>Use the method clearSubject(), but to apply when you are to call getMessage() method, let this example over here

    $transport = $this
        ->transportBuilder
        ->setTemplateIdentifier('send_email_email_template')
        ->setTemplateOptions( [
            'area' => \Magento\Framework\App\Area::AREA_FRONTEND,
            'store' => \Magento\Store\Model\Store::DEFAULT_STORE_ID,
        ])
        ->setTemplateVars(array())
        ->setFrom($sender)
        ->addTo($toEmail, '')
        >getTransport();
    $transport
        ->getMessage()
        ->setMessageType( \Magento\Framework\Mail\MessageInterface::TYPE_HTML)
        ->setBody($MyHtml)
        ->clearSubject()
        ->setSubject("MySubject");
    $transport->sendMessage();