It is indeed unfortunate that the causes of gender dysphoria are not well understood at this point of time. I am inclined to think that there are multiple causation factors that can be considered.
First, medical explanations. Fluctuations or imbalance in hormones during pregnancy may predispose to the development of gender dysphoria. There are links that have been found between transgender identity and brain structure. Brain structure of transsexuals seems to be intermediate between men and women.
No specific gene for transexuality has been identified so far. It is thought that certain brain alterations, when they interact with hormones during fetal development, can predispose the person to transsexualism. However, many of these findings are non conclusive as the sample size is small and they merely include a small number of individuals.
Second, psychological factors. Many individuals seen at my clinic report that they are aware that they are transgender from their earliest memories. One psychological theory proposes that a small boy may admire his mother to such a degree that he ends up wanting to be like her.
However, it is also believed that the boy would eventually lose his desire as long as his parents set firm limits when raising him, or he has the right genetic predisposition. Nevertheless, many people also argue that parental influence through punishment and reward of behaviour, can affect gender expression but not gender identity (a person's internal sense of self).
When discussing psychological factor, its is relevant to look at a condition called autogynephilia, where the individual is aroused by the thought of being a woman. This may explain late onset transsexuals. They tend to be even more gender dysphoric then men with no autogynephilia.
Third, cultural issues. There are cultures that believe that individuals have freedom of choice and are hence free to choose whatever is right for them. Also, cultures vary in their definition of masculinity and femininity. Some cultures have created specific ways for people to live in roles that are different from that assigned to them at birth.
As to how we can support individuals who are transgender, the best way is to lean to accept them as who they are. It is hard for them to change their gender identity. Many of them feel anxious or depressed as they find that society at large tends not to accept them.
They often times feel lonely and isolated. You can also advise your friend to seek further help and emotional support from a mental health professionals.