Base by Base

Sirvydis K et al., Nat Commun - A recurrent de novo MIDEAS p.Tyr654Ser variant disrupts an autoinhibitory loop in the MiDAC complex, increasing HDAC1 deacetylase activity and causing a multisystem neurodevelopmental disorder. Key terms: MIDEAS, MiDAC, HDAC1, neurodevelopmental disorder, Y654S.

Study Highlights:
Two unrelated probands carry the same de novo heterozygous MIDEAS p.Tyr654Ser variant and present with speech delay, progressive joint contractures, facial dysmorphism and gastrointestinal dysmotility. A 2.9 Å cryo-EM structure shows Y654 lies in a conserved loop of MIDEAS that covers the HDAC1 active site and positions I659 into the active site channel. The Y654S change creates an STP CDK consensus site that is highly phosphorylated and leads to displacement of the inhibitory loop, producing a 3–5-fold increase in MiDAC deacetylase activity in vitro. Patient fibroblast transcriptomes display largely reciprocal gene expression changes compared with MiDAC-depleted cells, and MiDAC loss upregulates MAP2K6 and MAP2K3 implicating p38 MAPK pathway involvement.

Conclusion:
MIDEAS p.Tyr654Ser is a dominant monogenic cause of a neurodevelopmental syndrome driven by hyperactivity of the MiDAC HDAC complex

Music:
Enjoy the music based on this article at the end of the episode.

First author:
Sirvydis K

Journal:
Nat Commun

DOI:
10.1038/s41467-025-65472-x

Reference:
Sirvydis K., Fairall L., Knottnerus SJG., Gonchar O., Muskett FW., Jukes-Jones R., van Brussel L., van de Geer E., van Gassen K., Badenhorst P., van Hasselt PM., van Jaarsveld RH., Schwabe J.W.R., et al. A de novo missense variant in MIDEAS results in increased deacetylase activity of the MiDAC HDAC complex causing a neurodevelopmental syndrome. Nat Commun. 2025;16:10472. https://doi.org/10.1038/s41467-025-65472-x

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/mideas-y654s-midac-hyperactivity

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-17.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript's presentation of the paper's central mechanism: Y654S in MIDEAS causing MiDAC hyperactivity via disruption of an autoinhibitory loop; structural basis from cryo-EM; enzymatic gain-of-function; downstream gene expression and MAPK pathway implications; clinical phenotype overlap with related syndr
- transcript topics: MiDAC/MIDEAS composition and function; Y654S de novo variant and clinical phenotype; Cryo-EM structure showing autoinhibitory loop; HDAC activity assays and gain-of-function; CDK phosphorylation site creation and PTMs; Reciprocal gene expression changes and MAPK signaling

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Two unrelated probands carry de novo MIDEAS p.Tyr654Ser (Y654S) variant with overlapping neurodevelopmental features
- Y654S disrupts an autoinhibitory loop over the HDAC1 active site, leading to MiDAC hyperactivity
- Y654S creates a CDK phosphorylation site (STP) with phosphorylation detected, plausibly driving loop displacement
- Y654S complex shows 3–5-fold increased deacetylase activity compared with wild-type/loop-present complex
- Patient fibroblast expression changes reciprocally with MiDAC depletion; MAP2K6/MAP2K3 upregulation linked to MAPK signaling
- MiDAC acts as a brake on the p38 MAPK cascade; hyperactivity may drive the neurodevelopmental syndrome

QC result: Pass.

Wang L et al., Nat Commun - Elevated PCBP2 forms liquid-like condensates that sequester mitochondrial and RNA-binding proteins, stabilize BACE1 mRNA, and promote amyloid pathology while the small molecule CN-0928 reduces PCBP2 via INTS1 to lower Aβ and improve cognition in AD models. Key terms: PCBP2, biomolecular condensates, BACE1, CN-0928, mitochondria.

Study Highlights:
PCBP2 protein is increased in AD patient brains and AD mouse models and forms enlarged, dynamic cytoplasmic condensates that undergo LLPS in vitro and in cells. PCBP2 condensates concentrate mitochondrial proteins and RNA-binding/NMD factors including UPF1, correlating with disrupted mitochondrial morphology, increased ROS, and reduced mitochondrial respiration. PCBP2 stabilizes BACE1 mRNA by sequestering NMD components into condensates and thereby impairs 3′UTR-dependent decay. The small molecule CN-0928 binds INTS1 at Arg-1404, lowers PCBP2 transcription and protein levels, reduces condensates, decreases BACE1 and Aβ, and improves cognitive performance in 5×FAD mice

Conclusion:
Targeting PCBP2 biomolecular condensates via INTS1 with CN-0928 offers a novel strategy to mitigate mitochondrial dysfunction and BACE1-driven amyloidogenesis in Alzheimer’s disease

Music:
Enjoy the music based on this article at the end of the episode.

First author:
Wang L

Journal:
Nat Commun

DOI:
10.1038/s41467-025-65547-9

Reference:
Wang L, Xie X-Y, Pan Q-L, Zhang J, Zhou G-F, Zhang Q-L, Yan X-X, Xiang Y, Li C-L, He Y, Xiang X-J, Deng X-J, Wang Y-J, Zhou J-Y, Nie S & Chen G-J. Pharmacologic inhibition of PCBP2 biomolecular condensates relieves Alzheimer’s disease. Nat Commun. 2025;16:10514. https://doi.org/10.1038/s41467-025-65547-9

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/pcbp2-condensates-alzheimers

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-15.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the central mechanistic narrative (PCBP2 condensates, LLPS, mitochondrial sequestration, UPF1/BACE1 3'UTR regulation) and the therapeutic axis (CN-0928/INTS1) with in vivo cognitive outcomes in mouse models.
- transcript topics: PCBP2 elevation and LLPS condensates in AD models; Sequestration of mitochondrial proteins and UPF1; Mitochondrial dysfunction and ROS/ respiration effects; BACE1 mRNA stability via 3'UTR and UPF1 sequestration; CN-0928 reduces PCBP2 condensates and lowers BACE1/Aβ; INTS1 as CN-0928 target and Arg-1404 binding site

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- PCBP2 levels elevated in AD brains and in AD mouse models
- PCBP2 forms biomolecular condensates that undergo LLPS
- PCBP2 condensates sequester mitochondrial proteins and UPF1
- Sequestration links to mitochondrial dysfunction (morphology, ROS, respiration)
- PCBP2 stabilizes BACE1 mRNA via 3'UTR and reduces mRNA decay
- CN-0928 reduces PCBP2 and condensates, lowers BACE1 and Aβ, improves cognition in 5×FAD mice

QC result: Pass.

Gopal AB et al., Nat Commun - Structural and functional characterization of two group 2 H3 HA stem antibodies, 2F02 and AG2-G02, shows distinct non-overlapping epitopes, protection in mice, and antigenic changes driven by HA2 position 32 that limit AG2-G02 binding. Key terms: influenza H3N2, hemagglutinin stem, broadly neutralizing antibodies, antigenic evolution, vaccine design.

Study Highlights:
Cryo-EM structures show 2F02 targets the central stem epitope while AG2-G02 targets the lower stem epitope and the two can bind concurrently to an HA trimer. Both antibodies neutralize diverse H3 strains in vitro and provide prophylactic protection in mice, with Fc-mediated effector functions contributing to in vivo efficacy. AG2-G02 binding is lost to recent human H3N2 HAs carrying R32 at HA2, whereas T32 or I32 permit binding. Human plasma binding profiles mirror the historical shift from T32 to I32 to R32, indicating altered population antigenicity of the lower stem over time.

Conclusion:
Natural evolution at HA2 position 32 has changed the antigenicity of the H3N2 HA lower stem, impacting binding of certain group 2 stem antibodies and informing vaccine design strategies

Music:
Enjoy the music based on this article at the end of the episode.

First author:
Gopal AB

Journal:
Nat Commun

DOI:
10.1038/s41467-025-65595-1

Reference:
Gopal AB, Lv H, Ouyang WO, Teo QW, Luo Y, Tang YS, Luo M, Mok CKP, Wu NC. Characterization of two non-competing antibodies to influenza H3N2 hemagglutinin stem reveals its evolving antigenicity. Nat Commun. 2025;16:10557. https://doi.org/10.1038/s41467-025-65595-1

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/h3n2-stem-antibodies-evolution

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-14.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited sections discussing: identification and epitopes of AG2-G02 and 2F02; structural/functional characterization; concurrent binding to an HA trimer; antigenic evolution at HA2 position 32; Fc-mediated protection in vivo; serological/population memory implications; vaccine-design implications.
- transcript topics: Identification and non-overlapping epitopes of AG2-G02 (lower stem) and 2F02 (central stem); Cryo-EM structural analysis and concurrent binding to an HA trimer; Antigenic evolution at HA2 position 32 (T32, I32, R32) and its effect on binding; In vivo Fc-mediated protection and importance of Fc effector functions; Serological analysis across pre-2003 adults, post-2011 adults, and post-2011 infants; Implications for universal influenza vaccine design targeting multiple stem epitopes

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- AG2-G02 targets the lower stem epitope; 2F02 targets the central stem epitope; epitopes are distinct and non-overlapping
- AG2-G02 and 2F02 can bind concurrently to the same HA trimer (non-competitive binding with six Fabs on a single trimer)
- AG2-G02 binding to H3 stem is abrogated by R32HA2; T32HA2 and I32HA2 permit binding
- Population plasma shows immune imprinting: pre-2003 adults bind more to T32HA2; post-2011 infants show stronger binding to R32HA2; post-2011 adults show intermediate patterns
- Fc-mediated effector functions are required for in vivo protection; LALA-PG variants reduce protection
- Two antibodies provide a blueprint for vaccines by targeting both central and lower stem epitopes

QC result: Pass.

Couvreu de Deckersberg E et al., Nat Commun (2025) - This study shows that spontaneous RPE differentiation eliminates most aneuploid human pluripotent stem cells but permits expansion of cells with chromosome 1q gains when they are co-cultured with wild-type cells. Key terms: aneuploidy, 1q gain, RPE differentiation, co-culture, wild-type rescue.

Study Highlights:
Large-scale single-cell genomics revealed pervasive low-grade mosaicism in genetically balanced hPSC cultures, with 3–6% of cells carrying various aneuploidies. During undirected RPE differentiation most aneuploid lineages are purged, except for cells bearing gains of chromosome arm 1q which persist. 1q-gain cells only complete neural/RPE specification when co-cultured with wild-type cells that provide paracrine ligands and induce neuroectodermal regulons, enabling rescued differentiation trajectories. Rescued RPE1q cells show comparable RPE marker expression but display transcriptional signs of aneuploidy-related stress and can outcompete wild-type and other aneuploid cells, whereas 20q11.21 gains, iso20q and trisomy 20 generally fail to be rescued.

Conclusion:
Spontaneous RPE differentiation acts as a selective bottleneck removing most aneuploid cells but permits expansion of 1q-gain clones via wild-type co-culture rescue, underscoring the importance of genomic surveillance for hPSC-derived therapies

Music:
Enjoy the music based on this article at the end of the episode.

First author:
Couvreu de Deckersberg E

Journal:
Nat Commun (2025)

DOI:
10.1038/s41467-025-66766-w

Reference:
Couvreu de Deckersberg E, Lei Y, Krivec N, Huyghebaert A, Duong MC, Janssens C, Regin M, Tsuiko O, Movahedi K, Verhulst S, van Grunsven LA, Sermon K, Al Delbany D, Spits C. 1q gain bypasses the selective barrier against aneuploidy in RPE differentiation via wild-type co-culture rescue. Nat Commun (2025). https://doi.org/10.1038/s41467-025-66766-w

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/1q-gain-wild-type-rescue

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-13.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the spoken content covering: baseline mosaicism in hPSCs, the selective bottleneck during RPE differentiation, the 1q-gain rescue via co-culture, the MDM4/p53 mechanism, signaling interactions with wild-type neighbors, and comparisons to other aneuploides; also covered limitations and safety considerations.
- transcript topics: hPSC mosaicism and common aneuploidies; undirected RPE differentiation bottleneck; 1q gain persistence and enrichment; wild-type co-culture rescue mechanism; MDM4/p53 axis and stress responses; signaling interactions between wt and 1q-gain cells

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Prevalence of low-grade mosaicism in hPSC cultures (3-6%).
- During undirected RPE differentiation, most aneuploidies are eliminated except 1q gains.
- 1q-gain cells differentiate efficiently only when co-cultured with wild-type cells via paracrine signals.
- 1q-gain cells can expand and dominate the culture (up to ~43% of final population in a line).
- MDM4 copy number in 1q gain inhibits p53, enabling survival through differentiation.
- Specific wt–1q ligand–receptor interactions (e.g., NRXN1–NLGN1, EFNA5–EPHA6, CALM1/2/3–RYR2/CACNA1C) mediate rescue.

QC result: Pass.

Wang S et al., Nat Commun - This study shows that podocyte-derived FGF4 is reduced in DKD and that recombinant FGF4 preserves podocyte survival and glomerular function in diabetic models via FGFR1-AMPK-FOXO1 signaling. Key terms: FGF4, FGFR1, podocyte, AMPK-FOXO1, diabetic kidney disease.

Study Highlights:
FGF4 expression is downregulated in kidneys from DKD patients and diabetic mouse models and localizes predominantly to podocytes. Podocyte-specific deletion of Fgf4 worsened albuminuria, reduced GFR, increased oxidative stress and podocyte loss in diabetic mice. Systemic treatment with a non-mitogenic recombinant FGF4 improved glucose in db/db mice, lowered UACR and BUN, reduced fibrosis, ROS and apoptosis, and restored podocyte markers in both T1D and T2D models. The protective effects of rFGF4 require podocyte FGFR1 and downstream AMPK-FOXO1 activity, as Fgfr1, Ampk, or Foxo1 podocyte knockouts abolished rFGF4 benefits. rFGF4 also reversed high glucose–induced injury and promoted nuclear FOXO1 in human podocytes and isolated human glomeruli

Conclusion:
FGF4 is a podocyte-derived regulator that promotes podocyte survival and mitigates DKD through FGFR1-mediated activation of the AMPK-FOXO1 axis, supporting rFGF4 as a potential therapeutic approach for diabetic kidney disease

Music:
Enjoy the music based on this article at the end of the episode.

First author:
Wang S

Journal:
Nat Commun

DOI:
10.1038/s41467-025-65978-4

Reference:
Wang S, Lou J, Pan B, Zhao M, Li Q, Zhou J, et al. FGF4-FGFR1 signaling promotes podocyte survival and glomerular function to ameliorate diabetic kidney disease in male mice. Nat Commun. 2025;16:10430. https://doi.org/10.1038/s41467-025-65978-4

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/fgf4-podocyte-protects-kidney

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-12.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the scientific content of the transcript, focusing on: DKD context and podocyte injury; FGF4 downregulation and podocyte-specific Fgf4 knockout effects; rFGF4 therapeutic effects in DKD mouse models; FGFR1-AMPK-FOXO1 signaling; human cell data; safety considerations; interactions with losartan and SGLT2 inhibit
- transcript topics: DKD and podocyte injury; FGF4 as a podocyte-protective factor; Podocyte-specific Fgf4 knockout model (PKO); Recombinant FGF4 therapy in DKD (db/db and STZ models); FGFR1-AMPK-FOXO1 signaling axis; Human podocyte/glomerulus data and translational relevance

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- DKD downregulates FGF4 in podocytes and correlates with disease severity
- Podocyte-specific deletion of Fgf4 worsens DKD outcomes (lower GFR, higher albuminuria, histological damage)
- Recombinant FGF4 (rFGF4) protects against DKD in two mouse models (db/db and STZ), reducing kidney injury and fibrosis
- FGFR1-AMPK-FOXO1 signaling mediates rFGF4's protective effects in podocytes
- Protection by rFGF4 is non-glycemic and can occur even when blood glucose remains high
- Human relevance: rFGF4 reverses injury in human podocytes and human glomeruli under high glucose

QC result: Pass.

Paouneskou D et al., Nature Communications - VRK-1 phosphorylates BAF-1 to remove chromatin from the nuclear periphery during early meiotic prophase in C. elegans, and failure of this step impairs pairing and synapsis and generates heritable genome lesions. Key terms: VRK-1, BAF-1, meiosis, chromatin tethering, genome integrity.

Study Highlights:
The authors used an auxin-inducible VRK-1 depletion system and genetic perturbations to show that VRK-1 phosphorylates BAF-1 (Ser4) to release chromatin–nuclear periphery contacts during leptotene–zygotene. VRK-1 loss or a BAF-1 Ser4 phospho-mutant increases chromatin tethering at the nuclear envelope, delays homolog pairing, slows and disrupts synaptonemal complex assembly, and elevates apoptosis. VRK-1 depletion produces oocytes with increased DAPI bodies, intrachromosomal bridges and fragmentation that depend on SPO-11 and MSH-5, while baf-1 RNAi rescues overtethering phenotypes. Transient VRK-1 loss during the chromosome movement window yields offspring with an increased burden of deletions and duplications detected by long-read sequencing, implicating VRK-1–BAF-1 in preserving genome integrity

Conclusion:
Timed VRK-1–mediated phosphorylation of BAF-1 is required to detach chromatin from the nuclear periphery during meiotic chromosome movements to ensure correct pairing, synapsis, and genome stability

Music:
Enjoy the music based on this article at the end of the episode.

First author:
Paouneskou D

Journal:
Nature Communications

DOI:
10.1038/s41467-025-65420-9

Reference:
Paouneskou D., Baudrimont A., Elkrewi M., Kölbl C., Tiemann-Boege I., Vicoso B., Jantsch V. BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. Nature Communications. 2025;16:10446. https://doi.org/10.1038/s41467-025-65420-9

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/vrk1-baf1-meiosis-integrity

️ Episode:
225: VRK-1 and BAF-1 release meiotic chromosomes

️ Season:
1

Article title:
BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-10.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript’s presentation of the VRK-1–BAF-1 mechanism, effects of VRK-1 depletion on chromatin tethering and meiosis (pairing, SC, CO), apoptosis, and the heritable genome-variant outcomes revealed by long-read sequencing, plus rescue and repair pathway details described in the article.
- transcript topics: Meiosis in C. elegans and rapid chromosome movements; Chromatin tethering to nuclear periphery (BAF-1); VRK-1 kinase and BAF-1 Ser4 phosphorylation; AID timing window for VRK-1 depletion; Synapsis and CO formation (HTP-3, SYP-1, MSH-5, ZHP-3); DNA repair pathways and alternative repair (MUS-81, POLQ-1, NHEJ)

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- VRK-1 phosphorylates BAF-1 at Ser4 to detach chromatin from the nuclear periphery during early meiotic prophase
- VRK-1 depletion leads to chromatin tethering, delayed pairing and synapsis, and elevated apoptosis
- BAF-1 Ser4 phosphorylation is a VRK-1 target; BAF-1 Ser4 phospho-mutant phenocopies VRK-1 depletion regarding chromosome reorganization
- Synapsis is delayed and crossover (CO) formation is perturbed (MSH-5 recruitment delayed; ZHP-3 retraction delayed) in VRK-1–depleted cells
- Transient VRK-1 depletion yields offspring with increased deletions and duplications (SVs) detected by long-read sequencing; large SVs (>10 kb) increased >6-fold
- Alternative repair pathways (MUS-81, POLQ-1) are engaged under VRK-1 depletion and influence chromosome integrity

QC result: Pass.

Bilir A et al., Wireless in-body sensing through genetically engineered bacteria - A bio-hybrid, battery-free implant converts engineered bacterial activity into microwave backscatter signals by controlled degradation of a biodegradable antenna. Key terms: engineered bacteria, biodegradable antenna, backscatter communication, implantable sensor, cytochrome c.

Study Highlights:
The AntennAlive system uses a magnesium split-ring passive implant antenna coupled with genetically engineered Escherichia coli that accelerate metal degradation to convert molecular detection into an electromagnetic signature. E. coli BL21 engineered to express the CcmA–H cytochrome c maturation pathway degraded the magnesium prototype faster (≈8 h) than non-engineered cells (≈14 h), causing a controlled structural transition from split ring to segmented ring. Numerical and experimental work showed resonant frequencies near 1.16 GHz for the intact antenna and 1.91 GHz after degradation, and an on-body reader antenna covering 0.8–2.3 GHz enabled backscatter monitoring through a muscle phantom. A wireless, chipless link between the cell-based passive implant and an external receiver was demonstrated at 25 mm implant depth, showing potential for molecular-level in-body sensing without batteries or electronics.

Conclusion:
Genetically programmed bacteria can modulate biodegradable antenna properties to produce remotely detectable backscatter signals, enabling battery-free, implantable molecular sensing.

Music:
Enjoy the music based on this article at the end of the episode.

First author:
Bilir A

Journal:
Nature Communications

DOI:
10.1038/s41467-025-65416-5

Reference:
Bilir A., Yavuz M., Safak Seker U. O., Dumanli S. Wireless in-body sensing through genetically engineered bacteria. Nature Communications. 2025;16:10432. https://doi.org/10.1038/s41467-025-65416-5

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/antennalive-bacterial-implant

️ Episode:
224: AntennAlive — wireless in-body sensing with engineered bacteria

️ Season:
1

Article title:
Wireless in-body sensing through genetically engineered bacteria

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-10.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript's coverage of AntennAlive concept, magnesium-based passive implant, engineered E. coli (CcmA–H), degradation-driven resonant-frequency shift, experimental phantom setup, 25 mm depth demonstration, and discussed limitations/future work.
- transcript topics: AntennAlive concept and biohybrid sensing bridge; Magnesium-based passive implant antenna design and degradation; Engineering E. coli for extracellular electron transfer (CcmA–H); Degradation dynamics and resonance shift (1.16 GHz to 1.91 GHz); Experimental setup: muscle phantom, Mg foil, on-body reader, VNA; Phantom-based wireless backscatter demonstration at 25 mm depth

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Mg foil implant is 25 μm thick and degrades faster under engineered bacteria
- E. coli BL21 expressing CcmA–H accelerates magnesium degradation vs non-engineered BL21
- Degradation changes implant antenna from split ring to segmented ring
- Resonant frequency shifts from ~1.16 GHz (intact) to ~1.91 GHz (degraded)
- Wireless backscatter link detected by on-body reader at 25 mm depth in a muscle phantom
- Non-biodegradable implant resonance detectable up to 55 mm depth

QC result: Pass.

Xiaomeng Jia et al., Berger, Smita S - New single-molecule angular optical trap assays reveal that DNA torsion directly controls T7 replisome stalling and reactivation. Key terms: DNA replication, torsion, replisome, helicase, DNA polymerase.

Study Highlights:
A high-resolution, label-free angular optical trap (AOT) assay was developed to track T7 replisome-driven DNA rotation and torsional slowing in real time. The combined helicase–DNA polymerase (DNAP) replisome generates ∼22 pN·nm of stall torque, about twice that of E. coli RNA polymerase, while helicase or DNAP alone produce minimal positive torque. Loss of the helicase C‑terminal domain interaction with DNAP increases fork regression under torsion and reduces restart efficiency, and prolonged stalling leads to replisome inactivation. Excess free DNAP at the fork and gyrase-mediated torsional relaxation substantially improve restart after a torsion-induced stall

Conclusion:
Torsional stress is a central regulator of fork stability and restart, with helicase–DNAP synergy and timely topoisomerase activity determining whether stalled replisomes reactivate

Music:
Enjoy the music based on this article at the end of the episode.

First author:
Xiaomeng Jia

Journal:
Nature Communications

DOI:
10.1038/s41467-025-65567-5

Reference:
Xiaomeng Jia, Xiang Gao, Shuming Zhang, James T. Inman, Yifeng Hong, Anupam Singh, Fahad Rashid, James M. Berger, Smita S. Patel & Michelle D. Wang. Torsion is a dynamic regulator of DNA replication stalling and reactivation. Nat Commun. 2025;16:10543. https://doi.org/10.1038/s41467-025-65567-5

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/torsion-dna-replication-restart

️ Episode:
223: Torsion Regulates DNA Replication Stalling and Restart

️ Season:
1

Article title:
Torsion is a dynamic regulator of DNA replication stalling and reactivation

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-09.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the substantive scientific content describing torque generation by the T7 replisome, stall under torsion, fork regression, restart mechanisms (including excess DNAP and CTD recruitment), and gyrase effects; cross-checked against the original article.
- transcript topics: Torque generation by the T7 replisome (AOT measurements); Stalling of replication under torsion and stall torque values; CTD-mediated helicase–DNAP interaction and fork stability; Fork regression dynamics under torsion; Excess DNAP and DNAP exchange promoting fork restart; Gyrase/topoisomerase role in torque relief and restart

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- WT replisome stalls at ~21.9 ± 4.4 pN·nm (≈22 pN·nm) torque when helicase and DNAP act together
- DNAP alone and helicase alone generate minimal positive torsion (DNAP ≈ -1.5 ± 2.4 pN·nm; helicase ≈ 1.2 ± 5.0 pN·nm)
- ΔCt helicase (lacking CTD-DNAP interaction) replisome stalls with torque ~19.4 ± 3.0 pN·nm
- Fork regression distances under stall: WT ~80 bp; ΔCt ~240 bp; ΔCtexo ~340 bp
- Prolonged stalling reduces restart efficiency; short stalls restore better than long stalls
- Excess DNAP during a long stall increases restart fraction from ~40% to ~85%

QC result: Pass.

Zhou S et al., Nat Commun - This episode examines how the cancer-associated Pol III transcript snaR-A binds core splicing factors, localizes near nuclear speckles, perturbs U2-dependent splicing to increase intron retention, and promotes cell proliferation linked to poorer patient outcomes. Key terms: snaR-A, splicing, SF3B2, intron retention, nuclear speckles.

Study Highlights:
Proteomic pull-downs and CLIP analyses reveal snaR-A interactions with RNA chaperones (La, ILF3) and multiple splicing factors, with PAR-CLIP and CLIP-qPCR supporting a direct interaction with the U2 snRNP subunit SF3B2. HCR-RNA-FISH and SON TSA-seq place snaR-A in subnuclear foci adjacent to nuclear speckles and show snaR-A gene clusters are speckle-proximal. Functional genomics show snaR-A overexpression increases intron retention while snaR-A depletion reduces intron retention and enhances splicing of transcripts marked by high U2 occupancy and speckle proximity, and snaR-A overexpression selectively reduces SF3B2 protein levels. Phenotypically, snaR-A depletion lowers proliferation in HEK293T cells, snaR-A gene activity correlates with proliferation markers across primary tumors and predicts worse survival, and rescued splicing increases protein abundance for tumor-suppressive targets such as OGFR.

Conclusion:
snaR-A acts as a nuclear antagonist of U2-dependent splicing near speckles, promoting cell proliferation and providing a non-mutational route to splicing dysregulation in cancer

Music:
Enjoy the music based on this article at the end of the episode.

First author:
Zhou S

Journal:
Nature Communications

DOI:
10.1038/s41467-025-65448-x

Reference:
Zhou S, Lizarazo S, Chorghade S, Mouli L, Cheng R, KC R, Kalsotra A, Van Bortle K. Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations. Nat Commun. 2025;16:10460. https://doi.org/10.1038/s41467-025-65448-x

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/snar-a-splicing-disruption

️ Episode:
222: snaR-A hijacks splicing to drive proliferation

️ Season:
1

Article title:
Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-08.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript's core mechanistic and phenotypic claims described in the Nature Communications article: snaR-A interactions with SF3B2 and splicing machinery, subnuclear speckle localization, intron retention changes with overexpression/depletion, effects on proliferation and OGFR, and clinical correlations.
- transcript topics: Pol III overactivity and snaR-A origin in cancer; snaR-A interactions with splicing factors (SF3B2, U2 snRNP); subnuclear localization near nuclear speckles; intron retention and splicing efficiency changes; effects of snaR-A depletion/overexpression on proliferation and OGFR; clinical associations: snaR-A activity and patient survival

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- snaR-A interacts with core mRNA splicing machinery including SF3B2
- snaR-A localizes near nuclear speckles and associates with splicing factors
- overexpression of snaR-A increases intron retention, especially for U2-bound, speckle-proximal transcripts
- depletion of snaR-A reduces intron retention and improves splicing of U2-resident, speckle-proximal transcripts
- splicing improvements after snaR-A depletion correlate with increased OGFR protein levels (tumor suppressor)
- snaR-A depletion reduces cell proliferation in HEK293T cells

QC result: Pass.

Kindlova M et al., Nat Commun - Using phased long-read nanopore and short-read sequencing across eight trios, the study maps allele-specific DNA methylation and transcription in female human placentas, identifies hundreds of DMRs and novel imprinted genes, and reports somatic placental variants. Key terms: placenta, nanopore sequencing, DNA methylation, imprinting, allele-specific expression.

Study Highlights:
The authors combined >20x Oxford Nanopore whole-genome sequencing with Illumina WGS and RNA-seq in eight mother–father–placenta trios to phase reads into maternal and paternal alleles. They catalogued 723 differentially methylated regions, finding a strong bias toward paternal demethylation concentrated in partially methylated domains. Allele-resolved expression analysis identified 74 imprinted genes and revealed previously unreported imprinted loci including paternally expressed ILDR2 and maternally expressed RASA1. The study also detected widespread somatic point mutations and a small number of placenta-specific structural variants, including a CNDP1–ZNF407 duplication associated with altered gene expression

Conclusion:
Phased nanopore sequencing provides a high-resolution, allele-specific map of the placental methylome and transcriptome, revealing novel imprinted genes and somatic variation with potential relevance to placental biology

Music:
Enjoy the music based on this article at the end of the episode.

First author:
Kindlova M

Journal:
Nat Commun

DOI:
10.1038/s41467-025-65337-3

Reference:
Kindlova M, Byrne H, Kubler JM, Steane SE, Whyte JM, Borg D, Clifton VL & Ewing AD. An allele-resolved nanopore-guided tour of the human placental methylome. Nat Commun. 2025;16:10358. https://doi.org/10.1038/s41467-025-65337-3

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/allele-resolved-placental-methylome

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-07.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Substantively audited the transcript’s coverage of allele-resolved placental methylome mapping, DMRs, imprinting, specific imprinted genes ILDR2 and RASA1, the C19MC locus, SST1 repeats, somatic variation including CNDP1–ZNF407, and X-chromosome methylation, plus study limitations and conclusions.
- transcript topics: Allele-resolved methylome mapping by nanopore sequencing; Trio-based phasing and parental allele assignment; Global methylation patterns and PMDs in placenta; Differentially methylated regions (DMRs) and paternal demethylation bias; Imprinted genes ILDR2 and RASA1; C19MC locus and SST1 macro-satellite region

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Eight female placentas were sequenced in eight mother–father–placenta trios
- Long-read nanopore sequencing with trio-based phasing enables allele-specific methylation and transcription mapping, with EM-seq validation showing high concordance (~94%)
- Identified 723 differentially methylated regions (DMRs), including 184 novel DMRs
- Large majority of DMRs show paternal demethylation bias
- ILDR2 is paternally demethylated and expressed; RASA1 is maternally demethylated and expressed
- C19MC locus encodes paternally expressed miRNAs; SST1 macro-satellite region shows paternal methylation pattern with transcription initiated at a HERVH element

QC result: Pass.