Use the method clearSubject(), but to apply when you are to call getMessage() method, let this example over here
$transport = $this->transportBuilder->setTemplateIdentifier('send_email_email_template')
->transportBuilder
->setTemplateIdentifier('send_email_email_template')
->setTemplateOptions( [
'area' => \Magento\Framework\App\Area::AREA_FRONTEND,
'store' => \Magento\Store\Model\Store::DEFAULT_STORE_ID,
])
->setTemplateVars(array())
->setFrom($sender)
->addTo($toEmail, '')
->getTransport();
$transport
->getMessage()
->setMessageType( \Magento\Framework\Mail\MessageInterface::TYPE_HTML)
->setBody($MyHtml)
->clearSubject()
->setSubject("MySubject");
$transport->sendMessage();