Collaboration revenues decreased by $2.7 million in the three months ended September 30, 2024, compared to the three months ended September 30, 2023, primarily due to a decrease of $2.8 million from our collaboration with Ionis related to the completion of the combined licenses and research and discovery performance obligation in the second quarter of 2024.
Research and development expenses increased by $8.4 million in the three months ended September 30, 2024 compared to the three months ended September 30, 2023, due to increases of $10.2 million in clinical program expenses for zelenectide pevedotin due to the ongoing Phase II expansion portion of the Phase I/II clinical trial as well as the ongoing Phase II/III Duravelo-2 registrational trial which commenced recruiting patients in the first quarter of 2024, $3.6 million in employee and contractor related expenses primarily attributable to one-time severance-related costs of $1.9 million as well as increased headcount, $1.1 million of incremental share-based compensation expense primarily associated with equity grants issued since the same period in the prior year and $0.9 million in facility expenses. These increases were offset by decreases of $3.3 million of incremental U.K. research and development tax incentives primarily associated with the impact of U.K. R&D tax credit reimbursement rate changes enacted in February 2024, $3.2 million in Bicycle TICA program development expenses due to the timing of clinical program activities, and $1.5 million in discovery, platform and other expenses.
We begin to separately track program expenses at candidate nomination, at which point we accumulate all direct external program costs to support that program to date. Through September 30, 2024, we have incurred approximately $129.3 million, $46.6 million, and $15.7 million of direct external expenses for the development of zelenectide pevedotin, BT5528, and BT1718, respectively, since their candidate nominations, and an aggregate of $47.6 million of direct external expenses for the development of the two named Bicycle TICA candidates since their nominations.
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