavlina Plevova, Peter Byers, Agne Cerkauskaite, Martin Gregory, Rimante Cerkauskiene, Danica Galesic Ljubanovic, Francesca Becherucci, Carmela Errichiello, Laura Massella, Valeria Aiello, Rachel Lennon, Louise Hopkinson, Ania Koziell, Adrian Lungu, Hansjorg Martin Rothe, Julia Hoefele, Miriam Zacchia, Tamara Nikuseva Martic, Asheeta Gupta, Albertien van Eerde, Susie Gear, Samuela Landini, Viviana Palazzo, Laith al-Rabadi, Kathleen Claes, Anniek Corveleyn, Evelien Van Hoof, Micheel van Geel, Maggie Williams, Emma Ashton, Hendica Belge, Elisabet Ars, Agnieszka Bierzynska, Concetta Gangemi, Alessandra Renieri, Helen Storey, Frances Flinter, Savige, J, Lipska-Zietkiewicz, B, Watson, E, Hertz, Jm, Deltas, C, Mari, F, Hilbert, P, Plevova, P, Byers, P, Cerkauskaite, A, Gregory, M, Cerkauskiene, R, Ljubanovic, Dg, Becherucci, F, Errichiello, C, Massella, L, Aiello, V, Lennon, R, Hopkinson, L, Koziell, A, Lungu, A, Rothe, Hm, Hoefele, J, Zacchia, M, Martic, Tn, Gupta, A, van Eerde, A, Gear, S, Landini, S, Palazzo, V, Al-Rabadi, L, Claes, K, Corveleyn, A, Van Hoof, E, van Geel, M, Williams, M, Ashton, E, Belge, H, Ars, E, Bierzynska, A, Gangemi, C, Renieri, A, Storey, H, Flinter, F., RS: GROW - R3 - Innovative Cancer Diagnostics & Therapy, and MUMC+: DA KG Lab Centraal Lab (9)

Subjects
Feature, Collagen Type IV, KIDNEY-TRANSPLANTATION, RENAL-FAILURE, MICROSCOPIC HEMATURIA, Epidemiology, Nephritis, Hereditary, Alport syndrome, COL4A3, COL4A4, COL4A5, FSGS, collagen IV, digenic Alport syndrome, genetic testing, kidney cysts, thin basement membrane nephropathy, Critical Care and Intensive Care Medicine, urologic and male genital diseases, Autoantigens, DIGENIC INHERITANCE, SEQUENCE VARIANTS, Humans, GENOTYPE-PHENOTYPE CORRELATIONS, Transplantation, urogenital system, COL4A3/COL4A4 MUTATIONS, GLOMERULAR-BASEMENT-MEMBRANE, NATURAL-HISTORY, female genital diseases and pregnancy complications, Nephrology, Practice Guidelines as Topic, FAMILIAL HEMATURIA
Abstract

Genetic testing for pathogenic COL4A3-5 variants is usually undertaken to investigate the cause of persistent hematuria, especially with a family history of hematuria or kidney function impairment. Alport syndrome experts now advocate genetic testing for persistent hematuria, even when a heterozygous pathogenic COL4A3 or COL4A4 is suspected, and cascade testing of their first-degree family members because of their risk of impaired kidney function. The experts recommend too that COL4A3 or COL4A4 heterozygotes do not act as kidney donors. Testing for variants in the COL4A3-COL4A5 genes should also be performed for persistent proteinuria and steroid-resistant nephrotic syndrome due to suspected inherited FSGS and for familial IgA glomerulonephritis and kidney failure of unknown cause.

Published
2022
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5. Kidney organoids: A system to study human basement membrane assembly in health and disease

Author

Mychel Raony Paiva Teixeira Morais, Pinyuan Tian, Craig Lawless, Syed Murtuza-Baker, Louise Hopkinson, Steven Woods, Aleksandr Mironov, David Andrew Long, Daniel Gale, Telma Maria Tenorio Zorn, Susan Kimber, Roy Zent, and Rachel Lennon

Subjects
Gene isoform, Transcriptome, Type IV collagen, Kidney, medicine.anatomical_structure, Proteome, Organoid, medicine, Biology, Phenotype, Basement membrane assembly, Cell biology
Abstract

SUMMARYBasement membranes (BMs) are complex macromolecular networks underlying all continuous layers of cells. Essential components include type IV collagen and laminins, which are affected by human genetic defects leading to a range of debilitating conditions including kidney, muscle, and cerebrovascular phenotypes. We investigated the dynamics of BM assembly in human pluripotent stem cell-derived kidney organoids. We resolved their global BM composition and discovered a conserved temporal sequence in BM assembly that paralleled mammalian fetal kidneys. We identified the emergence of key BM isoforms, which were altered by a pathogenic variant in COL4A5. Integrating organoid, fetal and adult kidney proteomes we found dynamic regulation of BM composition through development to adulthood, and with single-cell transcriptomic analysis we mapped the cellular origins of BM components. Overall, we define the complex and dynamic nature of vertebrate BM assembly and provide a platform for understanding its wider relevance in human development and disease.

Published
2021
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6. Consensus statement on standards and guidelines for the molecular diagnostics of Alport syndrome: refining the ACMG criteria

Author

Tamara Nikuševa Martić, Carmela Errichiello, Albertien M. van Eerde, Anniek Corveleyn, Pascale Hilbert, Rimante Cerkauskiene, Micheel van Geel, Samuela Landini, Concetta Gangemi, Miriam Zacchia, Emma Ashton, Evelien Van Hoof, Valeria Aiello, Martin C. Gregory, Elisabeth Ars, Viviana Palazzo, Constantinos Deltas, Asheeta Gupta, Laura Massella, Susie Gear, Laith Al-Rabadi, Danica Galešić Ljubanović, Louise Hopkinson, Julia Hoefele, Jens Michael Hertz, Peter H. Byers, Elizabeth Watson, Judy Savige, Agnieszka Bierzynska, Francesca Becherucci, Pavlina Plevova, Beata S. Lipska-Ziętkiewicz, Maggie Williams, Adrian Lungu, Ania Koziell, Kathleen Claes, Agne Cerkauskaite, Francesca Mari, Hendica Belge, Alessandra Renieri, Helen Storey, Hansjorg Martin Rothe, Rachel Lennon, Savige, J., Storey, H., Watson, E., Hertz, J. M., Deltas, C., Renieri, A., Mari, F., Hilbert, P., Plevova, P., Byers, P., Cerkauskaite, A., Gregory, M., Cerkauskiene, R., Ljubanovic, D. G., Becherucci, F., Errichiello, C., Massella, L., Aiello, V., Lennon, R., Hopkinson, L., Koziell, A., Lungu, A., Rothe, H. M., Hoefele, J., Zacchia, M., Martic, T. N., Gupta, A., van Eerde, A., Gear, S., Landini, S., Palazzo, V., al-Rabadi, L., Claes, K., Corveleyn, A., Van Hoof, E., van Geel, M., Williams, M., Ashton, E., Belge, H., Ars, E., Bierzynska, A., Gangemi, C., Lipska-Zietkiewicz, B. S., RS: GROW - R3 - Innovative Cancer Diagnostics & Therapy, and MUMC+: DA KG Lab Centraal Lab (9)

Subjects
Collagen Type IV, medicine.medical_specialty, Consensus, IV COLLAGEN, 030232 urology & nephrology, AMINO-ACID-SEQUENCE, MEDICAL GENETICS, Diseases, Nephritis, Hereditary, AMERICAN-COLLEGE, Meeting Report, urologic and male genital diseases, Autoantigens, DISEASE, 03 medical and health sciences, diseases, Alport syndrome, 0302 clinical medicine, Genetics, medicine, GLYCINE SUBSTITUTIONS, Humans, Genetic Testing, Genetics (clinical), 030304 developmental biology, 0303 health sciences, business.industry, MUTATIONS, Molecular diagnostics, medicine.disease, Phenotype, female genital diseases and pregnancy complications, Minor allele frequency, OSTEOGENESIS IMPERFECTA, BASEMENT-MEMBRANE, Practice Guidelines as Topic, Medical genetics, CHAIN, business, Nephrotic syndrome, Minigene, Founder effect
Abstract

The recent Chandos House meeting of the Alport Variant Collaborative extended the indications for screening for pathogenic variants in the COL4A5, COL4A3 and COL4A4 genes beyond the classical Alport phenotype (haematuria, renal failure; family history of haematuria or renal failure) to include persistent proteinuria, steroid-resistant nephrotic syndrome, focal and segmental glomerulosclerosis (FSGS), familial IgA glomerulonephritis and end-stage kidney failure without an obvious cause. The meeting refined the ACMG criteria for variant assessment for the Alport genes (COL4A3–5). It identified ‘mutational hotspots’ (PM1) in the collagen IV α5, α3 and α4 chains including position 1 Glycine residues in the Gly-X-Y repeats in the intermediate collagenous domains; and Cysteine residues in the carboxy non-collagenous domain (PP3). It considered that ‘well-established’ functional assays (PS3, BS3) were still mainly research tools but sequencing and minigene assays were commonly used to confirm splicing variants. It was not possible to define the Minor Allele Frequency (MAF) threshold above which variants were considered Benign (BA1, BS1), because of the different modes of inheritances of Alport syndrome, and the occurrence of hypomorphic variants (often Glycine adjacent to a non-collagenous interruption) and local founder effects. Heterozygous COL4A3 and COL4A4 variants were common ‘incidental’ findings also present in normal reference databases. The recognition and interpretation of hypomorphic variants in the COL4A3–COL4A5 genes remains a challenge.

Published
2021
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7. Circadian rhythms in skin and other elastic tissues

Author

Mark Naven, Louise Hopkinson, Sarah A. Hibbert, Alexander Eckersley, Mike Bell, Victoria L. Newton, Matiss Ozols, Michael J. Sherratt, and Qing-Jun Meng

Subjects
0301 basic medicine, medicine.medical_treatment, Extracellular matrix, 03 medical and health sciences, 0302 clinical medicine, medicine, Animals, Homeostasis, Humans, Circadian rhythm, Molecular Biology, Skin, Extracellular Matrix Proteins, biology, Cartilage, Elastic Tissue, Chronotherapy (treatment scheduling), Cell biology, Circadian Rhythm, Extracellular Matrix, 030104 developmental biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, biology.protein, Wound healing, Elastin, Elastic fiber
Abstract

Circadian rhythms are daily oscillations that, in mammals, are driven by both a master clock, located in the brain, and peripheral clocks in cells and tissues. Approximately 10% of the transcriptome, including extracellular matrix components, is estimated to be under circadian control. Whilst it has been established that certain collagens and extracellular matrix proteases are diurnally regulated (for example in tendon, cartilage and intervertebral disc) the role played by circadian rhythms in mediating elastic fiber homeostasis is poorly understood. Skin, arteries and lungs are dynamic, resilient, elastic fiber-rich organs and tissues. In skin, circadian rhythms influence cell migration and proliferation, wound healing and susceptibility of the tissues to damage (from protease activity, oxidative stress and ultraviolet radiation). In the cardiovascular system, blood pressure and heart rate also follow age-dependent circadian rhythms whilst the lungs exhibit diurnal variations in immune response. In order to better understand these processes it will be necessary to characterise diurnal changes in extracellular matrix biology. In particular, given the sensitivity of peripheral clocks to external factors, the timed delivery of interventions (chronotherapy) has the potential to significantly improve the efficacy of treatments designed to repair and regenerate damaged cutaneous, vascular and pulmonary tissues.

Published
2019

8. List of contributors

Author

Zahra Akbari, Luis Almeida, Thafar Almela, Parisa Amdjadi, Pouya Amrollahi, Sahar Ansari, Rizwan Bader, Mohamadreza Baghaban Eslaminejad, Katie Bardsley, Sompop Bencharit, Priyadarshni Bindal, Aldo R. Boccaccini, Dewi Borkent, Ian Brook, Wen L. Chai, Helen Colley, Aileen Crawford, Ali Dabbagh, Erfan Dashtimoghadarm, Shima Dehghani, Michael Del Monico, Andrew R. Dentino, Tarek El-Bialy, Noha A. El-Wassefy, Farahnaz Fahimipour, Mina D. Fahmy, Jasmine Faldu, Masomeh Farahani, Dina S. Farahat, Atena Fatehinya, Hossein Golzar, Jose Gonzalez, Ourania-Menti Goudouri, Vanessa Hearnden, Louise Hopkinson, Samaneh Hosseini, Mohamed S. Ibrahim, Saso Ivanovski, Maissa Jafari, Shahrbanoo Jahangir, Hossein E. Jazayeri, Noor H. Abu Kasim, Arash Khojasteh, Kimia Khoshroo, Zohaib Khurshid, Eleana Kontonasaki, Lisetta Lam, Ryan S.B. Lee, Masoud Mazafari, Farzaneh Moghadam, Keyvan Moharamzadeh, Alireza Moshaverinia, Craig Murdoch, Shariq Najeeb, Pantea Nazeman, Touraj Nejatian, Zach Nicholson, Maysam Omidi, Meisam Omidi, Zahrasadat Paknejad, Thamil Selvee Ramasamy, Morteza Rasoulianboroujeni, Maryam Rezai Rad, Nasim Salehi-Nik, Farshid Sefat, Massoud Seifi, Brinda Shah, Saleheh Shahmoradi, Mohammadreza Tahriri, Lobat Tayebi, Daryoosh Vashaee, Jonathan Wirth, Benjamin M. Wu, Amir Yadegari, Wiley Yao, Fatemeh Yazdian, Mostafa Yazdimamaghani, Muhammad S. Zafar, Ehsan Zahedi, and Sana Zohaib

Published
2017
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