  Vacancies in materials structure -- lowering its atomic density -- take the
system closer to the atomic limit, to which all systems are topologically
trivial. Here we show a mechanism of mediated interaction between vacancies
inducing a topologically non-trivial phase. Within an {\it ab initio} approach
we explore topological transition dependence with the vacancy density in
transition metal dichalcogenides. As a case of study, we focus on the PtSe$_2$,
to which pristine form is a trivial semiconductor with an energy gap of
$1.2$\,eV. The vacancies states lead to a large topological gap of $180$\,meV
within the pristine system gap. We derive an effective model describing this
topological phase in other transition metal dichalcogenide systems. The
mechanism driving the topological phase allows the construction of
backscattering protected metallic channels embedded in a semiconducting host.
