At last the three paths of apoptosis (extrinsic, mitochondrial, and
endoplasmic reticulum stress) were enriched by abundant DEG/DEP
(Fig. 6 ). For instance in 145
negative miRNA-mRNA-protein pairs,
Hadha was downregulated and promoted cell apoptosis by decreasing the
acylation of monolysocardiolipin into cardiolipin via raised miR-1-2
(Taylor et al. 2012). And that
GRP78 is expressed in large quantities under low oxygen to maintain the
stability of the endoplasmic
reticulum and protect cells (Reddyet al. 2003). Upregulation of miR-457a led to endoplasmic
reticulum stress and hypoxia-induced apoptosis by targeting GRP78 inP. vachelli muscles (Table 1 and Fig. 5 ).
(3) Muscle dysfunction
Several of the KEGG enriched by multi-omics (P < 0.05)
were associated with impaired contraction or dilation of heart muscle
(DCM and HCM) and dyskinesia (Parkinson’s and Huntington’s disease),
which suggested that hypoxia induces muscle dysfunction (Fig. 2
and Fig. 3A ). In addition, “Vascular smooth muscle contraction” and
“Calcium signaling pathway” contained abnormal muscular and calcium
overload related proteins that were significantly enriched by down DEP.
For example, Atp2a1, a key regulator
of muscle performance, contributed to calcium sequestration involved in
muscular excitation/contraction (Odermattet al. 2000). Krt8 helps to link the contractile apparatus to
dystrophin at the costamere of striated muscle
(Ursitti et al. 2004). In our
results (Table 1 and Fig. 5 ), let-7b was upregulated, whereas
its target genes/proteins Atp2a1 and
Krt8 were significantly downregulated. This supported the idea that
calcium overload and muscle dysfunction were linked in hypoxia
adaptation in P. vachelli .
To date, understanding of small RNAs in fishes is limited and
informations regarding hypoxic miRNA markers are especially rare.
Compared with other animals or cell
models, 24 miRNAs reported previously as
hypoxia-responsive were identified
(e.g., miR-15b, 133b, 143, 146b, 181a, 193b, 27b, 301b, 338, 152, 18a,
30a/d, 126, 199a, 210, 214, 29b, 25, let-7b) from 39 DEMI in our
results. These are thought to exert broad pleiotropic effects by
targeting genes involved in cell
cycle arrest, metabolism, apoptosis, cell survival and mitochondrial
function (Bandara et al. 2017;
Guimbellot et al. 2009;
McCormick et al. 2010;
Pocock 2011). Additionally, in fishes,
the tendencies of miR-210, -193b, -181a expression among muscle were the
same as the liver of P. vachelli(Zhang et al. 2016b) or M.
amblycephala (Sun et al. 2017) . For
example, in negative miRNA-mRNA-protein pairs (Table S4 ),
several key enzymes of “TCA cycle”, e.g., miR-193b-OGDH and
miR-210-SDHb/SUCLA2, were detected in our conjoint analysis. Moreover,
the same result as Danio rerio that raised let-7b acts downstream
of HIF-1α to repress cell
proliferation through blocking cell cycle progression
(Huang et al. 2017).
Interestingly, several miRNA expressions
in P. vachelli muscle were
the opposite to that of liver (e.g., miR-27b, -143, -338), which may be
due to different tissues or a metabolic disorder in muscle induced by
hypoxia. For instance, data analysis of predicted multi-omics pairsin silico (Table S4 ), suggested that the possible
mechanism that GAPVD1, a protein required for efficient endocytosis
(Guillen et al. 2020), promoted
catabolism in muscles under hypoxia by downregulating miR-27b/143.
Furthermore, upregulating miR-338
negatively targeted key enzymes of glycolysis (HK1) and
“oxidative phosphorylation” (SDH,
Atp5a1, NDUFV1/S1) under hypoxic conditions in P. vachelli muscle
(Aschrafi et al. 2012).