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1.
NEJM Evid ; 3(5): EVIDoa2300289, 2024 May.
Article En | MEDLINE | ID: mdl-38815168

BACKGROUND: In the United States, Black men are at highest risk for being diagnosed with and dying from prostate cancer. Given this disparity, we examined relevant data to establish clinical prostate-specific antigen (PSA) screening guidelines for Black men in the United States. METHODS: A comprehensive literature search identified 1848 unique publications for screening. Of those screened, 287 studies were selected for full-text review, and 264 were considered relevant and form the basis for these guidelines. The numbers were reported according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. RESULTS: Three randomized controlled trials provided Level 1 evidence that regular PSA screening of men 50 to 74 years of age of average risk reduced metastasis and prostate cancer death at 16 to 22 years of follow-up. The best available evidence specifically for Black men comes from observational and modeling studies that consider age to obtain a baseline PSA, frequency of testing, and age when screening should end. Cohort studies suggest that discussions about baseline PSA testing between Black men and their clinicians should begin in the early 40s, and data from modeling studies indicate prostate cancer develops 3 to 9 years earlier in Black men compared with non-Black men. Lowering the age for baseline PSA testing to 40 to 45 years of age from 50 to 55 years of age, followed by regular screening until 70 years of age (informed by PSA values and health factors), could reduce prostate cancer mortality in Black men (approximately 30% relative risk reduction) without substantially increasing overdiagnosis. CONCLUSIONS: These guidelines recommend that Black men should obtain information about PSA screening for prostate cancer. Among Black men who elect screening, baseline PSA testing should occur between ages 40 and 45. Depending on PSA value and health status, annual screening should be strongly considered. (Supported by the Prostate Cancer Foundation.).


Black or African American , Early Detection of Cancer , Prostate-Specific Antigen , Prostatic Neoplasms , Male , Humans , Prostatic Neoplasms/diagnosis , Prostatic Neoplasms/ethnology , Prostatic Neoplasms/blood , Prostate-Specific Antigen/blood , United States/epidemiology , Middle Aged , Aged , Practice Guidelines as Topic , Mass Screening
2.
Am J Hum Genet ; 111(5): 809-824, 2024 May 02.
Article En | MEDLINE | ID: mdl-38642557

Advancements in genomic technologies have shown remarkable promise for improving health trajectories. The Human Genome Project has catalyzed the integration of genomic tools into clinical practice, such as disease risk assessment, prenatal testing and reproductive genomics, cancer diagnostics and prognostication, and therapeutic decision making. Despite the promise of genomic technologies, their full potential remains untapped without including individuals of diverse ancestries and integrating social determinants of health (SDOHs). The NHGRI launched the 2020 Strategic Vision with ten bold predictions by 2030, including "individuals from ancestrally diverse backgrounds will benefit equitably from advances in human genomics." Meeting this goal requires a holistic approach that brings together genomic advancements with careful consideration to healthcare access as well as SDOHs to ensure that translation of genetics research is inclusive, affordable, and accessible and ultimately narrows rather than widens health disparities. With this prediction in mind, this review delves into the two paramount applications of genetic testing-reproductive genomics and precision oncology. When discussing these applications of genomic advancements, we evaluate current accessibility limitations, highlight challenges in achieving representativeness, and propose paths forward to realize the ultimate goal of their equitable applications.


Genomics , Precision Medicine , Humans , Genomics/methods , Precision Medicine/methods , Genome, Human , Genetic Testing , Neoplasms/genetics , Health Services Accessibility
3.
Biol Methods Protoc ; 9(1): bpae012, 2024.
Article En | MEDLINE | ID: mdl-38566776

While the detection of single-nucleotide variants (SNVs) is important for evaluating human health and disease, most genotyping methods require a nucleic acid extraction step and lengthy analytical times. Here, we present a protocol which utilizes the integration of locked nucleic acids (LNAs) into self-annealing loop primers for the allelic discrimination of five isocitrate dehydrogenase 1 R132 (IDH1-R132) variants using loop-mediated isothermal amplification (LAMP). This genotyping panel was initially evaluated using purified synthetic DNA to show proof of specific SNV discrimination. Additional evaluation using glioma tumor lysates with known IDH1-R132 mutational status demonstrated specificity in approximately 35 min without the need for a nucleic acid extraction purification step. This LNA-LAMP-based genotyping assay can detect single base differences in purified nucleic acids or tissue homogenates, including instances where the variant of interest is present in an excess of background wild-type DNA. The pH-based colorimetric indicator of LNA-LAMP facilitates convenient visual interpretation of reactions, and we demonstrate successful translation to an end-point format using absorbance ratio, allowing for an alternative and objective approach for differentiating between positive and negative reactions. Importantly, the LNA-LAMP genotyping panel is highly reproducible, with no false-positive or false-negative results observed.

4.
Curr Oncol ; 31(3): 1129-1144, 2024 02 20.
Article En | MEDLINE | ID: mdl-38534917

BACKGROUND: Examining lung cancer (LC) cases in Virginia (VA) is essential due to its significant public health implications. By studying demographic, environmental, and socioeconomic variables, this paper aims to provide insights into the underlying drivers of LC prevalence in the state adjusted for spatial associations at the zipcode level. METHODS: We model the available VA zipcode-level LC counts via (spatial) Poisson and negative binomial regression models, taking into account missing covariate data, zipcode-level spatial association and allow for overdispersion. Under latent Gaussian Markov Random Field (GMRF) assumptions, our Bayesian hierarchical model powered by Integrated Nested Laplace Approximation (INLA) considers simultaneous (spatial) imputation of all missing covariates through elegant prediction. The spatial random effect across zip codes follows a Conditional Autoregressive (CAR) prior. RESULTS: Zip codes with elevated smoking indices demonstrated a corresponding increase in LC counts, underscoring the well-established connection between smoking and LC. Additionally, we observed a notable correlation between higher Social Deprivation Index (SDI) scores and increased LC counts, aligning with the prevalent pattern of heightened LC prevalence in regions characterized by lower income and education levels. On the demographic level, our findings indicated higher LC counts in zip codes with larger White and Black populations (with Whites having higher prevalence than Blacks), lower counts in zip codes with higher Hispanic populations (compared to non-Hispanics), and higher prevalence among women compared to men. Furthermore, zip codes with a larger population of elderly people (age ≥ 65 years) exhibited higher LC prevalence, consistent with established national patterns. CONCLUSIONS: This comprehensive analysis contributes to our understanding of the complex interplay of demographic and socioeconomic factors influencing LC disparities in VA at the zip code level, providing valuable information for targeted public health interventions and resource allocation. Implementation code is available at GitHub.


Lung Neoplasms , Male , Humans , Female , Aged , Virginia , Prevalence , Bayes Theorem , Socioeconomic Factors
5.
iScience ; 27(2): 108858, 2024 Feb 16.
Article En | MEDLINE | ID: mdl-38303720

Lung cancer is the third most common cancer with Black/AA men showing higher risk and poorer outcomes than NHW men. Lung cancer disparities are multifactorial, driven by tobacco exposure, inequities in care access, upstream health determinants, and molecular determinants including biological and genetic factors. Elevated expressions of protein arginine methyltransferases (PRMTs) correlating with poorer prognosis have been observed in many cancers. Most importantly, our study shows that PRMT6 displays higher expression in lung cancer tissues of Black/AA men compared to NHW men. In this study, we investigated the underlying mechanism of PRMT6 and its cooperation with PRMT1 to form a heteromer as a driver of lung cancer. Disrupting PRMT1/PRMT6 heteromer by a competitive peptide reduced proliferation in non-small cell lung cancer cell lines and patient-derived organoids, therefore, giving rise to a more strategic approach in the treatment of Black/AA men with lung cancer and to eliminate cancer health disparities.

6.
bioRxiv ; 2024 Jan 16.
Article En | MEDLINE | ID: mdl-38293106

Ubiquitination of histone H2A at lysine 119 residue (H2AK119ub) plays critical roles in a wide range of physiological processes, including Polycomb gene silencing 1,2 , replication 3-5 , DNA damage repair 6-10 , X inactivation 11,12 , and heterochromatin organization 13,14 . However, the underlying mechanism and structural basis of H2AK119ub remains largely elusive. In this study, we report that H2AK119ub nucleosomes have a unique composition, containing histone variants H2BC1 and H2AZ.2, and importantly, this composition is required for H2AK119ub and Polycomb gene silencing. Using the UAB domain of RSF1, we purified H2AK119ub nucleosomes to a sufficient amount and purity. Mass spectrometry analyses revealed that H2AK119ub nucleosomes contain the histone variants H2BC1 and H2AZ.2. A cryo-EM study resolved the structure of native H2AK119ub nucleosomes to a 2.6A resolution, confirming H2BC1 in one subgroup of H2AK119ub nucleosomes. Tandem GST-UAB pulldown, Flag-H2AZ.2, and HA-H2BC1 immunoprecipitation revealed that H2AK119ub nucleosomes could be separated into distinct subgroups, suggesting their composition heterogeneity and potential dynamic organization. Knockout or knockdown of H2BC1 or H2AZ.2 reduced cellular H2AK119ub levels, establishing H2BC1 and H2AZ.2 as critical determinants of H2AK119ub. Furthermore, genomic binding profiles of H2BC1 and H2AZ.2 overlapped significantly with H2AK119ub binding, with the most significant overlapping in the gene body and intergenic regions. Finally, assays in developing embryos reveal an interaction of H2AZ.2, H2BC1, and RING1A in vivo . Thus, this study revealed, for the first time, that the H2AK119ub nucleosome has a unique composition, and this composition is required for H2AK119ub and Polycomb gene silencing.

7.
J Natl Cancer Inst Monogr ; 2023(62): 167-172, 2023 11 08.
Article En | MEDLINE | ID: mdl-37947328

Despite significant progress in cancer research and treatment, a persistent knowledge gap exists in understanding and addressing cancer care disparities, particularly among populations that are marginalized. This knowledge deficit has led to a "data divide," where certain groups lack adequate representation in cancer-related data, hindering their access to personalized and data-driven cancer care. This divide disproportionately affects marginalized and minoritized communities such as the U.S. Black population. We explore the concept of "data deserts," wherein entire populations, often based on race, ethnicity, gender, disability, or geography, lack comprehensive and high-quality health data. Several factors contribute to data deserts, including underrepresentation in clinical trials, poor data quality, and limited access to digital technologies, particularly in rural and lower-socioeconomic communities.The consequences of data divides and data deserts are far-reaching, impeding equitable access to precision medicine and perpetuating health disparities. To bridge this divide, we highlight the role of the Cancer Intervention and Surveillance Modeling Network (CISNET), which employs population simulation modeling to quantify cancer care disparities, particularly among the U.S. Black population. We emphasize the importance of collecting quality data from various sources to improve model accuracy. CISNET's collaborative approach, utilizing multiple independent models, offers consistent results and identifies gaps in knowledge. It demonstrates the impact of systemic racism on cancer incidence and mortality, paving the way for evidence-based policies and interventions to eliminate health disparities. We suggest the potential use of voting districts/precincts as a unit of aggregation for future CISNET modeling, enabling targeted interventions and informed policy decisions.


Healthcare Disparities , Neoplasms , Humans , Delivery of Health Care , Ethnicity , Neoplasms/diagnosis , Neoplasms/epidemiology , Neoplasms/therapy , Black or African American
9.
Article En | MEDLINE | ID: mdl-37998280

Multiple evidence-based interventions (EBIs) have been developed to improve the completion of colorectal cancer (CRC) screening within Federally Qualified Health Centers (FQHCs) and other safety net settings in marginalized communities. Little effort has been made, however, to evaluate their relative effectiveness across different clinical contexts and populations. To this end, we tested the relative effectiveness of three EBIs (mailed birthday cards, lay navigation, and provider-delivered education) among a convenience sample of 1252 patients (aged 50-75 years old, who were due for CRC screening and scheduled for a visit at one of three clinics within a network of Federally Qualified Health Centers (FQHCs) in the United States. To be eligible for the study, patients had to identify as African American (AA) or Latino American (LA). We compared the effects of the three EBIs on CRC screening completion using logistic regression. Overall, 20% of the study population, an increase from a baseline of 13%, completed CRC screening. Clinical demographics appeared to influence the effectiveness of the EBIs. Mailed birthday reminders appeared to be the most effective within the multi-ethnic clinic (p = 0.03), provider-delivered education within the predominantly LA clinic (p = 0.02), and lay navigation within the predominantly AA clinic (p = 0.03). These findings highlight the importance of understanding clinical context when selecting which evidence-based interventions to deploy.


Colorectal Neoplasms , Aged , Humans , Middle Aged , Colorectal Neoplasms/diagnosis , Colorectal Neoplasms/epidemiology , Colorectal Neoplasms/ethnology , Early Detection of Cancer , Ethnic and Racial Minorities , Evidence-Based Medicine , Hispanic or Latino , Mass Screening , United States , Black or African American
10.
PLoS One ; 18(9): e0291666, 2023.
Article En | MEDLINE | ID: mdl-37733671

The R132H isocitrate dehydrogenase one (IDH1) mutation is a prognostic biomarker present in a subset of gliomas and is associated with heightened survival when paired with aggressive surgical resection. In this study, we establish proof-of-principle for rapid colorimetric detection of the IDH1-R132H mutation in tumor samples in under 1 hour without the need for a nucleic acid extraction. Colorimetric peptide nucleic acid loop-mediated isothermal amplification (CPNA-LAMP) utilizes 4 conventional LAMP primers, a blocking PNA probe complementary to the wild-type sequence, and a self-annealing loop primer complementary to the single nucleotide variant to only amplify the DNA sequence containing the mutation. This assay was evaluated using IDH1-WT or IDH1-R132H mutant synthetic DNA, wild-type or IDH1-R132H mutant U87MG cell lysates, and tumor lysates from archived patient samples in which the IDH1 status was previously determined using immunohistochemistry (IHC). Reactions were performed using a hot water bath and visually interpreted as positive by a pink-to-yellow color change. Results were subsequently verified using agarose gel electrophoresis. CPNA-LAMP successfully detected the R132H single nucleotide variant, and results from tumor lysates yielded 100% concordance with IHC results, including instances when the single nucleotide variant was limited to a portion of the tumor. Importantly, when testing the tumor lysates, there were no false positive or false negative results.


Glioma , Peptide Nucleic Acids , Humans , Isocitrate Dehydrogenase/genetics , Colorimetry , Glioma/diagnosis , Glioma/genetics , Mutation
11.
Eur Respir J ; 61(6)2023 06.
Article En | MEDLINE | ID: mdl-37024132

INTRODUCTION: Pulmonary arterial hypertension (PAH) is characterised by loss of microvessels. The Wnt pathways control pulmonary angiogenesis but their role in PAH is incompletely understood. We hypothesised that Wnt activation in pulmonary microvascular endothelial cells (PMVECs) is required for pulmonary angiogenesis, and its loss contributes to PAH. METHODS: Lung tissue and PMVECs from healthy and PAH patients were screened for Wnt production. Global and endothelial-specific Wnt7a -/- mice were generated and exposed to chronic hypoxia and Sugen-hypoxia (SuHx). RESULTS: Healthy PMVECs demonstrated >6-fold Wnt7a expression during angiogenesis that was absent in PAH PMVECs and lungs. Wnt7a expression correlated with the formation of tip cells, a migratory endothelial phenotype critical for angiogenesis. PAH PMVECs demonstrated reduced vascular endothelial growth factor (VEGF)-induced tip cell formation as evidenced by reduced filopodia formation and motility, which was partially rescued by recombinant Wnt7a. We discovered that Wnt7a promotes VEGF signalling by facilitating Y1175 tyrosine phosphorylation in vascular endothelial growth factor receptor 2 (VEGFR2) through receptor tyrosine kinase-like orphan receptor 2 (ROR2), a Wnt-specific receptor. We found that ROR2 knockdown mimics Wnt7a insufficiency and prevents recovery of tip cell formation with Wnt7a stimulation. While there was no difference between wild-type and endothelial-specific Wnt7a -/- mice under either chronic hypoxia or SuHx, global Wnt7a +/- mice in hypoxia demonstrated higher pulmonary pressures and severe right ventricular and lung vascular remodelling. Similar to PAH, Wnt7a +/- PMVECs exhibited an insufficient angiogenic response to VEGF-A that improved with Wnt7a. CONCLUSIONS: Wnt7a promotes VEGF signalling in lung PMVECs and its loss is associated with an insufficient VEGF-A angiogenic response. We propose that Wnt7a deficiency contributes to progressive small vessel loss in PAH.


Pulmonary Arterial Hypertension , Mice , Animals , Pulmonary Arterial Hypertension/complications , Vascular Endothelial Growth Factor A/metabolism , Endothelial Cells/metabolism , Familial Primary Pulmonary Hypertension/metabolism , Hypoxia/metabolism
12.
Health Equity ; 7(1): 80-88, 2023.
Article En | MEDLINE | ID: mdl-36876237

Purpose: To examine the association of cigarette use and smoking-related health conditions by race/ethnicity among diverse and low-income patients at a federally qualified health center (FQHC). Methods: Demographics, smoking status, health conditions, death, and health service use were extracted from electronic medical data for patients seen between September 1, 2018, and August 31, 2020 (n=51,670). Smoking categories included everyday/heavy smoker, someday/light smoker, former smoker, or never smoker. Results: Current and former smoking rates were 20.1% and 15.2%, respectively. Males, Black, White, non-partnered, older, and Medicaid/Medicare patients were more likely to smoke. Compared with never smokers, former and heavy smokers had higher odds for all health conditions except respiratory failure, and light smokers had higher odds of asthma, chronic obstructive pulmonary disease, emphysema, and peripheral vascular disease. All smoking categories had more emergency department visits and hospitalizations than never smokers. The associations between smoking status and health conditions differed by race/ethnicity. White patients who smoked had a greater increase in odds of stroke and other cardiovascular diseases compared with Hispanic and Black patients. Black patients who smoked had a greater increase in odds of emphysema and respiratory failure compared with Hispanic patients. Black and Hispanic patients who smoked had a greater increase in emergency care use compared with White patients. Conclusion: Smoking was associated with disease burden and emergency care and differed by race/ethnicity. Health Equity Implications: Resources to document smoking status and offer cessation services should be increased in FQHCs to promote health equity for lower income populations.

13.
Mol Psychiatry ; 28(4): 1494-1501, 2023 04.
Article En | MEDLINE | ID: mdl-36869227

The racial/ethnic disparities in cancer incidence and outcome are partially due to the inequities in neighborhood advantage. Mounting evidences supported a link between neighborhood deprivation and cancer outcomes including higher mortality. In this review, we discuss some of the findings related to work on area-level neighborhood variables and cancer outcomes, and the potential biological and built/natural environmental mechanisms that might explain this link. Studies have also shown that residents of deprived neighborhoods or of racially or economically segregated neighborhoods have worse health outcomes than residents of more affluent neighborhoods and/or less racially or economically segregated neighborhoods, even after adjusting for the individual-level socioeconomic status. To date, little research has been conducted investigating the biological mediators that may play roles in the associations of neighborhood deprivation and segregation with cancer outcomes. The psychophysiological stress induced by neighborhood disadvantage among people living in these neighborhoods could be a potential underlying biological mechanism. We examined a number of chronic stress-related pathways that may potentially mediate the relationship between area-level neighborhood factors and cancer outcomes, including higher allostatic load, stress hormones, altered epigenome and telomere maintenance and biological aging. In conclusion, the extant evidence supports the notion that neighborhood deprivation and racial segregation have unfavorable impacts on cancer. Understanding how neighborhood factors influence the biological stress response has the potential to inform where and what types of resources are needed within the community to improve cancer outcomes and reduce disparities. More studies are warranted to directly assess the role of biological and social mechanisms in mediating the relationship between neighborhood factors and cancer outcomes.


Neoplasms , Social Segregation , Humans , Risk , Social Class , Racial Groups , Residence Characteristics , Socioeconomic Factors
14.
J Natl Med Assoc ; 115(2S): S2-S7, 2023 May.
Article En | MEDLINE | ID: mdl-37002129

Cancer incidence and outcomes vary considerably between racial and ethnic groups. Non-Hispanic (NH) Blacks are disproportionately burdened with the most common cancer types, having the highest death rate of any group. Racial health disparities are complex and have been identified at each step of the cancer care continuum, encompassing patient and provider factors and health care system processes. The higher cancer mortality among NH Blacks may reflect underuse of prevention strategies such as vaccination and screening, resulting in later stage of disease at diagnosis and underuse of cancer-directed therapy. Inequalities in the quality of care, including access to health care and receipt of recommended diagnostic and therapeutic interventions as well as supportive care also contribute to the excess burden of cancer-related deaths among NH Blacks. Non-clinical factors such as structural racism and lower socioeconomic status are associated with unequal access to resources such as housing, healthy foods, employment, and education, which have been demonstrated to drive racial disparities in cancer. Concerted efforts to understand and target the causes of the observed differences in access, screening, and treatment utilization will be critical for achieving more equitable treatment delivery and outcomes for all patients with cancer. Moreover, ongoing efforts to enhance diversity in clinical trials enrollment and access to novel precision medicine initiatives are processes warranted to reduce healthcare inequalities.


Neoplasms , Precision Medicine , Humans , United States/epidemiology , Minority Groups , Ethnicity , Healthcare Disparities , Neoplasms/diagnosis , Neoplasms/therapy , Health Disparate Minority and Vulnerable Populations
15.
J Womens Health (Larchmt) ; 32(5): 553-560, 2023 05.
Article En | MEDLINE | ID: mdl-36897755

Background: The vaginal microbiome (VMB) plays an important role in the persistence of human papillomavirus (HPV) infection and differs by race and among women with cervical intraepithelial neoplasia (CIN). Materials and Methods: We explored these relationships using 16S rRNA VMB taxonomic profiles of 3050 predominantly Black women. VMB profiles were assigned to three subgroups based on taxonomic markers indicative of vaginal wellness: optimal (Lactobacillus crispatus, L. gasseri, and L. jensenii), moderate (L. iners), and suboptimal (Gardnerella vaginalis, Atopobium vaginae, Ca. Lachnocurva vaginae, and others). Multivariable Firth logistic regression models were adjusted for age, smoking, VMB, HPV, and pregnancy status. Results: VMB prevalence by subgroup was 18%, 30%, and 51% for the optimal, moderate, and suboptimal groups, respectively. In fully adjusted models, the risk of CIN grade 3 (CIN3) among non-Latina (nL) Blacks was twice that of nL Whites (odds ratio [OR] = 2.0, 95% confidence interval [CI]: 1.1, 3.9, p = 0.02). The VMB modified this association (p = 0.04) such that the risk of CIN3 was significantly higher for nL Blacks than for nL Whites only among women with optimal VMBs (OR = 7.8, 95% CI: 1.7, 74.5, p = 0.007). Within racial groups, the risk of CIN3 was only elevated among nL White women with suboptimal VMBs (OR = 6.0, 95% CI: 1.3, 56.9, p = 0.02) compared with their racial counterparts with optimal VMBs. Conclusions: Our findings suggest that race is a modifier of the VMB in HPV carcinogenesis. An optimal VMB does not appear to be protective for nL Black women compared with nL White women.


Microbiota , Papillomavirus Infections , Uterine Cervical Dysplasia , Female , Pregnancy , Humans , RNA, Ribosomal, 16S/genetics , Vagina , Uterine Cervical Dysplasia/epidemiology
16.
J Natl Compr Canc Netw ; 21(2): 117-124.e3, 2023 02.
Article En | MEDLINE | ID: mdl-36791757

The root causes of racial disparities in access to optimal cancer care and related cancer outcomes are complex, multifactorial, and not rooted in biology. Contributing factors to racial disparities in care delivery include implicit and explicit bias, lack of representation of people of color in the oncology care and research workforce, and homogenous research participants that are not representative of the larger community. Systemic and structural barriers include policies leading to lack of insurance and underinsurance, costs of cancer treatment and associated ancillary costs of care, disparate access to clinical trials, and social determinants of health, including exposure to environmental hazards, access to housing, childcare, and economic injustices. To address these issues, ACS CAN, NCCN, and NMQF convened the Elevating Cancer Equity (ECE) initiative. The ECE Working Group developed the Health Equity Report Card (HERC). In this manuscript, we describe the process taken by the ECE Working Group to develop the HERC recommendations, the strategies employed by NCCN to develop an implementation plan and scoring methodology for the HERC, and next steps to pilot the HERC tool in practice settings.


Health Equity , Neoplasms , Humans , Delivery of Health Care , Neoplasms/epidemiology , Neoplasms/therapy , Medical Oncology , Policy , Healthcare Disparities
17.
Proc Natl Acad Sci U S A ; 120(2): e2205371120, 2023 01 10.
Article En | MEDLINE | ID: mdl-36595695

Development of multicellular organisms is orchestrated by persistent cell-cell communication between neighboring partners. Direct interaction between different cell types can induce molecular signals that dictate lineage specification and cell fate decisions. Current single-cell RNA-seq technology cannot adequately analyze cell-cell contact-dependent gene expression, mainly due to the loss of spatial information. To overcome this obstacle and resolve cell-cell contact-specific gene expression during embryogenesis, we performed RNA sequencing of physically interacting cells (PIC-seq) and assessed them alongside similar single-cell transcriptomes derived from developing mouse embryos between embryonic day (E) 7.5 and E9.5. Analysis of the PIC-seq data identified gene expression signatures that were dependent on the presence of specific neighboring cell types. Our computational predictions, validated experimentally, demonstrated that neural progenitor (NP) cells upregulate Lhx5 and Nkx2-1 genes, when exclusively interacting with definitive endoderm (DE) cells. Moreover, there was a reciprocal impact on the transcriptome of DE cells, as they tend to upregulate Rax and Gsc when in contact with NP cells. Using individual cell transcriptome data, we formulated a means of computationally predicting the impact of one cell type on the transcriptome of its neighboring cell types. We have further developed a distinctive spatial-t-distributed stochastic neighboring embedding to display the pseudospatial distribution of cells in a 2-dimensional space. In summary, we describe an innovative approach to study contact-specific gene regulation during embryogenesis.


Embryonic Development , Gene Expression Regulation, Developmental , Animals , Mice , Embryonic Development/genetics , Cell Differentiation/genetics , Transcriptome , Sequence Analysis, RNA , Single-Cell Analysis/methods , Gene Expression Profiling
18.
Cancer Lett ; 555: 216025, 2023 Feb 28.
Article En | MEDLINE | ID: mdl-36538983

Targeting KRAS-mutated non-small-cell lung cancer (NSCLC) remains clinically challenging. Here we show that loss of function of Miz1 inhibits lung tumorigenesis in a mouse model of oncogenic KRAS-driven lung cancer. In vitro, knockout or silencing of Miz1 decreases cell proliferation, clonogenicity, migration, invasion, or anchorage-independent growth in mutant (MT) KRAS murine or human NSCLC cells but has unremarkable impact on non-tumorigenic cells or wild-type (WT) KRAS human NSCLC cells. RNA-sequencing reveals Protocadherin-10 (Pcdh10) as the top upregulated gene by Miz1 knockout in MT KRAS murine lung tumor cells. Chromatin immunoprecipitation shows Miz1 binding on the Pcdh10 promoter in MT KRAS lung tumor cells but not non-tumorigenic cells. Importantly, silencing of Pcdh10 rescues cell proliferation and clonogenicity in Miz1 knockout/knockdown MT KRAS murine or human tumor cells, and rescues allograft tumor growth of Miz1 knockout tumor cells in vivo. Miz1 is upregulated in MT KRAS lung tumor tissues compared with adjacent non-involved tissues in mice. Consistent with this, Miz1 is upregulated while Pcdh10 is downregulated in human lung adenocarcinomas (LUAD) compared with normal tissues, and high Miz1 levels or low Pcdh10 levels are associated with poor survival in lung cancer patients. Furthermore, the Miz1 signature is associated with worse survival in MT but not WT KRAS LUAD, and Pcdh10 is downregulated in MT compared to WT KRAS LUAD. Taken together, our studies implicate the Miz1/Pcdh10 axis in oncogenic KRAS-driven lung tumorigenesis.


Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Animals , Humans , Mice , Carcinogenesis/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Cell Line, Tumor , Lung/pathology , Lung Neoplasms/metabolism , Protein Inhibitors of Activated STAT/metabolism , Proto-Oncogene Proteins p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/metabolism , Protocadherins , Ubiquitin-Protein Ligases/metabolism
20.
Cancer Gene Ther ; 30(3): 414-423, 2023 03.
Article En | MEDLINE | ID: mdl-36385523

Lung cancer continues to be the leading cause of cancer death in the United States. Despite recent advances, the five-year survival rate for lung cancer compared to other cancers still remains fairly low. The discovery of molecular targets for lung cancer is key to the development of new approaches and therapies. Electrically silent voltage-gated potassium channel (KvS) subfamilies, which are unable to form functional homotetramers, are implicated in cell-cycle progression, cell proliferation and tumorigenesis. Here, we analyzed the expression of KvS subfamilies in human lung tumors and identified that potassium voltage-gated channel subfamily F member 1 (KCNF1) was up-regulated in non-small cell lung cancer (NSCLC). Silencing of KCNF1 in NSCLC cell lines reduced cell proliferation and tumor progression in mouse xenografts, re-established the integrity of the basement membrane, and enhanced cisplatin sensitivity. KCNF1 was predominately localized in the nucleoplasm and likely mediated its functions in an ion-independent manner. We identified integrin ß4 subunit (ITGB4) as a downstream target for KCNF1. Our findings suggest that KCNF1 promotes lung cancer by enhancing ITGB4 signaling and implicate KCNF1 as a novel therapeutic target for lung cancer.


Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Animals , Humans , Mice , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Cell Line, Tumor , Cell Proliferation/genetics , Gene Expression Regulation, Neoplastic , Integrin beta4/genetics , Integrin beta4/metabolism , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Signal Transduction
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