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The frequency of pathogenic/likely pathogenic (P/LP) germ line variants in patients with myelodysplastic syndrome (MDS) diagnosed at age 40 years or less is 15% to 20%. However, there are no comprehensive studies assessing the frequency of such variants across the age spectrum. We performed augmented whole-exome sequencing of peripheral blood samples from 404 patients with MDS and their related donors before allogeneic hematopoietic stem cell transplantation. Single-nucleotide and copy number variants in 233 genes were analyzed and interpreted. Germ line status was established by the presence of a variant in the patient and related donor or for those seen previously only as germ line alleles. We identified P/LP germ line variants in 28 of 404 patients with MDS (7%), present within all age deciles. Patients with P/LP variants were more likely to develop higher-grade MDS than those without (43% vs 25%; P = .04). There was no statistically significant difference in outcome parameters between patients with and without a germ line variant, but the analysis was underpowered. P/LP variants in bone marrow failure syndrome genes were found in 5 patients aged less than 40 years, whereas variants in DDX41 (n = 4), telomere biology disorder genes (n = 2), and general tumor predisposition genes (n = 17) were found in patients aged more than 40 years. If presumed germ line variants were included, the yield of P/LP variants would increase to 11%, and by adding suspicious variants of unknown significance, it would rise further to 12%. The high frequency of P/LP germ line variants in our study supports comprehensive germ line genetic testing for all patients with MDS regardless of their age at diagnosis.

Oral cavity squamous cell carcinoma (OCSCC) is a devastating disease, causing substantial morbidity and mortality. While many OCSCCs arise from an existing dysplastic lesion, not all oral premalignant lesions progress to OCSCC. Current methods for oral premalignancy and OCSCC diagnosis (visual and tactile exam followed by tissue biopsy and histologic evaluation) cannot discriminate between benign inflammatory changes and high-risk premalignant lesions that require interventions, underscoring the need for molecular-based biomarkers. The multi-step cancer progression from normal epithelium to premalignant lesion and invasive SCC is driven by the accumulation of genetic alterations, including changes in mitochondrial DNA (mtDNA). Due to the lack of protective histones and limited repair mechanisms, mtDNA is susceptible to damage by environmental carcinogens and reactive oxygen species, a byproduct of the oxidative phosphorylation system. As a result, mutation rate in mtDNA is ~10 times higher than in nuclear DNA, and may greatly facilitate the risk of mitochondrial dysfunction. Previous studies underscore that acquisition of somatic mtDNA mutations directly involved in tumorigenesis, and not merely epiphenomena. However, the impact of these studies is limited by an incomplete understanding of mitochondrial genomic alterations in the transition of preneoplastic lesions to invasive disease. In this study we used a unique cohort of 27 patients with matched longitudinally collected samples (histologically normal mucosa, dysplastic lesion, and SCC) coupled with novel ultra-deep mitochondrial sequencing (mtDNA-Seq) method to assess the mtDNA mutational landscape throughout the continuum of OCSCC progression. Using a custom bioinformatics workflow, somatic mutations were detected in a subset of the premalignant lesions, with overall higher mutational load observed in OCSCC specimens. While sequencing revealed a large degree of inter-patient heterogeneity, a panel of non-synonymous aberrations were present in both premalignant and invasive neoplasms. The majority of shared mutations showed an increase in fractional abundance in tumors, compared to the precursor lesions (suggesting a spatial expansion of these clones as they progressed histologically), and were enriched for coding mutations in complex-I subunits (critical region for ATP production), which is associated with an oncogenic phenotype. Additionally, mtDNA content increased in OCSCC tumor in a subset of patients, suggesting a cell compensation for defective oxidative phosphorylation and lower ATP production per mitochondria. Here we report the first comprehensive characterization of mitochondrial mutational landscape in dysplastic and invasive SCC lesions, and reveal key molecular events associated with the transition from non-invasive to invasive state. Citation Format: Alka Singh, Ashwin Lakshman Koppayi, Ping Wu, Mark Lingen, Vasudha Mishra, Alexander Pearson, Ari Rosenberg, Nishant Agrawal, Karthik Suresh, Evgeny Izumchenko. Ultra-deep sequencing of mitochondrial genome to explore the dynamic mutational changes associated with oral cavity squamous cell carcinoma progression. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4845.

Human ovarian follicle development is a complex process of the female reproductive system. The functional unit of the ovary i.e., follicle, consist of female germ cell, Oocyte, at the center and somatic cells like Granulosa and Theca cells surrounding the oocyte. These different cell types interact with each other through intracellular and intercellular metabolic communication to produce a mature oocyte for fertilization. Development competence of the oocyte that can render a successful pregnancy depends on the accumulation of the required metabolites and other materials (e.g., proteins, transcripts) essential for later stages, such as fertilization and subsequent embryo pre-implantation. Understanding the complex dynamic and bi-directional communication between the oocyte and granulosa cells to achieve a competent oocyte will help us improve the in-vitro maturation of oocyte that has lesser side effects and cost effective compared to in-vitro fertilization because synthetic hormone is not required for hyperstimulation of ovary. Genome-wide metabolic model of the human ovarian follicle was generated by overlaying human single-cell transcriptomic data from different stages of follicle development to the latest genome-scale human metabolic model (Recon3D) using FASTCORE. Analysis of previously published single cell RNA sequencing data revealed that there were 18,741 actively transcribed genes in the oocyte samples and 17,092 actively transcribed genes in granulosa samples at the different stages of follicle development. Using an unsupervised method, we identified five different clusters that were indeed associated with the different follicular stages (i.e., primordial, primary, secondary, antral, and pre-ovulatory) and cell-type (oocyte and granulosa cells). The Follicle metabolic model contains 10,538 reactions, 3,484 metabolites and 2,954 genes that encode enzymes. As expected, the follicle metabolic model included several key follicle metabolic pathways during follicle development in vivo (such as, pyruvate metabolism, steroid metabolism, androgen and estrogen synthesis and metabolism). In summary, we have developed a human follicle metabolic model for the first time that could help to better understand the biology of human ovarian follicle development and thus serve to develop novel treatments for reproductive diseases in the future, such as polycystic ovarian syndrome (PCOS), endometriosis, or improve in vitro maturation culture system.