1
|
Bassani S, Chrast J, Ambrosini G, Voisin N, Schütz F, Brusco A, Sirchia F, Turban L, Schubert S, Abou Jamra R, Schlump JU, DeMille D, Bayrak-Toydemir P, Nelson GR, Wong KN, Duncan L, Mosera M, Gilissen C, Vissers LELM, Pfundt R, Kersseboom R, Yttervik H, Hansen GÅM, Smeland MF, Butler KM, Lyons MJ, Carvalho CMB, Zhang C, Lupski JR, Potocki L, Flores-Gallegos L, Morales-Toquero R, Petit F, Yalcin B, Tuttle A, Elloumi HZ, McCormick L, Kukolich M, Klaas O, Horvath J, Scala M, Iacomino M, Operto F, Zara F, Writzl K, Maver A, Haanpää MK, Pohjola P, Arikka H, Kievit AJA, Calandrini C, Iseli C, Guex N, Reymond A. Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles. Genome Med 2024; 16:72. [PMID: 38811945 PMCID: PMC11137988 DOI: 10.1186/s13073-024-01339-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/19/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney, caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpression in zebrafish provided evidence for a dominant-negative mode of action, wherein an increased level of AFF3 resulted in pathological effects. METHODS Evolutionary constraints suggest that other modes-of-inheritance could be at play. We challenged this hypothesis by screening ID cohorts for individuals with predicted-to-be damaging variants in AFF3. We used both animal and cellular models to assess the deleteriousness of the identified variants. RESULTS We identified an individual with a KINSSHIP-like phenotype carrying a de novo partial duplication of AFF3 further strengthening the hypothesis that an increased level of AFF3 is pathological. We also detected seventeen individuals displaying a milder syndrome with either heterozygous Loss-of-Function (LoF) or biallelic missense variants in AFF3. Consistent with semi-dominance, we discovered three patients with homozygous LoF and one compound heterozygote for a LoF and a missense variant, who presented more severe phenotypes than their heterozygous parents. Matching zebrafish knockdowns exhibit neurological defects that could be rescued by expressing human AFF3 mRNA, confirming their association with the ablation of aff3. Conversely, some of the human AFF3 mRNAs carrying missense variants identified in affected individuals did not rescue these phenotypes. Overexpression of mutated AFF3 mRNAs in zebrafish embryos produced a significant increase of abnormal larvae compared to wild-type overexpression further demonstrating deleteriousness. To further assess the effect of AFF3 variation, we profiled the transcriptome of fibroblasts from affected individuals and engineered isogenic cells harboring + / + , KINSSHIP/KINSSHIP, LoF/ + , LoF/LoF or KINSSHIP/LoF AFF3 genotypes. The expression of more than a third of the AFF3 bound loci is modified in either the KINSSHIP/KINSSHIP or the LoF/LoF lines. While the same pathways are affected, only about one third of the differentially expressed genes are common to the homozygote datasets, indicating that AFF3 LoF and KINSSHIP variants largely modulate transcriptomes differently, e.g. the DNA repair pathway displayed opposite modulation. CONCLUSIONS Our results and the high pleiotropy shown by variation at this locus suggest that minute changes in AFF3 function are deleterious.
Collapse
Affiliation(s)
- Sissy Bassani
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, CH, 1015, Switzerland
- Present address: Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, CH, 1015, Switzerland
| | - Giovanna Ambrosini
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Norine Voisin
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, CH, 1015, Switzerland
- Present address: Sophia Genetics, St Sulpice, Switzerland
| | - Frédéric Schütz
- Biostatistics Platform, University of Lausanne, Lausanne, Switzerland
| | - Alfredo Brusco
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126, Turin, Italy
- Medical Genetics Unit, Città Della Salute E Della Scienza University Hospital, 10126, Turin, Italy
| | - Fabio Sirchia
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126, Turin, Italy
- Medical Genetics Unit, Città Della Salute E Della Scienza University Hospital, 10126, Turin, Italy
- Present address: Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Present address: Medical Genetics Unit, IRCCS San Matteo Foundation, Pavia, Italy
| | - Lydia Turban
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Susanna Schubert
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Jan-Ulrich Schlump
- Department of Pediatrics, Centre for Neuromedicine, Gemeinschaftskrankenhaus Herdecke Gerhard-Kienle-Weg, Herdecke, Germany
| | - Desiree DeMille
- Genomics Analysis 396, ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Gary Rex Nelson
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kristen Nicole Wong
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Laura Duncan
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, TN, USA
- Present address: Mayo Clinic, Rochester, MN, USA
| | - Mackenzie Mosera
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christian Gilissen
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rogier Kersseboom
- Center for Genetic Developmental Disorders Southwest, Zuidwester, Middelharnis, The Netherlands
| | - Hilde Yttervik
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | | | | | | | | | - Claudia M B Carvalho
- Pacific Northwest Research Institute (PNRI), Broadway, Seattle, WA, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chaofan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | | | | | | | - Binnaz Yalcin
- Inserm UMR1231, University of Burgundy, 21000, Dijon, France
| | | | | | - Lane McCormick
- Department of Genetics, Cook Children's Medical Center, Cook Children's Health Care System, Fort Worth, TX, USA
| | - Mary Kukolich
- Department of Genetics, Cook Children's Medical Center, Cook Children's Health Care System, Fort Worth, TX, USA
| | - Oliver Klaas
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Judit Horvath
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Marcello Scala
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, 16132, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Michele Iacomino
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Francesca Operto
- Department of Medicine, Child and Adolescent Neuropsychiatry Unit, Surgery and Dentistry, University of Salerno, Salerno, Italy
| | - Federico Zara
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, 16132, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maria K Haanpää
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Pia Pohjola
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Harri Arikka
- Department of Pediatric Neurology, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Anneke J A Kievit
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Camilla Calandrini
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, CH, 1015, Switzerland.
| |
Collapse
|
2
|
Bassani S, Chrast J, Ambrosini G, Voisin N, Schütz F, Brusco A, Sirchia F, Turban L, Schubert S, Jamra RA, Schlump JU, DeMille D, Bayrak-Toydemir P, Nelson GR, Wong KN, Duncan L, Mosera M, Gilissen C, Vissers LE, Pfundt R, Kersseboom R, Yttervik H, Hansen GÅM, Falkenberg Smeland M, Butler KM, Lyons MJ, Carvalho CM, Zhang C, Lupski JR, Potocki L, Flores-Gallegos L, Morales-Toquero R, Petit F, Yalcin B, Tuttle A, Elloumi HZ, Mccormick L, Kukolich M, Klaas O, Horvath J, Scala M, Iacomino M, Operto F, Zara F, Writzl K, Maver A, Haanpää MK, Pohjola P, Arikka H, Iseli C, Guex N, Reymond A. Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.14.24301100. [PMID: 38293053 PMCID: PMC10827271 DOI: 10.1101/2024.01.14.24301100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpression in zebrafish provided evidence for a dominant-negative (DN) mode-of-action, wherein an increased level of AFF3 resulted in pathological effects. Methods Evolutionary constraints suggest that other mode-of-inheritance could be at play. We challenged this hypothesis by screening ID cohorts for individuals with predicted-to-be deleterious variants in AFF3. We used both animal and cellular models to assess the deleteriousness of the identified variants. Results We identified an individual with a KINSSHIP-like phenotype carrying a de novo partial duplication of AFF3 further strengthening the hypothesis that an increased level of AFF3 is pathological. We also detected seventeen individuals displaying a milder syndrome with either heterozygous LoF or biallelic missense variants in AFF3. Consistent with semi-dominance, we discovered three patients with homozygous LoF and one compound heterozygote for a LoF and a missense variant, who presented more severe phenotypes than their heterozygous parents. Matching zebrafish knockdowns exhibit neurological defects that could be rescued by expressing human AFF3 mRNA, confirming their association with the ablation of aff3. Conversely, some of the human AFF3 mRNAs carrying missense variants identified in affected individuals did not complement. Overexpression of mutated AFF3 mRNAs in zebrafish embryos produced a significant increase of abnormal larvae compared to wild-type overexpression further demonstrating deleteriousness. To further assess the effect of AFF3 variation, we profiled the transcriptome of fibroblasts from affected individuals and engineered isogenic cells harboring +/+, DN/DN, LoF/+, LoF/LoF or DN/LoF AFF3 genotypes. The expression of more than a third of the AFF3 bound loci is modified in either the DN/DN or the LoF/LoF lines. While the same pathways are affected, only about one-third of the differentially expressed genes are common to these homozygote datasets, indicating that AFF3 LoF and DN variants largely modulate transcriptomes differently, e.g. the DNA repair pathway displayed opposite modulation. Conclusions Our results and the high pleiotropy shown by variation at this locus suggest that minute changes in AFF3 function are deleterious.
Collapse
Affiliation(s)
- Sissy Bassani
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Giovanna Ambrosini
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Norine Voisin
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Frédéric Schütz
- Biostatistics platform, University of Lausanne, Lausanne, Switzerland
| | - Alfredo Brusco
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Fabio Sirchia
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Lydia Turban
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Susanna Schubert
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Jan-Ulrich Schlump
- Department of Pediatrics, Centre for Neuromedicine, Gemeinschaftskrankenhaus Herdecke Gerhard-Kienle-Weg, Herdecke, Germany
| | - Desiree DeMille
- Genomics Analysis 396, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Pinar Bayrak-Toydemir
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Gary Rex Nelson
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Kristen Nicole Wong
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Laura Duncan
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mackenzie Mosera
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christian Gilissen
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lisenka E.L.M. Vissers
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rogier Kersseboom
- Center for genetic developmental disorders southwest, Zuidwester, Middelharnis, The Netherlands
| | - Hilde Yttervik
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | | | | | | | | | - Claudia M.B. Carvalho
- Pacific Northwest Research Institute (PNRI), Broadway, Seattle, Washington, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Chaofan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | | | | | | | - Binnaz Yalcin
- Inserm UMR1231, University of Burgundy, 21000 Dijon, France
| | | | | | - Lane Mccormick
- Department of Genetics, Cook Children’s Medical Center, Cook Children’s Health Care System, Fort Worth, Texas, USA
| | - Mary Kukolich
- Department of Genetics, Cook Children’s Medical Center, Cook Children’s Health Care System, Fort Worth, Texas, USA
| | - Oliver Klaas
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Judit Horvath
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Michele Iacomino
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Francesca Operto
- Child and Adolescent Neuropsychiatry Unit, Department of Medicine, Surgery and Dentistry, University of Salerno, Salerno, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maria K. Haanpää
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Pia Pohjola
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Harri Arikka
- Department of Pediatric Neurology, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|