Susan Bullman

Our work with the @CJohnstonLab1 lab out today @Nature demonstrating the intratumoral microbiota impacts spatial, cellular and transcriptional heterogeneity in human cancer. Monster tweetorial below from Chris.

New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing Have you heard about #cancer microbiome or #intratumor microbiome? Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very​ low-microbe tissue samples, how much of the microbial signal is real ❓ and how much is background noise from the lab or the environment ❓ We tackle this with a simple idea: look at DNA fragment sizes using #longread sequencing. If microbes are truly present as intact cells, their DNA should show up as long, genome-like fragment distributions, not mostly short broken (degraded) pieces. Long-read data lets us distinguish those two cases! To make this more robust across datasets, we developed a #metric that normalizes microbial DNA fragment lengths to human DNA fragment lengths within the same sample. Negative #controls: germ-free mice and human cell culture datasets, where true resident microbes are not expected and any microbial signal is most likely introduced during workflows (i.e. contaminations). Positive #controls: bacteria spike-in, and importantly, GI tumors with well established bacteria: e.g. #Helicobacter #pylori in #gastric cancer, #Fusobacterium in #colorectal cancer. Across multiple tumor types and tissues (public + new data), we find that long microbial reads are mainly seen in tissues with natural microbial exposure (such as #gut, #stomach, #skin, #vagina and #cervix, etc). Outside those settings, most microbial signals look more like fragmented, and the occasional long fragments often match well-known #contaminant organisms. One finding that stood out to us was the #lung, which is constantly exposed to microbes we breathe in, yet in our analysis, the microbial signal appeared mostly as short, fragmented DNA, which is more consistent with transient exposure and rapid clearance than with stable resident microbes in deep lung tissue. The new metric also helps #unify earlier debates about microbiomes reported in #placenta and #blood. When we reanalyzed long-read data from those settings using the same read length-based approach, we found no evidence for a stable resident microbiome under normal conditions, consistent with the current consensus that most signals reflect background contamination, with true positives mainly expected during active infection. Long story short, but this was a 4+ years effort led by Yanchun Zhang and Andy Mead. Grateful to all collaborators who contributed valuable samples and feedback: Mi Ni, @MagdalenaKsi, @clannabel7, @LauraZuluagaJim, Gintaras Deikus, Robert Sebra, Rachel Brody, Raymund Yong, @NYCRoboticTeam, @Xue_Song__Zhang. @SinaiGenetics @IcahnInstitute Link: biorxiv.org/content/10.648… We’d love your thoughts! #longread @PacBio @nanopore #metagenomics #pacbio #nanopore

We’re excited to announce that Anirban Maitra, MD (@Aiims1742)—a pre-eminent physician-scientist whose work has widely influenced the field of pancreatic cancer research—has been appointed the new director of @Perlmutter_CC here at NYU Langone. For more: bit.ly/4t2xDD2

Christopher Johnston (@CJohnstonLab1) is engineering human-derived bacteria to act as "cellular therapies," infiltrating solid tumors to deliver medicine directly into the most treatment-resistant environments. 🧫 @MDAndersonNews

New from the Bullman Lab in Cancer Cell! Tumor-infiltrating bacteria, including Fusobacterium, disrupt cell-cell contacts & trigger quiescence, uncovering a pathway of bacteria-induced therapy resistance 🔗 cell.com/cancer-cell/fu… Thanks to @MDAndersonNews, @FredHutch, @UTEPnews

These findings add to the increasing evidence that cancer is not driven solely by DNA mutations. 🧵

I’m happy to share our latest work on tumour necrosis! During my time in the @megeblad lab, we found that tumour necrosis is not a passive phenomenon secondary to tumour growth, but an active phenomenon driven by neutrophils and NETs! Thread below: (1/13) nature.com/articles/s4158…

Absolutely insane amount of data in this resource from @mason_lab The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs biorxiv.org/content/10.110… Spatial data on 15million cells from 100 donors across multiple ages, mainly GI

Stromal lipid species dictate melanoma metastasis and tropism dlvr.it/TLK2RT

Spatial Total RNA Sequencing of Formalin-Fixed Paraffin Embedded Tissues by spRandom-seq biorxiv.org/content/10.110…

Our team is hiring! 🦠 🧫 🥼🧑‍🔧 jobs.mdanderson.org/search/jobdeta…

What exactly does "Fusobacterium nucleatum" refer to? It depends who you ask (and when you asked them). Our new perspective on taxonomy and naming challenges @GutMicrobes, proposing a genomics-based framework for Fusobacterium species designations. 🦠 tandfonline.com/doi/full/10.10…

If your stack of images is full of defects, don't panic! InterpolaAI, a deep learning-based optical flow method, will fix issue tears, photobleaching and sticking artifacts for improved 3D imaging. Read our paper in Nature Methods: nature.com/articles/s4159…

Second paper on HMGA2 mediated basal identity in #PancreaticCancer from Sita Kugel @fredhutch. This one is an elegant mechanistic dissection of the multi step cascade through which HMGA2 overexpression orchestrates basal lineage state: nature.com/articles/s4146…

@JessicaRQueen1 @Nature_NPJ Congratulations, Jessica and team!

Thanks for the shoutout Susan! This work is now published at @Nature_NPJ Article here: rdcu.be/emQPk

Powerful new story from the Srivastava Lab @sriv4000

@AACR @PeterMKWestcott Congratulations, Peter!

Deconstructing Benign-to-Malignant Transition in the Colon: Gertrude B. Elion Cancer Research Award recipient Peter Maxwell Kienitz Westcott will address this topic in his award lecture at #AACR25 (Tuesday, April 29). Learn more: abstractsonline.com/pp8/#!/20273/s… @PeterMKWestcott

Looking forward to presenting and hearing from the other speakers this evening @AACR25, at the microbiota and cancer prevention, diagnosis, and treatment session! Room S105 @MDAndersonNews

Thrilled to share our latest study just out in @Nature 😄A major milestone in our collaboration with ⁦@Aiims1742⁩ Led by brilliant ⁦⁦⁦@GuangshengPei⁩ ⁦⁦⁦⁦⁦⁦⁦⁦⁦⁦⁦@jiminmin_v⁩ ⁦⁦@MDAndersonNews⁩ nature.com/articles/s4158…

Wonderful work @IamLinghua, @Aiims1742 and team! 👏

It was a quite a transformative experience to attend the inaugural Microbiome Accelerator from NatureAwards and @seedhealth in London last year. Highly recommend entrepreneurial microbiome scientists to apply for the 2025 cycle! nature.com/articles/d4247…