Only you can decide how to put all the elements together creatively, but I hope to give you some ideas to get your creative juices flowing. Inspiration and ideas can come from films you have seen, songs you like, characters you have liked in other books, and twists and turns in the plots of books or your favorite movies. Although you should never copy these directly, you can let them creatively inspire you in your own writing assignment. Most of all, use your own creativity.
You need a plot: think of a central problem/crisis for your story. How will your protagonists react to try to solve the problem/crisis? What major setbacks will they encounter to create suspense and drama before they beat the bad guys and solve the problem? That can be a basic outline for your new story.
One thing that can do to make your assignment easier is to break it down into fewer parts.
Reading comprehension/grammar could be a word puzzle that appears in the story, mathematics could be a number problem related to the word puzzle, and various artworks could contain visual symbols or clues to solving the mystery. These could be used in a puzzle or riddle your protagonist has to solve to stop a crime or save something (their family, city, or country, or the world) from disaster. This could drive the plot. A central character’s knowledge of literature could help them solve clues left behind by the bad guys as to what their intentions might be.
You could have the setting in Paris and insert some French into the dialogue, or you can have a French character. For PE, you could have one of your characters have a bad guy get the best of them early in the story when they are out of shape, only to have them get the better of them later in a chase scene or fight after the good character has improved their diet and started working out and become fit. For chemistry, you could have a crime lab or a character solve a crime scene by analysis of some chemicals involved and explain the chemistry or physics used to solve a crime scene.
Have the plot take place in more than one city around the world and incorporate some geography into the story. You could also have characters that use their expertise in biology to solve a murder.
Rather than as obstacles, view each of these subjects as an interesting opportunity to incorporate diverse scenes in a way that seems natural and helps you add interest to your story. As for economics, you can have the story take place in an economic boom or recession and describe what events have caused it and make it part of your story. Obviously, these are just options to start you thinking creatively to get the ball rolling. Good luck and have fun with it!