Biology subjects

Almeida, A. S.

Publications and source records attributed to Almeida, A. S..

4 recordsLinked to original sources

bioRxiv2026

Ground-truth in silico spike-ins reveal limits of microbiome biomarker recovery in colorectal cancer

Microbiome-based biomarkers have been proposed for colorectal cancer (CRC), yet candidate taxa are often interpreted without knowing whether taxonomic profiling workflows can reliably detect and quantify them in human samples. Existing ground-truth studies commonly rely on simplified communities that do not preserve the biological and technical complexity of clinical stool metagenomes. We hypothesized that weak CRC-associated signals, particularly those relevant to early-stage disease, may be missed through analytical non-recovery rather than biological absence. We developed an in silico spike-in framework that embeds CRC-associated signals into clinical stool metagenomes. Ten taxa were introduced individually at six fractions (0.01-5%) or as an equally weighted community at seven total fractions (0.01-10%; effective per-taxon fractions, 0.001-1%), generating 5,770 spike-in metagenomes from 310 samples. The resulting metagenomes were profiled with Kraken2/Bracken and MetaPhlAn 4 to quantify detection, abundance accuracy, false-positive signals, biomarker recovery, and calibration against a known ground truth. Recovery depended strongly on workflow, taxon, abundance, and clinical background. At 0.01%, four taxa- F. nucleatum, P. micra, P. stomatis, and P. intermedia-showed good recovery in 85-90% of samples under Kraken2/Bracken, whereas none achieved good recovery in at least 50% under MetaPhlAn 4. Greater low-abundance recovery was accompanied by a broader artefact-prone background (54.9% versus 0.5% of non-target taxa). Artefact-prone taxa accounted for 96.3% and 100% of enriched off-target differential-abundance calls, respectively. Spike-in-derived artefact exclusion substantially reduced off-target detections where present, while abundance-response modelling provided proof-of-principle correction of systematic abundance distortions in both evaluated configurations. Overall, the evaluated profiling configurations demonstrate that known low-abundance CRC-associated signals can be missed or distorted across a complete biomarker-discovery pipeline. Analytical non-recovery may cause early-detection biomarkers to be missed rather than indicate biological absence. Importantly, artefact-aware filtering and abundance calibration show that these limitations can be partially overcome. Improvements in taxonomic profiling may help bring reliable microbiome-based CRC diagnostics closer to clinical application.

bioinformatics↗

bioRxiv2021

Fiber-associated Lachnospiraceae reduce colon tumorigenesis by modulation of the tumor-immune microenvironment

Patients with colorectal cancer (CRC) harbor gut microbiomes that differ in structure and function from those of healthy individuals, suggesting this altered microbiome could contribute to tumorigenesis. Despite increasing evidence implicating the gut microbiome in CRC, the collective role of different microbial consortia in CRC carcinogenesis is unclear. We have previously described these consortia as co-abundance groups that co-exist at different abundance levels in the same patient. Here, we report that tumor biopsy tissue from patients with a "high-risk" Pathogen-type microbiome had a different immune transcriptome and immune cell infiltrate from those with a "low-risk" Lachnospiraceae-type microbiome. Transplantation from patients of the two fecal microbiome types into mice with an orthotopic tumor differentially affected tumor growth and the systemic anti-tumor immune response. The differences in tumor volume and immunophenotype between mice receiving the high-risk and the low-risk microbiome correlated with differences in the engrafted human microbial species and predicted microbiome-encoded metabolites in the two groups. Of twelve taxa whose abundance in recipient mice led to increased tumor onset, seven corresponded with differentially abundant taxa in a global dataset of 325 CRC patients versus 310 healthy controls. These data suggest that the enrichment for a Lachnospiraceae-type configuration of the gut microbiome may influence colon cancer progression and disease outcome by modulating the local and systemic anti-tumor immune response. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/432654v2_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1de9ff5org.highwire.dtl.DTLVardef@d790d5org.highwire.dtl.DTLVardef@65be8aorg.highwire.dtl.DTLVardef@1c096da_HPS_FORMAT_FIGEXP M_FIG C_FIG Proposed model of how the high-risk Pathogen and low-risk Lachnospiraceae CAGs differentially modulate the tumor immune response.

microbiology↗

bioRxiv2020

Activating a collaborative innate-adaptive immune response to control breast and ovarian cancer metastasis

Many cancers recruit monocytes/macrophages and polarize them into tumor-associated macrophages (TAMs). TAMs promote tumor growth and metastasis and inhibit cytotoxic T cells. Yet, macrophages can also kill cancer cells after polarization by e.g., lipopolysaccharide (LPS, a bacteria-derived toll-like receptor 4 [TLR4] agonist) and interferon gamma (IFN{gamma}). They do so via nitric oxide (NO), generated by inducible NO synthase (iNOS). Altering the polarization of macrophages could therefore be a strategy for controlling cancer. Here, we show that monophosphoryl lipid A (MPLA, a derivative of LPS) with IFN{gamma} activated macrophages isolated from metastatic pleural effusions of breast cancer patients to kill the corresponding patients cancer cells in vitro. Importantly, intratumoral injection of MPLA with IFN{gamma} not only controlled local tumor growth but also reduced metastasis in mouse models of luminal and triple negative breast cancers. Furthermore, intraperitoneal administration of MPLA with IFN{gamma} reprogrammed peritoneal macrophages, suppressed metastasis, and enhanced the response to chemotherapy in the ID8-p53-/- ovarian carcinoma mouse model. The combined MPLA+IFN{gamma} treatment reprogrammed the immunosuppressive microenvironment to be immunostimulatory by recruiting leukocytes, stimulating type I interferon signaling, decreasing tumor-associated (CD206+) macrophages, increasing tumoricidal (iNOS+) macrophages, and activating cytotoxic T cells through macrophage-secreted interleukin 12 (IL-12) and tumor necrosis factor (TNF). Both macrophages and T cells were critical for the anti-metastatic effects of MPLA+IFN{gamma}. MPLA and IFN{gamma} are already used individually in clinical practice, so our strategy to engage the anti-tumor immune response, which requires no knowledge of unique tumor antigens, may be ready for near-future clinical testing.

cancer biology↗

bioRxiv2018

Cancer cell CCR2 orchestrates suppression of the adaptive immune response

C-C chemokine receptor type 2 (CCR2) is expressed on monocytes and facilitates their recruitment to tumors. Though breast cancer cells also express CCR2, its functions in these cells are unclear. We found that Ccr2 deletion in cancer cells led to reduced tumor growth and [~]2-fold longer survival in an orthotopic, isograft breast cancer mouse model. Deletion of Ccr2 in cancer cells resulted in multiple alterations associated with better immune control: increased infiltration and activation of cytotoxic T lymphocytes (CTLs) and CD103+ cross-presenting dendritic cells (DCs), as well as upregulation of MHC class I and downregulation of checkpoint regulator PD-L1 on the cancer cells. Pharmacological or genetic targeting of CCR2 increased cancer cell sensitivity to CTLs and enabled the cancer cells to induce DC maturation toward the CD103+ subtype. Consistently, Ccr2-/- cancer cells did not induce immune suppression in Batf3-/- mice lacking CD103+ DCs. Our results establish that CCR2 signaling in cancer cells can orchestrate suppression of the immune response. SummaryC-C chemokine receptor type 2 (CCR2) expressed on monocytes facilitates their recruitment to tumors. Here, CCR2 signaling in cancer cells is shown to suppress immune control of tumors, in part by reducing CD103+ dendritic cell recruitment.

cancer biology↗