Autism is a spectrum disorder that can look very different in different students. Any suggestions will need to be adapted or modified to meet your particular child’s needs.
Your description of your four-year-old son is complex. I recommend that you meet with the preschool evaluation service of your neighborhood public school.
Your story is a sad one. It is because of such stories that I try so hard to educate parents on what to look for and how to address a school system that is not seeing what the parents are seeing.
You can do a lot to help your child practice. One way is to use modeling to introduce these skills. As you read to your child, sound out some of the words before you say them completely.
I cannot be specific about the cause. I can share your concern. You need to discuss these problems with the school professionals to explore what his problem areas are.