The denial of this I-485 this time is not end of the world, you should still
try keeping your F1 status valid, and at least you will be able to work
legally doing PhD level jobs with a good salary, and maybe file your own I-
140 soon. Your LG has always been illegal, so no worse than he was before
the denial. He needs to prove he is eligible for 245i, gather the required
document now, such as the evidence of timely filed ETA9089, and the DOL
decision letter (you said it was a denial, then there should be a denial
decision letter) He needs that, because don't expect USCIS to take his word
for it without those documents. Also, if his uncle did not even pay him
salary, how could he be sure that the uncle went through advertising and
recruitment,... all the costly steps to pre-qualify a filing for labor
certification with SESA, then to regional DOL? Those were complicated
procedures compared to simplified PERM since 2005. The denial decision
letter from DOL cannot have findings such as frivolous filing, not in good
faith, etc in its language.