Sidharth V. Puram

Oct 30, 2024 | nature.com | Reyka G. Jayasinghe |Michael Iglesia |John Herndon |Austin N. Southard-Smith |Jacqueline L. Mudd |Alla Karpova | +16 more

AbstractTo study the spatial interactions among cancer and non-cancer cells1, we here examined a cohort of 131 tumour sections from 78 cases across 6 cancer types by Visium spatial transcriptomics (ST). This was combined with 48 matched single-nucleus RNA sequencing samples and 22 matched co-detection by indexing (CODEX) samples. To describe tumour structures and habitats, we defined ‘tumour microregions’ as spatially distinct cancer cell clusters separated by stromal components.

Feb 27, 2024 | onlinelibrary.wiley.com | Jake Lee |Patrik Pipkorn |Sidharth V. Puram |Nicholas A. Rapoport

1 INTRODUCTION Base of tongue (BOT) malignancies pose a challenge to head and neck surgeons. The American Cancer Society estimates 17 860 new BOT cases and 2790 deaths in 2022 alone.1 Largely due to the high burden of human papillomavirus (HPV),2, 3 the incidence continues to rise.

Jan 12, 2024 | nature.com | Thomas Barrett |Bhuvic Patel |Saad Khan |Sangami Pugazenthi |Allegra Petti |Sidharth V. Puram

AbstractVestibular schwannomas (VS) are benign tumors that lead to significant neurologic and otologic morbidity. How VS heterogeneity and the tumor microenvironment (TME) contribute to VS pathogenesis remains poorly understood. In this study, we perform scRNA-seq on 15 VS, with paired scATAC-seq (n = 6) and exome sequencing (n = 12).

Nov 1, 2023 | nature.com | Alla Karpova |Yize Li |Austin N. Southard-Smith |Michael Iglesia |Reyka G. Jayasinghe |Matthew Wyczalkowski | +17 more

AbstractChromatin accessibility is essential in regulating gene expression and cellular identity, and alterations in accessibility have been implicated in driving cancer initiation, progression and metastasis1,2,3,4. Although the genetic contributions to oncogenic transitions have been investigated, epigenetic drivers remain less understood.

May 31, 2023 | nature.com | Michael Tyler |Rouven Hoefflin |Roi Tschernichovsky |Thomas Barrett |Michael Mints |Avishay Spitzer | +2 more

AbstractEach tumour contains diverse cellular states that underlie intratumour heterogeneity (ITH), a central challenge of cancer therapeutics1. Dozens of recent studies have begun to describe ITH by single-cell RNA sequencing, but each study typically profiled only a small number of tumours and provided a narrow view of transcriptional ITH2.