References

• Arab, A. H., & Elhawary, N. A. (2015). Association between ANKK1 (rs1800497) and LTA (rs909253) Genetic Variants and Risk of Schizophrenia. BioMed Research International, 1. https://doi.org/10.1155/2015/821827
   Web of Science ®Google Scholar
• Arranz, M. J., Gallego-Fabrega, C., Martín-Blanco, A., Soler, J., Elices, M., Dominguez-Clavé, E., Salazar, J., Vega, D., Briones-Buixassa, L., & Pascual, J. C. (2021). A genome-wide methylation study reveals X chromosome and childhood trauma methylation alterations associated with borderline personality disorder. Translational Psychiatry, 11(1), 5. https://doi.org/10.1038/s41398-020-01139-z
   PubMed Web of Science ®Google Scholar
• Bifulco, A., Bernazzani, O., Moran, P. M., & Jacobs, C. (2005). The childhood experience of care and abuse questionnaire (CECA.Q): Validation in a community series. British Journal of Clinical Psychology, 44(4), 563–581. https://doi.org/10.1348/014466505X35344
   PubMed Web of Science ®Google Scholar
• Catts, V. S., & Weickert, C. S. (2012). Gene expression analysis implicates a death receptor pathway in schizophrenia pathology. PLoS One, 7(4), e35511. https://doi.org/10.1371/journal.pone.0035511
   PubMed Web of Science ®Google Scholar
• Cecil, C. A. M., Smith, R. G., Walton, E., Mill, J., McCrory, E. J., & Viding, E. (2016). Epigenetic signatures of childhood abuse and neglect: Implications for psychiatric vulnerability. Journal of Psychiatric Research, 83, 184–194. https://doi.org/10.1016/j.jpsychires.2016.09.010
   PubMed Web of Science ®Google Scholar
• Dall’Aglio, L., Muka, T., Cecil, C. A. M., Bramer, W. M., Verbiest, M. M. P. J., Nano, J., Hidalgo, A. C., Franco, O. H., & Tiemeier, H. (2018). The role of epigenetic modifications in neurodevelopmental disorders: A systematic review. Neuroscience & Biobehavioral Reviews, 94, 17–30. https://doi.org/10.1016/j.neubiorev.2018.07.011
   PubMed Web of Science ®Google Scholar
• Dodd, S., Bauer, M., Carvalho, A. F., Eyre, H., Fava, M., Kasper, S., Kennedy, S. H., Khoo, J.-P., Lopez Jaramillo, C., Malhi, G. S., McIntyre, R. S., Mitchell, P. B., Castro, A. M. P., Ratheesh, A., Severus, E., Suppes, T., Trivedi, M. H., Thase, M. E., Yatham, L. N., … Berk, M. (2021). A clinical approach to treatment resistance in depressed patients: What to do when the usual treatments don’t work well enough? The World Journal of Biological Psychiatry, 22(7), 483–494. https://doi.org/10.1080/15622975.2020.1851052
   PubMed Web of Science ®Google Scholar
• Drago, A., Giegling, I., Schäfer, M., Hartmann, A. M., Konte, B., Friedl, M., Serretti, A., & Rujescu, D. (2014). Genome-wide association study supports the role of the immunological system and of the neurodevelopmental processes in response to haloperidol treatment. Pharmacogenetics and Genomics, 24(6), 314–319. https://doi.org/10.1097/FPC.0000000000000052
   PubMed Web of Science ®Google Scholar
• Du, P., Zhang, X., Huang, C.-C., Jafari, N., Kibbe, W. A., Hou, L., & Lin, S. M. (2010). Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics, 11(1), 587. https://doi.org/10.1186/1471-2105-11-587
   PubMedGoogle Scholar
• Flory, J. D., & Yehuda, R. (2015). Comorbidity between post-traumatic stress disorder and major depressive disorder: alternative explanations and treatment considerations. Dialogues in Clinical Neuroscience, 17(2), 141–150. https://doi.org/10.31887/DCNS.2015.17.2/jflory
   PubMed Web of Science ®Google Scholar
• Fortin, J.-P., Triche, T. J., & Hansen, K. D. (2017). Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. Bioinformatics (Oxford, England), 33(4), 558–560. https://doi.org/10.1093/bioinformatics/btw691
   PubMed Web of Science ®Google Scholar
• Gandal, M. J., Zhang, P., Hadjimichael, E., Walker, R. L., Chen, C., Liu, S., Won, H., van Bakel, H., Varghese, M., Wang, Y., Shieh, A. W., Haney, J., Parhami, S., Belmont, J., Kim, M., Moran Losada, P., Khan, Z., Mleczko, J., Xia, Y., … Geschwind, D. H. (2018). Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science, 362(6420), https://doi.org/10.1126/science.aat8127
   Web of Science ®Google Scholar
• GBD 2016. Disease and injury incidence and prevalence collaborators. (2016). Global, regional, and national incidence, prevalence, and years lived with disability for 310 diseases and injuries, 1990-2015: a systematic analysis for the Global Burden of Disease Study 2015. The Lancet, 388(10053), 1545–1602. https://doi.org/10.1016/S0140-6736(16)31678-6
   PubMed Web of Science ®Google Scholar
• Hasin, D. S., Sarvet, A. L., Meyers, J. L., Saha, T. D., Ruan, W. J., Stohl, M., & Grant, B. F. (2018). Epidemiology of Adult DSM-5 Major Depressive Disorder and Its Specifiers in the United States. JAMA Psychiatry, 75(4), 336–346. https://doi.org/10.1001/jamapsychiatry.2017.4602
   PubMed Web of Science ®Google Scholar
• Huang, G., He, X., & Wei, X.-L. (2018). lncRNA NEAT1 promotes cell proliferation and invasion by regulating miR–365/RGS20 in oral squamous cell carcinoma. Oncology Reports, 39(4), 1948–1956. https://doi.org/10.3892/or.2018.6283
   PubMed Web of Science ®Google Scholar
• Jaffe, D. H., Rive, B., & Denee, T. R. (2019). The humanistic and economic burden of treatment-resistant depression in Europe: a cross-sectional study. BMC Psychiatry, 19(1), 247. https://doi.org/10.1186/s12888-019-2222-4
   PubMed Web of Science ®Google Scholar
• Kautzky, A., Baldinger-Melich, P., Kranz, G. S., Vanicek, T., Souery, D., Montgomery, S., Mendlewicz, J., Zohar, J., Serretti, A., Lanzenberger, R., & Kasper, S. (2017). A New prediction model for evaluating treatment-resistant depression. The Journal of Clinical Psychiatry, 78(2), 215–222. https://doi.org/10.4088/JCP.15m10381
   PubMed Web of Science ®Google Scholar
• Keshavarz, F., Soltani, M., Mokhtarian, K., Beshkar, P., Majidi, J., Azadegan-Dehkordi, F., Anjomshoa, M., & Bagheri, N. (2022). Autoantibodies against central nervous system antigens and the serum levels of IL-32 in patients with schizophrenia. Neuroimmunomodulation, 29(4), 493–499. https://doi.org/10.1159/000526425
   PubMed Web of Science ®Google Scholar
• Kikuchi, M., Yamada, K., Toyota, T., Itokawa, M., Hattori, E., Yoshitsugu, K., Shimizu, H., & Yoshikawa, T. (2003). Two-step association analyses of the chromosome 18p11.2 region in schizophrenia detect a locus encompassing C18orf1. Molecular Psychiatry, 8(5), 467–469. https://doi.org/10.1038/sj.mp.4001280
   PubMed Web of Science ®Google Scholar
• Knoblich, N., Gundel, F., Brückmann, C., Becker-Sadzio, J., Frischholz, C., & Nieratschker, V. (2018). DNA methylation of APBA3 and MCF2 in borderline personality disorder: Potential biomarkers for response to psychotherapy. European Neuropsychopharmacology, 28(2), 252–263. https://doi.org/10.1016/j.euroneuro.2017.12.010
   PubMed Web of Science ®Google Scholar
• Kraus, C., Kadriu, B., Lanzenberger, R., Zarate, C. A., & Kasper, S. (2019). Prognosis and improved outcomes in major depression: a review. Translational Psychiatry, 9(1), 127. https://doi.org/10.1038/s41398-019-0460-3
   PubMed Web of Science ®Google Scholar
• Labonté, B., Suderman, M., Maussion, G., Navaro, L., Yerko, V., Mahar, I., Bureau, A., Mechawar, N., Szyf, M., Meaney, M. J., & Turecki, G. (2012). Genome-wide epigenetic regulation by early-life trauma. Archives of General Psychiatry, 69(7), 722–731. https://doi.org/10.1001/archgenpsychiatry.2011.2287
   PubMed Web of Science ®Google Scholar
• Lanz, T. A., Reinhart, V., Sheehan, M. J., Rizzo, S. J. S., Bove, S. E., James, L. C., Volfson, D., Lewis, D. A., & Kleiman, R. J. (2019). Postmortem transcriptional profiling reveals widespread increase in inflammation in schizophrenia: A comparison of prefrontal cortex, striatum, and hippocampus among matched tetrads of controls with subjects diagnosed with schizophrenia, bipolar or major. Translational Psychiatry, 9(1), 151. https://doi.org/10.1038/s41398-019-0492-8
   PubMedGoogle Scholar
• Liew, C.-C., Ma, J., Tang, H.-C., Zheng, R., & Dempsey, A. A. (2006). The peripheral blood transcriptome dynamically reflects system wide biology: A potential diagnostic tool. Journal of Laboratory and Clinical Medicine, 147(3), 126–132. https://doi.org/10.1016/j.lab.2005.10.005
   PubMed Web of Science ®Google Scholar
• Maffioletti, E., Minelli, A., Tardito, D., & Gennarelli, M. (2020). Blues in the brain and beyond: Molecular bases of major depressive disorder and relative pharmacological and Non-pharmacological treatments. Genes, 11(9), https://doi.org/10.3390/genes11091089
   PubMed Web of Science ®Google Scholar
• Marinova, Z., Maercker, A., Küffer, A., Robinson, M. D., Wojdacz, T. K., Walitza, S., Grünblatt, E., & Burri, A. (2017). DNA methylation profiles of elderly individuals subjected to indentured childhood labor and trauma. BMC Medical Genetics, 18(1), 21. https://doi.org/10.1186/s12881-017-0370-2
   PubMedGoogle Scholar
• Mehta, D., Klengel, T., Conneely, K. N., Smith, A. K., Altmann, A., Pace, T. W., Rex-Haffner, M., Loeschner, A., Gonik, M., Mercer, K. B., Bradley, B., Müller-Myhsok, B., Ressler, K. J., & Binder, E. B. (2013). Childhood maltreatment is associated with distinct genomic and epigenetic profiles in posttraumatic stress disorder. Proceedings of the National Academy of Sciences, 110(20), 8302–8307. https://doi.org/10.1073/pnas.1217750110
   PubMed Web of Science ®Google Scholar
• Minelli, A., Magri, C., Giacopuzzi, E., & Gennarelli, M. (2018). The effect of childhood trauma on blood transcriptome expression in major depressive disorder. Journal of Psychiatric Research, 104, 50–54. https://doi.org/10.1016/j.jpsychires.2018.06.014
   PubMed Web of Science ®Google Scholar
• Minelli, A., Zampieri, E., Sacco, C., Bazzanella, R., Mezzetti, N., Tessari, E., Barlati, S., & Bortolomasi, M. (2019). Clinical efficacy of trauma-focused psychotherapies in treatment-resistant depression (TRD) in-patients: A randomized, controlled pilot-study. Psychiatry Research, 273, 567–574. https://doi.org/10.1016/j.psychres.2019.01.070
   PubMed Web of Science ®Google Scholar
• Miyake, K., Miyashita, C., Ikeda-Araki, A., Miura, R., Itoh, S., Yamazaki, K., Kobayashi, S., Masuda, H., Ooka, T., Yamagata, Z., & Kishi, R. (2021). DNA methylation of GFI1 as a mediator of the association between prenatal smoking exposure and ADHD symptoms at 6 years: The Hokkaido Study on Environment and Children’s Health. Clinical Epigenetics, 13(1), 74. https://doi.org/10.1186/s13148-021-01063-z
   PubMed Web of Science ®Google Scholar
• Montgomery, S. A., & Asberg, M. (1979). A new depression scale designed to be sensitive to change. British Journal of Psychiatry, 134(4), 382–389. https://doi.org/10.1192/bjp.134.4.382
   PubMed Web of Science ®Google Scholar
• Moschny, N., Zindler, T., Jahn, K., Dorda, M., Davenport, C. F., Wiehlmann, L., Maier, H. B., Eberle, F., Bleich, S., Neyazi, A., & Frieling, H. (2020). Novel candidate genes for ECT response prediction-a pilot study analyzing the DNA methylome of depressed patients receiving electroconvulsive therapy. Clinical Epigenetics, 12(1), 114. https://doi.org/10.1186/s13148-020-00891-9
   PubMed Web of Science ®Google Scholar
• Müller, N., Krause, D., Barth, R., Myint, A.-M., Weidinger, E., Stettinger, W., Zill, P., Drexhage, H., & Schwarz, M. J. (2019). Childhood adversity and current stress are related to Pro- and anti-inflammatory cytokines in major depression. Journal of Affective Disorders, 253, 270–276. https://doi.org/10.1016/j.jad.2019.04.088
   PubMed Web of Science ®Google Scholar
• Neves, I., Dinis-Oliveira, R. J., & Magalhães, T. (2021). Epigenomic mediation after adverse childhood experiences: A systematic review and meta-analysis. Forensic Sciences Research, 6(2), 103–114. https://doi.org/10.1080/20961790.2019.1641954
   PubMed Web of Science ®Google Scholar
• O’Donnell, K. J., Chen, L., MacIsaac, J. L., McEwen, L. M., Nguyen, T., Beckmann, K., Zhu, Y., Chen, L. M., Brooks-Gunn, J., Goldman, D., Grigorenko, E. L., Leckman, J. F., Diorio, J., Karnani, N., Olds, D. L., Holbrook, J. D., Kobor, M. S., & Meaney, M. J. (2018). DNA methylome variation in a perinatal nurse-visitation program that reduces child maltreatment: A 27-year follow-up. Translational Psychiatry, 8(1), 15. https://doi.org/10.1038/s41398-017-0063-9
   PubMedGoogle Scholar
• Pandey, G. N., Rizavi, H. S., Zhang, H., & Ren, X. (2018). Abnormal gene and protein expression of inflammatory cytokines in the postmortem brain of schizophrenia patients. Schizophrenia Research, 192, 247–254. https://doi.org/10.1016/j.schres.2017.04.043
   PubMed Web of Science ®Google Scholar
• Parade, S. H., Huffhines, L., Daniels, T. E., Stroud, L. R., Nugent, N. R., & Tyrka, A. R. (2021). A systematic review of childhood maltreatment and DNA methylation: Candidate gene and epigenome-wide approaches. Translational Psychiatry, 11(1), 134. https://doi.org/10.1038/s41398-021-01207-y
   PubMed Web of Science ®Google Scholar
• Pedicone, C., Meyer, S. T., Chisholm, J. D., & Kerr, W. G. (2021). Targeting SHIP1 and SHIP2 in Cancer. Cancers, 13(4)), https://doi.org/10.3390/cancers13040890
   PubMed Web of Science ®Google Scholar
• Perroud, N., Salzmann, A., Prada, P., Nicastro, R., Hoeppli, M. E., Furrer, S., Ardu, S., Krejci, I., Karege, F., & Malafosse, A. (2013). Response to psychotherapy in borderline personality disorder and methylation status of the BDNF gene. Translational Psychiatry, 3(1), e207. https://doi.org/10.1038/tp.2012.140
   PubMedGoogle Scholar
• Pidsley, R., Zotenko, E., Peters, T. J., Lawrence, M. G., Risbridger, G. P., Molloy, P., Van Djik, S., Muhlhausler, B., Stirzaker, C., & Clark, S. J. (2016). Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. Genome Biology, 17(1), 208. https://doi.org/10.1186/s13059-016-1066-1
   PubMed Web of Science ®Google Scholar
• Sales, G., Calura, E., & Romualdi, C. (2019). metaGraphite-a new layer of pathway annotation to get metabolite networks. Bioinformatics (Oxford, England), 35(7), 1258–1260. https://doi.org/10.1093/bioinformatics/bty719
   PubMed Web of Science ®Google Scholar
• Silva, R. C., Maffioletti, E., Gennarelli, M., Baune, B. T., & Minelli, A. (2021). Biological correlates of early life stressful events in major depressive disorder. Psychoneuroendocrinology, 125, 105103. https://doi.org/10.1016/j.psyneuen.2020.105103
   PubMed Web of Science ®Google Scholar
• Sirignano, L., Frank, J., Kranaster, L., Witt, S. H., Streit, F., Zillich, L., Sartorius, A., Rietschel, M., & Foo, J. C. (2021). Methylome-wide change associated with response to electroconvulsive therapy in depressed patients. Translational Psychiatry, 11(1), 347. https://doi.org/10.1038/s41398-021-01474-9
   PubMed Web of Science ®Google Scholar
• Snijders, C., Maihofer, A. X., Ratanatharathorn, A., Baker, D. G., Boks, M. P., Geuze, E., Jain, S., Kessler, R. C., Pishva, E., Risbrough, V. B., Stein, M. B., Ursano, R. J., Vermetten, E., Vinkers, C. H., Smith, A. K., Uddin, M., Rutten, B. P. F., PGC PTSD EWAS Consortium, & Nievergelt, C. M. (2020). Longitudinal epigenome-wide association studies of three male military cohorts reveal multiple CpG sites associated with post-traumatic stress disorder. Clinical Epigenetics, 12(1), 11. https://doi.org/10.1186/s13148-019-0798-7
   PubMed Web of Science ®Google Scholar
• Thase, M. E., & Rush, A. J. (1997). When at first you don’t succeed: Sequential strategies for antidepressant nonresponders. The Journal of Clinical Psychiatry, 58(Suppl 1), 16–21. https://doi.org/10.4088/JCP.v58n0103
   PubMedGoogle Scholar
• Van Assche, E., Hohoff, C., Zang, J., Knight, M. J., & Baune, B. T. (2023). Epigenetic modification related to cognitive changes during a cognitive training intervention in depression. Progress in Neuro-Psychopharmacology and Biological Psychiatry, 127, 110835. https://doi.org/10.1016/j.pnpbp.2023.110835
   PubMed Web of Science ®Google Scholar
• Vinkers, C. H., Geuze, E., van Rooij, S. J. H., Kennis, M., Schür, R. R., Nispeling, D. M., Smith, A. K., Nievergelt, C. M., Uddin, M., Rutten, B. P. F., Vermetten, E., & Boks, M. P. (2021). Successful treatment of post-traumatic stress disorder reverses DNA methylation marks. Molecular Psychiatry, 26(4), 1264–1271. https://doi.org/10.1038/s41380-019-0549-3
   PubMed Web of Science ®Google Scholar
• Wang, P., Wang, H., Li, X., Liu, Y., Zhao, C., & Zhu, D. (2016). Srcin1 suppressed osteosarcoma cell proliferation and invasion. PLoS One, 11(8), e0155518. https://doi.org/10.1371/journal.pone.0155518
   PubMed Web of Science ®Google Scholar
• Wu, W., Howard, D., Sibille, E., & French, L. (2021). Differential and spatial expression meta-analysis of genes identified in genome-wide association studies of depression. Translational Psychiatry, 11(1), 8. https://doi.org/10.1038/s41398-020-01127-3
   PubMed Web of Science ®Google Scholar
• Yan, S., Shan, Y., Zhong, S., Miao, H., Luo, Y., Ran, H., & Jia, Y. (2021). The effectiveness of Eye movement desensitization and reprocessing toward adults with major depressive disorder: A meta-analysis of randomized controlled trials. Frontiers in Psychiatry, 12, 700458. https://doi.org/10.3389/fpsyt.2021.700458
   PubMed Web of Science ®Google Scholar
• Yang, R., Xu, C., Bierer, L. M., Flory, J. D., Gautam, A., Bader, H. N., Lehrner, A., Makotkine, I., Desarnaud, F., Miller, S. A., Jett, M., Hammamieh, R., & Yehuda, R. (2021). Longitudinal genome-wide methylation study of PTSD treatment using prolonged exposure and hydrocortisone. Translational Psychiatry, 11(1), 398. https://doi.org/10.1038/s41398-021-01513-5
   PubMed Web of Science ®Google Scholar
• Zhang, M., Ma, F., Xie, R., Wu, Y., Wu, M., Zhang, P., Peng, Y., Zhao, J., Xiong, J., Li, A., Kequan, C., Zhang, Y., Liu, S., Wang, J., & Chen, X. (2017). Overexpression of Srcin1 contributes to the growth and metastasis of colorectal cancer. International Journal of Oncology, 50(5), 1555–1566. https://doi.org/10.3892/ijo.2017.3952
   PubMed Web of Science ®Google Scholar
• Zhang, Z., Zheng, F., You, Y., Ma, Y., Lu, T., Yue, W., & Zhang, D. (2016). Growth arrest specific gene 7 is associated with schizophrenia and regulates neuronal migration and morphogenesis. Molecular Brain, 9(1), 54. https://doi.org/10.1186/s13041-016-0238-y
   PubMedGoogle Scholar
• Zheng, Y., Lunetta, K. L., Liu, C., Katrinli, S., Smith, A. K., Miller, M. W., & Logue, M. W. (2022). An evaluation of the genome-wide false positive rates of common methods for identifying differentially methylated regions using illumina methylation arrays. Epigenetics, 17(13), 2241–2258. https://doi.org/10.1080/15592294.2022.2115600
   PubMed Web of Science ®Google Scholar
• Zhuang, H., Wang, H., & Ji, Z. (2022). findPC: An R package to automatically select the number of principal components in single-cell analysis. Bioinformatics (Oxford, England), 38(10), 2949–2951. https://doi.org/10.1093/bioinformatics/btac235
   PubMed Web of Science ®Google Scholar
• Ziegler, C., Richter, J., Mahr, M., Gajewska, A., Schiele, M. A., Gehrmann, A., Schmidt, B., Lesch, K.-P., Lang, T., Helbig-Lang, S., Pauli, P., Kircher, T., Reif, A., Rief, W., Vossbeck-Elsebusch, A. N., Arolt, V., Wittchen, H.-U., Hamm, A. O., Deckert, J., & Domschke, K. (2016). MAOA gene hypomethylation in panic disorder-reversibility of an epigenetic risk pattern by psychotherapy. Translational Psychiatry, 6(4), e773. https://doi.org/10.1038/tp.2016.41
   PubMedGoogle Scholar