The statement followed a Twitter rant on Friday from her husband in response to an interview James had given to CNN.
The statement didn't criticize the president. In his interview with Lemon, he said he'd consider running for president if he believed he was the only person who could stop Trump from being re-elected. "A man who puts kids in classrooms or one who puts kids in cages?"
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The Croatian was pictured doing fitness work at the club's Melwood training base on his first day back from holiday after the World Cup.
In 2013, he congratulated James on winning Athlete of the Year at the ESPYs and "a great guy". He made Lebron look smart, which isnt easy to do..
Last year, Mr Trump rescinded an invitation for National Basketball Association champions Golden State Warriors to visit the White House after team captain Stephen Curry questioned the billionaire's presidency. James carefully dodged the question, but when asked what he would say if someone told him, "If you don't run, Trump's going to win", James responded with, "Well, in that case, I may [run]", James said.
Along with Jordan, a number of other athletes spoke out in support of James. He said the school prioritised a holistic experience for students that include sports, which he described as critical for healthy communities.
He also argued that Mr Trump's actions had encouraged racists, saying: "I think [racism's] always been there".
CNN, which Trump has repeatedly said is a purveyor of "fake news", then mocked the president and first lady about their television viewing habits and even slighted Melania's #BeBest platform. "Not shocked it happened during a week where LeBron literally opened a school for at-risk kids".
James, for his part, in his first comment since the insult, tweeted a celebration of his new school instead of responding directly to Trump.
The hashtag is the slogan for the first lady's childhood welfare initiative.