From Gut to Hormones: Unraveling the Role of Gut Microbiota in (Phyto)Estrogen Modulation in Health and Disease.

The human gut microbiota regulates estrogen metabolism through the "estrobolome," the collection of bacterial genes that encode enzymes like ß-glucuronidases and ß-glucosidases. These enzymes deconjugate and reactivate estrogen, influencing circulating levels. The estrobolome mediates the enterohepatic circulation and bioavailability of estrogen. Alterations in gut microbiota composition and estrobolome function have been associated with estrogen-related diseases like breast cancer, enometrial cancer, and polycystic ovarian syndrome (PCOS). This is likely due to dysregulated estrogen signaling partly contributed by the microbial impacts on estrogen metabolism. Dietary phytoestrogens also undergo bacterial metabolism into active metabolites like equol, which binds estrogen receptors and exhibits higher estrogenic potency than its precursor daidzein. However, the ability to produce equol varies across populations, depending on the presence of specific gut microbes. Characterizing the estrobolome and equol-producing genes across populations can provide microbiome-based biomarkers. Further research is needed to investigate specific components of the estrobolome, phytoestrogen-microbiota interactions, and mechanisms linking dysbiosis to estrogen-related pathology. However, current evidence suggests that the gut microbiota is an integral regulator of estrogen status with clinical relevance to women's health and hormonal disorders.

Variations in Genes Encoding Human Papillomavirus Binding Receptors and Susceptibility to Cervical Precancer.

BACKGROUND: Cervical cancer oncogenesis starts with human papillomavirus (HPV) cell entry after binding to host cell surface receptors; however, the mechanism is not fully known. We examined polymorphisms in receptor genes hypothesized to be necessary for HPV cell entry and assessed their associations with clinical progression to precancer. METHODS: African American women (N = 1,728) from the MACS/WIHS Combined Cohort Study were included. Two case-control study designs were used-cases with histology-based precancer (CIN3+) and controls without; and cases with cytology-based precancer [high-grade squamous intraepithelial lesions (HSIL)] and controls without. SNPs in candidate genes (SDC1, SDC2, SDC3, SDC4, GPC1, GPC2, GPC3, GPC4, GPC5, GPC6, and ITGA6) were genotyped using an Illumina Omni2.5-quad beadchip. Logistic regression was used to assess the associations in all participants and by HPV genotypes, after adjusting for age, human immunodeficiency virus serostatus, CD4 T cells, and three principal components for ancestry. RESULTS: Minor alleles in SNPs rs77122854 (SDC3), rs73971695, rs79336862 (ITGA6), rs57528020, rs201337456, rs11987725 (SDC2), rs115880588, rs115738853, and rs9301825 (GPC5) were associated with increased odds of both CIN3+ and HSIL, whereas, rs35927186 (GPC5) was found to decrease the odds for both outcomes (P value ≤ 0.01). Among those infected with Alpha-9 HPV types, rs722377 (SDC3), rs16860468, rs2356798 (ITGA6), rs11987725 (SDC2), and rs3848051 (GPC5) were associated with increased odds of both precancer outcomes. CONCLUSIONS: Polymorphisms in genes that encode binding receptors for HPV cell entry may play a role in cervical precancer progression. IMPACT: Our findings are hypothesis generating and support further exploration of mechanisms of HPV entry genes that may help prevent progression to cervical precancer.

Evaluating Nurses' Time to Response by Severity and Cancer Stage in a Remote Symptom Monitoring Program for Patients With Breast Cancer.

PURPOSE: Remote symptom monitoring (RSM) using electronic patient-reported outcomes enables patients with cancer to communicate symptoms between in-person visits. A better understanding of key RSM implementation outcomes is crucial to optimize efficiency and guide implementation efforts. This analysis evaluated the association between the severity of patient-reported symptom alerts and time to response by the health care team. METHODS: This secondary analysis included women with stage I-IV breast cancer who received care at a large academic medical center in the Southeastern United States (October 2020-September 2022). Symptom surveys with at least one severe symptom alert were categorized as severe. Response time was categorized as optimal if the alert was closed by a health care team member within 48 hours. Odds ratios (ORs), predicted probabilities, and 95% CIs were estimated using a patient-nested logistic regression model. RESULTS: Of 178 patients with breast cancer included in this analysis, 63% of patients identified as White and 85% of patients had a stage I-III or early-stage cancer. The median age at diagnosis was 55 years (IQR, 42-65). Of 1,087 surveys included, 36% reported at least one severe symptom alert and 77% had an optimal response time by the health care team. When compared with surveys that had no severe symptom alerts, surveys with at least one severe symptom alert had similar odds of having an optimal response time (OR, 0.97; 95% CI, 0.68 to 1.38). The results were similar when stratified by cancer stage. CONCLUSION: Response times to symptom alerts were similar for alerts with at least one severe symptom compared with alerts with no severe symptoms. This suggests that alert management is being incorporated into routine workflows and not prioritized based on disease or symptom alert severity.

Partnership status and retention in care among cisgender heterosexual newly diagnosed people with HIV: a cohort study.

This study examined the role of partnership status (married, unmarried-partnered, and unpartnered) on retention in care among newly diagnosed (2013-2017), cisgender heterosexual people with HIV in Birmingham, Alabama (n = 152). This study evaluated all scheduled HIV primary care provider visits for two years following diagnosis date. A kept-visit measure was calculated such that, if an individual attended ≥1 visit in each of the four 6-month intervals, they were considered to have high visit constancy. A missed-visit measure was categorized as ≥1 no-show vs. 0 no-show for first and second year after diagnosis. Odds ratios (OR) and 95% confidence intervals (CI) were calculated using logistic regression models. Models were adjusted for confounding sociodemographic and clinical characteristics. The study population was 76% Black, 57% male, median age of 37 years. Overall, 65% had high visit consistency and 34.5% had ≥1 no-show in both years. Compared to unpartnered, married individuals had higher visit constancy [AOR (95% CI): 2.88 (1.02, 8.16)]; no differences were observed among unmarried-partnered individuals. No differences in having ≥1 no-show among partnership status groups were observed for either year. These findings suggest potential success of interventions involving a social confidant in optimizing retention in care among newly diagnosed, heterosexual PWH.

Genome-wide variants and polygenic risk scores for cognitive impairment following blood or marrow transplantation.

Cognitive impairment is prevalent in blood or marrow transplantation (BMT) recipients, albeit with inter-individual variability. We conducted a genome-wide association study of objective cognitive function assessed longitudinally in 239 adult BMT recipients for discovery and replicated in an independent cohort of 540 BMT survivors. Weighted genome-wide polygenic risk scores (PRS) were constructed using linkage disequilibrium pruned significant SNPs. Forty-four genome-wide significant SNPs were identified using additive (n = 3); codominant (n = 20) and genotype models (n = 21). Each additional copy of a risk allele was associated with a 0.28-point (p = 1.07 × 10-8) to a 1.82-point (p = 6.7 × 10-12) increase in a global deficit score. We replicated two SNPs (rs11634183 and rs12486041) with links to neural integrity. Patients in the top PRS quintile were at increased risk of cognitive impairment in discovery (RR = 1.95, 95%CI: 1.28-2.96, p = 0.002) and replication cohorts (OR = 1.84, 95%CI, 1.02-3.32, p = 0.043). Associations were stronger among individuals with lowest clinical risk for cognitive impairment. These findings support potential utility of PRS-based risk classification in the development of targeted interventions aimed at improving cognitive outcomes in BMT survivors.

Partnership status and time to viral suppression and sustained viral suppression among newly diagnosed heterosexual people with HIV.

BACKGROUND: Previous studies examining the role of partnership on HIV care outcomes have primarily focused on the men who have sex with men population in the United States, leaving a gap in the literature on this phenomenon among the heterosexual persons with HIV (PWH). This study examined association between partnership around diagnosis (married, unmarried-partnered, and un-partnered) with time to viral suppression (TVS) and sustained viral suppression (SVS) in newly diagnosed heterosexual PWH from a HIV clinic in Birmingham, Alabama. METHODS: TVS [time to first viral load (VL) <200 copies/ml] was measured using VLs from 12 months following diagnosis using Kaplan-Meier and proportional hazard model for interval censoring (n=153) to calculate hazard ratios (HRs) and 95% confidence intervals (CIs). SVS was measured using VLs for 12 months after first VS using logistic regression model (n=137) to calculate odds ratios (ORs) and 95% CIs. Models were adjusted for confounding demographics and clinical characteristics. RESULTS: The study population comprised of 77% Black, 57% male, and 46% aged 31-49 years; 24% were married, 35% unmarried-partnered, and 41% un-partnered. The median TVS (days) was 57 for married, 73 for unmarried-partnered, and 75 for un-partnered. Compared to un-partnered individuals, unmarried-partnered had similar, whereas married had 69% higher [HR (95% CI): 1.69 (1.02, 2.78)] hazard of TVS. Compared to un-partnered, unmarried-partnered and married individuals had similar odds of achieving SVS. CONCLUSION: Married, newly diagnosed, heterosexual PWH had faster TVS than un-partnered individuals suggesting that intimate partners may help achieve HIV care goals.

Treatment-related Correlates of Growth in Children With Sickle Cell Disease in the DISPLACE Cohort.

Reduced growth and delayed maturation have been described in children with sickle cell disease (SCD). This study investigated growth and hemolysis in children with SCD in the DISPLACE (Dissemination and Implementation of Stroke Prevention Looking at the Care Environment) cohort. The database includes 5287 children, of which, 3305 had at least 2 growth measurements over a 5-year period. Body mass index was converted to z-scores (zBMI), and 19.8%, 66.1%, 14.2% of children were classified as underweight, normal, and overweight/obese, respectively. Multivariable analysis of growth was conducted and included variables: age, sex, blood pressure, hemoglobin, reticulocyte count, treatment with chronic red cell transfusion therapy (CRCT), or hydroxyurea therapy. Baseline hemoglobin levels were associated with the lower odds of being underweight (odds ratio [OR]=0.93, 95% confidence interval [CI]: 0.86-0.99), and higher odds of being overweight/obese (OR: 1.26, 95% CI: 1.17-1.36) compared with normal zBMI. CRCT was associated with being overweight/obese at baseline (OR: 1.85, 95% CI: 1.31-2.60). Overall, results showed that children who were underweight improved regardless of therapy over the 2-year time period. However, children on CRCT are at higher risk for being overweight and should be monitored closely.

Genomic alterations associated with mutational signatures, DNA damage repair and chromatin remodeling pathways in cervical carcinoma.

Despite recent advances in the prevention of cervical cancer, the disease remains a leading cause of cancer-related deaths in women worldwide. By applying the GISTIC2.0 and/or the MutSig2CV algorithms on 430 whole-exome-sequenced cervical carcinomas, we identified previously unreported significantly mutated genes (SMGs) (including MSN, GPX1, SPRED3, FAS, and KRT8), amplifications (including NFIA, GNL1, TGIF1, and WDR87) and deletions (including MIR562, PVRL1, and NTM). Subset analyses of 327 squamous cell carcinomas and 86 non-squamous cell carcinomas revealed previously unreported SMGs in BAP1 and IL28A, respectively. Distinctive copy number alterations related to tumors predominantly enriched for *CpG- and Tp*C mutations were observed. CD274, GRB2, KRAS, and EGFR were uniquely significantly amplified within the Tp*C-enriched tumors. A high frequency of aberrations within DNA damage repair and chromatin remodeling genes were detected. Facilitated by the large sample size derived from combining multiple datasets, this study reveals potential targets and prognostic markers for cervical cancer.

Genomic Characterization and Therapeutic Targeting of HPV Undetected Cervical Carcinomas.

Cervical cancer tumors with undetectable HPV (HPVU) have been underappreciated in clinical decision making. In this study, two independent CC datasets were used to characterize the largest cohort of HPVU tumors to date (HPVU = 35, HPV+ = 430). Genomic and transcriptome tumor profiles and patient survival outcomes were compared between HPV+ and HPVU tumors. In vitro analyses were done to determine efficacy of the selective CDK4/6 inhibitor palbociclib on HPVU cancer cell lines. Patients with HPVU CC tumors had worse progression-free and overall survival outcomes compared to HPV+ patients. TP53, ARID1A, PTEN, ARID5B, CTNNB1, CTCF, and CCND1 were identified as significantly mutated genes (SMGs) enriched in HPVU tumors, with converging functional roles in cell cycle progression. In vitro HPVU, but not HPV+, cancer cell lines with wild type RB1 were sensitive to palbociclib monotherapy. These results indicate that HPVU status can be translated into the clinic as a predictive biomarker of poor patient response to standard of care treatments. We suggest primary cervix tumors be routinely tested for HPV prior to treatment to identify patients who will benefit from more aggressive precision-driven therapy. Our results identify palbociclib as a lead candidate as an alternative treatment strategy for HPVU CC patients.

Dissection of PIK3CA Aberration for Cervical Adenocarcinoma Outcomes.

Personalized treatment of genetically stratified subgroups has the potential to improve outcomes in many malignant tumors. This study distills clinically meaningful prognostic/predictive genomic marker for cervical adenocarcinoma using signature genomic aberrations and single-point nonsynonymous mutation-specific droplet digital PCR (ddPCR). Mutations in PIK3CA E542K, E545K, or H1047R were detected in 41.7% of tumors. PIK3CA mutation detected in the patient's circulating DNA collected before treatment or during follow-up was significantly associated with decreased progression-free survival or overall survival. PIK3CA mutation in the circulating DNA during follow-up after treatment predicted recurrence with 100% sensitivity and 64.29% specificity. It is the first indication of the predictive power of PIK3CA mutations in cervical adenocarcinoma. The work contributes to the development of liquid biopsies for follow up surveillance and a possibility of tailoring management of this particular women's cancer.

Immunophenotype-associated gene signature in ductal breast tumors varies by receptor subtype, but the expression of individual signature genes remains consistent.

BACKGROUND: In silico deconvolution of invasive immune cell infiltration in bulk breast tumors helps characterize immunophenotype, expands treatment options, and influences survival endpoints. In this study, we identify the differential expression (DE) of the LM22 signature to classify immune-rich and -poor breast tumors and evaluate immune infiltration by receptor subtype and lymph node metastasis. METHODS: Using publicly available data, we applied the CIBERSORT algorithm to estimate immune cells infiltrating the tumor into immune-rich and immune-poor groups. We then tested the association of receptor subtype and nodal status with immune-rich/poor phenotype. We used DE to test individual signature genes and over-representation analysis for related pathways. RESULTS: CCL19 and CXCL9 expression differed between rich/poor signature groups regardless of subtype. Overexpression of CHI3L2 and FES was observed in triple negative breast cancers (TNBCs) relative to other subtypes in immune-rich tumors. Non-signature genes, LYZ, C1QB, CORO1A, EVI2B, GBP1, PSMB9, and CD52 were consistently overexpressed in immune-rich tumors, and SCUBE2 and GRIA2 were associated with immune-poor tumors. Immune-rich tumors had significant upregulation of genes/pathways while none were identified in immune-poor tumors. CONCLUSIONS: Overall, the proportion of immune-rich/poor tumors differed by subtype; however, a subset of 10 LM22 genes that marked immune-rich status remained the same across subtype. Non-LM22 genes differentially expressed between the phenotypes suggest that the biologic processes responsible for immune-poor phenotype are not yet well characterized.

Inhibiting ß-catenin disables nucleolar functions in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) patients with upregulated Wnt/ß-catenin signaling often have poor clinical prognoses. During pathological examinations of breast cancer sections stained for ß-catenin, we made the serendipitous observation that relative to non-TNBC, specimens from TNBC patients have a greater abundance of nucleoli. There was a remarkable direct relationship between nuclear ß-catenin and greater numbers of nucleoli in TNBC tissues. These surprising observations spurred our investigations to decipher the differential functional relevance of the nucleolus in TNBC versus non-TNBC cells. Comparative nucleolar proteomics revealed that the majority of the nucleolar proteins in TNBC cells were potential targets of ß-catenin signaling. Next, we undertook an analysis of the nucleolar proteome in TNBC cells in response to ß-catenin inhibition. This effort revealed that a vital component of pre-rRNA processing, LAS1 like ribosome biogenesis factor (LAS1L) was significantly decreased in the nucleoli of ß-catenin inhibited TNBC cells. Here we demonstrate that LAS1L protein expression is significantly elevated in TNBC patients, and it functionally is important for mammary tumor growth in xenograft models and enables invasive attributes. Our observations highlight a novel function for ß-catenin in orchestrating nucleolar activity in TNBCs.

A 10-gene prognostic signature points to LIMCH1 and HLA-DQB1 as important players in aggressive cervical cancer disease.

BACKGROUND: Advanced cervical cancer carries a particularly poor prognosis, and few treatment options exist. Identification of effective molecular markers is vital to improve the individualisation of treatment. We investigated transcriptional data from cervical carcinomas related to patient survival and recurrence to identify potential molecular drivers for aggressive disease. METHODS: Primary tumour RNA-sequencing profiles from 20 patients with recurrence and 53 patients with cured disease were compared. Protein levels and prognostic impact for selected markers were identified by immunohistochemistry in a population-based patient cohort. RESULTS: Comparison of tumours relative to recurrence status revealed 121 differentially expressed genes. From this gene set, a 10-gene signature with high prognostic significance (p = 0.001) was identified and validated in an independent patient cohort (p = 0.004). Protein levels of two signature genes, HLA-DQB1 (n = 389) and LIMCH1 (LIM and calponin homology domain 1) (n = 410), were independent predictors of survival (hazard ratio 2.50, p = 0.007 for HLA-DQB1 and 3.19, p = 0.007 for LIMCH1) when adjusting for established prognostic markers. HLA-DQB1 protein expression associated with programmed death ligand 1 positivity (p < 0.001). In gene set enrichment analyses, HLA-DQB1high tumours associated with immune activation and response to interferon-γ (IFN-γ). CONCLUSIONS: This study revealed a 10-gene signature with high prognostic power in cervical cancer. HLA-DQB1 and LIMCH1 are potential biomarkers guiding cervical cancer treatment.

Race/ethnicity, sex and insurance disparities in colorectal cancer screening among individuals with and without cardiovascular disease.

Colorectal cancer (CRC) and cardiovascular diseases (CVD) share several risk factors. We examined the relationships between CRC screening and CVD history by race/ethnicity and sex. Data from 15 states across the United States with high age-adjusted CVD rates from the 2012-2016 Behavioral Risk Factor Surveillance System were used to examine prevalence of self-reported screening for CRC among 179,276 adults ages 50-75 years with and without history of CVD. Multivariable logistic regression was used to evaluate the association between socio-demographics and CRC screening in the expansion and stable phases of the Affordable Care Act (ACA) era. Prevalence of CRC screening was high among those with history of CVD. After multivariable adjustment, Whites and Hispanics with CVD had 19% (95%[CI]: 1.13-1.26) and 50% (95%[CI]: 1.10-2.06) higher odds for CRC screening, respectively, versus those without CVD. Individuals in both sexes with CVD had higher odds for CRC screening compared those without CVD. Strikingly, the odds for CRC screening in Hispanics with history of CVD were 72% higher in the stable phase of the ACA era for the fully adjusted model. Whites and Hispanics with history of CVD are more likely to undergo CRC screening, perhaps due to greater exposure to the healthcare system due to CVD. This association was not observed in Blacks. Interventions are needed to improve CRC screening rates among Blacks, especially due to their well-documented higher risk of CVD.

HPV-EM: an accurate HPV detection and genotyping EM algorithm.

Accurate HPV genotyping is crucial in facilitating epidemiology studies, vaccine trials, and HPV-related cancer research. Contemporary HPV genotyping assays only detect < 25% of all known HPV genotypes and are not accurate for low-risk or mixed HPV genotypes. Current genomic HPV genotyping algorithms use a simple read-alignment and filtering strategy that has difficulty handling repeats and homology sequences. Therefore, we have developed an optimized expectation-maximization algorithm, designated HPV-EM, to address the ambiguities caused by repetitive sequencing reads. HPV-EM achieved 97-100% accuracy when benchmarked using cell line data and TCGA cervical cancer data. We also validated HPV-EM using DNA tiling data on an institutional cervical cancer cohort (96.5% accuracy). Using HPV-EM, we demonstrated HPV genotypic differences in recurrence and patient outcomes in cervical and head and neck cancers.

Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade-specific epigenome and transcriptome landscapes.

Cervical cancer is the most common cancer affecting sub-Saharan African women and is prevalent among HIV-positive (HIV+) individuals. No comprehensive profiling of cancer genomes, transcriptomes or epigenomes has been performed in this population thus far. We characterized 118 tumors from Ugandan patients, of whom 72 were HIV+, and performed extended mutation analysis on an additional 89 tumors. We detected human papillomavirus (HPV)-clade-specific differences in tumor DNA methylation, promoter- and enhancer-associated histone marks, gene expression and pathway dysregulation. Changes in histone modification at HPV integration events were correlated with upregulation of nearby genes and endogenous retroviruses.

Gain of function in somatic TP53 mutations is associated with immune-rich breast tumors and changes in tumor-associated macrophages.

BACKGROUND: Somatic mutations in TP53 are present in 20%-30% of all breast tumors. While there are numerous population-based analyses of TP53, yet none have examined the relationship between somatic mutations in TP53 and tumor invasive immune cells. METHODS: Clinical and genetic data from 601 women drawn from The Cancer Genome Atlas (TCGA) were used to test the association between somatic TP53 mutation and immune-rich or immune-poor tumor status; determined using the CIBERSORT-based gene expression signature of 22 immune cell types. Our validation dataset, the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), used a pathologist-determined measure of lymphocyte infiltration. RESULTS: Within TP53-mutated samples, a mutation at codon p.R175H was shown to be present at higher frequency in immune-rich tumors. In validation analysis, any somatic mutation in TP53 was associated with immune-rich status, and the mutation at p.R175H had a significant association with tumor-invasive lymphocytes. TCGA-only analysis of invasive immune cell type identified an increase in M0 macrophages associated with p.R175H. CONCLUSIONS: These findings suggest that TP53 somatic mutations, particularly at codon p.R175H, are enriched in tumors with infiltrating immune cells. Our results confirm recent research showing inflammation-related gain of function in specific TP53 mutations.

Two high-risk susceptibility loci at 6p25.3 and 14q32.13 for Waldenström macroglobulinemia.

Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a rare, chronic B-cell lymphoma with high heritability. We conduct a two-stage genome-wide association study of WM/LPL in 530 unrelated cases and 4362 controls of European ancestry and identify two high-risk loci associated with WM/LPL at 6p25.3 (rs116446171, near EXOC2 and IRF4; OR = 21.14, 95% CI: 14.40-31.03, P = 1.36 × 10-54) and 14q32.13 (rs117410836, near TCL1; OR = 4.90, 95% CI: 3.45-6.96, P = 8.75 × 10-19). Both risk alleles are observed at a low frequency among controls (~2-3%) and occur in excess in affected cases within families. In silico data suggest that rs116446171 may have functional importance, and in functional studies, we demonstrate increased reporter transcription and proliferation in cells transduced with the 6p25.3 risk allele. Although further studies are needed to fully elucidate underlying biological mechanisms, together these loci explain 4% of the familial risk and provide insights into genetic susceptibility to this malignancy.