Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro.

While evolution is often considered from a DNA- and protein-centric view, RNA-based regulation can also impact gene expression and protein sequences. Here we examined interspecies differences in RNA-protein interactions using the conserved neuronal RNA binding protein, Unkempt (UNK) as model. We find that roughly half of mRNAs bound in human are also bound in mouse. Unexpectedly, even when transcript-level binding was conserved across species differential motif usage was prevalent. To understand the biochemical basis of UNK-RNA interactions, we reconstituted the human and mouse UNK-RNA interactomes using a high-throughput biochemical assay. We uncover detailed features driving binding, show that in vivo patterns are captured in vitro, find that highly conserved sites are the strongest bound, and associate binding strength with downstream regulation. Furthermore, subtle sequence differences surrounding motifs are key determinants of species-specific binding. We highlight the complex features driving protein-RNA interactions and how these evolve to confer species-specific regulation.

SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells.

Scaffold attachment factor B (SAFB) is a conserved RNA-binding protein that is essential for early mammalian development. However, the functions of SAFB in mouse embryonic stem cells (ESCs) have not been characterized. Using RNA immunoprecipitation followed by RNA-seq (RIP-seq), we examined the RNAs associated with SAFB in wild-type and SAFB/SAFB2 double-knockout ESCs. SAFB predominantly associated with introns of protein-coding genes through purine-rich motifs. The transcript most enriched in SAFB association was the lncRNA Malat1, which also contains a purine-rich region in its 5' end. Knockout of SAFB/SAFB2 led to differential expression of approximately 1000 genes associated with multiple biological processes, including apoptosis, cell division, and cell migration. Knockout of SAFB/SAFB2 also led to splicing changes in a set of genes that were largely distinct from those that exhibited changes in expression level. The spliced and nascent transcripts of many genes whose expression levels were positively regulated by SAFB also associated with high levels of SAFB, implying that SAFB binding promotes their expression. Reintroduction of SAFB into double-knockout cells restored gene expression toward wild-type levels, an effect again observable at the level of spliced and nascent transcripts. Proteomics analysis revealed a significant enrichment of nuclear speckle-associated and RS domain-containing proteins among SAFB interactors. Neither Xist nor Polycomb functions were dramatically altered in SAFB/2 knockout ESCs. Our findings suggest that among other potential functions in ESCs, SAFB promotes the expression of certain genes through its ability to bind nascent RNA.

Association of Oncologist-Patient Communication With Functional Status and Physical Performance in Older Adults: A Secondary Analysis of a Cluster Randomized Clinical Trial.

Importance: The functional status and physical performance of older adults with cancer are underassessed and undertreated despite the high prevalence of impaired functional status and physical performance in this population and their associations with chemotherapy-induced toxic effects and mortality. Objective: To examine the association between providing oncologists with a geriatric assessment (GA) summary with recommendations and having oncologist-patient conversations about functional and physical performance. Design, Setting, and Participants: Data for this secondary analysis were collected from October 29, 2014, to April 28, 2017, for a national cluster randomized clinical trial conducted by the University of Rochester Cancer Center National Cancer Institute Community Oncology Research Program evaluating the effect of a GA intervention on patient satisfaction with communication about aging-related concerns. There were 17 practice clusters in the intervention group and 14 in the usual care group. All 541 participants underwent a GA including standardized functional and physical performance measures and had 1 clinical encounter audio-recorded, transcribed, and blindly coded to categorize conversations by GA domain. Participants were aged 70 years or older, with a stage III or IV solid tumor or lymphoma with palliative treatment intent, and impairment in 1 or more GA domain. Statistical analysis was performed from August 18, 2020, to January 10, 2022. Interventions: Oncologist practices randomized to the intervention received a GA summary and validated recommendations for each patient prior to the audio-recorded clinical encounter. Main Outcomes and Measures: The primary analysis of this clinical trial assessed the effect of the intervention on patient satisfaction with oncologist communication about aging-related concerns. This secondary analysis assessed the post hoc hypothesis that the intervention would be associated with an increase in the proportion of patients having conversations with their oncologists and receiving oncologist recommendations specific to functional and physical performance concerns. Results: A total of 541 patients (276 men [51%]; mean [SD] age, 77.5 [5.2] years [range, 70-96 years]) were analyzed at baseline. Excluding 13 patients without audio recordings, 86% of patients (95% CI, 78%-91%) in the intervention group vs 59% of patients (95% CI, 47%-69%; P < .001) receiving usual care had conversations about functional or physical performance. Conversations were more frequently initiated by oncologists in the intervention group (84%; 95% CI, 77%-90%) than oncologists in the usual care group (58%; 95% CI, 45%-70%; P < .001). Oncologists in the intervention group were more likely to address patients' concerns (43%; 95% CI, 33%-53%) than oncologists in the usual care group (17%; 95% CI, 10%-26%; P < .001). Conclusions and Relevance: In this secondary analysis of a cluster randomized clinical trial, providing oncologists with a GA summary was associated with an increase in the number of oncologist-patient conversations about functional and physical performance-related concerns with recommendations to address these concerns. These findings support the use of the GA summary and recommendations as important tools in caring for older adults with advanced cancer and functional or physical impairments. Trial Registration: ClinicalTrials.gov Identifier: NCT02107443.

Evaluating the association of frailty with communication about aging-related concerns between older patients with advanced cancer and their oncologists.

BACKGROUND: A geriatric assessment (GA) intervention improves communication about aging-related concerns, but its effect on communication in patients with various levels of frailty is unknown. METHODS: This was a secondary analysis of a nationwide trial of patients aged ≥70 years with incurable cancer and impairment on 1 or more GA domains (ClinicalTrials.gov Identifier NCT02107443; principal investigator Supriya G. Mohile). Practice sites were randomized to either the GA-intervention or usual care. Frailty was assessed with a deficit accumulation index (range, 0-1), and patients were stratified as robust (0 to <0.2), prefrail (0.2 to <0.35), or frail (≥0.35). The clinic visit after the GA-intervention was audio-recorded, transcribed, and coded to evaluate the number and quality of conversations about aging-related concerns. Linear mixed models examined differences in the number and quality of conversations within and between arms. All P values were 2-sided. RESULTS: Patients (n = 541) were classified as robust (27%), prefrail (42%), or frail (31%). In the usual care arm, frail patients (vs robust ones) engaged in more aging-related conversations (adjusted mean difference, 1.73; 95% confidence interval [CI], 0.59-2.87), conversations of higher quality (difference, 1.12; 95% CI, 0.24-2.0), and more discussions about evidence-based recommendations (difference, 0.71; 95% CI, 0.04-1.38; all P values ≤ .01). Similarly, in the GA intervention arm, frail patients (vs robust ones) engaged in more aging-related conversations (difference, 2.49; 95% CI, 1.51-3.47), conversations of higher quality (difference, 1.31; 95% CI, 0.56-2.06), and more discussions about evidence-based recommendations (difference, 0.87; 95% CI, 0.32-1.42; all P values ≤ .01). Furthermore, the GA-intervention significantly improved the number and quality of conversations in all patients: robust, prefrail, and frail (all P values ≤ .01). CONCLUSIONS: Patients with higher degrees of frailty and those exposed to the GA-intervention had more and higher quality conversations about aging-related concerns with oncologists. LAY SUMMARY: A geriatric assessment (GA) intervention improves communication about aging-related concerns, but its effect on communication in patients with various levels of frailty is unknown. This study conducted a secondary analysis of a nationwide trial of patients aged ≥70 years with incurable cancer and 1 or more GA domain impairments. Patients were stratified as robust, prefrail, or frail. The number and quality of conversations about aging-related concerns that occurred during the clinic visit after the GA-intervention were determined. Patients with higher degrees of frailty and those in the GA intervention arm had more and higher quality conversations about aging-related concerns with oncologists.