Table Info

Table 1.

Biological functions of caspase-2 substrates. GO enrichment analysis of significantly enriched biological processes within proteins described as caspase-2 substrates (compiled by MEROPS database)

GO biological process complete	FE	FDR
Female meiosis chromosome segregation	42.02	1.40 × 10^–2
Positive regulation of chromosome segregation	16.16	4.11 × 10^–3
Phosphatidylinositol-3-phosphate biosynthetic process	16.01	1.93 × 10^–2
Negative regulation of mRNA splicing, via spliceosome	16.01	1.92 × 10^–2
Cellular response to misfolded protein	15.28	2.12 × 10^–2
Protein quality control for misfolded or incompletely synthesized proteins	12.45	3.58 × 10^–2
Regulation of heterochromatin assembly	12.01	3.98 × 10^–2
Regulation of androgen receptor signaling pathway	12.01	3.96 × 10^–2
Positive regulation of chromosome separation	11.59	4.34 × 10^–2
Establishment of spindle orientation	10.77	1.66 × 10^–2
Regulation of mitotic sister chromatid segregation	10.70	1.44 × 10^–3
mRNA splicing, via spliceosome	8.79	5.12 × 10^–12
Histone deacetylation	8.69	1.22 × 10^–2
Neuron apoptotic process	7.64	5.00 × 10^–2
Regulation of mitotic metaphase/anaphase transition	7.39	3.29 × 10^–3
Positive regulation of chromosome organization	7.20	1.45 × 10^–3
Positive regulation of DNA recombination	7.10	2.60 × 10^–2
Regulation of translational initiation	6.15	4.46 × 10^–2
Positive regulation of translation	5.92	2.16 × 10^–3
Positive regulation of apoptotic signaling pathway	5.86	5.34 × 10^–3
Nuclear export	5.82	5.50 × 10^–3
Ribonucleoprotein complex assembly	5.81	2.02 × 10^–4
Regulation of mRNA stability	5.57	6.23 × 10^–4
Negative regulation of translation	5.03	6.51 × 10^–3
Positive regulation of proteasomal protein catabolic process	5.03	4.86 × 10^–2
mRNA transport	4.84	3.01 × 10^–2
Positive regulation of response to DNA damage stimulus	4.61	2.06 × 10^–2
Mitotic nuclear division	4.48	2.43 × 10^–2
Positive regulation of leukocyte differentiation	4.30	3.02 × 10^–2
Negative regulation of organelle organization	4.18	2.90 × 10^–4
Chromatin remodeling	3.97	5.46 × 10^–3
Negative regulation of catabolic process	3.36	1.92 × 10^–2
Translation	3.34	8.75 × 10^–3
Ubiquitin-dependent protein catabolic process	2.97	3.21 × 10^–3
Cell division	2.81	1.75 × 10^–2
DNA repair	2.74	2.96 × 10^–2
ncRNA metabolic process	2.73	2.24 × 10^–2
Regulation of plasma membrane bounded cell projection organization	2.70	1.00 × 10^–2
Intracellular signal transduction	2.17	1.57 × 10^–3
Cellular protein localization	2.06	1.40 × 10^–2
Protein transport	2.03	3.42 × 10^–2

The most specific GO term is shown (hierarchically sorted terms). Fold enrichment (FE) ≥ 2 and Fisher’s exact test with false discovery rate (FDR) less than 0.05 as calculated by the Benjamini-Hochberg procedure were used as thresholds in the enrichment analysis. ncRNA: noncoding RNA

Declarations

Acknowledgments

All the figures have been created with the BioRender program (BioRender.com).

Author contributions

ALP: conceptualization, formal analysis, visualization, writing original draft, review and editing. MC: critical review and editing. MA: funding acquisition, critical review and editing. CB: funding acquisition, critical review and editing. CH: critical review and editing. MAA: conceptualization, funding acquisition, critical review and editing. MGFB: conceptualization, funding acquisition, critical review and editing. All authors have read and agreed to the published version of the manuscript.

Conflicts of interest

ALP is employed by Kintsugi Therapeutics S.L. CH is Co-founder and CEO of Kintsugi Therapeutics S.L. MC is Co-founder and COO of Kintsugi Therapeutics S.L., a start-up developing capase-2 inhibitors as therapeutic agents for liver disease. MA, CB, MAA, MGFB declare no conflicts of interest.

Ethical approval

Not applicable.

Consent to participate

Not applicable.

Consent to publication

Not applicable.

Availability of data and materials

Not applicable.

Funding

Work in the authors’ laboratory is supported by: CIBERehd; grant PI19/00613 from Instituto de Salud Carlos III (ISCIII) co-financed by “Fondo Europeo de Desarrollo Regional” (FEDER) “Una manera de hacer Europa” grant 2018-055 from Gobierno de Navarra; grants SAF2014-54191-R, SAF2017-88933-R, PID2019-104878R-100/AEI/10.13039/501100011033 and PID2019-104265RB-100/AEI/10.13039/501100011033 from FEDER/Ministerio de Ciencia, Innovación y Universidades-Agencia Estatal de Investigación; AECC LAB Grant 2020; AECC post-doctoral fellowship POSTD18014AREC to MA and Ramón y Cajal Program contract RYC2018-024475-1 to MGFB; grant CPP2021-008411 “Proyectos de colaboración público-privada” co-founded by the Ministerio de Ciencia e Innovación and European Union NextGenerationEU/PRTR. The generous support of Mr. Eduardo Avila is acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright

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