Science with Angela

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Week 4 in the books!

Hello my fellow science-lovers and Abstract Watchers! I hope you all had a wonderful week, and if you're in the US that you had a nice break. I savored a manuscript and some lasagna and watched Eternal Sunshine of the Spotless Mind which is one of my all time favorite movies. The moral of the story - it might not end well, but the journey can still be worth it. Life, love, - are complex and sometimes have contradictions. It reminds me of the book "Lost and Found" (Kathryn Schulz) that I read recently - where theword 'and' does a lot of heavy lifting in our lives, juxtaposing profound and trite things, because that is the way they occur, from day to day.


In this sense, I find science a lot simpler than philosophy, so on to the abstracts!!


Have a great, complex day!



Abstract #21: Vaccination-based immunotherapy to target profibrotic cells in liver and lung from Dr. Christian Stockmann's lab. Open access, no preprint. Fibrosis is the final path of nearly every form of chronic disease, regardless of the pathogenesis. (We talked a bit about fibrosis and its connection to liver cancer and pancreatic cancer a couple of weeks ago on Abstract Watch) Upon chronic injury, activated, fibrogenic fibroblasts deposit excess extracellular matrix, and severe tissue fibrosis can occur in virtually any organ. However, antifibrotic therapies that target fibrogenic cells, while sparing homeostatic fibroblasts in healthy tissues, are limited. Here, the authors tested whether specific immunization against endogenous proteins that are strongly expressed in fibrogenic cells but not in quiescent fibroblasts can elicit an antigen-specific cytotoxic T cell response to ameliorate organ fibrosis. In silico epitope prediction revealed that activation of the genes Adam12 and Gli1 in profibrotic cells and the resulting “self-peptides” can be exploited for T cell vaccines to ablate fibrogenic cells. The authors demonstrate the efficacy of a vaccination approach to mount CD8+ T cell responses that reduce fibroblasts and fibrosis in the liver and lungs in mice. These results provide proof of principle for vaccination-based immunotherapies to treat fibrosis. - This abstract is super clear and compelling. The next step is obviously to see if this vaccine-based immunotherapy can elicit a comparable, targeted immune response in people, leading to a potential treatment for patients with organ fibrosis.


Abstract #22: The retroelement Lx9 puts a brake on the immune response to virus infection from Dr. Cecile King's lab. Open access, no preprint. Transposable elements (TEs) were proposed to operate as genomic regulatory elements over 60 years ago. The abundance and repertoire of TEs were revealed only recently (with technological advances). TEs constitute up to two-thirds of mammalian genomes. DNA regulatory regions (promoters, enhancers and transcription-factor-binding sites) are often within TEs, suggesting that TEs have been co-opted to regulate mammalian gene expression and cell phenotype. Mammalian TEs  include both recent acquisitions and ancient ones. Ancient conserved TEs are more likely to have a regulatory function, but their function needs to be uncovered experimentally. Here, the authors show that CRISPR–Cas9-mediated deletion of the LINE-1 retrotransposon Lx9c11in mice results in an exaggerated and lethal immune response to virus infection. Lx9c11 is critical for the neogenesis of a non-coding RNA (Lx9c11-RegoS) that functions as a natural antisense transcript to negatively regulate genes of the Schlafen family, reduce the hyperinflammatory phenotype and rescue lethality in virus-infected Lx9c11−/− mice. These findings provide evidence that a TE can control the immune system to favour host survival during virus infection.


Abstract #23: Pepinemab antibody blockade of SEMA4D in early Huntington’s disease: a randomized, placebo-controlled, phase 2 trial from Dr. Maurice Zauderer et al and the Huntington Study Group SIGNAL investigators. Open access, no preprint. SIGNAL is a multicenter, randomized, double-blind, placebo-controlled phase 2 study (no. NCT02481674) established to evaluate pepinemab, a semaphorin 4D (SEMA4D)-blocking antibody, for treatment of Huntington’s disease (HD). Pepinemab is being developed by Vaccinex to treat Huntington’s and other neurological disorders. It is designed to block the activity of SEMA4D, which is at higher levels in the brains of people with Huntington’s. Pepinemab is thought to act in part by normalizing the function of astrocytes, thereby preventing blood vessel, metabolic, and inflammatory changes that contribute to nerve cell loss in Huntington’s.The trial enrolled a total of 265 HD gene expansion carriers with either early manifest (EM, n = 179) or late prodromal (LP, n = 86) HD, randomized (1:1) to receive 18 monthly infusions of pepinemab (n = 91 EM, 41 LP) or placebo (n = 88 EM, 45 LP). Pepinemab was generally well tolerated. The trial had two primary efficacy goals, both assessed in the 179 people with an early-stage Huntington’s diagnosis. One goal looked at changes from study start in cognition with treatment using two components of the Huntington’s Disease Cognitive Assessment Battery (HD-CAB), one a test of executive function, and the other an assessment of timing and psychomotor coordination. The other efficacy goal was score changes on the Clinical Global Impression of Change (CGIC), which evaluates changes in planning ability and memory associated with disease progression. Little difference in HD-CAB scores were seen in patients with normal cognitive abilities at the study’s start regardless of pepinemab or placebo assignment. Significant differences, however, were observed among patients who began the trial with “some degree of cognitive deficit”: There was a steady decline in HD–CAB scores in the placebo group during 18 months of treatment, while these scores in the pepinemab group did not fall below baseline at any time point. Similarly, no differences in CGIC scores between pepinemab and placebo were observed for patients with normal functional abilities, ranging from managing personal finances to self-care and daily life activities, at the study’s start. But among those with baseline functional impairments, fewer pepinemab-treated patients experienced CGIC declines during the study. Therefore, early Huntington’s patients with existing cognitive impairments were most likely to benefit from the treatment. These data suggest pepinemab may target cellular processes that are not disturbed in very early disease. 


Abstract #24: A highly selective response to food in human visual cortex revealed by hypothesis-free voxel decomposition from Dr. Nancy Kanwisher's lab. Not open access, no preprint. Distinct cortical regions are selectively responsive to specific categories of visual stimuli but the role of these category selectivities in the functional organization of the visual cortex, or if other regions for different categoriy selectivities exist are not known. Furthermore, standard voxel-wise tests cannot detect distinct neural selectivities that coexist within voxels. To overcome these limitations, the authors used data-driven voxel decomposition methods to identify the main components underlying fMRI responses to thousands of complex photographic images. Their analysis rediscovered components selective for faces, places, bodies, and words, validating the method. The analysis also revealed an unexpected component with a distinct anatomical distribution that responded highly selectively to images of food. Alternative accounts based on low- to mid-level visual features, such as color, shape, or texture, failed to account for the food selectivity of this component. High-throughput testing and control experiments with matched stimuli on a highly accurate computational model of this component confirm its selectivity for food. We registered our methods and hypotheses before replicating them on held-out participants and in a novel dataset. These findings demonstrate the power of data-driven methods and show that the dominant neural responses of the ventral visual pathway include not only selectivities for faces, scenes, bodies, and words but also the visually heterogeneous category of food, thus constraining accounts of when and why functional specialization arises in the cortex.


Abstract #25: Topoisomerase 1-dependent R-loop deficiency drives accelerated replication and genomic instability from Dr. Batsheva Karem's lab. Open access, preprint available about 6 months earlier. Replication stress arising from endogenous or exogenous origins can compromise the fidelity of DNA replication and lead to genomic instability. It is commonly associated with slow and stalled replication forks. Accelerated replication has emerged as a non-canonical form of replication stress. However, the molecular basis underlying fork acceleration is largely unknown. Here, we show that mutated HRAS activation leads to increased topoisomerase 1 (TOP1) expression, causing aberrant replication fork acceleration and DNA damage by decreasing RNA-DNA hybrids or R-loops. In HRAS mutant cells, restoring TOP1 expression or mild replication inhibition rescues the perturbed replication and reduces DNA damage. Furthermore, TOP1 or RNaseH1 overexpression induces accelerated replication and DNA damage, highlighting the importance of TOP1 equilibrium in regulating R-loop homeostasis to ensure faithful DNA replication and genome integrity. Altogether, our results dissect a mechanism of oncogene-induced DNA damage by aberrant replication fork acceleration. (I thought R-loops were bad, so I did find this a bit surprising - decreasing them accelerates replication, still not clear to me why accelerated DNA replication is bad, or is the lack of R-loops bad - seems a bit chicken/egg so I might have to read the paper... ;) )


Abstract #26: Control of ribosomal RNA synthesis by hematopoietic transcription factors from Dr. Vikram Paralkar's lab. Not open acess, preprint posted about 4 months earlier. Despite substantial variation in rRNA transcription rates across cell types, little is known about cell-type-specific factors that bind rDNA and regulate rRNA transcription to meet tissue-specific needs. Using hematopoiesis as a model system, the authors mapped about 2,200 ChIP-seq datasets for 250 transcription factors (TFs) and chromatin proteins to human and mouse rDNA and identified robust binding of multiple TF families to canonical TF motifs on rDNA. They developed a 47S-FISH-Flow assay for nascent rRNA quantification, and demonstrated that targeted degradation of C/EBP alpha (CEBPA), a critical hematopoietic TF with conserved rDNA binding, caused rapid reduction in rRNA transcription due to reduced RNA Pol I occupancy. Thus, multiple cell-type-specific TFs bind canonical motifs on rDNA, revealing numerous potential rRNA regulators. Seems related to ribosomopathies, particularly Diamond Blackfan anemia. The authors also mention in the Discussion "The direct binding of CEBPA to mammalian rDNA, and its regulation of rRNA transcription, has implications for normal and malignant hematopoiesis. Mice with knockout of CEBPA suffer fatal loss of GMPs (Zhang et al., 2004), one of the populations with high rRNA transcription rates in the hematopoietic tree (Hayashi et al., 2014). Our work suggests that loss of CEBPA in vivo may lead to reduced ribosome biogenesis in GMPs, and its knockout phenotype may result partly from such an impairment. In the context of malignancy, leukemic blast cells have characteristic prominent nucleoli (Smetana, 2009), and CEBPA knockout is known to cause reduced growth in most AML lines (Tsherniak et al., 2017). We speculate that CEBPA binding to rDNA may drive high rRNA transcription rates in AML, and, if so, may serve as a cell-type-specific ribosome biogenesis vulnerability that could be exploited for treatment."


Abstract #27: Engineering human mini-bones for the standardized modeling of healthy hematopoiesis, leukemia, and solid tumor metastasis from Dr. Paul Bourgine's lab. Not open access, preprint available 1 month earlier. The bone marrow microenvironment provides factors to sustain blood production throughout life. is a hotspot for the progression of hematologic disorders, and the most frequent site of solid tumor metastasis. Preclinical research relies on xenograft mouse models, but these models preclude the human-specific functional interactions of stem cells with their bone marrow microenvironment. Human mesenchymal cells can be exploited for the in vivo engineering of humanized niches, which confer robust engraftment of human healthy and malignant blood samples. However, mesenchymal cells are associated with major reproducibility issues in tissue formation. Here, the authors report the fast and standardized generation of human mini-bones by a custom-designed human mesenchymal cell line. They generated mini-bones (ossicles, hOss) in mice by modifying a human mesenchymal cell line engineered to express bone morphogenetic protein 2. This line generates hOss by endochondral (EC) and intramembranous (IM) ossifications,  by culturing them under chondrogenic or osteogenic conditions, respectively, and then implanting the cells subcutaneously. hOss consist of fully mature bone and bone marrow structures hosting a human mesenchymal niche with retained stem cell properties. As compared to mouse bones, we demonstrate superior engraftment of human cord blood hematopoietic cells and primary acute myeloid leukemia samples and also validate hOss as a metastatic site for breast cancer cells. We further report the engraftment of neuroblastoma patient-derived xenograft cells in a humanized model, recapitulating clinically described osteolytic lesions. Collectively, our human mini-bones constitute a powerful preclinical platform to model bone-developing tumors using patient-derived materials. The authors further highlight the advance in the Discussion: "Preexisting hOss approaches demonstrated the functional advantage of engineering a human bone marrow niche, but protocols are relatively complex and use primary MSCs, challenging their reproducibility. Instead, the MSOD-B consists of a mesenchymal cell line conserving lineage plasticity, capable of undergoing EC and IM ossifications. The process is highly efficient and in appearance limitless, with the same clonal population exploited for the engineering of over 1000 hOss. The 3 weeks in vitro priming followed by in vivo implantation led to the formation of bone organs as early as 4-week post-implantation (7 weeks total), harboring a mature architecture comparable to native bones and composed of a functional human mesenchymal niche. In comparison, selected batches of primary MSCs required 5 weeks of in vitro differentiation to reach hypertrophy, and 8 to 12 weeks of in vivo development (15-19 weeks total)."


"The woods are lovely, dark and deep"

Robert Frost