TY - JOUR
T1 - Development of ultra-deep targeted RNA sequencing for analyzing X-chromosome inactivation in female Dent disease
AU - Minamikawa, Shogo
AU - Nozu, Kandai
AU - Nozu, Yoshimi
AU - Yamamura, Tomohiko
AU - Taniguchi-Ikeda, Mariko
AU - Nakanishi, Keita
AU - Fujimura, Junya
AU - Horinouchi, Tomoko
AU - Shima, Yuko
AU - Nakanishi, Koichi
AU - Hattori, Masuji
AU - Kanda, Kyoko
AU - Tanaka, Ryojiro
AU - Morisada, Naoya
AU - Nagano, China
AU - Sakakibara, Nana
AU - Nagase, Hiroaki
AU - Morioka, Ichiro
AU - Kaito, Hiroshi
AU - Iijima, Kazumoto
N1 - Funding Information:
Funding All phases of this study were supported by a grant from the Ministry of Health, Labour and Welfare (Japan) for Research on Rare Intractable Diseases in Kidney and Urinary Tract [H24-nanchitou (nan)-ippan-041 to Kazumoto Iijima] in the Research on Measures for Intractable Diseases Project and a Grant-in-Aid from the Ministry of Culture, Sports, Science and Technology [KAKENHI] (Subject ID: 15K09691 to Kandai Nozu, 26293203 to Kazumoto Iijima and 17K16087 to Shogo Minamikawa).
Publisher Copyright:
© 2018 The Author(s) under exclusive licence to The Japan Society of Human Genetics.
PY - 2018/5/1
Y1 - 2018/5/1
N2 - The pattern of X-chromosome inactivation (XCI) can affect the clinical severity of X-linked disorders in females. XCI pattern analysis has been conducted mainly by HUMARA assay, a polymerase chain reaction-based assay using a methylation-sensitive restriction enzyme. However, this assay examines the XCI ratio of the androgen receptor gene at the genomic DNA level and does not reflect the ratio of either targeted gene directly or at the mRNA level. Here, we report four females with Dent disease, and we clarified the correlation between XCI and female cases of Dent disease using not only HUMARA assay but also a novel analytical method by RNA sequencing. We constructed genetic analysis for 4 female cases showing high level of urinary low-molecular-weight proteinuria and their parents. Their XCI pattern was analyzed by both HUMARA assay and an ultra-deep targeted RNA sequencing of the CLCN5 gene using genomic DNA and mRNA extracted from both leukocytes and urine sediment. All four cases possessed pathogenic variants of the CLCN5 gene. XCI analysis revealed skewed XCI in only two cases, while the other two showed random XCI. All assay results of HUMARA and targeted RNA sequencing in both leukocytes and urinary sediment were clearly identical in all four cases. We developed a novel XCI analytical assay of ultra-deep targeted RNA sequencing and revealed that skewed XCI explains the mechanism of onset of female Dent disease in only half of such cases.
AB - The pattern of X-chromosome inactivation (XCI) can affect the clinical severity of X-linked disorders in females. XCI pattern analysis has been conducted mainly by HUMARA assay, a polymerase chain reaction-based assay using a methylation-sensitive restriction enzyme. However, this assay examines the XCI ratio of the androgen receptor gene at the genomic DNA level and does not reflect the ratio of either targeted gene directly or at the mRNA level. Here, we report four females with Dent disease, and we clarified the correlation between XCI and female cases of Dent disease using not only HUMARA assay but also a novel analytical method by RNA sequencing. We constructed genetic analysis for 4 female cases showing high level of urinary low-molecular-weight proteinuria and their parents. Their XCI pattern was analyzed by both HUMARA assay and an ultra-deep targeted RNA sequencing of the CLCN5 gene using genomic DNA and mRNA extracted from both leukocytes and urine sediment. All four cases possessed pathogenic variants of the CLCN5 gene. XCI analysis revealed skewed XCI in only two cases, while the other two showed random XCI. All assay results of HUMARA and targeted RNA sequencing in both leukocytes and urinary sediment were clearly identical in all four cases. We developed a novel XCI analytical assay of ultra-deep targeted RNA sequencing and revealed that skewed XCI explains the mechanism of onset of female Dent disease in only half of such cases.
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U2 - 10.1038/s10038-018-0415-1
DO - 10.1038/s10038-018-0415-1
M3 - Article
C2 - 29459630
AN - SCOPUS:85042190561
VL - 63
SP - 589
EP - 595
JO - Jinrui idengaku zasshi. The Japanese journal of human genetics
JF - Jinrui idengaku zasshi. The Japanese journal of human genetics
SN - 1434-5161
IS - 5
ER -