Insight Genetics (United States)

Proteases rely on their active sites for substrate specificity, but these sites have inherent limitations that impact enzymatic efficiency and regulation. Exosites and cofactors help overcome these constraints by enhancing the protease's substrate interactions, specificity, and inhibition. Recent research by Gangemi etal. highlights the role of exosites in regulating the inhibition of the protease neutrophil elastase by the serpin alpha-1-antitrypsin. Understanding these mechanisms is crucial for developing therapeutic applications. Advances in computational analysis provide new insights into exosite function, complementing traditional structural studies and expanding potential biotechnological applications of protease inhibitors.

Introduction Squamous cell carcinoma of the thyroid (SCCT) is a rare, aggressive thyroid cancer distinguished by the emergence of squamous cells due to chronic inflammation or metaplasia. It poses diagnostic and therapeutic challenges, often identified at an advanced stage with a poor prognosis. The rarity of SCCT underscores the necessity for advanced research on effective treatments and diagnostic strategies. The current data utilized the Surveillance, Epidemiology, and End Results (SEER) database to determine the characteristics and outcomes of patients with primary SCCT. Methods De-identified data from patients with primary SCCT from 2000 to 2020 were collected using the SEER database. Demographic data, including age, sex, race, income, and housing, and clinical data including tumor size, tumor stage, nodal status, metastases, treatment modality, survival, and the patient's status, were extracted. Exclusion criteria were patients with unknown outcomes and missing death certificates. A detailed comparison of the two patient cohorts and univariate and multivariate Cox proportional hazard regression survival analyses were conducted. Results Among the 159 primary SCCT patients, the median age was 71 ± 21 years, with 83 females (52.2%) and 76 males (47.8%). The median overall follow-up was 6.0 years (4.41-7.59). The majority were White (108, 67.9%), followed by Hispanic (19, 11.9%). The five-year overall survival (OS) of the study group was 17.6% (95% CI = 14.5-20.7). The five-year disease-specific survival (DSS) was 37.6% (95% CI = 32.7-42.5). There was no significant difference based on surgery, chemotherapy, or radiation (p = 0.134). Age, tumor stage, nodal status, and distant metastases were negative prognostic factors. Sex, race, income, and housing were not predictive of survival. Conclusion The current study on SCCT highlights a low five-year OS rate of 17.6% and a DSS rate of 37.6%, with no significant difference in survival based on surgery, chemotherapy, or radiation. The negative prognostic factors included age, tumor stage, nodal status, and distant metastases, whereas sex, race, income, and housing did not significantly predict survival outcomes. These findings underscore the critical need for early detection and the development of more effective treatment strategies to manage SCCT.

Abstract The roles of the serine/glycine metabolic pathway (SGP) have recently been evident in certain types of tumor physiology; however, the pathological relevance of SGP in undifferentiated thyroid cancer remains unexplored. Herein, we employed a comparative transcriptome analysis of bulk RNA sequencing coupled with single-cell RNA sequencing, showing that the high expression of SHMT2 and MTHFD2 is tightly associated with a low thyroid differentiation score (TDS) and poor clinical features in thyroid cancer. In addition, unique metabolic reprogramming of SGP-relevant pathways in dedifferentiated cancer cells, and a distinct trajectory of a subpopulation of tumor cells with a high mitochondrial one-carbon pathway was observed. More importantly, such dramatic changes are functionally relevant, as inhibition of SHMT2 significantly compromises mitochondrial respiration and decreases tumor size by upregulating TDS markers. Taken together, our results highlight the importance of the mitochondrial one-carbon pathway, including SGP, in undifferentiated thyroid cancer and suggest that SHMT2 is a novel therapeutic target.

PURPOSELehmann et al have identified four molecular subtypes of triple-negative breast cancer (TNBC)—basal-like (BL) 1, BL2, mesenchymal (M), and luminal androgen receptor—and an immunomodulatory (IM) gene expression signature modifier. Our group previously showed that the response of TNBC to neoadjuvant systemic chemotherapy (NST) differs by molecular subtype, but whether NST affects the subtype was unknown. Here, we tested the hypothesis that in patients without pathologic complete response, TNBC subtypes can change after NST. Moreover, in cases with the changed subtype, we determined whether epithelial-to-mesenchymal transition (EMT) had occurred.MATERIALS AND METHODSFrom the Pan-Pacific TNBC Consortium data set containing TNBC patient samples from four countries, we examined 64 formalin-fixed, paraffin-embedded pairs of matched pre- and post-NST tumor samples. The TNBC subtype was determined using the TNBCtype-IM assay. We analyzed a partial EMT gene expression scoring metric using mRNA data.RESULTSOf the 64 matched pairs, 36 (56%) showed a change in the TNBC subtype after NST. The most frequent change was from BL1 to M subtypes (38%). No tumors changed from M to BL1. The IM signature was positive in 14 (22%) patients before NST and eight (12.5%) patients after NST. The EMT score increased after NST in 28 (78%) of the 36 patients with the changed subtype (v 39% of the 28 patients without change; P = .002254).CONCLUSIONWe report, to our knowledge, for the first time that the TNBC molecular subtype and IM signature frequently change after NST. Our results also suggest that EMT is promoted by NST. Our findings may lead to innovative adjuvant therapy strategies in TNBC cases with residual tumor after NST.

BackgroundThe Special Supplemental Nutrition Assistance Program for Women, Infants, and Children (WIC) is a federal nutrition program that provides nutritious food, education, and health care referrals to low-income women, infants, and children up to the age of 5 years. Although WIC is associated with positive health outcomes for each participant category, modernization and efficiency are needed at the clinic and shopping levels to increase program satisfaction and participation rates. New technologies, such as electronic benefits transfer (EBT), online nutrition education, and mobile apps, can provide opportunities to improve the WIC experience for participants.ObjectiveThis formative study applies user-centered design principles to inform the layout and prioritization of features in mobile apps for low-income families participating in the WIC program.MethodsTo identify and prioritize desirable app features, caregivers (N=22) of the children enrolled in WIC participated in individual semistructured interviews with a card sorting activity. Interviews were transcribed verbatim and analyzed using constant comparative analysis for themes. App features were ranked and placed into natural groupings by each participant. The sum and average of the rankings were calculated to understand which features were prioritized by the users. Natural groupings of features were labeled according to participant descriptions.ResultsNatural groupings focused on the following categories: clinics/appointments, shopping/stores, education/assessments, location, and recipes/food. Themes from the interviews triangulated the results from the ranking activity. The priority app features were balance checking, an item scanner, and appointment scheduling. Other app features discussed and ranked included appointment reminders, nutrition training and quizzes, shopping lists, clinic and store locators, recipe gallery, produce calculator, and dietary preferences/allergies.ConclusionsThis study demonstrates how a user-centered design process can aid the development of an app for low-income families participating in WIC to inform the effective design of the app features and user interface.

ABSTRACT The study aimed to determine the variation of Y-chromosome-bearing sperm content among individual ejaculates. A real-time polymerase chain reaction (qPCR) with unique primers was developed and used to calculate the percentage of Y-chromosome-bearing sperm in individual ejaculates from 50 randomly selected men. There was a significant difference in the overall mean ± SD between the proportion of Y-chromosome-bearing sperm and X-chromosome-bearing sperm (45.36 ± 7.88 vs. 54.42 ± 7.88). Of the 50 ejaculates, 17 had more than, and 14 had less than the 99% confidence interval of the mean of the Y-chromosome-bearing sperm (45.58 ± 2.87). These results suggest that the inconsistency in sperm-based sex-selection outcomes appears to be a function of differences in the ejaculates and highlights the need for further study in environmental and genetic factors contributing to X or Y bearing spermatozoan instability. Abbreviations: qPCR: real-time polymerase chain reaction; ROS: reactive oxygen species; DTT: dithiothreitol; SRY: sex-determining region Y.

Abstract Although the profile of immune cells changes during the natural course of SARS-CoV-2 inflection in human patients, few studies have used a longitudinal approach to reveal their dynamic features. Here, we performed single-cell RNA sequencing of bronchoalveolar lavage fluid cells longitudinally obtained from SARS-CoV-2-infected ferrets. Landscape analysis of the lung immune microenvironment showed dynamic changes in cell proportions and characteristics in uninfected control, at 2 days post-infection (dpi) (early stage of SARS-CoV-2 infection with peak viral titer), and 5 dpi (resolution phase). NK cells and CD8+ T cells exhibited activated subclusters with interferon-stimulated features, which were peaked at 2 dpi. Intriguingly, macrophages were classified into 10 distinct subpopulations, and their relative proportions changed over the time. We observed prominent transcriptome changes among monocyte-derived infiltrating macrophages and differentiated M1/M2 macrophages, especially at 2 dpi. Moreover, trajectory analysis revealed gene expression changes from monocyte-derived infiltrating macrophages toward M1 or M2 macrophages and identified the distinct macrophage subpopulation that had rapidly undergone SARS-CoV-2-mediated activation of inflammatory responses. Finally, we found that different spectrums of M1 or M2 macrophages showed distinct patterns of gene modules downregulated by immune-modulatory drugs. Overall, these results elucidate fundamental aspects of the immune response dynamics provoked by SARS-CoV-2 infection.

In many states, abortion laws are becoming increasingly restrictive. Prenatal genetic counselors often see patients after the diagnosis of a fetal abnormality or genetic disorder and discuss the option of termination of pregnancy. The purpose of this study was to understand prenatal genetic counselors' perspectives on how state abortion laws impact their practice. Qualitative semi-structured interviews were conducted with 16 prenatal genetic counselors in states with restrictive abortion laws who were recruited from the National Society of Genetic Counselors' online directory. Verbatim transcripts were analyzed thematically, yielding five themes: genetic counselors in this study described (a) how state laws restrict access to abortion; (b) how they navigate state laws and institutional policies regarding abortion; (c) how they tailor their professional practice in the context of state abortion laws; (d) how abortion laws burden patients; and (e) how they engage in forms of advocacy. Participants described the financial and emotional burden placed on their patients by state abortion laws and how the laws influence their patient interactions. As access to abortion becomes more restricted, it is important to be aware of how this will impact genetic counselors and their patients.

In patients with triple-negative breast cancer (TNBC), tumor-infiltrating lymphocytes (TILs) are associated with improved survival. Lehmann et al. identified 4 molecular subtypes of TNBC [basal-like (BL) 1, BL2, mesenchymal (M), and luminal androgen receptor (LAR)], and an immunomodulatory (IM) gene expression signature indicates the presence of TILs and modifies these subtypes. The association between TNBC subtype and TILs is not known. Also, the association between inflammatory breast cancer (IBC) and the presence of TILs is not known. Therefore, we studied the IM subtype distribution among different TNBC subtypes. We retrospectively analyzed patients with TNBC from the World IBC Consortium dataset. The molecular subtype and the IM signature [positive (IM+) or negative (IM-)] were analyzed. Fisher’s exact test was used to analyze the distribution of positivity for the IM signature according to the TNBC molecular subtype and IBC status. There were 88 patients with TNBC in the dataset, and among them 39 patients (44%) had IBC and 49 (56%) had non-IBC. The frequency of IM+ cases differed by TNBC subtype (p = 0.001). The frequency of IM+ cases by subtype was as follows: BL1, 48% (14/29); BL2, 30% (3/10); LAR, 18% (3/17); and M, 0% (0/21) (in 11 patients, the subtype could not be determined). The frequency of IM+ cases did not differ between patients with IBC and non-IBC (23% and 33%, respectively; p = 0.35). In conclusion, the IM signature representing the underlying molecular correlate of TILs in the tumor may differ by TNBC subtype but not by IBC status.