Synthetic messenger RNA vaccines and transcriptomic dysregulation: Evidence from new-onset adverse events and cancers post-vaccination

Table 1 Summary of study participants, clinical manifestations, and diagnostic groupings

Patient ID	Group	Condition/symptoms
P1	1: Non-malignant adverse events	Brain fog and chronic fatigue
P2	1: Non-malignant adverse events	Cardiovascular injury, thrombosis, and chronic fatigue
P3	1: Non-malignant adverse events	Cardiovascular injury, thrombosis, and chronic fatigue
P4	2: Cancer	Glioblastoma multiforme
P5	2: Cancer	Prostate adenocarcinoma
P6	2: Cancer	Bladder tumor
P7	2: Cancer	Follicular lymphoma
P8	2: Cancer	Prostate cancer
P9	2: Cancer	Glioblastoma multiforme
P10	2: Cancer	Follicular lymphoma

Table 2 Gene set enrichment results for group 1 categorized by molecular pathway

Molecular pathways	MSigDB standard name	Normalized Enrichment Score	False discovery rate
Mitochondrial electron transport dysfunction and reactive oxygen species	KEGG_MEDICUS_REFERENCE_MITOCHONDRIAL_COMPLEX_UCP1_IN_THERMOGENESIS	1.86	0.11
	KEGG_MEDICUS_REFERENCE_ELECTRON_TRANSFER_IN_COMPLEX_I	1.70	0.10
	KEGG_MEDICUS_VARIANT_MUTATION_INACTIVATED_PINK1_TO_ELECTRON_TRANSFER_IN_COMPLEX_I	1.73	0.09
	KEGG_MEDICUS_VARIANT_MUTATION_CAUSED_ABERRANT_ABETA_TO_ELECTRON_TRANSFER_IN_COMPLEX_I	1.69	0.09
	KEGG_MEDICUS_VARIANT_MUTATION_CAUSED_ABERRANT_SNCA_TO_ELECTRON_TRANSFER_IN_COMPLEX_I	1.66	0.11
	HALLMARK_OXIDATIVE_PHOSPHORYLATION	1.43	> 0.001
Proteasome-mediated protein degradation stress	KEGG_MEDICUS_VARIANT_MUTATION_CAUSED_ABERRANT_ABETA_TO_26S_PROTEASOME_MEDIATED_PROTEIN_DEGRADATION	1.78	0.12
	KEGG_MEDICUS_VARIANT_MUTATION_INACTIVATED_VCP_TO_26S_PROTEASOME_MEDIATED_PROTEIN_DEGRADATION	1.74	0.13
	KEGG_MEDICUS_VARIANT_MUTATION_CAUSED_ABERRANT_SOD1_TO_26S_PROTEASOME_MEDIATED_PROTEIN_DEGRADATION	1.73	0.09
	GOBP_PROTEIN_CONTAINING_COMPLEX_REMODELING	-2.11	> 0.001
Transcriptomic instability and translational stress	REACTOME_EUKARYOTIC_TRANSLATION_INITIATION	3.11	> 0.001
	REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE	3.08	> 0.001
	REACTOME_NONSENSE_MEDIATED_DECAY_NMD	2.9	> 0.001
	KEGG_MEDICUS_REFERENCE_TRANSLATION_INITIATION	3.0	> 0.001
	GOBP_CYTOPLASMIC_TRANSLATION	2.60	> 0.001
	GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS	2.35	> 0.001
	GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS	2.34	> 0.001
Systemic inflammatory and immune response	GSE22886_NAIVE_TCELL_VS_DC_UP	2.43	> 0.001
	GSE2405_0H_VS_9H_A_PHAGOCYTOPHILUM_STIM_NEUTROPHILS_UP	2.36	> 0.001
	GSE7400_CTRL_VS_CSF3_IN_VIVO_TREATED_PBMC_UP	2.27	> 0.001
	GSE7400_CTRL_VS_CSF3_IN_VIVO_TREATED_PBMC_DN	-1.93	> 0.001
	GSE6269_E_COLI_VS_STREP_PNEUMO_INF_PBMC_DN	-1.9	> 0.001
	GOBP_ANTIMICROBIAL_HUMORAL_RESPONSE	-1.95	> 0.001
	GOBP_HUMORAL_IMMUNE_RESPONSE	-1.91	0.006
Endothelium dysfunction	HALLMARK_ANGIOGENESIS	-1.94	> 0.001
Proliferative signaling and suppressed tumor control	HALLMARK_MYC_TARGETS_V1	1.64	> 0.001
	GAVISH_3CA_MALIGNANT_METAPROGRAM_3_CELL_CYLCE_HMG_RICH	1.77	0.005
	HALLMARK_KRAS_SIGNALING_DN	-1.68	> 0.001
	HALLMARK_P53_PATHWAY	-1.50	0.038
	KEGG_MEDICUS_REFERENCE_WNT_SIGNALING_MODULATION_WNT_INHIBITOR	-1.56	0.89

The Table 2 displays the top gene sets within each category, along with their corresponding MSigDB identifiers, Normalized Enrichment Score (NES), and false discovery rate (FDR) q value. Positive NES values indicate upregulation, while negative NES values indicate downregulation of the gene sets in vaccinated samples (group 1) relative to controls. Gene sets were selected based on biological relevance and NES >|15| with FDR q < 0.25. Group 1 includes patients with new-onset adverse events following messenger RNA coronavirus disease 2019 vaccination (n = 3), compared with normal controls (n = 803 unvaccinated individuals from the GTEx dataset).

Table 3 Gene set enrichment results for group 2 categorized by molecular pathway

Molecular pathways	MSigDB standard name	Normalized Enrichment Score	False discovery rate
Transcriptomic instability and translational stress	REACTOME_SIRT1_NEGATIVELY_REGULATES_RRNA_EXPRESSION	3.08	> 0.001
	REACTOME_RNA_POLYMERASE_I_PROMOTER_ESCAPE	2.61	> 0.001
	REACTOME_TRANSCRIPTIONAL_REGULATION_BY_SMALL_RNAS	2.63	> 0.001
	REACTOME_B_WICH_COMPLEX_POSITIVELY_REGULATES_RRNA_EXPRESSION	2.60	> 0.001
	REACTOME_POSITIVE_EPIGENETIC_REGULATION_OF_RRNA_EXPRESSION	2.54	> 0.001
	REACTOME_RRNA_MODIFICATION_IN_THE_NUCLEUS_AND_CYTOSOL	2.03	0.027
Systemic inflammatory and immune response	KEGG_MEDICUS_REFERENCE_TYPE_I_INTERFERON_TO_JAK_STAT_SIGNALING_PATHWAY	2.64	> 0.001
	KEGG_MEDICUS_PATHOGEN_HIV_TAT_TO_TLR2_4_NFKB_SIGNALING_PATHWAY	2.73	> 0.001
	KEGG_MEDICUS_REFERENCE_TYPE_I_IFN_SIGNALING_PATHWAY	2.64	> 0.001
	KEGG_MEDICUS_REFERENCE_RIG_I_NFKB_SIGNALING_PATHWAY	2.54	> 0.001
	KEGG_MEDICUS_REFERENCE_TLR3_IRF7_SIGNALING_PATHWAY	2.46	> 0.001
	KEGG_MEDICUS_REFERENCE_TLR7_8_9_IRF5_SIGNALING_PATHWAY	2.29	> 0.001
	KEGG_MEDICUS_REFERENCE_TLR7_9_IRF7_SIGNALING_PATHWAY	2.27	> 0.001
	KEGG_MEDICUS_REFERENCE_MDA5_IRF7_3_SIGNALING_PATHWAY	2.0	0.006
	KEGG_MEDICUS_REFERENCE_IFN_RIPK1_3_SIGNALING_PATHWAY	2.0	0.006
	KEGG_MEDICUS_REFERENCE_RIG_I_IRF7_3_SIGNALING_PATHWAY	2.0	0.007
	GAVISH_3CA_METAPROGRAM_CD8_T_CELLS_CHROMATIN	1.78	0.068
Endothelium dysfunction	GOBP_NEGATIVE_REGULATION_OF_ENDOTHELIAL_CELL_PROLIFERATION	-1.98	0.0017
	GOBP_NEGATIVE_REGULATION_OF_COAGULATION	-1.98	0.0017
Proliferative signaling and suppressed tumor control	REACTOME_ASSEMBLY_OF_THE_ORC_COMPLEX_AT_THE_ORIGIN_OF_REPLICATION	2.93	> 0.001
Genomic instability and epigenetic shift	REACTOME_DNA_METHYLATION	3.18	> 0.001
	REACTOME_CONDENSATION_OF_PROPHASE_CHROMOSOMES	2.93	> 0.001
	KEGG_MEDICUS_REFERENCE_CGAS_STING_SIGNALING_PATHWAY	2.43	> 0.001
	GAVISH_3CA_MALIGNANT_METAPROGRAM_4_CHROMATIN	1.91	0.05
	GOBP_NUCLEOSOME_ORGANIZATION	2.33	0.01

The Table 3 displays the top gene sets within each category, along with their corresponding MSigDB identifiers, Normalized Enrichment Score (NES), and false discovery rate (FDR) q value. Positive NES values indicate upregulation, while negative NES values indicate downregulation of the gene sets in vaccinated samples relative to controls. Gene sets were selected based on biological relevance and NES >|15| with FDR q < 0.25. Group 2 includes patients with new-onset cancers diagnosed shortly after messenger RNA coronavirus disease 2019 vaccination (n = 7), compared with normal controls (n = 803 unvaccinated individuals from the GTEx dataset).