Github single pull request for changes to multiple repositories?

From what I can see of GitHub pull request, this operation is linked to a single GitHub repository:

By default, pull requests are assumed to be based on the parent-most repository’s integration branch.
In a great majority of cases, the defaults will be right; however, if any of this information is incorrect, press the Change Commits button.
The commit range selector will expand, allowing the base repository, base branch, and head branch to be customized.

Only one base repo can be entered.

So in your case, a note mentioning the dependency seems the relevant option here.