3126cdbdab060c22b0df1180b1053ce8 324031.pdf 7074dbf1a10a7b3bb00847effe00d020bf2958a1 324031.pdf 95c86fcd7376268d3c1c9029296670f29b304ea52f65a4ade35dd81ae1690048 324031.pdf Title: Frontotemporal lobar degeneration targets brain regions linked to expression of recently evolved genes Subject: DOI: 10.1093/brain/awae205; Brain, 147, 9, 2024-06-28.; Abstract: In frontotemporal lobar degeneration (FTLD), pathological protein aggregation in specific brain regions is associated with declines in human-specialized social-emotional and language functions. In most patients, disease protein aggregates contain either TDP-43 (FTLD-TDP) or tau (FTLD-tau). Here, we explored whether FTLD-associated regional degeneration patterns relate to regional gene expression of human accelerated regions (HARs), conserved sequences that have undergone positive selection during recent human evolution.To this end, we used structural neuroimaging from patients with FTLD and human brain regional transcriptomic data from controls to identify genes expressed in FTLD-targeted brain regions. We then integrated primate comparative genomic data to test our hypothesis that FTLD targets brain regions linked to expression levels of recently evolved genes. In addition, we asked whether genes whose expression correlates with FTLD atrophy are enriched for genes that undergo cryptic splicing when TDP-43 function is impaired.We found that FTLD-TDP and FTLD-tau subtypes target brain regions with overlapping and distinct gene expression correlates, highlighting many genes linked to neuromodulatory functions. FTLD atrophy-correlated genes were strongly enriched for HARs. Atrophy-correlated genes in FTLD-TDP showed greater overlap with TDP-43 cryptic splicing genes and genes with more numerous TDP-43 binding sites compared with atrophy-correlated genes in FTLD-tau. Cryptic splicing genes were enriched for HAR genes, and vice versa, but this effect was due to the confounding influence of gene length. Analyses performed at the individual-patient level revealed that the expression of HAR genes and cryptically spliced genes within putative regions of disease onset differed across FTLD-TDP subtypes.Overall, our findings suggest that FTLD targets brain regions that have undergone recent evolutionary speciali Keywords: frontotemporal lobar degeneration; cryptic exon; human accelerated regions; TDP-43; tau; gene expression Author: Lorenzo Pasquini Creator: Servigistics Arbortext Advanced Print Publisher 11.1.4546/W-x64 Producer: PDFlib+PDI 9.0.7p3 (C++/Win64) CreationDate: Mon Sep 2 11:26:54 2024 CEST ModDate: Tue Sep 3 09:42:50 2024 CEST Custom Metadata: yes Metadata Stream: yes Tagged: yes UserProperties: no Suspects: no Form: AcroForm JavaScript: no Pages: 16 Encrypted: no Page size: 612.283 x 790.866 pts Page rot: 0 File size: 1522508 bytes Optimized: no PDF version: 1.6 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- QOLAAF+CaeciliaLTStd-Bold Type 1C Custom yes yes yes 1493 0 RDUWRE+CaeciliaLTStd-BoldItalic Type 1C Custom yes yes yes 1498 0 BYIQHG+CaeciliaLTStd-Roman Type 1C Custom yes yes yes 1503 0 UZEBZO+CaeciliaLTStd-Heavy Type 1C Custom yes yes yes 75 0 QCFNHG+CaeciliaLTStd-Italic Type 1C Custom yes yes yes 80 0 NZVSYH+STIXGeneral-Regular Type 1C Custom yes yes yes 85 0 Greek_Medium Type 1 Builtin yes no yes 7 0 YBNOAR+TimesNewRomanPS-ItalicMT CID TrueType Identity-H yes yes yes 121 0 QJZMDP+TimesNewRomanPSMT CID TrueType Identity-H yes yes yes 64 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2026-01-14 04:22:37 CET RepresentationInformation: 324031.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2026-01-13 12:50:12 CET Size: 1522508 Format: PDF Version: 1.6 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf Profile: Tagged PDF PDFMetadata: Objects: 1580 FreeObjects: 4 IncrementalUpdates: 4 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: false CenterWindow: false DisplayDocTitle: true NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: OneColumn PageMode: UseOutlines Language: en Outlines: Item: Title: Frontotemporal lobar degeneration targetsbrain regions linked to expression of recentlyevolved genes Children: Item: Title: Introduction Destination: secawae205-s0 Item: Title: Materials and methods Destination: secawae205-s1 Children: Item: Title: Participants Destination: secawae205-s1.1 Item: Title: Neuropathology Destination: secawae205-s1.2 Item: Title: Structural neuroimaging Destination: secawae205-s1.3 Children: Item: Title: Acquisition and preprocessing Destination: secawae205-s1.3.1 Item: Title: W-score maps Destination: secawae205-s1.3.2 Item: Title: Gene expression Destination: secawae205-s1.4 Children: Item: Title: Allen human brain atlas Destination: secawae205-s1.4.1 Item: Title: Human accelerated region genes Destination: secawae205-s1.4.2 Item: Title: Cryptic splicing genes Destination: secawae205-s1.4.3 Item: Title: Spatial correlation analyses Destination: secawae205-s1.4.4 Item: Title: Gene set enrichment analysis Destination: secawae205-s1.4.5 Item: Title: Graph network Destination: secawae205-s1.4.6 Item: Title: Gene length Destination: secawae205-s1.4.7 Item: Title: Disease epicentres Destination: secawae205-s1.4.8 Item: Title: Results Destination: secawae205-s2 Children: Item: Title: FTLD subtypes target brain regions expressing shared and distinct genes Destination: secawae205-s2.1 Item: Title: Genes correlated with FTLD atrophy are enriched for HAR genes Destination: secawae205-s2.2 Item: Title: FTLD-TDP atrophy-correlated genes are linked to TDP-43 regulated genes Destination: secawae205-s2.3 Item: Title: HAR genes overlap with TDP-43 cryptic splicing genes Destination: secawae205-s2.4 Item: Title: Expression of cryptic splicing and HAR genes varies across FTLD-TDP subtypes and patient epicentres Destination: secawae205-s2.5 Item: Title: Discussion Destination: secawae205-s3 Item: Title: Data availability Destination: secawae205-s4 Item: Title: Acknowledgements Destination: acknow Item: Title: Funding Destination: secawae205-s5 Item: Title: Competing interests Destination: secawae205-s6 Item: Title: Supplementary material Destination: secawae205-s7 Item: Title: References Destination: reflist Info: Title: Frontotemporal lobar degeneration targets brain regions linked to expression of recently evolved genes Author: Lorenzo Pasquini Subject: DOI: 10.1093/brain/awae205; Brain, 147, 9, 2024-06-28.; Abstract: In frontotemporal lobar degeneration (FTLD), pathological protein aggregation in specific brain regions is associated with declines in human-specialized social-emotional and language functions. In most patients, disease protein aggregates contain either TDP-43 (FTLD-TDP) or tau (FTLD-tau). Here, we explored whether FTLD-associated regional degeneration patterns relate to regional gene expression of human accelerated regions (HARs), conserved sequences that have undergone positive selection during recent human evolution.To this end, we used structural neuroimaging from patients with FTLD and human brain regional transcriptomic data from controls to identify genes expressed in FTLD-targeted brain regions. We then integrated primate comparative genomic data to test our hypothesis that FTLD targets brain regions linked to expression levels of recently evolved genes. In addition, we asked whether genes whose expression correlates with FTLD atrophy are enriched for genes that undergo cryptic splicing when TDP-43 function is impaired.We found that FTLD-TDP and FTLD-tau subtypes target brain regions with overlapping and distinct gene expression correlates, highlighting many genes linked to neuromodulatory functions. FTLD atrophy-correlated genes were strongly enriched for HARs. Atrophy-correlated genes in FTLD-TDP showed greater overlap with TDP-43 cryptic splicing genes and genes with more numerous TDP-43 binding sites compared with atrophy-correlated genes in FTLD-tau. Cryptic splicing genes were enriched for HAR genes, and vice versa, but this effect was due to the confounding influence of gene length. Analyses performed at the individual-patient level revealed that the expression of HAR genes and cryptically spliced genes within putative regions of disease onset differed across FTLD-TDP subtypes.Overall, our findings suggest that FTLD targets brain regions that have undergone recent evolutionary speciali Keywords: frontotemporal lobar degeneration; cryptic exon; human accelerated regions; TDP-43; tau; gene expression Creator: Servigistics Arbortext Advanced Print Publisher 11.1.4546/W-x64 Producer: PDFlib+PDI 9.0.7p3 (C++/Win64) CreationDate: Mon Sep 02 11:56:54 CEST 2024 ModDate: Tue Sep 03 10:12:50 CEST 2024 ID: 0x4d1430e880c24471e38c07a09afe7423, 0x2600ea0552cfd247bc609da2401420e0 Filters: FilterPipeline: FlateDecode FilterPipeline: DCTDecode Images: Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 2236 ImageHeight: 254 BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 1143 ImageHeight: 1653 BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 1266 ImageHeight: 1485 BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 650 ImageHeight: 1114 BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 650 ImageHeight: 486 BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 650 ImageHeight: 425 BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 866 ImageHeight: 704 BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 1085 ImageHeight: 1626 BitsPerSample: 8 BitsPerSampleUnit: integer Fonts: Type0: Font: BaseFont: QJZMDP+TimesNewRomanPSMT Encoding: Identity-H ToUnicode: true Font: BaseFont: YBNOAR+TimesNewRomanPS-ItalicMT Encoding: Identity-H ToUnicode: true Type1: Font: BaseFont: QCFNHG+CaeciliaLTStd-Italic FontSubset: true FirstChar: 1 LastChar: 62 FontDescriptor: FontName: QCFNHG+CaeciliaLTStd-Italic Flags: Nonsymbolic, Italic FontBBox: -166, -270, 1053, 915 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: QOLAAF+CaeciliaLTStd-Bold FontSubset: true FirstChar: 1 LastChar: 69 FontDescriptor: FontName: QOLAAF+CaeciliaLTStd-Bold Flags: Nonsymbolic, ForceBold FontBBox: -166, -273, 1141, 938 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: NZVSYH+STIXGeneral-Regular FontSubset: true FirstChar: 1 LastChar: 8 FontDescriptor: FontName: NZVSYH+STIXGeneral-Regular Flags: Nonsymbolic FontBBox: -995, -455, 2000, 1055 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: Greek_Medium FirstChar: 32 LastChar: 207 FontDescriptor: FontName: Greek_Medium Flags: Symbolic FontBBox: -50, -180, 1000, 720 FontFile: true ToUnicode: true Font: BaseFont: RDUWRE+CaeciliaLTStd-BoldItalic FontSubset: true FirstChar: 1 LastChar: 5 FontDescriptor: FontName: RDUWRE+CaeciliaLTStd-BoldItalic Flags: Nonsymbolic, Italic, ForceBold FontBBox: -169, -273, 1082, 932 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: UZEBZO+CaeciliaLTStd-Heavy FontSubset: true FirstChar: 1 LastChar: 31 FontDescriptor: FontName: UZEBZO+CaeciliaLTStd-Heavy Flags: Nonsymbolic, ForceBold FontBBox: -170, -277, 1146, 970 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: BYIQHG+CaeciliaLTStd-Roman FontSubset: true FirstChar: 1 LastChar: 94 FontDescriptor: FontName: BYIQHG+CaeciliaLTStd-Roman Flags: Nonsymbolic FontBBox: -167, -270, 1136, 926 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true CIDFontType2: Font: BaseFont: QJZMDP+TimesNewRomanPSMT CIDSystemInfo: Registry: Adobe Registry: Identity Supplement: 0 FontDescriptor: FontName: QJZMDP+TimesNewRomanPSMT Flags: Nonsymbolic FontBBox: -568, -307, 2046, 1040 FontFile2: true Font: BaseFont: YBNOAR+TimesNewRomanPS-ItalicMT CIDSystemInfo: Registry: Adobe Registry: Identity Supplement: 0 FontDescriptor: FontName: YBNOAR+TimesNewRomanPS-ItalicMT Flags: Nonsymbolic, Italic FontBBox: -498, -307, 1333, 1023 FontFile2: true XMP: uuid:6c29bfcb-0493-4e6a-9b33-f0a80b486b62 uuid:8B07BFF6-371A-7AEB-7302-BB58897D6129 True frontotemporal lobar degeneration; cryptic exon; human accelerated regions; TDP-43; tau; gene expression PDFlib+PDI 9.0.7p3 (C++/Win64) application/pdf 10.1093/brain/awae205 en Oxford University Press Frontotemporal lobar degeneration targets brain regions linked to expression of recently evolved genes Lorenzo Pasquini Felipe L. Pereira Sahba Seddighi Yi Zeng Yongbin Wei Ignacio Illán-Gala Sarat C. Vatsavayai Adit Friedberg Alex J. Lee Jesse A. Brown Salvatore Spina Lea T. Grinberg Daniel W. Sirkis Luke W. Bonham Jennifer S. Yokoyama Adam L. Boxer Joel H. Kramer Howard J. Rosen Jack Humphrey Aaron D. Gitler Bruce L. Miller Katherine S. Pollard Michael E. Ward William W. Seeley DOI: 10.1093/brain/awae205; Brain, 147, 9, 2024-06-28.; Abstract: In frontotemporal lobar degeneration (FTLD), pathological protein aggregation in specific brain regions is associated with declines in human-specialized social-emotional and language functions. In most patients, disease protein aggregates contain either TDP-43 (FTLD-TDP) or tau (FTLD-tau). Here, we explored whether FTLD-associated regional degeneration patterns relate to regional gene expression of human accelerated regions (HARs), conserved sequences that have undergone positive selection during recent human evolution.To this end, we used structural neuroimaging from patients with FTLD and human brain regional transcriptomic data from controls to identify genes expressed in FTLD-targeted brain regions. We then integrated primate comparative genomic data to test our hypothesis that FTLD targets brain regions linked to expression levels of recently evolved genes. In addition, we asked whether genes whose expression correlates with FTLD atrophy are enriched for genes that undergo cryptic splicing when TDP-43 function is impaired.We found that FTLD-TDP and FTLD-tau subtypes target brain regions with overlapping and distinct gene expression correlates, highlighting many genes linked to neuromodulatory functions. FTLD atrophy-correlated genes were strongly enriched for HARs. Atrophy-correlated genes in FTLD-TDP showed greater overlap with TDP-43 cryptic splicing genes and genes with more numerous TDP-43 binding sites compared with atrophy-correlated genes in FTLD-tau. Cryptic splicing genes were enriched for HAR genes, and vice versa, but this effect was due to the confounding influence of gene length. Analyses performed at the individual-patient level revealed that the expression of HAR genes and cryptically spliced genes within putative regions of disease onset differed across FTLD-TDP subtypes.Overall, our findings suggest that FTLD targets brain regions that have undergone recent evolutionary speciali © The Author(s) 2024. Published by Oxford University Press on behalf of the Guarantors of Brain. frontotemporal lobar degeneration cryptic exon human accelerated regions TDP-43 tau gene expression Journal Brain © The Author(s) 2024. 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