Cancers

The significant sex differences that exist in cancer mechanisms, incidence, and survival, have yet to impact clinical practice. We hypothesized that one barrier to translation is that sex differences in cancer phenotypes resemble sex differences in height: highly overlapping, but distinct, male and female population distributions that vary continuously between female- and male-biased extremes. A consequence of this variance is that sex-specific treatments are rendered unrealistic, and our translational goal should be adaptation of treatment to the unique mix of sex-biased mechanisms that are present in each patient. To develop a tool that could advance this goal, we applied a Bayesian Nearest Neighbor (BNN) analysis to 8370 cancer transcriptomes from 26 different adult and 4 different pediatric cancer types to establish patient-specific Transcriptomic Sex Indices (TSI). TSI precisely partitions an individual patients whole transcriptome into female- and male-biased components such that cancer type, patient sex, and transcriptomics, provide a novel and patient-specific mechanistic identifier that can be used for sex-adapted, precision cancer treatment planning.

(1) BackgroundClear cell renal cell carcinoma extending into the inferior vena cava (ccRCCIVC) represents a clinical high-risk setting. However, there is substantial heterogeneity within this patient subgroup regarding survival outcomes. Previously, members of our group developed a microRNA(miR)-based risk classifier - containing miR-21, miR-126 and miR-221 expression - which significantly predicted cancer-specific survival (CSS) of ccRCCIVC patients. (2) MethodsExamining a single-center cohort of tumor tissue from n = 56 patients with ccRCCIVC, we measured expression levels of miR-21, miR-126 and miR-221 by qRT-PCR. Prognostic impact of clinicopathological parameters and miR expression were investigated via univariate and multivariate cox regression. Referring to the previously established risk classifier, we performed Kaplan Meier analyses for single miR expression levels and the combined risk classifier. Cut-off values and weights within the risk classifier were taken from the previous study. (3) ResultsmiR-21 and miR-126 expression were significantly associated with lymphonodal status at time of surgery, development of metastasis during follow-up, and cancer-related death. In Kaplan Meier analyses, miR-21 and miR-126 significantly impacted CSS in our cohort. Moreover, applying the miR-based risk classifier significantly stratified ccRCCIVC according to CSS. (4) ConclusionsIn our retrospective analysis, we successfully validated the miR-based risk classifier within an independent ccRCCIVC cohort.

BackgroundThe involvement of the androgen and androgen receptor (AR) pathway in the development of epithelial ovarian cancer is increasingly recognized. However, the specific mechanisms by which anti-androgen agents, such as flutamide, may prevent ovarian cancer and their efficacy remain unknown. We examined the effects of flutamide on the miRNA expression profile found in women at high risk (HR) for ovarian cancer. MethodsOvarian and tubal tissues, free from ovarian, tubal, peritoneal cancers, and serous tubal intraepithelial carcinoma (STIC), were collected from untreated and flutamide-treated HR women. Low-risk (LR) women served as controls. Transcriptomic miRNA sequencing was performed on these 3 sample cohorts. The miRNAs that showed the most notable differential expression were subjected to functional assays in primary ovarian epithelial cells and ovarian cancer cells. ResultsFlutamide treatment demonstrated a normalization effect on diminished miRNA levels in HR tissues compared to LR tissues. Particularly, the miR-449 family was significantly upregulated in HR ovarian tissues following flutamide treatment, reaching levels comparable to those in LR tissues. MiR-449a and miR-449b-5p, members of the miR-449 family, were computationally predicted to target the mRNAs of AR and colony-stimulating factor 1 receptor (CSF1R, also known as c-fms), both of which are known contributors to ovarian cancer progression, with emerging evidence also supporting their roles in ovarian cancer initiation. These findings were experimentally validated in primary ovarian epithelial cells and ovarian cancer cell lines (SKOV3 and Hey): flutamide treatment resulted in elevated levels of miR-449a and miR-449b-5p, and introducing mimics of these miRNAs reduced the mRNA and protein levels of CSF1R and AR. Furthermore, introducing miR-449a and miR-449b-5p mimics showed inhibitory effects on the migration and proliferation of ovarian cancer cells. ConclusionFlutamide treatment restored the reduced expression of miR-449a and miR-449b-5p in HR tissues, thereby decreasing the expression of CSF1R and AR, functional biomarkers associated with an increased risk of ovarian cancer. In addition to the known direct binding of flutamide to the AR, we found that flutamide also suppresses AR expression via miR-449a and miR-449b-5p upregulation, revealing a novel dual-inhibitory mechanism on the AR pathway. Taken together, our study highlights mechanisms supporting the chemopreventive potential of flutamide in ovarian cancer, particularly in HR patients with reduced miR-449 expression.

Background and objectivesAge influences the development and progression of clear cell renal cell carcinoma (ccRCC). Management of non-metastatic (M0) ccRCC involves surgery, adjuvant immune checkpoint inhibition (e.g., pembrolizumab) and surveillance. For metastatic (M1) ccRCC, treatment combines immune checkpoint inhibitors with anti-angiogenic therapies, achieving long-term remission in approximately 30% of patients. Despite these advancements, a definitive cure remains elusive for most individuals. Furthermore, predictive criteria for relapse that incorporate age-specific variations are lacking, highlighting the critical need for prognostic models to optimize outcomes across diverse age groups. This study aimed to validate tumor aggressiveness markers in ccRCC, focusing on age as a determinant factor. MethodsData from The Cancer Genome Atlas (TCGA) were analyzed to identify age-related gene expression differences, which were then validated using an independent cohort and ccRCC cell lines. Random Survival Forest models were employed to predict overall survival (OS) and disease-free survival (DFS) post nephrectomy and progression-free survival upon tyrosine kinase inhibitors and immunotherapies. Key findings and limitationsOf 110 age-differentiated genes identified, 31 were significantly correlated with OS and DFS. Poor prognostic markers included CIAO1, EIF2B1, NARF, UBE2G2, and SART3, while TMEM167B emerged as a good prognostic marker, and a potential predictive biomarker for immunotherapy efficacy. Limitations include the need for larger independent cohort validation and deeper exploration of gene mechanisms. Conclusions and clinical implicationsThe study presents age-informed prognostic models that integrate gene expression profiles, offering a foundation for personalized treatment strategies. TMEM167B stands out as a novel candidate for improving age-specific ccRCC management. Advancing PracticeWhat does the study add? This study explores age-dependent differentially expressed genes in clear cell renal cell carcinoma (ccRCC) and proposes a potential age-specific prognostic gene signature that could be applicable to both non-metastatic and metastatic patients. This signature may assist in identifying individuals at higher risk of relapse. Among the identified genes, TMEM167B is highlighted as a candidate associated with favorable prognosis and shows promise as a potential predictive biomarker for immunotherapy efficacy. Patient SummaryAggressiveness in ccRCC varies with age and gene expression. Tailored treatments based on these factors may enhance outcomes and minimize side effects, particularly for patients over 75 years of age.

BackgroundClinical management of patients with recurrent ovarian granulosa cell tumor (GCT) remains poor. Sirtuin-1 (SIRT1), a deacetylase enzyme involved in the regulation of tumor growth and metastasis, may represent a therapeutic target due to the availability of selective pharmacological inhibitors with minimal toxicity. MethodsWe assessed the possible overexpression of SIRT1 during tumorigenesis by Western blot and immunohistochemistry. We tested the effects of SIRT1 inhibition by EX-527 on growth, proliferation, death, migration and gene expression by RNA sequencing and RT-qPCR in vitro on three GCT cell lines (AT29, KGN, COV434). Tumor growth in response to EX-527 treatment was examined in nude mice carrying subcutaneous GCT cell grafts using an electronic caliper and in GCT of AT83 mice by 3D ultrasound imaging system. ResultsSIRT1 abundance increased during tumorigenesis. In vitro treatment with EX-527 efficiently reduced cell growth, either by inducing apoptosis or by inhibiting proliferation. EX-527 induced alterations in pathways driven by mTOR, Myc and E2F, and in pathways controlling cell metabolism and oxidative stress. The administration of this treatment for 4 weeks efficiently reduced tumor progression in vivo. ConclusionsOur study reveals a new therapeutic potential of SIRT1 targeting as a treatment option for patients with recurrent GCT.

Lung cancer is the leading cause of cancer deaths, with lung squamous cell carcinoma (LUSC) accounting for a substantial proportion of cases. LUSC exhibits significant variability in patient outcomes, influenced by clinicopathological factors such as stage, age, and sex, with men exhibiting higher rates of incidence and poorer outcomes compared to women. Therefore, prognosis modeling and customized approaches to LUSC therapy require the characterization of the biological mechanisms that differentiate tumors and patient outcomes across sexes. Using data from The Cancer Genome Atlas (TCGA), this study characterized gene expression patterns that distinguish male and female LUSC. Specifically, differential expression, survival, and Cox regression analyses assessed the prognostic value of ANO1 (Anoctamin 1) expression and methylation in LUSC. Analyses uncovered a significant overexpression of ANO1 in a subset of male LUSC tumors compared to a much lower expression in normal lung and female LUSC tumors. High ANO1 expression was associated with poor survival outcomes in male subjects. High ANO1 gene body methylation mirrored gene expression and was similarly associated with poor survival outcomes. ANO1s prognostic value remained significant in a multivariate Cox regression analysis, establishing it as an independent prognostic biomarker. ANO1s marked sex-specific differences in expression and prognostic value indicate its role in the sex disparity of LUSC survival, highlighting its potential as a biomarker and a target for sex-specific customized therapies.

Right-sided colon cancer (RCC) and left-sided colon cancer (LCC) exhibit distinct clinical and molecular characteristics, influencing prognosis and therapeutic strategies. This study analyzed 750 patients with histologically confirmed adenocarcinoma (RCC: 387, LCC: 363) from the AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) Biopharma Collaborative (BPC) dataset. Tumor mutation burden (TMB) was significantly higher in RCC (6.65 {+/-} 11.3) than in LCC (3.17 {+/-} 4.35, adjusted p = 3.12 x 10-32). After filtering for functionally significant mutations, RCC exhibited enrichment for BRAF (23.1% vs. 6.7%, adjusted p = 1.64 x 10-8), KMT2D (8.6% vs. 3.2%, adjusted p = 9.27 x 10-3), and SMAD4 (13.1% vs. 7.3%, adjusted p = 2.97 x 10-2) mutations, while LCC demonstrated a higher frequency of TP53 (40.6% vs. 31.8%, adjusted p = 2.97 x 10-2). Multivariate Cox regression analysis showed significantly poorer overall survival (OS) in RCC than in LCC (HR: 1.30, 95% CI: 1.02-1.66, p = 0.033). KRAS mutations were identified as an independent predictor of worse OS in RCC (HR: 1.68, 95% CI: 1.06-2.70, p = 0.027), while BRAF mutations were associated with poorer OS in LCC (HR: 1.58, 95% CI: 1.05-2.37, p = 0.028).

Colorectal cancer (CRC) is the second cause of death worldwide. Up to 70% of CRC patients will metastasize. Identify new biomarkers of progression to prevent/delay disease evolution is urgent. Epithelial-to-mesenchymal transition (EMT) is a major program engaged during metastasis. We aim at identifying a combination of new genes that further identify signs of EMT in cancer tissues. We treated HT-29 cells grown in 3D with an EMT Inducing cocktail, and collect them before during and after treatment. For each condition, pan-transcriptomic analyses were done. Genes that were both induced upon EMT induction and inhibited upon EMT release (mesenchymal-to-epithelial transition or MET) were selected. We identified new genes for EMT-MET programs. These genes were used to build a metagene that, when applied to a database of transcriptomic data from primary colorectal tumors (n= 2,239), had an independent prognosis value. Finally, we submitted this metagene to CMap and identified drugs that might affect EMT-MET programs. Statins, well-known inhibitors of cholesterol synthesis, were among them and effectively delayed MET. These data show that cholesterol and EMT pathways are opposite regulators and impact differently tumor differentiation and outcome. TRANSLATIONAL RELEVANCEMetastases are the main cause of death of colorectal cancer (CRC) and the major issue in CRC management. Understanding the chain of events that lead to metastasis occurrence is urgent to identify new biomarkers of progression and/or new potential targets. Epithelial to mesenchymal transition (EMT) is a major player in cancer dissemination that remains non-targetable due to its broad involvement in tissue homeostasis. Here, we used a relevant in vitro dynamic model to identify the pathways triggered during EMT in CRC and how this might improve tumors classification, prognosis and open therapeutic avenue for this deadly disease. The cholesterol pathway surprisingly popped-out from this model and turned out to be a good prognosis factor of disease-free survival for CRC. Altogether, our results showed that an active EMT program lowers the cholesterol pathway, which further influence the differentiation of colon tumor toward the most aggressive subtypes.

IntroductionThe association of body composition with checkpoint inhibitor outcomes in melanoma is a matter of ongoing debate. In this study, we aim to add to previous evidence by investigating body mass index (BMI) alongside CT derived body composition metrics in the largest cohort to date. MethodPatients treated with first-line anti-PD1 {+/-} anti-CTLA4 for advanced melanoma were retrospectively identified from 11 melanoma reference centers in The Netherlands. Age, sex, Eastern Cooperative Oncology Group performance status, serum lactate dehydrogenase, presence of brain and liver metastases, number of affected organs and BMI at baseline were extracted from electronic patient files. From baseline CT scans, five body composition metrics were automatically extracted: skeletal muscle index, skeletal muscle density, skeletal muscle gauge, subcutaneous adipose tissue index and visceral adipose tissue index. All predictors were correlated in uni- and multivariable analysis to progression-free, overall and melanoma-specific survival (PFS, OS and MSS) using Cox proportional hazards models. ResultsA total of 1471 eligible patients were included. Median PFS and OS were 8.8 and 34.8 months, respectively. A significantly worse PFS was observed in underweight patients (multivariable HR=1.87, 95% CI 1.14-3.07). Furthermore, better OS was observed in patients with higher skeletal muscle density (multivariable HR=0.91, 95% CI 0.83-0.99) and gauge (multivariable HR=0.88, 95% CI 0.84-0.996), and a worse OS with higher visceral adipose tissue index (multivariable HR=1.13, 95% CI 1.04-1.22). No association with survival outcomes was found for overweightness or obesity and survival outcomes, or for subcutaneous adipose tissue. DiscussionOur findings suggest that underweight BMI is associated with worse PFS, whereas higher skeletal muscle density and lower visceral adipose tissue index were associated with better OS. These associations were independent of previously identified predictors, including sex, age, performance status and extent of disease. No significant association between higher BMI and survival outcomes was observed.

Colorectal cancer contributes to cancer-related deaths and health disparities in the Hispanic and Latino community. To probe both the biological and genetic bases of the disparities, we characterized features of colorectal cancer in terms of somatic alterations and genetic similarity. Specifically, we conducted a comprehensive genome-scale analysis of 67 Hispanic and Latino samples. We performed DNA exome sequencing for somatic mutations, somatic copy number alterations, and genetic similarity. We also performed RNA sequencing for differential gene expression, cellular pathways, and gene fusions. We analyzed all samples for 22 important CRC gene mutations, 8 gene amplifications, and 25 CRC gene fusions. Then, we compared our data from the Hispanic and Latino samples to publicly available, Non-Hispanic White (NHW) cohorts. According to our analyses, twenty-four percent of colorectal carcinomas were hypermutated when patients were of Peruvians-from-Lima-like (1KG-PEL-like) genetic similarity population from the 1000 genome project. Moreover, most of these cases occurred in patients who were less than fifty years old age at diagnosis. Excluding hypermutated tumors, approximately 55% of colon cancers and 58% of rectum cancers exhibited two similar features: 1) the patterns of genomic alterations; 2) percentage of 1KG-PEL-like. We analyzed all samples -- which had a median 1KG-PEL-like proportion of 55% -- for 22 important CRC gene mutations, 8 gene amplifications, and 25 CRC gene fusions. One notable example of a frequently observed gene mutation was SMAD4. Samples with SMAD4 alterations, which are known to support tumor growth and progression, had the highest 1KG-PEL-like proportion (63%). According to our results from risk association analyses and differential gene expression, SMAD4 alterations were significant when we compared Hispanic and Latino samples to NHW cohorts. Of the 8 drug-targetable amplifications, PIK3CA and PI3K exhibited an average 1KG-PEL-like of over 55%. Of the 25 relevant CRC gene fusions, targetable genes included ALK, FGFR1, RAF1, and PTPRK; PTPRK was observed in a sample with the highest 1KG-PEL-like proportion (95%). Using integrative analysis, we also detected recurrent alterations in the WNT, TGFB, TP53, IGF2/PI3K, and RTK/RAS pathways. Importantly, these alterations mostly occurred in young patients with high 1KG-PEL-like. These findings highlight the potential for tailoring precision medicine therapeutics to an underrepresented population. Our study advances the molecular profiling of CRC in Hispanics and Latinos. In toto, genetic similarity appears to be an important component in understanding colorectal carcinogenesis and has the potential to advance cancer health disparities research. SignificanceOur study provides molecular profiles of colorectal cancer in an underserved community, probes the impact of genetic similarity, and sheds light on cancer health disparities. This study provides a comprehensive, genome-scale analysis of colorectal cancers (CRCs) taken from 67 Hispanic and Latino patients. We performed DNA exome sequencing for somatic mutations, somatic copy number alterations, and genetic similarity. We also performed RNA sequencing for differential gene expression, cellular pathways, and gene fusions. Our data from the Hispanic and Latino samples was compared to publicly available, Non-Hispanic White cohorts. In general, colorectal carcinomas from our cohort presented a high proportion (55%) of Peruvians-from-Lima-like (1KG-PEL-like) population from the 1000 genome project. Moreover, hypermutated colorectal carcinomas (24% of cases) predominantly occurred in individuals with 1KG-PEL-like. Most hypermutated cases occurred in young (<50) patients. We assessed our cohort for 22 important CRC gene mutations, 8 gene amplifications, and 25 CRC gene fusions. We cross-referenced results with percentage of 1KG-PEL-like. For example, frequent mutations were observed in a tumor suppressor called SMAD4; samples with SMAD4 alterations had 63% 1KG-PEL-like. Of the 8 drug-targetable amplifications, PIK3CA and PI3K exhibited an average 1KG-PEL-like of over 55%. Of the 25 CRC gene fusions, targetable genes included ALK, FGFR1, RAF1, and PTPRK. PTPRK was observed in a sample with 95% 1KG-PEL-like proportion. Using integrative analysis, we also detected recurrent alterations in the WNT, TGFB, TP53, IGF2/PI3K, and RTK/RAS pathways. Our study thus advances the molecular profiling of CRC in Hispanics and Latinos; suggests precision medicine therapeutics can be tailored to an underrepresented community; and demonstrates genetic similarity can be an important component in understanding colorectal carcinogenesis.

PurposeTriple-negative breast cancer (TNBC) has a higher incidence, a younger age of onset, and a more aggressive behavior in African-ancestry women. Biological disparities have been suggested as an important factor influencing the ancestry-associated TNBC discrepancy. In this study, we sought to identify ancestry-associated differential gene and protein expression between African-ancestry and White TNBC patients, controlling for patients menopause status and pathological staging at diagnosis. MethodsDifferential gene expression analyses (DGEA) were performed using RNA-sequencing data from The Cancer Genome Atlas (TCGA). Gene set enrichment analysis (GSEA) and Ingenuity Pathway Analysis (IPA), with focus on network design, were performed to highlight candidate genes for further validation through immunohistochemistry of TNBC samples from patients followed in Portugal. ResultsWith 52 African-American and 90 White TNBC patients included, TCGAs data corroborate that African-American patients have a higher TNBC incidence (28.42% vs 11.89%, p<0.0001). Particularly, premenopausal and stage II disease African-American patients also have significantly lower survival probability, comparing with White patients (log-rank p=0.019 and 0.0038, respectively). DGEA results suggest that expression profile differences are more associated with TNBC staging than with patients menopause status. Hippo pathway and cellular community gene sets are downregulated, while breast cancer gene set is upregulated in African-Americans, comparing with White TNBC patients. Furthermore, MAPK pathway gene set is upregulated when controlling for stage II disease. Due to their central role in highly scored networks resulted from IPAs network design, EGFR, Myc and Bcl2 genes were selected for further validation through immunohistochemistry. We also included {beta}-Catenin in the validation study as it is consensually reported to be required in TNBC tumorigenesis. Although patients used in the DGEA and in the immunohistochemistry experiments are geographically and culturally distinct, both groups of African-ancestry patients are mostly of western-African ancestry and, interesting, differential gene and protein expression matched. ConclusionsWe found ancestry-associated gene expression patterns between African-ancestry and White TNBCs, particularly when controlling for menopause status or staging. EGFR, Myc, Bcl2 and {beta}-catenin gene and protein differential expression matching results in distinct populations suggest these markers as being important indicators of TNBCs ancestry-associated development.

Colorectal cancer (CRC) has increased at an alarming rate amongst younger (< 50 years) individuals. Such early-onset colorectal cancer (EOCRC) has been particularly notable within the Hispanic/Latino population. Yet, this population has not been sufficiently profiled in terms of two critical elements of CRC -- the MYC proto-oncogene and WNT signaling pathway. Here, we performed a comprehensive multi-omics analysis on 30 early-onset and 37 late-onset CRC ([&ge;] 50 years) samples from Hispanic/Latino patients. Our analysis included DNA exome sequencing for somatic mutations, somatic copy number alterations, and global and local genetic similarity. Using RNA sequencing, we also assessed differential gene expression, cellular pathways, and gene fusions. We then compared our findings from early-onset Hispanic/Latino patient samples with publicly available data from Non-Hispanic White cohorts. Across all early-onset patients, which had a median 1000 Genomes Project Peruvian-in-Lima-like (1KG-PEL-like) genetic similarity proportion of 60%, we identified 41 WNT pathway genes with significant mutations. Six important examples were APC, TCF7L2, DKK1, DKK2, FZD10, and LRP5. Notably, patients with mutations in DKK1 and DKK2 had the highest 1KG-PEL-like proportion (79%). When we compared the Hispanic/Latino cohort to the Non-Hispanic White cohorts, four of these key genes -- DKK1, DKK2, FZD10, and LRP5 -- were significant in both risk association analyses and differential gene expression. Interestingly, early-onset tumors (vs. late-onset) exhibited distinct somatic copy number alterations and gene expression profiles; the differences included MYC and drug-targetable WNT pathway genes. We also identified a novel WNT gene fusion, RSPO3, in early-onset tumors; it was associated with enhanced WNT signaling. This integrative analysis underscores the distinct molecular features of EOCRC cancer in the Hispanic/Latino population; reveals potential avenues for tailored precision medicine therapies; and emphasizes the importance of multi-omics approaches in studying colorectal carcinogenesis. We expect this data to help contribute towards reducing cancer health disparities. SignificanceThis study offers multi-omics profiling analysis of early-onset colorectal cancer (EOCRC) in an underserved community, explores the implications of MYC gene and WNT pathway alterations, and provides critical insights into cancer health disparities. ABSTRACT(short version)Colorectal cancer (CRC) has risen at an alarming rate in early-onset (<50 yrs) cases. Both its increased incidence and higher rates of mortality are especially pronounced within the Hispanic/Latino population. Although the MYC gene and WNT signaling pathway are well-established in CRC, we lack sufficient data about what role these elements play in young Hispanic/Latino patients. Here, we assess how both the MYC gene and WNT pathway are altered in Hispanic/Latino patients with early-onset CRC. We analyzed 30 early-onset and 37 late-onset CRC samples using multi-omics approaches, including DNA exome and RNA sequencing. The strategy allowed us to identify significant differences between early and late-onset tumors. Specifically, early-onset CRC had prevalent alterations in WNT pathway genes: APC, TCF7L2, DKK1, DKK2, and FZD10. Unique mutational profiles were linked to a high proportion of Peruvians-from-Lima-like (1KG-PEL-like) genetic similarity. These findings highlight the need for targeted precision medicine approaches to address the distinct molecular characteristics of early-onset CRC in underrepresented populations.

Osteosarcoma is a rare primary bone tumor for which no significant therapeutic advancement has been made since the late 1980s despite ongoing efforts. Overall, the five-year survival rate remains about 65%, and is much lower in patients with tumors unresponsive to methotrexate, doxorubicin, and cisplatin therapy. Genetic studies have not revealed actionable drug targets, but our group, and others, have reported that epigenomic biomarkers, including regulatory RNAs, may be useful prognostic tools for osteosarcoma. We tested if microRNA (miRNA) transcriptional patterns mark the transition from a chemotherapy sensitive to resistant tumor phenotype. Small RNA sequencing was performed using 14 patient matched pre-chemotherapy biopsy and post-chemotherapy resection high-grade osteosarcoma frozen tumor samples. Independently, small RNA sequencing was performed using 14 patient matched biopsy and resection samples from untreated tumors. Separately, miRNA specific Illumina DASL arrays were used to assay an independent cohort of 65 pre-chemotherapy biopsy and 26 patient matched post-chemotherapy resection formalin fixed paraffin embedded (FFPE) tumor samples. mRNA specific Illumina DASL arrays were used to profile 37 pre-chemotherapy biopsy and five post-chemotherapy resection FFPE samples, all of which were also used for Illumina DASL miRNA profiling. The National Cancer Institute Therapeutically Applicable Research to Generate Effective Treatments dataset, including PCR based miRNA profiling and RNA-seq data for 86 and 93 pre-chemotherapy tumor samples, respectively, was also used. Paired differential expression testing revealed a profile of 17 miRNAs with significantly different transcriptional levels following chemotherapy. Genes targeted by the miRNAs were differentially expressed following chemotherapy, suggesting the miRNAs may regulate transcriptional networks. Finally, an in vitro pharmacogenomic screen using miRNAs and their target transcripts predicted response to a set of candidate small molecule therapeutics which potentially reverse the chemotherapy resistance phenotype and synergize with chemotherapy in otherwise treatment resistant tumors. Importantly, these novel therapeutic targets are distinct from targets identified by a similar pharmacogenomic analysis of previously published prognostic miRNA profiles from pre chemotherapy biopsy specimens.

Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer defined by the lack of expression of estrogen receptor, progesterone receptors, and of the human epithelial growth factor receptor 2. Neoadjuvant chemotherapy has proven efficacy in the treatment of TNBC, and a pathological complete response (pCR) is predictive of improved long-term survival. The immune response exerts a vital role in response to neoadjuvant chemotherapy, as indicated by the relation between the percentage of stromal tumor-infiltrating lymphocytes (TILs) in pre-treated tumor tissue samples and the likelihood of achieving pCR. Despite this, the relationship between the systemic immune response and the tumor microenvironment is unclear. In this prospective study, we determined the systemic plasma immune profile of TNBC patients before treatment using a panel of 27 immune mediators and measured the percentage of TILs from the same patients. Patients who demonstrated pCR had significantly higher systemic immune mediators; GM-CSF, FGF-basic, VEGF, IL-2, and IL-5, than the non-responders. Moreover, responders displayed a strong positive correlation between the cytokines IFN-{gamma} and IL-7 with the percentage of TILs, while non-responders had a negative or no correlation. Finally, systemic immune mediator levels before treatment predict pCR (AUC range 0.64 - 0.71), and the combination of immune mediators and TILs improved pCR prediction (AUC 0.71 - 0.82). In conclusion, increased systemic immune mediators reflect increased TILs percentage and act as potential predictive biomarkers of pCR for TNBC patients submitted to neoadjuvant chemotherapy.

BackgroundLung adenocarcinoma (LUAD) is the most common subtype of non-small cell lung cancer (NSCLC) and frequently affects non-smokers, especially women. It is characterized by a complex genetic profile and interactions with its microenvironment, which contribute to its aggressive and adaptable nature. Early symptoms are often subtle, leading to late diagnoses. Treatment approaches have advanced with targeted therapies and immunotherapy supplementing traditional chemotherapy and radiation. Despite these advancements, the prognosis remains variable, highlighting the need for continued research into new treatment strategies to improve outcomes. MethodIn this study, we employed Single-cell RNA Sequencing (scRNA-seq) to comprehensively analyze the impact of chemotherapy on lung adenocarcinoma at the individual cell level. By comparing before and after treatment samples, we assessed the differential expression of genes and pathways, revealing insights into how different cell types within the tumour respond to chemotherapy. This approach enabled us to pinpoint specific mechanisms of drug resistance and highlight potential therapeutic targets for overcoming these challenges. ResultsOur analysis uncovered substantial changes in gene expression between primary tumour cells and metastatic cells following chemotherapy. Notably, we observed that 45 pathways were shared between the top 50 upregulated pathways in the primary tumour and the top 50 downregulated pathways in the metastatic tumour post-chemotherapy. Conversely, there was no overlap between the top 50 downregulated pathways in the primary tumour and the top 50 upregulated pathways in the metastatic tumour after chemotherapy. This suggests that chemotherapy effectively downregulated the major upregulated pathways but did not upregulate the key downregulated pathways in metastatic tumours. ConclusionsIntegrating single-cell transcriptomics into LUAD research offers detailed insights into the tumours response to chemotherapy and its interaction with the immune system. This approach enhances our understanding of LUAD and aids in developing targeted and effective treatments. Based on our analysis, we hypothesize that combining chemotherapy with drugs designed to upregulate the downregulated pathways in primary tumour cells could significantly enhance treatment efficacy and improve patient outcomes.

Introduction Stark disparities in endometrial cancer (EC) risk and mortality exist between non-Hispanic Black and White women, with Black women experiencing higher incidence and worse survival. This disparity has been attributed to biological and socioeconomic factors, though how these factors interact to influence EC disparities remains unclear. This study modeled EC outcomes using race, area-level socioeconomic deprivation, clinical phenotypes, genetic ancestry, and molecular alterations. Methods We identified 281 cases of EC diagnosed from 2013-2023 in women who underwent clinical genomic sequencing as part of routine care across multiple Northwell Health sites. We estimated genetic ancestry, oncogenic alterations in 324 genes, microsatellite instability, and molecular classification. Geocoded patient addresses were used to derive the state-level Area Deprivation Index to estimate socioeconomic deprivation. Results African ancestry patients were enriched for high-grade disease (89% vs 64%), serous histology (57% vs 26%), and the TP53-mutant molecular classification (71% vs 51%) compared to European ancestry patients (p-value<0.05). Socioeconomic deprivation quintiles were associated with race, with more deprived quintiles enriched for Black patients (p-value<0.001). Both race and genetic ancestry, but not area-level deprivation, were independently associated with differences in progression-free survival. TP53 mutations were enriched in African ancestry patients, while KRAS, PTEN, and ARID1A mutations were enriched in European ancestry patients (q<0.10). Cox proportional hazards modeling, adjusting for these factors, showed that African ancestry patients had worse progression-free survival (HR 1.91, p-value<0.05). Conclusion Our findings indicate that EC disparities persist after adjusting for socioeconomic, clinical, and molecular factors, highlighting the need to further investigate additional drivers of disparity.

In the last decade, genetic analysis has aided lymphoma classification, alongside traditional phenotypic subdivision. Lymphomas exhibit sex differences in disease incidence and prevalence; therefore, scope existed to explore sex-specific genetic variation. Harnessing UK Biobank genetic data (185,000 females, 176,000 males), sex-specific genome-wide genetic variation significantly associated with lymphoma subtypes was determined in both autosomal and sex chromosome genes. Sex-specific genetic variation significantly associated with sex-related characteristics was also identified. Functional predictions for those genes containing significant (p<5x10-5) genetic variation was carried out via ViSEAGO. For each lymphoma subtype, approximately 10-12% of the genes containing significantly associated genetic variants were shared between the sexes, highlighting largely sex-specific profiles for lymphoma subtypes. Significantly associated X chromosome genetic variants were identified for Non-Hodgkins lymphoma (NHL) and Diffuse large B-cell lymphoma (DLBCL), such as variants within SYTL5 (in males) and PPP2R3B (in females); genes previously implicated in haematological malignancy biological processes. Additionally, in female NHL patients, a genetic variant mapped to ESR1, the gene coding for oestrogen receptor- was identified, adding to the body of evidence highlighting the relevance of oestrogen regulation for haematological malignancy subtypes. Indeed, up to 9.1% of overlap was observed between those genes containing significant genetic variation associated with specific lymphoma subtypes, and those significantly associated with oestrogen level determination. Gene ontology analysis further emphasised functional overlaps between lymphoma and oestrogen level determination in females, highlighting predicted involvement in epigenetic modification, gene expression, and signalling. This study revealed sex-specific genetic variation significantly associated with lymphoma, as well as hormone level determination, and revealed biological pathways potentially disrupted during lymphoma pathogenesis which are influenced by oestrogen. Exploring these pathways may advance our understanding of the sex-specificities of lymphoma, and may reveal therapeutic targets to advance patient care.

Lung adenocarcinoma (LUAD) has been observed to have significant sex differences in incidence, prognosis, and response to therapy. However, the molecular mechanisms responsible for these disparities have not been investigated extensively. Sample-specific gene regulatory network methods were used to analyze RNA sequencing data from non-cancerous human lung samples from The Genotype Tissue Expression Project (GTEx) and lung adenocarcinoma primary tumor samples from The Cancer Genome Atlas (TCGA); results were validated on independent data. We observe that genes associated with key biological pathways including cell proliferation, immune response and drug metabolism are differentially regulated between males and females in both healthy lung tissue, as well as in tumor, and that these regulatory differences are further perturbed by tobacco smoking. We also uncovered significant sex bias in transcription factor targeting patterns of clinically actionable oncogenes and tumor suppressor genes, including AKT2 and KRAS. Using differentially regulated genes between healthy and tumor samples in conjunction with a drug repurposing tool, we identified several small-molecule drugs that might have sex-biased efficacy as cancer therapeutics and further validated this observation using an independent cell line database. These findings underscore the importance of including sex as a biological variable and considering gene regulatory processes in developing strategies for disease prevention and management.

BackgroundHigh-grade serous ovarian cancer (HGSOC) is a highly lethal gynecologic cancer, in part due to resistance to platinum-based chemotherapy reported among 20% of patients. This study aims to elucidate the biological mechanisms underlying chemotherapy resistance, which remain poorly understood. MethodsSequencing data (mRNA and microRNA) from HGSOC patients were analyzed to identify differentially expressed genes and co-expressed transcript networks associated with chemotherapy response. Initial analyses used datasets from The Cancer Genome Atlas and then replicated in two independent cancer cohorts. Moreover, transcript expression datasets and genomics data (i.e. single nucleotide polymorphisms) were integrated to determine potential regulation of the associated mRNA networks by microRNAs and expression quantitative trait loci (eQTLs). ResultsIn total, 196 differentially expressed mRNAs were enriched for adaptive immunity and translation, and 21 differentially expressed microRNAs were associated with angiogenesis. Moreover, co-expression network analysis identified two mRNA networks associated with chemotherapy response, which were enriched for ubiquitination and lipid metabolism, as well as three associated microRNA networks enriched for lipoprotein transport and oncogenic pathways. In addition, integrative analyses revealed potential regulation of the mRNA networks by the associated microRNAs and eQTLs. ConclusionWe report novel transcriptional networks and pathways associated with resistance to platinum-based chemotherapy among HGSOC patients. These results aid our understanding of the effector networks and regulators of chemotherapy response, which will improve drug efficacy and identify novel therapeutic targets for ovarian cancer.

Examining LncRNA-driven cancer biology, our study represents the first comprehensive investigation of the LncRNA CDKN2B-AS1 across multiple cancer types, revealing its genetic basis for cancer susceptibility, and associations with thromboembolic risks and immunological dynamics. Stratification across hematological and non-hematological cancers revealed predominant prevalence rates of the CDKN2B-AS1 C-allele, notably higher in solid tumor malignancies, peaking at 86.8% in colorectal carcinoma (CRC). CRC-C-carriers exhibited worse outcomes, marked by reduced overall survival, increased venous-thromboembolism, elevated frequencies of thromboembolic-associated gene polymorphisms and BRAF mutations, and decreased MSI-H. Key tumor progression aspects in CRC-C-carriers included an inflammatory profile (reduced Th2 and increased Th1/Th17 cells), angiogenesis and endothelial activity (elevated CD14+, CD31+, CD144+, and VEGFR2+ cells), decreases in tumor suppressor-CD146+ cells (elevated tissue-adherent TA-EPCs lacking CD146), and marked elevation in tumor activity markers (Ki-67, CEA, CA 19-9, EGFR, VEGF-A, PD-1, and CTLA-4). Palbociclib significantly improved progression-free survival relative to baseline, primarily through suppression of tumor cell proliferation, with a more pronounced clinical and biomarker response observed in CDKN2B-AS1 non-C-allele carriers, whereas C-allele carriers exhibited an attenuated response consistent with relative treatment resistance. This underscores the multifaceted role of LncRNA CDKN2B-AS1, presenting it not just as a genetic determinant but also as a potential prognostic biomarker in cancer dynamics, paving the way for targeted personalized interventions, representing promising advancements in cancer therapeutics.