We are running out of Helium.
There's lots of helium in the solar system. You could harvest the atmosphere of Jupiter or Saturn for it. Obviously this has an energy cost, but s stated in the article energy is the only real resource that we use up. Everything else is renewable.
In what sense? The problem of potential helium scarcity has been (effectively) solved in the last few years by just looking for more helium deposits.In a sense, we are "running out" (because there's only a finite supply of Helium), we're just running out very, very slowly.