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bioRxiv2017

Potential clinical benefits of CBD-rich Cannabis extracts over purified CBD in treatment-resistant epilepsy: observational data meta-analysis

Potential clinical benefits of CBD-rich Cannabis extracts over purified CBD in treatment-resistant epilepsy: observational data meta-analysis\n\nDifferent therapies involving cannabinoid compounds have become popular on the past few years, particularly the use of canabidiol (CBD) based products for the treatment of child refractory epilepsy. In this segment we highlight genetic disorders such as the Dravet Syndrome, which has received a lot of attention in Brazil. Our country has been giving visibility for this issue after the public discussion regarding the patient Anne Fischer, who benefited from a treatment with hemp based products, imported from the United States of America as a nutritional supplement, and still unregistered in Brazil. To this moment there is no cannabinoid based product registered for clinical indication for epilepsy, so patients have at their disposal products considered nutritional supplements, in general produced from a type of Cannabis known as \"hemp\", which are commercialized in Brazil through medical prescription. Despite several anecdotal evidences from patients and family members, until now there is no consensus on medical literature over the efficacy and safety of these products. Some observational studies are available on scientific literature, but there is still a scarcity of clinical studies conducted under the logic, rigor and organization necessary for clinical trial dedicated to the register of a pharmaceutical product. The objective of this paper is to describe the analysis of several observational clinical studies available on the literature regarding the treatment of child refractory epilepsy with cannabinoid based products. Beyond attempting to establish the safety and efficacy of such products, when possible, the present analysis also intended to investigate if there is enough evidence between the different aspects of safety and efficacy between CBD enriched extracts compared to purified CBD products. Results: a systematic search for papers in the \"PubMed\" search system with the words \"Dravet\", \"Lennox-Gastaut\" and \"epilepsy\" combined with the terms \"Cannabis\", \"cannabinoid\" and \"child\" yielded 30 papers. From those, 24 were not considered for the systematic review, for not having valid content (13), for being opinion only papers (6), showed not clinical data (4) and reported different subjects (1), resulting in 6 valid papers published between 2013 and 2016. One additional study was in press at the moment of the search was added manually (1) resulting in 7 valid references for analysis, with an average impact factor of 5,9 (2,3 to 21,8). Public data from partial reports of controlled randomized studies conducted in order to register a medication (2) were also considered, when appropriated and were mentioned in the text. The categorical data were analyzed by the Fischer test. Overall, the papers analyzed report observational clinical data of 442 patients, treated with CBD rich extracts or purified CBD, with he average daily dose between 1 and 50 mg/kg, with treatment length from 3 to 12 months (average of 6,2 months). A considerable amount of 66% (292/442) of the patients reported improvement in the frequency of convulsive crisis. There were more reports of improvement from patients treated with purified CBD (242/285) than patients treated with purified CBD (68/157), with statistical significance (p<0,0001). Nevertheless, when the standard clinical threshold of a \"50% reduction or more in the frequency of convulsive crisis\" was applied, only 40% of the individuals are considered respondent, and there were no difference (p=0,57) between the treatments with extract (64/168) and purified CBD (65/157). However, even that both treatments have similar efficacy, the patients treated with CBD enriched extracts reported a lower average dose than purified CBD patients. The average CBD equivalent dose on the extracts was 7,1 mg/kg/day, while the purified CBD was 22,9 mg/kg/day, suggesting that CBD is about 3x more potent in the extract than in its purified form. Looking only at the data relative to genetic originated disorders, there is evidence of a superior efficacy on Dravet Syndrome patients (37/72, p=0,01), but not for Lennox-Gastaut Syndrome (78/188, p=0,18), compared to the number of refractory epilepsy respondents in general (107/305). There is also an advantage of the CBD enriched extracts related to the occurrence of side effects. The report of mild side effects (109/285 vs. 291/346, p<0,0001) and severe (23/285 vs. 77/346, p<0,0001) are more frequent in products containing purified CBD than on CBD enriched extracts. Important to mention that these are the numbers of total reports of side effects, it is not possible to infer which fraction of these numbers are related to the treatment. In conclusion, this meta analysis suggests that treatments using CBD enriched extracts are more potent and have a better profile of adverse effects (but not more efficacy) than products containing purified CBD, at least in this population of patients with refractory epilepsy. The lack of standardization between extracts containing Cannabis does not allow us to infer directly which characteristics of the product that confer this therapeutic advantage, but it is likely related to other compounds present in the formulation that act sinergistically with CBD. Controlled studies with standardized Cannabis based extracts are necessary to confirm these observations.\n\n*Presented as an abstract and lecture to the 2017 CannMed event, at the Harvard Medical School, Boston, USA, in may 2017.

pharmacology and toxicology↗

bioRxiv2019

PDXGEM: Patient-Derived Tumor Xenograft based Gene Expression Model for Predicting Clinical Response to Anticancer Therapy in Cancer Patients

BackgroundCancer is a highly heterogeneous disease and shows varying responses to anti-cancer drugs. Although several approaches have been attempted to predict the drug responses by analyzing molecular profiling data of tumors from preclinical cancer models or cancer patients, there is still a great need of developing highly accurate prediction models of response to the anti-cancer drugs for clinical applications toward personalized medicine. Here, we present PDXGEM pipeline to build a predictive gene expression model (GEM) for cancer patients drug responses on the basis of data on gene expression and drug activity in patient-derived xenograft (PDX) models.\n\nResultsDrug sensitivity biomarkers were identified by an association analysis between gene expression levels and post-treatment tumor volume changes in PDX models. Only biomarkers with concordant co-expression patterns between the PDX and cancer patient tumors were used in random-forest algorithm to build a drug response prediction model, so called PDXGEM. We applied PDXGEM to several cytotoxic chemotherapy as well as targeted therapy agents that are used to treat breast cancer, pancreatic cancer, colorectal cancer, or non-small cell lung cancer. Significantly accurate predictions of PDXGEM for pathological and survival outcomes were observed through extensive validation analyses of multiple independent cancer patient datasets obtained from retrospective observational study and prospective clinical trials.\n\nConclusionOur results demonstrated a strong potential of utilizing molecular profiles and drug activity data of PDX tumors for developing a clinically translatable predictive cancer biomarkers for cancer patients. PDXGEM web application is publicly available at http://pdxgem.moffitt.org.

bioinformatics↗

bioRxiv2022

Paxlovid-like nirmatrelvir/ritonavir fails to block SARS-CoV-2 transmission in ferrets

Despite the continued spread of SARS-CoV-2 and emergence of variants of concern (VOC) that are capable of escaping preexisting immunity, therapeutic options are underutilized. In addition to preventing severe disease in high-risk patients, antivirals may contribute to interrupting transmission chains. The FDA has granted emergency use authorizations for two oral drugs, molnupiravir and paxlovid. Initial clinical trials suggested an efficacy advantage of paxlovid, giving it a standard-of-care-like status in the United States. However, recent retrospective clinical studies suggested a more comparable efficacy of both drugs in preventing complicated disease and case-fatalities in older adults. For a direct efficacy comparison under controlled conditions, we assessed potency of both drugs against SARS-CoV-2 in two relevant animal models; the Roborovski dwarf hamster model for severe COVID-19 in high-risk patients and the ferret model of upper respiratory tract disease and transmission. After infection of dwarf hamsters with VOC omicron, paxlovid and molnupiravir were efficacious in mitigating severe disease and preventing death. However, a pharmacokinetics-confirmed human equivalent dose of paxlovid did not significantly reduce shed SARS-CoV-2 titers in ferrets and failed to block virus transmission to untreated direct-contact ferrets, whereas transmission was fully suppressed in a group of animals treated with a human-equivalent dose of molnupiravir. Prophylactic administration of molnupiravir to uninfected ferrets in direct contact with infected animals blocked productive SARS-CoV-2 transmission, whereas all contacts treated with prophylactic paxlovid became infected. These data confirm retrospective reports of similar therapeutic benefit of both drugs for older adults, and reveal that treatment with molnupiravir, but not paxlovid, may be suitable to reduce the risk of SARS-CoV-2 transmission.

microbiology↗

bioRxiv2026

Neutrophils orchestrate pre-metastatic immunosuppressive bone marrow remodeling during prostate cancer metastasis

The dynamic reprogramming of the bone marrow (BM) microenvironment during metastatic progression is poorly defined. Through single-cell profiling of BM samples spanning benign conditions, high-risk bone metastatic potential localized prostate cancer (HMP) and established bone metastatic prostate cancer (PCa), we uncovered a primary tumor-to-BM signaling axis that orchestrates niche formation through neutrophil-mediated remodeling. Tumor-associated neutrophils (TANs) emerge during the HMP stage, persist throughout metastatic progression, correlate with poor patient prognosis, and exhibit direct immunosuppressive activity that contributes to a BM environment permissive to metastatic colonization. Functional and genetic studies showed that tumor-associated systemic IGF1 reprogrammed BM neutrophils through IGF1R-MAPK/ERK-KLF4 signaling, with IL-1{beta}, reactive oxygen species and nitric oxide contributing to TAN-mediated T cell suppression. Tumor-cell Igf1 perturbation, IGF1R blockade and neutrophil-specific Igf1r deletion attenuated TAN-associated BM remodeling, and reduced subsequent bone metastatic progression. In bone-metastasis models, combined IGF1R and PD-1 blockade suppressed bone-metastatic progression. Translationally, our investigator-initiated clinical trial (NCT06866548) of teprotumumab plus tislelizumab in patients with established metastatic castration-resistant prostate cancer (mCRPC) provided initial safety data and exploratory clinical observations. Together, these findings identify IGF1R-dependent neutrophil reprogramming as a functionally important component of the evolving PCa bone metastatic microenvironment and provide a rationale for therapeutic targeting of IGF1R signaling together with immune checkpoint blockade.

cancer biology↗

bioRxiv2017

Heterogeneity in the tumour size dynamics differentiates Vemurafenib, Dabrafenib and Trametinib in metastatic melanoma

Molecular heterogeneity in tumours leads to variability in drug response both between patients and across lesions within a patient. These sources of variability could be explored through analysis of routinely collected clinical trial imaging data. We applied a mathematical model of tumour growth to analyse both within and between patient variability in tumour size dynamics to clinical data from three drugs, Vemurafenib, Dabrafenib and Trametinib, used in the treatment of metastatic melanoma. The analysis revealed: 1) existence of homogeneity in drug response and resistance development within a patient; 2) tumour shrinkage rate does not relate to rate of resistance development; 3) Vemurafenib and Dabrafenib, two BRAF inhibitors, have different variability in tumour shrinkage rates. Overall these results show how analysis of the dynamics of individual lesions can shed light on the within and between patient differences in tumour shrinkage and resistance rates, which could be used to gain a macroscopic understanding of tumour heterogeneity.

cancer biology↗

bioRxiv2023

Broad-spectrum antiviral activity of clinically approved CYP3A inhibitors against pathogenic human coronaviruses in vitro

Coronaviruses pose a permanent risk of outbreaks, with three highly pathogenic species and strains (SARS-CoV, MERS-CoV, SARS-CoV-2) having emerged in the last twenty years. Limited antiviral therapies are currently available and their efficacy in randomized clinical trials enrolling SARS-CoV-2 patients has not been consistent, highlighting the need for more potent treatments. We previously showed that cobicistat, a clinically approved inhibitor of Cytochrome P450-3A (CYP3A), has direct antiviral activity against early circulating SARS-CoV-2 strains in vitro and in Syrian hamsters. Cobicistat is a derivative of ritonavir, which is co-administered as pharmacoenhancer with the SARS-CoV-2 protease inhibitor nirmatrelvir, to inhibit its metabolization by CPY3A and preserve its antiviral efficacy. Here, we used automated imaging and analysis for a screening and parallel comparison of the anti-coronavirus effects of cobicistat and ritonavir. Our data show that both drugs display antiviral activity at low micromolar concentrations against multiple SARS-CoV-2 variants in vitro, including epidemiologically relevant Omicron subvariants. Despite their close structural similarity, we found that cobicistat is more potent than ritonavir, as shown by significantly lower EC50 values in monotherapy and higher levels of viral suppression when used in combination with nirmatrelvir. Finally, we show that the antiviral activity of both cobicistat and ritonavir is maintained against other human coronaviruses, including HCoV-229E and the highly pathogenic MERS-CoV. Overall, our results demonstrate that cobicistat has more potent anti-coronavirus activity than ritonavir and suggest that dose adjustments could pave the way to the use of both drugs as broad-spectrum antivirals against highly pathogenic human coronaviruses.

microbiology↗

bioRxiv2025

B7-H3 as a Dual Clinically Relevant Checkpoint and Antibody Drug Conjugate Target Expressed Across Adenocarcinoma and Neuroendocrine Prostate Cancers

Background and ObjectivesCD276 (B7-H3) has recently emerged as a promising presumptive immune checkpoint inhibitor (ICI) and a potential antibody-drug conjugate (ADC) target for prostate cancer (PCa). We evaluated B7-H3 and 15 other clinically relevant ADC and ICI targets for expression at the RNA and protein level across the PCa continuum--hormone-sensitive, castration-resistant, and neuroendocrine. MethodsCCLE data analysis and western blot experiments were performed for quantifying RNA and protein expression variability across PCa cell lines. Inter- and intratumoral heterogeneity was evaluated by integrating single-cell RNA sequencing data across 595k cells and 102 patients, spanning the disease continuum. AR and B7-H3 knockouts of PCa cell lines were developed and investigated using R1881 and Enzalutamide to elucidate the AR-CD276 signaling pathway through qRT-PCR and flow cytometry. Key FindingsB7-H3 showed high expression in tumor and myeloid cells (tumor microenvironment - TME), lowest heterogeneity across all ADC and ICI targets, and was negatively regulated by androgen signaling. LimitationsFurther validation of ADC and ICI target protein expression in human samples and more exhaustive exploration of the AR-CD276 signaling cascade is required. ConclusionB7-H3 demonstrates the least susceptibility to selective pressure due to its stable expression across PCa disease states. Clinical ImplicationsB7-H3 represents an important ADC target for PCa due to its potential to minimize drug resistance and likely ability to be a valid target across the prostate cancer continuum. Additionally, its expression in myeloid cells supports a dual role as an ICI, further enhancing its therapeutic relevance. Graphical AbstractDiscovery of optimal checkpoints and antibody drug conjugates (ADCs) in Prostate Cancer (PCa). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/632253v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@1af1115org.highwire.dtl.DTLVardef@8a9d70org.highwire.dtl.DTLVardef@6659aeorg.highwire.dtl.DTLVardef@189e200_HPS_FORMAT_FIGEXP M_FIG C_FIG Patient SummaryIn this study, we demonstrate that prostate cancer expresses high amounts of a cell surface protein called B7-H3 both when first diagnosed and throughout various stages of metastatic disease. Furthermore, we demonstrate a clear and yet to be fully resolved cross-talk between B7-H3 and the androgen signaling pathway central to prostate cancer development. We conclude that B7-H3 is therefore a highly promising therapeutic cell surface protein expressed by prostate cancer due to its stable expression potentially leading to low selective pressure and reduced drug resistance--thereby having significant implications for clinical trial design and patient inclusion considerations. Advancing PracticePCa is a highly heterogeneous disease with an increasingly wide treatment landscape, governed by various factors including clinical covariates, histopathological features, and molecular factors. B7-H3 has recently emerged as a promising clinical target for immunotherapy in the localized setting and antibody drug targeting in the metastatic setting. Despite the clinical significance, B7-H3 expression has not yet been thoroughly evaluated against other clinically relevant immune checkpoint and antibody drug targets, especially along the continuum of PCa treatment stages--hormone sensitive, castration resistant, and neuroendocrine. To our knowledge, this is the first study to characterize B7-H3 in this continuum using representative cell lines and the largest collection of PCa patient single cell sequencing data yet assembled in the literature, thus accounting for the substantial heterogeneity across PCa disease states as well as between datasets. Take Home MessageThis article explores the therapeutic relevance of clinical stage ADC targets and immune checkpoints for Prostate Cancer (PCa). We show that B7-H3 is a highly promising therapeutic candidate for PCa due to its stable expression across various disease states.

cancer biology↗

bioRxiv2025

Preclinical efficacy of combinatorial B7-H3 CAR T cells and ONC206 against diffuse intrinsic pontine glioma

BackgroundDiffuse intrinsic pontine glioma (DIPG) is a fatal pediatric brain tumor affecting over 300 children annually in the United States. Chimeric antigen receptor (CAR) T cells are a targeted immune effector cell therapy with substantial clinical benefit against hematologic cancers. Against CNS tumors, CAR T cells targeting B7-H3, a protein highly expressed on DIPG, have rapidly advanced from preclinical studies to clinical trials. BrainChild-03 (NCT04185038), a phase 1 trial of repeatedly delivered intracerebroventricular (ICV) B7-H3-targeting CAR T cells (B7-H3 CAR T cells), demonstrated tolerability and potential efficacy for children and young adults with DIPG. However, clinical benefits were not uniformly seen, and multi-agent treatment strategies may be required against such an aggressive disease. Here, we combined B7-H3 CAR T cells with ONC206, an imipridone molecule also under clinical investigation. MethodsWe tested B7-H3 CAR T cells combined with ONC206 across multiple DIPG cell cultures and orthotopic xenograft mouse models. ResultsB7-H3 CAR T cell monotherapy induced robust cytotoxicity while ONC206 treatment resulted in significant mitochondrial dysfunction against DMG/DIPG cells. The combination of low effector-to-target ratios of B7-H3 CAR T cells and IC50 concentrations of ONC206 led to significantly enhanced cytotoxicity in vitro (p<0.003) and increased IL-2, IL-29, VEGF-A, and Granzyme B levels. In vivo combinatorial studies of ONC206 and a single ICV dose of B7-H3 CAR T cells significantly extended survival in multiple DIPG xenograft mouse models (p<0.05). ConclusionsB7-H3 CAR T cells combined with ONC206 is a feasible and efficacious multi-agent approach against multiple DIPG models. Importance of the studyDiffuse intrinsic pontine glioma (DIPG) is a fatal pediatric brain tumor. While B7-H3 CAR T cells have shown tolerability and potential benefit in early trials, combinatorial regimens may be required for consistent cures against this aggressive disease. This study demonstrates that a preclinical therapeutic regimen of B7-H3 CAR T cells with ONC206, a second-generation imipridone, increases anti-tumor efficacy in vitro and in orthotopic DIPG mouse models. To our knowledge, this is the first study to evaluate ONC206 in combination with CAR T cells. Our findings provide a preclinical roadmap for evaluating small molecules with CAR T cells to interrogate both their combined benefit and the effect of small molecules on T cells themselves. This work offers a biologically-informed, clinically translatable strategy integrating small molecule therapeutics with CAR T cell therapy and support the development of multi-agent immunotherapy trials for children with DIPG and other high-grade brain and spinal cord tumors. Key PointsO_LIB7-H3 CAR T cells are cytotoxic against preclinical DMG models. C_LIO_LIONC206 causes metabolic apoptosis in preclinical DMG models. C_LIO_LIB7-H3 CAR T cells and ONC206 have combinatorial efficacy against DMG. C_LI

cancer biology↗

bioRxiv2023

Dual therapy with corticosteroid ablates the beneficial effect of DP2 antagonism in chronic experimental asthma.

BackgroundProstaglandin D2 (PGD2) signals via the DP1 and DP2 receptors. In Phase II trials, DP2 antagonism decreased airway inflammation and airway smooth muscle (ASM) area in patients with moderate-to-severe asthma, but in the Phase III clinical trials, DP2 antagonism failed to significantly lower the rate of exacerbations. Here, we hypothesised that DP2 antagonism resolves established ASM remodeling via endogenous PGD2/DP1 activation and that this beneficial effect is ablated by dual corticosteroid therapy. MethodsNeonatal mice were co-exposed to pneumonia virus of mice (PVM) and cockroach extract in early life to induce severe bronchiolitis, then re-infected with PVM and challenged to cockroach extract in adulthood to progress disease to chronic experimental asthma (CEA). The efficacy of DP2 antagonism monotherapy or various dual therapies was assessed in the setting of a rhinovirus (RV)-induced exacerbation. ResultsRV inoculation increased PGD2 release, mucus production, collagen deposition, transforming growth factor (TGF)-{beta}1 expression and type-2 inflammation. Treatment with a DP2 antagonist or DP1 agonist ablated the aforementioned phenotypes, increased type-1 immunity, and decreased ASM area. Dual DP1-DP2 antagonism or dual corticosteroid/DP2 antagonism, which attenuated endogenous PGD2 levels, prevented the resolution of ASM area induced by DP2 antagonism alone. The resolution of ASM remodelling following DP2 antagonism was mediated by IFN-{gamma} and associated with decreased TGF-{beta}1 expression. ConclusionDP2 antagonism resolved ASM remodelling via PGD2/DP1-mediated upregulation of interferon-{gamma} expression. Dual DP2 antagonism/corticosteroid therapy, as occurred in many of the human trials, suppressed PGD2 and IFN-{gamma} production, impairing the efficacy of DP2 antagonism.

immunology↗

bioRxiv2024

Computational modeling of drug response identifies mutant-specific constraints for dosing panRAF and MEK inhibitors in melanoma

Purpose: This study explores the potential of preclinical in vitro cell line response data and computational modeling in identifying optimal dosage requirements of pan-RAF (Belvarafenib) and MEK (Cobimetinib) inhibitors in melanoma treatment. Our research is motivated by the critical role of drug combinations in enhancing anti-cancer responses and the need to close the knowledge gap around selecting effective dosing strategies to maximize their potential. Results: In a drug combination screen of 43 melanoma cell lines, we identified unique dosage landscapes of panRAF and MEK inhibitors for NRAS vs BRAF mutant melanomas. Both experienced benefits, but with a notably more synergistic and narrow dosage range for NRAS mutant melanoma. Computational modeling and molecular experiments attributed the difference to a mechanism of adaptive resistance by negative feedback. We validated in vivo translatability of in vitro dose-response maps by accurately predicting tumor growth in xenografts. Then, we analyzed pharmacokinetic and tumor growth data from Phase 1 clinical trials of Belvarafenib with Cobimetinib to show that the synergy requirement imposes stricter precision dose constraints in NRAS mutant melanoma patients. Conclusion: Leveraging pre-clinical data and computational modeling, our approach proposes dosage strategies that can optimize synergy in drug combinations, while also bringing forth the real-world challenges of staying within a precise dose range. Simple SummaryCombining drugs is crucial for enhancing anti-cancer responses. However, the potential of pre-clinical data in identifying suitable combinations and dosage is often underutilized. In this study, we leverage preclinical in vitro cell line drug response data and computational modeling of signal transduction and of pharmacokinetics to elucidate distinct dose requirements for the combination of pan-RAF and MEK inhibitors in melanoma. Our findings reveal a more synergistic, but narrower dosing landscape in NRAS vs BRAF mutant melanoma, which we linked to a mechanism of adaptive resistance through negative feedback. Further, our analysis suggests the importance of drug dosing strategies to optimize synergy based on mutational context, yet highlights the real-world challenges of maintaining a narrow dose range. This approach establishes a framework for translational investigation of drug responses in the refinement of combination therapy, balancing the potential for synergy and practical feasibility in cancer treatment planning.

systems biology↗

bioRxiv2025

B-cell precursor acute lymphoblastic leukaemia with IGH::CEBP rearrangement: what have we learnt over the years?

B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) is a haematologic malignancy marked by the rapid proliferation of immature B cells in the bone marrow. While BCP-ALL most commonly affects children aged 1-5 years, it remains the most prevalent subtype of ALL in adolescence and adulthood. Chromosomal translocations involving the immunoglobulin (IG) locus and partner genes are proven useful for risk stratification and guiding clinical trials for therapeutic decision. This includes translocations with CCAAT/enhancer-binding proteins (CEBP), which are particularly rare. This rarity has limited efforts to characterise their genetic and clinical profiles, making risk stratification for IGH::CEBP-rearranged BCP-ALL challenging. In this letter, we review the clinical and demographic characteristics of all reported IGH::CEBP cases prior to 2024 and introduce new cases, with preliminary analysis to encourage further investigation into this poorly understood subtype. This study delivers new insights into the molecular and cytogenetic landscape of IGH::CEBP rearrangements in BCP-ALL, and lays a foundation for further investigation into CEBP family roles in haematopoietic development and leukemogenesis, especially in the context of Down syndrome. Finally, it introduces the ongoing international collaborative effort to assemble the largest known IGH::CEBP cohort for comprehensive risk stratification and prognostic evaluation.

cancer biology↗

bioRxiv2019

Auditory processing atypicalities for pure tones and complex speech sounds in Rett Syndrome: towards neuromarkers of disease progression.

Due to severe motor impairments and the lack of expressive language abilities seen in most patients with Rett Syndrome (RTT), it has proven extremely difficult to obtain accurate measures of auditory processing capabilities in this population. Here, we examined early auditory cortical processing of pure tones and more complex phonemes females with confirmed mutation of the MECP2 gene. We recorded high-density auditory evoked potentials (AEP), which allow for objective evaluation of the timing and severity of processing deficits along the auditory processing hierarchy. We compared AEPs of 12 females with RTT to those of 21 typically developing (TD) peers aged 4-21 years, interrogating the first four major components of the AEP (P1: 60-90ms; N1: 100-130ms; P2: 135-165ms; N2: 245-275ms). Atypicalities were evident in RTT at the initial stage of processing. Whereas the initial P1 showed increased amplitude to phonemic inputs relative to tones in TD participants, this modulation by stimulus complexity was absent in RTT. Interestingly, the subsequent N1 did not differ between groups, whereas the following P2 was hugely diminished in RTT, regardless of stimulus complexity. The N2 was similarly smaller in RTT, and did not differ as a function of stimulus type. The P2 effect was remarkably robust in differentiating between groups with near perfect separation between the two groups despite the wide age range of our samples. Given this robustness, along with the observation that P2 amplitude was significantly associated with RTT symptom severity, the P2 has the potential to serve as a biomarker of treatment efficacy.\n\nSignificance statementOur study points to dramatic reduction of the P2 component of the auditory evoked potential (AEP) as a potentially reliable biomarker of Rett Syndrome severity, with prospective applicability as an objective readout (neuromarker) of change in functional brain activity following therapeutic interventions administered in the context of clinical trials. Compellingly, the reduction of P2 amplitude in patients with RTT mimics findings in animal models of RTT, providing a translational bridge between pre-clinical and human research.

neuroscience↗

bioRxiv2026

Azacitidine Response in Myelodysplastic Syndromes is Marked by NK-like CD8 T-Cell Expansion and CXCL12+ Reticular Cell Remodeling

Myelodysplastic syndromes (MDS) are driven by somatic mutations in hematopoietic stem and progenitor cells (HSPCs), leading to clonal expansion and ineffective hematopoiesis. Hypomethylating agents (HMAs; azacitidine or decitabine) are the standard of care for higher-risk MDS. However, their effects on the bone marrow (BM) microenvironment, and the extent to which these changes correlate with clinical response, remain poorly understood. We performed longitudinal analyses of BM aspirates, trephine biopsies, and peripheral blood samples from MDS patients treated with azacitidine in a clinical trial (NCT03493646), integrating CyTOF, 5' single-cell RNA and TCR sequencing, plasma proteomics, and multiplex immunofluorescence microscopy to characterize changes associated with azacitidine response. Clinical responders showed expansion of GzmBCD56CD8 T cells together with increased type I and type II interferon signaling within the T-cell compartment. Responders also exhibited marked alterations in circulating platelet- and myeloid-derived factors with the potential to remodel the BM niche. Spatial analyses revealed expansion of "neighborhoods" enriched for CXCL12-abundant reticular cells and CD8 T cells in responders, whereas HSPC-enriched neighborhoods were largely unchanged. In contrast, several HSPC-enriched neighborhoods expanded in non-responders. These microenvironmental changes were accompanied by evidence of enhanced myelopoiesis in clinical responders. Our findings support a model in which azacitidine response extends beyond direct effects on malignant hematopoietic cells to involve coordinated remodeling of the BM microenvironment which may be reinforced by platelet- and myeloid-derived signals that establish a feed-forward circuit promoting productive hematopoiesis. One Sentence SummaryLongitudinal bone marrow profiling reveals stromal and immune correlates of azacitidine response in myelodysplastic syndrome.

cancer biology↗

bioRxiv2026

Modeling CISH-KO TIL therapy: T-cell persistence and endogenous competition determine response in gastrointestinal cancer

BackgroundTumor-infiltrating lymphocyte (TIL) therapies have shown promise in murine models; however, early-phase clinical trials reveal substantial heterogeneity in treatment response across patients. Elucidating the biological drivers of this variability is critical for improving patient selection and therapeutic design. MethodsWe developed a mechanistic mathematical model of Cish-inactivated TIL therapy capturing interactions among tumor cells, endogenous TILs, and infused CISH-KO (Cish gene knockout) T-cells. The model was calibrated to longitudinal tumor size data from two murine studies and also fitted to clinical data from a first-in-human phase 1 trial enrolling 22 and treating 12 patients with metastatic gastrointestinal cancers (27 independently tracked tumor lesions). We used the calibrated model to identify patient-level determinants of response and to simulate combination and fractionation treatment strategies in silico. FindingsFour mechanistically distinct parameters emerged as dominant determinants of therapeutic outcome: CISH-KO T-cell persistence (r = 0.827, p < 10-4) was the single strongest predictor of therapeutic failure; other major determinants included endogenous T-cell proliferation rate (r = 0.648, p < 10-4) , CISH-KO T-cell killing rate, and intrinsic tumor growth rate. In silico simulations predicted that the addition of anti-PD-1 checkpoint blockade to standard-dose CISH-KO TIL therapy achieved comparable or superior tumor control relative to dose doubling, while maintaining lower peak T-cell level. Additionally, fractionating the same total dose across multiple delayed infusions further improved predicted tumor control by prolonging CISH-KO T-cell persistence, again without raising peak effector burden. InterpretationThe efficacy of current CISH-KO TIL protocols is influenced not only by the cytotoxic potency of infused T-cells, but also by their persistence within the tumor microenvironment and competitive pressure from the reconstituting host immune compartment. These findings support strategies that enhance the functional efficiency and prolong the availability of infused T-cells--such as concurrent PD-1 blockade or fractionated dosing of the same total cell product--rather than dose escalation alone and identify CISH-KO T-cell persistence and endogenous immune competition as actionable targets for improving TIL-based immunotherapies.

Cancer Biology↗

bioRxiv2021

A tissue-level phenome-wide network map of colocalized genes and phenotypes in the UK Biobank

BackgroundPhenome-wide association studies conducted in electronic health record (EHR)-linked biobanks have uncovered a large number of genomic loci associated with traits and diseases. However, interpretation of the complex relationships of associated genes and phenotypes is challenging. ResultsWe constructed a tissue-level phenome-wide network map of colocalized genes and phenotypes. First, we generated colocalized expression quantitative trait loci from 48 tissues of the Genotype-Tissue Expression project and from publicly available genome-wide association study summary statistics from the UK Biobank. We identified 9,151 colocalized genes for 1,411 phenotypes across 48 tissues. Then, we constructed a bipartite network using the colocalized signals to establish links between genes and phenotypes in each tissue. The majority of links are observed in a single tissue whereas only a few are present in all tissues. Finally, we applied the biLouvain clustering algorithm in each tissue-specific bipartite network to identify co-clusters of non-overlapping genes and phenotypes. The majority of co-clusters contains a small number of genes and phenotypes, and 88.6% of co-clusters are found in only one tissue. To demonstrate functionality of the phenome-wide map, we tested if these co-clusters were enriched with known biological and functional gene classes and observed several significant enrichments. Furthermore, we observed that tissue-specific co-clusters are enriched with reported drug side effects for the corresponding drug target genes in clinical trial data. ConclusionsThe phenome-wide map provides links between genes, phenotypes and tissues across a wide spectrum of biological classes and can yield biological and clinical discoveries. The phenome-wide map is publicly available at https://rstudio-connect.hpc.mssm.edu/biPheMap/.

genomics↗

bioRxiv2022

Clemizole and Trazodone are Effective Antiseizure Treatments in a Zebrafish Model of STXBP1 Disorder

ObjectiveCRISPR-Cas9-generated zebrafish carrying a 12 base-pair deletion in stxbpb1b, a paralog sharing 79% amino acid sequence identity with human, exhibit spontaneous electrographic seizures during larval stages of development. Zebrafish stxbp1b mutants provide an efficient preclinical platform to test antiseizure therapeutics. The present study was designed to test prototype antiepileptic drugs approved for clinical use and two recently identified repurposed drugs with antiseizure activity. MethodsLarval homozygous stxbp1b zebrafish (4 days post-fertilization) were agarose-embedded and monitored for electrographic seizure activity using a local field recording electrode placed in midbrain. Frequency of ictal-like events was evaluated at baseline and following 45 min of continuous drug exposure (1 mM, bath application). Analysis was performed on coded files by an experimenter blinded to drug treatment and genotype. ResultsPhenytoin, valproate, ethosuximide, levetiracetam, and diazepam had no effect on ictal-like event frequency in stxbp1b mutant zebrafish. Clemizole and trazodone decreased ictal-like event frequency in stxbp1b mutant zebrafish by 80% and 83%, respectively. These results suggest that repurposed drugs with serotonin receptor binding affinities could be effective antiseizure treatments. SignificanceClemizole and trazodone were identified in a larval zebrafish model for Dravet syndrome. Based primarily on these preclinical zebrafish studies, compassionate-use and double-blind clinical trials with both drugs have progressed. The present study extends this approach to a preclinical zebrafish model representing STXBP1-related disorders, and suggests that future clinical studies may be warranted.

neuroscience↗

bioRxiv2023

Reusability Report: Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients

Machine learning (ML) and artificial intelligence (AI) methods are increasingly used in personalized medicine, including precision oncology. Ma et al. (Nature Cancer 2021) developed a new method c alled "Transfer of Cell Line Response Prediction" (TCRP) to train predictors of drug response in cancer cell lines and optimize their performance in higher complex cancer model systems via few-shot learning. TCRP was presented as a successful modeling approach in multiple case studies. Given the importance of this approach to assist clinicians in their treatment decision process, we sought to reproduce independently the authors findings and improve the reusability of TCRP in new case studies, including validation in clinical trial datasets, a high bar for drug response prediction. Our results support the superiority of TCRP over established statistical and machine learning approaches in preclinical and clinical settings. We developed new resources to increase the reusability of the TCRP model for future improvements and validation studies.

bioinformatics↗

bioRxiv2025

FOXJ1 mediates taxane resistance through regulation of microtubule dynamics

Docetaxel is the first-line chemotherapy for metastatic castration-resistant prostate cancer (PC), but clinically meaningful mechanisms of resistance remain to be established. We generated an in vivo model of docetaxel resistance using castration-resistant patient-derived xenografts and found increased expression of genes that drive development of multiciliated cells, including FOXJ1 and its effector genes, many of which regulate ciliary microtubules (MTs). Mechanistically, FOXJ1 overexpression conferred docetaxel resistance in vitro and in vivo, which was associated with decreased docetaxel-mediated MT bundling. Overexpression of a MT-associated FOXJ1-regulated gene (TPPP3) had similar effects. Conversely, FOXJ1 knockdown impaired basal MT function, enhanced taxane binding to MTs, and increased docetaxel sensitivity. These results establish mechanistic causality between the FOXJ1 signaling axis, MT biology, and taxane resistance. Clinically, FOXJ1 gene amplification was increased in taxane-treated PC patients. Moreover, in the CHAARTED clinical trial of docetaxel combined with androgen deprivation for metastatic PC, higher baseline FOXJ1 was predictive of decreased survival in PC patients treated with docetaxel, further supporting clinical relevance. Together these findings identify a previously unrecognized clinically impactful mechanism of taxane resistance whose exploitation could stratify patients that will not benefit from taxane treatment. Statement of SignificanceThe early use of docetaxel in combination with androgen receptor targeted therapy can enhance survival in a subset of PC. This study indicates that increased FOXJ1 is predictive of tumors that will not benefit from docetaxel, and that agents targeting FOXJ1 or downstream effectors may enhance taxane responses and improve patient outcomes.

cancer biology↗