The author of the article doesn't understand the process of...

The author of the article doesn't understand the process of creating a GMO nor the outcome of a GMO.

A GMO is when DNA in an organism is altered.
Often a gene is disrupted to prevent its protein product from being produced hence a previous produced protein is no longer produced.
Often a new promoter is added to increase the transcription of a gene which will increase the level of transcription/translation of a genes leading to more of a protein product
Often a new gene is inserted eg) the insulin gene has been inserted into bacteria to mass produce insulin.

Can you explain that if no new proteins are being consumed how it would cause issues for the immune system?