The Cocaine and Oxycodone Biobanks, Two Repositories from Genetically Diverse and Behaviorally Characterized Rats for the Study of Addiction

Abstract

Visual Abstract

Glucocorticoid Receptor-Regulated Enhancers Play a Central Role in the Gene Regulatory Networks Underlying Drug Addiction

“…csRNA-seq overcomes these limitations by quantifying the level of transcription initiation at regulatory elements, such as enhancers, from total RNA, which can be easily obtained from frozen tissues (e.g., samples from a tissue repository). Using csRNA-seq on < 1 µg of total RNA isolated from repository brain tissues, we identified > 100k TSRs across PFC and NAc from naive rats or rats with addiction-like behavior following oxycodone or cocaine IVSA (Carrette et al, 2021). Most TSRs represent eRNAs as they initiate transcripts in regions associated with known features of enhancer elements, including open chromatin, histones harboring the H3K27ac mark, and bidirectional transcription.…”

“…For the cocaine cohorts, rats were characterized for motivation (progressive ratio responding), compulsive-responding for drug use (contingent footshock), and irritability-like behavior (bottle-brush test). An Addiction Index was computed by integrating all the behavioral measures (Kallupi et al, 2020;Carrette et al, 2021;Sedighim et al, 2021). HS rats classified as having a high Addiction Index were used for this study.…”

“…1A). Samples from six animals were obtained from a tissue repository (Carrette et al, 2021), including two naive rats, two rats subjected to oxycodone intravenous self-administration (IVSA), and two rats subjected to cocaine IVSA (Arnold et al, 2019;Adhikary et al, 2021;Carrette et al, 2021). We further generated total small RNA-seq libraries that were used as input in csRNA-seq peak calling to mitigate the identification of false TSS from potential RNA degradation-related biases or other high abundance short RNA species.…”

“…Brain samples from male heterogeneous stock (HS) rats (2 naive, 2 cocaine, 2 oxycodone) were obtained from the cocaine oxycodone (www.oxycodonebiobank.org) and (www.cocainebiobank.org) tissue repositories at UCSD and are part of a large and ongoing study of addiction that uses outbred HS rats (www.ratgenes.org) (Solberg Woods and Palmer, 2019). We selected samples that were collected during prolonged abstinence after the last session of extended access of oxycodone or cocaine IVSA (Carrette et al, 2021). In this model, male Heterogenous Stock (HS) rats were trained to selfadminister drugs in short access conditions (2 h/day for 4 days for oxycodone or 2 h/day for 10 days for cocaine) followed by long access conditions (12 h/day for oxycodone and 6 h /day for cocaine) for 14 days to develop escalation of drug intake.…”

“…Here, we compared transcription initiation profiles by csRNA-seq using brain tissues isolated from rats that were not exposed to drugs or were subjected to a well-validated extended access model of intravenous self-administration (IVSA) of oxycodone or cocaine (Ahmed and Koob, 1998;Ahmed et al, 2000Ahmed et al, , 2002George et al, 2008;Chen et al, 2013;Koob et al, 2014;de Guglielmo et al, 2019;Carrette et al, 2021). Tissues were collected after five weeks of prolonged abstinence to study the long-term effects of voluntary drug intake and were obtained from a tissue repository (Carrette et al, 2021). We selected NAc for its role in mediating the reinforcing effects of substances of abuse and the prefrontal cortex (PFC) for its role in inhibitory control behavior altered in addiction (Everitt, 2014).…”