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. 2024 Feb 10;27(3):109203.
doi: 10.1016/j.isci.2024.109203. eCollection 2024 Mar 15.

Identification of a strong genetic risk factor for major depressive disorder in the human virome

Nobuyuki Kobayashi  1 , Kazuya Shimada  1 , Azusa Ishii  1 , Rui Osaka  1 , Toshiko Nishiyama  2 , Masahiro Shigeta  3 , Hiroyuki Yanagisawa  2 , Naomi Oka  1 , Kazuhiro Kondo  1
Affiliations

Identification of a strong genetic risk factor for major depressive disorder in the human virome

Nobuyuki Kobayashi et al. iScience. .

Abstract

The heritability of major depressive disorder (MDD) is reportedly 30-50%. However, the genetic basis of its heritability remains unknown. Within SITH-1, a risk factor for MDD in human herpesvirus 6B (HHV-6B), we discovered a gene polymorphism with a large odds ratio for an association with MDD. It was a sequence whose number of repeats was inversely correlated with SITH-1 expression. This number was significantly lower in MDD patients. Rates for 17 or fewer repeats of the sequence were 67.9% for MDD and 28.6% for normal controls, with an odds ratio of 5.28. For patients with 17 or less repeats, the rate for presence of another MDD patient in their families was 47.4%, whereas there were no MDD patients in the families of patients with more than 17 repeats. Since HHV-6B is transmitted primarily mother to child and within families and persists for life, this gene polymorphism could potentially influence heritability of MDD.

Keywords: Behavioral neuroscience; Genetics; Virology.

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Conflict of interest statement

K.K. and N.K. have submitted a patent application entitled “Factor involved in latent infection with herpesvirus, and use thereof,” US patent application publication 2010/0281550 A1. N.O., K.K., and N.K. have submitted a patent application entitled “Method for detecting antibody against SITH-1 in biological sample,” US patent application publication 2012/0107842 A1. K.K. has stock in Virus Ikagaku Kenkyusho Inc.

Figures

None
Graphical abstract
Figure 1
Figure 1
Analysis of repeat sequences present in HHV-6B SITH-1 enhancer region (A) HHV-6B latent transcripts and repeat sequences. The upper portion shows the positions and arrangements of the major repeat elements, R1, R2, and R3, and the structure of the direct repeat (DR) termini. The middle portion shows the positions of the HHV-6 latent transcripts (H6LTs). The bottom portion shows the positions of SITH-1 mRNA, R1, R2 and R3. The drawings of the mRNAs are all in the same orientation relative to the HHV-6 genome. Thin lines, introns; thick arrows, exons. All exons and introns are drawn to scale. (B) Design of nested primers for DNA amplification in R1 region. Shows positional relationships of PCR primers and R1 repeat sequences. (C) Base sequences and structure of repeat sequences in R1 region of HHV-6B HST strain. Sequences with less than 12 bases are underlined. Light blue: R1A, Green: R1B、Yellow: R1C, Dark blue: R1D. (D) Repeat sequences present in R1 region. Shows base sequences and identifiers.
Figure 2
Figure 2
Association of repeat sequences in R1 region and MDD (A) Comparison of total numbers of R1 elements between NCs and MDD patients. (B) Comparison of numbers of R1A elements between NCs and MDD patients. (C) Comparison of numbers of R1B elements between NCs and MDD patients. (D) Anti-SITH-1 Ab titers in NCs and MDD patients. (E) Correlation between total number of R1 elements and Anti-SITH-1 Ab titers in NCs and all MDD patients. (F) Correlation between number of R1A elements and Anti-SITH-1 Ab titers in NCs and all MDD patients. (G) Correlation between total number of R1B elements and Anti-SITH-1 Ab titers in NCs and all MDD patients. (H) ROC analysis regarding R1A element numbers and MDD onset. (A, B, C, and D) Bars represent median values; Mann-Whitney U-test. (E, F and G) Spearman’s rank correlation coefficient.
Figure 3
Figure 3
Association of number of R1A repeats and MDD patient symptoms (A) Difference in Anti-SITH-1 antibody titers in MDD patients depending on whether number of R1A elements is 17 or less or greater than 17 Bars represent median values. (B) HAMD_3 score in MDD patients depending on whether number of R1A elements is 17 or less or greater than 17. (C) HAMD_8 score in MDD patients depending on whether number of R1A elements is 17 or less or greater than 17. (D) HAMD_12 score in MDD patients depending on whether number of R1A elements is 17 or less or greater than 17. (A, B, C, and D) Mann-Whitney U-test.
Figure 4
Figure 4
Effect of MDD-related repeat R1A sequences on gene expression in astrocyte cell line U373 (A) Structure of SEAP expression reporter plasmid Shows NF-kB binding site, TATA-like promoter (PTAL), R1 element insertion sites, SEAP genes and position of SEAP Kozak sequences. (B) Suppression of SEAP production by 17 R1A elements and R1B elements Comparison of SEAP production for reporter plasmid with no R1 elements inserted, one with 17 R1A elements inserted, one with 17 R1B elements inserted. (C) Comparison of SEAP production for plasmids with 7, 12 or 17 R1A elements inserted. (D) Comparison of SEAP production for plasmids with 7, 12 or 17 R1B elements inserted. (B) One-way ANOVA followed by Tukey’s multiple comparisons test. (C and D) One-way ANOVA followed by Dunnett’s multiple comparisons test.
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