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Suva Lab

@suvalab.bsky.social
905 followers 97 following 2 posts

Brain cancer, single cell and spatial genomics. Mass General. Broad Institute. Harvard Medical School.

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alissa greenwald @alissacg.bsky.social · 15/09/2026
Thank you to Daniel Silver, Chang Xu, and Justin Lathia for the beautiful companion perspective piece: www.cell.com/cancer-cell/...
cell.com
Scherer’s map, remapped
Scherer’s century-old classification of expansive and infiltrative glioma growth remains foundational to neuro-oncology. In this issue of Cancer Cell, Hoefflin et al. use spatial RNA and protein profi...
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alissa greenwald @alissacg.bsky.social · 15/09/2026
Out in @cp-cancercell.bsky.social our work w/ Rouven Hoefflin, @itaytirosh.bsky.social, @suvalab.bsky.social, Noam Galili, & Christopher Mount quantitatively maps two independent axes of tumour organization, revealing how they emerge at different stages of progression & in distinct tissue contexts.
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alissa greenwald @alissacg.bsky.social · 15/09/2026
IDH-mutant gliomas often progress slowly, but inevitably recur and progress. Are there spatial organizing principles at the level of cell states that repeat across tumours during stages of tumour progression? www.cell.com/cancer-cell/...
cell.com
Spatial analysis reveals the evolving organization of IDH-mutant glioma
Hoefflin et al. define organizational principles of IDH-mutant gliomas using multimodal spatial profiling. They identify three spatial archetypes across histological grades and reveal that brain anato...
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Masashi Nomura @masashi-nomura.bsky.social · 22/06/2026
10/12 Our study connects DNA methylation loss to alterations in glioma cell states encoding and heritability, and suggests that DNA methylation loss may mark tumors with more aggressive clinical course in IDH-munant gliomas.
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Masashi Nomura @masashi-nomura.bsky.social · 22/06/2026
8/12 Leveraging unique expertise of the Landau Lab, we reconstructed high-resolution phylogenetic trees from DNAme data to trace the evolutionary relationships among tumor cells and ask a fundamental question in cancer biology: how does cell state dynamics change over the course of tumor evolution?
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Masashi Nomura @masashi-nomura.bsky.social · 22/06/2026
7/12 Unlike previous bulk studies that compared G-CIMP-high and G-CIMP-low tumors, our single-cell approach enabled direct comparisons between G-CIMP-high cells and G-CIMP-low cells, revealing potential mechanisms underlying the acquisition of stem-like states.
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Masashi Nomura @masashi-nomura.bsky.social · 22/06/2026
6/12 These findings suggest that G-CIMP loss is not merely a consequence of the expansion of stem-like cells, but rather that the reduction in DNA methylation may underlie the acquisition of stem-like states.
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Masashi Nomura @masashi-nomura.bsky.social · 22/06/2026
5/12 Notably, the intratumoral variance in G-CIMP DNA methylation level was relatively low, revealing that DNA methylation loss occurs uniformly across tumor cells rather than within a distinct subpopulation—an insight uniquely enabled by single-cell analysis.
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Masashi Nomura @masashi-nomura.bsky.social · 22/06/2026
4/12 Longitudinal single-cell methylation data demonstrated that G-CIMP methylation level progressively decreased over time in malignant cells. In pararell, single-cell transcriptomic analyses revealed an increase in the stem-like state during malignant progression.
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Masashi Nomura @masashi-nomura.bsky.social · 22/06/2026
3/12 We collected 36 primary and matched recurrent IDH-G samples from 19 patients and profiled them using our unique single-cell multiomics platform, which simultaneously captures DNA methylation and transcriptomic information from individual cells.
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Masashi Nomura @masashi-nomura.bsky.social · 22/06/2026
2/12 IDH-G are generally characterized by a hypermethylated phenotype (G-CIMP-high). However, as these tumors undergo malignant progression over time, they gradually lose DNA methylation (G-CIMP-low). This study provides the first single-cell characterization of this phenomenon.
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Masashi Nomura @masashi-nomura.bsky.social · 22/06/2026
11/12 I am deeply grateful to my great mentor, @suvalab.bsky.social. A big thank you to my co-mentor, @landau.bsky.social, and co-first authors, Ramya Raviram and Joshua S. Schiffman.
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Masashi Nomura @masashi-nomura.bsky.social · 22/06/2026
1/12 Excited to share that our new paper on IDH-mutant glioma (IDH-G) is now out in Nature Genetics! This work was a fantastic collaborativ effort of laboratories of @suvalab.bsky.social and @landau.bsky.social, co-lead by Ramya Raviram and Joshua S. Schiffman. www.nature.com/articles/s41...
nature.com
Longitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation - Nature Genetics
The authors use single-cell multi-omics to interrogate longitudinal samples of isocitrate dehydrogenase mutant gliomas. Their analyses couple progression and hypomethylation with changes in differenti...
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
15/ This of course wouldn't have been possible without the generous contribution of the patients and their families, for which we are ever thankful.
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
14/ Big thanks also to the institutions that provided tumor samples @dukepress.bsky.social, @mdanderson.bsky.social, Tokyo University Hospital, Pitié-Salpêtrière Hospital, St. Michael's Hospital, Seoul National University and NORLUX and funders NIH, NCI, Mark Foundation and Sontag Foundation.
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
13/ @weizmanninstitute.bsky.social, Mass General Brigham (Cancer Center, Pathology), @broadinstitute.org, @yalepress.bsky.social and University of Miami.
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
12/ Big thanks to the PIs that supervised the project @itaytirosh.bsky.social, @suvalab.bsky.social, @roelverhaak.bsky.social, Antonio Iavarone and Anna Lasorella, all collaborators and institutions involved in the CARE consortium >
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
11/ To sum-up, our multi-center study offers a high-resolution atlas of GBM recurrence dynamics, shaped by treatment response and TME context and underscores the tremendous heterogeneity of this devastating disease.
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
10/ Overall genetic divergence (SNVs + CNAs) correlated with transcriptional evolution, suggesting that GBM cell state shifts during recurrence are at least partially genomically driven.
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
9/ Small deletion phenotype (linked to radiotherapy) was associated with hypoxia-related states at recurrence, likely reflecting selection of radioresistant subpopulations. SBS21 (MMR-deficiency signature) also increased post-treatment in both CARE and GLASS cohorts.
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
8/ Interestingly, quantifying MGMT activity from the single-cell expression data outperformed promoter methylation as a prognostic marker in this cohort.
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
7/ However, in certain sub-groups, specific trajectories do tend to recur more often. First, MGMT-Low tumors (likely TMZ responders) tend to lose MES-like states whereas MGMT-High tumors (likely non-responders) tend to gain MES-like at recurrence.
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
6/ Despite global conservation, individual matched tumor pairs showed frequent divergence, with the majority switching at least one transcriptional layer. Overall, 72% of all possible transitions were observed across the cohort.
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
5/ Contrary to previous studies, we did not observe a significant enrichment of mesenchymal-like (MES-like) states at recurrence. Instead, recurrence trajectories were diverse and patient-specific, with no single state dominating across the cohort.
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
4/ And now for the results! Across the cohort the most consistent change at recurrence was reduced malignant cell fraction, with a reciprocal increase in glial and neuronal TME cells. This was observed in ~66% of patients, suggesting increased tumor integration into brain tissue.
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
3/ We first leveraged this large cohort to revisit the intra- and inter-tumor heterogeneity in GBM and characterized three multi-layered transcriptional ecosystems. Read more about this study in this great thread by @masashi-nomura.bsky.social → bsky.app/profile/masa...
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
2/ In this study we profiled the longitudinal evolution of glioblastoma at single-cell resolution - altogether 121 treatment-naïve and exposed tumors from 59 patients, 430K nuclei, full clinical annotation and whole exome/genome sequencing.
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Avishay Spitzer, MD, PhD @avishayspitzer.bsky.social · 10/05/2025
1/ Truly excited to share our new study that I had to privilege to co-lead during my PhD alongside great friends and collaborators @masashi-nomura.bsky.social, @kevin-johnson.bsky.social and Luciano Garofano, published at Nature Genetics @natureportfolio.nature.com! www.nature.com/articles/s41...
nature.com
Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics - Nature Genetics
Comparison of paired primary and recurrent glioblastomas at the single-cell transcriptomic level describes molecular and cellular trajectories associated with tumor recurrence, highlighting extensive ...
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Masashi Nomura @masashi-nomura.bsky.social · 09/05/2025
I thank my great mentor/boss @suvalab.bsky.social and outstanding co-PIs @itaytirosh.bsky.social, @roelverhaak.bsky.social, Antonio Iavarone and Anna Lasorella. Also appreciate all collaborators, patients and their families who generously provided the samples.
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Masashi Nomura @masashi-nomura.bsky.social · 09/05/2025
12/ Before that, I would like to say thank wonderful co-first authors/friends, @avishayspitzer.bsky.social, @kevin-johnson.bsky.social and Luciano Garofano.
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Masashi Nomura @masashi-nomura.bsky.social · 09/05/2025
11/ How this architecture evolves during progression from primary to recurrent GBM is addressed in the second paper, that will be introduced by @avishayspitzer.bsky.social in the following threads later.
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Masashi Nomura @masashi-nomura.bsky.social · 09/05/2025
10/ These three layers of heterogeneity are inter-related and partially associated with specific genetic aberrations, thereby defining three stereotypic ecosystems in GBM. This work provides an unparalleled view of the multi-layered transcriptional architecture of GBM.
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Masashi Nomura @masashi-nomura.bsky.social · 09/05/2025
9/ Third, after controlling for the frequencies of cellular states, we find that the remaining variation between GBM samples highlights three baseline gene expression programs which we labeled Neuronal, Glial, and Extracellular Matrix.
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Masashi Nomura @masashi-nomura.bsky.social · 09/05/2025
8/ Second, we describe the diversity of cellular states and their pathway-based functional activities, with an expanded set of malignant cell states, including glial progenitor cell-like, neuronal-like, and cilia-like states that were previously depleted by tumor dissociation
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Masashi Nomura @masashi-nomura.bsky.social · 09/05/2025
7/ First, GBMs can be classified by their broad cellular composition, encompassing malignant, immune, vascular, neuronal, and glial cell types.
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Masashi Nomura @masashi-nomura.bsky.social · 09/05/2025
6/ In the first paper, we intensively analyzed GBM cellular heterogeneity, irrespective of time points. Our analyses reveled three transcriptomic layers that contribute to GBM heterogeneity.
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Masashi Nomura @masashi-nomura.bsky.social · 09/05/2025
4/ We thank @mdanderson.bsky.social, @dukecancer.bsky.social, @uoft.bsky.social, @pitiesalpetriere.bsky.social, NORLUX Neuro-Oncology laboratory, Seoul National University and @utokyoofficial.bsky.social for providing precious primary and recurrent GBM cohorts.
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Masashi Nomura @masashi-nomura.bsky.social · 09/05/2025
3/ In these studies, we collected 121 longitudinal GBM samples from 6 countries under GBM CARE (Cellular Analysis of Resistance and Evolution) consortium, and profiled them by single-nucleus RNA-seq (total 420 k cells).
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Masashi Nomura @masashi-nomura.bsky.social · 09/05/2025
2/These are the fantastic collaborative effort between Suva, Tirosh, Verhaak and Iavarone/Lasorella labs. We appreciate all supports from Mass General Brigham (Cancer Center, Pathology), @broadinstitute.org, Weizmann Institute of Science, @yalepress.bsky.social and University of Miami.
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Masashi Nomura @masashi-nomura.bsky.social · 09/05/2025
1/ Thrilled to share our TWO back-to-back papers published in Nature Genetics today! www.nature.com/articles/s41... , www.nature.com/articles/s41...
nature.com
The multilayered transcriptional architecture of glioblastoma ecosystems - Nature Genetics
Integrated single-cell transcriptomic and genetic characterization of 121 adult glioblastomas identifies heterogeneity at cell type, cell state and baseline expression program levels associated with s...
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American Association for Cancer Research (AACR) @theaacr.bsky.social · 06/05/2025
Today, the American Association for Cancer Research (AACR) called on Congress to reject the Administration's nearly 40% cut to the NIH budget and allocate a bipartisan funding increase to $51.3 billion for the agency to accelerate progress for patients. www.aacr.org/about-the-aa...
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rantao2023.bsky.social @rantao2023.bsky.social · 07/01/2025
Thrilled to share our recent work published in @naturegenet.bsky.social, where we uncover how ZIC1 is regulated by distinct genetic and epigenetic mechanisms in SHH vs. Group 4 medulloblastoma—revealing it as a context-dependent driver. tinyurl.com/2c3jnhn2
tinyurl.com
ZIC1 is a context-dependent medulloblastoma driver in the rhombic lip - Nature Genetics
Analysis of medulloblastomas in humans and mice shows that the functional consequences of ZIC1 mutations are exquisitely dependent on the cells of origin that give rise to different subgroups of medul...
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Itai Yanai @itaiyanai.bsky.social · 24/12/2024
You can plan ahead all of the different aspects of the project, except for the bits of discovery that will make it actually worthwhile.
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Christian Frezza @frezzalab.bsky.social · 21/11/2024
Like ‘old Twitter’: The scientific community finds a new home on Bluesky another incredible piece of news! www.science.org/content/arti...
science.org
Like ‘old Twitter’: The scientific community finds a new home on Bluesky
After recent changes to Elon Musk’s X, a gradual migration turns into a stampede
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Timothy Caulfield @caulfieldtim.bsky.social · 21/11/2024
Bluesky is the new destination for X/Twitter’s health and science community. Here’s why statnews.com/2024/11/21/b... via @statnews.bsky.social
statnews.com
Bluesky is the new destination for X/Twitter’s health and science community. Here's why
#MedTwitter is migrating en masse from X to Bluesky, suddenly making it an essential hub for scientific discourse. Here's why.
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