By now, I hope your daughter has gotten into the swing of her first year in middle school and that she already has at least one friend with whom she feels comfortable and happy. Middle school can be a very challenging time for kids (and their parents). The changes are many and they keep coming! From the increased number of teachers a student has to deal with, plus the course work and need for greater organization skills than most 11-12 years old have yet to develop. Then there's all the social stuff, the shifting friendships, the Bf/Gf Zone, and, what I call, Peer Approval Addiction (i.e., the compulsion to do or say whatever it takes to fit it, even stuff you may not be particularly proud of). In spite of all that, parents can and must stay tuned in and place themselves at the epicenter of your middle schooler's support system.
By keeping the lines of communication open while respecting your daughter's increasing need for privacy (a tricky balance) you and she can support each other as you navigate these waters together.
I would say the best thing that you could tell her is that she will make new friends and the other kids may feel the same way. I would tell her to try and see if there is someone that wants to have a new friend. I would encourage her by telling her all the things that she is good at and that others maybe interested as well and that they could start a friendship that way. I would let her know that other kids feel that way as well and that they are going to feel scared and lonely. I know my daughter went through something like this and when she found a girl that liked to swim like her and they were inseparable.