. 2019 Dec;22(12):1966-1974.

doi: 10.1038/s41593-019-0530-0. Epub 2019 Nov 25.

Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7, encoding a heat-shock protein

Sali M K Farhan^{1

2

3}, Daniel P Howrigan^{4

5

6}, Liam E Abbott^{4

5

6}, Joseph R Klim⁷, Simon D Topp⁸, Andrea E Byrnes^{4

5

6}, Claire Churchhouse^{4

5

6}, Hemali Phatnani⁹, Bradley N Smith⁸, Evadnie Rampersaud¹⁰, Gang Wu¹⁰, Joanne Wuu¹¹, Aleksey Shatunov¹², Alfredo Iacoangeli^{12

13}, Ahmad Al Khleifat¹², Daniel A Mordes⁷, Sulagna Ghosh^{6

7}; ALSGENS Consortium; FALS Consortium; Project MinE Consortium; CReATe Consortium; Kevin Eggan^{6

7}, Rosa Rademakers¹⁴, Jacob L McCauley^{15

16}, Rebecca Schüle¹⁷, Stephan Züchner^{15

16}, Michael Benatar¹¹, J Paul Taylor^{18

19}, Michael Nalls^{20

21}, Marc Gotkine²², Pamela J Shaw²³, Karen E Morrison²⁴, Ammar Al-Chalabi^{12

25}, Bryan Traynor^{20

26}, Christopher E Shaw^{8

27}, David B Goldstein²⁸, Matthew B Harms²⁹, Mark J Daly^{4

5

6}, Benjamin M Neale^{30

31

32}

Affiliations

¹ Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. sfarhan@broadinstitute.org.
² Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA. sfarhan@broadinstitute.org.
³ Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA. sfarhan@broadinstitute.org.
⁴ Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
⁵ Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
⁶ Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
⁷ Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
⁸ United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
⁹ Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA.
¹⁰ Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
¹¹ Department of Neurology, University of Miami, Miami, FL, USA.
¹² Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.
¹³ Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
¹⁴ Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
¹⁵ John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA.
¹⁶ The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA.
¹⁷ Center for Neurology and Hertie Institute für Clinical Brain Research, University of Tübingen, German Center for Neurodegenerative Diseases, Tübingen, Germany.
¹⁸ Howard Hughes Medical Institute, Chevy Chase, MD, USA.
¹⁹ Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
²⁰ Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA.
²¹ Data Tecnica International, Glen Echo, MD, USA.
²² Department of Neurology, The Agnes Ginges Center for Human Neurogenetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
²³ Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK.
²⁴ Faculty of Medicine, University of Southampton and Department of Neurology, University Hospital Southampton, Southampton, UK.
²⁵ Department of Neurology, King's College Hospital, London, UK.
²⁶ Department of Neurology, Johns Hopkins University, Baltimore, MD, USA.
²⁷ Centre for Brain Research, University of Auckland, Auckland, New Zealand.
²⁸ Institute for Genomic Medicine, Columbia University, New York, NY, USA.
²⁹ Department of Neurology, Columbia University, New York, NY, USA.
³⁰ Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. bneale@broadinstitute.org.
³¹ Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA. bneale@broadinstitute.org.
³² Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA. bneale@broadinstitute.org.

PMID: 31768050
PMCID: PMC6919277
DOI: 10.1038/s41593-019-0530-0

Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7, encoding a heat-shock protein

Sali M K Farhan et al. Nat Neurosci. 2019 Dec.

. 2019 Dec;22(12):1966-1974.

doi: 10.1038/s41593-019-0530-0. Epub 2019 Nov 25.

Authors

Affiliations

¹ Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. sfarhan@broadinstitute.org.
² Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA. sfarhan@broadinstitute.org.
³ Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA. sfarhan@broadinstitute.org.
⁴ Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
⁵ Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
⁶ Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
⁷ Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
⁸ United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
⁹ Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA.
¹⁰ Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
¹¹ Department of Neurology, University of Miami, Miami, FL, USA.
¹² Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.
¹³ Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
¹⁴ Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
¹⁵ John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA.
¹⁶ The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA.
¹⁷ Center for Neurology and Hertie Institute für Clinical Brain Research, University of Tübingen, German Center for Neurodegenerative Diseases, Tübingen, Germany.
¹⁸ Howard Hughes Medical Institute, Chevy Chase, MD, USA.
¹⁹ Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
²⁰ Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA.
²¹ Data Tecnica International, Glen Echo, MD, USA.
²² Department of Neurology, The Agnes Ginges Center for Human Neurogenetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
²³ Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK.
²⁴ Faculty of Medicine, University of Southampton and Department of Neurology, University Hospital Southampton, Southampton, UK.
²⁵ Department of Neurology, King's College Hospital, London, UK.
²⁶ Department of Neurology, Johns Hopkins University, Baltimore, MD, USA.
²⁷ Centre for Brain Research, University of Auckland, Auckland, New Zealand.
²⁸ Institute for Genomic Medicine, Columbia University, New York, NY, USA.
²⁹ Department of Neurology, Columbia University, New York, NY, USA.
³⁰ Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. bneale@broadinstitute.org.
³¹ Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA. bneale@broadinstitute.org.
³² Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA. bneale@broadinstitute.org.

PMID: 31768050
PMCID: PMC6919277
DOI: 10.1038/s41593-019-0530-0

Erratum in

Publisher Correction: Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7, encoding a heat-shock protein.
Farhan SMK, Howrigan DP, Abbott LE, Klim JR, Topp SD, Byrnes AE, Churchhouse C, Phatnani H, Smith BN, Rampersaud E, Wu G, Wuu J, Shatunov A, Iacoangeli A, Khleifat AA, Mordes DA, Ghosh S; ALSGENS Consortium; FALS Consortium; Project MinE Consortium; CReATe Consortium; Eggan K, Rademakers R, McCauley JL, Schüle R, Züchner S, Benatar M, Taylor JP, Nalls M, Gotkine M, Shaw PJ, Morrison KE, Al-Chalabi A, Traynor B, Shaw CE, Goldstein DB, Harms MB, Daly MJ, Neale BM. Farhan SMK, et al. Nat Neurosci. 2020 Feb;23(2):295. doi: 10.1038/s41593-019-0570-5. Nat Neurosci. 2020. PMID: 31857710

Abstract

To discover novel genes underlying amyotrophic lateral sclerosis (ALS), we aggregated exomes from 3,864 cases and 7,839 ancestry-matched controls. We observed a significant excess of rare protein-truncating variants among ALS cases, and these variants were concentrated in constrained genes. Through gene level analyses, we replicated known ALS genes including SOD1, NEK1 and FUS. We also observed multiple distinct protein-truncating variants in a highly constrained gene, DNAJC7. The signal in DNAJC7 exceeded genome-wide significance, and immunoblotting assays showed depletion of DNAJC7 protein in fibroblasts in a patient with ALS carrying the p.Arg156Ter variant. DNAJC7 encodes a member of the heat-shock protein family, HSP40, which, along with HSP70 proteins, facilitates protein homeostasis, including folding of newly synthesized polypeptides and clearance of degraded proteins. When these processes are not regulated, misfolding and accumulation of aberrant proteins can occur and lead to protein aggregation, which is a pathological hallmark of neurodegeneration. Our results highlight DNAJC7 as a novel gene for ALS.

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Conflict of interest statement

COMPETING INTERESTS

MN participation is supported by a consulting contract between Data Tecnica International and the National Institute on Aging, NIH, Bethesda, MD, USA, as a possible conflict of interest. MN also consults for Lysosomal Therapeutics Inc, the Michael J. Fox Foundation and Vivid Genomics among others. The other authors declare no competing interests.

Figures

**Fig. 1.. Exome wide enrichment of protein-truncating variants in ALS cases**
Exome wide analysis of synonymous variants, benign missense variants, damaging missense variants, and protein-truncating variants within singletons, doubletons, ultra-rare singletons, and rare variants. Odds ratios and 95% confidence intervals for each class of variation are depicted by different colors. P-values from firth logistic regression test are also displayed. Multiple test correction P-value: 0.0125. N=3,864 ALS cases; N=7,839 controls. The graph display the mean and standard deviation.

**Fig. 2.. Enrichment of protein-truncating variants in constrained genes in ALS cases**
a, Analysis of constrained genes only in synonymous variants, benign missense variants, damaging missense variants, and protein-truncating variants within ultra-rare singletons and rare variants. Odds ratios and 95% confidence intervals for each class of variation are depicted by different colors. P-values from firth logistic regression test are also displayed. Multiple test correction P-value: 0.0125. N=3,864 ALS cases; N=7,839 controls. The graphs display the mean and standard deviation. b, Exome-wide analysis with constrained genes removed.

**Fig. 3.. No enrichment of variants in known ALS genes, other related neurodegenerative disease genes, or brain specific genes**
a, Analysis of ALS genes. Synonymous variants, benign missense variants, damaging missense variants, and protein-truncating variants within singletons, doubletons, ultra-rare singletons, and rare variants are shown. Odds ratios and 95% confidence intervals for each class of variation are depicted by different colors. P-values from firth logistic regression test are also displayed. Multiple test correction P-value: 0.0125. N=3,864 ALS cases; N=7,839 controls. The graphs display the mean and standard deviation. b, Analysis of other neurodegenerative disease genes. c, Analysis of brain specific genes.

**Fig. 4.. Quantile-quantile plot of discovery results for rare variants**
a, Rare protein-truncating variants in ALS dataset. X and Y axis represent the negative logarithm P-value. N=3,864 ALS cases; N=7,839 controls. The top 10 genes with their P-values are displayed. Genes in red and blue pass or approach exome-wide significance, respectively. The results displayed are from a burden analysis using Fisher’s exact test as well as SKAT, with previously defined covariates (sample sex, PC1-PC10, and total exome count). Exome-wide correction for multiple testing was set at (P<2.5×10–6), which was the 5% type-I error rate multiplied by the number of genes tested. b, Rare damaging missense variants in ALS dataset. c, Rare protein-truncating variants in ALS cases with an additional 21,071 non-Finnish European controls for a total of 28,910 controls. Genes in blue were the most significant genes in the discovery analysis. Genes in green were the most significant genes in the secondary analysis. d, Rare damaging missense variants in ALS cases and 28,910 controls. The top 10 genes with their P-values are displayed.

**Fig. 5.. Effects of *DNAJC7* protein-truncating variant p.Arg156Ter on transcript and protein levels.**
a, qRT-PCR analysis of *DNAJC7* transcripts in human fibroblasts from healthy controls or a patient harboring a *DNAJC7* protein-truncating variant p.Arg156Ter. Data were normalized to GAPDH and displayed as mean of 3 technical replicates with s.d. from two independent experiments with n=12 control and 1 patient lines (unpaired t test, two-sided, P<0.05). P-value is displayed, 0.1312. b, Immunoblot analysis for DNAJC7 protein levels in human fibroblast lysates. Protein levels were normalized to GAPDH and displayed relative to the average levels in healthy controls. Data are displayed as mean with s.d. of n=3 technical replicates (unpaired t test, two-sided, P< 0.05). P-value is displayed, <0.0001. The blot image was cropped to make this figure, for the full scan of the blot, please see Supplementary Fig. 10.

See this image and copyright information in PMC

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Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7, encoding a heat-shock protein

Affiliations

Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7, encoding a heat-shock protein

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Erratum in

Abstract

Conflict of interest statement

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