Single-cell transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a serious and poorly understood disease. To understand immune dysregulation in ME/CFS, we use single-cell RNA sequencing (scRNA-seq) to examine immune cells in patient and control cohorts. Postexertional malaise (PEM), an exacerbation of symptoms following strenuous exercise, is a characteristic symptom of ME/CFS. To detect changes coincident with PEM, we applied scRNA-seq on the same cohorts following exercise. At baseline, ME/CFS patients display classical monocyte dysregulation suggestive of inappropriate differentiation and migration to tissue. We identify both diseased and more normal monocytes within patients, and the fraction of diseased cells correlates with disease severity. Comparing the transcriptome at baseline and postexercise challenge, we discover patterns indicative of improper platelet activation in patients, with minimal changes elsewhere in the immune system. Taken together, these data identify immunological defects present at baseline in patients and an additional layer of dysregulation in platelets.

Chemical, Molecular, and Single-nucleus Analysis Reveal Chondroitin Sulfate Proteoglycan Aberrancy in Fibrolamellar Carcinoma

Fibrolamellar carcinoma (FLC) is an aggressive liver cancer with no effective therapeutic options. The extracellular environment of FLC tumors is poorly characterized and may contribute to cancer growth and/or metastasis. To bridge this knowledge gap, we assessed pathways relevant to proteoglycans, a major component of the extracellular matrix. We first analyzed gene expression data from FLC and nonmalignant liver tissue (n = 27) to identify changes in glycosaminoglycan (GAG) biosynthesis pathways and found that genes associated with production of chondroitin sulfate, but not other GAGs, are significantly increased by 8-fold. We then implemented a novel LC/MS-MS based method to quantify the abundance of different types of GAGs in patient tumors (n = 16) and found that chondroitin sulfate is significantly more abundant in FLC tumors by 6-fold. Upon further analysis of GAG-associated proteins, we found that versican (VCAN) expression is significantly upregulated at the mRNA and protein levels, the latter of which was validated by IHC. Finally, we performed single-cell assay for transposase-accessible chromatin sequencing on FLC tumors (n = 3), which revealed for the first time the different cell types in FLC tumors and also showed that VCAN is likely produced not only from FLC tumor epithelial cells but also activated stellate cells. Our results reveal a pathologic aberrancy in chondroitin (but not heparan) sulfate proteoglycans in FLC and highlight a potential role for activated stellate cells.

Significance

This study leverages a multi-disciplinary approach, including state-of-the-art chemical analyses and cutting-edge single-cell genomic technologies, to identify for the first time a marked chondroitin sulfate aberrancy in FLC that could open novel therapeutic avenues in the future.

Abstract 1460: Decoding the tumor biology of the orphan malignancy fibrolamellar carcinoma at single-cell resolution

The World Health Organization (WHO) recognized fibrolamellar carcinoma (FLC) in 2010 as a rare and aggressive form of liver cancer that predominately afflicts adolescents and young adults. There are currently no effective therapies. Surgical resection remains the only option to date, but it is not viable for patients who present with metastasis. Thus, there is an urgent need to identify therapeutic targets. The hallmark genetic lesion of FLC, occurring in >80% of patients, was recently identified to be a ~400kb heterozygous deletion on chromosome 19, leading to the oncogenic fusion protein DNAJB1-PRKACA (DP).

We recently used FLC primary tumors and matched non-malignant liver samples to map the chromatin activity landscape of FLC by chromatin run-on sequencing, or ChRO-seq, which is a state-of-the-art technology for quantifying nascent transcription and defining active regulatory elements across the genome. We identified nearly 7000 FLC-specific enhancers and ~150 “super-enhancers” (SEs) - dense clusters of highly active enhancers that mark nearby critical oncogenes. Despite these advances, a major limitation is the bulk tissue nature of the study - that is, these data reflect an average profile across numerous different cell types (hepatocytes, stellate cells, fibroblasts, macrophages, endothelial cells, etc.), and therefore it is not evident which enhancers and genes are active in which cell types. This represents a major knowledge gap. If we could learn the specific cell types in which FLC enhancers and genes are active, we could then study the functions of these genes in FLC with greater precision and develop more effective targeted therapeutics. I recently conducted single-cell Assay for Transposase Accessible Chromatin ATAC-seq (scATAC-seq) to bridge this knowledge gap. I identified eight clusters from FLC-Primary, FLC-Metastatic, and non-malignant liver (NML) samples. Dimensionality reduction reveals two FLC-Primary, and FLC-Metastatic derived clusters that exhibit an epithelial-like identity most closely related to NML-epithelial cells. Using this scATAC-seq dataset, I have deconvoluted and resolved the bulk resolution limitations of ChRO-seq signal. ScATAC-seq reveals ChRO-seq defined candidate genes are highly accessible in FLC-Primary and FLC-Metastatic transformed Epithelial Cells. I have also dissected ChRO-seq defined SE’s and detailed the proportion of active constituent enhancers within each cell type. Further analysis revealed cell-type-specific transcriptional networks. Together, these studies provide the first single-cell resolution understanding of the transcriptional network in FLC.

Citation Format: Alaa R. Farghli, Bo Shui, Seoyeon Lee, Paul R. Munn, Yutong Zhu, Paul Soloway, Praveen Sethupathy. Decoding the tumor biology of the orphan malignancy fibrolamellar carcinoma at single-cell resolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1460.

Multiple stages of evolutionary change in anthrax toxin receptor expression in humans

The advent of animal husbandry and hunting increased human exposure to zoonotic pathogens. To understand how a zoonotic disease may have influenced human evolution, we study changes in human expression of anthrax toxin receptor 2 (ANTXR2), which encodes a cell surface protein necessary for Bacillus anthracis virulence toxins to cause anthrax disease. In immune cells, ANTXR2 is 8-fold down-regulated in all available human samples compared to non-human primates, indicating regulatory changes early in the evolution of modern humans. We also observe multiple genetic signatures consistent with recent positive selection driving a European-specific decrease in ANTXR2 expression in multiple tissues affected by anthrax toxins. Our observations fit a model in which humans adapted to anthrax disease following early ecological changes associated with hunting and scavenging, as well as a second period of adaptation after the rise of modern agriculture.

Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock

Heat shock (HS) initiates rapid, extensive, and evolutionarily conserved changes in transcription that are accompanied by chromatin decondensation and nucleosome loss at HS loci. Here we have employed in situ Hi-C to determine how heat stress affects long-range chromatin conformation in human and Drosophila cells. We found that compartments and topologically associating domains (TADs) remain unchanged by an acute HS. Knockdown of Heat Shock Factor 1 (HSF1), the master transcriptional regulator of the HS response, identified HSF1-dependent genes and revealed that up-regulation is often mediated by distal HSF1 bound enhancers. HSF1-dependent genes were usually found in the same TAD as the nearest HSF1 binding site. Although most interactions between HSF1 binding sites and target promoters were established in the nonheat shock (NHS) condition, a subset increased contact frequency following HS. Integrating information about HSF1 binding strength, RNA polymerase abundance at the HSF1 bound sites (putative enhancers), and contact frequency with a target promoter accurately predicted which up-regulated genes were direct targets of HSF1 during HS. Our results suggest that the chromatin conformation necessary for a robust HS response is preestablished in NHS cells of diverse metazoan species.