Northrop‐Albrecht, Emmalee J.

Abstract INTRODUCTION: Colorectal cancer (CRC) is the 2nd most fatal cancer in the U.S.; most benefits of CRC screening are from detection of advanced pre-cancerous lesions (APLs). With a goal to improve non-invasive stool test APL sensitivity, we sought novel APL signatures in stool metaproteomes (host- and gut microbiome-derived proteins) among cancer-free controls (CTRL), APL, and CRC patients. Since dysbiosis in gut microbiota is associated with CRC initiation, we also examined the microbial source of differentially expressed proteins (DEPs). METHODS: Mass spectrometry was performed on archival stool supernatants (n=63 patients; 15 CTRL, 32 APL [16 adenomas & 16 sessile serrated lesions], 16 CRC). A sectioning and database-enrichment strategy was applied for peptide-spectrum matching. Microbial and human-derived proteins were searched against the Integrated Gene Catalogue (IGC) and UniProt human reference proteome. DEPs were identified using thresholds of P < 0.05 and fold-change ≥ 1.5. Pathway annotation of human DEPs was performed with the REVIGO webserver, while gut microbial DEPs were functionally categorized using the KEGG Automatic Annotation Server (KAAS). To assess the taxonomic distribution of microbial DEPs, sequences were aligned against the NCBI non-redundant database using BLASTP. RESULTS: Mass spectrometry detected 879 human and 32,514 microbiome-derived proteins. When limiting detection to proteins present in ≥ 75% of patients, only 117 human and 204 microbial proteins remained. There were 17 (4,875), 288 (9,638), and 63 (3,053) unique human (microbial) proteins detected in CTRL, APL, and CRC groups, respectively. When the protein presence cutoff was set at >30% of patients, there were 52 (13 human [11 upregulated, 2 downregulated], 39 microbial [28 upregulated, 11 downregulated]) DEPs detected for the CRC + APL vs CTRL comparison. Some pathways associated with upregulated human DEPs included: inflammatory response, cellular response to iron, and endothelial cell migration. The top upregulated microbial DEPs were derived from the Phocaeicola, Lachnospiraceae, and Oscillospiraceae genera. The top downregulated microbial DEPs belonged to the Bacteroides, Eubacterium, Agathobacter, Coprococcus, and Blautia genera. CONCLUSION: This work highlights the biological diversity and molecular heterogeneity of the stool proteome. We identified several host and microbial protein markers that differentiate APLs and early CRC from controls. These results provide a foundation for future validation studies, which are necessary to determine the clinical utility of these protein biomarkers prior to their integration into a noninvasive stool test. Citation Format: Emmalee J. Northrop-Albrecht, Vinod K. Gupta, William R. Taylor, Jason P. Sinnwell, Doug W. Mahoney, Patrick H. Foote, Kelli N. Burger, Jaeyun Sung, John B. Kisiel, . Comprehensive investigation of stool metaproteomes among patients with precancerous lesions and colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7656.

Abstract Identifying the genetic architecture of complex traits is important to many geneticists, including those interested in human disease, plant and animal breeding, and evolutionary genetics. Advances in sequencing technology and statistical methods for genome-wide association studies have allowed for the identification of more variants with smaller effect sizes, however, many of these identified polymorphisms fail to be replicated in subsequent studies. In addition to sampling variation, this failure to replicate reflects the complexities introduced by factors including environmental variation, genetic background, and differences in allele frequencies among populations. Using Drosophila melanogaster wing shape, we ask if we can replicate allelic effects of polymorphisms first identified in a genome-wide association studies in three genes: dachsous, extra-macrochaete, and neuralized, using artificial selection in the lab, and bulk segregant mapping in natural populations. We demonstrate that multivariate wing shape changes associated with these genes are aligned with major axes of phenotypic and genetic variation in natural populations. Following seven generations of artificial selection along the dachsous shape change vector, we observe genetic differentiation of variants in dachsous and genomic regions containing other genes in the hippo signaling pathway. This suggests a shared direction of effects within a developmental network. We also performed artificial selection with the extra-macrochaete shape change vector, which is not a part of the hippo signaling network, but showed a largely shared direction of effects. The response to selection along the emc vector was similar to that of dachsous, suggesting that the available genetic diversity of a population, summarized by the genetic (co)variance matrix (G), influenced alleles captured by selection. Despite the success with artificial selection, bulk segregant analysis using natural populations did not detect these same variants, likely due to the contribution of environmental variation and low minor allele frequencies, coupled with small effect sizes of the contributing variants.

AbstractExtracellular vesicles (EVs) are of growing interest due to their potential diagnostic, disease surveillance, and therapeutic applications. While several studies have evaluated EV isolation methods in various biofluids, there are few if any data on these techniques when applied to stool. The latter is an ideal biospecimen for studying EVs and colorectal cancer (CRC) because the release of tumour markers by luminal exfoliation into stool occurs earlier than vascular invasion. Since EV release is a conserved mechanism, bacteria in stool contribute to the overall EV population. In this study, we assessed five EV separation methods (ultracentrifugation [UC], precipitation [EQ‐O, EQ‐TC], size exclusion chromatography [SEC], and ultrafiltration [UF]) for total recovery, reproducibility, purity, RNA composition, and protein expression in stool supernatant. CD63, TSG101, and ompA proteins were present in EV fractions from all methods except UC. Human (18s) and bacterial (16s) rRNA was detected in stool EV preparations. Enzymatic treatment prior to extraction is necessary to avoid non‐vesicular RNA contamination. Ultrafiltration had the highest recovery, RNA, and protein yield. After assessing purity further, SEC was the isolation method of choice. These findings serve as the groundwork for future studies that use high throughput omics technologies to investigate the potential of stool‐derived EVs as a source for novel biomarkers for early CRC detection.

Abstract Increased numbers of antral follicles are associated with greater fertility and a uterine environment that is more supportive of early embryonic development in beef heifers. Glucose is a primary energy source for embryos and glucose concentrations are elevated in uterine luminal fluid (ULF) of pregnant heifers. We hypothesized that ULF glucose concentrations and endometrial transcript abundance for glucose transporters at d16 after insemination would be greater in heifers with increased numbers of antral follicles. Heifers classified with either increased (32 ± 1.1) or diminished (14.7 ± 1.1) antral follicle counts were selected and artificially inseminated following the Select Synch protocol (d0). At d16 after insemination, heifers were sent to the abattoir and reproductive tracts were collected to retrieve conceptuses to determine pregnancy. Uterine luminal fluid was collected, the endometrium was biopsied, total RNA was extracted and glucose transporter transcript abundance was determined. Data were analyzed using the MIXED procedure of SAS with antral follicle group, pregnancy status, and the interaction as fixed effects. Glucose concentrations in ULF were greater (P < 0.05) in heifers with increased antral follicle numbers compared to heifers with diminished numbers (122.65 ± 11.91 vs 84.12 ± 12.42 mg/dL). Glucose ULF concentrations were increased (P < 0.05) in pregnant vs. non-pregnant heifers (124.84 ± 12.81 vs 81.93 ± 11.50 mg/dL). Endometrial glucose transporter 1 (GLUT1) transcript abundance was increased in pregnant heifers (P < 0.01) but was not different due to antral follicle number or the interaction. Therefore, differences in glucose concentrations associated with antral follicle number may be due to differences in GLUT1 transcription before d16 or due to differences in protein abundance or functionality. Taken together, heifers with increased number of antral follicles may have increased energy availability in the uterus for trophoblast proliferation and function. USDA is an equal opportunity provider and employer.

Abstract Transcript abundance of two forms of GnRH and its receptor have been characterized in bovine ovaries. The objective was to investigate the relationship of GnRH-1, GnRH-2, GnRH-R, intrafollicular estradiol (E2) and progesterone (P4) during follicular development. Ovaries were collected from beef cows at specific stages of follicular development [pre-selection (PRE, n = 9), post-selection (POST, n = 9), and post-selection 24h after luteal regression (PG, n = 9)]. The largest follicle per stage was aspirated to obtain granulosa cells (GC) and follicular fluid (FF). Total cellular RNA was extracted from GC and RT-PCR was performed for GnRH-1, GnRH-2, GnRH-R and GAPDH. Radioimmunoassays were performed to determine FF concentrations of E2 and P4. Data were analyzed using the MIXED and REG procedures in SAS. There was no difference (P ≥ 0.23) in mRNA abundance of GnRH-2, GnRH-R or FF concentrations of P4 across follicular stages. There was an effect of stage on FF E2 (PRE: 17,925±20,273, POST: 28,458±21,503, and PG: 252,616±21,503 pg/mL; P < 0.01). Stage affected GnRH-1 mRNA abundance (PRE: 2.28±0.55, POST: 0.92±0.55, and PG: 0.11±0.55; P = 0.03). There was no relationship of GnRH-1 and GnRH-2 mRNA abundance or effect of FF P4 on GnRH-R mRNA abundance (P ≥ 0.23). There was no effect of FF P4 on GnRH-1 mRNA abundance (P = 0.68). There was no effect of FF E2 on GnRH-2 mRNA abundance (P = 0.66). As FF E2 increased GnRH-R mRNA abundance tended to increase (P = 0.10;r2=0.13). As FF P4 concentrations increased GnRH-2 mRNA abundance tended to decrease (P = 0.09;r2=0.12). As FF E2 increased GnRH-1 mRNA abundance decreased (P = 0.02;r2=0.20). In conclusion, there were differences in peptide and receptor mRNA abundance of GnRH in relation to FF E2 and P4 at specific stages of follicular development. This is supportive of a regulatory relationship between ovarian GnRH and steroidogenesis. This work is supported by AFRI Grant No.2018-67016-27578 from USDA. USDA is an equal opportunity provider and employer.

Abstract The relationship of ovarian reserve parameters to fertility in mammalian females continues to be debated. We demonstrated improved uterine function, creating an environment that is more supportive of early embryonic development in beef heifers with increased numbers of follicles. In the present study we hypothesized that timing of luteolysis differs between heifers with increased compared to heifers with diminished numbers of follicles. Angus heifers (n = 20/ group) were classified as low (14.7 ± 1.1) or high (32 ± 1.1) antral follicle number based on ovarian ultrasonography, and artificially inseminated (d0) following a Select Synch protocol. At d16 after insemination, heifers were slaughtered, and reproductive tracts collected. Tracts were flushed with 20 mL of physiological saline to determine pregnancy status by presence of a conceptus and endometrial samples from the horn ipsilateral to the CL were frozen for determination of transcript abundance. Real-time RT-PCR was performed to determine relative transcript abundance of oxytocin receptor (OXTR) and interferon-stimulated gene-15 (ISG15) with glyceraldehyde-3-phospate dehydrogenase as the endogenous reference gene. Transcript abundance was analyzed using the MIXED procedure of SAS with follicle group, pregnancy status and the interaction as fixed effects. Transcript abundance of ISG15 was greater in pregnant endometrium than non-pregnant endometrium (2.75 ± 0.25 vs 0.16 ± 0.22-fold; P < 0.0001) with no influence of follicle group or the interaction. The interaction of follicle group and pregnancy status influenced OXTR transcript abundance (P = 0.06). Luteolytic mechanisms were activated in non-pregnant heifers with diminished numbers of follicles (1.46 ± 0.25-fold) and were not activated in pregnant heifers (0.06 ± 0.22-fold) or heifers with increased numbers of follicles that were not pregnant (0.32 ± 0.30-fold). These data indicate a wider window of recognition of pregnancy in beef heifers with increased numbers of ovarian follicles. USDA is an equal opportunity provider and employer.