Nintendo's official statement is as follows: 

"Nintendo Co., Ltd. deeply regrets to announce that President Satoru Iwata passed away on July 11, 2015 due to a bile duct growth." 

Satoru Iwata was 55 at the time of his untimely death. Satoru had battled the growth on his bile duct for the past few years. This would explain his absence from last year's E3.

Nintendo fans and gamers in general will surely miss Mr. Satoru Iwata and we thank him for his accomplishments for Nintendo. 

Thank you Satoru Iwata and Goodnight. Rest in peace. 9/6/59 - 7/11/15