You can embed HTML in Markdown. Type literally what you want, with no indent.
<code class="prettyprint">
code_line(1);
// a code comment
class More Code { }
</code>
For the specific case of syntax highlighting following the back ticks at the start of a fenced code block with the language works just about everywhere these days.
```js
code_line(1);
// a code comment
class MoreCode { }
```