Biology subjects

Martini, R.

Publications and source records attributed to Martini, R..

8 recordsLinked to original sources

bioRxiv2026

An explainable boosting machine model for identifying artifacts caused by formalin-fixed paraffin embedding

BackgroundFormalin-fixed paraffin-embedding (FFPE) is a widely used, cost-effective method for long-term storage of clinical samples. However, fixation is known to introduce damage to nucleic acids that can present as artifactual bases in sequencing otherwise absent from higher fidelity storage methods such as fresh freezing (FF). Various machine learning methods exist for filtering these variant artifacts, but benchmarking performance can be difficult without reliable truth sets. In this study, we employ a collection of 90 paired fresh-frozen and formalin-fixed paraffin embedded samples from the same tumor to robustly define real and FFPE-derived, artifactual variation and enable objective evaluation of filtering methods. To address existing shortcomings, we propose a novel explainable boosting machine (EBM) model that improves performance, can be easily updated with new data, requires modest computational resources, and is analysis pipeline agnostic, making it broadly accessible. ResultsWe evaluated several methods for limiting FFPE-derived variant artifacts using cohorts of B-cell lymphoma samples. We found capturing local context around variants to be a highly informative, under-utilized feature set not commonly incorporated into many existing machine learning methods. Consequently, we developed a novel algorithm, FIFA, for filtering FFPE artifacts, which uses an EBM model, an interpretable decision-tree-based learning algorithm, to address some of the existing shortcomings. We used four independent cohorts composed of paired lymphoma and cervical cancer samples and a breast cancer cell line with both FF and FFPE samples to define clearly annotated training and test sets and demonstrated improved performance over existing methods. Additionally, FIFA filtering increased relevant biological signals in FFPE breast cancer datasets distinct from the training and testing sets. The EBM framework employed by FIFA is computationally efficient and easily amenable to incorporation of additional datasets due to its generalized additive modeling of features making it straightforward to incorporate new data into existing models dynamically over time. ConclusionsOur novel FFPE variant artifact filtering tool, FIFA, is a marked improvement over existing methods. It can be easily implemented, post hoc, to supplement existing somatic calling pipelines, training and inference can be run quickly across most compute environments, and it can be easily updated online as new training data becomes available. Accordingly, FIFA represents an important advance in retrospective cancer genomics research by further enhancing access to the vast stores of FFPE-archived tumor samples currently in existence.

bioinformatics↗

bioRxiv2025

Uncovering Functional Sequence Gaps in Human Reference Genomes using African Pan Genome Contig Sequences

Human reference genomes underpin biomedical discovery but remain incomplete and biased toward European populations, constraining interpretation of genetic variation in underrepresented populations. Here we characterize African Pan Genome (APG) contigs totaling 296.5 Mb to define the sequence and functional landscape of genomic regions absent from current references. Most contigs align to the telomere-to-telomere (T2T-CHM13) genome and across 47 haplotype-resolved Human Pangenome Reference Consortium (HPRC) assemblies, with T2T-CHM13 placements enriched in centromeric and satellite repeats and overlapping 373 genes, including disease-associated loci. Mapping across HPRC assemblies revealed ancestry-associated contig enrichment, particularly in African genomes. Notably, 742 contigs remained unmapped under both stringent and relaxed criteria. These sequences are largely nonrepetitive and exhibit strong functional potential, including predicted protein-coding genes, CpG islands and transcriptional activity. Together, these results demonstrate that functionally relevant, ancestry-enriched genomic sequences remain absent from current references, with important implications for disease variant interpretation and precision medicine.

genomics↗

bioRxiv2023

Kinome focused CRISPR-Cas9 screens in African ancestry patient-derived breast cancer organoids identifies essential kinases and synergy of EGFR and FGFR1 inhibition.

Precision medicine approaches to cancer treatment aim to exploit genomic alterations that are specific to individual patients to tailor therapy strategies. These alterations are usually revealed via next generation sequencing of the tumor tissue. Yet, it is clear that some targetable genes and pathways are essential for tumor cell viability even in the absence of direct genomic alterations. This is especially important in under-represented populations, whose mutational landscape and determinants of response to existing therapies are poorly characterized due to limited inclusion in clinical trials and studies. One way to reveal tumor essential genes is with genetic screens. Most screens are conducted on cell lines that bear little resemblance to patient tumors, after years of culture in non-physiological conditions. To address this problem, we aimed to develop a CRISPR screening pipeline in 3D-grown patient-derived tumor organoid (PDTO) models. We focused on identifying essential kinases that may translate to options for targeted therapies, including combination therapies. We first established a breast cancer PDTO biobank focused on underrepresented populations, including West African patients. We then performed a negative selection kinome-focused CRISPR screen to identify kinases essential for organoid growth and potential targets for combination therapy with EGFR or MEK inhibitors. We identified several previously unidentified kinase targets and showed that combination of FGFR1 and EGFR inhibitors synergizes to block organoids proliferation. Together these data demonstrate feasibility of CRISPR-based genetic screens in patient-derived tumor models, including PDTOs from under-represented cancer patients, and identify new targets for cancer therapy.

cancer biology↗

bioRxiv2023

Genetically perturbed myelin as a risk factor for neuroinflammation-driven axon degeneration

Axon degeneration and functional decline in myelin diseases are often attributed to loss of myelin but their relation is not fully understood. Perturbed myelinating glia can instigate chronic neuroinflammation and contribute to demyelination and axonal damage. Here we study mice with distinct defects in the proteolipid protein 1 gene that develop axonal damage which is driven by cytotoxic T cells targeting myelinating oligodendrocytes. We show that persistent ensheathment with perturbed myelin poses a risk for axon degeneration, neuron loss, and behavioral decline. We demonstrate that CD8+ T cell-driven axonal damage is less likely to progress towards degeneration when axons are efficiently demyelinated by activated microglia. Mechanistically, we show that cytotoxic T cell effector molecules induce cytoskeletal alterations within myelinating glia and aberrant actomyosin constriction of axons at paranodal domains. Our study identifies detrimental axon-glia-immune interactions which promote neurodegeneration and possible therapeutic targets for disorders associated with myelin defects and neuroinflammation.

neuroscience↗

bioRxiv2023

Patient-derived tumor organoids with p53 mutations, and not wild-type p53, are sensitive to synergistic combination PARP inhibitor treatment

Poly (ADP-ribose) polymerase inhibitors (PARPi) are used for patients with BRCA1/2 mutations, but patients with other mutations may benefit from PARPi treatment. Another mutation that is present in more cancers than BRCA1/2 is mutation to the TP53 gene. In 2D breast cancer cell lines, mutant p53 (mtp53) proteins tightly associate with replicating DNA and Poly (ADP-ribose) polymerase (PARP) protein. Combination drug treatment with the alkylating agent temozolomide and the PARPi talazoparib kills mtp53 expressing 2D grown breast cancer cell lines. We evaluated the sensitivity to the combination of temozolomide plus PARPi talazoparib treatment to breast and lung cancer patient-derived tumor organoids (PDTOs). The combination of the two drugs was synergistic for a cytotoxic response in PDTOs with mtp53 but not for PDTOs with wtp53. The combination of talazoparib and temozolomide induced more DNA double-strand breaks in mtp53 expressing organoids than in wild-type p53 expressing organoids as shown by increased {psi}-H2AX protein expression. Moreover, breast cancer tissue microarrays (TMAs) showed a positive correlation between stable p53 and high PARP1 expression in sub-groups of breast cancers, which may indicate sub-classes of breast cancers sensitive to PARPi therapy. These results suggest that mtp53 could be a biomarker to predict response to the combination of PARPi talazoparib-temozolomide treatment.

cancer biology↗

bioRxiv2023

TREM2 limits necrotic core formation during atherogenesis by controlling macrophage survival and efferocytosis

Atherosclerosis is a chronic disease of the vascular wall driven by lipid accumulation and inflammation in the intimal layer of arteries [1], [2], and its main complications, myocardial infarction and stroke, are the leading cause of mortality worldwide [3]. Recent studies have identified Triggering receptor expressed on myeloid cells 2 (TREM2), a lipid-sensing receptor regulating several key myeloid cell functions [4], as a highly expressed marker of macrophage foam cells in experimental and human atherosclerosis [5]. However, the function of TREM2 in the development of atherosclerosis is unknown. Here, we show that hematopoietic or global TREM2 deficiency increases necrotic core formation in early experimental atherosclerosis. We further demonstrate that TREM2 is essential for the efferocytosis capacities of macrophages, and to the survival of lipid-laden macrophages, altogether indicating a crucial role of TREM2 in maintaining the balance between foam cell death and their clearance in atherosclerotic lesions, thereby controlling plaque necrosis.

immunology↗

bioRxiv2023

Cytotoxic CNS-associated T cells drive axon degeneration by targeting perturbed myelinating oligodendrocytes in PLP1 mutant mice

Myelin defects lead to neurological dysfunction in various diseases and in normal aging. Chronic neuroinflammation often contributes to axon-myelin damage in these conditions and can be initiated and/or sustained by perturbed myelinating glia. We have previously shown that distinct mutations in the PLP1 gene result in neurodegeneration that is largely driven by adaptive immune cells. Here we characterize CD8+ CNS-associated T cells in these myelin mutants using single-cell transcriptomics and identify population heterogeneity and disease-associated changes. We demonstrate that early sphingosine-1-phosphate receptor modulation attenuates the recruitment of T cells and neural damage, while later targeting of CNS-associated T cell populations is inefficient and has no effect on neurodegeneration. Applying bone marrow chimerism and utilizing random X chromosome inactivation, we provide evidence that axonal damage is driven by cytotoxic, antigen specific CD8+ T cells that target mutant myelinating oligodendrocytes. These findings offer insights into neural-immune interactions and are of translational relevance for neurological conditions associated with myelin defects and neuroinflammation.

neuroscience↗

bioRxiv2019

Extinctions in marine plankton preceded by stabilizing selection

Unless they adapt, populations facing persistent stress are threatened by extinction. Theoretically, populations facing stress can react by either disruption, increasing trait variation, or stabilisation, decreasing trait variation. In the short term, the more economical response is stabilisation, because it quickly transfers a large part of the population closer to a new ecological optimum. However, canalisation is deleterious in the face of persistently increasing stress because it reduces variability and thus decreases the ability to react to further change in stress. Understanding how natural populations react to intensifying stress reaching terminal levels is key to assessing their resilience to environmental change such as that caused by global warming. Because extinctions are hard to predict, observational data on the adaptive reaction of populations facing extinction are rare. In this study, we make use of the glacial salinity rise in the Red Sea as a natural experiment allowing us to analyse the reaction of planktonic Foraminifera to stress escalation in the geological past. We analyse morphological trait state and variance in two species across a salinity rise leading to their local extinction. One species reacted by stabilisation in shape and size, detectable several thousand years prior to extinction. The second species reacted by trait divergence, but each of the two divergent populations remains stable or reacted by further stabilisation. These observations indicate that the default reaction of the studied Foraminifera is stabilisation and that stress escalation did not lead to the local emergence of adapted forms. Inability to breach the global adaptive threshold would explain why communities of Foraminifera, and many other groups of marine plankton, reacted to Quaternary climate change by faithfully tracking their zonally shifting environments. It also means that populations of marine species adapted to response by migration, when exposed to stress outside of the adaptive range, will be at risk of extinction.

ecology↗