TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer.

Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications. The effect of 3D chromatin topology on TE regulation remains elusive. Here, by integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. In cancer, perturbation of the hierarchical chromatin topology can lead to co-option of LTRs as functional alternative promoters in a context-dependent manner and drive aberrant transcriptional activation of novel oncogenes and other divergent transcripts. These data uncovered a new layer of regulatory mechanism of TE expression beyond DNA and chromatin modification in human genome. They also posit the TAD hierarchy dysregulation as a novel mechanism for alternative promoter-mediated oncogene activation and transcriptional diversity in cancer, which may be exploited therapeutically.

Impact of race-neutral eGFR calculations on African American kidney transplant candidate wait time: A single center retrospective analysis.

Race-inclusive estimated glomerular filtration rate (eGFR) could contribute to racial disparity in access to kidney transplantation. The Organ Procurement and Transplantation Network (OPTN) issued a policy allowing waiting time modification for candidates affected by race-inclusive eGFR calculations. Implementation of the new OPTN policy at the kidney transplant program of the Mount Sinai Hospital involved review of 921 African American candidates, of whom 240 (26%) candidates gained a median of 1 year and 10 months. The duration of time candidates gained varied from a minimum of 5 days to a maximum of 12 years and 3 months; 45.4% gained at least 2 years, and 12% gained at least 4 years of wait time. Among those who gained wait time, 20 (8.3%) candidates received deceased donor kidney transplants. Candidates who gained wait time had similar sociodemographic characteristics as those who did not, except that the median age for the former was higher by 3 years (59 vs. 56). Our early data suggest that the current policy on waiting time modification for candidates affected by race-inclusive estimation of GFR has the potential to improve racial disparity in access to kidney transplantation. However, the generalizability of our findings to other centers requires further study.

Surgery Improves Patient-Reported Outcomes in Patients with Intestinal and Pancreatic NETs: A Prospective Analysis.

BACKGROUND: Incorporation of patient-reported outcomes such as health-related quality of life has become increasingly important in the management of chronic diseases such as cancer. In this prospective study, we examined the effect of surgical resection on quality of life in patients with intestinal and pancreatic neuroendocrine tumors (NETs). METHODS: Thirty-two patients underwent NET resection at our institution from January 2020 to January 2022. All patients completed the 12-item short-form quality-of-life survey prior to surgery, as well as at the 3-, 6-, and 12-month postoperative time points. The presence and severity of specific carcinoid syndrome symptoms (diarrhea, flushing, and abdominal pain) were also recorded during pre- and postoperative appointments. RESULTS: Patients experienced significant increases in both mental and physical health after surgery. Mental health scores significantly increased at all three time points (baseline: 51.33; 3-month: 53.17, p = 0.02; 6-month: 57.20, p < 0.001; 12-month: 57.34, p = 0.002), and physical health scores increased at 6 and 12 months (baseline: 50.39; 6-month: 53.16, p = 0.04; 12-month: 55.02, p = 0.003). Younger patients benefited more in terms of physical health, while older patients had more significant increases in mental health. Patients with metastatic disease, larger primary tumors, and those receiving medical therapy had lower baseline quality-of-life scores and greater improvements after surgery. The vast majority of patients in this study also experienced alleviation of carcinoid syndrome symptoms. CONCLUSIONS: In addition to prolonging survival, resection of intestinal and pancreatic NETs leads to significantly improved patient-reported quality of life.

Early Ambulation is Associated with Improved Outcomes Following Colorectal Surgery.

BACKGROUND: The Enhanced Recovery After Surgery (ERAS) society lists early mobilization as one of their recommendations for improving patient outcomes following colorectal surgery. The level of supporting evidence, however, is relatively weak, and furthermore, the ERAS guidelines do not clearly define "early" mobilization. In this study, we define mobilization in terms of time to first ambulation after surgery and develop an outcome-based cutoff for early mobilization. METHODS: This is a retrospective cohort study comprised of 291 patients who underwent colorectal operations at a large, academic medical center from June to December 2019. Three cutoffs (12 hours, 24 hours, and 48 hours) were used to divide patients into early and late ambulation groups for each cutoff, and statistical analysis was performed to determine differences in postoperative outcomes between the corresponding groups. RESULTS: Multivariate analysis showed no difference between the early and late ambulation groups for the 12-hour and 48-hour cutoffs; however, ambulation before 24 hours was associated with a decreased rate of severe complications as well as fewer adverse events overall. Patients who ambulated within 24 hours had a 4.1% rate of severe complications and a 22.1% rate of experiencing some adverse event (complication, return to the emergency department, and/or readmission). In comparison, 11.8% of patients who ambulated later experienced a severe complication (P = 0.026), while 36.1% of patients experienced some adverse event (P = 0.011). CONCLUSIONS: Ambulation within 24 hours after colorectal surgery is associated with improved postoperative outcomes, particularly a decreased rate of severe complications.