Haplotype-resolved germline and somatic alterations in renal medullary carcinomas

BACKGROUND

Renal medullary carcinomas (RMCs) are rare kidney cancers that occur in adolescents and young adults of African ancestry. Although RMC is associated with the sickle cell trait and somatic loss of the tumor suppressor, SMARCB1, the ancestral origins of RMC remain unknown. Further, characterization of structural variants (SVs) involving SMARCB1 in RMC remains limited.

METHODS

We used linked-read genome sequencing to reconstruct germline and somatic haplotypes in 15 unrelated patients with RMC registered on the Children's Oncology Group (COG) AREN03B2 study between 2006 and 2017 or from our prior study. We performed fine-mapping of the HBB locus and assessed the germline for cancer predisposition genes. Subsequently, we assessed the tumor samples for mutations outside of SMARCB1 and integrated RNA sequencing to interrogate the structural variants at the SMARCB1 locus.

RESULTS

We find that the haplotype of the sickle cell mutation in patients with RMC originated from three geographical regions in Africa. In addition, fine-mapping of the HBB locus identified the sickle cell mutation as the sole candidate variant. We further identify that the SMARCB1 structural variants are characterized by blunt or 1-bp homology events.

CONCLUSIONS

Our findings suggest that RMC does not arise from a single founder population and that the HbS allele is a strong candidate germline allele which confers risk for RMC. Furthermore, we find that the SVs that disrupt SMARCB1 function are likely repaired by non-homologous end-joining. These findings highlight how haplotype-based analyses using linked-read genome sequencing can be applied to identify potential risk variants in small and rare disease cohorts and provide nucleotide resolution to structural variants.

Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ

RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here, we present a new method, Smart-3SEQ, that accurately quantifies transcript abundance even with small amounts of total RNA and effectively characterizes small samples extracted by laser-capture microdissection (LCM) from FFPE tissue. We also obtain distinct biological profiles from FFPE single cells, which have been impossible to study with previous RNA-seq protocols, and we use these data to identify possible new macrophage phenotypes associated with the tumor microenvironment. We propose Smart-3SEQ as a highly cost-effective method to enable large gene expression profiling experiments unconstrained by sample size and tissue availability. In particular, Smart-3SEQ's compatibility with FFPE tissue unlocks an enormous number of archived clinical samples; combined with LCM it allows unprecedented studies of small cell populations and single cells isolated by their in situ context.

Perspectives of women participating in a cervical cancer screening campaign with community-based HPV self-sampling in rural western Kenya: a qualitative study

BACKGROUND

Despite cervical cancer being preventable with effective screening programs, it is the most common cancer and the leading cause of cancer-related death among women in many countries in Africa. Screening involving pelvic examination may not be feasible or acceptable in limited-resource settings. We sought to evaluate women's perspectives on human papillomavirus (HPV) self-sampling as part of a larger trial on cervical cancer prevention implementation strategies in rural western Kenya.

METHODS

We invited 120 women participating in a cluster randomized trial of cervical cancer screening implementation strategies in Migori County, Kenya for in-depth interviews. We explored reasons for testing, experience with and ability to complete HPV self-sampling, importance of clinician involvement during screening, factors and people contributing to screening decision-making, and ways to encourage other women to come for screening. We used validated theoretical frameworks to analyze the qualitative data.

RESULTS

Women reported having positive experiences with the HPV self-sampling strategy. The factors facilitating uptake included knowledge and beliefs such as prior awareness of HPV, personal perception of cervical cancer risk, desire for improved health outcomes, and peer and partner encouragement. Logistical and screening facilitators included confidence in the ability to complete HPV self-sampling strategy, proximity to screening sites and feelings of privacy and comfort conducting the HPV self- sampling. The barriers to screening included fear of need for a pelvic exam, fear of disease and death associated with cervical cancer. We classified these findings as capabilities, opportunities and motivations for health behavior using the COM-B framework.

CONCLUSIONS

Overall, HPV self-sampling was an acceptable cervical cancer screening strategy that seemed to meet the needs of the women in this community. These findings will further inform aspects of implementation, including outreach messaging, health education, screening sites and emphasis on availability and effectiveness of preventative treatment for women who screen positive.