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. 2025 Jun 25;5(5):100558.
doi: 10.1016/j.bpsgos.2025.100558. eCollection 2025 Sep.

Pathway-Specific Polygenic Scores for Predicting Clinical Lithium Treatment Response in Patients With Bipolar Disorder

Nigussie T Sharew  1   2 Scott R Clark  1 Sergi Papiol  3   4 Urs Heilbronner  3 Franziska Degenhardt  5   6 Janice M Fullerton  7   8 Liping Hou  9 Tatyana Shekhtman  10 Mazda Adli  11 Nirmala Akula  9 Kazufumi Akiyama  12 Raffaella Ardau  13 Bárbara Arias  14 Roland Hasler  15 Hélène Richard-Lepouriel  15 Nader Perroud  15 Lena Backlund  16   17 Abesh Kumar Bhattacharjee  10 Frank Bellivier  18 Antonio Benabarre  19 Susanne Bengesser  20 Joanna M Biernacka  21   22 Armin Birner  20 Cynthia Marie-Claire  18   23 Pablo Cervantes  24 Hsi-Chung Chen  25 Caterina Chillotti  13 Sven Cichon  26   27   28 Cristiana Cruceanu  29 Piotr M Czerski  30 Nina Dalkner  20 Maria Del Zompo  31 J Raymond DePaulo  32 Bruno Étain  18 Stephane Jamain  33 Peter Falkai  4   34 Andreas J Forstner  5   28 Louise Frisen  16   35 Mark A Frye  22 Sébastien Gard  36 Julie S Garnham  37 Fernando S Goes  32 Maria Grigoroiu-Serbanescu  37 Andreas J Fallgatter  38 Sophia Stegmaier  39 Thomas Ethofer  40   41 Silvia Biere  42 Kristiyana Petrova  42 Ceylan Schuster  42 Kristina Adorjan  3   43 Monika Budde  3 Maria Heilbronner  3 Janos L Kalman  3   4 Mojtaba Oraki Kohshour  3   44 Daniela Reich-Erkelenz  3 Sabrina K Schaupp  3 Eva C Schulte  3   4 Fanny Senner  3   4 Thomas Vogl  3 Ion-George Anghelescu  45 Volker Arolt  46 Udo Dannlowski  46 Detlef E Dietrich  47   48 Christian Figge  49 Markus Jäger  50 Fabian U Lang  50 Georg Juckel  51 Carsten Konrad  52 Jens Reimer  53   54 Max Schmauß  55 Andrea Schmitt  4   56 Carsten Spitzer  57 Martin von Hagen  58 Jens Wiltfang  59   60 Jörg Zimmermann  61 Till F M Andlauer  62 Andre Fischer  60 Felix Bermpohl  11 Philipp Ritter  63 Silke Matura  42 Anna Gryaznova  3 Irina Falkenberg  64 Cüneyt Yildiz  64 Tilo Kircher  64 Julia Schmidt  65 Marius Koch  65 Kathrin Gade  59 Sarah Trost  59 Ida S Haussleiter  51 Martin Lambert  53 Anja C Rohenkohl  53 Vivien Kraft  53 Paul Grof  66 Ryota Hashimoto  67 Joanna Hauser  30 Stefan Herms  5   27 Per Hoffmann  5   27 Esther Jiménez  19 Jean-Pierre Kahn  68 Layla Kassem  11 Po-Hsiu Kuo  69 Tadafumi Kato  70 John Kelsoe  10 Sarah Kittel-Schneider  71   72 Ewa Ferensztajn-Rochowiak  73 Barbara König  74 Ichiro Kusumi  75 Gonzalo Laje  11 Mikael Landén  76   77 Catharina Lavebratt  16   17 Marion Leboyer  78 Susan G Leckband  79 Alfonso Tortorella  80 Mirko Manchia  81   82 Lina Martinsson  83 Michael J McCarthy  10   84 Susan McElroy  85 Francesc Colom  86   87 Vincent Millischer  16   17   88 Marina Mitjans  87   89   90   91 Francis M Mondimore  32 Palmiero Monteleone  92   93 Caroline M Nievergelt  10 Markus M Nöthen  5 Tomas Novák  94 Claire O'Donovan  37 Norio Ozaki  95 Andrea Pfennig  63 Claudia Pisanu  31 James B Potash  32 Andreas Reif  71 Eva Reininghaus  20 Guy A Rouleau  96 Janusz K Rybakowski  73 Martin Schalling  16   17 Peter R Schofield  7   8 Barbara W Schweizer  32 Giovanni Severino  31 Paul D Shilling  10 Katzutaka Shimoda  97 Christian Simhandl  98 Claire M Slaney  37 Alessio Squassina  31 Thomas Stamm  11   99 Pavla Stopkova  94 Mario Maj  93 Gustavo Turecki  29 Eduard Vieta  19 Julia Veeh  76 Biju Viswanath  100 Stephanie H Witt  101 Adam Wright  102 Peter P Zandi  103 Philip B Mitchell  102 Michael Bauer  63 Martin Alda  37   94 Marcella Rietschel  101 Francis J McMahon  9 Thomas G Schulze  3   9   32   101   104   105 Bernhard T Baune  106   107   108 Klaus Oliver Schubert  1   109 Azmeraw T Amare  1
Affiliations

Pathway-Specific Polygenic Scores for Predicting Clinical Lithium Treatment Response in Patients With Bipolar Disorder

Nigussie T Sharew et al. Biol Psychiatry Glob Open Sci. .

Abstract

Background: Polygenic scores (PGSs) hold the potential to identify patients who respond favorably to specific psychiatric treatments. However, their biological interpretation remains unclear. In this study, we developed pathway-specific PGSs (PSPGSs) for lithium response and assessed their association with clinical lithium response in patients with bipolar disorder.

Methods: Using sets of genes involved in pathways affected by lithium, we developed 9 PSPGSs and evaluated their associations with lithium response in the International Consortium on Lithium Genetics (ConLi+Gen) (N = 2367), with validation in combined PsyCourse (Pathomechanisms and Signatures in the Longitudinal Course of Psychosis) (N = 105) and BipoLife (N = 102) cohorts. The association between each PSPGS and lithium response-defined both as a continuous ALDA score and a categorical outcome (good vs. poor responses)-was evaluated using regression models, with adjustment for confounders. The cutoff for a significant association was p < .05 after multiple testing correction.

Results: The PGSs for acetylcholine, GABA (gamma-aminobutyric acid), and mitochondria were associated with response to lithium in both categorical and continuous outcomes. However, the PGSs for calcium channel, circadian rhythm, and GSK (glycogen synthase kinase) were associated only with the continuous outcome. Each score explained 0.29% to 1.91% of the variance in the categorical and 0.30% to 1.54% of the variance in the continuous outcomes. A multivariate model combining PSPGSs that showed significant associations in the univariate analysis (combined PSPGS) increased the percentage of variance explained (R 2) to 3.71% and 3.18% for the categorical and continuous outcomes, respectively. Associations for PGSs for GABA and circadian rhythm were replicated. Patients with the highest genetic loading (10th decile) for acetylcholine variants were 3.03 times more likely (95% CI, 1.95 to 4.69) to show a good lithium response (categorical outcome) than patients with the lowest genetic loading (1st decile).

Conclusions: PSPGSs achieved predictive performance comparable to the conventional genome-wide PGSs, with the added advantage of biological interpretability using a smaller list of genetic variants.

Keywords: Bipolar disorder; Lithium; Pharmacogenomics; Polygenic score; Psychiatry.

Plain language summary

Polygenic scores (PGSs) have the potential to identify patients likely to respond to specific psychiatric treatments, but their biological interpretation remains unclear. In this study, we developed 9 pathway-specific PGSs (PSPGSs) for lithium response by aggregating genetic variants involved in pathways affected by lithium. We assessed their associations with lithium response in the International Consortium on Lithium Genetics (ConLi+Gen) (N = 2367) cohort and validated the findings in the PsyCourse (N = 105) and BipoLife (N = 102) cohorts. Clinical response to lithium treatment was significantly associated with PSPGSs for acetylcholine, GABA (gamma-aminobutyric acid), calcium channel signaling, mitochondria, circadian rhythm, and GSK pathways, with explained variance (R 2) ranging from 0.29% to 1.91%. The combined PSPGS explained up to 3.71% of the variability. Associations for GABA and circadian rhythm PGSs were successfully replicated. In a decile-based analysis, patients with the highest genetic load (10th decile) for acetylcholine pathway variants were 3.03 times more likely to respond well to lithium compared with those in the lowest decile (1st decile). PSPGSs achieved predictive performance comparable to conventional genome-wide PGSs, with better biological interpretability and a more focused set of genetic variants.

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Figures

Figure 1
Figure 1
Examples of potential targets of lithium (pathways) and detailed steps of the data analysis process. Ach, acetylcholine; Ca2+, calcium ion; GABA, gamma-aminobutyric acid; GSEA, Gene Set Enrichment Analysis; GSK, glycogen synthase kinase; GWAS, genome-wide association study; HGNC, HUGO Gene Nomenclature Committee; KEGG, Kyoto Encyclopedia of Genes and Genomes; Li+, lithium; LOC, leave-one-country-out; PRS-CS, polygenic risk score with continuous shrinkage; PSPGS, pathway-specific polygenic score; SNP, single nucleotide polymorphism.
Figure 2
Figure 2
Trends in the odds ratios for favorable lithium treatment response [with the categorical (A) and beta coefficeints in the continuous (B) outcomes in patients with bipolar disorder, comparing patients with a high pathway-specific PGS, deciles (2nd–10th) with patients with the lowest genetic scores (1st decile; n = 2367)] for the pathways that had a significant association after multiple testing. The dot points and error bars represent the odds ratios and 95% CIs for the respective polygenic deciles. The PGS deciles that crossed an odds ratio of 1 on the y-axis in the categorical outcome (A) and a beta coefficient of 0 in the continuous outcome (B) are not statistically significant. GABA, gamma-aminobutyric acid; GSK, glycogen synthase kinase; PGS, polygenic score.

Update of

  • Pathway-Specific Polygenic Scores for Lithium Response for Predicting Clinical Lithium Treatment Response in Patients with Bipolar Disorder.
    Sharew NT, Clark SR, Papiol S, Heilbronner U, Degenhardt F, Fullerton JM, Hou L, Shekhtman T, Adli M, Akula N, Akiyama K, Ardau R, Arias B, Hasler R, Richard-Lepouriel H, Perroud N, Backlund L, Bhattacharjee AK, Bellivier F, Benabarre A, Bengesser S, Biernacka JM, Birner A, Marie-Claire C, Cervantes P, Chen HC, Chillotti C, Cichon S, Cruceanu C, Czerski PM, Dalkner N, Del Zompo M, DePaulo JR, Étain B, Jamain S, Falkai P, Forstner AJ, Frisen L, Frye MA, Gard S, Garnham JS, Goes FS, Grigoroiu-Serbanescu M, Fallgatter AJ, Stegmaier S, Ethofer T, Biere S, Petrova K, Schuster C, Adorjan K, Budde M, Heilbronner M, Kalman JL, Kohshour MO, Reich-Erkelenz D, Schaupp SK, Schulte EC, Senner F, Vogl T, Anghelescu IG, Arolt V, Dannlowski U, Dietrich DE, Figge C, Jäger M, Lang FU, Juckel G, Konrad C, Reimer J, Schmauß M, Schmitt A, Spitzer C, von Hagen M, Wiltfang J, Zimmermann J, Andlauer TFM, Fischer A, Bermpohl F, Ritter P, Matura S, Gryaznova A, Falkenberg I, Yildiz C, Kircher T, Schmidt J, Koch M, Gade K, Trost S, Haussleiter IS, Lambert M, Rohenkohl AC, Kraft V, Grof P, Hashimoto R, Hauser J, Herms S, Hoffmann P, Jiménez E, Kahn JP, Kassem L, Kuo PH, Kato T, Kelsoe J, Kittel-Schneider S, … See abstract for full author list ➔ Sharew NT, et al. medRxiv [Preprint]. 2025 Mar 24:2025.03.20.25324216. doi: 10.1101/2025.03.20.25324216. medRxiv. 2025. Update in: Biol Psychiatry Glob Open Sci. 2025 Jun 25;5(5):100558. doi: 10.1016/j.bpsgos.2025.100558. PMID: 40196273 Free PMC article. Updated. Preprint.

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