Rephrasing for clarity: you want to know if there is a graph $G_0=(\omega,E_0)$ such that every graph on $\mathfrak c=2^{\aleph_0}$ vertices is isomorphic to an induced subgraph of the powerset graph $\operatorname{Pow}(G_0)$. That powerset graph has vertex set $\mathcal P(\omega)$, and two vertices $X,Y\subseteq\omega$ are adjacent iff $\{a,b\}\in E_0$ for some $a\in X\setminus Y$ and some $b\in Y\setminus X$. We prove the negative answer by showing that any induced subgraph $\operatorname{Pow}(G_0)[\mathcal S]$ has a special property: for any uncountable set of nonisolated vertices, some vertex has uncountably many neighbors in that set.
For $a,b\in\omega$ let $\mathcal E_{a,b}=\{X\subseteq\omega:a\in X,\,b\notin X\}$.
Consider a set $\mathcal S\subseteq\mathcal P(\omega)$ and suppose $\mathcal S_0\subseteq\mathcal S$ is an uncountable set of nonisolated vertices in $\operatorname{Pow}(G_0)[\mathcal S]$. For each $X\in\mathcal S_0$ choose $a_X,b_X\in\omega$ so that $\{a,b\}\in E_0$, $a\in X$, $b\notin X$, and $\mathcal S\cap\mathcal E_{b,a}\ne\varnothing$. Since $\mathcal S_0$ is uncountable, there exist $a,b\in\omega$ and an uncountable set $S_1\subseteq S_0$ such that $a_X=a$ and $b_X=b$ for all $X\in\mathcal S_1$. Choose $Y\in\mathcal S\cap\mathcal E_{b,a}$; then every member of $\mathcal S_1$ is adjacent to $Y$.
P.S. Maybe I misinterpreted the definition of the graph on $\mathcal P(\omega)$. In a comment the OP seems to say that $S,T\in\mathcal P(\omega)$ are adjacent iff "both $e\cap S$ and $e\cap T$ are non-empty" for some $e\in E_0$; thus $\{X\in\mathcal P(\omega):X\cap e\ne\varnothing\}$ is a clique for $e\in E_0$. In that case, if the subgraph induced by $\mathcal S$ is a tree, then $\mathcal S$ must be countable; but there are only $\mathfrak c$ countable subsets of $\mathcal P(\omega)$ while there are $2^\mathfrak c$ nonisomorphic trees on $\mathfrak c$ vertices.